Serial Endosymbiosis and Intelligent Design

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

It's very gratifying to see Lynn Margulis finally getting the recognition that she deserves. As the originator of the serial endosymbiosis theory (SET) for the origin of eukaryotes, Lynn's work provides an excellent example of how ID should (but currently doesn't) proceed. During the late 1960s, Lynn published a series of revolutionary papers on the evolution of eukaryotic cells, culminating in her landmark book Symbiosis and Cell Evolution, in which she carefully laid out the empirical evidence supporting the theory that mitochondria, choloroplasts, and undulapodia (eukaryotic cilia and flagella) were once free living bacteria (purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).

Her theory was greeted with contempt and scorn by almost all evolutionary biologists (sound familiar?), who believed at the time that all eukaryotic cellular organelles evolved by gradual elaboration of invaginations of the plasma membrane. But Lynn didn't give up, or continue to simply restate her original theory (sound familiar?). Instead, she continued to do extensive field and laboratory research, publishing hundreds of papers and dozens of books in which she presented the accumulating empirical evidence supporting her theory. With time, other researchers (encouraged by the success of her field and lab research) began to test her hypotheses themselves, and discovered yet more empirical evidence supporting her theory.

And so today, Lynn Margulis's SET has become the dominant theory explaining not only the origin of eukaryotes, but also the origin of evolutionary novelty at dozens of different levels in biology (see her book, Acquiring Genomes for a comprehensive review). So well accepted has her work become by evolutionary biologists that finally, after almost four decades, creationists and ID supporters have begun to attack her theories. As she said at our Darwin Day celebration at Cornell this past February, no greater affirmation of one's "having arrived" as a major theorist in evolutionary biology could be imagined.

The point here is that, if ID wants to become accepted as part of evolutionary biology in the same way that Lynn Margulis's SET has become accepted, then ID supporters have to do the same thing she did: get out in the field and get your hands dirty, and get into the lab and do the same thing. Her ideas were just as unorthodox and unacceptable in 1969 as ID is now. However, she didn't put all of her effort into public relations and political propaganda. No "Symbiosis Institute" dumped millions into the production of deliberately distorted press kits and one-sided propaganda films. Legions of self-appointed experts whose only exposure to biology was in high school classes or what they read on Answers in Genesis or Uncommon Descent bloviated on SET and declared themselves experts after a week of superficial study of articles on Wikipedia.

No, Lynn and her colleagues did the hard work of finding the empirical evidence that eventually carried the day and established her SET as one of the bedrock foundations now worthy enough of respect as to earn the ire of the creationists and IDers. Her ideas are still radical, and still raise the blood pressure of many evolutionary biologists. Her dismissal of the "modern evolutionary synthesis" in particular is not popular among many evolutionary biologists, who are largely still mired in paradigms that are at least four decades of out of date. She has said some things about the "modern synthesis" that have brought smiles to the faces of the creationist quote-miners. The difference between her and them is that they can't even begin to claim any credibility in science; their "work" is entirely parasitic on hers, and deserves nothing but contempt.

When the history of evolutionary biology in the 20th century is written (I hope to contribute to it myself, if I live long enough), the work of Lynn Margulis will rank right up there with the work of Fisher, Haldane, Wright, Dobzhansky, Mayr, Simpson, Stebbins, Gould, Lewontin, Kimura, Williams, Hamilton, Trivers, and the two Wilsons. And unless and until IDers decide that it's finally time to stop doing agitprop and start doing science, they and the creationists will at best be a trivial footnote.

Comments, criticisms, and suggestions are warmly welcomed!

--Allen

Evolution and Ethics: Is Morality Natural?

ANNOUNCEMENT: Seminar in History of Biology

AUTHOR: Allen MacNeill

COMMENTARY: Allen MacNeill

First the announcement, followed by a brief commentary:

I am very excited to announce the following course, to be offered this summer in the six-week summer session at Cornell University:

COURSE LISTING: BioEE 467/B&Soc 447/Hist 415/S&TS 447 Seminar in History of Biology

SEMESTER: Cornell Six-Week Summer Session, 06/24/08 to 07/31/08

COURSE TITLE: Evolution and Ethics: Is Morality Natural?

COURSE INSTRUCTOR: Allen MacNeill, Senior Lecturer in Ecology & Evolutionary Biology, Cornell University

COURSE DESCRIPTION: This seminar addresses, in historical perspective, controversies about the cultural, philosophical, and scientific implications of evolutionary biology. Discussions focus upon questions about gods, free will, foundations for ethics, meaning in life, and life after death. Readings range from Charles Darwin to the present (see reading list, below).

In 1871, Charles Darwin wrote in The Descent of Man "…the first foundation of the moral sense lies in the social instincts…and these instincts no doubt were primarily gained…through natural selection.” A century later, Edward O. Wilson, in
Sociobiology: The New Synthesis, wrote “The biologist…realizes that self-knowledge is constrained and shaped by…natural selection. This simple statement must be pursued to explain ethics and ethical philosophers….”

And so it has: in the past few years the publication of hypotheses for the evolution of ethics and “the moral sense” has become an explosive growth industry and a hot topic of debate. In this seminar course, we will take up this debate by considering two alternative hypotheses:

(1) that ethics can be derived directly from human evolutionary biology, or

(2) that ethics can only be derived from philosophical principles, which are not directly derivable from evolutionary biology.

Included in this debate will be an extended consideration of the hypothesis that the capacity for ethical behavior is an evolutionary adaptation that has evolved by natural selection among our primate ancestors. We will read from some of the leading authors on the subject, including Frans de Waal, Paul Farber, Marc Hauser, T. H. Huxley, Richard Joyce, Elliott Sober, and David Sloan Wilson. Our intent will be to sort out the various issues at play, and to come to clarity on how those issues can be integrated into a perspective of the interplay between philosophy and the natural sciences.

In addition to in-class discussions, course participants will have the opportunity to participate in online debates and discussions via the instructor's weblog. Students registered for the course will also have an opportunity to present their original research paper(s) to the class and to the general public via publication on the course weblog and via THE EVOLUTION LIST.

INTENDED AUDIENCE: This course is intended primarily for students in biology, history, philosophy, and science & technology studies. The approach will be interdisciplinary, and the format will consist of in-depth readings across the disciplines and discussion of the issues raised by such readings.

PREREQUISITES: None, although a knowledge of philosophical ethics, evolutionary psychology, and general evolutionary theory would be helpful.

DAYS, TIMES, & PLACES: The course will meet on Tuesday and Thursday evenings from 6:00 to 9:00 PM in Mudd Hall, Room 409 (The Whittaker Seminar Room), beginning on Tuesday 24 June 2008 and ending on Thursday 31 July 2008. We will also have an end-of-course picnic on Friday 25 July 2008.

CREDIT & GRADES: The course will be offered for 4 hours of credit, regardless of which course listing students choose to register for. Unless otherwise noted, course credit in BioEE 467/B&Soc 447 can be used to fulfill biology/science distribution requirements and Hist 415/S&TS 447 can be used to fulfill humanities distribution requirements (check with your college registrar's office for more information). Letter grades for this course will be based on the quality of written work on original research papers written by students, plus participation in class discussion.

COURSE ENROLLMENT & REGISTRATION: All participants must be registered in the Cornell Six-Week Summer Session to attend class meetings and receive credit for the course (click here for for more information and to enroll for this course). Registration will be limited to the first 18 students who enroll for credit.

REQUIRED TEXTS (all texts will be available at The Cornell Store):

de Waal, Frans (2006) Primates and philosophers: How morality evolved. Princeton University Press, Princeton, NJ, ISBN #0691124477, $22.95 (hardcover), 230 pages.

Farber, Paul (1998) The temptations of evolutionary ethics. University of California Press, Berkeley, CA, ISBN # 0520213696, $25.00 (paperback). 224 pages.

Hauser, Marc (2006) Moral minds: How nature designed our universal sense of right and wrong. Ecco/Harper Collins, New York NY, ISBN #0060780703, $27.95 (hardcover), 512 pages.

Huxley, T. H. (2004). Evolution and ethics & science and morals. Prometheus Books, Amherst, NY, ISBN #159102126X, $13.00 (paperback), 151 pages. Available free online here.

Joyce, Richard (2007) The evolution of morality. MIT Press, Cambridge, MA, ISBN #0262600722, $18.00 (paperback), 288 pages.

Sober, Elliot and Wilson, David Sloan (1999) Unto others: The evolution and psychology of unselfish behavior. Harvard University Press, Cambridge, MA, ISBN #0674930479, $22.50 (paperback), 416 pages.

OPTIONAL TEXTS:
(all texts will be available at The Cornell Store)

Darwin, Charles (E. O. Wilson, ed.) (2006) From So Simple a Beginning: Darwin's Four Great Books. W. W. Norton, New York, NY, ISBN #0393061345, $39.95 (hardcover), 1,706 pages.

Dawkins, Richard (2006) The selfish gene: Thirtieth anniversary edition. Oxford University Press, Oxford, UK, ISBN # 0199291152, $16.95 (paperback), 384 pages.

Dennett, Daniel (1996) Darwin's dangerous idea: Evolution and the meanings of life. Simon & Schuster, New York, NY, ISBN #068482471X, $16.00 (paperback), 586 pages.

Katz, Leonard (ed.) (2000). Evolutionary origins of morality. Imprint Academic, Charlottesville, VA, ISBN # 090784507X, $29.90 (paperback). 352 pages.

MacKinnon, Barbara (2006) Ethics: Theory and contemporary issues. Wadsworth, Boston , MA, ISBN #0495007161, $95.95 (paperback), 504 pages.

Ridley, Matt (1998) The origins of virtue: Human instincts and the evolution of cooperation. Penguin, New York, NY, ISBN #0140264450, $15.00 (paperback), 304 pages.

Wright, Robert (1995) The moral animal: Why we are the way we are: The new science of evolutionary psychology. Vintage, New York, NY, ISBN #0679763996, $15.95 (paperback), 496 pages.

COMMENTARY:

Perhaps the most common fallacy in philosophy and science is the tendency to assume that because something is “natural” (whatever that means) it must, ipso facto, be “good” (whatever that means) as well. In
last summer’s evolution and history of biology seminar, we talked about this tendency at some length. This summer I intend to make it the primary focus of our discussions.

From a historical standpoint, the tendency to conflate “is” and “ought” statements has been one of the ongoing arguments about the implications of evolution ever since Darwin first proposed his theory in 1859. Indeed, Darwin himself wrote much on the subject, especially in The Descent of Man, and Selection in Relation to Sex, his second most popular (and controversial) book. It has also been one of the sources of both confusion and controversy about evolution today. In particular, evolutionary psychologists (among whom I number myself) have struggled with this problem, not always successfully.

Like last summer and the summer before, this is a fascinating topic and I hope that enough people will sign up for the course with opposing viewpoints on this subject to make for a very interesting and stimulating summer seminar.

So, watch this space; when the course blog goes up, I will announce it here and provide links to all and sundry. And remember:

"… the ethical progress of society depends, not on imitating [nature], still less in running away from it, but in combating it." – T. H. Huxley, Evolution and Ethics (1893)

--Allen

Godwin's Darwin

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

There has recently been a huge controversy generated around the upcoming movie, "Expelled: No Intelligence Allowed", featuring Ben Stein. Rather than rehash most of this, I recommend that those who are not yet "up to speed" check out the related posts at The Panda's Thumb.

Ben Stein (a former speech writer for Richard Nixon) interviewed many evolutionary biologists for this film, including Will Provine and me. As the various threads at The Panda's Thumb indicate, he did so under patently false pretenses. Then, when some of the interviews contradicted the particular propaganda point he was trying to make, those "inconvenient" interviews were cut from the film (see here).

But that's not what I want to talk about in this blog. Ben Stein has been quoted repeatedly as saying that the underlying message in "Expelled" is "No Darwin, no Hitler". Yes, this is a particularly egregious example of Godwin's Law, but it is cited so often by creationists and ID supporters that I have prepared the following refutation (including citations, most of which I found here) Enjoy!

While Hitler uses the word "evolution" in Mein Kampf, it is clear that he is not referring to Darwin's theory. Indeed, he never mentions Darwin at all. In fact, a look at his writings reveals his sentiments on the subject to be those of an orthodox creationist.

Like a creationist, Hitler asserts fixity of kinds:

"The fox remains always a fox, the goose remains a goose, and the tiger will retain the character of a tiger." - Adolf Hitler, Mein Kampf, vol. ii, ch. xi.

Like a creationist, Hitler claims that God made man:

"For it was by the Will of God that men were made of a certain bodily shape, were given their natures and their faculties." - Adolf Hitler, Mein Kampf, vol. ii, ch. x.

Like a creationist, Hitler affirms that humans existed "from the very beginning", and could not have evolved from apes:

"From where do we get the right to believe, that from the very beginning Man was not what he is today? Looking at Nature tells us, that in the realm of plants and animals changes and developments happen. But nowhere inside a kind shows such a development as the breadth of the jump , as Man must supposedly have made, if he has developed from an ape-like state to what he is today." - Adolf Hitler, Hitler's Tabletalk (Tischgesprache im Fuhrerhauptquartier).

Like a creationist, Hitler believes that man was made in God's image, and in the expulsion from Eden:

"Whoever would dare to raise a profane hand against that highest image of God among His creatures would sin against the bountiful Creator of this marvel and would collaborate in the expulsion from Paradise." - Adolf Hitler, Mein Kampf, vol ii, ch. i.

Like a creationist, Hitler believes that:

"God ... sent [us] into this world with the commission to struggle for our daily bread." - Adolf Hitler, Mein Kampf, vol ii, ch. xiv.

Like a creationist, Hitler claims Jesus as his inspiration:

"My feeling as a Christian points me to my Lord and Savior as a fighter. It points me to the man who once in loneliness, surrounded only by a few followers, recognized these Jews for what they were and summoned men to fight against them." - Adolf Hitler, speech, April 12 1922, published in My New Order.

Like a creationist, Hitler despises secular schooling:

"Secular schools can never be tolerated because such schools have no religious instruction, and a general moral instruction without a religious foundation is built on air; consequently, all character training and religion must be derived from faith . . . we need believing people." - Adolf Hitler, Speech, April 26, 1933.

Hitler even goes so far as to claim that Creationism is what sets humans apart from the animals:

"The most marvelous proof of the superiority of Man, which puts man ahead of the animals, is the fact that he understands that there must be a Creator." - Adolf Hitler, Hitler's Tabletalk (Tischgesprache im Fuhrerhauptquartier).

Hitler does not mention evolution explicitly anywhere in Mein Kampf. However, after declaring the fixity of the fox, goose, and tiger, as quoted above, he goes on to talk of differences within species:

"[T]he various degrees of structural strength and active power, in the intelligence, efficiency, endurance, etc., with which the individual specimens are endowed." Mein Kampf, vol. ii, ch. xi.

So, like a creationist, there is some evolution he is prepared to concede -- evolution within species, or "microevolution", to which people like Phillip Johnson and Michael Behe have no objection. It is on the basis of the one part of evolutionary theory which creationists accept that Hitler tried to find a scientific basis for his racism and his program of eugenics.

Ergo, Hitler did not base his eugenic and genocidal policies on evolutionary theory, but rather on views that are very similar to those held by most creationists and many ID supporters.


Comments, criticisms, and suggestions are warmly welcomed!

--Allen

On the Problem of Pain

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

As some long-time visitors may be aware, I have not been able to update this blog for a long time. While part of this has been due to the press of other business, much of it has been due to two health problems, both of which have at their core what C. S. Lewis referred to as “the problem of pain.” Late last fall, and continuing until after the turn of the year, I suffered from a kidney stone. Then, in mid-January, my wife’s stepmother died of emphysema, and we drove 1,200 miles to be present at her funeral in Michigan. It was a hellish drive, through wind-driven lake-effect snow all the way from Jamestown to Toledo. I gripped the wheel with white knuckles and hunched my shoulders like a linebacker all the way.

The next day I awoke in agonizing pain, similar in quality to that produced by the passage of a kidney stone. But, unlike the kidney stone, the pain did not relent. It is still present, although finally it has begun to subside as the result of intensive physical therapy and the passage of time.

What kind of pain? Well, to be precise, it’s phantom pain. The cause (as far as anyone can figure out) is inflammation of the right lateral cervical nerve passing through a foramen between my sixth and seventh cervical vertebrae. To be precise, I have right lateral radial radiculopathy.

But that doesn’t describe what it feels like. Throughout most of the past two months it has felt like there is a cable of red-hot twisted steel running from the right side of the back of my neck, across the top of my shoulder and down the outside of my right arm to the middle three fingers of my right hand. This pain begins as soon as I wake up, and intensifies throughout the day until, after nightfall, it becomes overwhelming and the only thing I can do is take two oxycodone and lie down and wait for unconsciousness.

I describe all of this, not to elicit your sympathy, but to introduce “the problem of pain” from the standpoint of evolutionary biology. All of the rest of our senses have a physical referent: heat receptors sense heat, cold receptors cold, taste receptors sugars and ions and acids and bases and certain amino acids in our food, rods and cones sense the presence of light photons, etc. But pain receptors do not sense the presence of “pain.” No, “pain” is an “artificial sensation.” What pain receptors are adapted to sensing is cellular damage.

Why does pain exist? From an evolutionary standpoint, pain is “good for us”: in the past, those individuals who could feel pain would stop doing whatever it was they were doing that was causing the cellular damage that was triggering the pain, and therefore survived and reproduced more often than other individuals who did not feel pain so acutely. To be specific, individuals who had the cellular machinery to transform the chemical signs of cellular damage into action potentials in pain dendrites, and whose pain dendrites are connected to their central nervous systems in such a way as to cause changes in their behavior in such a way as to reduce such damage (and therefore reduce the amount of pain such damage causes) passed on to their offspring the genetic and developmental programs that produced the cellular machinery that made such responses possible.

But the problem with pain is that it doesn’t necessarily happen only when avoidable cellular damage is happening as the result of something we are doing. This is most obvious in the case of the two sources of pain that have crippled me for the past few months.

Kidney stone pain is widely recognized as one of the most intense forms of pain that we can experience. I know several women who have had babies and kidney stones, and they all assert that kidney stone pain is much, much worse. I know a couple of men who have had massive heart attacks and kidney stones, and they assert that kidney stone pain is worse (yes, the terror of having a heart attack is horrific as well, but terror is not pain, although the two are evolutionarily related). I have myself suffered various injuries, from chopping a wedge out of my shin with a macheté to breaking a bone to rather serious burns (especially on my fingertips) and none of them comes close to the pain of passing a kidney stone.

Yet, two questions immediately present themselves: why should passing a kidney stone produce pain at all, and why is the pain so intense? It is only via modern medicine that we understand what causes kidney stones; the most common cause is a familial tendency to produce very concentrated urine, combined with a genetically inherited defect in a couple of enzymes that in most people prevent the precipitation of calcium oxalate and/or uric acid crystals in the lumen of the pelvis of the kidney. Furthermore, the behavioral and chemical events that predispose one to forming kidney stones are so “detached” from the process of passing a kidney stone that they almost certainly cannot cause a person to stop doing whatever it was that resulted in the formation of the stones themselves.

Also, it is a general principle of the evolution of sensory systems that if damage to a particular tissue is virtually universally fatal, no pain receptors are present in that tissue. For example, there are no pain receptors in brain tissue; as my friend Will Provine can attest, people can probe around in your exposed brain tissue without causing the slightest amount of pain (he was fully conscious during the surgery in which his brain tumor was removed). You can literally stick an ice pick into a human brain and swish it around, and although it will cause massive neurological deficits, it will not cause any pain (this is how “ice pick” lobotomies used to be performed, generally without anaesthesia).

So why are there so many exquisitely sensitive pain receptors in the lining of our ureters? It would seem to me that damage to something as deeply embedded in the body as a ureter would almost certainly be fatal, and so why are there pain receptors in them? And why is the pain so extravagantly severe?

One possibility is that the pain receptors are there because people who did not have them would contort or twist their bodies so much during vigorous or violent activity that they might rupture or tear their ureters, resulting in their death. However, that doesn’t explain why a kidney stone the size of a grain of sand should cause so much pain passing down a ureter with the inside diameter of a pencil lead.

And so on to my cervical radiculopathy. In the case of my right arm pain (which at times has been nearly as bad as passing a kidney stone), there isn’t any damage happening in my arm at all. Rather, the pain is the result of physical stimulation of the pain fibers in the seventh cervical nerve as it passes through the foramen between the vertebrae. That is, there is absolutely no connection between anything I am doing (or have done) with my right arm that has caused cellular damage in my arm, which has then been transformed into action potentials in the pain dendrites going to my central nervous system.

That this is the case is encapsulated in the term “radiculopathy.” What is causing the pain is cellular damage in the “root” (or “radicle”) of the seventh cervical nerve, rather than cellular damage in my right arm. In the beginning stages, this damage was so severe that I also had fasciculations in my arm, shoulder, pectorals, rhomboid, and trapezious muscles. That is, these muscles twitched and contracted spasmotically and uncontrollably, as “phantom” nerve impulses generated in the inflamed motor neurons of the seventh cervical nerve stimulated those muscles to contract.

And so I had both “phantom” pain and “phantom” muscle twitching, for months. Did any of this convince me that I should no longer drive out to Michigan with my hands clenched to the wheel and my shoulders hunched. You bet it did, but that can’t possibly explain how generations of my ancestors could have evolved an anatomical or physiological arrangement that is so prone to such derangements. For, as it turns out, cervical radiculopathy is one of the two most common forms (the other being lumbar radiculopathy, or “low back pain”, which I – along with nearly all of you – have suffered from repeatedly).

Once again, is there any “reason” for all of this extravagant pain? C. S. Lewis, in The Problem of Pain, used an analogy with sculpting stone: that each “blow” of the pain we all feel is what “hammers” us into shape as people. That is, God gives us the ability to experience pain as a means of making us better people.

Well, what about “meaningless” pain, such as that which we experience in the case of passing a kidney stone or suffering from cervical radiculopathy? Believe me, I honestly don’t think either of these has made me a “better” person. On the contrary, they have made me a more exhausted, more tentative, more fearful person. Every hint of the return of such pain makes me cringe, and so only if God wants me to be a more exhausted, more tentative, more fearful person who cringes at the slightest hint of a kidney stone or returning arm pain does such an explanation make sense.

What makes more sense to me is that such pain is an unintentional side effect of a system that is otherwise adaptive. In a world in which cellular damage is an ever-present possibility, pain receptors have clear adaptive value. And if, under certain conditions, they produce “unnecessary” pain, that’s the price we pay for being adaptive.

For moral reasons, I tend to favor the evolutionary explanation. That isn’t to say that one can’t use unnecessary pain; I have consciously tied the pain in my arm to an exercise and weight loss program, which seems to be working so far (although I worry about what will happen when and if the pain in my arm finally goes away). But this is the result of a conscious and deliberate process on my part, to harness what would otherwise be a completely meaningless affliction to something I would like to accomplish, but have had difficulty doing in the past. Maybe that’s what Lewis is really saying as well, although I suspect not.

So, does the experience of pain make us “better people?” Only if we make it so, and then it isn’t the pain that is doing it, but rather our own determination to do so, which isn’t “natural” in any way.

Here’s wishing you all a happy (and generally pain free) New Year!

Comments, criticisms, and suggestions are warmly welcomed!

--Allen

RM & NS: The Creationist and ID Strawman

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

Creationists and supporters of Intelligent Design Theory ("IDers") are fond of erecting a strawman in place of evolutionary theory, one that they can then dismantle and point to as "proof" that their "theories" are superior. Perhaps the most egregious such strawman is encapsulated in the phrase "RM & NS". Short for "random mutation and natural selection", RM & NS is held up by creationists and IDers as the core of evolutionary biology, and are then attacked as insufficient to explain the diversity of life and (in the case of some IDers) its origin and evolution as well.

Evolutionary biologists know that this is a classical "strawman" argument, because we know that evolution is not simply reducible to "random mutation and natural selection" alone. Indeed, Darwin himself proposed that natural selection was the best explanation for the origin of adaptations, and that natural selection itself was an outcome that necessarily arises from three prerequisites:
• variation (between individuals in populations),
• inheritance (of traits from parents to offspring), and
• fecundity (reproduction resulting in more offspring than necessary for replacement).
Given these prerequisites, some individuals survive and reproduce more often than others, and hence their characteristics become more common in their populations over time.

As I have alread pointed out in an earlier post, the real creative factor in evolution isn't natural selection per se, it's the source(s) of variation that natural selection "preserves" from generation to generation. According to the creationists and IDers, the only source of such variation is "random mutations", and so there simply isn't enough variation to provide the raw material for evolutionary change.

In my earlier post on the "engines of evolution" I promised a list of the real sources of variation that provide the raw material for evolutionary change. It's taken me a while, but here it is. This list includes "random mutation,' of course, but also 46 other sources of variation in either the genotypes or phenotypes of living organisms. Note that the list is not necessarily exhaustive, nor are any of the entries in the list necessarily limited to the level of structure or function under which they are listed. On the contrary, this is clearly a list of the minimum sources of variation between individuals in populations. A comprehensive list would almost certainly include hundreds (and possibly thousands) of more detailed processes. Also, the list includes processes that change either genotypes or phenotypes or both, but does not include processes that are combinations of other processes in the list, again implying that a comprehensive listing would be much longer and more detailed. Anyway, here it is, listed according to level of structure and function:

Sources of Heritable Variation (both genotypic and phenotypic) Among Individuals in Populations:

Gene Structure (in DNA)

1) single point mutations

2) deletion and insertion (“frame shift”) mutations

3) inversion and translocation mutations

Gene Expression in Prokaryotes

4) changes in promoter or terminator sequences (increasing or decreasing binding)

5) changes in repressor binding (in prokaryotes); increasing or decreasing binding to operator sites

6) changes in repressor binding (in prokaryotes); increasing or decreasing binding to inducers

7) changes in repressor binding (in prokaryotes); increasing or decreasing binding to corepressors

Gene Expression in Eukaryotes

8) changes in activation factor function in eukaryotes (increasing or decreasing binding to promoters)

9) changes in intron length, location, and/or editing by changes in specificity of SNRPs

10) changes in interference/antisense RNA regulation (increasing or decreasing binding to sense RNAs)

Gene Interactions

11) changes in substrates or products of biochemical pathways

12) addition or removal of gene products (especially enzymes) from biochemical pathways

13) splitting or combining of biochemical pathways

14) addition or alteration of pleiotropic effects, especially in response to changes in other genes/traits

Eukaryotic Chromosome Structure

15) gene duplication within chromosomes

16) gene duplication in multiple chromosomes

17) inversions involving one or more genes in one chromosome

18) translocations involving one or more genes between two or more chromosomes

19) deletion/insertion of one or more genes via transposons

20) fusion of two or more chromosomes or chromosome fragments

21) fission of one chromosome into two or more fragments

22) changes in chromosome number via nondisjunction (aneuploidy)

23) changes in chromosome number via autopolyploidy (especially in plants)

24) changes in chromosome number via allopolyploidy (especially in plants)

Eukaryotic Chromosome Function

25) changes in regulation of multiple genes in a chromosome as a result of the foregoing structural changes

26) changes in gene expression as result of DNA methylation

27) changes in gene expression as result of changes in DNA-histone binding

Genetic Recombination

28) the exchange of non-identical genetic material between two or more individuals (i.e. sex)

29) lateral gene transfer via plasmids and episomes (especially in prokaryotes)

30) crossing-over (reciprocal and non-reciprocal) between sister chromatids in meiosis

31) crossing-over (non-reciprocal) between sister chromatids in mitosis

32) Mendelian independent assortment during meiosis

33) hybridization

Genome Structure and Function

34) genome reorganization and/or reintegration

35) partial or complete genome duplication

36) partial or complete genome fusion

Development (among multicellular eukaryotes, especially animals)

37) changes in tempo and timing of gene regulation, especially in eukaryotes

38) changes in homeotic gene regulation in eukaryotes

39) genetic imprinting, especially via hormone-mediated DNA methylation

Symbiosis

40) partial or complete endosymbiosis

41) partial or complete incorporation of unrelated organisms as part of developmental pathways (especially larval forms)

42) changes in presence or absence of mutualists, commensals, and/or parasites

Behavior/Neurobiology

43) changes in behavioral anatomy, histology, and/or physiology in response to changes in biotic community

44) changes in behavioral anatomy, histology, and/or physiology in response to changes in abiotic environment

45) learning (including effects of use and disuse)

Physiological Ecology

46) changes in anatomy, histology, and/or physiology in response to changes in biotic community

47) changes in anatomy, histology, and/or physiology in response to changes in abiotic environment

So, next time you hear or read a creationist or IDer cite "RM & NS" as the sole explanation for evolutionary change, point out to them and everyone else that there are at least 47 different sources of variation (including "random mutations"), and at least three different processes that result from them: natural selection, sexual selection, and random genetic drift.

Comments, criticisms, and suggestions (especially additional items for the list) are warmly welcomed!

--Allen

Jerry Fodor on Why Pigs Don't Have Wings

AUTHOR: Jerry Fodor

SOURCE: Why Pigs Don't Have Wings
(London Review of Books 29(20):19-22, 18 October 2007)

COMMENTARY: Allen MacNeill

Cognitive scientist and frequent critic of evolutionary psychology, Jerry Fodor, has a long article in the most recent issue of the London Review of Books in which he attacks what most people think of as the core of evolutionary biology: natural selection and adaptations. Fodor has attacked evolutionary psychology before, and spends most of his ammunition attacking it again in this article. However, he now has bigger (Darwin) fish in his sights: "Darwinism" – yes, he uses exactly the same term as the one so favored by creationists and ID theorists. Indeed, the article under discussion here has been lauded by prominent young-Earth creationist and ID theorist, Paul Nelson.

This isn't the first time left-leaning philosophers such as Fodor have joined forces with creationists, nor will it be the last. However, what I would like to discuss (in later posts) is Fodor's serious misrepresentations of evolutionary biology in general, and evolutionary psychology in particular. But, before I do that, you should go and read Why Pigs Don't Have Wings, paying special attention to Fodor's criticisms of natural selection and its role in evolutionary biology. And while you're at it, you might check out this essay by Fodor as well: Against Darwinism.

Then come back here (in a day or two), and I'll get started fisking both articles.

--Allen

Darwin Day in America

TITLE: Darwin Day in America

AUTHOR: John West

COMMENTARY: Allen MacNeill:

Meanwhile, back at the Discovery Institute/Neo-Creationism Propaganda Ministry, John West has published a much-balleyhooed book that makes the case that virtually all of society’s ills can be traced to poor old Charles Darwin and his latter-day minions. I’m going to force myself to read Darwin Day in America, not because I expect to find any new arguments or evidence in it (IDers like John West and his fellow creationists aren’t interested in new ideas, and are positively repelled by evidence, especially if it involves entering a lab or going out into the field), but because I want to be prepared for the mini-tidal wave of disinformation that it might generate vis-a-vis the pernicious effects of “Darwinism” on society.

This despite the fact that (according to the DI/NCPM’s favorite statistics), less than 10% of Americans believe in non-theistic evolution, and even fewer are atheists. Two thoughts immediately come to mind:

• Shouldn’t the prisons be stuffed with evolutionary biologists and atheists (i.e. greater than 10% of the prison population), and

•Isn’t this in a perverse way empirical evidence that evolutionary biologists and atheists have an influence on society out of all proportion to our numbers?

Ah, but that would imply a direct contradition in logic: something that the DI/NCPM is, of course, perfectly comfortable with, but which strikes the <10% of the population that attempts to be rational as…well, irrational.

So it goes…

--Allen