A Response to David Gelernter’s Attack on Evolution

My ability to read the paper Brian has incorrectly referenced multiple times. Read the post where I explain this Bill. It’s been linked.

Your “therefore” doesn’t actually follow. Straight up non-sequitur.

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Seem to misrepresenting this paper.
They say:
“This made the problem of the Cambrian Explosion even more acute: 550 million years ago there were no animals at all, and 537 million years ago there were already fully developed crown-group arthropods like trilobites with sophisticated compound eyes, exoskeletons, and articulated legs. Does anybody seriously believe that such an enormous transition within 13 million years is a piece of cake? Gelernter is right to be skeptical, and mainstream science supports his arguments.”

From the paper they cite:
These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana , Rusophycus ) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma.
So are they just ignoring the existence of stem Euarthropods? They certainly were around 550mya. They are making it sound like nothing then all the sudden crown groups.

Also, I disagree with a lot in that paper they cite.

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So your opinion is you understand the material better than Brian does. That does not mean he is wrong. You are labeling him as being wrong yet it is just your opinion.

Also, I’m a little behind on Cambrian dating but isn’t 550ma Precambrian… soooo

Yes, that is my opinion. Demonstrably so. But the falsity of his claim is not contingent on my opinion. It is contingent on the contents of the Tawfik paper Brian cites to support his incorrect claim. But it does not support his claim as I have shown.

It is not merely the fact that I seem to understand the material better than him that makes him wrong. It’s that I SHOW him to be wrong. Read the link Bill.

What if he simply said that the same mutational combination combination in birds and humans is evidence for coordinated mutations given we observe the same changes in two different animals.

Mr Cole…

This paragraph has also thrown up redflags:

“What about the other Ediacaran trace fossils? All gone. A seminal study published in 2016 experimentally demonstrated that these Ediacaran trace fossils can be easily reproduced as artifacts of stirred up bacterial mats that covered the Ediacaran sea floors.”

I remember reading that paper and I’m
99% sure that is not the conclusion that paper reached. I reached out to the author and am awaiting his response before I really delve into this.

But here are two papers published two years after the study Bechly and company refer to. Showing evidence of bilaterian animals in the Ediacaran.

https://royalsocietypublishing.org/doi/10.1098/rsos.172250

Update: they are totally misrepresenting that paper. The paper did not conclude that all ediacaran trace fossils are ruled out. Only that a closer look is required and alternative explanations, like the ones put forward by the author, need to be ruled out before assigning them to biology. This is from
The author. Reproduced with his permission: “We need to look for 3D trace fossils (i.e,. penetrate into the sediment) that should be a stronger indicator of animals.”
This describes some trace fossils in the edicaran. See the second paper I link to! So Bechly and company are making grand claims the data does not support. Also the author was very humble and said, “ I have not followed up much on that topic since I published that paper…I cannot add much more since I know more about sediments and less about animals.”

So maybe the ID folks should slow down a bit promoting that paper.

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He is making a stronger conclusion than you think is warranted by the data. You could simply express that thought. Again your opinion but I agree more evidence is probably prudent here.

There are no specified changes in evolution. Neither human speech, bird calls or vertebrate eyes were specified in advance, and none of them had to evolve.

Your conclusions are based on a false premise.

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Yep. It’s the same “sharpshooter” logical fallacy ID-Creationists have been tripping over forever. The claim what we see was somehow targeted and is the only possible combination which will support life.

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Maybe for once you could try actually discussing the rebuttal scientific evidence instead of knee-jerk defending anything to do with Creationism.

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So, @bjmiller, in the paper you point to, exactly how many “specific, coordinated mutations” are described?

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Heres Bechly and company:

“What about the other Ediacaran trace fossils? All gone. A seminal study published in 2016 experimentally demonstrated that these Ediacaran trace fossils can be easily reproduced as artifacts of stirred up bacterial mats that covered the Ediacaran sea floors.”

Here’s the author of that study discussing this paper: https://royalsocietypublishing.org/doi/10.1098/rsos.172250

“Yes, that looks like an animal burrowing into the sediments

The mechanism I describe in my article would definitely not explain that.

Cheers

G”

Soooo yeah. Looks like all the Ediacaran trace fossils aren’t gone after all.

@bjmiller it isn’t hard to email these guys and make sure you got them right…

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Some have argued that catalytic antibody (abzyme) research challenges the argument for extreme protein rarity. In reality, the truth is the exact opposite. As a case study, Shahsavarian et al. used a phage display library of the size on the order of billions to generate catalytic antibodies approaching the efficiency of beta-lactamase enzymes in breaking down antibiotic molecules. Antibodies are highly specialized multicomponent proteins that are designed to maintain a stable structure as localized sections of the protein known as Fv regions dramatically vary. One Fv region resides at the end of each of the antibody’s two branches, and it consists of the variable domains within a heavy chain and a light chain. The immunoglobulin gene randomizes the variable regions allowing for a binding site to eventually appear that can bind to a target and possibly break it apart. Finding the right combination of amino acids to degrade an antibiotic molecule proved relatively easy.

Yet, abzymes function very differently from enzymes. In the former, the variable domains forming a binding site consist of localized sequences of amino acids held in fairly consistent positions by nonvarying sections known as constant regions. The constant regions also ensure the variable regions in the heavy and light chains reside at the right locations in close proximity. In contrast, an enzyme starts off with the amino acids which form the catalytic site residing at distant locations along the chain. The folding process forms the active site by moving the correct amino acids to the right locations and positioning them in the right orientations.

Moreover, in enzymes both the active site and amino acids throughout the protein structure are specified to assist in its target function. Specifically, an enzyme’s entire conformation morphs into multiple configurations. This complex dynamic is well summarized by Hammes et al.,

Multiple intermediates, multiple conformations, and cooperative conformational changes are shown to be an essential part of virtually all enzyme mechanisms.

Each reconfiguring involves the coordinated rearrangements of single amino acids and often entire secondary structures.

Therefore, the tasks of forming a functional abzyme and generating a novel functional enzyme represent fundamentally different problems. A new enzyme requires both finding a set of amino acids with the right chemical capacities and generating a new fold that brings those amino acids together properly in 3D space and provides structural support. The fold also must perform complex conformational changes to support specific chemical activities. The abzyme only needs to stumble upon the correct amino acid sequences in the variable regions for the catalytic activity. The amino acids are already positioned properly by the constant regions, and the latter also provide the needed structural support. In addition, abyzmes do not morph their overall conformations to assist specific chemical reactions. These differences explain abzymes’ limited capacities, and they result in enzymes having much greater functional sequence rarity.

Ironically, the abzyme research greatly strengthens the argument for the generality of extreme rarity, for it shows that degrading antibiotic molecules is a relatively easy function to achieve. In contrast, the enzyme HisA participates in an intermediate step in the synthesis of the amino acid histidine where it performs a highly specific molecular rearrangement. Namely, the enzyme detaches a hydrogen atom from one nitrogen molecule and attaches a hydrogen atom to another nitrogen. No abzyme or polypeptide generated in a randomized library has ever demonstrated a comparable ability to reengineer molecules.

The difference in the difficulty of antibiotic degradation and molecular reengineering explains beta-lactamase’s greater resilience to accumulating mutations than HisA’s. This difference directly translates into HisA’s more extreme sequence rarity. Many enzymes and structural proteins also perform more difficult tasks with greater specificity requirements than beta-lactamase, so a 10% populated target region should be an optimistic estimate for a large percentage of globular proteins.

There are those interesting moments where you read one sentence and can almost 100% guarantee that everything after that sentence will be wrong.

There are plenty of examples of standard enzymes where the residues responsible for catalytic activity are in a contiguous segment.

This is also false. There are plenty of enzymes where chunks of the protein can be removed without affecting activity. Also, “specified” is a meaningless term.

No, they don’t. In the case of abzymes, there is a ~10 amino acid section of the protein that is randomized. This is no different than the insertion of a random sequence (e.g. random recombination event) into a non-antibody protein.

Sharpshooter fallacy. You are painting the bulls eye around the bullet holes. Evolution isn’t trying to hit a target. All evolution is doing is selecting for genetic changes that increase fitness.

It is entirely possible that there would be additional enzyme functions if the variable region were located elsewhere in the protein. Again, you are committing the sharpshooter fallacy.

Perhaps you should tell Douglas Axe that.

B-lactamases take atoms from water and re-engineers the b-lactam with those atoms.

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But you never go on to explain why. You just wrote a huge wall of text that contains exactly zero valid reasons for reaching that conclusion.

So only sixty eight orders of magnitude higher than estimated by Axe.

Shouldn’t they have needed to generate 10^77 sequences before they found a beta-lactamase function?

But I’ve read on EN&V that it should only happen roughly 1 in 10^77 attempts.

But now you’re telling me relatively little evolutionary change is needed to discover a biologically useful function, such as catalyzing the breakdown of a specific antibiotic molecule?

Funny.

Uhm, no. The fact that it is “easy” to degrade antibiotic molecules does not at all strengthen the argument for the extreme rarity of functions. In any way. Straight up non-sequitur.

It seems to me to imply the diametrically opposite. If sequences with different but useful functions were all extremely are in sequence space, and isolated from each other (as they would need to be to prevent evolution from discovering new functions from already existing functional sequences by sampling into their immediate surroundings), then why is it so easy to turn an antibody protein into an enzyme with a biologically useful function? Shouldn’t those two be both incomprehensibly rare, and totally isolated from each other?

No, it doesn’t.

Every time it comes to supplying the evidence or reasoning that is purported to support your conclusion, it turns out the statement you make is either just flat out false, or at best a mere blind assertion. Or implies the diametrically opposite of the ID narrative.

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One must be very careful to distinguish between what some might imagine being true from what has been demonstrated to be true empirically. Dan Tawfik has stated that all theories about the origin of new protein folds are based primarily on speculation. Ignoring the implications of hard data by appealing to speculative theories is like a trial lawyer ignoring video footage of a crime in favor of the testimony of his client’s imaginary friends.

The hard evidence points to the following:

  • Enzymes can only evolve to the extent that the structure does not change, the active site remains basically the same, and the catalyzed chemistry is similar. Tawfik labeled these changes as micro-transitions.
  • Evolving a new protein fold requires an evolving gene to pass through regions of sequence space without any function.
  • A straightforward mathematical analysis of studies on the effect of random mutations on protein stability/function demonstrates that sequences corresponding to functional proteins are exceedingly rare.

The analysis of protein rarity is now much more accessible to the public. Doug Axe’s 2004 JMB article was extremely difficult to understand by anyone who was not an expert in the field. Consequently, critiques of his work could use erroneous arguments, and the public was powerless to identify the errors:

In contrast, Tawfik’s experiments can much more easily be interpreted. For instance, roughly half of all beta-lactamase mutants with three random amino acid changes are still functional. That change corresponds to a 1% alteration in the initial sequence. And, nearly all mutants with 10% of the sequence randomly altered are nonfunctional. In comparison, a 10% change in the letters of a short paragraph is still largely readable. Therefore, functional protein sequences are rarer than readable English paragraphs.

In addition, a large proportion of proteins consist of combinations of a limited number of domains just as a limited number of words are used in most sentences. This pattern was described by Scaiewicz and Levitt, and they identified numerous other similarities between protein sequences and human language including syntax, semantics, grammar, and the importance of context.

This observation relates to the common error of claiming that estimates of protein rarity exaggerate the difficulty of finding a functional target since other proteins or other distinct versions of the same protein might exist which could perform the same function. A multitude of alternative targets could dramatically increase the odds of finding one of them. Yet, this possibility seems remote given the extremely low probability of a random search entering a target region. It is also challenged by the fact that newly discovered multidomain proteins are very often “combinations of domains characterized by a limited number of sequence profiles.” If sequence space contained such vast numbers of targets, newly discovered proteins should not repeat the same sequence and structural patterns so often.

In addition, the bacteria population exceeds the population of most eukaryotic taxa by many orders of magnitude (e.g. 10^30 bacteria verses 10^13 trees). Yet, the percentage of taxonomically restricted genes (TRG) in ash trees is 25%, to name just one example, and this percentage is at least as large as the percentage in most taxa of bacteria. Some have argued that the TRG estimates are greatly exaggerated due to limited sampling, but a recent paper from Carvunis’ lab challenges this argument. The fact that TRG numbers in bacteria do not vastly outnumber those in eukaryotic species also strongly suggests that sequence space is not supersaturated with targets.

Um, beta lactamase is a hydrolase. There are more than just a few hydrolases in the biosphere, and their substrates are many and extremely varied.

So @bjmiller, how many papers can you cite in which someone has screened a random combinatorial library for a reaction that resembles the HisA reaction? If the answer is zero, then your point is meaningless.

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