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Michael Behe: New paper supports my “Darwin Devolves” thesis

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The beneficial mutations that helped yeast survive were losses:

An interesting paper that strongly reinforces the lessons of Darwin Devolves was recently published in Nature Ecology and Evolution.1 University of Michigan biologists Piaopiao Chen and Jianzhi Zhang looked at the effect of changing environments on the evolution of laboratory yeast Saccharomyces cerevisiae…

The most interesting point of their fine work to me is that all of the beneficial mutations almost certainly are loss- or degradation-of-function. That is, the mutations in the various conditions benefit the yeast by destroying pre-existing genes or diminishing their activity. Chen and Zhang followed two different categories of mutations: 1) mutations that substitute single nucleotide residues; and 2) mutations that delete chunks of DNA or cause a stop codon to appear in a gene. The latter category is highly likely to outright destroy the activity of the protein that the mutated gene codes for. Nonetheless, this category is actually the more frequently found of the two. The former category — substitution mutations — does not necessarily destroy a protein’s activity, but that’s certainly the way to bet here. The reason is that most of the selected genes that have substitution mutations (where the normal amino acid residue in the protein the gene codes for is swapped out for a different one) actually have multiple positions that can be beneficially substituted. That’s the signature of a mutation that is helping by degrading or destroying a protein’s activity, simply because there are many more positions where substitution will degrade activity than ones that will improve activity.

Michael Behe, “Helpful Devolutionary Mutations Are Rapid and Unavoidable: Paper Reinforces Darwin Devolves” at Evolution News and Science Today

Paper: Chen, P. and Zhang, J. 2020. Antagonistic pleiotropy conceals molecular adaptations in changing environments. Nature Ecology & Evolution 4:461-469. (paywall)

The trouble with Darwin Devolves is that it is likely to be both quite right and a big problem for schoolbook Darwinism. Just as it is much easier to—without thinking much—throw something out than fix or adapt it, life forms will far more likely randomly mutate by dumping complex equipment than by reengineering it. It’s not that life forms can’t develop complex new equipment. But such changes probably aren’t an instance of natural selection acting on random mutation. And in these times, that’s the controversial part: design in nature.

See also: Michael Behe and the broken wolves. In Darwin Devolves, he explains how much evolution depends on breaking genes. He picks up the theme in this video series. In the case of wolves, we call the broken ones dogs.

Comments
Apparently my offer (to discuss the material and organizational hurdles described in the literature) was unwanted by our neutral friend with the open mind. I bet there is a self-serving reason for that.Upright BiPed
March 10, 2020
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"Built-in responses to environmental cues"- Dr. Lee Spetner in "Not By Chance".ET
March 9, 2020
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I would suggest organisms were given the intellectual capacity to perceive environmental information, and then use that to alter their own biological information....aka their genes/physiology. The living organism is a mindful, creative entity. The environment is informative; the organism responds to it and changes itself adaptively.tommy hall
March 9, 2020
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ID says that organisms were intelligently designed with the ability to adapt and evolve. That would mean they were given the information to do so.ET
March 9, 2020
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From the OP: “ it. It’s not that life forms can’t develop complex new equipment. But such changes probably aren’t an instance of natural selection acting on random mutation.” Can you give me an example? And as far as how organisms change, how they adapt to their surroundings, Darwinian theory says that an external mechanism is the cause (natural selection which acts on random mutations), so ID is the opposite; adaptive change happens by endogenous mechanisms that are not random. On its fave it’s as simple as that, as the individual himself is his own creative force. “Evolution” over time is just a process of conscious individuals who are intelligently responding to environmental challenges with an array of endogenous mevchanusms.tommy hall
March 9, 2020
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JVL:
There are no goals! There is no “directive”, no target.
Just another reason why unguided evolution is impotent with respect to universal common descent and producing protein machines.ET
March 9, 2020
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@JVL 50
There are no goals! There is no “directive”, no target.
So I was right. Under naturalism, there is no purpose to anything.
You might not like the use of “beneficial”
-Of course I do not like arbitrary and non-sensical terminologies. Neither should you. Naturalism makes no sense. It contradicts it-self (pun intended).Truthfreedom
March 9, 2020
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Truthfreedom, 48: So survival + consequent reproduction are the ‘goals of evolution’? There are no goals! There is no "directive", no target. You might not like the use of "beneficial" or "selection" but it's clear what they mean in this context.JVL
March 9, 2020
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@47 PaV
As to the number of commentators here, I wrote a blog post about four years ago entitled, “The War is Over: We Won!” https://uncommondescent.com/intelligent-design/the-war-is-over-we-won/
Excellent blog post. Thank you for the link.Truthfreedom
March 8, 2020
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@19 JVL Truthfreedom asked (16):
'Beneficial' (mutations) for what?
JVL replied:
For the individual and its descendants, i.e the descendants/offspring will be better able to exploit the environmental conditions so that their population percentages increase with respect to the base population. So, they may be able to escape predators better, they may be able to reach more food, they may be better able to survive local climatic conditions, they may have larger ‘litters’, they may have smaller litters (thereby having more time to protect and guide their offspring, etc. There are lots of different survival techniques/ways of producing more descendants.
So survival + consequent reproduction are the 'goals of evolution'? Truthfreedom
March 8, 2020
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Jim Thibodeu:
Evolution is every bit the current scientific paradigm as it was when Paul said that.
I would slightly disagree with you here. I think Darwinian evolution is beginning to slip. However, there is a bigger point you haven't addressed: Behe's Darwin Devolves makes the case that what we know as Darwinian evolution borders on the trivial. The case Behe makes is that the "First Rule of Adaptation" is that organisms begin breaking and altering what already exists--that is, they don't bring anything of any consequence into existence; and, further, that the ease with which organisms can 'break' things puts typical Darwinian evolution/mechanisms at a severe disadvantage. So, while Darwinian evolution might be the "current paradigm," it looks feeble and inconsequential. Another way of putting this is that by using Darwinian thought, scientists end up "barking up the wrong tree." As to the number of commentators here, I wrote a blog post about four years ago entitled, "The War is Over: We Won!". I'm not interested in posting article and getting into discussions with Darwinists because they're simply wrong and take positions that are indefensible. IOW, I don't want to waste my time. The "Darwin Wars" are over--there is nothing left to say. With time, Darwinism will be seen to be more and more wrong. In the meantime, the Darwinists will enforce their orthodoxy and the "current paradigm" will remain Darwinism. Take an article, whenever you see the word "evolve" being used, either substitute "changed" or "adapted," and you'll find that nothing of value will have been lost. Darwinism is no more than a narrative gloss.PaV
March 8, 2020
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. Sorry for the delay, a rack of baby-back ribs took priority.
I suppose it’s first necessary to acknowledge that the answer must be: all or none.
So which is it? If you answer “all of them” then your answer is congruent with the fact that the symbol system was famously used predicted to exist prior to being found, then it was found, then it was carefully and unambiguously documented in the physics literature to be just as it was first predicted to be. If you answer “none of them” then your answer is a sweeping denial of the well-documented history of science, as well as its experimental results. If, on the other hand, your desire is simply to ignore the documented history and empirical facts surrounding the system — in the hopes that your personal assumptions about it will someday be shown to be true — then your position is plainly illogical, non-falsifiable, and anti-science. In other words, the symbol system is a symbol system based on the recorded science, regardless of whether or not you find it ideologically uncomfortable. As a materialist you can either acknowledge that your preferred metaphysical assumptions must produce a multi-referent symbol system (using discontinuous association, spatial orientation, language structure, and semantic-closure in order to exist and persist over time), or, you can be demonstrably anti-science and frankly anti-intellectual. If you’d like, we can start walking through the physical findings of the symbol system, one by one, and see how well you can ignore them.Upright BiPed
March 8, 2020
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It's pretty cool how I called that one, eh, JVL? Two of the papers referenced in your Wikipedia quote are from Yarus, et al. :cool: Don't feel like beating that dead horse again. But I am sure that upright biped will step in and help you out.ET
March 8, 2020
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Speigelman's Monster reign's supreme with respect to molecular replicators. Not a molecule?
Not in the sense we use that term now anyway.
Sort of like gibberish? And if there are RNA triplet to amino acid associations that just gets in the way of producing the system currently in use.ET
March 8, 2020
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ET, 41: Reference please. Hopefully you link to Yarus, et al. Some of the papers referenced in the Wikipedia article are behind a paywall which I can do nothing about but you can go to the link and see the references. Anyway, from: https://en.wikipedia.org/wiki/Genetic_code#Origin
Chemical principles govern specific RNA interaction with amino acids. Experiments with aptamers showed that some amino acids have a selective chemical affinity for their codons. Experiments showed that of 8 amino acids tested, 6 show some RNA triplet-amino acid association.
It uses chemical bonds to be carried out, yes. But how can it be based on chemical bonds? What determined which codon represented what amino acid? What chemical bonds? I guess you'll have to start tracking down some references. No. Molecules just don’t replicate. You need a catalyst and a template. But what if the first basic replicator was not a "molecule"? Not in the sense we use that term now anyway. And, again, why not wait until more work is done before making a fast and final call? What's the rush?JVL
March 8, 2020
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JVL:
But doesn’t it suggest to you that it’s possible that there could be a basic, simple replicator that could just reproduce exploiting existing environmental chemicals?
No. Molecules just don't replicate. You need a catalyst and a template. Then you need to go from that basic replicator to a coded information processing system. Why? Nature is fine with stones and minerals.ET
March 8, 2020
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JVL:
There is research which suggests that the genetic “code” isn’t a real “code” in that it might not be completely arbitrary.
Reference please. Hopefully you link to Yarus, et al.
IF it is based on chemical bonds then there would be no requirement for “a working multi-referent symbol system to be in place” since that wouldn’t be the basis of the system.
It uses chemical bonds to be carried out, yes. But how can it be based on chemical bonds? What determined which codon represented what amino acid? What chemical bonds?ET
March 8, 2020
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ET, 38: A virus doesn’t have the machinery to generate proteins. But viruses require a working multi-referent symbol system to be in place. Or nothing happens. But doesn't it suggest to you that it's possible that there could be a basic, simple replicator that could just reproduce exploiting existing environmental chemicals? I don't think we know the answer to that question yet. I'm happy to keep an open mind and decide after the work has been done. We both have our opinions and guesses but, honestly, don't we still have to wait until more work has been done?JVL
March 8, 2020
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UBP, 36: When you wrote “for the individual and its descendants”</i< did you not have something in mind? When you suggested ”they may be able to escape predators better“ did you make that suggestion without any conception whatsoever of any life form that it might apply to? Of course not. So what’s the problem? I didn't think it was clear (and I didn't want to assume) that when you asked your question that you were restricting it. I was trying to make sure you had the chance to be clear. So, since we now know you are referring to multicellular life forms . . . mutations require nothing, they just happen when cells reproduce. They're just mistakes. What you're really asking is: How many of these mutations require a "working multi-referent symbol system to be in place" in order to have an effect on the physiology of the organism and its offspring. I think. Please correct if necessary. I suppose it's first necessary to acknowledge that the answer must be: all or none. But, I suppose, a case can be made that neutral mutations do not require "a working multi-referent symbol system" to be in place since they have no effect on physiology. There is research which suggests that the genetic "code" isn't a real "code" in that it might not be completely arbitrary. IF it is based on chemical bonds then there would be no requirement for "a working multi-referent symbol system to be in place" since that wouldn't be the basis of the system. IF the genetic code really is a purely arbitrary, abstract code then YES the question of where it came from and how it got implemented and enforced is a huge question. I think that's what you wanted me to get to. But I seriously think there are reasons for questioning whether or not the "code" is actually arbitrary. So, I'm going to wait and see what the research suggests. I don't think it's correct to second guess work that hasn't been done yet. I'm happy to accept that everyone who claimed that there was a genetic "code" might have been wrong. Are you?JVL
March 8, 2020
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Holy whacko. Viruses require a working multi-referent symbol system to be in place. Or nothing happens. A virus doesn't have the machinery to generate proteins. But viruses require a working multi-referent symbol system to be in place. Or nothing happens. In order for a virus to mutate during replication it requires a working multi-referent symbol system to be in place. Or nothing happens.ET
March 8, 2020
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ET, 35: Why did you avoid the most important part? So they (mutations) can occur outside of a cell? Without proteins? Do tell. Do viruses generate proteins or just exploit them? Is their sequence a 'code' or just a chemical game that depends on basic chemical rules?JVL
March 8, 2020
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. Good grief JVL, you seem to really be struggling to answer an entirely unambiguous question about your own equally unambiguous statement. Is it indeed an unfounded assumption to think that you had some concept in your mind about the organisms you were speaking of? Is that really unfounded; it seems rather incoherent to think anything else. When you wrote “for the individual and its descendants”</i< did you not have something in mind? When you suggested ”they may be able to escape predators better“ did you make that suggestion without any conception whatsoever of any life form that it might apply to? Of course not. So what’s the problem? It is those organisms (the ones you were speaking about) that I asked my question. So, once again: How many of these advantageous or disadvantageous mutations require a working multi-referent symbol system to be in place?Upright BiPed
March 8, 2020
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JVL:
Thanks for that! I realise how significant that is for you.
Facts and reality should be significant for you, too. But I understand that you have issues with them. The book "Not By Chance" was published in 1997. You seem to be decades behind. Why did you avoid the most important part? So they (mutations) can occur outside of a cell? Without proteins? Do tell.
It’s just a chemical bonding sequence.
That requires a working multi-referent symbol system to be in place. Or nothing happens.ET
March 8, 2020
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From the Wikipedia article on viruses:
Viruses are considered by some to be a life form, because they carry genetic material, reproduce, and evolve through natural selection, although they lack key characteristics (such as cell structure) that are generally considered necessary to count as life. Because they possess some but not all such qualities, viruses have been described as "organisms at the edge of life" and as replicators.
ET, 32: That’s debatable, but I understand that is what mainstream evolution posits. Thanks for that! I realise how significant that is for you. 33: Viruses require a functioning, living organism for a host. Viruses have a nucleic acid sequences based on the same coding as the hosts use. But if they don't code for proteins then the sequence ain't a code for them is it? It's just a chemical bonding sequence. That's the question.JVL
March 8, 2020
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JVL:
Viruses are arguably alive (it’s contentious, granted) but they do not ‘code’ for proteins or more complicated structures.
Viruses require a functioning, living organism for a host. Viruses have a nucleic acid sequences based on the same coding as the hosts use.ET
March 8, 2020
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JVL:
Strictly speaking mutations require nothing,...
So they can occur outside of a cell? Without proteins? Do tell.
they just happen randomly.
That's debatable, but I understand that is what mainstream evolution posits.ET
March 8, 2020
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UBP, 29: Did you notice these two sentences in my previous comment (its the part of my comment that you did not include in your response): Yes, I did notice. I am responding to your original question again. I am going to go out on a limb and stand by my assumption that you had some idea of Life in mind when you wrote the words “for the individual and its descendants” in your comments above. Yes but I think the answer to your question might depend on whether you're asking about a basic self-replicator or something more complicated. Viruses are arguably alive (it's contentious, granted) but they do not 'code' for proteins or more complicated structures. They just get copied.JVL
March 8, 2020
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ET, 28: Every. Single. One. Strictly speaking mutations require nothing, they just happen randomly. But I was assuming that Ubp was getting at something more involved. And then I don't think it's clear.JVL
March 8, 2020
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. Did you notice these two sentences in my previous comment (its the part of my comment that you did not include in your response):
The “stage of development” I was referring to? I was asking you about your statement.
I am going to go out on a limb and stand by my assumption that you had some idea of Life in mind when you wrote the words “for the individual and its descendants” in your comments above. If that assumption is unfounded, then just let me know. If not, then my question stands. How many of these advantageous or disadvantageous mutations require a working multi-referent symbol system to be in place?Upright BiPed
March 8, 2020
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Upright Biped:
How many of these advantageous or disadvantageous mutations require a working multi-referent symbol system to be in place?
Every. Single. One. It's not that difficult, JVL.ET
March 8, 2020
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