Corante

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

Chemistry and Drug Data: Drugbank
Emolecules
ChemSpider
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
PubChem
Not Voodoo
DailyMed
Druglib
Clinicaltrials.gov

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
Kilomentor
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
ChemBark
Realizations in Biostatistics
Chemjobber
Pharmalot
ChemSpider Blog
Pharmagossip
Med-Chemist
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
SimBioSys
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Business|Bytes|Genes|Molecules
Eye on FDA
Chemical Forums
Depth-First
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa


Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
FuturePundit
Aetiology
Gene Expression (I)
Gene Expression (II)
Sciencebase
Pharyngula
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net


Medical Blogs
DB's Medical Rants
Science-Based Medicine
GruntDoc
Respectful Insolence
Diabetes Mine


Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem


Politics / Current Events
Virginia Postrel
Instapundit
Belmont Club
Mickey Kaus


Belles Lettres
Uncouth Reflections
Arts and Letters Daily

In the Pipeline

Category Archives

« The Dark Side | The Scientific Literature | Things I Won't Work With »

August 27, 2014

Life Is Too Short For Some Journal Feeds

Email This Entry

Posted by Derek

What scientific journals can you not be bothered to keep up with? I know, sometimes it's tempting to answer "all of them", but a well-informed chemist really should watch what comes out in the better ones. But how about the not-so-better ones? The "Life's too short" ones? Reading journals by RSS gives a person some perspective on signal-to-noise.

One problem is that Elsevier's RSS feeds are sort of perpetually hosed. Are they working now? I haven't checked in a while, because I finally gave up on them. And that means that I don't regularly look at Tetrahedron Letters or Bioorganic and Medicinal Chemistry Letters, even though (once in a while) something interesting turns up there. I look at ACS Medicinal Chemistry Letters more often, just because it has a working RSS feed (and I should note that I've rotated off their editorial board, by the way). Overall, though, I can't say that I miss either of those Elsevier journals, because you have to scroll through an awful lot of. . .stuff. . .to see something worth noting.

The same goes, I'm afraid, for Chemical Communications, and that makes me wonder if it's possible to keep up with the Letters/Communications style journals usefully at all. There are just so many papers pouring through them, and since Chem Comm takes them in from every sort of chemistry there is, vast numbers of them are of little interest to any particular reader. Their mini-review articles are perhaps an attempt to counteract this problem, and the journal also seems to have a slant towards "hot" topics. It's still in my RSS feed, but I look at the numbers of papers that pile up in it, and wonder if I should just delete and get it over with.

Organic Letters, on the other hand, I seem to be able to stay on top of, perhaps because it's focused down to at least organic chemistry (as opposed to Chem Comm). And I find a higher percentage of papers worth looking at than I do in Tet Lett (do others feel the same way?) And as for the other short-communications organic chemistry journals, I don't have them in the feed. Synthesis, Syn Comm, Synlett - writing this prompts me to go in and add them, but we'll see over the next couple of months if I regret it.

What it comes down to is that there's room for only a certain number of titles that can be followed as the papers publish. (The rest of them turn up in literature searches, responses to directed queries). And there are only a certain number of titles that are worth following in real time. So to get back to the question at the start of the post, which well-known journals do you find to be not worth the trouble?

Comments (16) + TrackBacks (0) | Category: The Scientific Literature

August 25, 2014

Citable Garbage

Email This Entry

Posted by Derek

Experimental and Clinical Cardiology used to be a reputable journal. Now it's a trash heap piled with crap. No, literally - the Ottawa Citizen newspaper has proof, thanks to reporter Tom Spears (who's an experienced hand at this). The journal was sold last year, and the new owners will publish absolutely anything you send them, as long as you send them $1200 to their bank account in the Turks and Caicos Islands. I wish I were making all that up, but that is exactly how it goes, offshore banking and all.

Spears whipped together a gibberish cardiology paper by taking one about HIV and doing a find-and-replace to substitute "cardiology" for "HIV" wherever it occurred. I'm sure it reads just fine, if you're high on crack. He stripped out all the graphics, wrote up some captions for new ones, but didn't send any graphs or figures with his submission. No problemo, dude! Paper accepted! As soon as the money shows up under that palm tree in the Caribbean, this junk will become the latest contribution to the medical literature.

The "journal" lists an affiliation with the International Academy of Cardiovascular Sciences in Winnipeg, which organization is pretty upset about that, since there's no connection at all any more. But how to get that fixed? The phone number listed for the editorial office doesn't work. And they don't respond to any emails that they don't feel like responding to, which I'd guess are all the ones that don't involve the possibility of $1200 wire transfers.

The wonderful people behind this scam will ride it as long as a shred of reputation clings to the journal's name, or as long as people send them money, whichever comes first. The journal's web site, which I will consider linking to if they pay me twelve hundred dollars, looks legit, except for the slightly-shaky-English-style notice that "Starting from Jan 1, 2013, Experimental and Clinical Cardiology Journal will operate under new publishing group". If you click "Editorial Board", it tells you that a new one is coming soon. And this part is pretty interesting, too - they say that they provide:

. . .outstanding service to authors through a clear and fast editorial process. Review and decision will be fast and our editorial policy is clear: we will either accept your manuscript for publication or not, our editors will not ask for additional research.

All submissions will be peer reviewed, and our reviewers are asked to focus their attention to data presented in the article. Your manuscript, after the review process can be or accepted or declined. Three independent reviewers are reviewing each manuscript and if two of them accept the manuscript then your work will be published without any further corrections. Note that we will not reject a manuscript because it is out of scope or for its perceived importance, novelty or ability to attract citations: we will publish any study that is scientifically sound.

Yeah boy! But as it says under "Publication Fees", "Open access publishing is not without its costs". One of those costs should be the scientific credibility of anyone who sends a paper in to the place these days. I've looked over the most recent papers listed on the web site - there's one from a hospital in Barcelona, a university in Turkey, an institute in China, some group from Italy whose paper doesn't load well, and a bunch of people with German-sounding names whose paper appears to be two pages long and consists of one figure and no text. An erratum? Who can tell? And who would bother? You might as well copy-and-paste some old Star Wars fan-fiction; no one's going to notice. Every single one of these lead authors probably had their paper turn around within a couple of days, and sent $1200 to the flipping Turks and Caicos without batting an eye, for a journal that's supposedly based in Switzerland. For shame.

No getting around it: if you send money to any of the publishers on Beall's List, you are funding a bunch of scam artists. And if you use such a paper to pad your own c.v., then you've decided to become a scam artist yourself.

Comments (7) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

July 11, 2014

My Imaginary Friends Would Be Glad to Serve as Referees

Email This Entry

Posted by Derek

Here's the biggest fake-peer-review operation I've heard of yet. Retraction Watch, which does not seem to be in any danger of running out of material, reports that a researcher in Taiwan decided to not leave the review process at the Journal of Vibration and Control up to chance. He set up scores of fake identities in their online submission database, with as many as 130 fabricated e-mail addresses, and guess who got to review his manuscripts?

The journal has retracted sixty papers going back to 2010, and I'd like to know if that's the record. I haven't heard of anything better - well, worse, you know what I mean. The professor involved has been removed from his position in Taiwan, as well he might, and the editor of the journal has resigned. As well he might, too - that editor is not implicated in the publication scam, as far as I can tell, but what exactly were his editorial duties? Dozens of papers come pouring in every year from some obscure university in Taiwan, all of them with overlapping lead or co-authors, and you don't even so much as look up from your desk? Hardly a month goes by without another bulletin from the wildly productive engineers at Pingtung U, sometimes four or five of the damn things at once, and you think you're doing your job? And nobody else who reads this journal - assuming anyone ever does - wonders what's going on, either?

If the professor involved was really getting something out of this (tenure, promotion, grant money, what have you), then the people who awarded those to him were idiots, too. In fact, that's how I'd sum up the whole affair: a fool, faking papers for a bunch of incompetents, and rewarded for it by idiots. What a crew. You really cannot underestimate the low end of the scientific publishing industry, nor its customers.

Comments (14) + TrackBacks (0) | Category: The Scientific Literature

July 7, 2014

That Retracted Stressed Stem Cell Work

Email This Entry

Posted by Derek

This article from David Cyranoski at Nature News is an excellent behind-the-scenes look at all the problems with the "STAP" stem-cell work, now retracted and apparently without any foundation at all. There were indeed problems with all of it from the start, and one of the key questions is whether these things could have been caught:

The committee was more vexed by instances of manipulated and duplicated images in the STAP papers. Obokata had spliced together gel lanes from different experiments to appear as one. And she had used an image of cells in a teratoma — a tumorous growth that includes multiple types of tissue — that had also appeared in her PhD dissertation. The captions indicated that the image was being used to represent different types of cell in each case. The committee judged that in both instances, although she might not have intended to mislead, she should have been “aware of the danger” and therefore found her guilty of misconduct. Obokata claimed that they were mistakes and has denied wrongdoing. . .

. . .Philip Campbell, editor-in-chief of Nature, says: “We have concluded that we and the referees could not have detected the problems that fatally undermined the papers.” But scientists and publishers say that catching even the less egregious mistakes raises alarm bells that, on further investigation, can lead to more serious problems being discovered.

Many say that the tests should be carried out on all papers. Christopher says that it takes about one-third of her working week to check all accepted manuscripts for the four journals published by EMBO Press. At Nature and the Nature research journals, papers are subjected to random spot-checking of images during the production process. Alice Henchley, a spokeswoman for Nature, says that the journal does not check the images in all papers because of limitations in resources, and that the STAP papers were not checked. But she adds that as one outcome of this episode, editors “have decided to increase the number of checks that we undertake on Nature’s papers. The exact number or proportion of papers that will be checked is still being decided.”

A complication is that some of the common image manipulations (splicing gel lanes, for example) are done in honest attempts to present the data more clearly, or just to save space in a figure. My guess is that admitting this up front, along with submitting copies of the original figures to the editors (and for inclusion in the Supplementary Material?) would help to clear that up. The article raises another good point - that editors are actually worried about confronting every example of image manipulation that they see, for fear of raising the competence of the average image manipulator. There's an evolutionary-arms-race aspect to all this that can't be ignored.

In the end, one gets the impression that Nature's editorial staff (a separate organization from the News people) very much regret ever having accepted the work, as well they might. Opinion seems divided about whether they could have caught the problems with the papers themselves - this was one of those cases where a number of reputable co-authors, at reputable institutions, all screwed up simultaneously when it came to cross-checking and verification. What remains is a portrait of how eager people can be to send in groundbreaking results for publication, and how eager editors can be to publish it. Neither of those are going to change any time soon, are they?

Update: from the comments, see also this timeline of events for a look at the whole story.

Comments (14) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

July 1, 2014

Scientific Journals: Who Pays What?

Email This Entry

Posted by Derek

If you've ever wondered about those deals where the large scientific publishers offer bundled discounts to libraries, wonder no more. There's a paper in PNAS whose authors used Freedom of Information Act requests to track down what various university libraries really paid for these deals, and it reveals that everyone paid something different.

Here's a comment in Nature on the study, which they can do with a straight face, since the Nature Publishing Group wasn't included in the study (although the authors seem to think, in retrospect, that they should have done so). These deals are always secret - the publishers make it a requirement not to disclose the terms. And that, as you might easily expect, benefits the publishers, since the library systems don't have a good way of finding out what the market price might be. The PNAS study reveals some odd discrepancies, with some universities getting noticeably better (and worse) deals than others. Wisconsin and Texas bargained hard, it appears, while BYU and Georgia could have done better for themselves.

As the article details, publishers used site licenses to take care of arbitrage opportunities, and the "Big Deal" bundles were used as incentives for the library systems and as tools for the publishers to figure out how much each customer might be willing to pay (using the print-based subscription data as a starting point). As you might have guessed, Elsevier comes out at the top of the pricing list when you just look at the dollar figures. On a cost-per-citation basis, though, they don't look so bad - in fact, they're the most cost-effective of the big publishers by that metric. (Sage and Taylor & Francis both look pretty bad in that table). For reference, the ACS bundle looks pretty decent, and it turns out that nearly 60% of the libraries that deal with the ACS choose the whole package (a high percentage compared to many other publishers). Interestingly, it turns out that some very wealthy schools (Harvard, MIT, Caltech) still don't take the full Elsevier bundle.

And the bundles are, naturally, a mixed bag. It's their whole purpose to be a mixed bag:

It would cost about $3.1 million at 2009 á la carte prices to buy all of the journals in Elsevier’s bundle, the “Freedom Collection.” The average research 1 university paid roughly $1.2 million, or 40% of the summed title-by- title prices, for access to the Freedom Collection. However, this bundle price is by no means equivalent to a 60% discount from journal-by-journal pricing. The Freedom Collection includes about 2,200 journals, many of which are expensive but rarely cited. The least cost-effective 1,100 journals contained in this collection supply fewer than 5% of the citations, but their prices add to more than 25% of the total of á la carte prices. A library that spent $1.2 million on Elsevier journals at listed catalog prices, selecting journals for cost-effectiveness, could obtain access to journals providing 79% of the citations to journals found in the Freedom Collection. Thus, for the average research 1 institution, the citation-scaled discount obtained from the Freedom Collection is about 21%.

Elsevier, though, drops its prices for smaller universities more quickly than many other publishers, and for Master's-level schools it's actually a better deal than many of the nonprofit publishers. We wouldn't know this, though, if these authors hadn't dug up all the info from FOIA requests, and I guess that's the take-home here: scientific publishing is a very opaque, inefficient market. And the publishers like it that way.

Comments (6) + TrackBacks (0) | Category: The Scientific Literature

June 27, 2014

Varieties of Scientific Deception

Email This Entry

Posted by Derek

Some may remember a paper from 2011 on the "reverse click" reaction, an interesting one where triazoles were pulled apart with mechanical force. This was an interesting system, because we really know surprisingly little, down on the molecular level, about what happens when bonds are physically stressed in this way. What do molecular orbitals look like when you grab both ends of the molecule and tug hard? Which bonds break first, and why? Do you get the reverse of the forward reaction, or do different mechanisms kick in (free radical intermediates, etc.)? (Note that the principle of microscopic reversibility doesn't necessarily apply when the conditions change like this).

Unfortunately, there seems to be trouble associated with this example. Science has an editorial "expression of concern" on the paper now, and it appears that much of it is not, in fact, reproducible (see this report in C&E News).

The paper was from the Bielawski lab at UT-Austin, and Bielawski is reported as saying that a former group member has confessed to manipulating data. But he also says that the conclusions of the paper are unchanged, which is interesting. My guess is that the "unclick" does happen, then, but nowhere as smoothly as reported. Someone may have sweetened things to make it all look better. At any rate, a correction is coming soon in Science, so we should get more information at that point.

This reminds me of the scheme I use to rate political and economic corruption. Stage I is paying someone off to do something they wouldn't normally do (or aren't authorized to do) for you. This happens everywhere, to some extent. Stage II is when you're bribing them just to do the job they're supposed to be doing in the first place. Many countries suffer from institutional cases of this, and it's supremely annoying, and a terrible drag on the economy. And Stage III, the worst, is when you're paying them not to harm you - a protection racket with the force of law behind it. Cynics may adduce examples from the US, but I'm thinking about countries (Russia, among others) where the problem is far worse.

Similar levels apply to fakery in the scientific literature. Here's how I break it down:

Stage I is what we may have in this case: actual conclusions and effects are made to look cleaner and better than reality. Zapping solvent peaks in the NMR is a perfect small-scale example of this - for organic chemists, solvent peaks are sometimes the training wheels of fakery. The problem is, once you're used to altering data, at what point do you find it convenient to stop? It's far better not to take that first step into matters-of-degree territory.

Stage II is unfortunately common as well, and there's a nice slippery path from Stage I that can land you here. This is when you're convinced that your results are correct, but you're having such a hard time getting things to work that you decide to "fake it until you make it". That's a stupendously bad idea, of course, because a lot of great results were never real in the first place, which leaves you hung out to dry, and even the ones that can be finally filled in don't have to do so in the way that you were faking them to happen. So now a real result is tainted by deception, which will call the whole thing into doubt when the inconsistencies become clear. And faked results are faked results, even if they're done in what you might think is a good cause. Many big cases of scientific fraud have started off this way, with someone just trying to fill in that one little gap, just for now.

Stage III, the bottom, is when something is faked from beginning to end. There was no question of it even working in the first place - it never did. Someone's just trying to get a paper, or a degree, or tenure, or fame, or something, and they're taking the shortcut. I think that there are two main classes of fakery in this category. In one group (IIIa?), you have people whipping up bogus results in low-profile cases where no one may notice for years, if ever, because no one cares. And you have IIIb, the famous high-profile cases (see Jan-Hendrik Schön, among too many others) where impressive, splashy, look-at-that stuff turns out to have been totally faked as well. Those cases are a study in human psychology. If you report a big result in superconductors, stem cells, cancer therapy or any other field where a lot of smart, competent people are paying very close attention, you will be found out at some point. How can you not be? We're in Bernie Madoff territory here, where someone comes into work every day of every week knowing that their whole reputation is a spray-painted scrim of deception that could have a hole punched through it any minute. How people can possibly live this way I don't really know, but people do. The self-confidence displayed by this sort of personality is a wonder of nature, in its way. IIIa cases are initiated by the desperate, stupid, and/or venal. IIIb cases, though, are brought on by people born to their task.

Update: as pointed out by several good comments, there are plenty of not-quite-fraud sins that neighbor these. Those are worth a separate post, partly because they're even more common than straight-up fraud.

Comments (53) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

June 6, 2014

The Robustness Test: Why Don't We Just Require It?

Email This Entry

Posted by Derek

There's a follow-up paper to that one on the robustness of new synthetic methods that I blogged about here. This one's in Nature Protocols, so it's a detailed look at just how you'd go about their procedure for shaking down a new reaction.

The reaction they've chosen is a rhodium-catalyzed indole formation (phenylhydrazine plus substituted alkyne), which is a good test bed for the real world (heterocycles, metal-catalyzed mechanism). The authors suggest a matrix of additives and reaction conditions, analyzed by GC, as in their original paper, to profile what can be tolerated and what can't. It's good to have the detailed reference out there, and I hope it gives referees and journal editors something to point at.

But will they? I can imagine a world where new reactions all have a "standard additives" grid somewhere in the paper, showing how the yields change. You could even color-code them (the old stoplight slide scheme, red/yellow/green, would be fine), and then we'd all have a way to compare synthetic methods immediately. Aldrich and others could sell the pre-assembled kit of the standard compounds to use. This would also point out reactions where more useful work could be done, since it would be immediately obvious that the new Whatsit Cyclization fails in the presence of tertiary amines, etc. Too often now you have to work that our for yourself, usually by seeing what the authors left out.

So why don't we all do this? It's more work, that's for sure, but not an incredible amount more work. If the major synthetic chemistry journals starting asking for it, that would be that. It would also make the publication landscape even more clear, because the titels that don't ask for an extra few days to be spent on the reaction conditions would be hard-pressed to make a case that they weren't just venues for hackwork (or for people with something to hide). I'd rather read about reactions with a clear statement of what they'll work on and what they won't - wouldn't you?

Comments (13) + TrackBacks (0) | Category: Chemical News | The Scientific Literature

June 2, 2014

No More Acid Stem Cells

Email This Entry

Posted by Derek

In case you hadn't seen it, the "acid-washed stem cells" business has gone as far into the dumper as it can possibly go. It now appears that the whole thing was a fraud, from start to finish - if that's not the case, I'll be quite surprised, anyway. The most senior author of the (now retracted) second paper, Teruhiko Wakayama, has said that he doesn't believe its results:

The trigger, he told Bioscience, was his discovery—which he reported to Riken a few weeks ago--that two key photos in the second paper were wrong. Obokata, lead author on both papers, had in April been found by Riken guilty of misconduct on the first paper: the falsification of a gel electrophoresis image proving her starting cells were mature cells, and the fabrication of images proving resulting STAP stem cells could form the three major tissue types of the body.

But Riken had not yet announced serious problems with the second paper.

Last week, however, there was a flurry of activity in the Japanese press, as papers reported that two photos—supposed to show placenta made from STAP cells, next to placenta made from embryonic stem (ES) cells—were actually photos of the same mouse placenta.

As with so many cases before this one, we now move on (as one of Doris Lessing's characters once put it) to having interesting thoughts about the psychology of lying. How and why someone does this sort of thing is, I'm relieved to say, apparently beyond me. The only way I can remotely see it is if these results were something that a person thought were really correct, but just needed a bit more work, which would be filled in in time to salvage everything. But how many times have people thought that? And how does it always seem to work out? I'm back to being baffled. The stem cell field has attracted its share of mentally unstable people, and more.

Comments (12) + TrackBacks (0) | Category: Biological News | The Dark Side | The Scientific Literature

May 28, 2014

The Science Chemogenomics Paper is Revised

Email This Entry

Posted by Derek

The Science paper on chemogenomic signatures that I went on about at great length has been revised. Figure 2, which drove me and every other chemist who saw it up the wall, has been completely reworked:

To improve clarity, the authors revised Fig. 2 by (i) illustrating the substitution sites of fragments; (ii) labeling fragments numerically for reference to supplementary materials containing details about their derivation; and (iii) representing the dominant tautomers of signature compounds. The authors also discovered an error in their fragment generation software that, when corrected, resulted in slightly fewer enriched fragments being identified. In the revised Fig. 2, they removed redundant substructures and, where applicable, illustrated larger substructures containing the enriched fragment common among signature compounds.

Looking it over in the revised version, it is indeed much improved. The chemical structures now look like chemical structures, and some of the more offensive "pharmacophores" (like tetrahydrofuran) have now disappeared. Several figures and tables have been added to the supplementary material to highlight where these fragments are in the active compounds (Figure S25, an especially large addition), and to cross-index things more thoroughly.

So the most teeth-gritting parts of the paper have been reworked, and that's a good thing. I definitely appreciate the work that the authors have put into making the work more accurate and interpretable, although these things really should have been caught earlier in the process.

Looking over the new Figure S25, though, you can still see what I think are the underlying problems with the entire study. That's the one where "Fragments that are significantly enriched in specific sets of signature compounds (FDR ≤ 0.1 and signature compounds fraction ≥ 0.2) are highlighted in blue within the relevant signature compounds. . .". It's a good idea to put something like that in there, but the annotations are a bit odd. For example, the compounds flagged as "6_cell wall" have their common pyridines highlighted, even though there's a common heterocyclic core that that all but one those pyridines are attached to (it only varies by alkyl substitutents). That single outlier compound seems to be the reason that the whole heterocycle isn't colored in - but there are plenty of other monosubstituted pyridines on the list that have completely different signatures, so it's not like "monosubstituted pyridine" carries much weight. Meanwhile, the next set ("7_cell wall") has more of the exact same series of heterocycles, but in this case, it's just the core heterocycle that's shaded in. That seems to be because one of them is a 2-substituted isomer, while the others are all 3-substituted, so the software just ignores them in favor of coloring in the central ring.

The same thing happens with "8_ubiquinone biosynthesis and proteosome". What gets shaded in is an adamantane ring, even though every single one of the compounds is also a Schiff base imine (which is a lot more likely to be doing something than the adamantane). But that functional group gets no recognition from the software, because some of the aryl substitution patterns are different. One could just as easily have colored in the imine, though, which is what happens with the next category ("9_ubiquinone biosynthesis and proteosome"), where many of the same compounds show up again.

I won't go into more detail; the whole thing is like this. Just one more example: "12_iron homeostasis" features more monosubstituted pyridines being highlighted as the active fragment. But look at the list: there's are 3-aminopyridine pieces, 4-aminomethylpyridines, 3-carboxylpyridines, all of them substituted with all kinds of stuff. The only common thread, according to the annotation software, is "pyridine", but those are, believe me, all sorts of different pyridines. (And as the above example shows, it's not like pyridines form some sort of unique category in this data set, anyway).

So although the most eye-rolling features of this work have been cleaned up, the underlying medicinal chemistry is still pretty bizarre, at least to anyone who knows any medicinal chemistry. I hate to be this way, but I still don't see anyone getting an awful lot of use out of this.

Comments (6) + TrackBacks (0) | Category: Biological News | Chemical Biology | Chemical News | The Scientific Literature

May 14, 2014

A Unique Correction

Email This Entry

Posted by Derek

A reader sent this correction notice along this morning, and I agree: I've never seen anything quite like it. Here's how it goes (emphasis added):

According to the recent reconsideration and re-evaluation of every author’s contribution of this work, all of authors have reached the final conclusion that we should rearrange the order of the authors and remove Dr. Usui from the author list as observed below.

(List of authors follows)

All of authors have already approved this correction. Dr. Usui, our supervisor, also authorized and approved it.

There's surely a story here, but I'm sure that I don't quite know what it is, either!

Comments (31) + TrackBacks (0) | Category: The Scientific Literature

April 22, 2014

J. Appl. Drivel or Gibberish Lett.? Choices, Choices.

Email This Entry

Posted by Derek

People keep hoaxing the predatory "scholarly" publishers out there, and the publishers keep falling for whatever drivel is slung at them. Here's the latest example from a reporter at the Ottawa Citizen, Tom Spears. He molded a pile of steaming gibberish into the rough shape of a manuscript, and that was more than enough:

I have just written the world’s worst science research paper: More than incompetent, it’s a mess of plagiarism and meaningless garble. . .

. . .I copied and pasted one phrase [in the title] from a geology paper online, and the rest from a medical one, on hematology.

I wrote the whole paper that way, copying and pasting from soil, then blood, then soil again, and so on. There are a couple of graphs from a paper about Mars. They had squiggly lines and looked cool, so I threw them in.

Footnotes came largely from a paper on wine chemistry. The finished product is completely meaningless.

The university where I claim to work doesn’t exist. Nor do the Nepean Desert or my co-author. Software that catches plagiarism identified 67 per cent of my paper as stolen (and that’s missing some). And geology and blood work don’t mix, even with my invention of seismic platelets.

And you guessed it - the acceptances came rolling in, and pretty damned quickly, too. Peer-reviewed, refereed, and edited within 24 hours - where are you going to find an honest journal with service like that? 16 of the 18 bottom-feeding "journals" accepted it, and one of the rejections suggested that it just needed a bit of tweaking to be accepted. And one of the publishers has asked Spears to serve on an editorial advisory board, so he's clearly got what it takes.

Of course, as yesterday's post shows, even a peer-reviewed journal with a recognizable name can publish gibberish. But I assume that Drug Discovery Today and Elsevier didn't charge the author $1000 to do it. On the other hand, they might have taken more than 18 hours to review the manuscript. Or not.

Comments (14) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

April 21, 2014

Molecular Printing of Drug Molecules. Say What?

Email This Entry

Posted by Derek

Update: the author of this paper has appeared in the comments here (and elsewhere) saying that he's withdrawing the paper. These are apparently reviewer's comments on it, although I have no way of verifying that. Many of them don't sound like the comments I might have expected. There's more here as well.

Here we have one of the oddest papers to appear in Drug Discovery Today, which is saying something. The journal has always ranged wider than some of the others in this space, but this is the furthest afield I've seen to date. The title is "DrugPrinter: print any drug instantly", and I don't think I can do better than letting the abstract speak for itself:

In drug discovery, de novo potent leads need to be synthesized for bioassay experiments in a very short time. Here, a protocol using DrugPrinter to print out any compound in just one step is proposed. The de novo compound could be designed by cloud computing big data. The computing systems could then search the optimal synthesis condition for each bond–bond interaction from databases. The compound would then be fabricated by many tiny reactors in one step. This type of fast, precise, without byproduct, reagent-sparing, environmentally friendly, small-volume, large-variety, nanofabrication technique will totally subvert the current view on the manufactured object and lead to a huge revolution in pharmaceutical companies in the very near future.

Now, you may well read that and ask yourself "What is this DrugPrinter, and how can I get one?" But note how it's all written in the conditional - lots of woulds and coulds, which should more properly be mights and maybes. Or maybe nots. The whole thing is a fantasy of atomic-level nanotechnology, which I, too, hope may be possible at some point. But to read about the DrugPrinter, you'd think that someone's ready to start prototyping. But no one is, believe me. This paper "tells" you all the "steps" that you would need to "print" a molecule, but it leaves out all the details and all the hard parts:

Thus, if DrugPrinter can one day become a reality it will be a huge step forward in drug discovery. The operator needs only to sit down in front of a computer and draw the structure of compound, which is then inputted into the computer, and the system will automatically search by cloud computing for suitable reaction conditions between bond and bond. . .

That actually captures the tone of this paper pretty well - it exists on a slightly different plane of reality, and what it's doing in Drug Discovery Today is a real mystery, because there's not much "Today" in it, for one thing. But there's something else about it, too - try this part out and see what you think:

Thus, this novel protocol only needs one step instead of the five-to-ten steps of the current synthesis process. In actual fact, it is even better than click chemistry, with lower costs and with better precision of synthesis. A world-leading group led by Lee Cronin has made advances with the technology named ‘Chemputer’. However, it is different to our concept. We specifically address the detail of how to pick up each atom and react. We also disagree that it is possible for anyone to simply download the software (app) from the internet and use it to print one's own drug. It is not feasible and should be illegal in the future.

Some of this, naturally, can be explained by non-native English usage, although the editorial staff at DDT really should have cleaned that up a bit. But there's an underlying strain of grandiose oddness about the whole manuscript. It makes for an interesting reading experience, for sure.

The paper proposes a molding process to fit the shape of the desired target molecule, which is not prima facie a crazy idea at all (templated synthesis). But remember, we're down on the atomic scale here. The only thing to build the mold out of is more atoms, at the same scale as the material filling the mold, and that's a lot harder than any macroscale molding process that you can make analogies to. The MIP (molecularly imprinted polymer) idea is the closest real-world attempt at this sort of thing, but it's been around for quite a while now without providing a quick route into molecular assembly. There is no quick route into molecular assembly, and you’re certainly not going to get one from stuff like this:

Benzene has six carbon atoms joined in a ring, with one hydrogen atom attached to each carbon atom. It can be divided into six reactors for three atoms: C, H and C (Fig. 3). After inputting the chemical structure of benzene, the system will search for the best synthesis condition for each bond. The best optimal condition will be elucidated by computer and controlled by a machine with optical tweezers to pick up the reactant and the atoms of carbon and hydrogen. The carbon atom will be picked up by optical tweezers in the right position in these tiny reactors (just like a color laser printer). DrugPrinter technology will work just like a color laser printer but instead of a four-color (red, yellow, blue and black) printer toner cartridge there will be various atoms.

Right. The computer will search for the best reaction conditions for building up benzene by individual carbon atoms? There are no best conditions for that. You can make benzene from acetylene, if you’re so minded, but you need meta