Approaching Difference, Not Likeness
by JoyThere were a couple of very interesting research news reports this week coming in from the fields. Turns out that biological scientists are beginning to understand why their simplistic model of evolution [a.k.a. Neodarwinian Synthesis] can't account for the empirically obvious differences between human beings and our closest relatives. They've been looking at things the wrong way, guided by that simplistic model.
First up is the report that Ancient Retroviruses Spurred Evolution of Gene Regulatory Networks. About the estimated 8% of the human genome that consists of primate-specific retroviral DNA insertions.
This expands on knowledge incoming that gene regulation networks, controlled by "Master Regulators" are responsible for orchestrating gene expression in higher vertebrates. Deal is, at least one of those "Master Regulators" [p53] was helped by a retroviral element akin to HIV that jumped repetitive elements around in the genome that p53 acts upon, enlisting new genes into its network. The researchers go ahead and state that these elements account for the most of the obvious differences between humans and other primates despite the similarity in genes across the genomes.
From the article:
Thus, p53 was crowned "guardian of the genome," as biologists now call it. Its job is to coordinate the surveillance system that monitors the well-being of cells. Indeed, p53 is so important that when it fails, cancer often results. About half of all human tumors contain a mutated or defective p53 gene.
Moreover, this challenges the NDS "conventional wisdom"…
These results raise new questions about the role of so-called "junk DNA," the vast regions of the genome that don't code for proteins. ERVs fall into that category. Many scientists once believed that such DNA served no purpose, but new data from the Haussler lab and other labs are challenging that view.
"We're starting to uncover the treasure in this junk," said Wang.
Moreover, the team has proposed a new mechanism for evolutionary change. Conventional wisdom says that evolution is driven by small changes–point mutations–to the genetic code. If a change is beneficial, the mutation is passed onto future generations.
Now it appears that another level of evolution occurs that is not driven by point mutations. Instead, retroviruses insert DNA sequences and rearrange the genome, which leads to changes in gene regulation and expression. If such a change in gene regulation is beneficial, it is passed onto future generations.
It gets worse, of course. These researchers now predict that ERV-mediated expansion of gene regulatory networks are responsible for other master gene regulators too. Not just p53.
The second article, Humans and Chimps Differ At Level of Gene Splicing begins to quantify a further means of differential expression, this one between humans and chimpanzees whose genomes are ~99% identical. This is about alternative splicing for producing alternative proteins.
This is interesting science. Both articles talk about findings garnered by a different approach to the material being examined, that weren't informed by the arbitrary brick wall NDS has erected around causation. I predict we'll see more and more of this from researchers who chafe under the restrictions NDS imposes on their approaches to biological issues. I suspect it's because so many researchers who have opted into private practice left the ideological restrictions behind and academic researchers would like to try and keep up.
But I could be wrong. It might be that non-culture warriors are just sick of ignorant, antiquated theoretics and want to know what's really going on.
November 16th, 2007 at 5:45 pm
Joy:
Another nutty post by Joy. Please Joy, why don't you explain to us exactly what you mean by NDS, so we can better follow your "logic" that leads you to conclude that NDS (whatever it is) is flabbergasted by mutations caused by viruses.
Comment by Raevmo — November 16, 2007 @ 5:45 pm
November 16th, 2007 at 6:33 pm
Another inane response from Raevmo. Please Raevmo, why don't you explain why you are inferring some non-ordinary, esoteric understanding of NDS. In order to illuminate your unwillingness to actually address the points she made - snide comments aside.
Comment by Doug — November 16, 2007 @ 6:33 pm
November 16th, 2007 at 8:38 pm
Inane, but not unexpected. NDS. Neodarwinian Synthesis. Mutation-selection. The 'standard model' of evolution. The "conventional wisdom" derived from that model of evolution, cited by the researchers as *what* their findings challenge.
And before Raevmo goes off on another tangent about *what* the challenge of those findings is, let me just go ahead and re-type the key-word phrases from the cited copy…
"New questions about the role of so-called 'junk DNA'."
"New data challenging that view."
"Treasure in the junk."
"New mechanism for evolutionary change."
"Another level of evolution."
"Not driven by point mutations."
"Alternative splicing."
"Alternative proteins."
Of course it is quite possible that both these reports are mere hype about mundane high-school level non-research nobody in their right mind would pay a real biologist to do. Lord knows there's a heck of a lot of that out there choking science these days.
But until and unless Raevmo can demonstrate that to my satisfaction, I'll remain hopeful that biologists are finally closing in on what they've been missing all these years. Jumping genes are nothing new. Retroviral insertions are nothing new (that's what they've been calling "junk"). Gene expression is nothing new. Orchestrated gene regulation and expression networks across whole genomes facilitated by the jumping insertions *is* fairly new, and it offers a whole different level of evolution beyond fortuitous point mutations in nucleotide bases selected by the parameters of life and the luck of the Irish.
We are learning why we are not chimpanzees. Ever since they discovered (contrary to the model's "conventional wisdom") that our genome is 99% chimpanzee, this question has loomed large. It simply cannot be explained by the "conventional wisdom."
Comment by Joy — November 16, 2007 @ 8:38 pm
November 17th, 2007 at 4:06 am
As I understand it, this paper is about the different mechanisms through which genetic variation might have happened in the past i.e. through retrovirus's. This is not a problem for NDS which never assumed that all variation was a point mutation (remember NDS was developed before the structure of DNA was known). In fact it helps explain why undirected (I think this is a better term than "random" which implies some kind of probability model) and relatively small change in the genonome can result in rapid, large, and coherent change in the phenotype. It also shows how under the NDS paradigm the field of evolutionary biology can grow and make signicant discoveries based on experimental and field data.
Comment by Mark Frank — November 17, 2007 @ 4:06 am
November 17th, 2007 at 10:40 am
Mark Frank:
Retroviruses themselves are latecomers to the genetic lineup, but are fascinating relief pitchers. Then again, it's been less than a decade that we've known we're 99% chimpanzee. …or even that we didn't have half the genes 'conventional wisdom' thought we had.
Perhaps not NDS specifically, but "modern evolutionary theory," "standard model of evolution" and whatever else you want to call it has always assumed evolution proceeds by incremental small changes in phenotype by virtue of the relative success of certain minor variations. This is simply a fact of scientific history, Mark. There's no sense pretending otherwise.
Gee. I wonder if the scions of biology ever got around to informing Stephen J. Gould that he was right about punk-eek, even though he didn't live long enough to accept his Nobel. I've never heard that story. Have you a link to the details?
Now you're back to NDS again? NDS doesn't and never did allow growth or significant discoveries that challenge its orthodox "paradigm," which is why biologists have fondly (and not-fondly) labeled the imposed framing as "dogma" and so love to offer challenge.
It looks to me like as the generations of working biologists have changed and the technological tools developed for investigation have improved, and as the knowledge base has grown well beyond the imposed dogmas of "Neodarwinian Orthodoxy," evolution isn't looking so Darwinian (Paleo or Neo) anymore. Maybe y'all need a new label that accounts for what we now know, and what we could hope to know very soon by different approaches to the actual evidence before us.
As if biology were a real science and not just a religious inquisition in defense of orthodoxy against heresy. I think that would be pretty cool.
Comment by Joy — November 17, 2007 @ 10:40 am
November 17th, 2007 at 11:27 am
As illustration of the issues before us as we become ever more familiar with what genomes actually are - as opposed to what they've been assumed to be for so long, the 99% figure on our likeness to chimpanzees could be juxtaposed to those strange, lowly voles.
Despite our 99% likeness to chimps, we are obviously, empirically, unquestionably NOT chimpanzees. Yet we don't have enough unique genes in our genome to account for that by the dying paradigm. Something else accounts for the difference, and it's NOT unique genes.
At the other end of the conundrum are the voles. The critter undergoing the fastest speciation that we know of at this point in time (by analyzing their wildly divergent genomes). Those genomes are nowhere near 90% alike, and there's a wide variety of numbers of chromosomes among the species. Heck, in one species males and females have different numbers of chromosomes! …yet all voles look alike. So much alike that biologists can only tell them apart by counting chromosomes under a microscope.
What are these facts telling us about genomes? I could, from my broad and non-biologist view, make a couple of suggestions about that. Not exactly "predictions," but certainly considerable possibilities…
1. Genomes are data storage devices, where basic codes for all the possible and all the historic protein families, protein forms and sub-protein adjuncts are recorded. To be read, shifted and re-read, post-modified and creatively deployed by the organism that relies for these jobs on the few that are evolutionarily conserved across deep time. Read-write-error correction, production modification, assembly and function (old or new) are processes, not 'things'. The pieces-parts of those machines are 'things'.
2. A life form *is not* its genome, and is not specified by its genome. It uses its genome to support the processes which define what it is. A life form is the expression of its life processes. And expression is primarily an epigenetic phenomenon, a constant, responsive information flow through feedback loops between the organism, its pieces-parts, its ancestral history and its current environment. A dynamic process, not a 'thing'.
Comment by Joy — November 17, 2007 @ 11:27 am
November 18th, 2007 at 7:18 pm
Joy, sorry, but I do not understand what in the articles supports your claim that evolution is not looking like NDS. As I understand it, the "standard model" of evolution acknowledges that some "junk" DNA has a use and also recognises a wide variety of mechanisms of variation. Sure, they are some details that are unclear, there are many surprises awaiting us, but in what sense would those articles lead us to abandon NDS? Will either of those papers break the NDS paradigm? I doubt it. Evolutionary theory will evolve to include the new findings.
Was that approach telic? I saw nothing to suggest it was. As far as I could tell this work was done by scientists who embrace a [i]non-telic[/i] theory of evolution - NDS if you like.
Like most scientists, in fact. It is what they do, afterall; try to find out what is going on. And have been doing for a long time. And that is why the NDS of today is quite different to the NDS of 30 years ago. There is no arbitrary brick wall, Joy. The development of NDS over the decades would seem to prove that.
Comment by The Pixie — November 18, 2007 @ 7:18 pm
November 20th, 2007 at 1:54 pm
"The development of NDS over the decades would seem to prove that."
By development, I presume you mean the arbitrary, ad-hoc, epicycle-upon-epicycle approach that attempts to salvage the central dogmatic principles?
Comment by Eric Anderson — November 20, 2007 @ 1:54 pm
November 21st, 2007 at 2:02 pm
"By development, I presume you mean the arbitrary, ad-hoc, epicycle-upon-epicycle approach that attempts to salvage the central dogmatic principles?"
By "ad-hoc, epicycle-upon-epicycle" I presume you mean empirical?
By "central dogmatic principles" I presume you mean principles that have stood the test of time?
Comment by The Pixie — November 21, 2007 @ 2:02 pm