Friday, March 27, 2009

The Modern Evolutionary Synthesis


In the years following the publication of the Origin of Species in 1859, Charles Darwin’s theory of evolution became widely accepted throughout most of the scientific community. Other naturalists, including such notable figures as Charles Lyell, Joseph Hooker, Asa Grey, and especially Thomas Henry Huxley quickly came to accept Darwin’s assertion that what he called “descent with modification” had in fact occurred.

However, scientific opinion was much more divided on the subject of natural selection, Darwin’s proposed mechanism for evolution. To understand why, consider the three preconditions Darwin proposed as the necessary prerequisites for natural selection. They are:

• Variation: There must be significant differences between the members of an evolving population. These variations need not be extreme, as illustrated by the relatively large changes that animal and plant breeders have accomplished, using relatively slight differences in physical appearance and behavior.

• Inheritance: The distinct variations noted above must be heritable from parents to offspring.

• Fecundity: Living organisms have a tendency to produce more offspring than can possibly survive. Among those individuals that do survive, those that also reproduce pass on to their offspring whatever characteristics made it possible for them to survive and reproduce.

Given these prerequisites, then the natural outcome is:

• Non-Random, Unequal Survival and Reproduction: Survival and reproduction are almost never random. Individuals survive and successfully reproduce because of their characteristics. It is these demographic characteristics that form the basis for evolutionary adaptations.

Considering these four ideas, we can ask the question, “What is the ultimate source of the new characteristics that are preserved and promulgated from generation to generation?” The answer is, “The ultimate source of all new characteristics is the ‘engines of variation’ – that is, those processes that produce the natural variation between individuals that Darwin emphasized as being absolutely necessary for the operation of natural selection". In a nutshell:
Variation between individuals is the key to evolution by natural selection.

However, in the Origin, Darwin summarized his presentation of his views on variation with this statement:
"Our ignorance of the laws of variation is profound."

Neither Darwin nor any of his contemporaries (that he knew of) had a coherent theory of heredity or variation. However, this was not an insuperable obstacle to Darwin. Instead of giving up his argument, he simply accepted as a given that many important traits of animals and plants are heritable (pointing again to the observable facts of inheritance in domesticated animals and plants). He also proposed that, although he had no explanation of how they arose, variations among the members of a species do indeed occur, and can provide the raw material for natural selection.

There were therefore two reasons why Darwin’s proposed mechanism of natural selection was not widely accepted, even among scientists:

• Many of Darwin's contemporaries (and, in fact, Darwin himself) believed in Lamark's assertion that acquired characteristics could be inherited through use and disuse. This process directly contradicts the blind and purposeless process of natural selection, and therefore held the door open for purpose in evolution.

• The consensus among naturalists was that inheritance worked by "blending" the characteristics of parents, which would cause any incipient adaptations to be diluted out of existence.


This second objection to Darwin's mechanism of natural selection was almost fatal to his theory. In an influential review of the Origin, written in 1867 by Fleeming Jenkin (a very well-respected English engineer and designer of the first trans-Atlantic telegraph cable), Jenkin pointed out that blending inheritance would eliminate variation within a few generations:
“However slow the rate of variation might be, even though it were only one part in a thousand per twenty or two thousand generations, yet if it were constant or erratic we might believe that, in untold time, it would lead to untold distance; but if in every case we find that deviation from an average individual can be rapidly effected at first, and that the rate of deviation steadily diminishes till it reaches an almost imperceptible amount, then we are as much entitled to assume a limit to the possible deviation as we are to the progress of a cannon-ball from a knowledge of the law of diminution in its speed.”

If (as most naturalists of Darwin's time believed) all traits were blended from generation to generation, all of the distinctiveness of each variation would be lost and the population would remain essentially unchanged. Darwin got around this objection by proposing that large numbers of new variations (i.e. mutations) occur with each new generation. He called these “continuous variations,” but did not propose a mechanism for how they might be produced.

Mendelian Genetics


However, at about the same time that Darwin was working out his ideas on natural selection and evolution, Gregor Mendel was working out a revolutionary new theory of genetics. Mendel was born in 1822 in Moravia, a province of the Austrian Empire (now part of the Czech Republic). Because he was a peasant's son, Mendel was expected to return to the family farm after finishing his education. However, Mendel was not satisfied with all that he had learned. The university, instead of answering his questions, instilled in him an insatiable curiosity about nature.

Mendel observed that some offspring of some organisms had traits that were similar to only one parent, rather than being intermediate between both. He explained this phenomenon by assuming that heredity was determined by tiny, discrete “particles of inheritance” that were passed from the parents to the offspring via the reproductive cells. This would explain how some traits could remain unblended in the next generation.

Such thinking stemmed from Mendel's university education in physics. Ever since Isaac Newton revolutionized the science of physics, all of nature has been considered by physicists to be subject to "natural laws" based on the existence of and interactions between small, indestructible particles of matter. The goal of a physicist is to learn about the laws that determine the behavior of the particles, and to use such laws to predict the behavior of material objects subject to natural forces, such as gravity. Central to this intellectual tradition is the idea that an investigator can often work out these laws through careful observation and experimentation.


Mendel believed that these same methods could be used to study inheritance in living things. Having become established as a monk in an Augustinian monastery in the city of Brünn (now Brno, in the Czech Republic). Over a period of seven years he studied the inheritance of various characters in garden peas. In his landmark paper, "Experiments in Plant Hybridization” ("Versuche über Pflanzen-hybriden" in the original German, published in 1866), Mendel tells how he used the garden pea plant to study the laws of heredity.

Mendel's techniques differed from those of other investigators in three ways:

(1) He looked at one trait at a time;

(2) He followed this trait from generation to generation over eight years; and

(3) He used larger numbers of organisms in his studies. At the end of his experiments, he had carefully observed over 29,000 plants.

In his most famous set of experiments, Mendel studied 22 varieties of plants of the same species: the common garden pea (Pisum sativum). He studied a total of seven different traits, each with two alternative forms, including seed shape, color, and seed coat color; pod shape and color, flower position on the stem, and stem height.

For example, in one series of experiments, Mendel crossed pea plants that produced round seeds with pea plants that produced wrinkled seeds, and then observed what kinds of seeds were produced as the result of this cross over two generations.


Mendel observed that the two forms of each of these traits did not blend with each other. Among the offspring of the first cross, only one form of each trait showed up; the alternative form seemed to be lost. For example, when peas with round seeds were crossed with peas with wrinkled seeds, the first generation of offspring only produced round seeds (as shown in the Punnett square, above).


However, in the second generation, the seemingly lost form showed up again. In our previous example, wrinkled seeds showed up again in the second generation of offspring, comprising approximately one-fourth of all of the offspring of that cross. Mendel explained this result by saying that the lost form of each trait was actually latent or cancelled by the expressed form. He called the prevailing form of a trait dominant and the latent form of a trait recessive. Mendel's definitions of dominance and recessiveness are sometimes called Mendel's Law of Dominance:
Dominant traits mask the appearance of recessive traits whenever dominant and recessive traits are combined in one individual.

In our example, the gene for seed shape has two different forms. One form produces round seeds; the other form produces wrinkled seeds. Different gene forms that produce different forms of a trait are called alleles (from the Greek allos for "other"). In this example, the allele that codes for round seeds is dominant to the allele that codes for wrinkled seeds.

Mendel observed that dominant and recessive forms of a trait did not become blended. Instead, the recessive form of the trait reappeared in an unaltered form in the second generation. Based on this observation, Mendel formulated his Law of Segregation, which states that:
The different forms of a trait remain separate and unblended from generation to generation.

Mendel was so convinced of the validity of his conclusions that his subsequent work with other plants, some of which failed to support his hypothesis, did not discourage him. As he wrote in 1866,
"It requires indeed some courage to undertake a labour of such far-reaching extent; this appears, however, to be the only right way by which we can finally reach the solution of a question the importance of which cannot be overestimated in connection with the history of the evolution of organic forms."

Late in his life, Mendel's time was mostly spent fighting political battles for the monastery and peasants of his village. In his lifetime, Mendel witnessed a complete change in his homeland. In his later years, the focus was no longer on agricultural advances but on political advances. The rise of the Hapsburg dynasty and the consolidation of the Austro-Hungarian Empire forced different values on the people. The days of intellectual freedom, when a monk could study agriculture in a monastery garden without interference by the government, were drawing to a close. Shortly before his death in 1884, Mendel said to a future abbot of the monastery:
"Though I have suffered some bitter moments in my life, I must thankfully admit that most of it has been pleasant and good. My scientific work has brought me a great deal of satisfaction, and I am convinced that it will not be long before the whole world acknowledges it."

Evolution by Mutation

Mendel's belief that his work would eventually be recognized was not mistaken. In 1900, only fourteen years after his death, his work was simultaneously rediscovered by three different geneticists – Carl Correns, Erich Tschermak, and Hugo de Vries – working in three different countries. They each realized that Mendel's particulate theory of inheritance fit patterns of inheritance they were observing.

It is interesting to speculate what Darwin would have thought had he known about Mendel's work. Genes that did not blend in each generation were the answer to Darwin's dilemma, and could have put him onto the right track as early as 1866, the year Mendel's most important paper was published. A copy of the journal containing Mendel's paper was found in Darwin's library at Down House, but it had apparently not been opened or read.

There is an even deeper irony: the rediscovery of Mendel's work led geneticists to reject natural selection as the mechanism for evolution, in favor of mutations. Hugo de Vries, one of the rediscoverers of Mendel's work, proposed that mutations (i.e. changes in the phenotype of an organism, occurring in just one generation) were the primary "engine" of evolutionary change. De Vries did his pioneering work in genetics using the evening primrose (Oenothera lamarkiana), which is now known for having sudden, large mutations (called "macromutations") in its overall phenotype.


De Vries argued that these kinds of mutations were the basis for the changes in phenotype to which Darwin referred in the Origin of Species, and that therefore natural selection was neither necessary nor likely as a cause of evolutionary change. Indeed, DeVries asserted that macromutations were responsible for the "origin of species", and that natural selection played little or no role at all in this process. The mutational theory of evolution promoted by DeVries and other pioneering Mendelian geneticists was accepted by most of the prominent geneticists at the turn of the century, and led to widespread public testimonials that "Darwinism was dead":
“Today, at the dawn of the new century, nothing is more certain than that Darwinism has lost its prestige among men of science. It has seen its day and will soon be reckoned a thing of the past. A few decades hence when people will look back upon the history of the doctrine of Descent, they will confess that the years between 1860 and 1880 were in many respects a time of carnival; and the enthusiasm which at that time took possession of the devotees of natural science will appear to them as the excitement attending some mad revel.” - Eberhard Dennert, At the Deathbed of Darwinism (1904)


The Hardy-Weinberg-Castle Genetic Equilibrium Law

However, like Mark Twain, reports of Darwinism's death were "greatly exaggerated." In the second decade of the 20th century, three other researchers, again working separately and mostly unbeknownst to each other, proposed a theory that would eventually lead to the re-establishment of natural selection as the prime mover of evolution.


G. H. Hardy, Wilhelm Weinberg, and William Castle all proposed a mathematical theory that describes in detail the conditions that must be met for evolution to not occur. This theory, often called the Hardy-Weinberg Equilibrium Law lays out the conditions that must be met for there to be no changes in the allele frequency in a population of interbreeding organisms over time.

Recall Mendel's definition of alleles: different forms of the same gene that produce different variations of a trait. In the context of evolution, alleles are what code for the phenotypes that change over time in an evolving population. Therefore, changes in the alleles present in a population will produce changes in the phenotypes present in that population. This, in a nutshell, is the genetic definition of evolution:
Evolution is the result of changes in allele frequency in a population over time.

What Hardy, Weinberg, and Castle all realized is that for allele frequencies to not change in a population, five conditions must be met:

There must be no mutations (i.e. alleles cannot change into other, different alleles).

There must be no gene flow (i.e. individuals cannot enter or leave the population).

The population must be very large (i.e. random accidents cannot significantly alter allele frequences).

Survival must be random (i.e. there can be no natural selection).

Reproduction must also be random (i.e. there can be no sexual selection).

Notice that the Hardy-Weinberg Equilibrium Law seems to say only that there are conditions under which evolution can't happen. Aren't we interested in those conditions in which evolution can happen? Yes, but notice what the Hardy-Weinberg Equilibrium Law gives us: it outlines exactly what processes are essential to prevent evolution, and therefore by negation shows us how evolution can happen.

That is, if any of the five conditions for maintaining a Hardy-Weinberg equilibrium are not met, then evolution must be occurring. And, of course, virtually none of these conditions is ever permanently met in any known natural population of organisms:

• Mutations occur at a slow but steady rate in all known populations.

• Many organisms, especially animals, enter (immigration) and leave (emigration) populations.

• Most populations are not large enough to be unaffected by random changes in allele frequencies.

• Survival is virtually never random.

• Reproduction in organisms that can choose their mates is also virtually never random.

Therefore, according to the Hardy-Weinberg Equilibrium Law, evolution (defined as changes in allele frequencies over time) must be occurring in virtually every population of living organisms. In other words,
Evolution is as ubiquitous and inescapable as gravity.


THE MODERN EVOLUTIONARY SYNTHESIS

The Hardy-Weinberg Equilibrium Law provided more than just a "null hypothesis" for genetic evolution. It also provided a mathematical basis for a much more comprehensive theory of evolution now known as the modern evolutionary synthesis (often called "neo-darwinism"). During the 1930s and 40s, R. A. Fisher, J. B. S. Haldane, Sewall Wright, and Theodosius Dobzhansky developed mathematical models for fitness, selection, and other evolutionary processes. These models were then applied to demographic data derived from artificial and natural populations of organisms in a rigorous (and ongoing) series of empirical tests of the validity of the neo-darwinian model for genetic evolution. As a result of their work, Darwin's theories of natural and sexual selection were combined with Mendelian genetics, biometry and statistics, demography, paleontology, comparative anatomy, botany, and (more recently) molecular genetics and ethology to produce a "grand unified theory" of the origin and evolution of life on Earth.

The Genetical Theory of Natural Selection


Ronald Aylmer Fisher built on the pioneering theoretical work of Hardy, Weinberg, and Castle by providing mathematical models that further undermined the Mendelian geneticist's theory of evolution via mutation. He did this by showing that continuous variation could provide the basis for natural selection as proposed by Darwin. In his most important work, The Genetical Theory of Natural Selection (published in 1930) Fisher showed that traits characterized by continuous variation (i.e. those that approximate a normal, or bell-shaped, distribution) were both common and could provide all the raw material necessary for Darwinian natural selection. This is because such traits, although being continuous in populations, do not blend from parents to offspring. Instead, as Mendel first showed, they are produced by unblending "particles" of inheritance (i.e. Mendelian "genes"). In other words,
Mendelian inheritance conserves, rather than eventually destroying, the genetic variation that exists in natural populations.

Fisher is perhaps best known for what he called the Fundamental Theorem of Natural Selection. Using a series of essentially mathematical arguments, Fisher showed that the rate of change via natural selection was a direct function of the amount of variation in a population. That is,
The more variation among alleles that exists in a population, the faster natural selection can causes changes in the allele frequencies in that population.

Conversely, the less variation among alleles that exists in a population, the slower natural selection can causes changes in the allele frequencies in that population.

R. A. Fisher's work formed the basis for a mathematical theory of evolution in which the process of natural selection is modeled mathematically in the same way that Newton modeled the force of gravity. Indeed, Fisher pointed out several times that the mathematics of natural selection were similar in many ways to such physical models as the ideal gas laws and the second law of thermodynamics. According to his mathematical models, alleles that were positively selected would increase in frequency in populations in much the same was as gas molecules spread out in an expanding balloon.

To many evolutionary biologists, this meant that natural selection would inevitably result in "fixation" of alleles that were not selected against. That is,
Any allele that results in increased survival and reproduction should, if given enough time, eventually become the only allele for that particular trait in a particular population.

This presented a problem to evolutionary biologists that was almost as severe as the “mutationism” of the early Mendelians. It implied that the inevitable result of natural selection would be the eventual elimination of all non-adaptive variation in natural populations. This would then cause natural selection to grind to a halt (or to become reduced to essentially the rate of production of new genetic mutations, which is slow in the extreme, much slower than the observed rate of evolution). Fisher suggested that constant environmental change would cause different alleles to be selected for and against, and that therefore fixation might not ever happen. However, this argument seemed to be "tacked on" to his argument for the relationship between the amount of variation in populations and the speed of evolutionary change via natural selection.

Adaptive Landscapes and Genetic Drift


A solution to this problem was provided by Sewall Wright, who discovered a process that has eventually become known as genetic drift. Wright, who worked primarily with domesticated animals in controlled breeding programs, proposed that in small populations of organisms, random sampling errors could cause significant changes in allele frequencies in those populations. He showed mathematically that the smaller a population was, the greater the effect of such random events on its allele frequencies. In other words,
Evolution can proceed by at least three primary mechanisms: natural selection, sexual selection, and random genetic drift.

Wright's discovery of genetic drift solved the problem that Fisher's Fundamental Theorem posed: how can natural selection be prevented from shutting itself down as the result of fixation? Wright proposed that allele frequencies could be visualized as forming what he came to call an "adaptive landscape". In an adaptive landscape, allele frequencies formed a series of hills and valleys, in which the top of a hill represented the highest an allele frequency could reach via natural selection. According to Fisher, there is an iron-clad rule operating here: if an allele is on a slope, it can only go up the slope via natural selection.


But this means "you can't get there from here": if a trait is at the top of one adaptive peak, it can't go down through a valley to get to the top of another, even higher (i.e. more adaptive) peak. What Wright showed was that "you can get there from here" if you drift there. That is, if a population becomes very small, it is possible for it to "drift" from one adaptive peak to another, without sliding down into the valley in between. This means that natural selection doesn't get "stuck"; populations at one adaptive peak can make it to another, even higher adaptive peak, so long as they drift randomly to it.

The Causes of Evolution


John Burdon Sanderson Haldane (usually referred to as J. B. S. Haldane) solidified the revolution in theoretical population genetics begun by Hardy, Weinberg, Castle, Fisher, and Wright. In his most important book, The Causes of Evolution, published in 1932, he showed that genetic mutations could provide the raw material for Darwinian natural selection. Furthermore, he showed mathematically that such mutations could do this even when their frequency in a population was initially so low that they would be "invisible" to statistical analysis. He also showed how dominance could evolve in populations by means of natural selection, even when the original expression of an allele was initially recessive.

Haldane is also remembered for two quips that are often repeated by evolutionary biologists. The first concerns a question posed to him by an Anglican minister, who asked him (supposedly at a dinner party) what his study of nature had led him to conclude about the principle concern of the Creator. Without batting an eyelash, Haldane replied: "An inordinate fondness for beetles," referring to the fact that there are more species of beetles on Earth than any other kind of organism.

During another conversation (supposedly in a pub), Haldane was confronted with the observation that natural selection should result in pure selfishness on the part of individuals, and therefore no one should be willing to risk his own life to save another. To this Haldane replied,
"I would be willing to risk my life to save two brothers or eight cousins."

This quip is based upon the observation that brothers share an average of one-half of their genetic material, whereas first cousins share an average of one-eighth. Therefore, saving two brothers or four cousins would result in the same genetic contribution to the next generation as that represented by one's own genome. This quip was later cited by one of the founders of what is now know as the theory of kin selection in which natural selection is considered to act at the level of genes, rather than individuals. I will discuss this idea in more detail in a later blog post.

R. A. Fisher, J. B. S. Haldane, and Sewall Wright are usually recognized as having laid the theoretical foundation for modern evolutionary theory. However, many evolutionary biologists and historians of science consider that the "modern evolutionary synthesis” was initiated by Theodosius Dobzhansky with the publication of his most famous book, Genetics and the Origin of Species published in 1937.

Genetics and the Origin of Species


Dobzhansky combined the Mendelian genetics, the mathematical models of Fisher, Haldane, and Wright, and the observations of evolution and natural selection in the wild in a theory that reinstated natural selection as the primary engine of evolution. He emphasized both the scientific aspects of evolutionary theory, and the implications of evolutionary theory for education and society in general. In a famous essay entitled "Nothing in biology makes sense except in the light of evolution” he showed how modern synthetic evolutionary theory provides a comprehensive explanation for the origin and evolution of life on Earth.

Dobzhansky also grounded the "modern evolutionary synthesis" in empirical investigation. Using the common fruit fly (Drosophila melanogaster). Dobzhansky and his colleagues showed that the patterns of variation and natural selection predicted by Fisher actually occurred in controlled populations of living organisms under laboratory conditions.


Most importantly, Dobzhansky showed empirically that the "continuous variation" that both Darwin and Fisher asserted were essential for natural selection actually occurred for many traits in nature. According to Dobzhansky, most traits are distributed in what is often referred to as a "bell-shaped curve". That is, for most traits there is an average value for the trait, which the majority of the members of the population share. There is also two "tails" to the bell-shaped curve, consisting of extreme versions of the trait.

Dobzhansky then went on to identify three different forms of natural selection, which depended upon which part of the bell-shaped curve of variation selection affected:


• Directional selection, in which selection against one extreme "tail" of the bell-shaped curve caused the average value for the trait to move over time;


• Stabilizing selection, in which selection against both extreme "tails" of the bell-shaped curve caused the average value for the trait to remain where it was; and


• Disruptive selection, in which selection against the average value of the bell-shaped curve caused the population to split into two diverging curves, corresponding to the two extreme versions of the trait.

The proponents of the "modern evolutionary synthesis" asserted that this last form of natural selection was the underlying explanation for the divergence of one species into two or more different species (for this reason, disruptive selection is sometimes referred to as "diversifying selection"). That is, Darwin's "mystery of mysteries" – the origin of species – was shown to have a mathematical basis which could be studied empirically and tested statistically, thereby making it a genuinely "scientific" study.

The Historical Importance of the "Modern Evolutionary Synthesis"

What, then, was the importance of the “modern evolutionary synthesis” to evolutionary theory? Perhaps J.B.S. Haldane said it best:
"The permeation of biology by mathematics is only beginning, but unless the history of science is an inadequate guide, it will continue, and the investigations here summarized represent the beginning of a new branch of applied mathematics."

The theory of evolution as Darwin first proposed it was essentially a qualitative theory; it had no mathematical basis, and could not be tested using statistical methods. Indeed, Darwin himself was a “mathophobe,” who had neither the training nor the inclination to provide a mathematical basis for his theories.

However, the founders of the modern synthesis were all well-versed in mathematics, as was Gregor Mendel. Indeed, R. A. Fisher not only provided the first solid mathematical framework for the theory of evolution by natural selection, he virtually founded the disciplines of biometry and statistics. Many of the statistical tests that are still used to test evolutionary hypotheses (indeed, hypotheses throughout the natural and social sciences) were first formulated by Fisher.

Providing a mathematical foundation for evolutionary theory literally meant converting evolution from “natural history” into a modern science. When a hypothesis can be tested by gathering numerical data (by counting or measuring objects and events), that data can then be statistically tested to determine if it verifies or falsifies that hypothesis. This is what happens in the other natural sciences, like chemistry and physics. Since the modern evolutionary synthesis, this is also what happens in evolutionary biology.

ESSENTIAL READING:

Mayr, Ernst & William Provine (eds.) (1998) The Evolutionary Synthesis: Perspectives on the Unification of Biology. Harvard University Press.

SUPPLEMENTAL READING:

Bowler, Peter J. (1983) The Eclipse of Darwinism: Anti-Darwinian Evolutionary Theories in the Decades Around 1900. The Johns Hopkins University Press.

Darwin, Charles (1868) The Variation of Animals and Plants Under Domestication. John Murray. Available online here.

Dobzhansky, Theodosius (1937) Genetics and the Origin of Species. Columbia University Press.

Dobzhansky, Theodosius (1973) Nothing in biology makes sense except in the light of evolution. The American Biology Teacher, March 1973, volume 35, pages 125-129. Available online here.

Fisher, R. A. (1930) The Genetical Theory of Natural Selection. Oxford University Press.

Haldane, J. B. S. (1932) The Causes of Evolution. Princeton University Press.

Jenkin, Fleeming (1867). [Review of] The Origin of Species. The North British Review, June 1867, 46, pp. 277-318. Available online here.

Mendel, Gregor (1866) Experiments in Plant Hybridization. Verhandlungen des naturforschenden Vereines in Brünn, volume 4, pages 3-47. Available (in English) online here.

Provine, W. (1971) The Origins of Theoretical Population Genetics. University of Chicago Press.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Wednesday, March 25, 2009

The Answer (Now, What Was The Question?)



For what it’s worth (and because I have been rather sneeringly referred to as an atheist at other websites), here is some information that readers of this blog may find interesting.

I am a Quaker. That is, I am a member of the Ithaca Monthly Meeting of the Religious Society of Friends. The actual name for “Quakers” is "Friends". When they started out (in England in the 17th century) they tended to refer to themselves (rather grandly, IMHO) as the “children of the light” and/or “the publishers of truth”. However, by the time they had come to America they had settled on the Society of Friends. “Quakers” was a somewhat derogatory name given to them by their opponents in Cromwell’s England.

It is important to note that there are two different kinds of Friends, known as “programmed” and “unprogrammed” (sometimes referred to as “evangelical” and “traditional”, respectively). The programmed/evangelical friends are a lot like Methodists: they meet on Sundays in buildings that look like churches (but generally without steeples), there is a minister who gives a sermon, there is often a choir, and the congregation sits auditorium-style facing the front of the “church” where the pastor speaks. Following the service there is generally “fellowship time”, with coffee and snacks in the fellowship room, etc. Herbert Hoover and Richard Nixon were both brought up in “programmed” Friends meetings.

The other kind (the original kind, the kind invented by the founder of the Friends, George Fox, and the kind of meeting that I belong to) meets in silence in a simple (often very plain) meeting house, with no minister, no choir, no hymns, no sermons, indeed no “program” at all. Everybody waits in silence for the “gathering of the spirit”, usually all facing each other in a roughly circular (or square) arrangement of chairs or short pews. Sometimes a person in meeting is “moved” to stand up and speak (or, much more rarely, to sing). This almost never happens until at least a half hour of silence has gone by. No one comments while they speak, although people sometimes join in with a familiar song. When they have finished speaking, they sit back down and all wait for the silence to “settle”. I’ve never been at a meeting at which more than a half dozen people spoke, and I’ve been at plenty at which nobody spoke for the entire hour (and sometimes much longer than that, as some special meetings have no set time limit).

In an unprogrammed/traditional meeting such as the one in Ithaca there are no officials except for the Clerk of the Meeting, whose responsibility it is to keep people informed of when and where meetings are happening, and to take notes at “meetings for worship with attention to business”, which generally happen once a month. The Clerk also “breaks” meeting by catching people’s eyes and turning to the people next to them to shake hands. At the “rise of meeting” the Clerk makes announcements and invites members of the meeting to share concerns. There is also a Treasurer, who keeps accounts, but is not considered to be an “officer” and is not elected. Both the Clerk and the Treasurer have assistants, and are usually chosen annually by the committee for ministry and oversight (which used to be referred to as the elders, a now archaic term). I was for many years a member of this committee.

Probably not surprisingly to some at this website, I am known to some of the older members of the Ithaca Meeting as a “minister”; that is, someone who is often moved to speak. I haven’t done so in about a year, but that’s not unusual, especially for our meeting. Some meetings have a tradition of recording and drawing attention to ministers, but this is rare and becoming more so among “traditional” Friends meetings.

Although as one might expect there are a number of Cornell and Ithaca College professors in our meeting, the overwhelming majority of our members are not professional academics. Rather, they are working people from the town; everything from secretaries to lumberjacks to farmers. Quite a few of these, as it turns out; Ithaca is “centrally isolated” and is known for having a "cow college" on east hill...and yes, I grew up in the middle of farm country and spent some of my summers and vacations in college milking cows (and I'm a proud graduate of Cornell's "Ag school", class of '69).

Membership in a traditional Friends meeting is gained by petition to the committee on ministry and oversight, who appoints a “clearness committee” for the prospective member. Clearness committees work together with members to “come to clearness” on particular issues. People can ask for a “clearness committee” to join the meeting, get married “under the care of the meeting” (FWIW, the Ithaca meeting has been recognizing marriages between same-sex couples “under the care of the meeting” for almost thirty years), decide on taking a particular job, pursue a particular academic degree, get divorced (yes, it happens, although not often) or whatever is of concern to them. Anyone can ask to join a meeting, and there is no prohibition against people becoming members of a Friends meeting while remaining full members of other churches or religions. Indeed, there are a number of agnostics and atheists in our meeting (but, as I stated earlier, I’m not one of them). Because of this process, we say that a person becomes a Friend by “convincement”, not conversion, and that “convincement” must come from within, not from a minister or the group.

Perhaps the most noticeable difference between “traditional” Friends and other religious groups is the total lack of a creed or “confession of faith”. Instead, we maintain a collection of written “Queries and Advises”, which are periodically read and revised by clearness committees. We feel that it is each person’s responsibility to come to whatever “measure of the light” we can. All decisions (and I mean ALL decisions) are made by pure consensus. There are no votes taken at any Friends meetings, including those held with attention to business. This means that some decisions take a generation or more to be reached, but when they are finally arrived at, everyone in the meeting has agreed to the decision and will back it wholeheartedly.

Friends are one of the three historic “peace churches” (along with the Brethren and Mennonites). To be a Friend means never to participate in war or the preparation for war in any form whatsoever. I was a conscientious objector during the Vietnam War, and remain one to this day.

This doesn’t mean that Friends are pacifists, however. Quite far from it; Friends are very active in our “peace witness”, often placing ourselves between combatants and doing humanitarian work around the world. The Friends service group, the American Friends Service Committee, received the 1947 Nobel Peace Prize on behalf of Friends worldwide, for our corporate work for peace and reconciliation.

Friends also don’t proselytize (indeed, there is a heavy but unspoken prohibition against doing so), and so the foregoing should be considered to be informational only. If you would like to learn more about the Society of Friends, I recommend this website, and here is the website for the Friends meeting I attend.
“Dearly beloved Friends, These things we do not lay upon you as a rule or form to walk by, but that all, with the measure of light which is pure and holy, may be guided: and so in the light, walking and abiding, these may be fulfilled in the Spirit, not from the letter, for the letter killeth, but the Spirit giveth life.”

– Given forth at a General Meeting of Friends in the Truth at Balby in Yorkshire, in the ninth month 1656, from the Spirit of Truth to the Children of Light

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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A Brief Note About Comment Moderation

Due to the behavior of certain unnamed and unscrupulous individuals, I have found it necessary to return to full-time comment moderation at THE EVOLUTION LIST. This means that comments will not appear here until they have been emailed to me and I have approved them for posting to the comment threads following each post. Please bear this in mind when you comment here. Thank you for your patience and understanding.
--Allen MacNeill

"I had at last got a theory by which to work"
-The Autobiography of Charles Darwin

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Tuesday, March 24, 2009

Intelligent Design is Boring


At a thread at another website discussing the idea that ID is "boring", an ID supporter wrote this:

"[ID] is boring to Will [Provine] I suspect (and to others for the same reason) because they rule out the possibility of an intelligent designer."

Actually, knowing Will Provine pretty well and hearing him say that ID is "boring" on several occasions, I can confidently state that the reason he finds it "boring" is that whenever something interesting in biology is discovered and somebody asks "Why is that thing the way it is?" Will hears most ID supporters answer "Goddidit". His opinion of ID is that it's a science-stopper because rather than suggesting new and interesting ways of trying to figure out how something came to be the way it is, he thinks that IDers simply throw up their hands and say "It's too complicated, so God / the Intelligent Designer must have done it".

Personally, I don't find ID boring for quite the same reason, as I don't always see ID supporters resorting to the "Goddidit" pseudoexplanation. No, the reason I tend to find most ID boring is it's relentlessly negative. That is, people like Michael Behe and William Dembski observe something marvelously complicated and say "That's Irreducibly Complex!" or "That's Complex Specified Information, so it couldn't have evolved via naturalistic means"...and then they leave it at that. No alternative means of creating the marvelously complicated thing is proposed (unless you credit Behe's "puff of smoke" pseudoargument).

Furthermore, I generally don't see ID supporters doing any original empirical research. In particular, I don't see any of them going out into the field (my favorite place to discover things) or into the lab and "getting down and dirty" with some biological phenomenon that they find absolutely fascinating.


My friend, Harry Greene (the world's authority on rattlesnakes) is my idea of a real scientist. He absolutely loves snakes, talks about them at the drop of a hat, has spent his entire professional life studying them in the field and in the lab, and has revolutionized our understanding of the ecology, ethology, and evolutionary biology of reptiles. To me, he's the epitome of an evolutionary biologist, because he has what we call "a feel for the organism" which goes far beyond simply studying it as an experimental subject.


And my friend, Lynn Margulis (the world's authority on endosymbiosis) is also my idea of a real scientist. She absolutely loves getting knee-deep in the mud of some tropical lagoon and scraping scum off of rocks to look at under the microscope. She's spent her entire professional life studying microorganisms in the field and in the lab, and has revolutionized our understanding of the evolutionary biology of microorganisms. Like Harry, she's the epitome of an evolutionary biologist, because she also "a feel for the organism" which leads her to discover things nobody ever thought to look for before, such as symbiotic bacteria embedded in the cell membranes of symbiotic protozoa from the guts of termites.

I have yet to meet or hear about or read about any ID supporter who does anything like what Harry and Lynn do. Yes, Michael Behe is a biochemist, but the things he does in his laboratory at Lehigh have little or nothing to do with ID. And William Dembski wouldn't know an actual living organism if it lunged out and bit him on the ankle.

Biology, and especially evolutionary biology, is that branch of the natural sciences founded and maintained by people who loved and were obsessed with nature and natural things. Darwin and Wallace and Fisher and Haldane and Wright and Dobzhansky and Mayr and Simpson and Stebbins and Hamilton and Trivers and Margulis and the two Wilsons (Edward O. and David Sloan): these are my heroes, and they are the "naturalists" (see how the word has another, much more positive meaning?) who have been the inspiration for my research, insignificant as it is compared with theirs.

And all that IDers can generally do is say "No, you're wrong, it can't happen that way, in fact it can't happen at all without a deus ex machina?" Ugh: boring, pointless, and most of all, no "feel for the organism".

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Monday, March 23, 2009

Just Another One of the Boyz in the Banned...

Just a quick note to say that I have apparently once again been "moderated" off of the threads at Uncommon Descent. Apparently my comments were cutting a little too close to the bone. One could almost say I'd been Expelled (No intelligence Allowed)...

And to Timaeus and others from UD: I will be indirectly responding to some of the posts at Uncommon Descent here (time and weather permitting, of course).

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Analogies, Metaphors, and Inference in Science


Mike Gene, the pseudonymous founder of Telic Thoughts and the author of The Design Matrix: A Consilience of Clues has written the following about metaphors and their application to the detection of intelligent design:
Metaphors such as “fear”, “cost”, “abhor” and “angry”, commonly share the projection of consciousness onto the world. Metaphors such as these represent the human tendency to view the world through anthropomorphic glasses. However, the metaphors employed by molecular biologists are not of this type.
...
Metaphors typically break down when we begin to take them literally.
...
[but] The design terminology that is used in the language of molecular biology does not break down when interpreted literally
...
[T]here is a basic and literal truth to the use of design terminology in molecular biology–these technological concepts are just too useful. Metaphors are certainly useful when explaining concepts to other human beings, yet the design terminology often goes beyond pedagogy–it provides true insight into the molecular and cellular processes. An understanding of our own designed artifacts, along with the principles required to make them, can guide the practice of molecular biology.

Metaphors are a special case of analogies (the other being similes). I have written extensively on the subject of the use of analogies and metaphors in science, and especially in the evolution/design debate here, here, and here. The fundamental question in this ongoing debate is, how do we know an analogy really exists? For example, do we have any objective way to determine if one rock is analogous with another? Or whether an anatomical feature (or a protein/substrate binding site) is analogous to another?

As in the case of agency detection, we think we can do this very easily (just as we can easily identify what looks like design), but I would argue that this is because both "finding" analogies and "finding" design and purpose are capabilities of the human mind (and the nervous system that supports it) that have conferred enormous adaptive value on our ancestors. As in the case of our hypothesized "innate agency/design/purpose detector" (which first becomes active in very early infancy), our "analogy detector" also appears to become active at a very early age, and operates entirely in the background. That is to say, we are almost totally unaware of its operation, and concentrate only on its output.

Our ability to detect (and construct) analogies is, IMO, the core of our intelligence, as demonstrated by the fact that identifying analogies has been traditionally used as one of the most sensitive gauges of general intelligence in intelligence tests (such as the Miller Analogies Test).

In the context of Mike Gene's ideas about metaphors, doing engineering (and especially mathematics) is essentially the construction of highly compact analogies, in which numerical (and sometimes physical) relationships are expressed in the form of abstract symbols. A blueprint is simply a metaphor for a building, just as a chemical formula is a metaphor for the product of the chemical reaction, and a recipe for a cake is a metaphor for the cake. Indeed, many mathematical relationships (especially in the natural sciences) are expressed as equations, which are quite literally metaphors expressed in symbolic form. For example, Newton's equation for force:
F = ma

is a metaphor linking the concept of force with the concepts of mass and acceleration.

In molecular biology we encounter once again the concept of metaphors, for what is the genome of an organism but a highly abstract metaphor for the fully embodied and operating organism itself? I agree with those (and I expect Mike Gene would number himself among them) who assert that the encoding of "life" into a string of nucleotides is indeed the crucial difference between biological "metaphors" and physical "direct necessities". Gravity isn't "encoded" in anything, but proteins are, and so are cells, tissues, organs, organ systems, organisms, and (at least at some level) their behaviors.

So, is there a way to verify if an analogy or metaphor is "real"? In the case of some analogies in biological systems we have an independent double-check on our identification of analogies. This is based on the evolutionary concept of homology, or derivation from a common ancestor. If two structures on two different organisms (say a small bone of the jaw of a reptile and the even smaller bone in the middle ear of a mammal) appear to be analogous (on the basis of size, location, relationship to other bones, etc.) there are at least two different, though related, methods of verifying that these structures are indeed analogous (and not just accidentally similar).

One way is by means of comparative paleoanatomy, in which a series of fossils of known age are compared to determine if there is a connection between the evolutionary pathways of derivation of the structures. If such a pathway can be empirically shown to exist, this would be strong evidence for both the analogous and homologous nature of the objects.

Alternatively one could compare the nucleotide sequences that code for the structures to determine if they are sufficiently similar to warrant a conclusion of homologous derivation. In both cases, evidence for homology, combined with our intuitive "identification" of analogous structure and/or function, both point to the same conclusion: that the two structures are both analogous and homologous.

This is why structures that appear to be analogous, but for which there is no convincing evidence of homology (as in the wings of birds and insects) can present a serious problem to evolutionary biologists, and especially those engaged in biological classification. Such apparent similarities (technically called homoplasies) can either be the result of "true" (i.e. partial) analogy at the functional (and/or structural) level (and therefore assumed to be the result of convergent evolution) or they can be completely accidental. Simple inspection is often insufficient to separate these two hypotheses, and lacking either fossil or genomic evidence, conclusions about the validity of such analogies can be extremely difficult to draw. However, if there is fossil and/or genomic evidence and it points away from homology (i.e. descent from a common ancestor), then the structures can be considered to be analogous, but not homologous.

One of the dangers in invoking analogies and metaphors is overusing the concept of analogy to mean almost anything. Indeed, it is essential in discussions such as these that we be as precise as possible about our definitions, as imprecision can only lead to confusion (at best) and unsupportable conclusions (at worst).

Perhaps the most essential distinction to be made in this regard is between "analogies of description" (which could also be called "semantic analogies") and "analogies of function/structure" (which could also be called "natural analogies"). The former (i.e. "semantic analogies") are merely artifacts of the structure of human cognition and language, as happens whenever we describe an analogy that we have perceived.

By contrast, the latter (i.e. "natural analogies") are the actual similarities in function/structure that we are describing (i.e. that resulted in our identification and description in the first place). As in the Zen koan about the roshi and the novice in the moonlit garden, much of the confusion about which of the two types of analogies we are discussing seems to stem from confusion between the moon that illuminates the garden and the finger pointing at the moon.

In the brief example from Mike Gene's The Design Matrix posted at the head of this thread, the implication is that the analogies we perceive between biological systems and those engineered by humans are "natural analogies"; that is, they are real analogies, and not simply a form of linguistic convenience. However, there is nothing about the finding of an analogy that necessarily verifies that the analogy is "natural" (i.e. "real"), as opposed to "semantic" (i.e. "imaginary"). This would be the case even if one found repeated analogies between complex systems engineered by humans and biological systems that evolved by natural selection. To verify that an analogy is "natural" requires an independent source of validation for the assertion that the analogy is "real" and not merely "semantic". At this stage in my reasoning about this subject I am not at all sure how one would go about this.

However, one thing I am sure of is that simply asserting over and over again that one has perceived an analogy, and that this is all that is necessary to validate the analogy, is not sufficient. Even I am but mad north-north-west: when the wind is southerly I know a hawk from a handsaw.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Saturday, March 07, 2009

Should Embryonic Stem Cells be Used for Medical Research?


On Monday 9 March 2009 President Obama signed an executive order reversing the Bush administration's ban on the use of Federal funding for embryonic stem cells for medical research (and presumably for any medical treatments that might eventually be developed as the result of that research). This policy change has raised a storm of controversy among right-to-life- advocates, and also among "intelligent design" supporters. This controversy has centered on the ethics of science, and whether scientists should be allowed to pursue their research wherever it leads.

Currently, most embryonic stem cells are derived from human egg cells that have been fertilized in vitro (that is, outside of the body of the egg-donor mother) as part of the process of in vitro fertilization (IVF) whereby childless couples can conceive of a baby using their own genetic material.

IVF clinics generally fertilize multiple donor eggs and then let them
divide by mitosis
until the blastula stage is reached. During this process the inner cell mass is formed inside the blastula, from which embryonic stem cells are derived. The point to this process is not to produce the embryonic stem cells in the inner cell mass, but rather to produce viable blastulas, which can then be implanted in the uterus of the egg donor (or, in rare cases, a surrogate).

The way this process is carried out necessarily produces multiple unused blastula-stage embryos for every one that is implanted. These unused blastula-stage embryos are usually frozen in liquid nitrogen, in case the egg donor requires a repeat implantation.

Currently, there are almost half a million such blastula-stage embryos frozen in liquid nitrogen in IVF clinics in the United States, which leads to the first ethical question:
What becomes of the unused frozen embryos, and who decides?

Here is what generally happens:
Any embryos that you do not use in your first IVF attempt can be frozen for later use. This will save you money if you undergo IVF a second or third time. If you do not want your leftover embryos, you may donate them to another infertile couple, or you and your partner can ask the clinic to destroy the embryos. Both you and your partner must agree before the clinic will destroy or donate your embryos. [source]

So, should the "parents" (i.e. the egg and sperm donors) have the right to decide that their unused blastula-stage embryos be destroyed? Despite some political efforts to deny them this right, there is no legal jurisdiction in the U.S. in which this right has been abrogated (yet).

One way to solve this particular ethic dilemma is to "adopt" the frozen embryos by having them implanted in an "adoptive" mother. There is an organization that advocates this, Nightlight Christian Adoptions, and has arranged for some of these frozen embryos (which the organization calls "snowflakes") to be "adopted" by implantation in "adoptive" mothers who are medically infertile (and married).

According to data at that website, the current number of successful "snowflake adoptions" is approximately 202 since the program was started in 1997. That works out to around 17 per year, or 0.0034% of the current half-million "snowflake backlog". At that rate, all of the frozen embryos currently in cryogenic suspended animation will be "adopted" by the year 31421.

However, this grossly underestimates how long this backlog will persist, as it assumes that no new "snowflakes" are generated by new IVF procedures. Currently, the rate of production of new frozen blastula-stage embryos at IVF clinics in the US is approximately 18,000 per year. The current rate of "snowflake adoption" is approximately 20 per year, so unless IVF is permanently stopped, it is mathematically impossible for the current "snowflake backlog" to eventually be "adopted".

One way to avoid the use of embryonic stem cells taken from frozen blastula-stage human embryos is to use adult stem cells instead. There are many different tissues in adult humans that qualify as pluripotent stem cells (that is, cells that can continue to divide by mitosis). Recent research has made it possible to "regress" adult stem cells almost to the embryonic stem cell stage, which raises the possibility of using adult stem cells instead of embryonic stem cells.

Personally, I strongly hope that adult stem cells can be used for all of the scientific and technical uses that most scientists originally thought only embryonic stem cells could be used for. However, this will then lead to two new, unforseen ethical dilemmas:
What will be done with the "snowflakes" that are currently frozen at IVF clinics, if they are not used for stem cell research and medical treatment?

and
What will be done with the adult stem cells that have been regressed to the embryonic stem cell stage, since these would then qualify genetically and developmentally as "snowflakes" themselves?

Clearly, one irony of the development of adult stem cell regression will be that the "snowflakes" now frozen in liquid nitrogen in all of those IVF labs will now almost certainly be disposed of (I suppose they defrost and incinerate them), rather than contributing to the advance of medical technology and human welfare.

The other irony, of course, is that by regressing adult stem cells to the embryonic stem cell stage, there would be many more "snowflakes", rather than fewer, thereby necessitating the destruction of many more "potential human beings" than is currently the case.

There are two other solutions, both of which avoid the ethical dilemmas outlined above. One alternative would be:
To consider that neither embryonic stem cells nor adult stem cells are "human beings" until they are implanted into a mother and are born as human babies.

This, of course, would require defining "human life" as beginning at birth, rather than "conception" (regardless of where that "conception" took place).

Another alternative would be:
To consider that all stem cells are "human beings", which would require that all stem cell research and treatment and all forms of in vitro fertilization be declared unethical, and presumably outlawed.
But this would also require that we outlaw all developmental research, because somewhere along the line some researcher somewhere might find out how to regress any human cell to the embryonic stem cell stage, and then simply scratching your head or drinking a cup of too-hot coffee would be equivalent to murder.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Friday, March 06, 2009

"Can Natural Selection Produce New Information?"


Here's another in a series of responses to some common assertions/misunderstandings of evolutionary biology by creationists and "intelligent design" supporters. One of the most common arguments against the theory of evolution is that natural selection cannot produce genuinely new information:
"Natural selection does not produce new information. On the contrary, it only reduces existing genetic information. Evolutionary biologists shouldn't invoke mutations as a source of new information, because all known mutations involve a net loss of information."

This viewpoint demonstrates a basic misunderstanding of the process of evolution bynatural selection. According to Darwin (and virtually all evolutionary biologists), natural selection has three prerequisites:

1) Variety, generated by the "engines of variation";

2) Heredity, mediated by the transfer of genetic material (either vertically - from parents to offspring - or horizontally - via viral transduction, retrotranscription, etc.); and

3) Fecundity, that is, reproduction, usually at a rate that exceeds replacement (according to Malthus).

Given these three prerequisites, the following outcome is virtually inevitable:

4) Demography: Some individuals survive and reproduce more often than others. Ergo, the heritable variations of such individuals become more common over time in populations of those organisms.

Natural selection is synonymous with #4; it is an outcome of the three processes listed as prerequisites, not a "mechanism" in and of itself.

Ergo, the real dispute between evolutionary biologists and "intelligent design" supporters is not over natural selection per se, but rather the properties and capabilities of the "engines of variation". I have written extensively about these here and here.

Yes, natural selection (i.e. #4, above) is conservative not creative. It produces no new genetic nor phenotypic information, which is why Darwin eventually came to prefer the term "natural preservation" rather than "natural selection". However, it is also clear that the "engines of variation" - that is, the processes the produce phenotypic variation among the members of populations of living organisms - are both extraordinarily creative and extraordinarily fecund. The real problem in biology is therefore not producing new variation, but rather limiting the production of new variation to the point that the "engines of variation" do not cause the inevitable disintegration of living systems.

As just one example of this problem, the genetic elements known as transposons generate a huge amount of new genetic variation, much of which is either phenotypically neutral or deleterious to the organism. There are biochemical mechanisms by which cells can monitor the incidence of transposition in themselves, and limit its consequences (up to and including the active self-destruction of the cell via apoptosis).

At the same time, there is very good evidence in the genomes of many organisms that retrotransposition events mediated by transposons have occasionally produced genetic changes that have resulted in increased survival and reproduction of the organisms in which such events have taken place. There is a large and growing literature on this phenomenon, all of which points to the inference that retrotransposition via transposons both creates new genetic and phenotypic variation, and that in some cases such variation can provide the raw material for evolutionary adaptations, which are preserved via natural selection.

So, if someone really wants to find out where the Intelligent Designer might create new variations, they should follow the lead of Darwin's good friend, Asa Gray, and look for the telltale evidence (if any) for such intervention in the "engines of variation". Of course, they would have to show pretty conclusively (using empirical investigations and statistical analysis) that such "creation events" are not the result of purely natural, unguided processes. If they can do this, they will undoubtedly win a Nobel Prize and a Crafoord Prize (plus a MacArthur or two).

Notice that this will involve looking carefully into the mechanisms by which new variations are produced, rather than pointing to the outcomes of such processes (i.e. natural selection) and simply asserting that "you can't get here from there". Simply asserting (without empirical evidence) that something can't happen isn't "doing science" at all. In fact, it's doing just the opposite...

...it's doing ID the way it's always been done up until now; by press release, rather than by empirical research.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Thursday, March 05, 2009

"Why Do We Have The Senses That We Have?"


A common debating tactic used by creationists and ID supporters is to ask, "why do we have the senses that we have, and not some other ones"? The answer they usually provide is something like, "because that's the way the Intelligent Designer intended them to be".

The question of why we have the senses that we do is a very interesting one. As just one example, consider the sense of sight. As a type G2V yellow dwarf star, the sun gives off a relatively narrow range of electromagnetic radiation, including (from longest wavelength to shortest) radio waves, infrared radiation, “visible (red, orange, yellow, green, blue, and purple) light", and ultraviolet light. Almost all of these wavelengths of electromagnetic radiation can penetrate the Earth’s atmosphere (although the shorter wavelengths of ultraviolet light are somewhat attenuated by absorption by ozone/O3 in the upper atmosphere).

So, which wavelengths of electromagnetic radiation can we perceive? The answer depends on who you define as “we". Vertebrates have visual pigments in the cone cells of the retina that can absorb only three of these wavelengths: red (absorbed by the rhodopsin protein erythrolabe, which absorbs sunlight in the range of 564–580 nanometers), green (absorbed by the rhodopsin protein chlorolabe, which absorbs sunlight in the range of 534–545 nanometers), and blue (absorbed by the rhodopsin protein cyanolabe, which absorbs sunlight in the range of 420–440 nanometers). So, we vertebrates can only directly perceive red, green, and blue light (that’s why color computer monitors generate only red, green, and blue pixels).

However, most insects (including honey bees) have different visual pigments, and so see very different colors than we do. They do not have a visual pigment that corresponds to vertebrate erythrolabe, and so cannot perceive the color we call “red". However, they have a visual pigment vertebrates do not have, which can absorb light in the near ultraviolet range. Hence, insects can see colors (including ultraviolet) that we cannot see, and so the world appears very different to them.

So far, no organism on Earth has been discovered that can perceive the radio waves given off by the sun. This is probably because to do so would require absorptive structures several meters in length (the wavelength of most radio waves).

So, one answer to the creationist's question is that, taken as a whole, living organisms can perceive (or at least absorb) a range of light from the far infrared to the near ultraviolet, but lack receptors for most of the electromagnetic spectrum (such as radio waves, gamma radiation, etc). In other words, the range of electromagnetic radiation that can be perceived by living organisms matches quite closely the range of electromagnetic radiation given off by the sun and transmitted through the Earth’s atmosphere (with the exception of radio waves, which are too long to by absorbed by any known biological molecule).

That this is the case is exactly what one would expect to have evolved by natural selection, which can only work with what is available. Furthermore, it illustrates one of the basic ideas of evolutionary descent with modification: that the solutions to evolutionary problems vary from group to group as the result of historical contingency. Vertebrates see red, green, and blue, while insects see green, blue, and ultraviolet because two of our visual pigments (chlorolabe and cyanolabe) evolved before the divergence of insects and vertebrates from our common ancestor, while the third visual pigment evolved independently in the two groups, resulting in two different sets of perceived colors.

Compare this to the answer that ID provides: vision is the way it is because that’s how the Intelligent Designer intended it to be. Which of these answers to the creationist's query involves detailed empirical scientific investigation, and which simply relies on unsupported assertions?

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Wednesday, March 04, 2009

Teleology vs Teleonomy: Can a "Program" Exist Before Its "Programmer"?


This post is a follow-up to the previous post on the subject of the "randomness" in the processes that generate the variation that is necessary for biological evolution.

Can a "program" exist before its "programmer" (and therefore bring it into being)? This seems to be the core of the disagreement between ID supporters and mainstream scientists. The former (which include Charles Darwin's very close friend, Asa Gray) advocate the idea that the variation upon which natural selection and other evolutionary processes work is neither random nor unintentional. The latter (which include Darwin and his intellectual heirs) do not disagree with the idea that such variation is not "random". What they disagree with is the idea that there is some "intention" or "plan" guiding the variation that occurs, so that certain outcomes (including, but not limited to, the origin of humans) are more likely than others.

To answer the question that stands at the head of this post, I think it's essential to emphasize (as I did in the original blogpost) that the terms “foresighted” and “goal-oriented” are not equivalent, nor are the processes to which they are applied. As I have pointed out in many posts, there is no inherent contradiction between a process being purely "natural" (i.e. the result of the operation of purely natural processes) and being "goal-oriented".

Ernst Mayr (surely no advocate of "intelligent design") argued forcefully (and, in my opinion, convincingly) that biological organisms are indeed "goal-oriented". That is, their genomes provide a program, the function of which is to bring about a particular state of affairs: the survival and reproduction of the organism via its interactions with its environment.

The origin of the genome (i.e. the "program" itself) is an entirely different situation, however. Ever since Darwin it has been a standard assumption that the evolutionary processes by which the genetic "programs" that direct the assembly and operation of living organisms are not goal-oriented. These evolutionary processes – natural selection, sexual selection, founder effects, genetic bottlenecks, neutral "drift" in deep evolutionary time, exaptation, heterochronic development, changes in homeotic development, interspecific competition, species-level selection, serial endosymbiosis, convergence/divergence, hybridization, phylogenetic fusion, background and mass extinction/adaptive radiation, and internal variance – do not require any kind of "goal orientation" to produce the living entities and processes we observe around and within us. And, since such processes do not require goal-orientation or intentionality, these are not included in evolutionary explanations. Some, but not all, evolutionary biologists extend this idea to the assumption that goal-orientation or intentionality do not exist in nature, in the absence of pre-existing genomic "programs").

The main reason for this assumption has been that it is extremely problematic to agree on how one would go about showing that the aforementioned evolutionary processes have indeed been goal-oriented. The most serious objection to this idea is that there seems to be nowhere for such a "directing agency" to exist in material form, nor any natural means by which its goals could be impressed upon physical organisms.

The genomes of organisms are physical/chemical "stuff", which is translated via physical/chemical "machinery" into biological entities and processes. That is, there is a physical/chemical "vehicle" in which the information for assembling and operating organisms is carried and expressed.

The same would not the case for the putative source of the "evolutionary program" which might direct the evolution of the genomes of living organisms. Since such an "evolutionary program" would cause the evolution of the "genomic programs" which direct the assembly and operation of living organisms, such a program would necessarily have to exist before the origin and evolution of biological genomes, as it would be necessary for it to do so to direct their coming into being.

This presents two serious problems:

• By what mechanism(s) would such an "evolutionary program" cause "genomic programs" to come into existence, and

• Precisely where in the physical universe would such a pre-existing "evolutionary program" itself exist?

We seem to have two direct logical contradictions in terms:

• How can a non-natural "evolutionary program" cause a natural "genomic program" to come into existence, and

• How can a programmer pre-exist the program which brings itself into existence?

There is a proposed answer to these two questions, but one which most ID supporters seem loathe to invoke:

• That the "pre-existing program" that directs the evolution of the genomic programs of living organisms is woven into the structure of physical reality itself.

This is the line of inquiry pursued by Ilya Prigogine and Stuart Kauffman (among others), but which is rejected out-of-hand by nearly all ID supporters (most notably Michael Behe, William Dembski, and Phillip Johnson), who prefer a purely "supernatural" source for the "pre-existing program" by which evolution has been directed).

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Monday, March 02, 2009

"Are the Mechanisms that Produce Phenotypic Variation "Random"?


Some "intelligent design" supporters have recently asserted that all of the 47+ mechanisms listed in my blog are “random” or “accidental", and therefore the old creationist argument that "RM & NS" doesn't explain the origin and evolution of life is still valid. However, this is simply not the case. On the contrary, a large percentage of these mechanisms are the result of processes that are not “random” by any reasonable definition of that term. I have repeatedly been very careful to point this out, but that clearly has been missed by many "intelligent design" supporters.

It is also not the case that the 47+ processes are not “guided". Indeed they are “guided”, by the various internal and environmental forces that produce both the variations and the various evolutionary mechanisms that operate upon them (i.e. natural selection, sexual selection, founder effects, genetic bottlenecks, neutral “drift” in deep evolutionary time, exaptation, heterochronic development, changes in homeotic development, interspecific competition, species-level selection, serial endosymbiosis, convergence/divergence, hybridization, phylogenetic fusion, background and mass extinction/adaptive radiation, and internal variance).

That said, however, it is also demonstrably the case that none of the mechanisms listed above can be shown empirically to be “foresighted". Indeed, the whole idea of “foresightedness” in natural processes seems to me to violate several very well-established principles of physics, including the Second Law of Thermodynamics.

How can any natural process be empirically shown to be genuinely “foresighted"? Do rocks fall “in order to” reach the ground? Do gas molecules move “in order to” produce the phenomena we describe with Boyle’s Law? Do the electrons in the valence energy shells of hydrogen and oxygen form shared couplets “in order to” produce water? Do particular genetic changes happen “in order to” produce phenotypic changes that have no effects on organisms’ survival and/or reproduction now, but might have in the future? And how can anyone show any of these to be the case?

It is important to note that the terms “foresighted” and “goal-oriented” are not equivalent. The latter term is entirely compatible with both physics in general and evolutionary biology in particular. Indeed, the genomes of all living organisms are “goal-oriented programs” (as most clearly pointed out by Ernst Mayr), in that they organize and control the assembly and operation of the living organisms for which they code.

However, the processes by which such genomes have come into being (i.e. the 47+ mechanisms listed here, operating through the various mechanisms of micro- and macroevolution listed above) have not been empirically shown to be either “foresighted” nor “goal-oriented". It seems to me that this would be extremely difficult, if not impossible to do. What kinds of empirical observations could one conduct that would unambiguously verify today that some component of an existing organism’s genome or phenome was present in that organism now because at some point in the future it might become necessary for that organism’s survival and/or reproduction?

Clearly, once an organism has survived and/or reproduced one can point to its various attributes and say “yes, that attribute appears to have contributed to the organism’s survival/reproduction". However, that is no more evidence of “foresightedness” than a lottery winner saying “I chose these lottery numbers (or bought those particular scratch-off tickets) because I knew they would be winners". This is known as the “fallacy of affirming the consequent” (also called post hoc, ergo propter hoc argumentation) and is logically inadmissible in the natural sciences.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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