Comment on The End of “Junk DNA”? by Sean Pitman.

@pauluc:

We return again to wonderland and to unique definition of species and argument;

Why do you continually misrepresent my position? As I’ve explained to you and Professor Kent several times now, I’m not presenting a new definition of “species” – not at all. The mainstream definition of species works just fine for its intended purpose and does have value. My definition is a definition of unique “kinds” of gene pools that contain qualitatively unique functionality that cannot be evolved by RM/NS. This is not the same thing as the species concept and I’m not sure why you both continue to try to equate the two? That is why different species can indeed evolve, quickly evolve, over short periods of time while different “kinds” of biological systems cannot evolve beyond very low levels of functional complexity regardless of how much time is allotted this side of a practical eternity of time.

Note also that you’ve presented several demonstrably false assertions so far in this particular thread. You started off with the claim that the increasing mutation rate for men with age is clearly too high to consider the Bible’s claim for antediluvian reproductive life spans of several hundred years remotely tenable. You were wrong. You also claimed that other forms of mutations besides SNP-type mutations are too high to be consistent with the Biblical model. You were wrong. And, your claim that deleterious mutations can be effectively removed from slowly reproducing gene pools (via some form of genetic recombination?) is also clearly mistaken.

Why not just admit that Neo-Darwinism is obviously bankrupt and move on? Still clinging to your top-down approach “as Darwin did”? How is that valid “science” when your mechanism is so obviously bankrupt?

Your glory seem to be that classification of phenotypic and genotypic diversity “means what I say it means” completely disregarding the conventions of 150 years of biology and biologist who have gone before.

Not at all. The classification conventions of 150 years of biology are just fine for what they do. However, they do not, as you well know, draw a distinction between what can and cannot evolve via the Darwinian mechanism of random mutations and natural selection (RM/NS). My definition of qualitatively unique “kinds” of biological systems at various levels of functional complexity does draw this distinction and is not a redefinition of the species concept – despite your repeated attempts to paint it as such. The reality is that mine a unique concept that is independent of the species concept.

What is on the line here is the neo-Darwinian mechanism of random mutations combined with natural selection vs. the Biblical model of origins.

Does the mechanism of RM/NS have limitations that can be clearly defined? The answer to that question is yes. Any qualitatively novel system of function that requires a minimum of more than 1000 specifically arranged amino acid residues has not been observed to evolve and statistically is extremely unlikely to evolve this side of a practical eternity of time.

As a practical illustration, let’s say that we are comparing eukaryotic vs. prokaryotic motility systems for single-celled organisms. One type is based on a rotating flagellar system while the other is based on a back-and-forth sliding system. These two systems are qualitatively unique and they both require a minimum of far more than 1000 specifically arranged amino acid residues to work as motility systems. It is quite safe to say, then, that these two populations did not share a common ancestor – unless one wishes to propose that the common ancestor of both had both types of motility systems “front-loaded” in the original parental gene pool.

Another example would be the different kinds of vision systems in existence from a single light-sensitive cluster of cells to a cup-shaped “eye” to a compound eye to an eye with an inverted retina to an eye with a verted retina to an eye with a lens, etc. All such visions systems are qualitatively unique beyond the level of 1000 specifically arranged residues. Therefore, any comparison between gene pools containing codes for vision systems with such differences would suggest that these two gene pools do not share a common evolutionary ancestor – unless one wishes to propose that the original parental gene pool contained codes for both types of vision systems being compared… etc.

The other issue in play here, of course, is the credibility of the Bible. Has the Biblical account of origins been effectively falsified by the claims of modern scientists so as to require a non-testable Divine miracle to overcome? So far, based on what you’ve personally presented, the answer to this question is clearly no. You’ve not come remotely close to falsifying the Biblical claims regarding origins or even calling them into serious question. If anything, you arguments have ended up supporting the Biblical model. In short, the significant weight of the empirical evidence that we currently have in hand fits very very well within the Biblical model while effectively falsifying the neo-Darwinian perspective on origins.

“The biosystems themselves within different gene pools are what can be evaluated as far as levels of functional complexity are concerned. This is not beyond the capabilities of modern science.”

Indeed that is true but as far as I can see it so far has been beyond you to use the tools of modern science to evaluate your hypothesis. Certainly you do not even seem to have attempted to do so. There are complete genomes of at least 30 mammalian species as I have given reference to before. You seem to believe that there are differences between the mammalian species that would conform to your criteria of limits insuperable by an evolutionary process. Most biologist have long since past the point of worrying about these supposed limits so you cannot rely on someone else to do your research. Sit down at your computer and use the available free online resources and compare these genomes and tell us what and where are the 1000faar limits in these genomes that unequivocally destroy the argument that these mammalian species have arisen from a common mammalian ancestor.

I have given you multiple examples of qualitatively unique systems that could not have evolved by RM/NS. Any such systems in any gene pool would be beyond the powers of Darwinian mechanisms. What you seem to want is an analysis of innumerable gene pools with published dividing lines for each. That simply isn’t needed before the basic concept becomes clear – that there is a limit to the creative powers of RM/NS to very low levels of functional complexity and a steady devolution of slowly reproducing gene pools.

If you really think I’m wrong, you’re the one who needs to show how the high level qualitatively unique systems within modern species of plants and animals could actually have evolved given only a few billion years (a drop in the bucket compared to what the average time needed to achieve anything beyond the 1000saa level)? – and get rid of detrimental mutations faster than they are currently entering all slowly reproducing gene pools? That is the just-so story telling fairytale that is beyond scientific tenability.

“All the Pitta species can interbreed and produce viable and virile offspring. Therefore, they share the same basic “kind” of gene pool.”

Pardon my scepticism but I am reluctant to take this on your say so. Please provide a reference for the statement “All the Pitta species can interbreed”.

There are many examples of hybrids between Pitta bird species and no reason to think that any particular Pitta cross breed would be genetically impossible.

http://www.bird-hybrids.com/engine.php?search=pitta&searchby=nomenclature&nomenclature=ALL&family=ALL

This is simply obfuscation and a restatement of your postulate and does not at all respond to the question. Of course there is incomplete lineage sorting as is included for example in the Scally et al paper on comparison of primate genomes (Nature 2012 483:169). You cannot however use this mechanism to say that the 1000fsaar differences have been lost from all the sequenced genomes. Either the differences between mammalian species includes genes or DNA sequences fulfilling your criteria of 1000fsaar or it does not. I find it hard to accept that there are 1000fsaar differences that limit evolution somewhere beyond the species level but at the same time that you insist that all extant canid species arose over 4000 years from 2 animals by a process of mutation and natural selection. You seem to be insisting there is a rapid natural mechanism for speciation and that speciation occurs by multiple minor mutations (very very low complexity) yet there is some profound barrier at some arbitary point that you then use to define a kind.

I’m afraid I do not follow you here? I don’t see that you’ve presented any barrier to rapid canid speciation or any example of any kind of qualitatively unique system within various species of canids that is beyond low levels of functional complexity?

I also don’t see where you’ve presented any example of any qualitatively novel system of function evolving beyond low levels of functional complexity or how this might even be statistically tenable?

I also don’t see where you’ve explained how any naturalistic mechanism can deal with the very high detrimental mutation rate that is realized in every individual in every generation within slowly reproducing gene pools?

Where then is the “science” behind your position?

Oh, you want to me to list off distinct differences innumerable gene pools that could not be evolved. To a limited, but sufficient degree, I’ve already done this – as noted above. Other examples I’ve discussed with you include various qualitatively unique differences between reptiles and birds at high levels of functional complexity (like the breathing system for instance). Or, what about the qualitatively unique differences between human and ape brain structure and function that are based on unique genetic sequences?

I really don’t see why I need to get much more detailed here to get my basic point across? If no higher level system can evolve via RM/NS and slowly reproducing gene pools are devolving, not evolving, over time, then Neo-Darwinism is rationally and scientifically untenable while the claims of the Bible are right in line with the significant weight of the scientific evidence that is currently in hand.

I am happy you can accept as a faith position these extraordinary contradictory positions because of a particular literal reading of the biblical text. But to say

“All that mainstream scientists really have to prop up this concept are fantastic just-so stories that have no more scientific value than fairytales for children.”

and to imagine that even a fraction of the genomic and genetic data supports your unique and peculiar models without even actually examining the genomic data with a view to testing your models compels me to think that you have little understanding of the process of science or the explanatory value of natural process.

It is not a blind faith position to recognize the clear limitations of the Darwinian mechanism of RM/NS or to see that humans and all other slowly reproducing species are devolving toward eventual extinction over time.

All of you who accept the claims of mainstream scientists at face value without considering the limitations of the proposed Darwinian mechanism are not buying into science, but into a popular philosophy of mainstream scientists – a fairytale story that should have no more status in science than any other fairytale told to children at bedtime…

Sean Pitman
www.DetectingDesign.com

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