ID theorists publish new paper in Journal of Theoretical Biology

_{Denyse O'Leary

August 19, 2021

Darwinism, Intelligent Design, Mathematics}

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On the improbability of Darwinian claims:

A new peer-reviewed paper in the Journal of Theoretical Biology, “On the waiting time until coordinated mutations get fixed in regulatory sequences,” is authored by three key scientists in the intelligent design (ID) research program: Ola Hössjer, Günter Bechly, Ann Gauger. The paper is part of the “Waiting Times” project, spurred by Discovery Institute as part of its ID 3.0 initiative, and it investigates a question of vital interest to the theory of intelligent design: How long does it take for traits to evolve when multiple mutations are required to give an advantage? A previous peer-reviewed publication from this team appeared as a chapter in the 2018 Springer volume Stochastic Processes and Applications. This latest paper is lengthy, technical, and math intensive. In other words, it’s not for the fainthearted, but it’s open access and free to read here.
Casey Luskin, “In Mainstream Journal, ID Theorists Explore “Waiting Times” for Coordinated Mutations” at Evolution News and Science Today (August 18, 2021)

We hope the journal isn’t intimidated by Darwin’s Outrage Machine, Inc. Just think, some people are now allowed to bring this up. And not just as an inhouse titter, followed promptly by dismissal of the question.

Ola Hössjer, Gunter Bechly, and Ann Gauger, are competent scientists who happen not to be Darwinists. It’ll be interesting to see what happens now. More from Luskin:

This paper develops a complex mathematical model for calculating the waiting time for the evolution of a trait that requires L nucleotides in order to function. Although this is strictly a methodological paper, one potential application could be the evolution of regulatory regions which control the expression of a gene. Changes to transcription are thought to be important to evolving new body plans or biological systems. Regulatory regions such as enhancers or promoters may have a length of 1000 nucleotides, and for expression to occur special proteins called transcription factors must bind to these regulatory regions at binding sites, which may be 6 to 10 nucleotides in length.
Casey Luskin, “In Mainstream Journal, ID Theorists Explore “Waiting Times” for Coordinated Mutations” at Evolution News and Science Today (August 18, 2021)

It’s like just hoping that random guesses on a multiple choice exam will net you 100% and that is what you need to graduate.

A friend comments that the paper basically shows that if many mutations must be coordinated to enable a new feature, Darwinism won’t do it. Note: Dense mathematics warning.

Update updated: Apparently, the disclaimer below applies only to an earlier article: “The Journal of Theoretical Biology and its co-Chief Editors do not endorse in any way the ideology of nor reasoning behind the concept of intelligent design. Since the publication of the paper it has now become evident that the authors are connected to a creationist group (although their addresses are given on the paper as departments in bona fide universities). We were unaware of this fact while the paper was being reviewed. Moreover, the keywords “intelligent design” were added by the authors after the review process during the proofing stage and we were unaware of this action by the authors. We have removed these from the online version of this paper. We believe that intelligent design is not in any way a suitable topic for the Journal of Theoretical Biology.”

Neither paper was retracted. A friend asks us to have pity on the poor editors who are like deer among the wolves, when it comes to dealing with Darwin mob. Very well. We shall. Kudos to them for publishing something despite the mob.

Note: Facebook is now subjecting posts from Uncommon Descent to inhouse review as “selling” something, so they may no longer be visible. You may need to come to this page yourself to see the news. If you voted for this, rejoice and be glad. Otherwise, think again. We may need to start reporting here on the valiant efforts to curb irrational Big Tech censorship. Note: They seem to have stopped doing it for the last couple of posts. But just remember, they don’t work for you. They work for a Big Guy. Stay tuned.

Comments

Yarrgonaut, =the promoters evolved in our library are of very low complexity= Yes, this is it. Exactly as I anticipated. They start from something really complex, degrade the initial complexity, find it still works and, voi la, evolution did it.EugeneS_{August 24, 2021
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BA,
The main flaw in Bob’s paper is that, number one, they never evolved anything over and above the original wild type bacteria, and they, therefore, never really demonstrated that Darwinian evolution has the capacity within itself to create anything above and beyond what already exists in the wild-type bacteria."
Reading Bob's paper, I don't think they even did that. It looks like all they did is delete the repressor and switch the promoter to a random sequence to evolve another sequence of TATAAT and TTGACA. Given 100 base pairs, that shouldn't be too hard. Regarding using it as a response to the ID paper mentioned above, note the authors say:
"the promoters evolved in our library are of very low complexity, as most of the activating mutations involved no additional factors but the two basic promoter motifs. Although the evolved promoters likely have no regulation, we hypothesize that such crude promoters might play an important role in the evolution of the transcriptional network, as newly activated genes do not necessarily require the regulated/induced expression in order to confer significant advantage."
In other words, the assumption in this paper - that newly activated genes do not need to be regulated to offer significant advantage - is essentially the opposite of what the new ID paper is trying to test - How long does it take for traits to evolve when multiple mutations are required to give an advantage? In short, it is perfectly irrelevant. Except for:
...in the two cases, RandSeq29 and RandSeq40, we observed that predicted promoters in the random sequences were not active before evolution until the activated mutations occurred downstream to their TATAAT element, but did not create a promoter motif.
It appears that there wasn't any expression until both the promoter, and the downstream mutations were in place. Ironically, this paper, which was touted on Panda's Thumb as evidence against the above paper, demonstrated the very reality that the paper was discussing - that the wait times, even at a very very low level of complexity aren't imaginary.Yarrgonaut_{August 24, 2021
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I actually had a look at it. Starting from a functional whole, deliberately breaking something and watching how it recovers, is not enough to claim that something has appeared de novo. An old poodle trick.EugeneS_{August 24, 2021
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Bob Of course, it is your choice. I think that in good conscience a lot of people have tried their best for years to explain to you where they believe you are making mistakes. And yet... So I can say exactly the same thing in return: is it worth investing my time in these comments? ET # 22 That is exactly why I am not even bothering to look into all this stuff because it is bound to be the same old poodle tricks. "Give us another 5 years and we will..." whereas in the actual fact, all they are doing is intelligent selection. My favorite slogan is, the best refutation of Intelligent Design nonsense has been provided by the researchers from the Institute of Protein Design.EugeneS_{August 24, 2021
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The paper Bob linked to is a perfect example of a cell repairing itself because it was intelligently designed to do so.ET_{August 24, 2021
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Bob claims, "they didn’t delete sequences, though" Yet they replaced "the lac promoter with various random sequences". How you replace something without first removing and/or deleting it I have no idea. To be more clear in what I was saying I admit that I should have used the term 'replace' instead of 'delete', but that is a minor and trivial point compared to the overall point that I was making. i.e. The experiment is nowhere near being the proof for functionality that Bob imagines it to be! Bob is, IMHO, being overly pedantic since he simply has nothing else to hang his hat on in that experiment.bornagain77_{August 24, 2021
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ba77 - they didn't delete sequences, though. So I've no idea what you mean.Bob O'H_{August 24, 2021
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Bob, they assumed that the (small) sequence they deleted could not be compensated for by other parts of the genome and/or by information in the cell body. In fact, It is far, far, more likely that whatever functionality was inherent in the deleted segment is being compensated for by other parts of the genome, i.e. ''genetic redundancy', than it is that some random sequence just so happened to have the functionality necessary to be a lac promoter. That much is, or should be, just plain common sense. As mentioned in post 10, the failure of Darwinists to take 'genetic redundancy' into consideration led them to, for years, severely underestimate the minimal genome size required for life.
Minimal genome should be twice the size – 2006 Excerpt: “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product. “When you knock out one gene, the genome can compensate by using an alternative gene. “But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead. “Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments. http://www.news-medical.net/news/2006/03/30/16976.aspx
In other words, contrary to what Darwinists believe, it is turning out that the genome is not some cobbled together, piecemeal, affair, but that the genome is instead best viewed as being, more or less, an integrated whole where all the 'pieces' contribute to the functionality of the whole. Here is a semi related note to that effect:
Theory Suggests That All Genes Affect Every Complex Trait - June 20, 2018 Excerpt: Mutations of a single gene are behind sickle cell anemia, for instance, and mutations in another are behind cystic fibrosis. But unfortunately for those who like things simple, these conditions are the exceptions. The roots of many traits, from how tall you are to your susceptibility to schizophrenia, are far more tangled. In fact, they may be so complex that almost the entire genome may be involved in some way,,, One very early genetic mapping study in 1999 suggested that “a large number of loci (perhaps > than 15)” might contribute to autism risk, recalled Jonathan Pritchard, now a geneticist at Stanford University. “That’s a lot!” he remembered thinking when the paper came out. Over the years, however, what scientists might consider “a lot” in this context has quietly inflated. Last June, Pritchard and his Stanford colleagues Evan Boyle and Yang Li (now at the University of Chicago) published a paper about this in Cell that immediately sparked controversy, although it also had many people nodding in cautious agreement. The authors described what they called the “omnigenic” model of complex traits. Drawing on GWAS analyses of three diseases, they concluded that in the cell types that are relevant to a disease, it appears that not 15, not 100, but essentially all genes contribute to the condition. The authors suggested that for some traits, “multiple” loci could mean more than 100,000. https://www.quantamagazine.org/omnigenic-model-suggests-that-all-genes-affect-every-complex-trait-20180620/
i.e. So much for Dawkins' entire 'selfish gene' concept!bornagain77_{August 24, 2021
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ba77 -
And even, via genetic redundancy, their one claim to have established functionality for random sequences is very much questionable.
Why? What mistakes did the authors make in the paper?Bob O'H_{August 24, 2021
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Earth to Bob O'H- the paper didn't have anything to do with blind and mindless processes. You are equivocating, again.ET_{August 23, 2021
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Whatever Bob. You got no evidence for you worldview. PERIOD! And even, via genetic redundancy, their one claim to have established functionality for random sequences is very much questionable. VERY questionable. So I really have no idea what you think the big deal is with that paper. You, as an evolutionist, simply have nothing solid to hang your hat on in that paper!bornagain77_{August 23, 2021
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ba77 -
actually is not what I want the paper to be about, it is about the fact that the results of the experiment are nowhere near showing that the unguided, mindless, processes of Darwinian evolution are capable of creating anything new, over and above, what already exists.
But that's not what the paper was investigating, though. The work described in the paper had a specific aim, and the paper describes those results. You're criticising the paper because it didn't show what it wasn't trying to show. I guess I could take the same approach and criticise you because you haven't provided a road map to peace in Afghanistan in this thread.Bob O'H_{August 23, 2021
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Bob. actually is not what I want the paper to be about, it is about the fact that the results of the experiment are nowhere near showing that the unguided, mindless, processes of Darwinian evolution are capable of creating anything new, over and above, what already exists. It is also not a minor failing that the authors just so happened to forget about 'genetic redundancy' which is now known to be ubiquitous within life. These are NOT minor failings for their experiment, nor is such a consistent lack of empirical support a minor failing for a theory that falsely claims to be as well established as Gravity. Again, It has nothing to do with my personal preferences and has everything to do with the actual experimental science at hand. Again, Darwinian evolution simply has no real-time empirical evidence whatsoever to support its grandiose claims that all life on earth arose via unguided, mindless, processes.
Darwin vs. Microbes (Where’s the substantiating evidence for Darwinian evolution?) https://docs.google.com/document/d/16umLl1dnEuGcRfGqErD_XzZXVbOxcAJmIRPaF7PBOVg/edit
bornagain77_{August 23, 2021
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LoL! @ Bob O'H- All you do is equivocate and bluff. Your comments are worth investing time on because it is easy to expose you as the poseur that you are.ET_{August 23, 2021
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ba77 @ 10 -
The main flaw in Bob’s paper is that, number one, they never evolved anything over and above the original wild type bacteria, and they, therefore, never really demonstrated that Darwinian evolution has the capacity within itself to create anything above and beyond what already exists in the wild-type bacteria.
Err, so the main flaw is that the paper was not about what you wanted it to be about. Not much of a flaw, really. EugeneS @ 11 - if you can't even be bothered to look at something before commenting on it, I don't think your comments are worth investing any more time on.Bob O'H_{August 23, 2021
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Bob I haven't even looked into that paper. Mine is a general statement that whatever "evolution can do it" proponents present as achievements of evolution, are results of carefully crafted and carefully controlled experimentation. "Carefully crafted" refers to making available at time 0 all the necessary components that are at the exactly right concentrations, purified to the industrial standards, at the exactly right temperature ranges, exactly right timing etc. In nature everything exists in mixtures. "Carefully controlled" means controlling the chemical synthesis by an intelligent experimenter, e.g. by removing or manipulating the intermediate reagents in order to achieve the end goal that is in the minds of the experimenters, which is bona fide Intelligent Design. Either of these two points, as any unbiased researcher would admit, defeats the purpose. Now, I pointed you to an earlier OP by GPuccio that deals with this and other issues. Amongst the other issues is the one that simple functions can really be achieved by evolution. BUT these functions are rather irrelevant to ID inference GP proposes, because they are not complex enough and consequently not identifiable as intelligently created. Second, often these simple functions are irrelevant because they are not naturally selectable.EugeneS_{August 23, 2021
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Bob O'H cites this following paper as (finally) providing experimental proof for Darwinian evolution.
Random sequences rapidly evolve into de novo promoters - 2018 How new functions arise de novo is a fundamental question in evolution. We studied de novo evolution of promoters in Escherichia coli by replacing the lac promoter with various random sequences of the same size (~100?bp) and evolving the cells in the presence of lactose. We find that ~60% of random sequences can evolve expression comparable to the wild-type with only one mutation, and that ~10% of random sequences can serve as active promoters even without evolution. https://www.nature.com/articles/s41467-018-04026-w
The main flaw in Bob's paper is that, number one, they never evolved anything over and above the original wild type bacteria, and they, therefore, never really demonstrated that Darwinian evolution has the capacity within itself to create anything above and beyond what already exists in the wild-type bacteria. Moreover, my bet is that is they if they more realistically mimicked what wild-type bacteria actually experience in a natural environment over a extended period of time, instead of using a 'comfy' artificial laboratory environment to see if the mutated bacteria are as fit as the wild-type bacteria, then they would eventually see small declines in fitness for the mutated bacteria when compared to the wild-type bacteria. But anyways,,, the second flaw in their paper is that the authors are apparently unaware that it is now known that there is a tremendous amount of 'genetic redundancy' that is 'Intelligently Designed" into cells that compensates for 'missing' elements in the genome. In fact, such inbuilt 'genetic redundancy' led Darwinists to, for years, severely underestimate what the minimal genome size for life should actually be. The following studies highlight the inherent fallacy in gene deletion/knockout experiments that have led many (Darwinian) scientists astray in the past as to underestimating what the minimal genome for life should actually be:
Minimal genome should be twice the size - 2006 Excerpt: “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product. “When you knock out one gene, the genome can compensate by using an alternative gene. “But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead. “Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments. http://www.news-medical.net/news/2006/03/30/16976.aspx How Many Genes Do Cells Need? Maybe Almost All of Them - May 2018 Excerpt: By knocking out genes three at a time, scientists have painstakingly deduced the web of genetic interactions that keeps a cell alive. Researchers long ago identified essential genes that yeast cells can’t live without, but new work, which appears today in Science, shows that looking only at those gives a skewed picture of what makes cells tick: Many genes that are inessential on their own become crucial as others disappear. The result implies that the true minimum number of genes that yeast — and perhaps, by extension, other complex organisms — need to survive and thrive may be surprisingly large,,, “Perhaps what we’re sampling here,” Andrews said, “are some functional connections in the cell that we weren’t able to see before.” One set of new connections, for example, was between genes involved in transporting proteins and genes involved in DNA repair. On the surface, it’s difficult to see what would connect these two functions. And in fact, the researchers still don’t have a mechanistic explanation. But they are sure there is one. “Our immediate reaction was, ‘Well, that’s kind of random,’” Andrews said. “But we’ve learned over the course of doing this project that it’s not random. We just don’t understand how the cell is connected. https://www.quantamagazine.org/how-many-genes-do-cells-need-maybe-almost-all-of-them-20180419/
Genetic Redundancy is incompatible with Darwinian evolution:
A Darwinian Paradox Excerpt: the very existence of genetic buffering, and the functional redundancies required for it, presents a paradox in light of the Darwinian (or: selectionist) concept. On one hand, for genetic buffering to take place there is a necessity for redundancies of gene function, on the other hand such redundancies are clearly unstable in face of natural selection and are therefore unlikely to be found in evolved genomes. Still, over 90% of the genes studies of model organisms were observed to be redundant [Conant GC et al, 2004; Kobayashi K et al, 2003; Baba T et al, 2006]. http://archive.is/YxXhd
Oh well, so much for Bob's supposed experimental proof for Darwinian evolution. Like everything else in Darwinian evolution, Bob's supposed evidence for Darwinian evolution is 'smoke and mirrors' that does not bear up to scrutiny. Darwinists simply have no substantiating scientific evidence whatsoever to support their grandiose claims that all life on earth evolved via mindless undirected processes..
Darwin vs. Microbes (Where’s the substantiating evidence for Darwinian evolution?) https://docs.google.com/document/d/16umLl1dnEuGcRfGqErD_XzZXVbOxcAJmIRPaF7PBOVg/edit
bornagain77_{August 22, 2021
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Wow. Earth to Bob O'H- evolution by means of blind and mindless processes is total nonsense. The DI promotes the approach because it proves that people like you are full of that nonsense.ET_{August 22, 2021
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EugeneS - OK, so you're saying that the JTB paper that the OP is about is irrelevant to ID. You might want to tell the DI about this, as they are promoting this approach.Bob O'H_{August 22, 2021
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Bob O'H is confused. There isn't any evidence that blind and mindless processes produced E. coli. There isn't any evidence that blind and mindless processes are what produced the results in the paper Bob linked to.ET_{August 22, 2021
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Bob Thank you. People can't back up their claims even in a controlled lab environment. That is reality. With random libraries and no control you can demonstrate non complex functions at best. ID inference kicks in at or beyond 140 functional bits. Please see GP's original posts here of three years back where he dealt with this at length. In particular, he quotes Hayashi paper presenting phage infectivity landscape and discusses in detail why this paper is actually evidence of ID claims. The OP is on the Texas sharpshooter fallacy and why it doesn't apply to ID.EugeneS_{August 22, 2021
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EugeneS - In reality they aren't "highly likely globally optimized" this is 10% of all the random sequences tested. I gave you think link, so at least you can read the abstract.Bob O'H_{August 22, 2021
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Bob, Re 10%: in many cases protein functions observed in reality are highly likely globally optimized, which is really hard to achieve even in a lab by guided search. Nowhere near 10%. Would you be willing to drive a car on a motorway if you knew that it was just 10% of the industry reliability standard?EugeneS_{August 20, 2021
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It’s like just hoping that random guesses on a multiple choice exam will net you 100% and that is what you need to graduate.
Whereas in reality (i.e. in an experiment that was done) a 10% pass mark is good enough. Or 60% if you're allowed 2 tries. Strange the authors didn't notice this.Bob O'H_{August 20, 2021
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Thanks, Polistra at 1. They seem to have stopped doing it - for now. But we can;t really know whether the posts were allowed to be visible. We would rather not have to start covering the need to reign in Big Tech half the time (it's not really our our mission) but we will if we must.News_{August 19, 2021
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Peer-reviewed, the stamp of official approval. It's harder for the outragers to bash a peer-reviewed paper. Facebook is doing weird and random stuff. Not just censorship. The way they disorganize comments now makes it impossible to use for 'news' purposes. Seems like they're trying to lose their customers in every possible way.polistra_{August 19, 2021
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