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we haven't figured out most of the "bugs"

When JBS Haldane was asked what his work in biology has taught him about God, he apparently replied, 'It has taught me that the ALmighty has an inordinate fondness for beetles.' It's estimated that there are several million species or which less than 400,000 have been described. So we certainly haven't figured out most of the bugs. ;)

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This paragraph really cuts to the heart of it:

[blockquote]The museum's research scientist, Dr Jason Lisle, has a PhD in astrophysics from the University of Colorado at Boulder. He realised he was a Christian while he was an undergraduate, but didn't spread it around: "People get very emotional about the issue. I don't believe we should ever be obnoxious about our faith. I just kept quiet." And how did he pass the exams? "I never lied, but if I was asked a question about the age of the universe, I answered from my knowledge of the topic, not my beliefs."[/blockquote]

What he may not realize is that museums like this are part of the reason people "get very emotional".

FWIW, this project doesn't make me mad - since I think the weaknesses of their approach ought to be pretty plain to their visitors - but they are wrong about evolution, and that makes me sad.

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FWIW, this project doesn't make me mad - since I think the weaknesses of their approach ought to be pretty plain to their visitors - but they are wrong about evolution, and that makes me sad.

The geologist Ron Peterson once defined "creation science" as "An attempt to give credibility to Hebrew mythology by making people believe that the the world's foremost biologists, paleontologists, and geologists are a bunch of incompetent nincompoops."

Harsh, perhaps, but true!

Archie

-------------------------------------------------------------------------------------------------------------------------

I am a bright.

A bright is a person who has a naturalistic worldview

A bright's worldview is free of supernatural and mystical elements

The ethics and actions of a bright are based on a naturalistic worldview

Visit The Brights' Net for more information.

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The geologist Ron Peterson once defined "creation science" as "An attempt to give credibility to Hebrew mythology by making people believe that the the world's foremost biologists, paleontologists, and geologists are a bunch of incompetent nincompoops."

Harsh, perhaps, but true!

At the risk of looking like a backwards Evangelical, I'd just like to point out a few bits in this definition that aren't entirely accurate. For one, "creation science" is a pretty generic term. One can accept "creation science" and still believe in evolution (as do many on this thread, myself included). It's called "creationist-evolutionism" (or something of the sort). Also, "to give credibility to Hebrew mythology" does not entail taking it literally. From a creationist-evolutionist perspective, the Hebrew creation account is entirely credible -- in what it is meant to communicate. I do not believe that it is meant to tell us that God created everything in a week, made Adam from a pile of dirt, made Eve from his rib, etc. There are underlying fundemental spiritual truths that are communicated figuratively and symbolically in these myths.

The last part of the definition, however (about making people believe that the world's foremost ... are a bunch of incompetent nincompoops), is an accurate assessment of ID's underlying assumption. <_<

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But creationism <> science, and I don't seen any need for a hybridized position. If anyone asks, I hold an "evolutionist" position. The only times I feel any need to interject anything resembling creationism into an otherwise non-religious discussion is when someone insists that evolution is inherently atheistic.

Oh, absolutely. Problem is, many people (read: Christians) will assume that because you believe in evolution, you're an atheist.

Which, of course, is absurd.

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Did you see the NYT article on Creationist Geologist from Sundays Magazine?

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This is not encouraging:

Normally, peer review is a valuable step in the publication of scientific research. Scholars submit new discoveries to academic journals, which, in turn, solicit independent experts to assess the reliability of the work. Answers Research Journal, a new "professional, peer-reviewed technical" publication of "interdisciplinary scientific

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Jeffrey O. recently pointed out Brett McCracken's post about Ben Stein's "Expelled", a docu-drama favorable toward Intelligent Design.

Here's an expanded version of the comment I left in response to McCracken's generally positive review:

The real problem is *not* that the scientific establishment refuses to fairly consider ID theory. The theory is simply less predictive, less helpful than evolutionary theory...though evolution is certainly not without weaknesses. Most theories are, in fact, incomplete; some are nearly contradictory (e.g. the standard model of particle physics must be part of some larger theory or else it's useless). But these theories are the best we have.

Rather, the real problem is our society which, by-and-large, has come to regard science as the only reputable truth-teller. Until the grip of effective materialism is loosened, other methods of meaningful experience and inquiry will always be judged under the strict and somewhat narrow laws of empiricism.

Edited by Jeff Kolb

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Ran across this story on PZ Myers' blog while researching Expelled (Myers also provides a link to a related article at National Geographic):

..in 1971, scientists started an experiment. They took 5 male lizards and 5 female lizards of the species Podarcis sicula from a tiny Adriatic island called Pod Kopiste, 0.09km2, and they placed them on an even tinier island, Pod Mrcaru, 0.03km2, which was also inhabited by another lizard species, Podarcis melisellensis. ... When scientists finally returned to the island and looked around, they discovered that something very interesting had happened.

The lizards' skulls were wider, deeper, and longer, and they had stronger bites

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The more I think about it, the more it seems to me that either the lizard evolution thing can't be what Myers and others are claiming, or else I fundamentally misunderstand how evolution is supposed to work. I'm not ruling out either possibility.

It is possible to bring about physiological changes in a population that do not represent mutative change, that do not represent fundamentally new genetic information, added complexity to the gene pool.

One way is by various kinds of selection: sexual, environmental, artificial, etc. For instance, the cock with the showiest plumage gets the hen. Alternatively, the cow that gives the richest milk is chosen by the farmer for calving. Such selectivity can within a few generations produce individuals who possess the desired attribute in greater degree than any of the original population: cows who give richer milk than any of the ones you started with, rats with longer tails, etc.

However, all you are doing is weeding through the existing gene pool to engineer the most felicitous genetic combination for the desired trait. At some point you reach a threshold beyond which no further gains can be reached, because the genetic potential isn't there. Barring mutative change, you will eventually get cows that give milk of a certain richness, and no further selective breeding will ever get you richer milk.

Such changes may illustrate Darwin's ideas about selection, but I don't see it as being of great import in the evolution debate, since you don't have mutative change.

Besides selection, physiological changes may also come about, as previously mentioned, through other environmental changes, like changes in diet and exercise. As per my earlier post, a population subsisting on a grain-based diet will be shorter than a population with more protein and calories in its diet; environmental changes in either case may cause the shorter population to suddenly increase in size or the taller population to suddenly decrease in size.

These, too, are not mutative changes and of no great evolutionary significance. Neither of these types of changes is at all controversial, even among the most diehard six-day Biblical literalists. Nor are such changes more than skin deep. Physiological changes brought about by environmental changes such as diet and exercise would disappear in a single generation without those factors. And changes resulting from selection produce less genetic variation, not more.

This brings us to the third source of physiological change, and the only proposed mechanism I know of for getting real evolutionary change, i.e., genetic mutation.

As I understand it, mutations are random, and essentially consist of random genetic sequencing changes. Randomness being what it is, most mutations, probably a large majority, are either incompatible with life or at least more or less debilitating. This, of course, is where natural selection comes in and wipes out Nature's unhappy mistakes.

Perhaps some small number of mutations consist of what might be thought of as lateral changes. The organism neither increases nor decreases in structural complexity and general physiological viability. Depending on extrinsic, environmental factors, there are essentially three possibilities for the impact of such lateral moves on the creature's success potential.

On the one hand, the change might have no significant success potential. For example, a pigmentation change in a fish, or a mouse with a different number of toes from other mice, might be neither disadvantaged or advantaged in the struggle for survival and reproduction.

On the other hand, a lateral change might either (and this also is random) increase or decrease the creature's success potential. A random pigmentation change in a mouse might have the effect of making it either easier to see or harder to see for predators. If it makes it easier to see, of course, once again natural selection will step in and take its course; but if it makes it harder to see the mutation is likely to succeed. (Of course, what counts as easier or harder to see may be environmentally determined, as the famous example with the light and dark colored moths illustrates.)

So, of that small subset of mutations that are lateral steps, some small fraction may be extrinsically beneficial under current circumstances, and may enhance the creature's success potential. Even so, it is a lateral step, not a step forward. There is no new complexity, no new information. The creature has taken a step away from his origins, possibly even a step toward becoming a different species, but not a step toward yielding a higher species.

The number of non-harmful mutations that actually increase structural complexity, that create new structures that are not debilitating and could potentially be useful given the right environmental factors, must be a very, very low fraction of all mutations. Yet in the case with the lizards, it seems that Myers claims that this is precisely what happened. If the changes in question are really mutative, evolutionary change, the claim seems to be that in just a few decades the lizard population happened to hit upon a genetic mutation, or more likely series of mutations, that produced a gut structure that -- wonder of wonders -- increased their adaptability to the new environment into which scientists dropped them.

On that scenario, sheer odds would seem to suggest that the lizards must have been mutating, and dying off from unsuccessful attempts, at a blazingly fast rate over the last thirty-odd years. Either that, or they're the luckiest dang creatures in the universe. I'm tempted to say they could go to Vegas and own the town in a week, but after the Expelled animation with the casino metaphor I'm not sure I want to borrow that image.

Or, perhaps, I'm missing something about how evolution is supposed to work. Perhaps there is a mechanism other than mutation that is supposed to account for these changes. If so, I don't know what it is, at least not in a way that makes sense of Myers' trumpeting of the results. Because as far as I know, if it isn't mutative change, it isn't of any interest in refuting evolution deniers.

Does anyone have any light to shed? Any of our resident skeptics or experts? Anyone?

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SDG wrote:

: On that scenario, sheer odds would seem to suggest that the lizards must have been mutating, and dying off from unsuccessful attempts, at a blazingly fast rate over the last thirty-odd years.

Yeah, that was my reaction to Myers' claims, too.

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Some of these alleged changes don't necessarily seem all that immediately impressive as evolutionary development. Changes like larger heads and harder bites might simply be physiological responses to a different diet and environment, just as if you transplant a family of Asians subsisting on a traditional grain-based diet to a country with a Western-style diet, subsequent generations will grow much taller.

But do they grow "wider, deeper, and longer" heads? Why are you trying to equivocate between a change in head shape and a change in head size?

The new gut structures, though, seem more striking. Are these really new structures representing a genetic development, an "evolutionary novelty" as Myers says?

An evolutionary novelty, yes. "A genetic development" has no meaning to me, as someone trained in genetics.

Or is this simply what happens to Italian wall lizard guts when you feed them on a veggie diet?

You just proposed an empirical test of a hypothesis, SDG! Why can't the entire ID movement accomplish in years what you just did in a matter of seconds?

If you moved more Italian wall lizards to the same island, would they quickly "develop" the exact same structure?

It would be a poor experiment if you didn't extirpate the previous lizards that had been transplanted first. Wouldn't a similar, neighboring island be a better test of your hypothesis?

Or if you moved the "new" lizards back home, would the new structures disappear in a single generation?

Why? Is that a prediction of modern evolutionary theory?

If the new structures are a genetic novelty, this seems to be a striking documented case of the kind of mutative advance that many anti-evolution polemicists say has never been documented.

That all depends on what you mean by "genetic novelty." Since your term "genetic development" made no sense to me as a geneticist, would you mind expanding on that?

If not, Myers (and others) would seem to be over-claiming in a way that would really undermine their credibility.
Why?

I suspect that you are laboring under a massive misconception about genetics that's been spread by the incompetence of the popular press. We humans have ~30,000 genes. If we sequenced the genomes of this lizard species, how many orthologs of our genes would you predict we'll find? How about for a mouse?

It's essential that we clear this up before any discussion of "genetic novelty."

Edited by Smokey

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The more I think about it, the more it seems to me that either the lizard evolution thing can't be what Myers and others are claiming, or else I fundamentally misunderstand how evolution is supposed to work. I'm not ruling out either possibility.

It's the latter.

It is possible to bring about physiological changes in a population that do not represent mutative change,

Sorry, but "mutative change" makes no sense to me either.

... that do not represent fundamentally new genetic information, added complexity to the gene pool.

That's precisely the most basic definition of "evolution": a change in allele frequency in a population over time. (alleles=different variations of a gene)

Question: did Darwin ever say anything about "mutation" or "random mutation"?

One way is by various kinds of selection: sexual, environmental, artificial, etc. For instance, the cock with the showiest plumage gets the hen. Alternatively, the cow that gives the richest milk is chosen by the farmer for calving. Such selectivity can within a few generations produce individuals who possess the desired attribute in greater degree than any of the original population: cows who give richer milk than any of the ones you started with, rats with longer tails, etc.

Yes, in that instance selection is operating on genetic heterogeneity (or polymorphism) within a population.

However, all you are doing is weeding through the existing gene pool to engineer the most felicitous genetic combination for the desired trait.

Don't look now, but you've just acknowledged that natural selection produces design, and you're also ignoring that new mutations occur constantly.

At some point you reach a threshold beyond which no further gains can be reached, because the genetic potential isn't there. Barring mutative change, you will eventually get cows that give milk of a certain richness, and no further selective breeding will ever get you richer milk.

Such changes may illustrate Darwin's ideas about selection, but I don't see it as being of great import in the evolution debate, since you don't have mutative change.

That's completely false, as new mutations occur all the time. That's why we continue to impose artificial selection upon cattle, for example.

Question: on average, how many mutations occur during each DNA replication preceding a cell division?

Besides selection, physiological changes may also come about, as previously mentioned, through other environmental changes, like changes in diet and exercise. As per my earlier post, a population subsisting on a grain-based diet will be shorter than a population with more protein and calories in its diet; environmental changes in either case may cause the shorter population to suddenly increase in size or the taller population to suddenly decrease in size.

These, too, are not mutative changes and of no great evolutionary significance.

Your terminology is impossibly twisted. These are not inherited changes. Claiming that they represent evolution is what Lamarck did. He was wrong.

And changes resulting from selection produce less genetic variation, not more.

What evidence supports this conclusion? For example, tell me more about how the vast spectrum of infectious diseases selects for less polymorphism in relevant genes. Why are cheetahs almost certainly going to become extinct, no matter what we do to preserve them?

This brings us to the third source of physiological change, and the only proposed mechanism I know of for getting real evolutionary change, i.e., genetic mutation.

As I understand it, mutations are random,...

You clearly don't understand it. Mutations are only random with respect to fitness. They are decidedly nonrandom wrt location, direction, etc.

... and essentially consist of random genetic sequencing changes.

Sequencing is only used as a verb (including as a gerund) to describe what humans do to DNA and proteins. Your sentence is basically meaningless in this context.

Randomness being what it is, most mutations, probably a large majority, are either incompatible with life or at least more or less debilitating.

Wrong again. The large majority have no effect at all.

This, of course, is where natural selection comes in and wipes out Nature's unhappy mistakes.

Your conclusion is based on a false premise.

Perhaps some small number of mutations consist of what might be thought of as lateral changes.

That's not useful at all. A better way to look at it is that the effects of mutations are highly dependent upon context.

On that scenario, sheer odds would seem to suggest that the lizards must have been mutating, and dying off from unsuccessful attempts, at a blazingly fast rate over the last thirty-odd years.

Well, the lizards don't mutate (their genomes do), and they do so regardless of selection. They also reproduce at a higher rate than they survive. That alone creates selection pressure.

Or, perhaps, I'm missing something about how evolution is supposed to work.

Just most of the basics!

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Smokey,

Side note: Don't shoot yourself in the foot here. I wouldn't have asked you to comment if I wasn't both aware of my own lack of expertise and willing to learn. Although I'm not qualified to instruct anyone on evolution, I'm eminently qualified to learn from a qualified instructor who is willing to teach. I am a smart guy with a lot of curiosity about lots of things outside the area of my formal training.

In my rather extensive experience dialoguing with people whose training has been different from mine, I have had a lot of success both helping other people come to a working understanding of things I understand better than they, and in coming to a working understanding of things other people understand better than I do.

I know what it looks like when someone is trying to use their superior knowledge to help someone else, and what it looks like when someone is trying to use their superior knowledge to avoid helping someone else. Asking me to guess, suppose or predict on technical questions is a very useful rhetorical strategy for showing up the limitations of my knowledge; it is not a useful pedagogical strategy for helping me understand the subject. Same goes for asking me whether Darwin ever spoke of mutation (which, BTW, he did not, AFAIK).

The "gotcha" style of some of your notes ("Don't look now, but you've just acknowledged...") seems to assume you think I'm someone or something I'm not. I take evolution in the full-blown sense (what some call "macroevolution") for granted, and I tend to be skeptical of the ID people. In my undergraduate days I (IIRC) aced my evolution elective, which I mention not to tout my knowledge but only my ability and willingness to learn.

But that's a side note: I'm willing to work under hostile conditions or friendly ones, at least up to a point. I am, however, limited by time considerations as I'm on my way out the door to a screening. I'll try to write more tonight.

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Smokey,

...I know what it looks like when someone is trying to use their superior knowledge to help someone else, and what it looks like when someone is trying to use their superior knowledge to avoid helping someone else. Asking me to guess, suppose or predict on technical questions is a very useful rhetorical strategy for showing up the limitations of my knowledge; it is not a useful pedagogical strategy for helping me understand the subject.

Well, testing predictions is the very foundation of science, its general absence is the crux of our nation's failure in science education, and it's not meant to show you up--it's meant to get you to take the fundamentally wrong assumption you appear to be applying to an unknown and apply it to a known.

Same goes for asking me whether Darwin ever spoke of mutation (which, BTW, he did not, AFAIK).

So I trust that you can see the absurdity of claiming that "Darwinism"=RM+NS, and then going on to claim that evolution itself is random.

The "gotcha" style of some of your notes ("Don't look now, but you've just acknowledged...") seems to assume you think I'm someone or something I'm not.

I'm not assuming, just extrapolating from our conversation on the other thread, your use of creationist myths, and what appears to be a desire to denigrate Myers. He's an outstanding teacher.

So, more to the point, when you say "genetic novelty," are you saying that you expect to see new genes that are responsible for these changes?

Edited by Smokey

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Checking in at the theater on my iPhone.

Couple of quick points: First, my earlier posts do not assume that "Darwinism" (or evolution for that matter) = RM + NS. I do assume that contemporary theory generally requires both of those mechanisms, but my posts were also more or less explicitly open to the possibility of other important mechanisms I don't know about.

You are wrong in thinking that I am somehow out to find fault with Myers. My initial impulse was to take his claims at face value. It was only on further reflection that his claims began to seem problematic to me.

By mutative change I meant to indicate genetic mutation. For reasons I'll try to clarify later, it seems to me that if the new structures do not reflect genetic mutations, the kind of evolution they represent is not what I think of as controversial.

Sorry for hasty and imprecise thoughts. Will be back.

Edited by SDG

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Some more thoughts.

But do they grow "wider, deeper, and longer" heads? Why are you trying to equivocate between a change in head shape and a change in head size?

I'm not. But isn't it also true that non-inherited factors can cause bone structures to develop different shapes? If I find a population of homo sapiens with strikingly conical-shaped skulls, say, can I automatically assume that these are inherited features?

Or if you moved the "new" lizards back home, would the new structures disappear in a single generation?
Why? Is that a prediction of modern evolutionary theory?

It was intended to help address the question of whether the changes were inherited or not.

That's precisely the most basic definition of "evolution": a change in allele frequency in a population over time. (alleles=different variations of a gene)

It is, however, a completely uncontroversial sense, one that would be acknowledged by the most diehard six-day creationist (as long as he admits that there are such things as genes in the first place). It is also a kind of evolution that in itself will never, ever get you a new species... right? Some other mechanism, such as mutation, is necessary for that. Right?

Don't look now, but you've just acknowledged that natural selection produces design, and you're also ignoring that new mutations occur constantly.

However, it is not yet clear to me that the examples just discussed imply that design occurs spontaneously. Rather, in the examples just discussed, design implies preexisting design, if not a designer. For instance, the ordering principle that produces the showier plumage in cocks is rooted in already more complex reality of the sexual preferences of the hens.

As for mutation, I was far from ignoring them; rather, I was bracketing other issues, in this case changes in allele frequency, in order to focus precisely on mutations as the topic of greatest interest.

That's completely false, as new mutations occur all the time. That's why we continue to impose artificial selection upon cattle, for example.

You see, bracketing the limitations of changes in allele frequency does underscore the necessity of mutation as a mechanism; the very fact that you bring it up here illustrates the point I was making.

That said, AFAIK no one has by artificial selection produced cows that give half and half, for instance, or even 5 percent milkfat. Perhaps the necessary mutations have been recalcitrant in occuring.

Your terminology is impossibly twisted. These are not inherited changes. Claiming that they represent evolution is what Lamarck did. He was wrong.

I know. That's my point. Perhaps you weren't following as closely as you thought.

And changes resulting from selection produce less genetic variation, not more.
What evidence supports this conclusion?

My conclusion, if that's the right word, is that if you start, say, with a base population of 100 individuals, choose 10 for selective breeding, produce 100 offspring from the chosen 10, from which you again choose 10 for selective breeding, and so on, on the basis of allele redistribution only each generation will contain less genetic diversity than the ones preceding it. Are you saying that's incorrect?

As I understand it, mutations are random,...
You clearly don't understand it. Mutations are only random with respect to fitness. They are decidedly nonrandom wrt location, direction, etc.

Yes, it is precisely randomness with respect to fitness I was speaking about.

... and essentially consist of random genetic sequencing changes.
Sequencing is only used as a verb (including as a gerund) to describe what humans do to DNA and proteins. Your sentence is basically meaningless in this context.

If I had said "sequence" instead of "sequencing," or perhaps "arrangement," "order," or some other word you might suggest, would my sentence acquire meaning?

I understand very well -- believe me -- the crucial importance of terminological precision, and therefore of nit-pickiness, in any area of study, as some on this board can attest. In similar circumstances I might easily correct an inquirer in a field I know something about over the misuse of a word. But I would rather help someone more accurately rephrase what he was trying to say than dismiss it as gibberish over an ill-chosen word. That seems like intellectual bullying to me.

Wrong again. The large majority have no effect at all.

Yes, this rings a bell. Would it be accurate to say that those that have an effect often have deleterious effects?

That's not useful at all. A better way to look at it is that the effects of mutations are highly dependent upon context.

Yes, I did try to make that point too. I was going after something slightly different with my comments about "lateral" changes.

Edited by SDG

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Well, the lizards don't mutate (their genomes do), and they do so regardless of selection. They also reproduce at a higher rate than they survive. That alone creates selection pressure.

Well, my outsider's impression is that the odds of lizard genomes mutating in such a way as to produce an entirely new gut structure that just happens to be precisely what the lizards need in their new context in such a short period of time are rather daunting. WDYT?

So, more to the point, when you say "genetic novelty," are you saying that you expect to see new genes that are responsible for these changes?

I don't know whether "new genes" is the right way to say it. I would rather say that I want to know whether we are talking about allele frequency redistribution and/or non-inherited factors, or whether, and to what extent, mutation is a key factor.

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Checking in at the theater on my iPhone.

Couple of quick points: First, my earlier posts do not assume that "Darwinism" (or evolution for that matter) = RM + NS. I do assume that contemporary theory generally requires both of those mechanisms, but my posts were also more or less explicitly open to the possibility of other important mechanisms I don't know about.

But contemporary theory involves many more mechanisms.

You are wrong in thinking that I am somehow out to find fault with Myers. My initial impulse was to take his claims at face value. It was only on further reflection that his claims began to seem problematic to me.

I don't see a problem.

By mutative change I meant to indicate genetic mutation.

I don't see your point. Are you claiming that there are mutations that aren't genetic? Please don't take offense, it's just that equivocation is the fundamental way in which evolution deniers mislead the public.

For reasons I'll try to clarify later, it seems to me that if the new structures do not reflect genetic mutations, the kind of evolution they represent is not what I think of as controversial.
What you don't seem to realize is that among scientists, evolution isn't controversial. Again, I don't see how a structure can reflect a mutation, genetic or otherwise. I also don't see any relevance to this case, as no new "designs" are necessarily involved.

Are you asking whether a new mutation had to have occurred since the transplantation of the lizards? Are you assuming that these changes would require large numbers of mutations, new or old?

Are you considering the effects of sexual reproduction and diploidy (the fact that the lizards have two alleles at every locus)? What if a single recessive allele causing the formation of cecal valves was produced by a mutation that occurred 2000 years ago and has a fitness when homozygous of 0.9, and has been maintained at a frequency of 2%, possibly by tight linkage to a high-fitness allele at a nearby locus (locus = roughly "gene")?

Edited by Smokey

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Some more thoughts.

I'm not. But isn't it also true that non-inherited factors can cause bone structures to develop different shapes?

Different identities and numbers, as with vertebrae. That's spectacularly inconsistent with intelligent design, wouldn't you say?

If I find a population of homo sapiens with strikingly conical-shaped skulls, say, can I automatically assume that these are inherited features?

No, but it would be the best initial hypothesis.

It is, however, a completely uncontroversial sense, one that would be acknowledged by the most diehard six-day creationist (as long as he admits that there are such things as genes in the first place). It is also a kind of evolution that in itself will never, ever get you a new species... right?

Definitely wrong! It's my hypothesis that you're getting these things so wrong because you're assuming design of the mechanisms underlying morphogenesis. You're simultaneously overestimating the extent to which structures are specified (you're assuming there's a metaphorical blueprint), while underestimating the extent to which morphogenesis is an emergent property of many simultaneous processes.

Some other mechanism, such as mutation, is necessary for that. Right?

No!

Rather, in the examples just discussed, design implies preexisting design, if not a designer.

Not really--see above.

For instance, the ordering principle that produces the showier plumage in cocks is rooted in already more complex reality of the sexual preferences of the hens.

I'd say that there's no "ordering principle," at least in any sense that I understand the term, and that the hens' sexual preferences are not very complex. The latter has been addressed experimentally, btw.

As for mutation, I was far from ignoring them; rather, I was bracketing other issues, in this case changes in allele frequency, in order to focus precisely on mutations as the topic of greatest interest.

They aren't easy to separate. Development of affordable mechanisms to sequence the genomes of individuals would be required.

That said, AFAIK no one has by artificial selection produced cows that give half and half, for instance, or even 5 percent milkfat. Perhaps the necessary mutations have been recalcitrant in occuring.

You're being unnecessarily anthropomorphic. It's the limitations on evolutionary change that demolish the very idea of design by an omnipotent God.

And changes resulting from selection produce less genetic variation, not more.
What evidence supports this conclusion?

My conclusion, if that's the right word, is that if you start, say, with a base population of 100 individuals, choose 10 for selective breeding, produce 100 offspring from the chosen 10, from which you again choose 10 for selective breeding, and so on, on the basis of allele redistribution only each generation will contain less genetic diversity than the ones preceding it. Are you saying that's incorrect?

No. One can artificially select for total homozygosity by brother-sister matings, as we have for mice (they have been virtually cloned for a century). We were discussing natural selection, though. Bottlenecks produce less fitness. Radiation produces polymorphism. Both represent evolution.

If I had said "sequence" instead of "sequencing," or perhaps "arrangement," "order," or some other word you might suggest, would my sentence acquire meaning?

No. It adds absolutely nothing to the sentence preceding it--that's why I objected.

I understand very well -- believe me -- the crucial importance of terminological precision, and therefore of nit-pickiness, in any area of study, as some on this board can attest. In similar circumstances I might easily correct an inquirer in a field I know something about over the misuse of a word. But I would rather help someone more accurately rephrase what he was trying to say than dismiss it as gibberish over an ill-chosen word. That seems like intellectual bullying to me.

I'm still trying to figure out what you're trying to say.

Would it be accurate to say that those that have an effect often have deleterious effects?

Most deleterious mutations are recessive, so those would be no effect unless they were homozygous. That would take a while unless there was inbreeding and/or drift. You're missing the enormous buffer effect of sexual reproduction.

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Well, the lizards don't mutate (their genomes do), and they do so regardless of selection. They also reproduce at a higher rate than they survive. That alone creates selection pressure.

Well, my outsider's impression is that the odds of lizard genomes mutating in such a way as to produce an entirely new gut structure that just happens to be precisely what the lizards need in their new context in such a short period of time are rather daunting. WDYT?

The polar opposite.

I can get you there hypothetically with a single base change in a growth-factor receptor in the inner epithelial cells, but not the outer ones, that increases its sensitivity to a growth factor. This produces folds on the inside of the tube, the smooth muscle is consequently thicker at the folds, and you have valves. Again, you're assuming that these structures are somehow specified by metaphorical blueprints instead of representing properties emerging from evolutionary processes. All of the data are consistent with the latter. This misunderstanding makes it easy for antievolutionists to hoodwink laypeople.

You can also get the convolutions of the human cerebral cortex by the same general mechanism. The cell types are layered in a stereotypical way, and connections are modified by experience. That's how you can get a brain that holds orders of magnitude more data than the genome that encodes its components, which is frankly miraculous, but by itself debunks every ID myth about information.

So, more to the point, when you say "genetic novelty," are you saying that you expect to see new genes that are responsible for these changes?

I don't know whether "new genes" is the right way to say it.

It's emphatically not, which is why I wanted to make the point dramatically by getting you to offer hypotheses about numbers of genes. How about trying it? You'll learn more that way.

Out of 30000 genes, how many do you think we have that have no ortholog in a mouse, or vice versa?

Why are there enormous gene/protein families?

How many of those 30000 proteins are based on a structure we call the "P-loop"?

I would rather say that I want to know whether we are talking about allele frequency redistribution and/or non-inherited factors, or whether, and to what extent, mutation is a key factor.

Both. The point you're missing is that the mutation in question (if the mutant allele is recessive) could have occurred thousands of years ago, but maintained since then because of the buffering provided by sexual reproduction. That, in turn, is the best hypothesis to explain the prevalence of sexual reproduction. It provides a huge (metaphorical) reservoir of alleles for future evolution, reducing the likelihood of bottlenecks and extinction.

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Smokey, I just want to make a point regarding 'net etiquette and the way you've responded in this thread (although it applies to the Expelled thread as well).

SDG wrote a post which addressed a lot of different questions, but did so in a somewhat unified fashion. Your reply chopped his post into 22 pieces, along with your 22 replies. Above and beyond the content of your reply, this stylistic choice makes it much harder to read and reply.

I, personally, when I reply to very long posts, try to find the central truth or message which the original poster was getting at and just respond to that. Then a conversation (rather than 22 micro-conversations) can actually take place.

This is not to say that there's not a place for pulling an essay apart, when it deserves it. But SDG doesn't seem to, in this case, because he was just asking a question, rather than, say, making extravagant claims or personal attacks (two mistakes which might justify a shredding of the kind I think you've delivered).

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Personally, I find the point-responding-to-point approach valid, in principle. But I'm afraid the increasingly technical terminology is beginning to fly over my head -- and THAT is what makes it hard for me to follow (the same way my eyes begin to glaze over when economists discuss tax policies). So a big-picture approach might help for explaining this stuff to dummies like me.

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Smokey, I just want to make a point regarding 'net etiquette and the way you've responded in this thread (although it applies to the Expelled thread as well).

SDG wrote a post which addressed a lot of different questions, but did so in a somewhat unified fashion. Your reply chopped his post into 22 pieces, along with your 22 replies. Above and beyond the content of your reply, this stylistic choice makes it much harder to read and reply.

I, personally, when I reply to very long posts, try to find the central truth or message which the original poster was getting at and just respond to that. Then a conversation (rather than 22 micro-conversations) can actually take place.

This is not to say that there's not a place for pulling an essay apart, when it deserves it. But SDG doesn't seem to, in this case, because he was just asking a question, rather than, say, making extravagant claims or personal attacks (two mistakes which might justify a shredding of the kind I think you've delivered).

David,

SDG was using the same approach, so I felt the same style would be appropriate in response. There was no central truth or message that I could see, just many misconceptions. I approached this as a series of questions, not as an essay.

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