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

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.

GIGO

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. ...

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

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?

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.

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.

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?

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.

Wow. Watch the Twitter-splosion: https://twitter.com/mbeisen

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.

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.

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. ;)

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

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.

Yes, the mutational load issue is serious. This was one of the reasons population geneticists accepted that much of the genome must consist of bases whose mutation would not reduce fitness. If "functional" means that a change in the sequence changes fitness, your argument is a strong one.

For a more detailed technical discussion, see my free ebook Theoretical Evolutionary Genetics, particularly section III.6 and the preceding material in Chapter III.

For a more detailed technical discussion, see my free ebook Theoretical Evolutionary Genetics, particularly section III.6 and the preceding material in Chapter III.

Flint said: 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?

Flint said: 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?

Follow on:

Think of it like an equilibrium reaction, or water flowing into a bucket that has a hole in the bottom. The flow into the bucket represents the rate of nonfunctional mutation. The flow out represents the cost to the organism. The water level is % population which has nonfunctinal genetic strings. If the hole in the bottom is big compared to the inflow, you get little or no water in the bucket. If the hole is small compared to the inflow, you get a full bucket (which = everyone has such strings). You can also get situations where the bucket remains partially full, if the inflow and hole size are similar enough that an equal flow state is reached.

We seem to be in an overflowing bucket world, but evolution is perfectly consistent with a partially full bucket world or even one-drop-going-through-the-bucket world. However, evolution is not consistent with a world in which the tap is turned off. At an absolute minimum, assuming the bucket is nothing but a cylinder open on both ends, evolution predicts that we should still be able to take a snapshot of a drop dropping through the bucket. Which = finding some still-developing individual with a nonfunctional mutation, even if they never make it to breeding age.

Rolf said:

Flint said: 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?

The problem is the creationists, they jump on everything in the hope that it may be a valid argument for creationism. You can always do that without any knowledge or understanding of the subject. What a comfortable position! I continuously have to think and make an effort to learn and understand. But I gladly do it, I've always lived that way.

About the mutational load, I know you all know this, but there are plenty of mutation events that don't actually make changes to how the resulting protein forms.

Even if there's a change in the amino acids, as long as it's not an active site and the change is between similar aminos (both are hydrophobic for example), then a mutation can be totally invisible until you sequence the genome.

eric said:

Flint said: 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?

Just a quibble (and this is IMO, IANAB), but an 'absolute zero' would be difficult to explain via evolution, because for that to occur every nonfunctional mutation would have to be fatal in the womb.

The more nonfatal, nonfunctional mutations that are theoretically possible, the more probable it is that someone's going to be carrying one.

Hovewever, the amount of n[o]nfunctional DNA could certainly be very low without much theoretical problem. That would be consistent with currently understood evolution + hypothesis that replicating unnecessary strings has a significant survival or reproductive cost to the organism. In such a situation, the (carriers of) nonfunctional strings would get weeded out pretty quickly.

Joe Felsenstein said:

eric said: Just a quibble (and this is IMO, IANAB), but an 'absolute zero' would be difficult to explain via evolution, because for that to occur every nonfunctional mutation would have to be fatal in the womb.

A fitness of zero (a selection coefficient of -1) would be possible either by having the individual survive but be sterile, or having it die before reproduction begins. It does not need to die in the womb.

The cost of replicating DNA does not appear to be that great.

Interesting discussion. I felt that the equilibrium idea made sense. But I'm aware that some genomes have almost no non-functional DNA (in the sense that it contributes nothing to fitness), and yet those organisms do just fine. So near-100% functionality (the creationist dream) isn't impossible.

eric said: ... Of course, if such a mutation results in sterility, its hard to see how it fits the category of 'nonfunctional' any more. :) Almost by definition/tautology, the sorts of mutations we are talking about cannot have an immediate and strong developmental influence on the organism. If they do, they are functional.

The cost of replicating DNA does not appear to be that great.

If it wasn't clear, I agree. The empirical evidence seems to indicate that we live in a 'full-bucket world,' where the hole is much smaller than the inflow.

Flint said: Interesting discussion. I felt that the equilibrium idea made sense. But I'm aware that some genomes have almost no non-functional DNA (in the sense that it contributes nothing to fitness), and yet those organisms do just fine. So near-100% functionality (the creationist dream) isn't impossible.

A correction: It turns out that the "congo eel" Amphiuma is not the genome size champion among vertebrates. That crown is worn by another salamander, Necturus lewisi, the Neuse River Waterdog, which has 120 picograms of DNA per genome, fully 34 times as much as humans have.

Nick Matzke's onions have only 6 times as much DNA as humans.

Interestingly, both Amphiuma and Necturus lewisi live in the southeastern U.S., where they are surrounded by creationists who deny the existence of most of their genomes.

ogremk5 said: Similar to dogs. The morphological differences between dog species is larger than the morphological difference between all other carnivores combined.

http://tolweb.org/Carnivora/15971

The order Carnivora includes dogs, cats, bears, raccoons, weasels, mongooses, hyenas, seals, walruses, etc.

So yeah, the ones in that list other than dogs seem to me to have more variety than dogs do by themselves.

BTW, whales are in the order Cetacean, shrews are in order Insectivora.

Unless something has changed in the last few years, the largest measured vertebrate genome belongs to the marbled lungfish (Australia's Protopterus aethiopicus, @ 133pg). Necturus lewisi is definitely up there, though.

As I found out a recently, good old daphnia (D. pulex, model organism and popular fish snack) has some interesting things going on in its DNA. Its genome is tiny by one metric, with just 200 million base pairs of DNA vs. humans @ 3+ billion. But it has ~30,000 protein coding genes vs. our ~20,000. It has a lot of duplicate genes and accumulated gene variants.

This might be due to its reproductive cycle. When conditions are favorable, they spawn only females parthenogenetically. When conditions take a turn for the worse, it triggers the parthenogenetic birth of males for sexual reproduction. So in fat times they simply clone themselves, but when times get lean they make the switch to sexual reproduction, with the resulting gene recombination helping to shuffle the population's genes. Combined with fast generation times, it may be a recipe for rapid evolutionary changes in response to the environment. Beneficial mutations can be generated quickly, spread around, and preserved (hence the large number of genes compared to humans).

A little more involved than the onion test, but it brings up another facet of evolution that most denialists don't want to deal with: the benefit of genetic diversity leading to improved chances of accumulating and exploiting beneficial mutations. Beneficial mutations are something many anti-evolutionists claim shouldn't even exist, or would be too rare to make a difference. So not only does the tiny, simple water flea have a larger number of genes than us, it also has a system to better utilize those rare beneficial mutations.

The amount of shape variation among domestic dogs far exceeds that in wild species, and it is comparable to the disparity throughout the Carnivora. The greatest shape distances between dog breeds clearly surpass the maximum divergence between species in the Carnivora.

ogremk5 said: OK, I may have exaggerated slightly. Here's the paper I referred to http://flywings.org.uk/PDF%20files/AmNat2010.pdf and a quote from the abstract:

The amount of shape variation among domestic dogs far exceeds that in wild species, and it is comparable to the disparity throughout the Carnivora. The greatest shape distances between dog breeds clearly surpass the maximum divergence between species in the Carnivora.

Henry J: BTW, whales are in the order Cetacean, shrews are in order Insectivora.

Well shazbot. The TOL's page on the clade Eutheria ( http://tolweb.org/Eutheria/15997 ) has a note on it that says it hasn't been updated this millennium.

It shows Cetacea in parallel with Artiodacyla, but has parallel lines instead of a solid bar leading into the later, which I think means there was some question about the tree structure at that time.

That page didn't mention Lipotyphla, but Wiki describes it as mostly a renaming of Insectivora, but with some rearrangements of the tree.

ksplawn said: Unless something has changed in the last few years, the largest measured vertebrate genome belongs to the marbled lungfish (Australia's Protopterus aethiopicus, @ 133pg). Necturus lewisi is definitely up there, though. ...

Henry J said: It shows Cetacea in parallel with Artiodacyla, but has parallel lines instead of a solid bar leading into the later, which I think means there was some question about the tree structure at that time.

No wonder design deniers are in a rut. They put credence in the silly onion test. What compels them to assume genome size is proportional to its complexity? Complexity lies elsewhere, duh. At least guys like Shapiro understand this and want to take biology in a more interesting and productive direction.

SteveP. said: No wonder design deniers are in a rut. They put credence in the silly onion test. What compels them to assume genome size is proportional to its complexity? Complexity lies elsewhere, duh. At least guys like Shapiro understand this and want to take biology in a more interesting and productive direction.

SteveP. said: No wonder design deniers are in a rut. They put credence in the silly onion test. What compels them to assume genome size is proportional to its complexity?

Plus, the genome size comparison is only one of the rather large number of pieces of evidence that fits ToE.

The theory isn't established by any one piece of evidence, but by several patterns observed repeatedly across all of it. (But for some reason, science deniers tend to continually overlook this point, even after it has been repeatedly mentioned.)

ksplawn said:

SteveP. said: No wonder design deniers are in a rut. They put credence in the silly onion test. What compels them to assume genome size is proportional to its complexity?

That's the point, actually. To a very great extent it's not proportional. But let me ask you, would William Dembski say that a large genome contains more Specified Complex Information than a short one?

apokryltaros said:

ksplawn said:

SteveP. said: No wonder design deniers are in a rut. They put credence in the silly onion test. What compels them to assume genome size is proportional to its complexity?

That's the point, actually. To a very great extent it's not proportional. But let me ask you, would William Dembski say that a large genome contains more Specified Complex Information than a short one?

Would Dembski determine a bluefinned tuna's genome has more Specified Complex Information than that of a fugu pufferfish's genome?

Wow, Steve P. likes to sneer and posture!

While you are here, condescending to tell us that 'Complexity lies elsewhere', perhaps you can define complexity for us? Give us a method anyone can apply to determine the complexity of two organisms? Maybe you could be so good as to walk through this method with a few different (suggested by the readership here) organisms, and show the work, the math, at each step so that folks can follow along & learn from the examples? For all the bluster and frantic hand-waving, design-proponents have failed to do this -- even when given a golden opportunity to do so in Dover.

So here are my predictions:
1} profound silence -- you will refuse to answer by ignoring this question; or,
2} verbal diarrhea -- you will use as many words as possible to avoid answering the question, up to, including, and beyond using already discredited 'reasoning', inventing or changing the meaning of words, claiming that you 'have already answered that' when you never have, using papers which have nothing at all to do with this discussion -- or which outright refute you -- as 'support', shifting the burden of proof or work (the classic 'I cannot possibly make my first tic-tac-toe move until after you have rigorously explained how all possible strategies of all possible games in the universe work! Show your math!' whine) to your opponent, or any of dozens of other sleazy & all-too-common-from-the-design-folks tactics.

If this goes as I expect it will, you will richly deserve yet another 'Please Do Not Feed The Troll' sign hung about your neck.

No wonder design deniers are in a rut.

They put credence in the silly onion test. What compels them to assume genome size is proportional to its complexity?

Complexity lies elsewhere, duh.

Wow, Steve P. likes to sneer and posture!

J. L. Brown said: Wow, Steve P. likes to sneer and posture! While you are here, condescending to tell us that 'Complexity lies elsewhere', perhaps you can define complexity for us? Give us a method anyone can apply to determine the complexity of two organisms? Maybe you could be so good as to walk through this method with a few different (suggested by the readership here) organisms, and show the work, the math, at each step so that folks can follow along & learn from the examples? For all the bluster and frantic hand-waving, design-proponents have failed to do this -- even when given a golden opportunity to do so in Dover. So here are my predictions: 1} profound silence -- you will refuse to answer by ignoring this question; or, 2} verbal diarrhea -- you will use as many words as possible to avoid answering the question, up to, including, and beyond using already discredited 'reasoning', inventing or changing the meaning of words, claiming that you 'have already answered that' when you never have, using papers which have nothing at all to do with this discussion -- or which outright refute you -- as 'support', shifting the burden of proof or work (the classic 'I cannot possibly make my first tic-tac-toe move until after you have rigorously explained how all possible strategies of all possible games in the universe work! Show your math!' whine) to your opponent, or any of dozens of other sleazy & all-too-common-from-the-design-folks tactics. If this goes as I expect it will, you will richly deserve yet another 'Please Do Not Feed The Troll' sign hung about your neck.

@JoeFelstein: I was about to post a comment on the very large anount of DNA in the large paedomorphic salamanders (Necturus, Cryptobranchus, Amphiuma) when I saw your post. Amphiuma also has some of the largest cells of any vertebrate.

Slightly off topic, but any ideas of why the large amounts of DNA and large cell sizes in these paedomorphs? I have asked this of several 'experts' and have not been able to get possible explanations or suggestions.

Rolf said: Would Dembski determine a bluefinned tuna's genome has more Specified Complex Information than that of a fugu pufferfish's genome?

Rolf said: I am unable to understand how the concept of CSI might have a meaning wrt evolution and development.

One thing that shouldn't be forgotten here is that certain types of "junk DNA" are grist for the evolutionary mill. Duplicated genes, in particular, have given rise to different adaptations, indeed, to gene families. Whole genome duplications are thought by many to have played a role in vertebrate evolution.

As far as evolutionary predictions go, there never was the sort of resolution to say how much junk DNA should remain in genomes. Natural selection tends to either weed it out, or to make some sort of regulatory or other use of it, while transposons, duplications, and other mechanisms tend to produce more.

So evolutionary theory hasn't had much of an opinion on how much DNA should be "junk," rather the estimates have been tentative, and based on empirical data with its apparent limitations. Research continues on "junk DNA" precisely because we haven't known how to interpret the empirical data.

What is hardly in question at all, though, is that really (otherwise) useless duplicated DNA has been important in evolution, although even there the question of the degree of importance has been in contention. It's enough in this "debate" to say that gene duplications have certainly provided evolutionary opportunities to point out that, once again, evolutionary science deals meaningfully with "junk DNA," while ID remains nothing but a pretended default explanation. Of course they'll never acknowledge the role of natural selection in making use of "junk DNA," demanding that magic be credited instead, but that's just pathetic.

Glen Davidson

vhison said: @JoeFelstein: I was about to post a comment on the very ...

As far as evolutionary predictions go, there never was the sort of resolution to say how much junk DNA should remain in genomes.

Rather, modern genetics unintentionally challenges, to put it mildly, ID/creationism.

@JoeFelsenstein. Sorry Joe, my bad due to thick thumbs!. I know your correct name quite well. BUT, cam you weigh in on my question?

vhutchison said: @JoeFelsenstein. Sorry Joe, my bad due to thick thumbs!. I know your correct name quite well. BUT, cam you weigh in on my question?

I was about to post a comment on the very large anount of DNA in the large paedomorphic salamanders (Necturus, Cryptobranchus, Amphiuma) when I saw your post. Amphiuma also has some of the largest cells of any vertebrate. Slightly off topic, but any ideas of why the large amounts of DNA and large cell sizes in these paedomorphs? I have asked this of several ‘experts’ and have not been able to get possible explanations or suggestions.

Joe Felsenstein said: ...the large cell sizes are probably a result of the large amount of DNA...

Paul Burnett said:

Joe Felsenstein said: ...the large cell sizes are probably a result of the large amount of DNA...

Is that because more of the salamanders' DNA is non-coding ("junk DNA")?

harold said:

Paul Burnett said:

Joe Felsenstein said: ...the large cell sizes are probably a result of the large amount of DNA...

Is that because more of the salamanders' DNA is non-coding ("junk DNA")?

I find the question extremely interesting as well. It is clear that in some eukaryotic lineages, there is less "junk" DNA. Perhaps this represents direct selection against excess junk DNA in those lineages, or perhaps, because selection against junk DNA is so weak, there is a random distribution of its amount throughout lineages. That's a question that could be studied. For example, if the amount of DNA/genome per some logically defined lineage group was distributed along a normal curve, that might argue that a strong element of randomness exists with regard to amount of DNA per genome. Some lineages might have enzymes that regulate genome size more, but such enzymes might not be strongly selected for or against, but merely passed on, or not, in a random way. This would imply a gradual increase in eukaryotic genome sizes over time(since it would be more likely to lose such a function to gain it), at least until some point at which larger genome actually is selected against, which may be reasonable. On the other hand, other types of distributions might imply selection in some lineages. As for cell size, in mammals (and to some degree in all eukaryotes), cell size varies according to a number of factors: 1) Smaller organisms tend to have slightly smaller versions of the same type of cell, but nowhere near in proportion to the size difference between adults of various species. This makes sense when one considers that even the smallest eukaryotic cells, which occur mainly in single celled algae, are a bit less than 1 micrometer in diameter (a size range where they overlap with bacterial cell size). Likewise, there is clearly an upper limit on cell sizes, so whales and elephants don't have gigantic individual cells in proportion to their size. 2) Function: For example, certain types of neurons are very large, both in terms of nucleus and cytoplasm, in all mammals, easily reaching 100 micrometers, not even counting axons and dendrites, in humans. This is the strongest association with the size of normal cells. Cytoplasmic volume is strongly associated with function. Nuclear volume is to a less extent, but still is. Within the immune system, some but not all types of cells respond to stimulation by going through a phase of more rapid cell cycle with larger nuclear size. The megakaryocytes of the bone marrow, which generate blood platelets, are so named because of their large size. 3) Neoplasm: On average, with many exceptions, malignant cells tend to have larger nuclei, as well as different nuclear features. This does tend to associate with DNA content and DNA abnormalities. 4) Radiation: Exposure to ionizing radiation, usually seen in the context of radiation therapy, can lead to transient presence of very large cells, extremely alarming to the untrained eye. Such changes can be morphologically distinguished from malignancy (*of course ionizing radiation exposure is a risk factor for malignancy later, but it causes short term, non-malignant changes as well*). For example the cells often have both increased nuclear size and a large amount of cytoplasm, which is perfectly possible, but less common, in cancer. There are a variety of other features that allow the distinction as well, although in individual cases, it can be tricky.

harold said:

harold said:

Paul Burnett said:

Joe Felsenstein said: ...the large cell sizes are probably a result of the large amount of DNA...

Is that because more of the salamanders' DNA is non-coding ("junk DNA")?

I find the question extremely interesting as well. It is clear that in some eukaryotic lineages, there is less "junk" DNA. Perhaps this represents direct selection against excess junk DNA in those lineages, or perhaps, because selection against junk DNA is so weak, there is a random distribution of its amount throughout lineages. That's a question that could be studied. For example, if the amount of DNA/genome per some logically defined lineage group was distributed along a normal curve, that might argue that a strong element of randomness exists with regard to amount of DNA per genome. Some lineages might have enzymes that regulate genome size more, but such enzymes might not be strongly selected for or against, but merely passed on, or not, in a random way. This would imply a gradual increase in eukaryotic genome sizes over time(since it would be more likely to lose such a function to gain it), at least until some point at which larger genome actually is selected against, which may be reasonable. On the other hand, other types of distributions might imply selection in some lineages. As for cell size, in mammals (and to some degree in all eukaryotes), cell size varies according to a number of factors: 1) Smaller organisms tend to have slightly smaller versions of the same type of cell, but nowhere near in proportion to the size difference between adults of various species. This makes sense when one considers that even the smallest eukaryotic cells, which occur mainly in single celled algae, are a bit less than 1 micrometer in diameter (a size range where they overlap with bacterial cell size). Likewise, there is clearly an upper limit on cell sizes, so whales and elephants don't have gigantic individual cells in proportion to their size. 2) Function: For example, certain types of neurons are very large, both in terms of nucleus and cytoplasm, in all mammals, easily reaching 100 micrometers, not even counting axons and dendrites, in humans. This is the strongest association with the size of normal cells. Cytoplasmic volume is strongly associated with function. Nuclear volume is to a less extent, but still is. Within the immune system, some but not all types of cells respond to stimulation by going through a phase of more rapid cell cycle with larger nuclear size. The megakaryocytes of the bone marrow, which generate blood platelets, are so named because of their large size. 3) Neoplasm: On average, with many exceptions, malignant cells tend to have larger nuclei, as well as different nuclear features. This does tend to associate with DNA content and DNA abnormalities. 4) Radiation: Exposure to ionizing radiation, usually seen in the context of radiation therapy, can lead to transient presence of very large cells, extremely alarming to the untrained eye. Such changes can be morphologically distinguished from malignancy (*of course ionizing radiation exposure is a risk factor for malignancy later, but it causes short term, non-malignant changes as well*). For example the cells often have both increased nuclear size and a large amount of cytoplasm, which is perfectly possible, but less common, in cancer. There are a variety of other features that allow the distinction as well, although in individual cases, it can be tricky.

I should note that we should strongly differentiate between ploidy (copies of the overall genome, or large parts of it), versus amount of junk DNA per single genome. When malignant cells have a lot of DNA, which can lead to either large, or hyperchromatic (by light microscopy with appropriate stains), nuclei, it is essentially because of high rate of replication and/or excess chromosomes. It is still "more DNA per genome" but clearly has different effects on cell morphology than large amounts of non-replicating junk DNA, most of which can be tightly packaged.

For completeness I will also note that existence of very large multinucleated cells, both in the human body and in the case of some very large "single celled organisms" these can sort of be considered multiple cells fused together.

Joe Felsenstein said:

vhutchison said: @JoeFelsenstein. Sorry Joe, my bad due to thick thumbs!. I know your correct name quite well. BUT, cam you weigh in on my question?

I was about to post a comment on the very large anount of DNA in the large paedomorphic salamanders (Necturus, Cryptobranchus, Amphiuma) when I saw your post. Amphiuma also has some of the largest cells of any vertebrate. Slightly off topic, but any ideas of why the large amounts of DNA and large cell sizes in these paedomorphs? I have asked this of several ‘experts’ and have not been able to get possible explanations or suggestions.

Short answer: I haven't a clue -- your guess is as good as mine. I'm a theoretician, so if you have a question about a term in an equation, I might be able to answer. I'd just add that (as I think you realize) the large cell sizes are probably a result of the large amount of DNA, as that is often observed.

Most of the explanations of large cell size given above are implausible in the case of the lungfish or the salamanders: they do not have cancer, they are not subject to more radiation than other similar creatures, and the types of cell function that they need are not much different from other vertebrates.

(PS Protopteus aethiopicus is the African lungfish, not the Australian one -- I had wondered about the species name which seems inappropriate for anything Australian!)

As for polyploidy, the number of chromosomes in lungfish is not unusual; they seem to be diploid. However they have lots of transposable elements. One paper assessing this (Metcalfe et al., Molecular Biology and Evolution, 2012) concluded that: "the very large Australian lungfish genome may be the result of a massive amplification of TEs followed by a long period with a very low rate of sequence removal and some ongoing TE activity." (TE = transposable element)

Joe Felsenstein said: Most of the explanations of large cell size given above are implausible in the case of the lungfish or the salamanders: they do not have cancer, they are not subject to more radiation than other similar creatures, and the types of cell function that they need are not much different from other vertebrates. (PS Protopteus aethiopicus is the African lungfish, not the Australian one -- I had wondered about the species name which seems inappropriate for anything Australian!) As for polyploidy, the number of chromosomes in lungfish is not unusual; they seem to be diploid. However they have lots of transposable elements. One paper assessing this (Metcalfe et al., Molecular Biology and Evolution, 2012) concluded that: "the very large Australian lungfish genome may be the result of a massive amplification of TEs followed by a long period with a very low rate of sequence removal and some ongoing TE activity." (TE = transposable element)

The correlation between DNA content and cell size is due to a nucleotypic effect, that is an effect of the amount of DNA regardless of sequence or coding function. Cells with more DNA tend to be larger, that is why some plant breeders want to make polyploid strains, so that the individual cells and the entire plant will be larger.

For more on mammalian cell size, here's a great reference -

http://www.ncbi.nlm.nih.gov/pubmed/17360590

The largest mammalian genome, in terms of base pairs, does belong to a very large animal, but modern whales and elephants have genomes that are not all that different in size from those of mice and humans (and even this is less than double a mouse genome).

http://news.nationalgeographic.com/news/2008/11/081119-mammoth-DNA_2.html

It's thought that birds benefit from an apparent ancestral dinosaur small genome size (smaller than mammals anyhow), hence smaller cells. Less weight for better flight, presumably better diffusion in and out of cells as well (O2, CO2, etc.). Of course they also have the better lungs, unlike God's Designer's end goal, humans.

For mammals, bats also apparently have relatively smaller genomes, but larger than those of birds I believe.

Glen Davidson

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: It's thought that birds benefit from an apparent ancestral dinosaur small genome size (smaller than mammals anyhow), hence smaller cells. Less weight for better flight, presumably better diffusion in and out of cells as well (O2, CO2, etc.). Of course they also have the better lungs, unlike God's Designer's end goal, humans. For mammals, bats also apparently have relatively smaller genomes, but larger than those of birds I believe. Glen Davidson

Joe Felsenstein said: (PS Protopteus aethiopicus is the African lungfish, not the Australian one -- I had wondered about the species name which seems inappropriate for anything Australian!)

Joe Felsenstein said: (PS Protopteus aethiopicus is the African lungfish, ...

The correlation between genome size (c-value) and cell size is well-known (although imperfect) -- well, well-known to people who are familiar with the genome size/c-value literature, but apparently not to the ENCODE project people and many other molbio/genomics types.

The hard part is the explanation. The correlation is there, but the causation could run in either direction. E.g.:

(a) skeletal DNA hypothesis: genome size (regardless of the sequence) controls nuclear volume which allometrically controls cell size. Cell size is under selection, e.g. higher metabolism/more rapid growth requires more surface area/smaller cells. Cell size might also be under selection for e.g. brain complexity -- it may be you can have a more complex set of neural connections if each cell is smaller. Ironically, this would mean that more complex creature = SMALLER genome, which is the opposite of creationist/naive functionalist interpretations.

(b) relaxed selection hypothesis -- organisms that grow more slowly have fewer replication events, longer generation times, and lower population sizes. Thus, selection is weaker in these species, and the cost of junk DNA is lower, often lower than the 1/2N neutral cutoff. Thus, it accumulates without negative effect, but if the lineage moves into a niche where it evolves a higher metabolism and faster growth, mutation events that delete junk start to be selectively advantageous, and the genome size starts to shrink.

Both of these hypotheses have strengths and weaknesses. The people to read are Thomas Cavalier-Smith and T. Ryan Gregory.

Any way you slice it, though, it looks like a lot of the genome is pretty dispensable/lacking any specific function (unless "filler" is a function). I am happy calling this "junk DNA", but even some people highly skeptical of functionalist assumptions don't like the label, because of its emotive qualities. Who wants to study "junk", or tell funding agencies that they want to study "junk"?

Also, two points that are often missed:

1. People often think that it must be energetically expensive to have a bigger genome. But apparently the energetic cost of DNA replication is tiny compared to the cost of protein expression, etc.

2. The size of the genome is relevant to the speed of genome replication in organisms with a single origin of replication (i.e. prokaryotes), but NOT (at least mostly) in eukaryotes, which have many, many origins of replication.

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: It's thought that birds benefit from an apparent ancestral dinosaur small genome size (smaller than mammals anyhow), hence smaller cells. Less weight for better flight, presumably better diffusion in and out of cells as well (O2, CO2, etc.). Of course they also have the better lungs, unlike God's Designer's end goal, humans. For mammals, bats also apparently have relatively smaller genomes, but larger than those of birds I believe. Glen Davidson

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.

Since transposons make up approximately 45% of the human genome, the majority of those being SINEs and LINEs it is virtually impossible for 80% of the human genome to have any functional significance. That's not even counting pseudogenes, inactivated mitochondrial genes, completely nonfunctional introns, tandem repeats, etc. We not only know that a lot of the human genome is worthless junk, we know where it came from. It might make sense to view it as raw material, not eliminated by natural selection, but having the potential to eventually mutate into something useful. It certainly doesn't make any sense at all from any intelligent design stand point. Once again, modern genetic discoveries confirm what Darwin claimed all along, descent with modification is true and it explains new discoveries that Darwin could never have dreamed of.

Henry J said:

Rather, modern genetics unintentionally challenges, to put it mildly, ID/creationism.

It certainly does. Modern genetics would have predicted (and generated) the theory of evolution if it wasn't already around before DNA was understood, Darwin or no Darwin. Henry

I think that the no-junk DNA meme is just a random response from the creationists. They could have easily said that junk DNA shows the generally deterioration of the genome since the Fall.

The correlation between genome size (c-value) and cell size is well-known (although imperfect) – well, well-known to people who are familiar with the genome size/c-value literature, but apparently not to the ENCODE project people and many other molbio/genomics types.

Ironically, this would mean that more complex creature = SMALLER genome, which is the opposite of creationist/naive functionalist interpretations.

Of course, it depends on what you mean by “complex”. The Kolmogorov complexity of a larger genome is greater than that of a smaller genome, at least in the context of sequencing base pairs, simply because it is larger. An argument could be made that ploidy doesn’t really count (because you only have to sequence a haploid genome and then add a byte or few to give the ploidy), but the certain lungfish genomes are unequivocally far more complex than the human genome by standard measure. If repetitive sequence representation could be represented in a compressed way that might also be relevant, but basically, more base pairs per haploid genome would tend to mean more Kolmogorov complexity if sequence is being analyzed. A strong argument could be made that many organisms are more “advanced” than humans in many ways. In fact, a traditional Christian, rather than a post-modern right wing ideologue trying to enforce and deny his own religion at the same time, would accept that as uncontroversial.

harold said: A strong argument could be made that many organisms are more "advanced" than humans in many ways.

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-a-shapiro/bob-dylan-encode-and-evol_b_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/columnists/faye_flam/20120910_Planet_of_the_Apes__What_is_that_big_hunk_of__junk__DNA_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/johnfarrell/2012/09/07/reports-of-junk-dnas-demise-have-been-greatly-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-a-shapiro/bob-dylan-encode-and-evol_b_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.

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/2012/09/junk-dna-theory-overturned.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/2012/09/junk-dna-theory-overturned.html

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/2012/09/junk-dna-theory-overturned.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.

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

http://sandwalk.blogspot.com/2012/09/james-shapiro-claims-credit-for.html

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/columnists/faye_flam/20120910_Planet_of_the_Apes__What_is_that_big_hunk_of__junk__DNA_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/johnfarrell/2012/09/07/reports-of-junk-dnas-demise-have-been-greatly-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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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-a-shapiro/further-thoughts-on-the-e_b_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.

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, 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-a-shapiro/could-bill-nye-have-done-_b_1919558.html

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