Tuesday, June 02, 2009

What's So "Intelligent" About "Intelligent Design"?


Many of the debates about "intelligent design" (ID) that I have read online have focused on the defintion of "intelligent". This is not necessarily because we all agree what "design" means, but rather because we know even less about that quality we refer to with the term "intelligent". If one cannot define what one means by "intelligent", then any attempt to define or investigate "intelligent design" would seem to me to be a futile exercise.

Some ID supporters have suggested substituting the term "purposeful design" for the term "intelligent design". To me, this sounds almost redundant; after all, design is all about "purpose", isn't it? And if that's the case, then "purposeful design" reduces to "purposeful purpose" or "designed design". Furthermore, it's not clear to me that the terms "intelligent" and "purposeful" are necessarily interchangeable, or mean even similar things.

Many ID supporters seem most upset about the implication that evolutionary theory is "random". That is, the processes by which new characteristics of living organisms come into being are not necessarily the result of intentional design. To many of them, this would eliminate a supernatural force or deity as the causal factor in biological evolution. Ergo, if one is committed to the intervention in nature of a supernatural force or deity, one must deny a priori the possibility that new characteristics of living organisms can come into being without "intention".

However, it is not necessarily the case that "purposeful" (i.e. teleological) objects and processes are necessarily non-random. First of all, it seems to me that "purposeful" is not an antonym for "random". For example, consider a falling rock: its movement as it falls is most definitely not random. Neither its trajectory nor its acceleration are "random" at all. On the contrary, they are predictable to such a degree that we call the mathematical description by which we can predict the movement of falling objects a "law" - the "law of gravity".

Ergo, it seems to me that the best antonym for "random" is "predictable", in the sense of being able to predict successive states in a dynamically changing system.

Given the foregoing, what is the best antonym for "purposeful"? Forgive me, but I think the only reasonable answer is "non-purposeful". This then forces one to define what one means by "purposeful". To me, the best definition of a "purposeful" (or "teleological", if you prefer the more technical term) object or process is "a dynamical process (or component of a dynamical process) in which the dynamical entity's actions are actively and homeotelically regulated by a cybernetic process that functions according to a pre-existing program, the outcome of which is a specified end state.
A homeotelic process is one in which a dynamical entity reacts to external perturbations from its original trajectory in such a way as to regain its original goal orientation. For example, an arrow fired from a bow is not homeotelic, whereas a heat-seeking missile is. By the same logic, a snowflake growing in a supercooled cloud is not homeotelic, whereas a virus replicating in a host cell is.

In my opinion, most of the arguments about "intelligent design" founder, not on the definition of "intelligent" but rather on the definition of "design". If one focuses not on "design" but rather on "purpose" (i.e. teleology), much of the disagreement (like a boojum) vanishes softly and silently away.

Indeed, I think the qualifier "intelligent" is unnecessary, and quite possibly redundant. Why argue over something – that is, "intelligence" – that is indefinable without self-reference?

That is to say, "purpose" is very clearly and unambiguously defined in cybernetics, as Gregory Bateson and Norbert Weiner pointed out a half a century ago. "Purpose" (aka "teleology") are what this argument is really about, and so it would help immensely if all of the participants on both sides of the debate would define it in such a way as to render its presence or absence empirically verifiable.

The same could also be wished about "intelligence", but I see no real hope for this, given that virtually every definition of "intelligence" given in this thread (and all previous threads) is neither empirically verifiable nor applicable to simple systems such as those found in viruses or very simple cells. How "intelligent" is the lambda bacteriophage? Compared to a human, not much; compared to a crystal of sodium chloride, tremendously so. Indeed, what separates crystallized viruses from crystallized salts is precisely the "quality" that separates life from non-life and "purposeful" from "non-purposeful" things.

Termites build termite mounds using a surprisingly simple set of "decision rules". For example, one decision rule (which is clearly "wired in" to the nervous system of worker termites) is the rule to stack particles of sand on top of each other and glue them together using a material like saliva in such a way as to produce an arch (this is beautifully illustrated in E. O. Wilson's masterpiece, The Insect Societies). In Höldobler and Wilson's new book, Superorganism, they explain in detail how insect societies produce astonishingly complex, adaptive, functional dwelling places, "highways" (army and driver ants), "farms" and "pharmacies" (leaf-cutter ants), etc. without anything that remotely resembles what we would call "intelligence" or "consciousness" (remember, their brains are smaller than a poppy seed and their life spans are measured in days).

Furthermore, none of the instructions for doing all of this "design" is encoded directly into the DNA of any given social insect. Rather, the instructions are "compiled" from the individual activities of thousands of individual insects performing very simple, stereotyped actions (mostly coordinated by chemical pheromones). In other words, the "intelligence" that produces the marvelous structures and functions of insect societies is a collective "intelligence" consisting of a small set of "decision rules" hard-wired into the nervous systems of individual insects.

Might it not be the case that this same process is the paradigm for all biological complexity? This would not only explain where the "designer" is (it's all around / inside us) and who the "designer" is (it's everyone, interacting collectively in producing the "superorganism"), it would also present what ID has so far completely lacked: an empirical research program. That is, one could search for the "decision rules" that produce biological complexity, in viruses, cells, insect societies, primate societies, and human societies, and figure out how the interaction of such rules produces biological complexity. And when you did that, you would have recreated the already-existing field of biology known as sociobiology, which is a branch of evolutionary biology.

Termites do not have "goals and foresight". Rather, they are quite literally programmed (i.e. "hard wired") to perform a surprisingly simple set of simple behaviors. They are born with this capability and do not have to learn it. Furthermore, their behaviors are extremely stereotyped and subject to quite a bit of essentially "random" variation. Despite this, and because there are so many of them (literally millions in some large hives), they collectively produce structures and functions that rival the most complex "artificial" factories and dwelling places designed by humans.

The point here is that "intelligence" is not being defined well at all, if it is restricted to humans and higher vertebrates, but not to insect societies. Each insect is definitely not "intelligent" (any more than each of our individual cells is), but collectively both the insect societies and our multicellular selves are intelligent. "Intelligence" is therefore an emergent property, rather than a pre-existing attribute. And evolution, of course, is all about emergent properties.

One of the points I tried to make earlier is that using human "intelligence" as a yardstick for intelligence in general is like using a Cray XMT as your yardstick for evaluating the "intelligence" of an abacus. In virtually every discussion I have read about "intelligence" at ID blogs, there seems to be an unspoken yet universal assumption that "intelligence" is an either/or phenomenon: either something is at least as intelligent as a human (or the Intelligent Designer aka God) or it isn't intelligent at all.

How "intelligent" a virus like the lambda bacteriophage? If "intelligence" is to be a useful (not to mention empirically measurable) phenomenon, it seems to me that it should fall somewhere along a spectrum, from the "intelligence" manifested by simple viruses up through the "intelligence" manifested by complex animal societies such as ours.

The latter point - that "intelligence" must somehow be massively multiplied as the result of social/collective interactions - is also non-trivial. As I pointed out earlier, an individual termite is extraordinarily "stupid", especially by human standards. Indeed, taken out of their social contexts, the behaviors of most social organisms seem pointless and almost random. However, what appear to be pointless and virtually random behaviors when viewed at the individual level become extraordinarily complex and "hyper-intelligent" when one moves up in organizational levels in animal societies.

How "intelligent" would each of us be, if we were forced to live in complete isolation from all other humans? If we were forced to do so from birth, our "intelligence" would be so limited as to result in almost instant death. Ergo, if one uses "able to live independently" as one's criterion for "intelligence", one would have to conclude that oak trees are immensely more intelligent than humans.

In my opinion, until ID theory comes to grips with the concept of "intelligence" in such a way as to make it both empirically verifiable and quantifiable, ID "theory" will continue to be not much more than unsupported speculation.

As a first approach to an operational definition of intelligence, consider whether learning is a necessary component of intelligence. Several commentators have strongly implied that this is the case. That is, the more an entity is capable of "learning", the more intelligent it is.

However, using the ability to learn as a criterion for intelligence is fraught with difficulties. For example, termites do not learn to build termite mounds, yet virtually everyone in this thread has agreed that mound-building behavior in termites indicates that termites (at least as a group) are indeed intelligent. Ergo, it is quite clear that an entity that is utterly incapable of "learning" can still qualify as being highly "intelligent".

This would also apply to some ID supporter's assertion that the Intelligent Designer is the God of the Abrahamic religions. This entity is universally recognized as being a "4-O deity": that is, He is omnibenevolent, omnipotent, omnipresent, and omniscient. However, this last quality also strongly implies that the ID/God does not learn from His actions, as to do so would be directly contradictory with His being forever omniscient (i.e. from the beginning to the end of time, assuming that time does indeed end). Ergo, the ability to learn is quite clearly not a criterion for determining intelligence, if one assumes that the Intelligent Designer of ID theory is the God of the Abrahamic religions.

If one is familiar with so-called "expert systems" in computing, the same would be the case. Expert systems (ESs) do not "learn" to do anything in the sense that animals with "wet" minds do. On the contrary, an ES performs a complex (sometimes recursive) calculation using data embedded in one or more "truth tables", producing a calculated outcome. This outcome is sometimes hedged with statistical error calculations, but it is a calculated (i.e. not learned) outcome nonetheless. While the final calculation produced by an ES can be modified, this happens only when the values in the "truth tables" are modified. Otherwise, the outcome is simply a calculation. Ergo, expert systems do not actually "learn" anything, at least in the same way that animals (and some other living organisms) do.

So, I believe that it is fair to conclude that the ability to "learn" is quite clearly not a necessary criterion for intelligence. Some highly intelligent entities (such as termite colonies and the God of Abraham) are clearly incapable of true "learning". Conversely, some very unintelligent entities, such as bacteria, are nonetheless capable of changing their behavior over time in response to changes in their environment (the standard operational definition of "learning" in the cognitive sciences).
CONCLUSION: Intelligence is fundamentally unrelated to the ability to learn.

Which brings us back once again to the fundamental question: what is "intelligence", how can it be observed, and can it be quantified in any way? If not, then ID is quite literally a "science" without an empirically definable subject, and therefore a pointless exercise in mental masturbation.

One might also be tempted to define "intelligence" as "adaptability". That is, an "intelligent" entity has the ability to adapt its behavior (and, presumably, its underlying cognitive machinery by means of which its behavior is generated and regulated) in response to changes in its environment. However, this presents two serious problems to an ID supporter:

1) "Adaptability" is what natural selection is all about. Why posit the existence of an "intelligent" entity that is capable of "adapting" to changes in the environment, when this is precisely what natural selection is supposed to be able to do?

2) Since ID is supposed to be a theory that explains adaptation, then saying that the Intelligent Designer (i.e. the entity that moulds adaptations) is adaptable is essentially defining "intelligence" via constructing a tautology:

• "intelligence" = "ability to produce adaptations"

• "intelligent design" = the process by which adaptations are created

Ergo, "intelligent design" reduces to "adaptability producing adaptations".


This is what is sometimes referred to in logic as the "dormative principle" argument, from Moliere's "The Imaginary invalid". When asked how or why opium produces sleep, the learned doctor replies "because it contains a 'dormative principle'"; that is, it causes sleep because it contains a material that causes sleep. In the same way, defining "intelligence" as "the ability to adapt to changes in the environment" (including changes that have not yet happened, i.e. foresight) reduces to "design that is 'adaptable' because it is 'adaptable'".

Where does this leave us in a search for an empirically quantifiable definition of "intelligence"? And if the answer is, "nowhere", then where does this leave "intelligent design"?

In the same line of argument, one clearly cannot define "intelligence" as "that principle/process/quality by which complex specified information is produced". To do so would once more be arguing via tautology:

Question: What produces "complex specified information"?

Answer: Intelligence.

Question: What is "intelligence"?

Answer: That principle/process/quality that produces complex specified information.

Ergo, "the principle/process/quality that produces complex specified information" is what produces "complex specified information".


Again, a pointless exercise in semantic gymnastics.

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

--Allen

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Saturday, May 02, 2009

How Not To Fight A "Culture War"


There has been an interesting and often heated discussion about "methodological naturalism" taking place at Uncommon Descent. After more than 350 comments, the dispute about what "methodological naturalism" was, and how long scientists have been practicing it was resolved in the way that most such discussions are resolved: with the participants agreeing to disagree.

I think it would be interesting for both sides in the debate around methodological naturalism (MN) to consider why this term has become so widely used in recent times. For the sake of argument, let us assume that the entire concept of MN only became "solidified" following Paul de Vries' coinage of the term in 1983. Also for the sake of argument, let us concede that prior to that time the use of "non-natural" assumptions was indeed legitimate for at least inspiring scientific research (as, indeed, history shows us was clearly the case). Let us then further assume that the current application of MN does indeed exclude any reference to "non-natural causes", either in the design of experimental tests of hypotheses or in their interpretation.

One might then reasonably ask, "What happened in the early 1980s that prompted such a dramatic shift in the perception of scientists, so dramatic that it led most scientists to reject what had previously been allowable: that is, the use of "non-natural" hypotheses as an inspiration for scientific research (if not necessarily also in the interpretation of the results of such research)?

I believe that if one examines what was happening the early 1980s vis-a-vis evolutionary biology, the answer to this question is obvious: the rise of "scientific creationism" (especially of the "young Earth" variety) as a political force in the U.S., culminating in the Supreme Court of the United States (SCOTUS)'s decision in Edwards v. Aguillard (
482 U.S. 578
) in 1987. During the 1960s, American science was promoted very vigorously, both by the U.S. government and by scientists themselves, as a reaction to scientific advances by the Soviet Union (particularly the launching of Sputnik, the first artificial satellite). Part of this promotion involved the formulation of the Biological Sciences Curriculum Study (BSCS) protocol and its associated textbooks (the "blue", "green", and "yellow" versions). All three versions stressed evolutionary theory as providing a foundation for the biological sciences. This was virtually the first time since 1925 (and the conviction of John T. Scopes for having violated Tennessee's Butler Act by teaching evolution in a public school classroom) that evolutionary theory had been so prominently featured in biology textbooks that were widely promoted in the American public school system.

This caused an immediate negative reaction among American evangelical Christian groups. Legislative bans on the teaching of evolution similar to the Butler Act were either reinstated or promoted in several states. At the same time, Henry Morris and other "scientific creationists" founded and promoted the "scientific creationism" movement, which sought to provide scientific evidence for their version of "young Earth creationism" (YEC). Not much actual science was done by these self-described YECs, but strenuous political efforts were undertaken to have their YEC reinterpretations of existing scientific information incorporated into public school curricula in several states (most notably Arkansas and Louisiana).

In reaction to these efforts by YECs, the scientific community partnered with the American Civil Liberties Union (ACLU) and allied organizations to bring such efforts to the attention of the SCOTUS, with the intention of having them outlawed as violating the first amendment to the US constitution. These efforts were ultimately successful, as both laws banning evolution from public school science classes and the attempts to insert YEC in public school science classes were struck down as unconstitutional by the SCOTUS. These events, and not the subsequent rise of Intelligent Design (ID), are the context within which the adoption of MN by the scientific community in the 1980s can most effectively be viewed.

From my interactions with them, I have found that some ID supporters are very strongly in sympathy with the YECs, and view ID as a way of getting their version of YEC back in the public schools. This was clearly the case in the Dover Area school board's 2005 attempt to provide students with alternative biology textbooks incorporating ID, as shown by the sworn testimony by several of the members of that school board and other members of the board who were present at meetings at which this plan was discussed and approved.

However, in my interactions with other ID supporters (and especially the members of the Cornell IDEA Club and some commentators at Uncommon Descent), I have come to understand that a significant fraction of ID supporters do not accept that YEC is a legitimate empirical science, nor support it's incorporation in public school science curricula.

The dispute that has occurred in this thread (and similar recent disputes elsewhere) seem to me to be examples of people "fighting the last war" rather than dealing with the situation as it exists today. ID supporters who are not YECs need to understand that most evolutionary biologists lump the two together, partly because of the behavior of the Dover Area school board and similar, more local situations in which YECs have persisted in pushing their views into the public schools. At the same time, evolutionary biologists and their political supporters need to understand that there is no necessary connection between YEC and ID, nor are they united in their conviction that YEC and ID must be incorporated into the public school curriculum today.

A recognition of the political contexts within which both evolutionary biologists and Intelligent Design supporters have come to their positions, and what these contexts imply about the value of possible further actions would be valuable for both sides in this debate. I have had many ID supporters say privately to me that Dover was a disaster for ID, and especially for its quest to be accepted as a legitimate empirical science. I have also had many evolutionary biologists express to me their opinion that there is essentially no difference between YEC and ID, a viewpoint that I have learned through experience is clearly in error.

Ergo, I have concluded that the most effective way to move forward in this debate is the way I have been conducting it since the mid-1990s. That is, to invite supporters of both sides of the debate to make presentations in my evolution courses and seminars at Cornell and to conduct such debates in public forums such as this website. Ironically, I find this venue to be much more congenial to such debates than places like AtBC, in which character assassination is the order of the day, rather than the last resort of people who are either confused about their own position or uncertain about its logical force.

And so, I recommend that all participants in this debate avoid name-calling and ad hominem arguments. For each committed commentator on both sides of this issue, there are many thousands of quiet observers who are trying to come to their own conclusions about the issues being debated. While mud-slinging is fun, it's fun in the same way that smoking or drinking heavily is fun; it provides short-term personal gratification, but in the long term it undermines everything one is trying to accomplish.

I believe that clarity should be our goal, not necessarily agreement. If we come to clarity about our positions and agree to disagree, then we have accomplished a great deal more than we would have accomplished if our goal was simply to attack our opponents' characters or to question their personal motives. Going forward I will do my best to pursue this course of action, and recommend that all who genuinely wish to come to clarity on these issues and, by doing so, help the "silent watchers" of this forum to do so as well, treat each other as colleagues (in the "collegiate" sense of that word) in their pursuit of what they perceive to be the truth, rather than as enemies in a culture war.

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

--Allen

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Wednesday, April 29, 2009

More on Teleology in Evolutionary Biology


I’ve been corresponding via email with a fellow evolutionary biologist (who shall remain nameless). I thought that some of her/his comments might be useful or interesting to those who read this blog, as they have a direct bearing on the "problem" of purpose (i.e. teleology) in evolutionary biology.

My correspondent's comments and questions are in block quotes:
I’ve been following the ‘Survival of the Sickest’ thread at Uncommon Descent, and have some comments on it and on your essay on the (un)reality of adaptations.

First, a major area of agreement between us is that the original post is fatally flawed by:

1) the assumption that “Darwinism” implies “constant progress”, and

2) failure to understand that fitness is always defined relative to a particular environment, and that environments change over time.

Now, on to some points of disagreement:

You mentioned Gould and Vrba’s 1982 paper on exaptation, and wrote:

"The reason is quite simple: if (as Gould, Lewontin, and Vrba argue) adaptation isn’t legitimately part of what evolutionary theory is about, then the whole idea of “design” and “function” is read completely out of evolution, leaving only descent with modification."

I have been very strongly influenced on this topic by Warren Allman, director of the Paleontological Research Institute here in Ithaca. He asserted that all adaptations should be considered to be exaptations. His rationale for this assertion was that the term “adaptation” has built into it an assumption of teleology. Literally translated, the word "adaptation" means “toward usefulness”. It’s the “toward” part that is the problem. As you and I both understand it, evolution (including natural selection, but not artificial selection) does not tend toward anything. It has no goal as far as we can tell. Ergo, it builds on what has gone before, but without any specific goal “in mind”.

This is why “exaptation” expresses better how we understand natural selection. It builds “away from” non-functionality (or even away from previous functionality), but never really “toward” anything at all as far as we can tell. And, if Sewall Wright’s “shifting balance” theory is a reasonable model of evolution, then it never really “arrives” anywhere at all, since the “goal” is constantly shifting anyway.
I’m wondering why you think that Gould and Vrba regard adaptation as being outside the legitimate scope of evolutionary theory. My take on the paper is not that they regard the concept of adaptation as illegitimate, but just that it has been typically construed too broadly and should be broken down into the categories of true ‘adaptation’ and ‘exaptation’, where they define a true adaptation thusly:

“Following Williams, we may designate as an adaptation any feature that promotes fitness and was built by selection for its current role.”

The problem I have with this definition is the inclusion of the words “promotes” and “for”. “Promotion” means exactly what it says: “motion towards” something. Ergo, using this word immediately suggests teleology, and as I have pointed out above, teleology cannot be a valid assumption in the origin of the products of evolution at any level. This is not because including teleology allows for “a divine foot in the door” (c.f. Lewontin, 1997), but rather because it requires that the “plan” for the teleological process must exist prior to the coming into being of that process. When we do things, this assumption is perfectly valid, but when something happens in nature, such an assumption is entirely unwarranted. Where, in nature, could such a pre-existing plan exist?

As for the word “for, I always point out to my students that teleological explanations virtually always reduce to sentences that include the phrase “in order to”. This can be shortened even further to “to” (leaving out the “in order”). However, the entire phrase “in order to” can be replaced with the word “for” without changing its meaning. Ergo, the definition quoted above is still irreducibly teleological, and therefore includes an assumption that we should not make in evolutionary biology.

In my paper on the evolution of the capacity for religious experience, I began with a succinct definition of “adaptation”, from which I lay out four criteria that a characteristic (i.e. a “trait”) must meet to be considered a genuine adaptation.

An evolutionary adaptation is any heritable phenotypic character whose frequency of appearance in a population is the result of increased reproductive success relative to alternative versions of that heritable phenotypic character.

Here are the four criteria that I believe must be met for a characteristic to be considered to be an adaptation:

1) An evolutionary adaptation will be expressed by most of the members of a given population, in a pattern that approximates a normal distribution;

2) An evolutionary adaptation can be correlated with underlying anatomical and physiological structures, which constitute the efficient (or proximate) cause of the evolution of the adaptation;

3) An evolutionary adaptation can be correlated with a pre-existing evolutionary environment of adaptation (EEA), the circumstances of which can then be correlated with differential survival and reproduction; and

4) An evolutionary adaptation can be correlated with the presence and expression of an underlying gene or gene complex, which directly or indirectly causes and influences the expression of the phenotypic trait that constitutes the adaptation.

I would now modify criterion #4 to state that such genes/gene complexes must be shown to have been conserved, relative to other sequences in the genome. However, one must keep in mind that such conservation, while necessary, is not sufficient. As we know now, some sequences are conserved, but can be knocked out, with no discernible effect on phenotype. Ergo, to fully satisfy criterion #4, a characteristic must be shown to be associated with a particular gene or gene complex, the knocking out of which can be shown to have significant negative effects on fitness.

Obviously, this means that a great many characteristics that we observe in living organisms will not qualify as adaptations. I believe that this is fully justified, following Williams’ assertion that the concept of adaptation is “onerous” and should only be resorted to “in the last resort”. It is only by doing so that we may avoid the otherwise almost inevitable pitfall of appealing to teleology in our explanations.
Gould and Vrba close their paper with this:

“The argument is not anti-selectionist, and we view this paper as a contribution to Darwinism, not as a skirmish in a nihilistic vendetta. The main theme is, after all, cooptability for fitness. Exaptations are vital components of any organism’s success.”

There’s that nasty little word “for” again! Fitness is immediately measurable as relative differential reproductive success, but “adaptation” can only be legitimately inferred retrospectively. We can’t say that something is a genuine adaptation until it already is, and this seems to me the kind of logical circularity that has also plagued Herbert Spencer’s phrase “survival of the fittest”. If we stick to the four criteria listed above, we will rarely fall into the trap that teleological thinking always sets for us.

Also, you later wrote the following, which seems to acknowledge that Gould and Vrba did regard adapation as a legitimate part of evolutionary theory:

“Yes, indeed, except that I believe that Gould, Lewontin (and later, Vrba) were, like Darwin, unwilling to take their principles to their logical conclusion: that adaptations (like species) are a figment of the human imagination, and do not actually exist in nature (or, to be even more precise, do not have to exist in nature).”

What I meant by this is that the only way we can actually “detect” the presence of adaptation is by inferring it. In that sense, adaptations are not “primary” characteristics; that is, characteristics that can be directly observed (such as differential reproductive success). Rather, such “secondary” characteristics must be indirectly inferred. In that sense, they are indeed “imaginary”; we must “imagine” that they exist (as the result of our application of inferential logic), as we cannot observe them directly.
Am I missing something? Are you trying to say that although Gould and Vrba regarded adaptations as real, they nevertheless thought they should be excluded from evolutionary theory?

No, I’m saying what Williams was saying, only I’m saying it more strongly and consistently: that we should never include any hint of teleology in our explanations, as such inclusion includes the biological equivalent of that old bugaboo of physics: “action at a distance” in physics is the equivalent of “goals preceding causes” in biology.

When I reread Williams’ famous 1966 book, Adaptation and Natural Selection, which supposedly reads teleology out of evolutionary biology, I was astonished to find it shot through with the same kind of teleological reasoning that he was supposedly trying to eliminate. I think I could find all the “hidden teleology” in Williams because I have spent so much time debating with ID supporters. They are the ultimate teleologists, and can always find where we have subtly woven teleological assumptions into our biology.
Finally, you wrote:

“To be as clear as I can, I believe that asserting a position of “metaphysical materialism” is just that: a metaphysical, not a scientific assertion. Confusing metaphysics with science is nearly as pernicious as confusing “ought” and “is”. The former makes for questionable science and the latter makes for questionable ethics.”

I would agree that science has no say on metaphysical questions that don’t have observable consequences (although I would argue that even then, Ockham’s razor should cause us to prefer simpler metaphysical systems to needlessly complex ones). However, some metaphysical assertions do have observable consequences. For example, I consider the existence of the Young Earth Creationists' God to be a metaphysical assertion that has nevertheless been decisively falsified by science.

I agree, but the same cannot be said for the more subtle versions of teleology found in Michael Behe or William Dembski's works. Their books (especially Dembski’s) present a much more subtle and less easily refuted version of teleological explanation, one that is easily reinforced by our own unwitting resort to teleological explanations.

Evolutionary adaptation is where the rubber of both evolutionary theory and ID hit the road.
Now on to your essay “Are Adaptations ‘Real’?”

You wrote:

“...although there are characteristics of organisms that are correlated with relatively high reproductive success (and would therefore be considered by most evolutionary biologists to qualify as “adaptations”), it becomes problematic to decide exactly which of those characteristics are the “real” adaptations and which are merely ‘accidental’”.

The problem, of course, is the words “real” and “accidental”. If we are genuinely dedicated to rooting out teleology in all of our explanations of the origins of biological objects and processes, then all adaptations are “accidental”, in the sense that they are all unplanned. We perceive them as having “functions” because our naive viewpoint of reality is always teleological. We can think non-teleologically only with very great difficulty. It’s like special relativity or quantum mechanics. We have to twist our minds to be able to even begin to conceive of them, and even then we constantly slide back into our naive (and unwarranted) views of reality.

True, if by “accidental” adaptations you mean exaptations. But while it may sometimes be difficult to tell whether an adaptation is “real” or “accidental”, that is not evidence that “real” adaptations don’t exist. Indeed, the only scenario I can envision in which “real” adaptations would not exist would be one in which every fitness-enhancing feature was an exaptation.

Exactly!
But that would mean, among other things, that every incremental improvement to the eye would have to have been the accidental result of changes that were selected for some reason other than improved vision. That seems far-fetched to me. Am I misunderstanding your position?

It’s not that that every incremental improvement to the eye would have to have been the accidental result of something, it’s that every incremental change to the eye would have had to originate accidentally, but then increase in frequency as the result of differential survival and reproduction. If we think the way you worded it (and we almost always think that way), then the teleological trap is that all of the incremental changes are somehow “predestined” and that complex eyes must be the inevitable result.

But this just plays into the hands of intelligent Design supporters. When we argue that “half an eye is still adaptive” we unwittingly include the assumption that “half an eye” is just that: half of what will ultimately evolve by natural selection. But our knowledge of the natural history of vision has shown us over and over again that “half an eye” is the whole thing in many cases. We can only say that the eyes of, say, flatworms, are “half an eye” because we already know that such a thing as a “whole eye” exists in cephalopods and vertebrates. We have to disabuse ourselves of the idea that any characteristic is only partially the whole deal. All characteristics of all organisms are the whole deal for those organisms, period, end of story, that’s all She wrote. Anything else contains the beginnings of teleology, and that way lies error, endlessly compounded.
We now have the ability to selectively delete individual characteristics from many different organisms. This makes possible something that natural selection does not: the precise determination of the selective “value” of particular characteristics. This has already been done, and the surprising outcome has been that even some gene sequences that were thought to have been very important in selection (due to having been “conserved” over deep evolutionary time) are apparently insignificant or useless. We know this because knocking them out of the genome has no discernible effect on the survival or reproduction of the “knock-out” progeny.

Precisely my point, above.
That interpretation seems to depend on the hidden assumption that the environment hasn’t changed significantly in the recent history of the organism, and that the experimental environment is fully representative of the historical environment over the entire time during which the features in question evolved. In the case of knocked-out sequences that have no apparent effect on fitness, how sure are we that the experimental environment is fully representative in this way?

No, but to assume that we are making the opposite mistake - assuming that some characteristic really has some function, even if that function is entirely unobservable - is once again to fall into the “teleology trap”. This is essentially the same argument that ID people make about “junk DNA”. Just because we haven’t found any function for it, doesn’t mean that all of it has no function. They argue that all of it must have some function. They are, like the evolutionary biologists for whom Williams, Gould and Lewontin, and Gould and Vrba wrote their warnings about, assuming teleology in evolution: they are, in a word, “pan-adaptationists”.
As a hypothetical example, imagine a bacterial DNA sequence that is expressed only during the formation of spores to protect the organism during periods of extreme environmental conditions. Knock out the sequence and test the viability of the resulting variant. If the experimental environment doesn’t include the extreme conditions that induce spore formation, the organism will never attempt to express the knocked-out sequence, and so its absence will not be noticed. If the experimenter concludes that the sequence is insignificant or useless, she is mistaken.

True, but I would strongly prefer that adaptation be considered a “diagnosis by exclusion” rather than our first and most important resort. By focusing on adaptation and natural selection, we teeter on the edge of the “teleology trap” and often (maybe even usually) fall in, despite our best efforts to avoid doing so.

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

--Allen

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Wednesday, April 22, 2009

Why Intelligent Design Supporters Insist That ID Must Be True


It has taken me a very long while, but I think I finally understand why Intelligent Design (ID) exists, why websites like Uncommon Descent exist, and why the regular commentators who support ID at those websites are so determined to assert the absolute reality of ID, in spite of a complete lack of empirical evidence.

It’s all right here in this quote about the ultimate justification for morality:
“Of course [the validity of an objective moral code] is all dependent upon the truth of the existence of God and the truthfulness of scripture - most of us here are aware of that.”

I believe that this is the crux of the whole science versus ID debate: if there is no empirical evidence for the existence of God, then it all comes down entirely to pure, unsupported supposition. Yes, one can assert that God exists, and can assert that therefore whatever God asserts must, by definition, be the absolute objective truth, but by the standards of scientific logic (which are now almost universally accepted as providing the most reliable evidence for descriptions of reality), arguments based purely and solely on assertion are no longer considered valid.

Ergo, without some independent source of evidence – independent of the original assertion, that is – then it all comes down to dueling assertions, which means that eventually it all comes down to force majeure: whoever can make the most forceful assertion gets to define the Truth.

Therefore, there must be some kind of empirical evidence for the existence of God. The fact that no one has ever found any is completely irrelevant, and will remain so indefinitely. It also explains why it is perfectly legitimate to deliberately distort, misinterpret, omit, or otherwise alter empirical evidence if it does not support the otherwise unsupportable assertion that God exists. [1]

Here is the way it looks to me:

Condition #1:

• If a moral code is not objective, it is ipso facto invalid.

• The moral code asserted by God is the only objective moral code. [2]

• If God does not exist, then there is no basis for the assertion that there is an objective moral code.

• Therefore, if God does not exist, anything is permitted.

Condition #2:

• An argument supported purely by assertion(s) is invalid. [3]

• Ever since Francis Bacon’s Novum Organum, it has generally been considered necessary that there should be empirical evidence (either direct or indirect) in support of arguments.

• Ergo, there must be empirical evidence in support of the assertion that God exists. Otherwise, there can be no objective morals, and therefore anything is permitted.

Conclusion:

Since God must exist (otherwise there are no morals and anything is permitted), then there must be empirical evidence for His existence. Finding none, it is therefore necessary to pretend that some exists, or to make some up. Otherwise there can be no objective basis for morals, society will necessarily collapse into chaos, and we will all inevitably become insatiable, maniacal, cannibalistic, orgiastic mass murderers, rapists, and thieves.

It also seems to me that this is the reason why ethical philosophers now virtually unanimously agree that ethical prescriptions cannot be derived from statements derived from empirical science (i.e. "ought" cannot be derived from "is"). To do so not only conflates two separate domains of logic (i.e. deductive versus inductive), but also requires that there be empirical evidence for something (i.e. ethical prescriptions) that are not and cannot be justified by empirical analysis (i.e. the workings of nature). Yes, we can use empirical analysis to determine if our ethical prescriptions have brought about the goals which we have decided to pursue, but we cannot use empirical analysis to formulate those goals.

Notes:

[1] Unsupportable on the basis of empirical evidence, that is.

[2] An obvious corollary to this is that each and every one of God’s moral prescriptions is both objective and absolutely True, by definition. Hence the argument that anything God prescribes (such as the massacre of the Canaanites) is morally right, simply by virtue of His saying so.

[3] To be specific, arguments based purely on deductive (i.e. Aristotelian) logic have been largely superseded by arguments based on inductive logic.

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

--Allen

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Monday, April 20, 2009

Evolution: Is Free Will An Illusion?


Every summer I teach a seminar course at Cornell in which we examine the historical, philosophical, religious, and scientific implications of evolutionary theory. This summer our seminar course will consider the question: Is free will an illusion?

On the 15th of July, 1838, Charles Darwin began a notebook which he labeled as “M”, in which he intended to write down his correspondence, discoveries, musings, and speculations on “Metaphysics on Morals and Speculations on Expression”. On page 27 of that notebook, he wrote
“…one doubts existence of free will every action determined by hereditary constitution, example of others or teaching of others. (…man…probably the only [animal] affected by various knowledge which is not heredetary & instinctive) & the others are learnt, what they teach by the same means & therefore properly no free will. [Emphasis added]

In his private musing on the question of free will, Darwin came to the conclusion that human free will is an illusion, and that all of our actions (and, by extension, our thoughts and intentions) are the result of our “hereditary constitution” and “the example…or teaching of others.”

Some evolutionary biologists, notably William Provine of Cornell University, have followed Darwin’s lead and asserted that human free will is an illusion. Most philosophers disagree, asserting that free will is the principle difference between humans and non-human animals. Many Christian theologians go further, asserting that free will is the foundation of all human action, without which no rational ethics or theology is possible.

In our seminar course this summer we will take up this debate by considering two alternative hypotheses: (1) that human free will is real and forms the basis for our morals and ethics, or (2) that human free will is an illusion, the capacity for which is a product of the same evolutionary processes that have shaped our anatomical and behavioral adaptations. Included in this debate will be an extended consideration of the hypothesis that the capacity for ethical decision making is an evolutionary adaptation that has evolved by natural selection. We will read from some of the leading authors on both sides of the subject, including George Ainslie, Daniel Dennett, Robert Kane, Daniel Wegner, and Edward O. 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.

Here are some particulars for the course:

INTENDED AUDIENCE: This course is intended primarily for students in biology, history, philosophy, religious studies, 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 general evolutionary theory, evolutionary psychology, sociobiology, and the philosophy of human free will would be useful.

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 23 June 2009 and ending on Thursday 30 July 2009.

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 4670 / BSOC 4471 can be used to fulfill biology/science distribution requirements and HIST 4150 / STS 4471 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. 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:

Ainslie, G. (2008) Breakdown of Will, Cambridge University Press, ISBN: 0521596947 (paperback: $34.99), 272 pages.

Dennett, D. (2004) Freedom Evolves, Penguin Books, ISBN: 0142003840 (paperback: $17.00), 368 pages.

Kane, R. (2005) A Contemporary Introduction to Free Will, Oxford University Press (USA), ISBN: 019514970X (paperback: $19.95), 208 pages.

Wegner, D. (2003) The Illusion of Conscious Will, MIT Press, ISBN-10: 0262731622 (paperback: $21.95), 419 pages.

Wilson, E. O. (2004) On Human Nature (Revised Edition), Harvard University Press, ISBN: 0674016386 (paperback: $22.00), 284 pages.

OPTIONAL TEXTS:

Darwin, Charles (E. O. Wilson, ed.) (2006) From So Simple a Beginning: Darwin's Four Great Books. W. W. Norton, ISBN-10: 0393061345 (hardcover, $39.95), 1,706 pages. Available online here.

Fisher, J., Kane, R., Pereboom, D., & Vargas, M. (2007) Four Views on Free Will, Wiley-Blackwell, ISBN: 1405134860 (paperback: $33.95), 240 pages.

Kane, R. (2001) Free Will (Blackwell Readings in Philosophy), Wiley-Blackwell, ISBN: 0631221026 (paperback: $33.95), 328 pages.

Wilson, E. O. (2000) Sociobiology: The New Synthesis (25th Anniversary Edition), Belknap Press, ISBN: 0674002350 (paperback: $44.00), 720 pages

Our summer seminar course is always fascinating, and often quite controversial (see this and this). Over the years we have explored many of the implications of Darwin's theory, and the participants have always found our discussions (perhaps they should be called "debates") enlightening. As always, the intent is not necessarily to reach unanimity, but rather for each participant to come to clarity on where they stand on the issues and to be able to defend that stance using evidence and rational argument.

So, please consider taking our seminar on free will this summer - the choice is yours!

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

--Allen

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Tuesday, April 14, 2009

Evolution: The Darwinian Revolutions


Long-time readers of this blog will know that every summer I teach an introductory evolution course for non-scientists at Cornell. This year the focus of the course will be somewhat different. In honor of the bicentennial of the birth of Charles Darwin and the 150th anniversary of the publication of his monumental book, On the Origin of Species..., we will be focusing on the impact of Darwin's concept of evolution by natural selection, both on the sciences and on society as a whole.

Darwin's theory of evolution is the most revolutionary idea ever entertained by the human mind. It fundamentally alters our perception of reality. In profound and unsettling ways the theory of evolution changes our understanding of who we are, where we come from, why we do the things we do, and where we might be going. It does this by making us look carefully and dispassionately at the world around us, asking questions and seeking answers in the things we can observe.

This summer we will explore Darwin's theory and the impact that it has had on the sciences and on human society. Here is the syllabus for the course:

EVOLUTION: THE DARWINIAN REVOLUTIONS
BIOEE 2070 / HIST 2870 / STS 2871
Cornell University Six-Week Summer Session – Summer 2009

PREREQUISITES: None - Intended for non-science majors with an interest in evolutionary theory

CREDIT HOURS: 3 (does not count toward evolution distribution requirement in biological sciences)

CLASS TIMES: Mondays and Wednesdays 6-9 PM, Monday 22 June 2009 to Wednesday 29 July 2009

CLASS LOCATION: Lectures in Morrison Room, Corson-Mudd Atrium. Discussions TBA in class.

COURSE FORMAT: The format for each class will be a two-hour interactive lecture/discussion, in which the professor outlines the major concepts, followed by a one-hour discussion section in which all participants present their interpretations and opinions of the concepts and readings under consideration. Participants will also have the opportunity to make full-length presentations of their original work. Grades will be based on the quality of three essays, due at the end of each two-week segment. Students may also opt to do one essay and a research paper (see description and point scores, below).

GRADE BASED ON: Attendance and participation in lecture and section, plus combined letter grade on three essays (suggested length = 4 to 8 pages) or one essay and one research paper (maximum length = 20 pages), for a total of 100 points (electronic/email submission encouraged, but not required)

COURSE DESCRIPTION: Evolution is the founding concept of the science of biology. This course examines evolution in historical and cultural contexts. Aims of the course include understanding the major issues in the history and current status of evolutionary theory and exploring the implications of evolution for culture and human psychology. Issues range from controversies over mechanisms of evolution in natural populations to the philosophical implications of evolutionary theory.

REQUIRED TEXTS:

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

Goldschmidt, Tijs (1998) Darwin's dreampond: Drama in Lake Victoria, MIT Press, ISBN: 0262571218 (paperback, $27.00), 274 pages.

Jabloka, Eva & Lamb, Marion J. (2006) Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life, MIT Press, ISBN: 0262600692 (paperback, $19.95), 474 pages.

Raup, David M. (1991) Extinction: Bad genes or bad luck? W.W. Norton, ISBN: 0393309274 (paperback, $14.95), 228 pages.

Ruse, Michael (2004) Darwin and design: Does evolution have a purpose? Harvard University Press, ISBN: 0674016319 (paperback, $19.50), 371 pages.

OPTIONAL TEXTS:

Darwin, Charles (1892) The autobiography of Charles Darwin (Nora Barlow, ed.), W.W. Norton, ISBN: 0393310698 (paperback, $14.95), 365 pages. Available online here

COURSE PACKET:

All of the course packet readings listed below are available from the course website. The password to access the course packet is “evolutioncp” (without the quotation marks). Alternate weblinks are provided for your convenience.

NOTE: Students will not be required to read all of these articles. Your instructor and/or TA will tell you which articles you are responsible for.

Ayala, F. (1970). Teleological explanations in evolutionary biology. Philosophy of Science, vol. 37, pp. 1–7.

Behe, M. (2002) Intelligent design as an alternative explanation for the existence of biomolecular machines. Unpublished manuscript.

Cosmides, L. & Tooby, J. (1997) Evolutionary psychology: A primer. Center for Evolutionary Psychology. Available online here

Dembski, W. (2005) What every theologian should know about creation, evolution, and design. Orthodoxy Today. Available online
here


Dobzhansky, T. (1973) Nothing in biology makes sense except in the light of evolution. The American Biology Teacher, vol. 35 (March 1973), pp. 125–129. Available online
here


Eldredge, N. and Gould, S. J. (1972) Punctuated equilibria: An alternative to phyletic gradualism. In Schopf, T. J. M. (1972) Models in Paleobiology, Freeman, Cooper, & Co., pp. 82–115. Available online here

Gould, S. J. And Lewontin, R. C. (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proceedings Of The Royal Society of London, Series B, vol. 205, no. 1161, pp. 581-598. Available online here

Huxley, T. H. (1860) Letter to Charles Kingsley, Available online
here


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

Kaviar, B. (2003) A history of the eugenics movement at Cornell. Unpublished manuscript.

MacNeill, A. (2004) The capacity for religious experience is an evolutionary adaptation for warfare. Evolution and Cognition 10:1, pages 43 to 60.

MacNeill, A. (2005) Natural selection, sparrows, and a stochastic God. Available online here

MacNeill, A. (2006) Vertical polygyny in modern America: An evolutionary perspective. Available online here

Mayr, E. (1974) Telological and teleonomic: A new analysis. Boston Studies in the Philosophy of Science, XIV, pages 91 to 117.

Mayr, E. (1982) The growth of biological thought. Harvard University Press. Chapters 12 & 13, pages 535 to 627.

Pinker, S. (2004) The evolutionary psychology of religion. Freedom From Religion Foundation. Available online here

Wegner, D. (2002) The illusion of conscious will. MIT Press: Cambridge. Chapter 3, pages 63 to 98.

PART ONE: THE ORIGIN OF EVOLUTIONARY THEORY
The science of evolutionary biology began with the publication of Charles Darwin's On the Origin of Species. It is one of the most important books ever written and should be read by any person who wants to understand who we are, where we come from, and why we are here (and how we know).

PART TWO: THE MODERN SYNTHESIS
Darwin's theory was accepted by most scientists of his generation within a surprisingly short time. Then, within just one more generation, it fell out of favor, replaced by genetic theories of evolution suggested by the rediscovered work of Gregor Mendel. Then, in another generation, the pendulum swung the other way, and Darwin's ideas were integrated with Mendel's and codified in the "modern synthesis."

PART THREE: MACROEVOLUTION, EVO-DEVO, AND BEYOND
Evolutionary theory has exploded in the fifty years since the "modern synthesis" was proclaimed. Sociobiology, punctuated equilibrium and new ideas about evolutionary psychology, genetic engineering, macroevolution, speciation…these are just a few of the directions that evolutionary theory and biology have expanded in the second half of the 20th century and the beginning of the 21st.

I would like to invite anyone who has found this blog interesting to take this course, or follow along with us by keeping up with the course materials posted at the course website. Either way, you will find your mind being stretched and your view of reality challenged. What better way could one spend a few summer evenings?

See you this summer!

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

--Allen

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Wednesday, April 08, 2009

Platonic Ideal Forms Versus Evolutionary Developmental Biology


In a recent thread at Uncommon Descent,
Salvador Cordova
wrote:
"[The existence of] platonic forms would strongly suggest that [evolutionary] transitional [form]s don’t exist. And if there are only lawful morphological forms, transitional forms, even in principle, couldn’t exist. Transitional forms and Platonic Forms don’t fit well together in any theory. It appears the two are mutually exculsive.

In engineering we have many platonic forms. As engineers we are taught to recognize and implement certain canned architectures. A lot of systems biology is mapping biological forms to the forms engineers recognize.

[The] quest for “correct designs” ... makes sense in a world of ideal forms, platonic forms. We instinctively have platonic forms in our mind. We have a sense that a defect is a defect, that an error is an error.

In the Darwinian world, it’s all about selective advantage. A blind cave fish is “selectively advantaged”. Defect is only a relative term. However in the eyes of plato, a blind cave fish is less than the ideal, it is a broken form. In such case, natural seleciton helped to infuse the defect in the population and thus introduce a defect that is not consistent with the ideal pattern.

The notion of platonic forms does not seem to be compatible with Darwinian evolution. [Emphasis added]

The idea of Platonic ideal forms in biology is an old one. The now mostly defunct tradition of orthogenesis is essentially a version of Platonic ideal forms applied to biology (and an argument can also be made that Lamarck’s progressive theory of evolution by means of the inheritance of acquired characteristics is as well). However, and contrary to what some might expect, applying the concepts of orthogenesis to "intelligent design theory" ("ID") is problematic, because in its early 20th century form, orthogenesis was considered to be progressive, but not goal oriented (i.e. teleological).

In addition to the early orthogenesists, two other names stand out in this tradition: D’Arcy Thompson and Stephen Jay Gould. Both were primarily concerned with the origin and evolution of form, and both developed theories of evolution based on this. Even J.B.S. Haldane (one of the founders of the “modern evolutionary synthesis”) wrote in this tradition in his essay "On Being the Right Size". Haldane’s musings on the relationship between size and constraints on form have become known as “Haldane’s Principle”, and have recently been applied to urban planning.

The newly emerging science of evolutionary developmental biology (”evo-devo”) has some similarities to orthogenesis, especially insofar as both are attempts to explain why the evolution of overall form (i.e. phenotype) appears to be constrained to certain types of forms, rather than all possible forms. The orthogenesists asserted that there are certain forms that are much more likely than others. These forms are similar in some ways to Platonic forms, in that there is no necessarily materialistic explanation for the predominance of certain forms, at least according to the theory of orthogenesis.

Evo-devo explains the similarities within “formal types” with reference to shared developmental programs, especially among eukaryotes. This shared developmental programming is based on the hierarchical gene regulation systems, most of which are based on homeotic gene regulatory mechanisms. Similar developmental constrains appear to exist among plants and fungi, but not so much among prokaryotes and multicellular protists. So, looking for things that resemble Platonic ideal forms in biology will probably involve identifying and categorizing the various developmental “channels” which are produced by these homeotic gene regulatory systems.

None of this, of course, says how the various hierarchical gene regulation systems originally evolved. This is another of those “deep time” problems, such as the origin of life and the origin of the genetic code. As I have commented repeatedly in the past, I believe that questions about such origins are almost certainly unanswerable using current empirical methods.

I also personally believe that the question of the origin of Platonic ideal forms (if such things exist and are empirically distinguishable from the various “channels” produced by the action of homeotic gene regulatory mechanisms) is both an open question and one that is almost certainly not answerable using empirical methods.

For more on the question of Platonic forms in biology, see this and this.

For a critique of my analysis of Platonic ideal forms in biology, see this.

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

--Allen

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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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