Sunday, November 30, 2008

Warfare Makes the Man, Woman, or Chimp


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.

Laura Moorhead

Book Review: Darwin’s Marginalia


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.

Laura Moorhead

Much ado about banknotes


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."

Brad Bauer

An ounce of prevention....or a dose of evolutionary biology


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.

Brad Bauer

Wednesday, November 26, 2008

Interactive HMS Beagle Voyage




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:

January 1832
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."


September 1832
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."


January-February 1835
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.

Roxanne Enman

Darwin Centre to Open in September 2009

The British Natural History Museum is expanding its facilities to include the ultra-modern Darwin Centre, just in time to mark Darwin’s bicentennial. Work is now underway to transition various museum collections and displays into this architectural masterpiece.

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

Roxanne Enman

Friday, November 21, 2008

Identifying non-native plants in the Galapagos



In this morning's New York Times, there is a brief article about non-native plants in the Galapagos.

http://www.nytimes.com/2008/11/25/science/25obplants.html

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.

Brad Bauer

DNA as an Historical Tool--Copernicus's Remains Identified


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.

Greg Priest

Thursday, November 20, 2008

Wallace: ‘The Man Who Wasn’t Darwin’

The latest National Geographic issue takes a look at Alfred Russel Wallace, a “the man who wasn’t Darwin.”

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

Laura Moorhead

Wednesday, November 19, 2008

Genes: The Older (Not) the Better

As we know, genes are linked to disease. In The Economist this week, there’s an article about how old genes cause more disease than young ones. “Old” in this case means historically old.

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

Laura Moorhead

Rock of Ages: The Evolution of Minerals

Living organisms, according to The Economist, don’t have a monopoly on evolution. Minerals, too, evolve. The gist of the article is that rocks are showing characteristics of evolution. When the Earth first came to be, few minerals existed; however, today there are more than 4,000 different minerals on the planet.

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.

Laura Moorhead

Tuesday, November 18, 2008

Darwin's Mockingbirds at the Natural History Museum

We’ve all heard about Darwin’s finches. Now, London's Natural History Museum is giving us the chance to see two never-before-exhibited mockingbirds collected by Charles Darwin in the Galapagos.

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

Roxanne Enman

Themes - Evolution's Genius: From memes to temes?

"TED adores great design. A growing number of speakers focus their talks on the most elegant designs that exist: those in the natural world." Below is video lecture by Susan Blackmore as a part of a lecture series that TED has dedicated to evolution. In the video Susan discusses her idea of temes an off shoot of the theory of memes. 

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...?

video

Here's a link to the rest of the video lectures. http://www.ted.com/index.php/themes/evolution_s_genius.html

Pamela Alexander-Beutler

Sunday, November 16, 2008

A New (er, Old) Meme on Evolution: It's Not Random, It’s Self-Correcting, and Wallace Was Right

Complexity vs. the “Blind Watchmaker": (Credit: iStockphoto/Sven Klaschik)

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.

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.”
Laura Moorhead

Darwin Mania!

Thank goodness we're not too far from the February anniversary date, as natural history museums and the reporters they invite to press conferences are getting desperate for news.

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.

Laura Moorhead

Friday, November 14, 2008

Our Closest Single-Celled Cousin


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.

Greg Priest

Bird-Brain: Not So Flighty

Charles Darwin believed that animals possess intelligence. In The Descent of Man, he dedicated a chapter to illustrating "that there is no fundamental difference between man and the higher mammals in their mental faculties" (p. 66), believing that the difference between human intelligence and animal intelligence is simply a matter of degree.

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:

http://www.npr.org/templates/story/story.php?storyId=96897162


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..."

http://www.pbs.org/wgbh/nova/sciencenow/3214/03-brain.html

Roxanne Enman

Tuesday, November 11, 2008

meaningoflife.tv/


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.
http://meaningoflife.tv/video.php?speaker=goodenough&topic=direvol

Books by Ursula Goodenough:
The Sacred Depths Of Nature

Books by Robert Wright:
Nonzero | The Moral Animal

Pamela Alexander-Beutler

Social Darwinism in the business world

I found this book while searching for some reference materials for work. 

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: 

http://www.dealingwithdarwin.com/theBook/introduction.php

Marta Cervantes

Monday, November 10, 2008

Ancient DNA, Modern Diseases


http://news.nationalgeographic.com/news/2008/10/081029-mummies-disease-evolution.html

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.

Roxanne Enman

Sunday, November 9, 2008

Evolution of Vampire Bats: A little history


(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

Marta Cervantes

Friday, November 7, 2008

Misinterpreting Phylogenetic Trees


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

Greg Priest

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.

Thursday, November 6, 2008

Saving Wild Salmon, in Hopes of Saving the Orca



So what does the president elect have to do with Science (let alone Darwin)? That's exactly what I said when I opened the science section of the NY Times this afternoon. Well there was no answer to be found. Just a questions. "What’s a president to do on issues like climate and population, particularly in an era of huge deficits and pressing real-time problems?" Nice hook. It got me, but gave me very little satisfaction...
But I did see an interesting article about Alexandra Morton a "supky hero" and the Jane Goodall of killer whales. "Alexandra Morton is a self-trained biologist, has been battling fish farms in British Columbia that she says are endangering wild salmon runs that in turn are adversely affectly the orca's ecosystem.

In 1984, 26 years old and armed only with a bachelor’s degree and enthusiasm for her task, she [and her family] moved to the Broughton Archipelago, in the Queen Charlotte Strait of British Columbia, where the whales, or orcas, were abundant." Her husband died 2 years later, but she stayed on and has earned the respect of scientist, fisherman and fishery experts alike.

Ray Hilborn, a researcher at the University of Washington. “She doesn’t come from a science background but she has had a lot of influence in highlighting the issue,” he said. Daniel Pauly, director of the Fisheries Center at the University of British Columbia, calls her “a spunky hero.”

Like the Grants, Morton has remain in one place long enough to identify issues that are missed even by specialists. She's in the NY Times because “the problem with this whole issue is if nobody sees it nothing happens,” she said one day recently as she motored past one of the farming operations. And because most of the fish farmed here end up in trucks heading down I-5 to California, she said, “it can’t just be the Canadian public. It has to be the American public.”
-Pamela Alexander-Beutler

Wednesday, November 5, 2008

The HMS Beagle Trust



Fundraising is underway to build a replica of the HMS Beagle, which will set sail on a two-year voyage commencing in 2009. The Beagle’s mission is to conduct scientific research (in particular, Metagenomics and DNA Barcoding) in much the way Darwin did while circling the globe 177 years ago.

The Trustees of this UK registered charity describe the undertaking as follows:

The HMS Beagle Project
Bringing the adventure of science to life

We aim to rebuild the ship that carried Charles Darwin around the world. The voyage of the new Beagle will inspire global audiences through unique public engagement and learning programmes, and original scientific research in evolutionary biology, biodiversity and climate change.

She will cross the North and South Atlantic, the Pacific and Indian Oceans, round both Cape Horn and the Cape of Good Hope. She will sail in her ancestor's wake, with international crews of young scientists and sailors aboard applying the tools of modern science to the work started by Darwin and Captain Fitzroy 170 years before.

The replica Beagle is not intended to be a museum ship; she will be equipped with laboratories and equipment to allow contemporary, original research. This is not only in keeping with Charles Darwin’s legacy but also creates an opportunity to engage students and teachers in the excitement of real scientific discovery.


You can peruse the details, or make a donation, at http://www.thebeagleproject.com/index.html

The HMS Beagle Trust also sponsors a blog, which is worth a look: http://thebeagleproject.blogspot.com/

The latest entry points to the Galapagos Conservation Trust (GCT) website, which is raising funds to save the Floreana mockingbird from extinction. An earlier post highlights that the Trust and NASA will work together “…on a joint science, education and outreach programme centered on a direct link between the International Space Station and the new Beagle as she retraces the 1831-1836 voyage that carried a certain young naturalist around the world.”



Finally, I came across an article that claims the remains of the original HMS Beagle, which became a coastguard vessel before being sold for scrap in 1870, were located in 2004. Here’s a link to the article: http://news.bbc.co.uk/2/hi/science/nature/3490564.stm



Roxanne Enman

Another brief note from the New York Times, this time about genetic variations--or the lack thereof--in commercially produced chickens. The link to this article is http://www.nytimes.com/2008/11/04/science/04obchicken.html?scp=1&sq=&st=nyt .

A new study shows that commercially produced chickens are less genetically diverse than they were 50 years ago....a troubling development since that means diseases can spread more easily through a larger number of chickens that lack varying means of resistance to these diseases. Rather than natural selection developing varieties that evolve into separate species on the one hand, or the variation under domestication described by Darwin in chapter 1 of "Origin of Species," which as he puts it, leads to a greater variety than what would be found in nature (using the example of his beloved pigeons), this article shows instead a form of domestication that unwittingly leads to uniformity. According to this study, published in the Proceedings of the National Academy of Science, around 50 percent of the ancestral breeds of these chickens have been lost.

However, this study was able to "reverse engineer," and through genetic studies reconstruct the genetic characteristics of the ancestral breeds and identify what is missing from the contemporary chickens. So, on one level an interesting contrast to Darwin's apparent view of evolution leading to a continuously growing level of diversity.

Brad Bauer

Cloning of Extinct Species?


Scientists working at the RIKEN Research Institute in Japan recently cloned mice, frozen for more than a decade and whose cells had burst, using the Somatic Cell Nuclear Transfer technique, and prompting speculation that nuclear transfer might be used to “resurrect” extinct species.

Somatic Cell Nuclear Transfer involves transplanting the nucleus from a somatic cell (any cell of the body other than a reproductive cell) into an egg cell.

“In this process, the nucleus of a somatic cell is removed and inserted into an unfertilized egg that has had its nucleus removed. The egg with its donated nucleus... divides until it becomes an embryo[, which] is then placed inside a surrogate mother [to] develop…” (http://biology.about.com/od/biotechnologycloning/a/aa062306a.htm).

Typically cells burst when frozen, damaging the DNA inside them. The article explains that “[c]hemicals called cryoprotectants can prevent this, but they must be used before the cells are frozen.” Because the cloned mice had damaged cells, and a cryoprotectant had not been used, the Japanese research team speculates that nuclear transfer might be used on other organisms frozen for long periods without cryopreservation (for example, to resurrect extinct species like mammoths, who have often been found preserved in ice). They further believe that the technique might be used to preserve endangered species.

The team reported in the Proceedings of the National Academy of Sciences. Here’s the link to the article: http://www.newsdaily.com/stories/tre4a26nv-us-clones-frozen/

Roxanne Enman

Tuesday, November 4, 2008

Extinction and evolution


Among checking on election news this afternoon during my lunch break, I found this article on the New York Times, which I thought could be of interest: http://www.nytimes.com/2008/11/04/science/04conv.html?pagewanted=1.


Namely, it is about the work that Prof. Stuart Pimm of Duke University is doing to study--and combat--the extinction of species (no, that is not Prof. Pimm in the picture, but one of the animals that he studies, the golden lion tamarin of Brazil). In studying Darwin one can read about the "tree of life," with the emphasis being on those branches of the tree that continue to evolve, but what happens to those dead-end branches that do not? Pimm's work gives current and vivid examples of such cases.

Unsurprisingly, the culprits that prevent such further evolution are often human beings, through the expansion of the human population and corresponding alteration of natural habitat, whether in the destruction of rain forests in Brazil, or the development (real-estate and agricultural)and importation of foreign species to the Hawaiian Islands, an example that Pimm discusses at the beginning of this article. When he first visited Hawaii over thirty years ago, he thought that it would harbor a rich and diverse native flora and fauna, like the Galapagos, and was disappointed at the paucity of native species (10 types of animals, with a further 10 on the brink of extinction).

Trying to think about this in Darwinian terms, I am reminded of Paul Ewald's book, "The Evolution of Infectious Diseases," which I began reading on the train this morning. One of the problems that Ewald outlines is that infectious diseases adapt more quickly than the biological beings that act as hosts for them (such as humans, animals, etc.) Using this analogy, it looks like human beings play the role of "infectious diseases" when compared to the wildlife that can't adapt quickly enough to ward off or at least adapt to our incursions.

One area of course where this analogy breaks down is that there are people like Pimm who are trying to find ways to save species, and there are no infectious diseases I know of that are trying to spare us the worst that they have to offer. If you take a look at the interview with Pimm, listen to his audio segements as well, where he discusses efforts to save the Florida panther (through importing female panthers from Texas)as well as saving the habitat of the golden lion tamarin in Brazil, purchasing land between shrinking islands of forest habitat so that "it will be possible for lonely hearts to meet members of the opposite sex and go forth and multiply."

Brad Bauer

Monday, November 3, 2008

Stephen Hawking Heads to the Vatican, on Behalf of Darwin

In October, I posted about the Anglican and Vatican unofficial apologies to Charles Darwin. Again, I found the whole news thread a non-issue. Still, I can’t resist giving you all an update: Pope Benedict XVI has invited Stephen Hawking to the Vatican, which is holding a week-long conference organized by the very offical sounding Pontifical Academy of Sciences.

In a London Times article, Hawking, explained that he took part in another scientific conference at the Vatican 30 years ago. At that time, he suggested that since the universe had no identifiable beginning, there had been no creation. Now, on his return to the Vatican, he’s hoping that the current is Pope was unaware of his remark for fear that he'll “share the fate of Galileo.”

The article reiterated the Catholic Church’s view on evolution, which included yet again a reminder that there’s no reason to formally apologize to Darwin. It also pulls out the cliché that oh-so-many Americans are fundamentalist Christians. Personally, I preferred the heydays of Dallas and Dukes of Hazzard, when most Brits simply assumed all Americans talked like a Texan or Daisy Duke.

Here’s the Pope’s latest thinking on the e-word, according to the Times:

The Catholic Church accepts evolution, but sees it as part of the divine plan. Pope Benedict has been described as a ‘theistic evolutionist’ who believes that God created life through evolution, and thus that there is no inherent clash between religion and science.

Laura Moorhead

Darwin's Gardens


There is a traveling exhibit about Darwin's botanical studies and his gardens at Down House that is ongoing near LA through January 5, 2009. The exhibition started at the New York Botanical Gardens, where it was described by the New York Times as "stunning."

The website for the New York version of the exhibition describes it as follows:

Charles Darwin is best known for his theory of evolution and other natural history achievements, but little is known about his enduring and insightful work with plants and the important role they played in formulating his ideas. Yet from cradle to grave, botany played a pivotal role in Darwin's life. From counting peonies and playing under the apple trees in his father's garden as a boy to collecting "all the plants in flower" on his famous voyage to the Galápagos as a young man and testing the sex and sensitivity of plants at his home, Down House, in his later years, plants were a lifelong preoccupation for Darwin.

Darwin's Garden: An Evolutionary Adventure explores the untold story of Darwin's botanical influences, his research, and his contribution to our understanding of plants, and ultimately, of life in general. The exhibition ... includes an "evolutionary tour" of living plants that demonstrate key points on the Tree of Life, which links all living beings through a common ancestry. [Also included is a] re-creation of Darwin’s garden at Down House, where he lived in the English countryside for the last 40 years of his life.

There is a catalog of the exhibition available for purchase at http://www.nybgshop.org/Darwins-Garden-An-Evolutionary-Adventure-p-18751.html
There is also a fascinating essay on the occasion of the exhibition in the latest New York Review of Books (the 45th Anniversary Issue of that august journal) here: http://www.nybooks.com/articles/22075
The essay is by Oliver Sacks. I say "on the occasion" because it is less a review of the exhibition itself and more an inquiry into the centrality of botany to Darwin's achievements. It is well worth a read.
If you are interested in going to the LA exhibit, here is a link to the website for the exhibit: http://www.huntington.org/Information/darwin.htm

Greg Priest

Sunday, November 2, 2008

Evolution in the Media

A recent report indicates that technology is causing the human brain to evolve while another report attempts to provide an explanation for why gay genes persist, despite their reproductive disadvantage.

In the first case, Dr. Gary Small, a neuroscientist at UCLA’s Memory & Aging Research Center states that the brain is very sensitive to changes in the environment such as those brought by technology.

According to Small, a study of 24 adults showed that experienced Internet users showed double the activity in areas of the brain that control decision-making and complex reasoning as Internet beginners.

The report quotes Small:

"The brain is very specialized in its circuitry and if you repeat mental tasks over and over it will strengthen certain neural circuits and ignore others. We are changing the environment. The average young person now spends nine hours a day exposing their brain to technology. Evolution is an advancement from moment to moment and what we are seeing is technology affecting our evolution."

Small goes on with:

"We're seeing an evolutionary change. The people in the next generation who are really going to have the edge are the ones who master the technological skills and also face-to-face skills."

This statement strikes me as particularly misleading – Small seems to be using the term evolution in a very loose sense. I believe he simply means that humans are using a different part of the brain when engaged with technology and with repeated use of technology, they are strengthening particular parts of the brain.

Does this mean that the human brain has evolved, from a biological sense of the word? I don’t think so. I don’t believe that Small can make the case for evolutionary change; however, the media seems to implying so with headlines like this one:

The Internet is not just changing the way people live but altering the way our brains work with a neuroscientist arguing this is an evolutionary change which will put the tech-savvy at the top of the new social order.

The article can be found here: http://news.zdnet.com/2424-9595_22-243997.html

The second article is from THE ECONOMIST and attempts to explain why homosexual traits survive. The question posed is:

“THE evidence suggests that homosexual behaviour is partly genetic. Studies of identical twins, for example, show that if one of a pair (regardless of sex) is homosexual, the other has a 50% chance of being so, too. That observation, though, raises a worrying evolutionary question: how could a trait so at odds with reproductive success survive the ruthless imperatives of natural selection?”

One idea proposed in the past is that the genes for gayness bring reproductive advantage to those who have them but are not actually gay themselves: “Originally, the thought was that whichever genes make men gay might make women more fecund, and possibly vice versa.”

In a paper to be published soon in EVOLUTION AND HUMAN BEHAVIOR, Brendan Zietsch of the Queensland Institute of Medical Research in Brisbane, Australia, and his colleagues suggest there IS an advantage to family members, but to relatives of the same sex – for example, to the brother of a gay man or to the sister of a lesbian.

Dr Zietsch and his colleagues tested their idea by doing a study of twins:

“They asked 4,904 individual twins, not all of them identical, to fill out anonymous questionnaires about their sexual orientation, their gender self-identification and the number of opposite-sex partners they had had during the course of their lives. (They used this figure as a proxy for reproductive fitness, since modern birth-control techniques mask actual reproductive fitness.)”

Their study revealed that a heterosexual male with a gay twin tended to have more sexual partners than a heterosexual with a heterosexual twin.

The full article can be found here:
http://www.economist.com/science/displaystory.cfm?story_id=12465295


These articles illustrate how evolution is portrayed sometimes incorrectly (something that "happens moment by moment" ) as well as how it is used to explain the human experience.

Does this mean that evolution is part of our consciouness? Our shared understanding? Has it become a meme?

Marta Cervantes