The Iceman's Genome Cometh

I don't know why this fascinates me so, but the Tyrolean mummy they call the "Iceman" has made (or unmade) more science careers than you can shake a stick at. Genome sequencing reveals Iceman Was a Medical Mess

Earlier computer scans had revealed Ötzi's severe arteriosclerosis, or hardening of the arteries. But the new analysis shows that Ötzi had a genetic predisposition to the condition, despite the fact that as a hunter-gatherer he had none of what are currently believed to be the relevant risk factors, such as being overweight, getting too little exercise, and smoking or drinking.... He was also the first known carrier of Lyme disease: the sequencing yielded genes from the disease-causing Borrelia burgdorferi bacterium.

I particularly enjoy the way the stories keep changing: Iceman May Have Been Buried in a Ceremony

Researchers have long thought that Ötzi, the 5000-year-old Iceman found in the Alps in 1991, died wounded and alone, perhaps the victim of a raging blizzard. But a provocative new paper tells a radically different story. The first comprehensive map of Ötzi's body and belongings suggests he was ceremoniously buried by his fellows in the warm summer months.

What I've Been Doing Lately

Here's a peek at what I've been up to lately:

I'm enjoying revisiting my ecology textbooks and reading new PLoS ONE articles. I wish I didn't have to do it on such a tight deadline, but that is the way these things usually go!

JSTOR Limited Free Access for Unmoored Scholars

jstor opens limited free access option non-subscribing scholars | Inside Higher Ed: "The depletion of the traditional professoriate has produced a new demographic of unmoored scholars who might not have “the consistency of access that they want,” says Heidi McGregor, a spokeswoman for JSTOR. The goal of Register & Read would be to better serve that population — as well as others that the organization might not have even known about."

Good news for us "unmoored scholars." The institutions that employ me as an adjunct faculty member don't subscribe to JSTOR.

'via Blog this'

Burgess Shale--A New (Very Old) Animal

A New Stalked Filter-Feeder from the Middle Cambrian Burgess Shale, British Columbia, Canada. 2012. L. J. O'Brien and J.-B. Caron. PLoS ONE 7(1): e29233.

This is a new member of the "Problematica," those strange Cambrian animals not assigned to any known phylum. And because it's published in PLoS ONE, the entire article (including many beautiful photos of fossils and some ecological notes) is freely-available on line. What a treat! Via Paleoblog.

Remembering "Cave of Forgotten Dreams"

My wild New Year's Eve activity was watching Netflix's streaming video of Werner Herzog's Cave of Forgotten Dreams. I was expecting something soothing and low-key, and, indeed, there were beautiful landscapes, expert interviews, and hushed voices. However, the effect was astounding, and I've been thinking about the amazing prehistoric artwork ever since. This April, 2011 interview with Hezog is from Scientific American's Youtube channel.

A Dialectic Between Bunnies

These videos made me laugh really hard. I have no idea why this amuses me, but I'm having Linux trouble today, can't figure it out, and haven't come up with a real blog post yet. Perhaps it's just fun to hear cartoon animals say "Derrida."

In my grad school experience, the faculty told us that we needed to be deep scientific thinkers with a "feel for the organism" and cold, calculating political animals with no regard for the truth. In fact, the same professor might tell you "profound, broad-ranging knowledge" on Monday and "political animal" on Tuesday, repeating as necessary until you ultimately loathe your research, your department, and all of academe. Guess you have that in the philosophy department too.

Snowflakes--"Gem Bestrewn Realm"

In all the years I worked in science, microscopy was my very favorite thing, so I was excited to find this timely video on a collection of early photomicrographs: Winter Forecast: Art to Blanket Region.

When it comes to photography, a Wilson Bentley image can be described much like his favorite subject, the snowflake: Each is one of a kind. After all, the Vermont farmer was the first to ever photograph one....At the age of 19, "Snowflake" Bentley jury-rigged a microscope to a bulky bellows camera and took the first-ever photograph of a snowflake....Bentley saw his microphotographs as more than scientific contribution. In a 1910 article published in the journal Technical World, he wrote, "Here is a gem bestrewn realm of nature possessing the charm of mystery, of the unknown, sure richly to reward the investigator."

I don't know what the kids are calling them these days, but when I was a member of the American Microscopical Society, we called them "photomicrographs," not "microphotographs." I found this wonderful article via /.

Call of the Tame

Via Slashdot, I read Soviet Scientist Turns Foxes Into Puppies, where I found these links to documentary excerpts. I don't know what brought these breeding experiments into the news--most of the related stories I found are at least a few years old. However, it was news to me, and offers some fascinating suggestions about how domestic animals came to be that way. Here's the abstract of a review article, Early Canid Domestication: The Farm-Fox Experiment, by Lyudmila Trut (1999):

Abstract: At an experimental farm in Novosibirsk, Siberia, geneticists have been working for four decades to turn foxes into dogs. They are not trying to create the next pet craze. Instead, author Trut and her predecessors hope to explain why domesticated animals such as pigs, cattle and dogs are so different from their wild ancestors. Selective breeding alone cannot explain all the differences. Trut's mentor, the eminent Russian geneticist Dmitri Belyaev, thought that the answers lay in the process of domestication itself, which might have dramatically changed wolves' appearance and behavior even in the absence of selective breeding. To test his hypothesis, Belyaev and his successors at the Institute have been breeding another canine species, silver foxes, for a single trait: friendliness toward people. Although no one would mistake them for dogs, the Siberian foxes appear to be on the same overall evolutionary path--a route that other domesticated animals also may have followed while coming in from the wild.

You can download the complete article: Early Canid Domestication: The Farm-Fox Experiment (pdf file). It's well worth reading, and not painfully technical. (That's my evaluation, but I've been told I'm a painfully technical kind of gal, so YMMV.)

A 2006 New York Times article describes some related research on rats: Nice Rats, Nasty Rats: Maybe It's All in the Genes.

Extinctions Inside Us

I've had this article sitting on my "to blog" list for a while: Bugs Inside: What Happens When the Microbes That Keep Us Healthy Disappear? The human body has more microbial than human cells, but this rich diversity of micro-helpers that has evolved along with us is undergoing a rapid shift--one that may have very macro health consequences. At my last "real" job at The Institute for Genomic Research (Now known as J. Craig Venter Institute, because that is the boss's name, and he's not a bashful fellow) I wrote some grants to sequence microbial ecosystems. It was too early in the microbial genome sequencing game for those proposals to fly, but now several organizations are doing just that. It's been 11 years since I left, so I guess I was right not to stick around waiting for it to happen, but I'm feeling a little envious of the folks who are getting to do that work now.

Sea water microbes, oil well flora, rumin ecosystems, and human "normal flora"--it's a way to get a look at bacteria in non-homogeneous culture, and characterize "bugs" that can't be cultured individually. Of course, the normal flora of humans are of particular interest.

Having evolved along with the human species, most of the miniscule beasties that live in and on us are actually helping to keep us healthy, just as our well-being promotes theirs. In fact, some researchers think of our bodies as superorganisms, rather than one organism teeming with hordes of subordinate invertebrates....

With rapid changes in sanitation, medicine and lifestyle in the past century, some of these indigenous species are facing decline, displacement and possibly even extinction. In many of the world's larger ecosystems, scientists can predict what might happen when one of the central species is lost, but in the human microbial environment—which is still largely uncharacterized—most of these rapid changes are not yet understood. "This is the next frontier and has real significance for human health, public health and medicine," says Betsy Foxman, a professor of epidemiology at the University of Michigan (U.M.) School of Public Health in Ann Arbor.

Meanwhile, each new generation in developed countries comes into the world with fewer of these native populations. "They're actually missing some component of their microbiota that they've evolved to have," Foxman says.

Marvelous Pre-Cambrian Fossils

If like me, you love the Burgess Shale fossils, you'll be taken with this news item: Eight-armed animal preceded dinosaurs. It's remarkable enough to find so many beautiful fossils of soft-bodied animals, but to find they are older than the "Cambrian explosion" is quite wonderful. Really, it makes dinosaurs seem recent and mundane.

[Zhu, Gehling and their colleagues] believe the animal was a soft-bodied, dome-shaped organism that lived on seabeds and fed by absorbing dissolved nutrients from the ambient environment.

Before the latest fossils were found, some researchers identified the creatures as lichens or fungus-like organisms, but Zhu and his team suspect that at least some Ediacara fossils represent now-extinct diploblastic animals, or creatures that possess only two cellular layers separated by a jelly-type substance.

"Diploblastic animals are common creatures on present day earth," he said, mentioning that jellyfish, corals and sea anemones belong to the group.

"These animals (display) radial symmetry but lack complex organs, as shown by E. octobrachiata," he adds.

The multi-armed creature, and several other early life forms, went extinct around 542 million years ago, which Zhu says, "left empty niches for the subsequent Cambrian explosion of complex animals."

Representatives of nearly all existent animals emerged at this time, when a rapid increase in oxygen made respiration and metabolism possible.

....In addition to the eight-armed creature, they describe other early living things that looked like leaves, shells, stars and something almost akin to a peace symbol.

The Discovery News report includes links to the scholarly articles, and lovely photographs.

West Virginia Politics and Reality-Based Stuff

Lincoln Walks At Midnight points to several articles on the presidential race in West Virginia, including The Washington Post's A New Political Geography: Role Reversals in Virginias Reflect National Shifts By Alec MacGillis (Sunday, June 29, 2008). While cable TV news seemed content to write off West Virginian support for Hillary Clinton as redneck racism (redneck sexism having died off, I reckon), the print journalists are analyzing demographic trends. (Bless their hearts.)

....As the gap grows between places that are prospering and those that are not, Democrats are strengthening their hold in major metropolitan areas, particularly in places faring well in the technology-driven economy.

The trend generally bodes well for Democrats. Major metro areas are growing faster than the country as a whole, the party's strength with young voters promises a lasting edge, and well-off, highly educated urban voters are valuable campaign contributors in the Internet age. The weak economy and soaring gas prices could accelerate the shift if more Americans move closer to urban hubs in search of good jobs and shorter commutes.

But the Democrats' ascendance in prosperous areas leaves them with weak spots in key swing states such as Ohio. And it presents questions about their identity: The party that fought for the little guy against the party of the wealthy has, while still representing racial minorities, increasingly become defined by the metropolitan middle and upper-middle class....

The transformation goes beyond politics. As the distance between the rich and the poor grows, so too does the gap between regions. In places such as Northern Virginia, success has fed on itself, as firms seek educated workers and proximity to rivals and clients, and people with college degrees flock to the opportunities. Such areas are also seeing a surge in foreign-born residents, who favor Democrats.

In places such as West Virginia, manufacturing and mining have been decimated by automation and foreign competition, and hopes for reinvention are undermined by the stream of young people leaving. "There is a realignment going on here. It's a long-term shift that has to do with the economic decline in some areas in the modern economy," said Larry Bartels, a political scientist at Princeton University.

The presidential campaigns seem ready to write West Virginia off, both parties. We don't expect to see much money spent on advertising, or see candidates and their surrogates appearing in person, now that the Clinton campaign is out of the race.

....Obama barely campaigned in West Virginia, lost it by 41 points and will probably spend little time campaigning there.

Leading Democrats in West Virginia lament Obama's lack of effort, contrasting it with the campaign of John F. Kennedy, who, like Obama, faced hurdles as a minority in West Virginia -- in Kennedy's case, as a Roman Catholic -- but set out to win the 1960 primary there.

....Democrats still control state government and all but one of the state's seats in Congress, and registered Democrats outnumber Republicans. But the state voted for Bush by six points over Gore and 13 points over Kerry. Its pro-Democrat unions have declined.

Since 2000, an argument has raged over why voters in West Virginia and elsewhere have voted against Democrats who offered health-care and tax plans that favor them. In his 2004 book "What's the Matter with Kansas?", Thomas Frank argued that Republicans have used social issues such as abortion to win poorer voters.

Bartels, at Princeton, disputed Frank with data showing that higher-income voters are more likely than poorer ones to cite issues such as abortion. Outside the South, low-income whites have stayed loyal to Democrats, he said.

These demographic shifts leave me feeling confused. My dad was a member of the Merchant Seaman's Union (busted as a bunch of Commies by Joseph McCarthy and his lawyer-for-hire Bobby Kennedy), and The New Deal and The Great Society made it possible for me to have an education. When I finally landed in the "liberal elite" world of academe, I didn't fit in, and eventually moved away from all that. I was rather miffed when the quiz Sherry Chandler posted called me "Reality Based Intellectualist."

My Liberal Identity:

You are a Reality-Based Intellectualist, also known as the liberal elite. You are a proud member of what's known as the reality-based community, where science, reason, and non-Jesus-based thought reign supreme.

Take the quiz at www.FightConservatives.com

It's just a silly quiz, I told myself, but I went back and changed answers until I qualified as "Working Class Warrior." It was the science-related material that sent me into that "liberal elite." Evolution is just a theory, like gravity. (That's not even funny, just true. After teaching sixth grade science for a semester, I can tell you that many Americans don't believe in Newtonian physics, either.) And I'd save The Origin of Species over those other books because it's more interesting and better written. (Darwin was an excellent prose stylist.) I don't even know what "non-Jesus-based thought" means.

Natural Selection of Creationist Museums

Last month Sherry informed me that Kentucky's Creation Science Museum is in some financial hot water. That's why, when I came across this article about a Texas creationism museum, I began to wonder if there was a trend. Creationist museum auctioning mastodon skull.

DALLAS, Texas (AP) -- A Texas museum that teaches creationism is counting on the auction of a prehistoric mastodon skull to stave off extinction.

The founder and curator of the Mt. Blanco Fossil Museum, which rejects evolution and claims that man and dinosaurs coexisted, said it will close unless the Volkswagen-sized skull finds a generous bidder.

"If it sells, well, then we can come another day," Joe Taylor said. "This is very important to our continuing."

Heritage Auction Galleries says the skull is estimated to be 40,000 years old, and projects it will fetch upward of $160,000. The artifact discovered in La Grange in 2004 is believed to be the largest of its kind, Heritage spokesman David Herskowitz said....

Claims on the museum's Web site include that Noah took dinosaurs aboard his ark...."We've struggled so long here just to keep this thing going," Taylor said. "We're kind of losing interest. You can just tread water for so long."

In the struggle for natural resources, some museums succeed and leave progeny, while unfit museums perish without offspring. Natural selection does not seem to smile upon creationist museums these days. Of course, if Noah had taken them on his ark like the dinosaurs (really? I thought that was why they died.), they would not have to tread water.

Amazing Paleozoic Annelid Fossil

Paleoblog points to an amazing fossil find, Prehistoric Armored Worms. The fossil in question is very lifelike, showing extensive soft tissue preservation. Check out the Press Release, which has an excellent photograph of the fossil, and a drawing to explain what you're seeing. From the press release:

First described over 150 years ago, armor plates of these strange animals have been found in marine fossil deposits worldwide covering the time span of their existence [from 485 to 305 million years ago], and indicating that they were an important component of ancient seafloor ecosystems....Previous patchy evidence was insufficient to reveal the relationships of the machaeridians to other animals and there was much speculation about their position in the tree of life. Different authors suggested relationships to groups as varied as mollusks (clams and snails), barnacles (crustaceans--including shrimps, crabs and crayfish), echinoderms (starfish and sea urchins) and annelid worms (aquatic bristle worms and garden earthworms).

This inch-long specimen that was recently discovered shows that, below the dorsal armor, the machaeridians had an elongate body with paired, soft, limb-like extensions on each segment, and two bundles of long, stiff bristles on each extension. The segmented nature of the body, and especially the presence of soft ¡Èlimbs¡É carrying bristles, unequivocally identified the machaeridians as annelid worms, say the scientists.

Here's the abstract to the actual article:

Machaeridians are Palaeozoic armoured annelids. Jakob Vinther, Peter Van Roy and Derek E. G. Briggs. Nature 451, 185-188 (10 January 2008)

The systematic affinities of several Palaeozoic skeletal taxa were only resolved when their soft-tissue morphology was revealed by the discovery of exceptionally preserved specimens. The conodonts provide a classic example, their tooth-like elements having been assigned to various invertebrate and vertebrate groups for more than 125 years until the discovery of their soft tissues revealed them to be crown-group vertebrates. Machaeridians, which are virtually ubiquitous as shell plates in benthic marine shelly assemblages ranging from Early Ordovician (Late Tremadoc) to Carboniferous, have proved no less enigmatic. The Machaeridia comprise three distinct families of worm-like animals, united by the possession of a dorsal skeleton of calcite plates that is rarely found articulated. Since they were first described 150 years ago machaeridians have been allied with barnacles, echinoderms, molluscs, or annelids. Here we describe a new machaeridian with preserved soft parts, including parapodia and chaetae, from the Upper Tremadoc of Morocco, demonstrating the annelid affinity of the group. This discovery shows that a lineage of annelids evolved a dorsal skeleton of calcareous plates early in their history; it also resolves the affinities of a group of problematic Palaeozoic invertebrates previously known only from isolated elements and occasional skeletal assemblages.

Larmarck: Another Textbook, Another Bad Rap

Last month, I substituted for a seventh grade science teacher. The topic du jour was evolution. There's been no controversy about course content in Pocahontas County since I've been here, but I must say that the text explained evolution so poorly that it's no wonder many people don't believe in it.

Among other flaws, the text juxtaposed natural selection with the inheritance of acquired characteristics. "Lamarck believed in the inheritance of acquired characteristics, while Darwin believed in the inheritance of inherited characteristics." I paraphrase, but the authors should be ashamed of both the non-parallel comparison and the tautology they attribute to Darwin. In fact, Darwin knew of no mechanism for inheritance, and didn't discount inheritance of acquired characteristics.

This set me thinking of all the biology textbooks I've had to use through the years. Poor Jean-Baptiste Lamarck took a beating in most of them. I spent a little time tracking down articles about him, and I felt even worse about all the Lamarck abuse, as he had a difficult life, and was eventually evicted even from his rented grave. The University of California Museum of Paleontology's biographical sketch of Lamarck points out Lamarck's great contributions to the study of invertebrate taxonomy and anatomy, a field dear to my heart.

Aside from a stint as tutor to Buffon's son during a tour of Europe in 1781, Lamarck continued as an underpaid assistant at the Jardin du Roi, living in poverty (and having to defend his job from cost-cutting bureaucrats in the National Assembly) until 1793. That year, the same year that Louis XVI and Marie Antoinette went to the guillotine, the old Jardin des Plantes was reorganized as the Musee National d'Histoire Naturelle (National Museum of Natural History), which was to be run by twelve professors in twelve different scientific fields. Lamarck, who had called for this reorganization, was appointed a professor -- of the natural history of insects and worms (that is, of all invertebrates), a subject he knew nothing about.

To be fair to Lamarck, we should mention that since the time of Linnaeus, few naturalists had considered the invertebrates worthy of study. The word "invertebrates" did not even exist at the time; Lamarck coined it. The invertebrate collections at the Musee were enormous and rapidly growing, but poorly organized and classified. Although the professors at the Musee were theoretically equal in rank, the professorship of "insects and worms" was definitely the least prestigious. But Lamarck took on the enormous challenge of learning -- and creating -- a new field of biology. The sheer number and diversity of invertebrates proved to be both a challenge and a rich source of knowledge.

Here are some links to biographical material, modern, well-informed discussions of Lamarck's ideas, and English translations of Lamarck's books. There's not an exposition of giraffe neck stretching among them.

• Jean-Baptiste Lamarck (1744-1829) from University of California Museum of Paleontology
• Jean-Baptiste Lamarck (1744-1829) from the The Victorian Web
• Jean-Baptiste de Monet de Lamarck biography from Strange Science: The Rocky Road to Modern Paleontology and Biology
• Early Concepts of Evolution: Jean Baptiste Lamarck
• A Division of Worms - Jean Baptiste Lamarck's contributions to evolutionary theory by Stephen Jay Gould (Natural History, February, 1999)
• The Imaginary Lamarck: A Look at Bogus "History" in Schoolbooks by Michael T. Ghiselin
• Zoological Philosophy or Exposition, the translated text of Lamark's 1809 treatise.
• A review of Lamarck's Signature: How Retrogenes Are Changing Darwin's Natural Selection Paradigm. Edward J. Steele, Robyn A. Lindley and Robert V. Blanden. 286 pp. Perseus Books, 1998.

Ernst Haeckel--Still Controversial a Century Later

I came across these plates from Ernst Haeckel: Kunstformen der Natur 1899-1904 a couple of weeks ago on a needlework design Web site. I was so pleased to find them I thought I'd post the link here, and add a few other Ernst Haeckel links for good measure. As I searched for sensible, informative Haeckel links, I was amazed at the large number of Web sites offering vitriolic attacks on the man and his work. I would not have expected a comparative invertebrate anatomist who died in 1919 to elicit so much venom, let alone interest. I found creationists denouncing him, biologists calling him "forger" and "fraud," and even Lenin offers a scathing critique, courtesy of Marxists.org.

Haeckel coined the terms "ecology" and "first world war," and he pioneered embryology and marine biology. His drawings and colored plates are breathtaking. Do check out Art Forms in Nature. The plate above, featuring trilobites, eurypterids and horseshoe crabs is plate 47 from this volume. I understand why creationists don't like him, because he was a proponent of evolution, but I'm not sure why biologists are so vexed that he was wrong about some stuff. Darwin was wrong about lots of things too, but I've observed a cult-like devotion to Darwin among some biologists. (Alfred Wallace is my personal favorite, but then, I like insect collecting and biogeography.)

Here are some of the more balanced accounts of Haeckel. In my opinion, researchers always present the data that best support their ideas. This isn't "fraud," (although sometimes it stretches facts far enough to be called "spin,") and it's necessary to get your papers published and your grant proposals funded. Several of these Web authors feel the need to apologize for Haeckel's inaccuracies, but I don't think it's necessary myself.

• Biography of Haeckel from University of California Museum of Paleontology
• Ernst Haeckel: Artforms in Nature Exhibit from the Marine Biology Lab of Woods Hole Oceanographic Institute Library. These science librarians seem to feel the need to justify their Haeckel exhibition:

  His watercolors and drawings, made during his sojourn in Ceylon (Travel Pictures) and on his scientific journeys (Art Forms in Nature), are landmarks in the field of naturalist illustration, although many would not pass strict scientific muster. Indeed, much of naturalist illustration is not natural at all but permits stylization and distortion for decorative effect. Haeckel aimed Art Forms in Nature at a broad audience rather than specialists. Each of the 100 plates was accompanied by a short, readable commentary that made biological concepts accessible to the public. Moreover Haeckel's use of Art Nouveau techniques made the book even more appealing and "fashionable." The publication was an immediate success and remains a treasure to this day.

• Ernst Haeckel: Evolution's controversial artist--an unnecessarily apologetic but interesting slide show from Slate.com, 2005.
• Wikipedia article on Ernst Haeckel
• Early Evolution and Development: Ernst Haeckel from Understanding Evolution

Botany of Desire

Reya tipped me off to a delightful book, The Botany of Desire: A Plant's-Eye View of the World by Michael Pollan (2001). It's the sort of popular book on evolutionary biology I usually don't enjoy, so I was both surprised and pleased to find it so interesting.

Pollan invokes coevolution to describe the ethnobotanical history of four different cultivated species, and he examines it using the "Which came first, the chicken or the egg?" dilemma that served Richard Dawkins' career so well in The Selfish Gene.

Did I choose to plant these potatoes, or did the potato make me do it? In fact, both statements are true. I can remember the exact moment that spud seduced me, showing off its knobby charms in the pages of a seed catalog. I think it was the tasty-sounding "buttery yellow flesh" that did it....That May afternoon, the garden suddenly appeared before me in a whole new light, the manifold delights it offered to the eye and nose and tongue no longer quite so innocent or passive. All these plants, which I'd always regarded as the objects of my desire, were also, I realized, subjects, acting on me, getting me to do things for them they couldn't do for themselves.

Dawkins' cranky atheism and self-promotion made reading his books in grad school an annoying chore, but Pollan's fondness for his horticultural subjects shines through and lends his book an engaging charm. I usually am either bored or irritated by popular accounts of evolution, but I found much engagingly presented new information in these four essays on cultivated plants. I especially enjoyed picturing Johnny Appleseed as a Dionysian emblem.

Here are my inevitable links for further reading.

• Michael Pollan's Web page. This is a rich reading resource, as it includes the full text of many of Pollan's published articles on food, gardening, agriculture, and what-all. He also has a list of links that will keep me clicking for a long time.
• Eat the Press: An interview with foodie author Michael Pollan by David Roberts in Grist, 2006.

Charles Lyell--Belated Happy Birthday

Michael J. Ryan's wonderful Paleoblog points out that yesterday, November 14, was the birthday of Charles Lyell, prominent geologist and popularizer of the concept called "Uniformitarianism"--that the forces at work in the natural world today are the same forces at work in the past. While it strikes me as a reasonable working hypothesis, and one that has been widely used for a long time, many people, ranging from school boards to Ann Coulter, find it impossible to swallow. Dr. Ryan provides links to a brief Lyell biography and some of his books still in print, including the 1830-1833 page-turner, Principles of Geology in three volumes.

To this, I'd add Charles Lyell's online books courtesy of U Penn's Online Books Page. You can read his most seminal works for free.

I admire Lyell's writing. He always acknowledged that his ideas were developed and shared by other researchers, and he seemed to me to be clear and plain-spoken, in contrast to many writers of his time. Here's an excerpt from his essay "The Progress of Geology:"

If we reflect on the history of the progress of geology we perceive that there have been great fluctuations of opinion respecting the nature of the causes to which all former changes of the earth's surface are referable. The first observers conceived the monuments which the geologist endeavours to decipher to relate to an original state of the earth, or to a period when there were causes in activity, distinct, in a kind and degree, from those now constituting the economy of nature....Many appearances, which had for a long time been regarded as indicating mysterious and extraordinary agency, were finally recognised as the necessary result of the laws now governing the material world; and the discovery of this unlooked-for conformity has at length induced some philosophers to infer, that, during the ages contemplated in geology, there has never been any interruption to the agency of the same uniform laws of change. The same assemblage of general causes, they conceive, may have been sufficient to produce, by their various combinations, the endless diversity of effects, of which the shell of the earth has preserved the memorials; and, consistently with these principles, the recurrence of analogous changes is expected by them in time to come.

....By degrees, many of the enigmas of the moral and physical world are explained, and, instead of being due to extrinsic and irregular causes, they are found to depend on fixed and invariable laws. The philosopher at last becomes convinced of the undeviating uniformity of secondary causes; and, guided by his faith in this principle, he determines the probability of accounts transmitted to him of former occurrences, and often rejects the fabulous tales of former times, on the ground of their being irreconcilable with the experience of more enlightened ages.

Host-Parasite Intimacy--Reaching a New Level

One Species' Genome Discovered Inside Another's. I thought this was an interesting article, and it comes out of the research institute where I used to work (now known as the J. Craig Venter Institute), although there's only one person I know in the author list. The actual article is Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes in the latest issue of Science.

Wohlbachia species are parasites of insects and other invertebrates, passed from one host generation to the next inside the germ cells. Wohlbachia genes have been discovered inserted into host genomes, but this paper documents cases in which the entire bacterial genome has been so inserted.

Lateral gene transfer between bacterial species is a common phenomenon, and has made me pessimistic about deducing evolutionary history of bacteria. This finding could throw a monkey wrench in molecular insect phylogeny as well. It's also likely to send genome sequencers to recheck their published data. In sequencing eukaryotic genomes, you often get bacterial genome contamination, and much of the software used in the process automatically recognizes and discards bacterial sequences. Someone's going to have to distinguish between contamination and real sequence data. (Glad it's not me.)

Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes,

Julie C. Dunning Hotopp, Michael E. Clark, Deodoro C. S. G. Oliveira, Jeremy M. Foster, Peter Fischer, Monica C. Munoz Torres, Jonathan D. Giebel, Nikhil Kumar, Nadeeza Ishmael, Shiliang Wang, Jessica Ingram, Rahul V. Nene, Jessica Shepard, Jeffrey Tomkins, Stephen Richards, David J. Spiro, Elodie Ghedin, Barton E. Slatko, Herve Tettelin, John H. Werren

Published Online August 30, 2007, Science, Reports

Although common among bacteria, lateral gene transfer (the movement of genes between distantly related organisms) is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of 4 insect and 4 nematode species that range from nearly the entire Wolbachia genome (>1 megabase) to short (<500 base pairs) insertions. Potential Wolbachia to host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.

Underwing Moth In Mourning For Taxonomic Stability

Underwing or Catocola moths are common on Droop Mountain, and there are quite a few species with colorfully-striped hindwings of yellow, orange, or pink. Thursday night's rain brought a nice crop of Friday morning moths, and of course I nudged this large individual, anticipating a surprising flash of color. I got a real surprise this time, for the moth took flight, with flashes of intense flat black. Lucky for me it didn't fly far or high, and I was able to get a picture of the hindwings.

There are Catocolas with specific epithets like lachrymosa and dejecta, and I've seen these funeral hindwings in field guides and collections, but this was my first black Underwing on the wing.

Historically, the Underwings are members of the Noctuidae, but that family was a taxonomic dumping ground, and lepidopterists have been working clean-up for some time. The Noctuoidea of Eastern Canada includes Catocola in the Noctuiidae. Bugguide.net has placed Catocola in the Eribidae. Curiously, both resources cite the same taxonomic authority: "Kitching, I.J., and J.E. Rawlins. 1999. (The Noctuoidea, pp. 355-401 in Kristensen N.P. (editor). Lepidoptera: Moths and butterflies. Volume 1: Evolution, systematics and biogeography. Handbook of Zoology/Handbuch der Zoologie. Walter de Gruyter. Berlin/New York)."

Shrubby St. John's Wort

The St. John's Wort has been in bloom the last couple of weeks. They're small but beautiful flowers. Don't you love that cloud of anthers? Ours is a woody shrub, and it's abundant around the locust and hawthorn thickets overtaking the old field on top of our ridge.

I wasn't sure what species we have, so I turned to the incredibly frustrating but essential Flora of West Virginia (Strausbaugh and Core, WVU Press, Revised Edition, 1970). I know St. John's Wort on sight--it's genus is Hypericum. The Flora of West Virginia has no index, so the only way to find it in the book is through the key to families at the front of Volume 1. I skip to the Dicots couplet, 35. Yup, "Polypetalous plants," sends me to couplet 78, "Stamens numerous, usually more than 10." As a well-brought-up taxonomist, I pause to curse the use of "usually" in a key to families. However, I know we have WAY more than 10 stamens, so I continue to couplet 79--"Calyx free from ovary" vs. "Calyx more or less jointed to the ovary." "MORE OR LESS!" I snort. I know the answer, (the calyx is definitely free) but I can see I'm down to a short list of families, so I start skimming. There's Guttiferae, one of Linnaeus' eight conserved family names, venerable designations like Graminae that are kept even though they don't consist of a genus-name root plus the "aceae" family ending. Modern botanists scorn the conserved names, and call the St. John's Wort family either Hypericaceae (splitters) or Clusiaceae (lumpers, who put Hypericum in the Mangosteen family).

There it is in the Flora of West Virginia, Family Guttiferae, page 630. Now, I know page 630 is in Volume 3, so I pick up volume 3, turn to page 630, which is Family Tiliaceae, the Basswood family. The pages are misnumbered in the key, so I start leafing forward and backward. Guttiferae is on page 638. (I turn to the Guttiferae couplet in the Key to Families, and pencil in the correct number. In a few years, I will have a useful Key to Families.)

There I read that there are 12 species of St. John's Wort in West Virginia, and learn that

The common name St. John's Wort alludes to the flowering of many of the plants about St. John the Baptist's Day (June 24).

The key to species works nicely, and sends me to a couplet giving me a choice between Hypericum prolificum and Hypericum densiflorum. The two species are distinguished from one another by the size of the seed capsule. Although size of seed capsule can vary due to environmental factors, I'm reasonably comfortable offering an identification of Hypericum prolificum--"Shrubby St. John's Wort." I was surprised that this common shrub of old pastures and roadsides is not the introduced Palearctic St. John's Wort, but a native species that is uncommon in some parts of its range.

Some Web references for Hypericum species:

• USDA's Plants Database entry for Hypericum prolificum..
• Hypericum prolificum. from Wisconsin's Robert W. Freckmann Herbarium.
• UConn Plant Database entry for Hypericum prolificum.
• USDA's Plants Database entry for Hypericum densiflorum.
• Hypericum densiflorum entry from US Fish and Wildlife Service's Native Plants for Wildlife Habitat and Conservation Landscaping: Chesapeake Bay Watershed.
• USDA's Plants Database entry for Hypericum perforatum..
• St. John's Wort from the "Herbs at a Glance" section of NIH's National Center for Complimentary and Alternative Medicine (NCCAM). They are talking about Hypericum perforatum, the Old World species that's a common exotic in North America.
• Cornell's Animal Science Department has a page on Hypericism, extreme photosensitivity in livestock, caused by ingestion of St. John's Wort.
• Arthur C. Gibson's essay on St. John's Wort observes that St. John's wort, like a fairy, supposedly protects against evil beings, chases demons, and can silence poltergeists (see A. R. Vickery, "Traditional uses and folklore of Hypericum in the British Isles," Economic Botany 35:289-295, 1981).