More Evidence of a Changing Paradigm
by JoyToday's New York Times carries a story in its 'science' section by Carol Kaesuk Yoon entitled From a Few Genes, Life's Myriad Shapes.
It's a story about Evo-Devo, with strong allusions to what we are familiar with around TT as Front-Loading. Some pertinent quotes from the article seem to speak obliquely to challenges Evo-Devo has presented to the standard Neo-Darwinian story line since it took off in the 1980s, a clear indication that it can take decades for new ideas and new evidence to rise to a level where the implications are marketed to a public universally taught the standard RM-NS pablum that still maintains its hegemony in public education by force of law…
…the advent of molecular biology reinvigorated the study of development in the 1980s, and evo-devo quickly got scientists' attention when early breakthroughs revealed that the same master genes were laying out fundamental body plans and parts across the animal kingdom. For example, researchers discovered that genes in the Pax6 family could switch on the development of eyes in animals as different as flies and people. More recent work has begun looking beyond the body's basic building blocks to reveal how changes in development have resulted in some of the world's most celebrated of evolutionary events.
The article goes into some depth about research into those famous finch beaks, even mentioning experiments where the BMP4 "toolkit gene" was turned on in chicken embryos, causing them to develop the variety of finch beaks! Nut-cracking finch beaks, cactus-driller finch beaks, the whole varied sheebang.
Worse, the same "toolkit gene" was found to account for some dramatic jaw adaptations in fish. Where does that lead?
And if being a major player in the evolution of African cichlids and Darwin's finches "” two of the most famous evolutionary radiations of species "” were not enough for BMP4, Dr. Peter R. Grant, an evolutionary biologist at Princeton University, predicted that the gene would probably be found to play an important role in the evolution of still other animals. He noted that jaw changes were a crucial element in the evolution of lizards, rabbits and mice, among others, making them prime candidates for evolution via BMP4.
"This is just the beginning," Dr. Grant said. "These are exciting times for us all."
Mimicry is another trait now traced to "toolkit genes" and their useful expression. Anotoher expression of these pre-existing genes was the surprising presence of wrists in ancient fish species making the early transition to land. The presence of the necessary genes in earlier forms, which looks a whole lot like front-loading…
Tetrapods include cows, people, birds, rodents and so on. In other words, the potential for making fingers, hands and feet, crucial innovations used in emerging from the water to a life of walking and crawling on land, appears to have been present in fish, long before they began flip-flopping their way out of the muck. "The genetic tools to build fingers and toes were in place for a long time," Dr. Shubin wrote in an e-mail message. "Lacking were the environmental conditions where these structures would be useful." He added, "Fingers arose when the right environments arose."
And here is another of the main themes to emerge from evo-devo. Major events in evolution like the transition from life in the water to life on land are not necessarily set off by the arising of the genetic mutations that will build the required body parts, or even the appearance of the body parts themselves, as had long been assumed. Instead, it is theorized that the right ecological situation, the right habitat in which such bold, new forms will prove to be particularly advantageous, may be what is required to set these major transitions in motion.
A nod to "fair and balanced," author Yoon did allow an urging of caution from the NDS orthodoxy:
Amid the enthusiast hubbub, cautionary notes have been sounded. Dr. Jerry Coyne, an evolutionary biologist at the University of Chicago, said that as dramatic as the changes in form caused by mutations in toolkit genes can be, it was premature to credit these genes with being the primary drivers of the evolution of novel forms and diversity. He said that too few studies had been done so far to support such broad claims, and that it could turn out that other, more mundane workaday genes, of the sort that were being studied long before evo-devo appeared on the scene, would play equally or even more important roles.
"I urge caution," Dr. Coyne said. "We just don't know."
Wow. decades' worth of empirical evidence and thousands of experiments and published papers, and we are told that Neodarwinian orthodoxy is still resisting – and urging the public to resist as well. About which the author concludes…
All of which goes to show that like all emerging fields, evo-devo's significance and the uniqueness of its contributions will continue to be reassessed. It will remain to be seen just how separate or incorporated into the rest of evolutionary thinking its findings will end up being. Paradoxically, it was during just such a flurry of intellectual synthesis and research activity, the watershed known as the New or Modern Synthesis in which modern evolutionary biology was born in the last century, that developmental thinking was almost entirely ejected from the science of evolution.
But perhaps today synthesizers can do better, broadening their focus without constricting their view of evolution as they try to take in all of the great pageant that is the history of life.
"We're still a very young field," Dr. Gilbert said. "But I think this is a new evolutionary synthesis, an emerging evolutionary synthesis. I think we're seeing it."
Hmmm. Maybe the die-hards have been wasting so much time battling ID in the sociopolitical arena that they've neglected the challenges arising within science itself. Perhaps believing their authoritarian 'orthodoxy' could keep those challenges under wraps automatically during the distraction of their ongoing holy war.
I'd suggest this lengthy and well-researched article in the NYT demonstrates they were mistaken about that.
June 27th, 2007 at 12:53 pm
I think these findings point quite clearly towards the possibility that the "blueprints" for creating organisms are not specified within the genome at all. . . Genomes code for the sequence of amino acids in proteins. Envisioning the genome as some kind of uber-machine that controls and directs every aspect of morphogenesis and behavior is looking more and more impossible as we see how similar are the genomes and proteins that radically different organisms share.
See this summary of Rupert Sheldrake's theory of morphic resonance for an elaboration of the possibility of non-genomic aspects of inheritance. . .
Comment by mcromer — June 27, 2007 @ 12:53 pm
June 27th, 2007 at 1:29 pm
Joy,
Please stop embarrasing yourself. It's painful to watch.
The article speaks of
and
In other words, good old-fashioned mutation + natural selection.
The article informs us that mutations in particular genes (tool-kit genes) may be responsible for a wide range of different adaptations. If anything, this strengthens rather than weakens the case for the importance of mutation and selection in organic evolution. Jerry Coyne was simply pointing out that we don't know yet just how important mutations in this particular class of developmental genes are for generating morphological novelties.
Comment by Raevmo — June 27, 2007 @ 1:29 pm
June 27th, 2007 at 2:01 pm
Hi, Joy,
This blog article, A Divine Materialims, though the title is a misnomer connotating religion, comes at the idea of front loading from a different perspective. I have to admit that the gist of it seems sound:
The function of proteins are derived from their shapes (form).
The forms are pre-determined by natural laws.
From my own cursory knowledge of biology, it seems apparent that molecular form does indeed determine function (behavior), and that the forms come about as a result of the attraction/repulsion forces (natural laws).
The author even mentions the term front loading in the post. I think that inanimate matter's role is given a short shrift (in that it is not even mentioned), but that's a bone I could pick with just about all the forums.
Comment by AnaxagorasRules — June 27, 2007 @ 2:01 pm
June 27th, 2007 at 2:17 pm
Actually if you calculate the attraction / repulsion forces, there are millions or billions of lowest energy conformations for each protein sequence.
They form into a characteristic conformation or (sometimes) set of conformations that provide their function.
The question why proteins fold into a characteristic shape, and do so within the tiniest fraction of a second, is a big mystery known as the "protein folding problem". Of course materialists are all convinced this is all explainable in terms of chemical bond forces, but they certainly can't provide the evidence for that.
Comment by mcromer — June 27, 2007 @ 2:17 pm
June 27th, 2007 at 2:44 pm
Raevmo wrote:
For these mechanisms to exist and endure, indeed for a universe to exist at all, has not been shown to not require a designer. Fundamental particles look for all the world to be designed objects. Is it just chance that made all electrons have identical masses and charge strength, etc? If I walked into a warehouse containing 100 billion identical spheres of half a centimeter diameter, my first thought wouldn't be, "Well, clearly these objects weren't designed!" A significant number of physical constants and magnitudes look as though they were very finely tuned with life in mind.
Your conclusion assumes 1) that there is life ordered by a hereditary code; and 2) that the physical world exhibits stable, lawlike regularity. Neither has been shown to be possible by virtue of unintentional processes alone. In fact, both 1 and 2 are colossally improbable given naturalism. The degree of regularity and hence predictability in natural phenomena is actually rather staggering upon the hypothesis of naturalism. There is no logical necessity (i.e., assuming there is no perfectly rational, moral, and almighty creator/sustainer of nature), that the world will not change drastically from one minute to the next. Another way to put it is that there are infinitely many logically possible worlds. And remind yourself of the mother's milk of empiricism: one cannot observe necessity. So appeals to natural necessity are simply unempirical.
The stability of nature—"”in other words, that there are any physical necessities, never mind enduring ones"”—is precisely what naturalism cannot account for. For it is simply incredible, given the infinite number of ways in which things logically could have been less regular, and more random and unpredictable.
But given a rational creator/sustainer, we should expect nature to be rationally ordered and stable. If unintentional processes are the whole story, there should not be objects that start out by being already finely tuned for producing enduring complex life in a complex environment, given the infinite number of ways an unintentional world could fail to be consistent with and conducive to complex life.
Comment by stunney — June 27, 2007 @ 2:44 pm
June 27th, 2007 at 2:47 pm
mcromer:
Yes indeed, it seems quite plausible as a working hypothesis that standard chemical/physical forces are sufficient to explain it. Don't forget, the three-body problem is already quite difficult. In protein folding we're talking about a lot of atoms moving around. Even so, the process is not entirely a mystery: a general rule appears to be that the core of proteins is hydrophobic and the outside more hydrophylic, which seems to make physical sense. The fact that proteins can fail to relax into their standard shape in solvents other than water tends to confirm this idea.
But what kind of immaterial causes are you postulating?
Comment by Raevmo — June 27, 2007 @ 2:47 pm
June 27th, 2007 at 2:57 pm
Good lord, stunney, as mtraven just pointed out as well in another thread, you are repeating yourself verbatim. I've seen this post of yours (or a minor mutation of it) several times before. Time for some fresh ammo, dude.
Comment by Raevmo — June 27, 2007 @ 2:57 pm
June 27th, 2007 at 3:02 pm
Raevmo:
Then my advice to you would be to not watch it. I am not responsible for your inability to control yourself.
That alterations – a.k.a. mutations – of genes occur is common knowledge no one denies. At issue are the mechanisms for these alterations, particularly in situations of these types of "tool-kit" genes where the requisite alterations occur well before the environment opens up a niche for them to move into. Fish don't need wrists. Mice don't need beaks.
Y'all may be coming at the evidence ass-backwards. Not surprising, given that Darwin originally came at evolution backwards. He had to start somewhere. Too bad things never really progressed from there.
Comment by Joy — June 27, 2007 @ 3:02 pm
June 27th, 2007 at 3:03 pm
Anaxagoras:
Of course they do. Including their beta (and in some cases, delta and gamma forms) as well.
Since when are the functional constructs of living processes "inanimate?" When they're dead?
Comment by Joy — June 27, 2007 @ 3:03 pm
June 27th, 2007 at 3:38 pm
You're delusional if you think that article has any support for ID, front-loading, or any of the other pet causes.
Battling ID fortunately does not take up that much time of actual practicing scientists. And please note that one of your bete noirs, PZ Myers, is a researcher in the evo-devo field and manages to find time to actually do science in between saying nasty things about religion.
Comment by mtraven — June 27, 2007 @ 3:38 pm
June 27th, 2007 at 3:46 pm
Raevmo, I know that it is perfectly obvious to you that this article is just expressing something about the nature of RM+NS. However, I am not able to read that in this statement:
Why the heck did fish have finger, hand and foot-making technology "long before" they had need of it? This looks like "anticipation" to me.
I remember a Star Treck TNG episode when they encountered little flying fighting machines. When they determined that the fighting machines "anticipated", they used that as conclusive proof that the machines were intelligent.
A primary hallmark of intelligence is anticipation, a primary incapacity of RM+NS is an inability to anticipate. This is clear evidence for front-loading ID.
Comment by bFast — June 27, 2007 @ 3:46 pm
June 27th, 2007 at 4:00 pm
keiths said in a comment now in the Hole:
Um… Nope. I mentioned that the data is no longer available, I don't know why, and made yet another movie joke about it.
I have run out of patience with your nastiness. Play stupid games on someone else's threads. You're done with mine. Further posts go straight to the Hole.
Bye.
Comment by Joy — June 27, 2007 @ 4:00 pm
June 27th, 2007 at 4:09 pm
bFast:
A gene that is currently important for the development of fingers used to be important for the development of something else before fingers even existed. As Francois Jacob (evolution is a tinkerer) put it: the constant reuse of the old to make the new. Who anticipated McGeiver?
Comment by Raevmo — June 27, 2007 @ 4:09 pm
June 27th, 2007 at 4:10 pm
They had fin-making technology that was repurposed for hands and feet. No anticipation required. It can look like anticipation in retrospect, but that's an illusion.
Hm, here's an even more suggestive passage from the article:
That sounds a lot like anticipation, but what it really means is that the genetic tools were around for a long time, doing something else that was useful in another environment, before they were used to make fingers and toes.
Comment by mtraven — June 27, 2007 @ 4:10 pm
June 27th, 2007 at 4:31 pm
Hi, Joy,
My specific point is that the article I linked to is soley concerned with protein binding, and how natural laws determine the forms. However, it also makes sense that the natural laws must determine the forms of inanimate matter as well (in this case, I'm referring to the elements that are not directly part of the composition of life forms, regardless if the form is alive or a decomposing corpse). My interests are more about matter in general, and that is the chief reason why I finally put away my biology book. Life is just an illusion as far as I'm concerned, which is just a small part of a larger illusion about matter itself.
One analogy that I can think of is this:
I'm standing in front of a hologram of a rock. Suddenly I have instruments which let me magnify its features, and in seeing them I notice that they are made up of tiny particles, arranged to produce the form that I've identified as a rock. In looking at the particles, I soon see that they are made up of other, smaller particles. Meanwhile, the rock has disappeared, or more correctly I realize that the rock is not real, that it is a delusion. The smallest particles seem to be appoaching what reality is, but that is also delusion. What is coming clearer and more certain, is my awareness of the delusion. What I want to see is what is making the particles, or to put it another way, from what are the particles coming? THAT is what is real and that is what I'm interested in. I could have also made this analogy using as an example the hologram of a human being. I didn't because I wanted to underscore my point about not being fixated on life forms.
The benefit to me of not fixating on life versus non-life is that I am better able to fixate on the delusions about matter. In my opinion, devoting mental resources toward separation and classification only makes it harder to rid onself of the delusions.
Comment by AnaxagorasRules — June 27, 2007 @ 4:31 pm
June 27th, 2007 at 5:35 pm
Joy:
You created this thread based on a NYT article that highlights progress in evolutionary biology, including an important role for natural selection. If that's your idea of trying to make Darwinists look bad, you need to go back to the drawing board.
Comment by Raevmo — June 27, 2007 @ 5:35 pm
June 27th, 2007 at 5:45 pm
Anaxagoras:
I can certainly appreciate where you're coming from, though for all practical purposes [FAPP] of science, the forms, mechanisms and tools of life are very important. If there are any practical purposes to which we could put the knowledge. In biology, that's mostly medicine.
And there is a difference between animate and inanimate form. Raw (non-organic) inanimate matter will never produce a protein one. Abiogenesists of course think otherwise, but they're a long, long way from demonstrating the feasibility of that. Since proteins are coded for by DNA, and they can't account for DNA either.
And while proteins still exist when their makers are dead (we call it "meat"), meat doesn't magically produce more meat while it's dead. While functioning in a protein-based life form, proteins are themselves animate. Many of them are state-switchers, meaning they spontaneously change configurations to present different binding sites which serve different functions for the life form. This is of course a physical dynamic, quantum states. On the level of what determines the results of quantum states you're right – there is no matter. But living on that level to the point of denying reality doesn't contribute a thing to science or to life.
In my opinion only. Your Milage May Vary [YMMV].
Comment by Joy — June 27, 2007 @ 5:45 pm
June 27th, 2007 at 5:59 pm
Raevmo:
I haven't made Darwinists look bad. They do that to themselves without any help from me. The subject of the article is development, using the very same genetic "tool-kit" genes – there aren't that many of them – in different classes and even kingdoms to produce different evolutionary developments. I thought the article was quite clear about that.
No one denies that natural selection is a significant factor in what can live, how long it lives, if it can reproduce and whether it lives long enough to get the kids out of diapers. Life's a crap shoot, and sh*t happens. Natural selection as often selects out the fit as the unfit, so it's as random as biologists have claimed mutations are. Moreso if random mutations aren't the real mechanism of evolution, but more pertinent to devolution. Development is expression intensive, and expression has been evidentially tied to endogenous mechanisms related to environmental sensitivity-response called "epigenetics."
I think life forms have a lot more to do with their forms and evolution than random accidents do, even though random accidents happen. Cancer is a good example. It's generally not considered evolutionary, but almost exclusively environmental with genetic weaknesses to environmental triggers.
My drawing board has some blanks to be filled in. But your say-so isn't going to make me start erasing things already there. Sorry.
Comment by Joy — June 27, 2007 @ 5:59 pm
June 27th, 2007 at 6:28 pm
Joy:
You are very opnionated about biology for someone who obviously doesn't know all that much about it. Let me help you fill the gaps in your knowledge. You might like Leo Buss' "The Evolution of Individuality". The book explains among other things why the germ line is usually sequestered from a very early stage onwards during development. Roughly speaking, it's to prevent cancerous cells from making it to the next generation. It's all about levels of selection. Hope that makes sense, and if not hope it makes you think.
Comment by Raevmo — June 27, 2007 @ 6:28 pm
June 27th, 2007 at 6:44 pm
Raevmo:
Um… you do know the so-called "Weissman Barrier" has been breached, don't you? This was a factor in recent suspension of gene therapy trials, when it was found the researchers 'neglected' to inform the patients that they couldn't ever donate eggs or semen because the transgenes were found to cross that barrier. Part of that "Informed Consent" thing FDA ordered them to include.
Which might be a good thing if we can ever get good enough at gene-splicing to avoid promoters like human leukemia virus. Cure the patient, cure their offspring and all that.
Comment by Joy — June 27, 2007 @ 6:44 pm
June 27th, 2007 at 7:11 pm
Joy, I suppose you mean the Weismann barrier (not Weissman). The barrier may not be unbreachable, but it's there for a good reason. That's one of the points of Buss' book.
Comment by Raevmo — June 27, 2007 @ 7:11 pm
June 27th, 2007 at 10:48 pm
Raevmo wrote:
I've seen this stuff trotted out umpteen times.
Time for some new ammo, dude.
Oh, you mean you should just be able to presuppose naturalism, and should not have to deal with criticisms of it?
Well, why didn't you just say so? And wtf are you doing at TT anyway?
Comment by stunney — June 27, 2007 @ 10:48 pm
June 28th, 2007 at 2:31 am
You're confusing "genetic" with "inherited." Cancer is a genetic disease. Even environmental factors (which, for most cancers, predict a very small proportion of the risk) cause genetic changes.
It's a series of genetic changes, some of which were inherited from parents.
If you disagree, how do you describe/explain things like the activating K-Ras mutations found in nearly all colon neoplasms? The Philadelphia Chromosome?
Comment by JAM — June 28, 2007 @ 2:31 am
June 28th, 2007 at 8:05 pm
I really don't see how, when there are millions to billions of essentially-lowest energy states.
Proteins have been likened to magnets attached to a strand of spaghetti. Why do the strands always fold up in the exact same way, or couple of ways? I don't see how electromagnetic field attraction is going to deliver a miracle here. . .
Comment by mcromer — June 28, 2007 @ 8:05 pm