Friday, October 31, 2008

Saving A Species


In attempt to prevent the extinction of a small porpoise, the Mexican government is paying fisherman NOT to fish using nets, and in some cases to not fish at all.

The porpoise, known as a vaquita, is often trapped and killed in the process of using nets to catch shrimp, mackerel, and shark of the Gulf of California.

It is estimated that there are no more than 150 vaquitas. This number is near the tipping point – a reduction would mean that there would be too few sexually mature porpoises for the species to recover.

Fishermen are being paid off to switch to other activities; in addition, new nets are being developed which do not trap the porpoises.

The vaquita has been on the critical list for some time but with the extinction of a close cousin last year, the Chinese River Dolphin, scientists, activists, and government officials felt it was necessary to intervene now.

For the full article, go to:
Marta Cervantes

Wednesday, October 29, 2008

The Evolution of Art, Through Darwin

The Yale Center for British Art is previewing its February “‘Endless Forms’: Charles Darwin, Natural Science and the Visual Arts” exhibit, which contemplates art before and after Darwin’s On the Origin of Species.

CATTLEYA ORCHID + THREE BRAZILIAN HUMMINGBIRDS:
Martin Johnson Heade, 1871


Surprisingly, this exhibit is “the first-ever examination” of the significance of visual imagery (as in paintings, drawings, and sculptures) in the public evolution of Darwin’s theories and their impact on artists, from the Victorian era and to our own.

FUTURE EVOLUTION: Alexis Rockman

“Endless Forms” is structured around the premise that Darwin’s ideas became embedded in “the consciousness of the great artists of the era.” His notions would go on to inspire visual representations of many of Darwin’s big ideas: struggle for survival, natural attraction and sexual selection, and the origins of man. They would move the Western world from images of Noah’s flood and Moses’ tablets to Odilo Redon’s half-man, half-monkey one-eyed creature.

HUMAN HYBRIDS: Odilo Redon

The exhibit includes paintings by renowned artists such as Degas, Monet, and Cézanne. Additionally, there’s a sampling from lesser-known artists, notably Edwin Henry Landseer and Joseph Mallord William Turner. “Endless Forms” also expands the traditional definition of art to include beetles, pigeon skulls, fossils, and taxidermy.

DOG RULE: Edwin Henry Landseer

Two of my favorite artists of the moment aren’t included in the exhibit, but I do think they also capture the gist of the premise and they openly channel Darwin. Alexis Rockman actually drew the cover for Peter Ward’s book “Future Evolution.” (Here’s an NPR interview with both Ward and Rockman.) There’s also the much-less-known Casey Weldon, whose work is less about science and more about the evolution of culture.


EARTH STORM: J. M. W. Turner

According to a Bloomberg article, “Endless Forms” isn’t designed to instill a wonder of an artist’s beautiful or visually inspiring work. Rather, the exhibit strives to tap into the current debate surrounding Darwin’s theories. (As with usual reports from Britain, all of the United States is judged by the press-attracting squawks of Christian fundamentalists.)

“Without question, Darwinian thinking has been discredited,” Amy Meyers, the center's director, told reporter Bloomberg Farah Nayeri. “It’s very important for us to critique this new flaring up of fear over Darwin’s ideas, and to really question the sets of ideas that are at play within the fundamentalist community.”

IN THE GREENHOUSE & PRECIOUS: Alexis Rockman & Casey Weldon

The Fitzwilliam Museum, University of Cambridge, organized the exhibit in association with the Yale Center for British Art. The two groups pulled together previously unseen works from both public and private collections in the United States and Europe.

Laura Moorhead

Tuesday, October 28, 2008


The threespine stickleback lives in Lake Washington and over the last 50 years the fish has changed from a soft-skinned fish to a partial or full body armor fish. The fish has now revered back to its saltwater armored origins. Apparently this change is due to a mutation that occurred after the lake was cleared of pollution. “A program started in the late 1960s to clear the lake of toxic sludge made the sticklebacks de-evolve.”

More precisely, according to PhysOrg “when the lake was polluted, the transparency of its water was low, affording a range of vision only about 30 inches deep. The tainted, mucky water provided the sticklebacks with an opaque blanket of security against predators such as cutthroat trout, and so the fish needed little bony armor to keep them from being eaten by the trout.
In 1968, after the cleanup was complete, the lake's transparency reached a depth of 10 feet. Today, the water's clarity approaches 25 feet. Lacking the cover of darkness they once enjoyed, over the past 40 years about half of Lake Washington sticklebacks have evolved to become fully armored, with bony plates protecting their bodies from head to tail.”

Here is yet another example of what we might not have discovered has someone not had the patience to watch a particular fish in a particular lake for 50 years! Here's the link to the original article for more details. http://www.physorg.com/news130073255.html

Pamela Alexander-Beutler

Darwin on Film


Break out the popcorn! To celebrate the bicentennial of Charles Darwin’s birth, a movie showcasing his private life will hit the big screen in 2009. “Annie’s Box,” written by Randal Keynes (Darwin’s great-great grandson), serves as inspiration for a close-up look at the naturalist’s private life, as a husband and a father, in the years leading up to the publication of “On The Origin of Species”. The movie will highlight Darwin’s relationship with his eldest daughter, Annie, who died at the age of 10 in 1851. Keynes believes that Darwin’s grief “influenced some of his most important ideas” and that Annie’s death contributed to his dwindling belief in Christianity (http://www.aboutdarwin.com/news/darwin_news.html).

Update: I found a few more details about the film, which has the working title, Creation. Paul Bettany will play Darwin, depicting him as someone who comes to question God’s role in life despite the views of his deeply religious wife, played by Jennifer Connelly (http://www.cinematical.com/2008/09/05/jennifer-connelly-and-paul-bettany-debate-creation/).

Roxanne Enman

Robert Sapolsky to Speak at Stanford


Robert Sapolsky is a Stanford biology professor and primatologist, and he will be interviewed on November 12 at 7:30 pm in a public event at Cubberly Auditorium. I'm the research assistant for the series of events that Sapolsky's interview is part of, so I've had to work on figuring out what kinds of questions to ask him. I can represent without hesitation that he is an absolutely fascinating guy.

He has studied baboons in Kenya for over 20 years, and has insights from that not only into baboon behavior, but also into the implications for human behavior. He also studies, both in the field and in the lab, how stress affects health and brain activity. He is an atheist, and quite aggressive about it (could be a fifth horseman of the apocolyspe, if they were hiring). And he has written a memoir about his field work that is really interesting.

His style has led him to be called, by one observer, "the secret love child of Hunter Thompson and Jane Goodall." It should be an enjoyable evening.

Greg Priest

Monday, October 27, 2008

Synaptic Proteins and The Evolution of Brain Complexity



According to a recent study published in Nature Neuroscience (“Evolutionary expansion and anatomical specialization of synapse proteome complexity,” Nature Neuroscience 11, 799 - 806 (2008), Published online: 8 June 2008), “understanding the origins and evolution of synapses may provide insight into species diversity and the organization of the brain.”

The study notes that scientists currently know little about “synaptic molecular evolution,” despite the fact that synapses play a key role in information processing. The authors hypothesized that “the evolution of synapse complexity… has contributed to invertebrate-vertebrate differences and to brain specialization.”

With this in mind, they compared human brains with the brains of 19 other species, ranging from single-celled organisms that do not have nervous systems (e.g., brewer’s yeast), to invertebrates (e.g., insects and worms), non-mammalian vertebrates (e.g., fish), and mammalian vertebrates (e.g., rats and chimpanzees).

In particular, researchers examined proteins located in the postsynaptic region of the synapse in each of the different species. They then compared which proteins the various species shared and what functions they served.



Results indicate that, as organisms become more complex, they possess a greater variety of postsynaptic proteins, as well as a higher number. In particular, “mammals have a higher percentage of proteins” in their synapses (about 600) than invertebrates (which show only half as many) or single-celled organisms (which contain only a quarter of the amount). These proteins evolved over time to become more complex, which ultimately contributed to differences in cognitive abilities between species and to the adaptation of different regions of the brain for different functions.

Professor Seth Grant, Head of the Genes to Cognition Programme at the Wellcome Trust Sanger Institute, explains that "[o]ur simple view that 'more nerves' is sufficient to explain 'more brain power' is simply not supported by our study. Although many studies have looked at the number of neurons, none has looked at the molecular composition of neuron connections. We found dramatic differences in the numbers of proteins in the neuron connections between different species".

ScientificBlogging.com reports that, “[s]ince the evolution of molecularly complex, 'big' synapses occurred before the emergence of large brains, it may be that these molecular evolutionary events were necessary to allow evolution of big brains found in humans, primates and other vertebrates.”

Professor Grant believes that “[t]his work leads to a new and simple model for understanding the origins and diversity of brains and behavior in all species. We are one step closer to understanding the logic behind the complexity of human brains.”

He equates "[t]he molecular evolution of the synapse" to "the evolution of computer chips - the increasing complexity has given them more power and those animals with the most powerful chips can do the most".

Here are links to the research study and the article that sparked my curiosity in the subject:
http://www.nature.com/neuro/journal/v11/n7/full/nn.2135.html
http://www.scientificblogging.com/news_releases/the_complex_synapses_that_drove_brain_evolution

Roxanne Enman

Sunday, October 26, 2008

Salamandra robotica



The Biologically Inspired Robotics Group (BIRG) at l’École Polytechnique Fédérale de Lausanne in Switzerland has designed a Tiktaalik-like robot, Salamandra robotica, that can swim, crawl, and walk, perhaps the first of its kind.

The group studies the “neural mechanisms underlying movement control and learning in animals, and … take[s] inspiration from animals [both] to design new control methods for robotics [and] novel robots capable of agile locomotion in complex environments.”

BIRG explains that this project addresses vertebrate locomotion, by looking at:

1) modifications made to spinal circuits during the evolutionary transition from aquatic to terrestrial locomotion;
(2) mechanisms necessary for coordination of limb and axial movements, and
(3) mechanisms that underlie gait transitions induced by simple electrical stimulation of the brain stem.

The group hopes to explain how creatures transition between swimming and walking. Results suggest this occurs “by simply varying the level of stimulation of the brain stem.”

http://birg.epfl.ch/page65446.html
video

Roxanne Enman

Thursday, October 23, 2008

Worm Grunters?



Who knew? Worm grunters, aka snorers and fiddlers, wander around poking and prodding the ground in search of earthworms for fish bait. They actually make a living doing this, and – apparently – they have Charles Darwin to thank, along with Wired News for highlighting their utterly intriguing work.

“It is often said that if the ground is beaten or otherwise made to tremble worms will believe that they are pursued by a mole and leave their burrows,” Charles Darwin wrote in The Formation of Vegetable Mould through the Action of Worms, a book that “reflects his enduring and instructive fascination” with a creature that people either ignore or step on.

Ken Catania, a biologist from Vanderbilt University, is testing Darwin’s theory that, essentially, these worm grunters sound an awful lot like burrowing, worm-hungry moles.



ABOVE: Sopchoppy Worm Grunting Festival

Of course, Darwin also reminds in a charming quotation about the large debt we owe to worms: "It may be doubted whether there are any other animals which have played so important a part in the history of the world as have these lowly, organized creatures." Of course, I do wonder if a white lab rat would second that or not....

New Species: Transition From Dinosaurs to Birds?


Archaeologists have unearthed a new fossil in northern China that might be a link between dinosaurs and birds.

Epidexipteryx hui, a small, feathered bird with a short tail and four (featherless) limbs, pre-dates Archaeopteryx, which lived 155 to 150 million years ago. Researchers believe Epidexipteryx may have existed from 176 to 146 million years ago (the Middle to Late Jurassic periods), and that it had large teeth similar to those of carnivores. They are not sure what the bird ate, but with 90% of the fossil’s remains recovered, researchers are in a good position to study the new creature.

Here are links to the article, as well as to the abstract in Nature (Nature 455, 1105-1108 (23 October 2008):

http://www.newsdaily.com/stories/tre49l66z-us-china-dinosaur/


http://www.nature.com/nature/journal/v455/n7216/full/nature07447.html


Roxanne Enman

Monday, October 20, 2008

The Edge: The Big Ideas of Science


"Edge Foundation, Inc., was established in 1988 as an outgrowth of a group known as The Reality Club. Its informal membership includes of some of the most interesting minds in the world.

The mandate of Edge Foundation is to promote inquiry into and discussion of intellectual, philosophical, artistic, and literary issues, as well as to work for the intellectual and social achievement of society."

Each year, the Edge Foundation poses a question on its website (http://www.edge.org/) to members of the "third culture". According to Brockman "the third culture consists of those scientists and other thinkers in the empirical world who, through their work and expository writing, are taking the place of the traditional intellectual in rendering visible the deeper meanings of our lives, redefining who and what we are." The 2006 question (published in July 2007 ) is "What is your dangerous idea? The references to both Dennett and therefore Darwin is obvious. If this seminar is the who's of who presenters, this books could easily be the companion piece with contributions from Daniel Dennett himself as well as Jared Diamond and Richard Dawkins who writes the afterword.

The book is engaging and well worth the read. I'm interested to see if there will be another installment and what the next question will be.

--Pamela Alexander-Beutler

Update! Next installment due in bookstores any time now... Go to http://www.edge.org/questioncenter.html to see the questions that have followed since 2006...

Friday, October 17, 2008

New Data on the Origin of Life


It has long been hypothesized, including by Darwin, that a warm "soup" of basic chemicals could have, by the action of heat and either lightning or volcanic activity, given rise to the first organic molecules.

In 1953, the Miller-Urey experiment tried to replicate in a laboratory the conditions that might have allowed the creation of life. A system of water, methane, ammonia and hydrogen was heated and exposed to sparks. The result was the formation of five amino acids.

Over the years, questions were apparently raised about the conditions in the experiment and about whether 5 amino acids were sufficient to form the basis for life. In the latest issue of Science, a group of researchers found the original vials with residues from the Miller-Urey experiment and went back and reanalyzed them. They focused on a variant where, in addition to the soup, the heat and the spark, there was steam injected into the system, which they thought might better simulate what would happen in a robustly volcanic environment. They analyzed the samples from that variant and found 22 amino acids and 5 amines (whatever those are) had been generated. Although this would not have occurred everywhere, the researchers hypothesize that there could have been a number of microclimates, if you will, like this, and that they have reaffirmed and extended the Miller-Urey findings.

Here is a link to the article in Science: (http://www.sciencemag.org/cgi/content/full/sci;322/5900/404?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=lazcano&andorexacttitle=or&andorexacttitleabs=or&andorexactfulltext=or&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=9/1/2008&tdate=10/31/2008&resourcetype=HWCIT,HWELTR).

I heard one of the researchers on Talk of the Nation Science Friday today. Here's a link to the interview: http://www.sciencefriday.com/program/archives/200810176.

Greg Priest

A Second Life for Darwin






Yes, it had to happen: Charles Darwins’ 1832 journey aboard the Beagle and his Galapagos adventures now exists in the multiplayer videogame Second Life. The University of Cincinnati -- specifically, programmer Chris Collins, aka “Fleep Tuque” in Second Life, and Dr. Ronald W. Millard, a professor of pharmacology and cell biophysics -- unveiled the beta version of the game October 16. Millard also chairs the school’s 2009 Darwin Sesquicentennial Celebration Program and Planning Committee, and he's having the school’s students test -- er, play -- the game until Darwin’s February anniversary. At that point, the game will be opened up to any interested Second Life player.


Second Life: Images from Darwin's new virtual world.

Collins and Millard created the game as an educational tool for students interested in building out Darwin’s journey and seeing indigenous species in their natural, albeit virtual, habitats. They’re also reaching out to scholars and students willing to share their photographs, videos, and materials collected during trips that are based on Darwin’s Beagle journey.

Of course, I cringed -- as I do with all things related to Second Life -- when I first read this story in The Chronicle of Higher Education. However, I do think Millard and Collins are on to something.

Darwin's Lizard: An image pulled from The Voyage of the Beagle. Is this tormented creature the new avatar?
Until now, I had never read the entire Voyage of the Beagle. I had no idea that Darwin was such an entertaining writer, with an endearing streak of naughtiness. I love the scene (390) when wicked Darwin tosses an innocent lizard into the ocean repeatedly. His stated goal: to see what the creature would do. Based on this “research,” Darwin writes that the “reptile has no enemy whatever on shore.” Yeah, well, that was until Mr. Darwin came to town. There’s another scene (393) when Darwin is again tormenting lizards. This time, he’s pulling their tails after watching them burrow into the sand. He writes, in his ever understated fashion, “I then walked up and pulled it by the tail; at this it was greatly astonished, and soon shuffled up to see what was the matter; and then stared at me in the face, as much as to say, ‘What made you pull my tail.’”


News flash:
Black-hat hacker dumps a slew of invasive species on islands! Lizards wait for Green Peace or grad-student rescue!


Perhaps, it’s me, but I will always smile when I imagine Darwin pulling the lizard’s tail. Now, I’ll also try to keep it in mind as I read the inevitable press reports of bad behavior in Darwin’s Second Life. I’ll try to remember that he started it all.

Laura Moorhead

Wednesday, October 15, 2008

Self-Replicating Macros and the Game of Life

Daniel Dennett’s discussion on Monday touched on the algorithmic nature of the natural selection process, which is able to generate complex forms in an automatic, non-designed manner.

This analogy to mechanical computation is further illustrated in chapter 7 of Dennett’s book. Here, Dennett provides a rebuttal to the idea that someone must have created the first living thing since its appearance could not have resulted from mere chance, given its complexity.
Dennett argues that this dilemma is solved by a LONG series of Darwinian processes: self-replicating “macros”.

Dennett borrows this term from computer programming, where macros are small chunks of code that perform a specific computation or task. An example of a macro in Excel or Word would be to “program” a key to enter a set of characters (eg: my name) followed by a newline (carriage return). I could then use this macro to close all of my correspondence with a single key stroke.

A much more interesting macro would be macro that is able to call itself; that is, a recursive macro. An example of a recursive macro is a bit of code that calculates a geometric sequence:

a(n )= r*a(n-1), for every integer n >= 1

It is the recursive property of this code that exhibits the “self-replicating” property of Dennett’s macros.

Thus, a basic, self-replicating process over a very long period of time is able to kick-start life and “out of next to nothing, the world we know and love created itself.” (Dennett p 185)

An Illustration: The Game of Life

Dennett illustrates how this process could work using a computer program called The Game of Life. It was created around 1970 by John Conway, a British mathematician.

The Game of Life is played on a two-dimensional grid. The grid is divided into squares or “cells.” Each cell has two mutually exclusive states: ON and OFF.

Each cell has eight neighboring cells: four adjacent and for diagonals. The rules for “playing” are as follows.

For each cell on the grid:

Count how many of its eight neighbors are ON at the present instant.
If the answer is:

2: the cell stays ON in the NEXT instant

3: the cell is ON in the NEXT instant

Under all other conditions, the cell is OFF in the NEXT instant.

Dennett describes the shapes that come to “life” when these basic rules are followed, starting from different initial positions (a cell with various neighbors ON or OFF).
It is much more fun to actually see it.

You can download the program from http://www.bitstorm.org/gameoflife/ and here’s what it looks like.

Here’s a screenshot of the grid with a starting position:



















And here's a view on the final position after running through several generations with the "exploder" initial position:

I suggest you try it on your own computer -- it's quite fun.
Marta Cervantes

Darwin Apparition in Tennessee

And just for fun, take a look at this Darwin parody in that unimpeachable standard-bearer of journalistic truth, The Onion: http://www.theonion.com/content/news/evolutionists_flock_to_darwin

The story reports on a mysterious shape that suddenly appeared on a concrete wall in downtown Dayton, Tennessee, and which was soon recognized to be none other than an image of.....DARWIN! Of course, such an apparition has drawn a large number of the devout to this small Tennessee town, site of the famous Scopes Trial, such as the mother who said "I brought my baby to touch the wall, so that the power of Darwin can purify her genetic makeup of undesirable inherited traits." Amid the faithful, there are of course vendors of splinters from the "one true Beagle" and other holy relics, as well as a few skeptics, such as those who maintain that the image is actually that of Carl Sagan or Stephen Jay Gould. Some have dismissed the authenticity of this vision altogether though, such as the professor from Oral Roberts University, who asserted "It's a stain on a wall, and nothing more," and who added "I only hope these heretics see the error of their ways before our Most Powerful God smites them all in His vengeance."

Anyway, enjoy and have a chuckle or two.....


Brad Bauer

From Fish to Land-Based Animal: A New Study Elaborates on This Transition

The New York Times reports today that a recently released study, to be published tomorrow in the journal Nature, reveals some of the intermediate steps in the evolution of marine vertebrates to land-based animals.

Researchers from the Academy of Natural Sciences in Philadelphia, studying fossilized skeletons of fish that had been excavated several years ago on Ellesmere Island in Canada, have been able to note changes in the cranial cavity, the development of a mobile neck, and the transformation of a bone that was used in underwater feeding and breathing. This latter bone eventually made up part of the hearing mechanism for subsequent land-based animals.

The object of this study, a fish that has been named Tiktaalik roseae, lived 375 million years ago. The significance of the development of the flexible neck and the reduction of the gills demonstrates, the study's scientists assert, that a fish previously suited for deep-water environments was adapting to shallow water. As Dr. Ted Daeschler, one of the study's participants said, "The new study reminds us that the gradual transition from aquatic to terrestrial lifestyles required much more than the evolution of limbs."

For the full-text of John Noble Wilford's article, see http://www.nytimes.com/2008/10/16/science/16fossil.html?hp

Brad Bauer

Monday, October 13, 2008

Computers + Biology = Virus Detector

With the talk about computer program and all. I think some of you might find this article interesting.

Joe DeRisi and Don Ganem have developed the Virochip. It is a broad-scale detection tool for identifying unknown pathogens. The chip currently has over approximately 22,000 viral sequences printed on it. DeRisi describest how the chip works like this, "If we are looking at a virus and trying to figure out what it is, we take some DNA and some RNA from a patient and we tag it with a fluorescent dye. Then we put that material onto the virus chip. Because matching genetic sequences stick to each other — the double helix — if there’s a match between what’s on the chip and our biological sample, a particular spot on the chip will glow. That tells us which virus the sample is. And, thanks to computers, we can do this with thousands of viruses at one time." http://www.nytimes.com/2008/10/07/health/research/07conv.html?_r=1&ei=5070&emc=eta1&oref=slogin

Dr. DeRisi is a Stanford alum and "currently an Howard Hughes Medical Institute (HHMI) Investigator and a Professor and Vice Chairman of the Department of Biochemistry and Biophysics at the University of California, San Francisco (UCSF) with a joint appointment at the California Institute for Quantitative Biomedical Research (QB3)." This is straight from Wikipedia, so go there for more info!

More interesting is http://derisilab.ucsf.edu/%20theDeRisi Lab website that showcases the genomic study of infectious disease. There are all sorts of abstracts about the work they are doing... lots of paper topics to be found!

-Pamela Alexander-Beutler

Sunday, October 12, 2008

Dawkins, Computer Viruses & Evolution

Greg’s report of computer-generated virtual creatures caused me to reread an old (1991) Richard Dawkins essay entitled Viruses of the Mind.  Tucked into his criticism of faith were a number of observations re computer viruses.  While Dawkins doesn’t claim that they “evolve”, he points to a number of features that selectively render computer viruses more transmittable (and more likely to reproduce).  While this doesn’t quite rise to “evolution”, it does come close.  Coupling computer viruses with a mechanism such as described by Lee Graham could lead to ever more “life-like” viruses with respect to reproducibility and adaptive means.  Dawkins suggests that future computer viruses may mutate and evolve by true natural selection and notes that “whether their evolution is steered by human designers may not make much difference to their eventually performance.”
Darwinian features of computer viruses include:

  • DNA viruses and computer viruses spread for the same reason: an environment exists in which there is machinery set well set up to duplicate and spread them around and to execute the instructions that the viruses embody.   Their success depends upon their ability to reproduce.
  • The practice of viruses being activated on a particular date is analogous to the Medawar/Williams theory of ageing (hosts are often victim of lethal and sub-lethal genes that are expressed only after the host has had time to reproduce).  By allowing a long dormancy period, the virus is able to infect more computers.
  • “A virus that clones itself too prolifically will soon be detected and annihilated” (a Darwinian disadvantage).  To circumvent this, many viruses examine their target host and determine if the host is already infected.  This ability is often exploited by antivirus software, which disables the malicious code of the virus, leaving its external signature (which Dawkins likens to a viral protein coat) intact.
  • A “computer virus that is too virulent will be rapidly detected and scotched”.  A virus that sabotages every computer it infects will not be effective because its ability to thrive depends upon the host.
  • Some viruses evade detection by being triggered probabilistically (i.e. erasing only one in sixteen of the disks they infect).

Some of Dawkins other ideas don’t stand the test of time. 

  • Dawkins spoke of a future in which computer systems would be advertised as being compatible with all viruses registered before a particular date (which presupposed a world wide entity that would register viruses).
  • “Gangs of mutually compatible viruses might grow up, in the same way as genomes can be regarded as gangs of mutually compatible genes.”  He later talks about “a time when … computer viruses may evolve toward compatibility with other viruses, to form communities or gangs.”
Cy Ashley Webb

 

Saturday, October 11, 2008

Evidence of Recent Human Evolution


It is commonly said that humans evolved as hunter gatherers on the plains of Africa and that today's humans are not significantly changed from our hunter-gatherer ancestors. The most recent issue of Seed Magazine has an article about recent work that suggests that humans may have evolved quite rapidly and significantly during the historical period.

Forgive me if I screw up the biology, but as I understand it, there are two key points that need to be understood as background:

First, DNA is inherited in blocks, with adjacent DNA sticking together and getting transmitted to the offspring. Such a block of of linked DNA is called a haplotype. Over the generations, mutations and recombinations nibble away at the edges of, and poke holes in, haplotypes. So if we look at two populations, the longer, on average, the haplotypes, the more recent the two populations have been connected (because the more time elapses, the more the haplotypes degrade).

Here is a visual representation of a haplotype:



Second, if there is a variation in a haplotype that is common to many individuals, that would tend to signal that natural selection is operating. In other words, out of 100 haplotypes of a related population, let’s say 90 are the same, and 10 are different, each in a different way. One would suspect that the 10 variations are likely random mutations or recombinations, and there is no reason to think natural selection has been involved. But if the 10 different show not different variations, but the same one, that suggests that the variation must confer some benefit, or it would not be reproducing itself.

What the researchers are looking for, then, are long haploptypes (indicating recency) with unusual variations that are showing up repeatedly in the population. When they find these, they believe they have found evidence of recent evolution. They have found several.

Here is an artist's rendering of the heights to which human evolution might ascend if we continue to evolve as rapidly as the researchers think we have:



There are a couple of problems with this. One, which the article does not mention, but which seems in principle a problem, is that, to the extent the holders of a particular shared long haplotype mostly interbreed, the shared variations could be due to genetic drift rather than selection. Second, they find these gene variants and assume they must be selected for, but they generally have no idea what the particular variant codes for, so a big piece of the puzzle is missing. Third, allowing for recent evolution in human populations suggests that different groups may be more or less genetically fit in certain ways, which is politically and philosophically a position with which most of us are uncomfortable at least. Even so, there does appear to be at least some evidence to support them (the recent evolution of the ability to metabolize lactose, more frequently present in some races than in others, for example).

There’s a lot more detail in the article (Seed Magazine, September/October 2008, p.66). It’s a fascinating magazine, by the way, concerning itself with the intersection between science and culture.


Greg Priest

Thursday, October 9, 2008

Threats to the Galapagos Island


[Photo credit: Steve Stroud / LA Times]

Yesterday's Los Angeles Times carried a story about the Ecuadorian government's attempts to protect the increasingly fragile environment of the Galapagos Islands by placing new limits on the numbers of its citizens who can live there. You can see this article at http://www.latimes.com/news/nationworld/world/la-fg-galapagos8-2008oct08,0,363527.story .

This move was apparently prompted by UNESCO's designation of the islands in 2007 as being "in danger," a status that was upheld this year as well. The problem is not only the increase in the human population, which has doubled in the past ten years, or the rapid increase in the number of tourists who visit the islands, which has trebled in roughly the same period of time. Rather, with increased human traffic comes stowaways as well: non-native species of animals such as goats, rats, cats, mosquitoes and fire ants, all of whom hitch rides on the boats and planes that bring new residents and tourists, and many of whom prey on local species and threaten to alter the unique ecological balance of these islands.

The Ecuadorian government feels that UNESCO's designation is unnecessarily alarmist, and claims that they had already taken action prior to restrict human migration to the islands prior to UNESCO's report. In regard to tourism, however, one could argue that the prohibitively expensive costs of travelling to the Galapagos promotes a different type of "survival of the fittest," or at least that of the most financially fit. This article points out that it costs in the neighborhood of $2,000-$3,000 for a typical four-to-seven day boat tour of the islands, excluding airfare to the islands.

Brad Bauer

Poetry in Motion

http://www.codeasart.com/poetry/darwin.html

Darwinian Poetry anyone? Software engineer David P. Rea designed “an experiment in collaborative composition based on genetic algorithms” that aims to create new poems using a modified form of natural selection.

Simply put, the idea is to create, or to evolve, new poems from 2 parent poems (species A and species B), using “non-negotiated collaboration.”

The program presents the user with two poems (“abysmal pieces of nonsensical garbage”) from a set of 1,200 randomly generated groups of words. Once the reader selects his/her preference, the program duplicates each parent and randomly chooses a "snip" point, where each poem is then cut. Next, the software combines the snipped portions of the parent poems, resulting in two new poems.

Rea describes the program in this way:
The Darwinian Poetry software relies primarily on a mechanism called "crossover", similar to the process that operates on chromosomes in biological evolution, except that here the basic genetic units are words rather than nucleic acids. When the program sees that there is room in the population for new poems (because some unfit poems were...um...culled from the herd) it chooses randomly, albeit weighted by popularity, two surviving poems to serve as parents. These two poems are cloned then crossed over, producing two new offspring.
For basic descriptions of crossover techniques and genetic recombination, please see http://en.wikipedia.org/wiki/Crossover_(genetic_algorithm)
and http://en.wikipedia.org/wiki/Genetic_recombination.

Rea notes that voter selection “[kills] off the "bad" [poems] and [breeds] the "good" ones with each other. …Over time the poems users select will interbreed. …If enough generations go by, and if the gene pool is rich enough, we should eventually start to see interesting poems emerge.”

Mutations, whereby word position within a line segment can change, occur about 10% of the time. As we know, mutations are important sources of new variation for natural selection to work upon.

In addition, it’s possible to track a poem’s lineage, and to see how many generations it has “lived”. Most poems, though not all, tend to be much shorter in length than their parents.

Though the Discussion Boards shut down in 2004, they remain a good place to sample the types of poems that “evolved”. If you’re interested in participating in this project, voting remains open.

Sample Random Poem, #5:
Track this poem’s offspring here: http://darwinianpoetry.com/servlet/ReportingServlet

distance
she that her
don you preferred lot
to I long
stoops laughing in
who a cup but

Sample Evolved Poem, #17717:
Track this poem’s lineage here: http://darwinianpoetry.com/servlet/ReportingServlet?action=showPoem&id=17717

you lie beautiful
beating beyond love
imagine
beneath chairs
dark stars magic
everything frozen strangely in
you

Rea explains that “breeding two poems won't necessarily produce a better poem. In fact, if either poem is any good to start with, it will probably produce a worse poem. But sometimes something better will be produced, and such offspring will tend to survive a long time, producing many more offspring. Evolution is all about preserving those rare beneficial developments amidst a sea of failed genetic experiments.”

Poetry may not be the realm Darwin had in mind to test his ideas about natural selection and evolution, but Rea’s program competently illustrates the concepts. Of course, natural selection is not a matter of conscious choice in nature, nor is it so simplistic. However, just as life complexifies over time in nature, these Darwinian poems did evolve from previously random words gaining meaning and complexity over time, some being species worth a read.

Roxanne Enman

Tuesday, October 7, 2008

God, Salvation, the End Times and the Natural World

Let's try this again. For a profound analysis of the complex theological issues involved in reconciling the natural world with theological concerns, see the following thoughtful debate. The churches are across the street from each other.











Greg Priest (ironic, I know)

Sunday, October 5, 2008

Our (Unofficial) Apologies, Mister Darwin

I’m loathe to bring up the topic of religion and evolution. Surely, we’ve covered that topic enough last week? Certainly, Professor Jeff Wine, a panelist from the Eugenie Scott discussion, put the matter in perspective for us quite nicely. I thought the professor of psychology, human biology, neurosciences, and pediatrics, though the least spoken, had a few wonderfully understated end points for the night.

For starters, Professor Wine asked, Why is it necessary to have this conversation in the twenty-first century? Then he added, “Faith is not susceptible to argument. It also serves people and individuals in a very personal way,” and, well, that’s essentially fine. It’s when, he adds, that "faith comes out of the personal and into the public – into medicine, foreign policy, economics. Then you see the trouble.” I could (and perhaps should) stop there, but a few newswire items caught my eye last week. From my perspective, these seemingly innocuous news items are what largely keep faith in the public realm.

For those not in a habit of scanning traditional newswires, here's a brief explanation: The Associated Press and Reuters have subscription-based, bare-bone databases that literally stream breaking headlines and in-process stories. It’s like a stock ticker running across your computer screen. Sometimes it interesting, sometimes it’s horrifying, but usually it’s quite dull and repetitive. On Friday, the news cycle typically slows down (as in the journos leave their offices) and people turn off their computers for the weekend. Not surprisingly, it proves to be a good time for organizations to issue retractions, clarifications, and rotten earning reports – all the cock-ups that most marketeers prefer to go unnoticed. (Truly serious, "let's keep this under the wire" cock-ups go out Sunday morning.)

One so-called news flash caught my eye: a clarification to the Vatican’s September announcement that “the theory of evolution was compatible with the Bible,” but – again – there would be no official apology to Charles Darwin. There’s no more information on the story (as in who happens to be confused or concerned by the matter), but here’s a link to the initial Reuters story. Interestingly – and really my "Hot and New" (er, "Mild and Molding") item – comes from some subsequent digging.

In all honesty, I was hoping for some juicy Vatican drama with U.S. priests behaving badly around election time. But there’s no apparent news there. I was surprised to see that the clarification is tied to the Anglican Church’s apology to Mister Darwin for, well, 150 years of “misunderstanding,” “getting our first reaction wrong, and encouraging others to misunderstand.” Reverend Malcolm Brown writes more on the church’s official website, and it was posted to mark the upcoming 150th anniversary of the publication of On the Origin of Species. The posting appears to have been well-covered in the U.K., then subsequently picked up by Scientific America. But SA learned from an Associated Press interview with Church of England officials, apparently more in the know than their official blogger, that the posted "position on Darwin isn’t an official apology.” (And yes, a few other announcements came out from some more bit-player religions clarifying their positions on the matter.)

For me these news items and clarifications, which would have been put at least in the front of the eyes of a few million in Europe and the U.S., somehow pushes Professor Wine’s question about, Why is it necessary to have this conversation in the twenty-first century? to something, but I’m not quite sure what. The expectedly absurd? A matter bigger than the United States? The biggest non-news news item of the week? Or must-know information? Gee, did any ministers or priests rewrite their Sunday sermons after the Friday news?

It may seem a non-issue to many, but it's still news – or seeming – news to potentially more.

Laura Moorhead

Genetics provide keys to missing evolutionary links.

DNA analysis identifies an individual's unique genetic pattern, called a genotype. This information can be compared with other genotypes for purposes of identification. mtDNA is the DNA from the maternal side which can trace the evolution of the H. sapien from which both modern man and neanderthals are derived.

In the below articles geneticists have used mtDNA to confirm that modern man and neanderthal man are not related although they both roamed some of the same territories during the same period. As I read Janet Browne's Darwin's Origin of Species I was struck by how the genetic sciences continue to reveal evidence of adaptation (or the lack thereof), confirm natural selection, fill in missing links and present physical evidence.

http://www.youtube.com/watch?v=rfBmFx-g13Q

http://www.pbs.org/wgbh/nova/neanderthals/mtdna.html

http://news.nationalgeographic.com/news/2008/09/080917-neanderthal-photo.html

-Pamela Alexander-Beutler

Theory of Evolution in Computer Games

Greg’s posting on the evolution simulator reminded me of the latest game from Will Wright, the creator of SimCity. The new game called Spore and was just released last month by Electronic Arts.Spore is described in the product documentation as

“[Spore is] your own personal universe. In this universe, you can create and evolve life, establish tribes, build civilizations, and even sculpt entire worlds.”

I was intrigued enough to buy it ($45) and start building my universe. The Spore universe is made up of five stages, each allegedly corresponding to “a stage of evolution: Cell, Creature, Tribal, Civilization, and Space."

Clearly these stages were made up as part of the game and appear to be mishmash of evolutionary concepts. For example, the process of becoming a Creature (evolved being) simply involves accumulating points during the Cellular stage by eating available vegetation or other organisms. Apparently, adaptability and natural selection have nothing to do with evolution!

Each stage presents different challenges and goals. The player begins life as a tiny cell, then progresses through the other stages on their journey.

Borrowing from theories on the origin of life on earth, life in Spore starts by hitching a ride to the newly named planet on the tail of a meteor.

Again, Spore makes vague references to the planetary conditions favorable to life, “Fortunately the conditions on the planet are just right for an explosion of life in the primordial soup.”

But the main connection to evolution in Spore seems to be the emphasis on competition and survival:

“Unfortunately for you, that explosion means there’s a lot of competition to see which species is going to rule the water.”

This then seems to be the core of the “evolutionary” mechanism in Spore:

“And the cutthroat competition doesn’t stop once you evolve onto land! Through each of the five stages in Spore it’s survival of the fittest as you try to adapt your species to stay one step, one tool, one weapon ahead of the others. It’s up to you whether your creature will play nice or rough as it advances and evolves. Will your simple amoeba go on to rule the galaxy?”

Spore may be about creating beings and progressing through stages of “life” but it has no basis in the theory of evolution. It borrows from evolutionary concepts but doesn’t simulate real evolutionary mechanisms in any meaningful way.

Spore is the most recent “evolutionary” game but it’s certainly not the only one. E.V.O: Search for Eden, is another game from a Nintendo that incorporates evolutionary concepts. E.V.O is described as a role playing game, where players do battle with enemies and:

“By eating defeated enemies, players gain "Evolution points" that can be used to modify the creature they are playing as. These improvements include bigger jaws, various armors, horns, fins, longer neck, better jumping, swimming ability, flying ability and more. By evolving, your character gains more hit points, greater speed, stronger attacks, and even certain special abilities such as flight.”

The real problem, if you will, with E.V.O is the storyline, which according to Wikipedia (http://en.wikipedia.org/wiki/E.V.O.:_Search_for_Eden) is a combination of creation mythology and Theistic Evolution.

In using the evolutionary concepts with creation mythology, quasi-religious and quasi-scientific ideas are merged:

“The player takes the role of one of many billions of life-forms created by Gaia, the nurturing and benevolent daughter of Sol, the Sun. Among the creatures known as "life", there is a competition to evolve, and the greatest life-form will eventually be granted the privilege of entering the Garden of Eden and becoming the husband and partner of Gaia." (Wikipedia)

I have no issue with fantasy role playing games – I rather enjoy them. However, I’m disappointed that in the popular imagination, evolution is reduced to survival of the fittest in the crudest manner and players are granted god-like powers to evolve their creations instead of simulating something more elegant like natural selection.

-Marta Cervantes

Understanding Evolution website



As a follow up to the weblink that I mentioned in the MLA 266 class at Stanford on Thursday night, www.evolution.berkeley.edu, I also wanted to add a few words about this website, which is called "Understanding Evolution."

This site, which I found while searching for information about uniformitarianism and Charles Lyell, is a rich resource for almost anybody interested in evolutionary theory and the history of its development. While it appears on first glance to be developed for school teachers seeking lesson plans on the topic, as well as for secondary school students seeking material for research papers, the articles are written to a sufficient level of depth to appeal to adults and any interested layperson. In fact, with an eye toward the research projects we will be working on this quarter, this website is a good resource for obtaining background information on most of the topics that we are likely to cover, and in that sense, can be an alternative to Wikipedia for getting quick information about topics as diverse as Lamarck and Linneaus, natural selection and genetic drift, speciation and mutation, as well as the tree of life.



One advantage that this site does have over Wikipedia, however, is that its sources are meticulously and authoritatively documented, and the site itself has even been evaluated by an outside firm that specializes in "technology interventions in education"(Rockman et. al.), with the results of its evaluations and surveys about the site posted online for all to see. Perhaps this is not so surprising, since the site is created by the University of California Museum of Paleontology, working with the National Center for Science Education (whose own Eugenie Scott we heard lecture at Stanford this past week). Nevertheless, it is certainly welcome to see a site like this crafted with such care, and this does increase the level of confidence and trust of any student wishing to use it as a research source.

In addition to sections explaining the basics of evolution (in great detail though, I might add), the evidence for evolution, its impact on everyday life, and the history of evolutionary theory, this site also contains sections on lesson plans for teachers and a featured news topic as well (currently focusing on the evolution of Tasmanian devils, and the development of cancerous lesions that are threatening to wipe out this species), which in addition to an article compiled by the website staff, also contains links to articles and other information resources on the topic.



Enough said for now......if you are looking to pass some time on a Sunday afternoon, I'd highly recommended browsing through this site. Enjoy.

Brad Bauer

Friday, October 3, 2008

Evolving Virtual Creatures

I have come across the coolest software application. As the guy who wrote the code describes it:
With this program you can watch a process of simulated Darwinian evolution unfold before your eyes.... The user is given control of many of the parameters of the evolution such as the size of the creature population, the mutation rate, the ability for which the creatures will be evolved, and many other settings.
The basic idea is that the software randomly sets initial conditions that define a set of creatures made of connected blocks. You define (from a limited set of options) how fitness is measured (e.g., speed, jumping ability). The creatures start to reproduce, with mutations, recombination, etc., and those creatures that are more "fit" as you've defined fitness are disproportionately favored with "offspring." As you run the application, the creatures "evolve" before your eyes.

On his website, he has a zoo of creatures that have evolved using his software. Here are a couple of them, just for fun:








He even has a bunch of videos on YouTube that show some of the creatures in action, like the following: http://www.youtube.com/watch?v=wRzA8_zoYmo

I haven't had the opportunity to work enough with the software to validate this, and I am not sure enough about what goes on behind the scenes to ever be really sure, but it strikes me as possible that the author is selling himself short when he says the application "simulates" evolution. Remember how Darwin explains evolution in the Origin:
If during the long course of ages and under varying conditions of life, organic beings vary at all in the several parts of their organisation, and I think this cannot be disputed; if there be, owing to the high geometrical powers of increase of each species, at some age, season, or year, a severe struggle for life, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of existence, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, I think it would be a most extraordinary fact if no variation ever had occurred useful to each being's own welfare.... But if variations useful to any organic being do occur, assuredly individuals thus characterised will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance they will tend to produce offspring similarly characterised. This principle of preservation, I have called, for the sake of brevity, Natural Selection. (127-128)

If we assume for the sake of argument that he was right, in order for evolution by natural selection to happen, you need (1) creatures that have offspring that inherit important attributes from their parents, (2) some mutation or other variation from perfect replication, (3) occasional cases where the variation is either more fit or less so to the environment and (4) a struggle for existence where some creatures die earlier (or, put more directly, where some creatures have more offspring than others). I would venture to suggest that all four of these attributes are present in the software. I'm not sure that it would not be accurate to say that the application does not "simulate" evolution but in fact instantiates it--that is that the software performs evolution, though not the same by any means as biological evolution. I'd be curious whether others agree that this is possible, or think I'm daft.

The author's name, by the way, is Lee Graham. He's a PhD student at Carleton University in Ottawa, Ontario. A link to his site and the software is here: http://www.stellaralchemy.com/lee/virtual_creatures.html

Greg Priest