RNA Polymerase II
by BradfordEvolution With A Restricted Number Of Genes is a Science Daily article which discusses research results published in the journal Science. The first paragraph:
The development of higher forms of life would appear to have been influenced by RNA polymerase II. This enzyme transcribes the information coded by genes from DNA into messenger-RNA (mRNA), which in turn is the basis for the production of proteins. RNA polymerase II is highly conserved through evolution, with many of its structural characteristics being conserved between bacteria and humans.
If enzyme possibilities for initial front loading were nominated RNA polymerase II would likely be a popular candidate. Found in organisms as diverse as bacteria and humans this enzyme plays an important role in gene transciption. In eukaryotes an enzyme structure dubbed the carboxyterminal domain or CTD is involved in gene expression. There is variation in amino acid sequence among different eukaryotic organisms. Interestingly, a form of splicing during transcription enables multiple variants in proteins from a single gene.
July 5th, 2009 at 9:21 am
So what exactly makes it a popular candidate? That it is found in diverse organisms? That it has a regulatory domain that affects gene expression? That is has splice variants? That it has this particular combination?
Or is it simply because it catalyzes what we think of as an elemental reaction for life as we know it?
PS: Now that we have this 'telic' interpretation or 'telic' hypothesis, could you tell us maybe how this would guide our research.
And let me make a prediction right up front: This research is already being done by scientists who relied on a non-telic interpretation. Odd how that is virtually always the case.
Comment by hrun — July 5, 2009 @ 9:21 am
July 5th, 2009 at 12:13 pm
This polymerase, from my limited understanding, simply copies chunks of DNA into mRNA and then it's done. It can copy virtually any sequence of nucleotides and simply attempts to make perfect copies, right? So what would the information theory model of RNA Polymerase as a front loading agent look like? There is information in a DNA strand, the polymerase copies that information unaltered. The polymerase doesn't seem to limit or extend the complexity of the information stored in the DNA. It doesn't evaluate or enforce any sort of grammar or code on the DNA. It doesn't understand what the resulting mRNA strand is used for. It doesn't change or effect the final usage of the mRNA strand. It doesn't know anything about proteins or the structure of the cell.
So I'm curious, what would the theoretical model of RNA Polymerase II as a front loading agent look like? You seem to claim every single old or nearly universal component of the cell is a candidate for assisting in front loading but I just don't understand what theoretical mechanism they might be using to carry out the front loading.
Comment by Todd Berkebile — July 5, 2009 @ 12:13 pm
July 5th, 2009 at 7:15 pm
Is everyone here familiar with Michael Sherman's Universal Genome hypothesis?
From the Abstract:
Couple that with this research into "arguably the simplest free-living animals"…
The Trichoplax genome and the nature of
placozoans
From the abstract:
…and you begin to see a pattern forming. "Simple" organisms with complex organization of cellular functions that – while not technically "useless" as Sherman predicts – definitely amount to an extreme case of "overkill". This is expected from a front-loading perspective. It is "surprising" from the currently accepted perspective.
Comment by Daniel Smith — July 5, 2009 @ 7:15 pm
July 5th, 2009 at 7:32 pm
Denial Smith:
It is common practice in science to deduce predictions from hypotheses/theories. You know, using logic. How is all this "expected" from a FL perspective?
Anyway, I'll bite. So how come bacteria have little or no functionally useless genetic information? Are you suggesting that Teh Deziner "skipped" the bacteria but front-loaded primitive eukaryotes?
From the currently accepted perspective, it is expected that bacteria with their huge effective population sizes (and therefore very efficient selection) have little or no useless stuff in their genome, while eukaryotes with relatively small populations are expected to accumulate crap because selection is often relatively weak compared to drift (s<1/N). What's the (logical) FL explanation for this?
PS: I see I have been banned from the Microbial Versatility thread without any specified reason, and long after my last comment there. Bradford, care to explain please?
Comment by Raevmo — July 5, 2009 @ 7:32 pm
July 5th, 2009 at 7:55 pm
His first prediction doesn't seem to match the empirical data. Oops.
To know if this is "expected" don't you have to make assumptions about the taxonomy of the species? I think you are suggesting that FLE theorizes that this simple organism with a complex genome is a precursor to later more complex organisms with complex genomes. (i.e. “useless” genes were front loaded into it and used by later species). There are many problems with this view when compared against the evidence, however. One, common descent suggests this organism is evolved from a common ancestor that includes Achaea and Bacteria which lack the complexity of Trichoplax, so where could this front loaded information have come from? Another, Trichoplax is the last survivor of an ancient branch of eukaryotes; we know very little about its taxonomy because there is so little to compare it against. We don't know if it's ancestors were as simple as it is or if they were more complex. Traditional evolution might suggest Trichoplax diverged from a complex organism with a complex genome and then evolved to be simpler.
Comment by Todd Berkebile — July 5, 2009 @ 7:55 pm
July 5th, 2009 at 8:12 pm
Wait, what? Is this supposed to be the answer to my question? How exactly does this telic interpretation guide the research?
Comment by hrun — July 5, 2009 @ 8:12 pm
July 5th, 2009 at 10:04 pm
That's close. Transcription is not only "elemental," it's an essential function as well. But there is more. RNA Polymerase II is highly specified with respect to its sensitivity to DNA damage. It may be more optimized in its damage recognition capacity than any other enzyme.
I've argued in the past for a threshhold capacity with regard to cellular viability or more specifically genomic integrity. Evolution can be viewed as a process requiring a balance between a biological need to maintain genomic integrity and the need for some degree of genomic instability. RNA polymerase II is a balancing agent in that process, allowing for change while guarding against genomic meltdown. More precise appreciation of RNA polymerase II capacities has implications for pathogens- both disease remedies and adaptive reactions to treatment. Many approaches to fighting pathogens can be thought of as identifying the balance point at which pathogens lose an ability to infect when genomic disruptions tilt the balance against them. I don't make the unnecessary assumption that a balance was sustainable at point of origin be it a prebiotic rybozyme or some other such theoretical construct.
Comment by Bradford — July 5, 2009 @ 10:04 pm
July 5th, 2009 at 10:13 pm
We are unable to correlate function to 100% of studied genomes. Sherman is entitled to work with his assumption. Oops Todd.
Comment by Bradford — July 5, 2009 @ 10:13 pm
July 6th, 2009 at 12:26 am
Ah, so even though 0% of the statistically significant cases that we do know don't fit the theory we aren't allowed to draw any inferences until we have 100% knowledge. Yet another example of only being allowed to draw inferences that match Bradford's metaphysical bias.
Comment by Todd Berkebile — July 6, 2009 @ 12:26 am
July 6th, 2009 at 12:36 am
I don't know of any scientist other than Sherman who is investigating this. Do you?
Nothing inferential about this. Either Sherman's suspicion will be shown to have some supporting data or it will be debunked by resulting evidence. I thought you wanted empirical investigations of design instead of inferences.
Comment by Bradford — July 6, 2009 @ 12:36 am
July 6th, 2009 at 12:53 am
I don't know what Sherman is doing these days, he's not exactly prolific. But I'm sure you can find people searching for the function of various genes. That's pretty much what molecular biologists and biochemists do. There are whole labs dedicated to mapping the genomes of various species. And I'm sure you've heard of gene knockout experiments. More and more of the genome is understood every day, and you aren't aware of anyone doing that sort of work?
The inference is that his theory has already failed. You deny that inference. I suspect that is due to your biases.
Comment by Todd Berkebile — July 6, 2009 @ 12:53 am
July 6th, 2009 at 12:57 am
They would not fit your conceptualization of genes if they are as Sherman suggests. You'd likely find a tract that is not transcribed and lacks the premature stop codon characteristic of pseudogenes.
Comment by Bradford — July 6, 2009 @ 12:57 am
July 6th, 2009 at 1:30 am
There are people studying protein coding regions, RNA coding regions, regulatory regions, now defunct pseudogenes, retrotransposons, and the c-value paradox. Honestly Bradford, given how large biology is I suspect there is nothing in genetics that is not being studied by someone someplace. This is part of why so much progress is being made in biology and yet none of that progress is helping your pet theories.
Comment by Todd Berkebile — July 6, 2009 @ 1:30 am
July 6th, 2009 at 6:42 am
My 'pet theory' entails the belief that design is evident in nature. The belief is not one that ultimately can be affirmed or debunked by scientific data as the data is too limited with respect to the broad questions raised. Nevertheless one is free to assume that matter and energy have some eternal property that allows their existence without attribution to a cause. OTOH, one can also assume that matter and energy are created entities. It's a rational belief invoking a prior cause.
As for the more specific issue Sherman raised, he would gain support for it IMO even with a pattern relating non-essential, peripheral value functions to proteins of ancient organisms and essential, highly conserved properties to slightly modified proteins found in descendents. Critics would argue the data fits the work of a blind watchmaker but that in itself would be a metaphysical interpretation of a physical process. In any case, to borrow imagary from Mike Gene, behavior of ducks toward rabbits indicates a belief by the former that organisms not possessing their aquatic outlook merit their emnity. We rabbits are a kinder gentler species.
Comment by Bradford — July 6, 2009 @ 6:42 am
July 6th, 2009 at 7:06 am
Bradford wrote:
So if no amount of data can debunk ID then perhaps it's out there with the pink invisible unicorns?
This assumption contributes nothing—diddly-squat—towards understanding the properties of matter and energy. Feel free to entertain it, but keep it to yourselves.
Comment by olegt — July 6, 2009 @ 7:06 am
July 6th, 2009 at 11:58 am
I think you may have answered your own question. Perhaps Achaea and Bacteria "evolved to be simpler" – since they had no use for much of the front-loaded complex genome.
Comment by Daniel Smith — July 6, 2009 @ 11:58 am
July 6th, 2009 at 1:02 pm
That's right. It was intended as a contrast to an opposite metaphysical presumption that starts and ends with "it just exists." Measuring properties of what exists is the proper purview of science.
Comment by Bradford — July 6, 2009 @ 1:02 pm
July 6th, 2009 at 3:29 pm
hrun Says: And let me make a prediction right up front: This research is already being done by scientists who relied on a non-telic interpretation. Odd how that is virtually always the case.
Not much of a prediction if it is “virtually always the case.” But if it is virtually always the case you should be able to easily identify these “non-telic interpretations” from the pertinent literature. I ask because I’m a bit fuzzy on what a “non-telic interpretation” is or how it is relied upon.
I’ll even provide some source material
http://www.jbc.org/cgi/reprint/280/52/42477
Comment by Rock — July 6, 2009 @ 3:29 pm
July 6th, 2009 at 3:41 pm
A non-telic interpretation is (in this context) obviously the opposite of a telic interpretation as it is understood by the proponents of FLE. I am fuzzy on it, too, so I always hope that somebody will explain to me how the two are properly contrasted.
Comment by hrun — July 6, 2009 @ 3:41 pm
July 6th, 2009 at 4:27 pm
Your narrow perspective belies the generalization you stated.
My prediction is that no one will support it.
Anyone?
Comment by Rock — July 6, 2009 @ 4:27 pm