Misc. – Page 177 – Jonathan Eisen's Lab

Darwin and Conservatives

The New York Times is reporting that Darwin (and by Darwin, they mean evolution by natural selection) is getting more and more support within the conservative community in the US.

Basically there appear to be two camps emerging. The anti-science group (not what they called them in the Times article but that is what they are) who cannot reconcile Darwinism (or many other scientific tenets) with their religious beliefs. And on the other side are conservatives who not only accept evolution by natural selection as a fact, but embrace it as supporting many of their conservative ideals. This second pro-evolution conservative clade includes fundamentalist types who, like Francis Collins, believe that evolution by natural selection is indirectly the hand of God. The pro-evolution clade also includes political and social conservatives, who are not particularly religiously conservative.

I found the article fascinating in many ways because finally philosophical conservatives are taking a stand against the religious right. For example:

“I do indeed believe conservatives need Charles Darwin,” said Larry Arnhart, a professor of political science at Northern Illinois University in DeKalb, who has spearheaded the cause. “The intellectual vitality of conservatism in the 21st century will depend on the success of conservatives in appealing to advances in the biology of human nature as confirming conservative thought.”

Also — from the article

What both sides do agree on is that conservatives who have shied away from these debates should speak up. Mr. Arnhart said that having been so badly burned by social Darwinism, many conservatives today did not want “to get involved in these moral and political debates, and I think that’s evasive.”

Yet getting involved is more important than ever, after “the disaster” of “President Bush’s compassionate conservatism,” he said, because the only hope for Republicans is a “fusion of libertarianism and traditionalism, and Darwinian nature supports that conservative fusion.”

So I say to all you social or political conservatives who think that anti-evolution talk is not necessary and potentially damaging, come out come out wherever you are. The time is now for evolutionary biologists to embrace these conservatives. Not because they agree or disagree with their politics. But because evolutionary biology does not itself make ANY moral judgements nor force one to make any political decisions. It is science. Just as quantum physics does not support the right or the left, evolutionary science is apolitical. That is not to say that evolutionary science cannot be used to inform political and social and moral decisions. It is just that evolutionary science is not about those things. It is about studying the way the world works.

open access hits the elections

Well, nice to see OA in the political arena. Obama is asking that the video from the Presidential Debates be released without copyright so that it can be freely blogged, etc.

See the SF-GATE article here.

Obama is quoted as saying

“Rather than restricting the product of those debates, we should instead make sure that our democracy and citizens have the chance to benefit from them in all the ways that technology makes possible.”

I could not agree more. Now if only that were the case for all scientific research.

Thanks to Melinda Simmons for pointing this out

BBB – Baseball, bioinformatics, and brothers

I know quite a few people in bioinformatics who are also pretty avid baseball fans. Ian Paulsen and I sneaked away from a conference to go see his beloved Padres last year get slaughtered in two playoff games. A resercher from Wash. U.’s Genome Center caught Mcgiure’s 70th home run a few years ago. An article in Bioinformatics even promotes a software package as being useful for viewing baseball stats.

I have tried to convince people there are connections between the two in the past. But the best article I have seen on this is, for better or worse, about my brother. What a scam he has pulled at Berkeley. He is teaching a course (with James Fraser) ostensibly about bioinformatics in some way. What is is really about? Baseball statistics. They are not even trying to pretend it is about bioinformatics. But they apparently hope that some of the stats rubs off enough that some students get into bioinformatics.

As an ex-baseball player I have some smpathy for their approach. Also, it was at a baseball game that my brother first convinced me that Open Access science was the way to go. But I think focusing on stats is the wrong way to use an interest in baseball to get an interest in biology. I think it would be better to get Drew Endy and his cohort into using one of their synthetic biology competitions to make some good new steroids. And then the stats course could be used to analyze the differences with and without the new drugs.

“I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome.”

OK. I could not help myself with this one after I was sent the quote by Francis Collins in this New York Times Article. Dr. Collins, in relation to a new study that showed that one region of one human chromosome apparently plays roles in heart disease and diabetes, said

I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome.”

Now, I have commented before about how Dr. Collins is doing a pretty good job about keeping his religious beliefs separate from his work. And since he is a strong supporter of evolutionary biology I like to give him the benefit of the doubt (I personally agree with him that there is no need for a conflict between evolutionary biology and non fundamentalist religious beliefs). But I think “the seat of the soul of the genome” is a bit much.

I frequently criticize researchers who observe something in the genome and immediately come up with an adaptive explanation for the observation. Such adaptationist, just so story responses, are common in molecular biology and many areas of biology and were written about extensively by Gould and Lewontin and others. But now I guess we have a new category of adaptationist-like explanations. Striking findings in a genome can now be called “just soul stories.”

Nice plea for Open Access in Harvard Crimson

An opinion piece in the Harvard Crimson (student newspaper) by GREGORY N. PRICE and ELIZABETH M. STARK pleas for students to lend more support to the Open Access movement. It is a well thought out piece and worth a look. I particuarly like the proposal for students to make their senior theses available somehow and for students to write letters to Congress supporting OA.

Fair Use and Open Access

Really interesting blog, with a collection of other information is available from Coturnix at Science Blogs. Basically the discussion revolves around the use of figures from non Open Access publications. She writes:

My esteemed colleague here at scienceblogs, Shelley Batts of the Retrospectacle blog, did what we all do all the time – what is one of the primary role of science blogs: compared what a scientific paper says to what the press releases and media say about the paper. It was a paper widely reported by the press about the potential health effects of drinks like daikiri. Shelley wrote in her post that the paper is fine, but that the media coverage is faulty (what’s new?). In order to demonstrate what the paper really says, she, as we often do, reprinted a table and one panel of a figure from the paper in her post.

The blog has lots of links to other blogs about this issue. My favorite line:

The old model will crumble and the dinosaurs can choose to adapt or go extinct.

My sentiments exactly. You go get ’em.

PS Thanks to Karl Mogel at the Innoculated Mind for pointing this out.

More on the Human Microbiome Program Workshop – Day1

As a follow up to my previous blog I am posting some additional information here about the NIH Roadmap Human Microbiome Project Workshop, which was held in Bethesda, MD.

The general outline of the meeting was as follows:

Sunday Night

Introduction

Welcome by Francis Collins (NHGRI), Hugh Auchincloss (NIAID) and Griffin Rodgers (NIDDK)

Comments by Gary Schoolnik

Overview of the NAS report on metagenomics by Jim Tiedje

Overview of the NIH Roadmap program by Francis Collins

Introductory talks on human microbiome

Jeff Gordon

David Relman

Gary Huffnagle

Jo Handelsman

Monday AM

Technological issues

Elaine Mardis

Jill Banfield

Deirdre Meldrum

Bioinformatics issues

Lior Pachter

Rolf Apweiler

Peer Bork

ELSI Issues Pilar Ossorio

Lunch
Monday PM – Breakout sessions and discussion

Group 1 – Reference microbiome (Claire Fraser and Martin Blaser)
Group 2 – Changes in microbiome and human health (Rita Colwell and Martin Rosenberg)
Group 3 – Enabling technologies (Bruce Birren and Mary Lidstrom)
Group 4 – Bioinformatics tools (Ewan Birney and Owen White)
Group 5 – Ethical legal and social issues (Midred Cho)

Wrap up

Overall, I found the Sunday night talks very useful to set the stage. The introductory talks by the representatives from NHGRI, NIAID, and NIDDK clearly indicated that NIH as well as others consider the human microbiome an incredibly important research area. Then Jim Tiedje gave a nice overview of the recent NAS report on metagenomics (which was about metagenomics in general, not specifically for the human microbiome). The main points of the report are basically: microbes rule the world, metagenomics is a very powerful tool in studying them, and there is a need for a more coordinated effort among funding agencies to push metagenomics as a tool and a field. (My only complaint about Tiedje’s presentation was he kept using the term “higher organisms” for those multicellular species with nuclei. But otherwise, he did a good job of concicely summarizing the report and the benefits as well as challenges of metagenomics).

Francis Collins then gave an overview of the NIH Roadmap Program. The Roadmap was started in ~2003 as an initaitive to identify projects that would need coordination across multiple NIH agencies. These projects should meet certain characteristics: truly transforming, require all NIH, must need incubator scape, and the outcome should produce material into the public domain. Collins then discussed how, from among hundreds of suggestions, the Human Microbiome was picked as one of five topic areas for in depth consideration for the new round of Roadmap competition. Thus the point of this workshop was to discuss this in more detail and help provide material and ideas for the full consideration of an HMP program.

I should note, I found one thing disappointing in the introduction which was a response to my question concerning whether this project would be limited only to studies of humans or would allow for studies of model systems that inform human work. The answer was basically that this would likely be limited to humans. I think this is a big mistake. The human genome project came to the realization that comparative studies with other species were critical to understanding and interpreting studies of the human genome. The same will be true of the human microbiome program.

Jeff Gordon then gave an overview of human microbiome studies, and focused on what are the key questions that need to be answered. Among the key questions: Do we share a core set of microbes? How should we view differences in microbes between people and over time? How do we relate communities of microbes to health and disease? How should we sample microbial communities to characterize them? What determines robustness of microbial communities in people?

To start to answer these and other questions, he suggested that we have three tiers of data collection: (1) deep draft assemblies of microbial communities and reference genomes, (2) reference microbiome work (deep characterization of individuals including information about the familiy history and genetics) (3) 16s surveys of communities (a global human microbial diversity survey). I basically liked all of his ideas. He did talk about work in model organisms too. His work has shown just how important this is … and I think as I said above it needs to be emphasized more in the HMP.

David Relman, from Stanford, then talked about patterns in human microbial diversity. He talked about some of the challenges in such studies as well as results of his and others work. He discussed many interesting aspects of the diversity of samples, and the shapes of diversity. Some of the patterns he emphasized were that history plays a role in the diversity, that archaea generally seem to have limited presence, that diversity is uneven and complex.

Then Gary Huffnagle discussed in more detail the interaction of microbes with the host immune system. And Jo Handelsman discussed what she calls functional metagenomics, which involves focusing on the functions of genes found in the environment on top of examining the phylogenetic diversity of communities. Unfortauntely, I did not take extensive notes for these two talks so do not have much to base my comments on here. In addition, I confess, the fact that the room in which the meeting was held was incredibly crowded and boiling hot, and the fact that I had flown in from California earlier in the day, made taking notes challenging at this point. However, that did not stop me from going out afterwards for a beer with Julian Parkhill, Ewan Birney, Owen White, and Jacques Ravel. The worst part of going out for the beer – I grew up in Bethesda but I made multiple wrong turns in the two blocks to the brew pub. I am sure from now on Julian and Ewan will never trust my directions. Fortunately, the fact that the pub had the RedSox pummeling the Yankees on TV made up for my direction problems.

I will post more about the second day soon.

Jonathan Badger on another reason not to publish in non Open Access journals

Jonathan Badger on his blog has a good little blurb about how he cannot examine a recent piece of research because his institution does not have a subscription to the journal. So the authors lose a reader becuase they published in a non OA journal. Worth a little read for microbiologists since many may not have access to the journal Geology where the paper was published. But the paper was about a fossil that may have been of a fungus.

A human microbiome program?

I am currently attending a workshop sponsored by NIH in which the participants are discussing whether there should be a Human Microbiome Project, and if so, what that should mean.

First, what is generally meant by the “Microbiome.” In essence the humn microbiome is the sum collection of all the microbes found in or on people. The human microbiome has become an important research field because the microbes that live in and among us play critical roles in human disease and health. An important aspect of this is the idea that microbes can be and are beneficial. For example, in the gut the normal microbes help with digestion and nutrient absorption as well as protect from infection. In addition, a variety of diseases (e.g., IBD, Krohns) seem likely to be caused by disruption in the normal microbial flora. In general, it seems likely that other ailments, like autoimmune diseases, allergies, etc will be found to have a connection to disruptions in the beneficial microbes that live among us.

Because of the importance of beneficial / commensal microbes in human biology, there have been growing efforts to characterize the microbes in various body locations – gut, mouth, lungs, skin, etc. But the efforts so far have simply given a tantalizing taste of how interesting and important these microbes are. So here comes this meeting. Organized by NIH (specifically, Francis Collins at NHGRI), this workshop is geared to discuss the possibility that studies of the human microbiome will be included in the next list of “NIH Roadmap” programs. More on the NIH Roadmap some other time.

Basically, the general idea is – do we need an big scale, organized program to tackle the human microbiome.? To get us in the mood, we had talks by many of the pioneers/leaders in the field (e.g., David Relman, Jeff Gordon, Jim Tiedje) as well as discussion of the NIH Roadmap program. I personally did not need any convincing but it was good to hear some of the ideas presented. In the end, I think there is no doubt that a large scale Human Microbiome Program is needed and would be very beneficial.

One of the reasons that an organized effort is needed is that studies of the human micribome are difficult. Reasons for this include:

1. Many of the microbes in the human system have not, and maybe cannot, be grown in isolation in the lab

2. The key features of the microbiome are determined by by populations of microbes and thus even if a representative of a species could be grown in the lab, it would not represent all the diversity in the population.

3. The best way to sample the populations is via “metagenomic” sequencing which involves isolating DNA and sequencing it directly without culturing.

4. Many of the important sites contain hundreds of species each with significant variation within species.

5. There likely will be ENORMOUS variation in and among people. Within a person, there will be variation over time as well as great variation in different sites. On top of that there will be great variation between people.

Given these and other complications, it seems a no brainer there is a need for a coordinated project to gather background information about the human microbiome that would then be useful to researchers, much like the human genome was useful to many researchers. So what would such a project do? Here are some possibilities

1. Sequence many “reference genomes.” By reference genomes here I mean genomes of cultured isolates that are closely related to organisms known in various human locations.

2. Do metagenomic sequencing of a variety of human mcirobiome samples.

3. Conduct large scale human microbiome diversity studies. This could involve rRNA PCR surveys as well as some amount of genome sequencing.

4. Develop the computational tools needed to analyze the massive amounts of data that will come out.

5. Encourage the development of new methods to aid in studies of the microbiome.

So today I guess we will be discussing what specific things are needed in more detail. But again, even though I do not really work on human microbiome projects much, I think it is pretty clear that the time is right for a Human Microbiome Program. And importantly, the methods and tools and discoveries that could come from this will be of use in all studies of microbes in the environment.

That’s all I have for now … will try to write more later.

From bad to good – how a parasite became a mutualist

Just saw this very cool paper in PLoS Biology on Wolbachia that appear to have converted from parasites to mutualists. Wolbachia are among my favorite organisms. They are intracellular bacteria that have been found to infect a wide diversity of invertebrate species. In many cases, the Wolbachia have male specific detrimental effects (I like to call the WMDs – Wolbachia of male destruction). In other cases (e.g., in filiarial nematodes), Wolbachia appear to be beneficial.

I had heard about the work in the new paper from one of the authors Michael Turelli, who was one of the main people to convince me to move to Davis. In this study, the authors returned to examine a population of Drosophila simulans that Turelli had studied some 20 years ago. In the previous studies Turelli and colleagues had found a “classic case” of Wolbachia infection spreading in nature. When they returned to study the population and did a suite of experiments, they found that the Wolbachia had acquired fecundity increasing mutations, making them mutualistic.

Though they have not yet figured out what mutations occurred, it seems that a little genome sequencing might help them. Just a little selfish plug there, since I led the first project to sequence a Wolbachia genome and would love to do some more …

For more information, see Weeks AR, Turelli M, Harcombe WR, Reynolds KT, Hoffmann AA (2007) From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila. PLoS Biol 5(5): e114 doi:10.1371/journal.pbio.0050114.

Weeks, A., Turelli, M., Harcombe, W., Reynolds, K., & Hoffmann, A. (2007). From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila PLoS Biology, 5 (5) DOI: 10.1371/journal.pbio.0050114

Wu, M., Sun, L., Vamathevan, J., Riegler, M., Deboy, R., Brownlie, J., McGraw, E., Martin, W., Esser, C., Ahmadinejad, N., Wiegand, C., Madupu, R., Beanan, M., Brinkac, L., Daugherty, S., Durkin, A., Kolonay, J., Nelson, W., Mohamoud, Y., Lee, P., Berry, K., Young, M., Utterback, T., Weidman, J., Nierman, W., Paulsen, I., Nelson, K., Tettelin, H., O’Neill, S., & Eisen, J. (2004). Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements PLoS Biology, 2 (3) DOI: 10.1371/journal.pbio.0020069

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