Wednesday, September 12, 2012

My challenge to critics of the ENCODE research

A number of commentators on this blog, as well as Darwinists on other blogs (Larry Moran at Sandwalk is an example) have been harshly critical of the published findings of the 400 scientists involved with the ENCODE project.

Specifically, these criticisms of the science center on the word "functional", as applied to DNA in the human genome.

Darwinists have argued for decades that most DNA in the eukaryotic genome is "junk", meaning DNA that is not functional and that has accumulated over eons and is isolated from natural selection. Junk DNA, in the Darwinist perspective, is tangible evidence of the "random" in "random mutation and natural selection". Accordingly, Darwinists have pointed to junk DNA as very strong evidence confirming Darwin's theory.

From an ID/teleology perspective, we would not expect the genome to contain much "junk". A genome evolved with purpose is an elegantly integrated system. A small amount of detritus may accumulate even in the most elegantly designed system, but, from the ID perspective, it should be a very small portion of the system.

The ENCODE research has created a firestorm, because the scientists have presented evidence that at least 80% of the human genome is "functional", and not junk.

The ENCODE lead investigator Ewan Birney writes:

It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. This question hinges on the word “functional” so let’s try to tackle this first. Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e., if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge. Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons.

He defines "function" quite clearly.

Here's my challenge to my Darwinist ENCODE critics ("deniers"?):


1) Define "junk DNA". Precisely. When you claim that most of the genome is junk (and you have claimed that for decades), what do you mean. Exactly. No weasel words. What is junk. What is not junk.

2) Define "function", in terms of DNA. What does it mean for DNA to be functional?


3) What relation does "junk" bear to "function"? Be precise. Can DNA be functional (by your definition) and still be "junk"?


4) How much of the human genome is "junk"? How much is "functional"? Explain what you mean.

If you are going to criticize the ENCODE research harshly, you need to define your terms, as the ENCODE scientists have defined theirs.

In my experience, Darwinism survives only because its faithful are permitted to evade defining terms. Ambiguity is Darwinism's defining adaptation. It is the only trait that keeps it from going extinct.

So, Darwinian interlocutors, define your terms. Answer my questions, if you feign to participate seriously in this debate.

I'll define the terms as well, and post on both. And then we'll review the ENCODE data in light of the definitions.

34 comments:

  1. !So Egnor finally admits he doesn't know the basic definitions of the stuff he's been arguing about! He wants professional biochemists to tutor him for free! What a lazy buffoon. He could just read sme of the biochemist blogs that have already been posted here, but, you know, that would require some honesty.

    The next time I'm in Stony Brook I'll make up some wild claims about how brain surgeons are all ideological crackpots, make up my own interpretations for "craniopharyngioma" and "laminectomy" and then demand that Egnor tutor me on the subject.



    ReplyDelete
  2. Michael,

    Leave it off. We are not criticizing the ENCODE scientists. We are criticizing your and other creationists' bizarre spin on the results of the ENCODE research.

    You still haven't explained why the human genome has many thousands of broken genes, including half of the 1000 genes in the olfactory receptor suit. What's the ID explanation? Also, why does the size of the genome vary so much across species, even similar ones? Why does the marbled lungfish have a genome of 130 billion base pairs, compared to humans' 3 billion base pairs?

    If you want a definition, I'd define 'junk' as having no current use, but isn't discarded, because it might turn out to have a use later (as an analogy, I have a lot of junk lying around the house, in contrast to garbage, which I discard immediately).

    Having a function means that if you delete the DNA, then it causes a change in the organism.

    The percentage of junk DNA varies across species. In humans, it's at least 50%. It could be 91% or more.

    We still don't have a complete understanding how the genome works. The presence or absence of junk DNA isn't evidence for or against evolutionary biology. The presence of large numbers of broken genes, though, is evidence against ID.

    ReplyDelete
  3. "If you want a definition, I'd define 'junk' as having no current use, but isn't discarded, because it might turn out to have a use later (as an analogy, I have a lot of junk lying around the house, in contrast to garbage, which I discard immediately)."

    Bachfiend the teleologist!

    So... NOW junk includes the material that has a purpose that has not been realized as of yet.
    Much like that extra button stitched into your shirts.... but who stitched it there, how did they know you may lose a button, and why did they give a shit if you do?
    Must be all random or 'emergent'- just like those buttons and Bach's 'junk' in his garage. Bach needs a hose for his vacuum and one forms from the oil residue from under his 4x4.

    As I noted on yesterday's post, Mike - these folks just seek to move the goal posts. They seek to redefine 'junk' so that it can safely be used and protect their nihilistic dogma.

    They are squirming, and it is delicious to see.

    ReplyDelete
    Replies
    1. CrusadeRex,

      I'm not a teleologist. I also don't wear shirts with buttons or have a 4x4 (you must be thinking of yourself). I'm not squirming about junk DNA. The thousands of broken genes in the human genome are much better evidence against ID (and also your brand of creationism). Why did God make humans prone to scurvy by including all the genes (present in most mammals) making vitamin C in the human genome, but made one of the genes defective and non-functional?

      Michael is engaging in the standard creationist trick of taking a small point over which there is debate, insisting that it disproves evolutionary biology (it doesn't), ignores all the other evidence and then insists that it means that ID (for which there isn't the slightest scrap of evidence) must therefore be true (it isn't).

      ID is a non-theory, going nowhere. God did something somewhere somewhen for unknown reasons and by unknown mechanisms doesn't make testable predictions, unless Michael wants to define how much a very small portion of the human genome is detritus accumulating after eons in a well designed system. 1%? 5%? It seems to be at least 50%. Is that a small portion?

      Delete
    2. bachfiend: "Why did God make humans prone to scurvy by including all the genes (present in most mammals) making vitamin C in the human genome, but made one of the genes defective and non-functional?"

      Because God wanted us to eat oranges!
      This answer is less idiotic than what Darwinists want us to believe.

      Delete
    3. So why are some people allergic to oranges? For humility?

      Delete
    4. Because God wanted them to eat Cantaloupe, Grapefruit, Kiwi fruit, Mango, Papaya, Pineapple, Strawberries, raspberries, blueberries, cranberries, Watermelon.

      Isn't God GREAT for having made fruits for Peter, Paul and Mary!

      Delete
    5. "Because God wanted us to eat oranges!"

      But not, apparently, apples

      Delete
    6. Only the very first apple! XD

      Delete
  4. mregnor,

    The problem is not with the ENCODE definition of functional or your definition of functional. The problem is with your false belief that the two are the same.

    ENCODE has a clear operational definiton to which you linked. I have no problem using that definition, but subsequent interpretations of the data need to keep that definition in mind, which you do not. The clearest you've come to an ID definition is the following.

    "From an ID/teleology perspective, we would not expect the genome to contain much "junk". A genome evolved with purpose is an elegantly integrated system. A small amount of detritus may accumulate even in the most elegantly designed system, but, from the ID perspective, it should be a very small portion of the system"

    From Ewan Birney's blog:

    “Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for.”

    As per Birney's description and your ID definition, the ID interpretation of the genome. Results in 20% "elegantly integrated system", 60% "detrius", and the remaining 20% has no discernable function.

    Please tell me that you at the very least understand that you and ENCODE are using different definitions for funtional.

    -L

    ReplyDelete
    Replies
    1. mregnor,

      I apologize, I skipped right over this part:

      "I'll define the terms as well, and post on both. And then we'll review the ENCODE data in light of the definitions."

      So you will give a full operational definition of function later. I've waited through three posts, I suppose I can wait for one more. Not sure how it will help though.

      If you use a different definition than the ENCODE project, then you are committing the error we have all claimed you are. If you use the same definition, then the leader of the ENCODE project disagrees with you.

      -L

      Delete
    2. @L:

      Where on earth do you get the idea that 60% of the genome is "detritus"?

      Birney's statement in my blog post makes it very clear that 80% of the genome has "specific biochemical activity". Not detritus or junk. Birney lists the assays on which he bases his conclusions.

      Why would you misrepresent the science so blatantly, in a way that can so easily be refuted?

      Delete
    3. Mike Egnor,

      “Where on earth do you get the idea that 60% of the genome is "detritus"?”

      From Birney’s blog: “Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling.”

      Of the 80% cited only 20% was of relevance to cell activity. The rest (80%-20%=60%) passed through the biochemical assays but appear to have no relevance or consequence on cell activity. I admit that detrius was your word. In his original press release, Birney wanted to make this distinction, but felt it would not make for good copy.

      “Why would you misrepresent the science so blatantly, in a way that can so easily be refuted?”

      I do not misrepresent science.

      Again from Birney’s blog: “But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for.”

      In short you are a prime example of the type of reader Birney was worried about: one who doesn’t have the patience to understand the full explanation. Reading two numbers and trying to figure out why they are different appears to be asking too much of you.

      -L

      Delete
    4. @L:

      Here's the rest of Birney's paragraph that you truncate:

      "(Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and 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."

      You're a liar, L. You intentionally didn't quote Birney in full, so you could change the context. He rigorously defended the 80% because it conveys that the genome is not "dead wood" but "alive with activity".

      You people are lying, spinning, spitting, doing anything you can think of to protect your shabby ideology.

      Delete
    5. mregnor,

      Yes , now I see how I used your word detrius (a word I wouldn't use on my own) in a manner that could lead to confusion. I assure you it was not intentional.

      Tell me though, if Birney is "rigorously defending" the 80% then why is he confusing people by mentioning the 20% figure? Why the difference between the two numbers? What does that 60% represent?

      -L

      Delete
    6. @L:

      Birney used 80%, as he explains clearly in the quote above, because 80% conveyed the truth about the data (specific biochemical activity) and it conveyed the truth that the genome is "alive with activity", and not dead with wood.

      Birney used 80% because it tells the truth. It is also obviously a way that he and his 400 collaborators could convey quite clearly that you and other Darwinists who peddle the junk DNA myth are ideologically motivated assholes.

      He gave you the middle finger, L.

      Delete
  5. In Egnor’s world the reality of situation is determined by the definition of the words used in describing the situation. The morality of abortion does not depend on the definition of “human being” or “person”, the nature of the universe does not depend on the construct of language in Aquinas’s 5 ways, and the reality of evolution has nothing to do with the precise definition of the word “functional“.

    The workings of nature are far too complicated to be pigeonholed by the definition of words in a few short declarative sentences. The more accurately your statements reflect the true nature of reality the more they will look like a stack of the ENCODE papers. Once again, Egnor’s argument comes down to little more than semantics and word games.

    -KW

    ReplyDelete
    Replies
    1. That's a very long-winded dodge on your part, KW. It certainly looks to me like you can't answer any of Dr. Egnor's questions regarding the specific meanings of terms, which demonstrates his point about Darwinists relying on ambiguity.

      Delete
  6. This is so much fun to watch. Another Icon of Evolution bites dust at the hand of real science, and evos are squealing like stuck pigs -- reduced to arguing that functioning really doesn't really mean functioning, and besides, "why would God (fill in the blank). Hahaha! Brilliant!

    ReplyDelete
  7. This is so much fun to watch! Another misunderstanding of basic science by the creationists, and they're squealing like stuck skunks - reduced to demanding definitions for things they don't really understand! Hahaha! Briliant!

    ReplyDelete
  8. For anyone who ever doubted that Darwinists were motivated by ideology, not science, the findings of the ENCODE Project will remove any and all doubt.

    Watching these people fight scientific progress solely because it refutes their stealth religion has been both thrilling and nauseating. It's quite the thrill to watch I.D. win the debate (and it has), however, it's nauseating knowing that these ideologues will stoop to any level to make sure their pseudoscience remains in the classroom.

    Even though I.D. has won the science battle, I'm certain these discoveries will lead to an increase in lying for Darwin in an attempt at winning the political battle. As their desperation and insecurity increases, so, too, does their level of dishonesty. Also, any attempt at bringing critical thinking into the classroom (as in Tennessee) just got a whole lot more threatening to the Darwinist, so expect to see them amp up their smear tactics against academic freedom bills.

    ReplyDelete
    Replies
    1. Even though I.D. has won the science battle

      For there to be a "science battle" there would need to be science in ID to begin with. There isn't. ID is crap, and ENCODE does nothing to change that. A couple years from now, IDers will be desperately trying to spin how the ENCODE data must be wrong because it will be clear even to their slow minds that it doesn't support them at all.

      As usual, IDer puff themselves up, glom onto the research done by others, misunderstand it and misrepresent it, and try to claim victory. And as usual, the claims of IDers will be ignored as the empty garbage they have always been.

      Delete
  9. Egnor:

    Junk DNA, in the Darwinist perspective, is tangible evidence of the "random" in "random mutation and natural selection". Accordingly, Darwinists have pointed to junk DNA as very strong evidence confirming Darwin's theory.

    Bullshit. You should read Michael Lynch's "The origins of genome architecture" to get a bit up to speed with modern views on junk DNA. The role of randomness in the spread of junk DNA is not random mutation, but rather that in small populations slightly deleterious DNA can become fixed by random genetic drift. That's why bacteria, with their huge population sizes, and therefore efficient purifying selection, have almost no junk DNA. The only known Darwinian mechanism that promotes spread of junk DNA is "selfish" elements like transposons multiplying within genomes.

    ReplyDelete
    Replies
    1. @troy:

      "purifying selection". I love it.

      Of course very little of eukaryotic DNA is junk, so your "purifying selection" fairy tale is another example of Darwinian junk science.

      Eukaryotic cells in multicellular organisms have much more elaborate physiological constraints than simple prokaryotes, and much more elaborate regulation of the genome is necessary. That's the ID prediction, and the ENCODE data supports it. It puts the lie to the Darwinist crap about "purifying selection" .

      What amazes me is the tenacity with which you Darwinian assholes stick to your fairy tale. The smartest thing would be to shut up (cf PZ Myers, Jerry Coyne, Richard Dawkins) and pretend ENCODE never happened.

      So please keep defending the junk DNA hypothesis, and link it intimately to Darwinism. It makes my job so much easier.

      Delete
    2. Haha, man are you ignorant.

      "purifying selection". I love it.

      That's standard terminology in biology. Of course you wouldn't know about that. Google it.

      Eukaryotic cells in multicellular organisms have much more elaborate physiological constraints than simple prokaryotes, and much more elaborate regulation of the genome is necessary. That's the ID prediction, and the ENCODE data supports it. It puts the lie to the Darwinist crap about "purifying selection" .

      Haha, nice bluff. What are those "more elaborate physiological constraints" then? How did you derive that from ID "theory"?

      Delete
    3. Michael,

      You keep on refusing to address the problem (to ID) of broken genes - pseudogenes- of which there are thousands in the human genome, some of which are copies and some of which are actually transcribed into RNA but not translated into protein, so by the very liberal ENCODE definition of functional, they're not 'junk' DNA.

      ENCODE is early work. You shouldn't be getting too excited about its results since it will take a long time to work out its meaning. Eukaryotic genomes aren't elegant and 100% functional (the enormous variation in genome size across species indicates that).

      The eukaryotic genome works adequately well (I used that clunky formulation, because if I wrote 'the eukaryotic genome works well enough', if you quote me, you'd leave out the 'enough' as creationist liars often do), but it's a clunky solution, similar to the left recurrent laryngeal nerve in the giraffe which descends along the entire length of the neck, loops around the aorta in the thorax and then ascends most of the neck to supply the larynx, reflecting its evolutionary history.

      The eukaryotic genome reflects the evolutionary history of their owners. There's no evidence that it reflects the loving care of an omnipotent god.

      Actually, the prokaryotic genome is apparently 'intelligently designed'; lean, mean, without very little of non-coding DNA and with no introns within genes. But there's an evolutionary explanation for that too. And bacteria are the true masters of the world, thriving in environments eukaryotes can't survive, such as in geysers and rocks kilometres beneath the Earth's surface.

      Delete
    4. @troy:

      Embryological development is one of those "more elaborate physiological constraints".

      Do I really have to make the case that multicellular organisms are more complex than single cell organisms?

      Is this another example of my Holocaust denial?

      Delete
    5. @troy:

      I know what "purifying selection" is. I think the term is hilarious.

      It sounds like a libation in some fringe religious cult.

      Which it is.

      Delete
    6. Michael,

      It seems as though your 'spam filter' is malfunctioning again. A comment I posted has subsequently disappeared.

      If multicellular organisms require more DNA because of physiological constraints due to the requirements of embryological development, then why do certain single-cell amoeba have much larger genomes than humans or even the marbled lungfish? More complex? Really?

      Not Holocaust denial. Just an example of your habit of taking tiny facts out of context and inflating them beyond all recognition to suit your preconceived ideas. Similar to what you did with Rachel Carson.

      Delete
    7. Michael,

      Your 'spam filter' still seems to be over functioning. The marked variation in genome size over different eukaryotic species gives lie to your claim that physiological constraints and complex embryological development necessitate the larger genome in eukaryotes, all of it functional. Why do certain single cell eukaryotic amoeba have a genome much larger than the marbled lungfish (130 billion base pairs) let alone humans (with 3 billion base pairs)?

      Delete
    8. Do I really have to make the case that multicellular organisms are more complex than single cell organisms?

      Your ignorance shows again. There are unicellular eukaryotes (e.g. amoebae) with larger genomes than humans. Indeed, within eukaryotes there is no correlation between genome size and developmental complexity.

      Delete
    9. But there is a close correlation between cellular/nuclear size and amount of "junk" DNA, which of course "purifying selection" has no explanation for.

      Are cells with larger nuclei less... purified?

      Think troy... WWDD (What Would Darwin Do?)

      Delete
    10. Michael,

      What exactly do you mean? Large cells tend to (but not necessarily) have large nuclei. Cells actively transcribing RNA tend to have larger but paler nuclei because they have less condensed DNA (heterochromatin).

      The evolutionary biology explanation for the absence of junk DNA in prokaryotes and its presence in eukaryotes is easy. Prokaryotes multiply so quickly that often their DNA isn't completely replicated and one daughter cell misses out on a large number of genes (so for example E col can vary by up to 30% in its genome). Bacteria also have horizontal gene transfer, so any important gene can be replaced by chance in some of the deficient offspring, giving an advantage to the fortunate bacteria.

      If junk DNA occurs in bacteria, having it is a disadvantage, losing it is an advantage and regaining it through horizontal gene transfer is a disadvantage, so bacteria will lose all the junk DNA eventually.

      In eukaryotes, junk DNA tends to arise through virus infections, duplications of genes and segments of chromosomes (and mutation in the extra copies of genes) or mutations within no longer necessary genes. And there's no method for safely removing DNA because there's no mechanism for safely replacing lost genes. Keeping junk is safer than throwing out important DNA inadvertently (similar to the fact that I have a lot of junk lying around the house, usually cables or cords for pieces of electronic equipment I no longer have, but which I keep because I don't know what it's actually for and if I throw it out, I'll probably then find out that it was important for something).

      Delete
  10. How can an ignoramus like Egnor who doesn't even know the meaning of "purifying selection" profess to know anything relevant to this debate? Good God, the stupidity - it hurts!

    ReplyDelete