Saturday, December 13, 2008
David Sloan Wilson’s “Evolution for Everyone” truly lives up to its title. Written in an engaging, accessible style, it is hard not to be carried away by the author’s enthusiasm for his topic. Although I am usually suspicious of authors who claim one pet theory can explain every known phenomenon under the sun (think of Freudians, behaviorists, etc.), Wilson ably demonstrates how evolution can indeed be applied to a variety of academic disciplines, and more importantly, to explain a variety of phenomena that one encounters in everyday life.
In this book, the author’s initial aim is both to introduce the reluctant reader to the basics of the theory of natural selection, as well as to clear away misconceptions about what it is and isn’t. In doing this, he seeks to demythologize science, assuring the reader that the scientific method consists of nothing more than “ensuring accountability for factual claims,” which when accumulated can build a sturdy scaffold to support a theory. Wilson repeatedly states that science is simply a “roll up your sleeves” activity like gardening or construction, that requires hard work and sweat, yet like gardening and (some) construction work, can be practiced by anybody.
I found the strongest parts of his book to be in the first half, in which he proceeds from a basic description of natural selection to fascinating examples of how adaptive behavior and traits evolve in various species, and eventually, how the theory can be applied to broader topics such as personality traits, perceptions of beauty, and social behavior. One of the underlying premises of his book is that evolutionary theory, even though it doesn’t always lead to behavior in the wild that humans would think of as benign (e.g., beetles and monkeys practicing infanticide), nevertheless favors cooperative social behavior in the long run, rather than the popular notion of “nature red in tooth and claw.” Although I found myself skeptical of some of the broader treatments of evolutionary life applied to nations and religions in the latter parts of the book, his cheerful and humane style disarms the reader, and keeps one engaged with his argument.
In short, I would heartily recommend this book.
Incidentally, on a related note, anybody who is interested in learning more about Wilson and his research should check out his website at http://evolution.binghamton.edu/dswilson/ . He refers to it several times in his book, and posts quite a few publications--not just his own but those of his students as well. And for those of us Stanford students from the Fall 2008 Darwin seminar, if you didn't get your fill, you should check the related link to a program that Wilson leads, EvoS, the Evolution Studies Program at Binghamton University. Their website is at http://evolution.binghamton.edu/evos/ .
Tuesday, December 9, 2008
The Autobiography of Charles Darwin, 1809-1882. Edited by Nora Barlow. New York: WWW. Norton & Company, Inc. 1993. Reissued 2005.
Darwin’s autobiography has gone through several evolutions of its own, and finally emerged in its intact, original & intended form about fifty years ago. It was later published in paperback by Norton Paperback and was reissued in 2005. That is the edition under review.
An autobiography is generally expected to provide insights on the author’s thoughts and feelings and experiences. In reality, most autobiographies are just another face that the author (or the author’s family, in this case) carefully presents to the world.
The author creates a persona he wants known as his “real self” – a persona that may contradict the known facts – or the author may edit out significant events of his or her life in order to create a perfect reality.
To gauge the extent that Darwin’s autobiography follows this strategy we’ll review, the origin of the autobiography, its publication history, as well as the content and omissions.
Genesis of the Autobiography
Darwin tells us, as a way of introduction, that the autobiography was suggested to him by a German editor; Darwin thought “the attempt would amuse me and might possibly interest my children or their children.” He began writing on May 31st, 1876, when was already sixty-seven years old, and almost seventeen years had passed since the publication of On the Origin of Species. Clearly, it was written at a time when Darwin had much to look back on. He may have taken this opportunity not just to amuse himself and his descendants but also to set the record straight, so to speak.
According to the introduction provided by Nora Barlow, Darwin’s granddaughter, Darwin wrote his autobiography in about three months but then expanded it by an additional sixty seven pages in the last six years of his life. The current edition represents the original draft plus the additions, grafted into the appropriate chapters.
History of Publication
That there was desire to mold and control the public perception of Darwin is never clearer than in the introduction provided by Barlow. The first publication in 1887, which was controlled by Darwin’s wife and surviving children, went through an editing process that excised some significant passages pertaining to Darwin’s religious beliefs, as well as some occasional commentary that may have offended still-living friends or colleagues of Darwin.
The need to protect the public image of Darwin would certainly be paramount to the family; though apparently some members thought that Darwin would have wanted the unexpurgated manuscript published. I think a case could easily be made for the latter viewpoint, after all Darwin certainly wrote it after a request from an editor. And the fact is he never instructed otherwise (that is, not to publish).
Barlow suggests that in reality Darwin’s thoughts were never intended for publication and certain family members (Henrietta Darwin, in particular) believed that publishing the manuscript as-is would damage his reputation. As a member of the succeeding generation, Barlow believed that the omissions were not of such great consequence as to necessitate expurgation. In fact, she had them restored in the 1958 edition of the Autobiography.
After reading the Autobiography, I would have to concur with Barlow – perhaps the passage of time and the general change in the centrality of religion was the significant factor affecting the perception.
Summary of the Text
Aside from the posthumous editing, the Autobiography is rather short—only about one hundred pages for the proper autobiographical section; that is, excluding the appendix, and notes.
The Autobiography briefly discusses growing up; his education; the seminal event of his life: the voyage of the Beagle, his marriage and; and finally his life at Down House, working and raising a family.
Upon my initial reading of the Autobiography, I was struck by how modest Darwin sounded. He downplayed his achievements (how could he only take a mere one hundred pages to tell the story of his long eventful life?) and exaggerated his faults.
To the degree that I was unfamiliar with his large body of work and the details of his efforts in producing the work, I fell for this humble act. I genuinely believed that he’d been extraordinarily lucky and it might well have been someone else who could easily have come up with the theory of evolution, much as he had done. Once I began reading his works, I realized how wrong I was.
Darwin was certainly modest, and the paragon of politeness and decency – his letters show his solicitousness. But, in his Autobiography I think the missing detail of his day-to-day work (captured in his notebooks and his actual publications) makes it hard to assess his industry and originality.
Darwin’s recollection of his time in Edinburgh and Cambridge as dissipated seems to be an obvious act of humility or simply the statements of an overachiever. He made too many scientific connections to have just been idling. He presented his first scientific paper at the age of 18 to the Plinian Society in Edinburgh. Rebecca Stott claims in Darwin and the Barnacle that Charles and his brother Erasmus checked out more books from the library during his first term at the University than most students did during the entire year.
Another interesting episode is that of the first publication of On the Origin of Species. He lets others take the responsibility (eg: Hooker and Lyell) for co-opting Wallace. Clearly, Darwin wanted to maintain his distance from the rough politics of science. And he certainly let T.H. Huxley fight his battles, after publication!
In the Autobiography, Darwin emerges as a solid family man, who loved his wife and children dearly. He was also a decent human being and a genius.As an introduction to Darwin or simply for insight into Darwin’s personality, I strongly recommend the Autobiography. But, do read some of his other works, or at least get an overview of the scope of his work. I think the Autobiography highly understates him.
Monday, December 8, 2008
Friday, December 5, 2008
For example, have you heard of Ilkley (or Otley) in Yorkshire? Well, Darwin stayed here “taking water cure treatments when On the Origin of Species was published in November 1859.”
The map can be accessed here: http://www.darwin200.org/darwins-britain/index.html
The map forms part of the Darwin200 website. The group’s mission is to celebrate Charles Darwin’s scientific ideas and their impact through a national program of events during this bicentenary year. Check out their website to see what they have planned at: http://www.darwin200.org/
Thursday, December 4, 2008
Keynes, Randal. Annie’s Box: Charles Darwin, His Daughter, and Human Evolution. London: Fourth Estate, 2001 (Published in the North America in 2002 under the title Darwin, His Daughter, and Human Evolution: New York: Riverhead Books, 2002)
If you’re curious about Charles Darwin, the man, look no further than Randal Keynes’ touching biography of his great-great-uncle. It’s all here: from the Darwins’ marriage and first home in London to the details of life at Downe House, Emma’s widowhood, and Annie’s Box, a writing-case which symbolizes the heartbreaking death of Darwin's ten-year-old daughter. The account spans from the time Darwin decided to “Marry – Marry – Marry. Q.E.D.” in 1938, dipping into some history at Cambridge and aboard the Beagle, until Emma’s death in 1896, and includes a deeply personal look at life along the way.
Keynes pays particular attention to Darwin as husband and father. Darwin, who adored his family, exhibited “a fine degree of paternal fervour” with his ten children, playing on his hands and knees with them, never silencing their "howls and screams,” and even allowing them into his study while he worked. Of all the children, Darwin doted most on Annie, his cherished, eldest daughter, who was the apple of her devoted father's eye.
On April 23, 1851, just two days after Easter, Annie died, possibly from tuberculosis. Paradoxically, Darwin’s religiosity suffered its final blow at this holiest time of year for Christians. Separated from his wife during Annie’s demise, Darwin could not draw on Emma’s religious fortitude to comfort him or to interpret Annie’s death, and he could not find the consolation he needed from the Church. Although Darwin’s theory of evolution was already well developed by the time Annie died, Keynes juxtaposes Darwin’s darkening sense of nature (and his efforts to understand suffering and death) with his continued work on the Origin of Species.
Keynes’ ultimate thesis is that Darwin’s private "life and his science were all of a piece," which he aptly portrays. The narrative left me with a greater appreciation of an iconic, and often misunderstood, man, someone who was both a brilliant scientist and a loving human being who made time in life for the things that matter most: family and friends.
(Posted as The Heart of Charles Darwin’s “Insufferable Grief” on Amazon.com at http://www.amazon.com/gp/product/1841150606/ref=cm_cr_mts_prod_img)
Shubin, Neil. Your Inner Fish: A Journey into the 3.5 Billion-Year History of the Human Body. New York: Pantheon, 2008.
Neil Shubin, an evolutionary biologist who works as Provost of the Field Museum of Natural History in Chicago, clearly chose the right career. In Your Inner Fish: A Journey into the 3.5 Billion-Year History of the Human Body, Shubin traces the history of our anatomy with a passion that leaps off the page. His conversational writing style, coupled with animated anecdotes and crisp descriptions, energized my reading so that two hundred pages seemed more like twenty.
The title of the book, Your Inner Fish, refers to the evolutionary history we humans share with other animals. Shubin, who also acts as Professor of Anatomy and Associate Dean at the University of Chicago, opens with the tale of how he co-discovered Tiktaalik roseae, sometimes called the “fish that crawled out of the water,” in the Canadian Arctic in 2006. This groundbreaking find provides compelling evidence of an intermediate stage between fish and early limbed animals, and serves as an illustration of the “history of life within us,” one example among many that Shubin highlights.
Of course, Charles Darwin predicted that transitional forms would illustrate a gradual evolutionary shift between two distinct groups, and Tiktaalik fits the bill. Like most fish, Tiktaalik possessed gills, scales, and webbed fins. Yet, it also sported innovations like wrists, lungs, and a mobile neck, and it denotes the earliest creature to possess all the bones of our arm, wrist, and palm. Previous to Tiktaalik, fish did not exhibit these joints. Thus, this creature laid the stepping-stones for later vertebrates to transition onto dry land.
The author tells us why we should care about this: "Virtually every illness we suffer has some historical component. ... [D]ifferent branches of the tree of life inside us – from ancient humans, to amphibians and fish, and finally to microbes – come back to pester us today … show[ing] that we were not designed rationally, but are products of a convoluted history."
He pinpoints the evolutionary history of our senses of smell, sight, and hearing, as well as that of our wrists, teeth, jaws, and skull, and he explains such common ailments as hiccups, hernias, and sleep apnea.
In a poignant passage about dissecting the human hand, Shubin recalls his personal introduction as a student to human anatomy. After spending months dissecting internal organs, he felt detached about the task before him. Seeing the hand jolted him back to reality: “[s]uddenly this mechanical exercise, dissection, became deeply and emotionally personal.” Similarly, when he examined Tiktaalik’s modified fin for the first time, he felt that he had “uncovered a deep connection between my humanity and [that of] another being,” which is the whole premise of his book.
Your Inner Fish provides a fascinating overview of the history of our own evolution, an introduction that is both readable and inviting. I suppose the simple explanations and introductory tone Shubin uses might give more well-read students seeking in-depth analysis or discussion, reason to criticize, but for a non-scientist reader such as myself, Shubin strikes the right note for piquing my interest further. And simply by asking what evolution from our animal ancestors really means for us, Shubin makes the book personally relevant in a modern context.
Shubin concludes with an inspiring message: "I can imagine few things more beautiful or intellectually profound than finding the basis for our humanity, and remedies for many of the ills we suffer, nestled inside some of the most humble creatures that ever lived on our planet."
(Posted as "Our Evolutionary Branch, Demystified" under the hardcover version on Amazon.com at http://www.amazon.com/Your-Inner-Fish-Journey-3-5-Billion-Year/dp/0375424474/ref=pd_rhf_p_t_1)
Wednesday, December 3, 2008
On Monday night, when George Levine recommended Darwin’s Plots, a book first published in 1983, he didn’t mention that he wrote the foreword to this book, penned by Gillian Beer. But the tie is far from surprising when one considers the topic — the evolutionary narrative found in Darwin’s writing.
Levine’s more recent Darwin Loves You, though original and enjoyable, echoes many of Beer’s notions, from the importance of considering Darwin’s metaphors and language to reconsidering Darwin “as much of a believer in cooperation” and “mutual aid as in ruthless competition.” Darwin’s Plots also pushes readers to consider Darwin as a careful writer and an ongoing influence on modern literature and language. In fact, Beer (and Levine) place Darwin in the realm of literature, alongside the likes of Charles Dickens, George Eliot, and Virginia Wolf. But Beer, through careful analysis of Darwin’s writing, notes that Darwin was also influenced by these writers and others. Beer notes similarities in Darwin’s prose and the likes of Milton, Wordsworth, Coleridge, and Dickens. She also labels the Victorian naturalist a “Romantic materialist,” which seems akin to calling someone a “nostalgic agnostic.” Considering Darwin as a Romantic materialist was, for me, considering him in an entirely new light. Additionally, Beer reminds readers that to skim Darwin’s writing is to miss out on his writerly charm and, on occasion, intended meaning.
Also, having spent time researching Victorian writer Edward Bulwer Lytton, I am fascinated by Beer’s notion that science was often considered fiction (or, perhaps, a twist on an old cliché — science was stranger than fiction):
“Most major scientific theories,” she explains, “rebuff common sense. They call on evidence beyond the reach of our senses and overturn the observable world. They disturb assumed relationships and shift what has been substantial into metaphor... Such major theories tax, affront, and exhilarate those who first encounter them, although in fifty years or so they will be taken for granted... When it is first advanced theory is at most fictive. The awkwardness of fit between the natural world as it is currently perceived and as it is hypothetically imagined holds the theory itself for a time within a provisional scope akin to that of fiction” (1).
Beer overlays Darwin’s language on the outline of the novel, and shows readers that his writing can be read as both science and poetry. Both Darwin and fiction writers tackle the notions of natural selection (er, daily life) through courtship, matchmaking, beauty, and utter brut force. To this day, as Levine points out, we still can reinterpret and reconsider Darwin’s prose. Amazingly, much of his writing and ideas still read fresh and relevant.
On November 21, the New York Times reported that a scientist in New Zealand found another species of penguins, while looking through museum specimens hundreds of years old. The scientist, Sanne Boessenkook of University of Otago was investigating the history of the yellow-eyed penguin, trying to determine if it had been more abundant in the past. It turns out that museum specimens included a completely undocumented species that is now extinct.
Another recent (Dec 1) article in the same magazine talks about the discovery of a new form of amoeba that throws into question the how of evolution of life on earth. Up until now, scientist have believed that multi-cellular organisms that have two halves that mirror each other came about in the pre-Cambrian period explosion of life (more than 500 M years ago). This idea was based on fossilized tracks. The thinking was that only a complex, bilateral form could leave those tracks. However, the new giant amoeba, called Gromia is unicellular and is capable of locomotion and leaves tracks very similar to those in the fossil record. The full article can be found here:
These findings reinforce that continued research is necessary to really understand evolution.
(Image source: New York Times Online)
New fossil discovery shows how turtle may have evolved their shells. Chinese scientist, Chun Li and other colleagues have come up with a new ancestral turtle species based on fossils found in Guizhou Province in southwestern China. The species they named Odontochelis semistestacea lived about 220 million years ago and was likely aquatic.
The unique characteristic that differentiates it from other later turtles is that it only has half a shell.
Based on its skeletal structure, the scientists believe that the shell evolved from skeletal changes.
The article appeared in the New York Times,
Tuesday, December 2, 2008
Inside: evolve your beliefs
The company believes it fills a niche, noting that “[n]early 15% of Americans identify themselves as ‘non-religious,’ [while] … surveys show that 95% of Americans celebrate Christmas.”
They offer eight designs at http://www.atheistholidaycards.com/ or http://www.cafepress.com/orderofstnick/6179512.
Inside: the evolution of tradition
Here’s a link to The Colbert Report episode (note: the segment begins at 14 minutes in):
Inside: It’s an evolutionary advantage
Happy Holidays, Everyone!
Monday, December 1, 2008
In Darwin’s Gift: To Science and Religion, Francisco Ayala provides a clear, concise, and readable introduction to the myriad ways in which evolutionary theory has been applied in the century and a half since Darwin’s publication of The Origin of Species. Although the motivation for writing this book appeared to be that of countering the views of “intelligent design” creationists, it can also be read by anyone interested in a brief overview of evolutionary theory. While not focusing at length on Darwin, this book does an effective job of explaining what the theory of natural selection consists of, and how it has been applied to such fields of study as paleontology and genetics in the century since Darwin. In fact, I’ve recently been reading of a number of works discussing evolution and have listened to a number of lectures on this topic (all as part of a university-level course on Darwin), and for a non-scientist like myself, I would’ve been helped much if I had read Ayala’s book first.
Of course, it is evident from the title that Ayala intends to allay any fears that religious believers may have about evolutionary theory, and he effectively demonstrates how this theory can complement rather than threaten the foundations of religious belief. The basis that he rests this view on, as noted by other reviewers, is the concept of NOMA, or the “non-overlapping magisterial areas” of science and religion, popularized by Stephen Jay Gould. In other words, it isn’t the business of religion to concern itself with strictly scientific questions, nor is it that of science to expound upon religious and philosophical questions (although this doesn’t mean that individuals who are religious can’t have an interest in science, and vice-versa). With this view as a departure point, Ayala shows not only what a gift Darwin’s theory has been to science—with ample description of the ways in which evolutionary theory has been applied to a number of areas of study—but also to religion. In explaining aspects of nature that seem cruel or poorly designed, he shows that a refutation of “intelligent design” and acceptance of natural selection lets God off the hook, so to speak, by providing a plausible explanation for an imperfect world. In a similar vein, he follows the lead of the theologian John Haught (who he cites) and the paleontologist Pierre Teilhard de Chardin (who he doesn’t) in showing how evolutionary theory can also provide an alternative explanation to the question of the existence of evil in the universe, solving the problem of theodicy (although admittedly this explanation doesn’t have much to say about individual evil, such as how Hitlers and Stalins come to be).
Yet, even aside from the big questions of religion and science, Ayala’s treatment of natural selection and evolution do a good job of demythologizing these concepts. For example, I found it helpful to learn that the process of natural selection is not the random, purposeless path it is often made out to be: while the mutations that lead to new species are indeed random, the process of natural selection that leads to such mutations becoming firmly established is not, but is instead a common-sense response of organisms adapting to a given environment over time.
In a time when the stridently atheistic views of bestselling evolutionists like Richard Dawkins, Daniel Dennett, and Christopher Hitchens have received much attention, it is refreshing to read the work of someone like Ayala, who can calmly make the case for the peaceful co-existence of both evolution and religion.
Sunday, November 30, 2008
The New Scientist considers why we fight. Apparently, warfare — “as ancient as humankind” — plays an “integral role” in our evolution. This doesn’t strike me as overly surprising, but apparently, such information should not be taken for granted:
“A new theory is emerging that challenges the prevailing view that warfare is a product of human culture and thus a relatively recent phenomenon. For the first time, anthropologists, archaeologists, primatologists, psychologists and political scientists are approaching a consensus. Not only is war as ancient as humankind, they say, but it has played an integral role in our evolution.”
The article, by Bob Holmes, considers research suggesting that warfare makes up 10 percent or more of all male deaths in present-day hunter-gatherers. “That’s enough to get your attention,” says Stephen LeBlanc, an archaeologist at Harvard University’s Peabody Museum in Boston quoted in the article. Primatologists, according to Holmes, have long known that orchestrated violence regularly occurs between gangs of warring chimpanzees, our closest relatives.
Much of the article veers into the realm of social science. However, anthropologist Mark Flinn of the University of Missouri at Columbia looked into group-oriented responses on the hormonal level. Flinn studied cricket players on the Caribbean island of Dominica and learned that they experience a testosterone surge after beating another village. Their hormonal group surge ends when the game — er, warfare — ends. “The net effect of all this,” according to Holmes, “is that groups of males take on their own special dynamic. Think soldiers in a platoon, or football fans out on the town: cohesive, confident, aggressive — just the traits a group of warriors needs.” And here’s a new flash: Women are less aggressive.
I'll be posting this book review on Amazon, but here it is, too:
As I’ve learned through this class, Darwin was a man with an agenda, and one devised at an early age. Now, I question the motives of “the man who walk[ed] with Henslow” (was he simply using his daily outings with the cleric-botanist as a way to infiltrate the close circle of Cambridge scientists?). What about Darwin’s instance that his grandfather Erasmus was of no influence on him? Certainly, I’ve come to read Darwin’s autobiography and letters with fresh eyes, no longer trusting words written by him for the eyes of another.
Now that Darwin seems calculating to me, I appreciate the Herculean effort of Mario A. Di Gregorio and his assistant N. W. Gill. Their 895-page volume Charles Darwin’s Marginalia is a find, largely because it captures what Darwin had no intention of publishing — his handwritten notes jotted in fourteen-hundred books from his personal library. (A subsequent, still-to-be-published book, is set to document the marginalia in Darwin’s journals.) The authors, who personally deciphered Darwin’s scrawl, track his notes line by line to the original text. They also include a “conceptual guide to annotations.”
Darwin was clearly a note taker, and oftentimes his humor, frustration, and cattiness come through. In Robert Chambers’ Vestiges, Darwin sketched out his approach for discussing evolution (“higher” and “lower” forms of life) and even wrote “Rubbish!” along side a line. In many respects, Darwin’s comments illustrate a sort of no-holds-barred conversation with authors — they comment and he responds. Often, he writes his personal view and how he would present his take to future readers (“remember to avoid...“).
Marginalia, though out of print, is also valuable for judging which writers and subjects were of particular interest to Darwin. By far, Charles Lyell is the most heavily annotated author (xxxiii). As a scholarly work (complete with a very elaborate system of abbreviations and symbols), this book is wonderful — a rare view into the occasional outbursts of a great, calculating mind. My only request is really that of a novice student: an overview that more simply considered the themes that can be culled from the tome.
Charles Darwin. Charles Darwin’s Marginalia. [Edited by] Mario A. Di Gregorio with the assistance of N. W. Gill. Volume 1. (Garland Reference Library of the Humanities, 783.) lxii + 895 pp., figs., indexes. New York/London: Garland Publishing, 1990. $102.
Incidentally, since Bob and some of the lecturers who have visited Stanford this quarter (e.g., Niles Eldredge, Janet Browne) have made mention of Charles Darwin's portrait gracing the new British ten-pound note, I thought that this recent piece in the Guardian might be of interest: http://www.guardian.co.uk/science/2008/nov/16/darwinbicentenary-currencies
In it, Professor Steve Jones of University College, London, points out that on this portrait, Darwin is shown facing an image of a hummingbird on the opposite side of the banknote, suggesting that Darwin received inspiration for the development of his theories through the study of such birds. Jones points out, though, that it was finches and mockingbirds that attracted Darwin's interest, and not hummingbirds, since none of the latter existed on the Galapagos Islands, nor were they mentioned in The Origin of Species. When asked why this bird appeared on the banknote, Jones suggested that the artist may have simply liked them. For Jones, however, such an apparent misrepresenation is no small matter, as he notes that "We are surprised by the numbers of people who believe in creationism and rubbish like that only to find the currency in which we place our trust is telling us lies about evolution."
For anybody interested in the Bank of England's take on this, their spokesperson simply said that the hummingbird was representative of birds found "in the region" of the Galapagos, while the Bank of England's web article about the currency (http://www.bankofengland.co.uk/banknotes/current/current_10.htm) states that the illustrations on the note represent "the flora and fauna that [Darwin] may have come across on his travels."
I hope that everybody reading this has made it through the Thanksgiving holidays healthy and whole. Wherever I have been these past few days though, I have been hearing more of the seasonal coughs and sneezes, which turns me to thinking about colds, and hoping that I don't sound too much like a hypochondriac, a couple of stories about viruses on the "Science Today" website caught my attention today.
The first article (http://www.sciencedaily.com/releases/2008/11/081120073115.htm)
was about the evolution of a virus that causes colds in young children, and which a new study shows originated in birds and "crossed the species barrier" about 200 years ago. This virus, human metapneumovirus (HMPV), is not the same as the rhinovirus that causes up to half of the common colds, yet the symptoms triggered by this virus are much like those typically associated with common colds (runny nose, sore throat, cough, etc.). Researchers in the Netherlands have determined that this virus is very similar to avian metapneumovirus (AMPV-C). What caught my attention in this article was the role that evolution played in the development and transmission of this virus, and how these scientists were able to establish when it migrated from birds to humans. The HMPV and AMPV are both "highly evolutionary," and in addition to determining when AMPV migrated from birds to humans, the researchers studied mutation rates and selection pressures on these viruses. As one of the principal researchers in the study, Dr. Ron Fouchier, summarized it, "An understanding of how viruses evolve and how they adapt to new hosts and their immune systems is important, especially if we are to prepare for new, potentially pandemic diseases."
The second article about colds that had an evolutionary twist was one that showed how viruses manipulate genes to create conditions favorable for the spread of the virus (http://www.sciencedaily.com/releases/2008/10/081024084206.htm). In a recent study conducted by researchers at the University of Calgary and the University of Virginia (with, interestingly, sponsorship from Proctor and Gamble), scientists identified two groups of genes that when "hijacked" by human rhinovirus (HRV), are either "up-regulated" or "down-regulated" by the virus, leading to an increase in production of pro-inflammatory cytokines and a change in the production of antiviral proteins (I was unclear from the article whether the virus lead to a decrease in the production of such proteins, as one would expect, or an increase, as the article at one point seemed to suggest).
In both articles, I was reminded of Gary Ewald's assertion in his book "The Evolution of Infectious Diseases," to the effect that it is important to understand the evolution of such viruses rather than merely trying to develop medicines that in the end simply treat symptoms or to which viruses eventually adapt. Both of these articles seem to be examples of the type of approach that he recommended.
Wednesday, November 26, 2008
The Natural History Museum in London recently unveiled an interactive tool that traces the route of the HMS Beagle.
Each virtual stop - sixteen are listed in total - features a quote from Charles Darwin that introduces his thoughts on that particular destination.
Here are a few examples:
Cape Verde Islands
Darwin is exhilarated by his first observations.
"It then first dawned on me that I might perhaps write a book on the geology of the various countries visited, and this made me thrill with delight."
Punta Alta, Argentina
Darwin is intrigued by the giant fossils he sees.
"I have been wonderfully lucky with fossil bones. Some of the animals must have been of great dimensions! I am almost sure that many of them are quite new."
Chiloe Island, Chile
Darwin sees Mount Osomo erupt while on the island of Chiloe and experiences the earthquake in the woods near Valdivia. Seeing the aftermath of the earthquake affected him tremendously.
"I believe this earthquake has done more in degrading or lessening the size of the island, than 100 years of ordinary wear and tear."
The tool provides a useful snapshot and reminder of the breadth of Darwin's voyages. Check it out here: http://www.nhm.ac.uk/nature-online/science-of-natural-history/expeditions-collecting/beagle-voyage.
Neil Greenwood, Programme Director for the Centre, explains that "[a]n innovative project like the Darwin Centre deserves to be housed in an iconic building."
C F Møller Architects, one of Scandinavia's most renowned architectural firms, delivered a distinctive, modern structure shaped like a cocoon. The state-of-the-art facility, which measures 65 meters long and 8 stories high, sits in a glass atrium that will allow the public to see behind the scenes. It will house both workspaces and close to 70 million insect and plant specimens, some of the world’s most valuable and historic collections. Environmental conditions will be carefully controlled to safeguard these scientific treasures, often “vulnerable to damage from light, humidity and pests.”
The Centre also aims to create a repository for world leaders in scientific research. Scientists from around the world will be able to collaborate on naming, identifying, and classifying organisms, as well as researching environmental changes.
The Darwin Centre is set to open in September 2009, and looks well worth a visit.
The Museum website can be accessed here: http://www.nhm.ac.uk/about-us/darwin-centre/index.html
Friday, November 21, 2008
In this morning's New York Times, there is a brief article about non-native plants in the Galapagos.
I posted here a couple of months back an article from the Los Angeles Times about the Ecuadorian government's attempts to limit the number of people living on and travelling to the Galapagos, due to the ecological impact of a growing human population, as well as the non-native flora and fauna that has hitchhiked to the islands.
Today's article is interesting since it shows that many varieties of plants that were thought to be non-native have actually turned out to be native after all. Why the reversal? Because scientists have located fossilized pollen grains of plants previously thought to have been non-native. It turns out that the fossilized pollen, though, is well over 8,000 years old.
This isn't meant to negate the need to protect the unique habitat of these islands, but has given some scientists pause for thought, as well as a new model to use in investigating the history of plant life on other Pacific islands.
It was widely reported this morning that the remains of Nicholas Copernicus have been identified by DNA testing. Polish and Swedish researchers accomplished the feat by comparing DNA from remains long-suspected to be Copernicus's, but buried in an unmarked grave, with remains of hair found in one of Copernicus's books.
Copernicus, of course, was the 16th century astronomer generally credited with being the first to realize that the earth revolves around the sun, rather than vice versa.
My favorite aspect of the story is that the researchers have also published a reconstruction of Copernicus's face, seen here.
I was curious how they could have come up with this level of detail simply with DNA. If you are as well, it appears that the explanation is "They can't." The explanation of why they are confident that the reconstruction is accurate is so hysterically inane as to deserve quotation in full. Here is Polish archaeologist Jerzy Gassowki on the subject:
[The reconstruction] bears striking resemblance to existing portraits of Copernicus. The reconstruction shows a broken nose and other features that resemble a self-portrait of Copernicus, and the skull bears a cut mark above the left eye that corresponds with a scar shown in the painting. Moreover, the skull belonged to a man aged around 70 -- Copernicus's age when he died in 1543.
In other words, we matched the DNA, then we went and looked at the skull and a bunch of old pictures of the guy, and created a face that fit both, and looks old to boot! Modern advances in science are indeed extraordinary.
Thursday, November 20, 2008
Aside from a nice biographical sketch of Wallace, author David Quammen poses the question that he says no scholar or biographer has answered adequately: “How to reconcile such brilliant achievements, radical convictions, and incautious zealotries within one human character — the character of a consummate empiricist and field naturalist?”
He partly looks to Wallace’s favorite books, those that Wallace himself say influenced his thinking most. The top two are of particular relevance to our class: Charles Darwin’s Journal and, according to the article, “the other, more daring and incendiary [...] best seller titled Vestiges of the Natural History of Creation.” I actually think this particular writer gets a lot wrong about Vestiges. Essentially, he is overly dismisive, but does rightly point out that “the book was a potpourri of interesting facts, absurd factoids, savvy insights, tenuous suppositions, and woozy deductive leaps, which variously satisfied or amused readers ranging from Queen Victoria to John Stuart Mill to Florence Nightingale.”
Though the author doesn’t source Janet Browne, he’s clearly referencing her when he writes that a young, impressionable Wallace found in Vestiges “an ingenious hypothesis” yet to be proved by further research.
I would have loved for the reporter to have teased about more about the notion of Wallace being dismissed as a crank. Frankly, he seems far more of crank than Robert Chambers, who wrote Vestiges:
Wallace’s story is complicated, heroic, and perplexing. Besides being one of the greatest field biologists of the 19th century, he was a man of crotchety independence and lurching enthusiasms, a restless soul never quite satisfied with the place in which he lived, a believer in spiritualism and séances, a devotee of phrenology, a dabbler in mesmerism, a later apostate from Darwinian theory when it came to the development of the human brain, an opponent of smallpox vaccination, and an advocate of nationalizing large private landholdings, who by these and other eccentricities gave his detractors some grounds for dismissing him as a crank.
Image: Wallace’s beetle collection, National Geographic
Wednesday, November 19, 2008
Using an approach called phylostratigraphy, Tomislav Domazet-Loso and Diethard Tautz of the Max-Planck Institute for Evolutionary Biology in Plön, Germany, compared genomes of species from different parts of the tree of life to figure out when a particular gene first appeared:
Something shared by multicellular animals but not found in protozoa, for example, probably arose about 700m years ago, when multicellularity appeared. Something found in amphibians, reptiles, birds and mammals, but not fish, would be about 370m years old—the point in history when limbs evolved. Using this information, the two researchers were able to trace the ages of genes implicated in genetic disease.In a paper published in Molecular Biology and Evolution, the researchers explain that “the majority of disease-causing genes were present in single-celled organisms and that most of the rest arose when multicellular creatures began to evolve. Genes specific to mammals, by contrast, barely ever carry diseases.”
The next step in the team’s research is to develop an explanation for why genetic diseases “seem to be caused so disproportionately by old genes.” Genes, that apparently, are crucial to our existence: “The older a gene is, the more likely it is to be part of the irreducible structure of being alive, and therefore the more likely it is that breaking that gene will be fatal.”
Image credit: DNA stub from Wikipedia
The article cites a study, just published in American Mineralogist, by Robert Hazen of the Carnegie Institution in Washington, DC, and a team of colleagues. The researchers worked to identify “how much of the diversity was created by the rocks alone and how much of it was created by the evolution of life.”
Of course, the researchers admit that minerals do not have genes and can’t mutate like living organisms. Still, they suggest that “when life appeared, the evolution of minerals and the diversity of life became entwined.” Hazen explains that contemplating minerals in evolutionary terms allows us to identify how far a planet has developed geologically. “Moreover,” he explains, “it can tell you whether life was present at some point—and even whether it is present now.”
Here’s a little nugget to track the thinking of Hazen and his crew:
With NASA’s Messenger probe now going into orbit around Mercury, Dr Hazen predicts that it will find only 300 or so minerals on the planet. If there are 500-1,000 detected, then it will suggest that there is a lot more to Mercury than anyone originally thought. And if minerals that depend upon life for their formation show up, then researchers will be flummoxed. The same is true for Mars and other planets—including the exoplanets that have been known about but which have just been seen for the first time orbiting stars outside the Solar System (see article).
Apologies to anyone trying to access the The Economist — it might be subscription only.
Tuesday, November 18, 2008
Like the finches, differences in these birds first led Darwin to muse about the "stability of species" in June 1836. They go on display in mid-November.
Randal Keynes, Darwin's great-great-grandson (pictured left), notes that the gifted naturalist noticed " … the small differences between the two birds on … two [different] islands” and realized it was a “most remarkable fact in the distribution of organic beings."
Ultimately, of course, Darwin concluded that all creatures had descended, with modification, from common ancestors.
The BBC article can be accessed here: http://news.bbc.co.uk/2/hi/science/nature/7713340.stm
Susan Blackmore studies memes: ideas that replicate themselves from brain to brain like a virus. She makes a bold new argument: Humanity has spawned a new kind of meme, the teme, which spreads itself via technology -- and invents ways to keep itself alive. Bruno Giussani say, "[Susan Blackmore], she took Richard Dawkins' intuition about memes (ideas that, like genes, take a life of their own) and turned it into a fully fledged theory." Metaphor or science...?
Here's a link to the rest of the video lectures. http://www.ted.com/index.php/themes/evolution_s_genius.html
Sunday, November 16, 2008
Princeton scientists say they’ve found chains of proteins that act like “adaptive machines, possessing the ability to control their own evolution.” These proteins, according to the scientists, are found in nearly all living organisms.
“The discovery answers an age-old question that has puzzled biologists since the time of Darwin,” says researcher Raj Chakrabarti in Science Daily. “How can organisms be so exquisitely complex, if evolution is completely random, operating like a
‘blind watchmaker’? Our new theory extends Darwin’s model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.”
I’m out of my element here with the science, but apparently the research zeroes in on a complex of proteins located in the mitochondria and offers “evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection.” Essentially, researchers say they’ve found that certain kinds of biological structures can “steer the process of evolution toward improved fitness.” (“Certain” = most.)
Princeton researchers: Herschel Rabitz (left) and Raj Chakrabarti are part of the research team. (Credit: Brian Wilson)
The researchers mention Darwin, but they really cite Alfred Wallace, saying that their laboratory efforts confirm an idea “first floated” by him in an 1858 essay. Unlike Darwin, they explain, Wallace believed that species themselves may develop the capacity to respond optimally to evolutionary stresses:
Wallace had suspected that certain systems undergoing natural selection can adjust their evolutionary course in a manner “exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident.” In Wallace’s time, the steam engine operating with a centrifugal governor was one of the only examples of what is now referred to as feedback control. Examples abound, however, in modern technology, including cruise control in autos and thermostats in homes and offices.
The researchers, having given credence to Wallace’s view, are now working to formulate a general theory that they’re calling “evolutionary control,” what they suspect will be the underlying cause for the self-correcting behavior in the protein chains they studied. They define this control theory as something that offers a direct explanation for an otherwise perplexing observation and indicates that “evolution is operating according to principles that every engineer knows.”
According to the Princeton news report,
Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems, the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car's cruise control or a home's thermostat, allowing them to fine-tune and control their subsequent evolution.Laura Moorhead
In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace’s original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks.”
The latest? Strands of beard hair "believed" to have been Charles Darwin's have been found. According to the BBC and other news agencies, Darwin's great-great grandson Randal Keynes found them in a box marked (of course!) "remaining hair." Keynes came across the hair -- found inside a small leather box, carefully wrapped in tissue paper -- as he was going through Darwin's Shropshire possessions. Apparently, the strands came with a message: "Found after his death in my father's papers." The hair is now part of a Natural History Museum exhibition.
Friday, November 14, 2008
Usually,when we want to understand the biology of humans and other complex animals, we use complex animal models--like primates, or canines, or fruitflies. A recent article I read pointed out that there are certain phenomena that are most easily understood with a much simpler model.
Recent work on how multicellularity evolved has focused in on a single-celled organism called a choanoflagellate. (I have shown two images here--one a highly magnified photograph, the other an artist's rendering.) Choanoflagellates have, according to the article, "a distinctive form: a cell with an apical flagellum, a kind of propeller that can move it through the water or drive a flow of water over it, and a ring or collar of microvilli, thin projections that act like a net to capture bacteria for food."
One interesting thing about choanoflagellates is that they have evolved cell-adhesion and signalling proteins to enable them to interact with other single-celled organisms. It is precisely these mechanisms, claims the article, that allowed for the development of multicellular life, because the same proteins that choanoflagellates use to interact with other cells are the proteins that more "advanced" forms of life use to negotiate between their own cells. Although the article does not make this point, this would seem to be a classic case of exaption--a mutation favorable to an earlier form for one reason (inter-organism interaction) being coopted by a later form for an entirely different purpose (integrity of a multicellular organism).
Two classes of proteins in particular are shared by choanoflagellates and multicellular animals: cadherins and integrins. Cadherins regulate cell adhesion though interaction with environmental calcium. And integrins help cells stick to the extracellular matrix. Without them, our cells would not be able to cohere into integral bodies.
In some senses, we may learn as much about complex animal life by studying these "simple" single-celled organisms as we do by looking at more obvious animal models.
The link to the article is http://www.seedmagazine.com/news/2008/10/the_masons_apprentice_1.php.
Dr. Irene Pepperberg would agree. Her groundbreaking, three-decade research on Alex, an African gray parrot, investigates animal thinking and mirrors earlier linguistic and cognitive work conducted on chimps and dolphins.
An Editorial Review on Amazon.com notes that when Dr. Pepperberg began her research, no one believed birds had the potential for "language, consciousness, or anything remotely comparable to human intelligence" (http://www.amazon.com/Alex-Me-Scientist-Discovered-Intelligence/dp/0061672475/ref=pd_bbs_sr_1?ie=UTF8&s=books&qid=1226735266&sr=8-1).
Parrots have small brains, about the size of a shelled walnut, but Alex learned to differentiate concepts like bigger or smaller, could count to 8, and could identify colors. He could even express emotions, being jealous, for example, when Dr. Pepperberg paid attention to others. Apparently, he also loved to dance, and play the occasional joke.
Dr. Pepperberg appeared on NPR this past Wednesday. Here is the link to her interview, which includes details on how she taught language to Alex:
Alex died in 2007, and Dr. Pepperberg penned Alex and Me: How a Scientist and a Parrot Discovered a Hidden World of Animal Intelligence-and Formed a Deep Bond in the Process
as a tribute and good-bye to a parrot with whom she shared a close bond. Alex's last words to her were "You be good. I love you."
Check out some of the data on PBS.org, where neurobiologist Erich Jarvis reports that "[f]ully 75 percent of the brains of parrots, hummingbirds, and thousands of other species of songbirds is actually made up of a sophisticated information processing system that works much the same way as the locus of human higher-mindedness, the cerebral cortex..."
Tuesday, November 11, 2008
Slate is a daily magazine on the Web. Founded in 1996, it is a general-interest publication offering analysis and commentary about politics, news, and culture. There are several interviews from people like Daniel Dennett, Robert Pollack, Freemany Dyson, etc. on topics like Being good without God, Consciousness, the Evolution of Religion and more...
The below link is to an interview of Ursula Goodenough, professor of biology at Washington University by Robert Wright.
Books by Ursula Goodenough:
The Sacred Depths Of Nature
Books by Robert Wright:
Nonzero | The Moral Animal
The book Dealing with Darwin: How Great Companies Innovate at every Phase of their Evolution is about “how today’s leading enterprises [can] compete successfully for revenues and profits in a globalized, commoditized, deregulated marketplace?”
And, hence the reference to Darwin, competition, and survival of the fittest … I did not read the book but the title reminded me of the recent discussion on the concept of social Darwinism.
Information about the book can be found here:
Monday, November 10, 2008
A recent National Geographic article reports that German scientists have discovered the earliest known cases of malaria – about 3,500 years old, to be exact. The researchers, who studied bone tissue samples in more than 90 Egyptian mummies, believe their findings could enlarge the current understanding of how modern diseases mutate in response to drugs. They also hope that "strategies to prevent the introduction of new infectious diseases or the re-emergence of ancient ones" might result.
Frank Rühli, head of the Swiss Mummy Project at the University of Zurich, asserts the importance of these findings:
"If you go back in the past and see th[e] genetic fingerprint [of a disease], say a hundred years ago or a thousand years ago or ten thousand years ago, it helps you to assess how it might actually react in the future."
There is no effective vaccine for malaria, and millions of people die from the disease every year. For this reason, the article claims that the findings take on additional importance: “Ancient samples of a microorganism's genetic code can show what its DNA looked like before any of its known mutations developed. An antibiotic designed to target a disease-causing bacteria in its earliest stages could then potentially cure its modern variations.”
Researchers are also studying ancient strains of tuberculosis, a potentially fatal bacterial infection. In 2007, they unearthed a 500,000 year old fragment of a Homo erectus skull with lesions that suggest TB, and recently, researchers located two of the oldest cases of TB in early humans to date. The article can be found here: http://news.nationalgeographic.com/news/2007/12/071207-tb-evolution.html.
With many diseases gaining resistance to antibiotics, this research has many potential benefits.
Sunday, November 9, 2008
(I first saw this article on 10/31 (how apropos!) but did not get a chance to write about it until today.)
Vampire bats are small winged mammals which live in the tropics of North and South America and gorge on blood from birds and livestock. New research has identified some of the genetic changes which allowed the vampire bat to evolve to subsist on a diet of pure blood.
These bats have made modification to the plasminogen activator – a gene that helps other animals (e.g. humans) produce proteins that bust up blood clots and clear vessels.
There are three species of vampire bats. Hairy-legged vampire bats feed on birds, while the white-winged vampire bats prey on both birds and mammals. One species (the common vampire bat) feeds exclusively on mammals; it prefers cattle but also is known to bite humans.
The plasminogen activator gene of the hairy-legged vampire resembles most the PA a closely related non-vampire bat. It seems that activating PA in saliva is enough to keep the bird blood flowing while it feeds.
The other two species that prey on mammals have an additional acquired mutation that prevent ther PA proteins from being silenced by a natural inhibitor. It appears that feeding on mammals was a key adaptation.
According to the scientists who made the discovery, the common vampire which feeds only on mammalian blood has also acquired several copies of the PA gene. “Two copies seem to be under tight evolutionary selection not to mutate, underscoring their biological importance.”
However, it’s possible that the copied genes are in the process of repurposing themselves. Or the genes could be atrophying from lack of use.
According to the article, there were probably other adaptations that evolved into the vampire bat. The first vampire bats emerged about 26 million years ago and are closely related to insect-eating bats.
“Vampire bats have very sharp incisors that erupt out of their mouths. Their tongues contain a specialized groove that allows a blood-meal to flow via capillary action, not sucking or slurping.”
To determine how these features evolved will quire a full sequencing of the vampire bat’s genome, which may happen within sometime soon.
Full article can be found here: http://www.newscientist.com/article/dn15083-how-vampires-evolved-to-live-on-blood-alone.html
Friday, November 7, 2008
Last night, Marta told us about the history of phylogenetic trees and touched on their modern incarnations. In yet another serendipity (we seem to be finding them everywhere), I just saw something this morning that expands on the modern part of the history, as well as supports Bob's comments last night about how misleading circular phylogenetic tree diagrams can be. I think it was Brad who first told us about the UC Berkeley evolution site, at http://evolution.berkeley.edu. There is a newly posted article that talks about how to read and interpret phylogenetic trees. It's written at an accessible level, and is completely understandable to those of us (guilty) who are not expert in biology.
One of the most interesting sections of the article is towards the end, where the author spells out the ten most common mistakes people make in interpreting phylogenetic trees.
I won't go through all ten, but here are a couple of the more interesting ones:
Misconception Number 1: Higher and Lower. Of particular interest to me since my first paper is on the idea of hierarchy of the natural world, the first misconception is that further up the tree is "higher" or "better" and further down the tree is "lower" or "less good." As the author puts it, "there is no scientifically defensible basis on which to rank living species in this way."
Misconception Number 2: Mainline vs. Sidetrack. Just by virtue of the use of the tree diagram, you visually see what looks like a main line of evolution, in the case of figure A from the root to a human, and all the other lines look like sidetracks. It's important not to take that seriously, as one could (as in figure B) simply reconfigure the exact same diagram to make the fish look like the main line and the human a sidetrack. Even T.H. Huxley made this conceptual error when he wrote that certain fish "appear to me to be off the main line of evolution—to represent, as it were, side tracks starting from certain points of that line."
Misconception Number 6: Long Branch Implies No Change. Visually, it can appear that the result of a long, unbranching line is more related to, or closer to, the root ancestor than something that is at the end of lots of branches. How many branches there are between the initial and terminal nodes is in no sense a measure of the how much evolutionary change there has been. Referring back to the figures A and B above, figure A could be misinterpreted to suggest that humans are very similar to the ancestral form, and figure B could be misinterpreted to mean that we are quite different. Of course, the diagrams are logically identical, and to draw either conclusion from the diagrams themselves would be a fallacy. (This is not to say, of course, that there are not some forms more like the ancestral forms than others, just that reading the long line of the diagram to be a measure of that similarity is a logical error).
Misconception Number 9: More Intervening Nodes Equals More Distantly Related. The author doesn't actually use this illustration to make this point, but it makes it quite clearly. If you interpret figure a naively, you might guess that frogs are more related to fish than to humans, being "closer" in a left to right sense. Figure B shows you another rendering of the identical phylogenetic tree that makes frogs look closer to humans. Of course, the right way to think about it is to look for the common ancestor. Frogs are more closely related to humans than to fish because the most recent common ancestor of the frog and the human is more recent than the most recent common ancestor between frogs and fish, a relationship that is apparent from either diagram.
Overall, none of this is rocket science, and we should be able to figure these things out on our own, but as the T.H. Huxley example shows, even the experts can think carelessly, and this article is a useful corrective. The url is http://www.springerlink.com/content/v41w288751r82653/fulltext.html
P.S. I am apparently a moron, unable to perform the simple tax of putting a live link that actually works into my posts. The links are correct, but the way I have inserted them is not working. Robbie has given me careful instructions, but I still am incapable of getting it right. I will get him to show me live, and meantime, you can copy the links into your browser.