On Tuesday, June 7, 2016 at 1:02:06 PM UTC-7, taf wrote: > On Tuesday, June 7, 2016 at 9:19:52 AM UTC-7, Thomas Milton Tinney, Sr. wrote: > > > TAF, though you are highly learned, your statements and conclusions appear > > to me to be intentionally and willfully misleading. > > The critical part of the sentence being 'to me'. > > First an aside: If you read the actual paper these stories are reporting on (I know, you don't actually read the scholarly papers on which you base your arguments, but one can hope), you will discover that there is nothing to see here. This was not a novel discovery. It was not dramatic. These two scientists simply wrote a review - they read a bunch of papers from the research literature and they summarized that research. All of the conclusions in their paper are not their own, they are just bringing together in one place the published conclusions of others. This hardly merits a press conference, let alone all of the over-hyped reporting in the popular media. The publicity department of the University of Western Australia should be congratulated for getting a non-finding reported as if it was an actual scientific discovery. Then they should be shot for getting a non-finding reported as if it was an actual scientific discovery. > > > Chromosome segregation is the process in eukaryotes by which two sister > > chromatids formed as a consequence of DNA replication, . . . > > https://en.wikipedia.org/wiki/Chromosome_segregation > > You are talking about mitosis here, where two identical chromosomes are separated into different cells. If this goes wrong and you end up with two identical copies in the same cell, how is that going to affect DNA testing? It's not because the answer is still the same - if some people have GATC and others have GAAC, then if a cell ends up with an extra copy of the same sequence, GAAC, and you test it, it will still show as GAAC. On the other hand, it could result in a cell missing the sequence all together and this will not report the other sequence - it will just produce a null result. A flaw in mitotic segregation does not change the identity of the DNA present, even if it changed the number of copies - it will give you the same result or a null result, not a different result. > > This specific report is about chromothripsis, the shattering of chromosomes that can occur in response to certain cellular insults. This usually results in cell death, but occasionally a cell patches back together all of the little pieces into a patchwork set of chromosomes, but here is the thing - all of the pieces are still the same, they are just strung together differently. Thus GATC is still GATC, even though it is now in a piece that is attached to chromosome 1 when it used to be on chromosome 15. When you do a SNP analysis, it will still show as GATC because the DNA analyses used in genetic and genealogic testing are micro-scale while the chromosomal rearrangements are macro-scale. But that is only half of the story. > > When this happens, it only happens in an occasional rare cell. Yes, that cell can give rise to a tumor, but it is just one cell. A cheek swab from someone who just smoked pot will still have 10s of thousands of normal cells for every 'shattered' one, so even if the shattering had an effect on DNA testing of that cell, which it doesn't, the signal from that cell would still be swamped by the 10,000 normal cells - you would never see the problem cell. > > When they talk about it possibly being passed down, they are referring to two entirely distinct phenomena, as again you would know had you read the paper. First, the shattering and rebuilding can theoretically happen in a gamete, in which case the progeny might have a rearranged chromosome, but all the chunks are there, just in different order, or are not there at all - again, the same result or a null result but not a changed result. They are also suggesting the possibility of epigenetic effects - these are chemical changes to the DNA that affect how it behaves in the cell, but do not affect its actual sequence - this will give you exactly the same result in DNA testing as unmodified DNA. > > So exactly which part of this is intentionally and willfully misleading? Do you have the expertise to know, or are you just the equivalent of the child who sticks his fingers in his ears and sings 'La, La, La' so as not to hear when someone else tries to tell them something they don't want to hear. > > taf ---------------- REPLY: TAF, your thoughts are interesting. Thomas A. Kunkel wrote back on Feb 26 2004, concerning DNA Replication Fidelity. He wrote: "interest in the fidelity of DNA copying mechanisms remains high because the balance between correct and incorrect DNA synthesis is relevant to a great deal of biology. High fidelity DNA synthesis is beneficial for maintaining genetic information over many generations and for avoiding mutations that can initiate and promote human diseases such as cancer and neurodegenerative diseases. Low fidelity DNA synthesis is beneficial for the evolution of species, for generating diversity leading to increased survival of viruses and microbes when subjected to changing environments, and for the development of a normal immune system." . . . "To perform these tasks, cells harbor multiple DNA polymerases (2, 3), many of which have only been discovered in the past 5 years and whose cellular functions are not fully understood. These polymerases differ in many features including their fidelity. This diversity and the sequence complexity of genomes provide the potential to vary DNA synthesis error rates over a wider range than was appreciated a few years ago. . . ." http://www.jbc.org/content/279/17/16895.full One, two, four, eight – lessons from dividing cells January 6, 2016 by Wei Theng Poh "By probing the mechanism(s) that leads to cells extinguishing checkpoint signaling in the presence of the DNA damage, we hope to gain a fundamental understanding of an event that possibly confers survival advantages to cancer cells types. And that would be half the battle in thinking about how to treat this disease." http://phys.org/news/2016-01-lessons-cells.html Scientists propose an algorithm to study DNA faster and more accurately January 18, 2016 "Bioinformatics is a very topical subject; every new sequenced genome raises so many additional questions that scientists simply do not have time to answer them all." http://phys.org/news/2016-01-scientists-algorithm-dna-faster-accurately.html It is intentionally and willfully misleading, to suggest, by companies, in public notices or by groups like this, as if you have all the answers; that current genetics can provide to unsuspecting new or advanced genealogy researchers, connective genetic data sets to written record sources. The power of positive prediction of similar results over time, is subject to cellular functions not yet fully understood, as noted in more current publications; and, which cells, from research undertaken and reviewed, in the recent past, have been found to be sensitive, re: DNA, to harmful drugs ingestion. Genetic data conclusions, at present, are like a beautiful 4th of July celebration, one great find after another lights the headlines sky, each having its 15 seconds of glory, then flowing down as burnt embers as a new theory and postulations follow the wake; ever learning, approximately, but not finding ultimate truth.

On Tuesday, June 7, 2016 at 8:55:46 PM UTC-7, Thomas Milton Tinney, Sr. wrote: > REPLY: > TAF, your thoughts are interesting. Thomas A. Kunkel wrote back on Feb 26 2004, concerning DNA Replication Fidelity . . . 12 years is a terribly long time in molecular biology terms. Any how, a discussion of how cellular polymerases optimize mutation frequency does nothing to affect the demonstrated consequences - enough mutations for divergens, not so much as to disguise shared origins. > One, two, four, eight – lessons from dividing cells > January 6, 2016 by Wei Theng Poh > > "By probing the mechanism(s) that leads to cells extinguishing checkpoint signaling in the presence of the DNA damage Note even remotely relevant. Here is a clue: DNA damage is not the same as DNA mutations. > Scientists propose an algorithm to study DNA faster and more accurately > January 18, 2016 > > "Bioinformatics is a very topical subject; every new sequenced genome > raises so many additional questions that scientists simply do not have > time to answer them all." And in what way is this even remotely relevant? Yes, with anywhere from millions to billions of nucleotides, encoding the signals for replication, transcription, translation.stability and function, there is so much information to be studied that interesting aspects than there are scientists to study them. This in no way invalidates the answer from any specific questions we do ask. These are all just completely irrelevant. > > It is intentionally and willfully misleading, to suggest, by companies, in > public notices or by groups like this, as if you have all the answers; Perhaps you want to try this again. It makes no sense. > that current genetics can provide to unsuspecting new or advanced > genealogy researchers, connective genetic data sets to written record > sources. Again, try English. > The power of positive prediction of similar results over time, is subject > to cellular functions not yet fully understood, as noted in more current > publications; Nonsense. > and, which cells, from research undertaken and reviewed, in the recent > past, have been found to be sensitive, re: DNA, to harmful drugs > ingestion. Irrelevant > Genetic data conclusions, at present, are like a beautiful 4th of July > celebration, one great find after another lights the headlines sky, each > having its 15 seconds of glory, then flowing down as burnt embers as a > new theory and postulations follow the wake; ever learning, approximately, > but not finding ultimate truth. Ultimate truth is unattainable, and that goes for science, history or theology (although I guess in the latter it could be said that you can achieve ultimate truth, and someone else can, but the two will be different ultimate truths). In science we don't have the ultimate truth behind gravity, but we can still measure it and characterize it and see that it follows certain principles, but our understanding of it too is subject to revision/optimization. That doesn't mean one day you will fly off into space. You suggest you won't accept DNA until we have the ultimate truth, but such an answer to life, the universe and everything is so complex we can't even frame the question. What you have 'discovered' by your Google search for DNA is not novel and it is not something that overturns the current model of genetics, any more than 'discovering' that some years do not have 365 days invalidates all chronology. The origins, effects and frequency of mutations has already been fully integrated into our understanding, and a full paradigm shift that would be required to subvert our understanding of DNA inheritance will not come from Googling for Wikipedia pages, decade-old science articles and over-blown stories from the popular press. taf