I have written about the Journal of Serendipitous and Unexpected Results before and now this just popped in my inbox from JSUR’s Google group. Apparently JSUR is now open for business.

JSUR Call for Participation

Submit your short (2-4page) and full length manuscripts to the Journal
of Serendipitous and Unexpected Results.

Over the past month we’ve received a great amount of press and
publicity for the Journal of Serendipitous and Unexpected Results
(JSUR). Thanks to everyone who helped spread the word, please keep it
up!

In Richard Feynman’s 1966 Nobel Lecture, he said, “We have a habit in
writing articles published in scientific journals to make the work as
finished as possible, to cover up all the tracks, to not worry about
the blind alleys or describe how you had the wrong idea first, and so
on. So there isn’t any place to publish, in a dignified manner, what
you actually did in order to do the work.”

We’re writing to invite you to solicit short (2-4page) and full length
submissions to JSUR.  Why not prepare a 2-4 page writeup discussing
side-investigations, alleyways, or false-starts in your latest
published or unpublished research? Papers of this length place a
minimal burden on the authors, while providing extremely valuable
research insights to a broad audience.

Journal website: http://www.jsur.org

Sincerely,
The JSUR Editorial Board

The most exciting phrase to hear in science, the one that heralds new
discoveries, is not ‘Eureka!’, but ‘That’s funny…’ -Isaac Asimov

Thanks to Ruchira Datta for pointing out this one.

Science is many things to many people, but any lab-rat will tell you that research is mainly long stretches of frustration, interspersed with flashes of satisfying success. The best laid schemes of mice and men gang aft agley. A scientist’s path contains leads to blind alleys more than anything else, and meticulous experimental preparation only serves to somehow mitigate the problem, if you’re lucky. This doesn’t work, that doesn’t work either and this technique worked perfectly in Dr. X’s lab, why can’t I get this to work for me?  My experiment was invalidated by my controls; my controls didn’t work the way the controls were supposed to work in the first place. I keep getting weird results from this assay. I can’t explain my latest results in any coherent way… these statements are typical of daily life in the lab.

This stumped and stymied day-to-day life is not the impression of science we get from reading a research paper, when listening to a lecture, or when watching a science documentary show. When science is actually presented, it seems that the path to discovery was carefully laid out, planned and  flawlessly executed, a far cry from the frustrating, bumbling mess that really led to the discovery. There are three chief reasons for the disparity between how research is presented, as opposed to what really goes on. First, no one wants to look like an idiot, least of all scientists whose part of their professional trappings is strutting their smarts. Second, there are only so many pages to write a paper, one hour to present a seminar or one hour for a documentary: there is no time to present all the stuff that did not work. Third, who cares about what didn‘t work? Science is linked to progress, not to regress. OK, you had a hard time finding this out, we sympathize and thank you for blazing the trail for the rest of us. Make a note for yourself not to go into those blind alleys that held you back for years and move on. We’re not interested in your tales of woe.

Only maybe these tales of woe should be interesting to other people. If you make your negative results public, that could help others avoid the same pitfalls you had. If you share the limits of a technique, a protocol or software then someone can avoid using it in a way that does not work. A lab’s publications are actually the tip of the sum total of its accumulated knowledge.Every lab has its own oral tradition of accumulated do’s and dont’s. Not oral in the literal sense: they may even be written down for internal use, but never published. UPDATE (2-FEB-2010): most peer-reviewed journals don’t like stuff that does not work. Thanks to Mickey Kosloff for pointing out the Journal of Negative Results in Biomedicine and The Journal of Negative Results – Ecology and Evolutionary Biology.

Until now.

The Journal of Serendipitous and Unexpected Results aims to help us examine the sunken eight-ninths of the scientific knowledge iceberg, in life science and in computer science. (So an additional field over JNRB and JNREEB). From JSUR’s homepage:

Help disseminate untapped knowledge in the Computational or Life Sciences

Can you demonstrate that:

* Technique X fails on problem Y.
* Hypothesis X can’t be proven using method Y.
* Protocol X performs poorly for task Y.
* Method X has unexpected fundamental limitations.
* While investigating X, you discovered Y.
* Model X can’t capture the behavior of phenomenon Y.
* Failure X is explained by Y.
* Assumption X doesn’t hold in domain Y.
* Event X shouldn’t happen, but it does.

The problem with the JSUR model, and the nature of discovery

I expect JSUR will be a great way to comment on  methods and techniques. Indeed it will codify a trend that has been going on for some time: public protocol knowledge sharing. Many sites like openwetware,  seqanswers or the UC Davis bioinformatics wiki have been doing this for a while. Not to mention a plethora of blogs. Scientists are willing to share their experience with working protocols and procedures, and if this sharing of knowledge can be now monetized to that all-important coin of academia, the  peer-reviewed publication, all the better.

So where is the problem? The problem lies with discovery, and credit given towards it. It would be very hard to get anyone to share awkward, unexpected or yet-uninterpreted results. First, as I said, no one wants to look like an idiot. Second, unexpected or yet uninterpreted results are often viewed as a precursor to yet another avenue of exploration. A scientist would rather pursue that avenue, with the hope of  the actual meaningful discovery occurring in the lab. At most, there will be a consultation with a handful of trusted colleagues in a closed forum. If the results are made public, someone else might take the published unexpected and uninterpreted results, interpret them using complementary knowledge gained in their lab, and publish them as a bona-fide research paper. The scientist who catalyzed the research paper with his JSUR publication receives, at best, secondary credit. The story of Rosalind Franklin’s under-appreciated contribution to the discovery of the structure of DNA comes to mind. Watson and Crick used the X-ray diffraction patterns generated by Franklin to solve the three dimensional structure of the DNA molecule. Yet she was not given a co-authorship on the paper. (And she did not even make the results public, they were shared without her knowledge.) Unexpected results are viewed either as an opportunity or an embarrassment, and given the competitive nature of science, no on wants to advertise either: the first due to the fear of getting scooped, the second for fear of soiling a reputation. I expect JSUR would have a harder time filling in the odd-results niche, but I hope I am wrong.

But if you have protocols you are willing to share…what are you waiting for? Get those old lab notebooks, 00README files, forum posts  and start editing them to a paper. You are sitting on a goldmine of publishable data and you did not even realize it.

Finally, here are two scientists who never declined sharing their unexpected results.

This post has been slashdotted. Exercise extreme caution.

A  small spike on my blog traffic yesterday led me to look for the source via Google Analytics. (If you are a blogger, you should really use this tool, lots of useful traffic information.) Seems like most of the traffic came from the page of a high school science teacher at Badin High School in Hamilton, OH. Apparently the students were to be quizzed today on two of my posts about endosymbiosis (and one from 80Beats; I’m in good company.) So they were very busy Sunday. It’s encouraging to know that some of my posts are accessible enough for high school science. Finally, quite a few Miami students come from Hamilton (we’re close). So I might see some of them next year.

Muahahaha!

Today is the 366th birthday of Sir Isaac Newton. Formulator of the three laws of motion, the theory of gravity, inventor of the first reflecting telescope, theory of color, calculus (with due credit to Gottfried Leibniz), the generalized binomial theorem, and president of the Royal Society.

Newton in a 1702 portrait by Godfrey Kneller

All which ties in directly to retail, and biodiversity. Huh?

Co-operative Farms (UK) recently bought 1,000  rare and endangered apple varieties, with colorful names like Great Expectations, Fairie Queen, Northern Spy, Forty Shilling, Duck’s Bill and Bloody Ploughman. (I wonder how the last name came to be; actually, maybe I shouldn’t.) This also includes Isaac’s Newton’s Tree: the apple variety cultivated from the descendants of the tree which inspired Newton to formulate the Theory of Gravity. Many of those apples were dessert apples, but some fell out of favor the strains were no longer grown, threatening to disappear.

Co-op Farms are bottling them up as the “Truly Irresistible Tillington 1,000″ pressed apple juice. I think it is great that a retail chain is funding crop diversity and finding a way to make some money in the process. Although with 7,500 cultivars worldwide, apples as are not exactly under an extinction threat. But there is also the matter of food variety, cultural heritage and, of course, preserving the history of physics. Or bottling it up, whichever the case may be.

Also, fruit, including apples, are important in the small-arms industry:

Here’s a really cool work, published this September in Nature.. Why did I choose this work?  Well, it’s a major discovery, and it’s all done using bioinformatics, and fairly simple bioinformatics at that. The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and how to look for it.

Obviously not CC licensed, but I couldn't resist using this very appropriate strip

Viruses as a bacterial genetic mechanism

Viruses follow some interesting and sometimes convoluted evolutionary paths.  One is “infect quick, reproduce fast, and make sure you can get to the next host before you kill this one”.  That is pretty extreme: smallpox was doing that, when there was smallpox. Ebola is doing that, but not very well: killing the host too quickly means that the disease is contained, especially in rural areas. Another strategy is: “slow and easy wins the race”. The herpes virus does that. Not lethal, but laying dormant in the central nervous system, it is  infectious, but rarely causes anything more than they occasional cold sore (which admittedly, is painful and disturbing). Still, it manages to infect up to 90% of the human population, most of which are completely unaware they harbor it, and would never develop any symptoms.

Most of the viruses on earth don’t infect humans, nor animals, nor plants. They infect microbes, where the same spectrum of evolutionary strategies applies. Some attack quickly, killing the microbial population they infect. Other can remain dormant for a long time. It is becoming clear to us that bacterial viruses or bacteriophages, are responsible for a large portion, if not the majority, of genetic variance in bacteria. In fact, viruses are a major component in bacterial genetics. The mechanism is called transduction, and it is illustrated below. Bacteriophages pick up DNA from bacteria they infect, and transfer it to other bacteria, creating genetic variance in the bacterial population.

Generalized transduction. Source: Indian River State College

Viral transduction also adapts

But viral transduction does not just carry random genes. Natural selection favors transduced genes that increase the bacterial host’s fitness. Because when a bacteria is infected by a virus, its protein making machinery is used to make viral genes. But when the viral genes include genes that are beneficial to the host as well, then everybody wins: the phage-infected bacterial species gets genes which enable it to compete better for resources with other bacterial species, while the phage gets a larger number of hosts to infect. Of course, this has to go hand in hand with a relatively benign virus that remains dormant long enough to let the bacterial host species enjoy the benefits of the transduced genes.

Such is the case of cyanophages and cyanobacteria. Cyanobacteria are photosynthetic bacteria, and cyanophages are the viruses that infect them. Several studies have shown that cyanophages have acquired whole photosynthetic genes from bacteria. Viruses do not photosynthesize, but when they infect cyanobaceria, the viral photosynthetic system is added to the bacterial one, boosting bacterial photosynthetic activity and ultimately increasing bacterial energy production.

The photosynthetic mechanism is  divided into two components: photosystem I and photosystem II (PSI and PSII). For a few years now, PSII has been known to be transduced by cyanophages.

A  more recent study by Itai Sharon and colleagues published in Nature this September shows that PSI proteins are also tranduced by cyanophages. Also, it seems like the viral PSI has some interesting properties that may make it advantageous over the cyanobacterial PSI. Two proteins in the bacterial PSI are called PsaJ and PsaF.  They found that the homologous protein in cyanophages is a fusion of the two, PsaJF. When they modeled an insert of PsaJF into the bacterial photosystem I it seemed that the bacterial PSI with the viral insert can now function more efficiently than the the original bacterial PSI. As a rule, PSI is a system that accepts electrons from PSII via a protein called plastocyanin. The donated electrons are excited by light, and the energized electrons are used to synthesize ATP and NADPH, the energy coinage of the cell, which are used to synthesize sugar from CO2. However, when the bacterial PsaJ and PsaF are replaced by the viral compound PsaJF, it seems like plastocyanin does not have to be the only electron donor to the newly minted virally-donated PSI. This means that the PSI may now accept electrons not only from plastocyanin, but from other electron-carrying proteins as well. Such proteins that are involved in the respiratory system, for example, which also donate electrons. The advantage of such a setup is that electrons whose reducing power would otherwise go to waste, got through PSII for formation of extra NADPH and ATP. Sharon and colleagues do not prove all this experimentally, but they make a pretty strong case, citing some analogous cases.

Electron transport from PSII to PSI via plastocyanin. Source: wikimedia commons.

a, The structure of T. elongatus PSI (subunits) was illustrated by PyMOL (http://pymol.sourceforge.net/) using a PSI monomer (adopted from Protein Data Bank (PDB) accession 1jb0). PsaF is in magenta, PsaJ is in blue, and all of the other subunits are in green. b, A model for the structure of the viral PsaJF fusion protein (red) substituting the original PsaF and PsaJ subunits. Reproduced under NPG Licensing terms for non-commercial / educational purposes. doi:10.1038/nature08284

Like I said,  this work is purely bioinformatics. They basically mined the Global Ocean Survey metagenomic data, over six million sequences from marine microbes collected by the J. Craig Venter Institute which I mentioned in another post. They then identified sequences that contain PSI genes, and sifted through those to find sequences that also contain genes that are exclusively viral. Having both a PSI gene and a viral gene on the same DNA clone ensures they were taken from a virus. I’m not sure how they did the structural modeling and insertion of the PsaJF. This seems to be missing both from the Nature article, and the supplementary material. Yes, it’s one of those Nature works with 3 pages of article, and 28 of supplementary. Great read though, there’s treasure everywhere.

Lindell, D., Jaffe, J., Johnson, Z., Church, G., & Chisholm, S. (2005). Photosynthesis genes in marine viruses yield proteins during host infection Nature, 438 (7064), 86-89 DOI: 10.1038/nature04111

Warren DeLano passed away suddenly and at a young age at his home Nov 3, 2009. He was the author of PyMol, a very popular molecular visualization program, and a strong advocate of open source software. The family of Warren Lyford DeLano has created a “In Memorium” page and blog. Also, a memorial award is being set up in his name, as per this email circulated on various mailing lists.

Dear friends and colleagues:

It’s now been over a week since Warren has passed away.  We are trying to
move toward a permanent way to honor Warren’s memory and what
he stood for: Open Source Computational Biosciences and molecular
visualization. To do this, Jim Wells and I put together a mission statement
with the approval of Warren’s family:
The Warren L. DeLano Memorial Award for Computational Biosciences

This award shall be given to a top computational bioscientist in
recognition of the contributions made by Warren L. DeLano to creating powerful
visualization tools for three dimensional structures and making them freely accessible.
The award, accompanying lecture, and honorium will be given annually in the context of a
national bioscience meeting or a Bay Area gathering of
computational bioscientists at Stanford, UCSF or UC Berkeley. For the award special emphasis
will be given for Open Source developments and service to the bioscience community.
The award selection committee, consisting of experts in the computational and
biological sciences, will accept nominations from anyone.
To make something like this happen in perpetuity would take about ~100K for
the endowment.

For donations, Warren’s family has set up a tax deductible fund:

Silicon Valley Community Foundation
memo:  Warren L. DeLano Memorial Fund
2440 West El Camino Real, Suite 300
Mountain View, CA 94040
tel: 650.450.5400

We hope that you’ll consider making a contribution (not matter
how small) in Warren’s honor.  Also, please forward this message
to anybody who might be able be willing to contribute.

Best regards,
Axel

Axel T. Brunger
Investigator,  Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University

This has been a topic of discussion since I was in grad school: when will the Nobel prize for the structure of the ribosome be finally awarded? Well, it finally has. Ada Yonath, Thomas Steitz and Venkatraman Ramakrishnan received the Nobel for work that has spanned three decades and an equal number of continents.

First, a victory dance:

Next, the scientific background:

And part of Ada Yonath’s model in this clip:

And the winners are…

Title:	2009 Nobel Prize in Physiology or Medicine
Description:	"Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak for the discovery of 'how chromosomes are protected by telomeres and the enzyme telomerase'

Yup, it’s those two weeks again, when that prize is being announced.  Sadly, BsB probably will not get it this year. Might have something to so with there being no category for blogging.

Credit: wikimedia commons

Prestige and controversy go hand in hand, mix in science and you have a concoction more explosive than the one Mr. Nobel himself invented. Who won, who didn’t win  and which achievement was never recognized.  This week’s BsB’s poll asks: which category would you add to the Nobel prize? Feel free to mark “other” and add your own in the comments.

Credit: wikimedia commons

By the way, Alfred Nobel’s wife did not sleep with a mathematician. That is not the reason why there is no Nobel prize in math. Get real.

Also, it might be a good idea to remember the spirit in which Nobel wanted the prize to be awarded:

The capital shall be invested by my executors in safe securities and shall constitute a fund, the interest on which shall be annually distributed in the form of prizes to those who, during the preceding year, shall have conferred the greatest benefit on mankind. The said interest shall be divided into five equal parts, which shall be apportioned as follows: one part to the person who shall have made the most important discovery or invention within the field of physics; one part to the person who shall have made the most important chemical discovery or improvement; one part to the person who shall have made the most important discovery within the domain of physiology or medicine; one part to the person who shall have produced in the field of literature the most outstanding work of an idealistic tendency; and one part to the person who shall have done the most or the best work for fraternity among nations, for the abolition or reduction of standing armies and for the holding and promotion of peace congresses.

A bit late in the day, but here are the Ig Nobel prize winners for 2009. Cut and pasted from Wikipedia. The prizes were awarded Thursday, Oct. 1, 2009 at
Sanders Theater, Harvard University, Cambridge, Massachusetts

At the 2009 ceremony, Public Health Prize winner Dr. Elena Bodnar demonstrates her invention — a brassiere that, in an emergency, can be quickly converted into a pair of face masks, one for the brassiere wearer and one to be given to some needy bystander. She is assisted by Nobel laureates Wolfgang Ketterle (left), Orhan Pamuk, and Paul Krugman (right). PHOTO: Alexey Eliseev. Source: improbable.com

2009

• Veterinary medicine: Catherine Douglas and Peter Rowlinson of Newcastle University, UK, for showing that cows with names give more milk than cows that are nameless.
• Peace: Stephan Bolliger, Steffen Ross, Lars Oesterhelweg, Michael Thali and Beat Kneubuehl of the University of Bern, Switzerland, for determining whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle.
• Biology: Fumiaki Taguchi, Song Guofu and Zhang Guanglei of Kitasato University Graduate School of Medical Sciences in Sagamihara, Japan, for demonstrating that kitchen refuse can be reduced more than 90% in mass by using bacteria extracted from the feces of giant pandas.
• Medicine: Donald L. Unger of Thousand Oaks, California, US, for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand but not his right hand every day for more than 60 years.
• Economics: The directors, executives, and auditors of four Icelandic banks — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa (and for demonstrating that similar things can be done to an entire national economy).
• Physics: Katherine K. Whitcome of the University of Cincinnati, Daniel E Lieberman of Harvard University and Liza J. Shapiro of the University of Texas, all in the US, for analytically determining why pregnant women do not tip over.
• Chemistry: Javier Morales, Miguel Apatiga and Victor M. Castano of Universidad Nacional Autonoma in Mexico, for creating diamond film from tequila.
• Literature: Ireland’s police service for writing and presenting more than 50 traffic tickets to the most frequent driving offender in the country – Prawo Jazdy – whose name in Polish means “Driving Licence”.
• Public Health: Elena N. Bodnar, Raphael C. Lee, and Sandra Marijan of Chicago, US, for inventing a bra that can be quickly converted into a pair of gas masks – one for the wearer and one to be given to a needy bystander.
• Mathematics: Gideon Gono, governor of Zimbabwe’s Reserve Bank, for giving people a simple, everyday way to cope with a wide range of numbers by having his bank print notes with denominations ranging from one cent to one hundred trillion dollars.

Open Notebook

Credit: hippie on Flickr

What is it? Open Notebook means “no insider information” You lab notebook is on a wiki, out there for everyone to see. Negative results & all.  You share your research process with the world as you go along. There are many shades to this process: you may share some of your data, edit it, sanitize it… but he general idea holds, that you share a major part of your data, methods and thoughts prior to the official publication.

Why doesn’t it work? Social and cultural reasons.  A basic tenet of science culture is that competition breeds quality and innovation.  Researchers need to pass a series of competitive thresholds to be able to continue and expand their research: secure a position to be able to start your independent research, compete for a grant to fund it (at a 10-15% funding rate in the US for biomedical research), compete for more grants so one can fund an expanding vision of one’s research, pass a threshold to receive tenure (or rather, not get fired after 6 years). In places with no tenure, pass periodic reviews. Search committees, grant review panels and tenure / periodic review committees judge a scientist by the number of publications, their innovation, how attributable they are to his group as opposed to the collaborating groups and how much impact they carry in the field. Of course the $$$ brought in by grant overheads.  To reach a truly innovative leap in research,  there is a period when you have to play your cards close to the chest, sharing your findings only with your lab, your collaborators and trusted colleagues. Revealing findings too early will get you scooped by a better equipped lab,  or at best dilute the innovative impact: your open lab notebook wiki can and will be construed as a prior publication.

Taking openness and collaboration to the extreme, if you put your notebook on a wiki, and your field is “hot” enough, you can be sure someone will use those ideas to their own benefit, very likely at your expense. It need not be malign: they could make an intuitive leap of reasoning reading your notebook before you can.  Even if they are honest and generous enough to credit you by co-authorship, how much of the innovation would be attributed to you?  And if you receive less credit for research innovation than you could, that would lower your evaluation score at whatever career stage you are in. By and large, this culture does not appear to be changing. The need to be identified with a certain type of research you can call “your own” and the need to innovate trump those collaborations that, in the eyes of your peers and evaluators, only serve to dilute your achievements.

Therefore, in the foreseeable future, I believe that the Open Science vision will be limited to non-competitive  endeavors that don’t have potential for high-impact research papers down the line. Those usually have more to do with tool and technology development rather than innovative research. That is actually a great thing: at least open-notebook science enables protocol, tool and software development more quickly. But anyone who has been involved with Free and Open Source Software has known that for three decades or more.

Different disciplines in science have different cultures. The biomedical field is known to be especially competitive.  Also, the field is going through very fast changes. I am referring to this field. I realize that things are different in physics, for example, where pre-publication of results is encouraged and credited. All the more proof that openness, or lack of it,  is a cultural issue, rather than inherent in academic research.

What does work? Collaborative technologies: wikis, blogs, discussion forums are great for publicizing oneself  (HEY!),  asking general questions about one’s methodologies, protocols, howtos, software or equipment. OpenWetWare is an example of such a success story for the experimental biology community, being a central repository for protocols and general lab how-tos. But the lab notebooks section only contains a handful of notebooks, most of them out of date. Social bookmarking like Delicious or specialized social bookmarking  like citeulike are catching on, maybe a bit slower than expected. Wikis (not open ones) are great for internal lab management as well, as more labs are discovering.

The free and open source software culture, where one is free to modify and distribute software so licensed,  has enabled new feats in scientific computation infrastructure by leveling the playing field so that anyone can use, modify and re-distribute software. In a similar vein,  grid technologies are leveling the field of computational power and hardware. Publications like PLoS-ONE, which accept research based on scientific rigor rather than innovation leaps and “exceptional interest” have filled the gap necessary to communicate research that is of interest, yet will not be accepted to journals demanding an innovative edge. Freely available data, post-publication, makes it easier to validate research by third parties, and build upon it. And of course, Open Access which makes publications available to all: not only to read, but to further publicize.

For another view that advocates a change in scientific culture that will make Open Science part of the academic incentive structure, just as publications are today, read here.

Community annotation

Credit: victoriapeckham Flickr

What is it? Genomics has become a data rich science. The deluge of genomes and metagenomes are to be too much to handle for a group of curators. The idea some genomic database maintainers have come up with is borrowed from the success of Wikipedia. If enough users would come in to annotate their favorite genes, we will eventually end up with a comprehensive collection of annotations for most if not all genes in a sequenced genome. If  ths system is good for Wikipedia entries, why not for genes?

Why doesn’t it work?

Why would anyone expect—or even worse, depend on—a community annotation effort? Imagine investing millions of dollars into state-of-the-art sequencing facilities, and then expecting volunteers from the community to stop by and run the sequencing machines. One might argue that this analogy is not valid because running a sequencing facility requires well-trained personnel, standardized protocols, clear procedures, quality controls and, most of all, tight coordination. Yet, the same professional standards are required for data curation, and it is precisely these aspects that are rarely achieved through a community contribution approach. Community annotation should be encouraged and facilitated, but the curation of biological data cannot depend solely on volunteer work. High standards and quality implies professionalism, and this, in turn, requires investing in dedicated professionals. Until this is done, data curation—and consequently the whole field of microbial genomics—will not move beyond the amateur stage.

Nikos Kyrpides Nature Biotechnology 27, 627 – 632 (2009)

What does work? The failure of community based annotations has brought the often overlooked but crucial activity of biocurators into the limelight. Recently, the International Society for Biocuration was formed. From the mission statement:

Strong support from the research community, the journal publishers, and the funding agencies is indispensable for databases to continue to provide the valuable tools on which a large fraction of research vitally depends. Structured ways for biocurators and associated developers to increase the sharing of tools and ideas through conferences and high quality peer-reviewed publications need to be developed. This will improve data capture, representation, and analysis. Secondly, biocurators, researchers and publishers need to collaborate to facilitate data integration into public resources. Researchers should be encouraged to directly participate in annotation. This will lead to improved productivity and better quality of published papers as well as stronger integrity of the data represented in databases. Thirdly, funding agencies need to recognize the importance of database for basic research by providing increased and stable funding. Finally, the recognition of biocuration as a professional career path will ensure the continued recruitment of highly qualified scientists to this field, which benefits the wider world of biomedical sciences.

– http://www.biocurator.org/mission.shtml

So it’s back to expert handling of data, perhaps with some community assistance. This goes back to the attribution problem discussed above: in the current culture, there is hardly any career-building attribution to community annotations. For true community involvement, this would need to change. At the same time, biocuration needs to be recognized as a valid and important career path.

Virtual Conferences

Credit: NASA

What is it? Why pay over $2000 for an international conference, suffer through delayed flights, lost baggage, forgotten poster tubes, jet lag, overpriced meals and hotels (“conference discount” my a$$), sweaty poster sessions and tight-fisted finance admins when you finally get home and try to get reimbursed (phew!) — when you can attend a conference using webcasting in the comfort of your home for a fraction of the price if not for free?

Why doesn’t it work? First: virtual conferencing technology sucks. It doesn’t matter if you use a free Skype on a $150 netbook, or a state-of-the art teleconferencing equipment with a 52″ screen and Dolby Surround, piped through at hundreds of Gigabits per second. You will get interruptions, cuts, lags, annoyances and embarrassing moments.  Second: social reasons. The important parts of a conference take place in the hallways, poster sessions, meals, banquets and, of course, the pub across the street. Incipient collaborations, exchange of ideas, brainstorming: all those take place around the dinner table and in the halls. With food, coffee and alcohol providing the social lubrication, and the talks and posters the intellectual one. A conference is much more than a series of talks.

To summarize: until we reach a level of virtuality akin to that of the Star-Trek holodeck, or at least something that manages to sync picture & sound without one or the other dropping every 3 minutes, we have no choice but to continue taking off our shoes and belts in front of  uniformed strangers.

What does work? live and archived webcasts can be an acceptable substitute to the lecture part if you could not make it to the meatspace meeting. Although you probably will not spend the time at home watching all the webcasts of all the keynote speakers you would have gone to in the conference. Microblogging is emerging as a time-saving device for those who were not there: you don’t need to devote 45 minutes to read a microblog from that talk you really wanted to attend. Done properly, perhaps with the speaker’s slides shared somewhere, it is less time consuming than watching a day’s worth of webcasts. And you can filter your interests using the microblogging notes taken by your colleagues, posted on friendfeed or such. No substitution for the real deal, which is shmoozing in the hallways. But at least you’ll get an idea about the latest & greatest in research in your field.

This is not to say that the Internet obviates socializing and work collaborations, quite the opposite of course.  Most of my collaborators are time zones away from me, and I use email, chat, wikis, Googledocs, and even (shudder) Skype conference calls for working with them. But the experience of a critical mass of people meeting for real and getting things done in a very short space of time has yet to be  duplicated by technological means.

The “End of Theory” science

What is it? I am referring to the Wired article penned by Wired’s editor-in-chief, Chris Anderson last  year. It generated a large response, and a resounding echo of “me too” and  “he’s so right” articles and blog posts.   The  message of this article was that with such a deluge of data in the natural scientists, scientists can stop going through the “hypothesize, model, test” cycle. Rather, they can simply look for statistical correlation and draw conclusions from them.

Why doesn’t it work? Because it was wrong from the get-go. I don’t think any serious scientist ever went through the cycle Anderson superficially outlined.  He neglected to prefix the “observe” phase to “hypothesize, model, test”. Observation – a.k.a. data collection is the foundation to whatever comes after. Scientists first observe, then if enough observations are made that seem to fit a certain trend, they formulate one or more hypotheses. Those are tested, and the hypotheses refined or discarded based on test results. Finally, some model may or may not emerge.  In any case, the empirical process of research is more of an “(1)observe,  (2)hypothesize, (3)test, (4)observe again, (5)retest, (5)correct hypothesis,(6) bumble through previous 5 stages for quite a while, if you’re lucky you may have a (6)model”. This is the way science is done regardless of whether you have  20 data points or 20 trillion. There are, of course, qualitative differences to large quantities of data: methods of observation and sifting through data become rather different, technology starts playing a major role: you really need that computer cluster power (see also above, on community annotation). It does not preclude the need to go through the previous stages, even more carefully than you have done with 20 data points.  In the end, science is about providing explanations for observed phenomena, and that is what a model is: an explanation, the best we can come up with at this time. If you don’t have hypotheses, models and theories you don’t have science.

What does work?

Hoffmann, R. (2008). A wiki for the life sciences where authorship matters Nature Genetics, 40 (9), 1047-1051 DOI: 10.1038/ng.f.217

Sagotsky, J., Zhang, L., Wang, Z., Martin, S., & Deisboeck, T. (2008). Life Sciences and the web: a new era for collaboration Molecular Systems Biology, 4 DOI: 10.1038/msb.2008.39

5. Question: “You know, our group has been working on this for a long time, and we found that…”

Really means: “How come you got invited to talk about this and not I?”

4. Question:  “Have you tried using Y instead of X?”

Really means: “We are doing the same thing using Y, since we can’t afford to use X on our budget. But we haven’t had results in the past two years, and you totally scooped us. Is there any way we can actually get results using Y?”

3. Question: “So where do you think this work is going?”

Really means: “I was just scratching my head, and the microphone runner thought I was raising my hand and handed me the mike.  Now that I actually have the mike, I might as well ask something”.

2. Question:  “You know, I was just talking about this recently with Bigshot1 and Bigshot2, and they said that…”

Really means:  “Hey, look at me!  I’m important enough to have engaged both Bigshot1 and Bigshot2 together in a conference. (They couldn’t get away because it was the conference dinner with free booze).”

1. Question:  “It seems that this whole field of…. is filled with very exciting prospects. We have been looking into…. and Bigshot3 has recently published in Science….(3-4 minutes more in the same vein)  so my question is: what are your thoughts?”

Really means: “Muahahaha. By hijacking Q&A time, I got to present at this conference even though I was not invited to. Sucks to the Program Committee”

Attendees at the CXXXVII Symposium on Whatever

When I say here “scientific websites”, I am not referring to education sites, science blogs, or scientific journal web sites. I am talking about sites scientists use for their day to day research. Sites like Entrez, EBI, FlyBase, ExPasy, PDB etc. The sites I just mentioned I deem quite virtuous, but there are many sinful sites out there. We all run into them, some of us are guilty of them at one time or another, as no-one is without sin   Sinful sites will drag you into the hellfire of obscurity, whereas virtuous sites will earn you the heaven of peer recognition, citations, and perhaps even some funding.

The Seven Deadly Sins:

1. Lust:   “form over function”: beautiful site design, lovely widgets, gadgets, interactive semi-transparent whachamallits but how exactly do I work this application? Where is the application?

2. Gluttony: stuffing my browser with Javascript code until it chokes and grinds to a halt.

3. Greed: lock your application, do not provide the source code. Also, if you want to make your site a paysite, fine. But if it’s free, (and definitely if it is paid) please keep it down to two  Google ads and one banner. If I see to another Flash drop-down  I will go away and never come back.

4. Sloth: Not updating your reference databases, not maintaining your code, broken links.

5. Wrath: not providing documentation to your application; not answering query emails (or worse, giving a half-hearted response).

6.  Envy: not designing your web site with an an API in mind. If you site is good and useful, don’t force your user to click their carpal tunnel into oblivion. Let them be able to write code to better use your site as a web-service. Throttle incoming traffic if you must, but let it come in.

7. Pride: not being able to take criticism, and make appropriate changes based on users’ comments. Also, a soul-sucking registration followed by too many emails.

The Seven Heavenly Virtues:

1. Chastity: a lean website. Minimal to zero use of Google web toolkit, Java applets, and other flashy yet often useless bells & whistles.

2. Temperance:  fast applications, with a load well split between server and browser.

3. Charity: open source you applications. Provide a downloadable, standalone version of your WWW application under an OSI open source license.

4. Diligence: maintain your code. Run periodic application checks to see that everything works. Don’t wait for the users to inform you of a crash or a bug. Keep  as close as possible to the latest version of your scripting language, web interface, OS, server software and DBI.

5. Patience: Take time and effort to document your web site and standalone applications well.  Make sure you answer all query emails within 24 hours, even if  your answer is “sorry, busy now.. please hold on another day”.

6. Kindness: Provide APIs and dynamic URLs,  so your site can be used as a web service. Document al URL formats, and API toolkits. Make sure error messages are meaningful. If you need to throttle traffic, advise users of the traffic throttling policy.

7. Humility: remember, those using your website are the best judges of its usefulness to them. Leave a clearly marked contact email for comments. Read those comments, and act on them.

Photos from [klf]photography on flickr under CC/attribution/non-commercial

Hypatia, detail from "School of Athens" (1510) by Raphael Sanzio. CC Wikimedia Commons

Hypatia  (b. ~360CE  d. 415CE) was a mathematician, philosopher, astronomer and teacher in Roman Alexandria. She was also quite probably the last librarian of the famous Library of Alexandria. Note that at the time, the definition of Philosophy was much broader, and encompassed what we term today the natural and exact sciences; and yes, she was also a techie. She is credited with inventing the hydrometer, for measuring the specific gravity of liquids.

In a time of political turmoil, she appeared to have supported the secular authority Prefect of Rome, Oresteus against the Pope of Alexandria, Cyril. Eventually, this cost her her life. Socrates Scholasticus (Socrates of Constantinople), a 5th Century Christian Church Historian wrote in Historia Ecclesiastica:

Chapter XV.–Of Hypatia the Female Philosopher.

There was a woman at Alexandria named Hypatia, daughter of the
philosopher Theon, who made such attainments in literature and science,
as to far surpass all the philosophers of her own time. Having
succeeded to the school of Plato and Plotinus, she explained the
principles of philosophy to her auditors, many of whom came from a
distance to receive her instructions. On account of the self-possession
and ease of manner, which she had acquired in consequence of the
cultivation of her mind, she not unfrequently appeared in public in
presence of the magistrates. Neither did she feel abashed in coming to
an assembly of men. For all men on account of her extraordinary dignity
and virtue admired her the more. Yet even she fell a victim to the
political jealousy which at that time prevailed. For as she had
frequent interviews with Orestes, it was calumniously reported among
the Christian populace, that it was she who prevented Orestes from
being reconciled to the bishop. Some of them therefore, hurried away by
a fierce and bigoted zeal, whose ringleader was a reader named Peter,
waylaid her returning home, and dragging her from her carriage, they
took her to the church called Caesareum, where they completely stripped
her, and then murdered her with tiles. After tearing her body in
pieces, they took her mangled limbs to a place called Cinaron, and
there burnt them. This affair brought not the least opprobrium, not
only upon Cyril, but also upon the whole Alexandrian church. And
surely nothing can be farther from the spirit of Christianity than the
allowance of massacres, fights, and transactions of that sort. This
happened in the month of March during Lent, in the fourth year of
Cyril’s episcopate, under the tenth consulate of Honorius, and the
sixth of Theodosius.

Ian Holmes introduced me to Ada Lovelace day. I pledged to blog this day, and here we are. Hypatia was an intelligent, courageous, free-thinking woman who paid dearly for her beliefs, her principles, and if you can read between the lines, her gender.

When the Moon is in the Seventh House, and Jupiter aligns with Mars, a bunch of people gather for their “Bioinformaticians anonymous” group therapy. There they metaphorically gather, commiserating about how bioinformatics is dead (or was it bioinformaticians?), just smells funny or suffers from identity theft, probably because it got drunk at the last ISMB, passed out, and left its driver’s license, along with most of its cash on the dresser at some floozy’s room.

Early Bioinformatics Conference

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