Home » 'Junk DNA', News » Biochemist Larry Moran responds to Jonathan M’s junk DNA post

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

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

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

  1. The Onion Test is a legitimate dilema for Intelligent Design Theory. Since computer programs are a useful analogy, please consider the following:
    What is the probability that (an) intelligent designer(s) would create two programs, the far simpler of the two requiring five times as many lines of code?

    I’m not sure how to go about that calculation, but I can use the analogy to offer some possible explanations:
    1. There are multiple designers with a wide-range of proficiency at genetic programming.
    2. It’s represents the genetic programming learning curve of the intelligent designer(s)
    3. Some portion of the genetic programming is non-functional (as in commented-out functions or comments left by one designer intended for another).

  2. RBH of Panda’s Thumb will be pleased as you are supporting his theory.

    Multiple Designer Theory
    http://pandasthumb.org/archive.....on-to.html

    Or, it could just be transposon remnants. But that’s just the dumb materialist Darwinist ideologues saying that.

  3. 4. the Designer is a malicious prankster, possibly related to the one that planted all those fake fossils, or the one that planted false evidence for the age of the earth.
    5. Onions are far more important to the Designer because they taste better.

  4. “. . . far simpler of the two requiring five times as many lines of code.”

    Let’s just be clear about one thing up front. This statement is an unsupported assertion.

    Of course, ID doesn’t have any issue with transposon remnants, Nick. ID certainly doesn’t dispute that systems and machines get messed up, degrade, break down over time.

    Petrushka, don’t mix age of the Earth in here. It is irrelevant and ID certainly doesn’t have any issue with the age of the Earth. I do like 5, though!

  5. Well if I were the Designer I would have made onions pre-fried!!!! ;)

  6. Not sure if I understood the biology under whloe this stuff, but we IT dudes know that something “simpler” can be “bigger” then what is seemingly more complex and smaller.

    It can be described as different software library reusage for particular tasks. Which means that your component have to carry out not only specific primary functionality, but libraries which your functionality relies upon.

    So if the original library was created with human genome in mind, then it is optimised for particular human functionality. But if you have to reuse the same libraries for onions and that is very natural thing to do for Designer (so you don’t reinvent the wheel) you take original library and reconfigure it for onion functionality. But this difference between original optimised library and non-human onion will emerge as additional code on the disk, where complexity may decrease.

    Ony my 2 cents.

    Other answer could be that Human Genome is designed very complex, optimised and loaded into system so it should be highly optimal. Where onion is just copy-paste chinese code simple as brick, without much optimisation as Designer does not care for onion wellbeeing as much as for human wellbeing.

    See… we IDists can produce proofs out of thin air too.

  7. Eric Andersson:

    “Of course, ID doesn’t have any issue with transposon remnants, Nick. ID certainly doesn’t dispute that systems and machines get messed up, degrade, break down over time.”
    ====

    Especially when environments have degenerated and degraded as a result of human misuse and abuse of science. Indeed, it has been excellerated by human ignorance, stupidity, greed and selfishness. But then wallowing in eror and imperfection seems to be the purposeful patterned lifestyle of choice now days as many of the arguments bare out across the Net. If there was a an Intelligent Designer, he wouldn’t have done such N such this way or that, therefore “Dice Theory” is true. You know how it works!
    —-

    Eric Andersson:

    “Petrushka, don’t mix age of the Earth in here. It is irrelevant and ID certainly doesn’t have any issue with the age of the Earth. I do like 5, though!”
    ====

    They can’t help themselves. They have a paasionate, strict need for an extreme Fundie take on the argument. Infact it’s imperative. It’s not so much that they need excuses, indeed they actually invest in them. Pimping I.D. as another Fundie invention allows them a chance of warding off a very real I.D. threat. Don’t expect their strategy to intelligently “evolve” any time soon.

    —-

  8. Honestly, this faffing around the comparisons between the onion and human non coding DNA. Perhaps a little thinking can help.

    The onion is member of the Alium genus, which contains 260-860 distinct species, with most authorities estimating the number to 760. (At least according to Wikipedia) There is a spectacular morphological diversity in this group, which includes onions, shallots, chives, garlic, and plenty of ornamental species also. Although I am not aware of a full-test of cross breeding, this paper shows that a lot of these species can cross breed:

    http://www.springerlink.com/co.....223817k20/

    Now having great morphological variety between species that can cross-breed indicate a compatible genome, where the emphasis is on various of the regulatory mechanisms. We know that at least some of the non-coding DNA has regulatory roles. As far as the morphology is concerned, the Alium genus seems to need a greater library of regulatory functions than humans.

    So, my theory is that the potential for greater morphological variety needs more detailed regulation. Pure ID. From this, one can start to research a) if this theory is true or not, b) if so how does it work exactly.

  9. And of course this evidence shouldn’t be considered in a vacuum. It must be viewed in light of the evidence for and against evolution, intelligent design and theism. So Darwinism would still fail even if the onion had a quintillion base pairs in its genome.

  10. Go do it then.

  11. bbigej:

    “And of course this evidence shouldn’t be considered in a vacuum. It must be viewed in light of the evidence for and against evolution, intelligent design and theism. So Darwinism would still fail even if the onion had a quintillion base pairs in its genome.”
    ====

    I found the first comment by ‘Negative Epiphany’ over at Larry “The Closet IDiot” Moran’s Sandbox blog humorous.

    ‘Negligent Entropy’:

    “Holy crap,

    Two things I didn’t know:

    1. That the C-value paradox was the same as the onion test.

    2. That onions were animals.

    Wow, I learned something new. These IDiots might be on to something … ”
    ====

    Time and again we hear that all lifeforms are cousins. Are not Onions our distant cousins ??? One has to wonder why such a mindless Vegy is so much more well endowed than a far superior human with all manner of intellectual superiority ???

    The “Junk DNA” lable is nothing more than pseudo-intellects not willing to admit to anyone that there are vast numbers of things they are ignorant of when it comes to function, that and the fact that antique Evolutionary vestigial features are forensic evidence of evolution’s past criminal activity. Now the responsible thing to do as opposed to investing in excuses to pimp and justify a worldview, would be to admit that we just don’t know everything about the function of DNA, but we are going to keep on researching forever until we have better understanding and we’ll keep everyone informed as we go along.

    Unfortunately we don’t live in a world that works that way. Hence we have the cowards way out of doing the responsible thing. This arrogant biligerant attitude has infected the thinking of other areas of science. Consider GMO Industrial Agriculture. Disrespecting the Laws of Nature with regards species barriers or boundaries(according to it’s kinds) has brought about an irresponsible technology which is spreading genetic pollution clear across the globe. They don’t know enough about DNA to make some of the disasterous decisions they have made in the pursuit of obscene wealth and power grabbing.

    Take for example the documentary called “A Silent Forest” narrated by a Canadian Geneticist named David Suzuki who hosts a science documentary series called “The Nature of Things” ? He helped put together a documentary called “A Silent Forest”. Below are some YouTube links which carries the entire documentary if you care to watch it. Give yourself some time, as it is about 46.16 mintutes in length.

    http://www.youtube.com/watch?v....._embedded#!

    http://www.youtube.com/watch?v.....re=related

    http://www.youtube.com/watch?v.....re=related

    When you listen to Geneticist David Suzuki explain it, it’s clearly one of the most responsible admissions a scientist could ever make and ALL scientists should have this same attitude. It doesn’t matter if their evolutionists, IDists or creationists – WHOEVER – this same responsible attitude should discipline and guide what science does. Once again, we unfortunately DON’T live in that kind of world. Hence when GMO scientists look at DNA as so much mindless junk for their freewilled right to manipulate, then as evidenced from the natural world today, we have catastrophic environmental ruin.

    And ultimately, this is what this whole debate mess is all about, showing moral respect for Laws and Rules. It’s not about the science. It’s about lifestyle choices and pursuit of self-determination the way any human(individully or as part of a collective) sees fit.

  12. rhampton7:

    The Onion Test is a legitimate dilema for Intelligent Design Theory.

    No, it isn’t. Why would it be? You obviously have no clue about Intelligent Design.

    Since computer programs are a useful analogy, please consider the following:
    What is the probability that (an) intelligent designer(s) would create two programs, the far simpler of the two requiring five times as many lines of code?

    Not even a useful analogy and not even required. ID does NOT exclude Darwinian processes from operating, duh.

    1. There are multiple designers with a wide-range of proficiency at genetic programming.

    ID is OK with multiple designers and Nick, I said so well before RBH.

    2. It’s represents the genetic programming learning curve of the intelligent designer(s)

    Nope, it could be redundancy or even the result of darwinian processes.

    3. Some portion of the genetic programming is non-functional (as in commented-out functions or comments left by one designer intended for another).

    Possible or perhaps some random error got inserted into the design and caused it to happen.

  13. The main point of my article was to demonstrate that Jonathan M doesn’t understand “The Onion Test.” That’s not a big surprise because he is, after all, an IDiot.

    Don’t the rest of you IDiots want to defend Jonathan M by showing that his interpretation of the Onion Test was correct? You could score lots of points for the anti-science crowd by doing this, especially since the inventor of “The Onion Test” (Ryan Gregory) will be reading your comments.

    Give it your best shot.

  14. Larry,

    The argument against junk DNA is against drawing a conclusion from insufficient information. In most cases whether it has function is unknown. We don’t know enough to make the next leap and say that it has no function. For all we do understand, we don’t know enough about how living things function to declare whether certain DNA is necessary or not.

    Perhaps it is all non-functional.
    Perhaps some is.
    Perhaps the excess DNA serves a known purpose less efficiently than in other cases.
    Perhaps is serves an unknown purpose efficiently or inefficiently.
    Perhaps we’re comparing the genome size to the requirements of an onion but the excess DNA serves a purpose unrelated to onions.

    The functions of both DNA and the organisms that use it are not yet such an open book that you or Ryan can confidently rule anything in or out.

    The argument against junk DNA is an argument against drawing conclusions from insufficient information.

  15. 15

    Isn’t the onion test based upon the idea that heritable information exists in the genome? Or shall we equivocate?

    Okay Larry, pull up a chair. Let’s talk about that information.

    Debate me right here right now.

  16. I think I speak for many of the daily lurkers here in saying that I’d love to see said debate.

    Unfortunately, knowing how Larry Moran operates, rather than debate you, he’ll call you a really witty name before scurrying back to the safety of his desolate blog.

    To Larry’s credit, most people his age are in nursing homes. Forget debating; the fact that he even knows how to work a computer is enough of a victory for him.

  17. I would hardly call “IDiot” a witty name. I mean it’s no better than the ultra-obvious: Larry Moron.

  18. “Of course, ID doesn’t have any issue with transposon remnants, Nick. ID certainly doesn’t dispute that systems and machines get messed up, degrade, break down over time.”

    Then ID should stop carping about how junk DNA is a crock and how dumb/mean/ignorant/etc. Darwinists are on this topic.

  19. Oh really, the question is completely up in the air? Then how can Jonathan Wells write a book declare junk DNA “a myth”?

  20. “Junk DNA: A perfectly reasonable idea that might be largely true” just doesn’t have the same ring to it, does it?

  21. 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.

  22. 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.

  23. 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.

  24. 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?

  25. 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!

  26. 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.

  27. 27
    material.infantacy

    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.

  28. 28

    too funny.

  29. 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.

  30. 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.

  31. 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?

  32. 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.

  33. 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.

  34. 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?

  35. 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.

  36. 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.

  37. 37
    material.infantacy

    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.

  38. 38

    Larry,

    Thank you for the response. I will return after a short break to offer a comment.

  39. 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.

  40. 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.

  41. 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.

  42. 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.

  43. 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.

  44. 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.

  45. 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?

  46. Marxist? Really?

    How do marxists like evolutionary biology, as a rule?

  47. 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.

  48. 48

    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.

  49. Kellyhomes, While I believe you make a good point, I just don’t agree. I am somewhat ashamed of myself for allowing this conversation to diverge into something irrelevant to the topic. SOo while I would love to address your points, even though you put an extreme amount of words in my mouth, I don’t feel this is the proper place to do so.

    Getting back on topic though, can someone please address my points and not the education I have.

  50. Kelly, your comparison to physics is deliciously appropriate: the standard model is in a flux. It’s an exciting time. Right now you could have a discussion with your physics professor about results that contradict “fundamental understandings” and unless he was an ideological tyrant he would be overjoyed to debate the possibilities. Oh and Guillermo Gonzales did question certain “fundamental understandings” of astrophysics. . .see his bio to find out the results.

  51. So I’m a little confused by your response Nick. Now I just want to make sure I undersand what you are saying…

    1: there were evolutionists who once rejected the idea of “Junk DNA”(just like Wells does)
    2: now its hard to find a “serious” evolutionist that does reject the idea of “junk DNA”
    3: Being that Molecular biologists don’t have proper training in evolution now-a-days, they are more likely to reject the idea of “junk dna”.

    Do I have this backwords or something for, although it does seem to prove your point, what I conclude is that molecular biolgists say there is “little junk DNA” but in fact they are wrong and we would expect “a lot of junk DNA”.

    I can’t be correct in my analysis here…could you help me please?

  52. 52

    Dr Moran, sorry for the delay. Other responsibilities intervened for a bit.

    Certainly the sequence in DNA is driving reactions. (And there are many varieties)

    In your comments you refer to the use of the term “information” within nucleic sequences as a useful analogy, and you say that there is no expectations that it should “conform to the meanings of “information” in other disciplines.” I certainly agree with you that it conforming to other meanings would be a telling turn of events. And I assume your comment suggests that the nucleotide sequence isn’t expected to share any of the same physical characteristics as other forms of information – given that we live in a physical universe where information has physical effects. Ones which we can observe.

    I think it makes an interesting comparison; the comparison between the physical characteristics of information transfer in the genome, versus information transfer in other forms. Just recently on this forum we were having a conversation about recorded information, and a question arose if a music box cylinder ‘contained information’. Speaking to its physical characteristics, the answer I gave was “yes”. Just like any other form of recorded information, the pins on a music box are an arrangement of matter to act as a representation within a system. No differently than ink on paper, or the state of a microprocessor, or the lines left on a recording tape, or an ant’s pheromones, or the tone of vibrations we make when we speak; they are all matter/energy arranged in order to represent an effect within a system.

    It was also pointed out that a physical arrangement of matter (like the pins on a music box cylinder) cannot by themselves convey information – they require a second coordinated physical object. This second object is easily referred to as a protocol, but physically its is a rule (a protocol) established in a material object. The necessity of this physical protocol is something easily understood; for one thing to represent another thing within a system, it must be separate from it, and if it is truly a separate thing, then there must be something to establish the relationship that exist between the representation and the effect it is to represent (within that system). That is what the second physical object accomplishes, it establishes the relationship between a representation and the effect it represents, which is a relationship that otherwise wouldn’t exist.

    There have been examples of this dynamic given in previous conversations. For instance, an apple is an apple, but the word “apple” is a separate thing altogether. Being a separate thing from the apple, there must be something that establishes the relationship between the two. In the case of the word “apple” we as humans have learned the protocols of our individual languages, and they physically exist as neural patterns within our brains. These neural patterns are material things, and they establish the immaterial relationship between a physical representation and its physical effect. This same dynamic is found in all other cases of recorded information. I have previously used the example of a bee’s dance; a bee dancing in a particular way during flight is a separate thing than having the other bees fly off in a particular direction, and the relationship between the two is brought about by a protocol which physically exist in the sensory system of the bee.

    In the dynamics of information transfer, the operative observation is that each of these physical things (the representations, the protocols, and their resulting effects) always remains discrete. This is one of the key observations that allows information to exist at all. The input of information is always discrete from the output effect, and the protocol that establishes the relationship between the two, remains discrete as well. They are three completely independent physical realities which share a relationship, with the protocol establishing the relationship between the representation and its effect within the system. In no case does the representation (or the protocol) ever become the effect.

    This same dynamic is found in all forms of recorded information; including those used in the information processing systems created by intelligence. As an example, the first automated fabric looms used an arrangement of holes punched into paper cards (which acted as physical representations of the resulting effects within the fabric). Sensors and pins within the machine would sense where the holes were punched, and it would use that information to change and control the colors of threads being woven. In this instance, the configuration of holes served as the representation, and the configuration of sensors served as the protocol, leading to the specified effects. Each of these is physically discrete, while sharing the immaterial relationship established by the protocol.

    So here we have a series of observations regarding the physicality of recorded information which repeat themselves throughout every form – no matter whether that information is bound to humans, or human intelligence, or other living things, or non-living machines. There is a list of physical entailments of recorded information that can therefore be generalized and compiled without regard to the source of the information. In other words, the list is only about the physical entailments of the information, not its source. I am using the word “entailment” in the standard sense – to impose as a necessary result (Merriam-Webster). These physical entailments are a necessary result of the existence of recorded information transfer. And they are observable.

    That list includes the four material observations as discussed in the previous paragraphs: a) the existence of an arrangement of matter acting as a physical representation, b) the existence of an arrangement of matter to establish the relationship between a representation and the effect it represents within a system (the protocol), c) the existence of physical effects being driven by the input of the representations, and d) the dynamic property that they each remain discrete. Observations of systems that satisfy these four requirements confirms the existence of actual (not analogous) information transfer.

    These same entailments are is found in the transfer of information from a nucleic sequence. During protein synthesis a selected sequence of nucleotides are copied, and the representations contained within that copy are fed into a ribosome. The output of that ribosome is a chain of amino acids which will then become the protein being prescribed by the input sequence. The input of information is therefore driving the output production. But the input and the output are physically discrete, as evidenced by the fact that the don’t directly interact, and that the material output is not assembled from the material input.

    The exchange of information (from input to output) is facilitated by a set of special physical objects – the protocols – tRNA and its entourage of aminoacyl synthetase. Acting together they make it possible for the input to alter the output, and they do so by allowing them to remain separate. The tRNA physically bridges the gap between the input and the output, acting as a passive carrier of the physical protocol. It accomplishes this by being charged with the correct amino acid by the synthetases (the only molecules in biology which actually hold the rules to the genetic code). The synthetases accomplish their tasks by being able to physically recognize both the tRNAs and the amino acids. They charge the tRNAs with their correct amino acids before they ever enter the ribosome. The actions of the synthetases are therefore completely isolated from both the input and output. In other words, the only molecules in biology that can set the rule that “this maps to that” are physically isolated from both the input and output, while the input and output remain isolated themselves.

    These observations establish that the entailed objects (and dynamic relationships) exist the same in the translation of genetic information as they do in any other type of recorded information (in every example from human language, to computer and machine code, to a bee’s dance). These observations have been attacked as being as a misuse of the definition of words (a semantic word game, as you call it). But I have already produced the definitions of the words from a standard dictionary; I’ve restated the observations using those definitions in place of the words themselves; and I have asked the question: “If in one instance we have a thing that actually is a symbolic representation, and in another we have something that just acts like a symbolic representation – then someone can surely look at the physical evidence and point to the distinction between the two. There is also the simple fact that there is nothing about the attachment of cytosine to thymine to adenine that intrinsically means “bind leucine to a nearby polypeptide” as an inherent property of its matter. That is a quality beyond its mere materiality, one it takes on by being in a system with the correct protocol to cause that effect from that arrangement of matter.

    There has also been the profoundly illogical objection that because these things follow physical law (and can be understood), they cannot be considered symbols or symbolic representations. Not only does this deny the existence of any symbol in the extreme, it fails for the obvious reason that everything follows physical law. If something can’t be true because it follows the same laws as everything else, then we have entered the Twilight Zone.

    So going back to your comment, a fair reading suggests that the information transfer in the genome shouldn’t be expected to adhere to the qualities of other forms of information transfer. But as it turns out, it faithfully follows the same physical dynamics as any other form of recorded information. As for “disciplines”, you will notice that these observations are very much in the domain of semiotics. Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments makes no reference to a mind. Certainly a living being with a mind can be tied to the observations of information transfer, but so can other living things and non-living machinery. It must be acknowledged, human beings did not invent iterative representative systems, or recorded information. We came along later and discovered they already existed.

    Therefore, the search for an answer to the rise of the recorded information in the genome needs to focus on mechanisms that can give rise to a semiotic state, since that is the way we find it. We need a mechanism that can cause an arrangement of matter to serve as a physical representation. We need a mechanism that can establish within a physical object a relationship between two discrete things. To explain the existence of recorded information, we need a mechanism to satisfy the observed physical consequences of recorded information

    Do you agree, or do you have evidence that attaching adenine to thymine to guanine is mapped to “start a new protein” in any physical context?

  53. @Upright BiPed,

    Sorry, I’m not interested in that kind of “debate.”

  54. ForJah says,

    Do I have this backwords or something for, although it does seem to prove your point, what I conclude is that molecular biolgists say there is “little junk DNA” but in fact they are wrong and we would expect “a lot of junk DNA”.

    Junk DNA is like the Spanish Inquisition, nobody “expected” it.

    The presence of large amounts of junk DNA is incompatible with Darwinism but compatible with modern evolutionary theory. Note that I said “compatible.” Large amounts of junk DNA were not predicted and were not anticipated.

    The presence of large amounts of junk DNA is not proof of evolution and if it turns out that most of the putative junk DNA is functional it will not refute evolution.

    Why do IDiots have such a hard time understanding basic evolution?

    I suppose I shouldn’t be surprised. If you were capable of understanding science you probably wouldn’t be IDiots in the first place.

  55. ForJah says,

    First, I don’t believe Wells thinks that all non-coding DNA was considered junk.

    That’s not the impression he conveys in his book. He never gives a proper scientific definition of “junk DNA.” He constantly uses “non-coding” DNA as a synonym for “junk.” And he “forgets” to mention that we were aware of many functions for non-coding DNA before the discovery of junk.

    He tells his readers about those functions (regulatory sequences, genes for RNA, centromeres) as though they were discoveries that came after the discovery of junk DNA and helped destroy the myth.

    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?

    I said “hardly anyone” because I’m well aware of the quote-mining powers of the IDiots. They can comb through the scientific literature and find the odd example of a scientist who implied that all non-coding DNA was junk. If I had said “nobody” those quotes would have popped up immediately in the comments.

    The quotes do not reflect the huge majority of scientists who were/are well aware of functional non-coding DNA. It’s just another example of how IDiots distort scientific consensus by selective quote-mining.

  56. This isn’t an answer to my question.

  57. So does that mean there were/are scientists who claim all non-coding DNA was or still is junk?

  58. Yes, of course, that’s exactly what I meant.

    IDiot.

  59. 59

    ahem…

    ;)

  60. Larry:

    Are we debating whether your understanding of the Onion Test is correct?

    Go for it

    UBP:

    [long post that has nothing to do with UBPs understanding of the Onion Test]

    Larry:

    @Upright BiPed,

    Sorry, I’m not interested in that kind of “debate.”

    UBP:

    ahem…
    ;)

    UBP, why don’t you want to debate your understanding of the Onion Test with Larry?

  61. 61

    Dr Liddle ,

    You might have noticed in my post where I stated:

    I am concerned with, its physical existence within the medium.

    To which Dr Moran responded with his comments on that subject.

    Are you suggesting that I should be limited in my comments and interests, or are you suggesting that I should be subjected to a test of bona fides on all subject matter in order to comment at all?

  62. Lol, as someone who is just getting used to the name calling tactic of evolutionists…I LOVE IT! haha…it’s like talking with a child. Thank you for finally answering my question and proving my point. I think I’m satisfied with stopping here.

  63. No, I’m suggesting that Larry offered to debate a specific topic and you seemed surprised when he declined to debate a different one.

    But I might come back to your post myself tomorrow. You seem to have laid out your thoughts in a nice essay format.

    Cheers

    Lizzie

  64. Elizabeth, in response to you complaint on the other thread, (paraphrase), ‘If God can do such powerful miracles why does he allow little children to die’:

    Natalie Grant – Held – music
    http://www.youtube.com/watch?v=8GDUBd2eWFw

  65. 65

    Dr Liddle, what is it about the following exchange that causes you to describe it with the word “surprise” and indicates to you in some way that the exchange is illegitimate in some sense. What I am asking – is why do you think Dr Moran needs your assistance in interpreting his exchange?

    BIPED: 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?

    MORAN: The specific order of nucleotides in DNA determines whether certain biochemical activities will occur at that site…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.

    I told Dr Moran upfront that I had a specific interest, he responded to that, and after describing my interest, he commented that he was not interested in the same thing. It seems pointless for you to be going on about it.

  66. Larry,

    ID is not anti-evolution and I would say that any and all regulatory sequences refute the claim that evolution occurs via blind, undirected chemical processes.

    ID claims that evolution occurs (mostly) via directed processes such as those found in targeted searches.

    But then again evotards like you don’t seem to understand anything about Intelligent design.

  67. Geez Kelly, even Richard Dawkins said it would make a difference- he said it would be a totally different type of biology- I would say something similar to the difference between geologists and archaeologists.

  68. ForJah,

    When someone such as Larry attempts to insult and intimidate me, I like to keep in mind that guys like him talk about how evolution works like they’re describing yesterday’s football game, that the thousands of them together with thousands of years of combined research have yet to use any evolutionary mechanisms to explain any evolutionary change greater than bird beaks, lizard heads, and bacteria that eat nylon.

    You can understand it or not, but it’s about as relevant the inner mythology of Harry Potter. Despite being hailed as the cornerstone of biology, it has yet to provide an explanation of anything that isn’t one third imagination and one third
    ‘somehow/something/evidently.’ It is the emperor’s new clothes. Only fools like you can I can’t see them.

    I remind myself of that and it’s like that old public speaking trick – imagining them naked.

  69. Larry Moron: Sorry, I’m not interested in that kind of “debate.”

    Dr. Moron, are you afraid to debate Upright Biped? You seemed so confident at first, yet after UB posted his opening entry, you seem to have gotten cold feet. Are you a coward, as I suspect?

    Also, am I correct in concluding that you are a bio-information denialist, i.e., one who denies that actual information exists in biology? That seems to be par-for-the-course with designophobes. It’s really quite telling.

  70. 70

    Att UD rebel forces:

    I think upright bipeds post should be moved to the reference area (or a version of it). this is a fundamental issue that rarely gets explained/understood in the manner posted @:

    Upright Biped 8.1.2.1.4

  71. Perhaps I wasn’t being very clear when I said …

    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.

    What I should have said was “I’m not going to debate the meaning of information in computer science or any other discipline and whether it applies to the ‘information’ contained in a sequence of nucleotides.”

    There are two reasons for my lack of interest in such a debate.

    1. I don’t think there’s any connection between the colloguial use of the word “information” in genetics and molecular biology and its use in other disciplines.

    2. I don’t know anything about the other disciplines and how they use the word “information.”

  72. Dear Jammer,

    Yes, in a sense I am “afraid” to debate the issue raised by Upright BiPed. When he/she/it said …

    These observations establish that the entailed objects (and dynamic relationships) exist the same in the translation of genetic information as they do in any other type of recorded information (in every example from human language, to computer and machine code, to a bee’s dance).

    … that goes well outside of my area of expertise. I don’t know anything about how the word “information” is used in human language and in computer code.

    I know that most IDiots are expects in almost everything so they are completely fearless about plunging into debates on all kinds of topics.

    Scientists like me, however, are much less intelligent. We tend to be experts on only a few things and we try to avoid pretending otherwise.

    I guess that means I’m a coward.

  73. ScottAndrews said,

    … I like to keep in mind that guys like him talk about how evolution works like they’re describing yesterday’s football game, that the thousands of them together with thousands of years of combined research have yet to use any evolutionary mechanisms to explain any evolutionary change greater than bird beaks, lizard heads, and bacteria that eat nylon.

    Are you saying that evolutionary biologists have never used evolutionary mechanisms to explain the fossil record of, say, chordates?

    Are you saying that they have never constructed phylogenetic trees of chordate proteins, noted that they are basically congruent with the morphological trees and the fossil record, but never offered an explanation based on evolutionary mechanisms?

    Do you actually think about what you’re writing before you click on “Post Comment”?

    Over on my blog I made note of the fact that Intelligent Design Creationists are notoriously deficient in the “explaining” game. They spend most of their time attacking evolution and hardly ever offer their own explanations.

    Here’s your big chance, ScottAndrews, how do you explain the fossil record and molecular phylogeny using Intelligent Design Creationism? You could start by telling me whether you accept the scientific evidence for the age of the Earth and the age of fossils and whether Intelligent Design Creationists have to accept the scientific evidence for common descent.

    I’m betting that you avoid the question. You and your fellow IDiots will probably launch into an attack on interpretations of the fossil record and the failings of molecular evolution.

    That’s why we call you IDiots. You always avoid the tough questions.

  74. Joseph says,

    ID is not anti-evolution …

    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.

    On the other hand, 99.9% of that literature is anti-evolution.

    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.

    Post your results here and then we can decided whether, to a first approximation, Intelligent Design Creationism is anti-evolution.

  75. ForJah, look at my comment #11.1 where I said,
    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.
    Later on I explained why I said “hardly anyone.” It’s because there are some examples in the scientific literature of scientists who said that all non-coding DNA is junk. (They probably just misspoke but that’s not relevant.)

    Then I said (#12.2) …

    The quotes do not reflect the huge majority of scientists who were/are well aware of functional non-coding DNA. It’s just another example of how IDiots distort scientific consensus by selective quote-mining.

    You immediately followed up with what you must have thought was a very important question …

    So does that mean there were/are scientists who claim all non-coding DNA was or still is junk?

    What kind of reply did you expect? When I said “huge majority” did you think I meant “every single scientist, without exception”?

    It was a stupid question.

    IDiot.

  76. Larry,

    Are you saying that they have never constructed phylogenetic trees of chordate proteins, noted that they are basically congruent with the morphological trees and the fossil record, but never offered an explanation based on evolutionary mechanisms?

    No, Larry, what I am saying it what I said, and what I cited.

    Evolutionary theory posits (today or last week at least) that unintentional variations and environmental pressures result in differential selection. Then it happens again. And again. Throw in drift, HGT, and whatever is popular that week.

    Now let me repeat my exact words: The thousands of them together with thousands of years of combined research have yet to use any evolutionary mechanisms to explain any evolutionary change greater than bird beaks, lizard heads, and bacteria that eat nylon.

    Then

    What changes have you explained in those terms – specific mutations, specific selective pressures, drift, HGT?

    You mention construction and comparison of trees as if that were the same thing. They are not, and that is what I am pointing out. How does a tree indicate the something was or was not selected, except tautologically?

    Only the most feeble-minded fool would be distracted from such details by name-calling and attempts to intimidate. I can’t tell whether I’m taking to a professor or a child. It is disgraceful. I wouldn’t let you teach my child arithmetic.

    That being said, my original statement stands. Let’s see if you avoid the tough questions.

    BTW, this is my big chance? Wow, you really are full of yourself.

  77. ScottAndrews says,

    BTW, this is my big chance? Wow, you really are full of yourself.

    Translation: “Intelligent Design Creationism can’t explain the fossil record or phylogenetic trees. I prefer to concentrate on attacking evolution.”

    When that doesn’t work you can always fall back on …

    Only the most feeble-minded fool would be distracted from such details by name-calling and attempts to intimidate. I can’t tell whether I’m taking to a professor or a child. It is disgraceful. I wouldn’t let you teach my child arithmetic.

  78. Larry,

    Natural selection is an integral part of evolutionary theory, unless someone decides tomorrow that it isn’t.

    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.

    Apparently those are the only parts of my post that you didn’t read.

    So I’m wrong. You didn’t run away from the tough question. You just dance in circles around it, waving your spear and chanting your holy incantations to make it disappear.

    Am I really asking you a difficult question? Would you like to refer me to an expert in the field?

  79. 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.

  80. 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!

  81. Hold on Dr. Moran! I can’t believe I didn’t ask you this but how much of Well’s book did you read?

  82. 82

    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.

  83. 83
    material.infantacy

    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.

  84. 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…

  85. 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.

  86. 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.

  87. 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?

  88. 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.

  89. 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.

  90. 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.

  91. 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.

  92. 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…

  93. 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?

  94. 95

    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.

  95. “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’.

  96. 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.

  97. 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’.

  98. 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

    Lizzie

  99. 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.

  100. 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….

  101. 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.

  102. 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.

  103. 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.

  104. 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.

  105. 106

    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.)

  106. 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.

  107. 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 genome

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