The important bit is at the 30 minute mark where he comments on a question about junk DNA. This is what Francis Collins said last week ...
I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.What seems like "hubris" to Francis Collins looks a lot like scientific evidence to me. We know enough to say, with a high degree of confidence, that most (~90%) of our genome is junk. And we know a great deal about the data that Collins is probably referring to (ENCODE)—enough to conclude that it is NOT saying what he thinks it says.
It would be bad enough if this were just another confused scientist who doesn't understand the data [see Five Things You Should Know if You Want to Participate in the Junk DNA Debate] but he's not just any scientist. He's a powerful man who talks to politicians all the time and deals with the leaders of large corporations (e.g. the J.P. Morgan Conference). If Francis Collins doesn't understand the fundamentals of genome science then he could mislead a lot of people.
Collins has many colleagues surrounding him at NIH and other agencies in Washington. These scientists also make important decisions about American science. I'm assuming that he reflects their opinion as well. If not, then why aren't they educating Francis Collins?
Hat Tip: Ryan Gregory
225 comments :
«Oldest ‹Older 201 – 225 of 225Mikkel:
"All DNA, once inside the nucleus, would start having some small activity in the sense ENCODE defines it, so it's a meaningless definition they use. "
Now, that's just silly. If that were true, ENCODE would have found 100% function.
Do you have a paper to show that your experiment has actually been done?
Ed Reynolds, click on the link below and read the page. Among other things you'll see this from Ewan Birney: "I was often asked whether that 80% goes to 100%, and that’s what I believe it will do."
Birney apparently likes to play games with the terms biological activity and biological function and he has been heavily criticized for equating 'activity' to 'function'. Based on his statements, and especially the one in quotes above, he obviously believes that ENCODE found at least 80% 'activity' or 'function' and that further studies would find and confirm 100%. It's also apparent that by saying 80% he thought that he would come across as being conservative, which backfired on him.
http://www.genomicron.evolverzone.com/2013/04/bbc-interview-with-ewan-birney/
Have you heard of genetic drift and neutral evolution?
You have been reading my posts here all this time and you are asking that question??
Constructive neutral evolution is a well known phenomenon. It likely played a much larger role in generating complexity during evolution than most people imagine.
However, constructive neutral evolution acts to lock things in an irreducibly complex state. Which is very different from what you are proposing.
Because let's imagine that your jDNA got to be there by drift (that's indeed exactly how it got there). The problem is that it stays there again because of drift and there is no selection mechanism to keep it there, for the same reasons why its presence could not have been selected for in the first place - the deletions would be too small to be visible for selection.
So we have extra DNA that got fixed by (nearly) neutral processes, and remains in the genome because of neutral processes. Why the hell do we need to ascribe any function to it if that is the case? That's a completely unnecessary additional explanatory layer. Everything is explained perfectly fine by the interplay between mutational processes, selection and drift. Sure, it can have causal influence on a wide variety of things. But the word "function" has not place here.
"Now, that's just silly. If that were true, ENCODE would have found 100% function."
No it isn't Ed, the problem is that you don't understand what the ENCODE project measured, or how they measured it. With even more sensitive essays, they'd pick up the rest of the genome as being active too.
And yes, I have a paper that shows random DNA to be "active" in the sense ENCODE defines it. Here is a nice blogpost on the paper, accessible to laymen: http://www.homolog.us/blogs/blog/2013/07/17/random-dna-sequence-mimics-encode/.
Mr. Reynolds, can you define function according to ID?
Instead of demanding proof for evolution, proof you won't accept and haven't accepted anyway, it's time for you to provide a definition of function according to ID.
And with the ID definition of function in mind, what's the percentage functional DNA in the human genome according to ID?
Georgi Marinov, Tuesday, February 03, 2015 11:35:00 PM:
“Because let's imagine that your jDNA got to be there by drift (that's indeed exactly how it got there). The problem is that it stays there again because of drift and there is no selection mechanism to keep it there, for the same reasons why its presence could not have been selected for in the first place - the deletions would be too small to be visible for selection. So we have extra DNA that got fixed by (nearly) neutral processes, and remains in the genome because of neutral processes. Why the hell do we need to ascribe any function to it if that is the case?”
Are you saying that the genomic sequences that “got to be there by drift” and “stays there again because of drift” cannot have biological functions?
Ed,
I've come across no "special" definition that ID uses.
I imagine most ID pro's defer to the experts who worked on the ENCODE project themselves.
Over 400 scientists.
About Half a Billion dollars worth of research.
I think they know what they're talking about.
Instead of crying about it like Morons, what the biochemists need to do is take that research ahead, by trying to determine what these active genes ARE doing.
So, grow up and giddyup. There's a whole world to explore in the genome; don't think you have it all figured out. That's bad for science.
"Over 400 scientists."
Almost none of which were behind reporting the "functional" number. This sensationalistic declaration was decided on by a small handful of people for PR reasons.
"About Half a Billion dollars worth of research.
I think they know what they're talking about."
On that sentiment alone it would seem incredibly hypocritical of you to simultaneously reject the theory of evolution, attested to by over 150 years of research and hundreds of thousands of scientists, while accepting the ENCODE project results simply because they agree with your preconceptions.
Rarely does one come upon a case of such obvious bias.
"what the biochemists need to do is take that research ahead, by trying to determine what these active genes ARE doing."
"Active genes"? Where the hell did you get this form Ed, it's not even in the ENCODE papers. You seem to have simply invented this phrasing out of thing air.
They aren't genes Ed, it's just strings of DNA that is "biochemically active" only in the sense that a transcription factor of some sort will occasionally bind itself weakly to it for a short time before letting go again or skirting along. That's it.
It is interesting to see how your psychology works here, putting in conclusions noone has argued for and the data does not support. So the ENCODE project alluded to the possibility that maybe as much as 80% of our genome is "functional" in the sense that it is "biochemically active", and now you've somehow got the idea in your head there are "active genes". Zero basis for this inference is given anywhere, you simply dreamt it up from your own preconceptions.
I wonder what 2000 years of having gullible people like you transmit the ENCODE project PR stunts by memory and word of mouth would end up with. I can sort of imagine.
Apologies for the spelling, can't be bothered correcting it now. :P
Curious how Mr. Reynolds is quick to choose new areas of debate to pursue without acknowledging or answering corrections of his misconceptions.
CREDIBILITY ALERT: Famous Darwinist caught twisting the words of opponents - AGAIN.
Mikkel says:
"But all by itself, it doesn't try to explain how either the features or the ancestor got there in the first place, or why descendants differ."
And thus Michael Behe is directly lying to you. Directly lying. Yes, I repeat, Michael Behe is unambigously and directly lying to you Ed. And you're buying it, because you don't have enough of a background in the subject to know whether it's true or not. You just trust it, blindly.
...
Do you understand the question here Ed? Michael Behe says evolution merely tries to account for the fact that there are shared similarities. This is what is a lie...
-----------------------------
If you had any idea what Behe was saying in Chapter 1 of EDGE OF EVOLUTION, you probably wouldn't have called him a liar.
Behe's discussion here rests on his statement:
"...Darwin's theory has to be sifted carefully, because it isn't just a single concept - it actually is a mixture of several unrelated, entirely separate ideas. The three most important ideas to be kept straight from the start are random mutation, natural selection, and common descent."
Behe said that COMMON DESCENT on its own only explains the similarities between species, and cannot explain HOW the DIFFERENCES arise in the first place.
He then proceeds to say:
"In contrast, Darwin's hypothesized MECHANISM of evolution - the compound concept of random mutation paired with natural selection...tries to account for the DIFFERENCES between creatures."
This is all within the FIRST FIVE PAGES of his book - simple stage-setting for a clear understanding of his topic.
This is the SECOND TIME I've caught you twisting of your opponents' concepts in order to argue against a straw man. This, along with your childish accusation that he was lying, compromises your scientific integrity and shows your dishonest nature. From now on, I need not take any of your explanations at face value, because, from uniform and repeated experience, you are a Moron.
Ed Reynolds said: "So, grow up and giddyup. There's a whole world to explore in the genome; don't think you have it all figured out. That's bad for science."
Yep, there's a lot to explore in genomes and everything else in nature. No credible scientists think that they have everything figured out, and that's why they're still exploring. Religious people like you are the ones who think that you have all the answers, or at least the 'ultimate' answer.
'God-did-it' is not a legitimate answer/conclusion and it's certainly not scientific, especially when considering the impossible fairy tales that have been and/or are used in lame attempts to support the existence, powers, and deeds of alleged 'Gods'.
In addition to the questions I asked you above, which you haven't answered, I have some more questions:
Why don't you believe in and worship Zeus, or Odin, or Ra, or the Mahadevas, or some other 'God(s)', instead of yhwh-jesus-holy-ghost?
What scientific evidence can you provide that was found via scientific exploration that supports the alleged existence, powers, and deeds of your chosen 'God' over the alleged existence, powers, and deeds of every other alleged 'God' that has ever been imagined, believed in, worshiped, and promoted?
If somehow it were discovered that there was/is a 'creator' of the universe (including life, humans, etc.) and the 'creator' was/is nothing at all like your chosen 'God', would you accept and admit that your beliefs are wrong and discard them?
Do you believe that everyone who didn't and doesn't believe in and worship yhwh-jesus-holy-ghost will suffer in a lake of fire for eternity and will deserve to do so?
Do you believe that Satan and demons exist?
Mr. Reynolds,
"I imagine most ID pro's defer to the experts who worked on the ENCODE project themselves."
One of the scientists of ENCODE, Georgi, has tried many times to explain to you, but your own bias prevents you to sit down, listen and learn, that your warped conclusions aren't what ENCODE said.
But, when confronted with these unconvienient answers you just STICK THE FINGERS IN THE EARS AND GO BLAH BLAH BLAH out loud.
Anyway, if you can't find an ID definition of function, and ENCODE doesn't support your warped and biased conclusions, do tell, how can the ID crew know there's no junk DNA and everything has a function?
Mr. Reynolds, I have his fucking book. Tell me where he gives the ID account for substitution biases.
Fuck, tell me where he even MENTIONS substitution bias.
I'll tell you: Nowhere in the entire book. Nowhere. Not a smidgeon is mentioned about the particular mutational distributions one gets from transition bias, nothing is mentioned about that these are actually found in comparative genetics, and nothing is done to give an ID account for them.
You DON'T get a clear understanding of the topic from Behe, he gives you deliberate misinformation, because he leaves out (deliberately, one cannot so consistently happen to forget it in all of one's written work) extremely important details.
So Mr. Reynolds, here's what I want YOU to do: Find where substituion bias is predicted in the ID litterature, where it is mentioned, and where it is accounted for with an ID explanation.
I can give you a quick first hint to save you some time: Don't bother looking in any of Michael Behe's books.
Ed R, Cellular mechanisms have to 'examine' DNA in order to determine what, if anything, to do with it. Frequently, it will be converted to RNA first before it is found to be nonsense. Therefore, all DNA is potentially a substrate for something. This is what ENCODE looked at - binding, transcription. This does not equate to function, any more than a random string of bits is functional because it can be parsed by software.
Over the last few weeks, Quest has left several comments on this and other threads I was also commenting, only to see them deleted, I presume by our host Larry. Yesterday, for example, he left this rather insightful comment here:
“Quest, Wednesday, February 04, 2015 8:02:00 AM
Claudia Bandea,
Giorgi is desperately trying "to stop the bleeding" but has not means...It is pretty painful to watch people like that who claim to be intelligent who are trying to hang on to their beliefs at any cost...No scientific integrity...Just pride....”
Well, Quest did not spell my name right, which is one of his colorful trademarks, but I thought that his comment, which was a fine example of clear and confident reading comprehension, was right on the money. To quote Quest, it is indeed “pretty painful to watch people like that who claim to be intelligent who are trying to hang on to their beliefs at any cost… No scientific integrity...”
However, as I have pointed out before, ultimately, it is not their fault, as these scientists are themselves victims of the distressing science system in which we operate, which encourages and rewards dishonesty and hype (see my comments at: http://www.ncbi.nlm.nih.gov/pubmed/23479647, and http://liorpachter.wordpress.com/2014/04/30/estimating-number-of-transcripts-from-rna-seq-measurements-and-why-i-believe-in-paywall/).
Claudiu, I don't see any comments by you or anyone else at the PubMed page that you linked to.
On another note, after reading the article and all of the comments at Lior Pachter's site I came away with the feeling that ENCODE was/is mostly a huge waste of money and that at least some of the ENCODE scientists have a lot to learn.
My comments at PubMed are on: Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA., 110:5294-300:
http://www.ncbi.nlm.nih.gov/pubmed/23479647
Here is a different link to my comments at PubMed Commons: http://www.ncbi.nlm.nih.gov/myncbi/claudiu.bandea.1/comments/
You can also go to PubMed Commons and search for comments by a specific author: http://www.ncbi.nlm.nih.gov/pubmedcommons/
Regarding the data produced by ENCODE it has some value, but not at the level described by the leaders of the project. On the other hand, the promotional fiasco set on the side by these leaders was an embarrassment to the entire field of genome biology.
Claudiu, thanks for the links.
Denyse "Old News" O'Leary has just put up a new OP at Uncommon Descent:
http://www.uncommondescent.com/junk-dna/is-dark-genome-becoming-the-new-name-for-junk-dna/
As for the author of the book: Professor Moran, please think twice before you click on the link below. It's dangerous, almost like the Monthy Python "Killer Joke".
http://www.nessacarey.co.uk/
And here's a Q&A page by someone who's just written a book about junk DNA. Just the basics.
(The same warning as above applies.)
I am taking long deep breaths and trying to calm down. I think Dan Graur might have a heart attack. I hope he doesn't learn about this book.
From the description on Amazon:
Junk DNA can play vital and unanticipated roles in the control of gene expression, from fine-tuning individual genes to switching off entire chromosomes.
Sigh...
Publisher: Columbia University Press
I have never had any dealing with them but my understanding is that university presses do review what they publish, don't they?
Bit it's "a cutting-edge, exhaustive guide to the rapidly changing, ever-more mysterious genome". Haven't you seen the New Scientist review?
As Mr. Kurtz put it, 'The horror! The horror!'
Larry, every year that goes by your ravings about junk DNA will appear to be more and more insane. Keep going. I think it's funny.
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