Random De Novo sequences are easy to make, making a sequence that codes for a structurally integrated protein, not so easy by random chance, and not so easy by selection if the whole integrated system won’t be selected for unless all the parts are in place simultaneously. In fact I guess the chances of this are astronomically remote!
So de novo is easy to make if one sets the bar low for what constitutes de novo. I’d say for even modestly well fitting systems such as those below, it’s outrageous to think this could happen by chance.
Two good illustrations of the well-fitting parts (I count 21 or so proteins):
Some have used “phylogenetic methods” to argue that this complex could easily arise by saying one of the proteins has some passing similarity to helicases. I find that phylogenetic “explanation” to be a total non-sequitur.
Another example of well fitting parts is below. This is the PRC2 complex with several proteins.
Notice how nicely all the little shapes join with other shapes! The space filling diagram on the lower right shows the fitting of the PRC2 parts quite well. The SUZ12/VEFS in beige is especially astonishing as it has to properly connect to multiple proteins in addition to connecting to a lincRNA from a totally different chromosome (chromosome 12) than the one it is positioned on (often the Hox cluster in chromosome 2).
Look at all the necessary domains (the colored boxes) in the EZH2 protein (of the above PRC2 complex) that have to be properly positioned and in the right order. Holy smokes!
Each of the boxes is a domain composed of a subsequence of 30 to 130 amino acids long and which collectively together form a protein of 950 amino acids, which would require not quite 3000 DNA nucleotides in its gene to code (at least). These are like nice little modules!
Many of the domains are mix-and-match. As in the domains violate a simple protein phylogeny since it would require odd sorts of gene fusions where several parts from several genes are slapped together to make a new functional gene, but each of the part need modification too! This is a known problem in evolutionary biology called “Promiscuous Domains.”
The “ZNx3” under the CXC domain is probably a suspected Cysteine zinc finger array, but it hasn’t been fully resolved according to literature I’ve read. If it is, I’ve argued before why its absurd to think zinc finger arrays can become functional by random mutation and selection.
But in actual fact, you have no idea whatsoever. All you have is your guess, based on nothing at all.
Doesn’t matter what you think is outrageous. That’s not an argument.
No, there is nobody who says “it can easily arise because one of the proteins is actually homologus to hexameric helicases”.
Yeah so do I, no wonder nobody actually made an argument that “evolving ATP synthase is easy” just because the F1 subunits alpha and beta are homologous to hexameric helicases(though, they actually are no matter how much you want to insist they merely have “some passing similarity”).
By the way there’s an error in the figure, it incorrectly shows that the membrane spanning ring is a “proton channel”, and that the protons appear to enter the center of the c-ring, and exit at the center of the alpha-beta hexamer of the F1 subunit. That’s incorrect, the proton channel actually split in two in the a-protein, and is at the interface between the protein labeled a(base of the stator), and the ring labeled c(rotor).
I have corrected your figure:
Protons enter into a half-channel at the base of the stator(the a-protein), becomes bound to aspartatic acid(forming aspartate) in the middle of a c-ring subunit, causing the c-ring to rotate and pick up more protons. Eventually the c-ring has turned all the way around and can release the proton back into the other half-channel in the a-protein, releasing it into the outer membrane space of the mitochondria.
The c-ring, even by itself, can actually function as a protein translocase able to move proteins across the membrane.
You have not answered the questions I asked in the OP. IIRC, you no longer consider yourself a supported of ID. But since you were an important part of the movement for several years, I presume you will have some hlepful insights.
And yet that basically forms the basis for the adaptive immune system. First the initial VDJ recombination, followed by recurring rounds of random mutation of a protein, such that it forms a well-fitting interface that can bind another. From a stage where the first iteration of binding Ig’s might be relatively weak and imprecise.
The bottom line is that T-urf13 is a new protein, encoded by a gene that has no protein-coding antecedents; it is, bluntly, a new protein that arose “from scratch”, through a series of duplications, recombinations, and other mutations that occurred spontaneously in the course of the breeding process that gave rise to the cmsT line.
These points are already problematic for the assertion by ID proponents that new protein-coding information cannot arise by natural processes. But T-urf13 is more than a nondescript polypeptide that happens to affect male fertility in corn. It turns out that T-urf13 is a membrane protein, and in membranes it forms oligomeric structures (I am not sure if the stoichiometries have been firmly established, but that it is oligomeric is not in question). This is the first biochemical trait I would ask readers to file away – this protein is capable of protein-protein interactions, between like subunits. This means that the T-urf13 polypeptide must possess interfaces that mediate protein-protein interactions. (Readers may recall Behe and Snokes, who argued that such interfaces are very unlikely to occur by chance.)
T-urf13 also binds to the toxin produced by the fungal pathogen. But it does not just bind the toxin “passively” – upon binding, a non-selective ion channel is opened, leading to dissipation of transmembrane ion gradients, and all of the resulting events that accompany collapse of proton-motive force. (In mitochondria, this will lead to uncoupling and crippling of mitochondrial function; this is probably why cmsT plants are so devastated by the disease.) This is the second biochemical trait that readers should keep fresh in their minds – T-urf13 is a gated ion channel. (This an the other interesting biochemical properties of Turf13 are reviewed in reference 7.)
Until you have some actual numbers all you have is your wild and baselss estimates.
What you need to show us is that all of those parts came about at the same time. You need to show us the organisms just before and just after this complex emerged. Otherwise, you are just assuming they came about at the same time with that exact function.
I’m working on them, but diagrams like that show why the folds have to be pretty precise, doesn’t it?
What you need to show us is that all of those parts came about at the same time.
No I don’t. You guys claim selection will do it but never show why. That’s basically an appeal to an unknown untestable mechanism. That’s pure faith based, not deduction from physical first principles.
You tried to invoke the immune system as a model, and I showed the first flaw in that reasoning because those aren’t germline cells. Try mutating other parts of the DNA like that in a germline and see what disaster happens.
I mentioned the EZH2 proteins. Variations in it are implicated in disease. It should be obvious why mutations causing structural variation would compromise the functioning of the complex. That’s good prima facie evidence that it can’t be reached by natural selection since the intermediates are mal-functioning. You could of course appeal to imagined, unknowable, untestable, un deducible evolutionary pathways, but let’s not represent that as science.
@stcordova, you don’t know this. Your incredulous assertions do not constitute evidence that the bolded statement is correct, and your tortured logic likewise does not make it so.
No, there is no actual inference being made. You really do just sort of “hunch” it. You do not have a logical argument(that you have given anywhere here) that logically entails, or somehow probabilistically implies, that the “intermediates” are too unlikely to be functional. You seem to be basically just winging it based on some sort of Hoyle-fallacy.
