The Evilutionary Biologist

Virus Evolution

2009-10-20T09:48:00.005-04:00

Here is a short video on virus evolution from the Instituto de Biologia Molecular y Celular de Plantas and the Santa Fe Institute Professor Santiago Elena.

Synopsis

Viruses can evolve fast and sometimes adapt quickly to a new host species. For example, an influenza virus that normally infects birds can become adapted to humans. The tobacco etch virus normally infects tobacco plants. Professor Santiago Elena from Valencia wants to find out what it takes to make the tobacco virus capable of infecting another plant: Arabidopsis. The movie shows how Santiago Elena does the evolutionary experiment and we see that after 30 rounds of experimental evolution the virus is indeed adapted to the new host plant! After the experiment, Elena looks at the genetic code of the adapted virus and finds that there are just three differences between the genetic code of the normal (tobacco loving) virus and the virus that is now adapted to Arabidopsis.

Lawrence Basil Slobodkin (1928-2009)

2009-09-17T14:50:00.007-04:00

Larry Slobodkin, eminent ecologist, founding chairman of the Stony Brook University Ecology and Evolution Department, and Fellow of the American Academy of Arts and Sciences passed away last Saturday.

Larry's impact on the science of ecology is immeasurable, particularly with regards to linking population dynamics with ecosystem ecology. A concrete example of this is his famous HSS paper. With coauthors Nelson Hairston Sr. and Jerry Smith, Slobodkin use a simple observation (the world is green) to deduce that predators limit herbivore abundance, thus allow plants to flourish.

Beyond his scientific contributions, Slobodkin is reknown for creating the world's first graduate program in ecology and evolutionary biology (at Stony Brook University). Many of the best and brightest in the field have either taught or schooled in this program.

Larry's (academic) nephew, ecologist Mike Rosenzweig, wrote a great piece about him for Evolutionary Ecology Research. Larry contributed this autobiographical article. More articles in the EER special issue in his honor are available here.

NY Times Obituary

Update: Carol Reid wrote a nice tribute to Larry here.

Phage Hunters

2009-09-10T12:12:00.004-04:00

18 freshmen students have enrolled in my Genomics Research Experience course aka Phage Hunters. This course is supported by the Howard Hughes Medical Institute's Science Education Alliance. My students have begun the process of isolating novel Mycobacteriophages by collecting soil samples from the wild and plating them on lawns of Mycobacterium smegmatis, a M. tuberculosis relative. Unlike M. tuberculosis, M. smegmatis is non-pathogenic and is easier to grow and manipulate under experimental conditions. Nonetheless, by virtue of their close phylogenetic relationship, the two bacteria are quite similar in many respects. Thus, M. smegmatis may be an excellent model for deriving treatments against tuberculosis.

Collecting Mycophage is already paying handsome dividends. Albert Einstein College of Medicine Professor William Jacobs isolated a phage he named the Bronx Bomber from soil from his own backyard in the Bronx. With University of Pittsburgh Professor Graham Hatfull, Jacobs characterized this phage in the laboratory. They found that this phage is able to insert itself into the genome of M. smegmatis at a very specific location in the groEL1 gene, thus disabling the gene. One of groEL1's functions is to facilitate the production of biofilms.

Biofilms are extracellular polymeric substances that aid and protect microbes. They allow bacteria to persist in the face of antibiotics. It's estimated that 80% of infections involve biofilm formation. While biofilm formation in tuberculosis has not yet been uneqivocally confirmed, M. tuberculosis does have a groEL1 gene with 90% similarity to that of M. smegmatis.

If the phage is able to infect M. tuberculosis or is mutated to infect M. tuberculosis, it is possible that some day the phage could be used as therapy against tuberculosis. As one of the three primary diseases of poverty, tuberculosis has a devastating impact in the developing world.

Top Photo: Bxb1 is a mycobacteriophage that was originally isolated from Dr. Jacobs' backyard in the Bronx. It is affectionately called "The Bronx Bomber" as it forms large plaques on a plate with lawn of Mycobacterium smegmatis cells (left panel). The Bxb1 phage plaques are characterized with their clear centers surrounded by turbid rings. The turbid rings represent lysogens (i.e. M. smegmatis bacterial cells into which Bxb1 has integrated) of M. smegmatis that are resistant to superinfection with Bxb1 phage. These lysogens are defective in biofilm formation. A transmission electron micrograph of Bxb1 is shown in the right panel. Courtesy of Jordan Kriakov, William R. Jacobs, Jr.

Middle photo: Image shows Mycobacterium smegmatis growing as a biofilm on a liquid surface, with its characteristically textured folds. Courtesy of Anil Ojha, Tom Harper, Graham Hatfull.

Bigfoot or Mistaken Identity?

2009-07-02T14:39:00.017-04:00

Ecological Niche Modeling is a great tool for conservation biology, phylogeography and evolutionary biology. However, as Jeff Lozier and colleagues point out in a paper in Journal of Biogeography, the models are only as good as the data they are based on.

The basic premise of the ENM approach is to predict the occurrence of species on a landscape from georeferenced site locality data and sets of spatially explicit environmental data layers that are assumed to correlate with the species’ range.

This is fine if the researchers themselves collect the data, but many studies rely on publicly available online databases. While no doubt the validity of most of this data is unimpeachable, there can be instances of misidentification or poor taxonomy. These discrepancies have the potential to significantly skew the results. As an extreme example, the authors point to Sasquatch, the North America's purported other large primate. Using data from the Bigfoot Field Researchers Organization, Lozier et al. predict the Sasquatch's range in the Western US (see figure above).

(T)he ENM shows that Bigfoot should be broadly distributed in western North America, with a range comprising western North American mountain ranges such as the Sierra Nevada Mountains, the Cascades, the Blue Mountains, the southern Selkirk Mountains, and the Coastal Range of the Pacific Northwest.

Interestingly, Bigfoot's supposed range overlaps considerably with another large American mammal, Ursus americanus, the Black Bear. Naturally, it is quite possible that the Black Bear and Sasquatch could share similar habitat requirements, but perhaps a more parsimonious hypothesis is that Black Bears are being misidentified as Sasquatch.

Thus, the two ‘species’ do not demonstrate significant niche differentiation with respect to the selected bioclimatic variables. Although it is possible that Sasquatch and U. americanus share such remarkably similar bioclimatic requirements, we nonetheless suspect that many Bigfoot sightings are, in fact, of black bears.

Photo of mangy bear

The take-home message is that scientists should carefully scrutinze literature records and/or public databases. Validate taxonomy. Rely on recognized experts. Don't be afraid to disregard questionable specimens. Ecological Niche Modeling has a bright future, but like any technique it can be properly or improperly applied. The authors should be commended for their clever approach to pointing out the need for scrutiny.

Lozier, J., Aniello, P., & Hickerson, M. (2009). Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling Journal of Biogeography DOI: 10.1111/j.1365-2699.2009.02152.x

Left-handed Snails Beat Snail-eating Snakes

2009-06-13T16:43:00.008-04:00

Masaki Hoso reported that the snail-eating snake, Pareas iwasakii, has lopsided jaws to better enable it to tug snails out of their shells. Most snails have shells that whirl clockwise (to the right) so P. iwasakii has evolved an upper jaw with more teeth on the right side than the left. In a sample of 28 snakes, the Hoso found each one had an average of 17.5 teeth on its left jaw and 24.9 teeth on the right.
The lack of symmetry helps the snake pry the snails out of their shells with alternate retractions of their left and right jaws, a technique called "mandible walking".

Here's a video of the snake preying upon a "right-handed" snail.

The snail, Satsuma c. caliginosa, has countered the snake's adaptation by evolving a left-handed swirling pattern.

Hoso et al. write in Biology Letters:

In addition, our experiments demonstrate a defensive function of sinistrality for snails against snake predators. Sinistral variants have been generally considered to suffer selective disadvantages on account of the overwhelming predominance of dextrals (Vermeij 1975, 2002; Johnson 1982; Gould et al. 1985; Asami et al. 1998; but see Dietl & Hendricks 2006). However, sinistrals should enjoy a selective advantage over dextrals under chirally biased predation by snakes. The remarkable diversity of sinistral snails in Southeast Asia (Vermeij 1975; Hoso et al. 2006, unpublished data) may be attributable to ‘right-handed predation’ by the snakes.

In the video below, P. iwasakii attacks but fails to consume the lefty snail.

How cool is that?

Hoso, M., Asami, T., & Hori, M. (2007). Right-handed snakes: convergent evolution of asymmetry for functional specialization Biology Letters, 3 (2), 169-172 DOI: 10.1098/rsbl.2006.0600

Evolution 2009 Moscow, ID

2009-06-12T21:05:00.003-04:00

I have finally arrived in Moscow, ID for the the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). It was a long and enjoyable drive from Salt Lake City where I met up with Weber State evolutionary biologist and fellow blogger Jon Marshall. Along the way we stopped at Waterfall Canyon and the Hot Pots in Ogden, the Craters of the Moon, Ernest Hemingway's grave, and more hot springs in Stanley.

Several other bloggers are participating in the festivities.

I'll be posting about the scientific content as time permits over the weekend, but now it's time for a few beers at the opening reception and Genie Scott's Stephen Jay Gould Award Lecture "The Public Understanding of Evolution and the KISS Principle."

Roald Dahl on Vaccines

2009-06-05T09:03:00.003-04:00

When I was younger, my favorite book was James and the Giant Peach by Roald Dahl (also author of Charlie and the Chocolate Factory and Matilda). Turns out that book was dedicated to his daughter Olivia, who tragically died of measles. In this article, Dahl stresses the importance of vaccinations.

Dahl writes "...there is today something that parents can do to make sure that this sort of tragedy does not happen to a child of theirs. They can insist that their child is immunised against measles. I was unable to do that for Olivia in 1962 because in those days a reliable measles vaccine had not been discovered. Today a good and safe vaccine is available to every family and all you have to do is to ask your doctor to administer it. It is not yet generally accepted that measles can be a dangerous illness. Believe me, it is. In my opinion parents who now refuse to have their children immunised are putting the lives of those children at risk.... It really is almost a crime to allow your child to go unimmunised."

Vaccine Wars: The Phantom Menace

2009-05-27T12:28:00.006-04:00

It's been 9 months since I read Autism's False Prophets and participated in a discussion over at Science Blogs Book Club. The good news is that there is increased awareness of the overwhelming scientific evidence refutating a link between vaccines and autism. Many organizations including the CDC, the Courts and the National Academy of Science, have all rejected a link between vaccines and autism.

There's even a Jenny McCarthy Body Count. (Former playmate Jenny McCarthy is the most prominent of the anti-vaccine advocates).

So why is the anti-vaccine movement still strong? Oprah has notably given Jenny McCarthy a highly visible platform. Despite overwhelming evidence that vaccines don't cause autism, one in four Americans still think they do. This has led to upsurges in measles, mumps and whooping cough among other easily preventable diseases. Large numbers of unvaccinated kids are dropping the population immunity below the herd immunity threshold for many diseases.

A great article investigating this tragedy is now available at PLoS Biology.

As the article points out, there is a conflict between individual interests and community interests. Pediatrician Jeffrey Baker says that "parents who claim nonmedical exemptions seem to become so focused on their own children that they “lose the bigger picture,” not accepting responsibility for the impacts their actions may have on the health of the community."

Autism's False Prophet's author Paul Offit blames "the media for keeping the myth alive by following the journalistic mantra of ‘balance,’ perpetually presenting two sides of an issue even when only one side is supported by the science. And shows like “Larry King Live” have been “just awful on this issue,” he adds, placing ratings and controversy above public health by repeatedly giving McCarthy and other “true believers” a platform to peddle fear and misinformation."

Medical anthropologist Sharon Kauffman thinks that the easy access to information online has exacerbated the crisis. Kaufman says, “many parents see even the most respected vaccine experts' perspective on the issue as just one more opinion.”

Article author Liza Gross writes, "Scientists on TV and radio are hard-pressed to compete with the emotional appeals of activists....McCarthy emerged as a hero for some parents by telling her story. Personal stories resonate most with those who see trust in experts as a risk in itself—a possibility whenever people must grapple with science-based decisions that affect them, whether they're asked to make sacrifices to help curb global warming or vaccinate their kids for public health. Researchers might consider taking a page out of the hero's handbook by embracing the power of stories—that is, adding a bit of drama—to show that even though scientists can't say just what causes autism or how to prevent it, the evidence tells us not to blame vaccines. As news of epidemics spreads along with newly unfettered infectious diseases, those clinging to doubt about vaccines may come to realize that several potentially deadly diseases are just a plane ride, or playground, away—and that vaccines really do save lives.

"Embracing the power of stories" sounds like framing to me. The notion was abhorrent to me when I first read the Nisbit and Mooney article, but lately I've been feeling less certain regarding the role of scientists in their intersection with the media.

Gross, L. (2009). A Broken Trust: Lessons from the Vaccine–Autism Wars PLoS Biology, 7 (5) DOI: 10.1371/journal.pbio.1000114

Scientia Pro Publica #4 - In Memory of Stephen Jay Gould

2009-05-20T12:19:00.003-04:00

Stephen Jay Gould is my homeboy. True story, he grew up in my present hometown of Bayside, NY. I am honored to be included in a blog carnival in his memory: Scientia Pro Publica #4.

I never met SJG, but I did bump into him once. Literally! When I was a junior in college, I visited MCZ at Harvard on my way to the Ernst Mayr Library. (Back in olden days, we didn't have access to "online" articles. If you wanted an article, you had to go to the library and photocopy it from a bound volume.) As I was climbing the stairs to the library, a door swung open and SJG came barreling out, and collided with me. He hardly hesitated save to glance back and scowl at me. Or maybe it was a look of surprise. Hard to say since it happened so fast. I haven't been so thrilled to see a celebrity since the time I sat next to Bobby Orr at a hockey game.

Missing Link Found?

2009-05-19T11:09:00.004-04:00

Franzen et al. announced the discovery of the most complete transitional fossil primate ever found. The fossil, described as Darwinius masillae, shows prosimian characteristics (e.g. a grooming claw on the second digit of the foot, and a fused row of teeth in the middle of her lower jaw known as a toothcomb), but has toe and fingernails, opposable thumbs, and a humanlike talus bone.

The Conclusions/Significance section of the abstract tells us,

Darwinius masillae represents the most complete fossil primate ever found, including both skeleton, soft body outline and contents of the digestive tract. Study of all these features allows a fairly complete reconstruction of life history, locomotion, and diet. Any future study of Eocene-Oligocene primates should benefit from information preserved in the Darwinius holotype. Of particular importance to phylogenetic studies, the absence of a toilet claw and a toothcomb demonstrates that Darwinius masillae is not simply a fossil lemur, but part of a larger group of primates, Adapoidea, representative of the early haplorhine diversification.

The announcement accompanies a veritable "media tsunami", including a American Museum of Natural History unveiling, a New York Times article, and a two-hour documentary to be broadcast on the History Channel on Memorial Day (May 25th).

Hype? Uberhype?

Probably, but I am withholding judgment until I find out more about it. Generally speaking, I am in favor greater public awareness of transitional evolutionary fossils. Even if this turns out to be somewhat inaccurate, and the precise phylogenetic position isn't directly linked to man, it will still raise awareness of evolutionary theory among an ill-educated public.

Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009). Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005723

The Giant’s Shoulders #11

2009-05-16T16:10:00.002-04:00

The Giant's Shoulders #11 is up at Curving Normality. This month's issue has excellent reads from Schrodinger, Faraday, Darwin, et al. I particularly liked the article by Eric Michael Johnson, who blogs at The Primate Diaries. In the article, Rivalry Among the Reefs, Johnson writes about Darwin's little known coral reef work.

Coral reefs hold an important place in the history of evolutionary theory, as they were the subject of Darwin’s first scientific monograph and his official entrance into the scientific community. It was this research, and his eight-year study of barnacles, that led to the Royal Society awarding him the Copley Medal for outstanding achievement in science. Based on depth measurements taken of the coral reefs at Cook, Keeling and Mauritius Islands, Darwin developed his theory of “subsidence” to explain their development. Darwin didn’t know just how coral reefs grew, but he was aware that the living coral formed fringing reefs just below sea level along many coastlines. He was also aware of white strips of limestone that encircled volcanoes throughout the South Pacific. Darwin theorized that these were the remnants of fringing reefs that had been raised above sea level by the rising volcano. The same logic should therefore operate in reverse; if the coast were sinking then the coral would continue to grow upwards in order to remain in the warm, sunlit waters. Eventually, once the coastline was completely submerged, all that would remain would be the coral atoll. After arguing away every problem that had previously plagued coral reef formation, Darwin was left with his triumphant conclusion.

"On this view every difficulty vanishes; fringing-reefs are thus converted into barrier-reefs; and barrier-reefs, when encircling islands, are thus converted into atolls, the instant the last pinnacle of land sinks beneath the surface of the ocean."

Darwin was later shown to be correct by Dr. Harry Ladd, a researcher for the US Geological Survey. Ladd convinced the US War Department to drill holes deep into the Bikini and Eniwetok Atolls just prior to their obliteration in 1952 by hydrogen bombs.

After digging nearly 5,000 feet through the coral of Eniwetok Atoll, the drill finally passed through and hit pay dirt. The atoll had been built up from coral as the land had sunk from view, just as the theory of subsidence had predicted. Tiny organisms, just millimeters across, had pulled themselves up by their own bootstraps to create the largest natural structures ever created by a living being. Just next to the borehole that ended the debate, Ladd erected a small sign that still stands today. It reads, simply “Darwin was right!”

Figure: Darwin's drawing of a reef from Voyage of the Beagle.

Evolver Zone

2009-05-10T08:53:00.002-04:00

University of Guelph Professor Ryan Gregory's Evolver Zone is now online. Evolver Zone is a one-stop shop for everything evolution related.

EZ contains links to multimedia, software, databases, professional societies, journals, and books, with new content added regularly. The site is 100% free to use, but is subsidized by the sale of original evolution related merchandise available through the EZ store. Any surplus funds will be used to support student research.

Content should be useful to everyone from the casual student to the professional scientist. Kudos to Dr. Gregory.

Homo floresiensis: Our Clown-footed Cousins

2009-05-06T14:37:00.005-04:00

I was fascinated by the discovery of the dwarfed hominin Homo floresiensis back in 2004 when it was first announced, but was skeptical that it was really a separate species. Later when I saw a cast of the skull, I admit to being more enthused with the possibility of a new species. Not being a anthropologist, I couldn't discount the possibility of microcephaly and/or dwarfism.

However, a recent pair of articles in Nature discount this possibility, and I'm convinced. Jungers et al. analyzed the H. floresiensis foot and report that it is quite unhumanlike. For a meter-high hominin, it sure has a big foot! At 20 cm, it is much longer than would be expected for a proportionately smaller human. In fact, the foot is much closer in length to that of a chimpanzee.

I think it is pretty unlikely that, if island dwarfism or microcephaly were the cause, the creature would have showed smaller features except for the feet. In other words, all features should have been reduced proportionately.

So if it isn't human, what is it? Most wagers are on a descendent of H. erectus. A close relationship of H. floresiensis with H. erectus is to be expected. H. erectus is believed to be the first hominim to leave Africa (ca 2 mya). In fact, the first H. erectus found was Dubois' Java Man (Java is ~1000 km from Flores). It is not a stretch to speculate that H. erectus arrived on Flores, was isolated, and evolved smaller stature over time, thus becoming H. floresiensis, a contemporary of modern man.

However, additional primitive features of the foot, such as long, curved and robust lateral toes; a short big toe; and a weight-bearing process on a crucial bone, imply that H. floresiensis was better suited for walking than running. This feature is important because modern feet first appeared in H. erectus, thus suggesting that H. floresiensis split off from H. erectus before the evolution of the modern foot.

Other primitive anatomical features, such as a relatively short, very curved clavicle; a straight humerus that lacked the normal degree of twisting between the shoulder and the elbow; an ape-like wrist; flared iliac blades, relatively small joints and relatively short leg bones, all imply a close relationship to early Homo or even Australopithecines.

If the article is to be believed in full, and this is the point I have most difficulty swallowing,

"these new findings raise the possibility that the ancestor of H. floresiensis was not Homo erectus but instead some other, more primitive, hominin whose dispersal into southeast Asia is still undocumented."

So we have another possible Out of Africa event! First, H. floresiensis (or its immediate ancestor). Then H. erectus. Then H. sapiens.

Jungers, W., Harcourt-Smith, W., Wunderlich, R., Tocheri, M., Larson, S., Sutikna, T., Due, R., & Morwood, M. (2009). The foot of Homo floresiensis Nature, 459 (7243), 81-84 DOI: 10.1038/nature07989

Biology of B-Movie Monsters

2009-05-01T09:02:00.004-04:00

One of the tragedies of the Hollywood movie industry is that they don't make "so bad they are funny movies" anymore. Sure they make plenty of mediocre movies, bad movies, "so bad you want to pluck your eyes out movies" and occasionally even good movies, but the "so bad they are good movies" are a lost art. They were a perfect storm of low production values, wildly contrived plots, abysmal writing, and budgets running into the hundreds of dollars.

Representatives of this genre include The Incredible Shrinking Man, Godzilla vs. Mothra, Plan 9 from Outer Space, Fire Maidens from Outer Space (the "from Outer Space" is a genre of its own), and Fantastic Voyage. A common feature of these movies was a complete and utter disregard for the Laws of Physics, Biology, Chemistry or other intellectual endeavor. If it can be imagined, no matter how fantastic, somebody probably made it a central plot point for a movie in the 50's.

It was to my great surprise that someone actually considered the biological implications of these old B-Movies. I give you "The Biology of B-Movie Monsters" by Michael C. LaBarbera.

Remember the scene in The Incredible Shrinking Man, where our hero fights a giant sized spider. Turns out it would have been no contest.

"As for the contest with the spider, the battle is indeed biased, but not the way the movie would have you believe. Certainly the spider has a wicked set of poison fangs and some advantage because it wears its skeleton on the outside, where it can function as armor. But our hero, because of his increased metabolic rate, will be bouncing around like a mouse on amphetamines. He wouldn't struggle to lift the sewing needle--he'd wield it like a rapier because his relative strength has increased about 70 fold. The forces that a muscle can produce are proportional to its cross-sectional area (length squared), while body mass is proportional to volume (length cubed). The ratio of an animal's ability to generate force to its body mass scales approximately as 1/length; smaller animals are proportionally stronger. This geometric truth explains why an ant can famously life 50 times its body weight, while we can barely get the groceries up the stairs; were we the size of ants, we could lift 50 times our body weight, too. As for the Shrinking Man, pity the poor spider."

Michael C. LaBarbera is a professor in Organismal Biology & Anatomy, Geophysical Sciences, the Committee on Evolutionary Biology, and the College of the University of Chicago.

Darwin Live in Concert

2009-04-23T13:36:00.007-04:00

Richard Milner is an anthropologist and former Senior Editor at Natural History magazine at the American Museum of Natural History. He also happens to be the foremost practitioner of Darwinian entertainment.

Between April 24th and May 3rd, you can catch Darwin Live in Cambridge, New York City, Chicago, Los Angeles and elsewhere.

I'll be catching Darwin Live April 29th at the Graduate Center of the City University of New York. The New York Times' John Tierney published an article on the show earlier this year.

“Everyone should find his own Darwin,” Mr. Milner says. “The man was so large. He was a zoologist, a botanist, an explorer, a travel writer, a philosopher, an abolitionist, a doting father, a radical intellectual revolutionary with an utterly conservative and blemish-free lifestyle. He revolutionized every field he touched, and he was trained in none of them.”

If you can't make the show, you can get a copy of the CD.

Milner grew up with famous evilutionary biologist Stephen Jay Gould in my current hometown of Bayside, where they were known to classmates as Fossilface and Dino. Below is a photo of Gould (l) and Milner at age 12.

The Giant's Shoulders X

2009-04-16T15:36:00.003-04:00

The latest edition of The Giant's Shoulders is up at Stochastic Scribbles. I particularly like the Open Helix's pick. It's an article on computational sequence analysis ... from 1962!

Belated Birthdays

2009-04-10T21:27:00.003-04:00

The Evilutionary Biologist is now 5 days into its second year of existence.

I was late last year too.

If I ever get a cake, I'd like one like the one Arthur Kornberg got. It has some Rube Goldberg action going on there. Check out the hi res version.

Irony

2009-04-09T17:33:00.002-04:00

New Scientist published an editorial by Simon Baron-Cohen on media distortion of Science.

Is this... uhh... the same New Scientist that claimed Darwin Was Wrong on the cover?

Larry Moran, Jerry Coyne and PZ Myers among others called them out on this.

Fight Infection with Infection

2009-04-09T08:55:00.003-04:00

There was a recent article in Popular Science magazine on bacteriophage therapy. Scientists, including d'Herelle the discoverer of phages, have long recognized the value of phage therapy. In fact, the protagonist of Sinclair Lewis's novel Arrowsmith (publ. in 1925) cured the residents of a fictitious Caribbean island of plague using phage.

Despite its early popularity, phage therapy never quite caught on in the West. Most speculate that the arrival of antibiotics precluded their widespread acceptance, except in the former Soviet Union (e.g. Georgia).

The article discusses some of the advantages of phage therapy.

They prey only on bacteria, never human cells, they rarely spread from person to person, and, perhaps most important, bacteria have trouble becoming immune to them. As living organisms, phages are constantly changing and adapting in tandem with their host bacteria to kill them more effectively. Phage therapy could therefore eliminate the vicious cycle in which bacteria evolve resistance to antibiotics, necessitating the development of new, even more powerful drugs, at which point the process begins all over again.

I'm skeptical that phages rarely spread from person to person (but the research on this is minimal if not nonexistent), and bacteria DO become immune. In fact, bacteria frequently win arms races with phage in coevolution experiments.( A good example is the trap cells I used in my virus trap experiments. Several attempts to generate phage able to infect these trap cells have failed). Nonetheless, the article is correct in that, unlike antibiotics, phage evolve. This is a powerful tool to generate new phage variants.

Unfortunately, as the article points out, this precise point makes it difficult for phage treatments to past muster at the FDA.

Although there have been no reports of adverse effects resulting from mutations, phages that don't normally nest inside the human body could potentially swap genes with other phages that do and produce foreign proteins that trigger an immune reaction. And it's impossible to say exactly how a virus might mutate when exposed to different bacteria, says Paul Sullam, a microbiologist at the University of California at San Francisco.

FDA regulation, which some would say is excessive, has slowed phage therapy research in the US.

"People in this country have a right to be incensed that we have a very different situation here than in Europe with regards to phage," says Betty Kutter, a phage researcher at Evergreen State College. "Our whole regulatory environment has been one major thing that has slowed people down."

So where does one go when they have an uncurable infection? The Eliava Institute of of Bacteriophage, Microbiology and Virology.

Randy Wolcott calls Eliava the "mother ship of phage research," a worldwide Mecca for people suffering from antibiotic-resistant infections. Only it doesn't look like the sort of place you'd want to go with a health problem. When Wolcott visited to hunt down alternatives for his patients, the four-story facility bore a closer resemblance to a neglected sanatorium. The walls were unpainted, the rooms were dark, and the equipment looked like museum pieces. "The conditions were abysmal," he says. "Yet the science is amazing."

Perhaps, as Rockefeller's Vincent Fishetti says , the way to go is phage-based therapy.

This distinction might seem arcane to nonbiologists, but in Fischetti's mind, it's a crucial one. While Wolcott sees phages as a major therapeutic coup, Fischetti sees them as merely an intermediate step toward a new generation of even better bacteria-fighters. He contends that the uphill regulatory battle phages face, as well as the risk of mutations, make them too big a gamble for American drug companies. "Phages are going to be a boutique treatment, nothing more," he says. So he is taking an alternative approach, purifying the phage to extract the lysin, the enzyme it uses to dissolve the bacterial cell wall and kill the bacterium. Having observed that lysins were the phages' "active ingredients," Fischetti aims to harvest the lysins from them and turn them into stable antibacterial drugs. If successful, he could accomplish a double feat previously thought impossible: getting the bacteria-fighting benefits of phages to patients, while doing an end run around the regulatory Rube Goldberg machine that researchers like Wolcott face.

Incidentally, I am currently hosting a doctoral student from the Eliava Institute, Sophie Rigvava, who is characterizing the phages of Enterococcus faecalis in my laboratory.

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

Photo: Phages [in orange] prey on a lone bacterium, using prong-like proteins to anchor themselves to the cell before they inject their genes into it Lee D. Simon/Photo Researchers

Darwin Rocks

2009-04-04T08:56:00.003-04:00

A small team of evolutionary ecologists from Tuebingen, Germany, just finished a rock music clip about evolution which is called "Struggle for love", together with a computer program that allows the user to "select and evolve" music tunes following biological principles. This program was also used to generate the underlying tunes for the song.

All this is the result of a one-year project that was generously supported by the VolkswagenFoundation (www.volkswagenstiftung.de) following a creativity contest called "Evolution Today". We cooperated with composers, musicians, film-makers, informaticians and a whole series of creative students, about one hundred in total!

Both the clip and the program are meant to attract the attention from non-biologists and make them think and talk about evolution. Hence, if you like it, please feel free to share it with your friends, relatives and students.

The Darwin Rocks! Team:
Johannes Faber
Suska Sahm
Gregor Schulte
Nico Michiels

Science journalism: Supplanting the old media?

2009-03-19T11:21:00.002-04:00

This week's issue of Nature has an interesting article on scientific blogging. Geoff Brumfiel asks whether science blogging will replace a declining scientific journalism.

In part because of a generalized downturn, especially in newspaper revenues, the traditional media are shedding full-time science journalists along with various other specialist and indeed generalist reporters. A Nature survey of 493 science journalists shows that jobs are being lost and the workloads of those who remain are on the rise (for full results see http://tinyurl.com/c38kp6). At the same time, researcher-run blogs and websites are growing apace in both number and readership. Some are labours of love; others are subsidized philanthropically, or trying to run as businesses.

I think diversity in media is a great thing. Throughout the 80s and 90s, it was apparent that the media was coming under the control of a few large corporations e.g. the News Corp, Time Warner etc. Controlling the media means controlling the message. The rise of the internet makes monopolizing the means of communication more difficult.

However, the article cites the example of Robert Lee Hotz, a science journalist for The Wall Street Journal, who doubts that blogs can fulfill the additional roles of watchdog and critic that the traditional media at their best aim to fulfill.

I seriously doubt this. In my opinion, investigative journalism is best a bottom-up enterprise. With the advent of venues such as wikileaks and reddit, anyone can be an investigative journalist.

Others say that science reporting will fail to reach a broad audience.

Press releases and blogs will not find the same broad audience once served by the mass media, says Peter Dykstra, who was executive producer of CNN's science, technology, environment and weather unit until it was closed down last year. Now at the Woodrow Wilson International Center for Scholars, an independent think tank in Washington DC, he says that science and environment news will be "ghettoized and available only to those who choose to seek it out".

So citizens will have to be active consumers of media rather than spoon fed "the news" during a 6:30 PM nightly broadcast? Oh catastrophe!

The idea that science journalism will suffer because major newspapers and tv stations are dropping coverage is ridiculous. What was that coverage anyway?

"You get a press release that is slightly rehashed by somebody in the newsroom and it goes in the paper! It's wrong, its sensationalist, it erodes the public trust in scientific endeavour," says Bora Zivkovic, author of A Blog Around the Clock on ScienceBlogs and an online community manager for the Public Library of Science journals. Myers takes a similar view. "Newspapers realize that they can get their audience by peddling crap instead of real science," he says. Not surprisingly, those who came to blogging from journalism — such as Carl Zimmer, who writes for a range of publications, including The New York Times, and blogs at Discover — tend to disagree. But Larry Moran, a biochemistry professor at the University of Toronto, Ontario, who blogs at Sandwalk, seemed to speak for many bloggers when he recently wrote "Most of what passes for science journalism is so bad we will be better of [sic] without it".

If anything blogging has enhanced scientific coverage. PZ Meyer's Pharyngula is getting 500k hits per week. The best thing is that scientists are generating news, reporting it, commenting on it and interacting with the general public in a manner that was impossible pre-web. Talk about tearing down the Ivory Tower! Readers can ask questions of actual scientists in the comment box, receive expert answers and opinions, and the end result will likely be a more science literate, engaged society.

The Giant's Shoulders #9

2009-03-10T14:21:00.012-04:00

"The Giants' Shoulders" is a monthly science blogging event, in which authors are invited to submit posts on "classic" scientific papers. Information about the carnival can be found here. The last Giants' was hosted at Greg Laden's Blog. The next issue will be hosted at Stochastic Scribbles.

The name "The Giants' Shoulders" refers to a passage in a letter from Issac Newton to his rival Robert Hooke dated February 5, 1676: "What Descartes did was a good step. You have added much several ways, and especially in taking the colours of thin plates into philosophical consideration. If I have seen a little further it is by standing on the shoulders of Giants." It's a bit of a taunt, really. Oh if I seem smarter than you, it's because I understand the work of our forebears much better than you. Newton and Hooke were famously at odds.

The phrase is believed to significantly predate Newton. Wikipedia attributes it to Bernard of Chartres based on a passage in 1159 in John of Salisbury's Metalogicon.

"Bernard of Chartres used to say that we are like dwarfs on the shoulders of giants, so that we can see more than they, and things at a greater distance, not by virtue of any sharpness of sight on our part, or any physical distinction, but because we are carried high and raised up by their giant size."

This month we celebrate the following works of genius. I've posted them in the order in which they were received.

1. "The irreducibility of the space of curves of given genus" by Pierre Deligne and David Mumford in 1969 was submitted by Charles Siegel of Rigorous Trivialities. The significance of the paper is, as Siegel writes, "Aside from the great achievement of solving this long standing open problem, the real value here is that Deligne and Mumford made algebraic geometers start taking the notion of stacks seriously, because they could be used to solve actual mathematical problems. Nowadays, stacks are essential to large branches of mathematics research."

2. Quantum Science Philippines submits Einstein's 1905 article on E = hf or The Equation That Changed The World. Here Einstein claimed that light was not only emitted in integral units or bundles of energy but it was also absorbed in such bundles - bundles that came to be known as photons.

3. GG of Skull in the Stars serves up this goodie on the unification of light and magnetism: “Experimental Researches in Electricity,” published in the Philosophical Transactions (vol 136, pp. 1-20) in 1846. GG writes, "The more I read of Michael Faraday’s work, the more I am in awe of the scientist’s insights and abilities." We all should be.

4. My own contribution to this list is comes from the Venerable George Williams who, in the words of no less a luminary than Stephen Pinker, "was instrumental in making natural selection an intellectually rigorous theory". In 1959 Williams published, "Pleiotropy, natural selection, and the evolution of senescence. Evolution, 11: 398-411" thus providing one of the first intellectually rigorous hypotheses for the question of "Why Do We Get Old and Die?" Click here to find out Why!

5. Kylie Sturgess of PodBlack Cat cites Expert Performance. Its Structure and Acquisition by K. Anders Ericsson and Neil Chamess (1994) and writes about talent versus training debate. Are poets born that way or do they become poets after years of hard work? She concludes, "I think research demonstrates how some Expert Performances were indeed gained from Structure and Acquisition. And I didn’t even have to go much further than the Romantic era poetry." Read more here.

6. A fascinating article was submitted by Scicurious of Neurotopia, Philip, APW. "On the nature of death" Philosophical Transactions of the Royal Society of London, 1834. As Scicurious writes, "Dr. Philip undertook in this publication to explain the nature of death. Not what happens after death. He was very specific that he would not cover anything "metaphysical". His concern was, well, with HOW people die."Phillip realized that breathing was critical to staying alive, thus was the first to attempt "artificial resuscitation".

7. Materialia Indica's Guru serves up this classic in materials science: L. Vegard. 1921. Die Konstitution der Mischkristalle und die Raumfüllung der Atome. Zeitschrift für Physik. The popularity of the law [stems from] the fact that the lattice parameter change with concentration is one of the important pieces (and, as Denton and Ashcroft note in their paper, rather fundamental piece) of information in understanding many interesting properties of alloys — for example, the wiki entry on the law mentions the determination of semiconductor band gap energies — and, a linear relationship is the minimum that one needs to assume.

8. Greg Laden, biological anthropologist extraordinaire and author of Greg Laden's Blog, thinks we all should read Mark Pagel (2009). Natural selection 150 years on Nature, 457 (7231), 808-811 DOI: 10.1038/nature07889 . Pagel addresses the question: How has Darwin's theory of Natural Selection fared over the last 150 years, and what needs to be done to bring this theoretical approach to bear as we increasingly examine complex systems, including human society?

9. Underemployed, grumpy, aging liberal John J. McKay of Archy has been busy lately and submitted four posts about mammoths: Fragments of my research - VII, Fragments of my research - VIII, Mastodon nightmares and A mammoth literary mystery. There's a wonderful melange of Eurasian history, skullduggery and entertainment; very much worth a read.

10. The eternal student John Wilkins of Evolving Thoughts writes about Polly Winsor's article in Taxon. Winsor thinks taxonomy was critical for Darwin's Big Idea; "she holds that what set up Darwin's problems was the hierarchical arrangement of organisms in the Linnean system that had effectively swept all before it in the early 19th century." Fascinating article.

11. Grad student Jeremy Yoder of Denim and Tweed cites Verne Grant's 1949 discovery of cleverly indirect evidence that pollinator isolation shapes the evolution of flowers. More than fifty years after Grant's study, pollinator isolation is a well-established mechanism for speciation. And the principle that Grant proposed, that increased divergence in floral traits is a sign of pollinator isolation, is still very useful.

12. And our last post is from Providentia who writes about psychologically profiling Hitler. The work was done by the Office of Strategic Services (the predecessor of the CIA) and was published here. (It's no longer top secret).

That's it for this month's edition of The Giant's Shoulders. Tune in next month at Stochastic Scribbles.

Very Gradual Change We Can Believe In

2009-02-23T10:12:00.003-05:00

Although I am heartily sick of the Obamicon and its iterations, I must give high praise to Mike Rosulek for the excellent Darwinia poster. I'll be buying a tshirt from Zazzle because all profits will be donated to The National Center for Science Education (NCSE). As I'm writing this, already over ~~$130 $250 $550~~ $700 has been raised. Awesome Mike!

Evolution 2009

2009-02-19T11:11:00.004-05:00

The Society for the Study of Evolution, the American Society of Naturalists and the Society of Systematic Biologists will be holding their annual joint meeting this summer in lovely Moscow, Idaho. I received my Master's degree from the Department of Biological Sciences at the University of Idaho so the event will be something of a homecoming for me.

The meeting will be held June 12-16, 2009.

The venue of the meeting, Moscow, Idaho, is a western college town situated at the transition between the Northern Rockies and the rolling palouse grasslands of the interior Pacific Northwest. Moscow (pronounced "Mos-coh" by locals) was settled in 1871, and became home to the University of Idaho, Idaho's land-grant university, in 1889. UI and Washington State University (which is only six miles away in the town of Pullman, Washington) form a major center of biological research in the Pacific Northwest. Idaho is the state where protected wildernesses was first created, and within a short drive from Moscow you can enjoy world-class whitewater rafting, fishing, backcountry hiking and mountain climbing; go west and you'll cross the geological marvels of the channelled scablands to reach Washington's premier wine country.

Following the meeting, I am trying to arrange a raft trip to one of the fantastic wild rivers of Idaho: Selway, Lochsa, Salmon or Snake. Failing that, I will backpack in the largest contiguous wilderness area in the lower 48. I am looking forward to the woods almost as much as I am looking forward to the scientific program.

Call for Submissions: Citation Classics

2009-02-18T16:41:00.002-05:00

I will be hosting the next edition of The Giant's Shoulders here at The Evilutionary Biologist.

The Giant's Shoulders is a monthly blog carnival dedicated to classic science papers. My original aim when I started The Evilutionary Biologist was to write about one classic biology paper each week. The rationale was three-fold. One, to increase science appreciation by discussing the great science experiments of yesteryear. Two, to foster awareness of the human side of science by highlighting personal anecdotes. Three, to personally learn more about how to do good science by reading the work of the masters. Although my posting has been ever more stochastic due to the constraints of life on the tenure-track, I still post as often as I am able.

I've been a regular participant in The Giant's Shoulders since I found out about it (except for last month's edition), and enjoy learning about the work that others feel is classic. I urge you to participate, write about a science classic that really floats your boat, and submit it at Blog Carnival. Submissions need to be received by March 15th.

About “The Giant’s Shoulders”

“If I have seen a little further it is by standing on the shoulders of Giants.” - Isaac Newton, in a letter to Robert Hooke, 1676. (Though the metaphor goes back much further.)

“The Giant’s Shoulders” is a monthly science blogging event, in which authors are invited to submit posts on “classic” scientific papers. Submissions are due on the fifteenth of each month, and entries will be aggregated and linked to on the host blog of the month. Links to entries should be sent to that month’s host blog.

What defines a “classic” paper? This depends upon the field in question, but one expects that the work should have somewhat stood the test of time: we suggest perhaps 10 years old, or more. Contributors should not only describe the research involved but also put it in a broader historical/scientific context: why is the work in question important/groundbreaking/revolutionary/nifty?