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About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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In the Pipeline

Category Archives

November 24, 2014

Holiday Blogging

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Posted by Derek

I'm doing research today and tomorrow, but after that I'll be taking the rest of the week off, so blogging will be intermittent. Wednesday I'll be home making the traditional chocolate pecan pie (recipe here, with many helpful suggestions in the comment section), along with some of the other Thanksgiving food that can be prepared ahead of time. The menu this year will be the same as last year, by popular demand.

After consulting my wife and her mother, I'll see if I can post a recipe for the Iranian rice dish (javaher polow) that we serve along with everything. Problem is, it seems that Iranian food is one of those cuisines that varies so much from region to region (and household to household) that it's hard to put up a recipe without causing a fight of some sort. The closest situation to that in America is with barbecue - what one part of the country considers the pinnacle of the art would be rated as the next thing to cannibalism somewhere else. And so it is with Iranians. Common phrases include "Oh, well, so-and-so doesn't know how to cook (Dish X) the right way", or "They don't know how to make any decent (insert whole swath of cuisine) in (insert Iranian city or region), anyway". Add in some "Well, you used to be able to get good (type of food), but you can't any more", and I can see how my Southern upbringing blends with my wife's Iranian one pretty smoothly. But about the food we make at home, ourselves, I have no dispute at all!

Comments (20) + TrackBacks (0) | Category: Blog Housekeeping

November 10, 2014

On the Road: GSK and Duke

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Posted by Derek

I'm speaking at GSK today, in a forum along with Bernard Munos, which should be fun (I hope they think the same way when the day is finished!) And tomorrow I'll be giving a talk at the Duke Chemistry Department, which should be a very weird feeling indeed, since I haven't set foot there for many years now. They've moved out of the not-so-beloved "Gross Chem" building, but I do hope to see what they did during its remodeling about the chromium stain I left on the ceiling there. (I know from eyewitnesses that it persisted for some years).

Comments (13) + TrackBacks (0) | Category: Blog Housekeeping

October 2, 2014

Speaking at Northeastern

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Posted by Derek

For anyone at Northeastern University here in Boston who would be interested in attending, I'll be speaking this evening at 6 to the student affiliate ACS there, in Hurtig Hall (Room 115). If you'd like to attend, let them know at acs.neu@gmail.com. And don't eat my portion of pizza before I get there - I'll need it to remain coherent. Turn down too much free pizza and they'll kick you out of almost any scientific society there is, you know.

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September 25, 2014

En Route

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Posted by Derek

Traveling today, so no time for a blog entry. More science and stuff tomorrow, though!

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September 18, 2014

The Worst Seminar

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Posted by Derek

Thinking of good seminars and bad ones reminds me of a story, which I'm surprised that I haven't told here, because it's a favorite memory of mine from grad school. Like everyone else, I've attended some pretty deadly talks over the years - some of them had decent subject matter, but were presented murderously, while others had such grim content that they would not have been redeemed by substituting the best speaker available. Combine those two, and you have a section of the Venn diagram that makes you wonder what you've done with your life (or with a previous one) to be sitting through the thing.

I remember coming back upstairs after one of those. Like most grad students, I didn't have the nerve to just bail on a speaker if they turned out to be horrible (heck, I sometimes don't have the nerve now). So I'd sat through a real forced march, or forced stagger, though a bunch of uninteresting stuff delivered at dictation speed in a nasal monotone. At this remove, I couldn't tell you what it was about even for a large reward; all I remember was the pointlessness.

So I was back in front of my hood when my labmate at the time appeared in the doorway. "That was the WORST seminar I have EVER heard in my LIFE!" he proclaimed, and I could only agree with him, which I did with a strange expression on my face. "Why are you grinning like that?" he asked. "Because the seminar speaker just walked behind you when you said that", I told him (truthfully). "No!" he said in horror, and looked off to his right down the hall. "Oh my God! Oh, well. He's heard it before." And maybe he had. Nominations for your own worst seminar experience are welcome in the comments, if you haven't blocked them out of your mind by now.

By the way, I checked to see if I'd told this story on the site by a Google trick, which is useful for searching the site as a whole. Just start your query with site:pipeline.corante.com, and you'll search only within that domain. It works quite well, but to be sure, I went and checked a text backup of the site (I make one from time to time, via an "Export" command. In case you're wondering, the whole site (posts and comments) rendered in 10-point Courier with standard margins on letter-sized paper, now comes to over 28,000 pages. Dang. I did a search for "worst seminar" and didn't find the phrase, but at this point you'd have to do a search for "Swann" to find the text of "Rememberance of Things Past" in there.

Comments (93) + TrackBacks (0) | Category: Blog Housekeeping | Graduate School

Conference in Basel

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Posted by Derek

I wanted to let people know that next week I'll be attending the FBLD (Fragment-Based Ligand Design) meeting in Basel, Switzerland. I'm looking forward to it - there are a number of good talks on the agenda, and it's always nice to attend a specialized conference where you're interested in the great majority of what's on offer. (Sitting through bad or irrelevant talks, as I've mentioned, becomes harder and harder for me every year). I hope to do some blogging from the conference itself as interesting topics come up.

If there are folks in Basel who'd like to meet up while I'm in town, it looks like I'll be free on Monday and Wednesday evening, so drop me an e-mail and maybe we can find a place to meet.

Comments (4) + TrackBacks (0) | Category: Blog Housekeeping

August 29, 2014

A Last Summer Day Off

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Posted by Derek

I'm going to be taking an extra day of vacation before the kids start back to school, so I'm adding to the Labor Day weekend today. Blogging will resume on Tuesday, unless something gigantic happens before then. If I can come up with something appropriate, maybe I'll put up a recipe!

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August 4, 2014

Summer Blogging Continues

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Posted by Derek

Irregular summer blogging will continue until later this week - I'm on the road at the moment, and internet access is spotty. I'll be able to see my e-mail at some point, and occasionally clear out the spam that silts up the comments section, but otherwise I'll be hard to communicate with.

Comments (7) + TrackBacks (0) | Category: Blog Housekeeping

July 28, 2014

Summer Blogging

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Posted by Derek

I wanted to let everyone know that blogging will be irregular around here for the next week or so. I'll be taking some time off here and there, and while I'll surely get a few blog posts in, they won't show up at the usual times. (I started the whole time-off process over the weekend, with a trip to Stellafane, the big amateur astronomy gathering up in Vermont. Despite earlier weather forecasts, Saturday night was clear and dark, the best night skies I've seen in years. My wife and kids joined me (their first star party), and as we were getting pulled pork sandwiches from the food tent, my son looked around and said "Wow, there sure are a lot of barbecue-eating, telescope-owning guys with beards around here. You fit right in!"

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July 4, 2014

Happy Fourth of July, 2014

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Posted by Derek

This, at least, I have observed in forty-five years: that there are men who search for it [truth], whatever it is, wherever it may lie, patiently, honestly, with due humility, and that there are other men who battle endlessly to put it down, even though they don't know what it is. To the first class belong the scientists, the experimenters, the men of curiosity. To the second belong politicians, bishops, professors, mullahs, tin pot messiahs, frauds and exploiters of all sorts - in brief, the men of authority. . .All I find there is a vast enmity to the free functioning of the spirit of man. There may be, for all I know, some truth there, but it is truth made into whips, rolled into bitter pills. . .

I find myself out of sympathy with such men. I shall keep on challenging them until the last galoot's ashore.

- H. L. Mencken, "Off the Grand Banks", 1925

In those days the New York dockers were renowned for their truculence, inefficiency and sheer slowness. Four hours was supposed to be the standard and we got the standard. Neverthless, the difference from the British equivalent did not strike me as very marked, and by the time we sailed out into the dusk. . .among the wondrous multi-colored lights of the New Jersey Turnpike, at that time utterly unparalleled at home - by then I knew. . .that this was my second country and always would be.

. . .I only ever spent a few nights in (New York City), but made a lot of day and evening trips and saw quite enough of the place to convince me that anyone who makes a business of hating it or being superior to it, and there were plenty then, home-grown and foreign, is a creep, and that anyone who walks up Fifth Avenue (say) on a sunny morning without feeling his spirits lift is an ***hole.

- Kingsley Amis, "Memoirs", 1991

There must be no barriers to freedom of inquiry. There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors. ... Our political life is also predicated on openness. We know that the only way to avoid error is to detect it and that the only way to detect it is to be free to inquire. And we know that as long as men are free to ask what they must, free to say what they think, free to think what they will, freedom can never be lost, and science can never regress.

- J. Robert Oppenheimer, 1949

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July 3, 2014

An Early Day Off

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Posted by Derek

Since the Fourth of July looks to be a rainy washout around here, I'm taking a day off to get a head start on the holiday weekend here. So instead of advancing the cause of science in the lab today, I'm home with a big pork shoulder, which I rubbed down with salt and dry spices last night. It's now cooking over a low charcoal fire with plenty of green hickory wood (from a small shagbark hickory tree I spotted over in the forest near the back yard). That will cook the rest of the day, and be ready for dinner. Here's a prep for barbecued pork ribs from a couple of years ago.

Dessert will be the lime sorbet I mentioned here last year. If you're at all into lemon or lime as a flavor, give that one a try - it's easy, and the results from fresh lime juice are spectacular. Two large-scale, tested preparations, then, for today - I just have to keep an eye on things to make sure that everything is going according to plan.

Comments (12) + TrackBacks (0) | Category: Blog Housekeeping

June 13, 2014

"In the Pipeline" Will Be Moving

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Posted by Derek

Everyone who's visited the blog in the last few weeks has noticed the ongoing server problems. I've been working on solutions, and I think that the time has come to move the blog. I've had offers over the years to do so, but for one reason or another, I haven't made the jump. But several very good situations have been offered to me recently, and one way or another, it looks like I'll be picking up stakes soon.

Corante.com has been this blog's home for over ten years now, and it's been quite a run. I am extremely grateful to Hylton Joliffe, the man behind it, for all the effort and for the space to do whatever I wanted to do here. Looking back, I can't believe how much I've written over that time (the archives will be moving too). But I plan to keep going without interruption, and I'll have more details soon about the new location.

Comments (17) + TrackBacks (0) | Category: Blog Housekeeping

June 2, 2014

More Server Problems

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Posted by Derek

The server here continues to throw electric fits, so I ask everyone to bear with the site while things get fixed. Longer-term solutions are being investigated as well. . .

Comments (6) + TrackBacks (0) | Category: Blog Housekeeping

May 6, 2014

Technical Problems

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Posted by Derek

The site has been glitching a lot recently, especially when it comes to displaying entries with comments. I hope to have this fixed shortly, but I wanted to let everyone know that I'm aware of the problem (and how), and that repairs are underway.

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April 22, 2014

Days Off

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Posted by Derek

I'm going to be traveling on Wednesday and Thursday, so blogging will resume again here for Friday morning. This means that something completely insane will no doubt occur in the chemistry/drug discovery world sometime Wednesday afternoon, but it can't be helped. The Pfizer/Disney merger will have to wait until Friday morning for comment from me!

Comments (4) + TrackBacks (0) | Category: Blog Housekeeping

April 1, 2014

Off To the Publishers

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Posted by Derek

I don't know if my publisher was pulling my leg by having the deadline for the manuscript of "The Chemistry Book" be April 1, but that's what the contract says. And I've sent the thing off, so it's now in the hands of the editors. There's more to be done - I have some more dates to track down, for one, and I'd like to insert some more references for further reading. And then there are the illustrations, for which I've sent along many suggestions, and I'll need to write the captions for those once we've settled on what pictures to use. But the bulk writing is done, I'm glad to say.

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March 31, 2014

A Quick Clean-Up

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Posted by Derek

Well, while I wasn't watching over the weekend, the comments section to this post kind of veered off the road. I've deleted a number of trolling comments, and all the various replies to them, and further comments to that entry are now closed. I rarely do this sort of thing, but (ironically) I was just saying the other evening that pretty much the only time I delete comments is when they're nothing but ad hominem. There are plenty of other places on the web to trade insults and gibberish (some sites specialize in nothing but), so I don't think it's any great loss to the world if this site doesn't join in. We'll now resume our regularly scheduled programming.

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March 20, 2014

For Some Folks, It's New Year's Day

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Posted by Derek

A quick "eid-e shoma mubarak" to all those out there who are celebrating Norouz, the spring-equinox version of New Year's Day. My Iranian wife certainly is, and I will be pitching in by consuming large amounts of the home-made sweets that her mother has produced, and by frying a large quantity of fish for a big meal later on. For once, there's actually some blue sky and sunshine out there today (albeit with heaps of melting snow everywhere). But it sure beats a faceful of sleet, which has been the case several times in years past. (If you've ever seen the old W. C. Fields short, "The Fatal Glass of Beer", you'll get the idea of what my wife goes through on a typical New England Norouz!)

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March 5, 2014

Traveling Interruption

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Posted by Derek

My visit to Illinois went well, and I had a very good time talking to the students and faculty here in Champaign/Urbana. But American Airlines has decided not to fly anyone to Chicago today, so I've had to round up alternative transportation and reschedule flights, which isn't going to leave much time for blogging, from the looks of it. So normal service, or what passes for it around here, will resume on Thursday!

Update: traveling interruption is right. I was supposed to fly out of Champaign at 8 AM, go through O'Hare, and land in Boston at 1:45. As mentioned above, that 8 AM flight disappeared, so I took a shuttle bus up to Chicago - which, because of the snow and thick traffic, ended up taking over four hours to get to ORD. But I was still in time for my rebooked flight - if American hadn't rebooked me for that flight departing Thursday instead of Wednesday. The guy at the airport desk was as puzzled as I was about why anyone would do that, but got me on direct flight to Boston leaving at 1:20. Which was delayed. And delayed again. I did finally make it back to Logan close to 6 PM, feeling a bit as if I'd made the trip back on a pogo stick! I know that ORD is capable of far more than this, though, and I'm glad that I escaped any worse fate.

Comments (13) + TrackBacks (0) | Category: Blog Housekeeping

March 3, 2014

Out to Illinois

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Posted by Derek

I'll be visiting Illinois tomorrow to give a talk as part of the university's Chemistry-Biology Interface program. The first week of March is probably not the time to see the Champaign-Urbana landscape at its best, but then, I'm not leaving a lot of scenic grandeur behind in the Boston area this time of year, either. By March, winter's the guy who hasn't realized that everyone else at the party left a while ago. Fortunately, the snow that was forecast to mess with my flights today seems to have vanished, for once. . .

Comments (8) + TrackBacks (0) | Category: Blog Housekeeping

February 24, 2014

ACS Webinars on Drug Discovery

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Posted by Derek

I wanted to mention the ACS Webinar series on Drug Discovery, which will be going on every so often throughout the year. I'm going to be doing the introductory overview one, along with Rick Connell of Pfizer and Nick Meanwell of BMS, this Thursday, 2PM to 3PM EST. As you'll note from the schedule, there are plenty more of these coming up that go into more detail, so we're going to be setting the stage and taking questions from the audience.

Comments (10) + TrackBacks (0) | Category: Blog Housekeeping

January 2, 2014

Back Blogging (Bonus Biographical Begging)

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Posted by Derek

Blogging is now resuming at the usual pace around here, even though I'm actually still off work today and tomorrow, for various reasons. It's snowing merrily out there, anyway, so I'm just as glad not to be doing the commute. We look to get a foot or so of the stuff during the day and tonight, and tomorrow night we're supposed to get down to -11 F (-24 C), which means the only reason I'm going out is to fill the bird feeder.

I spent the holidays lounging around with family, cooking various unhealthy foods, reading a stack of books given to me for Christmas, and writing away on The Chemistry Book. I'm now up to about 140-odd entries of the 250 I need, and I'm on a pace to finish well before my deadline. I still have a dozen or so open slots to fill as new topics occur to me or turn out to need to exist.

For each topic I'm trying to give credit where it's due, and erring on the side of generosity. But each person mentioned has to have birthdates (and date of death, when applicable), and that's led me on a few research chases. There are still a few people I've been unable to run down, so I thought I'd put them out here to try to tap into sources of knowledge greater than my own. Here are my mystery people at the moment:

Hennig Brand (first isolation of phosphorus): I have c. 1630 to c. 1692, and I don't know if there are any better dates out there.

Eduard Simon fl. 1840, inadvertent discoverer of polystyrene

Carl Friedrich Claus, (1829 - ????) inventor of the Claus sulfur extraction process

Charles Watt, fl. 1850, first separated cell for the chlor-alkali process

Christian Dantsizen, one of the many people who helped come up with stainless steel

E. A. Prudhomme, helped develop the Houdry petroleum cracking process

Reginald Gibson and Eric Fawcett, polyethylene pioneers

Fred Joyner, with Harry Coover, developing cyanoacrylates at Eastman

Arthur Rosinger and Edward McLaughlin, developers of the magnetic stirrer

Peter L. Pauson, Thomas J. Kealy, John F. Tremaine from the discovery of ferrocene (I have the other players dated).

William G. Eversole, synthetic diamond researcher (I have several others).

Denis L. Rousseau from the polywater story

Andreas Ludi Modern structure determination of Prussian Blue pigment

Those are my missing biographical dates at the moment, but there will probably be more as things go along. If anyone has any information on these people, I would be very happy to hear about it! Thanks very much. . .

Comments (24) + TrackBacks (0) | Category: Blog Housekeeping

December 31, 2013

Cold-Weather Chicken Soup

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Posted by Derek

Since the weather forecast around here is for snow, and temperatures down to -9 F (-22 C), I thought a recipe or two for some cold-weather food might be appropriate. Here's a chicken soup recipe adapted from Craig Claiborne that I've been making for twenty years now - that is, it's pretty reliable.

1 chicken (in the 3-to-4 pound or 1.5 kilo range)
Corn (fresh or frozen), about 2 cups or 500 mL volume (or more to taste)
Egg noodles (4 oz. / 0.15 kg or more, depending on taste)
Two hard-boiled eggs
Fresh parsley

Take the chicken, cover it in water, add a teaspoon of salt (6g) and some ground pepper, bring to a boil, then turn the heat down to a simmer. Cook it this way until the meat begins to come off the bone a bit - that will take at least an hour, perhaps closer to 90 minutes. Take the chicken out of the broth and let it cool enough to shred the meat off by hand.

Skim some of the fat from the broth - depending on the chicken you started with, there will probably be more of that than you want. (If you have lots of time, such as making this soup for the next day, you can chill the whole thing and remove the fat that way). Either way, get things back to a low simmer and add the corn at this point - if you're using frozen corn kernels, give the soup about five or ten minutes to heat back up. Then add the egg noodles - the quantities of both of these can be adjusted to how thick you'd like the soup to be, but the amounts given are a good starting point. Simmer for 8 or 10 minutes to get the noodles cooked, then grate the hard-boiled eggs into the soup and add the reserved chicken meat. Serve with chopped fresh parsley in each bowl.

Comments (14) + TrackBacks (0) | Category: Blog Housekeeping

November 27, 2013

Russian Soured Cabbage

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Posted by Derek

Here's a recipe that I'm trying out this year from The Joy of Pickling, an excellent book full of all sorts of pickle recipes. I have a good-sized batch of this going right now, and samples so far confirm that it's good stuff.

1 2 1/2 pound cabbage (1 kilo), shredded
1 tablespoon salt (17 to 18 grams, table or pickling, not kosher, unless you want to adjust the amounts)
1 medium carrot, shredded
1 apple, sliced
1/2 cup cranberries (55g)
1 tablespoon caraway seeds (7g)

Cut the core from the cabbage, save a couple of outer leaves, and shred it. Add the salt to it in a large bowl, mixing it in well and pressing it together. Add the carrot, the apple (cored and sliced into 16th, the book says), the cranberries and the caraway seeds, and mix gently. Place this mixture in some sort of deep crock or jar (jars, if need be). Press the mixture in tight and lay some of the reserved cabbage leaves (or a piece thereof) on top. Weight this down with a small plastic bag (one that's OK for food) full of brine (made from 1.5 tablespoons of salt (24g) in one quart (950 mL) water) - this will keep the cabbage under the liquid layer. If your cabbage was fresh, it should make enough liquid to submerge itself. If not, you can check it after sitting overnight and add some brine (1 tablespoon of salt (18g) in one quart (950 mL) water) to just cover the shredded cabbage.

Leave the jar or jars at room temperature. Twice a day, you'll want to stick a wooden spoon handle down in there a few times to vent the carbon dioxide that will develop. If you don't, especially at first, you're like to have an overflow, so be warned. Four or five days, at a minimum, should do the trick - after that, you can keep it in a cold room or refrigerator. If you ferment it from the start in a cooler room, it'll take longer, but may have even better flavor. According to the Joy of Pickling, the initial burst of gas is from Leuconostoc mesenteroides, which produces good anaerobic conditions for Lactobacillus plantarum, among others, whose acid fermentation products give the sour flavor.

If you like sauerkraut, you'll be very much up for this. If you're not a big kraut fan, have no fear - this is a lot milder and more delicate than the store-bought stuff, and tastes something like rye bread with all that caraway in there. Enjoy!

Comments (14) + TrackBacks (0) | Category: Blog Housekeeping

Thanksgiving: Never Trust An Organic Chemist Who Can't Cook

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Posted by Derek

I wanted to note that I'm home today, and will soon be starting my traditional chocolate pecan pie. If you haven't seen it, that link will lead you to a detailed prep, with both US and metric measurements. It's based on Craig Claiborne's recipe, and he certainly knew what he was talking about when it came to Southern food (and much else besides). I've been making it for twenty years now, and if I didn't, there would be a mutiny around here.

I have a pumpkin pie to make as well, and I'd like to get the base of the gravy going, so it can be turkey-enhanced tomorrow. (As for the turkey, for some years now we've bought a kosher one, so it's already been brined. A 17-pound specimen is waiting for tomorrow efforts). I hope to also make some green beans with country ham, since that reheats just fine, and will save on stove space tomorrow. For country ham, I can recommend Burger's from the Ozarks, available through that Amazon link. Pan-fried country ham has been my traditional Christmas breakfast for my entire life, and my wife and kids now join in with me on that one, but I break it out for Thanksgiving with the green beans. For me, it's wintertime food - I wouldn't turn it down if someone served it to my in July, but it certainly would be a new experience. I grew up eating a brand called Mar-Tenn from west Tennessee, but I don't even know if they exist any more.

The rest of the Thanksgiving meal will include an Iranian basmati rice (with saffron, slivered almonds, sour dried zereshk berries, pistachios, and bits of orange zest), home-made mashed potatoes, creamed onions with sage, pan-roasted Brussels sprouts, and stuffing (my Iranian mother-in-law's own recipe, with bread cubes, cranberries, celery, onion, and pepperoni - how she thought that one up, I don't know, but it's excellent). And this year I'm trying out some Russian sour cabbage (with apples, cranberries, and caraway seeds), which is fermenting away in the basement right now. I'll post the recipe for that later on in the afternoon, after I've made some culinary headway. Update: forgot the stuffed mushrooms and the roasted acorn squash. It's hard to keep track of it all after a certain point!

Comments (28) + TrackBacks (0) | Category: Blog Housekeeping

November 22, 2013

Things People Won't Listen To?

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Posted by Derek

Here's a podcast interview I did recently for "Science For the People" (formerly known as "Skeptically Speaking", where they quizzed me about some of the "Things I Won't Work With" compounds. The whole show is worth listening to (there's Scicurious and ZeFrank in there, but I come in at about the 38 minutes mark.

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November 1, 2013

Chemist At Work

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Posted by Derek

1113CW-In-the-pipeline_630m.jpg
Well, now I know the previously-obscured downside of writing a monthly column for Chemistry World. This month's entry is on emulating enzymes, and it's adorned by the illustration shown here (© "The Hit Man", so it says). I just emailed the link to my wife, and after she caught her breath from laughing, she noted the following for verisimilitude: "Tell them that you don't wear a tie. And that your height-to-width ratio is better. And that your beard isn't all that fearsome." Nothing, you'll note, about my tongue hanging out. That part is apparently true to life.

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Chemistry Job Postings: Worth a Try

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Posted by Derek

Once in a while I've mentioned open chemistry positions here on the site, but I've decided that I really should make it a more regular feature. I've been worried about the extra workload that it might bring on here, but I think it might work. Chemjobber already does this, of course, and I'd recommend that everyone in the market keep an eye on his blog for information. But on a trial basis, I'll posting occasional notices that I get through e-mail, from people specifically trying to reach this blog's audience. I've created a new category ("Job Postings") for anyone wanting to put all of these together.

So here's an open call for anyone who has openings that the chemists around this site might be able to fill. Send along your details, with some sort of contact information, and I'll put them up as separate short notices here. No warranty is expressed or implied on either side, naturally - I'll just be serving as a middleman, and no money is changing hands. This is pro bono, and we'll see how it works out!

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October 28, 2013

Back to Hendrix

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Posted by Derek

It was a very strange experience to speak to a crowd of students in the same room where I had my first college chemistry course. I could see the row of seats where I used to sit 34 years ago, and I was glad that I was speaking later in the morning than that old class used to start (7:40 AM, and no, my notes were not always coherent). I wasn't able to relive the experience of walking into the old labs, though, because they've been extensively renovated and are far nicer (and more functional) than they were back then. The building itself has been expanded, like many other parts of the campus - from some angles, the place looked almost exactly as it did in the early 1980s, but from others, it looked the way your old school does when you have a dream about it, with odd buildings somehow added to the landscape.

The students themselves were excellent hosts, and seemed more poised and on top of things than I remember us being back then. But I think that's a common impression that people have during such visits. My guess is that we simultaneously over- and under-rate our previous selves; the accurate picture is the hardest one to get into focus. I fielded a lot of good questions about chemistry and drug research, but I also had sympathy for the guy who was falling asleep during the first class I spoke to. I'd already done the math: here I was, thirty years after graduating, and what would I have made back then of some guy from the class of 1953? I'd have been sure that I was looking at a figure from the nearly unimaginable past. And he wouldn't have been able to tell my twenty-year-old self what I couldn't tell these students: that they'd be surprised how fast that amount of time can seem to pass, and that seeing the campus from some angles made it feel as if I'd been gone for maybe six months. Not so.

Tom Goodwin, who launched me on my own chemical career, turns up everywhere when you look into the literature on mammalian chemical communication. If you'd told him back in 1981 that he'd be collaborating with people around the world and spending his time flying around to places like Rwanda and New Zealand, he might have had a little trouble believing you. He was the only organic professor when I was an undergraduate, but they've now added Chris Marvin, and talking with his students about ruthenium-catalyzed photochemistry, which I'd been doing recently in my own lab, was a lot of fun. I didn't try to tell them about how odd it felt to see a 400 MHz NMR in a building where the highest-field instrument used to be a 60 MHz EM-360. There was a 30 MHz machine in the teaching labs - it was a doorstop even when I was a student, and most people (fortunately) will have never seen an NMR with a field so puny. (At least it didn't look like this).

That picture in the upper right left is me when I was in one of the (now reworked) labs back in 1983. That's a collection of T. S. Eliot that I'm reading next to my gravity column, and I managed to quote him during one of the classes I spoke to, to keep up my liberal arts credentials. Thanks again to everyone there for having me!

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October 24, 2013

Travel (Back to Arkansas)

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Posted by Derek

I'm writing this entry from my old school, Hendrix College, who are having me back for an awards ceremony. I'll be speaking to some of the classes while I'm here, and trying to find my way around after 30 years of building and renovation. But it's nice to see where I first learned chemistry, I have to say. . .

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October 10, 2013

Cambridge Meetup Final Plans: Noon by Broad Canal Way

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Posted by Derek

OK, after investigating several options, I think that we'll stick with the courtyard down by the kayaks/parking kiosk on Broad Canal Way. It'll be a bit on the cool and cloudy side, but it is October. I'll be there at noon, and everyone should just round up whatever lunch they like and bring it along with them. Looking forward to seeing what sort of crowd turns up!

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October 7, 2013

Cambridge "In the Pipeline" Reader Meetup: October 10

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Posted by Derek

Update: we're on for noon Thursday, at the courtyard down by the kayaks/parking kiosk on Broad Canal Way.

Looking at the response, it looks like this Thursday the 10th would work out for a good number of people who've expressed interest, and the weather forecast looks good. So let's try for it then - say, 12 noon?

Now, the venue. I think the MIT food truck area makes sense for throughput and number of options, but there's not much seating around there, or even standing room. The indoor food court across the street is an option for rain, but it looks like we won't need it. Further down, the plaza near the kayak place on the canal has more seating and room in general, but I'd guess that we would overwhelm the burrito place's window there. So we could try to meet there, with each person bringing their food from wherever they like. Or if there's another option near the food truck area for people to gather, I'd be glad to hear about that. I'll update this post with more details

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October 2, 2013

An "In the Pipeline" Meetup in Cambridge?

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Posted by Derek

Update: we're on for noon on Thursday, at the courtyard down by the kayaks/parking kiosk on Broad Canal Way.

I've been meaning to do this for some time, and more than one reader has mentioned the idea to me in e-mails. Would the local (Cambridge/Boston) readership be interested in an informal get-together at lunchtime next week (Oct 6 - Oct 12)? The only day that's out for me is Wednesday, October 9th, otherwise my schedule looks like can take whatever comes.

My guess for somewhere to congregate might be the line of food trucks near MIT, but other suggestions are welcome. This will depend on the weather, of course, which is unknowable at this point. But if you're interested and have a preference for which days might work, leave a note in the comments section. Thanks!

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September 30, 2013

A War On Expertise?

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Posted by Derek

I see that Popular Science is shutting down the comments function on their web site. Like a lot of news organizations, I think that their signal/noise was pretty low in the comments. (And that prompts me to express, again, my appreciation for the commenters on this blog - one of the first questions I get when I talk to anyone else who runs a web site is how on Earth the comments section around here stays so readable and sane!)

They're citing some experiments that seem to show that fractious comments sections actually make the original posts above them seem less reliable, and that may be how it works. In reality, my impression is that if a site seems to have a lot of fist-waving in the comments section, that pretty soon most readers don't even bother with it, and the only ones that show up are there for the fights. I'll say this for the Popular Science folks - they're not doing this for monetary/traffic reasons, because wildly argumentative comments sections also drive traffic from the people who just can't stay away (and hit "Refresh" over and over in the process).

Here's the key quote from their article:

A politically motivated, decades-long war on expertise has eroded the popular consensus on a wide variety of scientifically validated topics. Everything, from evolution to the origins of climate change, is mistakenly up for grabs again. Scientific certainty is just another thing for two people to "debate" on television. And because comments sections tend to be a grotesque reflection of the media culture surrounding them, the cynical work of undermining bedrock scientific doctrine is now being done beneath our own stories, within a website devoted to championing science.

I know where they're coming from, but I'm not so sure about that "again". My belief is that there hasn't been a time when evolution was not controversial with many people, nor climate change/global warming. The internet, it's true, gives everyone with a point of view a chance to ventilate, so it brings this sort of thing to the surface much more easily than in the past. (Look back a few decades, and ask yourself what was available to someone with a strong opinion. Letters to the editor? Soapbox in the park? Handling out flyers on the corner?)

And I don't think that there's been any big, coherent, "decades-long war on expertise". If there is, then there always has been. It makes a person feel better to believe these things, but that's the sort of self-congratulatory thinking that I believe one has to avoid. "I'm too smart for the crowd, the mob - a member of a persecuted minority just because I see the truth. . ." That doesn't do anything to help your own reasoning.

No, most people don't understand scientific topics, but most people never have. If anything, I'd be willing to bet that the population today is more literate in these matters than ever before. The sorts of people who go hunting through web sites looking for things to confirm their own opinions have always been with us. As have groups who'd rather obfuscate topics than debate them, for reasons of their own. We just have a better look at the whole process these days.

Comments (45) + TrackBacks (0) | Category: Blog Housekeeping | General Scientific News

September 2, 2013

A Quick Recipe: Lime Sorbet

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Posted by Derek

This is not a complicated thing to make, but it's terrific. My family and I polished off a large batch of it last night - it's still warm and humid enough around here to make it an excellent dessert. The only thing you need is some sort of stirring ice-cream freezer - we have one of those where you put the cylinder in the freezer for a day, and then turn a hand crank. But anything will work, as long as it's cold enough and allows you to keep mixing.

The ingredient list is short. Fresh lime juice really is essential, though, although if you have lemons around, lemon sorbet is (naturally) the same recipe, and is also excellent.

1 cup (250 mL) fresh-squeezed lime juice
1.5 cups granulated white sugar (300 grams)
Enough water to take the volume to 4 cups (1 liter)

Squeeze the lime juice. If you want a really smooth texture in the finished product, you can strain the pulp out, but I don't bother. Add the sugar, adjust to the final volume with water, and stir to dissolve. The sorbet will form more quickly, of course, if you chill this mixture beforehand. Add this solution to the ice-cream maker, and stir steadily until the mixture is very thick. Constant stirring will keep the sides from icing up, and make the finished product more homogeneous. I've found that you need to keep freezing things past when you think it looks ready, as the sorbet gets looser once it's being dished out. You'll also probably need to stir it again during that process; some syrup tends to pool up in it as it stands.

If you like the flavor of lemon or lime, this is probably going to be the best sorbet you've ever tasted. There's nothing like the fresh juice, and this will give you a cold, concentrated blast of it. These proportions are a little more sour than the ones given by Harold McGee for a "sweet fruit ice" in his book The Curious Cook, so if you find this a bit acidic, you can add four tablespoons more sugar (50g) to the mix next time. McGee's book has a chapter which includes tested recipes for doing this sort of thing with a huge variety of fruits, so it's worth seeking out if you find that this is your favorite route for self-administering vitamin C.

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August 30, 2013

Totally Off Topic: My Appearance on Jeopardy!

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Posted by Derek

I've had several requests for details about the time I was a Jeopardy! contestant, since I mentioned it in passing the other day. So for the holiday weekend, I thought I'd provide the story. This was all back in 1995-1996, when I lived in New Jersey, and that's actually how I got into the entire business. Coworkers had told me about how the Merv Griffin production people would be administering the test to get on the show down at the Resort International casino in Atlantic City (also owned by the Griffin company), so I drove down to try it out.

The test was only a short one, meant to be done quickly as a screen, and none of the questions seemed particularly hard. I spent the rest of my time in AC working on my card-counting skills at the blackjack table, which was not too lucrative. In fact, under the rules then - and I'm sure they've gotten no better - the same amount of time and effort applied to almost any other activity would surely have provided a greater return. (But at least they couldn't throw you out, as opposed to Las Vegas).

Not too many days later I got the invite to come down for the longer test, which had many more questions, all of which, I think, were from the $1000 category on the show. This was at the same casino, and I knew that morning, on the drive down, that I was in trouble. I'd gotten a late start, it was rainy, and there was more traffic than I'd counted on. I pulled in a few minutes late, bounded up the escalators, and was met by a lady sitting at a long table in front of a closed door. "I'm sorry", she said, "the test has already started".

"But there's another one in a couple of hours", she said, to my surprise and relief, "so we'll just put you down for that". Just then, there was the sound of someone frantically taking the escalator steps two at a time. Into view came a guy who looked even more frantic than I had - shoes untied, shirt half tucked in, hair sticking up on one side. "Don't worry!" I called. "There's another test later!" He caught his breath while taking in this news, and it was then that I noticed that his hands were full of almanacs and trivia books and the like. We walked off together, and he said "Good, good. . .this will give me time to study up some more!"

"I'm pretty much done with it", I told him. I had been brushing up over the last week on things that I didn't have covered so well - opera, Academy Award winners, some sports records and American presidential trivia - but I wasn't lying to him at all. I figured that if I didn't know something by the day of the test, I was unlikely to remember it when I needed to. "No, I've got to read up on things," the guy said, then turned to me and said "For example, what's the capital of Uzbekistan?"

"Tashkent", I told him, with no hesitation. Science, literature, history, and geography were my strong areas. He looked startled. "Oh s$%&!" he said, and sped off for parts unknown, there to clarify his map of Central Asia. After lunch it was time to take the test (much more challenging), and to wait around while the staff graded our sheets. They then called everyone together and read off the names of the people who had passed. Mister Tashkent did not seem to be among them, and I wondered if I'd fatally psyched him out. We did some dry runs of the game at that point, which served (from what I could see) to weed out the people who kept going "Ah. . .ah. . .um. . ." whenever it came time to answer a question.

And that was that, for a few months. They'd told us that we were on the list as possible contestants, and there was no way of knowing when or if we'd be called. But one day I had a message from LA, with the day of a taping, and I flew out for it quite happily. (I should note that the show covered not one penny of expenses, at least for the regular daily contestants). I showed up at the studio nervous but ready to go.

I got to see a couple of shows taped with some of the other crop of contestants before my turn came, and that gave me a chance to see some of the workings. The key to the whole thing was the moment of picking and answering. You had a chance to read the clue off the monitor while Alex Trebek was reading it out loud, and that was the time to figure out if you knew it and to prepare to try to answer it in the form of a flippin' question. You could not press your contestant's button too early, though - as they explained in detail, that locked you out for a delay period if you tried it, which would almost surely leave you without a shot. Timing was crucial. You had to wait for Trebek to stop speaking, wait about a sixteenth note of time, and then hit your button.

With the other two guys in my taping, that generally meant that all of us sat there poised while Trebek read off an answer, and then suddenly clickityclickityclickclick we'd all hit the buttons, so close to simultaneously as seemed to make no difference. There were a few times that I knew I'd reached out and snatched the right to answer a question, but others where I thought I had (but hadn't), along with a couple where I was as surprised as anyone else when my light came on.

It all happened very quickly, and took a lot of concentration and fast thinking. The effort of reading answers and coming with questions, while simultaneously watching the timing, deciding which category to go for, and keeping up with the score of the game was plenty to deal with. I remember two parts of the game very clearly, though. At one point, the taping paused for the commercial break, and some staff members came out to reapply makeup. I needed quite a bit, and Trebek remarked to the guy "You don't spend that much time on my makeup". "You don't sweat this much, Alex" came the response.

The other part I recall clearly was the Daily Double, which I was actively prospecting for whenever I had control of the board in the second round. I'd lost out on a few questions, and needed it to get back in the game. To my happiness, it came up in Geography, and I bet most of what I could. Up came the answer: "Lake Nasser sits on the border of these two African countries". My brain immediately pictured a map, while I played for time. Nasser could only mean Egypt, but I was having trouble figuring out the second country. "What are Egypt and. . . ." I started, while thinking to myself that it couldn't be Libya, that was a total desert out there. . .and the other side of the country, that was a coastline, the Red Sea. Trebek was looking at me, eyebrows raising a bit in anticipation, as if to say "You're not going to blow this one, are you?", as I finished with ". . .Sudan!". He gave a quick smile, and we were off again.

By the end of the game, I was in second place by $200 or so, a close race. The final Jeopardy category was English Literature, which gave me great happiness. The clue was "Mellors is the gamekeeper in this novel", and I immediately wrote "Lady Chatterly's Lover" on the scraggly, time-delayed screen. My only hope was that the guy ahead of me didn't get it, but alas, we all did. I lost, $13,300 to $13,100. The sensation was exactly that of coming off a carnival ride; the first thing I wanted was to go around again.

What valuable prizes did I win? Furniture, which I decided later to decline. I believe that a lot of it gets turned down like this, and probably for similar reasons to mine. I didn't care for the style, and had no place to put it. I could have perhaps sold it to someone, but this was pre-Craigslist, and in the meantime I was going to be paying tax on the full retail value, both to the IRS and to the state of California (a state tax form had been included in my going-away packet). A couple of weeks after I got back home, a package showed up with some boxes of Miracle-Gro, various flavors of cough drops, and other "Some contestants may also receive. . ." items (but alas, no Rice-a-Roni, which my family never ate while I was growing up, and which I always associated solely with game shows).

So that was my Jeopardy! experience. I enjoyed it tremendously, and I told people when I got back that I would have liked to be a contestant on the show for a living. A diet of Miracle-Gro and cough drops might have eventually impaired my button-pressing response times, though.

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July 23, 2013

A Chemical Biology Conference

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Posted by Derek

I wanted to mention that I'll be attending this conference ("Challenges in Chemical Biology") over the next few days, and hope to blog some from the sessions. It's not much of a trip - MIT is just down the street from my office - but it looks to be a good meeting. Any readers who might also be attending, feel free to get in touch!

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July 12, 2013

Comment Troubles

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Posted by Derek

As many of you have discovered, something is currently hosed up with the commenting function on the site. It's a glitch, and behind-the-scenes work is underway. So if you get some sort of error message when you try to leave a comment, hold those thoughts and try again later - thanks!

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July 4, 2013

A Fourth of July Recipe: Pork Tenderloin and Sour Onion Salsa

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Posted by Derek

In keeping with tradition around here, I wanted to put up a recipe for the holiday. It's pretty hot out there for standing next to a grill (but I'll be doing that later today anyway!) Here's one that gets made around here at Pipeline Headquarters fairly often. It's not something that can be whipped up quickly (it needs some marinating time), but maybe for the coming weekend. The pork tenderloin recipe is similar to many others floating around, and can be added to and adapted as needed. The onion salsa is adapted from a Steve Raichlen recipe in The Barbecue Bible, a book I've had a very high success rate with.

Grilled Pork Tenderloin
Here are the quantities for marinating one pork tenderloin (400 to 500 grams / circa one pound). You can adjust to suit your needs, of course:

40g salt (see Note 1)
50g brown sugar (or three tablespoons)
15g Dijon mustard (one tablespoon)
Two cups water
One pod of star anise
1g whole black peppercorns (1/2 teaspoon)
Two bay leaves

Dissolve the salt, sugar, and mustard in the water. Crush the anise pod and peppercorns (mortar and pestle if you have one, whacked in foil or plastic wrap if not) and add them and the bay leaves to the mix. Soak the pork tenderloin in this brine (plastic bag or covered bowl) for several hours in a refrigerator - overnight is good.

Remove the pork from the treatment vat and grill it over high heat for ten minutes, turning it to brown the surface. Then reduce the heat, or move it to a less directly heated part of your grill, and cook it there until its juices run clear. (See Note 2). Let the meat rest off the grill for a few minutes, then slice and serve.

Note 1: this is in the "2 or three tablespoons" range of something like Morton kosher salt, but salts vary tremendously in density. Notoriously, the two leading brands of kosher salt in the US, Morton's and Diamond Crystal, are off by nearly a factor of two, a conversion which has led many to grief. Table salt is denser still - see the link.

Note 2: These are not very scientific directions, but grilling is not a very scientific form of cooking - everyone's heat source is different, and things are hard to quantify. The brining treatment will generally keep this meat from drying out so quickly - a good think, since unbrined pork tenderloin can get that way quite easily. But you'll need to use your own judgment here. If you're not grilling this, you can brown the outside in a hot oiled pan and then bake it, or carefully broil it, with frequent turning, to achieve a similar effect.


Sour Onion Salsa

1 large red onion
125 mL fresh lime juice
125 mL orange juice
12 g salt (two teaspoons of table salt)

Peel the onion and cut a slice off the stem end. Place that flat side down and cut the onion into six or eight wedges. Grill these on both sides (the root end will hold them together as they cook) until they're somewhat charred. Remove them from the grill, let them cool a bit, then trim off the root ends and add the salt and citrus juices. Let these marinate at least a half hour at room temperature, stirring every so often.

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July 2, 2013

A Quick Traffic Update

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Posted by Derek

I'm traveling today, and have no time for a blog post, but I wanted to thank everyone for another record month of traffic around here. Nearly 820,000 page views beats even the previous outlier, back in April when I was linked to by xkcd.com. And I owe that, of course, to those Eight Toxic Food Additives, a post that got picked up all over the place (and is still echoing around). But I also owe that figure, naturally, to everyone who's taken the time to stop by - so thanks!

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July 1, 2013

Travel and Upcoming Posts

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Posted by Derek

I'm traveling for the next couple of days, and then we have the July 4th holiday coming up. So blogging will be a bit irregular around here this week. By popular demand, I am planning a couple of large posts that follow up on the "Eight Toxic Foods" craziness, though. One will look at why some of the allowed US ingredients are banned in some other countries, and the other will look at the reverse: ingredients and additives that are banned in the US, but allowed abroad. Those will start showing up next week.

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June 18, 2013

New Photos, Same Blather

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Posted by Derek

I've been meaning for some time to put up some new photos on the site, what with the original one being over ten years old by now. So here we are - a progress through time. The beard remains a constant, and I still have the T. S. Eliot paperback that I'm reading in the 1983 shot. That's an old flash column next to me, drying out because I was too lazy to clean it out, and some TLC plates on the bench. I was doing carbohydrate chemistry, forming nitrones and doing cycloadditions, and I'm not at all sure that I've ever done a nitrone reaction since!

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May 1, 2013

Best Sites for a Medicinal Chemist?

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Posted by Derek

I'm going to be traveling today, mostly through airports without good Wi-Fi (for which read "Wi-Fi that they don't want me to pay $10 for during my 90-minute layover"). But I wanted to put out a question sent in by a reader that I think would be worthwhile:

What are the best web sites for a medicinal chemist to have bookmarked? Resources for medicine and biology, organic chemistry, analytical chemist, and pharma development would be appropriate. There are shorter lists available here and there, but I don't think that there's One Big List that easily findable, and I think that there needs to be one. Suggestions in the comments - that should put together something pretty useful.

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April 30, 2013

Travel (University of Wisconsin)

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Posted by Derek

I'm in Madison, Wisconsin, where I'll be giving the Organic Chemistry McElvain Seminar later on today. The title of my talk, which I'm not sure if I'll live up to or not, is "Medicinal Chemistry: Getting Old, Or Just Starting to Grow Up?". It's at 3:30 in the Seminar Hall, room 1315, if you're passing through (!)

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April 19, 2013

Not the Usual Morning Around Here

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Posted by Derek

Things are a bit. . .unusual around here today. I'm home; my company (and others in Cambridge) called about 6 AM to tell all employees to stay put. What with mass transit shut down and everyone off the streets, I can see the point! And truth be told, I feel a bit odd, knowing that the gunfire, etc. last night started a few blocks from where I work. This is all happening miles to the east of where I live, but it still looks like a good day to stay off the roads. . .

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April 15, 2013

Traffic and More Traffic

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Posted by Derek

Well, although this is only the 15th of the month, today I'll already break my monthly traffic record for the site. That's thanks to a link from xkcd's "What If" page, which led to a couple of mentions on Reddit, which led to a front-page link at ycombinator's Hacker News, and who knows what else. Update: such as a mention on Twitter from Adam Savage of Mythbusters! Many thanks to everyone who's stopped by, and especially to those who have been linking!

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March 26, 2013

A Malfunctioning Spambot

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Posted by Derek

A quick behind-the-scenes note: anyone who has a blog has to contend with comment spam. It seems like something that has no chance of leading to any clicks or any money, but it piles up anyway. Hundreds of junk comments sometimes show up in a single day around here, most all of which automatically go right into the bit-bucket and are never seen (by me or anyone else). As a side effect, that means legitimate comments that end up in the spam folder have to be rescued pretty quickly, or they'll scroll off into the void, pushed along by illiterate come-ons for replica sports jerseys and implausible money-making schemes.

A few of them make it in each day, though, and I noticed this morning while taking out the blog-trash that one spammer seems to have glitched up. Behold, pretty much every vague, oddly worded blogspam comment all at once, complete with Mad-Lib style word lists at every opportunity. I couldn't help but {laugh | cackle | snort} at the {stupidity | incompetence | cluelessness} of this {garbage | crap}.

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March 23, 2013

Quick E-mail Housekeeping Note

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Posted by Derek

I wanted to mention that several e-mails sent to me last night and this morning (Friday night and Saturday AM, EST) got deleted inadvertently while I was fumbling through them early this morning. There were some that I'd like to respond to, so if you sent me something recently, please feel free to re-send it. Note: this request does not apply to the people who keep asking if I will be a speaker at the First World International Summit Congress of Everything for Everybody, to be held somewhere in southern China, or to anyone who starts off by saying "Dear Purchasing Manager".

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March 20, 2013

Off Topic: Happy New Year, In March

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Posted by Derek

For those of my readers who are celebrating it, eid-e shoma mubarak! That's "Happy New Year" for Iran, Afghanistan, and a number of nearby areas. It's a Zoroastrian-derived holiday, on the solar calendar, and thanks to my Iranian wife we celebrate it at home. I can fully endorse the emphasis on special holiday sweets (such as sohan, which I'd describe as a dark saffron-flavored almond brittle) and large quantities of other festive foods. We'll be having a traditional meal of spicy fried fish later on, which fits my Arkansan sensibilities just fine. So, happy new year!

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February 25, 2013

An Interview

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Posted by Derek

For those of you with subscriptions to Trends in Pharmacological Sciences, they have an interview with me up at the journal's site. It's in the "Scientific Life" section, and I was very happy to be asked to do it.

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February 8, 2013

Snow Versus Scientific Progress

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Posted by Derek

In case anyone's wondering, I'm not even at work today - no one at my company is; they announced last night that they were closing down for the day, which was welcome news. For those of you not living in the Northeast US, it's been snowing merrily along since earlier this morning, and by the time it finishes tomorrow, we look to have about two feet of the stuff.

Research will be slow today in this part of the country. I'm sure to see that in the traffic figures for the site - there's always a spike at lunchtime EST, a slight dip, and then another spike at lunchtime on the west coast. I think that the Central and Pacific zones will win out this time!

The largest single snowfall I've ever experienced was in January 1996, back in New Jersey, where we had 39 inches (one solid meter) in a single storm. I remembering opening one of those doors at the bottom of the apartment-complex building and staring in amazement at a drifted wall of snow that came up past the middle of my chest. This was one of those hunt-for-the-cars kind of storms. And I well remember the winter of 1977-78, which is still a standard in many parts of the country. I experienced that one in high school back in Arkansas, so I didn't get the apocalyptic snow mountains, but it was certainly impressive enough by the standards of the area (complete with a record amount of missed school!)

So for those of you not getting snowed on, well, you have to make up for the rest of us today. I think I'll get everyone to start on the Elements Jigsaw Puzzle, myself. Note: corrected this from the earlier "crossword". If anyone has a periodic table crossword puzzle, though, I'd be glad to hear about it).

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February 1, 2013

A Traffic Record

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Posted by Derek

I wanted to thank everyone who comes here for making January the biggest traffic month ever on the site: just over 480,000 page views. That seems like a lot for a site that features no cat videos (not that there's anything wrong with cat videos), no partially clad women (not that there's anything wrong with them, either), and no continually raging flamewars in the comments section. Actually, the comments section here has one of the highest signal-to-noise ratios in the whole blogging world.. Other blog owners have asked me many times how I do that last part, and I just have to tell them honestly that I don't - the people who read the site are responsible. So thanks again to everyone who visits!

Thanks are also due to those who have hit the various Amazon links that I put up from time to time. The affiliate payments those bring in get spent in, among other things, swelling the book collections around here to even more alarming levels.

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January 1, 2013

Another Recipe: Cornbread

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Posted by Derek

Here's the cornbread that I made to go along with the bean soup - in fact, I'm eating a piece now as I write this. This is adapted from the Cook's Illustrated people, and I've found this to be one of the better all-cornmeal recipes I've tried (a lot of recipes have half wheat flour and half cornmeal, but some of the other all-cornmeal preps come out with an odd soapy flavor, in my experience.

The quantities below are for an 8-inch (20 cm) cast-iron pan. An old black iron skillet is the traditional cornbread implement, and it's probably not possible to improve on it. I've doubled the recipe, though, and done it in a 9-inch round Calphalon frying pan, which worked fine. A Pyrex dish also works, but doesn't produce as good a crust. Using something that can be heated is key.

So what you want to do is heat an oven to 450F (230C). Take your pan, whatever its material, and put enough oil in it to cover the bottom plus a bit more. Bacon grease is traditional, and cooking a slice or two of bacon in the pan while it's heating up will provide just what you need. Update: At any rate, you want to heat up the pan in the oven while you're getting the batter ready.

While things are heating, take 1/3 of a cup (45 grams) of corn meal and put it in a medium-sized bowl. Then take 2/3 of a cup (90 grams) of corn meal and mix it, in another bowl, with a bit over a teaspoon (5 grams) of granulated sugar, 1/2 teaspoon (3.2 grams) of salt, 1 teaspoon (5 grams) of baking powder, and 1/4 teaspoon (1.25 grams) of baking soda (sodium bicarbonate). Blend these dry ingredients together.

Now bring 1/3 cup of water (just under 80 mL) to a full boil, and add this to the plain corn meal in that first dish. Stir it around to make a homogeneous mush out of it, then add 3/4 cup (about 175 mL) buttermilk to that (regular milk can be substituted; the product will be a bit less assertive). Mix this until homogeneous, then mix in one beaten egg.

Add the dry ingredients from the other bowl and stir to form a batter. Now it's time to get that hot pan out of the oven. Quickly swirl the oil or bacon grease around in it to make sure everything's coated, then pour any excess over into the batter and give it a fast stir, then pour the mixture into the hot pan before anything cools down. Back into the oven it goes for about 20 minutes. If you've doubled the recipe in a larger pan, that'll be 25 minutes, perhaps a bit more.

This should make cornbread that any Southerner would be glad to eat. It's not sweet corn-colored cake, like a Northern corn muffin - those were quite a surprise to me when I first moved up to New Jersey. The hot pan will give it a thin brown crust, and you'll often see these served with that side up on a plate, the way that they fall out of the pan. It is, I can testify, excellent with the bean soup recipe posted earlier today, but will also stand up to almost any soup or stew that you care to throw at it.

Variations are legion; many of them are good. You can add creamed corn to the batter, in which case you'd cut down on the milk. Whole-kernal corn is another classic addition, as are chopped jalapeños. I've seen diced red onion go in there as well. Some shredded cheese will make the whole thing richer. Crumbled bacon (perhaps from the slices you used to grease the pan) is another fine addition, and if you have access to pork cracklings, then you'll be making a variation that I first had in Tennessee over 40 years ago. Enjoy!

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A Bean Soup Recipe, With Bonus Country Ham Talk, And a Cameo By Frederick the Great

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Posted by Derek

I haven't put up any recipes during this break, so I thought I'd get moving on that a bit. Today I'm making a simple one - it's over across the kitchen from me as I write. It's a bean soup that my father often made for New Year's Day, as sort of a counter to the richer, fancier stuff that preceded it during the holidays.

Sitting out in the back yard during the summer, I tried a thought experiment out on my kids. What, I asked, if we had to grow all our own food, on the land we have here in the yard? Could it be done? And if so, what crops would you pick? Some favorites, such as tomatoes and cucumbers (the very things we had growing over in the sunnier part) were eliminated early as not providing enough food value for the space and effort. I pointed out that our yard was not a very large plot of arable land, which meant that we'd have to go first for the maximum yield of calories per area planted, with an aesthetic factors coming in way down the list, if at all. The life, that is, of a peasant. My first choice was potatoes, based on the survival of the Irish farmers (well, at least until the rot) and the gunpoint recommendation of Frederick the Great. Then corn and beans, based on New World agriculture. All three also rank high for their winter keeping qualities - as I mentioned to the kids, we'd have to pile up as much food as possible in the basement and garage to make it through a Massachusetts winter. They didn't find the prospect too appealing, which was one point of the whole exercise.

So here's the bean part of the equation. No doubt it's the sort of thing my own ancestors used to eat this time of the year:

Take 1 pound (or around 0.5 kilo) of dried white beans. I use Great Northern, but just about anything should work, I'd think. Soak them overnight at room temperature in four volumes of water or so - they can sit for longer, if you want to make them later the next day, but I'm sure there's an eventual limit imposed by incipient fermentation, which I would definitely not recommend testing.

Discard the soaking water. Put the beans in a pot and cover with water again, adding one or two bay leaves and salt and ground pepper to taste. You can adjust those later on. Some people like to add chopped onion at this stage; I prefer to put a little raw on the top of the beans when they're served. De gustibus non disputandem est.

Before bringing the beans to a low simmer, I also add some pieces of country ham, a specialty of my native part of the US. Different regions have different ideas about country ham (note that the Virginia/Smithfield ones are rather a different breed), but it's always salty, so if you're doing this, you'll probably want to add no extraneous salt at all until you've tasted the finished product. The amount of ham is also to taste - by the standards of my ancestors, some of them, anyway, this sort of things was no doubt a luxury item, and they'd have put in a mostly bare bone, at most. I'm happy adding a half pound (0.25 kilo), in pieces. If you'd like to try the stuff, I can recommend Burger's (I'm about to go downstairs and get some myself). Tripp is also a reliable brand. I grew up on Mar-Tenn brand, but I'm not even sure if it exists any more. It's not just for bean soup, of course - my Southern roots call for the sliced ham to be gently pan-fried for a winter breakfast and served with biscuits, a fine meal which will have you drinking water at an increased rate for several hours.

So heat the beans gently for two to three hours, depending on how long the earlier soaking has gone (and of course, what sort of bean you might have started with). I like them to the point where the soup has thickened some, but not to where the beans themselves are breaking up. I don't recommend any strong boiling; that'll bring on the bean-mush stage for sure. You'll have to check over so often to make sure that things haven't gotten out of hand. Adding extra water, if needed, is no sin. I eat the resulting bean soup with homemade cornbread, for bonus exiled-Southerner points, and I'll put up a recipe for that, too.

You can start from the straight dried beans, too, if you're a real buckaroo, but you're going to have to get going in the morning to have them for dinner.

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December 24, 2012

A Christmas Break

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Posted by Derek

Blogging will be light and irregular around here until after the first of the year. I'll probably post a recipe or two, as I tend to during this season, but unless something gigantic happens in the science/chemistry/pharma world, I'll be taking a blogging break. I hope that everyone out there celebrating Christmas (or other such midwinter holidays) has an enjoyable time of it. I'm lounging around myself: making cookies, roasting a leg of lamb, wrapping presents, and wishing that the full moon didn't fall smack in the middle of the break so that I could get my telescope out. Although, come to think of it, it's supposed to cloud over and snow, which I guess is Christmas-y enough. See everyone in the new year!

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November 23, 2012

Chemistry Software Questions Answered Monday

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Posted by Derek

After that ChemDraw post from a few days ago, I had some contact from Philip Skinner, one of the Perkin-Elmer employees who helps support their chemical software (ChemDraw, ChemDraw4Excel, E-Notebook, Inventory, Registration, Spotfire, Chem3D, and so on). He's agreed to hang around on Monday here at the site to answer whatever questions people might have about the programs - I'll start a post on the subject, and he'll handle things in the comment thread. So if you have some technical or usage questions for those programs, be sure to stop by!

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November 21, 2012

Thanksgiving Synthesis

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Posted by Derek

Well, I know that it's an odd time for me to be posting here, but I'm up working on some Thanksgiving food for tomorrow. The chocolate pecan pie recipe that I've posted here is back, by popular demand of my family (and me), and one of them is going to be coming out of the oven in about ten minutes. I've made a pumpkin pie as well; America is all about having a multitude of options.

Tomorrow we'll be roasting a large turkey (we buy a kosher one, which takes care of the brining step that really improves the bird). And there will be stuffing - my Iranian mother-in-law's recipe, which features seasoned bread cubes, onion, celery, cranberries, and pepperoni (trust me, it works). Alongside this will be homemade mashed potatoes (with turkey gravy), sweet potatoes, green beans cooked with some Tennessee country ham, creamed onions with thyme, pan-roasted Brussell sprouts, and a huge Iranian basmati rice pullao with saffron, orange zest, pistachios, and tart red zereshk berries.

That should pretty much hold everyone. If not, well, there's not much more I can do. Never trust an organic chemist who can't cook.

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October 30, 2012

Back On the Air

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Posted by Derek

Over here to the west of Boston, we had a real storm - downed tree branches all around my neighborhood, power outages - but fortunately nothing like what they had further south of here, starting in Connecticut and really picking up in New York and New Jersey. So it's back to work, on the somewhat-delayed MBTA, and back to blogging on the train! I hope that readers on the East Coast made it through OK (and people on towards the Great Lakes, too, since I see that this is hitting in Cleveland and Detroit as well). What a mess.

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October 29, 2012

Blogging Outage

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Posted by Derek

Well, all of us in the Northeast are battening down today for the storm, and a lot of companies and research labs either didn't open or are closing early. In that world, my sympathies go out to the people in the cell culture labs and the animal facilities, who can't just shut off the stir plates and go home immediately for the duration. Running those labs is like having a lot of very demanding pets, but ones that can cost you huge sums of money and time if they become unhappy. Good luck to everyone, and here's hoping that the maintenance on all those backup generators was actually kept up! Regular blogging will resume tomorrow. . .

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October 25, 2012

Travel (For C&E News)

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Posted by Derek

I'm in Washington today for a meeting of the C&E News editorial board (which I believe is the last one I'll be attending during my term on it). I'll be able to check the blog during the day for comments, but I don't know if I'll have time to put up a post until later on this afternoon. (In theory, I should be downstairs right now, having breakfast!)

But anyone with thoughts on the magazine, its news coverage, and what you as a reader might want to see more or less of in it, please add your comments. I can assure you that the staff will see them!

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September 24, 2012

Conference Travel

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Posted by Derek

I wanted to mention that later this week I'll be in Heidelberg, attending the EMBO Chemical Biology conference (agenda). So anyone in Hesse or Baden-Württemberg who's been trying to track me down in person, well, you're in luck. It'll be the first time I've been back in Heidelberg in nearly 25 years, although I believe one of its main selling points is that it doesn't change too much (!)

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July 6, 2012

Vacation!

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Posted by Derek

I wanted to let everyone know that I'll be taking a summer break - as of yesterday, I've cleared myself and my family out of the house and off for some R&R. I'll be lounging around all next week, and will return to blogdom (and research-dom) on Monday the 16th. I've already told folks in the lab not to discover anything gigantic while I'm gone (it looks bad, y'know).

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June 28, 2012

R. B. Woodward Does Furnish A Room

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Posted by Derek

If you're looking for an R. B. Woodward-themed decoration for you lab, look no further: Chemjobber has you covered.

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June 6, 2012

Drew University Visit

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Posted by Derek

I'm writing this from Logan Airport, on my way down to New Jersey, where later this afternoon I'll be giving a talk at the Drew University medicinal chemistry school. I took that course back in 1990, so it's rather odd to be coming back as the keynote speaker. Thinking about some of the people who were there with me, I can see that quite a few of them are no longer in the industry (although everyone that I know about on that list has still done fine for themselves and their families).

I suspect that many readers here may have been through the Drew course as well, especially if they started out with one of the big NJ companies back when. I'll try to give everyone an interesting talk!

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May 7, 2012

More Details

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Posted by Derek

A couple of notes: in the previous post, I forgot to include the link to Wavefunction's article on the "negative rate constant" brouhaha - it's here, and well worth a look.

And I wanted to note that the post that discusses the Dobson and Kell theories about how compounds make their way into cells now has a comment from Douglas Kell himself, which is also worth a look if you're into this topic.

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April 17, 2012

Day Off

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Posted by Derek

I'll be traveling today, so no time to do a blog post this morning. Regular blogging will resume tomorrow - see you then!

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March 22, 2012

Shortage of Blogification

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Posted by Derek

No time to update today, unfortunately - a blizzard of Real Science (TM) is keeping things hopping, and my new laptop died on the train this morning during my usual blogging time.

So I'll use this chance to throw out a question: what topics haven't come up around here lately that we should be talking about? Blogfodder comes in around here pretty regularly, and I have a few topics in the queue, but I want to be sure not to miss out on interesting stuff. Thanks, and I'll see everyone tomorrow. . .

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January 25, 2012

Comments (And Everything Else) Are Back

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Posted by Derek

Things are running around here again, after some problems with the comment system. Unfortunately, it looks like everything from about Monday mid-day disappeared into the Great Bit Bucket. That's unfortunate, since I know that there must have been some good stories in that "Weirdest Presentation" post - if anyone has the energy to add them again, there would be an audience for them!

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January 23, 2012

Comment Trouble

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Posted by Derek

I've noticed that comments to today's posts seem to have stopped appearing sometime around noon EST. Rooting around under the hood is ongoing; I'll let everyone know what the outcome is. With any luck, things can be rescued!

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January 11, 2012

Ten Years of Science Blogging. Already?

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Posted by Derek

Today marks my ten-year blogging anniversary. That doesn't seem possible, but there it is: ten years since I sat down and chose a Blogger template and starting typing away into the void. So what have I learned in all that time (and after all that blather?)

Where It Fits and How It's Done
I may well have been the first science blogger, because it didn't take me long to start talking about drug discovery, as opposed to current events and the like. (Even in 2002, I thought that blogging the news was an overcrowded field, and little did I know how much more crowded it would become). But blogging drug discovery still isn't a very crowded field at all, for various reasons. One of those surely is that most of it is done in an industrial setting, and very few people have felt comfortable blogging from inside a drug company.

The fact that I do so might be due to circumstances that are hard to repeat. It helped that I started out before most people had any idea of what a blog was, and it probably helped that my company's highest management levels at the time were on another continent and spoke another language. And naturally, it's also helped that I've carefully avoided ever being seen as a spokesperson for any company I've worked for. (Or a source of inside information, God forbid). But there are so many topics to write about that this has never been a real problem. When I started, I wondered if I'd be able to keep things up, but there's hardly a day when I don't find something to write about. The material just keeps coming, and I'm glad of it.

That's because I actually enjoy doing this - I don't suppose I could have lasted this long if I didn't! I compose quickly, and type quickly, which helps keep blogging from becoming a chore. As for what to write about, keeping up with the literature and the industry is something that I would have been doing already, and it really doesn't add much time to sit down and write up something about what I've been reading and thinking. (It helps, in fact, to clarify my thoughts - I'm sure that I retain a lot more information for having blogged about it).

Who Reads It, Anyway?
As it happens, a lot of people really do seem to be interested in this stuff. That was my hope - one reason for blogging was that every time I talked to people outside science about what I did for a living, they seemed to think (1) that it was a really neat job, and (2) that they'd never heard of it being a job at all. No one really seemed to know where drugs came from, and despite my efforts (!), most people still don't.

I get letters all the time, though, from non-scientists who read the site, and they make me very happy. Not everything here is accessible or interesting to non-scientists, but I try to make sure that enough of it is to keep people hanging around. And then there are the scientist readers themselves, who make of the bulk of the audience around here. To them I owe a rare distinction: one of the highest signal-to-noise ratios in in the entire world of blog comments. That's really the case - other bloggers have asked me many times what I do to keep things from devolving, and I tell them that it isn't me, it's the people who come here. It's not like every comment thread is a river of gold, but there's a lot more gold there than you'd expect from general run of the blog world.

Readership has increased steadily over the years. Here's the chart, minus the first couple of years, which tail off just the way you'd think, and minus a few months back in 2006, around the time the Wonder Drug Factory was running into trouble and I forgot to save the stats.
blog%20traffic%20chart.png
Basically, every time I think that the numbers have plateaued, they haven't. Most recently, mid-2010 to mid-2011 had pretty much the same readership levels, but lately things seem to be rising yet again. (And note that my stats don't pick up people who see the blog on RSS feeds, which I think has been an increasing percentage over the years). Far more people are willing to read about chemistry and drug discovery than I ever imagined.

Day-to-day, posts about misery (huge layoffs and the like) get a lot of traffic, which says something about human nature that close observers will have already noted. But a steady diet of misery lacks a number of essential nutrients. The "Things I Won't Work With" posts get the largest non-scientific readership, which is why I'm whacking them into book shape (to appear first on the Kindle, etc.) And posts about patents and IP issues almost always drive a small but noticeable number of people away - if I did a solid week or two of those, who knows if the site would ever recover.

Overall, though, the site has had what I think is a fairly consistent tone over its whole history. That may be because I have a fairly consistent tone myself. A few years ago, I was unnerved when I started looking over some of my older posts and thought that they were clearly better than anything I was turning out at the time. But that seems to be a general psychological effect - older posts always, eventually, look more polished to me because I still have the fresh experience of tumbling the new ones out onto the page. The old ones felt the same way at the time, though. Hindsight polishes them up.

What's Changed
The drug industry is a very different place than it was when I started blogging. Basically, every time I've thought that the worst had passed, it hadn't. I hate to be that negative-sounding, but it's hard to deny that the last ten years - especially the last six or seven of them - have been some of the roughest water that drug R&D has ever experienced. I never thought that I'd have to work at keeping the site from becoming the Blog of Constant Pharma Layoffs, but I've had to.

But that said, the way the industry works hasn't really changed over that time, not in any fundamental ways. (Those two trends may not be unrelated). We have some techniques now that weren't used much back then, but the broad strokes of the business are identical: find some hits, most likely through screening. Develop them into leads, and turn the med-chem people loose on them to do SAR. Fix the potency, fix the selectivity, fix the PK, and then put them into tox and cross your fingers. Send the winning compound to the clinic, put it into Phase I and cross your fingers, this time on both hands. Send it to Phase II, crossing all your fingers, your toes, and your lower intestines. And send it to Phase III, crossing all those body parts while sacrificing a two-headed goat and barbecuing it over bales of money. You know, the usual grind.

The scientific literature has changed, though - and in almost every way, it's become more like blogging and less like it used to be. Print journals have looked archaic for some time, and will likely continue their vanishing act. I haven't seen a hard copy of any of the journals I read in. . .months? Years? Articles get published online, discussed online (shared, boosted, or picked apart), and their authors, their publishers, and their readers are paying attention to things like traffic stats, comments, and links. That'll continue, too, and I think that science will be better off for it.

What's Coming
For the industry? I have no idea. Well, that's not completely true. I have several ideas, but they can't all be right at the same time. For this blog? That's easier - I have every intention of keeping it going, because I still enjoy it. And it's opened up a lot of opportunities that I never would have had otherwise. I had no idea what was going to happen when I started it, although it's safe to say that I wasn't exactly planning on it becoming one of the key turning points of my life. But that's what happened. Here's to more of it!

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December 23, 2011

Media Note

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Posted by Derek

I'm going to be on a short segment of Marketplace on public radio tonight, talking about cancer therapy. So if your holidays aren't complete without hearing me vent my opinions - and my wife, among others, tells me that hers aren't! - then tune in.

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Holiday Break

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Posted by Derek

Posting will be irregular next week for the holidays. I may put up a recipe or two, the way I did last year, and I'll certainly jump in for any big stories that might pop up. Otherwise, I'll be lounging around, gathering my strength for the new year. And hoping that we don't get what we got last year - relentless snowstorms, pounding in one after the other, which started about one day after Christmas. The less time I spend slogging through 40 inches of the stuff to go out and rake it off the roof, the better. Makes it rather difficult for a guy to set up a telescope, too, even in the unlikely event of a clear sky.

So I'd like to take this opportunity to wish everyone who's celebrating it a Merry Christmas, and I'll certainly throw in a Happy Hanukah as well. The Iranians have already celebrated the winter solstice, but a belated best wishes go out to them, too. Anyone I've missed?

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December 2, 2011

Blog Traffic: A Thank-You

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Posted by Derek

Just wanted to note that November saw nearly 441,000 page views here, for one of the best months ever on the site. Thanks to everyone who stops by! I never thought a blog about drug discovery, smelly chemicals, and other such compelling topics could ever get that sort of exposure. . .

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November 29, 2011

A "Things I Won't Work With" Request

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Posted by Derek

I've been putting together a revised-and-expanded "Things I Won't Work With" collection, which I hope to release first as a Kindle e-book (with other platforms following close behind). Each entry in the series has been revisited, with more useful (or not so useful) information and raised-eyebrow opinions added, and I'm throwing in some bonus chapters that haven't appeared on the blog yet.

But I'd like to expand the list, both for the e-book and for future blog entries. So, what will you not work with? I'd be glad to take suggestions for the unpredictably explosive, alarmingly toxic, overwhelmingly stinky stuff that everyone with any sense avoids on sight. There have to be a lot of them that I've never come across, and I'd be glad to give them the full TIWWW treatment!

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November 24, 2011

Happy Thanksgiving

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Posted by Derek

My US readers will mostly be sitting around digesting turkey by now -that's about all I'm doing, although I hope to work up enough energy to take the telescope out into the back yard and show the relatives what's going on on Jupiter.

The menu here was pretty much our standard: an 18-pound kosher turkey (I like the brining), stuffed with my mother-in-law's proprietary mixture of bread cubes, apples, celery, onions, and pepperoni. (Not sure where she came up with that one, either, but it gets demolished by the entire table of guests every year). The big side dish is shirin pullo, also from the Iranian side of the family - that's basmati rice with slivered almonds, thin bits of orange peel, dried barberries, and saffron). Then mashed potatoes (only time I ever use the potato ricer gadget), gravy (from the turkey pan, with some added mushrooms and onions and thickened with roux), green beans with country ham (from my Arkansas side of things), brussel sprouts (caramelized in the pan a bit), sauteed mushrooms, my wife's homemade cranberry sauce, and some sweet potatoes with brown sugar. Add the two pies I made last night (pumpkin and chocolate pecan), and I'm not sure if I'm going to make it out to the yard or not. . .

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November 23, 2011

Lab Preparation: Key Lime Pie

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Posted by Derek

Thanksgiving approaches for readers in the US, which means that I turn my attention around here to lab preparations that have already been through trials in my own kitchen. I've posted my procedure for chocolate pecan pie here in the past, and I plan to make it again this year (my kids will brook no change in this menu). And I should also note another reliable recipe from here at Pipeline HQ, chicken pot pie, which should adapt very easily to using up whatever leftover turkey you need to clear out. Personally, I can clear out quite a bit of it in the form of turkey sandwiches with mayonnaise-and-horseradish. My wife puts hoisin sauce on hers instead, in a wrap or flour torilla with fresh scallions to make a sort of turkey-for-duck Asian substitution, but you may need other options.

But I wanted to provide another well-tested prep, so for those of you looking for something a bit different, here's one for key lime pie, adapted from the Cooks Illustrated version. I've checked this procedure several times, and the only defect of the resulting pie is that it tends to have a short half-life, especially if left unwatched. It is, in theory, more of a summer dessert (being served cold), but no one's ever objected when I've made it at other times of the year.

First, the only tedious part of the whole recipe. You'll need to zest some limes - if you haven't done this before, it involves scraping the green peel off in small flakes or strips from the limes (wash 'em first), while not getting deep into the bitter white pith below. There's a lot of flavor in the volatile oils in that layer; this step really is important. Fellow blogger Megan McArdle has long recommended a Microplane Zesterfor this, and I may have to break down and buy one myself. There are other zesters, which are basically small, shallow grating tools. Judicious use of a standard grater, or even a peeler or sharp paring knife if you have a steady hand, will do the trick. You'll want to come up with four teaspoons of lime zest, and I have been unable to come up with a weight equivalent for that (I'll weigh it next time I do this recipe and amend this post!) But that's three limes worth if you're pretty efficient, but more likely four limes of zest, if that helps. Note: I'm talking about the amount from usual-sized "Persian" limes here, not the authentic Key limes, which are smaller. If you have the latter, feel free to use them, although zesting them is more of a pain and (to my palate, anyway) there's not too much difference in the finished product. Floridians disagree.

Take four eggs and separate out the yolks into a bowl (no use for the whites in this recipe, unfortunately). Mix the lime zest into the yolks - you'll notice that they'll extract some color, and they're doubtless doing the same with the flavor constituents as well. While that stands, take some of those ugly sheared limes you've created and squeeze out 1/2 cup (about 120 mL) of lime juice. If you're particular, you can run this through a strainer to remove pulp, which will give you a more homogeneous pie, but I sometimes don't bother. Stir the juice into the yolk mixture, and then mix in one 14 oz can of sweetened condensed milk. That's a standard can size here in North America, about 390 mL, but I have to confess that I'm less clear on the product's availability and packaging size in the rest of the world - clarifications welcome in the comments. Leave this mixture standing during the next part of the recipe; it'll set up a bit as the lime juice goes to work denaturing the casein protein in the milk (and probably albumin in the egg yolks). It will be an interesting yellow-green color.

Now, a crust. You'll need the oven heating to 325F (160 to 165C). The recipe calls for 11 full-sized Graham crackers to be put into a food processor (or crushed up in a bag) and thus turned into crumbs.That quantity is easy enough to round up in North America, but I'm not sure about the rest of the world. It comes to about 154g of Graham cracker, which might help. As for substitutions, I think that British wholemeal digestive biscuits (McVitie'sor equivalent) would work out fine, although they seem more open-textured than Graham crackers, so you might want to watch and not over-process them. The idea is to produce crumbs, not dust).

Combine these crumbs with 3 tablespoons (about 37g) granulated sugar. Melt 5 tablespoons (65 to 70 grams) of (unsalted) butter, and mix this into the crumb/sugar preparation. Press this into an even layer in a 9-inch round pie pan, up the edges as well. (I'm not sure about standard pan sizes in other parts of the world, but that's about 23 cm diameter and about 3 to 4 cm deep). Bake this for 15 minutes and let it cool to room temperature or a bit above. It's worth taking the time to make the crust, by the way - I think this pie is much better with a crumb crust than a standard pie crust, and the homemade one, although quite easy to make, will wipe out any store-bought version.

Pour the lime/milk/egg mixture into the crust, and bake the whole thing at the same temperature for about 17 minutes - the interior will still look a bit fluid, but it should be fine on cooling. Cool to room temperature, and then chill thoroughly before serving.

As mentioned above, these things don't last long around here - fresh limes (juice and zest) are sui generis, and if you like the flavor, you'll eat more of this than is good for you. Of course, there is the vitamin C content, which is no doubt substantial. Lemons for limes is an obvious substitution, although I haven't tried it - that's the equivalent of para-chloro for para-fluoro in a med-chem SAR (although I've seen that one fail, while lemon-for-lime is foolproof outside of the expected flavor change). I suspect that this would work with oranges as well, although you would probably want to add some extra lemon juice to take the acidity up in the first step. And for that matter, it would probably work with grapefruit, although you'd probably run into some bitterness problems that would require experimentation. Sugar won't cancel that out (consider the quinine-driven taste of bitter lemon, which you can hardly find in the US any more, and which I pounded down while in England the other month). I'd be glad to hear about any such research, naturally!

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September 13, 2011

Conferencing

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Posted by Derek

In response to several queries, my talk today went fine, as far as I can tell. I brought in some thoughts from Tyler Cowen's The Great Stagnation, among other sources, and tried to tie some widely scattered thoughts together. And since I've also had some requests from readers for the slides, I'm thinking about turning the thing into a video and just putting it up on YouTube for anyone who wants to see it. Of course, that'll mean that I'll have to come up with *another* talk next time someone invites me to a conference, but still. . .

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September 10, 2011

Conference Travel, With Blogging

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Posted by Derek

I wanted to mention that I'm going to be attending this med-chem symposium in the UK next week, a joint conference of the Royal Society of Chemistry and the Society for Chemical Industry.

I'll be giving a talk on Tuesday, which will probably be the only one without a single chemical structure in it. They've asked me to talk about the state of drug discovery, which is certainly a topic I've given a lot of thought to. Problem is, everyone else has given a lot of thought to it as well, so the challenge is to come up with something worthwhile to say. I'm dragging in some material from well outside the field, which I think (and hope) is relevant.

Blogging should continue while I'm gone, though. I'll be commenting on some of the things that I hear about at the conference, although I won't be live-blogging anyone's talk or anything. I look forward to meeting some interesting people, and since I've never been to Cambridge (or Oxford, another stop on the trip), that should be worthwhile all by itself. . .

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August 19, 2011

Day Off - Some Links and Some Ancient Greek

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Posted by Derek

I'm adding a day to the weekend, so science is going to have to march on without me for a while. I do have a few miscellaneous links to things that have been piling up, though: here's the Chronicle of Higher Education on growing links between drug company research and academia, and (for something completely different) here's a rather crazed editorial at Marketwatch calling for the immediate abolishment of the FDA. ("Everyone would start marketing crazy drugs to cure cancer, impotence, etc. And my response is – so what?").

And here's a short review in Organic Process R&D on a reaction that I've never done, but which looks interesting: direct amine substitution of C-H bonds. You do that with various semi-exotic rhodium catalysts, and I'm not aware of any other useful ways to do it at all. Anyone out there had any experience with this?

To cap things off, if anyone's looking for something to do in their spare time, well, do what I've been doing on the train rides home: help transcribe some ancient Greek papyri. No, I'm not kidding. These are unstudied examples of the Oxyrhynchus papyri, a trove of discarded writings from an Egyptian city of Roman and post-Roman times, excavated in the 1890s and still being worked through. (The book City of the Sharp-Nosed Fishis a good overview of what's been found so far).

They'll put scanned ones up on the screen for you, and you can transcribe the Greek letters for their database. I'd recommend hitting the "Next" button at first until you get one that's in nice, dark, all-capital lettering; those are pretty easy to work with. Some of the dashed-off script ones, though, are a real challenge, and you'll be surprised at how much handwriting varies. Here's a useful comparison of that sort of thing, and this is another excellent resource on reading papyri. If (like me) you don't have a whole lot of ancient Greek at your disposal, you can always try to translate text strings you find using this tool at Tufts' Perseus site. Mind you, these guys mashed all their words together with no spaces, so it can be a bit tricky - one help is that kappa-alpha-iota ("and") shows up a lot. Enjoy! I find it, weirdly, to be a lot of fun.

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August 9, 2011

What An Offer

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Posted by Derek

The glamorous side of blogging is that you get chances like this, delivered right to your e-mail queue:

". . .I am working with a couple of small-cap biotech companies who have good fundamental technologies, but are not on the radar screen of a lot of investors. We are looking for some influential bloggers to put some spotlight on these companies, so more people can be exposed to the value proposition and opportunities available. In the past we have worked with some bloggers who have written both paid as well as unpaid articles on these companies. I would like to explore your interest and to discuss this further. . .

I explained to this person just what my level of interest was, in terms that I don't think were misinterpretable, and pointed out that if their operation was not, in fact, a pump-and-dump penny stock scheme, then they should take more care not to make it sound exactly like one. But I thought I would at least get some use of of this sleazy offer by getting a few things on the record.

I write paid columns for Contract Pharma and Chemistry World, and I occasionally do paid pieces for other (respectable!) outlets. But in none of those do I tout stocks, companies, or products. As for the material on this blog, it's produced for free, which (by no coincidence) is what I charge for reading it. The only money that changes hands around here is if someone buys something through an Amazon link, and I try to keep those down to things that people could actually find useful and relevant - no links to plasma TV sales, for example, although if you want to buy one through Amazon, please do feel free.

And of course, I stay away from anything that might involve (or be thought to involve) material information concerning my place of work. But there are no commercial considerations involved in my choice of topics or my expressed opinions on them. If I have a stock position in a company - a rare event, these days, since my kids and my mortgage have seen to it that I don't have a vast fund of free-floating investment capital - then I say so. (A careful look though the archives would show that depending on me for investment advice is not necessarily a winning plan, although it would at least be full of excitement).

So there you have it. No pay-for-play around here. But if you across someone going on about what a great thing this tiny biotech you've never heard of is, well, exercise the usual amount of caution.

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July 19, 2011

Back to Blogging

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Posted by Derek

Just wanted to let everyone know that I'm back, and back to blogging. As usual, I'm spending some of my morning working out again what it is that I do for a living - although, again as usual, many people have been coming by my office trying to remind me. And I'll be putting up a post at lunchtime.

But in the meantime, since I've been totally out of most any loop you could name, what have I missed in the last week? Anything interesting?

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July 11, 2011

On and Off

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Posted by Derek

I'm going to be traveling this week, so posting will be intermittent. (It's summer, after all). I'll surface now and then, but for the most part, things will be quiet around here. Enjoy the weather, if you have weather to enjoy!

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May 30, 2011

Memorial Day

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Posted by Derek

I'm enjoying myself at home this long weekend - fencing in a vegetable garden to keep the marauding groundhogs out, hoping the sky clears up enough to use my telescope tonight, and cooking some food in the backyard. And being glad to have the opportunity to do these things - luxuries, all of them - because of the sacrifices made over the last 225 years or so. Happy Memorial Day to my U.S. readers, and I'll see everyone tomorrow!

With my Arkansas/Tennessee background, I don't have to go out for barbecue. Just get started early, and make it yourself. . .

Update: As one person in the comments section put it, "What is this, Tet. Lett.?" So, here's the procedure for this prep:

That's about 7 pounds of ribs, which is all I can hold on that smoker/grill. The key, as far as I'm concerned, is to cook them a long time over rather low heat, with plenty of wood smoke. I use no sauce at all - people from Kansas City, St. Louis, Georgia and other locales will have their own opinions about that, but I'm true to the Memphis "dry rib" tradition.

Accordingly, take the raw ribs and season them with (at a minimum) seasoning salt and ground black pepper. That's what's on the ones in the photo. There are all kinds of dry-rub recipes out there, with paprika, cumin, brown sugar, mustard powder, and who knows what else in them. If you want to try those, you can find proportions for them all over the web, or buy a commercial mix from some Memphis outfit. My advice is to go easy on anything with sugar in it - it'll get too dark, or burn outright during the cooking. That's another reason that I don't sauce things while cooking them - that, and finding most commercial sauces way too sweet and gooey. I've always had a suspicion that barbeque places that make too big a deal out of their sauce must have something to hide where the meat is concerned.

Leave the dry seasoning on the ribs overnight if you can, or at least a couple of hours. Start an indirect fire to cook them over - to the side, if you have a big cooking surface, or at least a foot below the meat if you're doing it in a tubular meat smoker like the one the in the picture. You'll also need some hickory wood chips or chunks - soaking it in water before hand will give you more smoke - but I can't say exactly how much, since different batches give varying amounts of wood smoke.

Cook the ribs over low heat - not quite enough for audible sizzling - for several hours, with frequent addition of fresh hickory wood to the fire. You'll need to add some more charcoal to the fire itself over that long a period, too, naturally, but don't go too wild, or things will get too hot. Four or five hours should about do it, but (since there are so many variables in play here), you'll need to judge for yourself. You can finish them off (carefully) on a hot grill at the end if you wish, which will render out some of the fat.

Sauce - well, that's up to you. If you're the type, then add it in the last hour or so of cooking. I serve mine on the side, and often don't take any, but (as mentioned above) I grew up near Memphis.
Rib%20shot.jpg

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May 23, 2011

Inadvertent Day Off

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Posted by Derek

Sorry about no new post today - it's been a lively day around here, for a number of reasons (none of them bad). New content tomorrow!

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April 28, 2011

Conference Time

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Posted by Derek

As it turns out, I'm not at the bench cranking out the wonder drugs today (or tomorrow) - I'm at this flow chemistry conference, right across the river in Boston, hoping to learn about new ways to, well, pump out the wonder drugs instead from our flow machines. No live-blogging, but I do have wireless in here, and will be keeping an eye on any interesting developments out there.

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April 22, 2011

Day Off

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Posted by Derek

I think that attendance across the pharma/academic/blog-reading-at-work world is rather low today (and I'm not at work myself), so I'll take a blogging holiday. Regular service will resume on Monday - see everyone then!

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January 27, 2011

Another Snow Day

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Posted by Derek

Well, the snow is now well up over my knees here at headquarters, which accounts for the lack of posting today. There's only so much the snowplow guy can do out there; it's hard to fine places to shove the stuff to. I've been out moving piles of it around, off the driveway and off the roof, which leaves little time for Science. More tomorrow!

Um, I mean more science. Not more snow. At least, I sure hope not.

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January 12, 2011

Snow and Chance Happeneth To Them All

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Posted by Derek

In case anyone's wondering, the pace of discovery has slowed a bit around these parts today. We've got a whalloping pile of snow out there, verging on about half a meter, and I'm blogging from my fortified position at home. No French onion soup today, although I do have a couple of home-made pizzas in the oven as I speak.

Science should be resuming tomorrow, though, thanks to the snow plows. I find, having grown up in a part of the country where there were none (and where everything just shut down a couple of times per winter), that I'm still impressed at the efforts that go into cleaning the roads. My thinking, though, is that people who grow up under these conditions take road-clearing as some sort of natural process - of course the highways will be clear; they always are. A good look at a local street that's had traffic and a foot of unplowed snow on it for a week would be quite a revelation.

Update: for those who've asked, my company was officially closed today, which I very much appreciated, even though I do take the train in to work. Driving in to work, now that would have have been a real treat. . .

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December 30, 2010

Another Cold-Weather Recipe: Chicken Pot Pie

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Posted by Derek

Here, as promised, is another dish for weather like the present. It takes some time, but if the snow is coming down and the wind is rattling the windows, you may well have some. You'll need, at a minimum: a chicken, vegetables (carrots, celery, onions, peas, etc.), some flour and milk, and some source of pie crust, either home-made or bought. (Note that if you're going to make your own crust, that needs to be started early in the process so it'll be ready to roll out - see below. If you're a make-your-own-crust type, though, you probably already knew that, though).

First take the chicken (up to a 3-pound / 1.4kg one) and simmer it in water (to cover). I season this with salt, black pepper, and a bay leaf, but you can modify this to taste - you're going to have extra chicken broth when this is over (no bad thing!), so season it the way you like it. A half hour should take care of the bird - take it out of the broth and let it cool down enough to handle, then remove the skin and pull the meat off the bones. You'll need to cut the larger pieces down to size - 1 to 2 cm on a side, say. I usually put the chicken pieces into a large bowl; you'll be adding more to it in a few minutes.

Now, the vegetables: peel and cut up 3 or 4 medium-sized carrots into similar-sized pieces as the chicken, and do the same with two large stalks of celery. For the onions, you can chop up a large one, or do what I often do - take half to 3/4 of a bag of frozen pearl onions (8 to 12 oz., 230 to 340 g) and let them thaw while working on the other vegetables. If you like mushrooms, you can also add some to taste; I often do. If they're fresh, you'll want to saute them along with the other vegetables in the coming step, or you can add canned ones at any point.

Take the cut vegetables and saute them in a large pot in oil over medium-to-high heat for five minutes or a bit more - you just want to get them started cooking, and not brown them or make them actually soft. You can add salt and black pepper as desired at this point. Then turn them out into the same bowl as the cut chicken. Take the same pot and melt about 4 tablespoons butter (50g) in it, then add 1/2 cup flour (which I think should be about 60 to 65 g), and stir that in. Cook the butter-flour mixture (which will be pretty solid) for a minute or two, then add 2 cups (475 mL) of the chicken broth you have, whisking it in to break up that flour lump, followed by 1 1/2 cups of milk (350 to 360 mL). Continue to whisk this around vigorously while it's heating - it'll thicken into a sauce (more specifically, into a béchamel sauce).

This is a good time to get the oven going - heat it to 400F, or 200 to 210C. Now Season the sauce with some more ground black pepper and about a half teaspoon of dried thyme (0.75 g), then add the vegetables and chicken, and stir to mix everything. At this point, you can add a cup of frozen peas, as they are, to the mix - they'll come out festively green at the end. If you have some fresh parsley on hand, you can chop a small handful and add it now. It goes well, but I've made it without as well, and it's still completely edible.

This mixture is ready to go into whatever sort of form you wish your chicken pot pie to take. Store-bought pie crust, the kind that comes refrigerated and rolled up, can be used to line a large oven-proof bowl. You than empty the pot pie mixture into that and use the second crust in the package across the top. (Some people like a bottom/side crust, others don't). You can use a wider, shallower pan and just have a top crust, or break the recipe up into individual oven-proof bowls. Your call! They all work fine.

If you're going to go all the way and make your own crust, then I'm going to have to refer you to your favorite recipe for it, since I rarely make my own, to be honest. (I wouldn't recommend making your first one at the same time you're doing all the rest of this). Remember, though, jome-made pie crust has to be refrigerated for a half hour or so to get it ready to be worked. You can also use a biscuit topping, if you've got a recipe you like for that - I haven't tried it myself, but it seems like it would work fine.

Cook the pie at the above-mentioned 400F until the crust is starting to brown. Depending on the format of your pie (or pies, if you broke it up into smaller servings for a group), this could be as short as 20 minutes or more like 35 to 40. And there you have it! And as a side effect, you now have some chicken stock to freeze for later on. Enjoy!

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December 28, 2010

A Cold-Weather Recipe, By Request: Onion Soup

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Posted by Derek

If there's big pharmaceutical news going on right now, it hasn't reached me. So in the spirit of taking time off, here are some things I've been making here at home while the wind rattles the windows.

First up is French onion soup. I use pretty much the procedure that the Cooks Illustrated people recommend. Take half a dozen onions (this should be a bit over 3 lbs, or 1.5 kg) and slice them fairly thinly. The Cooks people recommend red onions, and those certainly work well, but I've used all sorts (and mixtures of whatever's on hand). Now comes the only time-consuming part: cook these in a pot with butter (2 tablespoons, or about 30 grams) over medium-to-low heat, stirring frequently, until they're quite dark but not burnt. This will take at least half an hour, and probably more. If you're using a conventional pot (not nonstick), you'll have a lot of stuff stuck to the sides, so be careful that it doesn't burn. This is the key step in the whole preparation: well-browned onions are the crucial ingredient, without which all is lost.

Now add a mixture of beef broth (2 cups, 500 mL) and chicken broth (6 cups, 1500 mL). I sometimes have the latter around frozen from previous chicken preparations, otherwise, you can use canned. Beef broth I almost never have around, for one reason or another, so that's almost always canned. (Note - using all canned beef broth makes a fairly nasty soup, while using all chicken broth makes an edible, but rather chicken-centric one). This step will loosen up all the caramelized onion stuff and get things into suspension, if not into solution. You can also add a half cup or so (125 mL) of red wine at this point if you like. Season it all with dried thyme, salt, and pepper to taste, add a bay leaf, and simmer the mixture gently for at least fifteen minutes. (If it goes longer, you can add a bit of water to bring the volume back up). Check the taste at this point - you might like it with more of a bite, in which case a few mLs of balsamic vinegar added to the pot will help out.

You can have this as is, or go the traditional gratineé method, with toasted bread and cheese on top. I use whatever's on hand in the bread department, just making sure that it's cut fairly thick and is well toasted, and then add some sort of Swiss-ish cheese - your choice. (You can even go as far, and as non-traditional, as mild Provolone, but I don't think that sharp cheddar (for example) would be a very good idea). The best way to do all this is probably to put the soup in some sort of heat-resistant bowl, plop in the bread, cover that with cheese, and run the whole thing under a broiler.

This, to me, is one of the best meals for very cold weather - I can't imagine eating it in July. Next post: chicken pot pie.

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December 27, 2010

Weather Delay

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Posted by Derek

My company closes down between Christmas and New Year's (or at least it has the last couple of years), and I have to tell you that this is a good thing today. We've had between one and two feet of snow, starting late yesterday, and it's now being blown all over the landscape by 40 mile-per-hour winds. Commuting in to work does not appeal.

Neither does even setting foot outside, actually - I haven't even put my hand on a doorknob today. Instead, I'm teaching my kids how to play table tennis, and they're whipping me at Mario Kart. Dinner last night was a big pot of French onion soup, which I've always considered an excellent response to weather like this, and tonight I'm making a chicken pot pie from scratch. Recipes on request!

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December 22, 2010

Holiday Break

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Posted by Derek

Starting today, I'm going to switch over to Holiday Blogging Hours. Unless something gigantic happens, there won't be anything else here until Monday at the earliest. And blogging next week will be spotty as well, while I lounge around with the family. I've already been contributing on the cookie-baking, tree-decorating, and shopping fronts, and plan to start working soon on the important sleeping-in-late effort. With any luck, I'll have a couple of clear nights over the vacation to break out the telescope. The Christmas lights tend to brighten up the sky background a bit during this season, but one takes what one can get.

I hope that everyone out there who's celebrating has a good break, too. See you next week, and after that, next year. . .

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November 25, 2010

Blogging Break

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Posted by Derek

No blogging until Monday around here - US readers will mostly be taking today off for Thanksgiving, and people around the rest of the world have learned not to expect too much out of America on this day. My chocolate pecan pie preparation worked flawlessly (well, it looks flawless - we'll put it to the test this afternoon), and a home-made pumpkin pie is next to it.

My next job is getting a turkey underway. For some years now, we've cooked a kosher one, because the salt treatment they get really seems to help. (You can brine one at home, if you have space to store the bird, which is a marginal proposition around here most years). Many of the kosher turkeys do need a bit of minor re-plucking before cooking, though, so you have to be ready for that.

We have several traditional side dishes, but add some Iranian rice, like morasa polo, which fits in perfectly. And we have my Iranian mother-in-law's stuffing recipe, an excellent but decidedly non-Iranian mixture involving bread, onions, celery, cranberries and pepperoni. We'll make some mashed potatoes, the kids have requested stuffed mushrooms, I generally make some green beans seasoned with country ham, and we'll pan-roast some Brussels sprouts. My wife makes the cranberry sauce, and we'll have some gravy, too.

So no, I'm not going to be good for much useful work today. And tomorrow I'll eat it all again, so I hope no one's expecting much from me then, either. A happy Thanksgiving to everyone who's celebrating it!

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November 24, 2010

Holiday Organic Synthesis: Chocolate Pecan Pie

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Posted by Derek

Here's a recipe that I've put up here for the Thanksgiving and holiday season - I'm at home today, and I'm going to be following this exact prep a bit later in the day. I've made it for years this way, as have some friends, so you can consider this the Org Syn procedure for chocolate pecan pie:

Melt 2 squares (2 oz.) baking chocolate (see below if you can't find this) with 3 tablespoons (about 43g) butter in a microwave or double boiler. Combine 1 cup (240 mL) corn syrup (see below if you don't have this) and 3/4 cup sugar (150g) in a saucepan and bring to boil for 2 minutes, then mix the melted chocolate and butter into it. Meanwhile, in a large bowl, beat three eggs, then add the chocolate mixture to them, slowly and with vigorous stirring (you don't want to end up making scrambled eggs with chocolate sauce).

Add one teaspoon (5 mL) of vanilla, and mix in about 1 1/2 cups of broken-up pecans, which I think should be about 150g. You can push that to nearly two cups and still get the whole mixture into a deep-dish pie shell, and I recommend going heavy on the nuts, since the pecan/goop ratio is one thing that distinguishes a home-made pie from some of the abominations that people will sell you. Bake for about 40 to 45 minutes at 375 F (190C), and let cool completely before you attack it. Note that this product has an extremely high energy density - it's not shock-sensitive or anything, but I wouldn't want to see what it would do to a calorimeter.

Note for non-US readers: the baking chocolate can be replaced by 40 grams of cocoa powder (not the Dutch-processed kind) with 28 grams of some sort of shortening (unsalted butter, vegetable shortening, oil, etc.) If you don't have corn syrup, then just use a total of 350g white sugar instead, and add 60 mL water to the recipe.

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September 28, 2010

Open Thread

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Posted by Derek

I'm out of touch at a meeting all day today, so I thought I'd put up a request thread. What topics would people like to see covered here in the coming days and weeks? I have some chemical biology posts queued up, and current events will always intervene, but if you have any other topics for a medium-to-long horizon, feel free to suggest 'em. Thanks!

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September 6, 2010

Day Off

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Posted by Derek

Science (and blogging) will march along without me today, in honor of Labor Day in the US. I hope it doesn't get too far out ahead, so I can catch up.

I'm home preparing for a big dinner of some of my native Arkansas food (catfish and hushpuppies), planting flower bulbs, and teaching my two children to play seven-card stud high-low poker. Busy, busy, busy.

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August 27, 2010

Blogroll Update

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Posted by Derek

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August 24, 2010

Housekeeping Note

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Posted by Derek

My time's been in short supply the last few days, so I haven't had a chance to blog about the latest response from Sirtris regarding their compounds and assays. It's coming! I'm doing a side-by-side with the earlier papers calling their results into question.

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August 23, 2010

Lunch at the Boston ACS Meeting

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Posted by Derek

A reminder, for those in town for the ACS meeting. If you're interested, there will be a "Lunch and Learn" panel discussion on chem/pharma blogging in the Ballroom West tomorrow, from 12 to 2 (PDF flyer). As the longest-standing chemistry blogger (perhaps the longest standing science blogger, for all I know), I'm glad to have a chance to speak.

I was just telling a reader by e-mail that when I started this site in 2002, that I wasn't sure how much I'd find to write about. But (for better or worse) the material just keeps on coming. . .

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August 13, 2010

By The Way. . .

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. . .next week. Less depressing. I promise!

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July 28, 2010

Out in the Public

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Posted by Derek

I wanted to mention a couple of meetings that I'll be attending over the next month or so, in hopes of meeting people there. First off, this weekend I'll be at the 2010 Sci Foo Camp, out at Google's headquarters in Mountain View, CA. I'm happy to have received an invitation to this one, and I'm looking forward to seeing what it's like.

And in August, I'll be attending some of the sessions at the Boston ACS meeting, and speaking at a "Lunch and Learn" session on scientific blogging and communication. It's on Tuesday, August 24, from 12 to 2 at the Boston Convention Center. Here's a PDF flyer for the event. My fellow lunch-and-learners will be Ed Silverman of Pharmalot, David Kroll (aka "Abel Pharmboy" of Terra Sigillata, and Michael Tarselli of Scripps Florida. I hope to meet some of you there!

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July 22, 2010

Back in Business

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Posted by Derek

I wanted to let everyone know that I'm back from my break, and will resume regular blogging tomorrow. I have a few topics queued up, but in case I've missed something - any big stories out there that we should be talking about?

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July 13, 2010

Midsummer

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I wanted to let everyone know that posting is going to be scanty around here for the rest of the week and into the first part of next. Any gigantic events that may happen I'll try to cover, but otherwise I'll be fairly scarce. . .

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July 5, 2010

More From the Fourth

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Posted by Derek

And here's what we had at "In the Pipeline"'s headquarters for the Fourth - yep, a down-home old-fashioned Iranian kebab feast. Works just fine!
kebab%20feast%20small.jpg

Update: Since several people have pointed out that this is an experimental result without sufficient preparative details, here's the Supporting Information file: for the meat, you'll want beef tenderloin, cut into reasonable-size pieces (say, 3x4x4 cm). Chop up onions sufficient to cover the meat pieces (roughly one large onion per pound), and stir both of these together with salt (at your discretion, but roughly 10g per pound of meat), and lemon or lime juice - enough to moisten things, perhaps one half lemon per pound of meat. Let the meat marinate for at least two hours, then skewer it (broad Middle Eastern skewers work much better than the typical wiry ones you can get here). Whack the meat gently with the back (blunt) side of a cleaver once it's on the skewer and grill it over high heat, brushing it with a mixture of saffron (Iranian if you can get it, widely considered the best, at least by Iranians) steeped in hot water and melted butter.

As for the chicken, it gets a very similar treatment with the onions, salt, and lime juice. Brush that with the saffron as it grills (I just use the aqueous form, but feel free to use the butter mixture if you desire). You have now prepared kebab-e-bargh and juje kebab, either of which should be served with basmati rice. I was smart enough not to include a picture of that, so its recipe can wait until another time (!). Master those and the ground-meat kebab-e-kubideh and you can open a food stall for sure.

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Holiday

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Pretty much everyone in the US pharma/biotech industry has the day off today, added on for the Fourth of July. So here's one of my traditional posts for this holiday, never more true than now:

This, at least, I have observed in forty-five years: that there are men who search for it [truth], whatever it is, wherever it may lie, patiently, honestly, with due humility, and that there are other men who battle endlessly to put it down, even though they don't know what it is. To the first class belong the scientists, the experimenters, the men of curiosity. To the second belong politicians, bishops, professors, mullahs, tin pot messiahs, frauds and exploiters of all sorts - in brief, the men of authority. . .All I find there is a vast enmity to the free functioning of the spirit of man. There may be, for all I know, some truth there, but it is truth made into whips, rolled into bitter pills. . .

I find myself out of sympathy with such men. I shall keep on challenging them until the last galoot's ashore.

- H. L. Mencken, "Off the Grand Banks", 1925

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June 10, 2010

Nativis: In Which the Distant Footfalls of Lawyers Can Be Heard

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I've received a letter from John Kingma, the Chief Financial Officer of Nativis. I reproduce it below word-for-word (Here's the PDF of the original, in case anyone would like to check):

Dear Dr. Lowe,

The scientific nature of your blog seems to have taken a turn for the worse with the negative personal attacks on John and Lisa Butters and othe rmatters related to Nativis. The comments have gone far beyond reasoned scientific debate, skepticism and criticism. In fact, the overall tone seems to have degenerated into something resembling the Internet bulletin boards of old, with personal attacks, sexual comments and statements that may well amount to libel and defamation of character.

It appears to us that that the same person, using multiple names, is responsible for many of the negative personal comments (indications are that this is a person who bears a personal grudge against John Butters, and who now seems intent on ruining his reputation and that of Nativis). It seems clear to us that you have permitted unprofessional, bizarre, and even potentially activity prohibited by law to be conducted by this commenter and others on your blog site, activity that clearly overrides the scientific debate.

No one in the Nativis family has experienced anything so outrageous and unprofessional as the content of your blog site. I don't know if the current non-scientific banter is what you intended for your blog - essentially now a forum for personal attacks. Not only have you allowed theses attacks to be posted, you have also been selective in posting (screening out) information that would be more favorable to Nativis, such as the positive pre-clinical research data that John Butters provided you, showing how drug signal therapy reduced tumors in mouse models.

Moreover, apart from personal attack comments, your blog also contains comments from a person who announced his attempts to gain access to Nativis's facility. In fact, he visited Nativis's site, posing as a representative of your blog, The Pathfinder. When he was turned away by security, he reportedly took photographs or videos through office windows. His actions were reported and encouraged on your site. His actions may well have been illegal.

We have asked counsel to take a look at what is happening on your blog and the activities by commenters promoted there, and to recommend a course of action. But everyone at Nativis would rather get past this unfortunate situation and spend 100 percent of our time advancing our technology.

In that regard, may we suggest that in the best interest of all parties that you moderate your blog, focus on the scientific debate, delete all personal attacks and prevent personal attacks from occurring in the future? That would seem fair and reasonable, while also keeping the scientific debate going.

Thank you, in advance, for the consideration. I look forward to your response.

Sincerely,

John E. Kingma
Chief Financial Officer

Well. I suppose that the rest of this post should begin with "Dear Mr. Kingma:"

I am, as you see, in receipt of your letter of June 9. Allow me to comment on it, so that we may understand each other.

Your first objection is that the tone of some of the comments to my two posts on Nativis have "gone far beyond reasoned scientific debate". A less charitable observer might say that the claims that Nativis makes for its technology have long since occupied that territory. But I've actually tried to be charitable. Until your letter arrived, most of the criticism I'd received from readers and colleagues in the industry was that I'd been far too tolerant in my discussion of your company.

Your CEO, in addition to sending me papers on such disparate subjects as the Mossbauer effect (and offering generously to send along a large book on quantum electrodynamics), did indeed provide a graph of what is said to be the effect of your most advanced. . .well, let's call it a "therapeutic agent" in a mouse model. This does not help me as much as you seem to believe it does. Imagine some other company claiming that they can show effects in a mouse xenograft model though the intervention of invisible pink unicorns - and providing a dose-response curve as proof. Extraordinary claims, which yours surely are, require extraordinary evidence, and I don't see how you can possibly provide enough in a blog forum to convince your critics. Besides, this would be a waste of your time. You will surely be generating a tremendous amount of data in preparation for your company's IND application, and I certainly can't ask you to share all of it. Convince the FDA, and you'll have gone a long way to convincing everyone else.

Now, to your observations about my blog's comment section: I do not actively moderate it, except to occasionally remove duplicate posts. No real moderation has been needed: the tone of discussion around here is unusually civil, for the most part. It's especially so compared to the rest of the blog world and the Internet as a whole - not just "of old", but every day of the week. If no one in the "Nativis family" has ever experienced anything so outrageous as the contents of this blog, permit me to observe that you appear to have led sheltered lives.

Believe me, you will hear worse from other people as you go on developing your company's approach to drug therapy. I mean this in the best possible way, but the material that Nativis uses to explain and promote its technology does not inspire confidence in trained observers. I assume that you're well aware of this; if you're not, you should be. And that's fine - huge breakthroughs in the sciences often have that effect on people. But the problem is, nonsense has the same effect. If I may quote the late Carl Sagan on this very problem, "They laughed at Galileo. They laughed at Einstein. But they also laughed at Bozo the Clown."

Your company's claims are so startling, and so far beyond what most scientists would assume to be possible, that you truly have no alternative but to fall into one of those two categories. A red nose, a fuzzy wig, and floppy shoes are waiting for anyone who makes such claims. Your job is avoid being fitted for them. To that end, you do not have to convince me, or any random bunch of people on the internet. You have to convince the patent offices, the journal editors, and the regulatory authorities. My advice is to devote your time and effort to that task, and to stop worrying about what people say about you on blogs.

Worse things have been said on this site about other (far larger) companies; worse things are said all over the internet a thousand times a second. I certainly do not endorse the making of defamatory comments about people, but I fear that some of the very comments you might object to might not be seen that way by every observer. If I start taking down every comment that offends anyone who writes to me, there will be no end to it.

If you read my posts, you will see that I have not encouraged anyone to engage in illegal conduct. That goes for the entire 8-year archives of the blog, for that matter. I did not encourage anyone to visit your site in any way, and did not comment when someone reported that they did so. I live and work on the other side of the country from you, and my readers are responsible for their own actions. By the way, if the person you speak of did identify themselves as a representative of "The Pathfinder", as you state, then their connection to a blog called "In the Pipeline" is unclear.

As to whether some individual is engaging in a campaign of defamation against your company and your CEO, I can see no evidence of that in my blog's records. The uncomplimentary comments seem, from what I can tell, to have come in from a wide variety of separate sources - you truly have brought people together. On the other hand, some of the glowing endorsements and defenses of your company have come in under different names from the exact same IP addresses. Make of that what you will.

Mr. Kingma, you (and John Butters, and all the other officers and employees at Nativis) should be out there working to revolutionize the entire drug industry. If you can do what you say you can, that's exactly what will happen. Any scientist on the trail of something this wonderful, this huge - and potentially this profitable - would not allow anything to deter them from claiming their place in history. Go do that. I'll be overjoyed if you manage to pull it off. But having heard, after only two blog posts, from both the CEO and the CFO of your company makes me wonder about how you choose to use your time.

Sincerely,

Derek Lowe

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Coming Soon

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Just wanted people to know that I'll have what should be a very interesting post up a bit later on (around lunchtime). I'm traveling today, but I'll have a layover in which to post. See everyone then!

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April 29, 2010

Chemistry In (Ahem) Everyday Life

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Posted by Derek

I'm not sure how to interpret this, but my wife just sent me this link. She points out that the item is not only on sale, but that I can get free one-day shipping. Time, however, appears to be running out on that last option, so I must (yes!) act without delay.

I'm thinking of counteroffering with a different allotrope. I'll let everyone know how that goes.

Update: her latest offer is an equitable 50:50 deal - I buy her the ring, and she gets the graphite rod for me. That plan is, I think, that this way I get the shaft twice.

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April 28, 2010

Delivery Via Kindle

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Posted by Derek

I've had a few requests to make the blog available in a Kindle
version. So after a visit to the innards of Amazon, here it is, for those of you who'd like things delivered in that format. I don't own one of them myself, but I can definitely see the point of one (or something like it).

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April 27, 2010

Of Cambridge, MA Interest Only

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Posted by Derek

Every year there's a big Cambridge Science Festival, which many companies and institutions around here get involved with. My own company is no exception, and we're holding a "Networking Event" for students in academia tomorrow afternoon. Flyers for it went out a while back to all sorts of institutions around the area, but for anyone who's also a reader of this blog, I wanted to mention that I'll be giving a 30 minute talk at this one. So if you're in the target audience, feel free to stop by (4 PM Wednesday, 200 Sidney Street). I believe that there was an RSVP by last Friday, but drop me an email if you missed it, because I don't think we're going to lock anyone out if you really want to come, either.

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April 19, 2010

More on C&E News

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Thanks for all the comments to the previous post! And please, non-chemists who read or have a use for the magazine, please feel free to chime in as well.

Just to clear up some confusion, though, this is only an advisory position, and there are plenty of other people from academia and industry who also serve in the same capacity. I'm doing the same job I have been (and writing this blog the same way I have been as well!) Nothing's been affected, but it seems from the comments that some people have thought otherwise.

What will be affected around here this week is posting, which will be irregular. I'll try to get some things up, but it'll be haphazard. And I'll report back on the meeting with the C&E News folks as well.

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April 2, 2010

Day Off

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Posted by Derek

I'll be taking advantage of the fact that it's not actually raining today, and adding a day to the weekend. The rising rivers around the Boston area have made me glad that I live on a hill! Regular posting returns for Monday. . .

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March 17, 2010

More Blogroll

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Posted by Derek

Here's another addition: A New Merck, Reviewed, which is someone's attempt to dig through everything about the new Merck/Schering-Plough hybrid. I'm not sure that all the info is reliable, of course, and whoever writes this has a strange way with italics, but it's worth a look.

Update: this turns out to be the Wordpress backup site for Shearlings Got Plowed, which I've mentioned here before. With the merger, the blog's author is covering his bases.

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March 12, 2010

Blogroll Update

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Posted by Derek

Time to sweep out the inactive chemistry sites and bring in some new ones. Welcome to Chemistry Blog, Pharma Strategy Blog, Practical Fragments, Fragment -Based Drug Discovery Literature, Symyx Blog, and All Things Metathesis! And in the resources section, there's Chempedia Lab, a chemistry-question site that's looking for a broader user base.

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March 1, 2010

Blog Traffic - Thanks!

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Just a quick note to say that traffic here broke all the house records last month - over 440,000 page views (partly thanks to a late surge in interest in the wonderful properties of dioxygen difluoride). The number of people interested in this sort of thing continues to exceed my estimates. . .!

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February 24, 2010

Write A Book, Why Don't You

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Posted by Derek

Yesterday's "Things I Won't Work With" post has brought on calls to turn these (and some other parts of the blog) into a book. And you know, I'm game, actually - but I have no real contacts in the publishing world. If anyone out there in the readership knows a good agent, or knows someone who does, I'd be glad to have some contact information. Thanks!

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February 16, 2010

Twitter and Science, Revisited

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Posted by Derek

So I have a number of people trying to set me straight about Twitter. . .well, I'll see what I can do. For some time I've had it set up just to take 140 characters off the top of each post I do here, to serve as a sort of "I've posted something" alert, and that'll continue. I hardly follow anyone there, true. . .and many of them are non-chemical sources (Iranian politics and the like). What I probably need to do is set up more than one Twitter account, with one reserved for blogging and science. But even then, I don't see how I'll have time to look at it during the day, so people who fire messages back to me via Twitter are still going to come away disappointed.

Comments (8) + TrackBacks (0) | Category: Blog Housekeeping | The Scientific Literature

January 29, 2010

Sure Thing

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Posted by Derek

I get a lot of press releases around here - not a day goes by that several don't show up in the e-mail queue. I glance over the titles, and I'll open up the more interesting ones and look at them in more detail. Since I feel no obligation to read unsolicited bulk mail (who does?), the less interesting ones get deleted without opening.

Most of what shows up is reasonably well targeted, from university press offices or scientific publishers, and once in a while one of them will lead to a blog post. The PR from small pharma/biotech companies is also probably well targeted, but it's much less likely to lead to anything, simply because there's so much of that stuff around and because it tends, on the average, to be decidedly less interesting: "Spamozyme, Inc. announces its new ZippyChip assay, now with the great taste of fish!" (I don't have the heart to ask Google if "ZippyChip" is the name of a real technology; I fear the answer).

But I also get things that are seriously misguided. Publicists ask me if I want to talk to someone who's just published "Nineteen All-Natural Ways to Quantum Healing" or some damn thing, and the answer is, no, of course I don't. I'd rather drop an Erlenmeyer flask on my foot. Come to that, I'd rather read press releases about the ZippyChip. I know somebody's getting value for their publicity dollar when I get an e-mail pitch asking if my readers would be interested in learning the ways to holistic health without resorting to dangerous and toxic pharmaceuticals

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January 15, 2010

Physics, for Dogs and Others

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Posted by Derek

Allow me to recommend a book I received a copy of recently, Chad Orzel's How to Teach Physics to Your Dog. Chad's a fellow scientific blogger from way back, and I have had a chance to consume chicken wings and trade lab stories with him. His new book is a fine addition to the what-the-heck-is-quantum-mechanics field, with some very good analogies and explanations. The format is conversational (which has a long history in the teaching of science), but this time, Orzel's dog is holding up the other end of the dialog. It's a device that lets him get at some pretty complex subjects - complex even for humans, I mean. (The famous Gary Larson "Far Side" cartoon, about dogs being so cute when they try to comprehend quantum mechanics does come to mind). Definitely worth a look.

Comments (12) + TrackBacks (0) | Category: Blog Housekeeping | Book Recommendations

December 24, 2009

Holiday Time Off

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Posted by Derek

Well, with the holidays and all, I'll be taking blog-time off until Monday. The pace of scientific discovery has slowed noticeably around here in the last few days (and from the traffic stats, I can tell it's slowing in lots of other places, too!) As usual, I've made notes about what I'm up to in the lab, so I can pick up the threads in January. I also have an interesting manuscript that I'm submitting for publication, which I hope to talk about here soon. I'd like to wish all my readers who are celebrating a Merry Christmas!

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December 18, 2009

Day Off!

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Posted by Derek

I'll be out doing non-scientific things all day, so the march of progress is going to have to lurch along without me for a bit. I'll see everyone on Monday!

And if you're in need of something to waste a bit of time on, this site will make your sense of order shudder: There, I Fixed It. It's a favorite around the Lowe household; I'm trying to turn my kids into the sorts of people who will never do any of those things.

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December 8, 2009

Another Blogroll Update

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Posted by Derek

Time for some more useful sites! In the blog category, welcome to Intermolecular, Natural Product Man, Experimental Error. And in the chemistry data section, I've added Synthetic Pages, Not Voodoo, and the Organic Chemistry Portal. And finally, I'd inexplicably left Ben Goldacre's Bad Science
off the blogroll, even though I've linked to it several times, so I've fixed that. Enjoy!

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November 25, 2009

Light Blogging

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Posted by Derek

I'll have the Grand Recommended Med-Chem Book List up later today, but otherwise, blogging will be light over the next few days, what with Thanksgiving and all. A very happy feast to my readers who are celebrating, and hey, those of you in other countries, feel free to enjoy yourselves, too!

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November 24, 2009

Applied Organic Synthesis: Chocolate Pecan Pie

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Posted by Derek

I first published this recipe on the blog a couple of years ago, and I'd like to put it out there again for those readers who will be celebrating Thanksgiving this week. This is a slightly modified version of Craig Claiborne's recipe in the New York Times Cookbook
. He was a Southerner himself, so he knew his pecan pie. Substitutions for the ingredients are listed after the recipe:

Melt 2 squares (2 oz.) baking chocolate with 3 tablespoons (about 43g) butter in a microwave or double boiler. Combine 1 cup (240 mL) corn syrup and 3/4 cup sugar (150g) in a saucepan and bring to boil for 2 minutes, then mix the melted chocolate and butter into it. Meanwhile, in a large bowl, beat three eggs, then slowly add the chocolate mixture to them, stirring vigorously (you don't want to cook them with the hot chocolate goop).

Add one teaspoon (5 mL) of vanilla, and mix in about 1 1/2 cups of broken-up pecans, which I think should be about 150g. You can push that to nearly two cups and still get the whole mixture into a deep-dish pie shell, and I recommend going heavy on the nuts, since the pecan/goop ratio is one thing that distinguishes a home-made pie. Bake for about 45 minutes at 375 F (190C), and let cool completely before you attack it. Note that this product has an extremely high energy density - it's not shock-sensitive or anything, but make the slices fairly small.

Note for non-US readers: the baking chocolate can be replaced by 40 grams of cocoa powder (not Dutch-processed) and 28 grams of some sort of shortening (unsalted butter, vegetable shortening, oil, etc.) If you don't have corn syrup, then just use a total of 350g white sugar, and add 60 mL water to the recipe.

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November 18, 2009

More For the Blogroll

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Posted by Derek

Two more blogs that I've forgotten to add are now on the blogroll: Pharma Conduct and Chemical Space. Welcome!

Update: oh yeah, Pharmalot returns, too!

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November 17, 2009

A Blogroll Update

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Posted by Derek

I've gone through the blogroll, clearing out inactive sites and adding new ones. So welcome to Med-Chemist, Chemical Crystallinity,
Synthetic Nature, , Chiral Jones, and P212121!

And I've also added another category for chemistry and pharma database sites. There you'll find a quick way to access the copious piles of information from Drugbank, Emolecules, ChemSpider, PubChem, DailyMed, Druglib, and Clinicaltrials.gov.

As always, if I've left a blog (or your blog!) off the list, drop me an e-mail and let me know about it. If it's of potential interest to the readership here, on it goes.

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October 21, 2009

"Back to School"

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Posted by Derek

I just wanted to note that the entire BioCentury "Back to School" issue mentioned in the post below can now be read for free (PDF). Thanks to the folks over there for doing this! The original post has been updated as well.

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October 12, 2009

Day Off

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Posted by Derek

I'm taking the day off today (it's a school holiday, so I'll be out doing fall-ish stuff with the family rather than pushing back the boundaries of human knowledge. The frontiers of science will come under fresh assault tomorrow, though (as will the frontiers of science blogging).

I did want to mention, though, that Pharmalot is active again - Ed Silverman has his old domain, and is posting as time allows from his day job over at Elsevier. Welcome back!

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October 6, 2009

Traveling, Updates Later

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Posted by Derek

I've been traveling since Saturday, and have just spent an unplanned night in Atlanta, so things are a bit behind schedule around here. Regular posting will resume here tomorrow, when we'll have news of the Nobel in chemistry for this year. See everyone then!

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October 1, 2009

Traffic Record

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Posted by Derek

By the way, I just wanted to thank everyone who's been stopping by here. Traffic for last month broke all records: 260,000 visits, 350,000 page views. And that's not too bad for a site that talks about smelly chemicals and the people who work with them! Much appreciated.

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September 1, 2009

Back

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Posted by Derek

Just wanted to let people know that I am actually around. Yesterday was a home improvement day, so I didn't contribute much to the march of science (or to the blog!). And this morning I have a lot of catching up to do on that march-of-science front, but I'll have a post up at lunchtime.

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August 19, 2009

Time to Sing the Alma Mater

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Posted by Derek

Many of you may have looked at the short bio on the left-hand side of the site and wondered where the heck Hendrix College is. To my surprise, I opened up the New York Times today and found this article, which is surely the most coverage the school has ever received from them. (No science or chemistry connection in the article, though).

Last year I saluted Warfield Teague, my now-retired inorganic chem professor there, and I've mentioned the school's (in)famous organic professor, Tom Goodwin, several times (most recently here).

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August 18, 2009

H-h-h-holy C-c-c-c-cow

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Posted by Derek

I was going to put up another post here at lunchtime, but they've been tearing up the street or something right outside my building all morning. It's like a gigantic dental drill is trying to break in here - my desk vibrates. I've hardly had two sequential thoughts all morning - any more of this, and I'll be fit to be a managerial consultant.

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August 10, 2009

Blogroll Update

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Posted by Derek

A few more additions to the list at left today - welcome Node in the Noosphere, The LouRoe, and Heterocyclic Chemistry. In general, if you can't find anything worth reading here, there's generally something good over in the blogroll. . .

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July 29, 2009

Return From Travel: A Note About Cheaptickets.com

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Posted by Derek

I've now returned from a family vacation, so regular blogging is set to resume. Before it does, though, I have a brief public service announcement for readers who are looking for airfare deals: beware of Cheaptickets.com. I went with them this time because they beat what I could find on Kayak, but TANSTAAFL, or even necessarily a cheaper one.

Even when you've paid for your tickets and picked out your seats two months before, even after Cheaptickets sends you an e-mail with your reservation info, one that lists all your seat numbers and says "Your Seats Are Confirmed", don't just go and assume that those are, you know, your confirmed seat numbers. They aren't. You and your family can easily end up scattered throughout the plane - we sure did, at least until a helpful person from United was able to rearrange things.

Turns out the Cheaptickets people "forward your seat preferences" to the airlines, who then are free to do what they like with these suggestions. The whole seating-map thing is just a sort of gedankenversuch, not meant to have any real-world application. So keep that in mind.

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July 27, 2009

Travel Continues. . .

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Posted by Derek

I'm still on the road - just wanted to let everyone know that I'm still out here, and piling up topics to cover here. Should be another day or two before regular posting resumes. See you then!

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July 22, 2009

Travel

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Posted by Derek

Just wanted to let people know that posting will be irregular around here for the next few days, due to some traveling. I'll probably be able to put some stuff up, but it'll show up at odd intervals. I assume that no gigantic science/pharma stories will break in late July, but I guess one never knows. . .!

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July 3, 2009

Day Off

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Posted by Derek

I'll be taking today off, as an addition to the Fourth of July weekend. I hope that my American readers enjoy some warm, sunny weather (of the kind that's been in very short supply around here). No matter what the conditions, though, I'll be making a large slow-cooked pork shoulder with plenty of hickory wood. I'll see everyone on Monday!

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July 1, 2009

Blogroll Update

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Posted by Derek

Time for a quick blogroll update. Heading into the various science and pharma blog category over on the left are PK/PD, BBSRC/Douglas Kell, and Sigma-Aldrich ChemBlogs. Enjoy!

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June 23, 2009

Proxy Server Update

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Posted by Derek

I appreciate the mail I've had on this subject, and wanted to provide a brief update for those who are interested. If you've set up a proxy server for Iran, you can submit it here - Austin Heap is the guy running this part of the effort. There's also a test page where you can see if you have things configured correctly. Anyone needing more technical details, please drop me a note - I'll either answer it myself or send you on to someone who can. I am, truth be told, not exactly one of the 1337-est haxors around, but one does what one can.

Comments (4) + TrackBacks (0) | Category: Blog Housekeeping | Current Events

June 16, 2009

Proxies for Iran (More Politics - Mixed With Technology)

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Posted by Derek

Many thanks to the people who've e-mailed me about the situation in Iran. My wife's relatives there are all OK (so far!); she's spoken to them several times. Things remain unstable and impossible to predict. It's been thirty years since huge crowds marched through the streets shouting "Death to the Dictator", so everyone's a bit out of practice.

One thing that the more technically inclined readers might consider doing is setting up proxy servers for use by the Iranian protesters. Two web sites that will give you details on this are here and here. The government is blocking all the obvious IP addresses for people trying to organize and get news out of the country, but anonymous proxies provide a lot of non-obvious routes onto the net. I'm trying to get something set up at home myself.

There are a lot of punches being thrown by both sides - for example, some people with proxy servers have reported a lot of denial-of-service garbage coming in from blocks of Russian and Chinese IP addresses. But if you configure things to accept only Iranian domains (those sites above have IP address lists) you should be able to screen that stuff. If you're up for it, please consider helping out. It's one of the few concrete steps I can think of from this distance. A general guide to the current cyberwarfare situation is here. Update - link went dead, but this new one will stay alive. BoingBoing has enough bandwidth!

Comments (20) + TrackBacks (0) | Category: Blog Housekeeping | Current Events

June 14, 2009

And Now Some Politics

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Posted by Derek

My Twitter account usually only gets my posts on this blog (the first 140 characters of them, that is). But those of you who follow me there have been flooded with updates of a very different kind for the last 24 hours or so. My Iranian-born wife and I have been watching the news carefully, as the Iranian election situation seems to be getting out of control. She's been translating Farsi-language updates, and I've been reposting them - there will probably be more of this over the next few days.

You can imagine where my sympathies lie, as a non-religious guy with libertarian leanings. Confusion and bad luck to the mullahs, to everyone who helped them steal this election, and to their henchmen beating members of the opposition in the streets. Freedom of speech, freedom of assembly, and freedom of electoral choice are easy to take for granted in some parts of the world, but none of them come easy.

And more to the usual subject of this blog: the Iranians have produced a lot of top-notch people in science, medicine, and engineering - I've seen and worked with many of them. But I'd love to be able to see what they could accomplish working from a free and stable country, and I hope I get the chance. We'll see.

If you're looking for news, #iranelection on Twitter is a firehouse of information, good and bad, and will lead you to plenty of other sites. The National Iranian American Council is an excellent source, and Andrew Sullivan is doing a fine job covering the situation, too.

Comments (16) + TrackBacks (0) | Category: Blog Housekeeping | Current Events

June 8, 2009

Quick Blogroll Update

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Posted by Derek

In an effort never to let the blogroll slip like I did throughout 2007-2008, here are a few more chemistry/science blogs. Welcome to Zusammen, Chemical Crosspatch, Culture of Chemistry, and Chemical Professionals. As always, suggestions for new inclusions are welcome!

Update: Drug Discovery Opinion, too!

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June 5, 2009

Blog Contestification

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Posted by Derek

Voting ends Monday at the 3Quarks science blogging contest, so anyone who hasn't put their chip in can do so over the weekend. They're trying to make sure that everyone only votes once, which is a good plan. Looks like I have an entry or two doing well, and I've learned about several other blogs that I hadn't heard of before by looking over the tallies so far. Another blogroll update is pending!

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June 2, 2009

Blog Contestiness

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Posted by Derek

Voting has started on that 3Quarks science blog prize - here's the voting page. I have several posts on their nominees list, so I'll probably be diluted a bit, but please vote for your favorites (and discover some blogs that you probably haven't heard about).

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May 28, 2009

A Science Writing Award

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Posted by Derek

The folks over at the science-and-culture blog 3 Quarks are running a blog award for science writing, to be judged by Harvard's Steven Pinker. I figure that the readership here sees a lot of science blog posts from a lot of sources, so feel free to nominate anything that you've found especially memorable. They're looking for pieces written during the last 12 months, and it looks like their nomination process ends rather soon - wouldn't surprise me if they're working off of Pinker's schedule, which must be rather tightly articulated. . .

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May 11, 2009

Still More Blogroll Additions

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Posted by Derek

I did indeed miss a few in the latest update, so (before I let things sit for months, again), welcome Chemjobber, Science-Based Medicine, Chemical Quantum Images, Noel O'Blog, My Chemical Journey, and Eigenfunction/Eigenvalue. Good grief.

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May 8, 2009

Blogroll Update

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Posted by Derek

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April 20, 2009

More Travel!

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Posted by Derek

Posting will be irregular this week - I'm off traveling again, this time in the Washington, DC area. (This hasn't been the single most scientifically productive April I've ever had, unfortunately). I do hope to get some posts up, but not today - whatever news is happening, I'll catch up on it for tomorrow!

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April 6, 2009

San Diego

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Posted by Derek

Thanks to the readership for all the suggestions. Today I managed to survive on fish tacos for lunch and a fearsome bacon burger at Hodad's over in Ocean Beach for dinner. Good thing the hotel has a gym. No one's going to mistake Newport Street there for La Jolla, are they? Tomorrow I'm having a working lunch, a light one, I should hope, and at some point I'll do my Mexican thing over on University Avenue (Super Cocina has come highly recommended).

And yes, for the folks back at the shop who read the site, I am doing something here other than plow through the local food. Honest. I have witnesses that I was in every single talk at the meeting today, and y'all know from experience how rare that is.

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Travel

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Posted by Derek

Most of my last 24 hours have been spent in travel mode, of one sort or another, so I doubt if I'll have a full blog post this morning. I'm out in San Diego for a conference, so if any of you are doing the same, perhaps I'll run into you.

I won't be blogging the meeting itself. I'll be taking a lot of incoherent notes for my own use, naturally, and putting them into immediate readable sentences takes a lot of mental overhead. And naturally, proprietary concerns might well keep me from revealing which parts of the meeting I find most important. Of course, you could say that about the literature that I mention here on the blog as well. It's something that crosses my mind, but I try to arrange things so that I'm not giving away much. I also make sure to talk about fields about which I have no (current) professional irons in the fire, so that evens things out a bit.

But daily blogging will continue here during the week, just at odd times as my schedule and scrambled time zones allow.

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March 22, 2009

Blogs and Journalism

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Posted by Derek

Nature is out with a piece on the state of science journalism, and I'm quoted several times as a representative science blogger. They've overstated my blog traffic, though, which is gratifying but inaccurate. Instead of 200,000 page views per week, that's more like my traffic per month. Give it time, I guess! I also am an occasional contributor to an Atlantic web site, not a regular columnist for them.

Update: And in a response to the Nature article by science writer Francis Sedgemore, there's this:

One successful science blog identified by Brumfiel is that of pharmaceutical industry researcher Derek Lowe. “In the Pipeline” is a very well-written blog, but here we have a classic example of a blogospheric closed ecosystem. Lowe’s writing is not journalism, and can never be so given the author’s declared affiliation. More genuinely independent sources of online science news and comment include the web magazines Wired and Seed.

I guess it depends on whether opinion journalism is journalism - since that's what I write much of the time. And how about when I'm writing about something that has no connection to the pharmaceutical industry; do I slip back over the line then? To tell you the truth, I'm not necessarily sold on the idea of journalism as a particular professional category - as far as I know, the whole idea of the dispassionate truth-seeking journalist is a pretty recent one.

But that said, I don't consider myself a journalist, either, under almost anyone's definition. I'll take "writer", although that should really be "part-time writer": I'm a scientist by trade; the writing is something I do on my train rides or in the evenings. If I had to support my family on earnings from my written work, we'd all be eating weeds out of the back yard.

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February 20, 2009

Hexacyclinol - Another Request

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Posted by Derek

I'm taking the day off from cranking out the medicines of tomorrow (OK, the day after tomorrow), so there will be no post today.

I did want to add something about yesterday's post on the La Clair/hexacyclinol controversy. I'd like to ask that people not fill up the comments with ad hominem remarks or potentially libelous statements about La Clair himself. I don't mind saying that the evidence so far makes it very hard for me to believe his original paper, and I also have to say that I haven't seen any convincing explanations for all the discrepancies that have turned up. And I think that those opinions are shared by many people who've followed the story.

But let's keep it on a scientific plane, if possible. Opinions on NMR spectra and the like are one thing, but personal insults are another, and those we don't need. I try not to have to go in and hose out the comments sections around here.

Comments (15) + TrackBacks (0) | Category: Blog Housekeeping | Chemical News | The Scientific Literature

February 16, 2009

Day Off

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Posted by Derek

Today is a holiday in many workplaces around the US today, and so it is at mine. I'm home at stately Lowe Manor, breaking ice off the shady front steps and cleaning out the cage of my daughter's guinea pig. The comparatively relaxing (and comparatively nice-smelling) business of drug discovery will resume tomorrow, as will blogging. See everyone then!

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January 15, 2009

The Blogroll

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Posted by Derek

This is long, long, overdue, but I've finally gone through the blogroll and cleared out the dead sites, of which there are (were) many. Stage Two will be adding news ones. I already have a list going, with an eye on getting them in this weekend, but I'd be glad to hear about others that I might have missed. Chemistry / biology / pharma / science blogs that I don't yet link to, anyone? Add 'em to the comments if you have some, and thanks!

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December 23, 2008

Holiday Break

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Posted by Derek

Posting will be intermittent around here until after January 1st. I'm going to be doing various important tasks at home, such as wrapping presents and making another chocolate pecan pie for folks who didn't get any the last time around. There's also some snow to be shoveled, particularly if I want to get the telescope out during this period of new moon. There's 15 to 20 inches out there on the ground, which is not much of a stable surface for the equatorial platform to sit on, nor do I relish wading through it while hauling the telescope tube itself.

My workplace is very quiet indeed today, I can report, and later on I'll be doing my part to keep it that way. I suspect it's the same across a lot of labs today and for the next few days, and that's a good thing. It's impossible to have good ideas when you're grindstoning away the whole time; you need to clear your head every so often and take a look at what you're actually doing versus what you should be.

This is one of the only times when sleeping late and eating pecan pie come under the heading of "clearing one's head", so I'm going to take full advantage of it. I hope that many of you can do the same!

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November 26, 2008

How Slow is Research Today? Here's a Recipe!

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Posted by Derek

The pace of research has noticeably slowed today here in the US. Most industrial labs will be empty tomorrow, Friday, and through the weekend, and even the academic labs will have fewer grad students and post-docs hanging out in them. I'll be cleaning up some previously run reactions, setting up anything that can comfortably go for a few days, and otherwise getting ready for Monday myself. This is not a day to try any tricky chemistry.

I also have a manuscript that I'm working on, and it would be a good use of my time to try to finish up its experimental section. The paper will likely be of interest to the readership here, so I'll be sure to note when it makes it into print. It'll be good to hit the scientific literature again; everything that's gone onto my list for the last year or two has been residual stuff from the Wonder Drug Factory, and there's not much of that left, naturally.

And I'll be observing a blog holiday until Monday as well, unless of course, something big happens. (I rather doubt that anything will, and considering what "something big" usually means, I rather hope nothing does). I'd like to wish all the US readers a happy Thanksgiving, and if anyone in the rest of the readership wants to try cooking a turkey, well, it's not as hard as it's cracked up to be. If you soak it in some salt water beforehand, it's quite tasty (my wife and I usually buy a kosher turkey, since they've already been salted). Allow me to finish up by furnishing the details of last night's synthetic work, at home in the kitchen with my two children:

Melt 3 tablespoons (43 grams) of butter and two squares of unsweetened baking chocolate (I used a coffee cup set in a pan of boiling water). Beat 3 eggs in a good-sized bowl. Then, in a small saucepan, combine 1 cup (240 mL) of corn syrup and 1/2 cup table sugar (100 g), and bring the mixture to a boil for about two minutes. (It doesn't look at first as if the sugar will go into solution, but it will - you naturally don't want this to cool down, though, once it has). Add the butter/chocolate mixture to the sugar syrup (they're not all that miscible, but do what you can), and add this gemisch slowly to the beaten eggs, stirring vigorously. (As I explained to my kids, if you were to dump these together with no stirring, you'd end up with chocolate-covered scrambled eggs; I try to teach them some technique along the way). Stir in a teaspoon (5 mL) of vanilla extract, 1 1/4 cups of pecan pieces (about 130 grams, I think), and pour the resulting slurry into a pie crust, your own or the store's. Bake about 45 minutes at 375F (190C, gas mark 5 for you subjects of the Queen). Yield: one chocolate pecan pie.

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October 3, 2008

Day Off

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Posted by Derek

No time for a post this morning, unfortunately. The arguments are continuing full speed in the comments to Hard Times: A Manifesto, though, and I plan to do a long-overdue blogroll update this weekend. There are several sites that have needed to be added for quite a while now, and several others that have fallen into inactivity.

Inactivity doesn't seem to be a problem around here, anyway - today's an exception! Have a good weekend, and I'll see everyone on Monday.

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August 15, 2008

Back

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Posted by Derek

Just wanted to let people know that yes, I'm still out here. I've returned from vacation, and am dealing with the usual catch-up on everything that's going on. That includes a flood of interesting data at work, thanks to my summer student, which is always nice to come back to!

Regular posting will resume on Monday, and we'll get back to what passes for normal around here.

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August 5, 2008

Time Off

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Posted by Derek

I wanted to let people know that starting tomorrow I'll be taking some vacation time. Internet access will be rather limited - I'll be checking my mail some in the evenings, but there will be no posting until the middle of next week. Science will have to march on without me for a few days!

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July 4, 2008

Happy Fourth of July

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Posted by Derek

This, at least, I have observed in forty-five years: that there are men who search for it [truth], whatever it is, wherever it may lie, patiently, honestly, with due humility, and that there are other men who battle endlessly to put it down, even though they don't know what it is. To the first class belong the scientists, the experimenters, the men of curiosity. To the second belong politicians, bishops, professors, mullahs, tin pot messiahs, frauds and exploiters of all sorts - in brief, the men of authority. . .All I find there is a vast enmity to the free functioning of the spirit of man. There may be, for all I know, some truth there, but it is truth made into whips, rolled into bitter pills. . .

I find myself out of sympathy with such men. I shall keep on challenging them until the last galoot's ashore.

- H. L. Mencken, "Off the Grand Banks", 1925

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July 1, 2008

Leaving Comments: A Fix

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Posted by Derek

I know that a lot of people have been having trouble leaving comments here over the past few weeks, with plenty of "Too Many Comments" error messages coming up. I see from today's comment thread that there's a brute-force fix for this - deleting the cookie that this site leaves.

In Firefox, you can do that by going to Preferences, then Privacy, then Show Cookies. Find the "Corante.com" one and kill it - here's hoping that fixes the problem and that it doesn't show up again!

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May 12, 2008

Explaining It All

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Posted by Derek

One of the reasons I starting this blog was that many people I met were interested in my job. Very few of them had ever talked to someone who discovered new medicines for a living, and a surprising number of them (well, surprising to me) had no idea of where medicines came from in the first place.

Talking to such folks (interested, but with no particular training in science) gave me some good practice in explaining the work. It helps that the kind of work I do is actually fairly easy to explain. There are a lot of details – as with any branch of science, the closer you look, the more you see – but I haven’t run across any key concepts that can’t be communicated in plain language. (It also helps that medicinal chemistry, as it’s actually practiced, uses an embarrassingly small amount of actual mathematics).

The toughest things to deal with are the parts of the field that actually touch on physics and math. My vote for the hardest everyday phenomenon to explain at anything past a superficial level is magnetism. So that means that explaining how an NMR machine works is not trivial. At least, explaining it in a way that a listener has a chance of understanding you isn’t – a while ago, I took up the challenge to try to explain it here in lay terms, and I haven’t done it yet, for good reason.

Explaining statistical significance is doable, but going much past that (principal components, the difference between Bayesian and frequentist approaches) takes some real care. And, of course, when you open the hood on chemical reactivity, the mechanisms of bond-forming and bond-breaking, you quickly find yourself in physics up to your armpits. It’s easier to stipulate, openly or by assumption, that there are such thing as chemical bonds, and that some of them are stronger than others. You don’t want to start answering a question about why one group falls off your drug molecule easier than another one does, only to find yourself fifteen minutes later trying to explain the Pauli exclusion principle. Counterproductive.

But the basics of medicinal chemistry can be sketched out pretty quickly, which makes some of the more curious listeners wonder, after a while, why we aren’t better at it. The best example I can give them is to advance a quick, hand-waving explanation of, for example, how compounds get into cells. Then I point out that that explanation is unnervingly close to the best understanding we have of how compounds get into cells. The same holds for a number of other important processes, way too many of them.

And that's why drug discovery is simultaneously frustrating and fascinating. We know huge numbers of things, great masses of detail that can take years to piece together. And it's not enough. Some of the most important puzzle pieces are still weirdly ill-defined, and there are probably others whose existence we haven't even realized yet. I'd be willing to bet that if you scanned the whole history of pharmaceutical discovery, you'd find people at every point thinking "You know, in any thirty years they should have all this figured out". But the years go by, and they - we - don't. Give it another thirty years, you think?

Comments (13) + TrackBacks (0) | Category: Blog Housekeeping | Life in the Drug Labs

April 20, 2008

Quick Note

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Posted by Derek

Just wanted to let everyone know that there probably won't be a post for Monday - I'm doing some traveling, and will have irregular access to the internet. No doubt huge stories will break during the day, while I'm unable to comment on them! At any rate, we'll see if I can get something up for Tuesday. See you then!

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March 20, 2008

Anonymity?

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Posted by Derek

I see that “Kyle Finchsigmate” over at The Chem Blog is having some problems maintaining his pseudonymity at his own institution:

” I’m still befuddled why people walk up to me in the hall and talk to me about it. It’s more irritating than you can imagine. I feel like people treat me differently when they find out. . .

It has also become a liability and I’m not in the mood to juggle liabilities. Faculty and students around here have too much time on their hands to deeply contemplate the idiotic musings of a graduate student and it has handicapped me considerably. . .”

I’m not surprised. He’s given out enough details over the course of his blog for someone at his own school to figure out who he is without too much trouble, and I suspect that his distinctive habits of speech carry over into daily life as well. I enjoy some of his posts, but others (as I said about Dylan Stiles's blog) just serve to confirm for me that I am not, in fact, 25 years old.

I very briefly considered going anonymous back in 2002 when I started blogging, but realized that anyone who really wanted to would be able to do the same to me eventually. My writing isn’t as full of copulating inanimate objects as Kyle’s, but it’s also my own, and it’s also recognizable. (And if it’s not your vocabulary that’ll give you away, then it’s your opinions and your outlook).

I also figured that, one way or another, I’d like to be able to take credit for what I wrote. I lost the chance for some anonymous satire and griping by going the public route, but that’s just the sort of thing that would have caused even more trouble if (when) it was eventually traced back to me. So public disclosure it was. It’s worked out well, and I’ve never regretted it.

But I’m very glad that there were no blogging opportunities when I was a grad student. I had an awful lot to get off my chest about my grad school experience, and the opportunity to do it would have been hard to pass up. Sorrow would have been the only possible result. Actually, I’m just glad that there was no Web, period, when I was in grad school, since there’s no telling how long it would have taken me to get out of there if I’d that distraction constantly available.

So a word of warning for those of you thinking of starting a pseudonymous site: you’re heading toward a contradiction. If you’re doing so because you’re going to say things that you can’t say under your own name, you raise the chances considerably of eventually finding them there. And since the internet, for all practical purposes, Is Forever, your opinions and actions will follow you around whether you want them to or not.

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February 19, 2008

Day Off

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Posted by Derek

No post today - I'm taking an extra day to the long weekend, and going in with my kids to see the lizards at the Museum of Science in Boston. Just wanted to let everyone know that nothing is down, and things will be back to their usual levels tomorrow!

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February 1, 2008

Commenting Issues

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Posted by Derek

As many of your have noticed, there's been some software upheaval behind the scenes here the last few days. Many comments aren't getting through at all, and the others are showing up in the system, but not on the public site. Hammers and screwdrivers are being wielded, and I hope things are fixed up soon. . .

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January 2, 2008

Back On the Air

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Posted by Derek

Just wanted everyone to know that we're back in business around here, after a holiday break and some technical problems behind the scenes. Regular blogging resumes tomorrow!

In the meantime (and for some time to come, since there's a lot of it) I can recommend this year's Edge.org question: "What have you changed your mind about?". The index page will get you started. Plenty of good essays are to be found - for example, I just read some extremely sensible stuff from Brian Eno. Enjoy!

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December 20, 2007

Snow Day

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Posted by Derek

No real post today - too much snow shoveling, etc. Things will be a bit irregular around here during the holiday season, as usual, and I think that today will kick it off.

People have asked me how I'm liking Cambridge now that I've been up here a few months. The answer is, just fine. This Christmas season is a great improvement over last year's, that's for sure. Mind you, right now we've got between two and three feet of snow on the ground out here to the west of town, and my wife and I have taken a couple of unplanned sled rides down our steep driveway, with a Honda Accord substituting for the traditional sled.

And although I've spent the last twenty years moving to higher and higher latitudes, I have yet, it seems, made it far enough North to where traffic doesn't go to pieces when it snows. I take the train myself, which works out fine, but last Thursday people were taking hours just to get across Cambridge. (That's as opposed to a weekday morning, where those three miles only take 45 minutes - I did say I was taking the train in. . .)

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November 21, 2007

Synthetic Prep of the Day: Chocolate Pecan Pie

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Posted by Derek

I've had several requests, so here we go. This is a slightly modified version of Craig Claiborne's recipe in the New York Times Cookbook. He was a Southerner himself, Claiborne, so he knew his pecan pie:

Melt 2 squares (2 oz.) baking chocolate with 3 tablespoons butter in a microwave or double boiler. Combine 1 cup corn syrup and 3/4 cup sugar in a saucepan and bring to boil for 2 minutes, then mix the melted chocolate and butter into it. Meanwhile, in a large bowl, beat three eggs, then slowly add the chocolate mixture to them, stirring vigorously (you don't want to scramble 'em with the hot chocolate goop).

Add one teaspoon of vanilla, and mix in about 1 1/2 cups of broken-up pecans. You can push that to nearly two cups and still get the whole mixture into a deep-dish pie shell, and I recommend going heavy on the nuts, since the pecan/goop ratio is one thing that distinguishes a home-made pie. Bake for about 45 minutes at 375, and let cool completely before you attack it. Note that this thing has an extremely high energy density - it's not shock-sensitive or anything, but make the slices fairly small.

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Holiday Break

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Posted by Derek

Well, the drug labs are emptying out today, like many other workplaces around the US. My American readers will be celebrating Thanksgiving tomorrow (and Friday as well, in most cases), and so will I. This will be our first since the new job and the move, and I have a turkey to thaw and a chocolate pecan pie to make. Tomorrow I'll be in charge of roasting the bird, since my wife has washed her hands of the oven in this house until we can get it replaced. I've had my incidents with it too, but I figure that if I can make 100 grams of alkynylaluminum reagent without setting anything on fire (a near thing, though, as I recall), then a sixteen-pound non-pyrophoric turkey should be no problem.

Last Thanksgiving I was doing roughly the same things, but in the knowledge that in two months I'd be out of a job. I prefer this year, hostile kitchen appliances and all. I hope that everyone reading this and celebrating the holiday has a good time at it, and for my readers outside the US, the best to all of you, too. You don't have to eat turkey to be glad for what you have (hey, in some countries serving a turkey would actually make that more difficult). I'll see everyone on Monday, at which point science will get up off the couch and start marching on again.

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November 5, 2007

Bright Lights and Applause?

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Posted by Derek

I see that this blog is getting creamed in the Weblog Awards voting, which is similar to what happened last year. Pharyngula and Bad Astronomy are once again fighting it out for supremacy, this year joined by the fans of Climate Audit.

That last one not a blog I've read yet, since I regard most arguing about global warming to be as much religious as scientific. In my college years I largely lost my taste for arguing with people whose views were not susceptible to change, and too many people on both sides of that one fall into that category as far as I can see.

But the fierce arguing does lead to a lot of blog traffic, that's for sure - the same goes for a lot of the discussion on Pharyngula, as far as I can see. Disputes about sulfonamides and logP don't stir up the same passions, though, but if you're inclined, throw in a vote for this site to keep things from looking too disgraceful.

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October 9, 2007

Blogroll Update

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Posted by Derek

For those of you who were taking the day off yesterday, there's a Nobel speculation post just below this one. Today, it's time for a long-overdue blogroll update. We have the In Vivo Blog to lead things off, and Away From the Bench, which I guess describes me right now, the fine line between Drugs and Poisons, industry news site Fierce Biotech, England's Peter Murray-Rust, the all-fluorous all the time F- Blog, a reluctant chemist doing Closeted Chemistry, Making Graphite Work (something I've never been able to do), the weirdly named Power of Goo, and the most aptly named Great Molecular Crapshoot.

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August 7, 2007

Meet the Blogger?

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Posted by Derek

When I mentioned that I was moving to a company in the Boston area, I had a number of responses from readers of the site about meeting up in person. Now that I'm (sort of!) settled in, I wanted to see if there was still some interest in that idea. It's an odd thought for me, I have to say, but this is the first time I've lived in an area with enough readership density to make such an idea practical. Being recognized at several recent gatherings has brought home to me (in a way that Sitemeter can't quite manage) that a lot of people drop by here.

Lunch would probably be easiest, and I can get to most of the locations that people would think of in the Cambridge research zone. Those who are interested can leave suggestions for a venue in the comments. I've only lived here a month, so I'll defer to the people who know the area better. As for food, I'll eat most things that were once alive, so that won't be a problem on my end.

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August 3, 2007

Not Necessarily So

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Posted by Derek

My travel schedule has left me little time for blogging this morning, so I wanted just to report that I'll be revisiting some of the recent topics around here. My post on virtual companies led to a number of examples being sent to me - I want to look them over and report back. It's my guess that many of these deal with generic drugs or abandoned products, but we'll see. I still don't see how this model would work on a large scale (Pfizer, anyone?), but perhaps there's room for it on a smaller one.

And my post on abandoning the likes of tin, HMPA, and other nasties in med-chem research bought in quite a few counterexamples. I put a note up on that entry to direct new readers of it to the comments, so as not to miss them. I think that different companies treat these issues differently - in some shops, the med chem labs are encouraged to do whatever it takes to make the compounds, with the expectations that process chemistry will straighten out the kinks. Other companies, though, frown on that as irresponsibly throwing the problem over the wall to the next group, and want their med-chem people to forestall such problems if they can. I'll do a whole post on that subject next week, if possible, and we'll take an informal head count.

These bring up a general thought: as with any blog, this one is a reflection of my own experience and biases. (That's the whole point of a blog, eh?) I like the fact, though, that there are so many readers around the industry to confirm or disprove things as they come up. It's my hope that the non-industry audience finds the back and forth on these topics worth reading - I have a mixed crowd around here, and I try to keep things readable for anyone interested who happens by.

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June 26, 2007

Two Weeks Off

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Posted by Derek

Apologies to everyone for the gap in posting around here. As you probably gathered from the most recent one, things are hectic. We're preparing our house (Stately Lowe Manor, if you will) for listing on the local market - it's in good shape, but we've accumulated a lot of stuff over the last ten years, much of which won't make the move to Massachusetts. At the same time, we're visiting lists of houses up there. Things aren't dull.

So I'm going to go on hiatus for a couple of weeks while all this gets sorted out. I start at my new position then, and at that point blogging will resume. Until then, I have a question for everyone: what am I going to call the place? I'd like to be able to refer to the Wonder Drug Factory in the past tense, so I'll retire that name. Calling the new place the New Wonder Drug Factory seems cumbersome, and besides, it's only new for me.

Suggestions are welcome, and I'm very happy to be in a position to ask. I'll start things up here again in the second week of July, and see everyone then.

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June 21, 2007

Real Life, Which Costs Real Money

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Posted by Derek

No time for a new post today, unfortunately. I'm on the road, up in the unexplored (by me) territory of suburban Boston, looking at schools and houses today and tomorrow. At the moment, I'm sitting in one of those free-wireless sandwich places, catching my breath and getting ready to look at real estate.

When I was a kid, if you'd told me that I'd be living in a place that cost what these do, I'd have expected the full James-Bond-villian setup: missile launching facility, access to underground submarine base, etc. Looking at the listings, I can only assume that the fashion for these amenities has passed. Probably just as well - I'm not sure I could get the wife and kids to wear the matching jumpsuit uniforms.

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May 18, 2007

But Enough About You

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Posted by Derek

Over at Nature's Sceptical Chymist blog they have a Friday interview feature, and this week you can see them interrogate me. (The blog's name is lifted from Robert Boyle, one that I liked so much that I also wrote it on the front of one of my undergraduate lab notebooks.) Note: I had this post up for a couple of hours attributing the title to Robert Hooke instead. It was early in the morning, really.)

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May 9, 2007

Blogroll Update

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Posted by Derek

I'm short for time this morning, so I wanted to just put up some new links to still more chemistry / pharma sites. First off is Pharmalot, which I thought I'd added to the blogroll but hadn't. Its author has covered the industry for years, and the site is a solid source for how drug-company news is playing in the press.

New to the chem-blog section of the blogroll are Syntheticness, A Chemist's Lab Notebook, Jungfreudlich, Carbon Tet, Two-Headed Chemical Mayhem, and Liquid Carbon. And the list keeps on growing!

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April 4, 2007

Linkage!

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Posted by Derek

I'll be posting later on today as well, but I wanted to mention another crop of science blogs that have been added to the blogroll.

First off, I'm glad to report that there's another pharma drug discovery blogger at One in Ten Thousand. And there's The Futile Cycle, on the biology side, which includes the only poem I've ever seen written about ion channels. I've also added a new blog called Science, Theory, and Liberty, which I hope keeps going. Those air-sensitive organometallic folks now have representation of their own with Organometallic Current. And finally, there's Med Tech Sentinel, with news from the whole medical-device world, which is an area that I don't manage to cover very much. Enjoy!

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February 22, 2007

Back From DC

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Posted by Derek

There's a whole list of posts below live-blogged from the CMPI conference that I attended on Wednesday, and I think that the organizers will be putting up some audio files of the proceedings soon. It was an enjoyable meeting, and I met a number of interesting people. Since it also involved politics (on which everyone's an expert), the discussion was often livelier than at many scientific conferences. The entry barrier for speaking up about (say) the effect of efflux transporters on toxicokinetics, fascinating subject though that is, is higher than for talking about where the FDA should get its money and how they should spend it.

While in DC, I also got a chance to meet Megan "Jane Galt" McArdle, and we had a nice talk on economics, scientific research, academia, kitchen implements and the eighteenth-century novel. (Get yourself a liberal arts education, and you'll never run out of conversational topics, is my advice). Next time I'm in the area, she threatened to get Tyler Cowen to show up, who will probably take us to some Papuan or Zanzibarean restaurant in a decrepit strip mall. (Not that he's wrong about those being reliable places for good ethnic food).

Blogging will now resume its one-a-day pace here: five per day in real time is about my limit (particularly in a room where there's no place to plug in the laptop - although the CMPI people did well by us in getting wireless access set up outside the hotel's usual exorbitant charges).

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February 19, 2007

You Want Me to Just Talk? No Problem.

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Posted by Derek

I'm headed out tomorrow afternoon to Washington, DC, for this conference on "The Media and Medical Science", sponsored by the Center for Medicine in the Public Interest. They've asked me to participate on one of the panels, namely "Does Media Coverage Reflect Reality, and Does It Matter?"

Since I've no problem unburdening myself of my opinions, this should be pretty enjoyable (for me, anyway - the audience will have to take its chances). Should any readers be in the area and able to attend, I'll look forward to meeting you!

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February 16, 2007

Comments on Comments

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Posted by Derek

I know that people have been having some problems leaving comments here the last few days - I've had some myself; it's rather disconcerting to find that comments you're making to your own blog are being treated like radioactive spam. But I think the issue has been resolved, so if anything else odd happens, please let me know.

If you don't blog yourself, you'd probably be amazed at the volume of comment spam that comes in. Well, if your e-mail address is out on a web page like mine, maybe you wouldn't, considering what that does to your inbox. I pull two or three hundred offers of winning lotteries, African fortunes, dubious business propositions, and outright gibberish per day into my address. But there's a nearly equal volume of comment spam, which was always seemed to me one of the most pathetic attempts at advertising I've ever seen. Why bother? Well, because it's basically free, and hey, one out of every ten million people might click by accident. . .

There are keyword and lookup filters behind the scenes here that do an excellent job of catching all this garbage. Before they were implemented, I'd come in to take a look at the site in the morning and find the last fifty comments were a repeated offer to do things with farm animals or something, which was a welcome way to start the day, naturally. But if the setting get a little too aggressive, actual comments start getting flung into the bit-bucket. Every day or so I take a look at the pile and rescue a few strays, but we'll see how things look under the current settings.

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January 29, 2007

Blogroll Update

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Posted by Derek

Some may have noticed that the blogroll at left has been modernized a bit. I've tried to separate out the chemistry and drug industry sites - please let me know if yours has come down on the wrong side of the line.

And more sites have been added, as the relentless wave of chemical blogging continues to crest. Some of these sites are young, and others I just had neglected to link. Welcome to Occam's Blog, Pharma's Cutting Edge (the renamed Crownstone blog), the QDIS Blog, Curly Arrows, Thesis Sprint (which I hope can eventually get renamed once everything is done), Molecule of the Day, Hdreioplus, Levorotation, The Crimson Canary, the Chemistry World Blog from the folks who are now carrying a regular column of mine, Totally Mechanistic, The Synthetic Referee, Regulatory Affairs of the Heart, and Synthetic Environment!

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January 24, 2007

Back on the Air

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Posted by Derek

I just wanted everyone to know that things have been quiet here because of some Movable Type maintenance behind the Corante scenes. Things seem to be working now, though, and rather more zippily than before. There seem to be a number of comments that were backed up in the pipes which have now appeared, too. I have a backlog of things to talk about (Pfizer! Dichloroacetate!) and regular blogging will resume this evening or tomorrow morning. Even though I'm soon to be unemployed, the blog will live on.

Another update: my manuscript for the "Vial Thirty-Three" paper has been put on hold for a bit, because of some data in it, not related to its main point but still unremovable, that need to wait before being disclosed. A little later on this year I should be clear to publish, though. It's frustrating, but since I did this work at the company's expense, they certainly have the right to say when it gets released.

Comments (4) + TrackBacks (0) | Category: Birth of an Idea | Blog Housekeeping

December 26, 2006

Work At Home! It's Easy; It's Fun!

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Posted by Derek

Well, I took a load of data home with me, along with a first draft of the paper I'm working on. But as usual, my attempts to get any actual work done over the Christmas holidays have shriveled up on contact with the actual days off. I'm not sure why this always seems so plausible while I'm finishing up the last working days of the year, and so laughable three or four days later.

My two children probably have a lot to do with it. They're ready to take me on in a whole list of games, and since they know as well as anyone that these days don't run on a normal schedule, they don't see any reason for me not to be available. (And they have a point!) I find that when I'm thinking hard about a problem, and most especially when I'm writing, that I can't do it with interruptions or extraneous noise. I was better about those when I was in college, but I've lost the ability to deal with them. Or, perhaps I'm just dealing with things that require more thought.

At any rate, my brain needs room to work in, so I'm an awful conversationalist when I have to think hard about something. There's a period in the first few seconds, especially, when I'm working on formulating an answer to something, where any interruption will send the whole thing crashing down. It's hard to describe - thinking about the problem in front of me, I can start to see how this piece might fit over here, and this section seems to be matching up with this one over here, and it feels right to make an analogy to this part, which was the thing that worked when - what? What? We're out of peanuts, and have I watered the Christmas tree today, and do I feel like being pulverized at foosball?

Ah well, my manuscript can wait a few days - it's not like I'm not going to have plenty of opportunities to work on it when I get back. Meeting will not interrupt: my work calendar has attained a state of clarity that Zen rock gardens can only strive for. For now, I need to go show my eight-year-old son that foosball wasn't invented yesterday.

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December 21, 2006

Holiday Schedule

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Posted by Derek

Well, since it's the Christmas season around here, posting will be intermittent. I'm going to be making cookies with my two children tomorrow, for example. (I've explained to them that you should be suspicious of an organic chemist who can't cook). Further kitchen work over the next few days will include crown roast of pork, leg of lamb for a crowd (I'm hoping it's good enough weather to do it outside on a spit), and the traditional (for me!) Christmas breakfast of country ham, scrambled eggs, biscuits, and red-eye gravy.

I'll post occasionally, though, in between all this cooking, present-wrapping, and the like, but the regular schedule won't resume until after New Year's. I hope to do some work on my "Vial 33" paper while I'm home, but that may be wishful thinking. I did mention that I have two young children, after all. . .

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December 8, 2006

Shameless Self-Promotion

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Posted by Derek

As that discreet logo over on the left sidebar shows, this site has been nominated for a weblog award. This is the vote-once-a-day-per-computer one, and clicking on the banner will take you to the voting page. First prize, as I understand it, is basically a hearty handshake, but if you feel inclined to help out the site's standing in the vote tally, by all means please do. I've already got several of the other finalists on the blogroll, but I encourage you to check them out as well if you're not familiar with them.

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November 14, 2006

Elsewhere

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Posted by Derek

Just a few days after I commented on the troubles that Isis Pharmaceuticals has had developing antisense DNA therapies, they've popped up with impressive clinical cardiovascular clinical data. Their latest hope, ISIS 301302, has shown some strong LDL-lowering effects, both as a single agent and in combination with statin therapy.

It's aimed at the production of a key LDL-transporting lipoprotein, apoB-100, which target the company correctly describes as "undruggable" through standard med-chem approaches. Of course, the RNA people are hot on its trail, too (these guys, for example). It's a good opportunity for these approaches, since the protein is of clear biochemical importance, and the site of its synthesis is in the liver and gut wall. Those, of course, are the first tissues that an oral drug sees, and (in the case of many antisense and RNAi attempts) the last ones, too. Going after something that lives there is a good strategy.

On a different topic, welcome more additions to the blogroll, such as Totally Medicinal, a med-chem blogger who's concentrating on the synthetic chemistry end of things. And there's Xcovery, a good kinase-o-centric site for those who can't get enough of 'em.

We now return you to our regularly scheduled site closure, already in progress. I've started a new category, "Closing Time", where my posts on that topic will go. There are a lot of odd blogworthy issues and loose ends associated with shutting down an operation like this. I'll be writing on them in the coming weeks, since many people will (fortunately) not have experienced the process firsthand.

Comments (6) + TrackBacks (0) | Category: Blog Housekeeping | Cardiovascular Disease

November 8, 2006

Watch This Space

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Posted by Derek

No post this evening, for reasons that should become very clear in the late morning (EST) on Thursday. I'll update then. . .

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Links and Such

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Posted by Derek

As many of you have noticed, there's some Movable Type construction work going on behind the scenes over here, which seems to have knocked out the commenting function for the moment. I hope that it'll be back quickly, and that the various service interruptions will diminish.

I was up late eating Indian food and following the election, with little time to post last night. No matter which side you were cheering for, I can recommend plenty of tandoori chicken and papads. My wife's home-made basmati rice, curried cauliflower, and cucumber yogurt are not (as of yet) available online, though, so you're on your own there.

So for today, I've updated the blogroll to the left. A few inactive sites have departed, but there's more than enough new linkage to make up for them. Welcome to Omics! Omics!, from longtime reader Keith Robison, Molecule of the Day (waving the chemistry flag at Scienceblogs), the clearly obsessed Kinase Pro, and the up-to-your-elbows lab details of Org Prep Daily. And there are plenty more these days: Whistling in the Wind, The Curious Wavefunction, Carbon-Based Curiosities, the Half-Decent Pharmaceutical Chemistry Blog, Dreaming Spirals, Chemical Forums, Mining Drugs, Chemical Musings (the former Interfacial Science), Atom Pusher, She Blinded Me With Science, Transition State, Chemoblog, Culture of Chemistry, and Lamentations on Chemistry.

Man, blogging does seem to have finally reached takeoff in the chemistry world over the last few months. Enjoy!

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September 22, 2006

Darn Photons

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Posted by Derek

No time for a post for today, unfortunately - I was up late last night, trying to see this from my backyard. No dice - like most amateur astronomers, I need a darker sky. Even if I'd been able to see the galaxies, they wouldn't exactly look like that photo from Kitt Peak, though - visually in my 11-inch scope, they're going to be a lot more like the first one of this series. And as for this view: well, not without my own space program.

Coming up next week: more Ariad craziness, and we'll tackle (in a separate post!) the perplexing question of whether you have an infrared spectrometer in your nose or not.

Update: forgot to mention this. I've noticed that the comment spam filters seem to be set a bit more aggressively here these days. A number of comments are wrongly ending up in the junkpile. I'm rescuing them, but often not in a very timely manner. This weekend I'll try to tweak things back a bit.

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August 15, 2006

Here and There

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Posted by Derek

I'm going to be doing some traveling for the next few days, so posting will be intermittent, depending on time and internet access. E-mail, similarly, will stack up until the middle of next week - anyone with lucrative publishing offers, please wait until then to send 'em to the top of the queue. I think the drug industry will manage just fine without me. . .

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July 13, 2006

A Friday Linkfest

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Posted by Derek

There are a lot of interesting blogs that I need to catch up with, so here we go. First off is On Pharma, which focuses on the manufacturing end of things, with a lot of good stuff about FDA approvals and the clinical world. Note this recent post on the "cGMP Priesthood", which is something I fortunately don't have to deal with.

Life of a Lab Rat is a view from the bench in Sydney (no, not the beach, the bench), and Pipette Monkeys provides one from Heidelberg. Is This Thing On? has a biotech/bioinformatic perspective, and I've been wondering when someone was finally going to invent the Eastern Blot. And finally, the group at Nobel Intent is always worth checking.

Update: And how could I forget The Chemblog?

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May 25, 2006

Back on the Air

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Posted by Derek

Things were pretty disrupted on the servers around here yesterday, and we seem to have lost a few of the most recent comments. I couldn't get on last night to put up a new post, and won't be able to until this evening (work, y'know).

For my readers with a lab right outside their door, my advice is to go set up something weird. It always helps to have something going that's off track from your regular work. Mind you, the stuff I have going on in that category is in the process of ruining my health, because we still haven't been able to analyze my control experiments. But if you pick something that doesn't depend on one critical piece of machinery, you should be fine.

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May 2, 2006

Travel

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Posted by Derek

I've been out of town for the last few days, and just got back around midnight last night. So there will be no new post today - I'll have my hands full just staggering around my lab trying to figure out what's going on. The Wonder Drug Factory seems to have done just fine in my absence.

I told my lab associates that they were under orders not to discover anything while I was gone, so I could be back in time to take the credit. Motivational speeches like this are important. I can't quite reach the levels of a colleague of mine, though, who used to lean out of his office and call out "Work! Work! The harder you work, the faster I get promoted!"

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April 10, 2006

Linkorama

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Posted by Derek

I have Schedule D to wrestle with tonight, so it's time for some linking and blogroll additions. I'll start with a relatively new blog from a pharma consultant, Eye on FDA, and that'll do it from the industrial side this time.

The rest are from academia, some pure chemistry sites such as Dylan Stiles', which I've already linked to. I enjoy his site a lot, but one thing that it tells me is something that I already knew - namely, that I'm not 25 any more. Another blogging chem grad student is Paul Bracher, at Harvard. Another site for hard-core organic chemistry fans is Totally Synthetic. I did just this sort of thing for my PhD, and it's a lot more fun to read about than it is to do. Another blog from inside academia, this time from a post-doc, is Interfacial Science. Another post-doc can be found at Post Doc Ergo Propter Doc.

I can also recommend Nature's venture into chem-blogging, the group-written Sceptical Chymist. (That's the name I put on my first notebook in my first-year Quantitative Analysis course, actually - Robert Boyle is definitely worth remembering).

And finally, there's Peter Rost, famously ex-Pfizer. You're unlikely to find very many points of agreement between his worldview and mine, but you can see for yourself here.

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March 30, 2006

Missed One!

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Posted by Derek

Sorry about the lack of a post this morning. I took the day off from the Wonder Drug Factory to do some work here at home. Let me just say that if any of you are suffering from an excess of energy, it's nothing that going through a pound and a half of decking screws won't cure.

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March 22, 2006

A Lengthy Day

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Posted by Derek

Well, it was a long day at the Wonder Drug Factory - I got in early to start a large reaction, and took it through a workup and column during the rest of the day. I'm taking tomorrow off to take my kids out and around, and since people were waiting on the stuff I made today, or so I'm told, there had better be something missing from the batch when I come back. (Of course, I don't have much room to get haughty, since the reason that there's a shortage was because I made the wrong isomer of the stuff by mistake last time. Ah, how we laughed, except me.)

So rather than crank out something aggressively substandard tonight, I'll leave everyone to their own devices. A run up and down the blogroll at left should be enough to impair your productivity - I'll see everyone on Friday.

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March 2, 2006

Technical Difficulties

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Posted by Derek

Today's posts (on Matthias Rath and Procter and Gamble, respectively) disappeared well before noon due to a Movable Type problem back at Corante HQ. I think we should be back to normal soon, but wanted to leave this placeholder up for now. I'll leave those two up for Friday, and we'll get back on track next week. . .

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February 23, 2006

Blogroll Revamp

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Posted by Derek

Well, I'm going to try to post tomorrow morning about the Sanofi-Aventis investors meeting, when we should (in fact, had darn well better) hear some more about the rimonabant situation. And the debate over the New England Journal of Medicine and Merck is going on briskly in the comments to yesterday's post, so please take a look over there if you haven't yet.

So tonight I'll take a few minutes to rework the blogroll. Welcome newcomers Terra Sigillata, Science, Shrimp and Grits, the Mass Spectrometry Blog, Tobias Sing's Bioinformatics Blog, Snowdeal, Cosmic Variance, On Pharma, and Oncology Updates.

And note also the new locations of Uncertain Principles, Adventures in Ethics and Science, Aetiology, Gene Expression, Pharyngula, and Respectful Insolence at Scienceblogs.

No doubt there are other sites I should be linking to - suggestions are welcome!

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January 16, 2006

Various Updates

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Posted by Derek

In all the server-migrating of the last week, it appears that some of the recent comments have been hosed. I just wanted to let everyone know that it's unintentional - hey, I even let the comments that show up on the Intelligent Design posts around here stand. I also think I've fixed the "comment held for moderation" problem that was afflicting all of us, so if it happens again, please drop me an e-mail.

In other blog-news, I'd like to take this opportunity to welcome the advent of the Scienceblogs site, which incorporates several of the blogs over there on the left-hand side of the page. I'll be updating the blogroll shortly.

There's an interview with me up over at the financial site The Stalwart. Unfortunately, I don't think I've revealed enough to make anyone rich, but do write if I turn out to be wrong about that.

Finally, via Chad Orzel's new Uncertain Principles site over there, I found this useful companion to the Edge.org "Dangerous Questions" page. As you'd figure, not all of the submissions there are of equal quality, so these guys have taken the trouble of digging out the best ones.

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January 3, 2006

Comments Welcome - Really

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Posted by Derek

Over the last month or so, the commenting system here has been rather erratic. Despite having Movable Type set to allow anyone to comment, people keep getting "held for moderation" messages - it happens to me, too. At the same time, an increasing amount of junk is making its way through. I'm going in manually every so often to clean out the stables, but that's not the best solution. My intention is to let anyone comment at any time, except the people who are robotically offering us all opportunities to play poker or to all-naturally extend various organs of our bodies. Anyone with experience in dealing with MT's current treatment of junk comments is welcome to offer suggestions on how to fix things.

I should also mention that Corante is going to be trying some server migrations, probably starting this coming weekend. The hope is that posting on this and the other blogs won't be disrupted, but if there's an outage, that'll be the reason. . .

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November 25, 2005

Instead of Working

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Posted by Derek

Well, like many of my fellow Americans, I'm taking today as the second day of Thanksgiving. The Wonder Drug Factory where I work is closed for the day, and I'm here at home with my two children while my wife braves the shopping crowds. (I'm positive that I got the better end of that deal). My hardest task will be keeping the two of them from eating the rest of the chocolate pecan pie I made, which they've already decided would be a reasonable breakfast. And no, I have no reason to complain about anything if these are the sorts of problems that occupy me: Thanksgiving, indeed.

At any rate, I can recommend a browse through the blogroll over there on the left. There are some new additions today, namely TP With Page Numbers, Aetiology, Adventures in Ethics and Science, Politics and Ethics of Science, and the fine new group blog Nature Erratum. (That last one makes me wonder why no political blogger has titled a site "The New York Times Regrets the Error"). And if you don't know the medblogger Dr. Charles, then you've got even more to read instead of doing work. I'll see everyone on Monday!

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October 19, 2005

Procrastination Assistance

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Posted by Derek

Looking for another way to avoid doing some work for a bit? The latest Tangled Bank roundup of science-blogging is up. This weekend, I update the blogroll. There are too many good ones that I'm missing.

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October 6, 2005

Outside Reading, and Plenty of It

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Posted by Derek

For a huge festival of science-blogging, check out the latest Tangled Bank. It's getting hard to keep up with the number of worthwhile sites out there.

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September 30, 2005

And Another Thing. . .

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Posted by Derek

I wanted to let people know that I have an opinion piece up at the Manhattan Institute's "Medical Progress Today" site, on the FDA's conflict of interest rules for their advisory panels. There are some proposed changes that I don't think will work out very well. . .

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August 14, 2005

Blogging About Science Blogging

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Posted by Derek

There seem to be enough science bloggers around now that we're starting to wonder what it is that we're doing, and why. The recent article in The Scientist has started some of this, with its focus on why more scientists don't blog. Living the Scientific Life as well as Chad Orzel at Uncertain Principles have weighed in, among others (and I'd like to thank both of them for the kind words they've said about this site, while I'm at it.)

GrrlScientist, in that first link, points out that the Scientist article seems to miss one of the reasons that scientists blog (or might want to): explaining just what it is that they do. That's an important point - it's a big reason why I started and a big reason why I continue. I had had several experiences over the years where people found out what I did and pumped me for all kinds of information. And it hit me that although few people had any idea about drug discovery, they tended to say "Wow, that sounds like a really neat job" once they did. (It was a big improvement from the usual response you get when you tell people that you're a professional chemist, I can tell you.)

Chad Orzel goes on to note that large numbers of people see science as something that's difficult, boring, and beyond them, so they just tune out. I'm afraid he's right. But I used to explain my experiments to the janitorial staff when I worked late at my first job, which showed me that this didn't have to be the situation. To be sure, none of my explanations started off with the phrase "Consider the Hamiltonian. . .", but none of my conversations with my colleagues start that way, either, not if I can help it.

Instead, we talk about how we're not getting good blood levels with our latest series of compounds, wonder about whether that's because they're not getting absorbed through the gut or are getting cleared from circulation too quickly, and outline some experiments that would tell us one way or another. Now, it's true that we use a lot of verbal and scientific shorthand to discuss these things - a conversation like that could go "See the screening PK yet?" "Yeah, what a rotten AUC. Do we have an i.v. tee-one-half on that stuff yet?" "No, but we could probably get a slot in the next cannulated rat run." And that wouldn't mean much to one of the Uruguayan janitors that used to ask about my work.

But with a few extra minutes to explain what we were trying to do and why, they could appreciate what was going on. And they could see that it wasn't easy, and that we often didn't know why things were happening, and that we had to wait a long time between chances to run around high-fiving each other. Considering how television and movies treat science (which, to be fair, could be the only way to treat it for the purposes of mass entertainment), knowing these things was a real step up.

So when I found out about blogging, I didn't hesitate very long before jumping in. Here was a chance to do just the kind of thing I did when talking to people one-on-one, but for as many visitors as cared to stop by. It sounded like just what I'd been waiting for, and it still is. The pharmaceutical industry has been taking a beating the last few years, some of it (not all!) deserved, and I think there's an ecological niche in the blog world for someone who can talk about it from personal experience.

The majority of my readers, as far as I can tell, are not involved in drug discovery themselves. I certainly enjoy having people from the field reading and commenting, and I try to pitch my posts to both levels at once, as much as possible. But I've never pictured my site being exclusively a peer-to-peer experience. Since I'm in the drug industry, it couldn't very well be, in any case. We drug-industry types obviously can't talk about the specifics of what we're doing, and I don't. (That's why the "Birth of an Idea" posts are so maddeningly vague, and even those don't apply to any specific drug or drug target.) There's just not much chance for blogging to help me out with any current problems in my research, because those problems are all proprietary. It can give me a broader perspective on my industry, which might come in handy, but it's going to do zilch for what's stirring in my fume hood.

(I should note that both of the posts I linked to in the first paragraph put the public-outreach issue in terms of the teaching-intelligent-design debate. More on that another day. . .)

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August 6, 2005

Even More Worthwhile Stuff

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Posted by Derek

I've finally updated and cleaned up my blogroll over on the left - removed some inactive sites, fixed broken links, and added quite a few others. There may be some folks over there you haven't heard of, so give 'em a try.

On the home front, I'm nearly through adding all my old Lagniappe posts to the archive pages. Next up will be the earlier days of "In the Pipeline", finally categorized for your time-wasting pleasure.

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July 28, 2005

Like, Er, Fine Wine. I Hope.

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Posted by Derek

I wanted to mention that I've been gradually adding to the archives and category pages over there on the right-hand side of the page. My original blog, Lagniappe, has been difficult to access on the web due to some ancient HTML, so I'm taking the still-relevant posts from there (2002 into early 2003) and putting them into the appropriate categories.

Three dozen or so have been added in the last week or two, and more are coming. I'm fishing everything out of the Internet Archive, so all links are in there, although they're not all guaranteed to still work. (I do have the day job at the Wonder Drug Factory, y'know.) After that I'm going to categorize the Pipeline posts from the pre-Movable Type days, so those will start showing up over there, too. Enjoy (I hope), and keep an eye out for more (semi-)new content.

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July 9, 2005

Summer Hours

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Posted by Derek

Just wanted to let everyone know that posting will be light to nonexistent this week. I'll pop up if something big happens, but otherwise I'm going to be taking it easy for a few days. The regular schedule of fist-waving and table-pounding will resume a week from Monday, though, never fear.

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July 5, 2005

Continued Slacking

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Posted by Derek

I'm taking another vacation day today. No doubt my labmates are cranking out the discoveries in my abscence - just like working at the sawmill, I tell people.

While I'm lounging around here, you might check out Princeton's "Art of Science" competition here. See you tomorrow!

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May 20, 2005

Outside Reading

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Posted by Derek

Home and work have conspired to leave no time for a post this morning - man, I wish those two wouldn't team up so often; they're supposed to not even be friends or anything.

But you can head over to the science/medicine blogfest called Tangled Bank and find a lot of good stuff, written by a lot of good people that I need to blogroll. Enjoy, and I'll see everyone on Monday.

(Oh, one other thing on the outside-reading front. Glenn "Instapundit" Reynolds mentions that he has a law-school colleague who tried to build a Dune-style "stillsuit" some years back, and adduces this as proof of her geek credentials. Point taken, but let me pull my papers out for inspection. A more technically inclined geek would have realized the physics problem that Frank Herbert sort of, er, skipped over. The major point of sweating in hot weather is evaporative cooling. What happens when you trap that moisture and try to recycle it? Condensative heating, that's what, which you don't hear about as much but is as real as the laws of thermodynamics can make it. A stillsuit would cook you like a crock-pot.)

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March 12, 2005

New Address

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Posted by Derek

I wanted to point out that my email address has changed. After fifteen years (!), my old AOL address is no more. DSL connectivity has finally crept into our corner of the world, so now send your comments, complaints, and (not least) offers of gainful freelance goodness to me at: derek-lowe@sbcglobal.net.

The fine print: No immediate family members of deceased strongmen, please. No offers to elongate any part of my body will be considered. And I already have all the cheap insurance and discount toner cartridges that one man can handle.

Oh, and the next post here will be Tuesday evening/Wednesday morning. For plenty of science-themed reading material (more than a couple of day's worth, that's for sure), try the Tangled Bank.

Also, William Tozier has an interesting pile of science and art-related stuff here, and the latter is well represented, as usual, over at Two Blowhards. There, I've done my part for productivity.

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February 7, 2005

One Problem Solved, Anyway

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Posted by Derek

Before I start off tonight, I wanted to welcome another advertiser on the site, the folks at GenomeWeb over there in the corner. Glad to have 'em!

Thanks to the people who commented on yesterday's question. My Corantean overlord(s) suggested a useful solution as well, since (as Jack Vinson guessed), I'm set up to only display the most recent posts on the front page. Pasting in the old material, saving it as a draft, and then changing its date sends it directly to the category without having it appear up front.

So, the first thing I've added from the archives is my series on chemical warfare, which was written in September of 2002. It's in that "Chem/Bio Warfare" category over on the right, naturally enough. (This was written in the run-up to the Iraq war, and the last post in the series was soon overtaken by events. I note, though, that I speculated that Iraq might have far less in its stockpiles than people had estimated - I just didn't realize quite how much less.) But most of the series is still worth a read, if you're interested in that sort of thing. You'll learn about the morning that a German chemist first synthesized a human nerve gas, not realizing quite what he'd made until it was time to dive for the door. And you'll hear about my own cold-sweat encounter with phosgene gas, which I hope not to repeat any time soon.

This'll be it for tonight. I'll be heading into the lab tomorrow morning to see if I have a useful one-pot way to make a five-membered heterocycle, or if I have an orange mess in the bottom of my flask. The most likely outcome is that it won't work, and if it works, the most likely result is two different isomers (with the wrong one predominating.) But I don't know any of that for sure, and that's why we run the darn experiments, y'know. Hope springs eternal - that's one thing we prove in research every morning.

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February 6, 2005

A Technical Question

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Posted by Derek

A quick question to those of you who are Movable Type gurus - and you're probably more of an MT guru than me, even if you just rolled off the back of a turnip truck.

Is there an easy way to publish directly to a category archive? I have some older posts (from the pre-MT days) that I'd like to bring back into circulation, but they don't need to show up here on the main page. I'd just like to have 'em appear under the relevent categories (with a quick note to that effect out here.)

Among the things I want to bring back are my series on chemical weapons, which I've had requests for. There's also a series of posts that will go into "Birth of an Idea". They chronicle the long gestation of an idea that I've had to increase the drug discovery success rate, and they're a good overview of the mood swings that a really powerful idea will bring on. I haven't worked in that area much in the last few months, but I'm looking for a good way to bring it back to the front burner in my lab. Once I do, the mood swings will no doubt recur. . .

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January 21, 2005

And Now A Word. . .

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Posted by Derek

BTW, you may have noticed that the site has picked up some sponsorship, over there on the right. I'm glad to have 'em. Anyone who wants to reach the Pipeline readership - working in or interested in science, well-read, and (judging from my mail) not the sorts to keep things all bottled up inside them - feel free to apply within.

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December 29, 2004

Schedule Update

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Posted by Derek

Blogging will resume here on Monday night (EST), with a review of what the last twelve months have been like in my line of work. (After that I'll do something cheerful, promise!) In the meantime, I hope that all my readers have a safe New Year's Eve, and I encourage everyone, if they can, to donate to one of the tsunami relief funds out there. See you in a few days. . .

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December 23, 2004

Holiday Blogging

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Posted by Derek

Just wanted everyone to know that I'll be on break until sometime early next week. I'll post a bit between Christmas and New Year's, but full Pipelining won't resume until January. There are several threads to pick up - the Lab of the Future post attracted some great comments, which I'll come back to, for one. And I've received a reply from Gary Becker on the subject of pharmaceutical patents - he's looking over the arguments made over here, and I hope to get his thoughts on them. Howard Simon of TheStreet.com is also checking out the responses to the drug-optioning idea.

But for the next few days, I'll be occupied with many other important tasks: making cookies with my two children, wrapping presents, eating food of dubious nutritional value, etc. Merry Christmas (and whatever else) to everyone!

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December 12, 2004

Stocking Stuffers, of a Sort

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Posted by Derek

It seems to be the season for book recommendations in the blog world. If anyone's wondering what the favorites here are, let me recommend some classics of the scientist's trade:

First, Primo Levi's The Periodic Table. Levi was (famously) a survivor of Auschwitz, and wrote extraordinarily about that experience. But he was also a professional chemist, and in this unique memoir he lets various elements bring back incidents in his past. I'm not aware of another book like it.

Next, Oliver Sacks's memoir Uncle Tungsten. Sacks is famous, of course, as a neurologist and author, but he had an intense boyhood love affair with the field of chemistry. Anything by Sacks is worth reading if you're not familiar with him, though.

I can also recommend just about anything by Peter Medawar. The Nobel-winning immunologist was a graceful writer about science and other subjects - look for one of the essay collections. His takedown of Teilhard de Chardin is not to be missed, if you're into that sort of thing.

And on the subject of scientific essays, let me also recommend Freeman Dyson. He's getting up in years, but still very much with us, and I consider him to be my definition of scientific royalty.

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November 1, 2004

Now With The Great Taste of Fish

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Posted by Derek

You'll notice a new design here this morning - the Corantean Heirarchy is switching everyone over to a newer template. You can now adjust the text size, for example, which is something I know a lot of people have asked for (in both directions.) And if you get the blog by e-mail, you can now subscribe to specific categories of posts (or, more to the point I suppose, specifically leave some categories out!)

Let me know how things are working, and if you have some other features that you'd like to see. Other than the content of the posts, anyway - unfixable, that is.

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October 2, 2004

Comment Problems

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Posted by Derek

Something appears to have unraveled in the site's commenting function; it won't let anyone post anything. We'll try to have that fixed soon - in the meantime, I'll try to think of ways to abuse this newfound freedom from contradiction.

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September 20, 2004

Two Days Off (From This, Anyway)

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Posted by Derek

No blogging time left this evening, and tomorrow night will be blank as well. I'm giving a talk to the local section of the American Chemical Society, so I'll be off scarfing up a free meal and enlightening whoever shows up. If you turn down too much free food, the ACS revokes your membership - at least, that's how I've always understood it to work.

Instead of preparing for my talk this evening, I've been outside in the back yard observing a passing visitor to the solar system, Toutatis. I found it without much trouble at all, to my surprise, and it was intruiging (and a bit alarming) to note its position, go off to other parts of the sky for an hour, and come back to find that it had noticably moved against the stars. I'm just glad that we're not getting any better view than we are; it's coming close enough for me as it is.

Anyway, I hope to have some time tomorrow to think about my presentation. Otherwise, I'm going to be extra coherent. . .

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September 19, 2004

No Coming Attractions Here

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Posted by Derek

I promise, this week the blog won't be all-NIH-all-the-time. There are plenty of other things to talk about, but if I list them, I won't get around to writing them. I've done that several times over the last two years, and I think that I'm catching on to how that part of my brain works. Blocking up on that kind of thing doesn't seem to bode well for a career as a Famous Journalist, but if I'm not mistaken, others have overcome even more difficult mental habits.

There's an analogy to an odd thing that I do in the lab. Starting in graduate school, I noticed that if I opened a solvent bottle while I was concentrating on something else, I would tend to lose the cap for it. After searching around the bench for a while, I'd find that, for some reason, I would tend to put the cap right on top of another identical solvent bottle, resting on top of its cap. This was a pretty good technique for making it completely disappear, as you can imagine.

It took a few of those, but I finally realized that this was my technique - or at least the technique of whatever region of my brain was delegated to do that kind of thing. So I took it into account. Now when I have a missing stopper or cap, I know just where to look, and most of the time I'm right. I still do it, all the time, but at least it doesn't slow me down. We'll see if this latest technique does the trick. Stick around this week and find out. . .

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July 28, 2004

A Question For the Audience

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Posted by Derek

You know, it does feel odd not to be writing anything about the political season, what with all the conventioneering going on. But world events, for the most part, sort of wash over and around this blog, which is a decision I made back in my early days. Political opinions are piling up unsold in every market stall, but who offers commentary on chemistry?

Of course, there's always the question of market size. A single-subject site is never going to pull in the traffic of the big generalist ones, unless the subject is something rather more stimulating than organic chemistry (if you know what I mean and I think you do, as Joe Bob Briggs used to say.) But I've been encouraged by the responses I've had from people completely outside the sciences who've enjoyed visiting them by reading here.

Still, knowing that I have a widely mixed audience makes it tricky sometimes. There are some subjects that are harder to cover, and there are jokes that are hard to make. For example, I guarantee that every organic chemist will at least smile at a phrase like, oh, "plutonium enolate." But that's not going to make 'em spill their beer down at the comedy club, unless they're spilling it on the person trying to tell the joke.

So I'd like to take advantage of this slow news period to ask people if there are topics they'd like to see more (or less) of: current pharma news, stock market stuff, lab stories, med-chem background, purple-faced rants about price controls? Comment below, or feel free to e-mail me.

I hesitate to mention topics that I'm planning to post on, because it seems that I never get around to them, but the future should hold pieces on combination drugs (boon or gimmick?), salts and why I'm making a bunch of them right now, and (if I can summon the energy) a whack at Martha Angell and her recent NY Review of Books broadside against my industry. She has a book coming out this fall, and naturally I can hardly keep my enthusiasm from just foaming up all over the place. Sheesh.

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June 24, 2004

Summer Hours

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Posted by Derek

I'm only going to be at the Wonder Drug Factory for a half day on Friday, and there's not much time to post tonight, either. I wanted to let everyone know that I'm not going to hit the once-a-day update schedule reliably during the summer, what with all the summery activities going on (and with two small children, I'll be seeing plenty.)

I also hope to be working on some chemistry/pharma writing that will bring in some actual income - inquiries and suggestions are welcome. That's as opposed to blogging, which runs on the Free Ice Cream model (or some days, admittedly, Free Pickled Lemons.)

Next week looks like it'll feature some more drug-price blogging, to judge from the comments piling up below (and thanks for the links, from (among others) Marginal Revolution and LeftCenterLeft.

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May 14, 2004

The Last Word on Taste

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Posted by Derek

No time for real blogging for today, but I couldn't let this one go by: Reader Steve C. passes on what has to be one of the worst examples from the old days of tasting new compounds. Back in 1886, Victor Meyer was the first to achieve a reasonable synthesis of bis(2-chloroethyl)sulfide. So, as people did back then, he put some of the damned stuff on his tongue.

A good part of my readership has already grimaced in pain, but the rest of you are about to join them. That compound is better known as mustard gas. Meyer's gourmet experience must have resulted in an excruciating round of terrible blisters - which, depending on the amount he sampled, could have gone on for quite some time. I wonder how many things he taste-tested after that episode?

A blog housekeeping note - my blogroll was shattered in the conversion to Movable Type. It had a number of inactive sites on it, anyway, and there are plenty more I should have added as well. A rebuild is in the works.

Next week we'll talk about method of treatment patents (and won't that be fun, eh?) and about an outfit with the unusual name of Essential Inventions, Inc. The phrase "March-In Rights" will feature prominently, which I hope is not a phrase I'll be using very often.

Comments (2) + TrackBacks (0) | Category: Blog Housekeeping | Drug Industry History | Life in the Drug Labs

April 23, 2004

Categories

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Posted by Derek

I've noticed many visitors hitting the category topics over there on the right side of the page. Unfortunately, some of those headings don't have any posts in them yet, because we're still transferring the contents of the old site over here.

As of this writing, we only have about the last fifty posts or so, but I'm a much wordier guy than that. The usefulness of the topic links will increase as time goes on, so be sure to give them a try again in a few weeks. They'll fill out into their intended glorious (cough) shape.

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April 16, 2004

Welcome Back!

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Posted by Derek

It's a relief to finally be able to post again. My previous platform ran into a major glitch last week, and it was only after a few days that I realized that none of my new posts were getting through. So here's the new site, run from a spiffy Movable Type interface.

That means that comments are now available, and I'm categorizing all my past posts as they get grandfathered in. All the rants about drug pricing, for example, will be available in one place for those who feel a dearth of spleen in their lives.

My apologies for leaving everyone hanging. We now proceed with our regularly scheduled weblog. . .

(Note: the blogroll is coming back, too, in pieces - this will give me a chance to update it and add a number of worthy sites I've been meaning to list. Any other features or questions, just comment or drop me a line. MT will do everything short of emptying the cat's litter box.)

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March 2, 2004

Catching Up

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Posted by Hylton Jolliffe

Little time for blogging the last day or two. I've been finishing up a paper to send to Bioorganic and Medicinal Chemistry Letters, the first one I've written in a while, and I'm checking over another paper that I'm a coauthor on. We're deciding on where to send that one - the lead author suggested Tetrahedron Letters as a possibility, and I thought "Hmm. I haven't had a paper in Tet. Lett. for quite a while." Which was true - a moment later, I realized that the last time was twenty years ago this year! I'm just glad that I usually don't feel as old as that makes me sound. (Talk to me twenty years from now.)


Matthew Holt has a long article on his site that's well worth reading. I'm going to write in response to it this week, because I think a few of its assumptions are incorrect, but it's a good piece nonetheless. It's yet another in the saga of drug prices and research costs, whichs bids fair to be an inexhaustible topic. I am not, though, an inexhaustible blogger. After this round, I'm going to take some time off the topic to recharge my argumentative batteries.


I have a number of other topics backed up in my queue. And I'm going to start off a new occasional feature, a complement to my "How Not to Do It" series of lab stories. This one will be "Things I Won't Touch", and will feature a different reagent each time that I refuse to ever work with. It's a fairly lengthy list, and I'm only a moderately cautious guy. (If anyone else out there has made fluorosulfonic acid from scratch, starting with concentrated hydrofluoric acid and KOH pellets, I'd be glad to hear from you. We can start a club. Admittedly, I was young and foolish at the time, but I made it through without destroying any property. Mostly.)


And one more thing tonight: I'd like to thank everyone for making February by far my highest-traffic month ever. There were about 25,000 page views, which is a roundoff error for the likes of Glenn Reynolds, but thoroughly broke my old record. Much of that was due to my broadside against Gregg Easterbrook, which he certainly seemed to recover from nicely.

Comments (0) + TrackBacks (0) | Category: Blog Housekeeping | The Scientific Literature

January 13, 2004

Here and There

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Posted by Derek

I wanted to take a moment to mention some interesting posts around Blogdom that readers may not have seen. In a response to the news on secretin for autism (see my post below), Dwight Meredith writes on what it was like at its peak of interest:


Human secretin, swine secretin, herbal secretin (which as far as I can tell is an oxymoron) and synthetic secretin were all hawked relentlessly to the parents of autistic children. The price of secretin skyrocketed. People were paying $2,000 for an amount of secretin that before the buzz had cost about $30. It is not an exaggeration to say that parents were mortgaging their homes to purchase secretin for their kids. We now know that a sugar pill would have been equally effective.


Please note that all of that buzz was generated by the fact that a few autistic children had improved after being given secretin for digestive problems. The autism community could not wait for double blind and placebo tested trials. We wanted our miracle and we wanted it now.


This is a man who writes from personal experience, I should note. And I can understand the desperation (well, as much as anyone in my position can - I have two small children, neither of whom have - thus far - shown any neurological abnormalities.) What I have trouble imagining, though, is what goes through the mind of someone who peddles "herbal secretin" to parents who are begging for something to help their autistic child.


Herbal secretin? They didn't even bother making it sound like anything but a heartless scam. Figured the customer base would be too desperate to care, I suppose. I'm ashamed to be in the same phylum with creatures who would do something like this.


There's a larger point about the wait for double-blinded trials, too, of course, which I should save for a longer post. The short form is that I can see the point that some people make, that it would be better to require safety (Phase I) trials, then stand back and let efficacy be sorted out in the marketplace. (SMU's Steve Postrel and I had a long e-mail exchange on that subject a year or so ago.) But then I hear about this sort of thing, and start to think that this is one of those sensible ideas that would only work on some other species than humans.


The other post I wanted to mention is over at Colby Cosh's site. Talking about medical progress, he hits on the idea of looking at the causes of death in the records of ballplayers from the old days, who were in their physical prime. It's an alarming list, and most of the things on it are, fortunately, in the process of disappearing from the world. And good riddance. As Cosh says: "I don't know how anybody kept from just going insane before antibiotics existed, with death lurking around every corner."


One final note - I've forgotten to mention that Charles Murtaugh is back blogging again. There's lots of good new stuff; just start at the top and work your way down.

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