Thursday, September 20, 2012

Are All IDiots Irony Deficient?

As I'm sure you can imagine, the Intelligent Design Creationists are delighted with the ENCODE publicity. This is a case where some expert scientists support one of their pet beliefs; namely, that there's no such thing as junk DNA. The IDiots tend not to talk about other expert evolutionary biologists who disagree with them—those experts are biased Darwinists or are part of a vast conspiracy to mislead the public.

You might think that distinguishing between these two types of expert scientists would be a real challenge and you would be right. Let's watch how David Klinghoffer manoeuvres through this logical minefield at: ENCODE Results Separate Science Advocates from Propagandists. He begins with ....
"I must say," observes an email correspondent of ours, who is also a biologist, "I'm getting a kick out of watching evolutionary biologists attack molecular biologists for 'hyping' the ENCODE results."

True, and equally enjoyable -- in the sense of confirming something you strongly suspected already -- is seeing the way the ENCODE news has drawn a bright line between voices in the science world that care about science and those that are more focussed on the politics of science, even as they profess otherwise.
Okay, you can see where this is headed. There are two type of scientists: those who focus on real science and those who let their biases interfere with real science. You can imagine which ones the IDiots think are on which side of the ENCODE/junk DNA publicity fiasco.

Still, it might be interesting to see which examples he chooses.
An article in Science by Elizabeth Pennisi offers an illustration of the former -- science writing that's about science -- pulling no punches and offering no apology for making it unambiguous how big the ENCODE results really are.
Interesting choice. Elizabeth Pennisi is a Staff Writer for Science magazine. She has an undergraduate degree in biology and a Masters degree in science writing. Her article in Science [ENCODE Project Writes Eulogy for Junk DNA] is a classic example of something Chris DiCarlo covered in our class yesterday. It's called ""confirmation bias." In this case, Pennisi has long been troubled by the fact that humans don't seem to be very special compared to other species and she has written extensively about the mysterious "dark matter" in our genome. She ignores all of the evidence that we really do have only 25,000 genes and that most of our genome is junk. Instead, she writes major stories about those studies that claim to have discovered functions for all that junk. I discussed this in: Science Writes Eulogy for Junk DNA.

Creationists in general, and Intelligent Design Creationists in particular, are classic examples of confirmation bias in action. As Klinghoffer says above, "confirming something you strongly suspected already" is "enjoyable."

When's the last time you've seen a creationist fairly discuss both sides of a genuine scientific controversy?

Returning to the main point, who does Klinghoffer choose to represent the other side of his false dichotomy (science advocates and propagandists)?
Get that? It's the "death knell" of junk DNA. The title of the article, "ENCODE Project Writes Eulogy for Junk DNA," is not one bit less forthright than the title of our own Jonathan Wells's Myth of Junk DNA, which (prophetically) appeared in print more than a year before the ENCODE "flotilla" of articles (as another biologist friend aptly puts it) did.

...

Now compare that to a writeup for Scientific American, which focuses almost exclusively on the political management of the ENCODE crisis. Of top importance: not the science, but the dread that somehow this will grant a victory to the bogeymen, "creationists."

Under the title "Junk DNA, Junky PR," Athena Andreadis complains: ...
Isn't that interesting? Athena Andreadis is a practicing scientist, a professor in the Department of Cell and Developmental Biology at the University of Massachusetts Medical School whose lab works on the expression of human genes.1 Her article in Scientific American points out why the story put out by the ENCODE consortium is misleading [Junk DNA, Junky PR] and she supports it with actual scientific evidence for junk DNA—something that Elizabeth Pennisi didn't do. (I don't think Athena Andreadis got everything right as I discuss in: Athena Andreadis Writes for Scientific American: Junk DNA, Junky PR.)

Andreadis explains why the ENCODE consortium got it wrong and what their motives might be. She concludes that the ENCODE workers are guilty of "hype" in order to promote their work and garner maximum fame and glory for what turns out to be just a lot of boring data. She is correct. Lot's of scientists who work in this field agree with her.

Klinghoffer concludes, ....
Yet writing for Science, and having nothing to say about the PR implications but simply sticking to the science, Pennisi leaves you in no doubt that a once precious myth has, indeed, passed into oblivion. Just, I emphasize, as Discovery Institute's Jonathan Wells said more than a year ago.

So, one writer who seems to have missed her calling as a public-relations specialist says one thing. Another writer who appears wholly uninterested in PR says another. Who are you going to believe?
Not much of a choice as far as I'm concerned. On the one hand you have a scientist who discusses both sides of this scientific controversy and presents evidence on both sides. She concludes that the controversy is still alive.

On the other hand, you have a science writer with an obvious bias who completely ignores the scientific controversy and piles on the hype in support of the ENCODE publicity campaign.

Let's remind ourselves how Klnighoffer started his post.
True, and equally enjoyable -- in the sense of confirming something you strongly suspected already -- is seeing the way the ENCODE news has drawn a bright line between voices in the science world that care about science and those that are more focussed on the politics of science, even as they profess otherwise.
The voice that "cares about science" is a science writer for Science and the voice that's focused on the "politics of science" is the practicing molecular biologist who presents both sides of the controversy.

Keep in mind that the author of this post on Evolution News & Views is David Klinghoffer, a writer who presumably is completely innocent of any charge of bias, especially confirmation bias.

Can anyone answer the question in the title?


1. Andreadis is a molecular biologist. The criticisms of the ENCODE consortium are by and large comping from biochemists and molecular biologists and not from evolutionary biologists as Klinghoffer's source states. Just another example of the incredible skill of IDiots in getting everything wrong.

17 comments :

  1. It occurs to me the Pennisi also wrote the 'What Poison? Bacterium Uses Arsenic to Build DNA and other Molecules' News of the Week article for Wolfe-Simon's train wreck of an article.

    Unfortunately these reports are 'news' in the way FOX news is news. These articles are written to help sell Science subscriptions, not to provide an objective analysis of the articles and science in question. Pennisi's role is analogous to the White House press secretary's role. She disseminates the in house viewpoint.

    I do find it interesting that the News of the Week articles for the last two PR fiascoes were both written by Pennisi.

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  2. Today I'm being attacked by name on James Shapiro's anti-Junk blog post here. HuffPost publishes this attack on me, but HuffPost has also blocked my comments and will not allow me to defend myself in a comment there.

    However, our own Anthony McCarthy, aka The Thought Criminal, has shown up there-- to declare that, despite his having no knowledge of or interest in, or even curiosity about molecular biology, nevertheless, he knows for sure that the controversy is all about atheism and the closed-mindedness of atheists.

    Psychoanalysis, they're good at it! Science is boring to them.

    I will have to write about this at my blog, because HuffPost lets Shapiro's and McCarthy's evidence-free accusations through, but blocks whatever evidence I present.

    ReplyDelete
    Replies
    1. Apparently, Mr. Diogenes didn't get the message from Mr. McCarthy the other day that he was saying adios to this blog.

      Mr. McCarthy is truly a world class pompous jackass who writes at great length on subjects on which he is entirely ignorant.

      Delete
  3. I think the criticisms of the ENCODE announcement are coming from both evolutionary biologists and molecular biologists who have some familiarity with work on molecular evolution. Evolutionary biologists whose work is far from molecular evolution are holding back out of unfamiliarity with the molecular issues. Molecular biologists who are tempted by the dramatic ENCODE conclusions are ones who are tempted by a picture of all parts of the cell and all parts of the genome being fine-tuned; they are less familiar with molecular evolution.

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    1. I don't think most molecular biologists believe in the death of Junk DNA. Most molecular biologists can immediately see the fallacy in the media hype.

      It's true that most of the ENCODE scientists don't understand population genetics, and hardly grasp the positive arguments for Junk DNA (or know that there are positive arguments), as is shown clearly by the Reddit interview. But if you explain it to them, most molecular biologists grasp the issue immediately.

      It's not molecular biologists versus population geneticists. Guys like James Shapiro are the fringe.

      Even Ewan Birney knows that Junk DNA is probably real-- he understands the issue-- as he explained on his blog, he cooked up the 80% figure, because he burns, burns, for publicity. He's not challenged by the science, just the ethics.

      Delete
    2. Diogenes: Even Ewan Birney knows that Junk DNA is probably real-- he understands the issue-- as he explained on his blog, he cooked up the 80% figure, because he burns, burns, for publicity. He's not challenged by the science, just the ethics.

      Indeed, without the “80% figure,” ENCODE would have got little publicity and, therefore, their chances for new funding would have been diminished. So, why should we blame them for their dishonesty? After all, it is for a good cause, isn’t it?

      Delete
  4. Keep in mind, it's easy to refute the main claims in the ENCODE news stories without invoking evolution at all, from biochemical arguments. What happens to transposable elements? They promote their own transcription. What do transcription factors recognize? Short, degenerate sequences that crop up all over the genome.

    Synthesize 1000 random DNA sequences (as I did this summer), and stick them in front of a reporter gene. What happens is exactly what any self-respectiing molecular biologist should expect - many drive transcription, are bound, get marked etc.

    Pennisi's article didn't just fail on evolution, it failed on molecular biology too.

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    Replies
    1. @Mike White

      That’s a great point and experiment. So, Mike, when will we see your study in print?

      Delete
  5. Pennisi has long been troubled by the fact that humans don't seem to be very special compared to other species and she has written extensively about the mysterious "dark matter" in our genome
    And how does encode help. Even if ENCODE's claims are 100% correct*, they would be expected to hold true for all other species as well. Meaning we are just as un-special, as our ~20K genes + 80% "functional" junk would be equivalent to the other eukaryotes with their genes and "functional" junk. Heck, the onion gets to be extra special as (if I recall its genome correctly), not only does it have waaay more junk, but it has slightly more genes, then us lowly hominids.

    *which we know they are not.

    Bryan

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    Replies
    1. @Bryan

      Your point is excellent! However, they can easily spin it into: 'we are more special than them, the onions, because the regulatory sequences controlling our genes (i.e. the 'brains' of our genes) is better than theirs’.

      Delete
  6. Id folks are not irony deficient . Few people are anywhere like that.

    I say there is no such thing as confirmation bias.
    its just a phrase to excuse careless reasoning or investigation.
    All kids have "confirmation bias" because they are dumber.
    If a conclusion claims to be from proper form of investigation or proper form of reasoning and then its wrong well its just incompetence in that investigation or reasoning!

    Confirmation bias seems to be a invented word to ease the shame of error within the above educated class.
    Its just plain old, down on the farm, failing to pay attention.

    Yes this YEC creationist would see this "error phrase" in much of evolutionary biological conclusions.
    Yet closer attention to reason and investigation can correct error.
    No need to invent new strains of human nature as confirmation bias is plainly trying to do.
    I see this phrase everywhere and everywhere it is wrong as a analysis of why people get things wrong.

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    1. When you perform careless reasoning or investigation on the the things you don't think are true because you don't think they are true, that is confirmation bias, and to think it doesn't exist is hilarious.

      Delete
    2. Nope.
      Its just careless scholarship.
      No excuse for it if one claims to be a scholar.
      There is no such thing in human nature as confirmation bias it seems to me.
      Scholarship demands and can demand it is not in play unless it is being done accurately.
      It probably is a smaller clan then everyone who gets a degree in their early or middle twenties from these school places.
      Schools today reward studious kids more then scholarly ones.
      Do modern times produce, relative to numbers and resources and desire, more or less able scholarship as opposed to the old days?
      I don't think it does. I wish it would!

      Delete
  7. So, has Klinghoffer opened up the comments section on his site yet?

    Or is he still a hypocritical pseudo-intellectual coward/bully?

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  8. Replies
    1. Agreed, but I prefer the term "mendacious intellectual pornographer" as a better, more apt, description of what he does.

      John Kwok

      Delete
  9. DH Kaye reports: Court should consider ENCODE.
    link: http://for-sci-law-now.blogspot.de/2012/09/dear-judges-letters-to-ninth-circuit.html

    Genomics Law Report:
    ENCODE, CODIS, and the Urgent Need to Focus on what is Scientifically and Legally Relevant to the DNA Fingerprinting Debate
    link: http://www.genomicslawreport.com/index.php/2012/09/21/encode-codis-and-the-urgent-need-to-focus-on-what-is-scientifically-and-legally-relevant-to-the-dna-fingerprinting-debate/

    ReplyDelete