Monday, November 5, 2012

Darwinist Larry Moran: "[ENCODE] is going to make my life very complicated."



Darwinist biochemist Larry Moran is panicked. The recent publication in Nature and several other science journals of 30 papers by the ENCODE project that demonstrate that at least 80% of the human genome has biochemical function is a catastrophe for Darwinists like Moran and others who have misrepresented science in service of their personal ideology.

Moran is an atheist, and accordingly he restricts his science to materialist interpretations. The junk DNA fiasco is a direct consequence of forcing materialist interpretations on science.

The discovery in the 1970's that much of the genome contains DNA that does not code for proteins could be interpreted in two basic ways. Either the DNA had function, yet to be discovered, or the DNA was "junk", left over from eons of evolution in which random mutations that did not have phenotypic expression accumulated in the genome, like dust in an unswept room.

Scientists who did not restrict their inferences to materialist inferences-- such as scientists who accept intelligent design or at least do not rule out intelligent agency in nature-- generally inferred that the "junk" DNA in fact had function, which was yet to be discovered. They predicted that the genome would be found to be an elegant highly integrated system of gene expression and regulation, not a trash can for genetic garbage.

Darwinists and materialists predicted that the DNA without apparent function indeed was without function, and that it was in fact a physical manifestation of the "randomness" that underlies all of biological change, as understood in the materialist paradigm.

Over the past several years, evidence has accumulated that has tended to support the ID view of junk DNA.

Now the publication of 30 papers in three leading journals demolishes the Darwinist/materialist prediction, and as you can imagine, the folks who guard the materialist inference in science are in a lather.

Moran in particular is apoplectic. He denies the findings of the ENCODE consortium:

... All of this evidence indicates that most of our genome is junk. This conclusion is consistent with what we know about evolution...

Contra Moran, the lead scientist on the project, Ewan Birney, explains the conclusion that 80% of the human genome is functional:

we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.
We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity. [emphasis mine]

Moran has threatened the ENCODE scientists on the project with thinly-veiled retribution, and has fixated on his obsession with the term "functional" used by the ENCODE scientists to describe the findings in their data. Moran's obsession with the term function is a distraction. Any biological function "alive with activity" is evidence that it is not "dead wood". And that is clear evidence against the Darwinist prediction.


Moran is candid at least. He pulls no punches. He has advocated the targeted academic destruction of students and scientists who do not share his atheist beliefs, and he threatened the ENCODE scientists with thinly-veiled retribution:

I reserve my harshest criticism for the scientists, especially Ewan Birney who is the lead analysis coordinator for the project and who has taken on the role as spokesperson for the consortium. Unless other members of the consortium speak out, I'll assume they agree with Ewan Birney. They bear the same responsibility for what has happened.

Now he admits (about the ENCODE breakthrough):

"This is going to make my life very complicated"

Damn right, Larry. Let me add this: those of us who have been appalled for years by your ideologically-skewed junk science and your public threats against Christian students and scientists are going to make this remarkable scientific breakthrough as complicated for you as possible. 

30 comments:

  1. Michael,

    You are an absolute idiot. Larry Moran's blogs on 'junk' DNA are absolutely correct and measured.

    His comment that you started your thread; ' [ENCODE] is going to make my life very difficult' is inaccurate and taken out of context. You've used the double inverted commas, which according to your previous bizarre claim means that it's a direct quote, not a paraphrase (which you've claimed is indicated by single inverted commas - claimed by you to be the American convention).

    His thread to which you've linked with the quote 'This is going to make my life very complicated' was actually a quote of what Larry Moran had previously written, on September 5, discussing what Ed Yong, a science writer had written about ENCODE, quoting what Tom Gingaras, one of the study's scientists, had said 'Almost every nucleotide is associated with a function of some sort or another'.

    Moran was annoyed that science writers didn't know enough to ask the right questions. 50% defective transposons. 2% pseudogenes for starters - and allows 'almost every nucleotide' go through unchallenged.

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    1. Michael,

      You've previously claimed that almost all of the human genome will be shown to have a function, presumably because God wouldn't put useless DNA into the genome. What percentage of useless DNA would you expect to be the maximum? I've asked you this question before, but you've refused to answer it.

      Doesn't the thousands of broken genes - pseudogenes - worry you, if you're insisting that all the human genome is functional? There are about the same number of broken genes as there are functioning genes in the human genome, including about half of the 1000 or so olfactory receptor genes all mammals have (in whales they're all broken).

      How do you explain the wide variation in genome size across species, including the marbled lungfish which has a genome of 130 billion base pairs (cf humans' 3 billion base pairs).

      And anyway, 'junk' DNA wasn't a prediction of Darwinism. Nor was its absence a prediction of Paleyism. In the early days of genetics, it was assumed that DNA was actually compact, with little waste areas - actually rather like the genomes of bacteria - and when it was found not to be the case, apparently, it was thought that having excess DNA wasn't that much of a handicap, so it was tolerated.

      That said 'junk' DNA is still a robust hypothesis. Much of the human genome is still without function and could be deleted without harm.

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  2. The 80% number was a publicity stunt meant to get the paper into Nature and to attract the press. That is a charitable interpretation.

    Here is what reputable scientists are saying about this brouhaha. Ed Yong at Discover Magazine has a nice roundup.

    Indeed, to many scientists, these are the questions that matter, and ones that ENCODE has dodged through a liberal definition of “functional”. That, say the critics, critically weakens its claims of having found a genome rife with activity. Most of the ENCODE’s “functional elements” are little more than sequences being transcribed to RNA, with little heed to their physiological or evolutionary importance. These include repetitive remains of genetic parasites that have copied themselves ad infinitum, the corpses of dead and once-useful genes, and more.

    To include all such sequences within the bracket of “functional” sets a very low bar. Michael Eisen from the Howard Hughes Medical Institute said that ENCODE’s definition as a “meaningless measure of functional significance” and Leonid Kruglyak from Princeton University noted that it’s “barely more interesting” than saying that a sequence gets copied (which all of them are). To put it more simply: our genomic city’s got lots of new players in it, but they may largely be bums.


    So, tell us, guys, what was God's purpose in creating these "bums"? The answer is, of course, you don't know and, furthermore, don't care. You are just certain that they were designed. That sums up ID nicely, doesn't it?

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  3. It will be quite amusing in a year or two to watch Egnor and all his DI buddies desperately trying to explain away the ENCODE data when it has becomes painfully obvious even to them that it doesn't support their precious fantasies.

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  4. Seems Dr Moran is not alone in his denial.

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    1. Transcription is not what the ID movement means by "functional." Once you understand that, you understand that junk DNA is still very much alive and well.

      And that's not even getting in to the fact that there is nothing in ID which predicts the lack of junk DNA. ID posits an unknown designer using unknown methods for unknown purposes. Junk DNA is perfectly compatible with the ID assertion. Junk DNA could be a byproduct of the designer's designs, or could be a way for the designer to amuse itself, or any number of other reasons.

      Boo

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    2. Boo,

      You seem to miss the point, just as the others have. This is not a proof of ID or any other theory / idea. Some would say ID predicted this, but that is hardly a proof in itself.
      Rather, this is a blow to the people who have been attempting to prove their own historical science via the 'junk dna' hypothesis.
      I do not see a proof, I see a DISPROOF.
      This does not mean the ID people or creationists are proven correct, it just means that the mouthpieces of the Darwinian and Atheist movements have been grossly incorrect in their assumptions on the SCIENCE of the matter.
      It means the ID prediction was closer than the Darwinian prediction.
      Spin it all you want - 'thems the breaks'.
      Boo hoo?

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    3. crusader,

      Could you be a little bit more specific and state what exactly that "Darwinian prediction" was? I have a nagging feeling that you simply don't know what you are talking about.

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    4. I agree with crus. The ENCODE data doesn't "disprove" or "prove" anything. We ID folks are more modest and responsible than that.

      What ENCODE does is three things:

      1) It debunks a major prediction of Darwinism-- junk DNA was used as evidence for Darwinism for decades. So sorry...

      2) It is evidence that many mainstream scientists are willing to defy Darwinian orthodoxy. The Darwinist censors are pissed about this (eg Moran). The ENCODE scientists-- the best in their field-- just gave the Darwinists the middle finger. They're not going to lie for them anymore.

      3) The junk DNA hypothesis impeded molecular genetic research for decades. Darwinism was a major science-stopper.

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    5. Anon,
      We ALL now have a nagging feeling the arch bishops of nihilism simply don't know what they're are talking about.
      The prediction was junk DNA makes up most of our genome. They were incorrect.
      The genetic 'archaeology' that is the ENCODE project has proved the Darwinian version incorrect - while hinting at some sort of essential function for this 'junk'.
      Again, that does not prove anything, but it does DISPROVE something: Junk DNA was a lousy argument.
      Further it proves the 'censors' (as Dr Egnor calls them) are more interested in preserving their intellectual dogma than looking for real answers.
      That will have to suffice, as that is all there is!

      If you want a more detailed polemic from someone in the field of hard sciences, simply reread the Doctor's post and his above response.

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    6. Before spewing this nonsense, the two of you should read Ohno's original paper, So much "junk" DNA in our genome.

      And crus, ENCODE findings don't hint "at some sort of essential function." They found that DNA elements are transcribed, but most of them don't have any useful function. In fact, we know for certain that certain portions of the DNA are senseless repeats and also that a substantial portion of the DNA can be removed without causing any problems for the organisms.

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    7. If you want a more detailed polemic from someone in the field of hard sciences, simply reread the Doctor's post and his above response.

      So now Egnor is in the field of hard sciences, huh?

      Egnor may know a thing or two about hydrocephalus but he knows diddly squat about the fields he likes to criticize because they offend his childish beliefs in fairy tales: evolutionary biology and climate science.

      I bet he (and you for that matter) hasn't read a single one of the Encode papers, nor the Ohno paper. If you had, and if you understood them, you would realize that Moran's critique is spot on. The human genome is riddled with junk.

      If you understood something about transposons and different levels of selection, it would be easy to see why transposons can multiply and clutter genomes, especially in species with relatively small effective population sizes. See Michael Lynch' excellent book "The Origins of Genome Architecture" if you're really interested - but I know you aren't since you only read what you expect to reinforce your beliefs.





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    8. Anon,
      I will read the paper this afternoon when I get a few minutes free.

      Troy,
      Once something meaningful is posted, I will respond.
      So far.....
      Accusations of stupidity, dishonesty and invective?
      Sorry, too busy today.

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  5. CrusadeREX- Junk DNA that is transcribed is still junk. The prediction was not disproven. Sorry, I have nothing to cry about. Read the actual paper. I double dog dare you.

    Boo

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    1. I will, no worries there.
      I am having lunch right now. I will get at it when I get home.

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    2. Okay so I have read the paper.
      What exactly was I supposed to take away from it?
      Here is what I got: If we assume the 'junk' DNA is what the author assumes it is (he is an expert, after all) then it is far more likely for the genome to degenerate (devolve) than it would be for it to mutate in a positive way thus creating a new species or whatever.
      Further this argument seems to suggest that the 'junk' is important for 'doing nothing'. A kind of space holder for new genes that may be required by the teleological force of evolution. It KNOWS it needs more space, because it.... well because it does.
      Fascinating stuff, but I wonder if the scientist's déformation professionnelle prevents him from seeing the implications of some of his assumptions? Or if he simply prefers to leave that to the philosophers?
      I don't see any refutation of the ENCODE data, or anything that counters Dr Egnor's argument.
      Perhaps I am missing something?

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  6. The mapping of the human genome is similar to the memory dump of a computer program. Biologists, who are not trained in Information Technologies, could recognize some of the code, the portion that produces proteins, but the rest, because they could not see any usefulness to it, they labeled as junk.

    This is like looking at the memory dump of Microsoft's Words program. If you don't know any better, you will be able to recognize some letters and digits, the stuff you have typed and the program's help statements, but the rest will look like garbage to you and you will say it's junk. Evidently, you would be seriously mistaken.

    This is exactly what Darwinists have done with the human genome!

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    1. Pépé,
      Well put, mate.
      Let's hope that now they have released the ENCODE data that some of the more open minded scientists can try to understand the function and relation of the 'junk'.

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    2. Pepe- just saying all that doesn't actually make it true. We already know what a lot of junk DNA is, and it is in fact junk. ERV fragments are junk. Psuedogenes are junk. The telomeres in the center of the human chromosome #2, leftover from when two seperate chromosomes fused in our primate ancestors, are junk. I'm sure people who know the science better than I do could come up with more examples.

      Boo

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    3. Boo,

      The genome has the job of making a full organism from a zygote. It would be a "miracle" if junk could do that!

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    4. The junk doesn't do that. That's why it's junk.

      Boo

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  7. I'm so happy I live in a country where nobody cares about creationism (sorry, "intelligent design").

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    1. How is Pyongyang this time of year?
      LOL

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    2. I live 9000 km from Pyongyang. Try again.
      LOL

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  8. Michael,

    You still refuse to 'predict' the maximum amount of non-functional DNA in the human genome that's consistent with your assertion that almost all of the human genome has a function.

    As an aside, there's an iPad app for ENCODE. Just go to the Apps store, and type encode nature into the search box. It includes a lot of discussion from the authors, and no, 'Paleyism' (sorry Intelligent Design) isn't mentioned at all, although 'evolution' is mentioned often.

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    1. Bach,
      You know as well as I that Paleyism and Darwinism are both evolutionary theories. They simply draw different conclusions in terms of WHY. Paleyism admits there must be a WHY (and validates inquiry) and Darwinism relies on purely random forces and proposes a scientific foundation for nihilism. It is a philosophical argument using historical data in scientific drag.
      We both KNOW that, even if we don't both acknowledged it.
      Evolution is a term used by BOTH sides. It is a latin based word meaning the unfolding. It was used in the medical field LONG before it was co-opted by the Darwinian sects.

      Any mention of Darwinism or the lack of meaning to the universe in your APP?
      Maybe it was written by a new age advocate of galactic pan-spermia, for all we know?

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    2. CrusadeRex,

      I'm still waiting for a response from Michael. If you have an iPad, then you can look at the ENCODE app for yourself and make up your own mind.

      Criticism of evolution is a bit much, coming from a creationist. Intelligent Design could be anything. The ID film 'Darwin's Dilemma' (about the Cambrian 'explosion' - actually radiation - 540 MYA) was produced by Paul Nelson (a YEC - how's that for cognitive dissonance?) and Stephen Meyers.

      You're an idiot. Paley didn't propose an evolutionary theory. 'Natural Theology' was published in 1802. At that time, it was assumed that no species had gone extinct. Fossils of animals not known to exist in living form indicated that they were still alive in unexplored regions. For example, one of Clarke and Lewis' assignments was to look for living mastodons in the course of their explorations. It was all based on the erroneous idea that 'God wouldn't allow species he created to go extinct' (I'm actually quoting myself).

      And Darwinism is science. Evidence based.

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  9. This is really funny stuff. We can now add junk DNA to the long and ever-growing list of things that Egnor thinks he understands but doesn't: constitutional interpretation, quantum physics, separation of church and state, evolution, ...

    How did hel ever become a brain surgeon? I wouldn't trust him anywhere near me with a scalpel.

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