Alzheimer disease evolved alongside human intelligence, says Nature article

43 Replies to “Alzheimer disease evolved alongside human intelligence, says Nature article”

1. 1
   wd400 says:

   May 24, 2015 at 3:04 pm

   The paper is here[pdf] for anyone that wants to read it. I don’t quite what “darwinbabble” has to do with it, or understand this question.

   One must already be a human being to have these kinds of problems. Where is the evolution, exactly?

   The paper shows that genes associated with alzheimers in humans show a population-genetic signal expected from natural selection. That’s pretty obviously evolution, isn’t it?
2. 2
   bornagain77 says:

   May 24, 2015 at 3:19 pm

   as to:

   “That’s pretty obviously evolution, isn’t it?”

   The Meanings of Evolution – Stephen Meyer
   Excerpt: Principal Meanings of Evolution in Biology Textbooks
   1. Change over time; history of nature; any sequence of events in nature.
   2. Changes in the frequencies of alleles in the gene pool of a population.
   3. Limited common descent: the idea that particular groups of organisms have descended from a common ancestor.
   4. The mechanisms responsible for the change required to produce limited descent with modification, chiefly natural selection acting on random variations or mutations.
   5. Universal common descent: the idea that all organisms have descended from a single common ancestor.
   6. “Blind watchmaker” thesis: the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms.
   ,,, attempts to exclude scientific dissent (from neo-Darwinism) often employ ambiguous or shifting definitions of the term evolution. Many defenders of evolution #5 and/or #6 will offer evidence and argument for evolution in the first four senses of the term and then treat evolution in the latter two senses as equally well established. In the following section, we will show how educational policy statements and advocates for evolution often equivocate (the definitions of evolution) in their discussion of evolution,,,
   http://www.discovery.org/scrip.....php?id=305
3. 3
   wd400 says:

   May 24, 2015 at 3:34 pm

   … I guess News should specify which definition of evolution she thinks doesn’t apply to this result then?
4. 4
   News says:

   May 24, 2015 at 3:47 pm

   wd400 is likely to continue to fail to see the problem:

   Absent any way of determining how Alzheimer would affect a non-human, it’ not clear what “evolution” has to do with it.

   First, the human evolution claims are vague (*”Still, even the most powerful genomic-analysis methods can be limited by the vagaries of history.” = It’s rubbish).

   And second (in this case, far more important), animal models are necessarily lacking. (Animals don’t know phone numbers or why they matter, let alone forget them.)

   The point of the post is that Alzheimer is a problem for human intelligence. We simply don’t know how it would affect grizzly bears, if they suffer from it.

   If this is the best “evolutionary medicine” can do (and it probably is)…
5. 5
   bornagain77 says:

   May 24, 2015 at 3:58 pm

   News: “One must already be a human being to have these kinds of problems.”

   apparently 5 and 6 don’t apply. Perhaps you would like to tell us where the human brain came from?

   The Half-Truths of Materialist Evolution – DONALD DeMARCO – 02/06/2015
   Excerpt: but I would like to direct attention to the unsupportable notion that the human brain, to focus on a single phenomenon, could possibly have evolved by sheer chance. One of the great stumbling blocks for Darwin and other chance evolutionists is explaining how a multitude of factors simultaneously coalesce to form a unified, functioning system. The human brain could not have evolved as a result of the addition of one factor at a time. Its unity and phantasmagorical complexity defies any explanation that relies on pure chance. It would be an underestimation of the first magnitude to say that today’s neurophysiologists know more about the structure and workings of the brain than did Darwin and his associates.
   Scientists in the field of brain research now inform us that a single human brain contains more molecular-scale switches than all the computers, routers and Internet connections on the entire planet! According to Stephen Smith, a professor of molecular and cellular physiology at the Stanford University School of Medicine, the brain’s complexity is staggering, beyond anything his team of researchers had ever imagined, almost to the point of being beyond belief. In the cerebral cortex alone, each neuron has between 1,000 to 10,000 synapses that result, roughly, in a total of 125 trillion synapses, which is about how many stars fill 1,500 Milky Way galaxies!
   A single synapse may contain 1,000 molecular-scale switches. A synapse, simply stated, is the place where a nerve impulse passes from one nerve cell to another.
   Phantasmagorical as this level of unified complexity is, it places us merely at the doorway of the brain’s even deeper mind-boggling organization. Glial cells in the brain assist in neuron speed. These cells outnumber neurons 10 times over, with 860 billion cells. All of this activity is monitored by microglia cells that not only clean up damaged cells but also prune dendrites, forming part of the learning process. The cortex alone contains 100,000 miles of myelin-covered, insulated nerve fibers.
   The process of mapping the brain would indeed be time-consuming. It would entail identifying every synaptic neuron. If it took a mere second to identify each neuron, it would require four billion years to complete the project.
   http://www.ncregister.com/dail.....evolution/

   Of note: Alzheimer’s is a personal issue for Denyse:

   There is a country for old men – DENYSE O’LEARY
   Excerpt: In January of his 90th year, my father had a stroke. He had been struggling with Alzheimer’s for some time. The hospital staff had seen many like him, and they quietly conveyed to us that we should not expect too much. It was even spelled out, not merely hinted, that, beyond what common humanity required, the quality of his care would likely not matter much, and we ought not to spend his estate on it.,,,
   Circumstances prevented me visiting my father one Friday in January. But I received a phone call that evening from his closest sister, about 93, who lives in an old-age home in a midwestern city.

   She told me that after sixty years of practical atheism, anti-Catholicism, and anti-Christianity, Dad wanted to be reconciled to the Church. He had a dream, she said. His parents appeared and were calling him, urging this course on him, so that he could one day join them in glory. He told her he hoped that I, as a Catholic, could help.

   Unlike some family members, I did not think his wish proceeded from an addled mind. I recognized its source instinctively. He wanted someone from heaven to forgive him, someone whose word he need never doubt.

   I lost no time finding a priest. A relative in medicine had warned me that Dad’s next stroke would likely be his last contact with normal cognition. By Wednesday afternoon, the priest and I were sitting in the apartment with Dad. The priest was an affable man with an interest in World War II, born perhaps of his vocation to older folk. I distracted my stepmom by asking to see the crafts room, and when we returned, my father said, steadily and with composure, “I have been reconciled to the Catholic Church, and my sins have been forgiven.”,,,
   http://www.catholiceducation.o.....d-men.html
6. 6
   Mung says:

   May 24, 2015 at 4:08 pm

   wd400:

   The paper shows that genes associated with alzheimers in humans show a population-genetic signal expected from natural selection. That’s pretty obviously evolution, isn’t it?

   How did they rule out genetic drift?
7. 7
   mahuna says:

   May 24, 2015 at 4:23 pm

   Alzheimer’s is a disease of VERY old human beings. Most humans for most of our history died before they were 35. Many other people parts also wear out if we live to be 60 years old. Is anyone suggesting that at any point in human development we had perfect (non-corruptible) bodies and only died when we were stepped on by dinosaurs or kicked by a mammoth or something?

   Most animals live MUCH longer in captivity than they do in the wild. In the wild, it doesn’t matter that a horse’s teeth wear down to nubs because the horse is going to die of something else LONG before it dies of starvation.

   It’s much more significant, from a species continuity point of view, that human females stop menstruating and human males become impotent. Or that our knee joints and hip joints wear out, and we develop back problems.
8. 8
   wd400 says:

   May 24, 2015 at 4:49 pm

   Absent any way of determining how Alzheimer would affect a non-human, it’ not clear what “evolution” has to do with it.

   You will have to explain why you think this. If genes that cause Alzheimer’s were fixed/maintained by selection then evolution has rather a lot to do with it, whether animals get the disease or not.

   First, the human evolution claims are vague (*”Still, even the most powerful genomic-analysis methods can be limited by the vagaries of history.” = It’s rubbish).

   No. That comment is about the fact it’s much easier to see these ancient patterns in African rather than other populations. Not a great surprise given the low diversity of non-African populations.

   The point of the post is that Alzheimer is a problem for human intelligence. We simply don’t know how it would affect grizzly bears, if they suffer from it.

   Again, I am left wondering how this is mean to relate to anything to do with the research. (And it hardly matters, but there are some pretty good animal models of Alzheimers)
9. 9
   wd400 says:

   May 24, 2015 at 4:57 pm

   Mung,

   How did they rule out genetic drift?

   You can read the paper for yourself. But, basically, they find the distribution of time to most recent common ancestor for all pairs of samples in their samples across the genome. Because we know what that distribution should look like under neutrality, you make a statistical test for non-neutral patterns like selection.
10. 10
    bornagain77 says:

    May 24, 2015 at 4:59 pm

    Of note: Neo-Darwinism is excellent at explaining the degeneration of already existent, fantastically complex, organs and is atrocious at demonstrating, or even explaining, how even a single protein of those fantastically complex organs could possibly arise by unguided material processes:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations
    Michael J. Behe – 2013
    http://www.worldscientific.com.....08728_0020

    Biological Information – Loss-of-Function Mutations by Paul Giem 2015 – video playlist
    (Behe – Loss of function mutations are far more likely to fix in a population than gain of function mutations)
    https://www.youtube.com/watch?v=hzD3hhvepK8&index=20&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

    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

    Biological Information – Mutation Count & Synergistic Epistasis (mutation accumulation) 1-17-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6gdoZk_NbmU
11. 11
    Mung says:

    May 24, 2015 at 5:08 pm

    Mung: How did they rule out genetic drift?

    wd400:

    You can read the paper for yourself. But, basically, they find the distribution of time to most recent common ancestor for all pairs of samples in their samples across the genome. Because we know what that distribution should look like under neutrality, you make a statistical test for non-neutral patterns like selection.

    You’re confusing neutral evolution with drift. As you know, the two are not the same. I’m asking specifically about genetic drift.

    How does one distinguish genetic drift as a cause from selection as a cause?
12. 12
    wd400 says:

    May 24, 2015 at 5:18 pm

    Certainly one of us is confused…

    If some observed data is unlikely to arise under neutrality (i.e. by drift alone) then it is likely that selection was involved in generating that data. Isn’t it?
13. 13
    Mapou says:

    May 24, 2015 at 5:38 pm

    If Darwinian evolution had a bucket to spit in, genetic diseases would simply not exist. Heck, we would be immortal because people find it easier to procreate when they’re not dead. This is the kind of crap one can expect from a dirt-did-it theory ducttaped together with stupidity?
14. 14
    Mung says:

    May 24, 2015 at 6:11 pm

    wd400:

    If some observed data is unlikely to arise under neutrality (i.e. by drift alone) then it is likely that selection was involved in generating that data. Isn’t it?

    Like I said, you’re confusing neutrality with drift. Surely you know better, so why pretend you don’t?

    There is nothing at all in the definition of genetic drift that requires it to act only on neutral alleles.

    http://en.wikipedia.org/wiki/Genetic_drift

    http://en.wikipedia.org/wiki/P.....etic_drift

    Added in Edit: How does random sampling know to sample only neutral alleles?

    If I am wrong, please explain why.
15. 15
    ppolish says:

    May 24, 2015 at 6:18 pm

    From the paper (thx WD400 for the link):

    “Abundant signals of BS were detected”
    No kidding. Grab 3 Neanderthals and build a model. Abundant BS sure to be found there.

    “AD remains arguably a disease unique to humans. Not observed in chimps”
    Why are evolutionists so obsessed with chimps. How many chimps have been observed? Dogs & Cats suffer dementia. AD probably.

    Look, AD is based on some Design Rule. Find that Design Rule fcol. “AD due to NS” what a useless pile of BS. Useless & BS.
16. 16
    wd400 says:

    May 24, 2015 at 6:20 pm

    It’s really not my job to teach you intro pop gen. But here’s the brief summary.

    Under neutrality (and excluding demographic changes which are handled neatly in this model, and inbreeding which is unlikely to be an issue here) the only thing changing allele frequencies is drift. When you exclude neutrality you are effectively saying “could this result have arisen by drift alone”. If the answer is ‘no’ then you have evidence of some other force, in this cases selection.
17. 17
    bornagain77 says:

    May 24, 2015 at 6:31 pm

    “It’s really not my job to teach you intro pop gen. But here’s the brief summary.”

    Here’s a bit more summary with the ugly pieces included that wd400 left out:

    As to Neutral Evolution:

    Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.

    Neutral theory was not developed because of any empirical observation, but was developed because it was forced upon Darwinism by the mathematics. (i.e. neutral theory is actually the result of a theoretical failure of Darwinism within mathematics!)

    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

    Walter ReMine on Haldane’s Dilemma – interview
    http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in response 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’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    https://vimeo.com/91162565

    John Sanford has indeed backed up his claim that the mathematics of population genetics could be used to argue against the very validity of Darwinism.

    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

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage.
    Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real.
    Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”.
    http://media.wix.com/ugd/a704d.....fa9c20.pdf

    Here is a recent article, not associated with Dr. Sanford, that also found a insurmountable barrier in the theoretical framework of Darwinism:

    Neo-Darwinism’s Catch-22: Before Evolving New Features, Organisms Would Be Swamped by Genetic Junk – Casey Luskin – April 10, 2015
    Excerpt: A new peer-reviewed paper in the journal Complexity presents a computational model of evolution which shows that evolving new biological structures may be deterred by an unavoidable catch-22 problem.,,,
    This is a bit complex — let’s go over it again. Darwinian evolution either (1) produces nothing new, or (2) it’s destined to produce boatloads of deadly junk. In the case of (2), the reward for trying new things is high compared to the cost of building new structures. But in order for the ratio to be high enough for complexity to increase, the cost of building new things must be negligible. Novelties proliferate, but the fraction,, that’s vestigial grows, and the organism is eventually swamped and overwhelmed by harmful vestigial features. However, if you try to avoid the problem of (2) by making the reward-to-cost ratio lower, as in (1), then nothing new ever evolves.
    The authors think real biological organisms are closer to position (1). Indeed, study in the field of systems biology increasingly finds that biological systems contain very little junk.,,,
    per ENV

    There are also other strong theoretical and empirical reasons to believe neutral theory is incorrect:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, 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

    “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’

    etc.. etc..

    here are some supplemental comments/quips as to neutral theory:

    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

    With the adoption of the ‘neutral theory’ of evolution by many prominent Darwinists, and the casting under the bus of Natural Selection as a major player in evolution, William J Murray quipped,,,

    “One wonders what would have become of evolution had Darwin originally claimed that it was simply the accumulation of random, neutral variations that generated all of the deeply complex, organized, interdependent structures we find in biology? Would we even know his name today?
    What exactly is Darwin really famous for now? Advancing a really popular, disproven idea (of Natural Selection), along the lines of Luminiferous Aether?
    Without the erroneous but powerful meme of “survival of the fittest” to act as an opiate for the Victorian intelligentsia and as a rationale for 20th century fascism, how might history have proceeded under the influence of the less vitriolic maxim, “Survival of the Happenstance”?”
    – William J Murray

    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

    as to drift specifically

    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/

    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 (greater than 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.
    per Evolution News and Views

    Natural Selection Struggles to Fix Advantageous Traits in Populations – Casey Luskin – October 23, 2014
    Excerpt: Michael Lynch, an evolutionary biologist at Indiana University,, writes that “random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes.”2 He notes that the effect of drift is “encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations.”3 Likewise, Eugene Koonin, a leading scientist at the National Institutes of Health, explains that genetic drift leads to “random fixation of neutral or even deleterious changes.”4
    http://www.evolutionnews.org/2.....90571.html
18. 18
    Mung says:

    May 24, 2015 at 6:56 pm

    wd400:

    It’s really not my job to teach you intro pop gen.

    Indeed it isn’t. But you claimed one of is confused and I’ve seen no evidence that I was the one confused. If I am the one confused I thought I’d try to learn why.

    wd400:

    Under neutrality … the only thing changing allele frequencies is drift.

    So what? I’ve said repeatedly now that you are conflating genetic drift with neutrality and you’re doing nothing to change that.

    Genetic drift is due to [caused by] random sampling, and it’s not checking to see whether some allele is neutral or not before taking the sample. Of course, you know this, or should.

    wd400:

    When you exclude neutrality you are effectively saying “could this result have arisen by drift alone”. If the answer is ‘no’ then you have evidence of some other force, in this cases selection.

    Tell me how one can distinguish between selection [non random sampling] as the cause and genetic drift [random sampling] as the cause when the effect is the same.

    That’s what I want to know.
19. 19
    wd400 says:

    May 24, 2015 at 7:17 pm

    As I said in my first comment on this,

    Because we know what that distribution should look like under neutrality, you make a statistical test for non-neutral patterns like selection.

    Under neutrality all you have is random sampling (drift). If that pattern can’t easily be explained by neutral, random sampling only, model then it’s likely non-random-sampling (selection) happened. Yes?
20. 20
    Mung says:

    May 24, 2015 at 7:39 pm

    wd400:

    Under neutrality all you have is random sampling (drift). If that pattern can’t easily be explained by neutral, random sampling only, model then it’s likely non-random-sampling (selection) happened. Yes?

    Why would you model all genetic drift as neutral evolution when that’s not the way genetic drift works? What justifies the assumption?

    If an allele becomes fixed (or lost) you can’t from that infer it was fixed (or lost) because of selection.

    Genetic drift does not have a preference for neutral alleles. Isn’t that true?

    I asked Dr. Moran at what population size is genetic drift likely to swamp selection. Still waiting for an answer.
21. 21
    wd400 says:

    May 24, 2015 at 7:54 pm

    I can’t diagnose all of your misunderstanding here, so I’ll just encourage you to learn som more. Perhaps start by thinking about the question you first asked — how can you tell the difference between drift and selection, and how selection relates to neutrality.

    If an allele becomes fixed (or lost) you can’t from that infer it was fixed (or lost) because of selection.

    Correct. Nothing in this method tries to do that.

    Genetic drift does not have a preference for neutral alleles. Isn’t that true?

    I don’t know what you mean by preference, but drift is not a strong force for alleles with large fitness differences. (That is, the fate of all allele depends very little on random sampling when selection coefficients are large)

    I asked Dr. Moran at what population size is genetic drift likely to swamp selection. Still waiting for an answer.

    To a first approximation, selection will dominate when twice the (effective) population size times the selection coefficient (2.Ne.s) is greater than 1.
22. 22
    Mung says:

    May 24, 2015 at 7:58 pm

    wd400, thank you.

    Let me attempt a different approach.

    Say I want to create a model of evolutionary mechanisms. For now I’ll stick with genetic drift and selection.

    I create an initial population of organisms and assign to each some selective value. Just for grins and because I don’t really know what the hack i’m doing I will assign to most of them a neutral or nearly neutral selective value.

    Now I want to create from this population the members of the next generation. How do I decide the composition of the next generation?

    Should I perform the random sampling first or look at the selective value first?
23. 23
    wd400 says:

    May 24, 2015 at 8:07 pm

    You can’t separate to the two — you draw with probabilities determined by the selection coefficients.

    For moderately large populations, if the difference in fitnesses if large, then the randomness of sampling will have little effect on the alleles that make it through. If all alleles have the same fitness then the random sampling is the only thing deciding which alleles make it.
24. 24
    Mung says:

    May 24, 2015 at 9:02 pm

    wd400:

    You can’t separate to the two — you draw with probabilities determined by the selection coefficients.

    No, you cannot separate the two, and that’s my point.

    The only mechanism you’re offering is selection unless the allele is neutral. If the drawing is based only on the selection coefficients as you say, then the sampling is not random. If the sampling is not random then there is no random genetic drift.

    You are conflating genetic drift with neutral evolution.

    It may in fact be the case that genetic drift is the only mechanism by which neutral alleles can become fixed, but it does not follow that selection is the only mechanism by which non-neutral alleles can become fixed.

    But then, you already know this.

    What I am struggling to understand is why you think alleles which are not selectively neutral cannot be fixed by random genetic drift [as well as by selection].

    I actually don’t think you think this, but you keep arguing as if you do.

    wd400:

    To a first approximation, selection will dominate when twice the (effective) population size times the selection coefficient (2.Ne.s) is greater than 1.

    Else what? Random genetic drift will dominate and neutral alleles will be fixed at a greater frequency than non-neutral alleles? Or at this point is the selection coefficient pretty much irrelevant.
25. 25
    wd400 says:

    May 24, 2015 at 9:13 pm

    If the drawing is based only on the selection coefficients as you say, then the sampling is not random

    This is simply not true, and seems to be that root of your other errors.
26. 26
    Robert Byers says:

    May 24, 2015 at 9:26 pm

    The author of the thread is right.
    I say animals also would have this disease. Likewise the clues in it are the memory problems.
    It is just a memory problem or rather a triggering problem in the memory from old age . I say this confidently.
    Nothing to do with selection on man over long times. Its dumb and very poor research even by evolution standards if i may say so.
    The symtoms are the same if one is drinking booze too much. The same mechanism.
    I think it can be healed.
    By the way all this mixing of Communist dictatorship China with the west must mean China is okay morally and politically eh!!
    Nope. Keep it home folks and it will be better anyways.
27. 27
    Mung says:

    May 24, 2015 at 11:21 pm

    Mung: If the drawing is based only on the selection coefficients as you say, then the sampling is not random

    wd400: This is simply not true, and seems to be that root of your other errors.

    I’ve made no errors.

    You, otoh, have consistently conflated the neutral theory of evolution with random genetic drift.
28. 28
    phoodoo says:

    May 24, 2015 at 11:48 pm

    Mapou at @13,

    ” This is the kind of crap one can expect from a dirt-did-it theory ducttaped together with stupidity?”

    One of the best lines I read here.
29. 29
    phoodoo says:

    May 24, 2015 at 11:51 pm

    wd400,

    How is selection a force?
30. 30
    wd400 says:

    May 25, 2015 at 12:21 am

    Is this a prelude to some first year philosophy discussion about the meaning of “force”? If so count me out. If not, it’s a force in the same sense, say, erosion is a often described as a force: it’s a process that changes the thing on which it acts.
31. 31
    Andre says:

    May 25, 2015 at 3:47 am

    Is it drift? Neutral? Selection? Nobody knows but what we do know as an absolute fact, it was not by design. Anything and nothing can do it. By design? Absolutely not!
32. 32
    logically_speaking says:

    May 25, 2015 at 5:05 am

    I have to say that the exchange between Mung and Wd400 has been excellent so far. The way Mung has schooled wd400 without wd400 even realising it seems, is an stellar example of how to debate these people.

    Wd400 tried in vain to use the “you don’t know enough and I am not going to tell you!” tactic. When that didn’t work, Mung got wd400 to say what the whole problem is in the first place, classic.
33. 33
    Zachriel says:

    May 25, 2015 at 7:16 am

    News: For one thing, Alzheimer is probably mainly noticed in humans.

    Good question. Alzheimer’s disease causes observable changes in the brain, so it can be studied in animals. See Finch & Austad, Commentary: is Alzheimer’s disease uniquely human?, Neurobiology of Aging 2015.

    Mung: How did they rule out genetic drift?

    Because the rates of change exceed those expected by the statistics of drift alone. The authors were able to estimate the influence of positive, negative and balancing selection, as well as neutrality, and over how many generations selection was acting.
34. 34
    Silver Asiatic says:

    May 25, 2015 at 10:06 am

    LS @32 Agreed. wd400 fell right into it and his illogical response @25 is a perfect example of how empty the theorizing actually is. Larry Moran did the same thing. He can’t distinguish between selection and random sampling of non-neutral alleles.
35. 35
    ppolish says:

    May 25, 2015 at 10:18 am

    “Humans get AD because they evolved to be so smart”.

    But Dogs & Cats develop AD. Convergent Evolution. Evolution is so cool.

    http://www.drsfostersmith.com/.....cleid=1346

    http://vetmedicine.about.com/o.....mentia.htm
36. 36
    wd400 says:

    May 25, 2015 at 10:28 am

    SA,

    Do you seriously think my comment in 25 is wrong? That drawing a sample from a probability distribution is not a type of random sampling?
37. 37
    wd400 says:

    May 25, 2015 at 10:41 am

    LS,

    If you think Mung had made a “telling” criticism, then can you explain that criticism on your own words? I genuinely can’t find anything coherent, let alone telling, in his/her posts.
38. 38
    Silver Asiatic says:

    May 25, 2015 at 10:41 am

    wd400

    If selection coefficients are random, then you’re right.

    Selection is random and drift is random.
39. 39
    ppolish says:

    May 25, 2015 at 10:42 am

    Probability Sample built from data of three Neanderthals. Random? What a joke this paper is. Probably peer reviewed.
40. 40
    wd400 says:

    May 25, 2015 at 10:53 am

    Can you just answer the question SA?
41. 41
    ppolish says:

    May 25, 2015 at 11:04 am

    “Computational Biologists” building models to show evolution is true. What a waste of resources. It would not be as bad if a study fraught with errors gave some benefit – but this AD study does not even stumble on to anything useful.
42. 42
    Mung says:

    June 13, 2015 at 12:08 am

    Meanwhile, back in the real world:

    The Drift Barrier
43. 43
    Mung says:

    June 13, 2015 at 12:31 am

    “It all comes down to one parameter, but the problem is there is a lot of biology in this one parameter. Mutation is in there drift is in there and selection is in there.”

    – Michael Lynch

    27:40ff

    https://www.youtube.com/watch?v=GKo–DnOPwY