Comment on An apology to PUC by Sean Pitman.

@OTNT_Believer:

Well, I guess I get it. You know so uch more than me about genetics and evolution I can say no more. I do have a Ph.D. in molecular genetics with an emphasis on evolutionary genetics. I have also published a good number of peer-eviewed papers in scientific journals and a few boks to boot (not self-published, I might add). Now, of course, this likely means nothing to you, because you are obviously better read on these topics than I am. I mean I never even heard about the dog paper you cite. 😉

I’ve just asked you a few simple questions. Why not at least address them? Is your definition of “macroevolution” based on qualitatively novel functional differences within the underlying gene pools or not? If not, what is your definition of “macroevolution”? What types of differences would or would not qualify as “macro”?

Your example of the Galapagos “finches” is a good one. You note that they are so different than other types of finches or tanagers that they are difficult to classify. The question I have is, what is responsible for the difference in phenotypic appearance? What is the underlying genetic difference? Is it based on something new being added or lost from the common ancestral gene pool? Is this not a relevant question? After all, tanagers, in general, have been difficult to recognize as true tanagers. Only as genetic evidence has come into play in more modern times have many types of birds that were not originally recognized as tanagers surprised scientists by actually being part of the tanager family. There is an extreme diversity of phenotypic expression within this family. Yet, very phenotypically diverse tanagers can interbreed and produce viable and even fertile offspring.

http://creagrus.home.montereybay.com/tanagers.html

This fact strongly suggests to me that different “species” of tanagers are in fact part of the same original gene pool of phenotypic options that were already available in the original ancestral gene pool – and that there really has been no substantive change to that gene pool when it comes to the entrance of anything that is qualitatively unique with regard to functionality (that isn’t based on a loss of some pre-existing function or an alteration in the degree of expression of some pre-existing functional option).

This is reflected in the fact that:

“In contrast to the substantial differences in morphology, levels of sequence divergence among Darwin’s finches and their close relatives are surprisingly low, indicating they all share a very recent common ancestry…

Instead of identifying a single species as the closest living relative to Darwin’s finches, our results identifies a clade of six species (Tiaris canora, T. fuliginosa, T. obscura, T. bicolor, Loxigilla noctis, and Melanospiza richardsoni) that together form the sister taxon to Darwin’s finches. The ‘‘domed nest clade’’ represents a strongly supported monophyletic group not previously recognized. Thus, we propose the Latin name Tholospiza (meaning dome finch) to assist future communication concerning this group of birds…

Darwin’s finches and their relatives that build this unique type of nest as the ‘‘domed nest clade.’’ The species within the domed nest clade are genetically quite similar to each other, indicating they share a very recent common ancestry. Levels of sequence divergence range from 0.3% to 10.0% and average only 6.7%. By comparison, Johns and Avise
(1998) compiled cytochrome b sequence data for 88 avian genera and found that congeners show on average 7.8% sequence divergence. Thus, most species within the domed nest clade exhibit levels of genetic divergence less than that of pairs of congeneric, closely related species of birds. This contrasts with the traditional taxonomies that have placed these species into 13 different genera and three different families based on dramatic morphological differences in bill size and other characters.”

http://eebweb.arizona.edu/courses/galapagos/handouts%202009/articles%202009%20for%20web/phylogenetic%20relationships.pdf

As you know, when it comes to functionally neutral evolution, or even the loss of functional options that were originally present in the ancestral gene pool, such changes can be realized very rapidly. Consider, that the mutation rate is quite high – on the order of 200-300 mutations per individual per generation.

The problem with rapid speciation, it seems to me, is really only a problem if one’s definition of “species” is based, at least somewhat, on the entrance of functionally novel elements to the gene pool that were not already present within the ancestral gene pool.

I too have a real problem wth macroevolution, and thus my surprise at how you propose the earth was repopulated after the flood and the rapidity with which new taxa would have to arisen. I don’t know what you think Noah took into the ark, but even if he took a very broad sampling of the world’s taxa there would have to have been some macroevolution to get where we are now. Even if you define macroevolution more in the way creationists do, Darwin’s Finches represent a good example of this, as would a lot of isolated endemic species. They are the best examples, because they “appear” to have been separated from other related taxa for so long that their taxonomic affinities are often obscured.

And that’s the main question here. You think that it would have to take a very long time for Darwin’s finches to have achieve the degree of phenotypic uniqueness that we observe today. Why do you believe this? Upon what is this belief based? Please do educate me at least a little bit in regard to your understanding of population genetics and the rate at which genomes can mutate and pre-existing trait options can become isolated or enhanced over time…

I notice in some past post either you or someone else suggested that they knew no one who accepted a local flood and a short term chronology. Well, I am not one that falls into that category, but I certainly lean that way. It would help solve at least some of the problems.

But it would create many more problems than it really solves. How is a few thousand more years going to help solve your finch evolution problem anyway? That’s a drop in the bucked compared to the mainstream understanding of geology and the fossil record… to include the origin of the Galapagos.

One thing I do know. the Egyptian dynasties, based on their written records go back more than 6,000 years, so that at least would suggest we need to push things back a few thousand years.

The dates for various Egyptian dynasties are not very reliable. There are several reasons for this, to include the possibility that some Egyptian kings may have been contemporaneous – parallel rather than serial. Not knowing whether their monarchies were simultaneous or sequential may lead to widely differing chronology interpretations. Also, the dates for the same pharaoh often vary substantially depending on the intermediate source that is used as a reference. For example, J.H. Breasted, writing in 1905, adds a ruler in the Twentieth dynasty that further research showed did not exist. Breasted also believed all the dynasties were sequential, whereas it is now known that several existed at the same time.

Because of these problems, Breasted’s dates, published in 1905 for the 1st and 2nd dynasties, were 3400–2980 B.C. These dates have been reduced by Ian Shaw (in 2000) to 3000–2686 B.C. – a difference of some 400 years for the start of the 1st dynasty. In other words, the first dynasty is currently dated at ~5,000 years ago… not “over 6,000 years ago” as you suggest.

Beyond this, the debated “New Chronology” developed by English Egyptologist David Rohl and other researchers, suggests that the start of the 1st Egyptian dynasty was another 350 years younger than Shaw’s estimate… or ~4,650 years ago.

http://en.wikipedia.org/wiki/New_Chronology_%28Rohl%29

Either way, I fail to see how this substantially helps your argument…

So, although I mioght poke in on occasion, I am afraid I have neither the time, inclination, or apparently the adequate knowledge to continue this. I still think you would do well to take a few graduate courses, one in genetics and one in molecular systematics. Of course, it might be that you know all you need to know, in which case those classes would be a waste of time.

I have taken graduate level genetics courses – though not yet a course specifically in systematics. I have done more than a bit of reading into the topic however, and would appreciate it if you would clarify your concerns and reasons why you think the current phenotypic diversity of living things could not have been achieved nearly as rapidly as I’m suggesting. What specific genetic feature, in your opinion, is unexplainable in my model?

Sean Pitman
www.DetectingDesign.com

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