Friday quote: The conserved versatility of eukaryotes
by KrauzeWhen surveying the battlefield, you can be forgiven for thinking that there are only two camps in the discussion over intelligent design: The creationists, who claim that the major types of life were separately created (birds, fishes, etc.), with evolution playing a minor role thereafter, and the ID critics, who claim that the first life was the product of geochemistry, with evolution proceeding from this sloppy beginning. Now that we're disposing of misleading dichotomies, let me just point out that there is a third alternative: That life was designed to evolve, and that the first lifeforms, although simple in appearance, were made with the future in mind. This alternative is also known as front-loading.
Front-loading has become increasingly plausible with discoveries indicating that evolution, far from being something that "just happens" is organisms, is in fact a biological function. A good place to look for these discoveries is the book The Plausibility of Life: Resolving Darwin's Dilemma, by molecular biologists Marc Kirschner and John Gerhart. They show how the regulatory logic of cells facilitates the evolution of complexity, by shuffling already existing modules around, rather than creating them anew. Furthermore, it seems that the core of this system has remained virtually unchanged since it appeared in the first eukaryotes.
"With a more complete tool kit for regulating protein levels and protein activity, the eukaryotic cell, sometime between two billion and one billion years ago, had achieved processes of sufficient power to regulate large combinations of genes through extremely complex circuits. Except for elaboration and diversification of the circuits, very little of the process has changed qualitatively since. These regulatory mechanisms apparently possessed enough power and versatility to facilitate all of the evolution that has occurred since the time of their invention, while they were themselves conserved. Therefore, eukaryotic gene regulation is perhaps the most powerful conserved core process, responsible for much of the phenotypic variation on which selection acts."
Marc W. Kirschner and John C. Gerhart, The Plausibility of Life: Resolving Darwin's Dilemma (Yale University Press, 2005), p. 119
June 3rd, 2006 at 12:24 am
I am extremely attracted to the concept of front-loading, though it seems to have been somewhat abandoned on this forum. I, however, view front loading as a variant of ID. The concept that the designer would grow the biosphere through a similar path as organisms grow makes a lot of sense.
Even when you read from the quote:
you notice "the time of their invention".
What I found intriguing, however, is that I went on Amazon, and read the reviews. Apparently there is a chapter in the book expressly differentiating the book's premise from that of ID. The reviewers seem to think that the book presents something that is fundimentally not ID. Alas I would love to read the book to see whether it supports or truly rejects a telic interpretation. Alas, reality strikes.
Comment by bFast — June 3, 2006 @ 12:24 am
June 3rd, 2006 at 6:04 am
Hi bFast,
"I am extremely attracted to the concept of front-loading, though it seems to have been somewhat abandoned on this forum."
For my own part, that's simply a function of how much spare time I have. Writing about front-loading requires a good deal of research, reading the professional literature and summarizing the results. It's much easier to poke fun at the latest histrionics from Dawkins or Coyne. But I'm still using front-loading to generate insights (which I'll write about in due time), and I believe Mike is preparing to pull some white furry animal out of his black hat in the near future.
"Apparently there is a chapter in the book expressly differentiating the book's premise from that of ID."
Well, neither Krischner nor Gerhart are AFAIK ID supporters, and they do take some pot-shots at intelligent design, undoubtedly to increase the market for their book. But what is interesting is that what they're criticizing is the anti-evolution camp mentioned in my post. They never consider (and therefore can't criticize) the proposition that life itself is designed to evolve. In fact, the weakest part of the book is the very short section in which they try to show how these "core processes" that facilitate evolution arose in the first place. For example, their argument that the eukaryotic cytoskeleton is derived from bacterial genes hasn't exactly been strengthened by recent research.
Comment by Krauze — June 3, 2006 @ 6:04 am
June 3rd, 2006 at 8:22 am
Front-loading is indistinguishable from RM+NS.
Are semantic gymnastics part of the Post Wedge World agenda? Just wondering
.
Comment by Art — June 3, 2006 @ 8:22 am
June 3rd, 2006 at 8:29 am
Apples and origins, the two subjects you refer to, Krauze.
Genome fusion and endosymbiosis are not completely the same thing. That the ancestral genomes did not out-and-out fuse to give rise to eukaryotes isn't particularly surprising, given what we what know (before the work MG cites, even). But this doesn't really speak to the ancestral relationship (or lack thereof) between, say, archaes and eukaryotes.
And it most definitely doesn't impact the evolutionary relationships between bacterial and eukaryotic "cytoskeletons".
Comment by Art — June 3, 2006 @ 8:29 am
June 3rd, 2006 at 8:41 am
Hi Art,
"Front-loading is indistinguishable from RM+NS."
Not long ago, you were claiming that the "hurricane in the cell" was a problem for teleological views. Considering that one such views, front-loading, is indistinguishable from "RM+NS", does this mean that "RM+NS" is also in trouble?
Comment by Krauze — June 3, 2006 @ 8:41 am
June 3rd, 2006 at 8:47 am
The hurricane is an apt metaphor for the relationship between energy flow and cellular organization. It meshes seamlessly with RM+NS. In fact, it demands Darwinian aspects of subcellular existence that teleologists cannot really wrap their brains around.
Comment by Art — June 3, 2006 @ 8:47 am
June 3rd, 2006 at 9:18 am
Everything meshes seamlessly with RM+NS. Oh, except for finding fossils of Homo Sapiens in the Jurassic. If you find that, then modern evolutionary theory is falsified. Otherwise, it's RM+NS all the way down!
Comment by MatthewCromer — June 3, 2006 @ 9:18 am
June 3rd, 2006 at 10:05 am
Hi Art,
"In fact, it demands Darwinian aspects of subcellular existence that teleologists cannot really wrap their brains around."
What? RM+NS isn't indistinguishable from front-loading?
Comment by Krauze — June 3, 2006 @ 10:05 am
June 3rd, 2006 at 10:18 am
Art:
Not really. What you have are two different views of evolution seen from different vantage points. The non-teleological vantage point sees only RM+NS. The teleological vantage point allows us the ability to contemplate the same thing in a different way "“ RM+NS under control.
No, there are no semantic gymanastics nor is there an agenda. Nor are you "just wondering" when you make these accusations. Writing in the journal Science, molecular biologist Francois Jacob offered some truly profound words:
Might it be Art's "agenda" to prevent this "certain idea of what this so-called reality might be" from getting off the ground? If front-loading really is indistinguishable from RM+NS, why doesn't Art just declare victory, pack up, and go home? Because he knows it's not.
Look, this is a true example of semantic gymnastics that is part of a Post Wedge World agenda: "Bald creationism and its absurdly mock-plausible alternative, "intelligent design", are everywhere being taught as alternative theories to Darwin's theory of evolution." A federal judge rules against teaching ID in the schools and provides such a powerful ruling that it can be used anywhere to discourage school boards from flirting with the idea, yet according to this rhetoric, ID (and creationism) and being taught everywhere! I originally wrote about the post wedge world here, noting "I am cynical enough to expect most will still cling to Wedge-centrism, and invent exotic and convoluted reasons as to why ID still must be viewed as a threat to our way of life and why our adrenalin levels need to remain high (after all, some have built quasi-careers around fighting the wedge)." The continued rumor that ID (and creationism) is everywhere being taught looks like it part of the Agenda of Fear to me. You'll notice that no critic either a) provided a list a schools where ID is being taught or b) criticized this very public claim.
Art:
Yet just recently we were told, "Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life." The fun continues.
Comment by MikeGene — June 3, 2006 @ 10:18 am
June 3rd, 2006 at 11:41 am
This can't be correct. After all, in the book Intelligent Thought we are told we can trust the scientists in that volume, and one of them wrtites:
Art writes:
This cannot be true. Front loading requires that something be front-loaded. RM&NS either denies this or assumes it. If it assumes it, then it fails as an explanation, therefore it must deny it.
Comment by Mung — June 3, 2006 @ 11:41 am
June 3rd, 2006 at 11:50 am
There is selection for the ability to evolve. For example, an organism whose systems are so tightly coupled and inflexible that a change in any one is catastrophic would tend to evolve very slowly, which would increase its risk of extinction in response to changing conditions (such as competition from more rapidly evolving organisms). Since existing creatures are the descendants of "successful evolvers," one would expect, purely on the basis of natural selection, that they will have inherited traits, such as flexible regulation, that are conducive to evolution.
Comment by trrll — June 3, 2006 @ 11:50 am
June 3rd, 2006 at 12:16 pm
Which of course, explains organisms like the horseshoe crab which have remained morphologically static for hundreds of millions of years. . .
Comment by MatthewCromer — June 3, 2006 @ 12:16 pm
June 3rd, 2006 at 1:30 pm
A successfully evolved non-evolver?
There is also selection for the ability to not evolve. I mean, what better way to ensure a majority of a particular genome in subsequent generations than to produce identical copies?
Comment by Mung — June 3, 2006 @ 1:30 pm
June 3rd, 2006 at 2:56 pm
Hi Trrll,
"Since existing creatures are the descendants of "successful evolvers," one would expect, purely on the basis of natural selection, that they will have inherited traits, such as flexible regulation, that are conducive to evolution."
If this was the case, we would face the question of why no one then did expect this mode of regulation, "purely on the basis of natural selection". Why were the first models of eukaryote genes, lacking this flexible regulation, not rejected as being contrary to what onw could reason from Darwinian first principles?
Furthermore, you are ignoring the second point from Gerhart and Kirschner: It isn't just that there exists these processes facilitating evolution; they are also ancient, existing in the first eukaryotes. Like the long history of Hox genes, this too was surprising.
Comment by Krauze — June 3, 2006 @ 2:56 pm
June 3rd, 2006 at 5:03 pm
Art:
Actually, hurricanes, and all similar-scale fluiddynamic phenomena are dominated by inertial forces. Masses keep going in a straight line at unchanging velocity unless forces acts to deflect them. Hurricanes are driven by a geostrophic balance of coriolis and pressure gradient forces and are intrinsically high reynolds number phenomena (i.e. inertially dominated). The interesting thing to know is how solar energy stored over a broad region as latent heat in water is released quickly in a small diameter columnar updraft to lift air in the eye, drawing in air radially while coriolis forces spin the inflowing air. It's the qualitative structure of the thing that is interesting, not the thermodynamic details. Every phenomenon involving 'winds' is likewise inertially dominated. In slow movements in tiny cells, inertial effects are completely negligible. So, the analogy is off the mark.
Cells typically squander energy in a profligate way. While every step of every process in a live cell uses energy, in stoichiometric proportion to all molecular action, I do not think the energy flux, per se, is conceptually important. Metaphorically, if you wanted to understand how different automobiles worked, the least interesting thing to know is that some burn gasoline, some diesel fuel, etc. Instead, you would want to know how, qualitatively, how the various engines, transmissions, differential gears, and so on worked. Knowing full details of what gets burned, and how much gets burned, will tell you almost nothing about how the device works.
Comment by Guts — June 3, 2006 @ 5:03 pm
June 3rd, 2006 at 5:10 pm
There is a lot more to evolution than morphology. If a creature is very well adapted morphologically to a particular niche, it is likely to maintain that morphology indefinitely, unless that niche changes or a new predator comes along. But that doesn't mean that it can stop evolving, because it will need to continue to upgrade its defenses against microorganisms and other parasites. So evolution at the molecular level is expected to continue.
Comment by trrll — June 3, 2006 @ 5:10 pm
June 3rd, 2006 at 5:14 pm
However, in fact, monitoring cellular energy consumption by methods such as fluordeoxyglucose PET scanning and functional MRI has turned out to be extremely informative, and has provided a great deal of information on how the brain works.
Comment by trrll — June 3, 2006 @ 5:14 pm
June 3rd, 2006 at 5:22 pm
I think that a lot of people expected it. I've certainly heard such concepts expressed by molecular biologists for decades. But back then it was very abstract, based purely upon natural selection, rather than detailed knowledge of how genes work. And I think that while the general concept was well accepted, the degree to which organisms are able to compensate for particular mutations certainly surprised people.
In science, a model is not rejected merely because it doesn't agree with theoretical expectations–it's a matter of evidence. And one always starts with the simplest theory possible, generally in the expectation that the model will have to be modified based upon further studies. Remember, science is about discovery, not "Truth," so a scientist will readily use a simple model as a starting point, even if he believes that reality will ultimately turn out to be more complicated.
Comment by trrll — June 3, 2006 @ 5:22 pm
June 3rd, 2006 at 5:25 pm
trll:
Yes , for localization information, and also there are interesting flow phenomena at low reynolds number (viscous-dominated) that you might use metaphorically, but for the reasons I pointed out , the "lego" metaphor is a superior one in understanding molecular machines of the cell. Fluid flow that is turbulent enough to agitate anything is also dominated by inertial forces.
Comment by Guts — June 3, 2006 @ 5:25 pm
June 3rd, 2006 at 5:26 pm
The general assumption has always been that fundamental mechanisms would turn out to be very ancient, although just how ancient, nobody was quite sure. This was, after all, the rationale for studying fruit flies in the first place–which are where the hox genes were discovered.
Comment by trrll — June 3, 2006 @ 5:26 pm
June 3rd, 2006 at 8:01 pm
Don't forget that fruit flies were studied in the first place simply because they are an excellent genetic model "“ lots of offspring, short generation times, multiple traits, and easy to work with. They were chosen as a model long before anyone knew that DNA was the genetic material.
The most successful evolver, according to neo-Darwinian measures, would have to be the bacteria. Yet there are no prokaryotic fruit flies or mice.
Comment by MikeGene — June 3, 2006 @ 8:01 pm
June 3rd, 2006 at 8:31 pm
Mike,
I already sent a message to the "submit an article" link but didn't get any response. Not sure if you got it or not.
I have four mainstream, recent biology papers that fit pretty well into the "frontloading" hypothesis, IMO.
I cannot post them online as they are under copyright. However the author has given me permission to forward them for discussion to people interested in the subject. I do not have your email address otherwise I would have already forwarded them to you. I'm sure you could quote from the abstracts in a TT article if you found them of interest.
Please send me an email to matthewcromer at blast dot com if you are interested in reading them so I can forward them on to you via email.
Comment by MatthewCromer — June 3, 2006 @ 8:31 pm
June 3rd, 2006 at 9:17 pm
Hi Matthew,
No, I did not your message. The best way to contact me is to go to my web page, scroll down, and click on "Mike Gene." Send 'em my way, as it sounds interesting.
Comment by MikeGene — June 3, 2006 @ 9:17 pm
June 3rd, 2006 at 9:47 pm
Fortunately, we had Darwin's theory, which led us to believe that the fundamental mechanisms of inheritance would be the same in fruit flies as in people–another example of the theory guiding science in a direction that has turned out to be highly productive.
The bacteria are indeed successful evolvers. By numbers and mass, they are probably the single most successful organisms on the globe. They are the formula racers of nature, stripped down for speed and efficiency. They are able to adapt to a wide variety of environmental conditions, and are flexible enough to adapt to many internal mutational changes as well. They have the most evolved proteins, highly efficient and remarkably resistant to toxins. However, they do not fill every niche, so there are still opportunities for multicellular organisms to fill. I can't imagine why anybody would think that multicellular organisms would be expected to have the same cellular organization as bacteria.Multicellular organisms are not so dependent upon maximizing efficiency and speed of reproduction, but must maintain complex systems for coordination of multiple cells, so it is not suprising that a different cellular organization has evolved.
Comment by trrll — June 3, 2006 @ 9:47 pm
June 3rd, 2006 at 9:56 pm
Thanks Mike. I've forwarded you the info. Hope you find it interesting.
Comment by MatthewCromer — June 3, 2006 @ 9:56 pm
June 3rd, 2006 at 10:50 pm
I've quoted from one of the papers here.
Comment by MatthewCromer — June 3, 2006 @ 10:50 pm
June 4th, 2006 at 1:25 am
Hi MikeGene,
Mike, if I understand frontloading, RM+NS isn't under control, since the designer simply put the eukaryote in place a couple of billions years ago then let nature take its course.
Comment by Aagcobb — June 4, 2006 @ 1:25 am
June 4th, 2006 at 12:41 pm
For anyone who finds the topic interesting, I've started a thread over at ARN on energy in organisms.
Why would this be a general assumption? Darwinian theory doesn't predict that any particular structure, process, or anything else will not evolve.
Comment by Mung — June 4, 2006 @ 12:41 pm
June 4th, 2006 at 5:24 pm
No, but what it does predict is that evolution will proceed fastest in large populations of very short-generation organisms. This led to the expection that the vast majority of fundamental mechanisms will have been "discovered" by microorganisms. And these core mechanisms tend to get "locked in" by evolution–that is, they gradually evolve a wide range of dependencies, all of which would have to be adjusted to make any large change, so they tend to remain in place. Such changes are particularly unlikely to evolve in larger, long-generation organisms.
Comment by trrll — June 4, 2006 @ 5:24 pm
June 4th, 2006 at 8:14 pm
Hmmm.
I'd say the most interesting discoveries of evolution came from the metazoans, not the bacteria.
ie: intelligence, flight, high optic quality eyes, sonar, social organizations, etc.
Comment by MatthewCromer — June 4, 2006 @ 8:14 pm
June 5th, 2006 at 11:09 am
I don't see how this is a prediction of the theory. Can you explain?
Do we mean by "fundamental mechanisms" those that have been discovered by microorganisms? Which fundamental mechanisms did evolutionary theory predict?
Descriptive, not predictive. That was my point. Evolution doesn't
predict that anything will be locked in. It can only describe what is the case, and then try to explain why that is the case. It was never predicted.
Why? What prevents larger, long-generation organisms from building up systems that are reliant upon prior systems to the point where the prior systems cannot evolve?
Comment by Mung — June 5, 2006 @ 11:09 am
June 5th, 2006 at 5:56 pm
I'm talking about discoveries at the gene level. As impressive as such physiological traits may appear, at the level of the gene they turn out to be implemented using quite ancient "technology"–proteins and regulatory mechanisms that have been passed down from tiny, short-generation-time ancestors.
Comment by trrll — June 5, 2006 @ 5:56 pm
June 5th, 2006 at 6:21 pm
Because mutation is random, the likelihood that a particular mutation will be present in a population is dependent upon population size. With very large populations such as those that are typical of microorganisms, it can be shown statistically that even quite rare events, like two mutations that must occur simultaneously to be beneficial, will occur frequently over the population as a whole. Selection depends upon reproduction. So the faster an organism reproduces, the more rapidly an advantageous mutation will spread through the population. Humans have a generation time of perhaps 20 years. Many micro-organisms have generation times on the order of half an hour. So selection will proceed 350,000 times faster in such a microorganism population than a human. On top of all that, replication of genetic material turns out to be a particularly vulnerable point when it comes to mutation, so microorganisms not only have faster selection, they also mutate faster.
Comment by trrll — June 5, 2006 @ 6:21 pm
June 5th, 2006 at 7:33 pm
Trrll, "even quite rare events, like two mutations that must occur simultaneously to be beneficial, will occur frequently over the population as a whole."
At least you recongnize that two simultaneous beneficial mutations is a "relatively rare event". How 'bout 3, 4 or 18? Alas, we get to the heart of the irreduceable complexity case.
Trrll, "Humans have a generation time of perhaps 20 years. Many micro-organisms have generation times on the order of half an hour." Sounds like you have an appreciation for Haldane's dilemma.
Comment by bFast — June 5, 2006 @ 7:33 pm
June 5th, 2006 at 8:07 pm
I doubt that very much.
That's like saying that skyscrapers are implemented by a slight change in the concrete recipe that you'd use on a small shed.
There is a missing factor here, and it isn't the concrete recipe.
Comment by MatthewCromer — June 5, 2006 @ 8:07 pm
June 6th, 2006 at 10:47 am
Yes, it is quite remarkable, and certainly would not make much sense from a design perspective–why would the designer of a skyscraper be constrained to make do with only minor modifications of the parts and methods used to build a shed? However, that is exactly what is predicted based on natural selection. And with more and more genome sequence data pouring in every day, this prediction seems to be holding up quite well.
Comment by trrll — June 6, 2006 @ 10:47 am
June 6th, 2006 at 11:13 am
You're missing the difference in morphological blueprints. It isn't DNA. There's something else.
Comment by MatthewCromer — June 6, 2006 @ 11:13 am
June 6th, 2006 at 11:46 am
What a one-sided perspective you have! By the same reasoning, what about deleterious mutations?
What a one-sided perspective you have! By the same reasoning, what about deleterious mutations?
And the organism with the advantageous mutatioon isn't reproducing in a vacuum. It's competing. In large populations, it has more competitors. In fast reproducing populations the competitors are also reproducing rapidly. In larger populations, a new mutation has "further" to go to reach fixation.
Why do you ignore all these other factors?
So what happens to probability of fixation of a new mutation as a function of population size?
Do you have any references on faster selection?
Comment by Mung — June 6, 2006 @ 11:46 am
June 6th, 2006 at 4:17 pm
Virtually all deleterious mutations will also be present in a large population, although not, of course, in the same individuals that bear the favorable mutations. But the favorable mutations increase from generation to generation, while the unfavorable mutations are held to a low level by negative selection.
Similarly, the faster an organism reproduces, the faster favorable mutations will increase, and the faster deleterious mutations will be filtered out.
That's what a favorable mutation means–better at competing. In a large population, many different favorable mutations and combinations of mutations will be present in the population at varying levels, depending upon how well they compete. Additional favorable (or unfavorable, but those get selected out) mutations can be added onto these, or complementary favorable mutations in different populations can be combined in a single population by genetic recombination.
It is independent of population size.
Comment by trrll — June 6, 2006 @ 4:17 pm
June 6th, 2006 at 4:20 pm
Not that anybody has been able to find. There are some complications, like regulation by methylation of DNA, but it still comes down to DNA (or in some organisms, RNA).
Comment by trrll — June 6, 2006 @ 4:20 pm
June 6th, 2006 at 6:16 pm
However, so far the irreducible complexity "case" seems to reduce to arbitrarily picking a number of mutations unlikely to accumulate in a single organism, and insisting without a shred of evidence that some complicated-looking structure must have required that many simultaneous changes at some point.
It's hardly surprising that these guys never seem to discover much of anything. Discoveries are made by the guys who figure that an evolutionary pathway must have existed and then try to figure out what it was. If you start with that viewpoint, you have a good chance of discovering something significant, even if your assumptions are wrong. On the other hand, if you start with the assumption that it couldn't have happened, you tend to end up sitting on your keister complaining that the guys who are making all of the discoveries have it all wrong.
Comment by trrll — June 6, 2006 @ 6:16 pm
November 1st, 2008 at 1:49 pm
[...] is a nice essay from Krauze posted on Telic Thoughts back in June [...]
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