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?

By development, I presume you mean the arbitrary, ad-hoc, epicycle-upon-epicycle approach that attempts to salvage the central dogmatic principles?

… evolution isn't looking so Darwinian (Paleo or Neo) anymore…

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.

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.

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.

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.

It might be that non-culture warriors are just sick of ignorant, antiquated theoretics and want to know what's really going on.

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.

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'.

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.

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.

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).

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.

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.

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?

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.

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.

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."

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.

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.