2/13/2008

SHOOTING FINCHES IN A BARREL


This one's a can of corn, but it's irresistible.

There is a legendarily cantankerous retired biology professor named John A. Davidson who is highly skeptical of Darwinian evolution, and he's got his own ideas on how evolution actualy happens. Nothing wrong with that. He blogs about it. Nothing wrong with that. He's created multiple blogs attempting to spark discussion on his alternative views. Nothing wrong with that. Virtually no working scientist reads his blogs or otherwise gives him the time of day, though, most likely because they've concluded he's a crank.

Here's an example of why he seems to have a hard time establishing his credibility. Posting over at ID sympathizer Ftk's place, Davidson makes the following remarks alluding to Darwin's finches:

The Darwinians have no "theory." "Theories" are verified hypotheses. All that has been verified through the most intensive of selection is the generation of intraspecific varieties none of which are incipient species. They don't even test their "theory" any more. The Galapagos finches, as nearly as can be ascertained from field observations, are all one species. Finches are among the easiest of birds to domesticate. The canary is a finch. Why haven't the Darwinians tested that material in the laboratory? I will tell you why. It is summarized in a single word - FEAR. Fear of failure. They have abandoned the experimental method.


Well, that's just ridiculous. Natural selection of finches has been rigorously tested both in the laboratory and the wild. David Lack (1910-1973) provided detailed natural history of Darwin's finches in nature in the 1950's, and a pair of Princeton researchers (Peter and Rosemary Grant) have combined detailed natural history with DNA analysis of patrimony and survivorship in a ongoing research programme that is on its third decade. This is such a well-known fact that it was the basis of a Pulitzer Prize-winning book (Jonathan Weiner's The Beak of the Finch ) and is discussed in Miller and Levine's widely-used high school biology text.

So, Professor Davidson, while you are free to argue that 'evolutionists' misinterpret the data you collect, you can not argue that they are not testing the claim that natural selection occurs in populations such as Darwin's finches. Only the fact that you are a retired academic long out of touch with mainstream biology can excuse your ignorance of the latter. Here's a thought for you, Professor: try doing a little research before you make a claim that can be easily debunked by a high school biology teacher.

12 comments:

Stan said...

Well gosh, I've posted this before, but here we go again.

The work of the famous Grants, as revealed in their book, "Evolutionary Dynamics of a Natural Population", reveals only that the beak size responds to wet years and dry years. Pages 280 -289 contain their summary, where they conclude that finch beaks do "respond to environmental fluctuations", but do not remain at the extremes, rather they simultaneously oscillate with the environmental challenges, reverting back to normal size as the seasons oscillate from extreme to normal(p282). In fact, the "experience" level of the mama bird is more determinate of success than genetics (p281, 282). And, "Overall, relative success or failure in surviving and breeding repeatedly is determined more by behavioral factors associated with experience than by morphological features"(p285). So natural selection favors birds that accumulate wisdom, not genetically favored physical genotypes.

There is no pretense of speciated evolution in the book, just natural selection within existing parametric limits. Such selection is a poor substitute for actual evolution, macro-style, into a different species. In fact the one speciation event that they thought they were observing turned out to be nothing at all: differentiated mating songs one year disappeared the next (p283, 284). Since there is no talk at all of macro or speciated evolution until the last page where the authors claim to believe that finches could be "capable of further change", one suspects that the word "evolution" was placed into the title by over zealous publishers.

Weiner's "Beak of the Finch" is similar to a docudrama, especially in playing fast and loose with facts. When I saw that portions of the Grant's data was reported falsely by Weiner, I put the book aside, where it remains.

Prof. Lack's data is generously sprinkled throughout the Grant's book. Presumably if Lack had found speciation, so would the Grants, led by his example. But the Grants didn't, so Lack probably didn't either.

I feel that it is going to take more data that reveals actual speciation than these sources provide, to refute Prof. Davidson, primarily because the charge of lack of actual data still stands. Of course, if one chooses to ignore speciation as a criterion for evolution, then one is left with pretty much a tautology: a "Q" finch is a "Q" finch, whether its beak is long or short.

Scott Hatfield . . . . said...

Stan: your quibbles, as with those raised by JAD, are one of interpretation. You and he are free to play the skeptic when the inference in the question leads to something unpalatable. We can argue back-and-forth on that all you like. My point is that JAD is saying that no one is testing the hypothesis, which is a crock. In fact, the Grants found hybridization between at least two of the 14 species during the drought, which in a sense could be said to falsify certain extreme selectionist models. This was not something they expected, but it is something that they discovered through investigation.

As for Weiner misrepresenting the Grants' data, if you can show me where the Grants object to how they were portrayed, I might regard your criticism of Weiner's work as well-founded. Do you have such a citation? Or should I just contact the Grants and ask if Weiner's book at anyone misrepresented their data?

BTW, as you should know, speciation events have been observed both in the wild and in the laboratory. Just how 'macro' would an event have to be in order to qualify as speciation?

Stan said...

I would have to read Weiner's book again which I don't intend to do, but maybe I earmarked it, I'll check. As for observed speciation events, I would appreciate any references that you have that aren't just microbes developing resistance or similar selection within the original genome.

Perhaps defining terms would help us out here. If evolution is responsible for all the creatures in all their varieties, then it must involve creatures moving outside and beyond their original genome. This means mutations, and the mutations would have to be non-disruptive to the fitness of the creature, to say the least. And in most cases the mutation would have to provide a new fitness capability, or at least be stored up to combine with other positive mutations to provide increased fitness at a later date.

If you have information on these types of mutations, I'd appreciate that reference. If you disagree with the definition above, I'd like to discuss that, too.

As an animal breeder, I am aware that hybridization provides an advantage only for the first generation of hybrids, at least amongst bovines. What is acheived by hybridization is a combination of dominant features of both parents, not something outside the genome. And if they can breed together, are they really different species, or subspecies?

My impression of the Grant's data is that the hybrids did not do so well in the long term.(p283) "Hybrids reproduced successfully but did not live long and contributed less than nonhybrids to total breeding". In fact, again p283, "...it is possible that a reduction in genetic variation had occurred as well, as a result of selection."

Again as a breeder, this is what I would expect to find: a reduction in variability between individuals. This is what you see in yellow dogs on Indian reservations.

You and I are both skeptics of the works of man; I am a skeptic of interpretation of data in a field involved with both a worldview and social program.

Scott Hatfield . . . . said...

If evolution is responsible for all the creatures in all their varieties, then it must involve creatures moving outside and beyond their original genome.

I'm sorry, but this seems like a misconception. Evolution is not a property of individuals, nor is it based on individual creatures changing their genome. Individuals don't evolve; populations do. We don't say that the leopard changes his spots. Rather, evolutionary biologists would say that if a population of leopards once isolated experiences selection pressures different from its ancestral population, then sufficient genetic change may occur that effectively isolates that population from exchanging genes with other leopards, and at that point they may be considered a new species.

This means mutations, and the mutations would have to be non-disruptive to the fitness of the creature, to say the least. And in most cases the mutation would have to provide a new fitness capability, or at least be stored up to combine with other positive mutations to provide increased fitness at a later date.

Well, first of all, new combinations of genes and changes in gene frequency within a population can be generated by mechanisms other than mutations, so it doesn't have to be mutations.

Secondly, fitness is 'situation-dependent'. What might be selectively-neutral in one environment could lead to strong selection one way or the other. The suggestion that fitness could be 'stored up', as if it were a thing in itself, thus comes across as another misconception to yours truly, because this seems to imply that the genome is somehow 'looking ahead' or anticipating its future environment.

Anyway, what healthy populations tend to do is continually generate loads of genetic variation by a variety of processes. This is one of the reasons biologists and their fellow travelers tend to wax poetic about diversity. But there is no guarantee that any of this variation is going to be of selective value to the population in the future, so it wouldn't be accurate to describe the generation of genetic variability as 'storing' fitness, IMHO. Nor due we have to invoke a special class of mutations to do it. Any and all mechanisms that generate genetic diversity (including, but not limited to, mutations) could in principle lead to an overall increase in the population's genetic diversity over time, a potential reservoir for selection.

As an animal breeder, I am aware that hybridization provides an advantage only for the first generation of hybrids, at least amongst bovines. What is acheived by hybridization is a combination of dominant features of both parents, not something outside the genome.

Hybrids between populations which have been classified as separate species are fascinating because you can find cases to illustrate any number of points. Some hybrids are fertile, some are not. Some freely occur in nature, and others must be provoked by human intervention. 'Hybrid vigor' occurs in some cases, and in others they don't. Some of Darwin's finches will hybridize, but others won't, and those that do tend not to do so. The question of the survivorship of fertile hybrids versus 'pure--bred' finches is, as I understand it, under investigation but I don't know anything definite. But, even if I did, I doubt that any particular finding would exercise me, because one of the goal of systematics is to reevaluate all phylogenies on the basis of genetic relatedness. At the present time, the vast majority of species (including Darwin's finches) are classified on the basis of behavioural and morphological differences, rather than on the actual genetic relatedness between the populations, so discoveries like the Grants of fertile hybrids in times of drought can not be said to contradict the claim that those populations were shaped by natural selection. They are happy problems for taxonomists, not evolutionary theorists.

Stan said...

I don't have a biology degree, so all that I can do is to apply basic logic (where I do have credentials) to the theory as it is represented.

Scott said: "Individuals don't evolve; populations do."

If as you say, evolution is not considered a function of individuals but of a group of individuals, my skepticism is not abated.

To say that a group has modified itself is not meaningful unless the individuals within the group first modified themselves. Seems fundamental to me, basic logic. A bucket of red marbles can't become a bucket of green marbles unless the marbles change first.

Scott also said:
"...then sufficient genetic change may occur that effectively isolates that population from exchanging genes with other leopards, and at that point they may be considered a new species."

The "sufficient genetic change" you reference can only happen to individuals; the "group" has no DNA other than that resident in the individuals. The group can't change unless the individuals change first. Still basic logic.

And Scott said:
"...new combinations of genes and changes in gene frequency within a population can be generated by mechanisms other than mutations, so it doesn't have to be mutations.

It would seem to me that the changes to the DNA to which you refer would be mutations, unless there is a special meaning for that word in the wierd world of evolution. Simple sexual selection by individuals with un-changed (non-mutated) DNA still cannot create something outside the choices that are available to it. I don't understand why it is necessary for biologists to deny this. In fact the Grants say (after pointing out the oscillatory nature of the beak changes): "The main generating processes are mutation, which we cannot study, and the introgression of genes"[hybrids].

"Storing up" mutations seems absurd to me also, yet the logic, such as it is, being used here requires it.

Scott replies:
"Nor due we have to invoke a special class of mutations to do it. Any and all mechanisms that generate genetic diversity (including, but not limited to, mutations) could in principle lead to an overall increase in the population's genetic diversity over time, a potential reservoir for selection."

To me this sounds like saying the same thing that I am saying, just using different words: All the changes (mutations) are "reservoired" (stored)for potential selection. This is just another way of saying it without using the same words. Why are these words not usable by biologists?

In fact, the reading I have done implied that biologists do not believe that the mutations (calling it what it is) are stored in any fashion. And the probabilities of an instantly successful single mutation are excruciatingly miniscule (I've seen calculations somewhere, I'll find them if need be).

It seems to me that the theory needs to be rational before being accepted. No competing theory? Well, apparently this Davidson fellow had one (sort of congruent with my objections from what little I read) and he receives, not rational assessment of his issues, for which he quotes sources, but ridicule. The use of ridicule in the scientific arena is foreign to me as an R&D Engineer, and it is highly objectionable and indicative of closed minds. For example I think PZ should call himself a master ridiculist, since his site has much more ridicule than science (but that's neither here nor there).

At any rate, I appreciate your thoughts and I also would appreciate reference to proper literature that demonstrates your ideas conclusively. (and hopefully clearly).

Thanks,
Stan

Scott Hatfield . . . . said...

To say that a group has modified itself is not meaningful unless the individuals within the group first modified themselves. Seems fundamental to me, basic logic. A bucket of red marbles can't become a bucket of green marbles unless the marbles change first.

Basic logic only works if the propositions are valid within the frame of reference. This is like the case of a thermostat, the logic of which can be 'reduced' to contradiction:

If a, then not-a;
If not-a, then a


That is, if a certain temperature threshold is exceeded, then turn off the heater, then the threshold will not be exceeded, then turn on the heater, etc.

This is what can happen when simple, logical but 'timeless' arguments are applied to evolving systems, for whom the role of time is integral. Apparent contradictions emerge that can only be resolved by explicitly invoking the role of time and space in the evolving system.

In the case of evolution, marbles don't reproduce. Organisms do, but they can't change what kind of 'marbles' (genes) they get. In fact, the population can't consciously change their 'marbles' either----excluding eugenic impulses in our own species, of course.

Rather, what happens is that a complex interaction of various inputs select for or against the frequency of a particular sort of 'marble' (we biologists call them alleles, alternate forms of a gene). This complex interaction takes place over time and space, and allele frequency typically oscillates over time within the environment, much like a thermostat, as if the population were attempting to constantly resum various 'on' and 'off' inputs. This is what leads to the appearance of statis within a species in everyday life.

The "sufficient genetic change" you reference can only happen to individuals; the "group" has no DNA other than that resident in the individuals. The group can't change unless the individuals change first. Still basic logic.

Again, this is a fundamental misconception. Individuals don't change their genes. Period. The only thing that is likely to change is the total number and frequency of various alleles within a population. Mutation can affect this, but so can other phenomena.

Look, perhaps this example will help you understand. Canis familiaris is, of course, considered a single species. But it is a well-known fact that Great Danes and Chihuahuas are unlikely to mate successfully; there are, as the biologist might say, prezygotic morphological barriers to reproduction. But a Great Dane might mate with a terrier, and a terrier might mate with a Chihuahua, and so it is still appropriate to consifer them all one species, albeit with varieties at various morphological extremes which are no longer able to breed. They are still one species because genes flow between the various varieties.

But what if some disaster were to strike the population of dogs worldwide, and eliminate every breed of dog but Great Danes and Chihuahuas?

If that happened, gene flow between the two varieties would come to a halt. You would now have two populations that are reproductively isolated and thus 'free to go their own way' barring intelligent intervention by a more advanced being....

The point of all this is that neither the Chihuahuas or the Great Danes have to 'change' their genes in order to become reproductively isolated. And, in this case, no special kind of mutation is involved, either. We biologists do think that populations that are isolated by some non-genetic barrier are likely to acquire genetic differences that will make interbreeding problematic should the non-genetic barrier go bye-bye at some time in the future, but that, as you say, is just simple logic. Populations that are 'free to go their own way' are likely to acquire genetic differences, and if they go their own way long enough, they will have quite a few genetic differences. Eventually, if you have enough genetic differences, your population will no longer be able to have fertile offspring with any other populations, even those for which you share a common ancestor.

Now, what is needed for all this to occur? As Hutton said, 'nothing but time,' and again simple logic is unlikely to encapsulate the power of 'deep time' to effect profound changes.

Simple sexual selection by individuals with un-changed (non-mutated) DNA still cannot create something outside the choices that are available to it. I don't understand why it is necessary for biologists to deny this.

See, the evolutionary biologists I know, they don't deny this. You're tilting at a windmill here, whether you realize it or not, because like a lot of evolutionary skeptics you're hung up on a paradox that doesn't exist. Mutations are a source of variation, but variation in and of itself is not information. We are NOT claiming that order comes from chaos, or that randomness creates information on its own.

Rather, the information comes from an interaction between the genes and the environment. If we say that the genes, mutations and all, are like a set of encylopedias, that still doesn't explain the organism. You still have to read the damn things, you still have to follow the instructions and build stuff, it still has to provide some outcome in the real world. It is the interaction between the environment and the genes that builds the organism.

Change the world, and the program may not work at all, or it may work in unexpected ways, and various individual bells and whistles that were never developmentally significant in the old world may become critical to the organism's success or failure.

Well, I have to run along. I'll try to provide some citations for ya at a later date. In general, anything by Mayr is likely to be helpful.

Stan said...

Scott,
Your apparent thermostat paradox seems to derive from the erroneous use of a single variable to describe two entities: temperature (Tambient) produced by a sensor, and switch position (Son/off) (two logically separate electrical components). There is also a threshold condition (Tmargin), that exists in order to prevent oscillation at the set point: Tmargin.

Initial condition: Tambient < Tset - Tmargin; Son/off = closed, power = on.

Instruction Set:
(IF condition sensed, THEN action produced).

If Tambient < Tset -Tmargin, then Son/off = closed.
If Tambient > Tset + Tmargin, then S on/off = open.

Likely values for Tambient and T margin:

Tambient = +72 degF.
Tmargin = +/- 0.25 degF.

If there were a paradox in a machine, generally the machine will either oscillate uncontrollably, or it will latch up at some extreme condition and refuse to move away from it.

The apparent paradox is a systemic misconception, and does not exist in a thermostat. (Or any other functional piece of equipment).

Scott:
In the case of evolution, marbles don't reproduce. Organisms do, but they can't change what kind of 'marbles' (genes) they get. In fact, the population can't consciously change their 'marbles' either----excluding eugenic impulses in our own species, of course.

Individuals don't change their genes. Period. The only thing that is likely to change is the total number and frequency of various alleles within a population. Mutation can affect this, but so can other phenomena.

Stan:
Individuals do receive genes including some that have changed. Only individuals have genes. Once again it is necessary to fully define our terms:

American Heritage Stedman's Medical Dictionary - Cite This Source - Share This
al·lele ( -l l )
n.
One member of a pair or series of genes that occupies a specific position on a specific chromosome. Also called allelomorph.

al·le lic ( -l l k, -l l k) adj.
The American Heritage® Stedman's Medical DictionaryCopyright © 2002, 2001, 1995 by Houghton Mifflin Company. Published by Houghton Mifflin Company.

Merriam-Webster's Medical Dictionary - Cite This Source - Share This
Main Entry: al·lele
Pronunciation: &-'lE(&)l
Function: noun
1 : any of the alternative forms of a gene that may occur at a given locus
2 : either of a pair of alternative Mendelian characters (as ability versus inability to taste the chemical phenylthiocarbamide) —al·le·lic /-'lE-lik, -'lel-ik/ adjective —al·lel·ism /-'lE(&)l-"iz-&m, -'lel-"iz-/ noun
Merriam-Webster's Medical Dictionary, © 2002 Merriam-Webster, Inc.


I am aware of my bovine’s individual alleles, and I can calculate a cumulative number, I suppose, that might represent the herd as a composite, human construct. More on this mathematical entity below.

The canine disaster scenario is interesting. At the moment of the disaster, both extreme “breeds” are still canines. Morphologically I suppose they can be given different human-designated classifications. But the presumed different paths from that point would still require some mechanism to change their canine genetics to canine-plus genetics. It is the mechanism and likelihood of occurrence that are not addressed here.

Scott:
Populations that are 'free to go their own way' are likely to acquire genetic differences, and if they go their own way long enough, they will have quite a few genetic differences.

This is the presumption that I think needs proof, not only of the statement, but of the mechanism that causes it. It is a basic statement of evolution. It is not in itself proof.

Scott:
Now, what is needed for all this to occur? As Hutton said, 'nothing but time,' and again simple logic is unlikely to encapsulate the power of 'deep time' to effect profound changes.

How is this not an invocation of unproven faith? “Given enough time anything can happen, anything at all”. It’s another “infinite monkeys on infinite typewriters for infinite time producing infinite literary works. There is no proof of anything involved in this statement, only faith that it happened due to “deep time”. (Related to the fallacy, “evolution must be true, we are here aren’t we?”).

Besides, “deep time” is not all that deep. Time is a finite creation starting at the Big Bang. Time opportunities for life on a kinder, gentler Earth are even less deep. And the jump from sponge to full featured dinosaur, not so deep still. Time cannot, by itself, be a mechanism to “effect profound changes” , it is a mechanical space that allows other mechanisms to occur. It is the other mechanisms that need to be defined, not an invocation of deep time. It is also odd that such a statement is used as a rejection of simple logic. This can only be called a faith statement.

Next, Stan Said:
Simple sexual selection by individuals with un-changed (non-mutated) DNA still cannot create something outside the choices that are available to it. I don't understand why it is necessary for biologists to deny this.

Then Scott Said:
See, the evolutionary biologists I know, they don't deny this. You're tilting at a windmill here, whether you realize it or not, because like a lot of evolutionary skeptics you're hung up on a paradox that doesn't exist. Mutations are a source of variation, but variation in and of itself is not information. We are NOT claiming that order comes from chaos, or that randomness creates information on its own.

Rather, the information comes from an interaction between the genes and the environment. If we say that the genes, mutations and all, are like a set of encylopedias, that still doesn't explain the organism. You still have to read the damn things, you still have to follow the instructions and build stuff, it still has to provide some outcome in the real world. It is the interaction between the environment and the genes that builds the organism.[some emphasis by Stan]

Stan says:
The paradox is one of specific statement:

Individuals don't change their genes. Period. The only thing that is likely to change is the total number and frequency of various alleles within a population. Mutation can affect this, but so can other phenomena.

I cannot see any way that the middle sentence can be a correct statement. Individuals do receive changed genes, or genes that change in the process of genetic transmission (usually deleterious to the organism). So to say that individuals do not change their genes is just beside the point, because changes are transmitted individual to individual. What happens to the group’s calculated record can only be based on individual data, accumulated one at a time, until a calculated value for the full group is recorded. The calculated value for a group is a mathematical entity, not a real entity in materialistic terms. The calculated value depends entirely upon individual genetics. Scott, I cannot help but suspect that this is a dodge commonly used in evolutionist circles to avoid discussion of the actual mechanisms, which are held in mystery.

Scott said:
…various individual bells and whistles that were never developmentally significant in the old world may become critical to the organism's success or failure.

Scott, aren’t “bells and whistles that were never developmentally significant in the old world” the same thing as “accumulated mutations” (using the full definition of the word, mutation)?

At any rate, I have read a little of Mayr, but I will try for more. I will, for one thing, look for the word “random”, which does indeed imply order from chaos. The denial of this appears to me to be a worldview position, not an unfettered intellectual position. If mutation is as the Grants say, mutations and introgressions, then random is a correct description, because both of these are random occurrences.

Scott, do you believe that information exists before as well as during the evolutionary process? If what is the source of this information?

And, thanks again for any “real data” references you can provide.

Stan

Stan said...

Scott,
Here is something that might be of interest to you. There is a true paradox situation in asynchronous digital logic circuitry involving R S Flip Flops.. (Reset-Set Flip Flops). The Set signal and the Reset signal are separate signals which assert opposing states of the flip flop output. If the two signals are asserted simultaneously (an input “race state”), the flip flop can’t decide which state to choose for its output, and since the choices for output signals are directly opposing to each other, the flip flop goes into a state called “metastability”, where the output oscillates between zero and one, and doesn’t find a way to stabilize until internal noise levels force the output to assume a random state.

The solution to this issue - a paradoxical logic state - is to differentiate between the input signals during the race. This involves a circuit called a “race arbiter”, a circuit located prior to the flip flop inputs, which detects the race condition, arbitrarily asserts one signal as the “winner”, and holds off the other signal to be re-asserted at a later, appropriate time.

This shows the lengths to which machine designers go, in order to prevent paradoxical conditions from being asserted to the machine.

Scott Hatfield . . . . said...

First of, I never meant to imply that thermostats can't work. Obviously, the components you describe distribute the 'timeless' argument over time and space, overcoming the apparent (but of course non-existent) paradox. Is it too much to suggest that cells and organisms and populations, all complex objects, do the same things?

I am aware of my bovine’s individual alleles, and I can calculate a cumulative number, I suppose, that might represent the herd as a composite, human construct. More on this mathematical entity below.

The canine disaster scenario is interesting. At the moment of the disaster, both extreme “breeds” are still canines. Morphologically I suppose they can be given different human-designated classifications. But the presumed different paths from that point would still require some mechanism to change their canine genetics to canine-plus genetics. It is the mechanism and likelihood of occurrence that are not addressed here.


What in the world are you talking about? You seem to almost be going out of your way to use biological terms, or obsessing about how the terms that you do apparently want to use are used ('allelic'...?)

What is 'canine-plus' genetics? Do you mean, as in, 'adding information' to the original genome? That's not necessary, the genome's are constantly being reshaped by the addition of new information. The imaginary 'canine disaster' would be an example of such. Why do you feel the need to specify an additional mechanism? Stan, my friend, in biology reproductive isolation, however it is accomplished, is such a mechanism.

To say that a group has modified itself is not meaningful unless the individuals within the group first modified themselves. Seems fundamental to me, basic logic. A bucket of red marbles can't become a bucket of green marbles unless the marbles change first.

No. No. No. Ack! Look, I know you must understand that the individuals don't modify themselves (somatic mutations) in any way that can be inherited. If we're talking about mutations, only germ-line mutations can be passed on. If I have a mutation in a sperm cell, it doesn't affect me one iota, Stan. It's just another defective swimmer. If, on the other hand, that swimmer manages to fertilize an egg that leads to fertile offspring, then maybe we have a 'new' allele, or else a 'new' instance of an allele found elsewhere in the population. Either would affect the allele frequency, but at no time does a leopard change his or her spots. What causes the change is not the individual, either the parent or the offspring. What causes the change is the interaction between the genome and the environment. I'm not sure why you keep returning to a formulation that is biologically unrealistic.

What happens to the group’s calculated record can only be based on individual data, accumulated one at a time, until a calculated value for the full group is recorded. The calculated value for a group is a mathematical entity, not a real entity in materialistic terms.

Stan, isn't that's like saying that since temperature is an average of the kinetic energy of a given system, that temperature is just a 'mathematical' entity, and thus similarly unreal? Surely, as a former engineer you're not going to start arguing that models based upon sampling at different times are somehow invalid because we didn't see the moment when 'new' alleles appeared?

And besides, you're wrong about harvesting individual data, at least in the case of bacterial populations. We don't attempt to isolate individual bacteria when harvesting their DNA. We go after entire populations, pretty much all at once.

However, to be fair let's consider metazoans. How about the Grant's work? I mean, they sample from one breeding season to the next, in between broods. They can measure if allele frequencies go up or down, and they do go up and down. That's a real property of a population. Is it based on the duplication of individual alleles? Sure. Do mutations occur which also affect relative allele frequency? Sure. Can I follow each individual allele, from moment to moment? No, that would be like asking an engineer to keep track of the precise motion of an individual molecule in a sample of gas. But no one denies that there are real molecules doing real things in those examples. I just don't see what you hope to accomplish with this kind of argument.

Scott, I cannot help but suspect that this is a dodge commonly used in evolutionist circles to avoid discussion of the actual mechanisms, which are held in mystery.

I would say that whether or not it was a 'dodge' would depend on the context. If a researcher blithely assumed a mechanism in experimental work, I don't think that would be terribly publishable unless the experiment was such that it could in principle falsify that claim. We biologists often get accused of bad faith when what we really are is lazy: for example, using 'theory of evolution' when what we mean is the 'theory of evolution by natural selection.'

Also, in fairness, there are plenty of times the actual mechanism for genetic change may not be terribly relevant. Another example: cancer represents a genetic change that is confined to an organism, wherein the population of cancerous cells as a frequency of all cells undergoes treatment. Would it be reasonable to suppose that we can identify the means by which cells metastasized in order to acknowledge the metastasis has occurred?

Scott, aren’t “bells and whistles that were never developmentally significant in the old world” the same thing as “accumulated mutations” (using the full definition of the word, mutation)?

No,they might simply be preexisting genes that lacked the right environmental triggers.

This is the presumption that I think needs proof, not only of the statement, but of the mechanism that causes it. It is a basic statement of evolution. It is not in itself proof.

Surely you realize that any population that is reproductively isolated fits this requirement by definition. If gene flow is not occurring between the populations, then by definition they are 'going their own way.'

If mutation is as the Grants say, mutations and introgressions, then random is a correct description, because both of these are random occurrences.

Mutation is random by definition, but all this randomness provides is a reservoir of variation for the action of natural selection. Selection is non-random. Evolution by natural selection is neither a purely random or entirely purposeful process. Rather, it is a stochastic process defined by the interaction between genome and environment.

And yes, there is information present before, during and after the process. Some of this becomes part of building new information.

(yawn) I've got to quit starting posts like this when I'm tired. Chat you up later...SH

Stan said...

Scott said (with a yawn):
"That's not necessary, the genome's are constantly being reshaped by the addition of new information. The imaginary 'canine disaster' would be an example of such. Why do you feel the need to specify an additional mechanism? Stan, my friend, in biology reproductive isolation, however it is accomplished, is such a mechanism."

This is the claim that I can't understand. Especially the part, "the genome's are constantly being reshaped by the addition of new information.

Where does this information come from? Or maybe it is called information because it is "useful", even though it didn't start out as information? This is slippery because information out randomness is denied both by skeptics and by evolutionists, afik.

Scott said No. No. No. Ack! and he was justified in so saying. I meant something other than what I said. I do understand that I do not mutate myself (unless I get cancer), and that the mutations occur in the transfer of genes from myself to my progeny.

Scott: I'm not sure why you keep returning to a formulation that is biologically unrealistic.


I misspoke, sorry.

I also understand about recessive genes putting older alleles into the progeny here and there.

But here is the part that is confusing (bear with me please):

Stan:Scott, aren’t “bells and whistles that were never developmentally significant in the old world” the same thing as “accumulated mutations” (using the full definition of the word, mutation)?

Scott: No,they might simply be preexisting genes that lacked the right environmental triggers.

Here's the part that just doesn't pop out of the text so far: If they are "preexisting genes" that have never yet been expressed, then why were they stored up? And where did they come from? Are they not the product of mutations?

If, as in the Grant's Finches, the long beak / short beak alleles crop up in response to environmental conditions, isn't it true that the genes for variable beak size were there to start with and did not get "created" with the first drought that the species encountered? Or am I still off the biological base? If so, then where did the genes come from?

Scott said:
Mutation is random by definition, but all this randomness provides is a reservoir of variation. for the action of natural selection. Selection is non-random. Evolution by natural selection is neither a purely random or entirely purposeful process. Rather, it is a stochastic process defined by the interaction between genome and environment.

Stan: Again I can't understand that this is not a refutation of the idea of storing up mutations. After all, stochastic means probabilistic or essentially random.

And Scott, thanks for your considered answers, despite your weariness...
Stan

p.s., I don't think that temperature taken as an average of molecule energy is as good an analogy as taking the "average personality" of black people, or the "average weight" of all the women in the world, which resolves to meaninglessness. Correct me with generous explanations if I am wrong.

Thanks again....Stan

Scott Hatfield . . . . said...

Stan, you are far too patient and good-natured for me not to reply, and I apologize in advance for where what I say is unclear, unconvincing or unsourced. I'll try and get you some sources when I have a moment.

However, setting aside the whole 'storing mutations' thing, I have a simple question for you: does a tree ring contain information?

CarlaCarlaCarlaCarla said...

I came here to comment that perhaps Davidson makes up hoax emails in his spare time.

After you two's elaorate comments though, I'm too tired now.