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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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September 14, 2009

Abstract Abstracts

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Posted by Derek

Maybe I'm just cranky, or cranky on the subject of design and presentation, but this sort of chemical structure drawing rubs me the wrong way. I'd have a much better chance of understanding the transformation without all the colored dots; they don't seem to be adding anything.

And while I'm in get-off-my-lawn mode, the similar trendlet of coloring the interiors of ring structures annoys me, too. Nicolaou seems to enjoy doing this (here's a recent example), and I can't say that it adds much to my understanding.

OK, Andy Rooney mode off. For now.

Comments (43) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. ian on September 14, 2009 10:00 AM writes...

I can understand the colour as an aid to understanding bond connectivity in a confusing transition state / intermediate, but one is also reminded of the line, 'Hey, there's Skittles in there!' from The Hangover.

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2. ian on September 14, 2009 10:01 AM writes...

I can understand the colour as an aid to understanding bond connectivity in a confusing transition state / intermediate, but one is also reminded of the line, 'Hey, there's Skittles in there!' from The Hangover.

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3. You're Pfizered on September 14, 2009 10:15 AM writes...

It could be worse, you could be at Lilly right about now, wondering about your future. Maybe those colors would come in handy in an interview seminar.

I was more put off by the fact that KC, despite all he's accomplished, still puts his name first on a paper.

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4. Martyn on September 14, 2009 10:15 AM writes...

Can anyone tell the structure of the archazolids from this abstract?

http://pubs.acs.org/doi/abs/10.1021/jo901565n

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5. Anonymous on September 14, 2009 10:18 AM writes...

What's going on at Lilly?

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6. john.spevacek@aspenresearch.com on September 14, 2009 10:24 AM writes...

Come on guys, the colors are so obvious. What really bugs me is when they use these obscure symbols to identify the individual carbon atoms. I mean really, what the ____ is "1", "2" or "3". How can anyone use such junk???

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7. HelicalZz on September 14, 2009 10:25 AM writes...

I recall in my early grad school days doing a homework assignment in a physical organic chemistry course on heavy isotope effects wherein I color coded the reactive sites of interest. The TA of course was completely color blind, and I had to sit down with him and explain my homework. I pretty much use numbering exclusively now.

Zz

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8. Sili on September 14, 2009 10:39 AM writes...

Not to say that there isn't a place for colours (I've used it to highlight interpenetrating structures in crystals) and I could even see some use of them in plain chickenwire drawings. But these both reak of "Hey! We can get colours printed for free! Go, us!"

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9. You're Pfizered on September 14, 2009 10:40 AM writes...

4-Lilly cutting over 12% of their workforce over the next two years.

http://finance.yahoo.com/news/Lilly-cutting-5500-jobs-rb-127809934.html?x=0&.v=5

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10. Roger Federer on September 14, 2009 11:09 AM writes...

Nationwide, prescription pills have become a societal force. Adults and children rely on them for a growing list of afflictions, including anxiety, depression, even shyness, for which few alternatives were available a generation ago. Nearly half of all Americans take at least one prescription drug, it indicates findrxonline in his article about this topic. Meanwhile, direct-to-consumer drug marketing that touts new and expanded uses has become widespread. Adults and children alike are exposed to print, television and radio ads promising happier, more fulfilled lives. For young people, experts say, all these factors appear to have blurred the line between the benefits and dangers of the medications.

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11. Anonymous on September 14, 2009 11:17 AM writes...

Ouch. Didn't realise - thanks YP

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12. startup on September 14, 2009 11:26 AM writes...

I see your point, but I had a supervisor who would out of hand dismiss a paper brought to his attention if it did not have a color abstract.

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13. Chemjobber on September 14, 2009 11:33 AM writes...

I was wondering if they had done labeling studies, but nope.

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14. daen on September 14, 2009 11:42 AM writes...

IANAC ...

... but those structures remind me of the retina-separating colours some people use to liven up otherwise mind-numbing PowerPoint presentations. What I would *love* to see is a large audience which is just about to be subjected to a presentation using the Microsoft 'Garish' (tm) template putting on their sunglasses in synchrony ... I think that might get the message across ...

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15. Oliver Morton on September 14, 2009 12:17 PM writes...

FWIW as a non-chemist I looked at the diagrams and found it easier, I think, to see what was going on with the colours added than I would have done with b&w. Numbers might do as well, but colours seem more direct and intuitive, associating more closely in terms of identity.

Making such diagrams easier for non-chemists to read probably makes little sense in itself, I agree, since overwhelmingly we won't be reading this sort of thing at all, easy or not. But it's not clear to me that coding the identity with colours is necessarily wrong just because it wasn't done when most of you went to school and publishing worked completely differently (I'm pretty sure that colour is as cheap as black and white on my monitor...). Is there a way in which the colours actively hinder comprehension that I'm missing?

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16. davesnyd on September 14, 2009 12:50 PM writes...

I have to agree with Oliver-- I'm also not a synthetic chemist and I found that the colors helped clarify how the rings were lining up.

But maybe that's making your point-- those of us who don't do this day-in and day-out benefit from it but the real target market-- you-- only find it an annoying distraction.

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17. Hap on September 14, 2009 1:12 PM writes...

I think it's a little deceptive - without some labeling, the dots imply more mechanistic knowledge than you actually have. Though it's nice to see that the cycloadditions can get you some thing useful (trying to make taxol-type ring systems this way looked suboptimal because you couldn't easily delete all the Ns).

Oh, and either tennis stars have been taking time from their busy schedule to comment on drug availability or everyone's favorite drug spammer is visiting again.

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18. Charlie Abrams on September 14, 2009 1:32 PM writes...

Oliver Morton - The point is not just numbers, but *sequential* numbers. This gives more information than colored dots for which there is no obvious sequence. There are just too many colors to keep track of.

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19. Philip on September 14, 2009 1:44 PM writes...

If you watch some of Professor Nicolaou's presentations or look over his web pages, you can't help but wonder if he has some type of color blindness.

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20. Hap on September 14, 2009 1:56 PM writes...

Prof. Nicolaou's colored rings bother me more than Sieburth's colored dots - the colored rings only seem to indicate that N's group has enough money to hire graphic design students to prettify his molecules. Maybe he's looking for a reality show: "Pimp My Natural Product" ("we have this plain old strained polycyclic terpenoid, but if we color the rings red in this structure, we get...WOW") or "Survivor, La Jolla: Maitotoxin" ("sorry, your yield on that fragment coupling isn't good enough - you need to pass the column chromatography immunity challenge or it's back to startups for you!")

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21. CMCguy on September 14, 2009 2:08 PM writes...

While use of colored atoms/bonds/structures can be implemented to great effect for emphasis, particularly in talks, it does seem to be getting out of hand. I correlate trend to several things: Computer Drawing programs allow more and more color capability so people automatically think this option has to be utilized. As noted above seems we live in a PowerPoint culture so again people get carried away fancy aspects rather than fundamental straightforward means of conveying information. Finally, except for perhaps modeling, most chemists in their normal publications rarely even thought about using color because was much more expensive to print (which may be no longer a factor). Biologists and Biochemists sometimes employed (i.e. tissue stains and the like just don't show much otherwise) so I think (other) chemists got jealous so now have to show-off to claim status.

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22. Lucifer on September 14, 2009 3:12 PM writes...

Note the date..
_______________
Eli Lilly to outsource half of research by 2010
December 17, 2007 — 7:59am ET

While other big pharma companies have been making headlines with big layoffs and global restructuring plans, Eli Lilly has been steadily chipping away at its own strategy--quietly outsourcing jobs and services for research and manufacturing around the world as it gradually lowers its head count. About 40 percent of its IT work has already been outsourced with outside partners expected to handle half of its research work by 2010.

Read more: http://www.fiercebiotech.com/story/eli-lilly-outsource-half-research-2010/2007-12-17#ixzz0R772GcTt

Permalink to Comment

23. Anonymous on September 14, 2009 3:42 PM writes...

"the colored rings only seem to indicate that N's group has enough money to hire graphic design students to prettify his molecules"

What could be prettier than a nicely-drawn, black-and-white polycyclic structure? Maybe a nicely drawn structure on a chalk board, by one of those professors with the legendary structure-drawing skills ...

Permalink to Comment

24. Chemjobber on September 14, 2009 4:49 PM writes...

I believe that KCN has a secretary that does the graphic design or something; I heard this from him, during a talk. He thanked an assistant of his for help with the art, etc.

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25. Too Much Color on September 14, 2009 7:32 PM writes...

startup: That's funny, I sort through JACS by skipping all the papers with colored abstracts.

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26. z on September 14, 2009 7:58 PM writes...

I agree that this is annoying and very difficult to follow. Numbers and arrows would have been better. Although at least the colors mean something relevant to the chemistry.

Compared to, say, KCN's color schemes. He seems to deliberately make it difficult for people to follow his chemistry. Coloring in a ring might (emphasize *might*) be OK if you are highlighting a ring being formed. But by indiscriminately highlighting all rings, it draws attention *away* from the area of the molecule where the chemistry is actually happening. It makes the rings look much more substantial and "important" than the rest of the molecule, when, usually, they are *not* more substantial or important.

Color is often a very useful tool, but only if it enhances and doesn't interfere with the ability to understand what the paper is about.

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27. InfMP on September 14, 2009 9:18 PM writes...

Nicolaou's book Molecules that changed the world has all rings colored for the entire duration.

I am a huge nicolaou fan, and love the colored rings. But if everyone did it, then it would be confusing.
this is his signature and the moment that people open their ASAPs in the morning, it is immdieately apparent that nicolaou had (yet another) paper. That is exactly why he does it.

My only complaint with nicolaou is trying to obscure low yields with very confusing sentences, like in Sporolide B's key step, and haplophytine (11% bottleneck early in).
just SAY [X% yeild, X% recovered], not X% if you do 2 cycles, X%, based on X% recovered if you were to do the reaction infinite times, running a column each time.
only he can turn what is 24% in the SI into 92% in the manuscript.

Permalink to Comment

28. Danilo on September 14, 2009 10:51 PM writes...

As an inorganic/organometallic chemist, I often don't pay too much attention to the content of Nicolaou's articles and therefore I can't really comment on them in that regard (though I'm sure there's some very good chemistry in there). However, his colouring habits and penchant for listing himself as first author always cause me to shudder slightly every time I come across one of his graphical abstracts.

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29. Jack Bauer on September 14, 2009 11:26 PM writes...

The dots aren't even highlighting anything. It looks terrible.

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30. Smoki on September 15, 2009 2:04 AM writes...

Ugh, but that Nicolau picture isn't even pretty. Red on bright blue, it's horrible. This is when people confuse graphic design with liberally splashing colors around.

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31. Jose on September 15, 2009 2:23 AM writes...

KCN has a graphic designer on staff to handle all of his fonts, colors and default schemes to make sure everything is consistent (-ly bad, IMHO). Good research speaks for itself and doesn't require technicolor highlighting.

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32. RB Woodweird on September 15, 2009 6:38 AM writes...

Good news everyone! The ACS is going to go all electronic next year, and now you will have to read the literature on your netbook or other portable, color screen device. This will allow Prof. Nicolau to present graphics which are not only in color but flash, spin, dart onto and off of the page, change size and shape, and talk to you in one of several robotic voices.

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33. milkshake on September 15, 2009 6:48 AM writes...

there is a special circle of Hell reserved to the chemists who like to color their molecules in these eye-bleeding combination. Or is it a hexagon...

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34. AR on September 15, 2009 6:56 AM writes...

I’m no chemist, but it bothers even me. It’s like chemistry for MTV. I was helping my daughter with geometry, referencing the text book at some points. Geeze, it was full of dumb little popups, cartoon-style talking clouds to accent points, and thrown on the page is a colorful collage that really clutters the page. Some pages used different colored font on every other line.

Maybe it works well on kids by making learning fun, but it sure sent my blood pressure up a couple of points.

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35. Sili on September 15, 2009 10:38 AM writes...

Never managed to write a whole article on my own (feel free to boo here), but what's the deal with the order of authors? (Someone is gonna link me to the Ph.D. comics on this one, aren't they.)

Having a family name early in the alphabet, I'm obviously biased, so I'dn't mind hearing what the professionals think.

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36. Giagan on September 15, 2009 10:53 AM writes...

I have no problem with Nicolaou and other authors putting their names first on papers. They sponsored the research after all. I think it can also preclude many authorship disputes (e.g., which student gets listed as first author).

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37. Hap on September 15, 2009 11:48 AM writes...

Not having had any articles either, I think that it's the prof's prerogative whether to put their name first, last, in alphabetical order, or some other way. I don't think people correlate the author order of the professor with contributions, so it seems like more of a matter of convenience than ego (it's easier to see a group's papers with the author first). It does occasionally distinguish contributions, as well - I knew someone out of a synthetic group whose advisor normally took first position but gave it up for a paper derived from his idea. In that (extraordinary) case, the difference in author order is significant.

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38. z on September 15, 2009 5:17 PM writes...

Regarding whose name goes first: I'm not sure why people seem to be getting so mad about professors putting their name first. Everyone who looks at that paper will know that KCN did not do any of the chemistry. Having his name first does not taking any credit away from the other authors. Regardless of the order of the names, when you discuss this synthesis do you say "Nicolaou's synthesis of haplophytine" or do you say "Dalby's synthesis of haplophytine"? You say Nicolaou's. You mentally categorize the paper on the basis of who the professor is.

There are many instances where I think it can be more useful to have the professor's name first--it is easier to skim over and get a sense of lists of references when the first author is also the author that you are paying attention to (i.e., the PI). This is especially true in longish series of, say, methodology papers where the students have changed--when the PI's name is first, it is easier to see at a glance whether the papers are all part of the same story from the same lab, or whether the references are about different methods from different labs.

The inconsistency in how people list their names bothers me when I'm reading my ACS RSS feeds--they only show "First author et al," so I probably skip over some papers whose abstracts don't catch my eye, but that I might have read if I was interested in the PI's work, except that his name is at the end of the list so I don't see it.

Permalink to Comment

39. Danilo on September 15, 2009 8:04 PM writes...

Granted, putting the PI's name first is convenient in many ways (like authorship disputes, ACS RSS feeds, etc.), but in my end of chemistry (organometallic), the vast majority of PIs put their name last and the primary contributor first. In this way, you can more accurately gauge a student/postdoc/tech's contributions to the project and differentiate someone who did the bulk of the chemistry and/or wrote the paper from someone who maybe made a couple of ligands and fixed a few errors in the manuscript.

Perhaps an ideal system would be to list the PI as first author, the rest alphabetically, and then detail their contributions at the end of the manuscript (a la PLoS journals, Nature, and many others). But, as it stands (and even though it's not really fair), I do automatically get a slightly negative impression of a first-author PI.

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40. InfMP on September 15, 2009 9:21 PM writes...

If EVERYONE did it, best would be prof, then all the order like normal. It would still pimp to be second, cause that's obviously first.

skimming references when they are all old corey or nicolaou or trost is SOOO easy. but because most don't do it, it makes them look cocky

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41. z on September 15, 2009 9:28 PM writes...

Re: Danilo, #30, "organometallic ... PIs put their name last ... you can more accurately gauge a student/postdoc/tech's contributions to the project and differentiate someone who did the bulk of the chemistry and/or wrote the paper from someone who maybe made a couple of ligands and fixed a few errors in the manuscript."

Does putting the PI last really provide any more information about someone's contributions than putting the PI first? Anyone who is reading an academic paper where the PI is listed first will automatically assume that the PI did not do any of the technical work. Same as if he was listed last. You assume that the people other than the PI are listed in order of decreasing contributions. There is no way to tell who contributed most to the actual writing, or to the actual chemistry, or to the ideas, or anything more detailed. Regardless of where the PI's name shows up.

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42. Danilo on September 15, 2009 10:42 PM writes...

I agree with InfMP. If you put the PI first, then the order like normal, that could provide you with the same information and give many benefits beyond that. Despite being quite obvious, I hadn't thought of that.

Regarding z's comment, I believe that author order (aside from the PI) can be quite useful in determining an individual's contributions. Without something that suggests otherwise (corresponding author first or obviously alphabetical author listing), I assume the authors have been listed in order of decreasing contribution. In the labs I have worked in, "first authored" - and, to a lesser degree, second authored - papers "count" far far more towards someone's record than others.

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43. molecular architect on September 16, 2009 8:02 AM writes...

In my experience, the listing of authors on Chemistry papers varies with the PI. My advisor always listed himself last, others go alphabetically, etc. When I entered industry and began collaborating with biologists and clinicians, I was surprised to see how much importance they assign to being the first author. In those fields, being first is judged to be critically important. When I served on study sections, I found that my non-chemistry co-panelists placed much importance on the number of first author publications when judging the qualifications of grant applicants.

I've always wondered why chemistry is different.

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