Golly.
I do, and have used it that way (presence/absence of THREE genes) throughout my career. No one has ever suggested that my use of “allele” is incorrect.
As for the value of your thoughts, I’ll also note that you think that searching PubMed for “alternative splicing” yields a “comprehensive” list of papers on the subject.
Shall we kill two of your arrogant false claims with a single paper?
Yes, please.
Yet you haven’t offered a single case of anyone other than Bill referring to a gene bring fixed.
Bill, as far as I can tell, is trying to deny the existence of orthologs:
Sure, because it doesn’t matter. But here you are:
https://www.pnas.org/doi/10.1073/pnas.2535513100#:~:text=Fixation%20of%20an%20unlinked%20duplicate,locus%20(11%2C%2013).
Several mentions in there of the fixation of genes. The more important point, though, is that you were attacking Bill for saying something whose intended meaning was perfectly clear, expressed in a way that made sense. Why attack him for that rather than for any of his countless word salad claims?
I fully admit that this entire conversation has been pointless.
Well, at the least he’s trying to redefine them in a way that doesn’t involve descent. Then again, the original definition of homology didn’t involve descent either. He’s merely trying to erase a couple of centuries of science.
Bill explicitly excluded duplications.
That quote isn’t saying what you think. Bill is talking about the genes in his favorite Venn diagram, present in some species but not others. He may be trying to deny the existence of paralogs. He also clearly, given his creationism, doesn’t think that any genes in different species are orthologs (in the common, modern sense), but that’s not the import of the quote. By “thousands of genes” he’s talking about different, non-orthologous (and possibly non-homologous) genes.
Not sure what you mean by that or of the context.
In vertebrates, which simply don’t have thousands of such genes.
Thanks. I see that the phrase “alternative splicing” does not appear in that paper (though several close equivalents do). Not sure how that’s a big problem. And I’m not sure what other arrogant false claim that paper refuted. The allele in question is of a single gene, though one of its introns does contain an insertaion that itself contains viral genes.
Yes they do. Every gene the zebrafish has that the mouse doesn’t is non-orthologous to any mouse gene. I will grant that most of them probably have paralogs in the mouse, but that doesn’t seem relevant to Bill’s statement.
Indeed! Fixed.
What you think doesn’t matter. The math says you are wrong.
To the best of my understanding the difference are the result of more-or-less random deletions or HGT. These difference, once present in the genome, follow the predicted nested heirarchy from that time on.
Your hypothesis “This better explains the data that does not follow the reproductive patterns”, or “separate origins” has been disproven.
No, they don’t, because Bill’s same/different dichotomy doesn’t exist. This is why we have terms like ortholog, paralog, and homolog, which still have fuzzy boundaries.
So searching only for “alternative splicing” and no equivalents is incompetent.
It refutes your arrogant claim that the paper you cited (apparently without bothering to read it), trying to support the preconceived notion alternative splicing isn’t common, was “comprehensive.”
Hi Dan
There is no mathematical model in the literature that reconciles this. I am not sure what you mean that the math says I am wrong.
Horizontal gene transfer is a mechanism primarily between prokaryotes. While it may be a contributing explanation it is much rarer in vertebrates.
There is currently no model of how random deletions can explain the data. To build a model you need to build up empirical data that gives you the frequency of gene deletions in a population along with the probability of a gene deletion being selection positive, neutral or deleterious.
The other problem is how do new genes get produced by the reproductive process. I don’t currently know of any evidence for this in vertebrates.
If you look at the diagram Bill keeps referring to, it’s referring specifically to orthologs.
On the basis of a single paper? What if most papers do mention the exact term?
It could be comprehensive without including every paper in the literature. So one counterexample shows little. You have to establish that the search misses a large fraction of such genes.
The presence of non-coding sequences in chimpanzees that are orthologous to proposed human ORFans is just such evidence.
No, but it was an instant indicator of incompetence.
Irrelevant, because you claimed it was “comprehensive.” That’s objectively false. It’s very amusing that your ego won’t let you admit that.
Do you know that you can do searches for more than one term? For title/abstract searches that include one term and don’t include another?
Oh, and as further evidence of incompetence and/or unethical cherry-picking, in their database they cited a much more recent paper and concluded that there was no evidence of functional splice isoforms.
You claimed to know that it is comprehensive. Again, your flailing is amusing.
No, you have to establish that it was comprehensive. Your claim, your evidentiary burden. You’ve also claimed that more comprehensive reviews with higher percentages were wrong, remember? You’ve touted this utter crap paper as the gold standard.
The ‘mathematical model’ is called division and multiplication. This isn’t science, this is grade school math.
It’s only incompetence if it produces poor results, which has not yet been demonstrated. Now, a useful citation would be to a better review. Do you have one?
I have no idea what you mean by that one.
No, I don’t remember. Then again I don’t recall claiming that the review in question was comprehensive either. What reviews are you talking about? I also don’t recall anyone mentioning them. What I’m doing is trusting that Larry Moran knows what he’s talking about, failing evidence to the contrary.
Hi John
This is based on the inference of common descent and the inference that the ORFans are non functional.
The evidence that is not available is reproduction generating a novel functional gene sequence. Given the vast quantity of differences this should be possible if there is indeed a working mechanism in the reproductive process.
regarding alternative splicing