Hi Ahmed
Alternative splicing is a process in vertebrate cells that allow for additional protein iso forms. The argument often made is that it is noise in most cases. The data surfacing over the last several years is that it is active in embryo development and this is supported by cancer research. Embryonic pathways are active in cancer formation and protein alternative splicing is active in cancer cells. A reasonable conclusion is that alternative splicing is active in embryo development even though it may be measured as noise in a mature animal.
Alternative splicing patterns can differentiate multicellular organisms. Here is a graph from a University of Toronto paper that shows how splicing activity in other animals compares to humans.
What do mean by âdetected as a different proteinâ?
Iâm not sure what that has to do with my comment, which was in response to John. I am also not convinced you know what is meant by neutral theory.
The point is that it is not knowledge, in the sense you are using the term. And the fact that it is innate, rather than learned, demonstrates that it is coded in the DNA.
When people graduate from engineering school, do they automatically start building a hydroelectric dam if you play them a recording of rushing water? Obviously not. That is because they have knowledge . What the beaver has is an instinct he inherited from his ancestors, which has persisted because it increased their odds of survival. One of his ancient ancestors had a mutation that made him (the ancestor) really, really hate the sound of rushing water, so he did whatever he could to get rid of it. And the easiest thing for a beaver to do to stop that sound is pile up a lot of wood to block the water. This had the effect of creating a new pond, and this was conducive to his survival, therefore he had many descendants who inherited his hatred of the sound of rushing water.
That is the account that, taking all the additional evidence at hand, most likely explains this observation. You disagree. You think Allah âtaughtâ the beaver somehow. So how exactly did this happen? Does Allah take the souls of the beavers up to heaven and enroll them into engineering school? Or what, exactly? You really havenât said.
And why is Allah such a lousy teacher that they go and build dams even where there is no water? If a human engineer came and built a dam on your front lawn because you were watering it, would think he had been taught well?
Alternative splicing takes place in basically all eukaryotic cells with the typical eukaryotic exon-intron gene architecture. And most of it really is noise.
No, itâs a conclusion to a long argument from making sense of enormous amounts of data.
It also straightforwardly contradicts how creationists such as yourself usually think about protein sequence space. Thinking that all or most alternative splice protein isoforms are functional proteins implies that there is much more relaxed constraints on protein sequence function than anything youâd normally be arguing. Youâre literally positing that you can take essential proteins, be it metabolic enzymes, transcriptional regulators, structural proteins or what have you, remove something like half or a third of one or multiple domains, copy-paste different parts together in new ways, and still get useful proteins with new functions that are active in anything from metabolism to multicellular and embryonic development.
If youâre so willing to believe that just because youâre simultaneously unwilling to believe there is that junk DNA, junk-activity, and much noise in biology, then I think perhaps your mind deserves a vacation from the sheer compartmentalization and cognitive dissonance you must be engaging in. Iâll be welcoming your support and agreement to what Iâve been arguing over in the Functions are not so rare at all, and definitely not isolated, in sequence space of biopolymers thread.
Bill Cole - super-evolutionist.
Active =/= has fitness-relevant functions. As the ENCODE fiasco should have taught you.
Alternative splicing is active in all tissues, at varying levels, for different genes. Mostly at low levels, and mostly itâs unavoidable byproducts of the inherent uncertainties in the splicing mechanism.
Different organisms show different levels of splicing activity, and it varies among tissues, but with more closely related species generally having more similar splicing patterns (just as any other molecular and genetics-related divergence), which is still entirely consistent with the vast majority of splicing constituting unavoidable biochemical noise.
No, you donât know anything of the sort. Many of the SNPs that are polymorphic in humans are non-silent. Changes to proteins can be neutral too, as indeed is suggested by the fact that most of the human polymorphisms seem to have no effect on fuction.
You mean that they made us human, though only a tiny percentage of them.
Sure. Those mutations, a tiny percentage of them, made them chimps.
Letâs say you measure splicing at exon 1 in protein A of a mature animal and it is occurring at low levels. Would you then claim that splicing of exon 1 never has biological activity?
No, it doesnât add up. Our common ancestor was neither a chimp nor a human. The mutations that happened in each lineage after branching off of from that common ancestor is what made chimps into chimps and humans into humans. The mutations that separate modern humans and chimps include the mutations that happened in the chimp lineage and the mutations that happened in the human lineage. We are both equally distant from our common ancestor.
A good analogy is French and Italian. Both of those languages descended from Latin. Once those language groups broke off from Latin they each changed in different ways. In the present, French and Italian are different from one another while also having similarities. However, neither of those languages is Latin.
I wanted to make another reply, but I have a âlimitâ that is for new members. So I have to edit my previous reply to make a new one.
I actually donât think it is weird. The âring of lifeâ depiction more accuratly shows how the three domains are related to each other. Eukaryotes inherited a lot of their aspects from both archaea (especially DNA replication and regulation) and bacteria (especially membrane energetics and metabolism). So the old tree of life where every branch bifurcates ignores the significance of endosymbiosis.
Figure 1. A representation of the history of biological diversification of all life, reflecting the role of introgressive hybridization and lateral exchange in the development of new lineages with mosaic genomes (from [8], as modified in [6]). Reprinted with permission from The American Association for the Advancement of Science [8].
Not quite. There will also be some alleles that were both segregating in the common ancestor population, but then drifted, or were selected, to fix for different alleles in human and in chimp.
I also like Bill Martinâs image, although it shows no horizontal gene transfer (wouldâve been more accurate if it were a bit more bushier).
The other image by @T_aquaticus does depict the horizontal gene transfer (although whether HGT was actually that severe is still debated of course), but it doesnât depict the endosymbiosis event for eukaryotes. Itâs almost like the three domains emerged at the same time from a common ancestor, but that is of course wrong as eukaryotes emerged quite later, like the two prokaryote domains are almost twice as old as the eukaryotes.
If you feel that way, I have to wonder why you have failed to acknowledge and correct the many, many of your errors that have been pointed out in this discussion.
@T_aquaticus
I think that mixing the merits of taxonomy with evolution is not productive⌠Evolution needs to have its own merits; it does not. This is the point.
All he was doing was pointing out that the fact that humans are great apes has nothing to do with evolution, as even Linnaeus, with little conception of evolution (certainly not macroevolution) classified us that way.
