Do you know any creationist who denies the existence of heritable traits and changes in them?
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Graur mentions it himself. If function is defined as causal role or activity, his paper is not applicable.
Graurâs definition has nothing to do with the actual activity/ contribution of the gene to an organism. His definition only deals with genes that contribute to reproductive fitness in a way that can be selected for.
Thatâs not the question. The question is whether Graurâs paper is âindependent of evolutionary theoryâ.
What does the opinions of creationists have to do with thatâŠ
You have to prove your claim that his paper is independent of evolutionary theory.
Wrong again. He does describe his definition of âfunctionâ, which is only to be expected since âfunctionâ is what the paper is about, but it does not depend on evolution being true, nor does that definition figure into his methodolgy. Here is his definition: A genomic segment is considered to possess a selected effect function if at least one out of all the possible mutations that can affect its sequence is deleterious
Anyway, it is clear you are just going to keep repeating your unsubstantiated claim in the face of continued explanations, some from respected professionals in the field, of why you are wrong. So I donât know what else is left for me to say here.
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It figures in his methodology because he measures the percentage of the genome that is functional based on projected reproductive fitness.
He is measuring how much of the genome will effect reproductive fitness if there is a deleterious mutation.
This is totally dependent on his definition of function. Depending on evolutionary history, the same trait could be either selected for or against.
Would you agree that Graurâs paper is based on an evolutionary framework?
And what exactly do you mean by evolution here? Of Graur is wrong, atleast somethings in population genetics is wrong. Isnât that a part of evolutionary theory?
If most genes have a role in the organism, then Graurâs definition of function would be useless in fields such as medicine
where did I talk about any creationist theory in this thread. That is something @Faizal_Ali misunderstood and you are misrepresenting me here.
Genes being conserved by natural selection does not have anything to do with common descent?
It seems your main argument is that mutations may not be random, and may be mostly beneficial.
Again, whether or not that is true has no bearing on evolution. It could have turned out that was the case and evolution would still be true.
As it happens, your claims are obviously false. Graur did not include the parameters he did in his paper because of his commitment to evolutionary theory. He included them because he is not completely clueless about basic facts regarding genetics.
Mutations not being random does not necessitate that they are mostly beneficial.
The definition of function has nothing to do with the basic facts of genetics.
The same trait could be considered functional in one population while it is not considered functional in others (for a example sickle cell anaemia).
Graurâs definition is not specific to genes. Itâs dependent on the populations evolutionary history.
I did not say it does. I intended that to be read as two separate claims. Does that help?
That is not one of the basic facts to which I am referring. That facts to which I am referring are:
- Mutations are random.
- Very few of them are beneficial.
In your capacity as an engineer, you profess to know more on these matters than the worldâs geneticists. Thatâs kind of cute.
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You are confusing âfunctionalâ with âbeneficial.â
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No it doesnât. I didnât claim mutations are mostly beneficial⊠and they donât need to be mostly beneficial for a high percentage of the human genome to have function.
This is possible through a combination of mutations being more regulated and controlled by selection.
Dr Graur only looks at the effect of selection on functional mutations in addition to having a vague circular definition of function.
I am not.why would my comment give you that idea
I used functional in terms of being selected for. Sickle cell anaemia is selected for in some population/environments while it is selected against in others.
I donât claim anything of the sort. All I said was that if more of the genome turns out to have have function (in terms activity that effects the organism), then the current understanding of mutations being random would be wrong.
I never made any claim about most mutations being beneficial.
I could swear you did, but I canât be arsed to go back and look. Iâll take your word for it. Itâs not crucial, anyway.
Sure, but I never suggested they did.
There is nothing vague or circular about his definition. It is quite specific and, moreover, seems to be the same definition you are tying to use, albeit in a clumsy and uninformed manner. His definition is quoted below. For some obscure reason, when you quoted this passage you left out the last sentence that I have bolded. Why was that?
Throughout this paper, the term âfunctionâ is used to denote selected effect function, that is, a capacity that has been shaped by and is maintained by natural selection (Wright 1973; Graur et al. 2013, 2015; Brunet and Doolittle 2014). The selected effect function stands in contradistinction with the causal role function (or activity), which is ahistorical and nonevolutionary, and merely describes what an entity does (Cummins 1975; Amundson and Lauder 1994). A genomic segment is considered to possess a selected effect function if at least one out of all the possible mutations that can affect its sequence is deleterious (Graur 2016, pp. 492â496).
Right there, you are making the very error I pointed out: Confusing âfunctionalâ with âbeneficialâ. If a gene is selected against, it is still functional. i.e. it has some effect on how the organism functions or interacts with its environment. If it did not, how could be it be selected against?
Also, as noted, you are endorsing the very definition that Graur used, and which you have tried to dismiss. In the example you use, either the sickle cell variant or the normal variant has a deleterious effect, depending on the environment (âvariantâ = mutation). So the gene that is affected by the disease is functional according to his definition.
And that is a nonsense claim. As I have already mentioned, bacteria have far less Junk DNA (i.e. their genomes have a higher proportion of functional DNA) than do eukaryotes. Yet mutations are still random in bacteria. It is not even clear to me why you think lower rates of Junk DNA means mutations are not random. Most likely, as with most of what we are discussing here, you believe that because your understanding of basic genetics is not very strong. Thatâs why at least one professional geneticist here is also disagreeing with your claims.
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It would in humans. If a large proportion of the genome were functional, then random mutations would be deleterious a much larger proportion of the time than mutations are observed to be. Therefore one must suppose, in order to reconcile function with mutation, that mutations are non-random and are biased against deleterious ones.
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Dan Graur famously said that
« if ENCODE is right, then Evolution is wrong ». And he wrote the paper to demonstrate his point. So obviously, the paper has all to do with the theory of evolution !
So who says he is correct? I donât.
You shouldnât get too worked up about it, because that doesnât mean what you think it does. Technically he was speaking about population genetics(the implication being that our undertanding of the frequency of deleterious to neutral and beneficial mutations would have to change), not whether you are an ape and share ancestors with Chimpanzees, Rhesus monkeys, and flounders. Encode hypothetically being right wouldnât alter that. But youâd have to actually read his papers to gather that, not just regurgitate that single sentence.
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Itâs relevant to the question, as that is what the paper is about.
Because the paper, which you obviously donât understand, is about directly observable parameters in real time.
I just did. It is about directly observable parameters in real time.
Not as cute as his claim to know more about the relative strengths and weaknesses of Indian vs. US education than someone who has held faculty positions in both countries. 
Then that gets us back to the question you asked @Ashwin_s earlier:
Now, if it did somehow turn out that most of the genome was functional, that would tell us that population genetic theory (not evolutionary theory, precisely) had some basic lack, somewhere. What do you suppose that lack could be? The only thing I can think of is what I proposed, that God (or something else) acts to prevent deleterious mutations from happening in the parts of the genome currently considered junk while freely allowing them in the parts currently considered functional.
To which, AFAIK, he suggested no answer other than saying that scientists donât know all that much about genetics. Not as much as engineers do, I guess.
He does not seen to appreciate that we have a rough idea of how often deleterious mutations occur in parts of the genome we know to be functional, and that Graurâs study is based on this. Itâs hard to comprehend how and why some mysterious force or process, while allowing mutations to occur at random in our protein coding genes, would at the same time be carefully curating which mutations occur in the various pseudogenes, transposable elements, viral remnants, etc. that litter our genomes. At the same time as the mutations that are allowed in those regions allow us to form phylogenetic trees that are highly congruent with each other, and with what would be expected from other sources of evidence such as the fossil record, when we treat those mutations as occurring randomly. Perhaps @Ashwin_s will enlighten us further.
It happens that I have carefully read Graurâs paper and there is no doubt that he wrote it in order to demonstrate that if « ENCODE is right, then evolution is wrong ». Maybe you should read it again.