Genetics Natural selection News

So now it’s the “creationists’” fault that Darwin’s followers can’t face facts?

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retirement planning for Darwin’s followers

Further to science ideas ready for retirement, Philip Cunningham draws attention to a curious admission on the part of Wired’s Kevin Kelly: His idea to retire is “fully random mutations:”

So to be clear: the evidence shows that chance plays a primary role in mutations, and there would be no natural selection without chance. But it is not random chance. It is loaded chance, with multiple constraints, multi-point biases, numerous clustering effects, and skewed distributions.

He considers the question of why the assumption of “random mutation” persists and notes that it was “a philosophical necessity to combat the erroneous earlier idea of inherited acquired traits, or what is commonly called Lamarckian evolution.” Today, we call it horizontal gene transfer, and many researchers would be surprised to hear it considered an erroneous idea.

As a rough first-order approximation, random mutation works pretty well as an intellectual and experimental framework. But the lack of direct evidence for actual random mutations has now reached a stage where the idea needs to be retired.

There are several related reasons why this unsubstantiated idea continues to be repeated without evidence. The first is fear that non-random mutations would be misunderstood and twisted by creationists to wrongly deny the reality and importance of evolution by natural selection. The second is that if mutations are not random and have some pattern, than that pattern creates a micro-direction in evolution. And since biological evolution is nothing but micro actions accumulating into macro actions, these micro-patterns leave open the possibility of macro directions in evolution. That raises all kinds of red flags. If there are evolutionary macro-directions, where do they originate? And what are the directions? To date, there is little consensus about evidence for macro-directions in evolution beyond an increase in complexity, but the very notion of evolution with any direction is so contrary to current dogma in modern evolution theory that it continues to embrace the assumption of randomness.

This is a beaut, a keeper, a classic. In short, biologists must be wrong in thinking that there is no direction to evolution but admitting that is too controversial? So they have to keep it quiet by misrepresenting to the rest of us what “random evolution” means? Or if Kelly doesn’t mean that, what does he mean?

I guess that is as much intellectual openness or curiosity as one could expect from Darwin’s latter day followers. In fairness, they probably don’t even understand people whose standards for both qualities are just plain higher.

And it’s not just some of the ideas that need to retire.

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46 Replies to “So now it’s the “creationists’” fault that Darwin’s followers can’t face facts?

  1. 1
    lifepsy says:

    There are several related reasons why this unsubstantiated idea continues to be repeated without evidence. The first is fear that non-random mutations would be misunderstood and twisted by creationists to wrongly deny the reality and importance of evolution by natural selection.

    Translation: We are intentionally obscuring and misrepresenting scientific data in order to deny any comfort to our political enemies.

  2. 2
    Mapou says:

    This was always the main reason behind Darwinian evolution: a hatred of Christianity, especially Christian fundamentalists. Science is always subservient to the political and ideological goals of atheists/materialists/Darwinists. But then again, the same can be said for some Christian fundamentalists. In the process, scientific progress takes a dive. Telling it like I see it, as always.

  3. 3
    Joe says:

    The “importance” of natural selection is contrived. Yes differential reproduction due to heritable happenstance variation, ie natural selection, exists, it’s just that it has never been observed doing anything beyond that-> differential reproduction due to heritable happenstance variation. I don’t see the importance to that and no one has been able to demonstrate any importance.

    Also Dr Spetner has already proposed a “non-random evolutionary hypothesis” in “Not By Chance”- a book that should be required reading for anyone involved in this debate.

  4. 4
    drc466 says:

    Q: Why do evolutionists

    fear that non-random mutations would be misunderstood and twisted by creationists to wrongly deny the reality and importance of evolution by natural selection.

    ?? As evolutionary scientists, shouldn’t what creationists think be irrelevant? Who could fear such a harmless, crackpot crew?

    A: They don’t fear creationists, they fear “fellow” evolutionists. Any scientific fact or theory* that provides support for the creationist viewpoint is used as a Hammer, not by creationists, but by rabid gatekeepers of evolution (think Myers, Coyne) to beat the scientist revealing that fact/proposing that theory either a) into submission or b) out of a job.

    This admission is another excellent indictment of how the evolutionary establishment works to stifle open and free inquiry, and thus, scientific advancement itself.
    *Tuning of the universe. Dino DNA. Fossil record stasis. Functionality of the entire DNA. Epigenetics. ID Theory. Et cetera ad nauseam.

  5. 5
    Mapou says:

    drc466 @4,

    Excellent point.

  6. 6
    bornagain77 says:

    Random Mutations? We ain’t got no Random Mutations. We don’t need no Random Mutations. I don’t have to show you any stinking Random Mutations! 🙂

    We don’t need no stinking badges! – video
    https://www.youtube.com/watch?v=VqomZQMZQCQ

    That’s right folks, Darwinists don’t need no stinking Random Mutations;

    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

    And Darwinists also don’t need no stinking Natural Selection:

    “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.”
    Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79
    http://www.uncommondescent.com/evolution/16037/

    And Darwinists also don’t need no stinking Mathematical foundation:

    Active Information in Metabiology – Winston Ewert, William A. Dembski, Robert J. Marks II – 2013
    Except page 9: (Gregory) Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work.
    http://bio-complexity.org/ojs/.....O-C.2013.4

    Shoot, Darwinists don’t need no stinking empirical evidence whatsoever:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    Excerpt of conclusion pg. 42: “To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.”
    http://www.ncbi.nlm.nih.gov/pm.....MC2662469/

    That’s right folks, Darwinists don’t need any stinking thing at all to declare that their theory is beyond reproach from any finding whatsoever and that you are an IDiot for not believing them.

    Talking Evolution With Evolutionists – Cornelius Hunter – December 2011
    Excerpt: “Like the cultist I spoke with, evolutionists are certain even though the facts do not support such certainty.,,,” “You can present the facts, you can walk through the logic, you can review the experiments, and you can tally up the findings. It doesn’t matter. It never did matter because, ultimately, evolution never was about the science.”
    http://darwins-god.blogspot.co.....nists.html

    Verse and Music:

    2 Peter 1:16
    For we have not followed cunningly devised fables, when we made known unto you the power and coming of our Lord Jesus Christ, but were eyewitnesses of his majesty.

    Evanescence – Lies Lyrics
    https://www.youtube.com/watch?v=1xx36Bfg4gE

  7. 7
    sixthbook says:

    “To date, there is little consensus about evidence for macro-directions in evolution beyond an increase in complexity”

    I can’t count the number of evolutionist who when I debate them would say that evolution is not goal oriented so the mutations aren’t trying to increase complexity in the organism. They say evolution is random, not increasing complexity at all.

    Apparently the article in the OP disagrees.

  8. 8
    wd400 says:

    Why do evolutionists “fear that non-random mutations would be misunderstood and twisted by creationists”.

    I can’t speak for “evolutionists”, but evolutionary biologits don’t. Kelly doesn’t come off as someone who knows what he is talking about here – the fact there are non-random patterns in mutations (including spatial, directional and temporal patterns) has long been known. The randomness of mutation refers to the fact mutations are random with respect to their fitness (ie, animals can’t induce particular mutations that are likely to benifit their offspring).

    This is the sort of thing you’d hope an undergrad could see through, why Edge thought it was worth including I can’t imagine.

  9. 9
    gpuccio says:

    I have rarely read such a confused and misleading piece of thought. I think that both IDists and neo darwinists can equally be irritated by it, and that is really something!

    Just as a curiosity, why should a skewed distribution be non random? Is the author convinced (like many) that only a uniform distribution, or maybe a normal distribution, can be considered a random distribution? Maybe just reading on wikipedia the list of probability distributions could help…

  10. 10
    gpuccio says:

    wd400:

    Kelly doesn’t come off as someone who knows what he is talking about here – the fact there are non-random patterns in mutations (including spatial, directional and temporal patterns) has long been known. The randomness of mutation refers to the fact mutations are random with respect to their fitness (ie, animals can’t induce particular mutations that are likely to benifit their offspring).

    For once, I perfectly agree with you.

    I would add that any genomic variation due to some physical process, and particularly to biochemical laws, is necessarily random with respect to the functional information implied, for example, by a functional protein sequence, for the simple fact that physical laws and biochemical laws that generate variation in the genome have no way of knowing what kind of sequence will generate protein functionality.

    Unless, obviously, the variation is designed.

  11. 11
    Joe says:

    gpuccio-

    Ernst Mayr basically says the same thing in “What Evolution Is”- ie that natural selection is non-random because what lives and what is eliminated is not form a uniform distribution:

    Not all individuals have an equal probability for survival because the individuals that have properties making their survival more probable are a restricted non-random component of the population.-page 118 WEI

    Darwin’s alleged designer mimic is nothing but a mirage.

  12. 12
    Joe says:

    wd400:

    The randomness of mutation refers to the fact mutations are random with respect to their fitness (ie, animals can’t induce particular mutations that are likely to benifit their offspring).

    That is incorrect. The randomness refers to their happenstance/ accidental nature-

    The first step in selection, the production of genetic variation, is almost exclusively a chance phenomenon except that the nature of the changes at a given locus is strongly constrained. Chance plays an important role even at the second step, the process of elimination of the less fit individuals. Chance may be particularly important in the haphazard survival during periods of mass extinction.- Mayr WEI page 281

  13. 13
    News says:

    wd400 and gpuccio at 8 through 10: Kelly writes at Wired and he was writing FOR The Edge. One senses that he knows how Darwinians think (and generally agrees with them, and seems to think they agree with him on this).

    It’s not clear he would be heard from in either venue if it were all as doubtful as you are representing here.

  14. 14
    bornagain77 says:

    as to wd400 trying to defect attention away from the happenstance/accidental (unguided) nature of the word random, especially as it is used in neo-Darwinian evolution. The unguided, happenstance, definition of the word random is a core theoretical mandate in the naturalist’s worldview

    “Random: A Carefully Selected Word” Dr. Michael Behe – video
    https://www.youtube.com/watch?v=x-MuGUVWeFs

    Unguided or Not? How Do Darwinian Evolutionists Define Their Theory? – Casey Luskin – August 11, 2012
    Excerpt: While many new atheists undoubtedly make poor philosophers, the “unguided” nature of Darwinian evolution is not a mere metaphysical “add on.” Rather, it’s a core part of how the theory of Darwinian evolution has been defined by its leading proponents. Unfortunately, even some eminent theistic and intelligent design-friendly philosophers appear unaware of the history and scientific development of neo-Darwinian theory.
    http://www.evolutionnews.org/2.....63191.html

  15. 15
    lifepsy says:

    wd400,

    The randomness of mutation refers to the fact mutations are random with respect to their fitness (ie, animals can’t induce particular mutations that are likely to benifit their offspring).

    This is really a strange definition. According to this, a mutation that only ever occurs in the same exact loci over millions of years would still technically be “random” because the mutation is not induced for fitness. I’m pretty sure I have never heard any evolutionist define the randomness of mutation this way.

  16. 16
    Querius says:

    In my opinion, the term “random mutation” is acceptable in the sense that it suggests that there’s no intelligent planning or implicit direction. The term is misleading in the sense that the sources/types of mutations make a difference–that not all mutations are equally likely.

    -Q

  17. 17
    bornagain77 says:

    The word ‘Random’ as it is used by Darwinists, as Dr. Behe clearly illustrated in the video I previously listed, is clearly meant by leading Darwinists to convey the sense that the ‘random’ event that occurred was unplanned and unguided. Especially in regards to God having planned or guided the event. Yet, if we look at the source for ‘randomness’ in this universe, we find that a random event means that a entropic event has occurred (i.e. such the decay of an unstable particle) in this universe. And though the entropic event is in itself not predictable by us in a specific, precise, sense, what gives the Darwinists the idea that the event was unguided or unplanned by God? In my humble opinion the Darwinists has no right whatsoever to claim that the random, seemingly chaotic, entropic events that happen in this universe are unguided and unplanned. The reason I have for this is two fold. One reason is that the initial entropy of the universe is found to be fine-tuned on the order of 1 in 10^10^123. The fine-tuning of that initial condition for entropy absolutely blows away all the other initial conditions of the universe in terms of precision. The number, if written out in ordinary notation, could not be written out even if a number were written on every sub-atomic particle in the universe. That by itself should give Darwinists severe pause with the claim that the ‘random’ entropic events of the universe are unplanned and unguided. But the second reason why I don’t think Darwinists have a leg to stand on when they claim that the random, entropic, events of the universe are unplanned and unguided is that it is now found, by advances in quantum mechanics, that the space-time of this universe is not a ‘closed system’ of cause and effect, as materialists have always assumed, but that every particle and photon of the universe is dependent upon a non-local, beyond space and time, cause in order to explain each particle and photon’s continued existence in this universe. i.e. God upholds the universe in its being!

    Hebrews 1:3
    sustaining all things by his powerful word.

    Thus scientifically, Darwinists have no right to claim that the random, entropic, events of the universe are unplanned or unguided. Scientifically, there is simply no reasonable room for debate on the matter. But Where this gets into Theological issues, not scientific issues, is when we look at what type of events are associated when entropy. Death, Disease, Cancer, Earthquakes, Tornadoes, etc.. etc.., are all traceable to entropic events at their base. But so are good things traceable to an entropic base, such as Gravity and the passage of time itself. Thus, Theologically, not scientifically, it is very easy to say that these bad things were unintended by God. In fact, I hold that it is very hard for mere humans mortals to understand why God would allow suffering in this lifetime. But that is a purely theological matter and is not a matter for science. As I said before, as far as the science itself is concerned, Darwinists have no reasonable right to contend that the random, entropic, events of the universe are unintended.

    Verse and poem

    Romans 8:18-25
    I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. For the creation waits in eager expectation for the children of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the freedom and glory of the children of God.
    We know that the whole creation has been groaning as in the pains of childbirth right up to the present time. Not only so, but we ourselves, who have the first fruits of the Spirit, groan inwardly as we wait eagerly for our adoption to sonship, the redemption of our bodies. For in this hope we were saved. But hope that is seen is no hope at all. Who hopes for what they already have? But if we hope for what we do not yet have, we wait for it patiently.

    Autumn Leafs Laughter
    Oh please do tell us of your secret
    you majestic autumn leaves,of regal red ,and shimmering golden yellow,
    Brilliantly coloring the landscapes of trees.
    Do you dare pass away in a rush of beauty while you are slowly dying?
    Pay ye no heed to all the other deaths so solemnly attended with tears and crying?
    or Does the essence in you somehow yearn jealously for a glorious life to come?
    And you somehow know that death shouldn’t be sad but fun?
    For I truly wish I could die like you and that I knew the secret of your story, so that my countenance should light up and glow as my soul is delivered to behold God,s glory.
    So please autumn leaves which mock death with such defiant belly laughter,
    Do tell us your secret over death so that we may properly enter the hereafter.

  18. 18
  19. 19
    gpuccio says:

    lifepsy and others:

    I think I should make more clear what I think:

    1) A random system is one whose behaviour is best described by a probability distribution. All known random systems, with the probable exception of quantum randomness (intrinsic randomness), are indeed deterministic systems, in the sense that their behaviour is in principle caused by necessity laws. But their peculiar nature makes it practically impossible, for us, to understand that behaviour in detail by an algorithmic computation, because too many variables are implied, or for intrinsic features of how the system evolves (chaotic systems). Therefore, the best way we have to describe and cognize those systems is by some probability distribution (a mathemathical object that assigns probabilities to the possible events).

    2) So, the random nature of a system is more a feature of how we cognize it scientifically that a fundamental property of the system itself. Again, quantum events are a probable and important exception to that.

    3) That said, the fact remains that many natural system are best explained by probability distributions that are not the uniform distribution or other symmetric distributions, like the normal distribution. In no way that means that those are not random systems. That’s why a skewed distribution is random just the same. That’s why Kelly does not know what he is talking about. Just to make an example, if we record the results of throwing a die with 1 on five sides and 2 on the sixth side. 1 here has 5/6 probability as a discrete event, and 2 has 1/6 probability. The probability distribution that best describes the form of the outcome is skewed and completely non symmetrical, but the system is still a random system. Nobody can tell in advance if a single outcome will be a 1 or a 2, but the results conform to a general form which is best described by a simple discrete probability distribution.

    3) In this sense, the random variations spontaneously happening in genomes are certainly a random system. Even if each event is certainly caused by biochemical laws, we cannot know in advance which event will take place in each case. So, we describe the system by a probability distribution.

    4) Which probability distribution? The best approximation is certainly a uniform distribution. For each nucleotide in a genome sequence, we assume an uniform probability of mutation to each other nucleotide. That means that the variation of any pre-existing sequence can best be described as a random walk.

    5) Obviously, that is not completely true. There are certainly slightly different probabilities for different mutations. And, if we consider all forms of variation (including deletions, insertions, inversions, and so on) the probabilities of each of those events are certainly different. But again, a uniform distribution is the best approximation we can use. As far as I know, no other known probability distribution describes biological RV more efficiently.

    6) At this point, we could ask: but is it possible that some more detailed probability distribution, which takes into account the more realistic probabilities of each variation event, could explain better the functional information in proteins? The answer is: no. And the reason is simple. The different probabilities of the various random events that take place at genomic level are certainly important, but in no way they are related to the functional sequences that make a protein functional. IOWs, as I have already said:

    “I would add that any genomic variation due to some physical process, and particularly to biochemical laws, is necessarily random with respect to the functional information implied, for example, by a functional protein sequence, for the simple fact that physical laws and biochemical laws that generate variation in the genome have no way of knowing what kind of sequence will generate protein functionality.

    Unless, obviously, the variation is designed.”

    7) Regarding the modeling of the random walk, I have already shown, elsewhere, that it is true that in a random walk where each single variation event is best approximated by an uniform distribution, the distribution of possible outcomes is not uniform, because obviously the states which are more similar to the starting state are by far more likely, at least after a limited number of variation events. But that’s exactly why the probability of all outcomes which are completely unrelated to the starting state can be considered best described by an uniform distribution, and the probability of each unrelated state is somewhat lower than 1/n (where n is the numerosity of the search space). That’s why 1/n, which is what we usually use in our ID reasoning, is a higher threshold for the true probability of each unrelated state in such a system.

    8) Last but not least, as everyone can see, I have never included NS in this reasoning. The reason is simple: NS is essentially a necessity mechanism which, even if it certainly operates on random variation, and can also include random components in the way it operates, a necessity (algorithmic) description of how it works can certainly be used. That’s why the possible effect of NS must be computed separately, as I have tried to do in specific models some time ago. I will not add the reference again, because I think that nobody really would take the time to consider those long and complex posts. 🙂

    IOWs, what NS can or cannot do must be evaluated on the basis of what we really know of the laws that imply NS in specific systems. Those points can never be solved by merely appealing to probability, exactly as we don’t appeal to probability to describe the trajectory of a moving object in mechanics.

  20. 20
    gpuccio says:

    Querius (#16):

    In my opinion, the term “random mutation” is acceptable in the sense that it suggests that there’s no intelligent planning or implicit direction. The term is misleading in the sense that the sources/types of mutations make a difference–that not all mutations are equally likely.

    Excuse me if I choose your post to correct again this error, but I believe that it is a very important point to be clarified.

    As I have tried to explain in my previous post, the simple fact that “not all mutations are equally likely” in no way means that the system is not a random system. So, the term “random mutation” is not misleading at all.

    This idea, that only a uniform distribution can be used to describe a random system, is very diffused. There is no problem with that, because most people are not familiar with probability theory. But I think that this misconception has already caused a lot of confusion here, so I believe it should be definitely corrected.

    So, for the last time, random does not mean that the outcomes are equally likely. Please, see my example of the die with only two outcomes, in my previous post.

  21. 21
    bornagain77 says:

    The Genome is a Read-Write Memory System-James Shapiro – video
    https://vimeo.com/74618934
    This clips describes why we now need to view the genome as Read-Write (RW) memory system rather than a Read-Only Memory (ROM) subject to accidental change.

    How life changes itself: the Read-Write (RW) genome.
    Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

  22. 22
    bornagain77 says:

    gpuccio, do you still believe these changes are random?

  23. 23
    gpuccio says:

    BA:

    I do believe that random variation happens continuously in the genome. I don’t believe, obviously, that RV explains functional information in the genome. Functional information is designed.

    I have often proposed guided variation and/or intelligent selection (even after random variation) as possible ways of design implementation in biological beings. Those are instances of design.

    But RV certainly exists. We see it all the time.

  24. 24
    gpuccio says:

    BA:

    Ah, another point.

    While your examples of intelligent working in the genome are wonderful, and very significant, I still think that any appearance of new dFSCI (like a new protein superfamily) requires an input of functional information from outside the existing genome. But many adaptations and variations can certainly be controlled by the existing genome itself.

    It is a fundamental point in my views of ID, however, that new dFSCI can only originate because of an input from a conscious intelligent being.

  25. 25
    bornagain77 says:

    gpuccio, Kelly states:

    “Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur.”

    Clearly Kelly is looking for what he terms spontaneous mutations, which is another way of saying mutations that he believes to be completely unguided, unplanned, i.e. non-directed. ‘Spontaneous mutations which are adamantly held by Darwinists to be the source for all the complexity in life we see. As I have briefly laid out, Shapiro has made the point clear that the vast majority of ‘mutations/changes’ to the genome are not ‘spontaneous’ in the Darwinian sense, in that sophisticated molecular machines are in fact making very specific changes to the genome in a very precise fashion. As to exactly how the decisions are being in the cell made as to how to make these precise changes/mutations to the genome, nobody knows. The reason nobody knows exactly how the decisions are being made is due to the extremely complex level of hierarchical information involved above genomic information. Do you believe these molecular machines are making these changes in a ‘spontaneous/random’ fashion. I certainly don’t!

    Notes:

    Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. – Jan 2013
    Excerpt: Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides.,,,
    Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles.
    http://www.ncbi.nlm.nih.gov/pubmed/23293005

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    etc.. etc..

  26. 26
    gpuccio says:

    BA:

    You quote a phrase by Kelly:

    “Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur.”

    That phrase, IMO, is simply wrong. Those mutations to which he refers, “errors in the repair process for damaged DNA”, are simply random. There are two kinds of errors, random error and systematic error. I some mutations are the result of systematic error, that only means that there is some definite repetitive malfunctioning in the repair mechanism. I don’t believe that to be the case.

    The simple truth is that errors are random, wherever they occur. Kelly just suggests that they are non random because of his completely wrong idea that random means equally probable, or for other wrong ideas of his. As far as he cannot give us a necessity explanations of the errors, errors are random, for the reasons I have tried to explain in my post #19.

    I think that you, instead, refer to intelligent variations implemented in the genome by functional mechanisms, whatever they are. Those are not “random errors”, but the working of a definite functional system.

    However, as I have tried to explain, I believe that any system which works algorithmically can do many things, but not generate new original dFSCI. IOWs, even those intelligent mechanisms cannot explain the appearance of a new protein superfamily.

    I believe that random errors can contribute practically nothing to functional information, the few documented cases of microevolution are all trivial, and mostly of the “burning the bridges” type, just to quote Behe.

    Instead, intelligent adaptations guided by existing algorithms in the genome, or however in the existing living beings, can certainly do much more. For example, many mechanisms in bacteria, including plasmidic systems, are probably very good adaptational systems. As I have said many times, antibody maturation in humans is a very good example of embedded protein engineering (although, being somatic, it does not produce heritable information).

    However, the generation of a new protein superfamily, or of a new protein network or regulation network, or even a new body plan, are good examples of new, original dFSCI. The only possible explanation for them is the input of new functional information from a conscious being, an agent who is outside the existing biological being, and who interacts with it to modify it.

  27. 27
    bornagain77 says:

    gpuccio, I think you are trying to split hairs with your definition between systematic and spontaneous mutations. Moreover,,

    Evolutionists Caught Again—But They Still Believe – Dr. Cornelius Hunter – May 2012
    Excerpt: As a new paper now explains, under evolution we must believe that mutations rates have been “evolutionarily optimized.” That is, evolution is now so brilliant that it created the means to not only control, but to optimize the actual mutation rates.,,, (Here is how they put their findings)
    “Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases.,, Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection.,, Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.,, Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. ,, The findings have important implications for our understanding of evolution and the control of mutations.,,”
    Dr. Hunter Comments: “These findings have important implications for our understanding of evolution? Well sure, if by that they mean how absurd are evolution truth claims.”
    http://darwins-god.blogspot.co.....-they.html

    A few additional notes that may be of interest:

    Proof reading of DNA polymerase (Reduces error rate to 1 in 100 million) – video
    http://www.youtube.com/watch?v=YcNhuYh34P4

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

    Protein Researchers Unravel the Molecular Dance of DNA Repair – March 2012
    Excerpt: Using state-of-the-art technology, scientists at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen and their international collaborators have successfully obtained molecular snapshots of tens of thousands processes involved in DNA damage repair.,,, “We first damaged the DNA of cells using radiation or chemical drugs and then used a technique called mass spectrometry, which is a way of precisely determining the identity of proteins and their chemical modifications,” Petra Beli says.
    “This allowed us to follow thousands of protein modifications that happened in the process of DNA repair, shedding new light on how the networks of biochemical signals are regulated and how the infrastructure of alerts works.”
    The data from the experiments is so extensive that it will require much further work by researchers to fully understand the significance and impact of these newly identified signaling pathways.
    http://www.sciencedaily.com/re.....123022.htm

    Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution)
    http://www.youtube.com/watch?v=dzh6Ct5cg1o

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

  28. 28
    bornagain77 says:

    New Research Elucidates Directed Mutation Mechanisms – Cornelius Hunter – January 7, 2013
    Excerpt: mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,,
    These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,,
    http://darwins-god.blogspot.co.....ected.html

  29. 29
    gpuccio says:

    BA:

    I have not spoken of “systematic and spontaneous mutations”. I have only mentioned the difference between systematic error and random error, which are two well known concepts in methodology.

    However, I have simply tried to clarify my opinions on a few important points. I am not sure that I understand what your opinions are on those points, but I am happy that you keep them.

  30. 30
    Joe says:

    gpuccio- Have you read “Not By Chance”, by Dr Lee Spetner? He has a “non-random evolutionary hypothsus” that posits “built-in responses to environmental cues”.

  31. 31
    bornagain77 says:

    gpuccio, ‘spontaneous/random’ mutations, in the sense of completely undirected, unplanned, mutations, mutations which are suppose to be the source for all creativity in the neo-Darwinian view of things, which is the sense in which leading Darwinists themselves adamantly mean the term ‘random mutation’ when they use the term (as amply illustrated in the Behe video I listed) is the primary type of mutations that Kelly is concerned with (this is where you are trying to split hairs and make things more complicated than they actually are). I have addressed the fact that, scientifically, Darwinists have no right to presume ‘spontaneous mutations’ to be completely undirected in the first place in post 17. I could go further in clarifying issues in this matter as to how it completely undermines Darwinian thinking, but I think it will fall on deaf ears since you seem to be more concerned with declaring him to be (IYO) wrong. So I will refrain.

  32. 32
    gpuccio says:

    BA:

    Just to understand.

    Do you believe that all mutations are guided?

    Do you deny that unguided mutations happen at all?

    Do you believe that SNPs which cause mendelian diseases in humans are guided mutations, and that they contribute to the evolution of functional information?

    I would like you to answer that, because my simple point is that random mutations exist, that they are random and unguided, and that they do not contribute to the evolution of functional information.

    I believe my points are clear enough. Could you please clarify your position?

  33. 33
    gpuccio says:

    Joe:

    No, I have not read that.

    But maybe you can clarify a point for me.

    I certainly believe that there are “non random responses” to “environmental cues”. I also believe that those processes, which can be understood as the working of intelligent algorithms in the genome, or however in the living being, can contribute significantly to intelligent adaptation. That can also mean the refinement of existing functions or proteins.

    What I don’t believe is that such mechanisms can generate new, original dFSCI: IOWs, new functions that require new complex digital sequences. New protein superfamilies are a good example of that.

    The simple reason why I don’t believe they can is that they must be essentially algorithmic processes, IOWs something similar to a computer program. And, as I have stated many times, I strongly believe that algorithmic processing, however complex and intelligent, cannot generate new dFSCI, and that an input of information from a conscious agent is necessary for that.

    But, if Spetner (or you) has convincing arguments against that, I am happy to hear them.

  34. 34
    bornagain77 says:

    gpuccio, do you believe anything happens in the universe apart from God’s permissive will?

  35. 35
    bornagain77 says:

    As to the first question:

    Do you believe that all mutations are guided?

    As clearly pointed out in post 17, Scientifically, there is no question that everything that happens in this universe has to pass through God’s permissive will first. Scientifically there is simply no room for debate on the matter. To deny that fact is to not understand what science has revealed to us and is to argue Theology instead of science. Scientifically, not Theologically, all mutations, ever decay of every unstable particle, every snowflake that falls to the ground, EVERYTHING!, are all guided. There is nothing that happens in this universe apart from God permissive will as far as science can tell us.

    Do you deny that unguided mutations happen at all?

    See the answer to your first question.

    Do you believe that SNPs which cause mendelian diseases in humans are guided mutations, and that they contribute to the evolution(?) of functional information?

    This following quote by Dr. John Avise is illuminating as to this question. In the following quote, Dr. John Avise explicitly uses (bad) Theodicy to try to make the case for Darwinism:

    It Is Unfathomable That a Loving Higher Intelligence Created the Species – Cornelius Hunter – June 2012
    Excerpt: “Approximately 0.1% of humans who survive to birth carry a duplicon-related disability, meaning that several million people worldwide currently are afflicted by this particular subcategory of inborn metabolic errors. Many more afflicted individuals probably die in utero before their conditions are diagnosed. Clearly, humanity bears a substantial health burden from duplicon-mediated genomic malfunctions. This inescapable empirical truth is as understandable in the light of mechanistic genetic operations as it is unfathomable as the act of a loving higher intelligence. [112]” – Dr. John Avise – “Inside The Human Genome”
    There you have it. Evil exists and a loving higher intelligence wouldn’t have done it that way.
    http://darwins-god.blogspot.co.....it-is.html

    Does it even phase John Avise that the scientific evidence, that he himself cites, is absolutely SCIENTIFICALLY crushing for Darwinism? Moreover, he goes on to state,,,

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”

    I went to the mutation database website cited by John Avise and found that the total number of known disease causing mutations has almost doubled since he wrote his book:

    Total Entries – 148,413
    http://www.hgmd.org/

    What’s completely ironic is that Dr. John Avise’s theological argumentation from detrimental mutations for Darwinian evolution, as to what God would and would not do, turns out to be, in fact (without Darwinian Theological blinders on), a very powerful ‘scientific’ argument against Darwinism since nobody can seem to find any truly beneficial mutations that are on their way to building up functional complexity/information that is greater than what is already present in life:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

    Thus scientifically, there is no question as to whether everything that happens in the universe is part of God’s will or not, and that ‘spontaneous mutations’, for the overwhelming majority of times, ALWAYS reduce functional information. What is a mystery is why do Darwinists insist on using Theological argumentation as to what God would or would not do in this universe to try to make the ‘scientific’ case for Darwinism. If I want bad Theology I would go to a Unitarian church! 🙂

  36. 36
    bornagain77 says:

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video
    https://vimeo.com/35088933

  37. 37
    Joe says:

    gpuccio:

    What I don’t believe is that such mechanisms can generate new, original dFSCI: IOWs, new functions that require new complex digital sequences. New protein superfamilies are a good example of that.

    In Spetner’s scenario all the information is already present- just as Meyer said in SitC- think genetic algorithms. They do not create any new information or produce dFSCI- all the information they need is already designed in. They cannot exceed that designed in dFSCI.

    Even if new proteins and superfamilies would be created it would be due to the design which would have all of that information already.

    Hopefully that helps.

  38. 38
    gpuccio says:

    BA:

    I have no doubts that “everything that happens in this universe has to pass through God’s permissive will first”. That is something I strongly believe for religious and philosophical reasons. I would not say, however, that it is “scientifically” obvious. If you believe that, it’s fine for me, but I would not support that argument in that way.

    But design detection in biological information is all another matter. The existence of dFSCI in biological objects strongly supports the inference to an explicit intervention of a conscious designer, an intervention which would be something very different from the “permissive will” of God. What is required is an active input of functional information in specific material objects.

    So, when I ask if, say, the mutation that originates a defective SMN1 protein and causes spinal muscolar atrophy in the newborn is a random event or not, I am not suggesting that it happens out of the “permissive will of God”. I am sure it does not, because, like you, I believe that nothing happens out of the permissive will of God.

    What I am asking is if you believe that such a mutation is a random error, similar to a typo or to the result of the tossing of a coin, or if you think that it is a specifically designed event, where a designer willingly modifies that single nucleotide in that genome to achieve a specific plan.

    And, anyway, even if you believe that, in that case the design would not be detectable, because the variation is not complex (one nucleotide), and for all scientific reasons a design inference cannot be made for a simple variation.

    Because ID theory is about detectable design, not about design in any case. And the main idea in ID is that design is detectable only if it generates complexity linked to some definite specification.

  39. 39
    gpuccio says:

    Joe:

    Thank you for the clarification.

    With all the limits of one who has not read the other’s arguments, I must say that I don’t agree. The facts we know are all for a gradual increase of complex functional information in the course of biological evolution.

    Moreover, I really don’t believe that new dFSCI can be generated algorithmically. Unless, obviously, the information itself is already in the algorithm.

    So, unless we can show that the sequences of all 2000 known protein superfamilies (or some equivalent information, like all the biochemical rules and computing power to calculate those sequences for definite functions) were already included in the original information (of the first living beings?), together with all the information needed to generate protein networks, organs, body plans, and so on, I cannot understand how all those things could come into existence at different times in natural history without many new, original, fresh inputs of functional information.

    Maybe I will read Spetner sometime, and then I can be more specific.

  40. 40
    Joe says:

    gpuccio- Spetner does not advocate universal common descent. He says the deck was stacked in the originally Created Kinds- several thousand of them- he isn’t sure how many.

    But anyway, you are not actually limiting the designer (or God, if you prefer) such that there could not have been a designed program insewrted into the originally designed organisms such that the diversity of life observed could arise?

    Granted I do not accept UCD- for lack of supporting data- but I am not going out on a limb to say it is impossible via all mechanisms- especially knowing what genetic and evolutionary algorithms can create starting from randomly generated virtual populations.

  41. 41
    gpuccio says:

    Joe:

    All that can be fine, but in a scientific discussion I need some facts in favor of those “Created Kinds”, whatever they are, existing on our planet at OOL and during natural history, and mechanically interacting with matter.

    You see, in the end it is not so important how the functional information is inputted. The designer can input it from his intuitive knowledge, or through some intelligent algorithm he implements, or he may have created Kinds (whatever they are) on some other plane, and then input the information from that plane. I don’t know, we can make any hypothesis, but then we have to match our hypotheses with known facts.

    Known facts about what we can observe (or infer) about material biological objects in natural history tell us that there is a constant (but probably non continuous) input of new information at definite times.

    When a new protein family appears, it appears. It was not there before. It is there at some time in natural history, and it is still there now.

    That we have to explain. That information comes from someplace. And it had to be generated originally from a conscious agent.

    As far as we can understand, the original designed organism was some prokaryote (LUCA or FUCA, which IMO are the same thing). As far as we can know from facts, it was not very different from modern bacteria or arches. I really can’t see how “a designed program such that the diversity of life observed could arise” can be found in that kind of biological being.

  42. 42
    Joe says:

    No one knows what the originally designed organisms were. The facts that favor the originaslly Created Kinds are the observences that reproduction produces very similar organisms to the parents. It is only when we cannot observe ddoes soemthing magical occur to bring about new body plans requiring new body parts.

    My only point is a clever enough designer should be able to program organisms to produce new protein superfamilies if that is what is required.

  43. 43
    bornagain77 says:

    gpuccio, contrary to what Darwinists claim to the contrary all completely random entropic events in this universe lose information from the initial information input that God put into the initial entropic state of the universe:

    “Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…”
    Siegfried, Dallas Morning News, 5/14/90, [Quotes Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin]

    “Bertalanffy (1968) called the relation between irreversible thermodynamics and information theory one of the most fundamental unsolved problems in biology.”
    Charles J. Smith – Biosystems, Vol.1, p259.

    “Gain in entropy always means loss of information, and nothing more.”
    Gilbert Newton Lewis – preeminent Chemist of the first half of last century

    Thus, if you want life, new proteins and/or new life forms in general in the universe, then a new input of ‘functional’ information into the universe will be required.

    Kerrie Roberts- No Matter What **With Lyrics**
    https://www.youtube.com/watch?v=OA3MSqufJP4

    Romans 8:18-25
    I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. For the creation waits in eager expectation for the children of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the freedom and glory of the children of God.
    We know that the whole creation has been groaning as in the pains of childbirth right up to the present time. Not only so, but we ourselves, who have the first fruits of the Spirit, groan inwardly as we wait eagerly for our adoption to sonship, the redemption of our bodies. For in this hope we were saved. But hope that is seen is no hope at all. Who hopes for what they already have? But if we hope for what we do not yet have, we wait for it patiently.

    Autumn Leafs Laughter
    Oh please do tell us of your secret
    you majestic autumn leaves,of regal red ,and shimmering golden yellow,
    Brilliantly coloring the landscapes of trees.
    Do you dare pass away in a rush of beauty while you are slowly dying?
    Pay ye no heed to all the other deaths so solemnly attended with tears and crying?
    or Does the essence in you somehow yearn jealously for a glorious life to come?
    And you somehow know that death shouldn’t be sad but fun?
    For I truly wish I could die like you and that I knew the secret of your story, so that my countenance should light up and glow as my soul is delivered to behold God,s glory.
    So please autumn leaves which mock death with such defiant belly laughter,
    Do tell us your secret over death so that we may properly enter the hereafter.

    Autumn Leaf’s Laughter – music poem
    http://www.metacafe.com/watch/.....onal_poem/

  44. 44
    gpuccio says:

    BA:

    “Thus, if you want life, new proteins and/or new life forms in general in the universe, then a new input of ‘functional’ information into the universe will be required.”

    But that’s exactly my point! 🙂

  45. 45
    bornagain77 says:

    Well sorry for any confusion. It is just the whole ‘unguided/random/spontaneous’ part is where the real controversy is at. Theists as well as Atheists completely mishandle the issue by not tracing out the entropic root. i.e. 1 in 10^10^123. There is nothing ‘unguided’ in the sense that atheists would like to mean it. That point can’t be stressed enough!

  46. 46
    Querius says:

    gpuccio stated

    As I have tried to explain in my previous post, the simple fact that “not all mutations are equally likely” in no way means that the system is not a random system. So, the term “random mutation” is not misleading at all.

    Within the scope of your definition for “random mutation,” I agree with you.

    However, you obviously know about mutability variation within genomic architecture, so you used the term “non-uniform” distribution of “random” mutations, which sounds like an oxymoron.

    My objection is that broadly applying the term “random mutations” blurs out the fact that certain organisms have an advantage with mutability in certain regions, and these regions are not random, but at least some have the appearance of design.

    -Q

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