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

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

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

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.

•
•    Yale News – discovery of 20-part SAGA complex.

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.

•
•    CSIRO/ABC Science – description of flagellum’s motor-like complexity.

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?

•
•    NASA Astrobiology/PNAS – ribosome core conservation and origin.

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.

•
•    MIT News (Feb 2025) – new splicing regulation layer via Luc7 proteins.

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.

•
•    EMBL News (2022) – Integrator complex structure and broad role in transcription control.

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.

•
•    ENCODE project summary (NIH) – function assigned to 80% of genome, 3D regulatory architecture.

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).

ditto.

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

ditto.  Do you realize how many different means to regulate gene transcription have evolved?  We probably haven't even identified them all.

•
•    Science (2012) – histone code complexity, 100+ modifications (summarized in Curr Opin Genet Dev).

You already have this one above.

•
•    Genetics (Durrett & Schmidt 2008) – waiting time for two mutations,  >100 million years in large mammals.

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:
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.
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.

•
•    Science (Davidson & Erwin 2006) – developmental GRN “kernels” constrain body plan evolution (Cambrian explosion context).

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."
https://wiki.santafe.edu/images/6/64/Erwin_and_Davidson_2009.pdf
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.
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.

So what?

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

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.
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.

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?
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.
Ron Okimoto