Darwinism Evolution Intelligent Design

The Dangers of Bad Paradigms and the Need for Evolutionary Teleonomy

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Dan Graur is on a crusade against ENCODE – the NIH project that is showing that, at least in general, the entire genome is functional. Unfortunately, his commitment to the neo-Darwinian view of mutations is blinding him.

Graur recently published a paper in the journal Genome Biology and Evolution saying that the upper limit on the functional fraction of the human genome is 25%.

This paper represents one of the worst instances of how the Modern Synthesis (colloquially known as neo-Darwinism) can blind someone to thinking, and why the concept of Evolutionary Teleonomy is desperately needed in evolutionary biology.

Graur’s Campaign against ENCODE

Graur has been a long-time critic of encode. In fact, Graur has been on record as saying that, essentially, if ENCODE is right, evolution is wrong (his earlier paper criticizing ENCODE for being an “evolution-free gospel” can be found here). At his personal website (very bottom), Graur shows a picture of his baby granddaughter, where Graur’s own caption for the photo is “My granddaughter, Lilla Keshet Graur, gives ENCODE the finger”.

Salvador Cordova has been an active critic of Graur’s attacks on ENCODE. You can find Sal’s previous criticisms of Graur in these links: Gambler’s Epistemology, ALUs, Introns, LncRNAs, and Pseudogenes, and Non-DNA Inheritance.

In the latest round, Graur has been doubling down on his insistence that ENCODE and evolution are at odds, and that the equations of population genetics prove that the genome must be almost entirely non-functional. We reported on Graur’s findings last week based on his slideshow presentation of the idea. This week, since his paper was published, I thought I would go a little deeper into exactly where Graur goes wrong.

Before I get into the meat of the criticism, I should point out that if you agree 100% with Graur’s applications of population genetics, you could not realistically believe in evolution. You would have to agree with John Sanford’s Genetic Entropy concept – that our genomes are not evolving, but are rather in a decaying stasis. Since Graur is obviously never going to agree with that, he is forced to instead simply ignore the problem of the arrival of the fittest, and just assume that it happens. But, once it arrives, it devolves to mostly junk. That’s an interesting thought on its own, but it is not the focus of this essay.

The problem we are going to focus on, is that Graur’s analysis, though seemingly based on empirical findings, is held together by the worst of modern evolutionary thinking – an assumption masquerading as data.

The Modern Synthesis: The Paradigm That Jumped the Shark

When I was newer to the debate, I had always assumed that the concept of “random mutations” was born out by experiment. That we knew for a fact, fact, fact that mutations are mere haphazard events in the cell. I had assumed that since this was emphasized, it must have been found empirically to be true, and we were just debating whether or not it could lead to evolution in the long term.

I was then quite floored when, over the years, I discovered that the idea of random mutations was a holdover from a pre-DNA view of inheritance. It was kept merely because when we discovered DNA we hadn’t yet developed another idea, and it fit in well with the modern synthesis view of mutations (i.e., neo-Darwinism).

Graur’s paper keeps this up par excellence. In his description of the model he is using, he is assuming “that the probability of a mutation occurring in a certain region of the genome is independent of the functionality or lack of functionality of the region in which the mutation arises.” He cites Lederberg and Luria-Delbruck for this. Both of these are pre-DNA papers, and I have shown previously the problem of using these papers to justify that idea of mutation.

This is not a side-issue, in fact, it is the cornerstone of his calculations. Without this assumption, you actually cannot calculate the things he is trying to calculate. The only way that the statistics he is using are combinable is if you assume that there is no prior coordination between mutability and fitness.

As an example, when he is estimating the deleterious mutation rate of missense mutations, he uses a calculation of the total fraction of possible missense mutations and their effect on function (the paper Graur cited is here). This paper is not looking at the actual mutations that organisms undergo, but rather look at all the ways in which mutations can be induced, and seeing how many of them are deleterious.

This is fallacious, unless you accept the neo-Darwinian position that mutations are not geared towards fitness. If you don’t, then these calculations are simply non-sensical.

The Evidence for Fitness-Directed Mutations

As has been shown by others, it appears that the genome is marked in such a way as to point mutation mechanisms to the locations where mutations are helpful (see this, for instance, and this paper showing evidence of coordination of mutations between sites).

This information based on is then combined with empirical data on epistasis. The measured epistasis rate is based on actual epistasis identified among populations that have bred together. Again, this data can only be reasonably combined if the neo-Darwinian picture of mutations is true. You can’t if it is false.

There are other problems with the paper. For instance, it presumes that any mutation that doesn’t affect selectability is essentially non-functional (that is one of the reasons for my recent post on this subject).

Going Forward: Evolutionary Teleonomy as a Replacement Paradigm

So what should we do? No field of study can operate without paradigms. The question is whether the paradigms you are using are moving you forward or inhibiting your progress. Assumptions about the nature of mutations have been hindering progress in evolutionary theory for decades.

My suggestion? Move to evolutionary teleonomy as the background paradigm for evolutionary biology. It comports much better with the data, and doesn’t leave people making ridiculous assumptions about the relationship between mutation and fitness. Biological processes are inherently teleonomical on every scale. Assuming that at the level of mutation biology suddenly becomes non-teleonomic is one of the big mistakes (or even catastrophes) of modern intellectual history.

50 Replies to “The Dangers of Bad Paradigms and the Need for Evolutionary Teleonomy

  1. 1
    bill cole says:

    The base assumption here is that the mutation rate is understood. I think this is a faulty assumption because even though you can measure mutation it can be repaired later. If the mutation rate was so high as to create all this junk in our genome why would you see so many repeating sequences. Mutations should break down repeating sequences. Ironically these repeating sequences are what Graur considers junk.

  2. 2
    PaV says:

    On johnnyb’s previous post on “Biologist Dan Graur Doubles Down” I have a fuller response. (See comments #30 and 31)

    But, for the sake of brevity, look at Fig 1 in this citation. You’ll see that CR is shown to have NO function. But this is wrong.

    The original distinction between CR and SE come from Amundsen and Lauder. You’ll notice from the abstract that they attribute ‘function’ to CR. There’s an intermediate paper that distinguishes CR and SE along ‘historical’ and ‘ahistorical’ function. [You’ll find this in my post noted above]

    Doolittle and Brunet simply drop all of this. Not good science.

    The people involved with ENCODE disagree with Graur, and affirm their belief that CR elements have function

  3. 3
    Dionisio says:

    johnnyb,

    Thank you for your insightful articles and for sharing all that interesting information here.

  4. 4
    rvb8 says:

    I do believe johnnyb, is the new BA77.

    I’ve started following links here at UD, and I followed most of johnnyb’s links.

    Many are ‘self refferential’, not in th kairosfocus way, in some vaguely defined psychobabble way, but actually, ‘self referrential’.

    They refer to his articles, posts, or other articles andposts here at UD.

    Or they lead us to youtube, that satndard barer of good science, every scientist is proud to point to.

    There was one interesting link to something called researchgate. But it appears this site, although set up as an open forum, instead pesters scientists with endless e-mails to publish. In 2014 it sent out 297 invitations to 38 people. (The usual way a good science journal works is that it peruses 297 submissions, and then a board of peers, selects the 38 most original.)

    It’s ‘criticisms’ from the likes of Nature, seem to point to catchall, we’ll publish anything forum.

    And still, since the publication of the ‘Wedge’ (which I still re-read occasionally, just for a laugh), we have seen zero ‘paradigm shift’.

    Now despite all the name calling, conspiracy theories, and feelings of being locked out of the argument, I have a suggestion.

    Theorise, Experiment, write a paper, get it published and discussed, and join the debate. (Oh, and try not to use Christian legislatures, and the courts.) All of these links to youtube, UD, and dodgy science sites, harms your cause rather than bolsters it.

  5. 5

    rvb8 @ 4: johnnyb has clearly struck a nerve. I’m loving it. Keep up the excellent work, johnnyb.

  6. 6
    rvb8 says:

    TWSYF,

    perhaps, but I don’t feel angry, or upset, threatened, or intimidated by this ‘bold’ internet trolling, ‘research’.

    This is for one good reason, it’s sloppy and lazy, and involves no more scientific rigour than clicking his index finger on a mouse.

    My question to Dionisio @3, and yourself is this; how low can your ‘evidence’ based position in ID get, if you don’t undertake any, and I really mean any, research?

    It remains a fair question, and since the ‘Wedge’, an utterly unanswered observation about ID.

  7. 7

    rvb8: The following is a quote from Philosopher of biology Will Provine.

    ” … Let me summarize my views on what modern evolutionary biology tells us loud and clear — and these are basically Darwin’s views. There are no gods, no purposes, and no goal-directed forces of any kind. There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end of me. There is no ultimate foundation for ethics, no ultimate meaning in life, and no free will for humans, either. (Darwinism: Science or Naturalistic Philosophy April 30 1994) … ”

    Since you appear to be the resident expert on modern evolutionary biology, would you please educate this non-expert on a part of Provine’s statement that puzzles me. That being “modern evolutionary biology tells us loud and clear … are no gods, no purposes, and no goal-directed forces of any kind.”

    Then why is it that virtually every part and function of the human body exhibits specific goals? From the Kinesin Motors in cells, to all of the internal organs, to the body itself and its limbs that are capable of a multitude of goal directed and purposeful activities?

    I have written about this further at
    https://ayearningforpublius.wordpress.com/2015/09/03/either-modern-evolutionary-biology-is-goal-directed-or-it-is-false/ if you care to follow my thinking.

    If you care to get down and dirty into the details of bodily functions, brouse through Dr. Howard Glicksman’s series at
    https://evolutionnews.org/tag/the-designed-body/

    Cheers

  8. 8

    rvb8 @ 6: Do you remember that list of books I referred you to a short time ago? It was only a partial list, just a small sampling of all the available ID (or ID friendly) books published over the past forty years. There is an overwhelming amount of strong evidence for ID in that small sampling of books.

    Your big mistake, made by most a/mats, is thinking that we are trying to ‘prove’ ID theory. We cannot prove ID theory any more than you can prove the theory of Darwinian evolution. The best any of us can do is to analyze the evidence and draw an inference to what we think is the best explanation.

  9. 9
    awstar says:

    rvb8 at #6

    how low can your ‘evidence’ based position in ID get, if you don’t undertake any, and I really mean any, research?

    Maybe all design based research and all biology research are exactly the same thing?
    How can any scientist who knows about Okazaki fragments not believe that each of the 100 trillion cells in each of our bodies was designed?

  10. 10
    MatSpirit says:

    Don Johnson, I hope this answers some of your questions:

    Will Provine: ” … Let me summarize my views on what modern evolutionary biology tells us loud and clear — and these are basically Darwin’s views. There are no gods…”

    This is true, but evolution does not tell us that. Evolution merely tells us that we were made by natural forces, not gods. There could still be goods, they just didn’t happen to create life.

    “… no purposes, and no goal-directed forces of any kind.”

    I assume here that Dr. Provine is talking about EXTERNAL purposes and goal-directed forces such as might be supplied by a creator if we had one. There are plenty of INTERNAL purposes and goals, especially those relating to remaining alive, making a living and reproducing the next generation. This confusion over external and internal goals is the source of much bewilderment.

    “There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end of me.”

    Sad, but true. Life turns out to be purely material and when the material decays beyond recovery, you’re dead. Sadly, promising eternal life turned out to be a giant selling point for otherwise unremarkable religious notions. Best of all, from the point of view of the promiser, you don’t realize the falsity of those promises until you’re dead, at which time you can’t realize you were suckered because you’re dead.

    “There is no ultimate foundation for ethics…”

    False! As I remarked in the ‘FFT: Gender as a social construct —” thread, the fact that sane humans universally dislike things like pain, disfigurement, death etc. allows us to found an objective morality on the Golden Rule. Jesus even endorses this idea. In practice, its not used much in religion because so little of religious morality can pass that test.

    “…no ultimate meaning in life”

    Yes, as far as some creator externally imposing a meaning is concerned. You’ll have to find your own meaning, which turns out to not be too hard.

    “…and no free will for humans, either.”

    Nonsense! Dr. Provine has spent too much time listening to Jerry Coyne. Basically, free will works like this: You develop likes and dislikes, partially from your genes (such as a fear of falling) and partially through your life experiences (ice cream tastes good, road tar tastes bad).

    When you have a choice, such as, “Should I eat this scoop of ice cream or this scoop of road tar?”, you weight the options, figure out which is more likely to lead to pleasing consequences and do it.

    Presto! You have Free Will! You had more than one possible action and you chose the one most compatible with your desires. And its all done with our material brain.

  11. 11
    Florabama says:

    “At his personal website (very bottom), Graur shows a picture of his baby granddaughter, where Graur’s own caption for the photo is “My granddaughter, Lilla Keshet Graur, gives ENCODE the finger”

    This repulsive level of animosity, where a man would involve his grandchild in vulgarity, is revealing to me although nothing new from that side of the debate, except that it does seem to me, as I’ve gotten more and more into the debate with a/mat/progs, I’ve found that as the science has made their position less and less tenable, the vitriol and dishonesty has increased in inverse proportions from their side. The desperation is palpable. This is personal for Graur because he rightly sees it as an all or nothing threat to his religious worldview. His creation myth is threaten to the point that he admits that he would have to acknowledge a Designer. If the genome is functional as Encode has said, then his worldview is shattered, so much so that it isn’t enough to argue about the science. He must get in the gutter and be vulgar. It is increasingly clear that that is all that is left to them. While it is difficult to deal with this level of guttural hatred, it should be very encouraging to those of us who do not, “suppress the truth by their unrighteousness,” (Rom 1:18) because suppressing the truth is all that is left to them.

  12. 12
    groovamos says:

    RVB This is for one good reason, it’s sloppy and lazy, and involves no more scientific rigour than clicking his index finger on a mouse.

    RVB has the rigor huh?. Now what type of rigorous scientific training has benefited RVB has never been apparent on here. Maybe it’s some kind of “brain science” hee hee. RVB claims mental illness is the result of some ill-defined electro-chemical or maybe even mechanical defects in the brains of sufferers. Was there a presentation by RVB of any rigorous basis for his assertion? Of course not.

    Also RVB seems not interested in discussion of the philosophical implications of suffering. Funny thing about that because there is plenty of philosophically based discussion in the consciousness research field to which RVB has been pointed by yours truly, with apparent zero interest resulting on his part.

    Yes and plenty of scientific rigor in the vast consciousness research community which is composed of psychiatrists, physiologists, anthropologists and other academics.

    RVB is fearful of rigor. You can’t base a life philosophy on rigor but you can base it on fear.

  13. 13
    Marfin says:

    Matspirit- Who exactly is the you who makes decisions is it not the chemicals in your brain which is having this ice cream flavour fight, or do you believe there is something more than these chemicals influencing the decision.
    And as for Morals and ethics , surely every deed, want, desire, action is just a product of mindless evolution so why is one deed more or less moral than the next.

  14. 14
    gpuccio says:

    MatSpirit:

    “Presto! You have Free Will! You had more than one possible action and you chose the one most compatible with your desires. And its all done with our material brain.”

    This is really strange. More than one possible action? Why?

    Please, explain. If the brain is a deterministic machine, you have only one possible action.

    Please, clarify. What are you, a compatibilist? (and if you imagined a shade of disdain in my quoting that word, well, you were right! 🙂 )

  15. 15
    gpuccio says:

    MatSpirit:

    Life turns out to be purely material and when the material decays beyond recovery, you’re dead. Sadly, promising eternal life turned out to be a giant selling point for otherwise unremarkable religious notions. Best of all, from the point of view of the promiser, you don’t realize the falsity of those promises until you’re dead, at which time you can’t realize you were suckered because you’re dead.

    On the other hand, but always sadly, promising no eternal life turned out to be a giant selling point for otherwise unremarkable anti-religious notions.

    Best of all, from the point of view of the promiser, you don’t realize the falsity of those promises until you’re dead, at which time you will be torn between the realization that you were suckered and a pleasurable amazement because you are still alive.

  16. 16
    MatSpirit says:

    gpuccio: “This is really strange. More than one possible action? Why?”

    What a curious question. Because you’ve somehow managed to have an ice cream cone in one hand and a gob of road tar in the other and you’re feeling peckish. As a non-deterministic being, how do you decide which one to eat? Flip a coin?

    gpuccio: “Please, explain. If the brain is a deterministic machine, you have only one possible action.”

    A microcomputer is a deterministic thing. It has more than one action. For instance, a PacMan machine does not play the same game every time. It reacts with the outside world and changes its internal operation accordingly. So do we.

    It might help understanding if you think that “non-deterministic” means “broken”.

    gpuccio: “What are you, a compatibilist?”

    Certainly. What are you? Noise? A random number generator? Are your thoughts controlled by some outside intelligence? Your typing doesnt look random to me. What is deciding the order of your typing? I’ll bet it’s your brain, using its knowledge of English.

    Good luck in the Happy Hunting Ground. If there’s anything you really want to do, do it while you’re alive.

  17. 17
    EricMH says:

    MatSpirit, why do you think determinism and randomness are the only possibilities?

    Also, if we are determined beings, how do we know our thoughts are determined by truth and not by falsity? For example, I can make a computer believe 1 = 2, and the computer has no way of knowing its belief is wrong.

  18. 18
    Seversky says:

    With reference to the OP, I see that Larry Moran has a timely post on the subject although he has covered this a number of times before. I thought his “Five Things You Should Know if You Want to Participate in the Junk DNA Debate” is a handy summary of the key points:

    Genetic Load
    Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.

    C-Value Paradox
    A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.

    Modern Evolutionary Theory
    Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome.

    Pseudogenes and broken genes are junk
    More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk.

    Most of the genome is not conserved
    Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can’t rule out some unknown function that doesn’t depend on sequence.

  19. 19
    rvb8 says:

    groovamos @12,

    thanks for the capitalization of my moniker RVB, you forgot the all important ‘8’, heh:) Much appreciated.

    I don’t ‘claim’ an ‘ill-defined’ elctro-chemical relationship between mental illness and the brain. Science does.

    Science also claims the natural balance of a healthy person’s ‘electro-chemical’ brain function can be impaired, without recourse to a soul, mind, God,spirit, or indeed the devil, or any other unmeasurable cause.

    Try this experiment; go to bar, drink an inordinate ammount of ethanol. See how your, ‘soul’, ‘mind’, ‘faith’, and all the other stuff you say is beyond ‘materialism’, are effected.

    Then come back and explain how God, could sober you up with the flick of afinger; I will say, not faith, or God, but time, sleep, and maybe coffee, can only help to restore the ‘electo-chemical’ balance; plus an almighty hangover.:)

  20. 20
    rvb8 says:

    Sev @18,

    ‘100 mutations not found in either parent.’

    That is indeed a spectacular piece of evidence pointing to non-functionality in the genetic code.

  21. 21
    gpuccio says:

    MatSpirit:

    It seems that you are not aware that a lot of thinking people believe in libertarian free will.

    That means very simply that you have more than one option, and that you can choose according to some intrinsic process of your consciousness, not at all deterministic, and that has nothing to do with “reacting with the outside world and changing our internal operation”.

    A very simple reflection could show you that is the only way to change your “options” is that you “react with the outside world and change your internal operation”, then there are no options at all, and it’s simply “the outside world” which is part of your deterministic processes.

    Random components, of course, do not change at all the simple fact that “you” (whatever you are) have no options at all.

    Ah, but what am I doing, trying to explain that to a compatibilist? I must have lost my mind.

    ” If there’s anything you really want to do, do it while you’re alive.”

    Thank you for the kind advice, but that’s exactly what I try to do. It’s the only way to be at ease in the Happy Hunting Ground. 🙂

  22. 22
    gpuccio says:

    rvb8:

    “That is indeed a spectacular piece of evidence pointing to non-functionality in the genetic code.”

    Why? We know a lot of mutations in protein coding genes that are perfectly tolerated, some of them as common polymorphisms. Does that mean that protein coding genes are junk?

    Tolerance to change does not mean lack of function. Not at all.

  23. 23
    butifnot says:

    Five things you should know if you want to participate in the junk dna debate…
    bla
    bla
    bla…

    Moran makes the bad paradigm case spectacularly!

  24. 24
    Mung says:

    rvb8:

    I do believe johnnyb, is the new BA77.

    Whatever floats your boat. I can’t recall ba77 ever posting an OP both here at UD and at TSZ.

    But Don’t Stop Believing!

    Even trolls believe in something.

  25. 25
    rvb8 says:

    Mung,

    my linking of johnnyb, and BA77, was their similar belief in what constitutes research.

    You remember BA’s posts? Endless links to creationist websites, uncommondescent, evoltionnews, and youtube, to name just afew of the more egregious non-research sites.

    johnnyb has an almost identical propensity to be completely oblivious to the concept of, ‘primary research!’

  26. 26
    Dionisio says:

    Florabama @11:

    I see your point.

    I have a 5-month grandson and a 2-week granddaughter and I relate to your sharp observation.

    Thanks.

  27. 27
    Marfin says:

    Matspirit- You keep using the word you in connection with the decision making process ,can you please explain how that works , what is this you, and how does it exert its influence in decision making.

  28. 28
    wd400 says:

    and this paper showing evidence of coordination of mutations between sites

    These are somatic mutations, and so irrelevant to the question Graur is asking and your claim that mutations are not random with respect to fitness.

  29. 29
    rvb8 says:

    Marfin,

    ‘you’ is the sum total of the experiences ‘you’ have during ‘your’ life as stored chemically/electrically in ‘your’ brain.

    When the memories stored in ‘your’ brain cease, by the sudden loss of function in ‘your’ chemically/electrically driven brain, ‘you’ cease to be. A/mats call it death, I have no idea what creationists call it; ‘rebirth?’

    But who knows Marfin, perhaps your spirit and mind, will achieve oneness in a divine nervana like state of being with God, in the endless bliss of eternity, that is your childish wishful dream.

    Good luck with that. Feel free to come back and haunt me.

  30. 30
    Marfin says:

    RVB8- you, your, your brain , please explain as the way you are saying it here almost seems like there is a you and there is your brain, surely as an atheist you must accept there is no you there is only the chemicals in your brain and its them that are the you.Its the chemicals in your brain, that are the sum total of your experiences and there is no you so when Matspirit speaks of you and decision making all I want to know is how this process works as there is only chemicals and no you controlling them.
    So in real terms some chemicals in my brain are telling me to punch my boss in the face, cheat on my wife , cheat on my taxes,steal, lie,get what I can at the expense of others, and another set of chemicals seem to be telling me to do the opposite , so are there good and evil chemicals, well thats the only conclusion my chemicals can draw from this, seeing as chemicals is all there is.

  31. 31
    gpuccio says:

    wd400 at #28:

    and this paper showing evidence of coordination of mutations between sites

    Why? It’s the darwinists, after all, who have often stated (incorrectly, of course) that somatic htpermutation in antibody maturation is a good model for neo-darwinian evolution! 🙂

    OK, I agree it is not. But it shows that partially guided mutation can occur in a biological process.

    The real model for what could be behind functional information is rather hinted at in the first paper, the one you smartly did not mention in your comment:

    Transposable elements as activators of cryptic genes in E. coli.

    I have suggested many times that transposons are a perfect tool for intelligent design. Their apparently random insertions and activities can well be, in some cases at least, directed to generate useful information.

    Anyway, if ID theory is true (and it is, believe me! 🙂 ), then some model of guided mutation is true, too.

    The simple truth is that the assumption that all mutations are random in respect to fitness is purely ideological, and it’s the same as accepting a priori the neo-darwinian paradigm as absolute truth, without any support from observed facts (which is, after all, what the vast majority of scientists has done in the last decades).

  32. 32
    gpuccio says:

    rvb8:

    “When the memories stored in ‘your’ brain cease, by the sudden loss of function in ‘your’ chemically/electrically driven brain, ‘you’ cease to be.”

    This is funny. OK, but please explain, when did that “you” start to be? And how, and why?

    You say:

    “‘you’ is the sum total of the experiences ‘you’ have during ‘your’ life as stored chemically/electrically in ‘your’ brain.”

    OK, but why shoud “you” have experiences at all? Why should the chemical and electrical activities in your brain become “experiences”?

    You see, the concept of “experiences” implies subjective perceptions. And nobody can explain how subjective perceptions and representation may arise from purely objective events.

    In case you don’t know, this is exactly what David Chalmers calls “the hard problem of consciousness”. It’s a very big and controversial issue in the whole human thought of the last decades, and yet you seem to bypass it happily in a couple of sentences!

    Of course, you have certainly undertaken a lot, and I really mean a lot, of research about that issue, before making your easy statements! (in case you don’t understand, that was ironic 🙂 ).

    “But who knows Marfin, perhaps your spirit and mind, will achieve oneness in a divine nervana like state of being with God, in the endless bliss of eternity, that is your childish wishful dream.”

    Take care! It could happen to you. 🙂

  33. 33
    Marfin says:

    gpuccio- I would be happy enough to spend eternity with the creator and maker of all in a place he made for us , and sharing any of his glory he chooses to share with me.

  34. 34

    MatSpirit:
    Thanks for your response.

    That evolution is not ‘goal directed’ seems to be a major plank in the Darwinian world view, supported by another major plank, that of ‘Deep Time.’ I believe it was Dawkins that said ‘given enough time and enough chances, anything is possible.’

    But I ask again — why does this mindless, non goal directed process of evolution result in the consistent construction of something having close to 100% purposeful, goal directed functionality?

  35. 35
  36. 36
    gpuccio says:

    Dionisio:

    Definitely!

    Nothing makes sense in biology except in the light of guided transposon activity! 🙂

  37. 37
    Dionisio says:

    Marfin @33:

    Amen! By grace alone through saving faith in Christ alone.

    BTW, the term ‘spend’ seems inappropriate in conjunction with the concept of eternity, doesn’t it?
    However, that’s how it’s been expressed through years.
    We lack vocabulary to express things accurately.

  38. 38
    Dionisio says:

    gpuccio @36:

    “Nothing makes sense in biology except in the light of guided transposon activity!”

    Well, maybe that’s because we don’t understand evolution?

    🙂

  39. 39
    wd400 says:

    The simple truth is that the assumption that all mutations are random in respect to fitness is purely ideological,

    I look forward to any experimental evidence that this is the case.

  40. 40
    Dionisio says:

    wd400 @39:

    Here’s an exquisitely prepared antipasto, to activate your palate:

    https://uncommondescent.com/intelligent-design/interesting-proteins-dna-binding-proteins-satb1-and-satb2/

    The main meal could come later.

    Actually, perhaps you’ll be served by the chef himself! Oh, la la!

    Bon appétit!

    🙂

    PS. you’ll be served very classic dishes from the best cuisine.

  41. 41
  42. 42
    johnnyb says:

    wd400 – in the links above is a paper of mine which shows why the classic papers about this (which Graur himself cited) do not lead to this conclusion. Making an assumption of the nature of the distribution based on a paradigm instead of evidence is the definition of ideological. If you can find experimental confirmation of the neo-Darwinian view post it here. Evidence to the contrary is presented in the Evolutionary Teleonomy video linked in the OP. If you look back through my author page you will find plenty more. Of particular interest is my criticism of Merlin’s paper on the subject.

  43. 43
    groovamos says:

    RVB: I don’t ‘claim’ an ‘ill-defined’ elctro-chemical relationship between mental illness and the brain. Science does.

    Completely bogus. As argument because that is not what RVB claimed. He claimed a CAUSAL NEXUS between some non-proven organic brain disease(s) and all mental illness, with an absolute absence of any rigor-based scientific support for his assertion.

    And in fact I can offer a rigor-based refutation right here, as I have always done with RVB’s faith-based assertions before when it comes to mental health. It is very simple. There is no scientific consensus on what any of those common organic brain diseases are. I say “common” because mental illness is quite common, and so those common organic brain diseases should be cured by science by now in widespread fashion. It would be laughable but for the tragedy of mental illness, that mainstream science has wasted untold trillions of dollars for the effort, and to this day materialistic science has contributed NOTHING to the world in the area of mental health. NOTHING.

    And what is laughable is the refusal by RVB to even acknowledge the vast scientific literature on consciousness research. Not once has this field been mentioned by RVB, a field that has documented a plethora of cases of mental illness transformed into forward evolutionary change.

    RVB: Science also claims the natural balance of a healthy person’s ‘electro-chemical’ brain function can be impaired, without recourse to a soul, mind, God,spirit, or indeed the devil, or any other unmeasurable cause.

    This is pathetic. This is supposed to be “science” from RVB, and rigor too? Intoxication?

    Why would say intoxication be better empirical science than say video of a firing squad putting a bullet through the brain and cessation of brain function? Because it’s equivalent “rigor” to the “rigor” from RVB. Yeah right, a bullet to the brain proves a causal nexus between the brain and mental illness.

  44. 44
    wd400 says:

    wd400 – in the links above is a paper of mine which shows why the classic papers about this (which Graur himself cited) do not lead to this conclusion. Making an assumption of the nature of the distribution based on a paradigm instead of evidence is the definition of ideological.

    If you are referring to teh Creation Research paper then I’m afraid there is no argument there. Just a longer version of the typical falsification-avoiding “what ifs” you often see in online comments about creationism.

  45. 45
    johnnyb says:

    wd400 –

    Let me make it more explicit. The only thing that the Lederberg and Luria-Delbruck experiment show is that, for a certain subset of mutations, that they occur independently of selection. That’s it. This is the set of experiments that Graur cited to justify that mutations are random. Please explain how the fact that a subset of mutations act independently of selection (or even if it were all) would lead to a conclusion that mutations are random with respect to fitness. The logic simply doesn’t follow.

  46. 46
    wd400 says:

    Your post above is a little imprecise (what subset of mutations, in what way are they acting?). But the L-D and Lederberg experiments show that mutations arise independent of selection, which is to say their fitness consequences (selection being what happens when alleles have different fitnesses).

  47. 47
    wd400 says:

    I should add, Graur’s assumption is probably wrong. The mutation rate in functional regions is likely to be slightly higher than the rate in non-functional regions. Just because transcribed and decondensed DNA is more likely to mutate. But the effect is small compared than the range of mutation rates he used, so it shouldn’t make a substantial difference to the estimate.

  48. 48
    PaV says:

    In #2, I demonstrate that Graur’s argument is defective. He dismisses Causal Role (CR) function out of hand following Doolittle and Brunet. This is an error. Doolittle and Brunet themselves are following the work of Amundsen and Lauder, who are philosophers of biology, and who do not deny CR as having function.

    In D and L’s Figure 1, they show NO function for CR. But this is a misrepresentation of the distinction philosophers of biology like Admundsen and Lauder have made between SE and CR: for them both are assumed to represent function (follow the link in #2). The only difference is that SE’s function is ‘historical’: that is, it can be ‘traced.’ CR is “ahistorical”: it cannot be traced. Yet the function exists nonetheless.

    What Graur inadvertantly proves is the neo-Darwinism can’t explain evolution (macroevolution). That’s the whole point of genetic load arguments, and why Kimura changed from a neo-Darwinian view to his Neutral Theory of Molecular Evolution.

    Graur’s argument–perhaps unconsciously–ends up as being no more than “sleight of hand” argumentation.

  49. 49
    PaV says:

    Here’s the summary of ENCODE 2012:

    Operationally, we define a functional element as a discrete genome segment that encodes a defined product (e.g., protein or non-coding RNA) or displays a reproducible biochemical signature (e.g., protein-binding, or a specific chromatin structure). Comparative genomic studies suggest that 3–8% of bases are under purifying (negative) selection 4–8 and therefore may be functional, although other analyses have suggested much higher estimates 9–11. In a pilot phase covering 1% of the genome, the ENCODE project annotated 60% of mammalian evolutionarily constrained bases, but also identified many additional putative functional elements without evidence of constraint2. The advent of more powerful DNA sequencing technologies now enables whole genome and more precise analyses with a broad repertoire of functional assays.

    Here, we describe production and initial analysis of 1,640 datasets designed to annotate functional elements in the entire human genome. We integrate results from diverse experiments within cell types, related experiments involving 147 different cell types, and all ENCODE data with other resources, such as candidate regions from genome-wide association studies (GWAS) and evolutionarily constrained regions. Together, these efforts reveal important features about the organization and function of the human genome, including:

    1. The vast majority (80.4%) of the human genome participates in at least one biochemical RNA and/or chromatin associated event in at least one cell type. Much of the genome lies close to a regulatory event: 95% of the genome lies within 8kb of a DNA-protein interaction (as assayed by bound ChIP-seq motifs or DNaseI footprints), and 99% is within 1.7kb of at least one of the biochemical events measured by ENCODE.

    2. Primate-specific elements as well as elements without detectable mammalian constraint show, in aggregate, evidence of negative selection; thus some of them are expected to be functional.

    3. Classifying the genome into seven chromatin states suggests an initial set of 399,124 regions with enhancer-like features and 70,292 regions with promoter-like features, as well hundreds of thousands of quiescent regions. High-resolution analyses further subdivide the genome into thousands of narrow states with distinct functional properties.

    4. It is possible to quantitatively correlate RNA sequence production and processing with both chromatin marks and transcription factor (TF) binding at promoters, indicating that promoter functionality can explain the majority of RNA expression variation.

    5. Many non-coding variants in individual genome sequences lie in ENCODE-annotated functional regions; this number is at least as large as those that lie in protein coding genes.

    6. SNPs associated with disease by GWAS are enriched within non-coding functional elements, with a majority residing in or near ENCODE-defined regions that are outside of protein coding genes. In many cases, the disease phenotypes can be associated with a specific cell type or TF.

  50. 50
    J-Mac says:

    “Before I get into the meat of the criticism, I should point out that if you agree 100% with Graur’s applications of population genetics, you could not realistically believe in evolution.

    Can you elaborate?

    Thanks.

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