ENCODE hype? From now on I’ll just reply: #oniontest

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The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.

However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”. People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.

Anyway, I’d write more, but I’m jammed and Ryan Gregory has said everything I would say, except better: http://www.genomicron.evolverzone.c[…]encode-hype/

See also Larry Moran: http://sandwalk.blogspot.com/2012/0[…]-of-our.html, especially the rather wry comments.

Hashtag: #oniontest

111 Comments

Yeah, it would have been better for everybody if the ENCODE team had dubbed their findings “potentially active” or something along those lines instead of hijacking a term that is used differently in the same field.

The creationists couldn’t care less what the actual result is, as long as SOME scientists said something else.

If creationists actually wanted to say anything about this, then they should have made a prediction long ago. The prediction needed to include an estimate of this perceived functionality and why their notions say so. They also need to explain why it is discriminatory between creationism (including ID) and science.

Just because someone is ‘wrong’ (for some value of wrong) about something, that doesn’t mean that the opposing side is right. Creationists NEVER EVER learn that simple truth. Which means that they are doomed to failure every single time.

Failure? Sorry. To fail, one must try. Creationists (including IDiots) never ever try.

Well, this just means that twenty percent of the genome isn’t functional, by even the most liberal definition of the term. So creationists lose again. Now why would they claim victory if the facts are actually still against them? What? … Oh. Never mind.

The interesting comment here to me is saying lots of SMART people go through education in “science” subjects but unless they concentrate their thinking on a particular subject then their opinion is not as relevant as those who do concentrate/study. Creationists always complain the “scientific community” agreeing by vote with evolution counts as intellectual understanding behind the merits of the contention. In fact only those who study “evolution’ etc can claim to be scientists in the subject and as authority that creationists must respect and address. Not the others and no points for family support.

When the DNA structure was first being defined and analyzed, it was asserted by someone that it mostly non-functional, an assertion based solely on initial and preliminary investigations. That view has changed over time as more and more research continues into DNA/RNA structures. However, that perspective is changing due to increased scrutiny and research of DNA as well as other biological experimentation. But so what. Even if DNA is 100% functional, so to speak, that has no implications regarding it as having been ‘designed’ by some supernatural deity. There is no credible link to be made, only empty creationist assertions to that effect.

If 100% of the genome, or 80% of the genome, is not “junk” then we just have to adjust to that. But these seem unlikely to be true. The most general definition of non-junk DNA I can think of is DNA whose base sequence (at a site) makes a noticeable difference to the organism’s fitness. And noticeable does not just mean noticeable by us in a lab, it means big enough to affect the outcome of evolution. Population genetic theory shows that this means that the selection coefficient (the fractional difference in fitness) is bigger than ±1/(4N), where N is the effective population size. That is a small number but not zero.

Just because something is transcribed into RNA does not necessarily mean that it makes that much difference in fitness. Is that the criterion they are using?

I should add some comments on why creationists are upset about there being any noticeable amount of junk DNA. I say “creationists” because it is creationism, not specifically ID arguments, that is at issue.

Creationists don’t like junk DNA because:

1. It is something that can’t be explained by a Designer, unless she is someone who is trying to confuse us or make us think that the organisms arose with common descent. If it is junk, then it is difficult to conceive of any functional purpose except perhaps as a message to us. And a confusing one at that.

2. Similarities in junk DNA are evidence for common descent. They can be explained by it. If you try to explain those similarities by “common design” you run afoul of point 1 – what could be the point of that design?

Creationist and ID debaters are quick to disparage “bad design” arguments. They usually argue that we cannot judge what is good and bad design in the mind of the Designer. But after taking that lofty position, they run into junk DNA and don’t like it because that would be bad design. It seems to me that they can’t have it both ways (but they of course do anyway).

They often argue that the absence of junk DNA is a prediction of Intelligent Design. I think that when they argue that, people should ask them exactly where this prediction was made. William Dembski’s arguments do not address the issue. Nor do Michael Behe’s. So where did this prediction take place? Is it a theological prediction rather than a scientific one?

They also often argue that “Darwinism” needs junk DNA to be present. Actually evolutionary biologists did not predict it originally, though they wondered in the 1950s how there could be that much DNA in the genome if it all was under natural selection. Ohno’s arguments in 1969 made the case, and eventually the reality of substantial amounts of junk DNA was accepted. You won’t find arguments favoring the existence of junk DNA in the pre-1969 papers of Fisher, Wright, and Haldane, and no mention of it in pre-1969 writings of founders of the Modern Synthesis such as Mayr, Simpson, Dobzhansky, Huxley, and Stebbins. (I wonder, though, whether H. J. Muller won’t be discovered to have suspected its existence).

DavidK said:

When the DNA structure was first being defined and analyzed, it was asserted by someone that it mostly non-functional, an assertion based solely on initial and preliminary investigations.

That’s news to me. Who? Have you got a reference? Maybe as a mention in a textbook?

The interesting comment here to me is saying lots of SMART people go through education in “science” subjects but unless they concentrate their thinking on a particular subject then their opinion is not as relevant as those who do concentrate/study

There there’s you, who knows pretty much nothing about any subject, and won’t ever shut up despite your throughly demonstrated incompetence in biology, geology, general science, history, theology, law, spelling, grammar and style. Your poorly-formatted and un-proofread ramblings do an excellent job of showing the abject ignorance and nonsense of your pet idea and its supporters every day, and for this I thank you.

Joe Felsenstein said:

If 100% of the genome, or 80% of the genome, is not “junk” then we just have to adjust to that. But these seem unlikely to be true. The most general definition of non-junk DNA I can think of is DNA whose base sequence (at a site) makes a noticeable difference to the organism’s fitness. And noticeable does not just mean noticeable by us in a lab, it means big enough to affect the outcome of evolution. Population genetic theory shows that this means that the selection coefficient (the fractional difference in fitness) is bigger than ±1/(4N), where N is the effective population size. That is a small number but not zero.

Just because something is transcribed into RNA does not necessarily mean that it makes that much difference in fitness. Is that the criterion they are using?

First of all, just creationists idiotically “celebrating” because an obvious piece of evidence against creationism has been in some way discussed (the authors here are obviously not arguing for creationism nor against the concept of non-functional DNA).

It’s also worth noting that is that “junk” is a relative and subjective term. I do agree that it’s the best widely accepted general term for a certain broad set of types of DNA sequences found in eukaryotic genomes.

Obviously, there are things like LINES, SINES, ERVs, pseudogenes, and so on, which we can explain the origins of, which were clearly not directly adaptive for humans at their time of origin. By human values, “junk” in a highly reasonable sense.

But lots of DNA that doesn’t code for a protein or miRNA is at least expressed, usually due to promiscuous expression.

Genes can be used no matter how they got there. An ERV protein has been co-opted by some but not all mammals (including humans) for an important role in placental biology.

If it’s DNA it can theoretically be expressed, either if it becomes associated with appropriate regulatory elements, or even at a low level without that. And if it’s DNA it can be transposed. And if those things happen it can hypothetically “do” something. And then, and not just with creationists, but also between scientists, the semantic question of whether or not it is still “junk” gets rolling. It may do something bad, in which case most would agree it’s still junk, but it may do something neutral or even beneficial.

Bacteria really don’t have “junk” DNA to any serious extent. It’s a eukaryotic phenomenon. Yet this is not evidence that bacteria were magically created.

I understand that the existence of “junk” DNA is taken as an argument for “bad design”, and I agree that it is, but I never liked the whole “bad design” approach anyway. It involves applying subjective human values to a hypothetical creator deity.

I prefer to note that if the “designer” did create all species instantaneously, she made it look exactly like evolution to me. The types of DNA we call junk certainly provide evidence for evolution, and still will if we begin calling them “platinum executive plan DNA”. Where’s the positive evidence, not silly selective denial of evidence against it, positive evidence for

Robert Byers said:

The interesting comment here to me is saying lots of SMART people go through education in “science” subjects but unless they concentrate their thinking on a particular subject then their opinion is not as relevant as those who do concentrate/study.

Robert, nobody is claiming the ENCODE scientists’ conclusions are wrong. They are claiming that how the ENCODE scientists define ‘functional’ does not match up with how you, I, and most other people would define ‘functional.’

I’m sure the work will be relevant and useful to future biological research. The issue is whether it supports the vernacular conclusion you (or I, or most people) might draw from the headline. The commenters are saying: it doesn’t.

Oops, forgot my ending comment:

Robert, this is a squabble about how to present results; over what a set of results means. It is not a squabble over whether the results are good science.

Robert Byers said:

The interesting comment here to me is saying lots of SMART people go through education in “science” subjects but unless they concentrate their thinking on a particular subject then their opinion is not as relevant as those who do concentrate/study. Creationists always complain the “scientific community” agreeing by vote with evolution counts as intellectual understanding behind the merits of the contention. In fact only those who study “evolution’ etc can claim to be scientists in the subject and as authority that creationists must respect and address. Not the others and no points for family support.

So why don’t you Byers? Why do you have no respect at all for any of the real professional biologists who study evolution for a living? Why are you so willing to dismiss all of the evidence and all of the conclusions drawn by the real experts simply because you don’t want to believe it? Do you do this in other fields as well? Why should anyone care what you think when you can’t even be bothered to spell Dna correctly? Keep it up dude. You are the best argument against creationism ever invented.

Now, are you willing to admit that at least twenty percent of your genome is “junk”? Are you willing to admit that no intelligent designer would do such a thing? Are you willing to admit that this is exactly what one would expect if the human genome evolved over millions of years? Are you willing to listen to the experts who you obviously respect so much? Or are you just gonna put your hands over your ears and scream “intelligent design” at the top of your lungs whether it makes any sense or not?

That’s what I thought.

FYI… From Discovery Magazine:

And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”

Joe Felsenstein said:

DavidK said:

When the DNA structure was first being defined and analyzed, it was asserted by someone that it mostly non-functional, an assertion based solely on initial and preliminary investigations.

That’s news to me. Who? Have you got a reference? Maybe as a mention in a textbook?

See the wikipedia article at http://en.wikipedia.org/wiki/Junk_DNA

under the subsection Junk DNA

More on the problem with how these results were reported. Unfortunately, due to bad reporting and the wording of the press release, the actual results (which give us a better understanding of the biochemistry going on inside the cell) are being overshadowed by all the hype.

Just for argument’s sake, let’s suppose that IDiocy makes any real predictions (how can they when the “designer” is neither identified nor characterized?) and that this actually fits their “prediction”.

OK, the real non-teleological evolutionary prediction is the slavishly derivative nature of life, whether horizontally where this is known to occur, or vertically in the case of most vertebrates and many other eukaryotes. How does ID account for life being fraught with evidence of such evolutionary limitations, which all known species of designer (us, essentially) readily transcend?

That’s right, it doesn’t, it just pretends that it doesn’t matter.

Any evidence of forethought, planning, complete novelty, or rationality in life? No? Then there is no evidence for design in life, and (see above) endless evidence of the evolution of life.

Glen Davidson

veritea - a completly unsurprising and unremarkable prediction given their uber-broad definition of ‘functional.’

Yeah, based on their defition of functional, 100% of the genome (or close to it) probably IS functional.

Why not? Is there any reason to believe that rearranging the ATCG subunits will make a biologically active polymer into a non-biologically active one?

There’s still the fact that the amoeba has a genome about ten times larger than ours. Is it all functional? And there’s a Japanese flower with a genome 50 times larger than ours. There must be some junk in there somewhere.

SensuousCurmudgeon said:

There’s still the fact that the amoeba has a genome about ten times larger than ours. Is it all functional? And there’s a Japanese flower with a genome 50 times larger than ours. There must be some junk in there somewhere.

That’s something I find interesting. If the position of ID finds “complexity” to be so important, and (by their apparent definition) man must be more “complex” than any other animal, then the obvious conclusion would be that man would have a larger genome than any other organism.

Conversely, since a creature that is essentially a little blob of goo has a larger genome than we do, maybe you could say that our complexity reduces the amount of genome necessary for us to exist. Of course since you can then point to organisms (of varying levels of apparent complexity) that have smaller genomes than man.

In other words, comparing genetic complexity grants a perfect example of what you would expect from a process of evolution: A sloppy, chaotic mess.

More on the topic of the OP: If IDers want to insist that all DNA is functional (which not all stand by) then there is a “victory” requirement that they commonly seem to ignore:

Proving 100% DNA functionality means proving that every gene in a human is meaningful and functional, as well as every gene in an amoeba, every gene in a radish, every gene in a diplodocus, every gene in a strange warthog-like creature that lives on a planet 2,000 light years away, etc., etc.,etc. Put simply, in order to claim that there is NO non-functional DNA, you must be able to show that ALL genetic material that ever existed has function.

SonOfHastur said: That’s something I find interesting. If the position of ID finds “complexity” to be so important, and (by their apparent definition) man must be more “complex” than any other animal, then the obvious conclusion would be that man would have a larger genome than any other organism.

Another obvious (and amusing) ID conclusion from the onion test is that what modern science considers different varieties of onions must actually be different “kinds” and separately created. Because in the genetic difference between some onion varieties is not just bigger than the genetic diffence between humans and chimps, the difference is bigger than the entire human genome. ;)

eric said:

SonOfHastur said: That’s something I find interesting. If the position of ID finds “complexity” to be so important, and (by their apparent definition) man must be more “complex” than any other animal, then the obvious conclusion would be that man would have a larger genome than any other organism.

Another obvious (and amusing) ID conclusion from the onion test is that what modern science considers different varieties of onions must actually be different “kinds” and separately created. Because in the genetic difference between some onion varieties is not just bigger than the genetic diffence between humans and chimps, the difference is bigger than the entire human genome. ;)

That’s very cool.

Similar to dogs. The morphological differences between dog species is larger than the morphological difference between all other carnivores combined.

DavidK said:

Joe Felsenstein said:

DavidK said:

When the DNA structure was first being defined and analyzed, it was asserted by someone that it mostly non-functional, an assertion based solely on initial and preliminary investigations.

That’s news to me. Who? Have you got a reference? Maybe as a mention in a textbook?

See the wikipedia article at http://en.wikipedia.org/wiki/Junk_DNA

under the subsection Junk DNA

OK, that’s Susumu Ohno in 1972, nearly 20 years after Watson and Crick. I was thinking you were talking about the period right after 1953. The only hint in the 1950s of an issue of whether the DNA was all functional was the “c value paradox” that amounts of DNA did not correlate with complexity of organisms.

It would be nice if the ENCODE people had at least mentioned the c-value paradox. Yet another example of biologists who concentrate unduly on model organisms forgetting the value of comparative studies. I wonder how they would respond on the question. Do other species (e.g. onions) have lots of junk, and it just happens that humans have very little? How would they deal with fugu? I doubt we’ll be seeing any answers to those questions.

And can anyone tell me how I stop being a masked panda and start being me instead? John H.

Never mind. I figured out a workaround

As far as I can tell, EVEN IF we should discover some function, either active or passive (like alignment) for 100% of the base pairs in our DNA, this would still be consistent with evolutionary processes. And if we should establish beyond reasonable doubt that some hefty percent does absolutely nothing, that’s consistent with evolutionary processes as well. And of course ANY finding whatsoever is consistent with an unknown designer doing unpredictable things for unknowable purposes.

So where’s the problem here?

I think there would be significant evolutionary problem if 80% of the genome really were functional(*). If 80% were functional, then every human would be born with ~60 new deleterious mutations. There has been a low-key debate for a long time about whether a deleterious mutation rate of ~3 per birth would impose too high a genetic load on humans; 60 strikes me as extremely unlikely.

(*) Where “functional” has any definition recognizable by competent speakers of English, i.e. not the idiotic definition used in the ENCODE papers.

harold said:

A strong argument could be made that many organisms are more “advanced” than humans in many ways.

The feline philosopher Hobbes (in the comic strip “Calvin and Hobbes”) says to the boy Calvin with disdain, “Your fingernails are a joke, you’ve got no fangs, you can’t see at night, your pink hides are ridiculous, your reflexes are nil, and you don’t even have tails!”

[There’s Treasure Everywhere, by Bill Watterson, 1996, page 157]

T. Ryan Gregory has links to several pieces critical of the ENCODE hype.

ksplawn said:

A piece just went up on Ars Technica about the writer’s frustration with the way the ENCODE team and the media have been crowing about “functional” DNA in their findings. Mostly he seems to be tired of the attention-seeking gimmick that any piece of non-coding DNA that turns out to maybe do something under some conditions is touted as a radical overturning everything we thought we knew about genetics, and how the University press offices and the researchers themselves seem to be more than just complicit in promoting this distortion.

James Shapiro has just posted his latest piece of breathtaking inanity over at HuffPo. Not surprisingly, he reminds his readers of the two papers he co-authored with Rick Sternbergy, now of the Dishonesty Institute, which he claims anticipated the ENCODE results. I’m not really qualified to comment further since I don’t have a background in molecular biology, but feel free to stop by to chime in:

http://www.huffingtonpost.com/james[…]1873935.html

IMHO this is but his latest effort in grossly distorting public understanding of science, using this as “evidence” of his proposed “paradigm shift” for biology that will feature his uniquely weird Neo-Lamarckian theory of evolution relying on “Natural Genetic Engineering” and the “cognitive behavior” of cells.

I’m sure some of you will appreciate these observations of Shapiro’s, replete in their breathtaking inanity:

In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”

These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.

The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.

Faye Flam has an excellent overview behind the history of science related to the ENCODE paper as well as what it really tells us about Junk DNA here:

http://www.philly.com/philly/column[…]up_to__.html

I’d also recommend John Farrell’s take over at Forbes, in which he cites Larry Moran extensively:

http://www.forbes.com/sites/johnfar[…]exaggerated/

Finally, I am indebted to Diogenes for stopping by at HuffPo to challenge Shapiro’s lies about the ENCODE paper. Hope others will follow suit:

http://www.huffingtonpost.com/james[…]1873935.html

John said:

James Shapiro has just posted his latest piece of breathtaking inanity over at HuffPo. Not surprisingly, he reminds his readers of the two papers he co-authored with Rick Sternbergy, now of the Dishonesty Institute, which he claims anticipated the ENCODE results. I’m not really qualified to comment further since I don’t have a background in molecular biology, but feel free to stop by to chime in:

http://www.huffingtonpost.com/james[…]1873935.html

IMHO this is but his latest effort in grossly distorting public understanding of science, using this as “evidence” of his proposed “paradigm shift” for biology that will feature his uniquely weird Neo-Lamarckian theory of evolution relying on “Natural Genetic Engineering” and the “cognitive behavior” of cells.

I’m sure some of you will appreciate these observations of Shapiro’s, replete in their breathtaking inanity:

In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”

These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.

The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.

That’s funny, I don’t recall him ever predicting that twenty percent of the human genome would turn out to have no discernable function at all, even given the most relaxed definition of “function” imaginable. The genome is definitely not well organized, or well ordered or intelligently designed, or anything like that. As for transposable elements, most of them do absolutely nothing, unless of course they harm the organism. Most of them could cause harm in the future, that would be their most likely “function”. You can’t say they might do something useful later unless you are willing to give up the “no beneficial mutations” and “no increase in information” and “no genetic innovation” nonsense.

The ENCODE results give absolutely no credence whatsoever to any creationist= scenario. Big surprise. And if you think that it does, just ask yourself, why aren’t they the ones who actually performed the research?

Why are you ignoring so much scientific research? Surely hundreds of scientists, 30 papers and 80 testing methods would have caught some sort of error before the finding was published.

Here’s my full critique of your article:

http://tcrcreation.blogspot.com/201[…]rturned.html

TChapman500 said:

Why are you ignoring so much scientific research? Surely hundreds of scientists, 30 papers and 80 testing methods would have caught some sort of error before the finding was published.

Here’s my full critique of your article:

http://tcrcreation.blogspot.com/201[…]rturned.html

Why are you ignoring the hundreds of thousands of papers that demonstrate that evolution has occurred?

By the way, you are incorrect when you claim that “the creationist prediction that entire genome has a function because it was designed to have a function has been fulfilled”. You seem to be ignoring the papers you claim that others are ignoring. Read them again.

DS said:

TChapman500 said:

Why are you ignoring so much scientific research? Surely hundreds of scientists, 30 papers and 80 testing methods would have caught some sort of error before the finding was published.

Here’s my full critique of your article:

http://tcrcreation.blogspot.com/201[…]rturned.html

Why are you ignoring the hundreds of thousands of papers that demonstrate that evolution has occurred?

If not millions of such papers. Then again, why should such papers be allowed to matter if they dare to contradict the sacred Holy Bible?

By the way, you are incorrect when you claim that “the creationist prediction that entire genome has a function because it was designed to have a function has been fulfilled”. You seem to be ignoring the papers you claim that others are ignoring. Read them again.

Plus, there is the problem of how creationists merely said that to merely to spite and contradict anything Evolutionary Biologists say.

And there is the worse problem of how creationists never actually did anything to discover or to research that “the entire genome has a function because it was designed to have a function” to begin with.

Larry Moran weighs in on Shapiro’s jubilation with the ENCODE papers:

http://sandwalk.blogspot.com/2012/0[…]dit-for.html

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

I see you haven’t lost your Klingonese accent. Anyway, why don’t you take in another visit to the MMoA. So much design on display. Sooner or later you will hopefully ‘stumble’ upon a Klingonese translation for design.

Btw, here is a new English word you ought to have translated. Biosemiotics. UP over at UD was nice enough to introduce this lovely word. Rolls nicely off the tongue.

Whats so funny is how much more science I am learning over at UD and ENV than I am here.

A curious thing.

John said:

Faye Flam has an excellent overview behind the history of science related to the ENCODE paper as well as what it really tells us about Junk DNA here:

http://www.philly.com/philly/column[…]up_to__.html

I’d also recommend John Farrell’s take over at Forbes, in which he cites Larry Moran extensively:

http://www.forbes.com/sites/johnfar[…]exaggerated/

Finally, I am indebted to Diogenes for stopping by at HuffPo to challenge Shapiro’s lies about the ENCODE paper. Hope others will follow suit:

http://www.huffingtonpost.com/james[…]1873935.html

Steve P. said:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

Too bad you leave out the part of exactly how “Diogenes got his ass handed to him,” by Shapiro. I read the comments and it looks like the typical Shapiro style of dodging the questions by providing non answers. Perhaps you should read the comments a second time. Maybe you should read them a first time, preferably with a little comprehension.

Btw, here is a new English word you ought to have translated. Biosemiotics. UP over at UD was nice enough to introduce this lovely word. Rolls nicely off the tongue.

So does BS.

Whats so funny is how much more science I am learning over at UD and ENV than I am here.

A curious thing.

There is nothing curious about it at all. It is totally expected of you. You merrily wave away real evidence and science that is provided to you for free here on Panda’s Thumb in favor of what you dogmatically believe is science on UD and ENV. The joke is still on you, silly.

Steve Proulx the delusional expatriate American rug merchant residing in Taiwan barfed:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

I see you haven’t lost your Klingonese accent. Anyway, why don’t you take in another visit to the MMoA. So much design on display. Sooner or later you will hopefully ‘stumble’ upon a Klingonese translation for design.

Actually, Shapiro exhibited typical “Disco Tute” behavior in his exchanges with Diogenes. (As an aside, I’ve recommended to Shapiro that a better home for his blogging would be ENV anyway, jackass.)

As for the Metropolitan Museum of Art, the next time you’re in New York City and want to have a “pow wow”, we’ll meet downstairs in the cafetaria; I’ll be sure to have friends from museum security keeping a very, very close eye on you, just to ensure that you don’t go apeshit crazy.

Steve P. said:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

I see you haven’t lost your Klingonese accent. Anyway, why don’t you take in another visit to the MMoA. So much design on display. Sooner or later you will hopefully ‘stumble’ upon a Klingonese translation for design.

Btw, here is a new English word you ought to have translated. Biosemiotics. UP over at UD was nice enough to introduce this lovely word. Rolls nicely off the tongue.

Whats so funny is how much more science I am learning over at UD and ENV than I am here.

A curious thing.

That’s funny, I completely missed the part where he explained why the intelligent designer put twenty percent junk into the human genome. I also missed the part where he explained the exact insertion points for many of the junk elements and how it is completely consistent with descent with modification and completely inconsistent with common design.

See the thing is that until creationists start dealing with the actual evidence instead of just making crap up and attacking straw men, they are not going to get anywhere. Now if Stevie would only learn some real science instead of swilling crap from liars and charlatans, then maybe he would eventually get the idea. UNtil then all of his bluff and bluster ring hollow.

DS said:

See the thing is that until creationists start dealing with the actual evidence instead of just making crap up and attacking straw men, they are not going to get anywhere.

Other than a few of them getting richer from swindling the stupid Faithful who have been ordered/conditioned to fork over money whenever a Fraud For Jesus says to.

Now if Stevie would only learn some real science instead of swilling crap from liars and charlatans, then maybe he would eventually get the idea.

SteveP repeatedly demonstrates that he would sooner commit suicide than make an attempt to learn real science instead of swallowing anti-science propaganda crap without hesitation. Hell, SteveP even said that he’s far too busy making money hand over fist in the fabric industry in Taiwan than to make an attempt to learn science (even though he hypocritically always makes time to troll here).

Until then all of his bluff and bluster ring hollow.

And the sadder thing is that SteveP remains pitifully unaware of this. But, how can one be aware that one’s bluff and bluster is impotent when one is programmed only to insult those who don’t share one’s mindless hatred of science?

Steve P. said:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

You lying piece of shit! I crushed that drooling moron Shapiro. If you think Shapiro made any good points at all, why don’t you copy and paste his best point right here, you pussy?

I normally don’t tangle with you, Steve, because slapping the mentally handicapped is beneath me.

But come on, you pussy, copy and paste Shapiro’s best point right here, or else go fuck yourself. Do it right now, you fuckhole.

I suggest you re-read Michael White’s blog post here. I posted 7-8 comments in which I gave about 2 dozen quotes of ENCODE scientists THEMSELVES admitting that they had not disproved the Junk DNA hypothesis.

Why are you disputing what the ENCODE scientists now admit– that most of the genome is probably still junk? They admitted it, and they admitted that they didn’t disprove the Junk DNA hypothesis.

HuffPost wouldn’t let me tell Shapiro how horrible his blog was– they ditched my comments. So come get me here, pussy. COME GET ME, PUSSY.

I listed about two dozen quotes over there. Why don’t you address that, asshole?

Keelyn said:

Steve P. said:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

Too bad you leave out the part of exactly how “Diogenes got his ass handed to him,” by Shapiro. I read the comments and it looks like the typical Shapiro style of dodging the questions by providing non answers. Perhaps you should read the comments a second time. Maybe you should read them a first time, preferably with a little comprehension.

Keelyn, several of the comments I posted at Shapiro’s blog, in which I listed quotes from ENCODE scientists admitting they hadn’t disproven Junk DNA, were never posted by HuffPost, for whatever reason. I got more and better comments through at Michael White’s blog, here. I plan to list them all in my blog. There are many.

diogeneslamp0 said:

Keelyn said:

Steve P. said:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

Too bad you leave out the part of exactly how “Diogenes got his ass handed to him,” by Shapiro. I read the comments and it looks like the typical Shapiro style of dodging the questions by providing non answers. Perhaps you should read the comments a second time. Maybe you should read them a first time, preferably with a little comprehension.

Keelyn, several of the comments I posted at Shapiro’s blog, in which I listed quotes from ENCODE scientists admitting they hadn’t disproven Junk DNA, were never posted by HuffPost, for whatever reason. I got more and better comments through at Michael White’s blog, here. I plan to list them all in my blog. There are many.

Diogenes, HuffPo thinks there is a genuine “debate” going on between Shapiro, White and the others, and are all too willing to bend over backwards in support of Shapiro and his delusional creationist fans like Wendell Read, who opted to stalk me online and sent me four unsolicited e-mails; three after I told him to stop and that I was going to complain about his behavior to the Huffington Post. (Read is Shapiro’s “pet”, and as intellectually challenged as Stevie Pee.)

As for Shapiro, Diogenes, his latest blog is devoted to you and your critiques:

http://www.huffingtonpost.com/james[…]1893984.html

I invite other long-time PT posters - not Stevie Pee and his fellow drive-by creotards - to stop by and give Shapiro a piece of their minds. Shapiro’s problem is that he’s a once great scientist who has lost touch with reality, as noted, for example, by his blatant lies regarding Darwin’s importance in the history of science and Darwin’s understanding of Natural Selection. Shapiro has claimed falasely that Darwin wasn’t the only one to think of a credible evolutionary theory, citing as examples, not only Lamarck, but also his grandfather, Erasmus Darwin, as examples. For more worrisome is his insistence that Darwin didn’t really understand Natural Selection as well as Wallace did, and that he didn’t understand it until he read Wallace’s 1858 essay.

John said: I invite other long-time PT posters - not Stevie Pee and his fellow drive-by creotards - to stop by and give Shapiro a piece of their minds.

I would do so, John, with very great pleasure, but pieces of my mind on the details of evolutionary biology and biochemistry are mere grains of sand. I lurk on threads dealing with those subjects, and keep my mouth shut, because I know so little of them. Let Shapiro make a pronouncement on history, theology or the Bible, and I’m your man.

John said:

Diogenes, HuffPo thinks there is a genuine “debate” going on between Shapiro, White and the others, and are all too willing to bend over backwards in support of Shapiro and his delusional creationist fans like Wendell Read, who opted to stalk me online and sent me four unsolicited e-mails; three after I told him to stop and that I was going to complain about his behavior to the Huffington Post. (Read is Shapiro’s “pet”, and as intellectually challenged as Stevie Pee.)

As for Shapiro, Diogenes, his latest blog is devoted to you and your critiques:

http://www.huffingtonpost.com/james[…]1893984.html

I invite other long-time PT posters - not Stevie Pee and his fellow drive-by creotards - to stop by and give Shapiro a piece of their minds. Shapiro’s problem is that he’s a once great scientist who has lost touch with reality, as noted, for example, by his blatant lies regarding Darwin’s importance in the history of science and Darwin’s understanding of Natural Selection. Shapiro has claimed falasely that Darwin wasn’t the only one to think of a credible evolutionary theory, citing as examples, not only Lamarck, but also his grandfather, Erasmus Darwin, as examples. For more worrisome is his insistence that Darwin didn’t really understand Natural Selection as well as Wallace did, and that he didn’t understand it until he read Wallace’s 1858 essay.

Thanks for the link John.

Unfortunately for Shapiro, his reasoning is tortured at best. He is willing to throw out all that we actually do know in hopes of some day discovering what he hopes to be true. He didn’t even deal with the substance of the argument. All he did was make the age old claim that science doesn’t provide certainly, therefore I could be proven right in the future. In so doing, he commits the exact same fallacy that he accuses others of. Now where have we seen that kind of behavior before? No wonder the creationists love this guy so much, except maybe for that guy who was trying to claim that Darwin was solely responsible for all of evolutionary biology.

diogeneslamp0 said:

Keelyn said:

Steve P. said:

Challenged? Yes, he did ‘challenge’ Shapiro. But of course you left out the part where Diogenes got his ass handed to him.

Too bad you leave out the part of exactly how “Diogenes got his ass handed to him,” by Shapiro. I read the comments and it looks like the typical Shapiro style of dodging the questions by providing non answers. Perhaps you should read the comments a second time. Maybe you should read them a first time, preferably with a little comprehension.

Keelyn, several of the comments I posted at Shapiro’s blog, in which I listed quotes from ENCODE scientists admitting they hadn’t disproven Junk DNA, were never posted by HuffPost, for whatever reason. I got more and better comments through at Michael White’s blog, here. I plan to list them all in my blog. There are many.

Diogenes, Shapiro’s delusional band of Huffington Post creationist fans have been influencing the moderators to remove your posts as well as some of mine at both Mike White and Shapiro’s blogs. I’ve e-mailed a complaint to them. If you access to Facebook try contacting me there; I’ll forward to you the e-mail addresses of those at Huffington Post whom you should contact. I have also alerted Mike White BTW.

Diogenes, this is somewhat off topic, but James Shapiro demonstrates again just how clueless he is with regards to promoting the teaching of sound basic science like biological evolution and modern evolutionary biology:

http://www.huffingtonpost.com/james[…]1919558.html

His condemnation of Bill Nye the Science Guy’s recent commentary is yet another example of Shapiro’s breathtaking inanity.

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This page contains a single entry by Nick Matzke published on September 5, 2012 7:47 PM.

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