REAL WEASEL Family of Genetic Algorithms

Weasel and other genetic algorithms have been falsely advertised as proof of concept of Darwinian evolution in nature. Use of the term “natural selection” is false advertising because what Darwin and evolutionary biologists claim is natural is actually NOT natural.

I had an offline exchange with EricMH as I’m thinking of contributing to the Blyth Communication journal regarding computational models to highlight Darwin’s false advertising of what natural selection is really capable of doing. Whether my ideas end up in the Blyth journal is a separate issue from the ideas themselves. I’m hoping EricMH will weigh in with some ideas too.

EricMH suggested some other ideas offline, and I asked if it would be ok with him to discuss this at TSZ to get editorial feedback. I suggested we avoid use of CSI but instead using things like common sense to dismantle Avida, Weasel, Tierra, and other GA’s used as “evidence” that natural selection actually provided the complexity we see in biology today

Bill Dembski attempted to do the what I’m trying to do with pure math, but I instead decided to use common sense.

I hope to post some ideas here in this OP, but also in the comment section. If people object to the simplicity of the models, they’ll have to justify why my models are less valid than their GA’s or computer models like Avida, Tierra, Weasel or whatever. The point is to highlight the absurdity of assuming that because something is a called a “GA” that it actually models the physical genetic “algorithms” in nature or that there is no need of miracles to make evolution happen.

So for starters, here are some ideas:

Frozen in Space Weasel — there is no requirement in nature that an organism be provided temperatures and atmospheric pressures appropriate for life and genetic inheritance to take place. In fact, MOST of the universe is inhospitable, and for that matter, it takes fine tuning for life to emerge. It certainly is NOT natural (in the sense of expectation from first principles) that life should be sustainable. It is an exceptional event. Why should we assume a GA will run naturally?

DOA Weasel — well, without the origin of life, there is no Genetic Algorithm in real life. Evolutionary theory, as always, needs a miracle to make it work, and in this case a miracle to even get it started.

Global Warming Weasel — because of the Faint Young Sun Paradox, the Earth should have been a frozen ice ball till now, and there shouldn’t have even been a Cambrian explosion. Supposedly green house gases were miraculously fine tuned to allow just the right amount of global warming to counter balance the Faint Young Sun. The global warming gases miraculously diminished just at the right time and in the right amounts over billions of years to enable habitable temperatures to enable life to evolve. As usual, evolution needs a miracle to make it work.

See: The Young Faint Sun Paradox

Devolving Weasel — this weasel gets simpler and simpler as natural selection destroys its complexity. It is even LESS likely than random chance to arrive at the magic phrase, “methinks it is like a weasel.” This seems the natural direction of evolution, not toward complexity. Thus again, evolution needs a miracle to make it work, because selection toward extravagance and complexity from a starting point of simplicity is not indicated by theory nor experiment. Thus evolution again needs miracles to make it work.

Thwarted by IC Weasel — This is a weasel that can’t evolve because irreducibly complex systems don’t provide a feedback path, or worse, a NEGATIVE feedback path toward evolving complexity. To quote Michael Lynch, ” many genomic features could not have emerged without a near-complete disengagement of the power of natural selection.” I had a conversation with Robert Marks about this, but then we ran out of time to finish out the idea…

Endagnered species Weasel — this weasel dies out BECAUSE natural selection as its habitat is taken away by other creatures. So, for natural selection to enable diversity, natural selection has to be absent!

So we may add a few more ideas, and then Python code, or whatever code to illustrate these ideas.

It would probably help, imho, if some humorous sounds and vizualizations were added to the python code to drive the point home with the above algorithms. The point is to mock the absurdity of using GAs as some sort of evidence in favor of Darwinian evolution in nature. Bill Dembski attempted this in several publications including No Free Lunch using piles math. But I feel a more common sense approach will resonate with a general audience as well as a scientific audience.

Because I feel these ideas more appropriate reflect the reality of how miraculously natural selection must work in order to evolve complexity, and to mock programs like Avida, Tierra, Weasel, I call these the REAL WEASEL family of Genetic Algorithms.

108 thoughts on “REAL WEASEL Family of Genetic Algorithms

  1. Entropy: If you accept evolution as an algorithm written by a magical being in the sky, because Dawkins wrote a program that shows that random variation with selection and reproduction can produce meaningful text, then you’ve been contradicting yourself for quite a while arguing against the possibility that evolutionary phenomena have been producing functional molecules.

    What is this? The Twilight Zone?
    I think Entropy really believes this not to mention Larry…😅
    Somebody stop me!!!

  2. Entropy,

    Are you insinuating that you accept evolution, but that it is some “algorithm” written by a magical being in the sky?

    I am insinuating that there is no know mechanism we can model for creating even minor quantities of functional DNA by evolutionary process from scratch. Until you do this your atheist claims are without merit.

    This problem is not going to disappear from rhetoric alone. You call it a “magical being” in the sky. I call your reasoning circular until you drop the magical straw-man argument from ignorance.

  3. stcordova: The only place it is NET cumulative is in the imaginations of evolutionary biologists, not actual experiments and observations.

    Not in actual experiments and observations huh?

    So the selection in the LTEE is not cumulative? The relative fitness of the population in any flask lineage has not gradually increased over the course of the experiment compared to the ancestor?

  4. Rumraket: Not in actual experiments and observations huh?

    So the selection in the LTEE is not cumulative? The relative fitness of the population in any flask lineage has not gradually increased over the course of the experiment compared to the ancestor?

    Can someone please tell me why the same people have been repeating the same nonsense for years thinking that major, unfulfilled evolutionary claims will jusf go away?

    Why would anyone, in the right frame of mind, continue to deceive himself?!
    I just don’t get it…
    I guess this means I have spent too much time TSZ hoping that reason has the power to prevail…Unfortunately reason doesn’t work for those who refuse to apply it…
    I’m done with this blog…again…

  5. J-Mac: Can someone please tell me why the same people have been repeating the same nonsense for years thinking that major, unfulfilled evolutionary claims will jusf go away?

    Again with the “bacteria are still bacteria” trope? Really? How come didn’t you get it the first time someone told you that bacteria is an entire fucking domain among the THREE domains in the whole tree of life?

  6. J-Mac:

    Why would anyone, in the right frame of mind, continue to deceive himself?!
    I just don’t get it…

    Beats me, but clearly those NOT in the right frame of mind deceive themselves with a sort of desperation. I’m going to guess it has to do with the conflict between actual reality and hardwired religious belief. To quote Dawkins writing about Wise, “there is no sensible limit to what the human mind is capable of believing, against any amount of contrary evidence.” It’s not that religious believers don’t get it or won’t get it, but rather because they CAN’T get it. Morton’s Demon has thrown away the key.

  7. J-Mac:
    …Unfortunately reason doesn’t work for those who refuse to apply it…

    J-Mac shooting him/herself in the foot once again.

  8. colewd:
    I am insinuating that there is no know mechanism we can model for creating even minor quantities of functional DNA by evolutionary process from scratch.

    This is not what you said Bill. You clearly said that the Weasel algorithm works because it was written by a “mind.” This implies that you accepted that we can make such models, but that you attribute their success to being put together by a “mind,” rather than for doing/modelling what they do, which implies, again, that you think that evolution works because it was written by a magical being in the sky.

    Again, you cannot have it both ways. Either you admit that Dawkins’ model works as an example that a commutative process (reproduction of successful mutants, plus generation of variability by a few random mutations) can generate interesting stuff, thus implying that evolution works, or you refuse to admit it in the face of evidence. Neither works in your favour.

    colewd:
    Until you do this your atheist claims are without merit.

    This has been done quite a bit. But I don’t “claim” atheism on the basis of models about what nature can or cannot do. I find it interesting that you’d think that I have to know everything so that no gods can be put into some gap in my knowledge. It doesn’t work that way. When I don’t know or understand something, I don’t start imagining gods as answers. I just admit to my ignorance. So, if the models didn’t work for “creating even minor quantities of functional DNA” I’d say, “hum, seems like we don’t have all the elements for a basic understanding of these phenomena.” That’s it.

    To start believing in gods, on the other hand, would require positive evidence for such gods, starting with a god that made sense, not one of the many incoherent fantasies imagined by humanity.

    colewd:
    This problem is not going to disappear from rhetoric alone.

    The problem that your lack of knowledge about models that produce “even minor quantities of functional DNAs”? Of course not. Rhetoric will never work. This requires your effort, and I cannot force you. It’s up to you.

    colewd:
    You call it a “magical being” in the sky. I call your reasoning circular until you drop the magical straw-man argument from ignorance.

    I suspect that you don’t know what “straw-man”, “”circular reasoning” and “argument from ignorance” mean.

  9. Rumraket: Not in actual experiments and observations huh?

    So the selection in the LTEE is not cumulative? The relative fitness of the population in any flask lineage has not gradually increased over the course of the experiment compared to the ancestor?

    LTEE is an isolated experiments, one has to survey other observations and experiments to acertain a net direction of evolution.

    To keep citing LTEE and ignoring other more numerous examples of the opposite is cherry picking.

  10. Flint: I’m not sure I follow this argument. Are you saying that the very first bird didn’t evolve flying ability by taking advantage of other inherited features (perhaps used for other things like body temperature regulation), buy rather was poofed whole cloth into existence by your creator.

    And are you saying that all of the hundreds of species of birds today, from hummingbirds to condors, are cumulatively degenerate forms of that first poofed bird, losing their ability to fly (even though some species rarely even land). Interestingly, the visual abilities of many of these birds has degenerated into something far superior to our own ability.

    I think your claims would beguile more readers if nobody ever bothered to look around at the biosphere and notice that the exact opposite of your claim, has actually been happening. Bummer when observation refutes preference, even when that preference is buttressed by utterly ineducable blind faith.

    I’m saying direct observation is that evolution is net reductive, not constructive. Lots more bird type/species are going extinct than being created. Same for plants.

    https://www.newsweek.com/plant-species-extinct-birds-mammals-amphibians-1443367

    he Earth is entering what scientists have described as the “sixth mass extinction crisis,” with some estimates indicating that current extinction rates are hundreds of times above what is considered “normal.”

    While threatened animal species, such as gorillas and the white rhino, tend to receive the most attention, plants are also dying out at an alarming rate. This is significant because plant extinctions endanger other organisms, ecosystems and the ability of humans to survive on our planet.

    Now a team of scientists from the Royal Botanic Gardens, Kew, in the U.K., and Stockholm University have put together the first global analysis of plant extinction data, covering around 90,000 species—and the results are sobering.

    Sooooo, selection has favored human expansion into the biosphere. This wipes out other species.

    I need to write a new book under a pen name.

  11. stcordova:

    Joe Felsenstein: You mean most individuals do not start out with genotypes that come from genes transmitted by their parents?

    That’s what makes for the “cumulative”. It’s not some mysterious property involving long-term cosmic resonance. It’s that, before that generation’s selection, each generation starts from where its parents were.

    Thank you for reading and responding, but that is NOT what I meant.

    Creatures tend to lose integrated function over time, not accumulate it.

    …. (etc.)

    You don’t get it that Dawkins’s Weasel was not meant to establish some empirical generalization about evolutionary change? You don’t get it that it was intended to explain what the evolutionary biologists meant by cumulative natural selection?

    Given what Dawkins intended, he made a good teaching example.

    Even if you can establish somehow that evolution involves only loss and degeneration. Even if you can establish somehow that it only lasted 6.,023 years till now. Even if you ignore that under your own scenario involving Noah’s Ark, there would have to have been hyperfast evolution, not all by loss and degeneration, as each “kind” had many variously-adapted descendants.

    It was a teaching example about cumulative selection. Not a universal proof of how evolutionary change happens, in all its messiness. Do you get that? Why not?

  12. keiths:
    Sal,

    Everyone who knows anything about genetic algorithms understands that their success depends on the shape of the fitness landscapes they navigate.

    If you want to show that evolution is impossible, you’ll need to demonstrate that the fitness landscapes have the wrong shapes.Good luck with that.

    I’ve demonstrated the fitness landscapes have the wrong shape by referencing observation and experiment, not imaginations of evolutionary biologists.

    I don’t need to show evolution is impossible, I show that it is inconsistent with direct observation and experiment, which is sufficient to show acceptance of it is faith-based, not fact-based because it is not consistent with accessible direct knowledge.

    Evolutionary biologists just pretend their claims are science, when in fact it is mostly a faith-based enterprise pretending to be science.

  13. Joe Felsenstein:

    You don’t get it that it was intended to explain what the evolutionary biologists meant by cumulative natural selection?

    I get it now. Thank you for your comment.

  14. Entropy,

    Again, you cannot have it both ways. Either you admit that Dawkins’ model works as an example that a commutative process (reproduction of successful mutants, plus generation of variability by a few random mutations) can generate interesting stuff, thus implying that evolution works, or you refuse to admit it in the face of evidence. Neither works in your favour.

    Dawkins model shows how difficult it is to find function inside a sequence. It implies that evolutionary mechanisms that are going to fail beyond micro evolutionary change. This is very clear once you spend time with the algorithm.

    You need to think about this clearly as you are a smart guy.

    When you use the word magic you are labeling and creating a circular argument.

    Why do you persist in denying that the evidence shows intelligent cause behind our universe?

  15. colewd:

    Dawkins model shows how difficult it is to find function inside a sequence.It implies that evolutionary mechanisms that are going to fail beyond micro evolutionary change. This is very clear once you spend time with the algorithm.

    So you think that the difference between (about) 1000 generations and 10^{40} generations is not important?

  16. Joe:

    So you think that the difference between (about) 1000 generations and 10^40 generations is not important?

    We should probably expand that for Bill’s benefit:

    So you think that the difference between (about) 1000 generations and 10,000,000,000,000,000,000,000,000,000,000,000,000,000 generations is not important?

  17. stcordova: LTEE is an isolated experiments, one has to survey other observations and experiments to acertain a net direction of evolution.

    To keep citing LTEE and ignoring other more numerous examples of the opposite is cherry picking.

    When the claim being made is that there is no NET cumulative selection in any observations or experiments, and that it is just some sort of fantasy invented by evolutionary biologists with no basis in fact (which was in fact what you claimed), then pointing out that cumulative selection is an observed fact, can’t be an example of cherry picking.

    By the way, cumulative selection is an observed fact in countless of experiments. Cumulative selection is what is used in artificial selection, even before the process was understood: The domestication of crops in the evolution of agriculture was cumulative selection. Millenia before someone was named Darwin.

    When you make an absolutist statement, a single counterexample is all it takes to collapse your case.

    Also, no one says evolution has a “net direction” whatever the hell that means.

    To say that there is cumulative selection is not to say that evolution has a “net direction”. It just means that some adaptation evolves by the accumulation of successive adaptive mutations.

  18. Cumulative selection drove the evolution of apples, pears, bananas, oranges, carrots, tomatoes, potatoes, corn, wheat, dogs and cats, cattle, pigs, chickens, different skin tones in humans, and so forth almost literally ad infinitum.¨

    Everything you see in this picture is the result of it’s own experiment in cumulative selection. Most of it before anyone even knew what cumulative selection was.

  19. colewd:
    Dawkins model shows how difficult it is to find function inside a sequence.

    Bill, you should think before writing those overly ridiculous statements. Your claim doesn’t make sense. The algorithm doesn’t even attempt to find a “function” inside a sequence. It “evolves” a random “sequence” into a sentence using random mutations, selection, and reproduction.

    Dawkins algorithm does what it’s supposed to do: show the effects of cumulative selection where variability is built randomly. It’s a success. It gets the sentence, and a few other interesting sentences, and it’s a great teaching tool.

    colewd:
    It implies that evolutionary mechanisms that are going to fail beyond micro evolutionary change.

    ?????

    colewd:
    This is very clear once you spend time with the algorithm.

    I have. I never saw anything there about microevolution, or about the impossibility of “finding” a function inside a sequence.

    colewd:
    You need to think about this clearly as you are a smart guy.

    I suspect I’ve thought about it a tad better than you have. Starting with understanding its intended purpose.

    colewd:
    When you use the word magic you are labeling and creating a circular argument.

    I’m just stating clearly what creationists are arguing for. They often forget that detail and start trying to ridicule evolutionary phenomena, without paying attention to the beams in their own eyes.

    colewd:
    Why do you persist in denying that the evidence shows intelligent cause behind our universe?

    I don’t deny any evidence Bill. I just see the foundational problems with the mere proposal. I have told you, the problems start with the philosophical, and continue into the scientific. There’s no saving creationism and its ID incantation from those problems.

  20. stcordova: I’ve demonstrated the fitness landscapes have the wrong shape by referencing observation and experiment, not imaginations of evolutionary biologists.

    I don’t need to show evolution is impossible, I show that it is inconsistent with direct observation and experiment, which is sufficient to show acceptance of it is faith-based, not fact-based because it is not consistent with accessible direct knowledge.

    Evolutionary biologists just pretend their claims are science, when in fact it is mostly a faith-based enterprise pretending to be science.

    If you have indeed “demonstrated” all that then why have you not published and collected your Nobel? I imagine they would probably name the replacement after you as well!

  21. stcordova: I show that it is inconsistent with direct observation and experiment

    If you had published, or just collected your disparate claims together in something other then a youtube video I’d be able to just look up your support for that claim. But I can’t. So, what is your support for that claim?

  22. Rumraket:
    Cumulative selection drove the evolution of apples, pears, bananas, oranges, carrots, tomatoes, potatoes, corn, wheat, dogs and cats, cattle, pigs, chickens, different skin tones in humans, and so forth almost literally ad infinitum.¨

    Everything you see in this picture is the result of it’s own experiment in cumulative selection. Most of it before anyone even knew what cumulative selection was.

    Right. Same with dog breeds. And virtually no one believes that this is a path to a new plant, a new animal or a new organism we have never seen before. It is variation within kinds. You would think that, just like with the lenski experiments, when one realizes that you can get plenty of variation, and still never create something new no matter how many generations we witness, that micro changes are not small steps to the macro.

    The evidence hits you in the head like a giant Brussels sprout.

  23. phoodoo:
    Right. Same with dog breeds. And virtually no one believes that this is a path to a new plant, a new animal or a new organism we have never seen before.

    Really? Nobody? Then why would anybody work on breeding? The industry is huge, and the results contradict your claim unambiguously.

    phoodoo:
    It is variation within kinds.

    Sure. A pack of wolves in the wild looks like a collection of different dog breeds. One wolf looks like a chihuahua, the other like a german shepherd, the next one like a collie, the next one like a boxer, the next like a great Dane, etc, etc. Surely demonstrating that dog breeds are mere variation within “kinds.”

    phoodoo:
    You would think that, just like with the lenski experiments, when one realizes that you can get plenty of variation, and still never create something new no matter how many generations we witness, that micro changes are not small steps to the macro.

    Should I continue listing now what teosinte looks like in the wild? One specimen like white corn, the other like blue corn, etc. Or what about bananas? Apples? Pears? All breeds look exactly like one or another specimen of their wild relatives! It’s just variation within kinds people! Obviously.

    phoodoo:
    The evidence hits you in the head like a giant Brussels sprout.

    It certainly does. I look at Brussels sprouts, then at a cabbage, then at a broccoli, etc, etc, and I’m convinced that you didn’t think carefully enough before writing that comment.

  24. phoodoo: Right.Same with dog breeds.And virtually no one believes that this is a path to a new plant, a new animal or a new organism we have never seen before.It is variation within kinds.

    When I read this, I start to wonder exactly how different something must become over many generations, before it would be considered “new”. If we start with teosinte, is corn “different” enough? Is a chihuahua different enough from a wolf to be considered new? These strike me as being obviously and wildly different. Where does “new” begin? If corn were to become ever more different from teosinte, say for another million years at a constant rate, surely somewhere along the line it would have to count as “new”, wouldn’t it?

    When we trace modern-day phyla back to the beginning of the Cambrian, we find that what evolved into completely different phyla were in fact very similar to one another. Over the eons, these phyla gradually diverged until today, even a creationist would consider, say, trees and grasses to be not the same “kind.” And if so, there must have been some point in time when these diverged enough to be considered “new”.

    To paraphrase Upton Sinclair, it is difficult to get a man to understand something when his religion depends on his NOT understanding it.

  25. Rumraket:
    Cumulative selection drove the evolution of apples, pears, bananas, oranges, carrots, tomatoes, potatoes, corn, wheat, dogs and cats, cattle, pigs, chickens, different skin tones in humans, and so forth almost literally ad infinitum.¨

    Everything you see in this picture is the result of it’s own experiment in cumulative selection. Most of it before anyone even knew what cumulative selection was.

    How do evolutionary biologists know the change wasn’t due to what is expected mostly from simple mendelian inheritance of pre-existing alleles? They don’t!

    The Brassica change were tracked by farm records, IIRC. Do you think that many mutations happened in such a short time?

    Evolutionary biologists insinuate the changes are mostly mutational per generation followed by selection, how do you know they weren’t just different combinations of alleles of pre-existing genes where the combinations were selected for. That actually suggests phenotypic change due to specialization and loss of allelic diveristy in the lineages, and less to gain of mutations. Jeason suggests there ways, in priniciple (not necessarily practice) that this could be tested.

    If that’s the case, this is yet another example of evolutionary biologists misrepresenting the evidence for one thing when in fact it represents the opposite.

    What is NOT modeled is adapativeness that destroys function such as loss of genes. I suppose we could model accumulating loss of functional genes.

    I mean look at only TWO loci and the varieties that can be generated independent of new mutations! Now think if were dealing with thousands of loci! So, evolutionary biologists have not proven the majority of phenotypic changes in recorded history are MOSTLY due to new mutations over that time period to the exclusion of changes do to simple Mendelian inheritance of pre-existing alleles over that same time period.

    I mean, look at what a single founding pea (generation 1) involving 2 loci could give rise to — 16 different phenotypes! No cumulative selection needed!

  26. And before one jumps to all sorts of conclusions about phenotypic variation in successive generations due MOSTLY to new mutations consider:

    https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/phenotypic-variation

    1. Phenotypic Variation
    Phenotypic variation is an important adaptive mechanism in rotifers, but has posed difficult problems for systematists. This variation arises by several mechanisms including cyclomorphosis, dietary- and predator-induced polymorphisms, polymorphisms in hatchlings from diapausing embryos, and dwarfism. Cyclomorphosis is the seasonal phenotypic change in body size, spine length, pigmentation, or ornamentation found in successive generations of zooplankton. These changes are phenotypic alterations in a single population that are related to physical, chemical, or biological features of the environment. Each different morphological form is called a morphotype (or morph). Specifically excluded from cyclomorphosis changes are seasonal succession of sibling species and clonal replacements of genotypes (both of which are genetic changes in populations) and the production of spines or changes in shape due to induction by the presence of specific biochemicals in the diet or reaction to predators.

  27. And:

    https://bioone.org/journals/journal-of-economic-entomology/volume-107/issue-2/EC13243/Shift-in-Phenotypic-Variation-Coupled-with-Rapid-Loss-of-Genetic/10.1603/EC13243.pdf

    Reduced genetic diversity in subsequent generations (F4 and F8) of the laboratory colony was found to be linked with phenotypic divergence.

    Uh, so changes in phenotype weren’t really due to selection for NEW mutations was it. So much for the assumption that Rumraket’s examples are NECESSARILY due to accumulation of new mutations from the common ancestor. We simply don’t know. This could be the case of Darwinists misrepresenting the evidence by attributing large phenotypic change due to accumulation of new mutations when it could be mostly just plain old mechanism of inheritance of pre-existing alleles.

    When we see siblings from of the same parent that look so different, do we quickly assume it was due to new mutations in each kid? NOPE!

    Consider not only the phenotypic diversity due to mixing of alleles, but flat out loss of genes! What does this pan genome profile of M. aeruginosa represent but the fact many strains of M. aeruginosa have reduced genome sizes (aka gene loss) from some supposed ancestral pool for HGT:

    https://www.frontiersin.org/articles/10.3389/fmicb.2015.00394/full

  28. https://www.sciencedirect.com/science/article/pii/S0092867419303848

    The recent decays of autosomal π diversity and heterozygosity suggest a severe reduction in horse breeding stock within the last few centuries,

    Again, cumulative selection means something mutates, then you fix that mutation in subsequent generations, and then mutate some more, and rinse and repeat, and hence there is a phyletic transformation.

    That’s not what happens when there are different breeds of creatures that have different phenotypes but share the same ancestor but are different simply because the descendants have a different mix of the alleles that already existed in ancestral population. That’s just an extension of the observed differences in kids from the same parent, but on larger scale.

    So a lot of these “new” horse breeds are mostly due to different sets of pre-existing alleles, with maybe a few new mutations along the way. To represent these radical changes as due mostly or soley to selection acting on NEW mutations per each generation is not accurate, or at best not established as fact.

    Besides, Weasel uses cumulative selection to argue complex integrated function can be cumulative selected for — like say multi-protein enzymes with quaternary structures requiring numerous interacting connections. The false assumption in applying weasel’s cumulative selection to a NEW protein architecture is that it falsely assumes the half-formed protein will be selected for and preserved until it become fully functional. This fails for certain classes of proteins that are life critical in principle, like helicases which have 6 identical copies that have to connect to each other to make a working multi-protein enzyme.

    See for yourself how difficult it might be to evolve a helicase from scratch since the organism would be dead without it. Note that the first requirement is that the helicase complex needs the identical copies to be able to connect to each other properly — that’s no trivial task, much less be a function unit that can leverage ATP to unwind DNA!

    https://www.youtube.com/watch?v=bePPQpoVUpM

  29. Here is a beautiful discussion of Helicase and a great example of why we don’t need the assumption of common descent (except as a foil for making arguments by contradiction):

    The ring-shaped hexameric helicases that function at DNA replication forks

    DNA replication requires separation of genomic duplex DNA strands, an operation that is performed by a hexameric ring-shaped helicase in all domains of life. The structures and chemomechanical actions of these fascinating machines are coming into sharper focus. Although there is no evolutionary relationship between the hexameric helicases of bacteria and those of archaea and eukaryotes, they share many fundamental features. Here we review recent studies of these two groups of hexameric helicases and the unexpected distinctions they have also unveiled.

    So a life-critical enzyme supposedly evolved independently in bacteria and eukaryotes?????

    Note panel D, in eukaryotes the helicase complex attaches to the leading strand and travels in the 3′ to 5′ direction, and in bacteria it attaches to the lagging strand and travels from the 5′ to 3′ direction!!! The Intelligent Designer has a sense of humor!

    But a helicase is no good without a ring loader protein:
    https://www.sciencedirect.com/science/article/pii/S0960982203005232

  30. stcordova: Besides, Weasel uses cumulative selection to argue complex integrated function can be cumulative selected for — like say multi-protein enzymes with quaternary structures requiring numerous interacting connections. The false assumption in applying weasel’s cumulative selection to a NEW protein architecture is that it falsely assumes the half-formed protein will be selected for and preserved until it become fully functional. This fails for certain classes of proteins that are life critical in principle, like helicases which have 6 identical copies that have to connect to each other to make a working multi-protein enzyme.

    No, Dawkins’ original Weasel argument was a demonstration that cumulative selection was very different than pure random wandering in genotype space.

    I thought we established that, a bit upthread.

  31. stcordova: I get it now. Thank you for your comment.

    stcordova: Weasel uses cumulative selection to argue complex integrated function can be cumulative selected for

    So you didn’t get it after all. Oh well

    ETA: Ninja’d!

  32. Epic tard.

    stcordova: If that’s the case, this is yet another example of evolutionary biologists misrepresenting the evidence for one thing when in fact it represents the opposite.

    And if it isn’ t the case, then this is yet another example of Sal misrepresenting the evidence for one thing when in fact it represents the opposite.

    stcordova: I mean, look at what a single founding pea (generation 1) involving 2 loci could give rise to — 16 different phenotypes! No cumulative selection needed!

    Wait a sec! Your diagram only shows 4 phenotypes.
    Have you confused genotypes and phenotypes again?
    Is that what you would call a “Howler”?
    😉

    stcordova: Consider not only the phenotypic diversity due to mixing of alleles, but flat out loss of genes! What does this pan genome profile of M. aeruginosa represent but the fact many strains of M. aeruginosa have reduced genome sizes (aka gene loss) from some supposed ancestral pool for HGT:

    Nope. Shows HGT, not gene loss. Your imagination is getting the better of you, almost as if you were misrepresenting the evid…
    I’ll get me coat.

  33. phoodoo: Right. Same with dog breeds. And virtually no one believes that this is a path to a new plant, a new animal or a new organism we have never seen before.

    And here the goalposts go flying off to outer space. Sal made a claim he couldn’t support, and which was trivial to demonstrate to be wrong, and now you’re here blathering about irrelevancies. LOOK, A SQUIRREL!

    It doesn’t matter what anyone believes, facts aren’t established by polls. Also, you haven’t defined new. And it doesn’t matter whether it “leads to something new”, the claim Sal made was that cumulative selection is a fantasy. Which is just plain false.

    You can drool and smear your feces all over this board all you want, it’s not going to make Sal’s silly absolutist declarations turn into facts.

    It is variation within kinds.

    You haven’t defined a kind. You have no clue. It’s just some hunch-like idea you brainlessly regurgitate because you’re still stuck in childlike, almost infantile “dogs are dogs, cats are cats” line of thinking.

    You would think that, just like with the lenski experiments, when one realizes that you can get plenty of variation, and still never create something new

    Still haven’t defined new. At what point does something change so much it qualifies as new? Here’s a hint: at any amount of change. If it’s smaller, bigger, shorter, fatter, slimmer, darker, brigther, has any change in sequence, if there has been any change at all, then there is now something different about it, it is not what it was before, so it’s new. By definition.

    Done. Now all evolutionary change results in something new.

    no matter how many generations we witness, that micro changes are not small steps to the macro.

    No matter how many?

    How can you be so unnaturally stupid that you can even get yourself to say type that sentence? Small changes can never lead to big changes? How does your skull not implode from the impossible level of stupidity it requires to declare that?

    That’s like saying no matter how many times I gain one dollar, I will never each a thousand.

    The evidence hits you in the head like a giant Brussels sprout.

    That’s hilarious coming from the guy who claimed there were no organisms that were poorly adapted to some particular environment. You would not recognize evidence if you had it surgically installed on your retina.

    You know that saying “if you could reason with religious people, there’d be no religious people”? It’s you they’re talking about. You are the perfect example of someone with that mindset.

  34. DNA_Jock:

    Wait a sec! Your diagram only shows 4 phenotypes.

    Ah yes, thank you, my mistake. Jeanson had the right diagram that involved more alleles. I’ll have to ask him for it. Thanks.

  35. Entropy,

    The important thing is to keep him occupied…
    😮

    stcordova: Ah yes, thank you, my mistake. Jeanson had the right diagram that involved more alleles. I’ll have to ask him for it. Thanks.

    Nice try, Sal, but you wrote:

    I mean, look at what a single founding pea (generation 1) involving 2 loci could give rise to — 16 different phenotypes!

    Everyone can see that you confused ‘genotype’ and ‘phenotype’, a veritable “Howler”. Now you are attempting (badly, I might add) to re-write history to hide your error. You appear vain.
    Even with incomplete dominance, you are going to have a tough time getting 16 phenotypes from “a single founding pea involving 2 loci”. Nine, sure; sixteen, tricky.
    [grabs popcorn]

  36. Nope. Shows HGT, not gene loss. Y

    https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002787

    Selection-Driven Gene Loss in Bacteria

    Gene loss by deletion is a common evolutionary process in bacteria, as exemplified by bacteria with small genomes that have evolved from bacteria with larger genomes by reductive processes. The driving force(s) for genome reduction remains unclear, and here we examined the hypothesis that gene loss is selected because carriage of superfluous genes confers a fitness cost to the bacterium. In the bacterium Salmonella enterica, we measured deletion rates at 11 chromosomal positions and the fitness effects of several spontaneous deletions. Deletion rates varied over 200-fold between different regions with the replication terminus region showing the highest rates. Approximately 25% of the examined deletions caused an increase in fitness under one or several growth conditions, and after serial passage of wild-type bacteria in rich medium for 1,000 generations we observed fixation of deletions that substantially increased bacterial fitness when reconstructed in a non-evolved bacterium. These results suggest that selection could be a significant driver of gene loss and reductive genome evolution.

    But even assuming HGT accounts for much of the pan-genome diagram, it shows a strong tendency not to retain genes because of (tada) natural selection. So there is a problem for species where HGT is not common or absent.

  37. Joe Felsenstein: No, Dawkins’ original Weasel argument was a demonstration that cumulative selection was very different than pure random wandering in genotype space.

    I thought we established that, a bit upthread.

    It’s that too, but it is also to resolve the improbability of finding certain architectures like functioning proteins. From Dawkins himself:

    A haemoglobin molecule consists of four chains of amino acids twisted together. Let us think about just one of these four chains. It consists of 146 amino acids. There are 20 different kinds of amino acids commonly found in living things. The number of possible ways of arranging 20 kinds of thing in chains 146 links long is an inconceivably large number, which Asimov calls the ‘haemoglobin number’. It is easy to calculate, but impossible to visualize the answer. The first link in the 146-long chain could be any one of the 20 possible amino acids. The second link could also be any one of the 20, so the number of possible 2-link chains is 20 x 10, or 400. The number of possible 3-link chains is 20 x 20 x 20, or 8,000. The number of possible 146-link chains is 20 times itself 146 times. This is a staggeringly large number. A million is a 1 with 6 noughts after it. A billion 11,000 million) is a 1 with 9 noughts after it. The number we seek, the ‘haemoglobin number’, is (near enough) a 1 with 190 noughts after it! This is the chance against happening to hit upon haemoglobin by luck. And a haemoglobin molecule has only a minute fraction of the complexity of a living body. Simple sieving, on its own, is obviously nowhere near capable of generating the amount of order in a living thing. Sieving is an essential ingredient in the generation of living order, but it is very far from being the whole story. Something else is needed. To explain the point, I shall need to make a distinction between ‘single-step’ selection and ‘cumulative’ selection. The simple sieves we have been considering so far in this chapter are all examples of single-step selection. Living organization is the product of cumulative selection.

    The essential difference between single-step selection and cumulative selection is this. In single-step selection the entities selected or sorted, pebbles or whatever they are, are sorted once and for all. In cumulative selection, on the other hand, they ‘reproduce’; or in some other way the results of one sieving process are fed into a subsequent sieving, which is fed into . . ., and so on. The entities are subjected to selection or sorting over many ‘generations’ in succession. The end-product of one generation of selection is the starting point for the next generation of selection, and so on for many generations. It is natural to borrow such words as ‘reproduce’ and ‘generation’, which have associations with living things, because living things are the main examples we know of things that participate in cumulative selection. They may in practice be the only things that do. But for the moment I don’t want to beg that question by saying so outright.

    http://dbanach.com/dawkins3.htm

    So Weasel describes how evolutionary biologists fantasize a protein like haemoglobin could emerge. I’d suggest Helicase or Topoisomerase as even better examples since they are so life critical to a wider variety of species.

    But, that cumulative selection only works if the intermediate stages exist and are favorable. Analysis of systems like Topoisomerase or Helicase shows that is not a justified premise. The cumulative selection of Weasel is thus illegtimate to explain evolution of certain protein architectures.

    The REAL FAMILY of GA’s is more in line with how nature is expected to work.

  38. stcordova: The REAL FAMILY of GA’s is more in line with how nature is expected to work.

    Run up to a wall at full speed.

  39. stcordova: So Weasel describes how evolutionary biologists fantasize a protein like haemoglobin could emerge.

    We all get that you’d love to be a biologist. It’s never going to happen.

  40. Rumraket: Cumulative selection

    I guess Rum can’t, or wishes not to mention, that the cumulative selection is nothing more but artificial selection…almost the equivalent of dog breeding from wolves to chihuahua…

    https://evolution.berkeley.edu/evolibrary/article/evo_30

    While the article Rum based his comment on says that all the variations are of one species Brassica oleracea (wild cabbage), others could consider it to be a possible variation, or change, within a kind…

    Kale, Brussels sprouts, cauliflower, and cabbage are all varieties of a single magical plant species
    https://www.vox.com/xpress/2014/8/6/5974989/kale-cauliflower-cabbage-broccoli-same-plant

    One can perform a similar experiment with a lowly dandelion…
    Just cut a few of them in half and plant one half in the shady, not well nourished desert or clay soil backyard like mine and another half in s high, sunny, well nourishes mountain…
    Amazing differences can be observed between the two halves of the same dandelion -size, color, flower, leafs – just withing few months…

    What could be responsible for such drastic changes of a lowly dandelion with the same DNA so quickly? Can anyone guess??? 😉

    BTW: Yes, I’m taking a looooooooooong break from TSZ but I just didn’t want to leave any loose ends regarding the hellvolution within kinds…;-)

  41. J-Mac: I guess Rum can’t, or wishes not to mention, that the cumulative selection is nothing more but artificial selection…almost the equivalent of dog breeding from wolves to chihuahua…

    So it’s never happened outside of human intervention? Is that your contention?

    J-Mac: BTW: Yes, I’m taking a looooooooooong break from TSZ but I just didn’t want to leave any loose ends regarding the hellvolution within kinds…;-)

    How do you know it’s within kinds? How would you know if evolution happened outside of a kind if you can’t actually say that?

  42. J-Mac: almost the equivalent

    Always the qualification. Always the “if”. Always the get out.

    To be honest, I think Dawkins had people like you and Sal in mind when he chose the phrase …Weasel. Must be psi-kick powers!

  43. J-Mac: hellvolution within kinds…;-)

    You say that and end with a smiley face. You know, when you first started here you said that you did not believe in the bible and now you are saying that biblical kinds encapsulate all possible evolution.

    How very strange…

  44. I’m quietly enjoying the way that Sal, in his attempt to defend his claim re selection

    The only place it is NET cumulative is in the imaginations of evolutionary biologists, not actual experiments and observations.

    and his further claim that the cyanobacterium M. aeruginosa is demonstrating gene loss, rather than HGT, has cited an experimental study on gene loss in the proteobacterium S. enterica (that’s a different analytical approach and, critically, a different bloody phylum, mate) that demonstrates the effects of cumulative selection. Best OG’s evah!

  45. J-Mac: I guess Rum can’t, or wishes not to mention, that the cumulative selection is nothing more but artificial selection…almost the equivalent of dog breeding from wolves to chihuahua…

    This seems like a frame of reference error. From your godlike perspective, dog breeds don’t count as new kinds because people selected which individuals to keep breeding. But consider it from the dogs’ frame of reference — for them, people ARE the environment, selecting for traits just as surely as any other environment. From their perspective, there’s nothing artificial about it at all.

    Or, looked at from a different angle, we could say that the creationist god exercises precise control over ALL environments, which only look natural to us because we are exactly the same sort of ignorant as the dogs being selectively bred. From this perspective, ALL selection is artificial.

    And it doesn’t matter, because that’s how evolution works, from any perspective.

  46. One of the triggers for the idea of natural selection was the observed effectiveness of animal and plant breeding. I believe it’s mentioned somewhere in “Origin.”

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