9 Responses to “Ancient Sleep and Flipping Switches”

1. Doug Says:
   January 24th, 2008 at 12:40 pm

   this unprecedented finding demonstrates that evolution can be driven by changes in the patterns of gene expression, rather than solely by changes in the genes, themselves.

   Sounds familiar.

   Note that conventional non-teleological views of evolution came with an expectation - new forms would require many new mutations or many new genes. Yet what we now find is that because of the architecture of life, evolution instead tweaks what it was handed. If novel forms can be spawned by making minor modifications in already existing genes and developmental plans, then front-loading is clearly plausible. Yet this need not be the case. The original thinking could have turned out to be correct, where novel forms required the spawning of an array of novel genes. Unless those novel genes were somehow front-loaded to appear, the thesis of front-loading would be fatally wounded.

   from: More on Front-Loading Evolution - Mike Gene

   Good call.

Comment by Doug — January 24, 2008 @ 12:40 pm

2. hrun Says:
   January 24th, 2008 at 4:06 pm

   Doug, why would is front loading severely wounded unless 'novel genes were somehow front-loaded' but not unless novel regulatory units were somehow front-loaded?

   From an evolutionary stand-point it is irrelevant whether new genes or new regulatory regions evolve. Or if genes or regulatory regions get modified. Either works just fine. Likewise, I don't see why front-loading cares one way or another if genes get front-loaded or regulatory regions get front loaded.

   And, by the way, the definition of a gene encompasses its regulatory regions. So when mutations alter a regulatory region of a gene, thus changing gene expression, they are actually 'changes in the genes'.

Comment by hrun — January 24, 2008 @ 4:06 pm

3. Bradford Says:
   January 24th, 2008 at 4:17 pm

   hrun: I don't see why front-loading cares one way or another if genes get front-loaded or regulatory regions get front loaded.

   The signifcance lies in what FL would indicate. A blind process is devoid of foresight. FL is not.

Comment by Bradford — January 24, 2008 @ 4:17 pm

4. Doug Says:
   January 24th, 2008 at 4:20 pm

   why would is front loading severely wounded unless 'novel genes were somehow front-loaded' but not unless novel regulatory units were somehow front-loaded?

   Did you follow the link and read the article, hrun? Have you been paying attention to Mike's series of posts over at The Design Matrix (he usually included them over here with a link that brought you to the DM).

   From an evolutionary stand-point it is irrelevant whether new genes or new regulatory regions evolve.

   Well sure, now it is. One set of predictions will be brushed aside while new ones are ushered in to meet the evidence.

   Or if genes or regulatory regions get modified. Either works just fine. Likewise, I don't see why front-loading cares one way or another if genes get front-loaded or regulatory regions get front loaded.

   Evolutionary trajectory… designing the future through the present…. and other phrases can be found if you follow the link provided.

   And, by the way, the definition of a gene encompasses its regulatory regions. So when mutations alter a regulatory region of a gene, thus changing gene expression, they are actually 'changes in the genes'.

   Would we not be playing with words if it specified "the active protein coding sequence of a gene"?

Comment by Doug — January 24, 2008 @ 4:20 pm

5. hrun Says:
   January 24th, 2008 at 4:36 pm

   The signifcance lies in what FL would indicate. A blind process is devoid of foresight. FL is not.

   I understand that a blind process is devoid of foresight. I don't understand what the fundamental difference in terms of front loading (or evolution for that matter) whether the ORF of a gene or the regulatory regions of a gene get modified to alter for example the development of an organism.

   Clearly, both mutations in the ORF and in the regulatory regions occur. Clearly, both types of mutations can have profound effects on the organism. What would FL indicate in this respect?

Comment by hrun — January 24, 2008 @ 4:36 pm

6. hrun Says:
   January 24th, 2008 at 4:45 pm

   Did you follow the link and read the article, hrun? Have you been paying attention to Mike's series of posts over at The Design Matrix (he usually included them over here with a link that brought you to the DM).

   Yes. I have been following Mike's series of posts. I certainly did not read all of them. I hope that's not a prerequisite to ask questions or find answers.

   Well sure, now it is. One set of predictions will be brushed aside while new ones are ushered in to meet the evidence.

   ? Did you see evolutionary biology discount the importance of mutations in regulatory regions AFTER they were discovered? Did you see front loading proponents tout the importance of mutations in the regulatory regions BEFORE they were discovered?

   My guess is that your answer to both of those questions would be NO. Thus, it seems that neither FL nor non-FL needs to 'brush aside' any set of predictions.

   Evolutionary trajectory"¦ designing the future through the present"¦. and other phrases can be found if you follow the link provided.

   Yes, fine. But why does this apply specifically to mutations in regulatory regions and not in the open reading frame?

   Would we not be playing with words if it specified "the active protein coding sequence of a gene"?

   Well, no. It's not just 'playing with words'. Apparently somewhere there is the impression that 'evolutionary biology' stipulated that mutations in genes were key to novel features of organisms but that these mutations exclude mutations in regulatory regions. Case in point, just a few paragraphs above you insinuated that allowing for mutations in regulatory regions for the non-FL hypothesis would be akin to brushing aside a set of predictions.

   The original prediction was that mutations in genes are responsible for the changes we see in different organisms. This appears to be true. Some are in the ORF or the genes. Some are in the regulatory regions of the genes. How is this brushing aside an old set of predictions? Especially since this prediction was made long before anything about the structure of genes was known?

Comment by hrun — January 24, 2008 @ 4:45 pm

7. Doug Says:
   January 24th, 2008 at 6:35 pm

   Hrun,

   Those are interesting points. Tonight I'm going to re-read through Mike's series of posts on this topic and then re-read this post of yours.
   Thanks for raising the questions. Sorry I don't have a quick response - but that's a good thing. Gives me a chance to re-read and re-think.

Comment by Doug — January 24, 2008 @ 6:35 pm

8. hrun Says:
   January 24th, 2008 at 7:51 pm

   Doug, just as an aside, check out the final paragraph from the linked text:

   Dr. Behringer describes the significance of his finding as such: "Darwin suggested that "successive slight modifications" would ultimately result in the evolution of diverse limb morphologies, like a hand, wing, or fin. The genetic change we engineered in mice may be one of those "slight modifications" to evolve a mammalian wing."

   This really does not sound like anybody is brushing aside any predictions, does it?

Comment by hrun — January 24, 2008 @ 7:51 pm

9. Doug Says:
   January 25th, 2008 at 6:58 pm

   Did you see evolutionary biology discount the importance of mutations in regulatory regions AFTER they were discovered?

   This is a good point that I was brashly overlooking when I made that earlier comment.
   However, the nature of the FL position is more subtle. You're right, mutations can occur in any of the genic regions (promoter, operator, leading strands and protein coding regions), but it's the nature and the effect of these mutations that are of significance.
   It was assumed that novel and complex forms would have been the product of numerous mutations or the advent of new genes; but it turns out that the tweaking of existing genes and developmental plans will yield these novel, complex forms. These avenues for obtaining new features and body plans are a significantly simpler process.

   The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another

   and

   But the real interest for evolutionary biologists is that these hierarchies not only favor the evolution of certain forms but also disallow the growth of others, determining what can and cannot arise not only in the course of the growth of an embryo, but also over the history of life itself. - C.K. Yoon

   Constrained and possibly determined evolutionary trajectories. This does appear to lend more support to Mike's notion of FL opposed to a blind process exploiting any evolutionary pathway that allows some temporary functional benefit.

   As the Yoon paper states, you have this large diversity of finch species marked off by variations in beak size. When examined closely it is discovered that slight variations on the BMP4 gene can account for this variety. Higher or lower productions of BMP4 can determine thickness and robustness of the beak.

   There's more:

   BMP4 is multitalented and can also act to direct early development, laying out a variety of architectural plans including signaling which part of the embryo is to be the backside and which the belly side.

   The effects of BMP4 on beak integrity is not limited to finches. Similar effects are noted in chickens when the activity of BMP4 is artificially increased. Size, shape, and strength of chick beak is impacted when the gene is manipulated.
   Yoon also highlights research by Craig Albertson and Thomas Kocher showing that the same manipulations, toggling with BMP4, can have an effect on jaw varieties in cichlids.

   Used to lay out body plans, build beaks and alter fish jaws, BMP4 illustrates perfectly one of the major recurring themes of evo-devo. New forms can arise via new uses of existing genes.

   Mike states:

   To front-load evolution is an attempt to design future states through the present. To accomplish this, future evolutionary events would be fundamentally dependent on the originally designed state that has in some way propagated across deep time.

   Yoon also mentions the Tiktaalik, a "water-loving fish" that had wrists. A phenotypic trait that was believed to be unique to land animals.

   This was telling us that a piece of the toolkit, to make arms, legs, hands and feet, could very well be present in fish limbs… . In other words, the genetic tools or toolkit genes for making limbs to walk on land might well have been present long before fish made that critical leap.

   Front-loaded. You have an evolutionary trajectory that is mapped out by what is already contained within the genetic make up of a species, that is currently lacking the need for that genetic region to be expressed.
   Again, this is showing how constrained evolutionary development actually is.

   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 particulary advantageous, may be what is required to set these major transitions in motion.

   The genetic potential already exists, it's more than likely not waiting to be blindly stumbled upon - fortuitously allowing the species access into a new environmental niche.
   Evironmental feedback appears to be helping the unfolding of evolutionary plans.

Comment by Doug — January 25, 2008 @ 6:58 pm

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