Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Human genome project oversold? sure but lets not undersell basic science

Well, the piling on the human genome project continues, it seems at an accelerating pace.  I think most of this comes from the fact that we are in the range of the 10 year anniversary right now.   Here are some examples of recent stories suggesting the human genome project (or projects, if you count the public effort and Craig Venter’s effort as separate) have had little benefit:

  • 7/31/10: The Human Genome Project: 10 Years Later, Progress but Still a Puzzle – WNYC. Interesting piece by Sarah Kate Kramer discussing the limited clinical value of the HGP.  Includes some criticisms of personalized genomic medicine. 
  • 7/29/10: Spiegel interview with Craig Venter with the headline “We have learned nothing from the genome”.  Has lots of interesting tidbits.  Love the Venter line “Well, nobody likes to be beaten — by superior intelligence, planning and technology. That gets people upset.”  But I note Craig emphasizes the basic science value of human genome data.
  • 7/6/10: Public Radio mini story about Mike Mandel’s article on the failure of the human genome project.
  • 6/12/10: Nick Wade’s NY Times article on “A decade later, genetic map yields few new cures“.  In this Wade discusses many of the issues with both the sequencing of the human genome and some of the spinoff projects (and also butchers some evolutionary biology for which I gave him a twisted tree of life award). 
These are but a small sampling of the many many blogs, articles, and other reports that either directly state or suggest that much of the money spent on the human genome project was a waste.

Certainly, contrary to the suggestion of some of these articles, there have been some practical benefits that have come directly or indirectly from human genome sequencing.  But equally certainly, these critiques have a segment of truth to them in that the practical benefits have been few and far between.

Normally, one would not expect too many direct practical benefit to come from this kind of science project.  But alas, the problem here is that many of the key players (e.g., Eric Lander, Francis Collins, Craig Venter) in the sequencing of the human genome(s) oversold the potential benefits that could come from the sequencing.  In a way, it was their job to oversell the sequencing, since each was a cheerleader in ways for getting others to do a lot of work.

Many people knew at the time that this overselling was going on.  It was talked about extensively at various genome conferences and even occasionally in the press and scientific literature (boy do I wish I had had a blog then, because I was one of those people at conferences practically begging people to not oversell the benefits of the project – I now even give out an “overselling genomics award” on my blog ).  The cautionary voices were mainly saying that there was no need to oversell the project and that we should stick to the benefits of “knowing” ourselves and not guess about how it will lead to immediate cures for diseases.  And many said “If you oversell this now, it will come back to bite you“

And thus it is not surprising to me that there is somewhat of a backlash now.  But there is a very dark side to the backlash that has potential to hurt science for many years to come.  If there is a need in the future for large scale science / medical projects, I can guarantee that some critics will step up and say things like “Well the war on cancer failed.  And the human genome project failed.  Why should we trust you now?”

The problem here is that the human genome project should never have been sold as a means to a series of practical ends.  It should have been sold as a massive basic science project, much like going to the moon or building a giant linear accelerator.  That is, the human genome project was, and still really is, about knowledge.  It is about knowing ourselves.  It has enormous potential benefits in all sorts of areas, like human medicine.  It should greatly aid and abet studies of human biology and genetics and disease.  But given that benefits that come from such studies are impossible to predict, the human genome project should have been presented in a different way.  We need to discuss more in public why basic science is important even if one cannot predict what the benefits are.

In many ways, this is very much like the “war on cancer” which some have argued failed because we still have cancer killing a lot of people.  But this is off base because in fact the war on cancer has provided us with an incredible baseline of information about the biology of cancer.  We need to do a better job in all of these cases of defending the need for knowledge, and discussing how fighting cancer and curing diseases is not the same as building a big bridge or road.

The best person discussing this issue for the last ten or so years in my opinion has been Harold Varmus, who was once the head of NIH and is now the new director of the National Cancer Institute.  I have heard him repeatedly defending the “war on cancer” in terms of its basic science benefits.  For example see his comments on Science Friday 1/30/2009 and 7/16/2010.  There just have not been too many people doing a good job of this with genomics.  Venter and Collins have been OK here and there.  But we need more.

On a related note, we probably should have more discussion about how the money spent on the genome project and the war on cancer pales in comparison to money we spend on other things (e.g., interest on the national dept, wars, etc) but perhaps that is a side discussion.

Most importantly, we need to bring out to the public more of a discussion of the benefits from basic science. Here are some useful resources if you want to try and help:

I also encourage people to look at the National Academy of Sciences report A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution.  I note, I was one of the coauthors.  You can download the PDF of the whole document after giving your email address.
I am going to start a new series here on this blog called “Benefits of basic science” where I will be discussing these issues.  I encourage others out there to also bring more to the forefront discussions of the need for basic science.

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UPDATE

Also see

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Twisted tree of life award #6: Scientific American Origins piece for dissing microbes

There is an interesting series of mini articles in the August 2010 Scientific American tracing the origins of various concepts and things: Origins: Going Back to Where the Story Really Starts: Scientific American
Not open access mind you, but if you have a subscription it is worth checking out. They track the origins of the following:

  • swiss cheese
  • paternal child care
  • computer viruses
  • animation
  • sexual reproduction
  • malaria
  • fireworks
  • barbed wire
  • hand washing in hospitals
  • human morality
  • electric cars
  • the influenza virus
  • wheeled vehicles
  • black holes
  • zero
  • biodiversity
  • noodles
Many of the discussions are interesting.  Some are a bit trite.  But that is not what I am here to report on.  I am here to complain about one aspects of the article series: too much emphasis on humans and multicellular organisms as “higher” creatures.  There are various subtle phrases here and there that I did not like too much but the parts that really grate on me are the two below:
  • In the article on biodiversity Melinda Moyer discusses the remarkable possibility that single celled creatures might have in fact had some diversity in them “Today we think of biodiversity in terms of multicellular life, but flowering plants and animals didn’t arrive until relatively recently” she writes.  And ends with “It is no comfort to know that the worst catastrophe would still preserve some biodiversity — even if only for the lowly cell.“
  • In the mini article on sex, Brendan Borrell writes “The truth is, nobody really knows why people — and other animals, plants and fungi — prefer sex to, say, budding.”  This of course leaves out all the other eukaryotes that are not plants, animals and fungi that have sex.  
And though these are certainly subtle small issues, I feel that Scientific American should do better.  So for directly and indirectly dissing the microbes on the planet – I am giving them my coveted Twisted Tree of Life Award #6.  Previous winners are listed below:
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Some quick links on #OSS2010 Open Science Summit 2010

Just posting some links from the web relating to the Open Science Summit 2010 meeting which is continuing today … started Thursday.  If you want to follow today, check out twitter with hashtag #OSS2010

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Science SPAMMER of the month: OMICS publishing group

Well, Science SPAM never seems to go away. Not sure exactly why it seems to come in waves, but recently I have been getting a lot of email messages from the OMICS publishing group OMICS Publishing Group: An Open Access Publisher

The latest is for the Journal of Bioanalysis & Biomedicine. I love how the message says

“This is not a spam message, and has been sent to you because of your eminence in the field. “

Interestingly, this is the EXACT same wording in messages I used to receive from the horrible Bentham OPEN group. (see one of my complaining posts about this here). I wonder, did Bentham somehow morph into OMICS publishing group? OMICS Publishing group is also trying to promote itself as an Open Access publisher in much the same way Bentham does. I hope for everyone’s sake they are not connected since the last thing we need is more SPAM out there. Anyway, since I have gotten a bunch of emails from various OMICS journals many of which I have no possible scientific connection to, I am giving OMICS my “Science SPAMMER of the month award”.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Yay: #DavisCA police come through quickly on issue of dangerous signs

So , Saturday I got really annoyed with some unsafe street signs in Davis. I wrote some emails to the police and some realtors. I took pictures. I posted a blog post. And so on (see blog here – Davis, CA: Getting more and more annoyed with dangerous Real Estate signs in #DavisCA). Basically, the issues were realtors putting their open house signs in the street and some others putting signs in areas to block the view of oncoming traffic.

And though I got a response from one of the realtors, it was not very convincing. Thus I was more than pleased this AM to get an email back from the Davis Police Department in response to the emails I had sent in to policeweb@cityofdavis.org

And they said two things. First, they had talked to the manager of the apartment complex that had been placing a sign obstructing traffic and the manager was taking it down. And the police were going to send an email to all realtors in the area reminding them that placing their signs in the street or other public right of way was illegal. May seem like a small thing to many, but I have seen a few near crashes due to the realtor signs and worried about crashes due to the apartment sign. And thus to have these issues fixed so quickly made my day.

I must say, I have had nothing but good interactions with the Davis Police when I have sent questions or emails to their non emergency email address.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Testing, testing – why we need more testing like this in genomic informatics & annotation methods

Just got an announcement regarding this challenge:

Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations | Automated Function Prediction 2011 July 15-16 2011, Vienna, Austria

Here is a description:

CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will take place September 15, 2010 through January 15, 2011.See here for more details on how you can enroll in CAFA.

This is near and dear to my heart as I have been working on methods to predict gene function from sequence for some 15 years now.  My first paper on this was in 1995 in which I showed that for genes in multigene families, phylogenetic trees of the gene family could help in predicting functions of uncharacterized members of the gene family.  More specifically, I suggested that the position of an uncharacterized gene in a gene tree relative to characterized genes could be used to predict its function.  I did this for one family in particular – the SNF2 family – but argued that it could be applied to other families.  (I think perhaps it was the first time someone had made this specific argument about using trees to predict function, but am not sure)

I then formalized this idea with a few papers (e.g., here and here) describing a “phylogenomic” approach to predicting function (alas, this is when I invented my first omics word).  And for many years since, I continued to work on functional prediction methods and continue to do so.  When I was at TIGR for eight years I did this both in my own research and helped others with their functional predictions.  I firmly believe that evolutionary approached approaches are critical in such functional prediction and have laid this out in a series of talks and papers (e.g., see this more recent one).

Anyway, enough about me.  I can argue all I want about how brilliant I am and about how evolutionary methods are the best approach.  But arguing is alas not science.  What we need are tests and experiments.  And that is where things like CAFA come in.  In CAFA one can test how well various functional prediction methods work.  And the people involved in CAFA (including organizers  Iddo Friedberg, Michal Linial, and Predrag Radivojac and others such as Amos Bairoch, Sean Mooney, Patricia Babbitt, Steven Brenner, Christine Orengo and Burkhard RoshRost)) are to be commended for putting this together because we do not have a lot of these activities and need more in all aspects of genomics (and metagenomics too).  Others have discussed doing tests of functional prediction methods before, but I am not sure if any have happened per se.

Have a favorite functional prediction method?  Enter it in the competition or give a talk on it.  And if you are feeling inspired, organize a similar activity in your area of science – testing is a good thing.

See also Iddo Friedberg’s post about this

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Burrowing Owls on Wildhorse Ag Buffer Trail

In addition to the crawdads, the burrowing owls have been out in full force on the Wildhorse Ag buffer trail recently. There are at least 20 if not more living in the tunnels along the trail. Always entertaining.

http://picasaweb.google.com/s/c/bin/slideshow.swf

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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More crawdad fishing in Wildhorse Creek, Davis, CA

Here are some pictures from another night of crawdad fishing. We have been going for some walks along the Wildhorse Ag. Buffer trail at night and keep coming upon a few families fishing for crawdads in the creek. This night, they also had one of their cats with them. It was quite entertaining, with the kids lowering McNuggets into the creek and reeling up crawdads in seconds. Then they dumped out the bucket and watched them crawl back to the creek.

http://picasaweb.google.com/s/c/bin/slideshow.swf

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Getting more and more annoyed with dangerous Real Estate signs in #DavisCA

I am getting more and more annoyed with the Davis Realtor crowd. They seem to think that they can place signs anywhere they want to promote their sales. Here are some examples I took today, including one sign by Mona DeMasi that forced a couple of kids further into the path of a car while the kids were trying to ride around a circle.

http://picasaweb.google.com/s/c/bin/slideshow.swf

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Crawdads from Wildhorse Creek, Davis, CA

Just a quick one here. Went for a walk last night on the Wildhorse Agricultural Buffer trail near Wildhorse and bumped into a few families “fishing” for crawdads on the bridge over the little creek there. They were catching them just for the kids to look at them and then let them go on the bridge, which entertained my kids quite a bit … here is a slide show of the crawdads:

http://picasaweb.google.com/s/c/bin/slideshow.swf

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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