Re: Observe the trend. It’s happening. Give it time.

On 10/03/2025 2:16 am, RonO wrote:

On 3/9/2025 12:56 AM, MarkE wrote:

On 9/03/2025 3:59 am, RonO wrote:

On 3/7/2025 9:18 PM, MarkE wrote:

On 7/03/2025 1:06 am, RonO wrote:

On 3/5/2025 9:24 PM, MarkE wrote:

On 6/03/2025 3:48 am, RonO wrote:

You need to better cite your sources so that it is easier to look them up.

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Appreciate your engagement and detailed detailed content. Don't appreciate your rudeness and oversimplified black-and-white stance, but we live with these.

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Dishonesty is not the best policy.  The good lie for god was made up to attack religious belief.  It was never meant to be used to support your religious beliefs.  The ID perps may live by the good lie for god adage, but it is not anything that you want to be involved with in the gray areas of reality that you want to believe exist.  Your gray areas no longer exist.  They haven't existed since the bait and switch started to go down, and the ID perps gave up and decided to just go with the obfuscation and denial for denial purposes.  It is just a fact that the ID creationist scam has just been used as bait for the last 23 years. What you keep trying to support is the use of this junk as bait.  You may believe that these types of arguments are leading somewhere that you want to go, but you already understand that they never will.  You do realize that your origin of life denial is not Biblical, but you still persist in going with the gap denial. Gap denial is all the ID scam ever was, and the switch scam is just obfuscation and denial where they do not mention that ID nor creationism ever existed.  It is just obfuscation and denial meant to keep the kids as ignorant as possible because they can't tell them why they are being lied to. That is their current means to continue their original Wedge political mission.
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There is no existing ID "science" that, if they ever do validate any of it, will support their Wedge mission.  If Behe ever finds his three neutral mutations that were needed to evolve the flagellum over a billion years ago the ID perps would lose most of their financial and political support.  The vast majority of creationists that compose their "Big Tent" are YEC.  Any valid ID science would just be more science for them to deny.  This is why Nelson has always told the rubes that they do not have any ID science at this time, but that they are just working on producing some.  About the last thing that Nelson wants to happen would be if Meyer ever was able to demonstrate design during the Cambrian explosion over half a billion years ago. Nelson is YEC and he would have never joined up for the ID perp's Wedge political mission if the other ID perps had, had any valid ID science.

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All human activity has political dimensions. None of us can claim unbiased objectivity. As I've conceded previously, ID has had political intent, such as the Wedge strategy (I'm not a fan). This is not automatically wrong though - Darwinists do the same thing, e.g. Dawkins and friends promoting atheism.

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The Atheists aren't allowed to teach their atheistic claims in the public schools either.  The ID scam has always been a religious political scam.  They may have been able to fool a few scientists in the beginning, but that ended with the start of the bait and switch scam. After that everyone left at the Discovery institute was just a perp perpetrating the bait and switch, and anyone that still supported the scam was just an IDiotic creationist rube.
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Is all ID only "bait and switch", "no science", "gap denial", "IDiots and perps" and "scam, obfuscation and denial"? (Did I miss any?) From my assessment over decades and careful consideration of its leading proponents' writing and speaking, I think definitely not, despite its shortcomings. So I suggest we agree to disagree on this.

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Nelson understood that, that was all IDiocy ever was or he would not have signed up for the Wedge mission.  If the other ID perps really did have any valid science supporting the ID scam Nelson would never have joined because it would just have been more science for Nelson to deny.
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Do you deny that the switch scam is just obfuscation and denial without mentioning creationism nor the ID scam?  The ID perps just had an article up on Wells being fondly remembered.  Wells' book (Icons of Evolution) was not ID science, but obfuscation and denial of existing science.  The book was used by the Ohio IDiots to create the first switch scam model lesson plan, and the creationists screwed up by including the Wellsian lie of "no moths on tree trunks" and including creationist web links in the lesson plan.  That was the extent of their switch scam scholarship.
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The leading proponents of the ID scam decided 23 years ago to only use ID as bait.  They all understood that they never had the ID science to teach in the public schools, and decided that using ID as bait was the only way forward for their Wedge religious political goals.  All of them agreed to do this because not one of them objected, nor resigned from the Discovery Institute when they decided to start running the bait and switch.  Phillip Johnson was the only ID perp to "retire" a month after the bait and switch started to go down.  The previous month Johnson had supported teaching ID in Ohio.  The claim is that Phillip Johnson never understood what science actually is.  He was likely fooled by the other ID perps.  Johnson came back and supported teaching ID in Dover along with then Senator Santorum.  The ID perp bait and switch attempt had failed and the Dover creationist rubes tried to teach ID anyway.  The ID perps were able to run the bait and switch on Santorum and he flip flopped on the issue during his reelection campaign and came out against teaching ID in the Dover public schools.  His Republican opponents in the primary questioned Santorum's religious convictions.  Santorum was not reelected. Phillip Johnson would not flip flop and claimed that ID would prevail on the court room steps.  Johnson sat in court every day of testimony, and decided that the ID science had never existed.
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http://web.archive.org/web/20070609131601/http:// sciencereview.berkeley.edu/articles.php?issue=10&article=evolution
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QUOTE:
I also don’t think that there is really a theory of intelligent design
at the present time to propose as a comparable alternative to the
Darwinian theory, which is, whatever errors it might contain, a fully
worked out scheme. There is no intelligent design theory that’s
comparable. Working out a positive theory is the job of the scientific
people that we have affiliated with the movement. Some of them are quite
convinced that it’s doable, but that’s for them to prove…No product is
ready for competition in the educational world.
END QUOTE:
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QUOTE:
For his part, Johnson agrees: “I think the fat lady has sung for any
efforts to change the approach in the public schools…the courts are just
not going to allow it. They never have. The efforts to change things in
the public schools generate more powerful opposition than accomplish
anything…I don’t think that means the end of the issue at all.” “In some
respects,” he later goes on, “I’m almost relieved, and glad. I think the
issue is properly settled. It’s clear to me now that the public schools
are not going to change their line in my lifetime.
END QUOTE:
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Johnson was only fooled until he had his face rubbed in the fact that ID had just been a creationist bait and switch scam for the previous 3 years because there wasn't any ID science worth teaching.
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The last IDiots on TO could no longer live with the lies and stopped supporting the ID scam when they had their faces rubbed in the fact that there wasn't any ID science that they wanted the ID perps to accomplish.   The Top Six should have killed your support for the ID scam, but for some reason you want to live in denial of what the ID scam has been all of these years.
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Would you agree that there are limits to NS as described, which lead to an upper limit to functional complexity in living things? How these limits might be determined is a separate issue, but the first step is establishing this premise.

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Natural selection works in the real world, as such there are expected to be limits on what can happen in this universe or in any particular environment.  Your problem is that all you have are claims about such limits, and none of the ID perps have been able to demonstrate that any impossible evolution ever happened.  The ID perp's focus on natural selection is just a dishonest ploy anyway. We already know that natural selection is only one factor in the evolution of life on earth. Biological evolution is just basically allele frequency change over time.  Behe's waiting time stupidity about 2 or 3 neutral mutations needed for the evolution of some new function depends on the fact that natural selection is not involved in a lot of the evolution of life on earth.  There are biologists that believe that genetic drift may have more influence on the diversity of life on this planet than natural selection.  Genetic drift and things like founder effects can do things that natural selection likely could not do, and would even work against such evolution happening, but those things still happen.  They still have happened because genetic drift and founder effects are a known part of the evolution of life on earth.
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You need to deal with why Behe needs a time limit for his junk argument, and why he can't find any examples of impossible evolution. Below I have a human and mouse example where there may already be 30 neutral mutations that have occurred in your average protein gene in each lineage (60 total).  Any existing pair or triplet could have a beneficial effect if the environment changed. The mutations already exist in these proteins, but it took 80 million years to accumulate them.  Behe is looking for 2 or 3 mutations that have occurred in the same lineage within a limited number of generations, but in reality that time limit is not required by most protein genes.
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You are just lying to yourself as you keep supporting a dishonest and bogus creationist scam.  A scam that was never going to accomplish what they wanted the rubes to believe could be accomplished.  The ID perps were never going to support Biblical creationism with their "science".

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The limits of NS are not simply due to "what can happen in this universe". The mechanism of "differential reproductive success" is a blunt instrument, rightly described as explaining the survival but not arrival of the fittest.

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This is just nuts.  Whatever limits natural selection may have has absolutely nothing to do with the simple fact that nature is not Biblical.  The ID perps have lied to creationist rubes like you about this simple fact.  None of the Top Six god-of-the-gaps stupidity was ever going to support Biblical creationism if the ID perps were ever able to do any legitimate science demonstrating designer design.
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Science is just the study of nature, and the ID perps have always lied to the creationist rubes about the ID science.  The Top Six in their order in which they must have occurred in this universe made the other TO creationists quit the ID scam because they could no longer live with the lies supporting the "Big Tent" creationist effort.
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But I would agree that ID does need to better define and demonstrate theses limits.

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It will never matter what limits to natural selection that the ID perps ever demonstrate exists.  Nature is not Biblical, and never was.  Any legitimate science would only demonstrate that to be true, just as all the existing science has already done.  We do not live in a geocentric universe, the firmament never existed over a flat earth, there never was global flood that humans had to survive, and the order of creation in Genesis is wrong.  The gaps are not what creationists have to deal with.   As you found out it is what is around the origin of life gap that creationists Biblical literalists cannot deal with. Even old earth literalists like Kalk and Bill can't deal with what nature actually is. As long as you are anti-evolution for Biblical reasons, science will never support those Biblical beliefs.
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"The ID perp's focus on natural selection is just a dishonest ploy anyway." Wrong, wrong, wrong. The *only* naturalistic means to increase functional complexity and genetic information is NS.

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It is just a dishonest ploy just as you have consistently demonstrated. Natural selection has been known not to be the "only" means to increase what you call functional complexity for a very long time.  This understanding predates the start of scientific creationism in the 1960's.
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Look up Sewall Wright and Chromosome evolution.  He started that in the 1920's and developed his ideas of genetic drift and founder effects that could accomplish evolution that natural selection would have worked against.
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The ID perp's focus on natural selection and what they call "Darwinism" was just a dishonest ploy from the beginning of it's use in the ID scam.
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Behe's 3 neutral mutation stupidity relies on the fact that natural selection is not responsible for all increases in complexity.  Behe understands that 2 neutral mutations can occur and increase complexity routinely, but he claims that 3 are impossible if they have to occur within a limited period of time.  Nature isn't restricted by Behe's time limit.  Behe has only found the expected 2 neutral mutations, but he has no examples of his "impossible" evolution of 3.  So even Behe understands that your focus on Natural Selection is just a dishonest ploy.
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How could you have posted to TO for over 2 decades and not understood that you are lying about natural selection?  The ID perps may want you to believe that natural selection is the only means available to biological evolution, but they have always lied about that, and they understand that they are lying, but keep lying in order to keep using ID as bait.
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ALL OTHER FACTORS INCLUDING GENETIC DRIFT ONLY DESTROY INFORMATION AND FUNCTION OVER TIME.

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Absolutely false.  Behe's 2 and 3 neutral mutations increasing complexity depends on the fact that genetic drift can increase what you are calling information and new function.  Behe understands that 2 neutral mutations can occur within a limited period of time routinely in a population of around 100 million.  His examples of 2 neutral mutations occurring were found in populations that were in the billions and trillions.  The flagellum would have evolved in such a large population.
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Genetic drift is merely a shuffling/randomising effect, like mutation. The net effect of which is degradation of any system. Natural selection is the only game in town when in comes to building functional complexity and the "appearance of design".

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How can you make this claim and not understand that all natural selection does is shuffle existing variation segregating in a population.  Whether the evolution occurs by selection or drift it is still evolution.  Whether parts of the flagellum evolved by neutral mutations and drift or each variant was individually selected for makes no difference to the effect of changing the function of existing proteins.
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Founder effects (sort of a sub type of genetic drift) can assemble parts whose assembly would have been selected against by natural selection, but once the whole forms the resulting new "complexity" can be selected for.
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What does it feel like to realize that decades of lying to yourself about a stupid and dishonest creationist scam is due to your misunderstanding of reality?  A reality that has likely existed for a century.
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Your fixation on natural selection does not change the fact that nature is not Biblical, and there is no science that will ever be accomplished that will change that simple fact.  The ID perps only lied to you about reality in order to use ID as bait so that they could sell you their obfuscation and denial switch scam.
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You should look up the Dembski quote where he admits that natural selection could be the designer of a lot of things in nature.  Natural selection has been known not to account for all evolution for a very long time.  Do you recall Behe's Evolution news article on whale evolution where he claimed that natural selection could account for the changes that occurred to evolve aquatic whales from a terrestrial tetrapod?  He stated that the type of evolution identified that occurred during the evolution of whales was the type of evolution that natural selection would have been expected to select for.  He tried to fool the rubes with the argument by claiming that it was a bad type of evolution.   Even though it had resulted in a spectacular change, that was expected to be due to natural selection, it was really devolution.  Such is the stupidity of ID perps and the IDiotic creationist rubes that believe them.
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Ron Okimoto

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Let's stay focused and be very, very clear about the unique role of natural selection. Here is a restatement of why NS is the only game in town:

 It has been explained on TO repeatedly that natural selection is not the only game in town.  For a quarter of a century you have lived through the ID perps lying about that simple fact, and you still want to lie to yourself about it for religious reasons, and not because of any actual understanding of reality.
 Continuing to lie to yourself about reality isn't going to change reality.  The bait and switch scam was needed for a very good reason, and it is still going down because there never was any valid ID science to discuss.
 

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Macroevolution involves the generation of significant amounts of novel genomic information and functional complexity.

 This is likely false as you have written it.  Macroevolution is the result of the genetic variation created every replication cycle of a lineage.  The genetic variation constantly occurs and once it occurs it can be propagated within a population as the lifeform reproduces.  Every existing population has a boat load of genetic variation segregating within it.  Humans went through a severe population bottle neck and even though chimp populations have been decimated they still have around 3 times the standing genetic variation as humans (Variants with a frequency over 0.1 in the population.  Around a million people in the human population have to have a particular genetic variant before it is counted among the standing genetic variation.  New mutations are not counted, just variants that have propagated within the human population to a significant degree, mostly due to drift).  The ID perps estimated that it would take a million years to generate the genetic variation in the human population from two individuals if their genomes started out identical.  This is close to other estimates, but in reality new species inherit a lot of genetic variation from their parent population.
 The only genetic variation that survives in a population is variation that still works within what is already working.  If the variation disrupts the system enough to be nonviable you do not see such mutations segregating in the population.  Eukaryotes became diploid and this allowed deleterious and lethal genetic variants to be allowed to exist and drift in a population, until further evolution associated them with some new adaptation, or the system evolved some second site reversion mechanism to make the variant tolerable.  Macroevolution occurs when enough genetic variation accumulates that make the lifeform significantly different so that it can be called a different species, genera, family etc.  We know that this is a fact because we have extant genomes to study and we can trace them back to the last common ancestor of eubacteria and Archaea (includes eukaryotes that evolved from within Archaea).
 Most mutations add no new functional complexity information.  As Behe understands they may later combine with other genetic variants to do something interesting, but when they first occur most of them do nothing much at all, and they drift through a population.  Some do something noticeable, but what they do has to work within what is already working, and they can be selected for or against.  We claim macroevolution when enough functionally acceptable variants have accumulated so that it makes the lifeform different enough to be called something different.
 

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For argument's sake, let's say natural selection is not operating. Hypothetically take NS off the table. Are you suggesting that macroevolution could and would still occur, with only the action of mutation, drift, gene transfer etc?

 Let's not, and simply admit the obvious like Dembski and Behe have admitted that Natural selection has been the designer for well enough understood evolutionary events like whale evolution.  It happens, can be measured in extant populations.  Natural selection is a fact of nature.
 Your god has obviously allowed it to happen for billions of years.
 Some biologists have run their simulations and shown that drift can arrive at similar outcomes as selection.  We have difficulty differentiating genetic drift from natural selection on short time scales.  There are proposals that it may be common for a lot of functional changes that evolve, have evolved due to drift assembling some type of new function that then can be selected for under some new environmental conditions.  Behe's 2 neutral mutations depend on this notion, and we do find examples of 2 neutral mutations producing a new function.
 Look at coelacanths they are called living fossils because their body shape and morphology is very similar to their ancestors 300 million years ago.  If you look closely, even though their heads are the same shape and proportion to the body all the skull bones are different sizes and shapes.  The body plan has been selected for, but there has still been neutral evolution due to drift to change the shape of the skull bones but maintain the shape of the skull.
 

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To reiterate, macroevolution if and only if NS. And the corollary, without NS, only the degradation of the genome and functionality of a population.

 Absolutely not true about macroevolution.  The example of the punctuated evolution of steppe bison has been put up on TO.  Steppe bison had evolved to be bison by the time some of them went to the Americas, but there was an abrupt change during the last ice age.  It turned out that founder effects were involved along with probable natural selection.  In some glacial valley Auroch hybridized with steppe bison to create a hybrid species, that differed significantly in morphology from both parent species.  This hybrid took over the population of steppe bison within a 50,000 year period and was a recent example of punctuated speciation.  The two parent species may have existed for millions of years, and a new species took over within the 50,000 to 100,000 year period that the punctuated equilibrium paleontologists had been claiming.
 Natural selection is obviously involved in maintaining the function of the genome because changes that are deleterious are selected against. What did you not understand about the fact that all new genetic variation has to work well enough within what is already working in order to be propagated within any population?

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No NS, no "ratcheting" mechanism to identify and accumulate small positive changes -- which is mandatory for macroevolution.

 The above example makes this claim false.  Natural selection was likely responsible for the new hybrid taking over the territory of the extant species, but it was not needed to evolve the new combination of functions that allowed that to happen.

When you say that natural selection "was not needed to evolve the new combination of functions", you're saying that purely random processes of mutation and genetic drift are capable of building new functions.
That's not Darwinism, that's a misunderstanding of what randomisation means.

 

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No NS, no purify selection on a population to preserve its genomic integrity and fitness.

 What does this matter?  Natural selection is a fact of nature.  We do not have to worry about it not being able to do what it obviously has done since life originated on this planet.
 I do not recall any ID perps claiming that Natural selection did not exist in nature.  Behe and Dembski have even claimed that natural selection can be the designer for some of the systems that they have looked at.  Behe just claims that whale evolution is a bad type of evolution and that his designer would have done it some other way.
 Ron Okimoto
 

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Ron Okimoto

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Sources:
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•    Behe, M. (1996). Darwin’s Black Box: The Biochemical Challenge to Evolution. (Concept of irreducible complexity introduced, flagellum as example).

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Still born and never amounted to anything.  Pretty much a complete failure.  Not a good source for much of anything.  What testable hypotheses ever came out of this book, and did Behe ever attempt to do any such testing?  The claim was that IC was testable, but both Minnich and Behe claimed that they had never bothered to attempt the testing. The test that they both proposed was bogus, and would not have been any type of valid test.  Has Behe ever been able to determine that his type of IC systems exist.  He has admitted that IC systems can evolve by natural means, but supposedly there exist IC systems that cannot evolve by natural means.  Demonstrate that any such systems have been found to exist.
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•    Yale News – discovery of 20-part SAGA complex.

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So what?  Do you understand how complex gene regulation has become in the last 3 billion years?  Behe could never come up with a number of parts for a system that would make it his type of IC. You can't either.   You need to determine how it evolved in order to make any determination as to whether it was designed by some god or not.  Do you even know how this system works?  Without that knowledge why use it to support an obvious religious bait and switch scam like ID? Both plants and animals have the same type of chromatin.  Histones are highly conserved proteins.  Angiosperms and mammals differ by only 2 amino acid substitutions for one of the Histone genes.  This system has been evolving for well over a billion years to use chromatin structure to regulate the transcription of genes in eukaryotes that have their genes on chromosomes packed in the nucleus as chromatin.
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•    CSIRO/ABC Science – description of flagellum’s motor-like complexity.

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So what?  Gish would put up a picture of the flagellum in his "debates" and used to claim that it was a designed machine.  Behe tried to do the same thing, and it was an utter failure.  Was the flagellum ever determined to be Behe's type of IC?  What good does failure do for the ID scam?
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•    NASA Astrobiology/PNAS – ribosome core conservation and origin.

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The RNA parts of the ribosome likely existed before the genetic code evolved.  You do understand that, right?  How much evolution could have occurred since proteins could be added to the ribosome. The original ribosome likely did not have any protein components because the genetic code had not yet evolved.  The current ribosome was reconstructed with proteins that could now be encoded by organisms with a functional translation system.  You have to figure out how you can prevent proteins from being added to the functional ribosome in some evolutionary sequence to end up with what we have today. The ribosome was already working before the ribosomal protein genes evolved and got added to an already functioning ribosome.
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•    MIT News (Feb 2025) – new splicing regulation layer via Luc7 proteins.

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We don't know how intron splicing evolved.  These are a group of proteins associated with binding the 5' splice site of around half the introns in the human genome.  This just means that there are at least two systems that identify 5' intron splice sites.  That is all.  Not only that, but the Luc7 system obviously evolved by gene duplication. Gene duplication is a very common natural mechanism for evolving proteins with new functions.  Why would some designer modify an existing gene when it would be much better engineering to design the best part for a particular system instead of cludging something together by using parts that could just do a good enough job by altering the sequence of an existing protein?  Minnich found out that the flagellum tail evolved by gene duplication.  I've put up Minnich's paper several times. There was once only one gene that made the flagellar tail and connected it to the hook, but there was a gene duplication, and one copy retained the ability to bind to the hook and the other specialized into elongating the tail.  It is undeniable that they both evolved from the same gene at one time. You can even compare the sequences and see what changes have occurred in each sequence since they duplicated.  The gene used to elongate the tail later duplicated again, and one of the copies evolved to be a little smaller and started to be added to the tail after the other.  This would have made a tail with a taper (narrower on the tip than at the base).  This smaller tail component later duplicated again and one copy evolved to be even smaller.  It started to be added to the tail after the other 3 making the taper even greater. All this means that gene duplication could make an IC tail where the parts could evolve and be added sequentially, but if you removed a part that bound to the hook you would lose flagellar function because no tail would be produced.
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•    EMBL News (2022) – Integrator complex structure and broad role in transcription control.

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Same for all your complex structure stupidity.  What you need to do is demonstrate that designer design was required for these systems, not just that they exist.  It is obvious that these complex systems can evolve, so what kind of limit is there for how many could have been produced in the over 3 billion years life has been evolving on this planet?  You do realize that life was limited to single celled organisms for around 2 billion years, and it took around 3 billion years to evolve all the genes used in the Cambrian explosion.  The flagellum evolved over a billion years ago.
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•    ENCODE project summary (NIH) – function assigned to 80% of genome, 3D regulatory architecture.

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The ENCODE results that you quoted have been determined to be bogus. Most of the genome is composed of transposon and retroviral sequence and these parasitic elements have their own trancriptional regulation.  As stupid as it may be the ENCODE idiots decided to count parasitic sequence as being functional. They do affect transcription of genes around them, but the system has to work in spite of this spurious transcription.  If the system can't work with the spurious trancription you have genetic defects.  A lot of the dominant spontaneous mutations observed in humans are due to transposons jumping into or around some important gene.  We have identified some rare cases where transposons are associated with something that got selected for. Just like any other type of mutations most of them don't do much of anything, some do something bad and a few might do something of interest to evolution.
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•    Cell (Hnisz et al. 2017) – phase separation model for transcriptional control (super-enhancers forming condensates).

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ditto.
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•    MDPI Genes (2022) – microRNA regulatory scope (~60% genes, ~200 targets/miRNA).

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ditto.  Do you realize how many different means to regulate gene transcription have evolved?  We probably haven't even identified them all.
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•    Science (2012) – histone code complexity, 100+ modifications (summarized in Curr Opin Genet Dev).

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You already have this one above.
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•    Genetics (Durrett & Schmidt 2008) – waiting time for two mutations,  >100 million years in large mammals.

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QUOTE:
Results of Nowak and collaborators concerning the onset of cancer due to the inactivation of tumor suppressor genes give the distribution of the time until some individual in a population has experienced two prespecified mutations and the time until this mutant phenotype becomes fixed in the population. In this article we apply these results to obtain insights into regulatory sequence evolution in Drosophila and humans. In particular, we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second of which creates a new one. Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take >100 million years. In addition, we use these results to expose flaws in some of Michael Behe's arguments concerning mathematical limits to Darwinian evolution.
END QUOTE:
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Oops no support for the ID scam.  What the ID perps need to do is demonstrate that two mutations have been needed for large animals. Behe has looked, and could not find any examples.  What Behe found were examples in species with populations in the billions, and he admitted that in a population of a hundred million 2 mutations would be expect to occurr in the same lineage routinely.  This argument doesn't matter unless you find such mutations in a species with a small population, and can demonstrate that the population was that small when the two mutations occurred. Thornton found that 2 neutral mutations were needed to evolve a new steroid hormone receptor by gene duplication, but those two neutral mutations occurred in a multicellular common ancestor whose population likely numbered in the trillions.  Behe put up Thornton's example as the "edge" of evolution, and Behe understood that Thornton had used how the two receptor types had evolved during the Cambrian explosion to figure out how the new receptor function had evolved.
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These estimates are for two specific mutations, but two neutral mutations occur in lineages all the time within single genes.  You can take the mouse gene and a human gene, and they retain the same function because you can put the human gene into mice and it still works in the mouse, but there has been 80 million years of evolution separating the two species and the two protein sequences may differ by 20% in amino acid sequence.  For an average protein sequence (300 amino acids in length) you have 60 mutations that cause a difference in protein sequence, around 30 in mice and 30 in humans that are basically neutral.   A bunch of possible pairs of neutral mutations have obviously occurred in both lineages. This means that even if you find some spectacularly rare instance where two specific neutral mutations did occur to produce some trait in large animals with small populations that there is no reason why it just did not happen by chance.  The occurrence is obviously not impossible just improbable. You would need to find that it occurred repeatedly in the evolution of some lineage before you have some issue.  So far there are no such instances.
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•    Science (Davidson & Erwin 2006) – developmental GRN “kernels” constrain body plan evolution (Cambrian explosion context).

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I can't find out if this ever developed into anything.  There is a 2009 opinion paper claiming that it might be possible to test their notions, but their notions were never verified.  They are cited as among the group pointing out the existence of conserved regulatory networks in multicellular organisms, but their contention that their proposed model of some type of mutational effects "arise from the regulatory changes depends on the hierarchical position of the changes within the GRN. This concept cannot be accomodated by microevolutionary nor macroevolutionary theory."
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https://wiki.santafe.edu/images/6/64/Erwin_and_Davidson_2009.pdf
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I can't find any evidence that anything came out of what they suspected.   The regulatory networks have been known to exist since the 1990's when enough sequence was available for comparison, but we likely haven't figured out everything about how these networks function.
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A lot of these systems are highly conserved among multicellular animals.   You should recall (you put up the paper) that nearly all the types of genes needed had evolved by the Cambrian explosion, and these systems regulated those genes.
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•    The Atlantic (Ed Yong 2016) – synthetic minimal cell with 473 genes, 149 unknown essential.

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So what?
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•    PNAS (Kocher & Dill 2024) – origin of life perspective highlighting need for prebiotic selection (needle-in-haystack problem).

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So what?  The origin of life on this planet is not Biblical. Origin of life denial is never going to support your religious beliefs. The Supreme court was correct when it ruled that gap denial was not scientific evidence for any particular creationist notion.  Just because something is not known at this time, does not mean that it is support for some alternative for which there is no evidence that the alternative is viable.  This is absolutely true. In the case of the YEC IDiots we already know that even if some god was involved in the origin of life on this planet the YEC alternative has already been excluded.  You found out that the origin of life was not Biblical when you tried to define the gap in detail in order to deny that it could not have happened by natural mechanism.  The gap is not Biblical, and does not support your creationist beliefs.  You have to deny the Bible and claim that some other god did it.  Most honest religious scientists have just made up their minds that the Bible is wrong about the creation, but that doesn't matter to their religious beliefs.  It doesn't matter how life arose on this planet.  It doesn't matter that the earth is not flat, and that there was never any firmament above the earth for the Biblical god to open up and let the rain fall through. The earth is not the center of our solar system nor the universe. There likely isn't an honest and competent religious scientist alive at this time that is a flat earth, geocentrist that still thinks that the Biblical firmament exists.  As far as I know there are no flat-earth geocentrist creationists among the existing ID perps at the Discovery Institute.
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The ID scam is just using ID as bait to push their religious political views.  There has been nothing worth supporting since the bait and switch started to go down, and the ID perps themselves gave up on their ID stupidity, but could not give up on their original mission of the ID scam unit to recreate a theocracy that likely never existed in this country.
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•    PNAS (Stumpf et al. 2008) – human interactome estimated ~650,000 interactions.

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I actually ate lunch with the interactome guy at a Plant and Animal Genomome meeting in San Diego almost 2 decades ago.  What possible good does this do the ID scam?  Whatever life is at this time, or how the genome has evolved means what in terms of the existence of some designer who obviously is not Biblical?
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None of the IDiots except for you and, possibly, Glenn, survived as IDiots after the ID perps put out their the Top Six in the order in which they must have occurred in this universe.  Getting their faces rubbed in the fact that all the evidence went against a Biblical god existing made them all quit the ID scam.  What good does such evidence do for you?  The god responsible for the Top Six is not the Biblical god.  The Supreme court was correct, gap denial is not evidence for your alternative.
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Ron Okimoto
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