Evolution of KRAB Zinc Finger Proteins vs. the Law of Large Numbers
There are patterns in biology that violate the law of large numbers, and thus suggests Intelligent Design or at the very least statistical miracles. The pattern involves KRAB-ZnF proteins that have multiple zinc finger domains side by side that are inexact copies of each other and would require a scenario of co-evolution of their DNA binding partners with every additional zinc-finger insertion — a scenario indistinguishable from a miracle.
The role of a zinc finger can be something like a clamp or a lock. Each zinc finger in a KRAB-ZnF protein is fine-tuned to connect with a DNA much like a lock (the zinc finger) can receive a key (like DNA). Here is a depiction of a KRAB-ZnF protein with 4 zinc fingers as part of a large chromatin modifying complex. The four zinc fingers are marked “ZN” and connect to DNA:
The evolutionary explanation of side-by-side repeated patterns of zinc fingers such as in KRAB-ZnF proteins shows a severe lack of critical thinking by evolutionary biologists who pretend “phylogenetic methods” are adequate explanations of mechanical feasibility of common descent.
To illustrate the problem, consider the KRAB-ZnF protein known as ZNF136. For reference, this is the amino acid sequence of ZNF136:
https://www.uniprot.org/uniprot/P52737.fasta
This is an amino acid fragment contained within the ZNF136 protein
TGEKLYDCKECGKTFFSLKRIRRHIITH
This short sequence is called a zinc finger domain which in 3D looks like this:
https://sciencescienceeverywhere.files.wordpress.com/2015/08/figure-11.jpg
Wiki gives a description of the function of zinc fingers in proteins that have them:
http://wikipedia.org/wiki/Zinc_finger
A zinc finger domain requires two “C” amino acids and two “H” amino acids placed in the right positions. It requires a few other things too…
There are 13 zinc fingers in the ZNF136 protein and these are their sequences:
TGEKLYDCKECGKTFFSLKRIRRHIITH
SGYTPYKCKVCGKAFDYPSRFRTHERSH
TGEKPYECQECGKAFTCITSVRRHMIKH
TGDGPYKCKVCGKPFHSLSSFQVHERIH
TGEKPFKCKQCGKAFSCSPTLRIHERTH
TGEKPYECKQCGKAFSYLPSLRLHERIH
TGEKPFVCKQCGKAFRSASTFQIHERTH
TGEKPYECKECGEAFSCIPSMRRHMIKH
TGEGPYKCKVCGKPFHSLSPFRIHERTH
TGEKPYVCKHCGKAFVSSTSIRIHERTH
TGEKPYECKQCGKAFSYLNSFRTHEMIH
TGEKPFECKRCGKAFRSSSSFRLHERTH
TGQKPYHCKECGKAYSCRASFQRHMLTH
For completeness, there is a degenerate zinc finger in ZNF136 with the sequence “YGEKPDTRNQCWKPFSSHHSFRTHEIIH”
Why are the Zinc Fingers so different in sequence (except for the conserved amino acids)? To target a section of DNA, the zinc finger must be tuned to target it. Think of the zinc finger like a lock and DNA as a key that fits into the lock. In fact, for both the study of biology and medical applications, humans have a desire to make their own zinc fingers — like lock smiths. To bind a large segments of DNA, side-by-side zinc-fingers have to be tuned to their respective side-by-side DNA partners such as illustrated here:
By the way, there is a website that helps researchers construct the right amino acid sequence to make a zinc finger for a particular DNA target:
https://www.scripps.edu/barbas/zfdesign/zfdesignhome.php
Now, to visualize the critical/conserved amino acids, see the protein sequence here with highlights on “C” and “H” amino acids.
http://theskepticalzone.com/wp/wp-content/uploads/2019/04/znf136_zfC2H21.png
Note one of the lines is not exactly like the other lines in that it is missing a “C”. This is the degenerate zinc finger mentioned above. So there is 1 degenerate zinc finger and 13 functional ones.
From this diagram it is apparent that the regular appearance of “C” and “H” is a violation of the law of large numbers, hence this pattern is not due to random point mutation alone. To “solve” this problem, Darwinist explain the pattern through segment duplication followed by some point mutation and natural selection, but this is not mechanically feasible either!
To understand why, let the reader first ponder the alignment I made of the Zinc Fingers in the ZNF136 protein using MEGA 6.0/MUSCLE software:
http://theskepticalzone.com/wp/wp-content/uploads/2019/04/znf136_zfC2H2_muscle1.png
Then let the reader, consider the distance matrix generated by MEGA 6.0 which measures the number of nucleotide and percent differences between the zinc fingers.
http://www.creationevolutionuniversity.org/public_blogs/reddit/znf136_distance_matrix.xls
(All of the above results are reproducible, so I leave it to interested parties wanting to confirm the results to do so.)
For the duplication to work, at a bare minimum the right 84 nucleotide segment must be chosen, and then perfectly positioned for insertion so as not to break a pre-existing zinc finger. But supposing the duplication succeeds, why are the zinc finger’s conserved features involving “C” and “H” and other amino acids preserved and not eventually erased by point mutation given we obviously see the zinc fingers are different from each other. To preserve the “C” and “H” and other necessary amino acids in a zinc finger, the new zinc finger needs to be under selection. But in that case one is simply concocting a “just so” story for those newly minted zinc fingers without any respect for the difficulty of such a “just so” story being probable — and it is not probable!
To understand the problem of such a “just so” story, recall zinc fingers bind to DNA regions. Btw, this includes DNA regions such as ERVs! And ERVs are indicated to participate in the Stem Cell Pluripotency regulatory network:
https://www.nature.com/articles/nature13804
Further, the KRAB-ZnF protein is part of an incredibly complex machine that does chromatin modification (as shown above) by often attaching to ERV targets. But this would require that ERVs (or whatever DNA target) needs to co-evolve with the KRAB-ZnFs that attach to them!
Do these researchers even consider the fact such evolution would have to be instantaneous otherwise it would degrade function and not let the genome have the opportunity to adapt to the new accidental copy of the zinc finger because the duplication would immediately be selected against!
The above KRAB-ZnF complex is like a read/write head acting on Chromatin. Chromatin itself is an amazing mind-boggling design akin to computer ROM and RAM in one.
Again, the difficulty of evolution via random insertion/duplication mutations followed by point mutations is that such events would disrupt the binding of an already operational set of zinc fingers. For example, suppose we have an array of 10 zinc fingers side-by-side that collectively bind to a target DNA. Suppose one zinc-finger is duplicated and the number of zinc fingers is increased from 10 to 11. Oh well, the binding ability is broken or at best compromised, much like adding a single letter to a pre-existing password!
In sum, there is a violation of the law of large numbers in KRAB-ZnF proteins which is not explained by random mutation, nor random segment duplication followed by some point mutation and fixed by natural selection. Some other mechanism for the emergence of such proteins is indicated and would likely be indistinguishable from a miracle. Given the importance of such zinc finger proteins in the control of ERVs which are important in the stem cell pluripotency regulatory circuits, the origin of KRAB-ZnFs is even more miraculous.
I disagree with Entropy.
And Rumraket.
phoodoo,
I’ve guano’d the one comment that is, in my view, rule-breaking (up to this point). If phoodoo or anyone else want to argue about other comments, do it in the appropriate thread. Hence I am now guanoing comments that, in my view, are making complaints about moderation.
Alan Fox,
I would just like to discuss the points raised by Entropy and Rumraket. We are allowed to do that right?
I am interested in hearing other posters points of view on Entropys ideas. Isn’t that what this thread is for?
Why would you think I am discussing moderation? How crazy.
Of course. Simply saying” I disagree” is not doing that. What point are you disagreeing with? What evidence can you show to support your disagreement?
The thread is to discuss Sal’s OP and his misconceptions regarding zinc fingers. If you have a view on that and have an argument with Entropy regarding the biology of zinc fingers that would be great. Bring it on.
Good one. You see the distinction between me being crazy (rule-breaking) and an expressed thought of mine being crazy, in your view (not rule-breaking).
One doesn’t need to know EXACTLY because one can see if it was biased distribution that made collagen, then that same distribution can’t explain TopoIsomerase or KRAB-ZFP or whatever! Proof by contradiction. An estimate of the distribution will do.
Besides the sword cuts both ways, Darwinists don’t know the exact distribution either yet they assert these things evolve naturally!
But the fact the proteins are so radically different in amino acid bias is good evidence we don’t have biased distributions of point mutation or some random copy and paste mechanism and delete mechanisms.
If you don’t find my arguments sufficient for your level of accepting Collagen and KRAB-ZFPs are improbable sequences, I respect that. We’re cool.
He appears to not actually have understood your example.
He picked out a subsection of the protein sequence and repeated it, apparently cutting the protein in half and repeating the same half over and over again, ending up with this:
SGYTPYKCKVCGKSGYTPYKCKVCGKSGYTPYKCKVCGKSGYTPYKCKVCGKSGYTPYKCKVCGK
…rather than expanding the the whole stretch on from the area of homologous alignment.
Of course I picked an example that would BREAK the zinc finger. Neither Entropy, you, DNA_Jock, Allan Miller nor any of the detractors here have justified why a blasted zinc finger domain has to be preferentially chosen for a tandem repeat over any other sequence! That’s the friggin point!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
I’m going to post on the zinc fingers of TFIII3A shortly. In the meantime this is a diagram of the context of TFIII3A in the complex machinery of transcription initiation of DNA.
Click here for the larger diagram, and you can see TFIII3A in the larger context of the Transcription Initiation machinery:
https://rgd.mcw.edu/pathway/PW0000128/RNA%20polymerase%20III%20transcription%20pathway/pwmap.png
The reason I wanted to show TF3A (TFIIIA) is to contrast it with ZNF136. The violation of the law of large numbers is apparent in ZNF136 because of the regularity of residues appearing. That regularity is not quite so apparent in TF3A zinc fingers.
I got the coordinates of the zinc fingers from Interpro/UNIPROT which I depict in the diagram below.
The lines in TF3A with colored boxes are zinc fingers, but they don’t line up quite so prettily as with ZNF136. So one can’t really use violation of the law of large numbers as I used it for ZNF136 to suggest a miracle.
One has to resort to the work of researchers like my mentor and friend John Sanford and invoke the waiting time problem for matching of protein/transcription factors to DNA binding sites. The peer-reviewed paper is here:
https://tbiomed.biomedcentral.com/articles/10.1186/s12976-015-0016-z
When I showed Dr. Sanford the KRAB-ZFP (like ZNF136 in the opening of this thread), he said the waiting time problem would apper to apply in the case of matching zinc fingers to corresponding DNA targets. By way of extension it would apply to the TF3A zinc fingers being optimized for DNA targets.
In fact, if there is co-regulation of genes by the same transcription factor, several genes need similar transcription factor binding motifs! This would also put a constraint on when the genes were supposedly duplicated from each other with the transcription binding motifs as well as the zinc fingers that target them. If the genes are radically different from each other but have the same TF binding sites, this is problematic for evolution. A question for future research….
Anyway, here is the picture of the TF3A sequence arranged to highlight the zinc fingers:
The “waiting time problem” in all cases I have seen creationists lay it out commits the texas sharpshooter fallacy.
One reason I raised this topic is that it is related to the supposed parasitic nature of transposons and retroviruses. I believe a lot of retroviruses were actually functional elements that went berzerk. The reason for that is viruses can’t live outside of the host for very long, therefore they originated most likely from a host.
I only found out recently a lot of virologists believe in cellular origins of viruses!
The function of transposable elements is demonstrated in regulation of adult tissues:
https://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30079-X
Here is the DNA binding logo of a zinc finger target. For this coordinated system to evolve it would require the absurd situation of zinc finger ZFP932 evolving simultaneously with the transposon and then integrating this interaction with the regulation of stem cells and adult tissues. The reason for the must co-evolve is that unregulated expression of the transposon is BAD juju.
The paper discusses a mouse-specific Zinc Finger Protein and it’s paralogs. So did a transposon pop up and then a mouse-specific Zinc Finger Protein pop up to regulate it?
Immediately below are the zinc fingers of ZFP932.
From the paper is a diagram in the next comment of a DNA binding target logo:
This is the DNA binding logo of the Zinc Fingers of ZFP932:
No it doesn’t. This is more like the problem of having a key that fits a lot. For the two to be functional, they have to match each other.
DNA binding targets are the key, and a zinc finger array is the lock, with the individual zinc fingers the tumblers of the lock.
That was my first thought, and yes, you’re right, rather than following the example he cut the zinc finger in half. Clearly Salvador missed the whole point. Not worth giving it another try after that one. Hopefully it helped someone else.
There’s no need for fucking arguments. Of course they’re improbably sequences you ass-hole, they’re biased because of both negative and positive selection, because they do not arise by random number generators, but by biochemical/biophysical phenomena. Because they’re restricted by their functionalities, by their interactions with other molecules. They’re not computer models, they’re biochemical entities.
stcordova,
But you are insisting it can’t, and the reason is the LLN. I think in order to do that, you need to show the probability, taking account of all mechanisms, is below a boundary. It’s not up to evolutionists to do the work for you. Darwin’s wasn’t a probabilistic argument in the first place. You have discovered a brilliant new proof that Darwinism is wrong, but when it comes to supporting it – your argument – you actually play “They haven’t shown it’s right”.
Biochemistry doesn’t say a KRAB and and array of zinc-fingers will naturally evolve to regulate a transposon. Non-existent function can’t be selected for! The Waiting Time problem examines the problem.
In order to be “chosen,” they have to be functional, which makes them subject to natural selection by definition. Broken, functionless, tandem repeats would eventually disappear. I haven’t bothered to explain something that obvious because I didn’t think you’d be that ignorant, you mindless imbecile!!!!
I understood that Entropy had no clue and he got called out on the actual problem. There is no law of biochemistry that says zinc fingers should be preferrentially selected for tandem repeats, but the repeats aren’t tandem are they!!!!
Look at ZFP932, are those zinc fingers tandem repeats? Nope!
So how did they come to be? A fortuitous preferentially copied tandem identical repeat that just happened to encomass a pre-existing zinc finger in an non-functioning gene segment that got activated and then randomly evolved to target a trasposon that just happen to appear in mice and then the ZFP932 and transposon do a tango together to regulate stem cell development???? Doubtful.
Biochemistry “says” that interactions occur between molecules having some or other moieties, and that such moieties are prone to provide varying degrees of affinities and thus varying degrees of potential functionalities that can be “scanned” and improved by natural selection. Such natural selection will result, all too obviously, in biased proteins.
Biochemistry “says” that DNA complementarity occurs, and that it’s not perfect. That rows of repetitive DNA can slip in, slip out, misalign, etc, resulting in small and large repeats. Biochemistry “says” that if a small protein unit binds DNA, two such units will bind better, and three even better. Biochemistry also “says” that introduced variety in those units can give them differential affinities towards more than one potential target and allow for natural selection against different DNA sequences when the interactions have functional consequences.
The “waiting time problem” is an example of people making shit up out of their ignorance of biochemistry.
Nope. Can’t select for non-existent function.
Reading for comprehension Salvador:
A Tandem Repeat amplification of Entropy’s Counter Argument:
That’s not much of a counter argument. Repeating it over and over doesn’t refute the problem of the coordination of the transcription factor ZFP932 zincfingers to the DNA binding logo . Neither will natural selection solve the problem for the reasons I’m about to state.
Here are the considerations:
taking the most conserved part of the DNA binding logo (position 4-16) of ZFP932 we have:
where “-” is the 16th position.
But there is a subtlety here that must not be lost. There is an important property of a classical C2H2 zinc finger which affects the probability of the composite array of 4 zinc fingers being able to coordinate to target a transposon logo like the one below.
From wiki on zinc fingers:
To depict the problem, I pose a possible scenario in light of the wiki I just quoted.
For each of the 4 zinc fingers of ZFP932 discussed above, I highlight in CAPS and in bold the bases that are targeted and leave in lower case the other bases for context. It may not be exactly like this, but it should be close and conveys the problem of targeting a logo with an array of zinc fingers:
ZincFinger 1: ACCTaagacagg
ZincFinger 2: accTAAGacagg
ZincFinger 3: acctaaGACAgg
ZincFinger 4: acctaagacAGG-
So, a tandem repeat won’t work to get this logo will it? Nope. And in fact, given the constraints of overlap, a Tandem repeat may not even bind because it would create target a string that doesn’t exist in principle.
For example, a zinc finger targeting the a string like “ACCT”, given the overlapping principle, there is no such string that can be targeted by an ARRAY of zinc fingers that recognize “ACCT” because “ACCT” is not symmetric.
If each zinc finger repeat recognized “ACCA” (or some other symmetric DNA), then a string recognizable by an array of identical zincfingers string is possible — like “ACCACCACCACCA…”
This means a tandem repeat will either not bind to anything or it’s just going to bind to random partners. Not exactly good for keeping an organism working if randomly mutated transcription factors are just floating around in the cell and creating traffic jams and blocking function. The effect could be toxic.
You didn’t explain to the readers why a tandem repeat should preferentially copy a segment containing a zinc finger, not to mention, you didn’t account for the origin of the zinc finger on some random protein.
Thanks for serving as my punching bag for the week. HAHAHA!
I didn’t? What is this then?
ETA:
You’ve been punching yourself Salvador.
Of course not. The interesting thing is that you missed this part, thus confirming the epithet I used to refer to you:
Of course not. They must be almost identical for no reason:
Yes, they will. Here the part of the explanation that you missed:
Molecular interactions are not perfect Salvador. Proteins, including zinc fingers, show varying affinities towards multiple potential “targets,”
Nope, What this means is that you really don’t understand that molecular interactions vary in strength and in specificity quite a bit. It’s not black and white. They’re not solid stone, they’re dynamic.
No they don’t for tandem repeats. Are Huntingon disease tandem repeats chosen for copying because they are functional.
You haven’t explained why the tandem repeat necessarily includes the zinc finger rather than some random segment in the pre-existing gene. Btw, for something like ZNF136, it has to keep choosing doing this trick 13 times!
So much for your ectopic duplication theory since they aren’t tandem repeats. I showed with the example of ZFP932 that if they started out as tandem repeats, they would be worthless to start with, not to mention the waiting time issues.
You’re not paying much attention (how surprising), they obviiusly started as tandem duplicates. It’s “written” all over their sequences (as I showed in the pretty picture), you’re just not looking carefully enough.
What you showed is that you have no idea about biochemistry, and that you cannot read for comprehension, wince I explained it to you and repeated the explanation at least twice. Here it goes again so that you can ignore it, again, and thus show how well the epithet I use to describe you suits you:
Yes, I have. again:
Note that my explanation contains this sentence: Broken, functionless, tandem repeats would eventually disappear.
It’s not that broken tandems never happen, it’s that complete ones are more likely to have some function. You’re asking me about the functional ones. Obviously functional ones must have complete zinc fingers. So simple and straightforward, yet you miss it.
No Salvador, as I explained above, only the first duplicate is difficult. The rest are straightforward. Look at the pretty picture.
ETA: If you had the understanding you’d quickly notice that it isn’t even 13 events required. Once we have two duplicates, three can easily happen. Once we have three: four, and five easily happen in one step. From a five-tuple we can easily get, again in one step, the six, seven, eight, nine-tuples. So, one more and we have from ten to seventeen tandem repeats. Four events Salvador.
That you felt the need to make an emphasis on the number of copies came only to show that you really did not understand the example, as Rum suggested.
I’ve only loosely been following this conversation, but has anyone else noted that there seems to be a duplicated block of 5 ZFs in ZF136?
I just noticed it in the alignment by eye, but then confirmed it by aligning the relevant sequences myself and seeing how they cluster in a phylogeny – 4 with 9, 5 with 10, etc.
evograd,
Thanks!
————–
Look at the pretty picture Salvador! (Too advanced for you I’m afraid, but heck, it’s pretty!)
Dear Salvador,
I truly, really, predict that you won’t even try understanding what I wrote. Every time you bring something, I’ve already dealt with it. It’s just that it won’t register with you. Maybe because you don’t want it to register, maybe because you don’t actually read it, and/or maybe because you really don’t have the background and the mental prowess for understanding any of it. I suspect that the answer is “all of the above.”
Given that, I leave you to feel triumphant imagining that everything you did not understand was false anyway. That you won. That you showed me the wrongness and evilness of relying on phenomena, many of which scientists have checked and/or measured in the lab themselves, to try and explain what we observe in the molecular workings and evolution of living cells.
The explanation surely must be some absurd magical being in the sky who died so that you could get away with such sins as pride (in the arrogance with which you present your most ignorant claims, and refusing to contemplate the very idea that you might be wrong), sloth (to even try and understand what’s explained to you), and lying for Jesus.
I disagree
I don’t think so.
I think you won’t.
Says you.
Oh really?
My evidence is this post of yours.
You don’t get to decide what is evidence, King Alan.
Alan, your bias is showing.
Pull your slip down.
Oh look, another in a long line of phoodoo meltdowns.
Ouch. It’s not preferentially copied, but the result of random processes is biased by selection towards functional sequence.
Thank goodness you didn’t mention it then. That would be like bringing abiogenesis into a discussion on evolution, which never happens.
Your triumphalism is decidedly misplaced, speaking as an observer.
Exactly!
A random copy of a segment of a pre-existing protein won’t necessarily grab a zinc finger and make another zinc finger will it. It has to be the right length and taken from the correct coordinates, right?
In fact this probably should be happening to a duplicate of a pre-existing protein, because doing a random cut-and-paste to a pre-existing FUNCTIONING protein would likely damage its function especially in the unlikely event it adds a binding zinc finger where it ought not to be.
So is the cut-and-paste operation happening to a functioning protein or its duplicate?
Thanks for analyzing. But this is exactly the sort of story telling that doesn’t account for the problem of change in binding logos. The binding logo for ZNF136 is not available, but the one for ZFP932 is. If you look my analysis of ZFP932 you’ll why see a phylogenetic story tale doesn’t work.
Good evidence of hierarchical control, not phylogeny of the zinc fingers for the reasons stated in the example of zfp932.
In fact a paper on developmental biology said Transposable Elements enable hierarchical regulation.
So, like I said, build a model genome with recombinational slippage and see how often it happens given realistic parameters.
Recombinational slippage would create a gamete with a loss and another with a gain. If loss is detrimental, that segment of the first gamete’s genome would ultimately fail through purifying selection. The other chromosome, however, has the intact finger plus a bit. By reciprocal exchange you are only reducing chances by 50%; hardly a deal breaker.
Copy and paste, really. Go on, build the model, and make it biologically realistic. The latter part of the exercise might help you understand what people are saying, should you wish to.
LOVELY IDEA! I’ll suggest it at the conference I’m speaking at.