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From the Biologic Institute, “A Facebook Dialogue”

Ann Gauger posted an amusing facebook dialogue on the blog of the Biologic Institute: “Sometimes it might be a good idea to actually read what ID proponents write before critiquing it.” Click here to read the rest.

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93 Responses to From the Biologic Institute, “A Facebook Dialogue”

  1. Ugh. Ann Gauger’s/BioLogic Institute’s posts on this thread, just linked from the DI blog, are silly. (1) They have presented no evidence, and there is not any particular reason to think, that entire new binding sites are required between humans and chimps. Ditto for multiple-mutations-required-before-function mutations. What is the evidence that *any* of these would have been required? (2) Even the source they cite, Durrett and Schmidt 2007, notes that they are only talking about one very specific sort of change, and most of the changes between humans and chimps were neutral (and thus fix at much higher rates, basically equal to the mutation rate), that many more mutations happen than fix, and that each for the sorts of changes they are talking about, they could have happened in less than 1% of the 20,000+ genes in the human genome, which significantly changes the odds and times even on the ridiculously pessimistic model Gauger is trying to fool her readers with.

  2. “there is not any particular reason to think, that entire new binding sites are required between humans and chimps.”

    That is a false statement:

    “Museum of Comparative Anthropogeny” Human Uniqueness Compared to “Great Apes” (Hundreds of differences listed between humans and ‘great apes’ with references for each difference listed)
    https://docs.google.com/document/d/1dx8I5qpsDlsIxTTPgeZc559pIHe_mnYtKehgDqE-_fo/edit

    To focus on the male reproductive system. It is completely different and would have required an entire reworking of many binding sites:

    Ian Juby’s sex video – (Can sexual reproduction plausibly evolve?) – video
    http://www.youtube.com/watch?v=Ab1VWQEnnwM

    A False Trichotomy
    Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”
    http://www.uncommondescent.com.....richotomy/

    as well:

    From Jerry Coyne, More Table-Pounding, Hand-Waving – May 2012
    Excerpt: “More than 6 percent of genes found in humans simply aren’t found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps.”
    Jerry Coyne – ardent and ‘angry’ neo-Darwinist – professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.

    As to the “ridiculously pessimistic model Gauger is trying to fool her readers with.”

    The Real Barrier to Unguided Human Evolution – Ann Gauger – April 25, 2012
    Excerpt: Their results? They calculated it would take six million years for a single base change to match the target and spread throughout the population, and 216 million years to get both base changes necessary to complete the eight base binding site. Note that the entire time span for our evolution from the last common ancestor with chimps is estimated to be about six million years. Time enough for one mutation to occur and be fixed, by their account.
    To be sure, they did say that since there are some 20,000 genes that could be evolving simultaneously, the problem is not impossible. But they overlooked this point. Mutations occur at random and most of the time independently, but their effects are not independent. (Random) Mutations that benefit one trait (are shown to) inhibit another (Negative Epistasis; Lenski e-coli after 50,000 generations).
    http://www.evolutionnews.org/2.....58951.html

    etc.. etc..

  3. Moreover,

    Transcription Factors: More Species-Specific Biology – Cornelius Hunter – October 2011
    Excerpt: In fact, the binding sites are often so-called “lineage-specific,” meaning that the transcription factor binds to a section of DNA that is unique to that species. As one writer explained: “Remarkably, many of these RABS [repeat-associated binding sites] were found in lineage-specific repeat elements that are absent in the comparison species, suggesting that large numbers of binding sites arose more recently in evolution and may have rewired the regulatory architecture in embryonic stem cells on a substantial scale.”
    http://darwins-god.blogspot.co.....ecies.html

    Humans, Chimpanzees and Monkeys Share DNA but Not Gene Regulatory Mechanisms – (Nov. 6, 2012)
    Excerpt: Dr. Gilad reported that up to 40% of the differences in the expression or activity patterns of genes between humans, chimpanzees and rhesus monkeys can be explained by regulatory mechanisms that determine whether and how a gene’s recipe for a protein is transcribed to the RNA molecule that carries the recipe instructions to the sites in cells where proteins are manufactured.,,,
    Dr. Gilad also determined that the epigenetics process known as histone modification also differs in the three species. The presence of histone marks during gene transcription indicates that the process is being prevented or modified. “These data allowed us to identify both conserved and species-specific enhancer and repressor regulatory elements, as well as characterize similarities and differences across species in transcription factor binding to these regulatory elements,” Dr. Gilad said.
    http://www.sciencedaily.com/re.....201124.htm

    The mouse is not enough – February 2011
    Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.”
    http://www.the-scientist.com/news/display/57986/

    Modern Synthesis of Neo-Darwinism Is Dead – No Evidence For Body Plan Morphogenesis From Embryonic Mutations – Paul Nelson – video
    http://www.metacafe.com/watch/5548184/

    Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011
    http://www.evolutionnews.org/2.....45581.html

  4. You are not an accident Nick!
    http://2.bp.blogspot.com/-U_oF.....offee.jpeg

  5. Nick:

    …most of the changes between humans and chimps were neutral (and thus fix at much higher rates, basically equal to the mutation rate)…

    Are you saying that there was no ‘selection’ at all going on during either lineage after the alleged split?

    If there was selection, does that really have no effect on the rate of fixation of a neutral mutation?

  6. This study just came out:

    Study suggests humans are slowly but surely losing intellectual and emotional abilities – November 12, 2012
    Excerpt: “Human intelligence and behavior require optimal functioning of a large number of genes, which requires enormous evolutionary pressures to maintain. A provocative hypothesis published in a recent set of Science and Society pieces published in the Cell Press journal Trends in Genetics suggests that we are losing our intellectual and emotional capabilities because the intricate web of genes endowing us with our brain power is particularly susceptible to mutations and that these mutations are not being selected against in our modern society.”
    http://medicalxpress.com/news/.....l.html#jCp

    A few related notes:

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video (Notes in description)
    http://vimeo.com/35088933

    Stark Differences Between Human and Chimp Brains – Brian Thomas, M.S. – Oct. 5, 2012
    Excerpt: The researchers used a new technique to peer in unprecedented detail at the methylation patterns of human and chimp DNA that they harvested from brain tissue of three cadavers of each species. They compared only those DNA sequences already known to have basically the same genes, ignoring the vast majority of DNA. If humans and chimps are close relatives, then they should have similar DNA methylation patterns in the areas of chromosomes that they have in common such as similar gene sequences.2 However, this team found major differences.
    In particular, human and chimp DNA methylation patterns, called “methylomes,” were very different between the two species’ brain tissue. The data statistically indicated that “major principal components separate humans and chimpanzees,” according to their report in American Journal of Human Genetics.1,3
    A second observation is that the very genes that were differently methylated “exhibit striking associations with several disorders, including neurological and psychological disorders and cancers.”1 These data show that methylation patterns in many cases can tolerate very little disruption, thus presenting another impossible hurdle for the evolutionary model to overcome.
    If humans evolved from chimpanzee-like creatures, then some unknown evolutionary process must have altered their methylomes. But since methylomes apparently cannot tolerate that much alteration, then the evolutionary story must be in error.
    Human and chimp species-specific and irreducibly complex methylomes refute human evolution.,,,
    (Zeng, J. et al. 2012. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. American Journal of Human Genetics. 91 (3):455-465.)
    http://www.icr.org/article/7067/

    Of note: This following study, in which the functional role of unique ORFan genes were analyzed, the (Darwinian) researchers were ‘very shocked’ and ‘taken aback’ by what they found;

    New Genes, New Brain – October 2011
    Excerpt: “This is one of the first studies to look at the role of completely novel genes” in primate brain development,,, A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex,,, Finally, 54 of the 280 genes found to be unique to humans were also highly expressed in the developing prefrontal cortex,,,, “We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures.,,, (From the PLoS article, author’s summary: We found these genes are scattered across the whole genome, demonstrating that they are generated by many independent events,,, Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination,,)
    http://the-scientist.com/2011/.....new-brain/

    Darwin’s mistake: explaining the discontinuity between human and nonhuman minds. – 2008
    Excerpt: Over the last quarter century, the dominant tendency in comparative cognitive psychology has been to emphasize the similarities between human and nonhuman minds and to downplay the differences as “one of degree and not of kind” (Darwin 1871).,,, To wit, there is a significant discontinuity in the degree to which human and nonhuman animals are able to approximate the higher-order, systematic, relational capabilities of a physical symbol system (PSS) (Newell 1980). We show that this symbolic-relational discontinuity pervades nearly every domain of cognition and runs much deeper than even the spectacular scaffolding provided by language or culture alone can explain,,,
    http://www.ncbi.nlm.nih.gov/pubmed/18479531

    “Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation.” –
    Alfred Russell Wallace, New Thoughts on Evolution, 1910

    of note:

    Human brain has more switches than all computers on Earth – November 2010
    Excerpt: They found that the brain’s complexity is beyond anything they’d imagined, almost to the point of being beyond belief, says Stephen Smith, a professor of molecular and cellular physiology and senior author of the paper describing the study: …One synapse, by itself, is more like a microprocessor–with both memory-storage and information-processing elements–than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth.
    http://news.cnet.com/8301-2708.....2-247.html

  7. Nick Matzke:

    (2) Even the source they cite, Durrett and Schmidt 2007, notes that they are only talking about one very specific sort of change, and most of the changes between humans and chimps were neutral (and thus fix at much higher rates, basically equal to the mutation rate), . . .

    Nick, what do you mean about neutral mutations fixing at “much higher rates”? I would think that ‘neutral’ mutations would fix at much lower rates than mutations affected by positive selection.

  8. To go well above my allotted two cents worth, ‘neutral’ mutations are a joke as far as the evidence, and theoretical considerations, are concerned:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

    Ann Gauger on genetic drift – August 2012
    Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter.
    http://www.uncommondescent.com.....tic-drift/

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.
    http://darwins-god.blogspot.co.....ay-of.html

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    Michael Behe on the theory of constructive neutral evolution – February 2012
    Excerpt: I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. – Michael Behe
    http://www.uncommondescent.com.....evolution/

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

    The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology
    Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation..
    http://www.biosignaling.com/co.....X-9-30.pdf

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    related notes:

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

  9. Nick Matzke,

    Your entire position is all about fooling people as you don’t have any evidence to support its claims. You don’t know how many mutations it takes to get an upright biped from a knuckle-walker/ quadraped. You don’t even know if any amount of mutational accumulation can do the job required.

    BTW Nick, no one knows how fast or slow neutral mutations take to become fixed. No one knows how long it takes beneficial mutations to become fixed.

  10. “Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle.”
    - John Sanford – Genetic Entropy and The Mystery of The Genome – pg. 21 – Inventor of the ‘Gene Gun’

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt:,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

  11. “Neutral evolution” as an engine for productive evolutionary change is such a joke.

    1. Anyone who thinks that adding random changes to a massive database can be anything but net deleterious over time needs to have their head examined. It doesn’t even pass the laugh test.

    2. As others have pointed out, adding new material costs resources in terms of maintenance, replication, etc.

    3. Most importantly, it does precisely nothing to help explain functional complex specified information in DNA. The only thing neutral mutations are supposed to do is provide more genetic material to work with. But we don’t need no stinkin’ new genetic material — sheesh, we’ve already got 90% of the genome that is pure junk; how much more do we need to work with!? :)

    The neutral mutations idea, boiled down, is this: getting a bunch of beneficial mutations to arise is way too improbable, so instead we’ll get a bunch of random, unrelated neutral mutations to arise and then at some glorious moment in time light will break through the mists of darkness and . . .

    wait for it . . .

    the neutral mutations suddenly poof into an information-rich sequence that performs a beneficial function.

    It is all so clear.

    Ya, see,

    (i) having a bunch of unrelated, random mutations suddenly poof into a beneficial, information-rich sequence is *way* more likely than

    (ii) having a bunch of unrelated, random mutations slowly form a beneficial, information-rich sequence over time.

    Yeah, that’s the ticket!

  12. PaV:

    Nick, what do you mean about neutral mutations fixing at “much higher rates”? I would think that ‘neutral’ mutations would fix at much lower rates than mutations affected by positive selection.

    What he means is that mutations that do nothing towards evolving a proto-human into a human are far more prevalent than ones that do, therefore, mutations that do nothing will become fixed at a higher rate than a mutation that never happens.

    It’s simple math.

  13. PaV @7:

    This relates directly to what we have been discussing on the other thread:

    http://www.uncommondescent.com.....r-answers/

    A bit painful to wade through 100 comments, but the upshot is this:

    Neutral mutations get “fixed” in the population at a high rate (i.e., the overall mutation rate) because we are not talking about any particular mutation. Any mutation at any point whether or not it has anything to do with forming any functional system gets added to the aggregate number of mutations in the lineage over time. It is really a definitional issue: (i) the kind of fixation Nick is talking about is really just the accumulation of mutations from generation to generation over time; (ii) this is quite different from selection acting to fix a particular beneficial mutation in a relatively-contemporaneous population. This is a legitimate use of the concept of fixation; just took me a bit to parse through and figure out that two separate processes were being called by the same name, but I understand what Nick and wd400 are saying on that front.

    The real problem with the neutral mutations idea is not whether neutral mutations aggregate from one generation to the next over time — they do. The real problem is that this accumulation of mutations over time does absolutely nothing to solve the issue of how we get functional complex specified information in DNA or in biology generally. The fantastical storyline is that neutral mutations silently accumulate until, one happy day in an explosion of creativity, they come together to do something wonderful.

    The real fundamental issue that Nick (and wd400 on the other thread) have with Gauger’s approach is that they think no specific mutations are required to get from organism A to B, because, ya see, evolution is just a contingent process and anything goes. So we don’t need to explain how a functional specified string of information arose in DNA, the thinking goes, because anything could have happened. It was just one of many random possibilities. Therefore, there is nothing to explain.

    This is another manifestation of what I will now term the Great Evolutionary Explanation,* namely: Stuff Happens.

    So the real issue is whether any coordinated mutations are required to get from organism A to B. From an engineering and biological standpoint it is quite obvious that significant coordination is required at some point along the path. Nick and wd400 appear to want to deny this.

    Check out, in particular, comments #47 and #99 on the other thread.

    —–
    * Otherwise known as “GEE” as in “gee-whiz”!

  14. The fantastical storyline is that neutral mutations silently accumulate until, one happy day in an explosion of creativity, they come together to do something wonderful.

    MET – Miraculous Evolutionary Transitions

  15. semi related:

    Complex Tool Discovery Argues for Early Human Smarts By Stephanie Pappas – Wed, Nov 7, 2012
    Excerpt: One potential sign of complex thought would be an elaborately produced artifact that would have required capabilities such as language to pass along the technique to future generations.,,,
    Continuity of history
    These artifacts were discovered over the course of nine years at a site known as Pinnacle Point, in a storm-prone area with a temperate climate like San Francisco’s. Initially, Marean found many artifacts and fossil bones on the beach. Then, one day, a storm exposed deposits of these materials from a cave higher up. So far the researchers have found sediments about 45 feet (14 meters) deep containing artifacts and fossils dating from approximately 50,000 to 90,000 years ago.
    “As an archaeologist and scientist, it is a privilege to work on a site that preserves a near-perfect layered sequence capturing almost 50,000 years of human prehistory,” said researcher Kyle Brown at the University of Cape Town, South Africa. “Our team has done a remarkable job of identifying some of the subtle but important clues to just how innovative these early humans on the south coast were.” The scientists uncovered thin blades of stone, known as microliths, each about 1.2 inches (3 centimeters) long at most. These were blunted along one edge so they could be glued onto slots carved in wood or bone. The stone used to produce these blades, silcrete (quartz grains cemented by silica), was carefully treated with heat to make it easier to shape.
    These microliths could have found use as the earliest known arrowheads. However, researchers suggest they were more likely incorporated into spear-hurling devices known as atlatls. These spear-throwers were essentially sticks with spurs or cups to hold the projectile. Swinging the atlatl provided leverage to increase the distance and killing power of the hurled dart or spear.
    The microliths may have served as spurs in these atlatls. [See images of the ancient tools]
    “They are parts of a complex composite weapon,” Marean said.
    Past research suggested microlithic technology appeared briefly between 60,000 and 65,000 years ago.
    “Eleven thousand years of continuity is, in reality, an almost unimaginable time span for people to consistently make tools the same way,” Marean said. “This is certainly not a flickering pattern.” Moreover, heat treatment of stone was seen at Pinnacle Point about 160,000 years ago, suggesting people there mastered this complex technique for nearly 100,000 years.
    http://news.yahoo.com/complex-.....13070.html

  16. I’ve been been doubling up with laughter recently at references to ‘enchanters’, ‘wizards’ and the like, being summoned by various kings in the O.T., such as Nebuchadnezzar, before being obliged to summon one or other of the Hebrew prophets, to get the truth.

    I couldn’t help thinking (implicitly) of the sovereignty of today’s corporations and (explicitly) of their own court ‘enchanters’ and ‘wizards’. And of course, your good selves, our own ‘bona fide’ scientific oracles.

  17. OT: “Is The Material World All There Is?” William Lane Craig, St Andrews 2012 – video
    http://www.youtube.com/watch?v=hOwe2TxisB8

    video description: In September 2012, during his visit to The University of St Andrews in Scotland, Dr William Lane Craig delivered a lecture entitled “Is The Material World All There Is?” followed by audience Q&A. In this lecture Dr Craig outlined seven reasons to think that the material world is not all there is but, quite to the contrary, that the material world contains “signposts of transcendence” pointing towards the truth of Christianity.

  18. Eric Anderson:

    I just posted something at the other thread. Hopefully it might illuminate some matters.

    Eric, you wrote:

    The real fundamental issue that Nick (and wd400 on the other thread) have with Gauger’s approach is that they think no specific mutations are required to get from organism A to B, because, ya see, evolution is just a contingent process and anything goes. So we don’t need to explain how a functional specified string of information arose in DNA, the thinking goes, because anything could have happened. It was just one of many random possibilities. Therefore, there is nothing to explain.

    I agree with you completely here.

    I’ve been thinking about this type of argument being made by wd400, Nick, Elizabeth Liddle, and others.

    It seems to me that what they’re arguing comes down to Dawkins’ “Me Thinks It Is a Weasel” model.

    What do I mean? Well, they want to invoke BOTH neutral evolution and positive selection as working at the same time, with neutral evolution coming up with all these ‘mutations’ and then positive selection promoting the ‘beneficial’ mutations to ‘fixation’.

    This is almost exactly like Dawkin’s and his chimps. He says for these chimps, typing away madly at their typewriters, to arrive at the phrase “Me Thinks It Is a Weasel” in an entirely ‘random’ manner would take forever. But, if, every time they struck a correct letter within the phrase this letter was kept (equivalent to positive selection ‘fixing’ a particular mutation), then in no time at all would the chimps arrive at the target phrase.

    But even Dawkins has to admit that this isn’t how ‘natural selection’ works, because NS doesn’t ‘know’ what the final target will be. So he considers this not to be a good analogy, or model, for how NS works.

    Here, what is happening, is this: wd400 is saying: “You don’t know what the ‘target phrase’ looks like either. It could be “Me Thinks It Is a Weasel”, or it could be “No Thanks if it wheezes” or “Me Stinks like a Weasel,” etc.

    And the assumption behind all of this is that some kind of final target phrase will eventually arise.

    Well, getting back to Dawkins and his chimps, if we are no longer concerned about what the final target phrase is–i.e., if it isn’t known in advance–then it hardly matters what the chimps type. Anything could be the ‘final target phrase’. But the process so described is nothing more than a random number generator.

    I can’t write anything here and be able to communicate unless there were a protocol for how the English language is used. To effect meaning, rules must be employed. Likewise, a process that contains no known rules cannot possibly generate meaning. Just as the chimps are doomed to typing gibberish, so, too, the process wd400 are clinging cannot possibly erect a system capable of interacting with itself.

    I think it’s like going to the movies for the Darwinists: i.e., “suspension of disbelief.” In their ‘movie’ the chimps come up with “Me Thinks It Is a Weasel” on the first try. And, as we all know, ‘movies’ don’t lie.

  19. Towards the end, my latest post should read:

    “Just as the chimps are doomed to typing gibberish, so, too the process wd400 and others are clinging to cannot possibly . . . .”

    Sorry for not proofreading this.

  20. PaV:

    Well, they want to invoke BOTH neutral evolution and positive selection as working at the same time, with neutral evolution coming up with all these ‘mutations’ and then positive selection promoting the ‘beneficial’ mutations to ‘fixation’.

    Not quite. They want to invoke whatever is required to save the phenomena.

    So if invoking onlyy neutral mutations will do so, invoke only neutral mutations.

    If invoking neutral mutations and beneficial mutations, invoke both, and argue that the rate of fixation is the same as the neutral mutation rate.

    If that doesn’t work, toss in some deleterious mutations, convergence, hgt, and symbiosis or whatever else seems even remotely possible.

    And blame Joe for being a math denier.

  21. This thread is incredibly silly! You guys are trying to play selection off against neutrality, but both clearly exist. Let me outline what actual mainstream evolutionary theory would assert:

    1. Neutrality is just what happens when s, the selection coefficient, is ~0. Even under neutrality, you will get a bunch of fixation events, even under the very slow rate of fixation under neutrality (about 1.5% divergence over 6 million years). The vast majority of genetic differences between humans and chimps are of this type.

    2. Some of the differences (probably a tiny number, perhaps a few thousand or tens of thousands) were indeed promoted by selection, and thus fixed on average much more quickly than the neutral mutations.

    3. Gauger claims that some large proportion of the differences between humans and chimps would have required multiple mutations to happen *before* selection could favor them. If there were a large number of these, there would indeed be not enough time for drift+selection to produce these specific features. But she gives only the vaguest argument that such features exist at all and ignores all the counterarguments that indicate we have no particular reason to think that they are needed (for example, human and chimp DNA sequence is so similar, most regulatory sequences probably only differ by a base pair or two, if at all).

    Worse, much of the discussion here and elsewhere gets 1, 2, and 3 confused, and you get assertions like 1.5% divergence couldn’t have happened, because drift is too slow because of #3, or whatever.

    Random other comment on this line from Jerry Coyne’s book:

    “More than 6 percent of genes found in humans simply aren’t found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps.”

    Any serious usage of this number would require consideration of the following:

    1. Even if true, this wouldn’t mean a bunch of new genes on the human line. It could just mean a bunch of losses on the chimpanzee line. E.g. we already know that hundreds of genes for smelling and taste receptors have been gradually lost as primates became more specialized on vision compared to nocturnal, rodentlike ancestors.

    2. Computer programs that find genes in genomes have a nonzero error rate, because ORFs (open reading frames) can be created by chance mutation (all you need is for a mutation to produce a start codon from a different codon). Not all ORFs are actual genes that get expressed and do something, although on rare occasions in evolution they might (emphasize might) be the beginning of a new gene. Furthermore, sequencing errors can produce fake ORFs if a base is misread so that it looks like a start codon. Sequencing error rates and mutation rates are low, but when there are 3,000,000,000+ nucleotides you are looking at, unlikely things happen all the time.

    3. Neither the human genome nor the chimp genome sequence is actually complete, for various technical reasons. This was particularly true of the chimp genome a few years ago when Coyne’s book was written.

  22. Nick Matzke:

    You guys are trying to play selection off against neutrality, but both clearly exist.

    THAT is incredibly silly and bodering on dishonesty.

    1. Neutrality is just what happens when s, the selection coefficient, is ~0. Even under neutrality, you will get a bunch of fixation events, even under the very slow rate of fixation under neutrality (about 1.5% divergence over 6 million years). The vast majority of genetic differences between humans and chimps are of this type.

    That is the assertion. Of course under a design scenario such a thing would be possible.

    BTW how many mutations does it take to get an upright biped from a knuckle-walker/ quadraped?

    2. Some of the differences (probably a tiny number, perhaps a few thousand or tens of thousands) were indeed promoted by selection, and thus fixed on average much more quickly than the neutral mutations.

    Via design or severe bottlenecks. Otherwise all bets are off as evidenced by experiments with fruit flies.

    3. Gauger claims that some large proportion of the differences between humans and chimps would have required multiple mutations to happen *before* selection could favor them. If there were a large number of these, there would indeed be not enough time for drift+selection to produce these specific features. But she gives only the vaguest argument that such features exist at all and ignores all the counterarguments that indicate we have no particular reason to think that they are needed (for example, human and chimp DNA sequence is so similar, most regulatory sequences probably only differ by a base pair or two, if at all).

    Earth to Nick, YOU are ignoring the fact that no one has any idea how many mutations it would take nor to what chromosomes they would have to occur, in order to do the job. You have no idea if the transformations required are even possible via genetic changes.

    So please stop with your bloviations already.

  23. Nick:

    This thread is incredibly silly!

    HMM Nick have you ever read evolutionary material?
    http://sphotos-b.xx.fbcdn.net/.....0664_n.jpg

  24. Nick:

    1. Neutrality is just what happens when s, the selection coefficient, is ~0. Even under neutrality, you will get a bunch of fixation events, even under the very slow rate of fixation under neutrality (about 1.5% divergence over 6 million years). The vast majority of genetic differences between humans and chimps are of this type.

    ok, that’s what I said. Invoke neutral mutations until they can’t do the job on their own. Then invoke something else.

    2. Some of the differences (probably a tiny number, perhaps a few thousand or tens of thousands) were indeed promoted by selection, and thus fixed on average much more quickly than the neutral mutations.

    1. How many and which ones?

    2. Wouldn’t the neutral mutations have ridden along and been fixed at the same rate?

    1. Even if true, this wouldn’t mean a bunch of new genes on the human line. It could just mean a bunch of losses on the chimpanzee line.

    Oh yeah, and if all the above doesn’t work invoke lost genes!

    Flexible theory that. Can use it to “explain” just about anything.

  25. Nick:

    Neither the human genome nor the chimp genome sequence is actually complete, for various technical reasons. This was particularly true of the chimp genome a few years ago when Coyne’s book was written.

    Hold on just a minute. Here we were being told that 98% (or was it 99% or 97% or whatever last week’s % was?) proved that humans and chimps share a common ancestor. Now you’re saying we don’t really know how similar the genomes are? :)

  26. Hold on just a minute. Here we were being told that 98% (or was it 99% or 97% or whatever last week’s % was?) proved that humans and chimps share a common ancestor. Now you’re saying we don’t really know how similar the genomes are?

    You do realize, I hope, that one can make a highly accurate statistical estimate based on an incomplete sample…right? That’s how polls work, after all. In the case of polls, you have a sample of <0.01% of the population, yet they are accurate. With genomes, we have 90%+. The last stuff to be sequenced is the hardest stuff to sequence, because it is highly repetitive DNA, which is junk and/or low-information structural DNA.

    Even long before there was any genome sequencing at all, we could tell that human DNA and chimp DNA were highly similar, based on DNA-DNA hybridization experiments.

  27. 1. How many and which ones?

    It will take hundreds of years to figure this out, heck, we only finished the first genome sequence a little bit ago, and we would have to have a much more thorough understanding of developmental biology, for starters. But using “you don’t have complete knowledge” as an argument against evolution would be like using “you don’t know what Jesus ate on Thursday, 15 A.D.” as an argument against Christianity. Science isn’t about complete knowledge, it’s about testing hypotheses.

    However, it’s very clear that most of the genetic differences between humans and chimps are just noise and aren’t meaningful — they are just the product of genetic drift, and are in noncoding regions/junk, are synonymous substitutions, etc. To get a sense of how much rarer the “meaningful” changes are, look at the non-synonymous changes in coding DNA:

    If you measure nonsynonymous base pair differences within protein coding regions, humans and chimps are 99.75 percent identical (Chimpanzee Sequencing 2005, fig. 9)

    2. Wouldn’t the neutral mutations have ridden along and been fixed at the same rate?

    A little bit, but not very much. The chromosomes are broken up by crossing-over events every generation, so the blocks that get dragged to fixation during selective sweeps end up pretty small. Actually there are whole subfields of genetics devoted to just the topic of chromosome blocks and their history as they get broken up under selection, drift, and migration. There is all kinds of information about ancestry, selective events, etc. in the size of blocks. There are probably more people that study just this than all the creationist/IDist “experts” put together.

  28. Nick Matzke:

    Even long before there was any genome sequencing at all, we could tell that human DNA and chimp DNA were highly similar, based on DNA-DNA hybridization experiments.

    LoL! Yes similar DNA sequences are similar! However no one knows how much of a genetic difference exists between chimps and humans and no one knows if changes to the genome can account for the transformations possible.

    IOW it ain’t science.

  29. Unfortunately for Nick there isn’t any field nor subfield which can produce positive evidence for his positions’ claims.

  30. Nick:

    Science isn’t about complete knowledge, it’s about testing hypotheses.

    No one is asking for complete knowledge Nick. We’re asking for any knowledge. My request wasn’t a request for everything, it was a request for anything.

    Instead, what we get are shifting explanations and ad hoc rationalizations, and it’s hard to think of that as knowledge.

    However, it’s very clear that most of the genetic differences between humans and chimps are just noise and aren’t meaningful — they are just the product of genetic drift, and are in noncoding regions/junk, are synonymous substitutions, etc.

    Yes. But when we ask about what it takes to get a chimp and a human from a common ancestor, we get tales of drift.

  31. Nick @26:

    I know, I know. I’m giving you a hard time. That’s why I threw in the little smiley face. I just think it is funny that we’ve heard so many claims of absolute certainty about this or that % over the years from everyone from Dawkins on down, how it proves evolution and is a problem for “creationists,” etc., and yet the % keeps changing, it is turning out the numbers have often been wildly inflated or are highly questionable in how they are calculated and so on.

    Of course, “similar” is subjective, so it can be used however one finds it convenient in the particular instance.

    I presume we can both agree that the exact percentage of identical DNA or even similar DNA does not either prove or disprove a Darwinian or ID origin?

  32. Nick, just curious as to your viewpoint:

    However, it’s very clear that most of the genetic differences between humans and chimps are just noise and aren’t meaningful — they are just the product of genetic drift, and are in noncoding regions/junk, are synonymous substitutions, etc.

    Assuming the above to be true, does this suggest that the differences between humans and chimps do not result primarily from changes in the DNA?

  33. However no one knows how much of a genetic difference exists between chimps and humans

    What? This is just sheer nonsense, inherited from desperate creationist poo-flinging to obscure the fact that basically no matter how you measure it, chimps and humans are the two most similar genomes known (unless you count the Neanderthal genome, of course). This isn’t just me saying this, go ask Todd Wodd of Bryan College:

    http://www.uncommondescent.com.....-identity/

  34. Assuming the above to be true, does this suggest that the differences between humans and chimps do not result primarily from changes in the DNA?

    Of course not.

  35. Of course, “similar” is subjective, so it can be used however one finds it convenient in the particular instance.

    I presume we can both agree that the exact percentage of identical DNA or even similar DNA does not either prove or disprove a Darwinian or ID origin?

    The exact percentage doesn’t matter for the question of evolution vs. ID, that is true. If chimps had gone extinct and an Australopithecus had survived instead, the similarity would be 1% instead of 1.5% (say), but the argument would be the same.

    The real point is that no matter how you slice it, chimps are the closest living relatives of humans, and the evidence for this is exactly the same sort of DNA evidence that we use to determine paternity, identify the source of blood samples at crime scenes, track who gave HIV to whom, determine what portion of the world various chunks of some American’s chromosomes came from, etc. DNA is what gets copied from cell-to-cell, from generation to generation. We know how it mutates and approximately how fast. That plus the observed DNA similarity is all you need to make the argument go through. It’s a very simple argument.

    You guys are the ones who want to toss logic and experience and the very regular process of inheritance to the wolves, in favor of divine creation, basically to defend a particular fundamentalist reading of the Bible.

  36. Nick @34:

    Sorry, I don’t mean to be pedantic, but there are two ways to interpret your response. Just to clarify, are you saying that:

    (i) “of course not” (i.e., the differences between humans and chimps of course do not result primarily from changes in the DNA),

    or

    (ii) “of course not” (i.e., you disagree with the statement and would instead say that the differences do indeed result primarily from changes in the DNA)

  37. Nick @35:

    You guys are the ones who want to toss logic and experience and the very regular process of inheritance to the wolves, in favor of divine creation, basically to defend a particular fundamentalist reading of the Bible.

    There you go, projecting again.

    You should know that I am not trying to defend any fundamentalist reading of the Bible and have never tried to do so. I find it quite amusing that you are the one who keeps bringing religion into the discussion. But I realize that is how you view the entire debate through your twisted creationism-in-a-cheap-tuxedo perspective that you unfortunately acquired and honed at that bastion of propaganda, the NCSE.

  38. as to “the similarity would be 1% instead of 1.5% (say), but the argument would be the same.”

    This statement is false:

    From Jerry Coyne, More Table-Pounding, Hand-Waving – May 2012
    Excerpt: “More than 6 percent of genes found in humans simply aren’t found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps.”
    Jerry Coyne – ardent and ‘angry’ neo-Darwinist – professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.
    http://www.evolutionnews.org/2.....60271.html

    The Demise of Junk DNA and Why It Matters – Jonathan M. – September 2012
    Excerpt: “the prized 98% sequence-identify figure between humans and chimpanzees relates to the 2% of DNA that codes for the production of proteins. The non-protein-coding (Junk) regions of DNA are far more species-specific.,,, these (Junk) stretches of non-coding DNA really are functional, then what becomes of this (98%) sequence-identity figure and its significance with respect to shared ancestry?”
    http://www.evolutionnews.org/2.....64061.html

    “Humans, Chimpanzees and Monkeys Share DNA but Not Gene Regulatory Mechanisms” – November 2012
    http://www.uncommondescent.com.....echanisms/

    Chimp chromosome creates puzzles – 2004
    Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in ‘Nature’ that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed “significant structural changes”. In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, “we have seen a much higher percentage of change than people speculated.” The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity.
    http://www.nature.com/news/199…..524-8.html

    Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity
    Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors.
    http://www.nature.com/news/199.....524-8.html

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida
    …Therefore the total similarity of the genomes could be below 70%.
    http://www.evolutionnews.org/2.....20401.html

    DNA Comparisons between Humans and Chimps – Fazale Rana
    Excerpt: It is interesting that when evolutionary biologists discuss genetic comparisons between human and chimpanzee genomes, the fact that, again, as much as 25 percent of the two genomes won’t align receives no mention. Instead, the focus is only on the portions of the genome that display a high-degree of similarity. This distorted emphasis makes the case for the evolutionary connection between humans and chimps seem more compelling than it may actually be.
    http://www.reasons.org/article.....del-part-2

    Genomic monkey business – similarity re-evaluated using omitted data – by Jeffrey Tomkins and Jerry Bergman
    Excerpt: A review of the common claim that the human and chimpanzee (chimp) genomes are nearly identical was found to be highly questionable solely by an analysis of the methodology and data outlined in an assortment of key research publications.,,,
    Based on the analysis of data provided in various publications, including the often cited 2005 chimpanzee genome report, it is safe to conclude that human–chimp genome similarity is not more than ~87% identical, and possibly not higher than 81%. These revised estimates are based on relevant data omitted from the final similarity estimates typically presented.,,,
    Finally, a very recent large-scale human–chimp genome comparison research report spectacularly confirms the data presented in this report. The human–chimp common ancestor paradigm is clearly based more on myth and propaganda than fact.
    http://creation.com/human-chim.....-evaluated

  39. Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2.....47041.html

    Peer-Reviewed Paper in Medical Journal Challenges Evolutionary Science and Inaccurate Evolution-Education – Casey Luskin – January, 2012
    Excerpt: DNA homology between ape and man has been reported to be 96% when considering only the current protein-mapping sequences, which represent only 2% of the total genome. However, the actual similarity of the DNA is approximately 70% to 75% when considering the full genome, including the previously presumed “junk DNA,” which has now been demonstrated to code for supporting elements in transcription or expression. The 25% difference represents almost 35 million single nucleotide changes and 5 million insertions or deletions.
    http://www.evolutionnews.org/2.....55221.html

    A simple statistical test for the alleged “99% genetic identity” between humans and chimps – September 2010
    Excerpt: The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%.
    http://www.uncommondescent.com.....nd-chimps/

    Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship?
    Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.]
    http://www.apologeticspress.org/articles/2070

    Recent Genetic Research Shows Chimps More Distant From Humans,,, – Jan. 2010
    Excerpt: A Nature paper from January, 2010 titled, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.”,,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,,”
    http://www.evolutionnews.org/2.....34291.html

    The Gorilla Who Broke the Tree – Doug Axe PhD. – March 2012
    Excerpt: Well, the recent publication of the gorilla genome sequence shows that the expected pattern just isn’t there. Instead of a nested hierarchy of similarities, we see something more like a mosaic. According to a recent report [1], “In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other…”
    That’s sufficiently difficult to square with Darwin’s tree that it ought to bring the whole theory into question. And in an ideal world where Darwinism is examined the way scientific theories ought to be examined, I think it would. But in the real world things aren’t always so simple.
    http://www.biologicinstitute.o.....e-the-tree

    Dr. Fazale Rana states the chimp genome is about 12% larger than the human genome.

  40. …no matter how you measure it, chimps and humans are the two most similar genomes known (unless you count the Neanderthal genome, of course).

    He’s right you know Joe. A monkey’s genome is closer to my genome than yours is.

  41. Nick Matzke:

    …and the evidence for this is exactly the same sort of DNA evidence that we use to determine paternity…

    That statement is patently false.

  42. Nick @34:

    Sorry, I don’t mean to be pedantic, but there are two ways to interpret your response. Just to clarify, are you saying that:

    (i) “of course not” (i.e., the differences between humans and chimps of course do not result primarily from changes in the DNA),

    or

    (ii) “of course not” (i.e., you disagree with the statement and would instead say that the differences do indeed result primarily from changes in the DNA)

    The second.

  43. 41
    MungNovember 16, 2012 at 2:23 pm

    Nick Matzke:

    …and the evidence for this is exactly the same sort of DNA evidence that we use to determine paternity…

    That statement is patently false.

    Oh really? Do paternity tests, DNA tests for blood samples, etc., rely on DNA similarity, or not?

  44. Eric AndersonNovember 16, 2012 at 12:54 pm

    Nick @35:

    You guys are the ones who want to toss logic and experience and the very regular process of inheritance to the wolves, in favor of divine creation, basically to defend a particular fundamentalist reading of the Bible.

    There you go, projecting again.

    You should know that I am not trying to defend any fundamentalist reading of the Bible and have never tried to do so. I find it quite amusing that you are the one who keeps bringing religion into the discussion. But I realize that is how you view the entire debate through your twisted creationism-in-a-cheap-tuxedo perspective that you unfortunately acquired and honed at that bastion of propaganda, the NCSE.

    Oh, my bad. What’s your position on the relationship of chimps and humans, then, and where do you think humans came from? Ditto for anyone else who disputes my characterization. All you have to do is say “the evidence is clear that humans and chimps share a common ancestor, and that humans don’t descend from only two humans (Adam and Eve)”, and I’ll believe you.

  45. You guys are the ones who want to toss logic and experience and the very regular process of inheritance to the wolves, in favor of divine creation, basically to defend a particular fundamentalist reading of the Bible.

    There you go, projecting again.

    Also, the origin of this thread is a facebook discussion of the Ann Gauger/Discovery Institute book, which attempts to disprove human evolution and argue for the historical reality of Adam and Eve as the sole ancestors of humans. That’s straight-up fundamentalist Genesis literalism, and creationism. That’s not me projecting, that’s their position, a position they are proud to take and to defend.

  46. Nick, tell us, how many generations does it take before you can no longer tell how closely related any two people are?

    And DNA testing to see who a sample of blood belongs to is the same as the determination of paternity, is the same as determining who the most recent common ancestor of humans and chimps was? Really?

  47. Hmm I wonder if we can make a case for humans being descended from the kangaroo lineage:

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

    First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007
    Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,,
    The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.
    http://news.nationalgeographic.....m-dna.html

    But then again why are we even discussing the modern synthesis of neo-Darwinism in the first place?

    The Fate of Darwinism: Evolution After the Modern Synthesis – David J. Depew and Bruce H. Weber – 2011
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,,
    http://www.springerlink.com/co.....03g3t7002/

    The next evolutionary synthesis: Jonathan BL Bard (2011)
    Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory!
    http://www.biosignaling.com/co.....X-9-30.pdf

    The Origin at 150: is a new evolutionary synthesis in sight? – Koonin – Nov. 2009
    Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair.
    http://www.arn.org/blogs/index....._synthesis

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    Revisiting the Central Dogma – David Tyler – Nov. 9, 2012
    Excerpt: “The past decade, however, has witnessed a rapid accumulation of evidence that challenges the linear logic of the central dogma (DNA makes RNA makes Protein). Four previously unassailable beliefs about the genome – that it is static throughout the life of the organism; that it is invariant between cell type and individual; that changes occurring in somatic cells cannot be inherited (also known as Lamarckian evolution); and that necessary and sufficient information for cellular function is contained in the gene sequence – have all been called into question in the last few years.”,,
    Undoubtedly, the trigger for change has been the discovery of extraordinary complexity in cellular processes as revealed by systems biology research. It is now necessary to refer to networks of interactions when explaining any aspect of cellular function. And the very existence of these networks defies the central dogma:
    http://www.arn.org/blogs/index.....tral_dogma

  48. So Nick do you disagree that new fossil lineages appear suddenly in the fossil record just because it may smack of ‘biblical fundamentalism’ to you??? i.e. do you think that neo-Darwinism must be true because the alternative is unthinkable for you??? And exactly why, scientifically, would this alternative be so unthinkable for you even though the evidence points to the sudden appearance of new forms in the fossil record???

    “No fossil is buried with its birth certificate. That, and the scarcity of fossils, means that it is effectively impossible to link fossils into chains of cause and effect in any valid way… To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story—amusing, perhaps even instructive, but not scientific.”
    Henry Gee, In Search of Deep Time: Beyond the Fossil Record to a New History of Life

    Here are some quotes by leading paleontologists on the true state of the fossil record:

    “The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find’ over and over again’ not gradual evolution, but the sudden explosion of one group at the expense of another.”
    Paleontologist, Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK)

    “It must be significant that nearly all the evolutionary stories I learned as a student from Trueman’s Ostrea/Gryphaea to Carruthers’ Zaphrentis delanouei, have now been ‘debunked’. Similarly, my own experience [sic] of more than twenty years looking for evolutionary lineages among the Mesozoic Brachiopoda has proved them equally elusive.’
    Dr. Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK), ‘The nature of the fossil record’. Proceedings of the Geologists’ Association, vol.87(2), 1976,p.132.

    “A major problem in proving the theory has been the fossil record; the imprints of vanished species preserved in the Earth’s geological formations. This record has never revealed traces of Darwin’s hypothetical intermediate variants – instead species appear and disappear abruptly, and this anomaly has fueled the creationist argument that each species was created by God.”
    Paleontologist, Mark Czarnecki

    “There is no need to apologize any longer for the poverty of the fossil record. In some ways, it has become almost unmanageably rich and discovery is outpacing integration. The fossil record nevertheless continues to be composed mainly of gaps.”
    Professor of paleontology – Glasgow University, T. Neville George

    “Evolution requires intermediate forms between species and paleontology does not provide them.”
    David Kitts – Paleontologist – D.B. Kitts, Paleontology and Evolutionary Theory (1974), p. 467.

    “The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists” –
    Stephen Jay Gould – Harvard

    “The sweep of anatomical diversity reached a maximum right after the initial diversification of multicellular animals. The later history of life proceeded by elimination not expansion.”
    Stephen J. Gould, Harvard, Wonderful Life, 1989, p.46

    “Given the fact of evolution, one would expect the fossils to document a gradual steady change from ancestral forms to the descendants. But this is not what the paleontologist finds. Instead, he or she finds gaps in just about every phyletic series.” -
    Ernst Mayr-Professor Emeritus, Museum of Comparative Zoology at Harvard University

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.” Robert L Carroll (born 1938) – vertebrate paleontologist who specialises in Paleozoic and Mesozoic amphibians

    “Now, after over 120 years of the most extensive and painstaking geological exploration of every continent and ocean bottom, the picture is infinitely more vivid and complete than it was in 1859. Formations have been discovered containing hundreds of billions of fossils and our museums now are filled with over 100 million fossils of 250,000 different species. The availability of this profusion of hard scientific data should permit objective investigators to determine if Darwin was on the right track. What is the picture which the fossils have given us? … The gaps between major groups of organisms have been growing even wider and more undeniable. They can no longer be ignored or rationalized away with appeals to imperfection of the fossil record.” Luther D. Sunderland, Darwin’s Enigma 1988, Fossils and Other Problems, 4th edition, Master Books, p. 9

    “The evidence we find in the geological record is not nearly as compatible with Darwinian natural selection as we would like it to be …. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than in Darwin’s time … so Darwin’s problem has not been alleviated”.
    David Raup, Curator of Geology at Chicago’s Field Museum of Natural History

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.” Fossils and Evolution, TS Kemp – Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.”
    George Gaylord Simpson (evolutionist), The Major Features of Evolution, New York, Columbia University Press, 1953 p. 360.

    “No wonder paleontologists shied away from evolution for so long. It seems never to happen. Assiduous collecting up cliff faces yields zigzags, minor oscillations, and the very occasional slight accumulation of change over millions of years, at a rate too slow to really account for all the prodigious change that has occurred in evolutionary history. When we do see the introduction of evolutionary novelty, it usually shows up with a bang, and often with no firm evidence that the organisms did not evolve elsewhere! Evolution cannot forever be going on someplace else. Yet that’s how the fossil record has struck many a forlorn paleontologist looking to learn something about evolution.” -
    Niles Eldredge , “Reinventing Darwin: The Great Evolutionary Debate,” 1996, p.95

    “Enthusiastic paleontologists in several countries have claimed pieces of this missing record, but the claims have all been disputed and in any case do not provide real connections. That brings me to the second most surprising feature of the fossil record…the abruptness of some of the major changes in the history of life.” Ager, D. – Author of “The Nature of the Stratigraphical Record”-1981

    “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology.”
    Stephen Jay Gould

    Donald Prothero: In evolution, stasis was general, gradualism rare, and that’s the consensus 40 years on – February 2012
    Excerpt: In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. Rather than answers, we have more questions—
    Donald Prothero – evolutionary biologist
    http://www.uncommondescent.com.....ars-later/

    Tar Pit Study Shows Complete Absence of Evolutionary Change – Douglas Axe – October 16, 2012
    Excerpt: [T]he data show that birds and mammals at Rancho La Brea show complete stasis and were unresponsive to the major climate change that occurred at 20 ka, consistent with other studies of Pleistocene animals and plants. Most explanations for such stasis (stabilizing selection, canalization) fail in this setting where climate is changing. One possible explanation is that most large birds and mammals are very broadly adapted and relatively insensitive to changes in their environments, although even the small mammals of the Pleistocene show stasis during climate change, too.
    - Donald Prothero and colleagues
    http://www.evolutionnews.org/2.....65321.html

    Stasis in Pleistocene mammals and birds – Oct. 26, 2012 – David Tyler
    Excerpt: “After six years of work and publication, the conclusion is clear: none of the common Ice Age mammals and birds responded to any of the climate changes at La Brea in the last 35,000 years, even though the region went from dry chaparral to snowy pinon-juniper forests during the peak glacial 20,000 years ago, and then back to the modern chaparral again.” ,,,

    “In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. ,,,

    “Such stasis, along with the examples documented from nearly all other Pleistocene mammals and birds, argues that organisms are not as responsive to environmental change as classical neo-Darwinian theory predicts.”
    http://www.arn.org/blogs/index....._and_birds

  49. Read Your References Carefully: Paul McBride’s Prized Citation on Skull-Sizes Supports My Thesis, Not His – Casey Luskin – August 31, 2012
    Excerpt of Conclusion: This has been a long article, but I hope it is instructive in showing how evolutionists deal with the fossil hominin evidence. As we’ve seen, multiple authorities recognize that our genus Homo appears in the fossil record abruptly with a complex suite of characteristics never-before-seen in any hominin. And that suite of characteristics has remained remarkably constant from the time Homo appears until the present day with you, me, and the rest of modern humanity. The one possible exception to this is brain size, where there are some skulls of intermediate cranial capacity, and there is some increase over time. But even there, when Homo appears, it does so with an abrupt increase in skull-size. ,,,
    The complex suite of traits associated with our genus Homo appears abruptly, and is distinctly different from the australopithecines which were supposedly our ancestors. There are no transitional fossils linking us to that group.,,,
    http://www.evolutionnews.org/2.....63841.html

    McBride Misstates My Arguments in Science and Human Origins – Casey Luskin September 5, 2012
    Excerpt: At the end of the day, I leave this exchange more confident than before that the evidence supports the abrupt appearance of our genus Homo.
    http://www.evolutionnews.org/2.....63931.html

  50. Nick @35 (and to also answer your question @44):

    The real point is that no matter how you slice it, chimps are the closest living relatives of humans . . .

    Almost. Let’s try this:

    Chimps and humans share many common features, and in several areas humans are more similar to chimps than to any other creatures currently alive. One possible explanation for this similarity is that both humans and chimps descended from a common ancestor. Indeed, there are some tantalizing pieces of data that would be consistent with and explainable on the theory of common descent. However, there are also some anomalies or exceptions. Further, we do not know (i) exactly which changes would be required to get to humans, (ii) whether evolutionary processes could actually produce those changes in the real world, and (iii) whether the time available or the population numbers available could reasonably be expected to result in those changes. Finally, there are some differences between humans and chimps that may or may not be reducible to DNA changes alone.

    —–

    I think that would be more accurate statement of the current state of knowledge.

  51. Nick @45:

    Nick, you indirectly raise a question I’ve been contemplating recently. I’m sincerely interested in your thoughts on this issue.

    The concept of a “mitochondrial Eve” has received a lot of press over the years. Do you think there is in fact a single female individual from whom all humans descended?

    That individual would presumably have come from two parents, who also each came from two parents, etc., in a broadening cone of ancestors, if you will. So this would suggest that there is a kind of “hourglass” shape to our descent: broad now, but converging in the past to a single mitochondrial Eve, and then broadening again after mitochondrial Eve.

    Does that make any sense, or am I not describing this clearly?


  52. However no one knows how much of a genetic difference exists between chimps and humans

    What? This is just sheer nonsense, inherited from desperate creationist poo-flinging to obscure the fact that basically no matter how you measure it, chimps and humans are the two most similar genomes known (unless you count the Neanderthal genome, of course). This isn’t just me saying this, go ask Todd Wodd of Bryan College:

    http://www.uncommondescent.com…..-identity/

    It is very noticeable that you didn’t give a number.

    Also genetic similarity is evidence for a COMMON DESIGN and the DNA sequences used to infer common ancestry is NOT the same DNA sequences used to infer paternity.

  53. And DNA testing to see who a sample of blood belongs to is the same as the determination of paternity, is the same as determining who the most recent common ancestor of humans and chimps was? Really?

    You know, mung, some people on other sites have been suggesting you are a deep-cover pro-Darwin agent trying to make ID proponents look bad. I think you are now making deep-cover pro-Darwin agents look bad!

    Yes, it’s the same process.

  54. Oops, now I am making disinterested observers look bad. Forgot blockquotes, first paragraph is quoting mung.

  55. Same process, different sequences of DNA. That means the DNA testing is NOT the same, Alan.

    For example paternity is not done via alleged pseudogenes and ERVs.

  56. Jee whizz, Joe, I take my hat off to you! You are determined to outshine mung!

  57. And you are just determined to be a pimple on the arse of progress. Congratulations, I would say that you have made it.

  58. Sure, joe.

    It doesn’t alter the fact that comparing DNA sequences is done by…

    …comparing DNA sequences. It is valid as a method for matching forensic samples to suspects, individuals to relatives and organisms into nested hierarchies.

  59. LoL! You don’t know what a nested hierarchy is. But thanks for admitting that I am correct and that you and Nick are deceivers.

  60. So what happened Alan? Did you really think I was totally wrong and when you bothered to looked it up found out I was correct?

    LoL!

  61. Well, Alan, I see neither you nor Nick saw fit to answer my question:

    If a relationship is in question, and you have suggested DNA testing for additional evidence, you must identify the specific genetic relationship to be tested. It is not sufficiently specific for you to ask whether two people are “related;” rather, you must indicate how you think they may be related – parent/child, grandparent/grandchild, siblings, etc. here

    Now just how does that work for humans, chimps, and their alleged common ancestor (for whom you have no DNA sample)?

    Who’s your momma?

    If you send in a sample of your DNA and a sample of DNA from a chimp and ask if the two of you are cousins, you think the answer is going to be yes? (Who knows, maybe it would be.)

  62. Alan Fox:

    It doesn’t alter the fact that comparing DNA sequences is done by…

    …comparing DNA sequences.

    What a genius. That’s your rebuttal?

  63. Nick @ 35,43
    What distinguishes using DNA in forensics or paternity testing from using it to infer phylogenetic relationships is that the former cases possess sufficient empirical warrant whereas the latter does not. We have abundant, incontrovertible evidence that gives us good reason to use DNA similarities WITHIN a species to infer relationships. Descent with modification is an observed fact in that limited context. However, to apply that same reasoning to trace out phylogenetic relationships is problematic. There is good reason to suspect that Neo-Darwinian mechanisms are not robust enough to account for the major changes that would be a part of the contiuous spectrum view of biology. No breeding experiment has ever shown a species to have the plasticity needed to make radical changes to its muscular, skeletal, reproductive, cardio-pulmonary, digestive, or nervous system whilst still maintaining (or even improving) fitness. Thus, the bare fact that humans and chimps have considerable similarity in their genomes (pick whatever percentage you fancy) is not sufficient to establish their evolutionary relatedness, much less so the mechanism responsible for such relatedness. In fact, it’s entirely possible that at some point in the future biology will progress to the point where human engineers could synthesize biological systems. This engineered life could possess genetic similarity to “natural” forms of life. What, then, would we make of genetic similarity arguments in that case?

  64. What distinguishes using DNA in forensics or paternity testing from using it to infer phylogenetic relationships is that the former cases possess sufficient empirical warrant whereas the latter does not.

    Comparing DNA sequences is the same process. Methods might differ and evolve (pun intended!). 40 years ago, I recall as an undergraduate performing crude experiments involving passing samples through an electrophoresis column and measuring the radioactive tritium levels of labelled samples. One could then extrapolate an approximate measure of the percentage similarity of samples. I remember our prof. claiming that from this simple test it was possible to infer that yeast samples and moth samples shared a common ancestor about a billion years ago. At the time I was skeptical.

    Research continues.

  65. Alan Fox:

    Comparing DNA sequences is the same process.

    But they use DIFFERENT DNA sequences, so it is NOT the same.

    Evos just have to use deception in order to “win”- pathetic, really.

  66. They use DNA, therefore they are the same, is a huge non sequitur.

  67. Alan Fox:

    Methods might differ…

    You think? Why would the methods need to differ?

    Maybe it’s because they are not asking the same question.

  68. Optimus:

    We have abundant, incontrovertible evidence that gives us good reason to use DNA similarities WITHIN a species to infer relationships.

    And the efficacy is even limited WITHIN species. And they do not use the same tools as those used in phylogenetic analysis.

    Joe Felsenstein:

    A quibble: within species, the molecular and morphological evidence does not show that the differentiation of individuals is treelike. My genealogy is not treelike because (shock! horror!) I actually had not one ancestor, but two: my mother and my father. Samples of individual gene loci have trees of ancestry — coalescent trees — but they differ from locus to locus.

    Above the species level the pattern rapidly becomes treelike, and that is where the dispute between PaV and Alan is mostly occurring, but within species the pattern is not a single tree.

  69. Nick @ 35,43
    What distinguishes using DNA in forensics or paternity testing from using it to infer phylogenetic relationships is that the former cases possess sufficient empirical warrant whereas the latter does not. We have abundant, incontrovertible evidence that gives us good reason to use DNA similarities WITHIN a species to infer relationships. Descent with modification is an observed fact in that limited context.

    Oh really? Please prove that aliens or God did not magically intervene in each fertilization event. Maybe the DNA similarity between you and your parents is due to common design, not common descent. Or did someone watch your egg get fertilized?

  70. Nick @45:

    Nick, you indirectly raise a question I’ve been contemplating recently. I’m sincerely interested in your thoughts on this issue.

    The concept of a “mitochondrial Eve” has received a lot of press over the years. Do you think there is in fact a single female individual from whom all humans descended?

    That individual would presumably have come from two parents, who also each came from two parents, etc., in a broadening cone of ancestors, if you will. So this would suggest that there is a kind of “hourglass” shape to our descent: broad now, but converging in the past to a single mitochondrial Eve, and then broadening again after mitochondrial Eve.

    Does that make any sense, or am I not describing this clearly?

    It makes a little bit of sense but it’s mostly wrong. You need an intro popgen course or textbook. I’ll give you some buzzwords to look up. The “cone of ancestors” indeed increases as you go back in time (you, your 2 parents, your 4 grandparents, etc.) but pretty soon you start having relatives mating, so it doesn’t expand forever. With genetic data for a population you can calculate an “inbreeding coefficient” that measures this. This is closely related to how you can calculate an effective population size given data about genetic diversity. Basically, small population size = more inbreeding = less genetic diversity.

    As for mitochondrial Eve, there is an “Eve”, i.e. a last common ancestor, for every locus in the genome — the mathematics of inbreeding mean that this must eventually happen. But essentially every one of these loci will have a different common ancestor at a different time. This is one of the (many) ways that genetic data disproves a literal Adam & Eve…

  71. Or did someone watch your egg get fertilized?

    Not beyond the realm of possibility.

  72. Nick Matzke:

    This is one of the (many) ways that genetic data disproves a literal Adam & Eve…

    So you are saying that YEC can indeed be tested. However to test it you need to know more about the MECHANISM. Sure under unguided evolution’s framework, a literal Adam & Eve doesn’t work in the timeframe of 6,000-12,000 years. But given a design scenario in which real GAs are free to manipulate the genome virtually at will in order to achieve the goal, your equations do not apply and neither does your “refutation”.

  73. Nick Matzke:

    Please prove that aliens or God did not magically intervene in each fertilization event.

    Please prove that you are not an infant. Or better yet please step up and demonstrate that unguided evolution can account for fertilization events and people may listen to you.

    Maybe the DNA similarity between you and your parents is due to common design, not common descent.

    ALL humans owe their similarities to a common design. And all observations say common design with common descent lead to more of the same- humans give rise to humans, chimps give rise to chimps.

    What you need to do Nick, is focus on the observed differences- the anatomical and physiological DIFFERENCES and link those to the genomes.

    Or did someone watch your egg get fertilized?

    Mung has/ had an egg?

    “I am the eggman
    I am the eggman
    I am the Mung(er) coo-coo-ca-chu”

    “Has anyone sen the egg?
    Where is that confounded egg?”

  74. Nick @ 69
    Thank you for taking the time to respond to my comment, though I am a bit disappointed in your lack of substance. It’s hard to see how aliens or God are relevant to what I posted previously. Perhaps I should be gratified, though, as off-topic replies generally indicate an inability to seriously engage a cogent argument. I was simply pointing out what seems to be obvious, namely that using genetic similarities to establish phylogenetic relationships requires the prior assumption that such relationships are in fact possible. If that assumption is invalid, then the inferences based on comparative analysis are likewise invalidated. And given what we know from direct observation, that assumption is hardly established.
    But perhaps your seemingly off-topic tirade conceals a genuine worry. Since you did not state it clearly, I shall endeavor to guess at it… Perhaps your concern is that a design inference could be used as a sort of explanatory panacea, invoked with reckless abandon to explain anything and everything. I think that fear is vastly overblown. Like any other inference, the inference to design should only be invoked when there is reason to. If you want an example of an idea that is absurdly over-applied, look no farther than Neo-Darwinism.

  75. Nick @70:

    I’m familiar with the cone idea, and also understand the idea that each DNA locus has its own “ancestor” (which may or may not be different from any other ancestor).

    I referred specifically to mitochondrial DNA, which presumably does not go through recombination and presumably is why we see statements like this (I know, I know, it’s Wikipedia, but you get the idea): “In the field of human genetics, Mitochondrial Eve refers to the matrilineal most recent common ancestor (MRCA) of modern humans. In other words, she was the most recent woman from whom all living humans today descend, on their mother’s side, and through the mothers of those mothers and so on, back until all lines converge on one person.”

    This statement would seem to suggest that the human lineage converges on a single person, no?

  76. Nick, tell us, how many generations does it take before you can no longer tell how closely related any two people are?

    Unless I am mistaken, we will of course reach a point bgeyond where we can’t determine the number of generations between two people.

    But the subject of determining genetic differences began already about 100 years ago with Cambridge professor Nuttall. Followed by Professor Goodman at Wayne State University School. Later, in the 1960′s Vincent Sarich, who said:

    I know my molecules had ancestors, the paleontologist can only hope that his fossils had descendants.
    That was long before the discovery of the double helix…
    Yet it was possible to determine to a certin degree relationships between species. It’s all in the DNA, but sequencing is of course the more accurate of any methods.
    Evolutionary trees had been growing for a long time before sequencing was invented… Scientists actually are smart, they make theories, perform testing, invent methods, do experiments, draw conclusions, make inferences – and repeat it all, again and again never at rest as long as new frontiers are coming into sight. How much evolution of ID during, say, the last decade?

  77. I trust you spot where the last part of my comment got nested into the “I know …” quote

  78. Unless I am mistaken, we will of course reach a point beyond where we can’t determine the number of generations between two people.

    That’s my belief as well. And Nick, if he doesn’t know it, ought to know it.

    It would also mean that not only are his facts wrong, but so is his reasoning.

  79. You’re misunderstanding the magic. You don’t count a number of generations to determine relatedness.

    First you assume that the two organisms are related by descent. Then you count the DNA differences to calculate the number of generations.

  80. Mung cites a random page from the US Immigration Service in some kind of desperate attempt to establish that paternity and forensic DNA tests are “totally different” from human-chimp DNA tests:

    If a relationship is in question, and you have suggested DNA testing for additional evidence, you must identify the specific genetic relationship to be tested. It is not sufficiently specific for you to ask whether two people are “related;” rather, you must indicate how you think they may be related – parent/child, grandparent/grandchild, siblings, etc.

    This requirement is here just for legal purposes. I.e., if you are someone’s child, perhaps that makes you eligible for citizenship, but not if you are someone’s brother.

  81. Mung cites a random page from the US Immigration Service in some kind of desperate attempt…

    Arbitrary maybe, but not random.

    A random search would not likely have turned up a document relevant to the subject matter from the US government. Yet one more case of design in action.

  82. Nick @70:

    I’m familiar with the cone idea, and also understand the idea that each DNA locus has its own “ancestor” (which may or may not be different from any other ancestor).

    I referred specifically to mitochondrial DNA, which presumably does not go through recombination and presumably is why we see statements like this (I know, I know, it’s Wikipedia, but you get the idea): “In the field of human genetics, Mitochondrial Eve refers to the matrilineal most recent common ancestor (MRCA) of modern humans. In other words, she was the most recent woman from whom all living humans today descend, on their mother’s side, and through the mothers of those mothers and so on, back until all lines converge on one person.”

    This statement would seem to suggest that the human lineage converges on a single person, no?

    It suggests it, sorta, but if so it’s a misinterpretation of the science. The “human lineage” does not converge to one person, just the human mitochondrial lineage. Every other locus converges to a different person — well, except that the “person” might be an ape that was part of the species ancestral to humans/chimps/gorillas, or in some cases might even be a rodentlike animal tens of millions of years ago.

    The human lineage converges back on an ancestral population, the rough charactersitics of which can be inferred from the histories of the individual loci in our genomes.

  83. Nick:

    Mung cites a random page from the US Immigration Service in some kind of desperate attempt to establish that paternity and forensic DNA tests are “totally different” from human-chimp DNA tests:

    Well Nick, I see you have to resort to a straw man and have tried to float a brick.

    Is this human-chimp DNA test available over the counter yet? I’d like to take that test.

  84. National Geographic Explorer-in-Residence Dr. Spencer Wells and team designed Geno 2.0 based on the new technologies and insights that emerged since the launch of the Genographic Project in 2005. Using an exclusive, custom-built genotyping chip, we test nearly 150,000 DNA markers that have been specifically selected to provide unprecedented ancestry-related information.

    https://genographic.nationalgeographic.com/science-behind/

    Maybe those are the same markers they use to test human-chimp ancestry, but I doubt it.

  85. nick:

    well, except that the “person” might be an ape that was part of the species ancestral to humans/chimps/gorillas, or in some cases might even be a rodentlike animal tens of millions of years ago.

    Or not.

    Such questions are even more remarkable in light of genetic evidence that we are all descended from a common African ancestor who lived only 140,000 years ago.

    https://genographic.nationalgeographic.com/science-behind/

  86. Nick Matzke:

    Mung cites a random page from the US Immigration Service in some kind of desperate attempt to establish that paternity and forensic DNA tests are “totally different” from human-chimp DNA tests:

    Nick doesn’t cite anything to support his desperate attempt to establish that paternity and forensic DNA tests are “like, totally the same” as human-chimp DNA tests.

  87. Mung,

    Why do you think ” are all descended from a common African ancestor who lived only 140,000 years ago” is evidence against the most recent common ancestor of some of our genes was found in ape? You don’t seem to have grasped the point that different genes have different histories (each of which can tell us about the population-level history of our species).

  88. wd400,

    Why do you think ”are all descended from a common African ancestor who lived only 140,000 years ago” is evidence against the most recent common ancestor of some of our genes was found in ape?

    I don’t.

    You don’t seem to have grasped the point that different genes have different histories (each of which can tell us about the population-level history of our species).

    I don’t think I have any problem with that point at all.

    The current debate with Nick is over the sequences, tools, methods and reasoning used. From the fact that we can do a DNA test on blood found at a crime scene it does not follow that humans and chimps share a common ancestor. From the fact that we can do a paternity test it does not follow that humans and chimps share a common ancestor.

    Nick claimed it’s all the same:

    The real point is that no matter how you slice it, chimps are the closest living relatives of humans, and the evidence for this is exactly the same sort of DNA evidence that we use to determine paternity, identify the source of blood samples at crime scenes, track who gave HIV to whom, determine what portion of the world various chunks of some American’s chromosomes came from, etc.

  89. The current debate with Nick is over the sequences, tools, methods and reasoning used. From the fact that we can do a DNA test on blood found at a crime scene it does not follow that humans and chimps share a common ancestor. From the fact that we can do a paternity test it does not follow that humans and chimps share a common ancestor.

    In both cases, similarity in DNA is the observation, inheritance of DNA through copying is the mechanism causing similarity, and common ancestry is the inferred, not observed, conclusion. Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.

  90. Nick Matzke:

    In both cases, similarity in DNA is the observation…

    Different sequences of DNA. One of which is explained by common descent and the other is easily explained by a common design.

    inheritance of DNA through copying is the mechanism causing similarity,

    Common design is another mechanism causing similarity.

    Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.

    So IEEE design standards are magical? Building codes are magical and miraculous? Cars are very similar to to common descent or common design? PC clones are very similar due to common descent or a common design?

    So do tell Nick, without the DNA similarities, what else do you have to supprt common descent? Ya see, Nick, inheriting SIMILAR DNA is NOT going to explain the physical DIFFERENCES required to get an upright biped from a knuckle-walker/ quadraped.

    Lactase persistence is not going to get an upright biped from a knuckle-walker/ quadraped.

    You have NOTHING to explain/ account for all the transformations required- you need to invoke magical, miraculous, mytery mutations. So shut up about non-testable positions already. Yours has been exposed as a big fraud.

  91. 91

    Nick Matzke:

    In both cases [paternity testing and common ancestry between species], similarity in DNA is the observation, inheritance of DNA through copying is the mechanism causing similarity, and common ancestry is the inferred, not observed, conclusion. Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.

    While the cause of similarity is the same, the cause of the differences is different — for paternity testing, it’s mixing with alleles from other ancestors, while the differences used to infer ancestry between species are due to mutation (with selection etc complicating things). I’d argue that this is a pretty significant difference. (However, at least as I understand it, tracking both HIV ancestry and human chromosome chunks do depend on mutations for their differences, and so are legitimate parallels for inferring common ancestry between species.)

    But both methods have been tested. Checking paternity tests is easy: check them on people with known parents, and you find that DNA testing generally agrees. Common ancestry is similar: we’d inferred a lot about the ancestral tree of different organisms before we even knew DNA existed, and we find that the tree inferred from DNA similarities generally agrees. There are two complications here: first, all those “generally”s, and second the fact that some of those here think the inferred common ancestry is wrong. I’ll deal with the second one first.

    Why should the agreement between the ancestral tree inferred by DNA similarities and that inferred by older phylogenetic techniques be significant if you don’t think either one works? It’s because of the principle of consilience — basically, if you get the same answer from several different methods, it’s a good indication that they’re all working.

    There have been attempts to explain the agreement in some other way, but I haven’t seen any that actually worked. For example, the obvious option is that DNA similarity is is measuring functional similarity, which is essentially the same thing older methods are based on. This doesn’t work for two reasons: first, a disproportionally large number of the DNA differences (at least within genes) are changes that don’t affect function — silent substitutions that don’t change the protein at all, or that change the amino acid sequence of the protein in ways that don’t change the protein’s function. Second, the pattern of DNA similarities doesn’t really match the pattern of functional similarities. In a recent comment, Robert Byers pointed out the functional similaries between certain marsupials and placental mammals:

    The marsupial wolf is just another wolf with a pouch. A marsupial lion likewise was a lion.
    There is no reason to classify them as a unrelated other group of animals.
    This is why they are unique to areas and not in other areas. tHey simply are the same creatures who upon migration had a general change in these details for good reasons back then.
    One can see moving or still pictures of the marsupial wolf and be convinced its just another dog.
    All the points of anatomy surely trump the few points of difference.

    So if the DNA similarities are due to functional similarities, we should expect the marsupial wolf’s DNA to be very similar to that of the placental wolf, and the marsupial lion’s DNA to be similar to the placental lion’s, right? While if the DNA similarities are due to common ancestry we’d expect for example the marsupial wolf’s DNA to be more similar to other marsupials than to any placentals, and not be significantly more similar to placental wolves than any other placental. Anyone want to bet which prediction is correct? And if you don’t want to bet against the common ancestry prediction, wny not?

    Joe mentioned another possibility: that DNA similarity might be due to common design. But how does this explain that some organisms have more similar DNA than others? Were the placentals designed by one designer, while the marsupials were designed by another?

    Now, the other point: that there are cases where both paternity testing and DNA-based inference of common ancestry sometimes disagree with what we “know” by other methods. This happens in both cases, and in both cases the interesting thing is that the DNA methods are thought to be more accurate than the methods they were tested against. Measurement methods in general have uncertainties and are subject to errors. The figures I’ve seen say that around 10% of the time, someone’s socially accepted father isn’t actually their biological father. So we expect DNA paternity testing to disagree with the “known” father about 10% of the time. I don’t know of a good way to quantify the agreement between DNA-inferred common ancestry and other methods (Nick might), but it seems to me that where there’s a disagreement, there’s usually some ambiguity in at least one of the methods, and the inferred trees are usually only slightly different.

  92. Nick Matzke:

    Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.

    No, I don’t.

  93. Nick:

    Thanks, that is helpful.

    Ultimately, though, everything is supposed to converge back on a smaller and smaller population and, eventually, a single organism, under the traditional evolutionary story. I guess there is no way to know at what point the widening cone stops widening and starts converging, so we can only guess as to that aspect . . .

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