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Junk DNA

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Commenter DK asks:

What is the official ID position on junk DNA? Has anyone proposed that it might be a mechanism to cause wholesale change in other parts of the DNA?

I thought this subject might be good for its own discusson thread so here it is. I don’t believe ID has any more “official” position on it than NDE does. It is largely regions of DNA with no known function and that isn’t to say it has no function at all. IDists tend to say there is a lot of function waiting to be discovered in it under the rubric that design is less wasteful than chance processes. The NDE position tends more toward much of it being detritus of an evolution driven by chance processes.

Clearly some of it is detritus, at least in sequence information. A good example is the remnants of retrovirus gene insertions. Absent selection pressure the useless DNA would first be peppered by point random mutations over time (it is) then discarded wholesale by larger random deletion events over larger timespans.

It seems to me that there is a larger accumulation of junk DNA than NDE would predict. Given the large amount of it in the human genome (some 98% if memory serves) natural selection should really favor larger deletion events that clean it out from the genome. In computer programming we call this “garbage collection” and go to great lengths to eliminate code and data that is no longer required. In a living cell, as in computer programs, useless code consumes resources and returns no value for it. Replication of DNA takes up time, energy, and raw materials. If it could be done faster, using less energy, and fewer raw materials that should be a strong selection factor in getting rid of stuff that isn’t used. Yet there’s a ton of it there.

When I’ve made this argument in the past the counter argument was that it’s really not that much extra burden in eukaryote cells because they are so big and have such slow reproductive rates to begin with regardless of how much DNA they have to replicate in the process of making a new cell. Prokayrotes have virtually no junk DNA in comparison and their reproductive success is largely due to how rapidly they can reproduce in great numbers. It’s a good counter argument but I’m not sure I buy it.

What really raises a red flag about how much junk is really in all our junk DNA is a how much information is required to build an organism as complex as a human. If every single bit of information in all 3 billion bases was being used for some purpose I still find it incredible that the schematics (or recipe) for a human can be contained in a gigabyte (a gigabyte is roughly how much information is in 3B bases). To posit that it can be contained in 20 megabytes (2% of one gigabyte) stretches the limit of credulity far beyond the breaking point.

So the idea that natural selection should work hard at eliminating useless DNA combined with the incredulity of a human organism being able to be specified in so little storage space makes me strongly suspect that just about every shred of it is being put to some use and then some. The “then some” is the structure of the rest of the cell or epigenetic information. Because we can see some of the junk getting peppered with point mutations it’s obvious that the specific sequence information isn’t important in some of it. To explain this I have proposed that useful information is also encoded into the 3 dimensional structure of the DNA molecule. Thus an apparently useless remant of a viral insertion would serve to subtly (or maybe not very subtly) change the shape of the molecule and thus have an effect on the organism it describes. This handily explains why so much junk is still hanging around in the human genome and where at least some extra storage space beyond codified sequence information is contained.

On the other hand maybe it is mostly junk and the answer is that there is far more epigenetic information than is known about or widely postulated.

Comments
That'll teech me to proof my poasts. (Maybe not) :) mike1962
John A Davison, You are correct, sir. mike1962
mik196 In your last sentence I think you meant ontogeny not ontology. John A. Davison
Great_Ape: "Okay, but that’s just another way to say that it’s a lousy explanation. I’d need to know which evidence in particular before I’d be inclined to agree with you. And it’s perfectly fine that you don’t accept my committment to ruling out materialistic explanations first; such acceptance is not a requirement for proving NDE is inconsistent with the historical evidence." I didn't use the word "inconsistent." Nor did I say any evidence contradicts NDE. What I said was it can’t be demonstrated to be responsible for the historical evidence. You can say God did it. you can say fairies did. You can say NDE did it. But if you say some unknown process did it that would the fairest statement. God, fairies and NDE are all "gap" theories. There is no gap-free physical paths proffered for the macro level differences in lifeforms for what is deemed "explained" by NDE. Having said that, I think there is evidence against NDE, namely the fossil record, despite all the attempts at justification. The evidence strongly favors a programmed evolution. A macro ontology, if you will. mike1962
NeoDarwimpianism is the joke of two centuries. "A past evolution is undeniable, a present evolution undemonstrable" John A. Davison John A. Davison
mike1962: "What I mean by lousy explanation is that it can’t be demonstrated to be responsible for the historical evidence" Okay, but that's just another way to say that it's a lousy explanation. I'd need to know which evidence in particular before I'd be inclined to agree with you. And it's perfectly fine that you don't accept my committment to ruling out materialistic explanations first; such acceptance is not a requirement for proving NDE is inconsistent with the historical evidence. great_ape
Great_Ape: "simply stating “NDE is a lousy explanation” gives me little with which to work." What I mean by lousy explanation is that it can't be demonstrated to be responsible for the historical evidence. And saying that it's the "best theory we've got" assumes a materialistic commitment which I don't share, and is not logically necessary. mike1962
Everything will fall in place once the Darwimps abandon any role for chance. Until that happens it is all nothing but hot air as this and every other blog so eloquently testifies. I am also confident that we WILL be able to understand everything in the universe. That is precisely what the ultimate purpose was in a prescribed phylogeny. That is if we don't do ourselves in first. EVERTHING is determined... by forces over which we have no control." Albert Einstein, my emphasis "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison Men believe most what they least understand." Montaigne "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison
ape we’re still stuck with not having provided an explanation for how immense complexity/intelligence/advanced beings came to exist originally That's just how the cookie crumbles. We'll always be stuck by a logical need for a first cause and an inability to scientifically investigate the universe beyond certain finite bounds in time and space. DaveScot
ape the nanotech revolution has seemed to remain “just around the corner” for some time now The signal event may be here already and the gov't has put a lockdown on it. Being able to program bacteria to complete any task that is physically possible for them can be used to make weapons that are far superior and far cheaper than anything in the history of mankind. It's far easier to destroy than it is to create. Much of the book "Engines of Creation" is devoted to hypothetical constraints that can be employed to prevent nanotechnology from being weaponized. As I recall (it's been 20 years since I read the book cover to cover) the most promising method included burning one of the bridges behind us. The key bridge to be burnt is the one where the first bacteria is reprogrammed to create the first general purpose assembler. Here's a link to more recent thinking on the containment problem - I just discovered it so can't comment on it yet. DaveScot
mike1962: "It may be “simpler”, but it’s an illusion. Your view is essentially the “this is the best materialistic explanation we’ve got” view. The problem is, that while it might be “simpler”, it’s a lousy explanation given the evidence." It is difficult to respond to "it's a lousy explanation given the evidence." Tell me which evidence is incongruent, and then I have something concrete to work with. mike1962: "But the pragmatic view is to find an explanation that fits the data best. Sometimes the simpler exlpanations are wrong. NDE is a lousy explanation." Again, simply stating "NDE is a lousy explanation" gives me little with which to work. I know that in some circles this statement is regarded as a self-evident, but to engage in a meaningful dialogue with someone who doesn't necessarily believe that, you have to be a bit more specific. mike1962"...conventiently forgets all about the origins of it’s philosophical position regarding natural law. Without that foundation modern science and it’s successes would not have occured." I agree that the notion of a Lawgiver played an important part in Western culture of instilling the idea of a rational, orderly, and intelligible universe . Even though we must appreciate the influence of the historical idea of a supreme lawgiver on our philosophy and science, that does not imply that we must invoke the lawgiver as the *proximal* cause of life, evolution, etc. Saying anything beyond this would be venturing into theology, and this probably isn't the place for it. great_ape
ds, I haven't read engines of creation; I will have a look. Personally, I'm anxiously awaiting significant nanotech progress because I'm hoping to have a set of tools for exploring the cell that are a little more subtle than a sledgehammer. That's about the level of refinement I feel we're currently dealing with at the moment. I'm a little discouraged, though, by the fact that the nanotech revolution has seemed to remain "just around the corner" for some time now. As for how this relates to life-begetting/life shaping intelligence, even if I were to accept that such an intelligence existed prior to humans--which I certainly don't rule out--and could account for observed life, we're still stuck with not having provided an explanation for how immense complexity/intelligence/advanced beings came to exist originally. Wouldn't it be ironic if our evolutionary speculations turn out to be completely incorrect in accounting for humans, but, instead, explained the origin of our advanced-being-progenitors...or their progenitors? In that case, I wonder which camp, if any, gets the rights to gloat? great_ape
"NDE is a lousy theory, it cannot be demonstrated to explain the grand sweep of life from molecules to man." I don't think scientists are claiming that it can explain molecules to man, or at least not teaching it. "Historical forensics of billions of years and the supernatural sort of have something in common: they cannot be dragged into a laboratory and examined first hand." Are you saying we can't infer it because it happened in the past? "My interest, beyond simple fascination with the evidence, is in public education, and dethroning the NDE priesthood who have held the castle too long." The best way to do that is for ID to become an accepted scientific theory by producing research. According to the Discovery Institute this is happening and I am very interested to see what happens. Chris Hyland
DaveScot said:
art2 You’re going to have give me some links to back up your claim that bacterial colonies can double in size in less time than it takes to replicate the DNA in one cell. That is simply preposterous on the face of it.
I guess from an engineering standpoint it sounds preposterous. But that's how things are. Go figure. You need access to a pretty good library to get ahold of the primary research papers. If that's not an option, Chapter 3 of this book should help. (BEWARE - the link downloads a ca 6 MB pdf file.) The parts around Figure 3.18, if my memory serves me correctly. The reference list at the end of the chapter is pretty remarkable as well. (Some of these papers might bring back memories for old-timers like Davison.) Don't forget my request - is there an empirical basis for the supposition that a 3 billion bp genome cannot be information enough to specify a human being? Art2
Sorry, the URL link didn't work out. Here is the article: http://www.mc.vanderbilt.edu/reporter/index.html?ID=5043 Jehu
Slightly off topic but relevant to the structure of DNA. Check out this new article about DNA from Vanderbilt The article explains about DNA:
“Somehow they have been shaped and optimized for a particular purpose.”
As an example of opitmizatin, the article explains how even slight changes such as adding an extra carbon molecule to the sugars on the backbone of DNA destroys its characteristics that allow it to store and transfer genetic information. Some highly amusing quotes
DNA's simple and elegant structure — the “twisted ladder,” with sugar-phosphate chains making up the “rails” and oxygen- and nitrogen-containing chemical “rungs” tenuously uniting the two halves — seems to be the work of an accomplished sculptor.
Seems to be?
Yet the graceful, sinuous profile of the DNA double helix is the result of random chemical reactions in a simmering, primordial stew.
Sure it is. :) Jehu
Chris Hyland: "I don’t think anyones denying the history of science, it’s simply for practical reasons that we cannot objectively attribute an effect to the supernatural." By practical I assume you mean it isn't empirically verifiable. Is NDE? Bottom line is, NDE is a lousy theory, it cannot be demonstrated to explain the grand sweep of life from molecules to man. Historical forensics of billions of years and the supernatural sort of have something in common: they cannot be dragged into a laboratory and examined first hand. Us ID-friendly types are simply tired of a worn out materialist philosophy that has led to NDE and it's failure. By all means keep on trying. Keep the faith. I don't care. My interest, beyond simple fascination with the evidence, is in public education, and dethroning the NDE priesthood who have held the castle too long. mike1962
ape I do, however, believe that the difference between human intelligence and the type of intelligence that could orchestrate life and evolution is so inconceivably large that it is different in not only degree but *kind* from our own. Have you read Engines of Creation? The rate of technologic progress isn't linear. It's exponential. Given what we can do now (sequence genomes, insert and delete genes with viral vectors, construct functional viral genomes from just sequence information, etcetera) how long will it be before we have the whole thing licked at the rate we're progressing? Even if it's a thousand or million years that's an eyeblink in the history of the universe. Will we be an essentially different kind of intelligence when our computers and robotic laboratory equipment can whip up any kind of organism we care to specify? I don't think so. You should read Engines. It makes a very good case that these kinds of capabilities are only decades away, not thousands of years. The signal event is when we understand any bacteria well enough to be able to reprogram it to build things out of sturdier stuff than proteins. The capabilities of true nanotechnology are mind blowing... please read it. You won't be disappointed. DaveScot
"It isn’t because those who steer the philosophy of science somehow answered the really big questions about existence of the universe, and why it has the nature it has. The Lawmaker was pushed out because he wasnt required for the limited scope of study these days, which has a basis of natural law, but conventiently forgets all about the origins of it’s philosophical position regarding natural law. Without that foundation modern science and it’s successes would not have occured." I don't think anyones denying the history of science, it's simply for practical reasons that we cannot objectively attribute an effect to the supernatural. "So while you’re quite willing to make gross extrapolations of micromutations that have never been demonstrated capable of creating novel cell types, tissue types, organs, or body plans you’re dismissing on an a priori basis a proven current mechanism in evolution (intelligent agency)." Envoking an alien intelligence in terestrial evolution would still be considered unparsimonious unless you could either definatively prove the theory of evolution or better provide positive evidence that intelligence was involved. As far as the novel cell types tissue types and body plans goes it appears to be mostly due to changes in gene expression and cell signalling, and I have not seen any evidence that the genetic differences involved are not within the capabilities of NDE. " I am suggesting here that organisms have a built-in capability of adapting to their environement. I am suggesting that to the extent that evolution occurs, it occurs at the level of the organism… Suppose a “biological engineer” is designing living organisms…build into the species the ability to switch among several forms…I am suggesting that living organisms have the capability of switching from one phenotype to another when cued by the environment. " It's called phenotypic plasticity, it's a well documented phenomenon. If it coutns as evidence against evolution, then someone should tell Massimo Pigliucci. "Very much as Bil Dembski has done, he employs complex mathematics. For example, he writes in Chapter Five:" Are you copying this stright from the book or of the web somewhere, because I cant see what he's getting at without the context. Chris Hyland
ds, just a few thoughts now, and I will try to respond to more concerns raised later. I agree it was a bit unfair to imply, without further justification, that intelligence was somehow unnatural when NDE at the same time contends intelligence is a natural component of the universe, and we observe human intelligence and its impact on life and evolution. The way I left it does entail a double standard; point taken. I do not think that humans are necessarily the only intelligence in the universe. I do, however, believe that the difference between human intelligence and the type of intelligence that could orchestrate life and evolution is so inconceivably large that it is different in not only degree but *kind* from our own. So observation of our own human intelligence and its effects does not mean we have precedent for directly observing an intelligence of that enormity in nature. Basically, my position is that our own limited biomanipulations do not amount to establishing a precedent for an intelligence capable of begetting and/or shaping life. great_ape
great_ape, I'd be interested in hearing what you think about pragmatic naturalism. Patrick
I don't believe Spetner is fringe, and at any rate, anyone (John A. Davison take heed) who "name calls" and doesn't address the arguments raised loses credibility, no matter what side of the fence he sits on. If the only people who can challenge atenet that controls so much of the "environment" in which we live are the "authorized authority", then folks, don't worry about Sharia law, we've got it already. I don't have to publish favors to question conclusions that appear untenable. It is best to read Spetner's book, which provides the detail necessary along with the mathematics he employs raising doubts about the role of "randomness" in living organisms. Very much as Bil Dembski has done, he employs complex mathematics. For example, he writes in Chapter Five:
Contrast the huge number of possible sequences of the DNA with the size of an animal population...Suppose the population is even a billion. The fraction of all sequences that could be stored in the population would be a billion divided by 10 to the power 24,082,400 or 1/10 to the power 24,082,400...The number is so close to zero it is negligible. The genome variety found in the population is in no way a match for the potential variety of the genome.... But so long as these stored genes are not active, there's no selection...without selection, all strings of DNA have the same right to be in the genenome. How can a population know to store a DNA string that will some day be useful? Only by brute force!
As to "Junk DNA", in Chapter 7 of Not By Chance! he writes based on examples that he sites, e.g., snails shells thicken when there are crabs in the environment, or barnacles shape changing when snails that prey on them are present.
I am suggesting here that organisms have a built-in capability of adapting to their environement. I am suggesting that to the extent that evolution occurs, it occurs at the level of the organism... Suppose a "biological engineer" is designing living organisms...build into the species the ability to switch among several forms...I am suggesting that living organisms have the capability of switching from one phenotype to another when cued by the environment.
I think these concepts are worth considering; Spetner believes that what here is referred to as "Junk" or the "vast amount of DNA...whose funciton is as yet unknown" could in fact play a role in this. I believe this is an avenue of constructive thought. Here's the book, which one can purchase anywhere. http://www.amazon.com/Not-Chance-Shattering-Theory-Evolution/dp/1880582244 And now I shall leave to let the "authority" ponder with their proven sense of humility and wonder. There is enough strife on earth; why shouls anyone wish to contribute? P. Phillips
great ape According to NDE, intelligence is a natural part of the universe. It posits humans as arising from natural processes. Humans are intelligent, humans can manipulate genomes, thus intelligent agency capable of changing the course of evolution is a natural part of the universe. Thus when you say that NDE is the best naturalistic explanation going you seem to be relying on a metaphysical belief that humanity is the only operative intelligence in the universe. I would point out that such belief is in direct defiance of both uniformitarianism (which you rely on in NDE) and the Copernican Principle of Mediocrity which pleads against special creation of the earth. We certainly DO see intelligent agency changing the course of events today including evolutionary events. You can't swing a dead cat without hearing about how humanity is causing mass extinctions, how geneticially modified organisms on our grocery shelves are insidious, how GMOs escaping into the wild will wreak havoc, pathogens "weaponized" by genetic engineering, and ecetera. So while you're quite willing to make gross extrapolations of micromutations that have never been demonstrated capable of creating novel cell types, tissue types, organs, or body plans you're dismissing on an a priori basis a proven current mechanism in evolution (intelligent agency). I'm not asking you to embrace intelligent causation I'm only asking you to acknowledge the facts and not apply double standards in uniformitarianism and what's natural and what isn't. DaveScot
art2 You're going to have give me some links to back up your claim that bacterial colonies can double in size in less time than it takes to replicate the DNA in one cell. That is simply preposterous on the face of it. DaveScot
P. Phillips I deleted two of your comments as they were way too long. Please refrain from quoting so much text in a comment. It makes it too difficult for people to scroll through. If you can't link to it then summarize it. Your comments won't be showing up right away any more. I'll be moderating them for a while to make sure you keep them reasonably brief. DaveScot
great_ape: "For one, it is the simpler assumption and does not entail additional nonmaterial or intelligent influences that we do not witness presently affecting population genetics. In this view, it’s an extension of occam’s razor." It may be "simpler", but it's an illusion. Your view is essentially the "this is the best materialistic explanation we've got" view. The problem is, that while it might be "simpler", it's a lousy explanation given the evidence. Lousy explanations are still lousy explanations even when one insists on a materialistic basis. Time has shown that the simpler explanations are not necessarily the best ones. Which is why a neutral view, the one that allows for the possibility of intelligence causes, is the more rational one. Occam's Razor may be a fine initial guiding principle when one sets out to explain a phenomenon. But it can't turn a lousy theory into a good one. Time to start looking around for better explanations that fit the evidence. great_ape: "Finally, philosophically, I am of the opinion that we should only abandon so-called “naturalistic” explanations only at last resort, after we have exhausted all other options. This philosophical position of mine is ultimately pragmatic in origin, and is based on the past success of sticking to naturalistic explanations during the history of science." Part of that success you speak of is due to the fact that earlier scientists (such as Newton) were about discovering the laws of nature because they accepted a Lawgiver. It was a natural inference. I'm all for people trying to find natural law-based direct causes for things. But the pragmatic view is to find an explanation that fits the data best. Sometimes the simpler exlpanations are wrong. NDE is a lousy explanation. ID pragmatically expands the explanation range to what just might be the true explanation. This is the sensible approach. By all means, keep trying to made NDE work. But forgive us if we open our minds to better fits for the evidence. The successes of science have largely been entirely agnostic with regards to direct causes, and the question of intelligence is not required, pro or con. Newton determined that gravity was directly related to mass. But I assure you, he thought an intelligence was behind the "laws" of nature that made it so. And it was that view that compelled him to look for mechanistic laws. At some point in the philsophy of science, only deistic explanations were "seen to be required", to explain the laws of nature. (How this is "simpler" overall is beyond me.) Then eventually only atheistic explanations, because the laws themselves might exist on their own of from some non-rational cause. Simpler? On what basis? In order for one to have the authority to weigh in on what is "simpler" or more "complex" about the orgin of natural Laws, one would have to know something about the origin of those laws. It isn't because those who steer the philosophy of science somehow answered the really big questions about existence of the universe, and why it has the nature it has. The Lawmaker was pushed out because he wasnt required for the limited scope of study these days, which has a basis of natural law, but conventiently forgets all about the origins of it's philosophical position regarding natural law. Without that foundation modern science and it's successes would not have occured. Don't forget to dance with the one that brung ya. mike1962
Get this folks. "Evolution is not possible." That is probably true only if you add the words - any more. There is no doubt that evolution occurred in the past or that it has steadily declined in extent. Just as in ontogeny, where the greatest changes occur early in the life of the organism, so did the greatest changes occur early in the evolutionary sequence, virtually instantaneously at the level of the animal Phyla and the plant Divisions. No Phylum or Division can even be rationally derived from another one. It would be like trying to derive one embryonic germ layer from another one. The final arbiter of evolution is the fossil record and absolutely nothing it has ever divulged could conceivably be reconciled with the Darwinian pipe dream. There is no point trying to communicate with Darwinian zealots. They are stone deaf and there is no hearing aid available to remedy their condition as it is not in the ear. It is in their central nervous system. They were born that way. It is hard to believe isn't it? I love it so! "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison "We age fastest when we are youngest" John A. Davison I join witjh Julian Huxley, Robert Broom and Pierre Grasse by concludimng that phylogeny is a thing of the past. At the genus level it ceased at least 2 million years ago and perhaps longer ago than that. I have proposed that a new species has not evolved in historical times and still not seen that challenge met with a single example. John A. Davison
DaveScot said (too long ago to recall, probably):
art2 That may be true in eukaryotes but in prokaryotes it’s not. You’ve essentially restated the counter argument others have given but without separating the cases for eukaryotes and prokaryotes. The practical absence of any junk in prokaryote genomes is testimony to it.
?? I think that, in prokaryotes as well as eukaryotes, the resources devoted to genome replication are pretty small. This is no explanation for the difference betweem prokaryotes and eukaryotes. Speed of growth isn't really the answer either. At least, this is what a curious aspect of bacterial growth suggests. Recall (even if for the first time) that bacteria can grow with a doubling time that is actually smaller than the time it takes a new copy of the genome to be made. (That's right - a new generation can arise faster than the genome can be replicated.) Also recall that genome replication is relatively constant over more than an order of magnitude of growth rate. These observations (made back in the golden era of molecular genetics, when John Davison was a spry young Turk) tell us that the "speed limit" for growth in bacteria isn't the size of the genome, but rather something else. Thus, constraints made by growth rate isn't the reason bacteria have no junk DNA (at least not the same sorts that we see in eukaryotes). In a few places on this blog, comments repeat the canard that a typical genome is too small to account for the amazing complexity of, say, humans. I think I explained the error of this POV in easy-to-follow mathematical terms, and rather that repeat myself, I thought I would ask those who hold to this canard - why do you think this? What tangible experimental or theoretical considerations lead to this suggestion? Art2
mike1962: "An ungrounded inference if there ever was one. What is uniformitarianism inferred from?" There are several reasons one might invoke uniformity--albeit an approximate uniformity-- of process for evolution. Here are some of my own thoughts; there are probably others that could offer superior arguments. For one, it is the simpler assumption and does not entail additional nonmaterial or intelligent influences that we do not witness presently affecting population genetics. In this view, it's an extension of occam's razor. This is in more or less the same spirit that Lyell applied uniformitarianism to geological formations 2) when we look at the genomes of various species, of different levels of kinship, the varieties of changes that separate them are the very same type of changes that we observe arising naturally in present populations. (duplications, point mutations, rearrangements, mobile element insertions, etc). So we have robust empirical evidence that the changes that do occur in macroevolution are in the repetoire of mutations currently occurring. Finally, philosophically, I am of the opinion that we should only abandon so-called "naturalistic" explanations only at last resort, after we have exhausted all other options. This philosophical position of mine is ultimately pragmatic in origin, and is based on the past success of sticking to naturalistic explanations during the history of science. Microevolution as the generator, ultimately, of macroevolution is the best contender we have for a naturalistic explanation for evolution, and I do not believe we have exhausted it as a explanation as yet. But since microevolution has not been definitely shown to be the source of macroevolution, the door remains open for it to be refuted convincingly. Until then, I place my bets and allegiance with the ND/RM+NS hypotheses. This comes with the extremely convenient benefit of not being crucified by my colleagues. The latter being an incidental perk and in no way influencing my thoughts on the matter. great_ape
great_ape: "3. invoking of uniformitarianism, we surmise that the types of changes that lead to evolution A were microevolutionary in nature. Under this view, what occurs then is basically what occurs now and is what occurred at all timepoints in between." An ungrounded inference if there ever was one. What is uniformitarianism inferred from? The physical evidence. But appeals to evidence cannot prove uniformitarianism. Uniformitarianism has to be assumed before the evidence proves anything. Thus uniformitarinism props up NDE, and NDE props up unformitarianism. Round and round the circle goes. mike1962
P. Phillips, I won't be able to address every point by Spetner--the essay touches a range of issues-- but I will highlight one or two key disagreements I have with his take on things. If you haven't done so already, everyone here should consider reading the lengthy exchange between Spetner and Max at talkorigins (for Max's synopsis) and at trueorigins (for spetner's synopsis) to see this all in context. I largely agree with Max's response there, as well as Chris's points above, so I'll try not to rehash them more than necessary. I will reiterate though, as Chris Hyland indicates above, that Spetner has an overly simplistic view of mutations, the shape and dimensionality of fitness landscapes, and how populations of organisms might be distributed and move about on those landscapes. His arguments about getting inevitably and irreversibly stuck on local maxima fail as a result. The system is immensely more complex and noisy than his depiction, peaks are broader, and more wandering in the landscape occurs than he suggests. Yet this isn't Spetner's main point, so I'll leave it at that. Where I agree with Spetner is that no one has observed and/or demonstrated microevolution translating into macroevolution. Or in his terminology, evolution A resulting from evolution B. Point taken. Sometimes, either due to ignorance or disingenuousness, pro-evolution folks will speak as though this has been definitively established. It has not. It remains, as I suspect it will remain for the forseeable future, an inference from circumstantial evidence. An inference to what we believe, for various reasons, to be the best account of Evolution A's mechanism. Most of us here agree that Evolution A--whatever the driving mechanism--is an undeniable fact. And virtually all of us agree that Evolution B (microevolution) is a fact. It is the inference from one the other which produces most of the sound and fury. The central issue is just how plausible is the link between the sort of "random" processes we see in Evolution B and the remarkable productions of Evolution A. Spetner writes, "Most evolutionists assume that long sequences of microevolutionary events can produce Evolution A, but no one has ever shown it to be so. " Sort of. Evolutionists infer this to be the case from several lines of circumstantial evidence. They may then use this inference as a premise/assumption for the purpose of conducting studies, etc. The inference goes something like this: 1. the fossil record and genetic archeology strongly indicate evolution A happened. 2. When we look around today, to the best of our ability, the types of changes we see are Evolution B (microevolutionary) in nature. 3. invoking of uniformitarianism, we surmise that the types of changes that lead to evolution A were microevolutionary in nature. Under this view, what occurs then is basically what occurs now and is what occurred at all timepoints in between. At the heart of Spetner's "not by chane" argument, as well as others, is that this relationship is simply not plausible. If we, for instance, consider the probability of the mutations that would have to occur to produce some given organism, the probabilities are astronomically low. Particularly given the lower population sizes and generation times as you move up the food chain. And yet, as Spetner himself admits: "There is some difficulty in calculating these probabilities because the values of the relevant parameters are not all known." Agreed. So what ultimately happens is that some generous and/or reasonable values are assumed, the calculations are attempted, and they indicate that it is astronomically unlikely for RM+NS to have produced such and such evolutionary progression, etc. It all sounds pretty gloomy for darwinism's prospects. And, save for one or two points, I'd be inclined to agree. Most of the parameters used are generous (conservative) enough, and one might quibble here and there but ultimately it wouldn't matter much. The thing thats missing in my opinion, though, the elephant that is often swept under the rug, is the shape of the "adaptive landscape" itself. What forms of life are possible? What transitions between those forms possible? Is the adaptive landscape sparsely populated with little islands of habitability or is it filled with possibility. It may be ridiculously unlikely to get horseform#473 specifically, but if the fitness landscape includes 40 trillion potential horse-forms, the notion of ending up with *one* of them is less insane. If you don't understand the landscape, you can do do all the probability calculations your heart desires, and you still won't have any idea whatsover about the plausibility RM+NS leading to evolution A (macroevolution). Combined with the fact that evolution isn't *aiming* at anything--it's simply exploring the available space--this suggests to me that understanding the space its wandering is crucial to understanding the plausibility question. And we know next to nothing about the possible pathways, the adaptive space, the possible adaptive landscapes of life. So I would argue the implausibility approach is hindered by this fundamental unknown, and this is the essence of my response to Spetner. In my opinion, what we're left with is the relative strengths of the evolutionists' inference [evolution B results evolution A] vs. the ID inference of design [design inferred from immense complexity]. And where one falls in these camps is tied to what one makes of the circumstantial evidence as well as one's philosophy of science. great_ape
Can "Gorilla my dreams" or what's his name, "Great Ape", comprehend this? Just in - The Spectator review today of Dawkins The God Delusion . You have to register to read the review, but I'll provide the link and an excerpt. I have quoted Charles Moore, i.e., this essay: http://www.telegraph.co.uk/opinion/main.jhtml?xml=/opinion/2005/01/08/do0801.xml Now, on to his review, and as I just did, he quotes Shakespeare: http://www.spectator.co.uk/the-magazine/books/25609/a-voice-crying-in-the-wilderness.thtml
There are many things in this entertaining book which should certainly give religious people pause. Dawkins makes powerful attacks on the shiftiness of many religious apologists, and gives good examples of the sheer absurdity of some deference to religious belief. Did you know, for instance, that in the United States the Reverend Green in Cluedo has been renamed ‘Mr Green’? His points about the abuse of power by religious leaders are not new, but that does not make them less telling. Because Dawkins is an evangelical, however, he never does his opponents the justice of taking their position seriously. Just as the televangelist takes disagreement as showing sin, so Dawkins, as his book’s title states, speaks of belief in God as a ‘delusion’. This may be an appropriate word for those who died in the Jonestown massacre, but it simply does not tell you anything worth knowing about John Henry Newman, or George Herbert, or Thomas Aquinas. If Dawkins really wants readers like myself to check into the atheist equivalent of the Priory for what he calls ‘recovery’, he must first of all understand the condition which he seeks to relieve. He doesn’t. One of the things which sends him into paroxysms of fury, for example, is the idea that children should be brought up in a particular faith. He thinks that this turns them into ‘demented parrots’ and may make them suicide bombers. It is wrong to speak of a ‘Catholic child’, he says, or a ‘Muslim child’, because such a child can give no real consent. One should speak only of ‘a child of Catholic parents’. The reason that Dawkins is so angry about this is that he conceives religion simply as a set of opinions: opinions, to be of value, must be genuinely, personally held, and children are not ready for this. (Actually, I don’t agree even with this: children can and must develop their opinions, and can and should be guided, though not coerced, in them by parents, and I bet Dawkins in practice thinks the same.) But religion is not, at root, a question of opinions. It is the collective (and personal) attempt to live life according to a belief about everything. The whole of each human life, from conception, is therefore part of it. Most, though not all, Christians hold that God’s grace is channelled through the sacraments, and that the sacrament of baptism makes a child a Christian — i.e. a member of Christ’s family, not a person with a set of views. It is the spiritual equivalent both of the polio vaccine and the birth certificate, and it would therefore be unnecessarily risky to withhold it. Dawkins would think this all rubbish, of course, but he ought to acknowledge that ‘brainwashing’ need not be involved. Most churches have a later rite (confirmation) which depends on the free assent to beliefs given by people judged old enough for that assent to be real. Similarly, the story of the Fall of Man excites Dawkins’s contempt because he thinks the punishment of Adam and Eve incredibly ‘vindictive’ for the minor offence of what he calls ‘scrumping’. That wasn’t the offence: it was disobedience of the one prohibition God had given them, the eating of the fruit which bestowed the knowledge of good and evil that would lead to death. Dawkins should acknowledge the internal logic of what he does not believe. If the tree guaranteed all life, then the intrusion of death by man’s wilfulness was indeed the ultimate wrong. It is interesting, however, that Dawkins’s devotion to Darwin’s theory of natural selection produces in him a simulacrum of religious belief. He describes the pity we feel for the unfortunate and the desire we feel for members of the opposite sex even when we cannot have children with them as ‘misfirings, Darwinian mistakes: blessed, precious mistakes’. This is the Dawkins version of the ‘felix culpa’ of Adam and Eve, ‘felix’ because it led to Christ’s incarnation as a man, and to his saving death and resurrection. And what Darwin called the ‘daily and hourly scrutinising’ carried out always and everywhere by natural selection ‘working … at the improvement of each organic being’ is expressed just as absolutely, and just as much in terms of intention (though Dawkins denies this), as is any statement about the purposes of the all-seeing God. Darwin was a very great man, but Darwinism can turn into a Victorian faith as dated as the Clapham Sect. It is important for Dawkins to deny a real distinction between ‘moderate’ religion and fundamentalist extremism. He needs the cannabis-leads-on-to-heroin argument so beloved of schoolmasters. Yes, there are lots of nice religious moderates, but they set children off on the slippery slope, he says. This reveals his misunderstanding of what he attacks. The difference between moderates and bigots in religion is just as vital as is the difference between liberals and fascists in politics. Moderates (inadequate word, but I haven’t got another) see man’s relationship to his creator differently from fanatics. Their religious belief in man’s sinfulness leads them to humility: how can fallen man, with his partial understanding of everything, kill in the name of God and thus arrogate Godlike powers to himself? The fanatic’s attitude is different not in degree, but in kind: God tells him to kill, he believes, and so he must. Dawkins appears not to accept this distinction, and it leads him to the most extraordinary omission in his book — the failure to discuss, beyond a couple of perfunctory, derisive mentions, the belief in divine love. Such a belief, which is at the heart of Christianity, does not, in itself, refute atheism. But it does explain the other aspects of faith which Dawkins barely notices — the lives devoted to teaching, medicine, care for the poor, the visiting of prisoners, the abandonment of material things, the creation of beauty, the dying that others might live — which a pathologist inspecting the corpse of religion might see as even more marked than the cruelties inflicted in its name. To ignore it is Hamlet without the prince, or rather, Lear without Cordelia. Dawkins does treat, briefly, of love. He links human ‘falling in love’ with religion, each being ‘an accidental by-product — a misfiring of something useful’. He is puzzled why the majority of the human race remains unpersuaded by such language. Could it be that this man, so clever, so confident, so scientific, so modern and so liberal, has nevertheless missed something? For all his advocacy of the inquiring mind, this is not a question that seems ever to have occurred to Professor Dawkins
P. Phillips
I better type "fast" not face. I don't believe in Freud either. P. Phillips
John, you wrote (and I better type face before Dave Scot hits the "terminate" key):
Organisms do not get to become adapted. They appear perfectly adapted at the moment of their first appearance. From that moment on it is all down hill toward an inevitable extinction.
Doesn't that statement contradict your signature line, and let me remind you since you are forgetful, “A past evolution is undeniable, a present evolution undemonstrable”? What about the comments that the genetic code just doesn't contain enough information? If I do get terminated, it's been sort of nice knowing you. Except for "great ape". He must be a lawyer in his "day job" -- he generates a lot of...I was going to say wind, but how about heat and no light! P. Phillips
Organisms do not get to become adapted. They appear perfectly adapted at the moment of their first appearance. From that moment on it is all down hill toward an inevitable extinction. There is no evidence that any species ever underwent any improvement during its stay on earth. Quite the contrary it was for the vast majority of all creatures a period of what Schindewolf called typostasis, followed by typolysis and ultimate extinction. Adaptation to a changing environment is nothing but another Darwinian opium dream. Any capacity to change was intrinsic in the creature at the moment of its inception and was in no sense the result of random mutation and natural selection. Continue with your fantasies folks. I prefer the real world myself, the world of the experimental laboratory which has never supported any aspect of the Darwinian fairy tale and never will. How do you Darwimps like them heresies? I hope they give you the runs. I love it so! "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison
franky172, I was actually thinking of the mice example when I made this comment in the Instincts thread:
I’ve seen examples where large chunks of “junk dna” is removed and the resulting animal turns out fine physically. So it’s assumed these sections are junk (though I’m curious if they’re not restored from a backup elsewhere in the process). But I’m wondering if a type of experiment has ever been performed where the resulting animals are tested for a loss of notable instinctual behavior.
Patrick
Let me excerpt this on defining "Evolution A":
At the outset, I shall establish an important and necessary guideline in this discussion of evolution. The word evolution is generally used in at least two different senses, and the distinction between them is important. On the one hand, the word evolution is used to denote the descent of all life from a putative single primitive source. It is the grand sweep of evolution that is supposed to have led from a simple beginning, something perhaps simpler than a bacterium, to all organisms living today, including humans. This descent is supposed to have occurred through purely natural means. Neo-Darwinian theory (NDT), which is the prevailing theory of evolution, teaches that this development occurred through random heritable variations in the organisms followed by natural selection. I shall denote the word evolution used in this sense as Evolution A. When evolution is discussed for popular consumption, it is most often Evolution A. The second sense in which the word evolution is used is to denote any kind of change of a population. The change can sometimes occur in response to environmental pressure (artificial or natural selection), and sometimes it can just be random (genetic drift). I shall denote the word used in this second sense as Evolution B. Evolution B has been observed. Evolution A is an inference, but is not observable. The distinction between these two meanings of evolution parallels the distinction between macroevolution and microevolution, but the two pairs of terms are not identical. Evolution A is certainly what is called macroevolution, but what is called macroevolution is not identical with Evolution A. In any case, I prefer to use the A and B to avoid having to carry whatever baggage might go with the macro/micro distinction. The distinction between these two meanings of evolution is often ignored by the defenders of Neo-Darwinian evolution. But the distinction is critical. The claim is made for Evolution A, but the proof offered is often limited to Evolution B. The implication is that the observation of Evolution B is a substantiation of Evolution A. But this is not so. Since Evolution A is not an observable, it can only be substantiated by circumstantial evidence. This circumstantial evidence is principally the fossil record, amino-acid-sequence comparisons, and comparative anatomy. Circumstantial evidence must be accompanied by a theory of how it relates to what is to be proved. NDT is generally accepted to be that theory. The strength of the circumstantial evidence for Evolution A can therefore be no better than the strength of NDT. The important claim of Neo-Darwinism is that it can account for Evolution A. The public perceives this claim as the core of the controversy over evolution. This claim is also the source of the contention by evolutionists that life is the result of purely natural processes, which ensue from well-known natural laws. I have examined this claim in my book Not By Chance!, and have found it to be empty. Evolution A is the principle message of evolution, namely that all life descended with modification from a putative single primitive source. The mechanism offered for the process of modification is basically the Darwinian one of a long series of steps of random variation, each followed by natural selection. The variation is generally understood today to be random mutations in the DNA. That primitive source of life is assumed to be sufficiently simple that it could have arisen from nonliving material by chance. There is no theory today that can account for such an event, but I shall refrain from addressing that issue here. That is for another place and another time. What is relevant to this discussion is that the requirement that life arose spontaneously sets, at the very least, a stringent upper limit on the complexity and information content of the putative first organism that could reproduce itself, and thus serve as a vehicle from which to launch Darwinian evolution. The issue I address here is the alleged development of all life by the Neo-Darwinian process of random mutation and natural selection, starting from a sufficiently simple beginning. Despite the insistence of evolutionists that evolution is a fact, it is really no more than an improbable story. No one has ever shown that the mechanism of NDT can result in Evolution A. Most evolutionists assume that long sequences of microevolutionary events can produce Evolution A, but no one has ever shown it to be so. (Those few evolutionists who hold that macroevolution is really different from microevolution have changed their story several times since they first came out with it, and their mechanism is so fuzzy that I have a hard time telling what it is.)
P. Phillips
Curses! The *Spam* filter, better known as Denyse (kidding!) got me, so here is the Spetner link: http://www.trueorigin.org/spetner1.asp http://www.trueorigin.org/spetner2.asp The most important point he makes, and I don't see how NDE can combat it is below, and he has calculated the mathematical probabilities:
One must understand that at the heart of NDT lies chance and randomness. Mutations are random events. The occurrence of a beneficial mutation at any given time in any given population is governed by chance. Even natural selection, which carries the burden of being the directive force of evolution, is subject to the laws of chance. Selection coefficients are average values. What happens in any particular instance is a random event. A mutation, even one that confers adaptive benefit on the organism, is likely to be wiped out by chance events (see Chapter 3 of my book). There is a good chance that it will disappear before it can take over the population. The question is not if it can happen, but, with what probability will it happen? NDT is a theory that is supposed to account for the natural development of all life from a simple beginning. I don’t know why we need such a theory, because the development of life from a simple beginning is not an observable. The theory is gratuitous; it comes to account for something that was never observed. Actually, evolutionary thinking goes like this. 1. One observes present life. 2. One then assumes that it arose in a natural way. 3. One then concocts a theory (e.g., the NDT) to account for the observation, given the assumption. I suppose that if the theory were really a good one, and could really explain well how life could have developed in a natural way, it would lend some credence to the assumption that life did indeed develop in a natural way. But it is not a good theory, and it does not account for what it is supposed to. Evolutionists, realizing this, have lately been reduced to arguing that if no one has a better theory that can account for the natural origin of life, then one must accept NDT. As you will see from some of Max’s comments below, he also adopts this approach. I don’t know why NDT merits the pedestal on which evolutionists have put it. Now let’s get back to the probability of occurrence of one of those evolutionary steps of Max’s. Since they are chance events, we cannot say with any certainty that they will happen. The best we can do is to say with what probability such an event will occur. So, evolutionists have offered us a theory (NDT) that postulates a long string of random events to account for the existence of life, assuming it developed in a natural way. If the probability of those events were to turn out to be close to 1, then one could say that the theory accounts for the observation. On the other hand, if, according to the theory, the probability of those events were very low, one would have to say that the theory does not account for the observation. If a theory predicts observed events to be highly improbable, then one cannot justifiably say that the theory accounts for those events. You would think that, since the issue of the probabilities of the evolutionary events is so crucial to the validity of the theory, the advocates of evolution would have calculated the necessary probabilities to make their case. But they haven’t. Since they have not made these calculations, Max is not entitled to assume that evolutionary steps can occur. There is some difficulty in calculating these probabilities because the values of the relevant parameters are not all known. In my book, I addressed the problem of the probability of getting enough successful evolutionary steps to account for the evolution of the horse. In spite of the difficulties I just mentioned, I was able to calculate an important result. I found that either the probability of the horse evolving was impossibly low, or else convergent evolution cannot occur. This result refutes NDT, and with it Evolution A. Not only is Max’s point here not substantiated, it stands refuted.
P. Phillips
From that same Wikipedia article: "A surprising recent finding was the discovery of nearly 500 ultraconserved elements[9], which are shared at extraordinarily high fidelity among the available vertebrate genomes, in what had previously been designated as junk DNA. The function of these sequences is currently under intense scrutiny, and there are preliminary indications[9][10][11] that some may play a regulatory role in vertebrate development from embryo to adult." Interesting mike1962
mike1962 I don't know of too many, but see: M.A. Nobrega, Y. Zhu, I. Plajzer-Frick, V. Afzal and E.M. Rubin (2004). "Megabase deletions of gene deserts result in viable mice". Nature 431 (7011): 988-993. DOI:10.1038/nature03022. For an example of deleting several million non-coding base-pairs with no visible effects to mouse health. (from http://en.wikipedia.org/wiki/Junk_DNA#_note-Nobrega) franky172
Dr. Pellionisz maintains a website that specifically tracks news about "junk DNA": http://www.junkdna.com/new_citations.html Patrick
Does anyone know if experiments have been done, modifying or removing non-coding "junk" regions to see what effect it would actually have on ontogeny? I've often thought the junk regions are spacers for the coding regions. After all, it's not enough that proteins code. They have to code at the right time and in the right position. Maybe it's the *length* of the "junk" sequences that matter, not their content. Seems to me that a smart designer might utilize such an approach because the length of a region would seems to be less susceptible to errors than the contents of a region. So where less neucleotide precision is required, use length, otherwise use specific nucleotide values. Moreover, when these non-coding regions are duplicated, it takes less effort to use random values since all that matters is their length, not their values. mike1962
"There were about five hundred stretches of DNA in the human genome that hadn't changed at all in the millions and millions of years that separated the human from the mouse and the rat," says Haussler. "I about fell off my chair. It's very unusual to have such an amount of conservation continually over such a long stretch of DNA." Why, fall of his chair? Because, he bought into the a priori assumption of gradual change? And was astonished at the conservation of information? "From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It's a tiny, tiny fraction. It's virtually impossible that this would happen by chance." oringally quoted from Science, 2004, research paper, funded byNHGRI, NCI, NIH HHMI. Research by David Haussler, director of the Center for Biomolecular Science and Engineering at the University of California at Santa Cruz. http://www.sciencentral.com/articles/view.php3?type=article&article_id=218392305 Why would the study of random mutations involve a school of Science and Engineering? Presumably because one wants to unravel the secret of life. But if life has a secret to unravel and it can be found thru complex scientific searches utilizing some of the largest computers with pattern recognition systems and complex mathematical precepts, then one must be looking for significant, repeatable and reconizeable structures. A system oriented informational construct pliable, yet conserved for survival. When one unlocks such a secret of life, then they can utilize repeated patterns learned from this discovery to design new life forms and powerful new computer technology. Another words, what good does it do someone like IBM to invest in the secret of life, if it's all random and unpredictable? And why are they continuing to look for "patterns"? And why when they look for patterns are they having success? A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes http://www.cell.com/content/article/abstract?uid=PIIS0092867406010993 "Intelligent Design is the study of patterns in nature that are best explained as the result of intelligence." -- William A. Dembski Michaels7
jerry: "Am I wrong to think that this is the main area of the genome that really controls the morphology of a species and should be the real focus of research for the formation of species." Jerry, this "switch" notion, in one form or another, has been a popular hypothesis for years among biologists. At least it was at the time I was in graduate school. The idea being that it was a lot easier to play around with the switches to create large-scale changes in relatively short order. The problem, as in much of macroevolution, is that we still don't have strong empirical data one way or the other so people haven't really pushed the idea much lately. Point mutations, etc, in proteins are easier to detect right now b/c we know where the proteins are and (on occassion) what they do. Yet you'll find no one who thinks this is the whole story. These switches (promoters, enhancers, chromatin regulators, splicing regulators, etc) we have a very poor handle on at the moment so it's not easy to track how they've changed across taxa and, more importantly, what those changes produced in the organisms. One exception, possibly, is that there's progress being made on determining the factors that have allowed the dog species to morph into all its current forms. It's been a while since I read about it, so I won't attempt to go into the details, but I'll try to find the article again. p. phillips, I will have to read and respond to your lengthy quote--if I have something meaningful to say--after the day job is over. great_ape
I see Chrs Hyland continues to spout Darwinian pablum. It is hard to believe isn't it? Why do I waste my time here? "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison
"There must be a long series of possible mutations, each of which conferring a selective advantage on the organism so that natural selection can make it take over the population." "There must be a long series of possible mutations, each of which conferring a selective advantage on the organism so that natural selection can make it take over the population." Except that many of the mutations that will be involved will be intitially neutral. "The chain must be continuous in that at each stage a change of a single base pair somewhere in the genome can lead to a more adaptive organism in some environmental context. That is, it should be possible to continue to climb an “adaptive” hill, one base change after another, without getting hung up on a local adaptive maximum. " This is wrong, mutations are not limited to single base pairs. "Now one might say that if evolution were hung up on a local Maximum, a large genetic change like a recombination or a transposition could bring it to another higher peak. Large adaptive changes are, however, highly improbable." Mutations don't have to be large at the DNA level to have an effect on the phenotype. It is quite possible for a single nucleotide mutation to move on an adaptive landscpae in the way he says. "Moreover, as I have noted in my book, the large mutations such as recombinations and transpositions are mediated by special enzymes and are executed with precision - not the sort of doings one would expect of events that were supposed to be the products of chance." There certainly is a large degree of randomness involved, and duplications can be very random. "But our inability to observe such series cannot be used as a justification for the assumption that the series Darwinian theory requires indeed exist." Or for the assumption that it doesn't. I've never heard anyone say 'we know that happened becuase we haven't seen it happen'. "Evolution requires a long series of steps each consisting of an adaptive mutation followed by natural selection. In this series, each mutation must have a higher selective value than the previous." Not really, see above. "Thus, the evolving population moves across the adaptive landscape always rising toward higher adaptivity." Not necessarily, and especially not in a changing environment. "This is particularly likely because the steps it takes are very small - only one nucleotide change at a time." Except it's not. "The problem is compounded by the lack of freedom of a single nucleotide substitution to cause a change in the encoded amino acid." However sinlge nucleotide changes can cause large phenotypic changes especially in places like promoter sequences. "To get a triple change would take 1014, or a hundred trillion, years. " Im not sure, but I dont think anyone claiming that much apaptive evolution involves specific multiple bases changing simeltaneously and independently of each other. Chris Hyland
I will bring up again the framework of Sean Carroll who believes that the area of the genome that is most responisble for morphological differences in species is not the genes but what he calls the dark matter. I gather this is everything but the genes and includes something he calls switches. From what I have read these swithces control the proteins which he just calls the toolbox of the genome (the nuts, bolts, other parts necessary to build an organism) and there are tens of thousands of these switches which orchestrate the building of the organism during gestation and I guess afterwards too. Few organisms are finished at birth. If anything appears to be similar to a computer program, it is the orchestration of these switches which control the expression of proteins, type of cells, placement in the developing embryo at very specific places and very specific times etc. The Time magazine article indicated that 2-3% of the genome are made up of these switches. Am I wrong to think that this is the main area of the genome that really controls the morphology of a species and should be the real focus of research for the formation of species. Duplication of genes, inversions, mutations, co-options etc. may be red herrings in this investigation and the real focus should be elsewhere. jerry
There is really a lot of evidence that non coding DNA has a great importance. Apart from molecular evidence of messenger RNA with regulatory functions only (that is, completely unrelated to protein synthesis), there is the classic argument made, for example, by Mattick, that the non-coding/coding ratio is the only quantitative data which correlates well enough with species complexity. Humans, with a non-coding percent higher than 98, are indeed the most complex species, but there is a rather continuos increase of the non-coding percent passing from prokaryotes to one-celled eukaryotes, and then fungi, invertebrates and so on. You can find the details, along with the corresponding article in Scientific American, on Mattick's site (www.noncodingDNA.com). I think there can be no doubt that we still understand very little of how DNA works. The "genetic code", certainly an important step in understanding that, but widely overrated in the general opinion, is only a specific code to synthetyze proteins, that is the ultimate effectors of biological information, but there is no reason to believe that it is the only way information is stored in DNA or anywhere else. DaveScot has stressed very well what we could call "the information problem" in biological beings: less than 1 GB of total information, less than 20 MB of supposed useful information (protein coding). And in that, we should have all the information necessary to build a human being from a single cell, to orderly differentiate billions of billions of cells in thousands of different patterns and states, each of them derived from a special, very fine tuned, "interpretation" of the same basic genome, from a specal regulation of which and how many genes have to be translated at a certain moment, and how much each of them has to be translated. In those 20 MB (or 1GB) we have also to find the necessary information about the space and time structure of the macroscopic human being, the pattern of tissues and organs, the pattern of neuronal connections, of humoral network regulatory systems destined to connect cells at a distance, or to fine-tune the immune response, and so on. I understand that the information in DNA, or epigenetic, or wherever it is, is certainly very efficient. I am sure, also because I do believe that it was very intelligently designed, that it is not certainly written in some kind of visual basic counterpart, but rather in the most synthetic biological machine language. But still, I can't believe that 20 MB will do, and I still have great problems with 1 GB. Perhaps we must admit a few things: 1) The protein coding information is only a tiny part of the information which must be available to the cell. 2) At present, we have no idea of where and how the missing information (the real "code" of life) is stored. 3) Non coding DNA must have an important regulatory function, which at present is only partly understood. 4) May be an important part of the information is not in the form we think (that is, in the base sequence intended as digital bits). Recent observations about the importance of non coding sequences to modify DNA space structure are very interesting. 5) We have still only few ideas of how DNA transcription (the key element in cell individualization and differentiation) works, and no idea at all of how transcription regulation is guided and regulated. 6) Maybe the new science of biophysics could give, in the next few years, some of the answers which biochemistry cannot at present give. gpuccio
Allelic mutations never had anything to do with creative evolution. Neither did natural selection, Mendelian genetics nor obligatory sexual reproduction, all of which are purely conservative, anti-evolutionary processes that serve only to maintain the status quo as long as possible. For the vast majority of all organisms, past and present, that has proven to be a losing proposition, leading inexorably to extinction. The era of creative evolution ended long ago. We are now in the age of extinction. It is impossible to imagine an hypothesis more completely divorced from reality than neoDarwinism. "Orthodoxy means not thinking - not needing to think. Orthodoxy is unconsciousness." George Orwell, 1984 "It is undesirable to believe a proposition when there is no ground whatsoever for believing it to be true." Bertrand Russell "An hypothesis does not cease to be an hypothesis when a lot of people believe it." Boris Ephrussi "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison
P. Phillips I appreciate your comment but in the future please provide a link to such long quotes and let readers use the link to get to it. DaveScot
art2 That may be true in eukaryotes but in prokaryotes it's not. You've essentially restated the counter argument others have given but without separating the cases for eukaryotes and prokaryotes. The practical absence of any junk in prokaryote genomes is testimony to it. DaveScot
bFast I can write a hello world program, a fully contained hello.com executable file, in assembler in 21 bytes including the 12 bytes to contain "Hello World!". It runs under DOS of course. DaveScot
Seriously now. I spent a few minutes today pondering the difficulty in factoring large numbers. Some of you probably know about the RSA challenge. $200,000 to the first one who factors the 2048 bit sub-prime. (http://www.rsasecurity.com/rsalabs/node.asp?id=2093). Well, quite frankly I could use the money. Who couldn't. Anyway, the random thought came to me that humans can't factor 1024 bit numbers very easily. Why does anyone suppose they know how the DNA system came to exist? This seems to be a problem several orders of magnitude beyond factoring numbers. Is this my intuition gone haywire? Or do I sense a real arrogance on the part of some who think they know? Pardon this post. It's from the part of my brain that thinks in red-neck logic. mike1962
As the old saying goes, one man's junk is another man's treasure. How does this relate? Heck if I know. mike1962
sorry steveh, that last bit was a bit jargon-heavy as I was in a rush. To paraphrase, there has been a running debate as to whether the process of creating new junk dna insertions (mobile element copies) in the genome is what is primarily harmful to the host---since it can disrupt genetic coding regions (and hence this is why mobile elements are often found to be repressed) OR whether the most harmful consequence of mobile elements is that the cell machinery gets "confused" when repairing or recombining DNA, and accidentally recombines similar-looking repetitive DNA from different locations, resulting in genetic loss/translocations/duplications, etc. Publications are increasingly pointing to the latter effect as being the more significant of the two. That's not to say that the insertional/disruptional effect is not important at all. There are a number of human diseases resulting from mobile element insertion. But basically, the fact the misalligned repair/recombination looks like its the most significant consequence of "junk" dna argues that the extent to which the DNA repair system or recombination system allows for such confusion will determine how detrimental the presence of repetitive/junk sequence will be. In mammals, which have a pretty good screening system for avoiding such recombinations--it's by no means perfect--the negative effects of interspersed repetitive sequence is greatly mitigated, allowing the tolerance of more of it. great_ape
In support of the above, there’s rapidly growing evidence that the primary cost associated with junk dna proliferation in many taxa is nonallelic (ectopic) recombination as opposed to insertional mutagenesis.
Here's where I suddenly realise that I'm really out of my depth and should stick to writing buggy software. steveh
The status quo, NDE as you call it, hasn't got a leg to stand on and never did. There is no need to challenge myths. As for chimps and humans we are practically identical at the DNA level anyway. The most obvious difference between us at the chromosome level is about a dozen recombinations of preexisting chromosome segments. There is not a shred of evidence that any new information was required for our differences to now exist. Until such information is forthcoming, I will assume it doesn't exist and probably never did. At present I regard Primate evolution as largely and possibly entirely a matter of position effect. I am sure this will not be accepted by many but it represents my present posture nevertheless. A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison
ds: "If it could be done faster, using less energy, and fewer raw materials that should be a strong selection factor in getting rid of stuff that isn’t used. Yet there’s a ton of it there." The amount of apparently "tolerated junk dna" in higher eukaryotes remains an enigma. The official amount of human repetitive DNA, largely derived from mobile elements, etc, is around 50%. This is rather conservative as much of it has mutated beyond our ability to recognize it as mobile element/ viral/ pseudogene derived. Somewhere between that 50% and the 98% figure you mentioned is the actual fraction. I suspect it is closer to 98% of dna that is "junkish" in origin (i.e. from transposons, etc); that is not to say it remains useless. A fraction of that supposed junk sequence has been established to have been co-opted by the organism for something useful. I suspect that fraction will continue to grow as we find out more. Like DS, I think that the ability of junk DNA to modulate the physical structure/size of DNA molecules, along with when and where various parts of the DNA molecule interact with the nuclear matrix, will turn out to be important. In conjunction with epigenetic regulation, there may be layers of complexity we haven't even imagined. One of the concerns always in the back of my mind is that the complexity is ultimately such that it may be fundamentallybeyond our intellectual capacities to wrap our heads around it. That said, the incorporation of "junk" dna for useful ends does not entail a teleological purpose for that DNA as junk DNA. Even many evolutionary biologists get confused on this point. Just because something gets incorporated into a functional component here or there doesn't mean its original appearance was teleological in nature. I might use an old tree stump for a chair, but few would argue that the stump was brought into existence to serve as my chair. Now, as to why a ton of this stuff is in say, mammals, as opposed to bacteria. Part of the NDE theory, as indicated above, is that it has been coopted in mammals for thus far unknown purposes. (Also there's the low-cost argument, which I don't altogether buy) Another important piece of the puzzle, though, lies in the details of DNA repair mechanisms and how they differ between these two types of organisms. Mammals repair their dna in such a way that they can tolerate a great deal more interspersed repetitive sequence; bacteria and lower eukaryotes can not. of course, this brings up a chicken and egg issue. It's plausible that the repetitive element proliferation (due to the lower population sizes of higher eukaryotes) forced this dna repair alterations in these lineages; this resulted in the tolerance of even *more* transposon proliferation, etc, leading to the stupendous amounts of "junk" sequence we observe. In support of the above, there's rapidly growing evidence that the primary cost associated with junk dna proliferation in many taxa is nonallelic (ectopic) recombination as opposed to insertional mutagenesis. great_ape
bfast, if you were to set out to write a "Hello World" problem from scratch, would you start out by writing a load of standard library functions which your program doesn't need? AIUI, the standard libraries provide for a wide variety of programming needs. Their presense suggests that there are a load of other programs already out there which are using some or all of the other functions. Also those standard libaries contain recognisable instructions similar to the ones your program makes use of (after compilation). It should be possible to produce a disassembly listing of those routines similar to the one you produce the the "Hello World" part. That's not always the case. Some of the entries to the obfuscated C contests have blocks of apparent junk which turn out to be compressed data, and the main program turns out to be a implemention of a decompression algorithm. Such programs can't survive even a single mutation. In others, the decompression occurs coutesy of the preprocessor (also very sensitive to mutations, and which, in any case, I don't think we need to consider here - TTBOMK, DNA is not a high level language processed by a succession of external preprocessors and compilers). OTOH maybe human DNA could be some sort of introductory student exercise in how to use the compiler. It may alienate some of the "humans are special" tent occupents. :) steveh
Two comments pertaining to DaveScot's blog entry.
When I’ve made this argument in the past the counter argument was that it’s really not that much extra burden in eukaryote cells because they are so big and have such slow reproductive rates to begin with regardless of how much DNA they have to replicate in the process of making a new cell. Prokayrotes have virtually no junk DNA in comparison and their reproductive success is largely due to how rapidly they can reproduce in great numbers. It’s a good counter argument but I’m not sure I buy it.
I think a better way to think about it is to consider the resources that a cell devotes to the maintenance and replication of its genome. It turns out that these resources are a rather small fraction of those spent by the cell or organism - small enough that natural selection probably would not promote either a smaller or larger genome. At least on this basis.
What really raises a red flag about how much junk is really in all our junk DNA is a how much information is required to build an organism as complex as a human. If every single bit of information in all 3 billion bases was being used for some purpose I still find it incredible that the schematics (or recipe) for a human can be contained in a gigabyte (a gigabyte is roughly how much information is in 3B bases). To posit that it can be contained in 20 megabytes (2% of one gigabyte) stretches the limit of credulity far beyond the breaking point.
This argument doesn't make much sense to me. Consider a very generous, if simple, scheme, whereby each and every cell in the human body is specified by a unique combination of transcription factors, each of which is either present or absent. How many such factors would suffice to uniquely specify each and every cell? Less than 50. Given that we have many more transcription factors than this, and given that control is not a binary proposition (on or off, present or absent), I think the resources present in a very modest genome easily suffice to account for, not just human life, but all life. Look at things another way - how many unique combinations of a subset of, say, 10,000 of the 30,000 genes in a human genome are there? Well, obviously, there are essentially innumerable combinations. Far more than the numbers of human cells on earth. And easily enough to account for the perceived complexity of a human, or orchid, or rainforest, or ..... IMO, 1 gigabyte of protein coding sequence can go a long way. Art2
Let me also address the issue of junk DNA from the perspective of a programmer. When I write a "hello world" program, and compile it up, the result is an executable that is around a megabyte in size. I could write the same thing in optimized machine language in a kilobyte or so. So it seems clear to me that modern programming methods produce significant quantities of "junk code". Therefore I personally do not find it unreasonable for an intelligent designer to produce junk code. Dr. Davison, I recognize your position that evolution is complete. You certainly have made a significant case for your claim. I wonder, however, if I understand your position, the first primate had within it all of the information necessary to differentiate into a human and into a chimp. If so, could it be possible that the chimp still contains remnants of the DNA that would have made it human if it had followed the other path? If segments of "this is human DNA" are found in a chimp, would that not offer significant support for your hypothesis, and seriously challenge the status quo view -- NDE? bFast
Front Loading~ Cascading genetic changes~ mutational functions gained lossed= Left over? or maybe Junk DNA does have a function? Sounds like the jurry is out on this one! rpf_ID
I misspoke in my earlier message . Commoner felt it was the nucleotides that had to be gotten rid of and replication of the DNA was the way the cell had of getting rid of them with the nucleus functioning as a kind of garbage disposal. Kind of far out eh? "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison
Junk DNA will remin Junk DNA until a function is demonstrated for it. I am also at a loss to understand what future evolutionary events might be expected. I see none on the horizon as I indicate with my signature. What do others expect I wonder? All is see is extinction myself, lots of it. "A past evolution is undeniable, a present evoluton undemonstrable." John A. Davison . John A. Davison
First of all, let me point out that I know nothing of DNA so my thoughts here should be taken with copious amounts of salt. It's all idle speculation from a run of the mill programmer's perspective and not intended as criticism. It seems to me that a designer who front-loaded information into ancester DNA and went to great trouble to ensure that different bits of code got activated at prescribed times, might also arrange for any junk to be systematically discarded as he went along if it was going to incur costs. That's what I always tried to do when allocating and freeing memory in a C program. Maybe that's an argument against a front-loading designer, or maybe it means that the cost isn't so great after all. If instead he were to use a garbage collector then he would need to mark the DNA as junk as soon as it's appropriate. Otherwise a garbage collector wouldn't know if a particular segment of DNA was pure junk, coding DNA or DNA that didn't code for anything but did influence something else somewhere along the line. One way a garbage collector running on a computer identifies junk is to traverse all of the memory still in use, marking valid objects as non-junk and then assuming everything no so marked is junk. However, in this case not-junk is defined as referenced by some extant object, the not-junk memory might still be random garbage. Also it should be noted that you need to allocate additional memory to store flags (or a generation number etc.) for the use of the garbage collector. I'm not sure how a cell's replicating mechanisms could decide if non-coding DNA might be "referenced" by which I mean it either had a useful effect in the past (and therefore needed for the next generation) or is likely to have a useful effect for the current organism sometime in the future. Again, the clever old designer probably would be the one to take care of that. I don't see how a RM+NS model could handle a build up of junk. If it is all conveniently located in one place, there is a change that it a fair chunk of it could be eliminated in one go providing an advantage. If, OTOH, the DNA is fragmented with junk here, there and everywhere, then getting one or two small pieces is probably not going to make a difference to the organism's survival. Getting lot's of non-contiguous sequences would involve lots of mutations with potential for a lot of harm done as well and the likelyhood of the introduction of new junk at the same time. Also, I wonder if some things might work out differently if there wasn't genuine junk, affecting timings. Finally, the idea of garbage collection is that the system frees up memory from time to time, or when memory use reaches a certain level, not every time a mutation produces some new junk. Would you have the GC() run, say, every 1000 generations or when junk content reached a particular percentage of the total? steveh
There certainly have been a few ID theorists who have placed a lot of weight on the hypothesis that much/most of the junk DNA will prove to be useful. Most noteably, not because he is a central theorist, but because of the strength of his statement, is Denton. In Nature's Destiny, pp 289,290 Denton says:
If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serious challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary evvents, when it would not in a strict sense be junk in any case, could the finding be reconsiled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. Teleology would be entirely discredited.
bFast
The ciliate protozoans are very large cells with incredible internal complexity and morphology. They may have whole "organ systems" contained inside a single reproductive unit. Correlated with large size they have a large macronucleus and typically one micronucleus which is diploid. The macronucleus originates by endomitotic duplication of the micronucleus. When the cell divides the micronucleus divides mitotically but the macronucleus just pinches in two without producing identical products. This leads to a physiological unbalance which has to be restored by making a new macronucleus. A new macronucleus is periodically produced by a series of mitotic duplications of the micronucleus (endomitosis). Otherwise the animal will degenerate and die. Cells which are prevented from doing this give rise to degenerating lines doomed to ultimate extinction. I always thought this might have something to do with junk DNA because when the macronuclei divide amititically they must lose their genetic specificity in the process. The macronucleus, when first restored by approximately 10 endomitiotic replications which make it 1024 ploid, it is perfectly balanced and only gradually becomes unbalanced with subsequent amitotic replications. The micronucleus ALWAYS reproduces mitotically and accordingly genetically faithfully. The junk DNA may just be DNA that failed to replicate properly and the cells just had to find a way to get it out of the way. Years ago Barry Commoner published a paper about what he called the "nuclear wastebasket theory." The idea was that the cell had to get rid of its DNA somehow so it stuck it in the nucleus. I was his colleague at Washington University at the time, he in Botany, I in Zoology and everybody thought he was crazy, everybody except me that is! Of course everybody thought I was crazy too, so Barry and I always hit it off rather well. The ciliate protozoa are extremely advanced creatures in many ways which I take to be support for the PEH. There is a picture of one, Diplodinium ecaudatum, which lives in huge numbers in the rumen of cattle, in section VII-2 of the Manifesto along with a key to its incredible intracellular structure. Leo Berg called this sort of thing "phylogenetic acceleration." I call it "phylogenetic derepression," That it could occur in a protozoan is compatible with a "prescribed evolution," being simply a premature demonstration of it. A true placenta in certain sharks is another example. The ciliate protozoa may provide a model for the "Junk DNA" notion. I just don't know. "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison

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