So now you’re relying on ChatGPT for advice? But evolution doesn’t work that way. You don’t start from a random point in sequence space and try to get to some specific location by random changes. This is not a real problem, despite what a chatbot may say.
More importantly, it has no relevance to common descent. As usual.
I am showing based on an aggregated search the problem is real.
You don’t start from a random point in sequence space and try to get to some specific location by random changes
This is right by current theory you duplicate an existing gene. Now the change has to happen through an enormous sequence space. The chance of moving away from function is much larger then the chance of moving toward it.
It is relevant to how many origin events occurred during the history of life.
Is that so? How did you arrive by this estimate?
If only there was some natural process by which such changes were, I don’t know… selected for? A sort of natural selection? What a novel concept!
The size of the total sequence space in the case of proteins is defined by the number of available proteins to the power of the length. An average primate protein 500 aa long and there are 20 active amino acids so the total sequence space is 20^500.
The question is how much functional space is there?
Based on empirical preservation studies it is most likely orders of magnitude lower and depends on the particular protein. If you run uniprot on beta catenin and alpha actin there is extreme preservation or almost no changes among mammals. If you run p53 you will see up to 25% differences among different mammals.
People here have provided speculation on how this is solved but no one can provide a model of how function is found after duplication especially if it requires more then a few changes.
Here is a link to the alignment data.UniProt
How does that show the problem is real?
The size of sequence space is irrelevant if there is a new function not far away. Selection eliminates the mutations that move away from function and preserves those that move toward it. That changes the expected outcome.
That is not true, as I have pointed out to you countless times.
That’s a question, not the question, and it’s not a useful one to ask. The real question is whether there are functional spots near to other functional spots. The size of sequence space would matter only if functional spots were evenly or even randomly distributed. They are not.
Sounds like the functional island, connected by small changes, is quite extensive for that protein. So what’s the problem?
That’s a useless data set you have there. Only three sites are variable at all and one of those is uninformative. Two of the taxa (what is CANLF?*) are identical, and there’s no outgroup. There’s no way to get a meaningful tree out of that mess.
*Ah, domestic dog.
A fun challenge:
@Gisteron, given John’s criticism of Bill’s attempt, what would you do?
My hypothesis: Bill has zero interest in learning if his ID hypothesis is correct.
Empirical prediction: if John and Cisteron go through all of this, there will be no coherent response from Bill.
Ahh yes, his experience and qualifications are impeccable. And accomplishments! Unlike everyone else who works in climate modeling I guess.
He must be right then. No doubt about it. Calm measured people who aren’t hysterical and don’t have purple hair generally are.
Matter: settled. Personal testimony = never wrong.
And if he’s not paid by a fossil fuel company he can have no bias or other influence otherwise. So since he’s also calm and polite, well I guess that’s that. Climate change, it’s a communist hoax invented by George Soros. At least if we read the youtube comments.
What a refreshing lack of hysteria. So nice not to hear the alarmism. What a calm rational person. Data driven. Not paid by big fossil fuel! Calm.
LOL It’s all the right-wing classics.
Calm and polite people are generally right, or something. Hysterical people with purple hair are more likely to be wrong and biased.
Emphatic denial means he’s not lying.
If he’s not directly paid by a fossil fuel company, so he can’t be influenced by them, or lie about it.
And you’re just here to inform, you’re not taking sides. And you don’t want to argue the facts, and we should watch it before commenting, and buy his book also and read it before commenting, and if we are to comment it’s not going to be about the facts and data because you don’t want to debate the facts you’re not a scientist. Just here to inform. And he sure is calm and polite. It’s such a refreshing rational discussion. So nice and calm. What a pleasure. What a breath of fresh air.
And as he says, CO2 is plant food. I mean plant food for God’s sake! PLANT FOOD.
Why do I find these types of comments all over everything that has to do with advancing conservative and right wing talking points? Eddie your post literally reads like it was produced by a chatbot programmed by a conservative lobbying organization.
Ahh yes of course, you’re just here to inform. You have no views on the matter yourself or you prefer not to say because then you at least look less biased amirite? The climate change informer version of the “look at the black crime statistics.” You just want to inform. And after all, there are data-based objections to having blacks in society by people who aren’t members of the KKK.
This staple of right-wing talking points is more transparent than intergalactic voids are to the passage neutrinoes. We hear this exact shite from people like Alex Jones.
Maybe it was. Have you checked it’s not from ChatGPT?
Naturally. You think he’s right, and don’t want to have to defend that view. So you ignore the data and turn instead to your usual credentialism and tone-policing.
Most often, people do not saw the branch on which they are sitting.
And this post is your idea of how you could change that impression?
I’m glad your haven’t lost your sense of humour since you last posted here.
So I’m as much of a lay person on this as you. Still, it would seem to me just on the face of it that there are more questions to consider here than just the size of functional sample space as a fraction of the size of the total sample space.
Suppose you were to toss a coin with two distinguishable circular faces with radius r, and a cylindrical mantle of height h. In principle, there is nothing to prevent it from landing on the side that wouldn’t also prevent it from landing on either face. Between the mantle and the two faces, there are three possible states it can land in, and one state we are concerned with. Does it therefore follow that the probability of it landing on a face is 2/3, or that the probability of it landing on the mantle is 1/3? Well, we could construct a particularly tall coin, more of a cylinder, whose probability to land on the mantle actually is 1/3. But if we are comparing the raw number of states to arrive at the probabilities, then we should predict it to be 1/3 irrespective of r and h. To fully characterize a probability space, therefore, we need not only the number of states in the sample space, but also the probability measure, a function that assigns weights to all subsets of the sample space.
But let’s grant you this, and say that all amino acid sequences are equally likely to occur prima facie. In the end we are concerned with the probability to move from any functional sequence to another functional sequence (already a smaller space of starting points, mind you), and how this compares with the probability to move from any functional sequence to any non-functional sequence. We could again only consider the number of states in each subset of the sample space. This would be fair consideration assuming that gene sequences are swapped out completely and arbitrarily between one generation and the next. However, if this were so, then genes would not correlate between parent and offspring, and could therefore not be the carrier of heritable traits.
From what I understand, what happens instead most times between generations are individual mutations of but a handful of base pairs at a time. So while the number of different amino acid sequences one amino acid sequence is free to mutate into is as large as you say, in order to say how far the new sequence may be from its parent’s we need to know the probability p that a mutation occurs between the two generations. The probability that multiple mutations occur in the same generation could be a lot lower than p still, depending on how correlated or anti-correlated mutations are.
Then we need to consider that not every single-point mutation actually changes the amino acid the given codon produces, since many amino acids correspond to more than one codon each. Then we need to consider that no amino is as close to all the others as a single base pair, anyway. So even if we are swapping to a different amino acid with our mutation, we are not swapping to just any of the 19 others, but rather to one of a select few that are accessible in a single step from the one we started with.
In the end, the probability to access completely foreign amino acid sequences should be rather very, very low, and the probability to access neighboring ones should be much higher. And since the one we started with already produced a viable organism, it may not be out of the question that the very similar amino acid sequences it can mutate into for the next generation may very well still also produce viable organisms. A few might not, but if the next organism is not viable, then it will be a dead end whose genome we are unlikely to recover many generations after the fact. Many others may produce viable organisms but with disadvantagious traits for the current environment. Again, those lineages are unlikely to survive in the long run, unless the environment they find themselves in changes to support their variant before extinction.
You mean if I were in John’s shoes or in Bill’s?
John seems to have had many confrontations with Bill, and witnessed yet more, and possibly made an attempt to answer Bill’s questions at one or more times in the past. I do sympathize with frustrations of this sort and have no doubt myself chosen some on the face of it harsh sounding words with the occasional interlocutor. It was no good showing on my part, and I believe it is not a graceful one on John’s either, but I understand and respect where it is coming from.
Empathizing with Bill is more difficult for me, since the reactions to him make it seem like his motivations are of a sort largely foreign to me. If I were so committed to my conclusion, then posing the questoin would have been a mere rhetorical device, though I may not recognize it as such. In that case, John’s reaction would serve as a confirmation to me that my challenges are frustrating those who consider themselves educated on the subject enough to become emotional towards me on occasion. If, on the other hand, my question is genuine, then I would perhaps first attempt to research the subject in encyclopedic texts first, introductory text books next, and only then begin asking teachers for clarification, researchers after that, and consult the current scientific literature only once my expertise has grown enough to comprehend it. However, I have enjoyed training, I learned how to go about learning things, and I appreciate that this may not be the case for everyone. Nevertheless, if conversations like these have been happening for a while, I’m sure Bill would have heard similar advice from people like myself, and could have implemented some of it, if this was genuine interest. I would have found it insulting to be called essentially unteachable ahead of any such advice, but if this happened to Bill a lot, then I don’t know how I would think and feel in his place, for the thinking and feeling that would have produced a history of conversations like this is a kind I have difficulty identifying with.
That this comment, and others like it, was moved here from the original thread is a tacit endorsement of @Eddie’s position that scientific debate is primarily a matter of tone rather than of substance, a position with which I respectfully disagree.
Without my consent and against my wishes, I might add.
That’s not “Eddie’s position.” His position is that scientific debate ought to be about data and the interpretation of data, about hypotheses and means of confirming or disconfirming them, and that political partisanship (which quite obviously motivates, e.g., Michael Mann, as his private emails prove), arguments from authority, ad hominem arguments, etc. should have no place, either in science itself, or in public policy debates that concern scientific matters.
As for “tone”, tone is a concern insofar as tone is routinely used by some scientists, and by many of their groupies, to convey disrespect toward trained scientists with whom they disagree, and the emanation of disrespect colors scientific discussion with an emotional and often political overlay which gets in the way of detached, dispassionate consideration of hypotheses and data. My submission of what I honestly thought was a calm and intelligent discussion about global warming has been met here with plain indications of disrespect, both toward me and toward the gentlemanly scientist who is heard in the video; it was this habitual expression of disrespect (scientific, academic, intellectual, professional, and personal) that produced my recent long absence from this site, and it is this that will produce the next one, starting sometime around now.
The actual words you write here bely what you claim to be saying. You are fooling no one.
See what I mean?