What would make more sense is to first make better use of all the wasted biomass from various agricultural systems and from solid waste. Lots of material is still being burned on farms for example (see pictures below of a fire near Davis --- these are going all the time, even on "spare the air" days). Sure - one can make lots of money from corn to fuel right now. But that does not make it the right thing to do when there are plenty of sources of biomass being wasted all around us. Lets hope that more of the biofuels projects work on converting leftovers not new crops.
Thursday, August 30, 2007
Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.
And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack
Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations. This is interesting because it is the first report of strong evidence for such "stable" transfers from bacteria into multicellular species. Of course, one could say that this finding is not that surprising given that Wolbachia infect germ cells and given that DNA transfer from organellar genomes to nuclear genomes is quite common. But Wolbachia are not organelles and since it appears that their DNA can readily move into genomes of multicellular species, this opens up a new window into our understanding of gene transfer.
This of course does not mean that the DNA is anything but "junk" in terms of functions in the host genome. And this is where the adaptationomics comes in. One of the press releases associated with the paper has a bit of an outrageous adaptationomics claim that I would like to counter. In response to their finding of a nearly complete Wolbachia genome in the nuclear genome of a fly
The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host.And Dunning Hotopp in a Nature article says:
The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. "You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."This notion that the DNA MUST have an beneficial function is pure adaptationomics. Consider the movement of DNA from organellar genomes into the nucleus. Such movement occurs at an incredibly high rate and the DNA seems to be maintained in the host genomes for millions of years. For example, when we were sequencing the Arabidospsis genome, we found at least one if not more whole copies of the mitochondrial genome embedded in the nuclear genome and we concluded this was likely a non adaptive event. That is, the mt DNA was not conferring some advantage on Arabidopsis plants. There is extensive work on what are called "numts" (nuclear mitochondrial DNA) in humans and other species that makes similar conclusions - the mtDNA in the nucleus is basically junk but it is maintained for long periods of time. Sure, occasionally, the DNA confers some selective advantage. But this is a very rare event and one cannot infer that some DNA is advantageous simply because it is present. This is especially the case for eukaryotes which are generally more able than bacteria to maintain DNA that confers little selective benefit.
So I would argue that
Anyway - as is the case more and more. Read the paper. Ignore the interviews and the press releases.
Tuesday, August 28, 2007
PRISM - Partnership for Research Integrity in Science and Medicine - Seems like a spoof but it is real, and sad
- "undermines the peer review process." Yes that's right. If an article is freely available for all to read, that must mean that peer review has been compromised. Nevermind that openness in other areas (e.g., politics, law, etc) is well established to promote critical review (anyone heard of freedom of the press). But apparently in science, openness is bad.
- "opens the door to scientific censorship". Yup. Making publications freely available apparently means that you will stifle communication. Again, the logic here is completely silly - how on earth is openness connected to censorship?
- "undermining the reasonable protections of copyright holders." Yup, the publishers of scientific articles, who do not deserve the copyright to articles in the first place, are now saying that because they have stolen the copyright from many scientists, now we should defend them because they have the copyright. Kind of like saying that someone who steals some money should not give it back because of finders keepers rules.
For more on Prism see
Thursday, August 16, 2007
The incoming messages included diverse messages - some with the word "FWD" in the subject line but some appearing as normal as can be.
Anyone else out there experiencing a sudden increase in missing email?
Wednesday, August 15, 2007
Using molecular markers to study the formation of skeletal cartilage in embryos of the spotted catshark, UF scientists isolated and tracked the activity of Hox genes, a group of genes that control how and where body parts develop in all animals, including people.Now admittedly, this is not genomics here - but the press release just had to use genomics in the title so my automated google search for "genome" and "evolution" picked it up. So - why do they get the overselling award? Read more in the press release:
The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, shedding light on how life on Earth developed and potentially providing insight for scientists seeking ways to cure human birth defects, which affect about 150,000 infants annually in the United States.Yes that is right, this genome-ish gene expression study in sharks is going to help cure human birth defects (note the paper in PLoS One seems entirely reasonable ... this is another case of press releases being disconnected from the science - and is another reason to support OA publications because here you can actually all go and read the paper and ignore the press release).
In addition, the press release says
“We’ve uncovered a surprising degree of genetic complexity in place at an early point in the evolution of appendages,” said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. “Genetic processes were not simple in early aquatic vertebrates only to become more complex as the animals adapted to terrestrial living. They were complex from the outset. Some major evolutionary innovations, like digits at the end of limbs, may have been achieved by prolonging the activity of a genetic program that existed in a common ancestor of sharks and bony fishes.”Now I accept that the specific details of Hox gene expression here might have been surprising but what friggin evolution textbook are these people reading if they are surprised that there is not a chain of life going from less complex to the pinnacle of complexity in humans? Hopefully not mine.
Monday, August 13, 2007
For Day 3, I got up early, packed up my bag, and then polished up my presentation for a session on "The Human Microbiome." This was particularly difficult for me since I do not really at this time work on the human microbiome much (although I want to). But I figured, of all the things microbial I know about, this would be the one that would be most fun to talk about to scifooers and would catalyze the most interest. So I searched around for slides and figures and ideas on the web for a while and then said "WTF - I can do a chalk talk if I need to" and I headed downstairs to the lobby in the hopes of getting over to Googleplex and enjoying the last bits of scifoo.
There was quite a crowd in the lobby and I ended up talking to a few other evolutionary biologists which was good and then finally got a bus ride over to camp. At Google, I had a bit of breakfast and then went inside to sit at a table to do the last bits of preparation for my talk. If I had been at a normal conference I would have simply skipped the first two sessions to prepare for my talk at 11:30 (the last session of the meeting). But I said this would be silly and decided to go to a session at 9:30. My choices were:
|Future health care delivery and transport models: When "science" is not enough, benefit of new research vehicles (Berman and Neelagaru)||Reforming Patent Systems, patent informatics and innovation||5 mins on your favorite science website / tell us your dream science web tool (Richard Akerman)||How to Celebrate Darwin in 2009 (Phil Campeck)||Innovation is Not Pointless...But It's So 20th Century (Bingham)|
And again, the choosing was brutal. Though I really wanted to go to Lincoln Steins Genome Voyeurism session, I followed my rule of going to things I did not know a lot about and went to the session on the International Polar Year. This was one of those sessions in a giant room and I expected a huge crowd. Instead, there were about seven people. But boy did the others miss something brilliant. Dave Carlson not only told us about the whole IPY project but proceeded to tell us about how their project was completely Open Science. That is, everyone involved was required to post their data on the web for anyone to use. OK - well apparently they are allowed to publish in non Open Access journals, which seems counter to their whole philosophy, but their openness about data is brilliant (Note - I just found out from a Google search that a childhood friend of mine, Thomas Nylen, is participating in the IPY project -- see this blog here for some of what Tom has been up to).
Unfortunately, I missed the next session due to my computer having issues and me freaking out about whether it would work for my presentation at 11:30. The choices for the session I skipped were:
|Science Blogging||Towards an open source science learning collaboratory (Ted Kahn Design Worlds)||Opening the scientific literature: OpenLibrary, Google Scholar (Aaron Swartz)||21st century medicine: electronic medical records, privacy, and data mining (Erez L. and Kevin F.)|
Then it was time for the final session. And I was up -- the Human Microbiome. Here is what I was up against
|Social limits of scientific knowledge - can too much information impede science? (Dalton Convoy)||Culture of Fear: Scientific Communication and Young Scientists|
(Alex Palazzo, Andrew Walkingshaw)
|Towards DataWiki (Hugh Rienhoff, Alan Littleford)||Do systems organize themselves to produce entropy at the maximum rate? (Ralph Lorenz)|
|Science on the Stage, "science-in-theatre" (Djerassi)||Human Microbiome, microbes in and on us (Jonathan Eisen)||Science fiction: what is it for? (Henry Gee)|
It would have been funny if I had gone to someone elses session and skipped mine, but I am glad I did not as actually quite a few people showed up to mine. I started by saying I had a presentation but would prefer if people just asked questions along the way. And the great part was - did they ever. This included some by Freeman Dyson - kind of cool to have the guru asking me questions about microbial colonization of babies. Finally, after I had spent too much time on background - Drew Endy said something to the effect of "Lets get to the technically hard stuff" and I briefly discussed using genome sequencing to study microbes that live in and on humans. And then - we just had to stop.
I decided to linger for the wrap up session after lunch so I had lunch, made some phone calls, and then we had a wrap up which was mostly an open mike for comments and this ended up being a bit too much of "It was great" and not enough of "How could we make it better." But hey - it was great so I guess I understand. I went around saying thanks to the Google team and the Nature and O'Reilly folks and then moseyed on to the train back to Davis.
Some brief notes about the end and the new beginnings:
- I got lots of ideas for new projects and new things to do from this meeting as with the last one.
- Over the next few weeks I will be posting about some of the other things I saw there and discussing why/how they are interesting.
- I think this "un-conference" style would be really good to emulate for other gatherings. Not sure how to pull it off though.
- I know I will get in trouble from some of my Open Access colleagues, but I definitely came away from the meeting being really impressed with some of the things Nature Publishing group is doing. They really seem to be trying to move into the Web 2.0 area for science communication with Nature Preceedings, and the Nature Network and Scintilla and Connotea and Podcasts and of course Scifoo. Sure there were probably too many people from Nature at Scifoo, but hey, they were sponsoring it so why shouldn't they send them? Here's hoping that they continue to experiment with Open forums and Open material and that they change to OA for all their publications as a way to bring in more people to their Web services. And lets hope other publishers, especially truly open ones build similar resources for the community.
- Thanks to Timo Hannay, Tim O'Reilly, and all the folks at Google, Nature, and O'Reilly for organizing this and inviting me.
The authors are Nicholas H. Barton, University of Edinburgh, U.K.; Derek E.G. Briggs, Yale University; UC Davis’s Eisen; David B. Goldstein, Duke University Medical Center; Nipam H. Patel, UC Berkeley. Eisen holds appointments at the Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology at UC Davis.
New textbook illuminates the close links between evolutionary and molecular biology
COLD SPRING HARBOR, N.Y. � In an innovative approach to the subject of evolutionary biology, a new book, Evolution, combines the contemporary fields of genetics and molecular biology with traditional evolutionary theories to provide an elegant, cohesive view of biology. The book, which was recently released by Cold Spring Harbor Laboratory Press (), is geared toward all biologists seeking a clear, current, and comprehensive account of evolutionary principles and processes. It is a new and innovative choice of textbook for undergraduate courses in evolution.
�It is the most comprehensive book out there, with an admirable and clear presentation of the facts,� wrote Trevor Price, Ph.D., in a pre-publication review of the text. �I personally learnt a great deal...the book as a whole would be useful for workers in the field as a source of reference and to give them breadth.�
The branches of biology concerned with molecular events and evolutionary principles have developed independently of one another. But with recent breakthroughs in fields such as genomics, developmental biology, human genetics, and biochemistry, it has become yet more evident that evolutionary principles guide biological phenomena at all levels, and are essential to a practical understanding of these phenomena.
The authors, who are world-renowned experts from diverse biological backgrounds, illustrate how basic processes such as natural selection, optimization, and conflict occur at the molecular level as well as the organismal and ecological levels. They illuminate evolutionary principles and mechanisms with examples from across the spectrum of life�from �jumping genes� and RNA molecules, to populations of yeast and E. coli reared in the laboratory, to dung flies, lizards, and deer in their natural habitats.
�Evolutionary biology underpins all our knowledge of the living world,� write the authors. �[It] is a synthesis of Darwinian natural selection and Mendelian genetics. It allows us to ask not just how life evolved, but why it is as it is: Why do organisms develop from a single cell? Why is the genetic code as it is? Why is there sexual reproduction?�
The book is divided into four sections. The first three sections detail the history of evolutionary and molecular biology, describe the origin and diversification of life over the past 3.5 billion years, and explain the fundamental mechanisms underlying evolutionary change. The final section is devoted to human evolution and diversity, merging recent insights from molecular techniques with paleontological evidence. For a complete table of contents, see .
David B. Goldstein�s principal interests include human genetic diversity, the genetics of neurological disease, population genomics, and pharmacogenetics. His laboratory currently investigates how human genetic variation influences the response to drug treatments for common neurological and cardiovascular disorders. He is Director of the Center for Population Genomics and Pharmacogenetics at the Duke University Medical Center.
Nipam H. Patel initially studied the development of several model and nonmodel species, including cows, chickens, grasshoppers, and Drosophila melanogaster. His research group studies the evolution of development, with a focus on the evolution of segmentation, neurogenesis, appendage patterning, and gene regulation. He is Professor in the Department of Molecular and Cell Biology and the Department of Integrative Biology at the University of California, Berkeley and an Investigator of the Howard Hughes Medical Institute.
- In the end we concluded that if there is to be a Terraforming effort it should be on a near Earth asteroid encosed in some type of shell to retain gases. Sort of Biosphere 4 or something like that. Now we just need an asteroid.
- Dinosaurs, ancient humans, expedition science (Paul Sereno, Gabrielle Lyon)
- Machine Learning in the Natural Sciences
- why does science suck on TV, and what can we do about it? (Adam Rutherford)
- Hunch Engines /Eric Bonabeau/
- For this one I was completely torn. I really wanted to go to Noel Gorelicks discussion of Google's efforts to collate scientific data. But then I remembered my vow to stay away from things I might know something about.
- So I went to a session on MicroUAV. That is, small unmanned aerial vehicles. Holy *$%$. This was the best session I went to. Simply put - it was incredible. The leader (who I found out later was Chris Anderson the editor in chief of Wired) showed the evolution of his attempts to make cheap small UAVs.
- Here is the deal. He started off with trying to figure out all the things he would need to make robust small UAVs - and originally pieced together multiple various gizmos to control the planes and do things like communicate with ground and get GPS signals and take pictures. And then he realized he could use a GPS enabled cell phone with a CAMERA for all the functions and this helped reduce the costs of the planes such that one can now make one for < $700. Really. See DIYDrones.com.
- And then he showed us pics he had taken that AM of a fly over of Google HQ. Friggin' incredible. It was amazing from the fun point of view but also - I hope to use such UAVs to do sampling of microbes in air ...
- And one of the last things I heard in the session "And the sky will darken with Robots"
Session 7. Here the choices were:
- Data Mining the Sky, knoledge extraction and real-time discovery (Tony Tyson)
- All-Fluidic Computing, large-scale biological
- Science vs. Capitalism: Utopian Effots in the Overshoot Century. (KIm Stanley Robinson)
- Buildings engergy use and behavior change - can the built environment be an interface?
- The Paperless Home (Martha Stewart)
- Provenance Analytics: Illuminating Science Trails and the Future of Scientific Publications
- And here I chose to see what Martha Stewart had to say about the Paperless Home.
- Just before the session, Bora asked her about whether that meant no toilet paper and she responded by saying everyone should use bidets (really).
- She started off really well I thought - saying that homemakers are underserved by technology.
- She also complained about organizers made by other companies including Microsoft and said her plan was to make a better organizer for the homemaker.
- She also said that people need this because they need time for their families and she mentioned that many men spend less than 15 minutes a day with their kids. She also said she wanted this to help support the family unit, whatever that family was (referring back to her introduction when she said that the family has changed a lot but not saying that she thought new family structures were bad).
- She made a bunch of digressions that were basically the equivalent of "My magazine is brilliant and perfect" but I guess this did not surprise me since I think it is good that she is a perfectionist
- She did say she considers herself a typical customer for such an organizer - which made many people literally groan. Yes, Martha, with her 100s of millions of dollars, her boyfriend who pays 30 million to go into space and her many homes and giant houses and teams of assistants, she is the perfect customer.
- She did make some insightful comments about home technology like "I don't mind my talking to my computer but I do not want my refrigerator talking to me" when she was complaining about all the noise some gadgets make.
- Then she said nobody wants a drier that buzzes when it is done (I agree with her that this is annoying). She then asked the crowd if anyone wanted the buzzer and Paul Ginsparg said yes. So she skeptically dissed him and asked him why when he could just wait a little bit and put in the load a bit later. So he said "He wants to get another load in as fast as possible so he can spend more time with his kids", referring back to her comment about fathers not spending time with their kids. She knew she had lost this argument and she moved on to another topic.
- She made a funny reference to "Nature" magazine as though it was about you know, plants and bugs and well, "nature."
- In the end, I guess I agree with Anna Kushnir in her brilliant "Letter to Martha" that she missed a chance to get technogeeks interested in helping the homemaker. I felt this was happening and asked her a leading question trying to get her to say something about what technogeeks could do to help but she misunderstood and answered some other question.
- In the end, I am glad I went to her talk --- it was off the beaten path and memorable even if it was not technogeeky enough for me.
And finally we had the last session. The choices here were:
- Reinventing scientific publication (Web 2.0, 3.0, and their impact on science)
- Piracy, Murder and a Media Revolution
- Engineering Living Instruments, android sensors
- Nanohype: The volumnious vacuous vapid world where only size matters.
- Biohacking science security society (Greg bear)
- The user-generated content I like (anyone can show the content they like on the internet)
- Science communication with comics... come turn your science into comic books
- And here I went to Greg Baer's session on Biohacking. It was quite interesting with a wi
- de ranging discussion of biohacking, biodefense, biosafety, etc.
- I am not sure everyone came out with the same conclusion though. I came out thinking -- we should not worry about biohecking compared to normal pathogens. But many other people said later they came out of it scared about hackers making nasty viruses and killing us all. I mean - I think the community should worry a bit about genetic engineering and put into place safeguards against terrorists and accidental released. But I still worry more about MRSA and XTR TB and so on.
- For the first session, the choices were:
The Next Big Programming Language /Josh Block & Bob Lee/ Open Science 2.0 /BoraZivkovic/ Digital Data Libraries /Mike Halle/ Citizen Science - Where Next? /John Durant/
Future of Healthcare /Richard Satava/
Visual Garage - We'll Fix Your Graphs and Visuals /Felice Frankel/ Quantum Computing - What, Why, How /Frank Wilczek/ Synthesizing Life /Steve Benner/
- Well, actually, I could not chose as I told Bora I would help with his session on Open Science. This one turned into a passionate conversation about many topics relating to Open Science. There was also quite a collection of people there including young and old. Much of the initial discussion was around the problems and difficulties in doing Open Science (see here and here and here for more detail on this and the session overall - in particular the young scientists, who I felt did not get enough time to talk in this session, had many concerns). I felt Pam Silver expressed the most important and interesting concern which was that she said that students in the Systems Biology program at Harvard seemed most dismayed by the slow pace of publishing). Some other comments by the village elders that were present (e.g., Eric Lander and Carl Djerassi) were not overly encouraging in terms of how people get jobs in the field (I am not sure Eric understood what the young scientist's concerns were completely and I think he may have made them feel worse about things when he was trying to make them feel better).
- I think I sent the session down the wrong path at the way beginning by talking about the need to identify roadblocks to Open Science and to figure out ways to circumvent them. This is a true need but it made the beginning of the session seem more about problems than visions for the ideal future, which is what most people seemed to have expected.
- But then Paul Ginsparg and Dave Carlson got us back to talking about the good, positive things about Open Science. Most importantly for me, we got a brief look at Jean Claude Bradley's Open Notebook system which I would like to use in my lab.
- Here the choices were:
Efficient Inverse Control: Through the Users Not the Resources /Wefi Vardi aka Neuman/ Clinical Problems in Neuroscience / Towards Practical Cognitive Augmentation /Vaughn Bell/ / Towards Practical Cognitive Augmentataion /Ed Boyden/ How to Build Intelligent Machines /Jeff Hawkins/ Why aren't there more Scientists on the Covers of Magazines /Jackie Floyd/ Future of Human Space Flight and Ocean Exploration /D Mindell/ Science and Art /Brian Derbey/ 3D Video Applications: How to Publish Science in Video /Steve Silverman/ The Nature of Time and Mathematics /Jaren Lanier & Neal Stephenson & Lee Smolin/ Alternate terms of Science Education Future History of Biology /Rob Carlson/ Human Cell and Regeneration Map or is it worth building a cellular resolution database for the whole human body? / AhilaAttila Csordas /
- I was completely torn here and even ended up being late because I was staring at the bulletin board trying to decide. Finally I went to "the future of human space and ocean exploration" since I thought this was going to be split into space for the first half hour and ocean for the second. Instead they talked about space the whole time I was there and the ocean exploration representative did not get too many words in. But the space discussion was actually really interesting with Pete Worden, the head of the NASA Ames Research Center there discussing future space flights and many other space afficionados present. I thought the most insightful and interesting comments in the session came when everyone was talking about how to better publicize space travel such that it got better attention. And then Larry Page from Google said, basically, that this was simply "marketing" and that the key was to do really cool things in space and not worry about the marketing. This also relates to the safety culture of NASA and other space travel agencies - many of us pointed out that 1000s of people die every day from various causes and that if space travel cannot take risks and accept that some people will die, we have no hope of doing anything interesting in space (e.g., Page pointed out that more people probably dies in the making and moving of the space shuttle than have died in the accidents).
- And though I promised myself I would go to things I knew nothing about, I simply had to go to this one by Eugenia Scott on evolution education.
- Here I found the discussion quite varied and interesting. Some people suggested that evolutionary biologists should be careful about what they say because intelligent design supporters might use it for their own good. Henry Gee and I were adamant that one should not temper ones science for such fears.
- Other interesting things in the session: Dwayne Spradlin did a good job of making everybody justify assumptions that they made about people and Sarah Keller pointed out that it would be useful to have evolution education in chemistry classes
- Then it was time for a Googlicious lunch (OK - it was not as good as I had expected but it was better than any other conference food I have had). Paul Ginsparg and I went through the line together and decided to sit outside the tent. Good choice as inside the tent was absurdly loud. Really good talking to Ginsparg for a while about PLoS and Open Access. He is one of those people who, when you find out he won a Macarthur "genious" award you are like "well, duh - how could he not win one?"
- After we sat down Larry Page and Lucy Southworth sat down as did some others who I have already spaced out on. The best part of the conversation at lunch was Larry Page giving Ginsparg grief about some technical annoyances Google found in their early days with the Arxiv preprint archive. Apparently, Google had to shut down some connections/services to Arxiv for a while and this was the first conversation about it.
- Also interesting was briefly hearing about Lucy's work at Stanford on mouse aging and changes in gene expression. This was particularly interesting to me since I hope to study how microbial populations inside animals change with aging. I unfortunately did not get enough time to interrogate her about her project - the perils of having too many interesting things going on.
Some more comments on Day 1.
- Paul Serano and colleagues had a display of dinosaur fossils in the main reception area. They announced that they did not want anyone publishing pictures of the fossils since they were unpublished, following the big trend among paleontologists to not be too open about anything. Funny since Serano also gave some lip service to the idea of openness and sharing --- clearly what he meant was different from what many others meant.
- I talked to Eugenia Scott for a bit before the sign ups and gave her the lowdown on SciFoo, and encouraged her to have a session on Evolution education, which thankfully she did.
- The three words I chose for my introduction were "Microbes Rule Planet, " which of course is true.
- Tim O'Reilly was the grandmaster of introductions. He was running around introducing as many people as he could to others he thought they would find interesting. He introduced me to Jim McBride (who is currently I think working with Howtoons). We had a good conversation about how the best way to attract good mathematicians to something in biology is to make sure the math is really hard (and why in general it is fun to work on something hard).
- Martha Stewart gave a brief summary of how she made food for Charles Simonyi's space flight and trip to the International Space Station.
- The food, as always at Google, was quite good.