Embedding the short and long videos here. Hat tip to Lisa Green for pointing these out.
Making the Web Work for Science – Short from Jordan Mendelson on Vimeo.
Making the Web Work for Science – Full from Jordan Mendelson on Vimeo.
Eisen Lab Blog
Overselling genomics award #6: Quake/Helicos & the "democratization" of sequencing
For those interested in so-called “third generation” DNA sequencing systems, this week has had some buzz with the release of a publication in Nature Biotechnology reporting the sequencing and analysis of a human genome using a Helicos Heliscope sequencer. In this paper Stephen Quake and colleagues generated short read sequences from Quake’s DNA using this machine and then analyzed them by comparing them to reference human genomes.
Certainly, what they did was cool. And the use of the Helicos equipment is a good thing for that company and it’s development of single molecule sequencing. And given the “race” if you want to call it that for the $1000 genome, it is thus not surprising that this paper received a lot of coverage from all sorts of angles because they claim it involved the cheapest sequencing of a human genome yet achieved.
So first I want to commend Quake and Helicos for an important step in third generation sequencing. Quake mind you is one guy who is constantly inventing cool new techniques of great use in genomics and biology and he is always worth checking out.
But in this case, there are some aspects of what they claim they achieved here that are very off putting. In particular, I am concerned with the supposed “democratization of sequencing” that they think this project embodies (e.g., see some of the quotes in this). The basis for their concluding that democratization has happened here is that they believe this sequencing (of Quake’s genome) was done at lower cost and with less effort than previous human genome sequencing efforts. To back this up they make a table (Supplemental Table 1) detailing estimates of these values for 8 human genome papers (the original Lander et al and Venter et al ones, as well as Watson’s genome, etc) that is meant to represent some of this information).
In essence Quake et al are doing the following math (my formula, not theirs, but their discussions imply basically this)
D = B/(E*C)
Democratization factor (D) = # of bases sequenced (B) / (amount of effort (E) * cost (C))
That is, with more sequence, less effort, or less cost, the more democratized sequencing is. Sounds fine in some ways. Except when you look at the details.
For example consider the cost (C) of the sequencing. They report that the cost for the sequencing was < $50,000. But this number is misleading since, for example, they do not include any aspect of the cost of actually buying and setting up the machine. For more detail on the flaws in the cost calculation and for more detail on the whole story see Times Online and Dan Macarthur at Genetic Future and GenomeWeb).
However, more disconcerting to me is what they do with the rest of the implied calculation.
For example, they treat all the projects in essence as though they are equal in terms of total number of bases sequenced (B) because I guess after all, all were sequencing human genomes. But this is not fair since the depth of sequencing and the quality of sequencing varies between the projects and more recent projects, such as theirs, make use of the data from prior projects, which allows them to gather less data (e.g., in their paper here they assemble the genome by tiling the reads against reference genomes, thus allowing them to do lower coverage than would be required for denovo assemblies of genomes).
But even worse – the way they calculate effort required (E) is flabbergasting.
They seem to infer this in two ways. First, they make use of the number of runs of the machine that are required. They apparently used four runs while they claim that the use of second generation sequencing methods required many more runs. And many have been questioning this claim (e.g., see Chad Nusbaum’s quotes in the GenomeWeb article).
It is the second way that they infer effort that is perhaps the most annoying. They infer this from number of authors on the papers describing the sequencing of these human genomes (e.g., In Supplemental Table 1 they say “number of authors” is “an estimate of labor.”) And the big thing for Quake et al is that there are only three authors on their paper and dozens to hundreds on other human genome papers. Based on this lower number of authors they conclude that their work required less effort and discuss this as evidence for further democratization of sequencing.
Now suppose we gloss over that there is no way to infer amount of effort by number of authors (e.g., letters to the editor, which usually do not require a lot of effort, can sometimes have hundreds of authors while Origin of Species had but one author and was, shall we say, a lot of work). Even worse to me is that they are trying to compare their paper which is focused almost entirely on the technical aspects of the sequencing with other papers that spend much more effort on studying and discussing what the genomes might mean. For example the Venter/Celera and the public human genome papers are complex detailed volumes with analysis of everything you could think of. To compare the effort required to do this with the effort required to do what they did in the Quake paper which was pretty much assembly and analysis of SNPs is inappropriate and actually offensive.
Given the number of areas that they have oversold how their project has reduced effort and cost for sequencing a human genome and how this implies democratization, I am giving Quake and Helicos my coveted “Overselling genomics award“. Again, not that what they did was not cool or interesting, but by overselling it, it detracts from everything they achieved.
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New York Times Book Review Use of a "Tree of Life"
Funny use of a “Tree of Life” in the New York Times book review section from a few months ago (The New York Times:Natural Selections)
In this, they overlay onto a somewhat strange Tree of Life, the images used for various book publishers and what types of organisms they use. They say that this represents a fair amount of biodiversity, but really only because they draw the tree in a skewed manner. Basically, there are animals and plants in the logos and the way they draw the tree makes this look like it is a lot of biodiversity … but really it is a small component compared to the whole tree of life. I also like that they put robots on the insect branch and they have mythology as a VERY deep branch in the tree.
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New Open Access journal: ‘‘J. of Computational Biology and Bioinformatics Research‘‘
NOTE – NOT A FULLY OPEN ACCESS JOURNAL – COPYRIGHT MUST BE SIGNED OVER TO THE JOURNAL – THOUGH THEY DO USE A CC LICENSE
Journal of Computational Biology and Bioinformatics Research
www.academicjournals.org/JCBBR
Dear Colleague,
The Journal of Computational Biology and Bioinformatics Research (JCBBR)
is a multidisciplinary peer-reviewed journal published monthly by Academic
Journals (www.academicjournals.org/JCBBR). JCBBR is dedicated to
increasing the depth of research across all areas of this subject.
Editors and reviewers
JCBBR is seeking qualified researchers to join its editorial team as
editors, subeditors or reviewers. Kindly send your resume to
jcbbr.journal@gmail.com.
Call for Papers
JCBBR welcomes the submission of manuscripts that meet the general
criteria of significance and scientific excellence in this subject area,
and will publish:
• Original articles in basic and applied research
• Case studies
• Critical reviews, surveys, opinions, commentaries and essays
We invite you to submit your manuscript(s) to jcbbr.journal@gmail.com for
publication in the Maiden Issue (October 2009). Our objective is to inform
authors of the decision on their manuscript(s) within four weeks of
submission. Following acceptance, a paper will normally be published in
the next issue. Instruction for authors and other details are available on
our website; http://www.academicjournals.org/JCBBR/Instruction.htm
JCBBR is an Open Access Journal
One key request of researchers across the world is unrestricted access to
research publications. Open access gives a worldwide audience larger than
that of any subscription-based journal ad thus increases the visibility
and impact of published work. It also enhances indexing, retrieval power
and eliminates the need for permissions to reproduce and distribute
content. JCBBR is fully committed to the Open Access Initiative and will
provide free access to all articles as soon as they are published.
Best regards,
Oyo Excel
Editorial Assistant
Journal of Computational Biology and Bioinformatics Research(JCBBR)
E-mail: jcbbr.journal@gmail.com
http://www.academicjournals.org/JCBBR
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Wanted – Bioinformatics Enginner to work on Metagenomics
A bioinformatics engineer position is available on a microbial metagenomics project called iSEEM (http://openwetware.org/wiki/ISEEM) under the direction of
Jonathan A. Eisen (UC Davis) http://128.120.136.15/mediawiki/index.php/Main_Page
Jessica L. Green (U Oregon) http://biology.uoregon.edu/people/green/
Katherine S. Pollard (Gladstone Institutes at UC San Francisco) http://docpollard.com
The engineer will work in an interdisciplinary research group of evolutionary biologists, ecologists, and statisticians. Applicants should have substantial experience with genome-scale bioinformatics, including comparative genomics, analysis of protein families, multiple sequence alignment, and phylogenetic analyses. Familiarity with SQL, Perl/Python, and standard bioinformatics tools are essential. Typical responsibilities for this position may include designing and managing an in-house MySQL database of metagenomic sequence data; running BLAST, HMMER, and AMPHORA on the Global Ocean Survey and other large metagenomic data sets; identifying OTUs (operational taxanomic units) based on 16S rRNA or proteins; writing Perl scripts to query databases, process data, or run simulations; distributing data, scripts, and information to project members on all three campuses. Strong project management skills are essential.
We will offer a generous salary and benefits commensurate with experience. The position is available immediately, and the initial appointment will be for one year. The engineer would ideally be located at UC Davis, although other arrangements will be considered.
TO APPLY: Applications should be submitted at
http://jobs.genomecenter.ucdavis.edu/start_app.php?job_id=78
and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, until the position is filled.
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A passionate call for a new war on cancer by James Watson
Sure, James Watson has been known, especially recently, to say some outrageous things. But here is something I think everyone, scientists and the public should read – an opinoin piece in the NY Times today by Watson ( Op-Ed Contributor – To Fight Cancer, Know the Enemy – NYTimes.com)
This piece is worth reading because it contains some critical ideas and wisdom which has been missing in discussions of the fight against cancer.
First, Watson discusses the critical importance of basic science and says that when he expressed this importance to the National Cancer Institute advisory board many years ago, he was eventually booted off.
Second, he discusses how we have only recently begun to understand the basic biology of cancer (he also mentions how the human genome project has helped in this). The genome project will, he says, allow for the determination of most/all of the major genetic changes that occur in cancer cells.
Third, he discusses some limitations of the FDA drug approval process that limit the ability to test combinations of drugs which Watson believes will be needed in the fight against cancer.
Fourth he suggests that the National Cancer Institute should help support small biotech companies in the development of new drugs since venture capital has dried up for such endeavors.
As usual, Watson would not be Watson if he did not say something potentially controversial. In this, the most controversial thing is probably how he discusses that the National Cancer Institute has become a “a largely rudderless ship in dire need of a bold captain who will settle only for total victory. ” Now, I do not have any opinion about this since I have not followed NCI or its leadership. But it is certainly worth considering Watson’s opinion here.
In the end, Watson says the time is now to reinvigorate the “War on Cancer.” Despite misgivings about many things he has been up to recently, I found myself agreeing with almost everything he said in this piece. Again, definitely worth a read.
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PLoS Medicine and NY Times open up can of worms regarding ghostwriting
Absolutely terrifying and intriguing story in the New York Times yesterday (Ghostwriters Paid by Wyeth Aided Its Drugs )
In the article Natasha Singer reports on how Wyeth commissioned the writing by a communication firm of a series of “draft” articles that were then published under the names of various medical professionals. It seems from the article that in some if not many cases the articles were in essence written by this company and then names of authors were placed on the papers which were then submitted to various journals and were published (they were generally review papers, and shockingly supported the use of Wyeth manufactured products).
The issues here are as always complex. But in the end, the articles did not disclose the role Wyeth played in paying for the writing of drafts and/or nearly complete forms of the papers and certainly should have. For more detail, read the Times article.
Interestingly, the documents that helped uncover the full details of the practice were obtained after a “a request in court from PLoS Medicine, a medical journal from the Public Library of Science, and The New York Times.” For more detail on this see the PLoS Medicine blog here. Kudos to PLoS Medicine for getting involved in this and for pushing hard for more disclosure in medical publishing.
All I can say is the practice of ghostwriting medical and scientific articles should stop. Getting help with editing a paper is one thing. But putting your name on a paper conceived of and written by someone else is unacceptable.
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Quick Post: Some free online children’s books with sciency/dental themes at MelTells.Com
Just got pointed to this site by the author … MelTells.Com has some online books for kids some of which have a sciency theme to them. All of them seem to have some dental connection, though not all in the same way. I have only looked at the bacteria one and it is not bad. Even though I have not looked at the others, since they are free, I am posting this bit here.
Also see review on ByteSizeBiology here
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Can’t get much worse than this: soaking my shorts before my 1st conference talk. Other bad experiences?
Well, I was talking with some people recently about someone who had a bad experience giving their first talk at a scientific conference. And so I said – you think that is bad – how about this? And I told them the story below. But before telling the story I am asking here for others to post comments about the worst thing that has happened to you during a talk at a scientific conference/meeting. Please fire away.
OK – so my talk. It was 1995. The SSE (Society of the Study of Evolution) meeting was in Montreal. And somehow I was going. I am not sure anymore how I ended up registering for the meeting. I do remember other evo-grad students who were or had been at Stanford like David Pollock, Joanna Mountain, maybe David Goldstein, maybe Sally Otto, Sarah Cohen, and a few others were going. And so I registered, got accepted to give a talk on the “Evolution of RecA” and made plane reservations to get to Montreal.
I arrived the night before my talk, found my dorm room on the McGill campus, and then went wandering around town for the Jazz Festival which was going on that night. After staying out pretty late, I got back to my room and had a bit of a panic attack when I looked at the schedule and found that the session in which I was talking started at 8:30 in the morning the next day and I did not have an alarm clock, nor was there one in my room. (I note, fortunately I was using real slides and could not spend the night modifying my talk in the way I do now with Keynote/PPT). Anyway – I pretty much knew I would sleep late without some work and so I made some notes with my room # and a plea to others to bang on my door if they could by 6:30 or 7 AM and I slipped these under the other doors in the hall. Fortunately in some ways, I barely slept b/c I was so scared of missing my first talk.
So at 6:30 AM or so I headed out to the conference area. I think I got some coffee and then headed to the room where my talk was to be. Nobody was even there so I wandered around for a bit and came back and the projectionist was there getting the room set up. When I said I was one of the speakers – he said “Are you planning on doing any side by side slides where you need two projectors?” Well, I had not thought of doing this, but now that he mentioned it, it sounded perfect b/c the main point of my talk was that the phylogenetic trees of RecA and rRNA were very similar to each other (see my 1995 J. Mol. Evol. paper on the topic here), supporting earlier suggestions by Lloyd and Sharp that RecA was a potentially useful phylogenetic marker. So I said “sure” and proceeded to load up two slide carousels for my talk. We checked them out and all looked good.
As the room started to fill up (I recall there were a lot of people interested in the “Molecular Evolution” session I was in) I decided to go grab a seat (in the far back on an aisle – I was a lurker even before blogging from meetings) and try to relax. I think I was the fourth talk and while speaker #3 (Michael Purugganan) was getting started I got nervous about the side by side slides so I went over to ask the projectionist if all was OK and he said it was. Alas, someone had grabbed my seat when I was up. I saw a table in the back back of the room with some misc. fliers on it so I went there to sit down for a few minutes and try to relax. And here was the trouble.
The table was also being used to hold some pitchers of water for people. And alas, someone had just spilled an entire pitcher of water on the table and I did not notice. I sat in the puddle. And there I was, in my tan shorts, now dripping wet. Minutes before my first talk. Looking like I had gotten a bit too nervous. Underwear showing through. As I desperately looked around to borrow a sweatshirt from someone to tie around my waist, the chair said “And our next speaker is Jonathan Eisen …”. Holy Crap. I was on.
So I went up there and I had thought to myself to crack a joke about just getting in from a swim. Or something. But as I still do, I entered another zone for my talk and forget everything but the talk. And so – there I was – dripping wet in my see through shorts – turning around and pointing to the screen talking about RecA as though all was fine.
Only when I was done with the talk did I re-remember that I was basically doing a “wet-shorts” contest for all in the audience. Yay. I can say truthfully that when I start to worry about things going wrong in talks, I remember this one and say “well, it could be worse …”
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Fwd: Sign-up now for Microbial Genomics & Metagenomics workshop September 14-18, 2009
Begin forwarded message:
Subject: Sign-up now for Microbial Genomics & Metagenomics workshop September 14-18, 2009
The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.
For more information, see:
http://www.jgi.doe.gov/meetings/mgm/index.html
Jonathan Eisen's Lab 