Biochemist Larry Moran responds to Jonathan M’s junk DNA post

_{Denyse O'Leary

October 13, 2011

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Here, at Sandwalk: “A twofer” Here’s Jonathan M’s post: “Thoughts on the ‘C-Value Enigma’, the ‘Onion Test’ and ‘Junk DNA.’”

Comments

Petrushka, Take a look in the mirror for YOUR position does not have a testable hypothesis. It has no hypothesis regarding how functional sequences are found. It postulates that huge sequences must be created with incremental evolution via accumulations of random variation, but fails to speculate on how this could be done.
Mainstream biology claims it is possible to get from the genome of one species to another in steps of sizes known to exist.
1- It is an untestable claim 2- Organisms are not the sum of their genomeJoe_{November 25, 2011
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How can you say it functions like a language if it has no syntax and no way of interpreting meaning. Let's be clear about some of the key things that have been said on both sides in this dispute. On the ID side we have a general consensus, most notably defended by Douglas Axe, that function (utility) is isolated in sequence space. Stripped of jargon, that means you can't get from one functional sequence to another by small steps. On the same side you have gpuccio saying it is impossible to model biology in software (possibly because we lack the computational power). On the other side of the argument we have mainstream biology, which has observed a number of kinds of genetic and genomic changes, and has mapped a couple thousand genomes, enabling comparisons of species that are claimed to be cousins. Mainstream biology claims it is possible to get from the genome of one species to another in steps of sizes known to exist. Mainstream biology hypothesizes that peaks of function are connected in ways that makes traversal possible. That doesn't mean you can get for one current sequence to another in easy steps, but it requires that historically, sequences are connected by change and descent. Those are the opposing claims in a nutshell. My point is that mainstream biology has a theory to account for the diversity, and that theory has entailments that can be tested. Researchers like Lenski and Thornton have tested in the laboratory whether gaps in function can be bridged by neutral mutations. My point about ID is that it has no theory of design. It has no hypothesis regarding how functional sequences are found. It postulates that huge sequences must be created without incremental evolution, but fails to speculate on how this could be done. It also fails to speculate on how the ultimate utility of sequences can be predicted -- something far more difficult than merely figuring out protein folding.Petrushka_{November 25, 2011
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It looks like a language and functions as a language, and if were any other language we'd try harder to comprehend it. But in this case it seems way too complicated to be a language. So let's just throw our hands in the air, give up, and figure that a language that difficult to form or interpret must be a naturally occurring phenomenon. And about that manned trip to the moon, that also sounds waaayyy too hard. It's impossible to even escape earth's gravity or leave the atmosphere. So let's just scratch that one off, too. (Oh, wait. That was the 19th century.)ScottAndrews2_{November 25, 2011
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The only selection is artificial selection. And in the design scenario the variation is directed towards the goal.
The argument was mad on another thread (and throughout the ID literature, that a Designer somehow just knows how to make functional sequences without trial and error.
Yes, that is a POSSIBILITY but please reference that ID literature so I can check it out.Joe_{November 25, 2011
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You seem to be agreeing with me. Perhaps if you go back you can follow the discussion thread. My point is that the only known way to steer toward utility is via fecundity, variation and selection. That's what a GA does; that's what biological evolution does. The argument was mad on another thread (and throughout the ID literature, that a Designer somehow just knows how to make functional sequences without trial and error.Petrushka_{November 25, 2011
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Petrushka:
At the level of ribosomes it’s just chemistry.
Reference please.
If you, as a designer, are going to steer sequences toward utility, that is what you need to know.
Reference please. As I have said before a well written GA would take care of that.
How will this sequence affect competitive reproductive success.
And with a big population there are plenty of trials for the GA.Joe_{November 25, 2011
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At the level of ribosomes it's just chemistry. The meaning of a sequence is found in its effect on reproductive fitness. If you, as a designer, are going to steer sequences toward utility, that is what you need to know. How will this sequence affect competitive reproductive success.Petrushka_{November 25, 2011
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Umm the ultimate interpreter of the symbols are ribsomes and ribosomes are genetic compilers. As for the theory of ID well I bet ypou doubt there is a theory of archaeology and forensic science too....Joe_{November 25, 2011
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You seem to have slung a lot of words arguing that DNA is a symbolic language, but you have a problem. th ultimate interpreter of the symbols is not deterministic chemistry, but an indeterminant environment. You have not demonstrated the one key property of the system that is important: whether you can read the language and predict the effect of a sequence in terms of utility. Until you can demonstrate the utility of sequences independently of actual implementation in living organisms, you cannot do what is commonly known as design. You certainly can't do design without doing evolution. This is why there is no theory of deign and none in sight.Petrushka_{November 25, 2011
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Upright BiPed: sorry for the long delay in responding to your nice essay at 8.1.2.1.4 I have written a response here: http://theskepticalzone.com/wp/?p=212 And would be delighted if you would like to drop by to comment, or at least, to leave a link here to any response you might have. But there would be some advantages to continuing the discussion there, as I know your time visits to UD are sporadic, and things move very fast here. And we now have a dedicated thread to your "semiotic argument" :) Cheers LizzieElizabeth Liddle_{October 30, 2011
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Shazard: "Where onion is just copy-paste chinese code simple as brick, without much optimisation " Except that there are also onions, within the same genus, that lack the optimization. I mean, that seems like a bit of a problem. You've got optimization in Humans, then no-optimization in onions, but then optimization in, not just any other onions, but onions of the same genus! Also, I think most biologists recognize that it's a fallacy to think that, 'onions aren't as complex as humans and should have small genomes'.Schenck_{October 18, 2011
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ScottAndrews, what's the difference between an organism that recognizes the higher 'nutrient value' of a foodstuff, and one that associates that recognition with the 'mmmm, tasty' sensation? It seems like the sensation is meaningless here. The evolution of taste will just be tracked with the evolution of tastebuds and the parts of the brain associated with it.Schenck_{October 18, 2011
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"create two programs, the far simpler of the two requiring five times as many lines of code?" You're also forgetting that within the same /genus/ there is a vastly different genome size, so its "whats the probability of creating two programs, that do the same basic thing, one requiring 5X the code" ALSO, to continue the analogy further, I think that the size difference isn't really for %X the LINES of code, because you have to consider that, for example, you can get alternative splicing (and thus two different proteins lets say) with much less than a "Line" of code. So you get basically two genes for the price of one. So 5X the 'size' could really mean "10, 20, mabybe even more X" the 'information'.Schenck_{October 18, 2011
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Gordon Davisson at 8.1.2.1.3 I did not mean to ignore your post:
So far, I haven’t seen a definition which can be shown to be present in DNA and also cannot be produced without intelligence.
Well, now you know the only definition that matters - the one based upon the physical evidence as we find it. You also now know the physical dynamics that every evolutionary algorithm ever devised simply ignores, then imports from its designer. You also know why direct templating via an RNA world is a hopelessly wrong model from the start. You also now know that information transfer is the most prevalent form of irreducible complexity on the planet (in the precise sense that Michael Behe presented it). You also know that when people claim that X material system can create FSCI "without intelligence", they are operating inside their ignorance of the I by taking its existence for granted.Upright BiPed_{October 17, 2011
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I hope you don't mind my questions...no matter how IDiotic they might be. My last two questions would be...Do most scientists agree with you that the genome is 90 percent junk? Second, so to you pseudo-genes are not functional right?ForJah_{October 17, 2011
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Larry Moran:
(1) Organisms that are very similar by other criteria (morphology, fossil record, embryology, biogeography) are also similar by protein sequence. For example, mice and rats cluster together in both types of analysis and so do sharks and rays. Birds look similar to reptiles.
Both common design and convergence explain similarities. And we observe common design in many enterprizes. What universal common descent lacks is a way to test the premise that teh changes required are even possible. Heck to date no one knows if a prokaryote can "evolve" into something other than a prokaryote. Larry Moran:
The explanation that best fits the data tells us that >99% of all evolutionary change is due to random genetic drift and not natural selection.
For uears I have been telling evotards that natural selection is a minor player. And for years I have been accused of not knowing what I was talking about. Now, here you are supporting what I have been saying for years. Sweet...Joseph_{October 17, 2011
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Larry, At least some folks are smart enough to go the "natural selection isn't random route." That takes a little bit more reasoning to see through.
The explanation that best fits the data tells us that >99% of all evolutionary change is due to random genetic drift and not natural selection.
Then it's just a total coincidence that random genetic drift produces organisms "adapted" to their environment. Without natural selection, how do you explain that penguins seem remarkably suited to freezing climates and swimming? If most change is jut random drift, then they could just as well have been ostriches. That's besides the point. So you are proposing that the mechanism is 99% genetic drift. Then I repeat, I'm asking a professor of evolutionary biology for an evolutionary account of any evolutionary event in terms of evolutionary mechanisms, you know, just that cornerstone of biology. Let me help you to understand what is eluding you. If you are an expert in the field of construction, then there must be at least one building in the world that you can explain from the bottom up. If, on the other hand, you've written books and given lectures on your theories of construction but there is not one building on earth that you can explain in terms of what you have written, then your theory is evidently crap. You don't get extra credit for using more words. That's where you're at, Larry. You're a professor of evolutionary biology and yet you can't explain the evolution of anything, ever, in the specific terms of your own theory. I'm sad for you just thinking about it, even though you call me an idiot. You're clearly someone who likes to impress people, and you've gotten your share. But the only people who critically analyze what you say and what you won't even attempt to say aren't impressed. That is obviously under your skin, and your inner child who didn't get enough praise acts out and starts calling names.ScottAndrews_{October 17, 2011
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ForJah says,
…it seems you are in quite a mess of defining your terms appropriately along with Well’s. I wonder why the terms need to be defined in the first place though…when I think of “junk” I would assume that there is absolutely no reason for it. But if the DNA in question has function, or “some” at least, why label it worthless or junk at all?
Junk DNA is DNA that has no function. What's wrong with that definition? It's the definition that every respectable scientist uses but you won't find it in Wells' book. I wonder why?
Even if Well’s is incorrect about the majority of scientists YOU still believe that 90% of is is junk. Well’s is saying that it most likely is NOT and to say it is is an argument from ignorance.
That's correct. I think that 90% of the DNA sequences in our genome have no function and are, therefore, junk. It's true that Wells describes my point of view as an argument from ignorance. He's dead wrong about that. There's plenty of evidence in support of functionless DNA (junk). You won't find any of that evidence described or explained in Wells' book. I wonder why? I guess it's because those of us who have been studying evolution and genomes for most of our lives must be really, really ignorant. We've fallen under the spell of a myth that's easily exposed by an Intelligent Design Creationist who can't even define the term "junk DNA" correctly.Larry Moran_{October 17, 2011
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ScottAndrews says,
I ask you to provide an evolutionary explanation of something, just pick something, that demonstrates the explanatory power of evolutionary theory. You respond with trees, which indicates that you are unable to integrate natural selection with your explanation, or that you view it tautologically. Natural selection is an integral part of evolutionary theory but you cannot incorporate it in an evolutionary explanation.
When you compare the sequences of unique genes in different chordates you will note that some of them are very similar and others are very different. You can construct a tree showing these relationships. The pattern you get does not rely on any assumptions about how the pattern is generated—you can get trees by comparing languages, minerals, and makes of automobile. There are several remarkable features of the protein sequence trees. (1) Organisms that are very similar by other criteria (morphology, fossil record, embryology, biogeography) are also similar by protein sequence. For example, mice and rats cluster together in both types of analysis and so do sharks and rays. Birds look similar to reptiles. (2) All of the nodes of the tree are connected to a single point. (3) The distances from this single point to the tips of each branch are approximately the same. For example, you get about the same number of amino acid changes in the line leading to amphioxus as you do in the lines leading to salmon, frogs, and kangaroos. How do we explain these observations? I'll leave it up to you to give us the Intelligent Design Creationist explanation but here's how evolutionary biologists explain the observations. The pattern is due to the descent of each protein from a common ancestor represented by the point where all the sequences are connected. The changes we see are almost exclusively due to the fixation of nearly neutral alleles by random genetic drift—a theory developed by population geneticists in the 1930s. None of the patterns (with a few rare exceptions) have anything to do with natural selection. (You didn't know that, did you?) Biochemists subsequently confirmed that the changes, for the most part, occur in regions of the proteins that are not crucial to function. The important functional regions show very few changes (sometimes none). Since random genetic drift is a stochastic process, there will be slight differences in the position of some branches when you compare different sets of genes. There will also be slight differences in the total length of each branch. The fact that all the species seem to have accumulated approximately the same number of changes is explained by population genetics because fixation of nearly neutral alleles by random genetic drift depends only on the mutation rate and that doesn't change very much. That's why there's an approximate molecular clock. It's explained by modern evolutionary theory. The fact that all the observations can be explained by modern evolutionary theory is powerful support for modern evolutionary theory (population genetics) and powerful support for the idea that what see today also operated throughout the history of chordates beginning more than 500 million years ago. The fact that two independent methods give the same (very similar) trees is probably the most powerful evidence that evolution accounts for the history of life. Nobody has come up with a better explanation than evolution. The explanation that best fits the data tells us that >99% of all evolutionary change is due to random genetic drift and not natural selection. Very few IDiots understand evolution well enough to appreciate this fact.Larry Moran_{October 17, 2011
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ForJah says,
... could you perhaps provide an example of the so called “misspokeen” statement that would back up your opinion that there were/are some scientists that did say that?
You don't need to rely on me. Here's what Jonathan Wells says in his book.
In the 1950s, neo-Darwinists equated genes with DNA sequences and assumed that their biological significance lay in the proteins they encoded. But when molecular biologists discovered in the 1970s that most DNA does not code for proteins, neo-Darwinists called ono-protein-coding DNA "junk" ...[p. 15]

Yet by 1970 biologists already knew that much of our DNA does not encode proteins. Although some suggested that non-protein-coding DNAmight help regulate the production of proteins from DNA templates, the dominant view was that non-protein-coding regions had no function. [p. 20]
All you have to do is look up the references Wells give to back up his claim and you'll have your answer.Larry Moran_{October 17, 2011
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Well actually haha...it doesn't. I have had friends critic philosophy articles just from reading a few paragraphs or pages. Now in college this is what lots of people do, especially after a mid-night party. I mean, I asked a yes or no question and you answered me with posts and another question! I will assume that yes, you did read it, and that's great because I know a lot of your other evo friends don't like to read ID literature. I am interested by a lot of what you blog says...it seems you are in quite a mess of defining your terms appropriately along with Well's. I wonder why the terms need to be defined in the first place though...when I think of "junk" I would assume that there is absolutely no reason for it. But if the DNA in question has function, or "some" at least, why label it worthless or junk at all? Maybe this is why science education sucks. Because scientists suck at defining their terms. Also, I think you are working very hard to distract from Well's point. Even if Well's is incorrect about the majority of scientists YOU still believe that 90% of is is junk. Well's is saying that it most likely is NOT and to say it is is an argument from ignorance. You have faith in the future of science to answer the claim that life started naturally, now why can't a ID advocate have faith in the future of science when it comes to functionality of the genome?ForJah_{October 17, 2011
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In his post at 8.1.2.1.14, Dr Moran states that he isn’t going to debate the “meaning” of information in computer science versus biology. Of course, it is his right not to do so. But I thought in my post at 8.1.2.1.4, I made it abundantly clear I was not talking about the “meaning” of information; I was talking about its very observable physical characteristics. And I certainly wasn’t talking about computer science (I never mentioned it) I was talking about any recorded information, including that within the genome. Given that the conversation was about observed physicality, and how that physicality relates specifically to biochemistry, I thought holding such a discussion with a famed biochemist and coauthor of six or eight collegiate-level books on biochemistry might have been entirely appropriate. But then Dr Moran returned to clarify any misunderstanding as to why he does not intend on entering into the conversation. And the reason he gives is a very simple one; it’s because he doesn’t “think there’s any connection”. In other words, he doesn’t want to debate the connection because he doesn’t think there is one. This actually turns out to be a very compact and reliable position to take; one with a great deal of historical significance I would expect. I suppose I will just leave it to his authority “addressing real science” to make sense out of it though - if there is any.Upright BiPed_{October 17, 2011
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Wow, apparently this was my big chance. Ask a professor of evolutionary biology for an evolutionary account of any evolutionary event in terms of evolutionary mechanisms, you know, just that cornerstone of biology, and the discussion ends. I'm being unfair. Perhaps Larry hasn't had time to visit the facility at Princeton where you plant your palm on the glass, get your retina scanned, and ride an elevator to a vault deep beneath the earth where they keep such secrets next to Darwin's glass-encased skull.ScottAndrews_{October 17, 2011
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ForJah asks,
Hold on Dr. Moran! I can’t believe I didn’t ask you this but how much of Well’s book did you read?
LOL Jonathan, Moonies, and Junk DNA Junk & Jonathan: Part I—Getting the History Correct Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA? Junk & Jonathan: Part 3—The Preface Junk & Jonathan: Part 4—Chapter 1 Junk & Jonathan: Part 5—Chapter 2 Junk & Jonathan: Part 6—Chapter 3 Junk & Jonathan: Part 7—Chapter 4 Junk & Jonathan: Part 8—Chapter 5 Junk & Jonathan: Part 9—Chapter 6 Junk & Jonathan: Part 10—Chapter 7 Junk & Jonathan: Part 11—Chapter 8 Junk & Jonathan: Part 12—Chapter 9 Does that answer your question?Larry Moran_{October 17, 2011
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Response to larry Moran- I said ID is not anti-evolution … Larry Moran:
You are correct. If one scours the Intelligent Design Creationist literature one will occasionally stumble upon some article or book that tries to offer some positive evidence for the existence of intelligent design in nature.
Intelligent Design Creationist exists only in the minds of the willfully ignorant.
On the other hand, 99.9% of that literature is anti-evolution.
Not by the way YOU define "evolution". Geez try some consistency.
Here’s a challenge for you, Joseph. Look at all the postings on Uncommon Descent over the past few months. Tote up the number that are anti-evolution and those that offer a positive case for Intelligent Design Creationism.
1- How are YOU defing "evolution" that makes ID anti-evolution? 2- We have already been over and over the positive evidence for ID
Post your results here and then we can decided whether, to a first approximation, Intelligent Design Creationism is anti-evolution.
Again according to YOUR definition of "evolution" posted on YOUR site says that ID is not anti-evolution. But ten again you are obviously ignorant of ID and you think your ignorance is meaningful discourse. Strange, that...Joseph_{October 17, 2011
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Upright Biped, It's my understanding that Larry Moran might have debated the nature of information with you, but he was busy yelling at kids to get off his lawn. It's rumored that he referred to them as idi-tots.material.infantacy_{October 16, 2011
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A quick "Thanks" for the kind words. Jammer, -- thanks for the sentiments. It has not been my desire to pull a pile-driver routine on Dr Moran. I asked if he wanted to talk about the physical evidence of information, and he says he doesn't and gave his reasons. Even among materialists, Dr Moran has cultivated the identity of being a rather crusty character who doesn't take any crap from IDiots. If he doesn't want to talk about it, then I don't need him to. As far as him turning down the opportunity, it is what it is (and nothing less). Junkdnaforlife, -- wow that was a nice thing to say. Thank You. My post above comes from bits and pieces of an unpublished essay on the subject. It will appear among others on a modest website I have been working on, hopefully by the end of the year. (I am doing my best to plow through code right now - it's not my specialty). Clearly, there is a huge group of people who carelessly throw around the word 'information' like it was a shapeless entity which can be taken for granted. Well, it can't. Its existence imposes (observable) physical requirements on matter when it's recorded and transferred (in any form). We live in a material universe, how could it be any other way? If the theory of material origins is actually true, then the idea itself predicts that the information in the genome is not semiotic - to borrow Dr Moran's term - it is only 'analogous' to the kind of information transfer we as sentient beings use. One is symbolic and the other is chemical. Indeed, that position is argued by materialists (one way or another) ever day on this forum. The information transfer in the genome is said to be no more than a cascade of physical reactions, but of course, all information transfer is a cascade of physical reactions, so that is no answer, and it never has been. But why does the truth of materialism predict this (chemical-only transfer) anyway? Because the representations and protocols involved in semiosis would have only appeared on the map after billions of years of evolutionary advancement in organisms. An imaginative materialists may see a chemically non-complex origin of inheritable Life in his or her mind's eye, but that image blows up if that heredity is accomplished by using representations and protocols. Ask a materialists “what came first on the great time-line of Life: a) molecular inheritance by genetics, or b) representations and protocols?” Typically confusions ensues, and the embattled assumptions of materialism are pushed to the very front of the defense. On the other hand, if ID is said to be true, then it's own prediction is on the line. That prediction has been that the information causing life to exist is semiotic. And again, that is exactly what is argued (one way or another) on this board every day. When nucleic sequences were finally elucidated, we did not find an incredible new and ingenious way in which physical law could record and transfer information, we found the exact same method of information transfer that living agents use; semiosis. And as it turns out, if one properly takes into account the observable physical entailments of information transfer during protein synthesis, and compares it to the physical entailments of any other type of recorded information transfer (without exception), they are precisely the same. It requires an arrangement of matter to serve as a representation within a system, it requires an arrangement of matter to physically establish an immaterial relationship between two discrete objects within that system (the input and output), it requires an effect to be driven by the input of the representations, and it requires that all these physical things remain discrete. The semiotic state of protein synthesis is therefore confirmed by the material evidence itself, and with it, one of the predictions of ID theory. Of course, I have no authority, and I am not speaking for ID writ large, just for myself and anyone else who might hold this view. :) Cheers... ps: the name of the site is Complexity Cafe.Upright BiPed_{October 16, 2011
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Hold on Dr. Moran! I can't believe I didn't ask you this but how much of Well's book did you read?ForJah_{October 16, 2011
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That's probably becuase you don't understand my point. Which is okay...could you perhaps provide an example of the so called "misspokeen" statement that would back up your opinion that there were/are some scientists that did say that? I like to take one post at a time Dr. Moran, nice and slow so that I can understand your points and not put words in your mouth...you could learn a lot from my process!ForJah_{October 16, 2011
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Prediction: Larry will offer another explanation that incorporates natural selection but that eliminates another integral part of evolutionary theory - incremental variation. He will describe some phenotypic change, and state that it would obviously be selected, or observedly was. He will overlook that the change he described would involve several incremental changes, but he will not indicate what the genetic variations were, what specific phenotypic change resulted, and why each of those smaller steps, starting with the first, were selected. Then Larry will come up with an example that incorporates both incremental variation and specific selection. In doing so he will drop off yet another integral aspect of evolutionary theory, that it must explain extensive change resulting in vast diversity. In other words, back to bigger lizard heads and nylon-eating bacteria. Or, perhaps he'll play dumb and produce some research carefully detailing genetic differences between two or more organisms, begging the question that the differences between them are the result of the aforementioned mechanisms. Or perhaps he'll just dodge the question entirely, bluster some more, and call me an idiot.ScottAndrews_{October 16, 2011
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