Yeah, it’s almost like they are under selection, or something. Wow, whodathunkit.
Even stranger, the vast majority of a standard mammalian genome does evolve at a rate consistent with neutral theory. Hmf, it’s almost like large swaths of those genomes have no function.
Assuming that is correct, it simply indicates that selection has occurred. (I also note that protein sequences may not be the best measurement of mutations because of synonymous mutations). And of course these sequences won’t capture the within-species variations, which is th3 major point of difference between Behe’s model and Lynch’s.
I don’t believe that follows at all. We know for a fact that Lynch’s model is more accurate because he is right on the major difference between the models. Even if Behe’s model happened to give more accurate results it’s not because it is more accurate. Errors that cancel out - if that is even occurring, which I doubt - are still errors.
I agree with your point on selection. Both models however are based on fixation and not in species variation.
The largest difference between the models is the waiting time for a gene duplication. This is required if most mutations are deleterious. A duplicated gene can theoretically mutate without selection removing it from the population.
From Behe’s discussion on the model differences:
Our model posited necessary intermediate mutations to be deleterious in the unduplicated gene; Lynch’s model assumes them to be neutral: “all 20 amino acids are equally substitutable in the intermediate neutral state” (Lynch 2005, this issue). All of his objections to our work stem from this difference.
However the main difference is variations which are not fixed.
Behe assumed that the intermediate mutations would be strongly deleterious if they occurred before duplication. Lynch did not, and that is how we know that Lynch’s model is better. The fact that Behe resorted to arguing that most would be very weakly deleterious shows that even Behe could not support his assumption. Very weak is not strong,
How many times and for how long have you been taking about these studies? And yet you still don’t understand the basics of what they said.
The waiting time for a duplication event is not even a factor in Behe’s model, because he did not even include that in his model. Lynch started from a single copy of the gene, and included the time for a duplication in his estimates. So that is one way in which his model is actually more restrictive than Behe’s, even though Lynch still ended up with far shorter waiting times. The reason for this difference is that Behe’s fanciful and fictitious model could not include such scenario, because he created a condition that the initial compatible mutations inactivated the gene and therefore would have been deleterious if the gene was not yet duplicated.
And here we observe the dumbfounding spectacle of Bill Cole quoting Behe admitting that his model fails because it is based on a completely arbitrary condition that does not exist in real life. And BIll does so thinking it makes Behe look good. Unbelievable.
Hi Paul
We agree on this point.
What I disagree with is that Lynch has claimed that the mutations are neutral and from the comparative sequence data his model is not accurate due to that assumption.
Your claim here is selection has occurred. This contradicts Lynch’s claim of all 20 amino acids being equally substitutable. The data strongly favors Behe’s assumptions as in many cases only zero to a few changes are occurring after millions of generations.
Here is Behe’s response to Lynch .http://dx.doi.org/10.1110/ps.051674105
I could be wrong! But you base your estimate of a person’s character on what you see of them, what they say and do.
Out-of-body experiences are one evidence, where people reported for example, a shoe that was outside on a ledge while they were flatlined.
Well, I choose to believe that the evidence of my senses and the machinations of my reasoning are suitably valid for forming conclusions.
But your view involves the conclusion that our thoughts are determined by mindless atoms.
If my reasoning is determined by mindless atoms, I am not in control of my thoughts.
Therefore I cannot trust my reasoning.
“Because he thinks that my thoughts result from an irrational cause, he therefore discounts them. All thoughts which are so caused are valueless. We never, in our ordinary thinking, admit any exceptions to this rule."
I think this is relevant to the discussion, if you know that a man’s delirium is at work, you don’t bother to look for spiders on the walls.
I added some emphasis to help you out:
Then you disagree with Behe’s response which implicitly admitted that Lynch was correct,
Not really, Lynch’s claim essentially amounts to the assertion that there will be variation in the gene sequences within the existing population. Your data does not even address that question.
That’s what’s known as a non sequitur. Why should mindless atoms be less reliable than a hypothetical, immaterial soul, or whatever it is you think is doing your reasoning? As for you not being in control of your thoughts, that way leads to questions about free will, which if you actually think about it deeply is seen to be an incoherent concept, and best avoided.
Neither model is actually accurate. Behe’s model that assumes all intermediate states are strongly deleterious is inaccurate, and Lynch’s simplified assumption that all possible substitutions are effectively neutral is also inaccurate.
Behe’s model is extremely unrealistically restrictive, and Lynch’s is unrealistically permissive.
In actual reality these ratios of deleterious:neutral:beneficial will vary widely between different proteins and at different points in time. No simple model can fully capture all these effects.
What we can say, however, is that when and if there are at least some neutral or beneficial mutations available to an existing protein sequence(which there is for most proteins most of the time), then that protein can and will wander into those areas over geological time, and that this demonstrable reality that there really are neutral and beneficial mutations surrounding real proteins are the pathways through which novel protein functions evolve.
And this is the reason why scientists can construct phylogenies for related proteins that have slowly drifted apart(slowly because most but not all mutations are deleterious), and for some evolved new functions over geological time. This is why protein sequence divergence is generally for almost all proteins lower than the rate expected from pure neutrality, but almost never zero, and in some cases the divergence is actually above the rate expected from neutrality, which instead implies positive selection.
This is why there are families and superfamilies of proteins that are related in sequence and structure, but have evolved new functions. This is why the ancestral states can be inferred with phylogenetic methods, reconstructed in the laboratory, tested for their ancestral functions, and their evolution towards their new(descendant) functions can be replayed in experiments.
That implies that things you are not in control of can’t be trusted. I’d hate to be married to you.
But seriously, first of all, that doesn’t follow either. The conclusion does not follow from the premise.
Premise: I am not in control of X
Conclusion: Therefore I cannot trust X
That conclusion obviously does not follow.
Perhaps you could add a premise:
Premise1: I am not in control of X
Premise2: Things I do not control cannot be trusted.
Conclusion: Therefore I cannot trust X.
But then we can see the problem is the 2nd premise, which just begs the question. Now we need another argument to show that it is logically entailed that things you can’t control can’t be trusted. You should start to see the problem now - what premises will you need in that argument to get to that conclusion?
Second: Now I think it’s pretty clear that you can’t really believe that. I’m pretty sure you’re not in control of God, and yet you have some apparently totally blind trust in Him anyway(and we’ve already seen that God could be untrustworthy for his own amusment, yet made you to be convinced he’s trustworthy, and you’d have no way to tell). And you’re not in control of gravity, yet you are probably trusting it’s ability to keep you in place. Etc.
Third: If your thoughts are determined by “mindless atoms”, you would be one and the same thing. Then it would be true to say you are your mindless atoms and what they do. It’s not clear why you would need to be in control of them, as if you’re separate from them. The very idea of controlling them seems to indicate you haven’t fully grasped what it means to say that your thoughts are due to those atoms. And it raises question about what “you” are.
Fourth: As far as I can tell atoms follow the laws to the letter.
Fifth: Something about free will, identity, substance and the like. What you are, how your thoughts are “determined”, what governs their properties and so on. Are you in control of those factors? Can you just choose to do whatever at any moment, and if you can doesn’t that actually make you fundamentally untrustworthy because you could in principle at any moment decide something completely unpredictable and irrational?
Sixth: Have you noticed that we often times make errors in reasoning? You’ve made several yourself. it seems to me this discussion about atoms and control is about some absurd dichotomy where we must choose between flawless logic machines or utterly chaotic thinking that never works. I think there’s a spectrum, and we some times reason correctly, and some times don’t (and some times we have periods where we perform better and others where we perform worse), and that (for reasons I think you have to wrestle with because they make perfect sense from the perspective of an evolved physical brain who’s cognitive performance depends on them) those can be due to all sorts of physical and material conditions, such as whether you’ve had enough sleep, a proper diet, your morning coffee, medication/drugs/alcohol, enough sunlight, the temperature of your surroundings, how many other tasks are taxing your cognitive resources, etc. etc.
Yes people can be mistaken, but it seems to me this is no less a problem for you than it is for me. If God is supposed to have made your thoughts trustworthy, why is it the case that they some times aren’t? Interestingly people who suffer certain forms of temporal lobe epilepsy will get seizures where they (often) hallucinate angels and other forms of supposedly supernatural beings and occurrences. There’s some rather famous conversion stories thought to have been due to this kind of brain malfunction. Saul of Tarsus, anyone?
No good evidence this actually happened. It’s just a story someone told. A couple students actually investigated and found this anecdote could not have happened as reported.
As do I. And I need believe in no god to do so.
Yes. Interestingly, in the article below, pretty much that exact argument is used as an illustration of the Fallacy of Composition (example #3).
I think Lynch and Behe can both be correct depending on the proteins you are observing. Since I am interested in vertebrate origins then Behe’s model appears to be the best fit.
The claim says that all substitutions are neutral and thus will not be removed from the population. If there is variation in the population it is not relevant if it is ultimately removed by selection. You identified selection as a reason for the lack of observed sequence variation which means they are not neutral as Lynch claims.
Lynch quoted a few bacterial enzymes to support his neutral claim and I would agree that his model will work for a limited amount of prokaryotic enzymes…For many vertebrate proteins Lynch’s model does not appear to be useful.
I disagree. Lynch’s model can easily be adjusted to deal with more slowly evolving genes, while Behe’s model would need to be made more like Lynch’s.
And of course, you cannot determine the speed of evolution by only looking at the genes which are evolving at the slowest rates. The fact that Behe’s model does not apply to all genes is sufficient to destroy his argument.
Why?
That’s utterly false. Let’s say there is a neutral amino acid substitution and it is present in 20% of individuals. Another mutation occurs in one of the individuals who carries that neutral amino acid substitution, and the interaction between the two mutations results in a beneficial phenotype which is selected for. Are you telling me this scenario can’t happen because the initial neutral mutation did not reach fixation?
Based on what evidence?
No, I’m saying that mindlessness does not produce mind.
Let’s try:
Premise1: I am in control of my thoughts
Premise2: My reasoning can be trustworthy
Premise3: Mindless atoms cannot be trusted to produce reliable reasoning
Conclusion: My thoughts cannot be controlled by mindless atoms
Freedom doesn’t mean complete unpredictability, though. What I do insist on is the validity of reasoning, when it is not controlled by unreasoning factors.
Yes, I don’t insist on perfect logic every time.
But the point is that we discount thoughts that have non-rational causes, without exception.
This then requires a perfect Reason as the source of my reason, if we are to trust reasoning, which I believe we all do.
But the people with him also saw the light (Acts 22:9). Hallucinations as you mention, are individual, i.e. not shared.
Because I believe I have experience in being a soul, and controlling my thoughts.
Do you believe that none of your choices are due to a person choosing, that mindless atoms do control you? Tell that to the judge.