Life doesn’t require specific protein functions or sequences. Axe committed the ever popular sharpshooter fallacy in claiming the extant protein he studied was the only possible way for life to exist. We’ve been over this same example with you dozens of times by now. Why do you keep regurgitating the same already falsified claim?
2 Likes
No you’re not Bill. You’re showing (or more precisely you’re repeating Axe’s nonsense about) a low end probability for one very specific protein. Sharpshooter fallacy Bill. Will you ever stop relying on it?
2 Likes
Here, you are committing the same mathematical fallacy many people make when they look at the 100 prisoner problem.
Probabilities may not be independent.
If conditions allow for a 10 nucleotide sequence to form, then the probability of a 100 nucleotide sequence or 1000 nucleotide sequence may be not much more than for 10 nucleotides.
Similarly for 10 amino acid protein vs 100 vs 1000.
Here is my post on the 100 prisoner problem
If you haven’t encountered the 100 prisoner problem, it goes like this
There are 100 prisoners, numbered 1 to 100. There are 100 envelopes numbered 1 to 100. There are 100 slips of paper, numbered 1 to 100, and randomly distributed with 1 slip of paper in each envelope. All the envelopes are placed in a sealed room.
The guards of the prison make a deal with the prisoners. Each prisoner will be permitted, one at a time, to enter the room with the envelopes, and open 50 envelopes of their choosing. Once a prisoner has been to the envelope room, they are sequestered in a separate part of the prison and have no further communication with the remaining prisoners. If all of the 100 prisoners find the envelope with their own number, then all the prisoners will be set free. Otherwise, they will rot in jail forever.
The prisoners are permitted to confer with one another before the challenge begins. What is the optimal strategy for the prisoners to agree on and implement, in order to maximize their chance of being freed?
On first glance, each prisoner has only 50% chance for successfully opening their own envelope. Given 100 prisoners, then the probability of all 100 prisoners opening their own envelope if each prisoner opened 50 envelopes at random is, yes indeed, (1/2)^100, which when evaluated is 7.9 x 10^-31. Truly, truly abysmal and unlikely to the extreme.
But optimal strategy results in a probability of 31%!!
This is because the probabilities are not independent.
If you increased the number of prisoners to 1000, 1000,000 prisoners, or even a googolplex (10^100) prisoners, the probability is still over 30%, as unintuitive as it may seem!!!
The same reasoning is why creationist probabilities fail.
They ignore that research has shown that newer, more recently evolved functional proteins are shorter, while older, more ancient proteins are longer.
The probability of one functional protein is not independent of other functional proteins.
Once one has evolved, further functional proteins become much much much more likely.
Evolution is the ratcheting mechanism allowing for longer and bigger proteins and DNA/RNA sequences and organisms from smaller and more simple ones, just like the optimal strategy in the 100 prisoner problem,
and thus changing what would otherwise be absurdly unlikely to the extreme to become highly possible.
3 Likes
I disagree and don’t think this analysis represents the real world. To support this claim you need a real biological model. Your model requires a mind and so you are supporting ID which is probably not what you intended 
Done for the night. Thanks for the conversation.
Started with an already unstable temperature-sensitive mutant, not wild-type.
Too lazy to measure activity. It’s so easy that there’s a kit.
As I said above, Axe’s analysis does not represent the real world. Would you care to address those concerns? To be clear, his assumptions are blatantly unrealistic.
2 Likes
Each protein that today make up ATP synthase evolved independently for other functions, could have begun considerably smaller and simpler, and then eventually came together in ATP synthase. How is that a problem?
By the way, the alpha and beta subunits of ATP synthase belong to the P-loop NTPase superfamily, and the likely ultimate origin of that protein superfamily has been elucidated:
https://www.pnas.org/content/115/51/E11943.short
It could have begun with a small peptide, essentially just the Walker-A motif, consisting only of the residues: GxxGxGK[T/S], sandwiched between a betasheet and an alpha helix.
2 Likes
So you understand what @Art wrote better than he understands it himself?
Why has Axe not tested his global claim on any other proteins in the last 16 years?
Why did Axe start with a mutant protein explicitly selected for its instability?
Why didn’t Axe do actual assays of enzyme activity if he was interested in function instead of tweaking every variable to give him a single factoid to use in deceptive propaganda?
The assay can be done in less than 2 hours:
https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/1/mak221bul.pdf
All in your own words please. TIA!
3 Likes
And, @colewd, the myosins, kinesins, and G proteins are in that family. The pathway by which the myosins and kinesins evolved from this core is pretty obvious.
1 Like
First: Thanks for following the conversation.
I don’t see how co option is a realistic solution. If you think of this from a short sequence being optimized for a specific function. How does that get it any closer to being part of a different and more complex function.
Your claim requires that all protein functions are similar and that is not what we are observing. Why would an enzyme that catalyzes a reaction to break down acetyl co a work as a stator component for the bacterial flagellum?
With evolution? They tested that too, and showed it can also function as a helicase enzyme.
Same protein unzips double-stranded DNA, like hexameric helicases do today. That’s essentially what sits on top of the ATP-synthase, a hexameric helicase. Those alpha and beta subunits of the catalytic hexamer (which bind dNTPs, wink wink) are hundreds of amino acids in modern proteins and self-assemble into that large hexameric structure (btw the beta and alpha subunits share common ancestry, they’re both P-loop NTPase proteins).
That function, unwinding double-stranded DNA can be performed by that same 40 amino acid β-(P-loop)-α motif.
We live in interesting times where advances in biochemical technology and computational methods are allowing scientists to work out very ancient evolutionary events. They really are piecing apart the evolution of that superfamily of proteins from it’s very origin into it’s many, and more complex modern descendants.
2 Likes
I was not aware that I had claimed this anywhere, nor that such a conclusion is required.
I don’t understand the question. Why would it? Why not?
2 Likes
Most proteins have several different domains that each perform different functions. You can get different functions by combining or linking these protein domains.
1 Like
Fair enough.
In a bacterial motor you need more than 30 well matched proteins that perform a function which need to be expressed in an order that allows them to be build during every cell division. This is about 100k nucleotides that require a high level of organization. This is 4^100000 possible arrangements. How many do you think will generate a bacterial motor mounted in the right location? You need enough such that evolutionary mechanisms can find this sequence. The ancestral protein argument does not really help this issue.
That is very confused. The structure made up of 30 different proteins don’t have to arise all at once. Each protein can evolve at different times for different functions, then some associate (likely already to begin with) and so essentially make up one structure, and later evolved proteins are added because these too have associations that are either beneficial, or evolve by a neutral ratchet, and the function of the system improves and/or changes over time.
Of course it does. It shows that, for example, six of the proteins comprising the ATP synthase catalytic hexamer(the 3 times repeated alpha-beta subunits) derives from a single, simple ancestral protein.
It means there was already hexameric helicases before ATP synthase evolved, and that ATP synthases existed before the flagellum. So it’s a simple case of exaptation. An existing structure is copied, possibly already fulfilling dual roles, and each copy diverges to improve and specialize. One continues to function as a helicase, the other to translocate nucleotide or amino acid polymers in and out of the cell.
3 Likes
Which species do you want to talk about? There are numerous flagellar motors from numerous species with different sequences. It would be good to know which motor you are using as your reference.
We could also talk about archaeal flagellum which have the same function as its bacterial counterpart but different structure.
1 Like
Bill Bill Bill…How many times do you need it explained evolution doesn’t just stumble on a working sequence all at once by accident? Evolution slowly arrived at what we see today over hundreds of millions of years of building on simpler working precursors. You never get anywhere near any accurate probability because you continually use the wrong model. You never include any iteration with selection feedback which we know was the actual process involved.
4 Likes
Rum you can make up a story of how this could possibly happen. I think you are appealing to a statistical miracle no matter how many ways you say this might happen. For evolution by known natural mechanisms or UCD to be true you need to have these statistical miracles repeated over and over. The problem is that science is about probable statistical outcomes. As biology moves from prokaryotic cells to eukaryotic cells the statistical miracles get more and more challenging.
You are not looking at the real detail of these challenges. Once your probability estimates get high enough a little help with an ancestral protein is irrelevant. It only helps if it has a very similar fold and is expressed at the right time during the cell cycle. The only reason this discussion gets any legs at all is if you accept very generous odds of a single protein evolving. The evidence is against this premise as you move forward to eukaryotic cells.
Heh. You’re still using the wrong method which produces your ridiculous “it’s too improbable” numbers. You’ll never learn because you don’t want to learn.
2 Likes
Everything I said is consistent with what we know about how proteins and their assemblies evolve, and with the evidence for the evolutionary histories of the proteins that make up these structures.
I can’t help what you think.
Please show that there is a “statistical miracle”.
No, science is the tool we use to find out how the world works. What you said is word salad.
You haven’t shown any statistical miracles. It’s just some new phrase you like to regurgitate.
No, you are not looking at the real details. You’re just blathering about large exponents and spewing incoherent technical jargon.
You don’t have any probability estimates. The only thing you’ve told us is some meaningless number that has nothing to do with what happens in the real world.
This protein is X long, we have Y many proteins. Take 20 and put YX in the exponent. Hoyle! Tornadoes! What are the odds?
Please point out this evidence.
3 Likes