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Monday, February 16, 2009

Variation and Natural Selection

 
Here's a photograph of many varieties of hybrid radish. It's from the Botany Photo of the Day posted on Darwin's birthday by Nhu Nguyen to illustrate speciation in action.



Please visit the UBC website to see the entire posting. I'd like to comment on one particular statement. Nhu Nguyen writes,
This is a weedy species that grows in coastal (and some central) areas of California. According to research by Norman Ellstrand's group at UC Riverside, this species is evolving in a quantifiable manner. It is a hybrid between Raphanus sativus, the common radish, and Raphanus raphanistrum.

Curiously, the same hybrid occurs elsewhere in similar climates such as that of South Africa, but something special about ecosytems in California allowed it to proliferate. It is now different enough from either of its parents that Ellstrand's group is considering describing this as a new species. This has occurred within the timespan that the two parents were brought together by humans in California."

There are many color variations of this evolving species. It is exactly through this variation that the process of natural selection works. If allowed to go its own way, some of these color morphs may persist, others may perish, all depending on the selective forces present where they occur. Eventually, each of these via time and selection could become a species of its own. California thus would be the center of diversity for a new group of Raphanus species.
What is the evidence that natural selection is acting one these variants? I doubt that there's any evidence at all.

While it's true that evolution may result in many of these variants becoming separate species, there's no reason to suppose that there are "selective forces" working on different colored flowers. It could just as easily happen that one or more colored variations could become fixed in a new species by random genetic drift.

I'm not sure what the problem is here. Is it just sloppy language on the part of some botanists? Do they use the words "natural selection" as a synonym for "evolution" without thinking about it? Or, are they confirmed adaptationists who actually believe that all visible phenotypes must be subject to selection?

There seem to be a large number of scientists who think that all speciation events are driven by natural selection. This was (mostly) what Darwin thought but I was previously under the impression that this had changed in the 20th century to recognize that random genetic drift plays an important role in speciation.


Does This Look Designed?

 
Check out today's Botany Photo of the Day from the University of British Columbia Botanical Garden and Centre for Plant Research. The species is Euphorbia caput-medusae L. from South Africa.

It's an example of a strange-looking species that most of us are not familiar with. We need to keep in mind that life is complicated and weird.


Sunday, February 15, 2009

Literary Darwinism

 
A reader tells me that Trent University (Peterborough, Ontario, Canada) celebrated Darwin's birthday with a talk by Joseph Carroll on The Historical Position of Literary Darwinism. She asked me what I thought of Literary Darwinism.

I had never heard of it so I asked my good friend "Google" and he (she?) didn't disappoint. There's a Wikipedia entry on Darwinian Literary Studies (aka Literary Darwinism).
As Leda Cosmides and John Tooby indicate in their essay "The Psychological Foundations of Culture," scientific models and theories allow us to sense abstract objects and relationships just as our eyes and ears allow us to sense concrete ones. In Darwinian literary studies, as in evolutionary psychology, "[t]he tools of evolutionary functional analysis function as an organ of perception, bringing the blurry world of human psychological and behavioral phenotypes into sharp focus and allowing one to discern the formerly obscured level of our richly organized species-typical functional architecture."[2] In other words, since the human mind is embodied in evolving organic structures such as the brain, researchers should be able to explain aspects--not only of cognitive systems such as language ability, but of cultural systems such as art and literature--in terms of the environmental factors, or selection pressure, that give rise to them. A chief goal of Darwinian literary studies is to show how the reading and writing of literature contributes to the inclusive fitness of the human organism. In this sense the discipline relates closely to adaptationism, and it shares with the adaptationist social sciences the ultimate goal of understanding human nature.
So it's closely related to adaptationism and evolutionary psychology, eh? I don't think I'm going to like literary Darwinism. Sounds like just another misinterpretation of evolution by a bunch of non-scientists.

Let's look at an example.
A good example of applied Darwinian criticism is Joseph Carroll's reading of Pride and Prejudice, which shows how the fundamental biological problem of mate choice informs the plot of Austen's novel[3]. In this view, the novel narrates a social order in which males compete on the basis of socioeconomic attributes such as money and rank, whereas females compete according to 'personal' attributes such as youth and beauty. The story of Darcy and Elizabeth's courtship establishes a model for partial subversion of this social order, since the couple manage to abide by it even though the proximate causes of their mutual attraction have more to do with the conventionally undervalued attributes of dignity, honesty, kindness, and intelligence. A Darwinian critic might argue that the whole book functions as a tool for humans to perceive, order, and make sense of the conflicting impulses that characterize romantic relationships.
I don't know whether I count as a "Darwinian critic" or not but it seems to me that Austen is pointing out that women can be either smart or stupid when it comes to choosing a mate and so can men. Jane Austin is describing the breakdown of an English social order that existed prior to the nineteenth century. That social order is very different than those in other societies at the same time (e.g. India, China, North American natives), which, in turn, is probably nothing like the society of our ancestors 50,000 years ago. I don't see what this has to do with human evolution—or whatever these English scholars mean by "Darwinism."


Dan Falk Gets It Right!

 
Dan Falk is a Toronto-based science writer and winner of 2002 Canadian Science Writers’ Association Science in Society Journalism Award. He writes for major Canadian newspapers and is a frequent contributer to the CBC television program Quirks and Quarks. He is the author of In Search of Time: Journeys Along a Curious Dimension, which I have not read—an oversight I plan to correct as soon as possible.

I'm critical of many science writers for misrepresenting science in their articles appearing in newspapers or magazines. It's even worse when ordinary journalists attempt to write about science [The Ottawa Citizen Should Be Ashamed of David Warren].

Today I'm deligheted to bring to your attention an excellent article by Dan Falk in today's Toronto Star "[You are here: Your microspot in the universe: What Galileo and Darwin should really be remembered for: making us feel smaller"].

You really should follow the link and read the whole article. Here's the conclusion—I hope it will tempt you.
As physicist Steven Weinberg famously said, "The more the universe seems comprehensible, the more it also seems pointless."

Both Galileo and Darwin showed us that our place in the cosmos is less central – perhaps less special – than we had imagined. For some it has been a bitter pill to swallow. But there is also every reason to rejoice in their discoveries. We are indeed animals, but we are animals that can comprehend the structure of DNA and the unity of life.

And yes, we live in one remote corner of the galaxy, itself one of billions of galaxies, but from this outpost we have probed the fabric of the universe, from the smallest quark to the most distant quasars.

Galileo and Darwin broadened our horizons, perhaps to a greater degree than any other two thinkers in history. As a result of their vision, we live in a larger, richer and more wonderful universe.
Thank-you Dan Falk. It's refreshing to see that kind of writing in a major newspaper. I'm looking forward to the letters to the editor, especially from those who haven't yet swallowed the bitter pill.


[Photo Credit: The photograph of Dan Falk on the University of Toronto campus is from his article, TIME TRAVEL AND THE DOWNING STREET DILEMMA, on the pagebooks.ca website.]

Congratulations Steve Darwin!

 
Steve Darwin is Steve #1000. Find out who he is (no relation to Charles) and why he is #1000 by visiting the website of the National Center for Science Education [Steve Darwin is Steve #1000].


Saturday, February 14, 2009

You Can Lead an Atheist to Evidence, But You Can't Make Him Think

 
Here's a video of Pat Robertson and Ray Comfort—two of the best secret weapons on the atheism side. Just watch this video to see why.




[Hat Tip: Friendly Atheist]

Jerry Coyne Meets Ken Miller

 
Read about it on Coyne's blog [Darwin Day, Philadelphia. 1. I meet Ken Miller].
At any rate, after dinner I met Ken and we chatted about things. The first thing he said to me was that one of his friends advised him to break a beer bottle over my head, which was more than a little intimidating when imparted to me by a guy well over six feet tall looking down on my puny five-foot-eight self! But we discussed our differences, tried to iron out misunderstandings on both of our parts, and amiably shook hands. We will never agree on the science-versus-faith thing, but on most issues we are on the same side, and I admire him in many ways. I was glad that we met.
I'd love to have been there.


Can You Guess Who Wrote This?

 
Yet how the former led to the latter, how it was that complexity emerged and is sustained even in that near-miracle of a chemical factory we call the cell is still largely enigmatic. Self-organisation is certainly involved, but one of the puzzles of evolution is the sheer versatility of many molecules, being employed in a myriad of different capacities. Indeed it is now legitimate to talk of a logic to biology, not a term you will hear on the lips of many neo-Darwinians. Nevertheless, evolution is evidently following more fundamental rules. Scientific certainly, but ones that transcend Darwinism. What! Darwinism not a total explanation? Why should it be? It is after all only a mechanism, but if evolution is predictive, indeed possesses a logic, then evidently it is being governed by deeper principles. Come to think about it so are all sciences; why should Darwinism be any exception?

But there is more. How to explain mind? Darwin fumbled it. Could he trust his thoughts any more than those of a dog? Or worse, perhaps here was one point (along, as it happens, with the origin of life) that his apparently all-embracing theory ran into the buffers? In some ways the former possibility, the woof-woof hypothesis, is the more entertaining. After all, being a product of evolution gives no warrant at all that what we perceive as rationality, and indeed one that science and mathematics employ with almost dizzying success, has as its basis anything more than sheer whimsy. If, however, the universe is actually the product of a rational Mind and evolution is simply the search engine that in leading to sentience and consciousness allows us to discover the fundamental architecture of the universe – a point many mathematicians intuitively sense when they speak of the unreasonable effectiveness of mathematics – then things not only start to make much better sense, but they are also much more interesting. Farewell bleak nihilism; the cold assurances that all is meaningless. Of course, Darwin told us how to get there and by what mechanism, but neither why it is in the first place, nor how on earth we actually understand it.

To reiterate: when physicists speak of not only a strange universe, but one even stranger than we can possibly imagine, they articulate a sense of unfinished business that most neo-Darwinians don't even want to think about. Of course our brains are a product of evolution, but does anybody seriously believe consciousness itself is material? Well, yes, some argue just as much, but their explanations seem to have made no headway. We are indeed dealing with unfinished business. God's funeral? I don't think so. Please join me beside the coffin marked Atheism. I fear, however, there will be very few mourners.
The answer is at ... Darwin was right. Up to a point.


[Hat Tip: RichardDawkins.net]

Friday, February 13, 2009

Moving Darwin

A statue of Charles Darwin was sculpted by Sir Joseph Boehm in 1885. It cost £2200. The money was raised by soliciting individual contributions from individuals around the world and so much money flowed in that there was enough left over to fund research in evolution.

The statue was unveiled on June 9, 1885. Charles Darwin was hugely popular, as you can see by the crowd of people outside the Natural History Museum. The statue was placed in a prominent position at the top of the main staircase in the Central Hall.

In 1927, Darwin wasn't as popular and his statue was moved to make way for an elephant display. The place of honor was soon taken up by a statue of Richard Owen, founder of the museum, and not a huge fan of Darwin [The North Hall Statues].

Darwin, and his friend Huxley, sat in the North Hall, under the main stairs in what became the museum cafeteria. This is not a place of honor and when I saw it there in 2006 I thought it looked very much like the museum was trying to hide Darwin from its visitors.



The Natural History Museum decided that they had better take steps to rehabilitate Darwin in preparation for the 2009 celebrations. So last Spring they moved Darwin back to the original position at the top of the stairs in the Central Hall.

You can watch a video of the statue on the move on the Natural History Museum website [Darwin's statue on the move].

I'm glad they decided to move the statue. While there's a danger of reading too much into the traveling statue, I think it reflects a time in the early 20th century when Darwin's reputation was somewhat eclipsed. At that time, there were many scientists who didn't think that natural selection could explain evolution.



Quotable Quotes

 
From PZ Myers [I get email].
One frequent motif recurs in creationist email: they may believe in god, but they don't believe in paragraphs.


On Re-reading the Origin of Species

 
It's been a great pleasure to read the Origin of Species in preparation for my talk tonight and for our book club meeting last Monday. I had forgotten how clever Darwin was and how he carefully weighs his arguments for evolution.

I had also fallen prey to several myths about the book. For example, I didn't realize that Origin of Species is all about speciation and the difference between species and varieties.

The editors of Current Biology asked several scientists to re-read Origin of Species in honor of Darwin's 200th birthday. The results are published on the journal's website [(Re)Reading The Origin].

I've already mentioned Jerry Coyne's defense of the term "Darwinism" [Jerry Coyne on Darwinism. The contribution from Christiane Nüsslein-Volhard is excellent—she points out one of Dawin's most important arguments and reminds us that it has been largely forgotten because it now seems so obvious.

Many of the scientists comment on the wonderful prose in Origin and on Darwin's delightful style of writing. I agree with them. Mark Ptashne doesn't. He couldn't read the book when he was younger and even today he had to read a condensed version because the original is too difficult! ("Who has the patience to dig through the convoluted sentences, extracting the buried nuggets?")1

At my book club meeting, and in many discussions with non-scientific friends, the dominant impression is that Darwin is a very humble man who almost apologizes for having a good idea. That's not the Darwin I see. Simon Conway Morris isn't fooled either ....

But what suddenly became clear is that this is a book haunted by the ghost of William Paley the grandfather of creationist thinking and exponent of seemingly irrefutable arguments for organic design. The Origin is Darwin's riposte. Its metaphorical power depends on suspense and a scattering of clues, but significantly Paley himself is mentioned only once. And cleverly not in the context of his ideas on organic design but in an oblique dig at the question of natural evil. First and foremost, The Origin is an exorcism of the doctrine of special creation, and conducted by one of the most skilled exorcists science has ever seen. The brief crescendo in the last chapter is preceded by repeated and sudden flashes of disdain, a quick insertion of the knife before the narrative calmly continues in its ostensibly more objective purpose of piling up the evidence. Darwin knew his enemy intimately, but was far too astute to engage in a head-on clash.

Darwin was right, and he knew it. His expressions of doubt are largely rhetorical and how seamless—at least from a distance—is the edifice upon which he constructs his theory. Yet, it is equally intriguing how he conceals his intellect: the carefully marshalled facts are allowed to speak for themselves and the implications introduced with restraint and circumspection—a sotto voce naturalist. Darwin never doubted his abilities.
Why are so many people not able to see this? I think it's because they aren't familiar with the typical English style of understatement and well-disguised sarcasm.

Darwin's contemporaries weren't fooled. You should read Brian Switek's posting on Darwin's Heartache to see how Darwin's friends responded to the book in November 1859. His old Cambridge mentor, Adam Sedgwick, was not happy.

Andrew Berry and Hopi Hoekstra didn't comment on their own reading of Origin of Species; instead they listed the comments of their students in the course evaluations! The good news is that some students actually liked the book.

My favorite review is by Peter Lawrence who, I must confess, is one of my favorite scientists. Peter noticed something that I also noticed; namely, that Darwin's style of argument is very much a lost art. Here's how Peter puts it ...
I had only dipped into this wonderful book in my student days. But what a revelation for a somewhat jaded scientist to read it now! It is not only the brilliance, farsighted and original nature of the ideas, there is the sheer diversity of knowledge, the pervading presence of thought, of simple direct experiments, of debate, of argument, the consideration of other views and the style. In writing and reading scientific articles nowadays, we become imprisoned, constrained in what is considered appropriate and our vocabulary is reduced. Also our sentences are stifled by fashion and by journals that kill invention and independence with their strict word limits and their 'house style.' Just one example: punctuation. Darwin used everything, even the long dash and the exclamation mark. In my scientific writing I have been frequently told that these are not allowed—OK for great literature, but banned from scientific usage. I don't know why, but dulling down our scientific writing is not in our best interest. By contrast, in Darwin's time, Victorian fashion encouraged a flowery style as well as intellectual freedom; he took full advantage of both. He could write explorative and educative prose. He could spend many pages explaining narrow but important distinctions between different viewpoints and, time and again, one can see the outcome of careful reading and deep reflection. Our data-dominated publications, pared down to fit them into limited space, would be much more comprehensible if there were more argument, more explanation and more justification; indeed, if we reflected more, I think we could make big reductions in our published pages by making sure they carry and convey at least one message of note.


1. I suspect he hasn't read The Structure of Evolutionary Theory , either.

Thursday, February 12, 2009

YouTube Birthday Card

 



Happy Birthday Charles Darwin

 
Charles Darwin was born on this day in 1809.

Here are the opening paragraphs of Janet Browne's wonderful biography of Charles Darwin.
He was born into Jane Austen's England. Indeed, the Darwins could have stepped straight out of the pages of Emma, the four girls sharply intelligent about the foibles of others, their father as perceptive as Mr. Knightly. The boys had several equally distinctive qualities. Charles Darwin and his older brother, Erasmus, were obliging and sympathetic young men full of the gentle humour, domestic attachments, and modest traits that made Austin's characters stand out in the drawing rooms of local notables, with a good range of idiosyncratic failings to match. These natural attributes were enhanced by a substantial family fortune. Like sensible Mr Weston with his warm heart and easy financial circumstances, the two were general favourites: "always acceptable," as Emma Woodhouse said of Weston. Behind the scenes presided Mrs. Darwin, a clever, well-educated woman, at one time a friend of the novelist Maria Edgeworth, who now led a retired life, the female counter part to Mr. Woodhouse, "never quite well & never quite ill," according to her sister Kitty.

The Darwins like Austen's fictional families, lived in a sleepy market town in the countryside, in their case in Shrewsbury, the county capital of Shropshire, standing on the River Severn halfway between the manufacturing Midlands and Wales. Further downstream in the Severn Gorge smouldered William Hazledine's ironworks, the driving force of the Industrial Revolution. North-east sat the smoking chimneys of the Potteries. But Shrewsbury itself was untouched by any signs of industrial change.




Dawkins on Chance

 
I know I'm going to be accused of beating a dead horse but as Emile Zucherkandl and Linus Pauling said in 1965 ...
Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.
It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).

Richard Dawkins
Richard Dawkins has reviewed Jerry Coyne's new book Why Evolution is True in The Times Literary Supplement. The text of the review is posted on RichardDawkins.net [Heat the Hornet].

As you might have guessed, when an adaptationist reviews a book by a fellow adapationist you can expect heaps of praise. Dawkins does not disappoint.

One particular claim caught my eye since Dawkins has made it in the past. I know for a fact that others have pointed out to Dawkins the flaws in this claim. Here's what he says,
Coyne is right to identify the most widespread misunderstanding about Darwinism as the idea that, in evolution, “everything happens by chance”. This common claim is flat wrong – obviously wrong, transparently wrong, even to the meanest intelligence (a phrase that has me actively restraining myself). If evolution worked by chance, it obviously couldn’t work at all.
It's true that to say everything happens by chance is wrong. However, it is not true to say that, "If evolution worked by chance, it obviously couldn’t work at all."

Here's a quotation from the most popular textbook on evolution, Evolution by Douglas J. Futuyma. It's in Chapter 10—a chapter titled Random Genetic Drift: Evolution at Random.

Almost all factors are affected simultaneously by both chance (unpredictable) and nonrandom, or deterministic (predictable), factors.... So it is with evolution. As we will see in the next chapter, natural selection is a deterministic, nonrandom process. But at the same time, there are important random processes in evolution, including mutation and random fluctuations in the frequencies of alleles or haplotypes: the process of random genetic drift.

Genetic drift and natural selection are the two most important causes of allele substitution—that is of evolutionary change—in populations
Futuyma closes the chapter with a summary of the important points. The first two are ...
  1. The frequencies of alleles that differ little or not at all in their effect on organisms' fitness (neutral alleles) fluctuate at random. This process, called random genetic drift, reduces genetic variation and leads eventually to the random fixation of one allele and the loss of the other., unless it is countered by other processes, such as gene flow or mutation.
  2. Different alleles are fixed by chance in different populations.
Thus, according to the textbook, evolution by chance occurs in spite of the fact that Dawkins says, "If evolution worked by chance, it obviously couldn’t work at all."

Now, the only way to reconcile his statement is to assume that either Dawkins doesn't know about random genetic drift, or he uses a non-standard definition of "evolution" (or he is wicked, but I’d rather not consider that ).

I know that Dawkins has written about random genetic drift so I have to assume that he uses a definition of the word "evolution" that excludes it. Since he is using a non-standard definition of evolution, I think it would be wise of him to make this clear in his writing. He should have written something like ...
In my opinion, the only valid mechanism of evolution is evolution by natural selection and that is definitely not a chance process. If natural selection worked by chance it obviously couldn't work at all.


Wednesday, February 11, 2009

Nobel Laureate: Christian de Duve

 

The Nobel Prize in Physiology or Medicine 1974

"for their discoveries concerning the structural and functional organization of the cell"

Christian de Duve (1917 - ) won the Noble Prize in 1974 for discovering lysosomes and peroxisomes. He shared the prize with two other cell biologists; Albert Claude and George Palade.

Here's the Press Release.

THEME:
Nobel Laureates
Whereas Palade is in the first hand the morphologist searching the chemical correlate of the structures he has observed Christian de Duve is the biochemist who through his work can make predictions about new structural entities. Also the work of de Duve was a direct consequence of Claude's contributions in the area of chemical fractionation of cell components. de Duve started his work using differential centrifugation and he looked for the distribution of different enzymes among the four fractions resulting from Claude's procedure. These were nuclei, mitochondria (energy producers of the cell), microsomes (fragmented endoplasmic reticulum) and cell sap. He then found that certain enzymes sedimented such that they could not belong to any of the known morphological components. He discovered that they would sediment with a special class of particles, a fifth fraction. Interestingly all the enzymes were of a kind attacking protoplasmic components and de Duve therefore postulated that they had to be confined to membrane limited particles in order not to damage the cell. In accordance with this he found that agents dissolving membranes liberated the enzymes. It was soon possible for de Duve in collaboration with electron microscopists to make a morphological identification of the isolated components which were named lysosomes.

Lysosomes have now been shown, by de Duve and others, to be engaged in a series of cellular activities during which biological material must be degraded. The lysosomes are used in defense mechanisms, against bacteria, during resorption and secretion. They can also be used for a controlled degradation of the cell in which they are contained, e.g. to remove worn out components. Normally the cell is protected from the aggressive enzymes by protecting membranes but during certain conditions the lysosomal membranes may break down and the lysosomes are then real suicide pills for the cell. In medicine the lysosomes are of interest in many areas. There are a number of hereditary diseases with lysosomal enzyme deficiencies. This leads to accumulation of undigestible material in the lysosomes which swell and engorge the cell so as to prevent its proper functioning.

de Duve has not only a highly dominating role in lysosome research, he is also the discoverer of another cell component, the peroxisome, the function of which is still enigmatic but which may very well offer a story as fascinating as that of the lysosomes in the future.


The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.