DNA and Man's origin

by D wiltshire 126 Replies latest jw friends

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  rem

  Hooberus,

  These assumptions regarding mtDNA mutation rates, with their margin of error calculations are based on the assumption that humans/chimpanzees shared a common ancestor millions of years ago.

  This is incorrect. There is no assumption that humans and chimpanzees share a common ancestor in the mutation rates used. The assumed mutation rate is calibrated against known mutation rates in current populations. There is a margin of error, however, because mutation rates can change. The issue is whether mutation rates can become rapid enough to make the margin of error so great that the two species could share common ancestry in a matter of a few thousand years rather than a few hundred thousand years.

  Anyway, there is no reason not to assume humans and chimpanzees did not share a common ancestor a few million years ago. So far, that's what all of the evidence points to.

  rem
• 

  hooberus

  rem said:

  This is incorrect. There is no assumption that humans and chimpanzees share a common ancestor in the mutation rates used. The assumed mutation rate is calibrated against known mutation rates in current populations.

  rem my earlier post from an AiG arcticle (the section I posted came from an evolutionist) seems to indicate that the assumption of a human/chimp common ancestor was used in the calculation.

  http://www.answersingenesis.org/docs/4218tj_v12n1.asp

  To estimate the time when the most recent ancestral sequence common to the Neandertal and modern human mtDNA sequences existed, we used an estimated divergence date between humans and chimpanzees of 4–5 million years ago and corrected the observed sequence differences for multiple substitutions at the same nucleotide site. This yielded a date of 550,000 to 690,000 years before present for the divergence of the Neandertal mtDNA and contemporary human mtDNAs. When the age of the modern human mtDNA ancestor is estimated using the same procedure, a date of 120,000 to 150,000 years is obtained, in agreement with previous estimates. Although these dates rely on the calibration point of the chimpanzee-human divergence and have errors of unknown magnitude associated with them, they indicate that the age of the common ancestor of the Neandertal sequence and modern human sequences is about four times greater than that of the common ancestor of modern human mtDNAs.39
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  hooberus

  Also the quote that Earnest provided also seemed to indicate this:

  The date of divergence between the mtDNAs of the Neandertal and contemporary humans is estimated to 465,000 years before the present, with confidence limits of 317,000 and 741,000 years. Taken together, the results support the concept that the Neandertal mtDNA evolved separately from that of modern humans for a substantial amount of time and lends no support to the idea that they contributed mtDNA to contemporary modern humans.

  Dates of Divergences. For the estimation of the ages of MRCAs [Most Recent Common Ancestors] of different groups of mtDNAs, the observed nucleotide differences were corrected for multiple substitutions by using the Tamura-Nei algorithm. The resulting genetic distances and the estimated age of the modern human-chimpanzee split of 4-5 million years were used to calculate the substitution rate of 0.94 × 10 7 substitutions per site per year per lineage with 5.92 × 10 8 and 1.38 × 10 7 as the lower and upper confidence limits. These estimates are in reasonable agreement with previous rate estimations for the mtDNA control region. Using these rates, the age of the MRCA of the Neandertal and modern human mtDNAs was estimated to be 465,000 years, with confidence limits of 317,000 and 741,000 years. This age is significantly older than that of the MRCA of modern human mtDNAs, which, by the same procedure, was determined to be 163,000 years, with 111,000 and 260,000 years as confidence limits. Finally, the age of the MRCA of the mtDNAs of the seven chimpanzees and the two bonobos was calculated as 2,844,000 years (confidence limits: 1,940,000 and 4,534,000 years).

  However, mtDNA sequences from more Neandertal individuals are needed to obtain a better understanding of the extent of separation between the mtDNA gene pools of Neandertals and modern humans.
• 

  hooberus

  For the sake of clarity, here is Earnest's post from page 6 as well as some of my observations from it in a post shortly thereafter (also on page 6).

  The date of divergence between the mtDNAs of the Neandertal and contemporary humans is estimated to 465,000 years before the present, with confidence limits of 317,000 and 741,000 years. Taken together, the results support the concept that the Neandertal mtDNA evolved separately from that of modern humans for a substantial amount of time and lends no support to the idea that they contributed mtDNA to contemporary modern humans.

  Dates of Divergences. For the estimation of the ages of MRCAs [Most Recent Common Ancestors] of different groups of mtDNAs, the observed nucleotide differences were corrected for multiple substitutions by using the Tamura-Nei algorithm. The resulting genetic distances and the estimated age of the modern human-chimpanzee split of 4-5 million years were used to calculate the substitution rate of 0.94 × 10 7 substitutions per site per year per lineage with 5.92 × 10 8 and 1.38 × 10 7 as the lower and upper confidence limits. These estimates are in reasonable agreement with previous rate estimations for the mtDNA control region. Using these rates, the age of the MRCA of the Neandertal and modern human mtDNAs was estimated to be 465,000 years, with confidence limits of 317,000 and 741,000 years. This age is significantly older than that of the MRCA of modern human mtDNAs, which, by the same procedure, was determined to be 163,000 years, with 111,000 and 260,000 years as confidence limits. Finally, the age of the MRCA of the mtDNAs of the seven chimpanzees and the two bonobos was calculated as 2,844,000 years (confidence limits: 1,940,000 and 4,534,000 years).

  However, mtDNA sequences from more Neandertal individuals are needed to obtain a better understanding of the extent of separation between the mtDNA gene pools of Neandertals and modern humans.

  These assumptions regarding mtDNA mutation rates, with their margin of error calculations are based on the assumption that humans/chimpanzees shared a common ancestor millions of years ago. However if this did not happen, then not only would the assumed mutation rates be potentially in error, but also the "margin of error" calculation (which is also based on the assumption of a shared common ancestor who lived millions of years ago) would also be invalidated.

  There is a tendency when people see figures such as "confidence limits of 317,000 and 741,000 years" to assume that the creature in question must be at least as old as the lower figure. However this is not necessarily true as even the lower figure is based on assumptions of a shared common ancestor living millions of years ago.
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  hooberus

  funky derek said: Hooberus, this is becoming rather an annoying pattern. You make a claim, someone refutes your claim clearly and specifically, you then repeat and rephrase the claim several times underlining irrelevancies ignoring all the evidence thrown at you. You seem to think that just repeating unfounded claims ad nauseum is a substitute for learning about the subject you're discussing and providing evidence and rational arguments to support your claims. It's not. Now make a case or stop wasting everyone's time.

  funkyderek, I don't think that my responses involve "underlining irrevelancies" nor do I ignore all the evidence thrown at me. I am trying to learn about the subject that we are discussing. Specifically I am trying to confirm the details of how these dates of 200,000, 853,000, etc are generated by evolutionists. So your above post was unwarranted.
• 

  rem

  Hooberus,

  Because I demand the same accuracy from you I will conceed that you are technically correct. The 4-5 million year human-chimpanzee split assumption was used to normalize the mutation rate calculations for the paper(s) you cited. Basically what happens is there are various differences between the DNA in the two species. the problem is that you never know if a part of DNA that matches in both cases is really a match because it could have mutated to something different and then back to the original. The same is true with mutated parts - you don't necessarily know how many times the DNA has mutated on that particular spot. So there are various algorithms used to account for these. Note that the Tamura-Nei algorithm used in conjunction with the 4-5 million year human-chimpanzee split produced "estimates in reasonable agreement with previous rate estimations for the mtDNA control region." This implies that other algorithms may have been used to calibrate the mtDNA control region which may not have used the human-chimpanzee split dating to calibrate them. To be honest, these papers are the first I've read that used the human-chimpanzee split to normalize the mutation rate calculations.

  rem
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  Shemittah

  EXTRACTS FROM "GENOME - THE AUTOBIOGRAPHY OF A SPECIES IN 23 CHAPTERS"
  
  These extracts are taken from the paperback edition (2000) which I read some months ago. The list here has been compiled by me, and so this is no 'cut and paste' post. It should be noted that the author (Matt Ridley) is an evolutionist as is made abundantly clear in Chapter 2 - Species. I recommend this book to anyone interested in human DNA, and particularly to those looking for an entertaining introduction to the subject.

  
  The "machine-code" quality of DNA is of particular interest to me, as I trained for and worked for some years as a computer programmer, even at the machine-code level. Years ago machine-code programmers would often work with Hexadecimal (base 16) numbers to represent, say a byte. Our usual denary (base 10) system uses digits 0 to 9 which gives us 10 permutations per column (units, tens, hundreds, etc). In Hexadecimal the letters A to F are used to represent 10 to 15 (hence 16 permutations) and a two digit system is used to represent the 256 different values of a byte. DNA, as a base 4, three 'digit' system, would yield 64 different values (see extract 1 below). That's like having 64 types of material to build a house, 64 colours to paint a picture, or sound intervals to create a piece of music. Or 64 different machine-code values to write a computer program. The question remains however, who/what wrote the original program(s), from which all the genetic photocopies were made? Is it Natural-Selection who, it is claimed, started off with one master program that randomly changes itself, or is it God-Sabaoth who, it is claimed, wrote a number of different programs specifically for a certain type of lifeform? The debate rages on!
  
  1. "Whereas English books are written in words of variable length using twenty-six letters, genomes are written entirely in three-letter words [called BASES], using only four letters: A, C, G and T (which stand for adenine, cytosine, guanine and thymine). And instead of being written on flat pages, they are written on long chains of sugar and phosphate called DNA molecules to which the bases are attached as side rungs. Each chromosome is one pair of (very) long DNA molecules. The genome is a very clever book, because in the right conditions it can both photocopy itself and read itself. The photocopying is known as REPLICATION, and the reading as TRANSLATION. Replication works because of an ingenious property of the four bases: A likes to pair with T, and G with C. So a single strand of DNA can copy itself by assembling a complementary strand with Ts opposite all the As, As opposite all the Ts, Cs opposite all the Gs and Gs opposite all the Cs. In fact, the usual state of DNA is the famous DOUBLE HELIX of the original strand and its complementary pair intertwined. To make a copy of the complementary strand therefore brings back the original text. So the sequence ACGT become TGCA in the copy, which transcribes back to ACGT in the copy of the copy. This enables DNA to replicate indefinitely, yet still contain the same information." - Page 7, paras. 2-4.
  
  2. "Big brains needed meat (vegans today avoid protein-deficiency only by eating pulses); food sharing allowed a meaty diet (because it freed the men to risk failure in pursuit of game); food sharing demanded big brains (without detailed calculating memories, you could be easily cheated by a freeloader); the sexual division of labour promoted monogomy (a pair-bond being now an economic unit); monogomy led to *neotenous sexual selection (by putting a premium on youthfulness in mates). And so on, round and round the theories we go in a spiral of comforting justification, proving how we came to be as we are. We have built a scientific house of cards on the flimsiest foundations of evidence, but we have reason to believe this it will one day be testable. The fossil record will tell us on a little about behaviour; the bones are too dry and random to speak. But the genetic record will tell us more." - Page 35, from para. 1 (*neoteny = the retention of juvenile features in adult life).
  
  3. "All was suddenly clear: DNA contained a code written along the length of an elegant, intertwined staircase of a double helix, of potentially infinite length. That code copied itself by means of chemical affinities between its letters and spelt out the recipes for proteins by means of an as yet unknown phrasebook linking DNA to protein. The stunning significance of the structure of DNA was how simple it made everything seem and yet how beautiful. As Richard Dawkins has put it [in 'River out of Eden'], 'What is truly revolutionary about molecular biology in the post-Watson-Crick era is that it has become digital ... the machine code of the genes is uncannily computer-like.'" - Page 50, from para. 1.

  4. "Science is supposed to advance by erecting hypotheses and testing them by seeking to falsify them. But it does not. Just as the genetic determinists of the 1920s looked always for confirmation of their ideas and never for falsification, so the environmental determinists of the 1960s looked always for supporting evidence and averted their eyes from contrary evidence, when they should have been actively seeking it. Paradoxically, this is a corner of science where the 'expert' has usually been more wrong than the layman. Ordinary people have always known that education matters, but equally they have always believed in some innate ability. It is the experts who have taken extreme and absurd positions at either end of the spectrum." - Page 79, from para. 2 (The author is here talking about what constitutes intelligence).
  5. "By studying the way human beings speak, Chomsky concluded that there were underlying similarities to all languages that bore witness to a universal human grammar. We all know how to use it, though we are rarely conscious of that ability. This must mean that part of the human brain comes equipped by its genes with a specialised ability to learn language." - Page 93, from para. 1 (The author makes reference to Noam Chomsky's book "Syntactic structures").

  6. "Pinker and Cosmides both contend that the same applies to the human brain. Its modules, like the different blades of a Swiss-army knife, are most probably designed for particular functions. The alternative, that the brain is equipped with random complexity, from which its different functions fall out as fortunate by-products of the physics of complexity - an idea still favoured by Chomsky - defies all evidence. There is simply nothing to support the conjecture that the more detailed you make a network of microprocessors, the more functions they will acquire. Indeed, the 'connectionist' approach to neural networks, largely misled by the image of the brain as a general-purpose network of neurons and synapses, has tested the idea thoroughly and found it wanting. Pre-programmed design is required for the solving of pre-ordained problems." - Page 103, para. 2.
  
  7. "The SRY gene is peculiar. Its sequence is remarkably consistent between different men: there are virtually no point mutations (i.e., one-letter spelling differences) in the human race. SRY is, in that sense, a variation-free gene that has changed almost not at all since the last common ancestor of all people 200,000 years ago or so. Yet our SRY is very different from that of a chimpanzee, and different again from that of a gorilla: there is, between species, ten times as much variation in this gene as is typical for other genes. Compared with other active (i.e., expressed) genes, SRY is one of the fastest evolving." - Page 112, para. 1 (The SRY gene "begins the whole cascade of events that leads to the masculinisation of the embryo").
  
  8. "Oncogenes, in the unmutated state, are needed for cells to grow and proliferate normally throughout life: skin must be replaced, new blood cells generated, wounds repaired and so on. The mechanism for suppressing potential cancers must allow exceptions for normal growth and proliferation. Cells must frequently be given permission to divide, and must be equipped with genes that encourage division, so long as they stop at the right moment. How this feat is achieved is beginning to become clear. If we were looking at a man-made thing, we would conclude that a fiendishly ingenious mind must be behind it." - Page 239, para. 2 ("Oncogenes are genes that cause division and growth but, surprisingly, several of them also trigger cell death.").
  
  Alex.