From: rokimoto557@gmail.com   
      
   On 8/29/2025 11:48 PM, MarkE wrote:   
   > On 29/08/2025 1:48 am, RonO wrote:   
   >   
   > ...   
   >   
   >>> My question then, is it reasonable, accurate and in good faith to   
   >>> characterise this as "science doesn't know X therefore God"?   
   >>>   
   >> Yes it is.  God-of-the-gaps is just that no matter if the gaps are   
   >> never going to be filled.  No one expects to figure out how life   
   >> actually arose on this planet.  The best that we can do without a time   
   >> machine is figure out the most likely way that life arose, and it   
   >> could have actually arisen in a much more unlikely way.  The first   
   >> organic conglomerate that produced the first self replicating   
   >> molecules might have been created by a random asteroid impact instead   
   >> of condensing in some crevice somewhere.   
   >>   
   >> Gaps like what caused the Big Bang may never be filled due to the   
   >> singularity that we can't get past to see what existed before.  Denton   
   >> is happy with using this gap because he can never be demonstrated to   
   >> be wrong.   
   >>   
   >> I was a genetics major as an undergraduate at Berkeley, and all the   
   >> geneticists told me that genetics was over and that the future was   
   >> molecular biology, so I did my PhD in molecular genetics.  During my   
   >> graduate studies tools for genomic analysis like PCR and   
   >> microsatellite genetic markers were created, and they had the promise   
   >> of allowing the unsolved issues in genetics to be answered.  I went   
   >> back into genetics because the new technology was opening up a new   
   >> frontier in genetics. There was finally the possibility that things   
   >> like why the infinite allele model worked so well in quantitative   
   >> genetics.  Quantitative genetic analysis was well worked out, but we   
   >> didn't understand why it worked.  I started my first post doc on   
   >> looking for quantitative trait loci (QTL) in 1992.  I retired in 2024   
   >> and we still do not know why the infinite allele model works for   
   >> quantitative genetic analysis.  We can sequence whole genomes now, but   
   >> somethings remain a mystery.  You do not see the ID perps claiming   
   >> that their designer is responsible for the success of the infinite   
   >> allele model in quantitative genetics.   
   >>   
   >> My guess for why it works is that due to the fall off in increased   
   >> accuracy with the inclusion of more past generations of data (about 3   
   >> past generations are enough to use for things like BLUP (best linear   
   >> unbiased prediction) is that linkage is the reason for the infinite   
   >> allele model working so well.  Most of it may be apparent linkage and   
   >> not actual linkage on the same chromosome.  We have found that an LD   
   >> (linkage disequalibrium) of only 0.3 within a population is sufficient   
   >> to use markers spaced along the genome to improve the accuracy of   
   >> predicting the best breeding values for individuals.  All the alleles   
   >> segregating in the genome have a minimum linkage of 0.5 (you inherit   
   >> half of one parent's genome) in the first cross.  Closely linked   
   >> markers have a linkage close to 1.0.  This means that the whole genome   
   >> can be considered to have a quantitative genetic value due to hundred   
   >> or thousands of genetic variants in that genome, and these variants   
   >> can be inherited together just by chance if they occur in the same   
   >> individual even if they are not linked.  This would create pseudo   
   >> haplotypes based on the whole genome, and not just haplotypes of the   
   >> same chromosomes. In the first cross half the QTL segregate together   
   >> in any individual. My guess is that this would create close enough to   
   >> an infinite number of pseudo haplotypes of unlinked QTL.  Half the   
   >> sires genome is inherited in the first cross, 25% in the next cross,   
   >> but if we are talking genome equivalents (and things that sire is   
   >> homozygous for) then all the homozygous alleles (1 genome equivalent)   
   >> is inherited among the progeny of the first cross, half a genome   
   >> equivalent in the second cross and 25% in the third cross.   
   >> Statistically these pseudo haplotypes could persist for multiple   
   >> generations.  Each individual starts with a new set of pseudo   
   >> haplotypes that add to the haplotypes due to actual linkage, so you   
   >> never see all the "alleles" possible in a single generation.  There   
   >> would be pretty much an infinite number of them.   
   >>   
   >> Ron Okimoto   
   >>   
   >   
   > How is retirement treating you?   
      
   Just fine.  I find myself researching more science topics because I am   
   no longer limited to what my job involved.   
      
   God of the gaps is just that no matter if science is ever going to fill   
   the gaps, and even if you can fill the OOL gap with some god, it is not   
   the god described in the Bible.  When the ID perps have to resort to   
   quote mining and ignoring catalytic alternatives in order to support   
   Tour you should understand that gap denial is bogus.   
      
   >   
   > Based on your experience as described above (credit where due btw) I'd   
   > be interested in your comments on mathematical vs simulation vs observe   
   > and infer approaches the study of population genetics.   
      
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