Here, at Sandwalk: “A twofer” Here’s Jonathan M’s post: “Thoughts on the ‘C-Value Enigma’, the ‘Onion Test’ and ‘Junk DNA.’”
Comments
Upright BiPed:
So firstly, I would like to ask if you agree that there is information in DNA, or not?
This depends a lot on exactly how you define "information", since there are a variety of very different definitions available. There are two major "mainstream" theories of information: statistical and algorithmic information theory; each provides several potentially relevant definitions. By most (perhaps all?) of these definitions, DNA sequences do indeed contain information.
But both of these theories allow for information production without intelligence (in fact, neither assigns intelligence any special role). In particular, evolution involves mechanisms that can clearly produce all of these types of information.
For example, point mutations will generally increase Kolmogorov complexity (the primary measure of the algorithmic theory) and Shannon entropy (one of many measures from the statistical theory).
Sequence duplication will generally increase Kolmogorov compressability.
Selection will generally decrease Shannon entropy (note that both entropy and lack of entropy are sometimes useful measures of information -- as I said, definitions vary greatly) and increase joint information of the gene pool and the selective constraints on the population (essentially, it adds information about what functions and what doesn't).
Genetic drift will generally decrease the Shannon entropy of a population (although not of the individual genomes in it), and increase Kolmogorov compressability (again, of the population not individuals).
ID advocates generally reject these definitions, and use their own. So far, I haven't seen a definition which can be shown to be present in DNA and also cannot be produced without intelligence.Gordon Davisson
October 14, 2011
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There is, or there used to be, a sort of biologist that thought that natural selection was the only important process in evolution, and that therefore every feature of every organism was adaptive, i.e., an adaptation shaped by natural selection. These became known as "adaptationists" or "panselectionists" or "hyper-selectionists".
The default instinct of adaptationists was therefore to object to the very idea of "junk DNA", and also neutral mutation and genetic drift.
This attitude was bashed by Stephen Jay Gould in the famous paper "The Spandrels of San Marcos", and was weakened greatly by the success of neutral theory, and, probably, by the C-value "paradox" (which is only a paradox if you assume (a) that mammals and humans are the most complex forms of life and (b) that complexity should correlate with the size of the genome).
After all this bashing, I think it would be hard to find a naive adaptationist among serious scholars of evolutionary theory, but you can still often find it commonly amongst people whose main training is not in evolution, e.g. evolutionary psychologists, molecular biologists, biophysicists, etc.
Amongst other things, the critics of naive adaptationism pointed out that adaptationists were essentially taking way too literally the idea that natural selection replaced Paley's Argument from Design, and making assumptions based on this pre-Darwinian assumption that everything was specially created by God and therefore everything had a Purpose.
So, when modern-day IDists come along and proclaim that "Darwinists" stupidly assumed that lots of DNA was junk, there are several things that have to be corrected:
1. It's a wrong statement as a matter of history -- in historical reality, the more throughly adaptationist and hyper-selectionist someone was, the less likely they were to like the "junk DNA" idea.
2. A lot of people came towards the junk DNA position *against* the initially strong selectionist instincts which were still quite strong in the 1970s. Amongst other things, the huge variation in genome size in organisms without detectable differences in functionality or complexity is difficult to fit with adaptationist assumptions.
3. As it turns out, the actual evidence for the functionality of the bulk of the genome in large-genome organisms like humans ranges from mediocre to nonexistent. Thus declaring junk DNA a "myth", bashing evolutionists for suggesting it is a reasonable idea, etc., are silly things to do.
4. All of the above is well-known to anyone who investigates the literature with a decent amount of rigour; any competent scholarship would know about this stuff, and cite it prominently up near the front so that the reader is well-informed about the basics of the case. But IDists seem wholly unable to manage this feat.NickMatzke_UD
October 14, 2011
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Marxist? Really?
How do marxists like evolutionary biology, as a rule?wd400
October 14, 2011
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ForJah,
The Marxist ideals and threats of losing one’s job have a lot to do with it.
Simply incorrect. You no doubt believe that to be the case because of the propaganda from here and others but really, there is no army of "doubters" out there. In survey after survey, totally anonymously and also not, people reaffirm their support for "evolution"
SO majority opinion means absolutely nothing to me.
Quite right too. But sometimes the majority are in fact right. When the other side cannot actually produce any evidence for their position it can hardly be taken seriously.
For example, tell me a single thing about Intelligent Design without referring to what Darwinism/Evolution can or cannot do.
So I do feel that I am educated enough to have a decent opinion on this subject.
I have to ask then, do you go to your mathematics or physics tutors and explain to them why their understanding is wrong about some fundamental things that relate to their field of expertise? Why not? Why is it only biology and evolution where you have decided that the mainstream opinion is so wrong as to be worthless?kellyhomes
October 14, 2011
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Thank you Kellyhomes for your encouragement to further my study of Biology. I would just like to say though, I have studied Biology. When I said "my field of study is not in biology", it’s not, it's in music. That isn't to say I know absolutely nothing about Biology or that I have never taken a Biology course. I have actually; I've taken two, as well as a general science course and a philosophy of science course. That aside, I have read a lot of books on the topic of evolution and Intelligent design and, of course, I have education in mathematics and physics which comes from High school. So I do feel that I am educated enough to have a decent opinion on this subject.
I don't think studying evolution will cause me to come to the conclusion of why so many accept it. I think that lies in the field of philosophy of science. I know why many accept it without having to know what it says (even though I do). The Marxist ideals and threats of losing one’s job have a lot to do with it. The same reason I know why so many people conformed to the Catholic Church in ancient times, because they would have killed you! SO majority opinion means absolutely nothing to me.ForJah
October 14, 2011
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ForJah,
Now, I wouldn’t say evolution has no cloths, but it certainly is missing a hat and scarf to go with that ridiculously mismatching outfit.
you also said:
my field of study is not in Biology
If you are interested in it so much so that you believe that (presumably) life was designed and so much to take part in a ID message board why don't you study biology and use the advantage of "knowing" that life is designed to get one step ahead? I know that nobody can actually come out and say specifically what that advantage would be but trust me, it'll make *all* the difference.
And perhaps after studying evolution you'll know why so many actual scientists accept it? Or not, as many here would note of course. But most do, of course.kellyhomes
October 14, 2011
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Wow Dr. Moran, I'm quite honored that you took time to critic my response! Thank you for that. You said a few things though that I'm not sure ID advocates are really saying. For instance:
"Hardly anyone thought that all non-coding DNA was junk"
First, I don't believe Wells thinks that all non-coding DNA was considered junk. Just that "most" of it was and by "some" scientists, and he has done an excellent job at providing evidence of that claim. Also, I find it very important to understand that most people know Richard Dawkins and PZ Myers, those are just two scientists but since most people like to quote them as the "best evolutionary scientists of our time" then Well's book is merely a response to their claims, even if they represent a small portion of scientists. Now forgive me my fellow “Idiots” if I am misrepresenting Well's point, for I have not read the book in full, but from studying ID literature this is a conclusion, I feel, is most appropriate.
Second, I find it interesting that you said "hardly anyone"...So does that mean there were/are scientists who claim all non-coding DNA was or still is junk? Interesting, they probably are evolutionists, I wouldn't doubt. I would say that NO ID advocates have ever believed all non-coding DNA was junk. SO in its simplest essence 100% of ID advocates were right all along.
When I said "and then half of the post Dr. Moran doesn't even understand what Jonathan M is saying...I meant to say "and then half of the post Dr. Moran “claims not to even” understand what Jonathan is saying". That is why I said later perhaps you should have asked Jonathan M what he did mean before debunking an argument you didn't even understand...does that make sense? That just seems fair to me.
I do believe that you are correct Dr. Moran. I believe that the argument against "junk DNA" is irrelevant to evolution or ID. Though I would say one might expect "some" junk DNA if you look at the world with an ID worldview. My car still works even if the air conditioner does not or if the radio knob falls off. If you are a Christian and believe in the fall, then you would expect some junk DNA to be there, right? But of course then we come close to when PZ Myers says that evolution predicts both similarities and differences which one can then conclude it predicts nothing. Which I guess then makes both theories inconsistent. But no one doubts that both theories have their problems. The ID movement’s purpose is to wipe off the wrong assumption that ID is not science not to claim they know the answer to everything!
I think you have a very narrow minded understanding of the purpose of Jonathan Wells’s book, and the entire ID movement. Forgive me for my ignorance though, for I am simply a college student and my field of study is not in Biology, so I'm sure you know more about Biology then I do. Sometimes though, it does takes a child to say the emporer has no cloths! Now, I wouldn't say evolution has no cloths, but it certainly is missing a hat and scarf to go with that ridiculously mismatching outfit.ForJah
October 14, 2011
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And then half of the post Dr. Moran doesn’t even understand what Jonathan M is saying.
I understand perfectly well what he's saying.
He's screwing up a discussion of The Onion Test because he never bothered to figure out what Ryan Gregory really meant.Larry Moran
October 14, 2011
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Scott, to put it nicely what does eating out provide outside of 'mmmmm that tastes good (or perhaps ewww bad)' and boy that was expensive regardless of the mmmm or ewwww assessment?
Your right I can't ask a shark if s/he enjoys what it eats but I can make observations on how fish feed. I feed lots of fish and it isn't diffiult to generate excitement in the tank by feeding them their favorite rations. Do the fish enjoy eating one prey/food item over another or is it just preference? If it is preference what drives that? Maybe it tastes better to them than other food items and they enjoy the better tasting prey/food. Their excitment and enthusiasm to feed seems to me an indication that they enjoy eating things and other things not so much and some not at all.
Another example: I just went out to check on my pigs. I took some ripe pears out there for each of them to eat. It seems obvious that their enthusiasm and the excitement that eating the pears generates suggests that they do, indeed, enjoy eating pears over their standard fare. Their regular feed ration remains untouched until all the goodies are eaten. If they don't enjoy eating one over the other what is the explanation...preference?
Another example: my dogs just followed my wife out to the kitchen where she is going to strip the chicken meat off some carcasses she boiled for stock. They each have kibble in their bowls that they can eat but they prefer the chicken meat they are hoping to get more than the kibble. Do they enjoy the chicken meat more than the kibble? Appears so to me since I can get them doing parlor tricks with great enthusiasm with the chicken but can't get much other than looks that appear to be disgust when I try the same thing with the kibble.
Yes, Scott, I think it is not beyond the realm of reality to suggest that animals enjoy eating some foods just like humans who are also animals.Acipenser
October 14, 2011
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There are many scientists who never thought that most of our genome was junk. They still don't. It's a controversial topic in molecular biology.
Hardly anyone thought that all non-coding DNA was junk. That's a "myth" made up by Jonathan Wells and his supporters. He should know better because he studied molecular biology.
There are hardly any scientists who claim that the existence of massive amounts of junk DNA is proof of evolution. It certainly isn't proof of "Darwinism" because it actually refutes the core concepts of Darwinism. That's another myth invented by Jonathan Wells. He's confusing the use of a few specific examples, such as the conserved position of some pseudogenes, with the more general argument about whether most of our genome is junk.
Wells is confused about a lot of things.
Bacteria have very little junk DNA. That's perfectly consistent with evolution. Mammals have tons of junk DNA. That's also perfectly consistent with evolution. It's very difficult for IDiots to understand this because they don't understand evolution (or biology).
They really should try harder.Larry Moran
October 14, 2011
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Larry,
Thank you for the response. I will return after a short break to offer a comment.Upright BiPed
October 14, 2011
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Why does food taste so good?
A) So we'll eat it.
B) To elicit joy.
C) Inexplicable.
D) All of the above.
E) Evolutionary psychology will explain it someday.material.infantacy
October 14, 2011
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The specific order of nucleotides in DNA determines whether certain biochemical activities will occur at that site. In some cases a specific sequence of six base pairs may ensure that an endonuclease binds to that site and cleaves the DNA molecule.
Other sites may be places where transcription complexes bind causing a stretch of DNA to be transcribed into RNA. Some sites serve as origins of DNA replication and those sites are identified by specific runs of nucleotides in a specified order.
It's easy to identify these sites by scanning the genome sequence.
In common parlance we refer to these sites as containing "information" in the form of specific nucleotide sequence. It's a very useful analogy and I think everyone knows what we mean when we use it. Nobody expects it to conform to the meanings of "information" in other disciplines.
Nobody, that is, except some IDiots who like to play semantic word games instead of addressing real science.
I hope you're not one of those people.Larry Moran
October 14, 2011
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Acipenser,
First, to put it nicely, perhaps you should try eating out more.
Second, at least in my population everyone has access to roughly the same foods. Some enjoy broccoli while others are revolted. I can't imagine someone not liking chocolate, but some people don't.
It's not about what we're used to. These variations exist among siblings eating together.
So what does that mean? Is broccoli good for me and not for my wife? Is good for raw but bad for me cooked while the reverse is true for my brother?
Third, you are attributing a human experience to a shark. You have no way of determining whether sharks enjoy food like we do. Your argument requires you to make up what can't know.ScottAndrews
October 14, 2011
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Petrushka,
The whole point of calling something junk is that you are storing it without using it. The rest of the analogy is that stuff in storage rusts or deteriorates, like an uninhabited house or unused tool.
The rest of the analogy is that everything in those storage units was designed and constructed, as was the abandoned house. (Otherwise I'd love to see what's in your garage.)
Why does a rusted-out Ford Model T require less explanation than a 2011 Mustang?ScottAndrews
October 14, 2011
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Scott, do you think there is a distinction between food preferences and enjoyment in eating that food? If enjoyment is nothing more than stating "mmmm that tastes good' then the shark is choosing to enjoy a meal of a pinniped with the ability to recogniz that humans taste terrible and look for something else...something more enjoyable to eat.
Venus flytraps will also close on a piece of hamburger and digest it as well. I think they can discriminate what is nutritional and what is not and from your example it appears you would agree with me on that.Acipenser
October 14, 2011
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Acipenser,
Are you saying that sharks enjoy what they eat? Who told you that, the guy in the suit?
You're missing the distinction I made. Yes, things will exhibit a preference for certain foods. If you drop a pebble into a venus flytrap it will close and then slowly open without attempting to digest it. Are you saying that enjoy insects? I suppose if you turn sideways they might be smiling.ScottAndrews
October 14, 2011
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Scott, what makes you think that living things were eating and not enjoying it in the past? White sharks prefer pinnipeds and spit out humans in pinniped disguises. Why would they eat one and not the other?
I think today you will still find many organisms, humans included, will eat anything they can get their hands on regardless of taste. Spoiled grain, grain with mercuric fungicides on them, rotten food from a dumpster, kraft mac and cheese. Why would they eat that instead of something more palatable? What is nutrient-rich food?Acipenser
October 14, 2011
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We IT dudes know that if a project is bloated with stuff that isn't used -- say a multi-megabyte DLL from which you only call one small function, then the stuff you don't call is junk.
The whole point of calling something junk is that you are storing it without using it. The rest of the analogy is that stuff in storage rusts or deteriorates, like an uninhabited house or unused tool.
Junk DNA may have been used at one time, but no longer. And no one is maintaining it, so it deteriorates.Petrushka
October 14, 2011
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That's a very interesting point. One could reason that the behavior of eating and the physical experience of hunger evolved as responses to the need for nutrients. But why do we enjoy it? Clearly living things were already doing it without enjoying it, so why start?
Fortunately I've been reading a lot so I now have the expertise to answer my own questions. You see, some populations were just eating anything they could get their teeth or beaks on. Then a mutation arose that conveniently caused some to respond with inexplicable pleasure when eating nutrient-rich food. This resulted in their attraction to better food, which was beneficial, and therefore selected. (Evolution searches thoroughly. Similar mutations had occurred with regard to tree bark, rocks, and feces. Those were not selected.) Our enjoyment of food is a vestigial remainder of that instinct.ScottAndrews
October 14, 2011
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too funny.Upright BiPed
October 14, 2011
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Exactly. Delicious selection is WAY more relevant than the natural variety in this context.
Does it taste great sauteed in butter? This is the butter test. If one believes that the content of a vegetable is largely an artifact of blind processes, one must also explain why it is delicious with butter.material.infantacy
October 14, 2011
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I agree that the "no junk DNA" is a dumb argument. ID doesn't make such a claim and we certainly don't need that to show how dumb/ mean/ ignorant/ etc. Darwinists are.Joseph
October 14, 2011
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Wait, when Jonathan Well's book came out, weren't some of the first responses that scientists never thought the human genome was mostly junk? I don't understand what Moran is doing in his response, I mean if he disagrees with Wells and Jonathan then he must also disagree with his fellow evolutionists who agreed with Well's point just that it never really was considered "junk" to begin with.
Not to mention, Dr. Moran doesn't really impress me with his response. I mean, saying I don't agree and then giving no citation to a study that disagrees...really? And then half of the post Dr. Moran doesn't even understand what Jonathan M is saying. If you don't understand, find out first, and then write a response. But of course it's hard to do any honest objective analysis when you are so heavily bias to evolution.
And I happen to like "IDiot's" I think it's funny...the more insults they make the less information they address, which is pretty typical of evolutionists and militant atheists. Go my fellow IDiots!ForJah
October 14, 2011
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Great.
Firstly, I think the Onion Test is a fascinating issue. When Dr Gregory proposed the Onion Test, he was making a valid observation from his database, and offering a challenge to those who wanted to name a "universal function for DNA". It is the information in DNA that I am concerned with, its physical existence within the medium.
So firstly, I would like to ask if you agree that there is information in DNA, or not? Is there a reason you call it information if you do? And if you don't, then what is it about its existence that causes you decline to call it information? Does its existence have any observable physical qualities that would or would not sway your view in one direction or the other?Upright BiPed
October 14, 2011
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Lol. No they are perfectly fine, and delicious, the way they are. My comment was intended as a bit of low satire on the "a Designer Would Have Done Like This, Therefore No Designer Exists" fallacy.MedsRex
October 14, 2011
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Isn’t the onion test based upon the idea that heritable information exists in the genome? Or shall we equivocate?
The Onion Test is based on the idea that one species of onion has a much larger genome than a human. It's also based on the idea that very similar species of onion can have hugely different genome sizes.
The challenge for those who postulate a function for most of our genome is to describe how this explanation applies to the onions.
Debate me right here right now.
Are we debating whether your understanding of the Onion Test is correct?
Go for it.Larry Moran
October 14, 2011
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Nick,
Myth, or saying something you can't possibly know as if you do. You're right, they aren't the same thing. Some difference.ScottAndrews
October 14, 2011
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"Junk DNA: A perfectly reasonable idea that might be largely true" just doesn't have the same ring to it, does it?NickMatzke_UD
October 14, 2011
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Oh really, the question is completely up in the air? Then how can Jonathan Wells write a book declare junk DNA "a myth"?NickMatzke_UD