Friday, September 14, 2012

Shapiro's and Sternberg's prescient 2005 paper on genome informatics

University of Chicago molecular geneticist James A. Shaprio has a fine essay on the Huff Post Blog on the landmark ENCODE research:

Last week, the ENCODE project (ENCyclopedia Of DnaElements) released a tremendous amount of new information about our genomes. The results of literally hundreds of millions of experiments using the most current "high throughput" technologies provided the data for over a dozen scientific papers in the journals Natureand Genome Research. The conclusions about organization and expression of the human genome were so significant that they were the topic of a front-page story in The New York Times.

The massive collaborative project examined how our genomes are copied into RNA, interact with regulatory proteins, and are compacted in chromatin, which organizes the genome for cellular differentiation. ENCODE examined DNA from dozens of cell types to find out if the results changed in specific ways from one kind of cell to another. Cell type specificity provides a strong indication that the data are biologically relevant.

ENCODE described their most striking finding as follows:

"One of the more remarkable findings described in the consortium's 'entrée' paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'. The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA's transcription into RNA is initiated) and numerous previously overlooked regions that encode RNA transcripts that are not translated into proteins but might have regulatory roles. Of note, these results show that many DNA variants previously correlated with certain diseases lie within or very near non-coding functional DNA elements, providing new leads for linking genetic variation and disease."

In other words, the old idea of the genome as a string of genes interspersed with unimportant noncoding DNA is no longer tenable. Many eminent scientists had opined that the noncoding DNA, much of it repeated at many different locations, is nothing more than "junk DNA." ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information.
Shapiro goes on to describe a prescient paper that he and Rick von Sternberg published in 2005 about the functionality of supposedly "junk" DNA repetitive segments.

He quotes from the abstract of their paper:


"ABSTRACT: There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist ' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component."
Shapiro observes:
Although we could not predict in detail all the ways repeated DNA would serve genome functions, I think our statements stand up well in light of the recent data. Without knowing the specifics, we were correct in asserting that the genome had to be highly formatted to serve as the marvelous information organelle it is in every living cell and organism.

It's worth noting that Shapiro's co-author on the ENCODE-vindicated 2005 paper-- Rick von Sternberg-- is the intelligent design scientist who was hounded out of the Smithsonian Institute because he published, in his capacity as a journal editor, a review article by Stephen Meyer of the Discovery Institute on the origin of biological information.

In October of 2006 the U.S. House of Representatives Committee on Government Reform released their investigation of the harassment of Sternberg. The report was titled:

"Intolerance and the Politicization of Science at the Smithsonian: Smithsonian's Top Officials Permit the Demotion and Harassment of Scientist Skeptical of Darwinian Evolution"
Seven years after the harassment and demotion of Sternberg, Shapiro and Sternberg's design-oriented approach to molecular genetics-- in Shapiro's words:

... [t]hinking of the genome informatically and of mobile DNA as a potent force for genome organization...


-- has been elegantly vindicated, and Darwinian junk-science so decisively repudiated, in the ENCODE research.

There's a satisfying irony that a notable example of the prescient science vindicated in the ENCODE research was written by a scientist who the Darwinists tried so fervently to destroy.

Darwinists understood the work Rick Sternberg was doing.

It's not a stretch to suggest that Nature's and two other first-rank journals' unapologetic publication of the 30 articles by 400 leading molecular geneticists that has left the Darwinian junk-DNA hypothesis in shambles is a not-so-subtle repudiation of the Darwinist Iron Curtain behind which so many scientists have worked for so many years.

The message running through all of the ENCODE publications is this: Enough with ideological purity. Let's stick to science, and follow the evidence where it leads.


22 comments:

  1. Rick von Sternberg-- is the intelligent design scientist who was hounded out of the Smithsonian Institute

    A lie, of course! (Not to mention the fact that Egnor seems to think it is called the "Smithsonian Institute"!)

    But pathological liars have to lie - it's just in their nature.

    ReplyDelete
    Replies
    1. "Expelled Exposed" Exposed - N.C.S.E. Exposed: No Victim Blaming Allowed

      So, who are we to side with here: A fact-filled government investigation which says that Sternberg was harassed, or the claims of an anonymous ideologue or questionable morals who says that he was not?

      Tough decision. ;)

      Delete
    2. You could always side with the government investigation's own appendix, which actually contradicts everything in the report itself.

      Delete
    3. A fact-filled government investigation

      1. It wasn't a government investigation. It was an investigation by the staff of a member of Congress.

      2. The documents in the appendix contradict everything in the report that Sounder's staff generated.

      3. The report was so badly written and diveroced from reality that the Congressional committee that Souder chaired rejected it out of hand. It was never adopted by any government organization.

      Delete
  2. @anon:

    And the U.S. House of Representatives Committee on Government Reform investigation reached conclusions that were lies, too? [http://www.discovery.org/a/3833]

    What part of the House Committee report was a lie?

    ReplyDelete
    Replies
    1. Michael,

      It wasn't a report of a House Committee. It was an unofficial report of one member which wasn't read into the official records.

      Delete
    2. And the U.S. House of Representatives Committee on Government Reform investigation reached conclusions that were lies, too?

      Citing the report of a single member's staff that was rejected by the Committee that was controlled by his own party as that Committee's "conclusions" is itself a lie. You just can't seem to help lying about things, can you?

      In any event, the report has no credibility, as its text is contradicted by the supporting documents that accompany it. In short, yes, the report is a lie. But, no, it wasn't a report put out by the Committee on Government Reform.

      Sternberg's claims are lies. Your claims are lies. The documents show this. You just think that if you keep telling the same lie over and over again it will somehow become true. But it won't. All your lying will do is demonstrate that you are, in fact, a liar.

      Delete
  3. Michael,

    There's a persistent problem with the 'spam filter'. Comments which pass the filter stay visible for only a short time before disappearing. I wonder what the problem is ...?

    ReplyDelete
    Replies
    1. bach:

      You're right. I found 3 of yours in the filter. I'm not sure what to do about it. I'll see if I can disable the filter. We get very little actual spam.

      Sorry for the inconvenience.

      Delete
  4. The subject is too interesting, thanks for sharing

    ReplyDelete
  5. Michael,

    You seem to have dropped the non-issue of junk DNA to move onto another non-issue. Science evolves. The consensus as to what is probably true evolves over time. Mavericks with radical hypotheses have to make a case to convince other scientists. Although usually they turn out to be wrong and we remember only the successful paradigm changing scientists.

    Sternberg wasn't persecuted. He had an unpaid position which gave him access to the collections of the institute. It was subsequently lengthened by 3 years. His editorship of 'Proceedings of the Biological Society of Washington' was a time limited one due to run out with the next issue.

    Stephen Meyer's review article wasn't appropriate for the journal, which deals with taxonomy. It was also a lame dishonest review (unfortunately I've read it). In one section he discusses what he thinks a Japanese geneticist lists as necessary genes for Cambrian species, and claims that they must have been pre-loaded (a favorite term for ID proponents) and then many (many many) pages later in an endnote actually writes what his source actually did write. Which was completely different.

    Dishonest. Similar to what he did in his film 'Darwin's Dilemma' where he shows the Cambrian fossil beds in northwestern Canada, the fossil beds in China and an oil exploration drilling ship in the Pacific Ocean between the two and asking, why haven't Cambrian fossils been found in the Pacific sediments?. Without revealing the answer.

    Because Stephen Meyer is either an idiot or a dishonest liar. Take your pick. The Pacific Ocean didn't exist during the Cambrian 540 million years ago. No current ocean is older than about 200 million years. Stephen Meyer should have known this. After all, he did get a BSc (his highest science degree) in Earth Sciences.

    Michael,

    You still haven't defined what percentage would be the vanishingly small amount of junk DNA in the human genome. 1%? 5%?

    And you still haven't explained why the many thousands of broken genes in the human genome aren't a problem for ID.

    ReplyDelete
    Replies
    1. Let's take a look at bachfiend's latest fib for Darwin:

      ────────────────────────
      bachfiend wrote: Stephen Meyer's review article wasn't appropriate for the journal, which deals with taxonomy. It was also a lame dishonest review (unfortunately I've read it)
      ────────────────────────

      The three referees who peer-reviewed the article for the Proceedings of the Biological Society of Washington -- you know, the people whose opinions actually matter -- disagreed, as they all three recommended it be published.

      "I have seen the review file and comments from 3 reviewers on the Meyer paper. All three with some differences among the comments recommended or suggested publication. I was surprised but concluded that there was not inappropriate behavior vs a vis the review process."
      --Dr. Roy McDiarmid, president of the Biological Society of Washington

      Furthermore, Sternberg shows that the journal covers a fairly wide range of subjects by citing both its self-description, which proudly illustrates this fact, and articles previously published in the journal.

      Your claim fails, bachfiend. Now, do us all a favor and quit lying before I call your mother and tell her how you're behaving on the Internet.

      Delete
    2. Jared,

      I'm not lying. And a lot of luck contacting my mother. She's been dead for 15 years.

      I've Read Meyer's review article. It was pathetic and dishonest. Have you read it?

      I don't take notice of Sternberg's self serving justification. Have you got anything independent?

      Delete
  6. There was no official report by the "U.S. House of Representatives Committee on Government Reform ". Instead, there was a report by staff of the committee to Mark Souder. You know, the lying, hypocritical, creationist weasel ex-Representative Mark Souder?

    Which part of the report was a lie? Nearly everything.

    A pathological liar always needs to buttress his initial lies with other lies.

    ReplyDelete
    Replies
    1. Get with the times, kiddo. Pseudoskeptic Mike Shermer's dishonest rant was refuted almost immediately after he posted it.

      CSC - Michael Shermer's Fact-Free Attack on 'Expelled' Exposes Intolerance of Darwinists towards Pro-Intelligent Design Scientists

      The whole article is an absolute gem, however, this segment was my personal favorite:

      ────────────────────────
      Shermer's method of dealing with these persecution instances is as follows:

      (1) Ignore all the facts showing there was persecution;

      (2) E-mail the persecutor and ask them if there was any anti-ID discrimination;

      (3) Withhold all skepticism from the statements of the persecutors, and then trumpet their response as evidence that there is no persecution against ID proponents, blaming the victim for losing their job and then claiming those who feel there is persecution are just promoting a "conspiracy."

      Shermer's record of consistently taking the side of the persecutors shows that he is part of the problem and is in no way an objective source to analyze this subject. For example, Shermer implies that Richard Sternberg's credibility is diminished because he's a fellow of the International Society for Complexity Information, and Design or because he "is a signatory of the Discovery Institute's '100 Scientists who Doubt Darwinism' statement." (By the way, it's over 700 scientists now, Dr. Shermer.) This shows that Shermer himself could be a potential persecutor of Darwin skeptics, for he isn't interested in giving Darwin-skeptics equal treatment.

      ────────────────────────

      Michael Shermer's claims that Sternberg wasn't harassed hold about as much water as a murder suspect's claims that he's innocent. His acceptance of anything pro-Darwin and anti-I.D. with nary an ounce of critical thought involved refutes his claims of being a skeptic.

      Point blank: Michael Shermer is a proven liar, and exactly the type of dogmatic ideologue who brings about the type of persecution that Dr. Sternberg faced.

      Forget about Shermer. Members of the U.S. government have spoken, and they've concluded that harassment did, in fact, take place, and they support their conclusion with mountains of evidence -- something Shermer's article is entirely lacking in.

      Delete
    2. Shermer had little to do with the article I linked to, which was written by Ed Brayton.

      And of course Brayton presents multiple pieces of evidence refuting the Sternberg claims, not one of which you actually address.

      Members of the U.S. government have spoken

      Sieg Heil! Spoken like a good little Nazi.

      Delete
    3. Members of the U.S. government have spoken, and they've concluded that harassment did, in fact, take place, and they support their conclusion with mountains of evidence -- something Shermer's article is entirely lacking in.

      You need to do some serious fact checking yourself. The "report" you cite is not actually a report by the U.S. government. The title of the article you linked to dishonestly tries to imply that it is, but it was not a U.S. Congressional Committee report. It was a staff report prepared by Souder's staff. It was rejected by the committee, a committee that chairman of no less.

      The "mountains of evidence" show no evidence of persecution. Sternberg kept his position. Sternberg was treated similarly to other individuals in his position. The Department head offered to sponsor Sternberg himself. The "report" is as divorced from the evidence as it is possible to be. One has to wonder why Souder's staff thought a report that was so clearly undermined by the backing documents would pass muster with anyone.

      Oh wait, there's people like you, who didn't bother to check the supporting documents.

      Delete
    4. International Society for Complexity Information, and Design or because he "is a signatory of the Discovery Institute's '100 Scientists who Doubt Darwinism' statement." (By the way, it's over 700 scientists now, Dr. Shermer.)

      well, except that most of the signatories aren't actual scientists. The list contains more mathematicians, computer engineers, and electrical engineers than actual scientists. The "Scientists who Doubt Darwinism" list is a dishonest piece of propaganda.

      Not only that, once you drill down to the actual scientists, a decent chunk of them don't want to be on the list, feel they were deceptively included, and are angry about their continued inclusion.

      Delete
  7. These debates get stupid in a hurry.

    JQ

    ReplyDelete
  8. Someone essentially help to make significantly articles I would state. That is the first time I frequented your web page and to this point? I amazed with the analysis you made to make this actual publish incredible. Great job!

    ReplyDelete
  9. Why is the whole comment thread just talking about whether Sternberg was discriminated against or not? I would have figured that the validation of ID theory about the usefulness of 'junk DNA' (which anyone could have seen coming), and perhaps the reliability of orthodox predictions about genetic theory, was of more note here.

    But since an excuse has been furnished: It sounds like kids at school. All the documentation I read on the email back and forth clearly showed a well-understood and not all that amazing disdain/distaste for the invasion of non-evolutionary suppositions in their territory, in which the carrier of supposed suppositions was thus regarded as an infectious agent that needed to be excised carefully or quarantined.

    They honestly believe 'science' is under threat (rather than just a materialistic paradigm), so you could almost forgive them, if our hearts didn't have a tendency to bleed for the nerds that get picked on. And the fact that most of them were ragingly unlikeable.

    Fact is, they discriminated, on religious grounds. They may not have been able to help it, they might have done their best not to get done in by it, they may have thought they had pure motives, but it did motivate exclusionary tactics. Whether or not it's a big deal is arguable (depends on how much you care about a single person, but obviously he's gonna care), but it's still a fact that it was against those wonderful qualities of fair-play that Americans love to bring up at social events. These dudes skipped out only by a technicality of affiliation.

    Hunh, guess Sternberg is basically all there is to talk about. Since the only thing to say about the article is that 'evolution sucks, ID rules, in your face douchebags!'. Which we all knew anyway, obviously (but privately, because I would never be so crass as to post a comment to that effect... o.O).

    Ummm... I predicted the appendix would be useful when I was a wee lad, do I get first dibs for credit on that one? (Because obviously it never occurred to the other 6.5 billion people at the time) :P

    ReplyDelete
  10. I would have figured that the validation of ID theory about the usefulness of 'junk DNA'

    Except it isn't, and that claim has been pretty handily disposed of. In a year or two, you IDers will be desperately trying to explain away the ENCODE data, since it doesn't support your claims at all.

    ReplyDelete