Dear Dr.Iddo Friedberg,    

Greeting from OMICS Group!

I came across your contribution entitled “Biopython: freely available Python tools for computational molecular biology and bioinformatics” published in the Journal of Bioinformatics and thought your expertise would be an excellent fit for Toxicology-2012 Conference that OMICS Group is hosting.

 

I’m just wondering how many legitimate calls for participation I am missing due to the increasing amounts of conference spam in my inbox.

A quick post for International Women’s Day: how did the gender symbols originate in biology? What do ♀ and ♂ actually stand for?

The answer starts in antiquity, when planets and gods were almost synonymous. Religious rites (at least in Europe) were also associated with the working of metals. Thus, each heavenly body was associated with a metal, a god and provided with a proper symbol, thus:

1. Sun (gold) 2. Moon (silver) 3. Saturn (lead) 4. Jupiter (tin) 5. Mars (iron) 6. Mercury (mercury, duh) 7. Venus (copper) After woodcuts by Friz Kredel, published in Stearn 1962.

But how did the symbols of Mars (iron) and Venus (copper) migrate to describe sex in biology? It seems obvious to us that of all symbols, that of the god of war be assigned to male, and the goddess of love to female (stereotypes nonwithstanding), but who was the first who did that?

The answer can be traced to one of the greatest biologists of all times: Carl Linnaeus. He is better known for being the father of modern taxonomy: Linnaeus  is the reason that we uniquely identify organisms using genus and species names in Latin grammatical form, a system known as Linneael binomial nomnclature. From Homo sapiens to Escherichia coli, we all owe our scientific names to Linnaeus.

But Linnaeus was also the one to appropriate the planet symbols to biology. In his notes, he used the Venus symbol as shorthand for female and the Mars symbol as shorthand for male. He also used Saturn to denote woody plants, the Sun for annual plants and Jupiter for perennials. As for gender, the Mercury symbol was used by Linnaeus for hermaphrodite plants. However, that symbol’s meaning has changed over the years, at least in scientific shorthand, and is now used to denote virgin female (e.g. in genetic analysis).  Mars was also used by Linnaeus, somewhat confusingly, for biennial plants.

But how did the symbols actually originate? The accepted thought now is that they were derived by the Roman from the Greek initial letters for the planets / deities. So Phosphoros  Φωσφόρος (Greek: “Morning Star” or later the planet Venus) was abbreviated to Φκ and Thouros (Mars) to θρ further contracted over the years, by metal workers, astrologers and alchemists to the modern symbols.

Kronos (saturn); Zeus (Jupiter); Thouros (Mars); Phosphoros (Venus) Stilbon (Mercury). After Stearn 1962

William T. Stearn (1962). The Origin of the Male and Female Symbols of Biology Taxon, 11 (4), 109-113

EDIT: I got a couple of concerned emails. No, this did not happen to me. Yet.

Once I lived the life of a PI so rich,
Research was going along without a hitch.
Lab manager, four postdocs and grad students eight,
My lab took up the whole floor, and that felt great.

Five years later it all went to hell,
My renewal was declined, because no papers in Cell.
But I just read an RFA that is out,
I’m going to apply, and get it, without a doubt.

Nobody knows you,
when you lose your grant.
In your funding, not one penny,
and as for postdocs, I haven’t any.

If I ever get back on my feet again,
My department chair will not treat me with disdain.
It’s mighty strange, which is why I’m doing this rant,
Nobody knows you when you lose your grant.

Best version of the original, IMHO:

It is with no inconsiderable degree of reluctance that I decline the offer of any Paper from you. I think, however, you will upon reconsideration of the subject be of opinion that I have no other alternative. The subjects you propose for a series of Mathematical and Metaphysical Essays are so very profound, that there is perhaps not a single subscriber to our Journal who could follow them.

David Brewster, physicist and mathematician and inventor acting as editor of The Edinburgh Journal of Science to Charles Babbage, mathematician, philosopher, inventor and mechanical engineer; father of the computer circa 1821.

The Scientist is one of my favorite go-to destinations for keeping up with current biomedical research. That’s why I was rather sad when it was recently announced that The Scientist will be closing down. However, it seems like The Scientist will continue to be published after all:

NEW YORK, NY–(Marketwire – Oct 14, 2011) – Sciencenow Inc., a member of The Science Navigation Group, and LabX Media Group are pleased to announce that they have signed a nonbinding Letter of Intent specifying terms for the acquisition of The Scientist by LabX Media Group. The parties hope to close a transaction by the end of October.

Sande Giaccone, Sales and Marketing Director of The Scientist, said, “We are delighted that, following the decision to cease publication of The Scientist, LabX Media Group has stepped in to save The Scientist and keep the majority of its existing team together. We hope to return to our normal high service level for all our readers, contributors, and advertisers in the next few weeks. We sincerely appreciate the support of our advertisers in the past and hope to regain their confidence going forward. The Scientist is complementary to LabX Media’s existing stable of products and, subject to closing of a transaction, we look forward to working with them in the future.”

Mary Beth Aberlin, Editor in Chief of The Scientist, said, “Naturally, we were all saddened by the decision to cease publication of The Scientist, and grateful to our readers and contributors for all their kind words concerning the magazine. The editorial team and I are delighted that LabX Media Group has been able to agree on terms with Sciencenow, Inc. with such dispatch. Our dedicated editorial team will remain intact and continue to produce a magazine that maintains our editorial standards.

Bob Kafato, President of LabX Media Group, said, “The quality life science content that The Scientist produces is second to none and we are happy to be adding this to our portfolio of media products for lab professionals.”

Kudos to LabX. You have rescued a fine journal. Thanks to Linda Kosta for calling my attention to this fortunate turn of events.

The IgNobel prizes are awarded annually for research that “makes you laugh, and then makes you think”. Actually, I liked their previous motto better: “research that cannot or should not be reproduced”. But like the Nobel prizes, IgNobels are not awarded only for science. For example, The mayor of Vilnius received the IgNobel Peace Prize for fulfilling every urban driver’s dream and running over an illegaly parked car with a BTR-60 (an armored personnel carrier mistakenly identified as “tank” by the IgNobel prize awarders, but what do these Harvard peaceneaks know about military stuff).

The Physiology Prize was given to Anna Wilkinson (of the UK), Natalie Sebanz (of THE NETHERLANDS, HUNGARY, and AUSTRIA), Isabella Mandl (of AUSTRIA) and Ludwig Huber (of AUSTRIA) for their study “No Evidence of Contagious Yawning in the Red-Footed Tortoise.”
REFERENCE: ‘No Evidence Of Contagious Yawning in the Red-Footed Tortoise Geochelone carbonaria,” Anna Wilkinson, Natalie Sebanz, Isabella Mandl, Ludwig Huber, Current Zoology, vol. 57, no. 4, 2011. pp. 477-84.

The prize I like best was the medicine prize awarded to : Mirjam Tuk (of THE NETHERLANDS and the UK), Debra Trampe (of THE NETHERLANDS) and Luk Warlop (of BELGIUM). and jointly to Matthew Lewis, Peter Snyder and Robert Feldman (of the USA), Robert Pietrzak, David Darby, and Paul Maruff (of AUSTRALIA) for demonstrating that people make better decisions about some kinds of things — but worse decisions about other kinds of things‚ when they have a strong urge to urinate.

In other entertaining, for want of a better term, the Wall Street Journal came out with an op-ed which made quite a few heads explode. Basically using a rather heavy-handed non-sequitur the author tried to unravel climate science:

The science [global warming] is not settled, not by a long shot. Last month, scientists at CERN, the prestigious high-energy physics lab in Switzerland, reported that neutrinos might—repeat, might—travel faster than the speed of light. If serious scientists can question Einstein’s theory of relativity, then there must be room for debate about the workings and complexities of the Earth’s atmosphere

For a full dissection of this weirdness, please go to Phil Plait’s response in Bad Astronomy.

 

For one, there is always room for questioning science. But that questioning must be done by science, using a scientific basis, and above all else be done above board and honestly. But that’s not how much of the climate science denial has been done. From witch hunts to the climategate manufactrovery, much of the attack on climate science has not been on the science itself, but on the people trying to study it. And when many of those attacks have at least a veneer of science, it’s found they are not showing us all the data, or are inconclusive but still getting spun as conclusive by climate change deniers. And if you point that out, the political attacks begin again (read the comments in that last link).

Second, the neutrino story has nothing to do with climate change at all. It’s a total 100% non sequitur, a don’t-look-behind-the-curtain tactic. Just because one aspect of science can be questioned — and I’m not even saying that, which I’ll get to in a sec — doesn’t mean anything about another field of science. Bryce might as well question the idea that gravity is holding us to the Earth’s surface.

The whole thing generated the delightful hashtag #WSJScience. Read the tweets before they expire.

Hats off to Jonathan Eisen for hosting this activity on his blog. (I’ll keep mine on, thank you. It’s raining cats and dogs here right now).

A couple of weeks ago I posted a discussion about two papers that challenged the ortholog conjecture. Briefly, both papers stated that orthologs may not be such great predictors for molecular function. One study from  Indiana University by  has shown that paralogs may be better predictors than orthologs for molecular function. Or, at the very least, paralogs should not be excluded as predictors. This paper has generated quite a bit of interest and controversy. Consequently, Eisen has invited Matthew Hahn, the lead author to write about “the story behind the story” in Eisen’s well-read blog. The post is a great read, and has generated an animated discussion in the comments area. You do need to clear quite a bit of time to go through both Hahn’s guest post and the comment thread: the topic is a rather complex one, and as explained in the comments thread, one problem is that the ‘ortholog conjecture’ itself seems to be not well-defined.

I kept checking in to Eisen’s blog to read the elongating comment thread. It seems that now a special session on the topic may be in the works for the 2012 annual meeting of the Society for Molecular Biology and Evolution following this discussion. So great to see such an involved community getting together.

1. This is crap. (Rare).

2. This is terrific. (Even rarer).

3. This can be OK, but they really need to fix A, B & C. (fairly common).

4. If I only knew what they meant in point A, I could say whether they need to fix A, B & C or just B & C, or maybe explaining A will clarify to me that B need not be fixed at all.(Really common!)

The things is, sometimes draft manuscript are good, but unclear on a very specific and crucial point. Like point A.  The lack of clarity is not necessarily due only to bad writing. Sometimes it is very hard to describe a new idea or method. After all, it is new, right? So no-one has described it before and finding the correct way to describe you new idea or method can be very tricky. Some people use analogies (like me, I love analogies). But an analogy can be over interpreted, and then mis-interpreted, and your intricately concocted explanation is all shot. Then again, some authors do not use analogies, but explain their methods very formally. A reader who is very visual (like myself) would like to see a some graphic depiction of the method, but that may not be possible, or the author’s graphic rendering skills are not good enough.  In any case, I seem to get a lot into the position where my opinion of the paper hinges around one or two crucial details. If this were a seminar, and the author was talking about her work, I would just ask her to clarify the point. But I cannot do that when reviewing an article. Which leaves me with asking to perform major revisions, which sets the paper into a serious delay mode or sometimes reject because other reviewers have been less amenable.   (As an aside, I have noticed some reviewers  just let  the ambiguity of point A slide. This usually happens if the last author is Dr. Bigschotte, holder of the Endowed Golden Chair professorship of Biowizardry).

But maybe I can ask that clarification question of the author, or even have a brief dialogue? Anonymous email/chat technology can do wonders for shortening the turnover time of papers and clarifying issues. I am not saying that writers are now given a free license to write badly. But if needed, a chat session or email exchange monitored by the editor could really help push a paper through (or away). The exchange should be very brief, topical, logged (with the referee anonymized). The session should be requested by the referee, with very specific questions. The number of back-and-forth exchanges should be limited.

As a referee, I see myself more as a midwife (or whatever is the male counterpart) than a gatekeeper. I am not interested so much in keeping bad papers out (that is actually fairly easy), but letting good science in, even when it presents itself feet first and covered in gunk (OK, that was a rotten analogy, but you know what I mean). Anything that can ease this process is more than welcome.

So… any takers? Or is this a terrible idea? Better yet, has something like this been done?

PS: actually, as an author, I sometimes receive reviewer comments which I do not quite understand. This is even worse, since if I don’t address the issue in the way the reviewer asked for, it can spell the death of my paper. So this mechanism of quick dialogue between reviewer and author can work well both ways.

After WWII, Pacific islands occupied by the US military were regularly receiving goods via air. Once the military evacuated , the goods stopped arriving. Some inhabitants of those islands mistakenly thought that receiving the cargo was due to some divine intervention that required rituals they saw American servicemen performing. This eventually led them to performing activities like making their own airfields, waving in non-existent planes while wearing coconut headphones, etc, all in the hopes that material would magically come from the sky. These attempts were called cargo cults. Since then, “cargo cult” has been used metaphorically to describe an attempt to recreate successful outcomes by replicating conditions associated with those outcomes, even though those conditions are either effects and not causes of those outcomes.[Wikipedia]

Science culture is not void of its own cargo-cult, despite the fact that science is supposed to be the ultimate cargo-cult dispeller.  I have written before about solicitations for author-pays publications whose quality, shall we say, is less than assured. Actually, it seems like some of these publications will print anything as long as you pay them.  Here is what my inbox brought in today, all bold-faced typing is mine:

____ is a peer-reviewed journal that includes an international board of accomplished editors and researchers in their fields. There will be submissions on subjects such as cheminformatics, computational drug discovery, experimental medicine and analysis tools, personalized medicines, cancer informatics, hematology, diagnostic imaging, medical imaging and methods and gene therapy, among other latest breathtaking topics.

Indeed, breathtaking. This journal seems to have a strong focus on, um, whatever. But what really takes your breath away is that you really have to work hard to  qualify for publication. Specifically, self-plagiarism is rigorously weeded out:

If you (sic) paper has been published in any other platform, a new version of your paper for ___ (Vol 1 No 1) must reflect at least 25% difference in content from the one published in any conference proceeding or any other journal.

So I have to justify a “25% difference” between my submission to this journal and my previous manuscript? Do I change every fourth word from a previously published paper? And how do I measure this “25% difference”? Use the cosine measure for similarity of text?  Extended Jaccard similarity? Something else?

Each published paper in the ___ is subject to a publication fee of USD 300 for a maximum of 6 pages. A complimentary copy (print version) of the ___ (Vol 1 No 1) issue that carries your reviewed paper will be mailed to your mailing address.

I guess we all saw that coming.

These actually work. Click for description

The new top-tier competitor to Science and Nature proposed by three leading funders of scientific research last week is a great idea, but I think runs a risk of opening the scientific process to a potentially damaging slander by opponents of science.

As practising academic scientists we’re all concerned, and intimately entangled, with the scientific publication process. We are authors, reviewers, editors, sometimes journal chiefs and, in a very real sense, our entire careers may hang upon whether and where our work is published. Impact factors, journal reputations, author counts and ordering, and other actuarial metrics are foremost in our minds every time a promotion case or job application is submitted. The cost of publishing work raises its head every time we have to dip into consumables to fund a colour figure. Each time we submit to peer review we set sail anew, all paranoid, on the Sea of Judgement by Anonymous Colleagues and Competitors. We are, as a group, highly sensitive to changes in the scientific publishing ecosystem. So it’s no surprise that the scientific world and its experimental dog have opinions on this potential competitor to Science, Nature and Cell.

And, at first glance, the new journal could be a beautiful thing.

The journal is planned to be fully Open Access, underwritten at least initially by the funding bodies, so there will be no, or reduced, author charges. Author charges can be a problem where projects lack money allocated to publication costs. I’ve usually been lucky enough to obtain support for Open Access publication, but this still adds a level of political and financial consideration when deciding where to submit work. Where funding bodies require OA publication (and this is increasingly a condition of funding) I think it is only right that they support this route financially, and the Howard Hughes Medical Institute, Wellcome Trust, and the Max Planck Society are to be congratulated for taking this stand.

Michael Eisen points out that the new journal is a triumph for Open Access, and I think he’s right, there. Even in the short 15 or so years that I’ve been an active researcher, the internet has transformed me from a troll at the library copy machine into a blasé, and heavy, consumer of online PDFs. As befits one of the driving personalities behind PLoS, he says a great many sensible and worthwhile things about the new journal in his blog article. But I do think he overstates the potential impact on peer review. In his article, Eisen identifies three key areas of peer review that this new journal wants to shake up:

1) Rapid review and turnover: I think there’s a realistic chance, particularly with a financial incentive, of encouraging scientists to prioritise reviews for this journal, reducing turnaround time. And if there’s a flat payment to the reviewer per manuscript reviewed, then there’s no perverse incentive to cycle through rounds of revision. I think this will work, but I do share Eisen’s worry that uncompensated review requests from other bodies could come somewhat down the list of Things To Do Today, as a result.

2) Fewer demands for changes and additional experiments: The press release from the funding bodies states their desire to limit reviewers’ calls for more work. But really, if a piece of work is unconvincing because it lacks a key experiment, then that’s the fault of the work and not the fault of the review process. A competent peer review process would bounce the manuscript until the supporting evidence is provided. All that an editorial policy of fewer requests for changes and experiments can do is either accept a manuscript with insufficient support and so dilute journal quality, or reject at an earlier stage in the process.

3) Arbitrary editorial decisions on the grounds of sexiness: The new journal will have an editorial team of experienced, active scientists, rather than “junior scientists who are no longer active researchers”. This is quite obviously a pointed comment about the editorial composition of publications such as Science and Nature, rather than fair comment about scientific publication on the whole. Most journals I deal with have editorial and review boards comprising active researchers, and I believe that outside the usual extremely high-impact suspects, it is the norm to have an editorial panel of experienced, active scientists. I don’t see this policy being particularly ground-shaking.

Where I think that the new journal will shake up peer review is in its intent to publish reviewers’ comments publicly, but anonymously. This cuts both ways: authors will no longer be able to “get away with” ignoring potentially serious criticisms from a minority reviewer, unnoticed, after publication; But nor will poor or unreasonable reviewers be able to hide behind the opaqueness of the current review process. If readers can comment on or rate the quality of reviews, as well as papers, honest and insightful reviewers could be rewarded at the expense of the half-hearted and overly pedantic.

But I do have one serious criticism, which comes not from being a scientist, but instead thinking about how the public sees science.

In recent times, public trust, or rather the lack of it, in science as a human endeavour has been exemplified by the events of ClimateGate, and European attitudes towards genetic modification. Popular media presentation of difficult ethical issues in science is, well, difficult, and it’s useful in the face of criticism to be able to fall back on demonstrable claims of the independence of results from financial inducements, and the anonymity and stringency of peer review in journals that are disinterested in the outcome of our work. And that is where I think the new journal risks offering an easy target to those who would seek to undermine public confidence in science.

In 2009, it was revealed that the publisher Elsevier had been paid by the pharmaceutical company Merck, Sharp and Dohme to “produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles–most of which presented data favourable to Merck products” : The Australasian Journal of Bone and Joint Medicine. Intuitively, suspicions of vested interests can be expected to arise where there is no obvious and transparent independence in the chain that links the funder of research to the lab that carries out that research, and to the journal that publishes it. Even PLoS Medicine‘s policy on research funded by tobacco companies perpetuates this common perception that, unless the source of funding can be decoupled in some way from the outcome of research, and ‘review’ for publication, then publication amounts to little more than advertising.

When a piece of work is carried out by scientists funded by body X, reviewed by scientists funded by body X (who are even paid to review the paper by body X), and published in a journal bankrolled by body X, this intuitively looks like self-publication or advertising by body X. Where ‘body X’ is “Big Tobacco”, or “Big Pharma”, the conflict of interest is so self-evident that it has become a cliché. When ‘body X’ is “HHMI/Wellcome/MPS”, as a scientist I recoil at the potential association of such respected investors in science with cheap and shady practices. I don’t have any doubt that, as the journal’s press release states, the “editorial team will be editorially independent of the funders”, and that all published manuscripts will be competently assessed and of the highest quality. But from the point of view of those outside the circle of science, there is always an option to suggest sleight of hand, however ethically clean the journal is. Without independence and transparency in the cycle of funding and publication, we risk delivering an opportunity for slander into the hands of those who would undermine science for political goals.

DISCLAIMER: L.P. adds that the views represented here are his own, and do not reflect those of his employer, or those of any other of his professional affiliations.