Thursday, October 28, 2010

The Story behind the Meeting: Lake Arrowhead Microbial Genomes 2010 #LAMG10

Well, I really wanted to write up some thoughtful piece about the Lake Arrowhead Microbial Genomes Meeting I just got back from.  But I am in the throes of prepping for beginning teaching a 700+ person class here at UC Davis and well, I just can't put enough effort into the meeting write up as I would like.  So perhaps my live blog page may be all that I will post directly about the meeting (and at the bottom of this post I am re-posting my feed from Friendfeed).

And if you want to see my slides here they are

And here is a little write up of sorts - more about the history of the meeting than this 2010 meeting.....

First, some background.  The Lake Arrowhead Microbial Genomes meeting was, well, in Lake Arrowhead California.  This is both a town and a lake and is in the San Bernadino Mountains East of Los Angeles.

Fortunately for all of us who were there, UCLA has a conference center in Lake Arrowhead, just off the lake itself.  And for the last at least 12 years, every two years, there is a meeting in September at this Conference Center that focuses on microbial genomes in one way or another.  The meeting has changed names, and has gone through a few different major financial supporters, but has always been organized in a large part by Jeffrey H. Miller from UCLA.  Do not confuse him, please, with Jeffrey F. Miller, another microbiologist from UCLA.  That would be a bad thing.  Sort of like confusing me with my brother Michael.

Anyway, Jeffrey H. Miller has been the major force behind organizing this meeting and he has always done a bang up job on fostering a great atmosphere for both science and interaction.  I am not sure what it is he does, but it always seems to work.  One component is that Miller clearly believe that a conference is not only about hearing talks.  Too many times recently I have been to meetings that were overscheduled with speakers and no time for relaxation or discussion or other activities (the Open Science Summit in Berkeley comes to mind - at that meeting I had to actually stage a coup of sorts to prevent the organizers from skipping lunch and all breaks just to have more talks).  At the Arrowhead meetings, Miller always leaves a few hours in the afternoons free and then has poster viewing/reception time before dinner, plus reception time after evening talks.  It works out well.

The Lake Arrowhead Microbial Genomes meeting has a bit of an unusual history.  It is in essence part of a yearly meeting that used to be go by the name "Small genomes." And every two years, it happens in Lake Arrowhead under the direction of Jeffrey H. Miller.  And since 1998 I have gone to this meeting each time it has come around: 1998, 2000, 2002, 2004, 2006, 2008, and now 2010.

It all started for me in 1998.  I originally signed up for the meeting to give a joint talk with A. John Clark.  I was finishing up my PhD at Stanford on Evolution of DNA Repair Genes, Proteins and Processes and had a post doc lined up to work with Clark at Berkeley.  John was the person who had discovered the recA gene many years before with his graduate student Ann Murgulies. Clark, Steven Sandler and others had been working on functional studies of archaeal homologs of recA and has recently turned their attention in collaboration with Norm Pace (who was then at Berkeley) to trying to use PCR amplification of the archaeal recA homologs to study uncultured archaea, much like Pace and others had done with rRNA. This was seemingly perfect for me as I had worked on both rRNA PCR of uncultured microbes and on evolution of recA (e.g., see here, here, and here) and on DNA repair in archaea.

Anyway, John was invited to give a talk at the Lake Arrowhead meeting and he asked if I would do a tag team talk with him where I could present the results of my phylogenomic analysis of DNA repair genes across the available genome sequences.  So I said sure.  I had no idea what I was getting into, but I went to the meeting.

Alas, there was some awkwardness there because after accepting the post-doc at Berkeley with Clark, I told him I was going to have to drop it.  That was because in the meantime I had finagled my way into going to a dinner with Craig Venter when he came to Stanford to give a talk.  At the dinner I proceeded to tell Craig that I thought some of the evolution stuff he was doing was sketchy and that the genome annotation at TIGR could be improved by phylogenetic analysis.  I drew on napkins, told him about some of my recent papers and eventually he invited me to interview for a job.  The interview went well and both I and my then fiancĂ© now wife were both offered faculty jobs at Craig's institute "TIGR", which we accepted.

So here I was giving a joint talk with Clark yet had just told him I was ditching him for another job.  Well, we soldiered through - but the rest of the meeting went well.  I met all sorts of interesting people, developed multiple collaborations, and had a very good time.  Shortly thereafter I moved to TIGR and began life as a genome sequencer.  For more on the 1998 meeting, alas, there is not much out there on the web.  But I did find my meeting book and some notes and I scanned them in (see below).

Tuesday, October 12, 2010

Figuring out figures in scientific papers: new search / ranking method outline in PLoS One paper

Just a quick post here.  A colleague just sent me a link to her fascinating new paper in PLoS One: PLoS ONE: Automatic Figure Ranking and User Interfacing for Intelligent Figure Search

In this paper Hong Yu from the University of Wisconsin in Milwaukee describes a system for better automated characterization of figures from scientific papers.  The system is available through their webserver "Ask Hermes".

If you want to learn more about the system I suggest you read the paper.  Or watch their video.



Basically the general idea is summarized in their background section of the abstract:
Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.
I particularly like that they also allow searching just for open access figures, which may be of significant value to people who want to do things like make a slide presentation with no copyrighted/protected material in it.  For example see the results of a search for open access figures using the keyword phylogenomics.

Anyway - definitely worth checking this out.

Yu, H., Liu, F., & Ramesh, B. (2010). Automatic Figure Ranking and User Interfacing for Intelligent Figure Search PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0012983

Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus

OK, though this is not as bad as printing the wrong form of DNA on the cover Nature has another faux pas. In a recent Nature News story discussing a recent paper on the characterization of venoms in the platypus, Ewen Callaway reports in Poisonous platypuses confirm convergent evolution : Nature News:
By some accounts, being poisoned by a platypus could qualify as punishment in one of Dante's circles of hell. In one case report2, Australian doctors described their treatment of a 57-year-old man a few hours after he grabbed one of the small marsupials while fishing. The pain was "so bad I started to become incoherent" the man said, and far worse than the shrapnel wounds he took as a soldier. Ibuprofen and morphine provided no relief, and one finger was swollen and ached more than 4 months after the run-in.
The only problem with this is that the platypus is a monotreme, not a marsupial.

From http://kaboodle.nescent.org/?q=node/594
Fortunately Nature does get this correct on the headline for the story "Genome analysis shows that the monotremes and snakes have similar venoms" but the damage is done in the middle.

The mistake in the middle of the article may seem a very minor thing to most of you out there.  But @an_dre_a is calling for action on twitter from the monotreme antidefamation league.  And I am now posting here and giving Nature my coveted "Twisted Tree of Life Award" (the ninth) to bring attention to this horrendous horrendous offense to monotremes everywhere.

Hat tip to @recher_she on twitter who called my attention to the Nature article because it mentions the "venome" a really #badomics word that I will be writing about later. 

Sunday, October 10, 2010

Saturday, October 09, 2010

Twisted Tree of Life Award #7 #8: Alroy on "Changing the rules of evolution"

Twisted Tree of Life
Every once in a while I give out an award here for bad discussions of evolution in the media or scientific publications. I call this the "Twisted Tree of Life Award." And here is a doozy. It comes from a recent paper in Science: The Shifting Balance of Diversity Among Major Marine Animal Groups -- Alroy 329 (5996): 1191 -- Science

The paper is actually pretty interesting. But the last line of the abstract. OMG. It is beyond awful. Here is the full abstract:
The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere’s taxonomic composition by changing the rules of evolution.
That last line saying that the current extinction crisis may change the rules of evolution really really really bugs me. Changing the rules? Please. If they are rules, then, just how, exactly do they change? If they do change, perhaps they should not be rules no?

And as an aside, what is up with Science not printing the full first name of authors? Does that really save space?

Anyway - not much to say here other than that J. Alroy is the winner of my the 8th "Twisted Tree of Life Award" for suggesting that the evidence presented in this Science paper changes the rules of evolution. And a half award goes to the editors of Science for letting this BS get into the abstract.

Previous recipients of this award are

Tuesday, October 05, 2010

Stanford Magazine and a veneer of science: helping the world buy "human pheromones"

Wow.  This ad for "Athena Pheromones" definitely caught my eye in Stanford Magazine in the September-October 2010 issue.   So I decided to scan it in and share.

The whole thing is, sadly, pretty lame actually.  These "pheromones" come from the Athena Institute, which they say was started by Winnifred Cutler who was a post doc at Stanford.  They claim, on their web site and in this ad, that she "Co-discovered human pheromones in 1986" and use this to I guess imply that whatever potions they sell must therefore work the way they claim.

Sure, the claims they make for what the potions they sell are not as outrageous as many things relating to sexual interactions.  In fact, they are pretty tame:

  • But 10X does this with the special power of human pheromones. 
  • Men who used 10X in their aftershave experienced increased romantic attention and affectionate behavior from women.
  • Some men report 10X improves their business relationships.
But what annoys me about this is the attempt to use science smoke and mirrors to support the claims.  As far as I can tell, they are using a series of tricks to make you think that this stuff really works.

First, they seem to be overinflating the scientific credentials of the founder of the company.  Sure she seems like she might be a decent scientist.  But they give her credit for the discovery of human pheromones.  And the evidence for this discovery is a bunch of news coverage from 1986.  But it seems from looking at the literature, not too many other scientists refer to these papers as having discovered human pheromones.  So my guess is one creatively written press release led to a lot of press and now, 24 years later they are still trying to ride the wave of publicity from the news coverage.

Second, they do some creative writing to make it seem that the scientific evidence of the effectiveness of the pheromones that they claim to include in their potions is overwhelming.  But upon closer examination, the work they cite is pretty minimal.  On one page they cite a poster abstract from a meeting in 1998.  On another they reference a 2002 paper by what appears to be an outside group that did a controlled trial of sorts - so at least there is some science here.  But it is pretty minimal.  Amazingly, and very annoyingly, if you want to read more detail about these studies they tell you: "to order reprint of full study click here)  and then you have to pay to get reprints.  

Third, and most troubling, is that it is very hard to figure out what exactly is in the little vials they sell for hundreds of dollars each.  Is it the same thing in the papers?  What is the concentration?  Is this homeopathic pheromonetherapy?  They say it is a trade secret - which does make some sense if it is real - but it is hard to evaluate without such information.

They must hope that we make the following connections (1) founder is a pioneer in scientific  studies of human pheromones (2) they have shown that some human pheromones really have effects (3) they sell vials supposedly with human pheromones -> therefore anyone interested in attracting more "mates" should buy the vials, since they must work. 

Many other aspects of the site are like this - referencing science, giving some sort of faux science veneer, but the science is actually pretty limited.  Not that I am saying human pheromones do not exist - most likely they do.  But is there something in these vials that is an effective human pheromone?  And if so, how much exactly do you get for $100?  My guess is, the true answers to these questions would lead most to stop buying this stuff.  

Sunday, October 03, 2010

Here's hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine

From Wu et al. 2009. A phylogeny driven genomic encyclopedia of bacteria and archaea. Nature 462, 1056-1060 doi:10.1038/nature08656  http://bit.ly/8Y8xea
Well, I am always hopeful.  Every year when the Nobel Prizes come around I am alway hoping that one of them goes to someone involved in studying microbial diversity in some way.  And really, there is a potential Nobel Prize in Physiology or Medicine out there in this area.  Sure they do not give out a Nobel in biology, or evolution or ecology.  But I think a good argument could be made for giving out a Nobel Prize in Physiology or Medicine to those who have worked on molecular systematics of cultured and uncultured microbes.

Why should this attract the attention of those giving out the Nobel Prizes?  Well, without molecular systematics of microbes we would be completely lost in a sea of microbial diversity.  And with such molecular systematics we can not only make much more sense out of the biology of cultured organisms, but we can go to environments and determine who is out there by sampling their genes.  And this type of work has undoubtedly revolutionized medicine, from determining what antibiotics are most likely to be useful in infections, to tracking emerging infectious diseases, to studying the vast diversity of microbes we have not yet cultured in the lab.  Certainly with the growing importance of the human microbiome in medical studies and the growing application of molecular systematics (e.g., rRNA surveys) to all sorts of aspects of microbiology, the time is ripe for an award in this area.

And who would get an award if one was given.  Well, certainly one of the people should be Carl Woese, who pioneered the use of comparative analysis of the sequences of rRNA genes to the study of systematics of microbes.  Woese of course was responsible for proposing the existence of a third branch in the tree of life - the archaea.  And even if you do not personally believe that the "three domain" tree of life is perfectly correct, Woese and colleagues (e.g., George Fox, who was a coauthor on some of the pioneering papers) were responsible for making microbial systematics a much more rigorous science than it had been.

And I think a good argument could be made for including Norm Pace in this Nobel as he was the one mostly responsible for pushing the sequencing and analysis of rRNA genes for studying microbes in the environment (though I note, others like Mitch Sogin also helped pioneer this field).  There is a direct path from Woese through Pace to much of modern molecular studies of microbes in the environment, including the latest approach - metagenomics.  In fact, there has even been a Nobel Prize already given that depended on much of this work - the one in 2005 to Barry Marshall and Robin Warren for discovery of the role of Helicobacteri pylori in causing stomach ulcers.

Anyway - just a short post about this - maybe more later.  But I sincerely think this would be a well deserved area in which to hand out one of those Nobel Prizes.  Not holding my breath, but always hopeful.

Here some potentially related things that I have written that may be useful to read:

Saturday, October 02, 2010

Foundation: Nobel Prizes to be awarded via reality shows incl. Nobel Survivor, Sweden's Next Model (System) & The Amazing Particle Race

In a surprise last minute press release the Nobel Foundation has announced that this year's Nobel Prizes will be given out via reality show style competitions rather than by the traditional committee deliberations.

Marcus Snorch, Chairman of the Board of Directors of the Nobel Foundation said in at a press conference announcing the new system "We have noticed that in the last 5-10 years there has been a diminishing interest in the Nobel Prizes. This decrease appears linked to the steady increase in popularity of so-called reality show competitions. We felt like it was time for the Nobel Prize to try and attract a younger audience. Our reality Nobel series should be highly popular."

Barbara Connon, chairman of the Nobel Foundation Board of Trustees concurred, "We all felt like a shake up was necessary. The Nobel Prize is so important for the world, yet nobody was paying attention anymore. Our new approach, where semifinalists are announced in advance and then a competition decides the winner, should bring new attention to the Prizes"

The announcement represents an agreement between the many institutions involved in awarding the Nobel Prizes including the Royal Swedish Academy of Sciences that presides over the prizes in Chemistry, Physics and Economics; the Nobel Assembly at the Karolinska which awards the Prize in Medicine, the Swedish Academy which awards the Literature prize and the Norwegian Nobel Committee that awards the Peace Prize.

At the press conference, the Nobel Foundation presented the new reality series, one for each Nobel Prize. The example they highlighted relates to this years prize in Physiology and Medicine which will be given out via "Nobel Survivor." This show will feature Nobel Semifinalists living on a remote tropical island and the competitions will feature major medical "events" that one member of each team will experience.  Each week the team that responds least well to the challenge will have to vote off one member.  The challenges will include infections by schistosomes and filarial nematodes, a series of autoimmune disorders, premature aging, erectile disfunction, and severe body odor.  The competitions will be presided over by Hugh Laurie.

"Many of the Physiology and Medicine prizes have been criticized for being too disconnected from actual Medicine.  So we figured what better way to pick the winner than to make them actually do some medicine, but without all the comforts of home," said Barbara Connon. This years semifinalists who will be participating include J. Craig Venter, Lee Hood, Joan Steitz, Alec Jeffreys, Carl Woese, Norm Pace, Mary Claire King, Douglas Coleman, Elaine Fuchs, and James Till.

Other shows for this and future year's prizes include:

Sweden's Next Model (System)
The 2011 Medicine and Physiology prize will feature a competition to determine what is the best model organism.

Real Literature Idol
The 2010 Nobel Prize in Literature will be given out via a literature reading and slam poetry series dubbed "Real Literature Idol"

The Amazing Particle Race
The 2010 Nobel Prize in Physics will be given out to the scientist who is best able to maneuver their particle through a month long journey around the globe.

Dancing Peacefully With the Stars
Enough with Peace Prizes being given to people who work on abstract global issues.  The 2010 Nobel Peace Prize will be given out through a dance competition.  All "stars" selected for the competition will be notorious for their difficulty in getting along with others and will include Mel Gibson, Alex Rodriguez, Lindsay Lohan, Barbara Streisand, Kanye West, Dick Cheney, Amy Winehouse, and Courtney Love.

The Swedish Chef
In order to make chemistry more "Real" for the public, the 2010 Nobel Prize in Chemistry will be awarded in a Swedish Cooking competition.

The Nobel Apprentice
The Prize in Economic Sciences (though not technically a formal Nobel Prize) will be awarded via a collaboration with an existing reality show "The Apprentice." Candidates for the prize will compete to be Donald Trumps economic advisor.

The Nobel Foundation is also soliciting feedback, right here on this blog, for ideas for other Nobel Prize related reality shows for future awards.  Please submit suggestions.