5/17/2008

QUESTIONS FROM THE GALLERY

About three weeks ago, in response to my rather animated public denunciation of a presentation of Don Patton, some folk who attended Patton's presentations at Bullard High School expressed some interest in learning what the textbooks actually teach where evolution and natural selection are concerned. I promised to answer questions about the text and my curriculum, so you can expect to see many of these posts over the next week or so.

A correspondent, referencing a paper of mine*, writes:

“In the paper you state the general definition of evolution to be "change over time". This sounds to me like any form that changes/mutates (not sure if I'm using the right terms) to another similar form of equal complexity (micro-evolution), i.e., Darwin's finches, as reported by Peter and Rosemary Grant, qualifies under the general definition of evolution. Is there a different definition for the situation where one form, the coelocanth, mutates/changes into a land animal (macro-evolution)? Or is this still under the general definition of evolution?”

There are at least three potential pitfalls here, and none of them are religious in origin.

PITFALL #1: WHAT EVOLVES?

First of all, it is not an individual’s form that changes, as the brief ‘the coelocanth...changes into a land animal” would suggest. Rather, it is the frequency of alleles within a population that changes. Individuals don’t evolve; populations do, and it is truly amazing how many educated people routinely confuse changes in an individual’s form during its life (development) with changes in a population’s genetic makeup (evolution).

This is a prevalent misconception that works much mischief. For example, in the rather disappointingly-staged Ivan Reitman ‘comedy’ Evolution (it’s not all that funny, either), a whole batch of organisms changes right before our eyes, supposedly morphing in the span of a few hours from simple to complex life forms.



Similarly, as part of the Pokemon craze that peaked a few years back, a character such as ‘Pikachu’ is said to ‘evolve’ into ‘Raichu’—and pretty much instantly! The popular culture, in other words, routinely confuses evolution with metamorphosis, an amazing distortion when you think about it, but one that it is routinely accepted by both proponents and detractors of evolution alike. It’s difficult for me to overstate how much harm is done by this trope. It would be like a physics teacher having to explain, on a daily basis, that gravity is not magnetism, and it could only prosper if there was widespread ignorance about one or the other.


PITFALL #2: DOES EVOLUTION IMPLY COMPLEXITY?


“This sounds to me like any form that changes/mutates (not sure if I'm using the right terms) to another similar form of equal complexity (micro-evolution)...”

The notion of complexity is almost always misleading when considering individual cases of evolution. In the first place, what measure of complexity would you use? In the second place, regardless of which metric chosen, there is no reason to assume that evolution necessarily promotes any particular outcome where complexity is concerned.

True, populations may acquire adaptations rendering their members more fit in a given environment, but does that make the population as a whole more complex than the ancestral population from which it sprang? By no means. The ancestral population might’ve been exquisitely well-adapted to its past environment, much more so than the newly tinkered-with daughter population which is but recently responding to environmental change. In and of itself, evolution does not imply complexity.
In fact, in and of itself, evolution does not even imply speciation (the production of new species)! Evolution is best thought of as a tree with many nodes, rather than a 'ladder of progress' leading ever-upward.

The truth is that biologists don't use the terms ‘micro-evolution’ and ‘macro-evolution’ all that much, and when we do, we don’t use them in the way that the professional creationists do. The latter typically use ‘micro-evolution’ to describe the undeniable genetic changes that occur within populations, but ‘macro-evolution’ to refer to speciation events, which they seem eager to deny.

Now, this leads to an entire can of worms which is in fact religiously motivated, so I will save discussion of the alleged ‘micro/macro’ distinction for another time, but the key point is that, being undirected, evolution itself can not be said to promote complexity, nor necessarily to be in any way progressive.

PITFALL #3: IS THERE A ‘BAIT-AND-SWITCH’?


Is there a different definition for the situation where one form, the coelocanth, mutates/changes into a land animal (macro-evolution)? Or is this still under the general definition of evolution?”

A minor quibble: coelocanths and other crossoptygerian fish are not believed to be ancestral to land animals. But, yes, whether we are talking about changes that occur in a single generation or changes that accrue over many generations, we are still talking about a ‘change over time’ in a population of organisms. Unlike the people in Darwin’s day, we now know that what changes is the frequency of alleles in a population, and so the more precise genetic definition of evolution is still in play, as well.

But, at this point, an unbiased observer might not only wonder when one definition might be preferred over another, they would also wonder if there might be times when one definition is intended, and the other inferred? Or, even more sinisterly, if there might be times where evidence for one definition is misrepresented as evidence for the other—a ‘bait-and-switch’?

Many creationists are convinced that the latter is the case, because there is direct experimental evidence for the latter in contemporary populations, but none (for obvious reasons) from populations past. These creationists often adopt the pose of scientific purist, as if they have discovered some horrible methodological flaw in evolutionary biology, as if (gasp!) drawing inferences was inherently unscientific. They would have you believe that ‘microevolution’ (which they accept) is an example of proven‘operational science’ whereas ‘macroevolution’ is unproven ‘origins science.’

Again, we can discuss the particulars of that distinction at a later date. The point I just want to address is that some creationists imply that biologists are either playing a ‘shell game’ with the word ‘evolution’ in order to deceive the faithful, or that evolutionary biologists are inattentive to important distinctions where that word is concerned. In other words, we’re either lying or blind, which is not a terribly helpful stance.

For my part, I am sure that much of the problem here lies not with the science, but with how the science is presented in the popular culture. My curriculum tries to address that by being very intentional. The first definition is used when presenting the historical context in which Darwin first developed his theory, and when I give it I tell students they will eventually be responsible for a second definition which was developed in part to test the original theory. Later on, when I give the second definition, I remind students of the earlier definition and point out that what makes a theory scientific is that it can be modified or rejected in the light of new data, and that includes how words are defined.

That’s not ‘bait-and-switch.’ That’s the way science works. After all, Aristotle thought there were two forces in the universe: ‘gravity’ (the tendency of heavy objects to fall) and ‘levity’ (the tendency of light objects to rise). No contemporary physicist would be accused of ‘bait-and-switch’ just because they didn’t use Aristotle’s definition of gravity.

* I'm going to put this paper on the Net as a PDF file later this week.

UPDATE: The paper, "Show Me A Walking Fish and We'll Talk", is now available as a PDF file here. However, I should note that there is a misleading passage at the end that implies that crossoptygerian fish like coelocanths are ancestral to modern tetrapods. This is probably not the case! Rather, coelocanths and other creatures show transitional features such as choane which are believed to be derived from a common ancestor to other transitional forms, such as Tiktaalik.




6 comments:

Stan said...

Scott, Good to see you back on-line. But I have to ask: why do you continue to use "frequency of alleles" as the definition of evolution? If the alleles aren't there in the first place - let's say warm bloodedness - then they cannot be selected for. It requires mutation, pure and simple. This is not "religiously motivated", it is both rational and it is the only definition supported in all the literature, which I previously gave you.

If all the alleles for the human genome were present in the very first strip of DNA, then the entire concept is not parsimonious. To say that evolution is "frequency of alleles" is to say just that. Are you denying that mutation is, in fact, a requirement - absolutely necessary? The texts all refer to "natural selection operating on mutations" as the source of evolution; changing frequency of alleles is a result, not a cause. It is both a result of simple selection on pre-existing genomes, and it is also a result of selection of mutations...two separate issues. This is not just my opinion, it is documented.

Mutations are not metamorphosis, they are changes in genes which are passed down - changes for any reason. You seem to disavow this concept as being "creationist", when it is not, as I showed you with many references from biological sources. It is the denial of this that leads to suspicion of hanky-panky in the conceptual stages. Because exactly what mutations have led to higher animal forms? No increase in complexity? Hmmm. Dubious, and not just from a creationist standpoint.

Scott Hatfield . . . . said...

Stan, why do you continue to misread the literature?

Evolution is not a cause. It is a result. A 'change of the frequency of alleles within a population over time' is not a cause, either. It is merely another way to describe the result, which is to say evolution.

Here's a pretty straightforward treatment, from wikipedia:

Because an individual's phenotype results from the interaction of its genotype with the environment, the variation in phenotypes in a population reflects the variation in these organisms' genotypes. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridization in plants.


Notice, Stan, that the article stipulates that modern evolutionary theory actually defines evolution in genetic terms. So, by using that definition, I am just following convention.

Notice, also that there is more than one source of variation. Mutation (while obviously important) is not necessarily essential for every case of evolution. What is required is genetic variation. If you have a textbook or source that implies otherwise, it is either badly-written or out of date.

As for this or that being 'creationist', please don't misunderstand me. There is nothing inherently 'creationist' about any scientific fact, but their world view does lead them to admit or emphasize some things, and deny or deemphasize others.

For example, the important thing here is that many creationists admit that mutations occur, and that there can be selection for different alleles within a population, but deny that the cumulative effects of these processes can ever lead to something fundamentally new. They think that there is something typological or fixed about species, or (as they often privately describe them) the Biblical 'kind'. In their terminology, they admit 'microevolution' but deny 'macroevolution', by which latter they typically mean speciation and (by implication, what really rubs them the wrong way) the inference of common descent.

Speaking of which, Stan, I think at this point that you should probably put your cards on the table. I suspect all this beating about the bush where mutation is concerned is meant to buttress some skepticism you have about 'macroevolution'. Let's just get real, shall we?

Is the Earth old, or isn't it?

Do living things share common descent, or not?

Is the evolutionary processes that you've heard about sufficient to account for the diversity of life, or isn't it?

And, if you've answered in the affirmative to every item above, then what, exactly, is your point where mutations are concerned?

Puzzled...SH

Stan said...

So what I get from that approach is that evolution is defined not as a process, but as a result which is defined as "frequency of alleles".

(a)If evolution is the result of a process, but is not the process, then what is the process?
(b)Where do alleles come from? If there are zero alleles for hair in the genome of fish, from which we all apparently derived, then where did the alleles come from?
(c)Are you denying the sources I gave you, which include the following (just one):

The Cambridge Encyclopedia of Human Evolution; (c)1992, reprint 1999. Nine years old. Richard Dawkins name on the cover. Ch 7.3, Mutation and Human Evolution:

"Evolution depends on genetic diversity. New species are full of inherited variants not found in their ancestors, and millions of new genes have appeared since the origin of life. All this depends on inherited changes in the structure of DNA (mutation). [emphasis in the original].

and on pg 273,

"Mutation is the source of all the diversity that has led to the evolution of modern humans and to their divergence from other primates. However, mutation is an undirected process: it canot lead to evolutionary progress unless natural selection is at work."


These are genetic terms, unless you have a different definition. It seems to me that you are denying the process by defining the result as all there is.

Now, as to your questions:
Is the Earth old, or isn't it?

Based on the Grand Canyon, I'd say that the earth is very old. It shows much sign of erosion as opposed to single wash-out.

Do living things share common descent, or not?

I am skeptical, based on the evidence that has been presented as "conclusive", yet is extrapolated; I have not completed the journey through the "talk origins" site yet, but I am willing to discuss the development of ears from jaw bones.

Is the evolutionary processes that you've heard about sufficient to account for the diversity of life, or isn't it?

Sorry it is not, especially based on the vagueness of such things as "frequency of alleles". Defining a result while ignoring or denying the process that causes the result does not fit the process of science, in my opinion. If discussing the source of new alleles is not part of the discussion of how evolution happened, then it has become a religious topic, not an objective subject. In other words, "evolution happened: allele frequency changed; end of story".

As for me, I need a mechanism that makes sense. No effects without corresponding causes, if you will.

If you're trying to pin a religious motive on me, I have none. But I am suspicious of any illogical tenet that is used for political and social agendas. So far, evolution has not been proven so far as I can see... and new alleles DO appear, and if not due to mutation (the very definition of it) then where did they come from??

BTW, I think that microevolution would be "variation of frequencies of existing alleles in a population", and macroevolution would be "variation of the frequency of alleles, including new alleles, in a population". If you deny that there is a difference, I'll need to see you logic in its completeness, not just a new definition.

Regardless of that, however, to maintain that new characteristics do not require mutations of DNA being transferred is, well, just not logical.

I mean no disrespect; but if evolution is real, then it would be rational; if it is not rational then it probably is not real, unless it is tied into quantum theory or some other non-rational process. I have never heard any claim that it is non-rational. So I have to expect it to make sense.

A question for you:
Do you deny the Cambridge Encyclopedia of Human Evolution as a valid source?

bemused,
Stan

Stan said...

Ooops, I didn't address your last question to me:

"And, if you've answered in the affirmative to every item above, then what, exactly, is your point where mutations are concerned?"

Well I didn't answer in the affirmative, but I'd like to get on to the real issue here:

By denying that the movement of a population's allele frequency to be outside the original genome requires genetic mutation (changes to the DNA from its original state), absolutely halts the conversation at a point of vagueness, so that the real question is avoided:

"How did mutation cause new alleles for things like warm-bloodedness, or two-sex reproduction, or other innovations (what exactly is the DNA mutation that occurred); and what is the probability of such an occurrance?"

This seems to be a question that is being strenuously avoided, including redefining evolution to be just a result, not a process. We can't get to that question if the basis is being denied; in fact if there is no process, only results, the conversation is halted completely.

Scott Hatfield . . . . said...

(a)If evolution is the result of a process, but is not the process, then what is the process?

That's what I'm getting at. There are multiple processes known to cause changes in allele frequency within a population over time. Some processes generate variation, such as mutation and the recombination that occurs as a result of sex. Other processes/phenomena 'filter' the existing variation, among them natural selection, genetic drift and endosymbiosis.

Overemphasizing the role of mutation in evolution not only masks the true richness of evolutionary biology as a discipline, but it feeds a common creationist canard, which is that the incredulous straw-man version of evolutionary theory in which diversity is a product of randomness alone.

(b)Where do alleles come from? If there are zero alleles for hair in the genome of fish, from which we all apparently derived, then where did the alleles come from?

That's a good question. The general answer is that any process that promotes either a diversification, a rearrangement or an enlargement of the genome effectively generates new alleles. Mutation can be one of those processes, but it's not the only one.

A more particular answer for mammalian hair may or may not be known, but allow me to indulge in a little speculation guided by theory rather than particular findings. The chances are that the proteins involved in building hair are not all that different from those involved in building, say, the scales of a fish. The big difference likely comes from when and where the alleles that code for hair-type proteins are turned 'on' or 'off' by regulatory elements. Comparative genomics is a new field, but it has already led to some pretty interesting cases in which we can see that proteins that serve one function in one species can be shown to be extremely similar to different proteins that serve a very different function in another species.

I recommend that you read 'The Making of the Fittest' by Sean Carroll for an explanation of this burgeoning research field, and its significant to evolutionary theory in general. I suspect that these are evolutionary processes that you haven't heard of! They are certainly not discussed in the 'Cambridge Encylopedia of Human Evolution.' And, in fact, I do find the book's gloss on mutation which you quote to be not only poorly-expressed to the point of being misleading, but really behind the times today. It was written before the Human Genome Project was completed and before there was any meaningful work in comparative genomics. And it doesn't even discuss Hox genes, which were discovered a decade before the book's publication. Perhaps most importantly, that book was not intended to be a primer on molecular genetics or evolutionary theory in general, but rather focuses on particulars of primate evolution. It's a nice book on that topic, but where the former are concerned, not a good source.

Do living things share common descent, or not?

(you answered):

I am skeptical, based on the evidence that has been presented as "conclusive", yet is extrapolated...

You engineers don't seem to put much stock in inference, but you must surely recognize that multiple independent research programs all support the inference of common descent:

1) biogeography

2) the fossil record

3) homologous structures

4) vestigial organs

5) common embryological features

6) population biology

7) genetics of model organisms

8) molecular biology


Why do embryos of different species have pharyngeal gill arches during development? Why do pythons have rudimentary leg bones, and humans a tail bone, and whales unattached pelvises 'floating' in their bulk? Why do the fossils found in South America, on average, more closely resemble living South American species than living species of other continents? Why is the pattern of interior bone arrangement in all tetrapods so similar when their outer appearance so different, and their functions so diverse?

These are just a few examples. Not only are these extremely difficult to square with special creation, it's non-parsimonious to reject common descent as an explanation for such phenomena unless you have a better model. Which is more logical, to make an inference that is supported by multiple lines of evidence, or to maintain a stance of skepticism largely as a result of an engineer's intuition about how design happens?

You want to make the point that you have no religious ax to grind? Fine. For the purpose of this discussion, I have none either. But what is the alternative to TENS based on natural causes that could justify our skepticism? I don't think it exists, but let's say that there was such a model, that predicts the independent emergence and diversification of all lineages on natural causes alone.

Even if such a model existed, you would still be well-advised to reject it as unparsimonious unless it could be shown that it explained a larger class of observations with greater precision than the model of common descent.

Occam's razor, right?

In other words, "evolution happened: allele frequency changed; end of story".

Stan, if in fact evolutionary theory was nothing more than the above, it would deserve our pity. But of course it is more. The claim that evolution happened was made a long time before it was possible to even know what the basis of variation was, much less measure the extent to which alleles changed. So the genetic definition of evidence was, at one time, a key test of the evolutionary model. It could've worked out differently, that the math would've said the natural selection can't occur, or that the actual pattern of inheritance was immune to natural selection. But it didn't. Instead, the emerging field of genetics provided a key test of Darwin's theory. Genetics could've falsified evolution and common descent in principle; instead, it provided a far more precise and robust means of measuring evolution in populations. So, historically, the two claims are not tautological with respect to each other.

Nor is it correct to say that it is the end of the story. Again, by focusing so narrowly on mutations, you are largely ignoring the non-random effects of selection. In individual cases, the observation that evolution occurred in a given population is defined genetically, but that leads naturally to the question of what could be causing that particular change. It could be natural selection, or it could be something else, or perhaps multiple factors are involved.

Imagine if someone went up to an engineer and said something like, "There is such a thing as current; a current is a moving electrical charge--that's the end of the story."

Would you think that was a fair summation of the field of electrical engineering?

Stan said...

Scott said,
"I recommend that you read 'The Making of the Fittest' by Sean Carroll for an explanation of this burgeoning research field, and its significant to evolutionary theory in general. I suspect that these are evolutionary processes that you haven't heard of!"

Scott, we're going in the same circles that we went in last year. Here's the quote I gave you from "MOTF by Carroll (pg 17):

"...But where does this variation come from? And what happens if useful variations are not available? How long might a population have to wait for new variations to appear?
[new section, still pg 17]:
"THE MUTATION LOTTERY: WE ARE ALL MUTANTS [section title]
The source of all variety is mutation."


Last year you wound up denying this source as valid, just as every other source I have found [a goodly number now]. Your fear seems to derive from I.D.phobia: that admitting this will give a leg up to creationists. I suggest the contrary: that denying it makes for suspicions amongst the seekers of valid data.

And once again, all the lists of areas that are supported by speculation do not serve to quench the thirst for that which is real, and not speculated.

I do not see where electrical current is speculated; it is physically visible if one wishes it to be. Not the same as speculating a current.

Now if you wish to discuss human tailbones as proof of evolution, speculation is definitely the technique; moreover I agree with Einstein's assessment of parsimony: sometimes it is flat wrong; it is not a law of physics.

Why is it wrong to insist upon proof of a scientific conjecture? This is what engineers do, all the time.

An example: you say - and have said before - that genetics and the DNA driven genome system of life are compatible with, and therefore support, evolution from common ancestry. Multiple genetic systems would have disproved evolution, and common ancestry.

But there are actually schools of thought within evolutionary science that suggest two or more "first ancestors", for just that reason (I will try to find the source for this assertion). So evolution as a theory is perfectly capable of subsuming such aberrations, and keeps on ticking. Same with the proverbial preCambrian rabbit; the theory would morph to accept it. We just haven't got the right fossil set yet..., you just don't understand the scientific process, etc.

And you said,
"... Again, by focusing so narrowly on mutations, you are largely ignoring the non-random effects of selection. In individual cases, the observation that evolution occurred in a given population is defined genetically, but that leads naturally to the question of what could be causing that particular change. It could be natural selection, or it could be something else, or perhaps multiple factors are involved."

Again, same ol' circles. Natural Selection works on something to create something different? You are imbueing too much power to a simple process of selection. The process of selection can't create: it only selects that which is already created; that which already exists.

Might be time to go our own ways on this issue; you don't seem to want to accept that which has been stated by many experts in the field, including your own choice of sources.

My friend, that is an indication of "denial".

But one question. Who is the keeper of the theory?

If 8 year old information is now invalid, then what about 4 year old information, or 2 year old information, or even (gulp) current publications, which are not privy to this morning's findings and thus this afternoon's publications? Who decides what the theory is officially allowed to assert, at any point in time? For electromagnetism, it was pretty much Maxwell; totally quantum electronics is still in the future, if ever.

Whoever is "keeper of the theory of evolution", I shall willingly consult once I know who it is.

The following sort of throws me, though:
" But what is the alternative to TENS based on natural causes that could justify our skepticism? I don't think it exists, but let's say that there was such a model, that predicts the independent emergence and diversification of all lineages on natural causes alone.

Even if such a model existed, you would still be well-advised to reject it as unparsimonious unless it could be shown that it explained a larger class of observations with greater precision than the model of common descent."


Since evolutionary theory rejects any truck with abiogenesis, even though it is required, logically, how can it reject multiple abiogeneses, with ever increasing complexity as ...say... the earth cools (a potentially linear relationship). It could be argued, very successfully I think, that this is more parsimonious than a single instance of abiogenesis, followed by natural selection of mutations. And if it is NOT "a-biogenesis", then it is definitely more parsimonious!

See how it always devolves, not to science, but to philosophy? This is not the case with electromagnetic cause and effect, per Maxwell.