Friday, February 29, 2008

Spora and Gaia: How Microbes Fly with Their Clouds

WD Hamilton is my favorite scientist of the 20th century. He may not have had the largest impact, nor may he have had the most awards, but his relentless creativity is an inspiration to us all. This week's citation classic is an example of his wide ranging interests.

WD Hamilton and TM Lenton. 1998. Spora and Gaia: How Microbes Fly with Their Clouds. Ethology, Ecology and Evolution 10:1-16.

In the paper, Hamilton and Lenton hypothesize that some microbes use chemical induction of water condensation (ice nuclei) to enhance their own dispersal between habitats. The bacteria are supposed to create ice nuclei by releasing a gas called dimethyl sulfide (DMS). But this is an example of a cheater-prone trait. Non-producers can reap the benefits of DMS production without paying the energetic costs. So why are microbes producing DMS?
The idea that algae might produce DMS to get themselves into the air occurred to Hamilton first. 'Tim had mentioned that DMSP has a possible function as an antifreeze,' he recalls. 'Now why would a cell in a tropical ocean need antifreeze? Perhaps they sometimes end up high in the air, shot up there by a waterspout. Or maybe there are other ways they could go. Convective energy created by cloud formation would help them.' Flying high, the algae would be exposed to very low temperatures. Idle speculation rapidly led to the formation of a theory that beautifully explains why algae produce DMS. 'Seldom have I had a run of reading where so many papers were relevant or connected and nothing contradicted my ideas," says Hamilton. "I felt certain that there was something interesting here.'

As the Hamilton and Lenton write, "Dispersal is extremely important to life, indeed for self or progeny, it can be considered an organism's third priority after survival and reproduction". Thus microbes may be creating wind, clouds, rain, and snow to carry them around the globe. A great synopsis of the article appeared in the New Scientist, when the paper was first published.

When I first heard about these ideas, I thought them sort of fuzzy, cute and entirely without substance.

But some recent reports are suggesting otherwise. An article by Brent Christner et al. in today's issue of Science shows that ice nucleators are microbial in origin.

"Despite the integral role of ice nucleators (IN) in atmospheric processes leading to precipitation, their sources and distributions have not been well established. We examined IN in snowfall from mid- and high-latitude locations and found that the most active were biological in origin. Of the IN larger than 0.2 micrometer that were active at temperatures warmer than -7C, 69 to 100% were biological, and a substantial fraction were bacteria. Our results indicate that the biosphere is a source of highly active IN and suggest that these biological particles may affect the precipitation cycle and/or their own precipitation during atmospheric transport."

One of the coolest aspects (to me) is that one of the organisms responsible may be Pseudomonas syringae, an organism I use in my own lab. Although it remains unclear which microbes may be most responsible for snowfall or rainstorms, one leading candidate is the plant pathogen Pseudomonas syringae, which infects wheat, corn and other crops. It is a major pest—and the target of genetic modification—because it causes immediate crop damage if the temperatures drop below freezing.

The reason I find this interesting is that I study P. syringae's phage: the cystoviridae. A recent report found that "phages isolated from single clovers were not consistently more similar to each other than to phages isolated from sites across the country [i.e. opposite coasts] or from other previously isolated phages... These data are thus consistent with frequent continent-wide migration in the Cystoviridae."

Olivia Judson writes about Life and Clouds.
A synopsis of Christner et al.'s work is available at Science Daily.
Photo from Nicholas T

Sunday, February 24, 2008

Science Debate Update

From the ScienceDebate2008 team:

In response to the broad and growing interest in Science Debate 2008, the AAAS held a candidates forum in Boston last week and we got terrific coverage, though only two campaigns sent representatives. You can read about it here, and find other news stories on our home page.

Former White House Chief of Staff John Podesta told the candidates in a video last week that they need to come to Science Debate 2008 in Philadelphia - it's important to the future of our country and to the future of the planet.

You can see John Podesta's video here, along with videos to the candidates from John Porter, Neal Lane, Rita Colwell, and other high-profile supporters. We encourage you to embed these videos in your own site and to email the links to them widely. Check back frequently as we post more.

Over 100 major universities and other leading organizations have now signed on, as have the CEOs of leading tech companies including Intel, Texas Instruments and many others, over 70 university presidents, congresspersons of both major parties, present and former presidential science advisory committee members, and over 17,000 of America's leading scientists, engineers, executives, and concerned citizens. The list is astonishing.

All told, we now represent over 125 million American voters. From the health of the economy to the health of our families to the health of the planet, Americans understand what the candidates have yet to fully grapple with: issues of science and technology are critical to our future.

Despite the importance of this discussion to all Americans, we haven't yet heard back from the campaigns.

So we need your help. This is a unique moment in American history when you can truly influence the future direction of the nation and the world by helping us elevate science and technology in our national political dialogue.

If you run an organization, we need your office to contact the campaigns, direct them to the videos and the invitation, urge them to RSVP to this debate for the sake of America and the planet, and encourage your members to action.

If you are an individual, we need you to contact the campaigns directly and urge them to accept our invitation, which they can see on our site, in case they have lost their copies. We suggest you watch the videos for ideas of what to say, or borrow from the written statements. We also encourage you to write letters to the editor of your local paper of 200 words or less, telling people about Science Debate 2008 and urging the candidates to attend for the good of America.

Please email, call, and write the campaigns here:

  • Email, call the Clinton campaign at (703) 469-2008 and write to Hillary Clinton for President 4420 North Fairfax Drive Arlington, VA 22203
  • Email, call the Huckabee campaign at (501) 324-2008 and write to Huckabee for President, Inc. P.O. Box 2008 Little Rock, Arkansas 72203
  • Email, call the McCain campaign at (703) 418-2008 and write to John McCain 2008 P.O. Box 16118 Arlington, VA 22215
  • Email, call the Obama campaign at (866) 675-2008, and write to Obama for America P.O. Box 8102 Chicago, IL 60680

Thanks for being a part of this important initiative. Finally, please consider making an online donation here to support our volunteer effort.

Friday, February 22, 2008

The Evolution of a Creationist

For those of you who have access, there is a great article in this week's Science magazine about Paleontologist Stephen Godfrey.

Godfrey was raised a young-earth creationist, but had a keen interest in biology from an early age. His parents did not dissuade him from his interests.

"I guess they figured that the young-Earth creationist position was strong enough, was robust enough, that he would believe in young-Earth creationism and he would be a biologist, and that would be fine," says Godfrey.

At college, Godfrey was convinced that scientists were engaged in a vast conspiracy to promote evolution. However, the more Godfrey learned about biology, the more he found his religious beliefs untenable.

"For example, there was the quandary of death. A literal reading of Genesis indicates that no animals perished before Adam and Eve ate the fateful apple--in other words, that there were no carnivores preying on other animals. But in his biology classes, Godfrey learned of predators perfectly framed to kill: cats with stereoscopic vision, enlarged canines, and claws; spiders that weave webs as traps; and sharks that replace serrated teeth throughout their life. "They're not eating seaweed," says Godfrey, who puzzled over how these animals had emerged if God hadn't intended them to prey on others. "That was the first thing at university that really started to disturb me," he says."

Following college, Godfrey entered graduate school in Paleontology at McGill University with Robert Carroll. The major shock came when, on a field expedition to Kansas with Robert Reisz, Godfrey was quarrying through thin layers of rock. "We started to come across footprints of terrestrial animals," says Godfrey. 'You can't imagine a global flood and animals finding ground to make footprints on. … That, more than anything, any other experience in my life, really shook me to the core.' Godfrey agonized about where these footprints might have come from.

Godfrey finally came to embrace evolutionary theory as a postdoc with Reisz. "Godfrey often drove southeast to Dinosaur Provincial Park [in Alberta], passing through a landscape of sediments laid atop one another: deposits from freshwater and terrestrial environments in one, marine organisms and mollusks in another, and a third that mimicked the first, a mix of fossils from fresh water and land. 'These animals were living here in this same place, but they couldn't have all been there at the same time,' he says, a fact that was irreconcilable with flood geology. It was then that 'the rest of the young-Earth creationist ideas kind of exploded.'"

What struck me most about the article is the personal and family difficulties faced by those making the transition.

"'The day I had to tell my mother I wasn't a young-Earth creationist was the scariest day of my life,' says Denis Lamoureux, who teaches science and religion at St. Joseph's College in the University of Alberta in Edmonton, Canada."

People like Godfrey tend not to advertise their painful transition from creationist to evolutionist, certainly not to scientific peers. When doubts about creationism begin to nag, they have no one to turn to: not Christians in their community, who espouse a literal reading of the Bible and equate rejecting creationism with rejecting God, and not scientists, who often dismiss creationists as ignorant or lunatic.

"Nothing else I have done in my life has made me such an outsider," says Brian Alters, director of McGill University's Evolution Education Research Centre in Montreal. Alters has written books on teaching evolution and testified in the 2005 Dover, Pennsylvania, trial against bringing intelligent design--a form of creationism-- into the classroom. But few of his friends or his enemies know that Alters, who had a fundamentalist Christian upbringing in southern California, rejected creationism in college. More than 2 decades later, he says, "I still have childhood friends and relatives who won't speak to me."

Personally I find the heated rhetoric on both sides of the debate distasteful (although I, too, confess to such rhetoric on occasion). Hopefully we can come to understand and have compassion for those of us that are struggling to understand our world.

Godfrey is the author of Paradigms on Pilgrimage: Creationism, Paleontology and Biblical Interpretation. A profile of Godfrey is available here.

Photo taken by R.A. Price. Steeply dipping axial plane cleavage. These folded sedimentary layers exposed near Sullivan River in southeastern British Columbia dramatically illustrate the awesome forces constantly at work reshaping the features of the earth. One of the Geological Survey of Canada's tasks is to examine, study, and report on the effects and the causes of such forces.

Tuesday, February 19, 2008

Are you a science blogger or know of any cool science blogs?

I've been meaning to update my blogroll, but haven't found the time. So I've got a small request for my readers.

If you are a science blogger and you would like for me to include you in my blogroll, please leave a comment.

If you know of a good science blog and think I should include it in my blogroll, please leave a comment.

Thanks kindly,

The Evilutionary Biologist

Monday, February 18, 2008

Whither Nanobacteria

Supposedly nanobacteria are cell-walled organisms much smaller than the generally accepted lower limits for cell size. The existence of nanobacteria has been a hot topic because of their putative roles in and heart disease and kidney stones.

There's even a company devoted to commercializing nanobacterial products: Nanobac. There's even a video of "nanobacteria" in action.

A new article in PLoS Pathogens says that's all balderdash. Here is the authors' summary:

"In the last decade, the exact nature of nanobacteria was one of the most controversial of scientific questions. An audacious theory proposed the existence of nanobacteria, initially discovered in Italian hot spring deposits, as a new life form responsible for a wide range of diseases in humans, thus qualifying them as new agents of emerging infectious diseases. The community of microbiologists remained therefore skeptical about the fact that such structures, 100 times smaller than bacteria and highly resistant to heat and other treatments that would normally kill the latter, could be living entities fully capable of self-replication. Other scientists wondered if they might be an unusual form of crystal rather than micro-organisms. The comprehensive characterization of nanobacteria was the focus of our study. Our results definitively ruled out the existence of nanobacteria as living entities and revealed that they correspond to self-propagating mineral-fetuin complexes that we called “nanons.”

If the authors are correct, the result is very interesting, despite putting a damper on hopes for a novel form of life. The authors suggest that the "nanobacteria" are in fact protein-mineral complexes, which no doubt precipitated confusion over their origins. The proteins in question, fetuins, are also known as binding proteins which mediate the transport and availability of a wide variety of substances in the blood stream. Usually they are known as potent inhibitors of sytemic calcification, so this new report is somewhat surprising.

The authors speculate:

"that the conformational change of the fetuin protein, equivalent to that observed in prions, can occur. This ... leads to a new 'pathogenic' fetuin isoform able to induce hydroxyapatite crystallization and to promote calcification."

If so, it would be highly novel and interesting. I don't believe, however, we have heard the last from the nanobacteria proponents, and this should be a controversial and interesting area of science for some time to come.

Photo: EM Analysis of Nanons Following Immunogold Staining (doi:10.1371/journal.ppat.0040041.g005)

Friday, February 15, 2008

What makes a great scientist...

Aiming high? Check out this article in this week's PLoS Computational Biology.

This Week's Citation Classic

This week's citation classic comes from John Tyler Bonner, an Emeritus Professor in the Department of Ecology and Evolutionary Biology at Princeton.

Bonner, JT. 1947. Evidence for the formation of cell aggregates by chemotaxis in the development of the slime mold, Dictyostelium discoideum. J. Exp. Zool. 106: 1-16.

Slime molds, despite their name, are pretty neat. Much of the time, they wander around as single ameboid cells. However, when food is restricted, they aggregate into multicellular body. The aggregated cells eventually form a stalk, and a fruiting body from which spores are released.

For one, slime molds are marvelous examples of the importance of dispersal. When the going gets rough, organisms have highly ingenious methods for relocating. More importantly, slime molds are a great model for studying the evolution of cooperation. In the multicellular form, the cells in the stalk sacrifice their lives to ensure the survival of the group. Only those cells in the fruiting body will leave offspring. This altruistic behavior usually can only occur via kin selection, and as such, slime molds provide scientists a great system to study how social cheating is prevented and evolutionary conflict is resolved.

In addition to evolutionary biology, slime molds are great models for studying cell motility, signal transduction, cell-type differentiation and developmental processes.

Much of the scientific success of this model organism can be attributed to John Tyler Bonner. Before Bonner's work, slime molds were mostly a biological curiosity. Bonner was casting about for a PhD thesis at Harvard when he decided to test whether D. dictyostelium aggregation was enabled by chemotaxis or by other means (e.g. contact guidance). Using a clever approach, Bonner showed that aggregation occurred by chemotaxis, and the chemical attractant was a compound later given the name acrasin1. The photo below is taken from Bonner's paper.

Bonner wrote, with characteristic humility, "[The paper] is cited so often [because] I devised a physiological salt solution... which has been used by many workers in the field. It is a simple mixture of NaCI, KCI, and CaCl2, which keeps the amoebae happy and healthy.... I was greatly elated by the fact that they referred to it as 'Bonner's solution.' What could be more impressive than having a 'solution' bearing one's name? ... I occasionally find bottles in our laboratory refrigerator labeled 'BS;' it gives me a feeling that one of my graduate students is sending me a message."

Cool site alert: DictyBase
Cool article

1. The term acrasin was descriptively named after Acrasia from Edmund Spenser's Faerie Queene, who seduced men against their will and then transformed them into beasts. Acrasia is itself a play on the Greek word akrasia, which describes the loss of free will.

Top Figure: Development of Dictyostelium (M. Grimson, R. Blanton, Texas Tech University)

Tuesday, February 12, 2008

Happy Birthday Charlie!!

History's greatest scientist, Charles Robert Darwin was born on this day in 1809. We celebrate Darwin Day in his honor. Here are some blogging posts celebrating Darwin's Birthday.

Sex, Genes and Evolution

Reconciliation Ecology

Semour Benzer

PLoS Biology has published Semour Benzer's obituary. Benzer died late last year and was an intellectual hero of mine. I blogged about his work here. Jonathan Weiner of Beak of the Finch fame also wrote a biography of Benzer: Time, Love and Memory. I highly recommend it.

Sunday, February 10, 2008

Darwin Day

February 12 is Darwin Day! This year we have no classes. OK well it's also President's Day, but its still a great day to celebrate the diversity and marvel of life.

Friday, February 8, 2008

Phage Therapy

Cesar Sanchez put together an excellent post on bacteriophage therapy over at Twisted Bacteria. The highlight includes a BBC documentary that I had previously been unaware of.

Phage therapy is the use of the parasites of bacteria to combat bacterial infections. It was once held in high regard, but use declined with the advent of antibiotics. However, now that antibiotic resistant microbes are becoming more common, scientists in the West are re-exploring phage therapies (some in the East never stopped).

I've posted a few times on phage therapy here and here.

Photo: Phi6 infecting Pseudomonas phaseolicola from Dennis Bamford.

Thursday, February 7, 2008

Double-blind reviews

The peer review process in science is typically single-blind, i.e. the authors do not know the identity of the reviewers, but the reviewers are aware of the identities of the authors. This situation always puzzled me; is it not better to have a double-blind system?

My own experience suggested that it is wise. I recently received a manuscript where I was aware of the authors' identities. The final author (of several) is quite well respected, if not eminent. The paper, however, was crap. As I sat down to write the review, I began to second-guess myself. Maybe I don't know what I am talking about and Dr. Eminent has a much better command of the subject, after all I am just a junior faculty and he is a big shot professor at a prominent university. In the end, after talking to colleagues, I decided I was correct in my initial assessment and returned a "reject" review. A few weeks later I received an email showing that my decision was supported by a similar conclusion from the other reviewer.

I can easily imagine a situation where this process could have gone the other way, that is accepting poor quality work because of the eminence of the author.

This week's Nature has an editorial on the subject. If access is denied, it can be accessed here.

The editorial makes the point that, "Knowing author identities also makes it easier to compare the new manuscript with the authors’ previously published work, to ensure that a true advance is being reported."

I don't agree. In my opinion, the reviewer's job is to comment on the quality of the present work, whereas it is the editor's job to judge on the novelty in light of previous work by the same author or by others. Obviously the reviewer can do this too, even without knowledge of the author's identity.

Another issue is that, "referees could identify at least one of the authors on about 40% of the papers, undermining the raison d’ĂȘtre for double-blinding."

Well of course you can play the guessing game (I've often tried to decipher the ID of a reviewer), but you never know for certain.

The editorial also suggests that double-blinding is contrary to openness. This is difficult to assess; however, I might have to agree with it. I've experienced several situations where I've become aware of another team's work by virtue of seeing their work in review. Collaborations were initiated before the work appeared in print. With double-blind, this might not be possible.

Anyway, PLoS abandoned double-blind reviews, supposedly because too few authors chose it. I was unable to find further information. I'd like to know more behind that decision.

You can comment on the editorial via Nature blogs.

Wednesday, February 6, 2008

This Week's Citation Classic: Joshua Lederberg

Joshua Lederberg passed away last Saturday. He was truly a giant in microbiology. When I first joined the Department of Ecology and Evolutionary Biology at Yale, I visited the building on a weekend, and having no key, couldn't enter. As I walked around the building looking for an open entrance, I noticed a plaque near the front portal. I forget the exact wording, but in effect it says, "Here, in this building, Joshua Lederberg made his most important discovery, genetic exchange in bacteria, for which he received the Nobel Prize in Physiology and Medicine in 1958." (He was only 33!). With that, I felt great pride and amazement that I would work in the same building (possibly even the same lab!) as one of the greats in my field.

One of Lederberg's most cited papers is: Lederberg, Joshua, E. L. Tatum, "Gene recombination in E. coli", Nature 158 p. 558, October 19, 1946. It was his first published paper. It is very short and only takes up a quarter of a page in Nature.

Its findings, however, were revolutionary. Previously it was unequivocally assumed that bacteria reproduced asexually by binary fission and no genetic exchange or recombination occured. Lederberg and Tatum were able to find evidence that a wild-type bacterium E. coli K-12, lacking the ability to grow on certain media was able to acquire genes that permitted it to grow on that media, when reared with strains that possessed those abilities.

The most important effect of this discovery was that it established bacteria, K-12 in particular, as appropriate organisms to study genetics.

The experiment is described in greater detail on the National Library of Medicine website and I post the relevant section:

[Lederberg] took two of Tatum's double mutants of the K12 strain, each unable to synthesize two different nutrients (the vitamin biotin and the amino acid methionine in the first mutant, the amino acids threonine and proline in the second), to minimize the possibility of reversion to prototrophy, which in double mutants is extremely rare. When he crossed the two double mutants, Lederberg discovered that some of their progeny regained the ability to synthesize the two respective nutrients which previously had to be supplied in the broth for them to grow, and that this ability was inherited by succeeding generations. Such prototrophs were obtained only when the two mutants were mixed, not when single strains were incubated separately. Moreover, all individual bacteria within a colony of recombinants had the same genotype, or genetic constitution. Furthermore, from among the double mutants Lederberg isolated several that in addition to having the nutritional requirements described above were resistant to a bacteriophage, a bacterial virus, that infected E. coli. Resistance to bacteriophage T1 provided a second, so-called unselected genetic marker in this sub-group of nutritional mutants. When Lederberg tested prototrophs for T1 resistance, he found that some were resistant while others remained sensitive to the virus. Most importantly, he was able to demonstrate that the ratio of resistance to sensitivity depended on which parent carried the resistance marker, and that this ratio was reversed in reciprocal crosses (i.e. when instead of parent strain A, parent strain B carried this marker)."

I still use K-12 today, as well as a phage discovered by Lederberg's wife, Esther, phage Lambda.

Photo: Lederberg receiving the Nobel Prize.