Thanks you Sean. Now the subsequent question is why do …

Comment on The Basis of Biblical Credibility by Sean Pitman.

Thanks you Sean. Now the subsequent question is why do you accept that boars and pig as genetically related by ancestory but not man and chimps. If you read the paper you will see that in fact there is greater genetic distance between pig and boar than between man and chimp. Loss of genes in the boar/pig is simply analogous to the y chromosome changes in human/chimp. Is this a 1000FSAAR or not?

I’m not talking about a loss of genes. I’m talking about a gain of a qualitatively novel protein-based function that requires a minimum of more than 1000 specifically arranged residues. Do you know of such a novel system or not? If so, please do present it here. Even if humans and chimps did have a common ancestor, how would this help you explain the evolution of higher level systems via RM/NS? – given that such has never been observed and is still statisically impossible this side of trillions of years of time? Such an argument has absolutely no explanatory power and is not scientific (being untestable in a potentially falsifiable manner).

Just for fun though, is there such a difference between humans and chimps? As I’ve explained to you before, there do seem to be such differences on a macro scale – to include structural brain differences that result in higher-level functional differences that require, not just specific 1000aa structures, but entire cellular structures that enable humans to do things that chimps cannot do – things like write books and speak in complex sentences, etc. These functional advantages are not based so much on novel genes, as previously explained, but on how the products of similar genes are used to make different types of structures and systems based on non-coding DNA (which is significantly different between humans and apes). And, as far as I’m aware, there are no such higher-level functional differences between boars and pigs. Consider also that boars and pigs can interbreed to produce viable offspring. This cannot happen between humans and chimps.

Again, you need to focus on functional systems, not genes. Do you have any example of any qualitatively novel system evolving that requires more than 1000 specifically arranged residues? You’ve yet to produce such an example or any mathematical argument that even allows for such an example. You seem to be trying to argue that it must happen because certain species simply must be related. Again, that’s not the same thing as producing an actual example or explaining how such evolution is statistically possible within the vastness of sequence space.

If you accept that pig and boar arose by a sequence of small genetic changes occurring by gene selection in a gene puddle then you must logically also accept that man and chimp arose by small genetic changes as well. Particularly as you have not identified either in pig/boar or in human/chimp any differences fulfilling your 1000FSAAR barrier beyond simply hinting that Y chromosome changes must be such. I do not believe there is such a barrier. You do but have never even attempted to identify it with any sort of specificity.

I have given you many specific examples of higher level systems. Yet again, the rotary bacterial flagellar motility system requires a minimum of over 5000 specifically arranged amino acid residues positions to be in place before this type of function will be realized. No system at this level of functional complexity or beyond has ever been shown to evolve nor are there any statistically tenable models on how this might be achieved via random mutations and function-based selection.

As far as this level of differences between pigs/boars, of course I am not aware of such – especially given that pigs and boars and interbreed to produce viable hybrids. As far as humans and chimps are concerned, more and more discoveries are coming to light that highlight fairly significant structural differences that are functionally relevant at a higher level of complexity. And, humans/chimps cannot interbreed. Why not? Well, for one thing the non-coding DNA is very different and is responsible for producing many of the structural/functional differences. And, for another thing, research carried out by scientists at the University of Oxford and the University of Chicago found that hotspot regions that determine the locations for genetic recombination during cellular meiosis in sexual reproduction showed “no overlap between humans and chimpanzees.” This was an “extraordinarily unexpected finding” given the assumed evolutionary relationship between humans and chimps. Professor McVean explains:

“Genetic recombination has been likened to shuffling a deck of cards, which ensures that children are given a different genetic ‘hand’ than their parents. We know that in many cases recombination occurs where a particular thirteen letter sequence is present — this is like a run of hearts from ace to king determining where we cut the deck of cards. Because humans and chimpanzees are genetically very similar, we might explain that you can only ‘cut the cards’ at the same point — in fact, we find that this is not true.”

http://www.sciencemag.org/content/336/6078/193

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

The Basis of Biblical Credibility

Your argument that evolution cannot work because Paul Cameron or anyone else lacks a precise mechanism to overcome your declared barrier (1000 fairly specified amino acid residues) is based on the fallacy of ignorance.

Then I suppose SETI science, forensic science, and anthropology are all based on the “fallacy of ignorance” as well? – since these scientists can’t think of any mindless natural mechanism to explain certain types of radio signals, murder victims with certain unnatural features, or pieces of rock with artefactual features?

I’m sorry, but there is no fallacy with the argument for the detection of intelligent design behind various kinds of artefacts – like the origin of a highly symmetrical polished granite cube. It isn’t that these scientists are ignorant of how the phenomenon in question could have been produced by intelligent design. They know how the features they’re considering could have been produced by many different intelligently designed methods. What they don’t know is how the artefact in question could have been produced by any known mindless mechanism of nature. That, my friend, is the very basis of all sciences dealing with the detection of true artefacts of intelligent design.

The very same thing is true of the biomachines within living things that I’m presenting. Clearly, these machines very closely resemble machines that we know were produced by intelligent design. We known and understand how such machines could be produced by various means by intelligent design. What we don’t know is how they could be produced by any mindless natural mechanism this side of a practical eternity of time (i.e., trillions upon trillions of years). This means, of course, that the very best scientific conclusion, the theory with the best predictive power, is that any such biomachine was almost certainly produced by intelligent design.

Now, does the intelligent designer of these biomachines have to be God? No. Not at all. Omnipotence is not required to explain something like a bacterial flagellar motility system. However, even though omnipotence is not required to explain the origin of such machines (to include things like a wrist watch or a granite cube), intelligence of some kind is required.

Does this therefore mean that God did not make something just because God-like power is not required? No. God can make simple stuff just as easily as you and I can make simple stuff. If it just that a God-like creative power is not required to explain everything that God can make. For example, is it possible for God to make a loaf of bread? – the same type of loaf of bread that your mother can make? Sure it is.

It’s funny, don’t you think, that you don’t argue against SETI radio signals or highly symmetrical granite cubes as being anything other than obvious artefacts of intelligent design. Why then the double standard for biological machines that are even farther beyond any known mindless mechanism while being at least closely approximated the creative powers of known intelligent agents?

Sean Pitman
www.DetectingDesign.com


The Basis of Biblical Credibility

You obviously can declare anything you want in terms mutation rates and how many SNP indels and genes were present in the 2 mythical pigs but how many can really be present in the original haplotypes. You have said before that copy number variation was not at all the basis for the genetic richness of the original 2.

I see no reason to argue for a significant difference in past mutation rates as compared to today’s rates. Consider that the pig genome is similar in size to the human genome, ~3 billion bases (haploid). The two pigs on the Ark could easily have had a 0.3% difference in genome sequences to start with (with regard to SNPs). Also, in each family line novel SNPs are produced in each generation for each individual at a fairly high rate (up to 100 per individual per generation). And, the generation time for pigs is ~1 year. A comparison between hundreds of pigs from different family lines, even within the same breeding population of average size, would yield a huge number of SNPs in very short order. So, I don’t see why this is an appeal to “magic”?

As far as “unique genes” are concerned, much of this can be explained by a loss of genetic information by one population vs. the other after the split. This is one of the reasons for the “hybrid vitality” already mentioned. Producing such hybrids gives the hybrid offspring access to genes that are missing from each separate gene pool, but were originally available in the ancestral gene pool.

Of course, the production of novel alleles is also a factor. And, in an average population, any beneficial allelic variation would become fixed in relatively short order.

The differences in indels is interesting, but I see no need to invoke magic to explain a few hundred thousand indels in a comparison of hundreds of pigs – especially since muticharacter mutations are quite common as well and would already have existed within the first pair on the Ark to begin with. For example, there are thought to be thousands of conversion mutations per individual in each generation. Combine this with what is generally assumed to be a high rate of inversions/translocations, ~10 duplications/insertions/deletions (changing up to 20 times the number bases that point mutations change per generation), and >100 satellite mutations, and you have yourself a very high overall mutation rate that adds up to many thousands of nucleotide changes per individual per generation.


The Basis of Biblical Credibility

“The discovery of the Cit + mutants in Lenski’s experiment has been a mote in the eye for those suggesting that major phenotypic innovations cannot be explained by micro-evolutionary (gradual) processes…

Do you know anything about the experiment where Lenski’s produced Cit+ E. coli bacteria?

What Lenski did was to grow E. coli under oxic conditions in citrate-rich media. E. coli bacteria are generally unable to use citrate under oxic conditions as a source of energy. However, they can use it under anoxic conditions. In other words, they already have the gene for citrase in their genome. It is just that it is normally turned off under oxic conditions. How is it turned off? Well, the promoter for the gene that transports citrate into the bacterium is not active under oxic conditions. So, all that needs to happen is to move the citrate transport gene close to a promoter that is actually active under oxic conditions. Once this is done, citrate will enter the bacterium and be used for energy.

And, this is exactly what happened. Nothing structurally new needed to be evolved. After about 31,000 generations, in a large population of bacteria, there was a single genetic mutation in a bacterium that ended up moving the citT gene and placing it under the control of a promoter (rnk) that is active under oxic conditions. The fact that just this single translocation mutation took so long to achieve should clue you in to how difficult it is to achieve even such low-level changes in function via random mutations. The protein product, however, remained the same – i.e., <500aa with no required amino acid changes to achieve a selectable effect. All that was required was to move a pre-existing gene close to a promoter to turn it on during oxic conditions. That's it. The protein itself didn't need to be changed for a useful advantage. Now, at this point, multiple copies of the gene were rapidly produced in some colonies. However, having just one copy was enough to produce a selectable advantage in the citrate-rich environment. It doesn't matter if there are 1 - 9 copies of the gene - the same function is realized to different levels - i.e., the cit+ function can exist, to a selectable degree, with just one copy of the gene producing the the very same protein. Additional "refinements" are easy once at least a minimum useful level of a particular type of function is realized - not a problem at all. Again, this "unicorn" of yours is a very low-level example of evolution in action where nothing structurally new was produced to achieve the function in question. The only thing that happened was a mutational move from one location to another within the genome. That's not a statistical problem for Darwinism at all...

Pubmed still does not have any reference to novel structure composed of 1000 amino acid residues. But indeed there is refence to uinicorns so your 100FSAAR is rarer than unicorns in the biomedical literature. Perhaps you should publish your obvservations.

Tell me, what is the minimum number of specifically arranged amino acids required to produce a rotary bacterial falgellar motility system? Is it possible to reduce it to less than 1000 specifically arranged residues? – without a complete loss of the motility function?

Again, the concept of functional complexity has been published and is well defined in literature, to include the minimum size requirement. I’ve already given you the references a couple times now.

Sean Pitman
www.DetectingDesign.com


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