Monday, December 30, 2013

1001 Ideas that Changed the Way We Think - "Not-junk DNA"

Glenn Branch of NCSE alerted me to this book: 1001 Ideas the Changed the Way We Think. He wrote some of the articles [see Creationism and Evolution in 1001 Ideas].

The last great idea that changed the way we think (#1001) is written by Simon Adams, a "historian and writer living and working in London." Simon Adams thinks that the discovery that most of our genome is not junk counts as a big idea. To his credit, Glenn Branch realizes that this is somewhat controversial.

That's putting it mildly. Knowledgeable scientists agree that most (~90%) of our DNA is junk in spite of what the ENCODE publicity campaign might have said back in September 2012. I'm reproducing the article that Simon Adams wrote to show you just how successful that publicity campaign was and how difficult it is for the corrections and rebuttals to make an impact on a gullible public. With apologies to Glenn, whose articles are probably accurate, you should not buy a book that makes such a serious mistake by allowing an amateur to write about genomes, a subject he knows nothing about.
NOT-JUNK DNA
Far more of the human genome has vital functions than was first realized


The ribbons of DNA (deoxyribonucleic acid) in our cells carry instructions for building proteins and thus continuing life, but it was long believed that stretches of them are useless. The idea of "junk DNA" was first formulated by the Japanese-American geneticist Susumu Ohno (1928-2000), writing in the Brookhaven Symposium in Biology in 1972. He argued that the human genome can only sustain a very limited number of genes and that, for the rest, "the importance of doing nothing" was crucial. In effect, he dismissed 98 percent of the total genetic sequence that lies between the 20,000 or so protein-coding genes.

Yet scientists always thought that such junk must have a purpose. And indeed, a breakthrough in 2012 revealed that this junk is in fact crucial to the way our human genome, that is the complete set of genetic information in our cells, actually works.

After mapping of the entire human genome was completed in 2003, scientists focused on the so-called junk DNA. Nine years later, in 2012, the international ENCODE (Encyclopedia of DNA Elements) project published the largest single genome update in Nature and other journals. It found that, far from useless, the so-called junk contained 10,000 genes—around 18% of the total—that help control how the protein-coding genes work. Also found were 4 million regulatory switches that turn genes on and off (it is the failure of these switches that leads to diseases such as type 2 diabetes and Crohn's disease). In total, ENCODE predicted that up to 80 percent of our DNA has some sort of biochemical function.

The discovery of these functioning genes will help scientists to understand common diseases and also to explain why diseases affect some people and not others. If that can be achieved, drugs can be devised to treat those diseases. Much work still needs to be done, but the breakthrough has been made.
The editor of this book is Robert Arp, a philosopher specializing in the philosophy of biology and evolutionary psychology. I assume that he approved of the article by Simon Adams, which means that even philosophers of biology were duped by the ENCODE leaders.1


The book was published on Oct. 29, 2013. That means there was plenty of time to read the critiques of the ENCODE publicity campaign and even the scientific articles that were published last winter and early spring. There's really no excuse for making such a mistake.

29 comments :

  1. The topics covered in the book include "Miracles", "Angels", "Creation Myth", "Flat Earth Myth", "Adam and Eve", "Santa Claus", "Feng Shui", "Homeopathy", and 993 other ideas, quite a few of them very, very wrong. In such company, "Not-Junk DNA" is not entirely out of place. They should have thought of a more suitable title, though (or might have stolen one from John Farrell: "Myth of the Myth of Junk DNA")

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  2. Who says these are the important ways we think? I don't think that way. maybe this is just Englishmen's thinking. How would the author know?
    is it thinking or drawing conclusions? In fact drawn conclusions stops thinking!
    i notice this in CERTAIN subjects!

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  3. Off topic: Larry, I'm taking the free course on evolution you recommended a while back-Introduction to Genetics and Evolution by Dr. Mohamed Noor At Duke University.
    Are you taking it too? If yes, I don't think you are going to like it that much.
    In the first few minutes if the introduction to evolution, I already began to wonder whether I'm not wasting my time.
    This is what Professor Noor said about what evolution in his introduction: "Evolution is change through time over generations."

    I'm not an evolutionist and I very well know that species change overtime or many generations. Most sane people know that and don't question that.

    Darwin and others noticed that change but I don't think that is what Darwin and others were hoping to find proof for in the fossil record and in real life.

    Are you taking the course? Anybody here is taking it? It's free but boring as hell for now.

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    1. Starting off a course with definitions that you are familiar with makes you wonder whether you're wasting your time? So they should have started with something about genetics and evolution you have no earthly idea of?

      Would you expect a course entitled "Introduction to Mathematics" to start off with partial differential equations?

      This is really a pathetic attempt at finding something to criticize.

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  4. Guess what the first example of evolution is by professor Noor? Pepper moth.OMG!!! I'm going to die of boredom. If he gets to Miller–Urey experiment in the first video, I think I'm going to shoot myself.

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    1. Miller-Urey is about the origin of life. You shouldn't expect, Louise, to hear about the origin of life in a course in genetics and evolution.

      Starting with peppered moths is a problem? I always thought courses should start with something simple, then build on top of that. Were you disappointed when you were taught the ABC when you were a little kid instead of giving you Shakespeare?

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  5. I think I spent too much time on this and other good blogs and learned critical thinking too much. If this is what is being taught about evolution at reputable universities, creationists have nothing to fear. If you ALL think I'm making it up, you can sign up for free and check it out yourselves. I'm done.

    https://www.coursera.org/course/geneticsevolution

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    1. You seem disappointed with the course, but why? What did you expect? What led you to those expectations?

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    2. Its the other way around John: "Swine before pearls"m ;)

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    3. Sigh. Mohammed Noor is a fly geneticist interested in the genetics of speciation. Of course he's going to teach from that perspective. I doubt he'll even get into the origin of life, if that's what you want. He may not even get into macroevolution, except for speciation. So what's wrong with what he's tried desperately to teach you so far?

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    4. You seem disappointed with the course, but why? What did you expect? What led you to those expectations?

      From a long experience of dealing with creationists and their imbecilities, I can tell you precisely what Louise G.'s problem was with the course: it was too reasonable. It made entirely too much sense. It wasn't the absurd caricature she assumed evolution was. There were no altars on which incense was burned to an effigy of Charles Darwin, no avowed declarations of faith in the inexhaustible potential of metamorphosis, no X-Men-style treatment of mutations, etc. It was all disturbingly normal. And since reality didn't confirm with Louise G.'s assumptions about what evolutionary biologists do and think, it's reality that must be in error. This class must simply be hiding what the biologists are really up to. Why would they put it online otherwise?

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    5. What? The course lacked worshipping of Darwin? No promises to keep the secrets of evolution away from outsiders? We have to talk seriously with this Duke Univ guy!

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    6. Really Harsh man wrote: "Sigh. Mohammed Noor is a fly geneticist interested in the genetics of speciation. Of course he's going to teach from that perspective. I doubt he'll even get into the origin of life, if that's what you want. He may not even get into macroevolution, except for speciation. So what's wrong with what he's tried desperately to teach you so far?"

      If professor Noor is not going to cover macroevolution why should I continue with the course? Even YEC believe in microevolution and most religions I know about maybe with and exception of JWs, but I'm not sure about that 100% as two older ladies came to my door last Saturday and they were not sure what I meant by microevolution. They came back this moring at 930. Don't they ever give up and know what time it is? What is wrong with those people? Anybody talked to them this early? I asked 2 question 3 months ago, they left me 5-6 brochures, few books, and 2 videos. Who pays for this? I hope its not my tax money. I have to admit the video about blood transfusion was interesting but I'm not sure if it is real. JWs left and Mormons came like almost immediately. Are they same church just different clothes? These want me to live on my own planet by myself. I said that I'm addicted to sex and not the self-fulfilling one and they left with anger lol.

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    7. If professor Noor is not going to cover macroevolution why should I continue with the course? Even YEC believe in microevolution and most religions I know about....

      Here's a wild thought: maybe you could learn something? Strange as it may seem, it's not obligatory to disagree with the instructor to learn something valuable from the course, and given your track record you could stand to learn something about all aspects of evolutionary theory, even the parts you claim to ostensibly believe in.

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  6. Mikkel Rumraket Rasmussen wrote: "You seem disappointed with the course, but why? What did you expect? What led you to those expectations?"

    Well, sign up for the course so you will see.
    I'm disappointed for people like you that they do not have courses on biogenesis, but then again; what would that course be called? "We have no idea"? I would be the shortest course on the planet too lol

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    1. I'm already doing the course, I didn't come into it with the expectation that they'd be discussing the origin of life. What led you to that expectation? Maybe you should read the course description next time before signing up?

      If you want to learn about what scientists think about the origin of life, why don't you look at what those scientists actually working on that problem do, instead of signing up to unrelated courses on genetics?

      Let me help you with that. Here's a list of publications of one such scientist working on a hydrothermal-vent-metabolism-first type model:
      http://science.jpl.nasa.gov/people/Russell/

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    2. Mikkel, If you have some brains left, answer me one question straight up: If scientists like my cousin Szostak create life, will this mean that life can be generated spontaneously? Yes or No answer only. I'm going to ask you one question at a time so as not to create confusion.

      BTW: I know pretty well this Danish woman Caroline Wozniaci. She is some kind of rocket-ball player? I'm not sure but she is one pretty goodlooking kid and that German friend of hers Julia Gorgeous. I'm telling you man, those women are stunning. And what a personality and manners. I love the way Danes and Germans bring up their kids. According to stats and Larry, Danes are the happiest and the most fulfilled people in the world and yet, they are 99,99 non-religious. How do they fill the gap? How do they "feed the receptors in their brains that respond to spirituality, alcohol, drugs, food, diet coke that some drink, sex (me:) ) etc? Is it their biking that keeps them alive because it is too expensive to drive?

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  7. Louise G, What about "Introduction to Genetics and Evolution by Dr. Mohamed Noor At Duke University" signals that (a)biogenesis would be a subject? I would have questioned Dr. Noor's sanity if he'd mentioned Miller-Urey in this intro to Genetics and Evolution. I question your attitude as well.

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  8. "LouiseG", pains me though it does to say it, does have half a point, however. I'm not sure why an intro to evolution class would start with the hoary old peppered moth story right up front. Surely there are other illustrations that people have not heard thousands of times already. Never mind the fact, if any creationists are taking the course (and we know there is at least one), they'll roll they're eyes and think "Oh, yeah, the peppered moth. My pastor told me about that one. It's all fake."

    Personally, I'd consider starting with something like antibiotic resistance, which has the advantage of illustrating that evolution is a dynamic process that is occurring at this moment, and also how a proper understanding of it is relevant to serious issues that are immediately confronting us.

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  9. My wife and I took the course with Mohammed Noor the first time it was offered. We both found it informative and interesting, especially the mathematical parts and getting some idea of how traits spread via selection and drift. We both knew a reasonable amount heading in out of interest and from our background as science (Physic, Chem, Biology) teachers. It was a worthwhile effort but LouiseG is not up to it - too closed a mind.

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  10. I took the course on a previous outing. It's excellent. Shame about the trolling creationists on the forums. Lots of nonsense from imbeciles who think looking at creationist websites ( or listening to their pastor) gives them knowledge of biology. The first mention of 'allele frequency' scared most of them away. They hate anything that sounds a little complicated. If you find it boring Louise then stay away. It's not for the likes of you.

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  11. I think all of you have to take courses on comprehension. Read my posts again and tell me where I said the course included the origin of life. If you find any of my comments stating that, I will send you $100.00 via paypal.

    However, I have alluded to that possibility and expressed my disappointment that Duke did not offer such courses at all for Mikkel's sake, but I have never said that the course I have been taking "evolution and genetics" included the topic of the origins of life-abiogenesis. It is obvious it would be self-defeating. Why would one start a course with A definition of life he does not have (yeah, that is still true. Nobody has a definition of life :) and then say he has not clue how it began and why scientist can't create it.

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    1. I think all of you have to take courses on comprehension. Read my posts again and tell me where I said the course included the origin of life.

      First, why don't you point out where anyone claimed you said that?

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    2. Good news for you LouiseG, a previous course on astrobiology and the origin of life has just restarted this year on coursera: https://class.coursera.org/astrobio-001. I guess it's time to go pollute the discussion forum with arguments from ignorance fallacies, hoyle's improbability calculation fallacy and other standard creationist nonsense.

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    3. Why don't you try to "create life" YOURSELF by the vents you have been bragging about? Be careful though! Last time one scientist tried that he not only didn't create any life, he turned himself into a lifeless barbecue chicken. You your case it would only be a burned danish LMAO!!!

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    4. I'm glad you think the idea of "creating life" is fatuous nonsense, but please don't tell creationists.

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    5. What else can you say? This is where science ends and unreasonable belief begins +

      Someone once said that if one askes why is there something rather than nothing? The answer to it is outside of science. Why should you question something that is NOW clearly outside of science scope?

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    6. So you believe in instantaneous magical divine creation through an act of will alone? On what basis other than blind faith? There's no evidence it's possible.

      Notice how an argument from ignorance(we don't know how..) does not logically entail your conclusion or even reasonably justifies belief in the above proposition. But of course, you don't do logic.

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