Friday, December 14, 2012

Fallout from the ENCODE Fiasco Makes It into the Globe & Mail

Most of us are aware of the ENCODE publicity fiasco. The leaders of the project made some outlandish claims about the function of most of our genome in order to attract attention and make their work seem much more significant than it really is [see Sean Eddy on Junk DNA and ENCODE].

Many scientists tried to set the record straight and they pretty much succeeded, at least in the scientific community. Most scientist now know that the case for junk DNA is a lot stronger than they thought.

Unfortunately, the criticisms didn't get much publicity and the average person is left with the impression that most of our genome has an important function, even if we don't know exactly what that function is. This means that good science writers have to work harder to educate the public about the true state of our genome.

Timothy Caulfield is a Professor in the Faculty of Law and the School of Public Health at the University of Alberta in Edmonton, Alberta, Canada. He's also Canada Research Chair in Health Law and Policy, a very prestigious award. He writes the following in today's issue of The Globe & Mail, Canada's most important newspaper [We’re overselling the health-care 'revolution' of personal genomics].
The relationship between our genome and disease is far more complicated than originally anticipated. Indeed, the more we learn about the human genome, the less we seem to know. For example, results from a major international initiative to explore all the elements of our genome (the ENCODE project) found that, despite decades-old conventional wisdom that much of our genome was nothing but “junk DNA,” as much as 80 per cent of our genome likely has some biological function. This work hints that things are much more convoluted than expected. So much so that one of ENCODE’s lead researchers, Yale’s Mark Gerstein, was quoted as saying that it’s “like opening a wire closet and seeing a hairball of wires.”
Statements like this from someone who is supposed to be knowledgeable about such issues show us that the ENCODE fiasco has far-reaching consequences. The misleading statements by Ewan Birney and others will take years to undo. It's all the more reason to criticize Nature and Science for aiding and abetting the spread of this false information.

How can we expect people like Timothy Caulfield to understand the science if the leading journals get it wrong?

[Hat Tip: Ryan Gregory, "The Bullshit Continues to Spread" on Facebook.]


  1. We subscribe to Science News, and I was disappointed to see them report the ENCODE story with hardly a hint of the dissenters.

  2. Most of DNA is junk and yet it is the source of the diversity of life on our planet. That's the ultimate free lunch: everything out of nothing. That makes a lot of sense!

    1. Pépé, seriously, you don't have to do this. The reason you are sure that most DNA is not junk is because you can't believe god would design like that. But it is only through scientific analysis we will learn how things are in this world and universe. The bible does not speak of these matters, no theologian or even the pope has any special revealed knowledge about these things. You can learn about the true nature of the universe, such as humans can discern, without it being a threat to your god. Your god, if it exists, could have done anything even if it doesnt make sense to you. Even if every story in the bible turns out to be human-made nonsense, this does does not imperil your god, if it really exists. You should be interested in what humans have discovered about the universe, if only to understand the true acts of your god, rather than insisting that the inspired words of other men (who have no more a conduit to god than you have) must be true. Is your faith in god so weak that you must deny his acts?

    2. Shawn, I thank you for your consideration towards my humble self.

      But my take has nothing to do with God, the Bible, philosophy, religion or what have you.

      I only use common sense and that common sense tells me that the diversity (and the beauty) on this wonderful earth of ours cannot be the result on dumb luck.

      Call me a poet!

    3. The very reason science was invented was that common sense turned out to be a poor guide to the workings of the universe. Common sense may be useful in our everyday practical experience, but it doesn't work well in other domains.

      A poet? What blatant self-flattery!

    4. dumb is a human term that has no currency beyond its trivial human use...and as for luck, why not? Just of your life alone, who would you have been if a different egg cell from your mother or a different sperm cell from your father were the rare successful gametes? Who would you have been if, as often happens, the blastocyst Pépé was spontaneously aborted? Also, as the events in Connecticut remind us, not all is beautiful, not all is wonderful, not everyone is lucky.

    5. But my take has nothing to do with God, the Bible, philosophy, religion or what have you.
      I only use common sense and....

      Ah! If that is true (and I rather doubt it is, but who knows) then there is hope for you yet Pépé!

      In matters not commonplace and intuitive (and what could be intuitive about DNA, proteins, and other things we cannot see and could scarcely conceive of without science) abandon the bulk of your commonsense and follow the evidence, however strange this universe becomes.

    6. Imagination is more important than knowledge.
      (Albert Einstein)

      Some of you might benefit from that.

    7. Pépé: That would have been a better comeback if you had ever displayed any imagination.

      And your posting in general would be a lot better if you didn't restrict it to little taunts and soundbites. This is not twitter. It you have an argument to make for your position and against Larry's, go ahead with it. Otherwise, you're just wasting everyone's time.

      Simple explanation: most of your DNA is junk, but not all of it. The parts that are responsible for the diversity of life aren't junk. We have ways of distinguishing junk from non-junk (first pass: rate of evolution); they aren't perfect, but they are good enough for estimates of quantity. The well-known onion test (or more generally, the c-value paradox) is incapable of identifying particular sequences as junk, but it does tell us that there's a lot of junk in species with big genomes. Encode tested for "functional" DNA using assays that would identify junk DNA as functional. If you disagree with any of that, present some kind of argument.

    8. It is comprehensible, though not scientific, to try to rescue the junk DNA paradigm. When one of the supposedly best proof of Darwinian evolution is shut down in flames, diehard Darwinists will do anything to salvage their beloved (and wrong) theory.

      But the fact is that most, if not all, of DNA is useful. Labeling the parts we don't yet understand as junk has probably greatly impeded our progress towards a better understanding of the genome.

    9. @Pepe - you really have no idea. Time to educate yourself.

    10. What blatant self-flattery!

      It's a dirty job but someone has to do it.

    11. Pépé to try to rescue the junk DNA paradigm

      Coming from one who doubles down the crazy in the field of "rescuing junk paradigms" I applaud your apparent lack of irony, overweening sense of projection and breathtaking hypocrisy in this and similar statements.

      Hitchens really wasn't too far off the mark when he said that religion poisons everything.

  3. "Many scientists tried to set the record straight and they pretty much succeeded, at least in the scientific community. Most scientist now know that the case for junk DNA is a lot stronger than they thought."

    do you have any data to back that up? Sure, there have been some blogs (you've linked to most of them), but how widespread is this view in the scientific community? I really would appreciate if you could point us to some clues

    (I really would because, even though a layman, I mostly agree with you on this)

  4. we really enjoy your atheist blog

    do a search on youtube for skepticality

    a little souvenir

    it is the video about the PIGS

    1. Looks like Mabus/ Markuze might be back. Ed Brayton is getting comments similar to the one above.

  5. This comment has been removed by the author.

  6. Larry MoranHow can we expect people like Timothy Caulfield to understand the science if the leading journals get it wrong?

    It might be more appropriate to question the competence of the ENCODE’s leading scientists and of those who peer-reviewed the papers. Certainly, these scientists are among the best scientists in the world. So, what’s going on?

    Possibly, it is not their fault, but the problem is with the current system of conducting science. This system encourages and rewards scientists based primarily on their ability to produce data, rather than on their ability to interpret and make sense of this data or to understand and develop rational concepts.

    Take, for example, the dogma of molecular biology as proposed by Crick half of century ago. There are so few scientists understanding this concept that they might be on the endangered list.

    Indeed, why bother understanding these concepts, when the call is for generating more data, whether relevant or not, so that scientists can get grants to generate more data, so they can get new grants …

    Why bother understanding what a ‘biological function’ means, or understanding that DNA can have other functions besides its informational role?

    1. @Claudiu,
      On BBC's 'Start The Week', a live radio show, Ewan Birney has just been interviewed. (The podcast will soon appear on the BBC r4 part of the website, I expect). He is unrepentant about the fuss that ENCODE causes. Most interesting comment I heard: he wants to do away with the phrase 'Junk DNA' - when asked for an alternative by Andrew Marr, he introduced 'Enigmatic DNA' to replace it.

    2. It reminds me I have to remove all that enigma from my garden shed.

    3. ... when asked for an alternative by Andrew Marr, he introduced 'Enigmatic DNA' to replace it

      How sad. It shows that Birney hasn't learned a thing from his mistake. I'd like to ask him what's "enigmatic" about defective transposons and what's "enigmatic" about pseudogenes. I wonder what's so "enigmatic" about the genetic load argument showing that the sequence most of our genome can't be important.

      I wonder if "enigmatic" is just code for "I don't know the scientific literature and I'm not going to bother to find out so it's all a mystery to me."

    4. Rkt: “Ewan Birney… wants to do away with the phrase 'Junk DNA' - when asked for an alternative by Andrew Marr, he introduced 'Enigmatic DNA' to replace it.”

      This is reminiscent of another recent vocabulary transition in the field of genomics and, possibly, inspired by it: introduction of a new term ‘C-value enigma’ to replace the traditional term ‘C-value paradox’.

      What about new terms and concepts that might be more useful, such as bringing forward the concepts of ‘informational DNA’ (iDNA) and ’structural DNA (sDNA) to indicate that genomic DNA can have functions that are based on sequence and functions that are independent of sequence (see:

    5. Larry Moran: ”I wonder what's so "enigmatic" about the genetic load argument showing that the sequence most of our genome can't be important. (emphasis mine)

      Maybe, I’m reading too much into it, but did I catch a glimpse at our host Larry reaching for a ‘get out of jail’ card, when he implies that most of our DNA is ‘junk’ only if perceived from its informational role?

      Here is previous comment ( in which I discussed this issue:

      I agree with you that in terms of “informational content as defined by its base sequences”, the structural DNA (sDNA) can be called “junk”. But, I think, you would agree that in terms of structural role, the informational DNA (iDNA) can also be called “junk.” However, from a scientific perspective, both sDNA and iDNA have a biological function, and neither is “junk.”

    6. At no time in the past several decades have I ever denied that parts of our genome could have a function that was independent of the sequence of nucleotides.

      All I ask is that speculations about function recognize that the proposed function cannot rely on sequence information.

      So far I haven't seen any speculations about sequence-independent function that are anything more than wishful thinking that doesn't make sense and doesn't explain the data.

    7. The reason that you haven’t seen any speculations about sequence-independent function of the so called ‘junk DNA’ (jDNA) might be that the time for speculations is over; indeed, the current evidence clearly shows that the old model on the evolution of genome size and the protective function of jDNA against insertion mutagenesis, which in humans and other species can lead to cancer, is a fact .

      Say goodbye to the concept of ‘junk DNA’! (come to think of it, this might be a catchy title for a paper, anyone!?)

  7. Some organs and their parts in our body have had modification, but not a single organ (with its parts) is without some function.Recently it has realized e.g. that our hair has important function.

    Therefore it is wery difficult to think, that our genome has non-functional parts.

    The other reason is, that our genomes many physical job`s and action`s surely are "functional" too.

    See e.g. "Genome physics" or "DNA-physics"

    1. Therefore it is wery difficult to think, that our genome has non-functional parts.

      Why? Please read this. There is evidence that a lot of our genome is not useful to us. Wishing this idea away is not helping.

    2. but not a single organ (with its parts) is without some function

      Nipples on guys.

      Next contention?

    3. "Next contention?"

      The hair around my buthole.

    4. The hair around your buthole? Very important:

      The millions of naturally occurring commensal bacteria in the skin -- collectively known as the skin microbiota -- also have a beneficial role.

  8. Nipples on guys have many important functions. If guys did not have nipples, many females did not have proper nibbles because of heredity.

    A lot of men use nibbles as sexual enjoyment-organ.

    Nipples on guys participate in many other functions too.

    Ask Larry, if you don`t believe.

    I personally have observed my male nibbles being involved in the lymph-circulation.

    1. There are vestigial organs. Hind legs or hip bones on a whale. Eyes of various blind organism. Eye sockets on eyeless fish. Limb bones in snakes. They are ex-organs on their way out due to non-use. But this is not an instantaneous event.

      In the genome, the junk DNA probably also at one time had "a use". Pseudogenes are the result of DNA duplication or molecular accidents that re-integrate RNA sequences into the genome. Genome or local DNA duplications often lead to loss-of-function and degradation of extra gene copies. Retrotransposon were selfish elements that invaded the genome, but the bulk of them have mutated and ceased their selfish duplication function (and make up at least 40% of our genomes).

      Now that they do not have a function, and they are in a state of decay. The persistence of the vestige element is then due to a balance between selection to dispose of the trait and the fitness cost of maintenance. DNA replication is a minor energy cost to a eukaryote, so the advantage of the loss is insufficient to drive allele frequencies, so they drift along under nearly-neutral evolution. Not to mention the very severe effects that are probable under large-scale random deletion events - the one mechanism that would efficiently loose excess DNA.

      So again, why do you think you analogy poses a problem?

    2. E.J.Slijper (1907–1968), famous whale-researcher, has written, that hip bones on whales are used in reproduction.Very plausible is, that same realizes to the snakes too.

      Blind fishes have important circadian rythm-apparat which some opsin-receptors in their eyes. Some other retina-cells have probably changed receiving some other function.

      Fishes and other water-animals with eye sockets are probably poisoned:

      I assume that you think me as some anti-evolutionist, who shoul be converted to evolutionist with pieces of evidence. Not so, at all. I define myself as not ID but IC-evolutionist, Intelligent Cell -evolutionist. New genetics is pointing at this.

      Every day does some aspect of the junk DNA find some function. And more and more researcher are waking up from old times dream.

    3. I assume that you think me as some anti-evolutionist, who shoul be converted to evolutionist with pieces of evidence.

      No. I thought you were one of the many molecular biologists that take the DNA as computer code / life is little machines metaphor too seriously. There are many about these days. But it is an easy affliction to overcome. Step 1 is put down the Shapiro books.

      New genetics is pointing at this.


      "An appeal to novelty is the opposite of an appeal to antiquity. Appeals to novelty assume that the newness of an idea is evidence of its truth. They are thus also related to the bandwagon fallacy.

      That an idea is new certainly doesn’t entail that it is true. Many recent ideas have no merit whatsoever, as history has shown; every idea, including those that we now reject as absurd beyond belief, were new at one time. Some ideas that are new now will surely go the same way.

      (1) String theory is the most recent development in physics.
      (2) String theory is true."

      Cummings 1972 had more meaningful content than the contentions ENCODE paper.

      Every day does some aspect of the junk DNA find some function.

      I think you are failing to recognize the scale involved here. Purely to illustrate the point, let's say that every month, 1000bp of the genome is described with some new, novel function. At a constant rate, 5% of the genome will be accounted for in 13,775 years. As I mentioned above 40% is degenerated retrotransposons. There is a lot.

    4. Comings (1972) has really been ahead time!

      But retrotransposons, it seems as of they almost all would be functional..or I may be mistaken.

    5. You are mistaken. Most are inactive.

    6. Not long ago neodarwinists had almost hundred examples of rudiments, which they believed non-functional. Still today some blogists suppose e.g. appendix, nibbles on guys, hair in humans, wisdom tooth etc. being non-functional.

      Wisdom tooth act as a biting organ and excellent source of stem cells.

      Because every organ has some function (often difficult to see), I have difficulties to believe, that some parts of the genome would be completely non-functional.

      I do well understand in a different way thinking people too.
      kei se rase ra..nähtäväksi jää..

    7. I thought we were having an interesting discussion, but you suddenly revert back to an argument from incredulity .

      But your mind is made up, so there is no point in discussing this with you any further.

      I'll just leave you with a few to ponder,

      8% of our genome is due to insertions from Bornavirus infections.
      Broken copies of mitochondrial DNA inserted into the nucleus account for >3,000,000 bp of our genome.

  9. Not a single organ (with its parts) is without some function

    Therefore it is wery difficult to think, that our genome has non-functional parts.

    Some genes could be scaffold-genes having only physical meaning, but when the genomics proceed as it now does bigger and bigger part of the genome proves to be useful.

  10. More apparent fallout -

    1. @Major: the use of the word "facts" is questionable in the article you refer to. It concerns itself mainly with measurements, or rankings. A subset. Other simple facts, such as elephants have a trunk, beach sand contains silicon, each living cell is surrounded by a membrane, Mars is less massive than the Earth .... fall into the category of things that will always be the case. The way the article is written the writer is taking skepticism to a whole new (and whacky!) level, don't you think?
      Come to think of it, ENCODE is right in the dangerous-zone for factually correct/incorrect knowledge so I take your point.

    2. The ENCODE project has generated large amounts of data. Likely much of this data is correct, which means that they are facts. For example, the project found that most of our DNA serves as binding sites for various proteins, so that’s a fact. And, if we insert large pieces of arbitrary DNA in our chromosomes and we find that they serve as biding sites for various proteins, that would also be regarded as a fact.

      However, the ENCODE data has not shown that most of our DNA has a functional role. That’s a fact. It is also a fact that most of our DNA has a protective function against insertional mutagenesis which can lead to cancer.

      What we do not know, is why have scientists working in this field failed to recognize and embrace this fact? Maybe, because we have not spent hundreds of millions of dollars figuring it out? Or, maybe, because it was published a couple of decades ago, and nobody has noticed it?