The ENCODE delusion

It's like they googled "functional," hit the DI (re)definition of it, and just went with it.

There's nothing new about the fact that much "junk DNA" interacts with something or other (hence this review of papers found as much), it just wasn't clear if that "junk DNA" was truly functional. And it still isn't.

Glen Davidson

It would have helped a lot if ECODE had considered where the activity of a biochemical reaction resides and what DNA actually is in the reactions they describe: sustrate, enzyme, co-enzymes, product?

It seems possible to me that the ENCODE hierarchy chose the misleading phrasing on purpose to increase the size of their media splash thinking that they benefit when random citizens recognize their acronym. The Kardashian family certainly operates on this thesis.

mandyvarda said: It seems possible to me that the ENCODE hierarchy chose the misleading phrasing on purpose to increase the size of their media splash thinking that they benefit when random citizens recognize their acronym. The Kardashian family certainly operates on this thesis.

However, on the other end of the scale – using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints; places where we are very confident that there is a specific DNA:protein contact, such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%. Given what most people thought earlier this decade, that the regulatory elements might account for perhaps a similar amount of bases as exons, this is surprisingly high for many people – certainly it was to me! [...] A conservative estimate of our expected coverage of exons + specific DNA:protein contacts gives us 18%, easily further justified (given our sampling) to 20%

Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints. We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.

If we define junk DNA as sequence whose change is not affected by natural selection because it has so little fitness effect, then ENCODE has not shown that most of its "functional" sequences are anything but junk. Which makes the Birney announcement of "functional" sequences misleading in a major way.

I am encouraged that quite a few researchers who have serious experience with molecular evolution have now weighed in saying that junk DNA is alive and well.

It is going to be a long, hard struggle to get to the point where the popular science press declares junk DNA to be back in the genome. But the initial steps have been taken.

Maybe what they should do is concentrate on the twenty percent that does absolutely nothing at all. Maybe they should explain what all of this junk is and how it got there. After all, this is some of the most powerful evidence that we have for evolution. The first priority should be to make sure that the creationists cannot misrepresent this to their own advantage. The next step should be to explain very carefully that about three quarters of the eighty percent doesn't really do anything important either. Make sure the science is sound, then make sure you are presenting it in the right way.

Of course, no matter what you do, the creationist will always say that they predicted that result all along. But then again, everyone will see that they didn't actually do any of the work or any of the analysis. So no one is going to be fooled by their hollow claims. If they really thought that the human genome provided evidence for creationism, they would have done the work themselves. The fact that they did not is all you need to know.

Just out of curiosity (and I probably have a distorted view of this because I'm not in it), do research proposals that aren't cool (dinosaurs, lasers, etc) or have plan to save humans/the world/the environment ever get funded?

I know, in my company, if you want funding for a project, then the research had better result in a marketable product or a method for saving large sums of money.

The know nothing Wells spews forth on ENV:

"The recent findings from ENCODE and related projects are significant for several reasons. First, the results from over a thousand experiments -- involving dozens of laboratories and hundreds of scientists on three continents, published simultaneously in dozens of articles in five different journals -- are remarkably consistent."

That's funny, so are the over one million articles published by hundreds of thousands of scientists in hundreds of journals over the last one hundred and fifty years. They demonstrate conclusively that descent with modification is real. Funny how he isn't willing to accept that conclusion.

"Second, by providing abundant evidence that 80% or more of our DNA is functional, the results have greatly expanded our biological knowledge and may shed valuable light on some diseases."

It's not 80% or more, it's 80% absolute maximum. He conveniently left out the part that, even according to the most liberal definition of "functional" possible, 20% is still junk. Now why do you suppose that is?

"Third, the results demolish the argument used by Richard Dawkins and some other Darwinists that most of our DNA is "junk," proving we could not have originated by design. As the journal Science put it, "Encode Project Writes Eulogy for Junk DNA."

So, if at least 20% is still junk, then intelligent design is falsified! That doesn't even incluide the result that nearly 60% doesn't seem to do anything important.

DS said: Maybe what they should do is concentrate on the twenty percent that does absolutely nothing at all.

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.”

https://www.google.com/accounts/o8/id?id=AItOawm-WhebH0itIDDTj06EQo2vtiF0BBqF10Q said:

DS said: Maybe what they should do is concentrate on the twenty percent that does absolutely nothing at all.

According to Ed Young's blog at Discover Magazine Ewan Birney beleaves that it will turn out that these 20% are functional as well (unde ENCODE's definition of course) once more cell types and developmental stages have been analyzed:

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.”

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.”

Birney: "For me, the driving concern was to avoid over-hyping the medical applications..."

Birney: "With hindsight, we could have used different terminology to convey the concepts..."

Birney: "I do think we got our point to the general public: that there is a staggering amount of activity in the genome..."

NPR: “Most of the human genome is out there mainly to control the genes,” said John Stamatoyannopoulis, a geneticist at the University of Washington School of Medicine, who also participated in the project.

The Independent: "Scientists have once and for all swept away any notion of “junk DNA” by showing that that the vast majority of the human genome does after all have a vital function by regulating the genes that build and maintain the body."

NY Times: "As scientists delved into the “junk” — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed."

Wash Post: "Indeed, the vast majority of human DNA seems to be involved in maintaining individuals’ well being — a view radically at odds with what biologists have thought for the past three decades"

USA Today: "International research teams have junked the notion of “junk” DNA, reporting that at least 80% of the human genetic blueprint contains gene switches, once thought useless, that control the genes that make us healthy or sick."

Birney: "ENCODE also had the chance of making our results comprehensible to the general public..."

Joe Felsenstein said: I am encouraged that quite a few researchers who have serious experience with molecular evolution have now weighed in saying that junk DNA is alive and well. It is going to be a long, hard struggle to get to the point where the popular science press declares junk DNA to be back in the genome. But the initial steps have been taken.

It seems to me the results of the ENCODE study spell even more doom for ID
if anything. The fact that much of the "junk" is transcribed means that there
is an awful lot of biochemical *noise* in the cell which has no function.

Which seems to me an even bigger problem for ID

“Third, the results demolish the argument used by Richard Dawkins and some other Darwinists that most of our DNA is “junk,” proving we could not have originated by design. As the journal Science put it, “Encode Project Writes Eulogy for Junk DNA.” So, if at least 20% is still junk, then intelligent design is falsified! That doesn’t even incluide the result that nearly 60% doesn’t seem to do anything important.

At any rate, ENCODE has great professional marketing. It's the greatest thing since sliced bread! Now what about social media? How many Facebook "likes" do they have?

We here see illustrated the dangers of thinking by analogy.

Mahavishnu Orchestra

SteveP. said: That's like saying, why bother having books on biology, car repair, and home improvement in your possession when you take a bus from your rented efficiency apartment to your job at 7-11. Maybe upon investigation we would find that this person once drove to his job at a lab from his house but due a bad economy, lost it all and is now struggling to hold on, waiting for better times. Why chuck the books when hope is not lost? No, holding on to your information is the smart play. Likewise, wouldn't orgainisms having a library of historical environmental records help in their survival? Wouldn't calling upon old records of climate change come in handy when a millennium long climate cycle is starting to repeat itself?

Speaking of which, wouldn't it be a much more intelligent design to give cells only those genes they need and not the other 90% that they don't? That should be easy for any real intelligence. Maybe the intelligent designer just wanted to make it easier to do human cloning.

SteveP. said: Does a car's cigarette lighter affect the function of the car? I could rip out the lighter, the radio, the air conditioning, the rear view mirror, all the seats, the tissue dispenser, the gps, the visors, the ash tray, the glove compartment, the shitload of maps and guidebooks and sunglasses in the center armrest, cup holder, etc. etc and could still drive my car without a hitch. but that is what you would expect if genome's came with lots of bells and whistles!

Any DNA in the human genome whatsoever that is viral in origin, a pseudogene, a repetitive element that can differ widely among individuals with no effect, etc, is a severe problem, essentially a death knell for ID.

Dave Luckett said: We here see illustrated the dangers of thinking by analogy.

Likewise, wouldn’t orgainisms having a library of historical environmental records help in their survival?

Maybe upon investigation we would find that this person once drove to his job at a lab from his house but due a bad economy, lost it all and is now struggling to hold on, waiting for better times. Why chuck the books when hope is not lost? No, holding on to your information is the smart play.

DS said:

SteveP. said: Does a car's cigarette lighter affect the function of the car? I could rip out the lighter, the radio, the air conditioning, the rear view mirror, all the seats, the tissue dispenser, the gps, the visors, the ash tray, the glove compartment, the shitload of maps and guidebooks and sunglasses in the center armrest, cup holder, etc. etc and could still drive my car without a hitch. but that is what you would expect if genome's came with lots of bells and whistles!

Any DNA in the human genome whatsoever that is viral in origin, a pseudogene, a repetitive element that can differ widely among individuals with no effect, etc, is a severe problem, essentially a death knell for ID.

Bullshit. Your car has twenty five radios, many of them without transistors and none of them work. That ain't bells and whistles, that's stark raving insanity. You can't even use the sixteen broken cigarette lighters to burn a cross into your arm cause they don't work either. Your car was not intelligently designed. Deal with it.

DS said:

SteveP. said: Does a car's cigarette lighter affect the function of the car? I could rip out the lighter, the radio, the air conditioning, the rear view mirror, all the seats, the tissue dispenser, the gps, the visors, the ash tray, the glove compartment, the shitload of maps and guidebooks and sunglasses in the center armrest, cup holder, etc. etc and could still drive my car without a hitch.

Bullshit. Your car has twenty five radios, many of them without transistors and none of them work. That ain't bells and whistles, that's stark raving insanity. You can't even use the sixteen broken cigarette lighters to burn a cross into your arm cause they don't work either.

A biology book, a book on car repair, and a book on home maintenence sitting on a shelf is junk???

SteveP.

Honestly, if you want to talk about evolution, biology, the genome or the ENCODE project, why don't you just talk about them? There is SO much information that we could discuss.

Instead you want to play word games with stupid analogies that don't even work. An analogy is a teaching tool. It's a device used to explain something that is difficult to someone without sufficient background. I used analogies in my classroom all the time, with the provision that they were analogies and that students should strive to understand the actual concepts. Very often, analogies were useful to my students to see relationships that they didn't have the content background to understand with the analogy.

You, however, are speaking to a bunch of people who have a very, very good understanding of science in general and biology and evolution in particular. Some of the people in this website are published scientists who do evolutionary work for a living. The rest are people who bother to study and learn about science, biology, biochemistry, evolution, population ecology and all that other stuff that is required to make valid judgments on the science.

You, however, are trying to make ridiculous analogies that you then use to dismiss the results of actual experiments. There are several words for that. The nicest I can come up with is "lame".

DNA is not a bookshelf, or a car, or spaghetti. It is DNA. People who know what they are talking about can discuss DNA as it is. We can talk about introns, exons, histones, translation, functions, repeats, ERVs, SINEs, etc. etc. etc.

When you use an analogy that has been proven wrong by experiment, the only thing you are accomplishing is to expose your own ignorance.

Now, do you want to talk about the ENCODE project? Or do you want to blather on about cars and books?

SteveP. said: Be careful here Diogenes. You advocate an evolutionary narrative not supported here. Evolution records jack shit. It has no goals, no purpose. Its pay as you go. There is no insurance plan, no pension plan, nada. Evolution as explained on this board has no way of recording anything. How could it? Its not in the business of planning ahead. Recording and remembering is an intelligent act of foresight...knowing bad times could be ahead so right it down and get ready for next seasons's drought or hurricane.

Look dipstick, I don't know how I can make this any clearer. You have a book on repair of Edsel Fords in every room in the house. Some are missing covers, some have lots of mistakes, some are missing pages, some are missing chapters. None of them are gong to do you any good whatsoever, even if you ever read them. And you are claiming not only that they are not junk, but that the house was built yesterday and nobody put any books in the house since! Gert a clue.

SteveP. said: Be careful here Diogenes. You advocate an evolutionary narrative not supported here. Evolution records jack shit. It has no goals, no purpose. Its pay as you go. There is no insurance plan, no pension plan, nada.

Steve P.

1) I think I said that yes, DNA stores information. It stores the information to make a complete organism. Sometimes that information changes and sometimes it affects what the organism looks like and does. It's called evolution.

2) Nature does not equal God.

3) Yes, emergent properties (behavior, shapes, etc) do resolve the 'conundrum' in the favor of the current understanding of the universe. An overriding intelligence is not needed. Since it is not needed, it is up to you to provide sufficient evidence that A) one exists and B) it is directly involved in such things as you claim (like making DNA, controlling body forms, performing miracles, etc.) Since everything that I mentioned (and all the other claims of deity that I've ever heard) is either done by scientifically observed natural processes (like body plans) or do not exist (like miracles), then there is zero evidence of a supernatural designer.

4) So you agree with JoeG that termites are intelligent. Since, I don't want to fall into the trap I accuse you of, I need to define intelligence. Here, I'm using intelligence as advanced cognitive skills such as, planning, innovation, abstract knowledge, sense of self, and problem solving. Just to clarify, is a single termite intelligent based on that definition of intelligence? Is a termite colony intelligent based on that definition?

BTW: I use that definition because that is what is required for the supernatural designer (aka God). If you claim that the designer can be a swarm intelligence, then I will claim that evolution is just as valid a designer in that case as God. You won't be able to tell the difference.

Of course, in your first reply, you say the exact same thing. Evolution 'designed' us. That's the problem with you guys, you never define anything. First design is used because it's implied that massively complex things can't evolve. Now you say that evolution results in the massively complex systems that are living things.

You really need to get together with Dembski and Behe and JoeG and hash out what you really think. One of these days, you are going to need to actually sit down and explain what you think and why. Until then, we just have to respond to your comments... which, on the face, seem to be contradictory.

BTW: Thanks for actually answering the questions.

SteveP. said: Ah, but DS, if I have a book on Edsel Fords in every room with some missing pages, and some missing chapters, I could go through all of them and paste together a minimum of one complete book. Remember I have that capability. Redundency solves the problem. Your attempt to knock this analogy down fails. In fact, my scenario is more than likely a truer picture than what you paint. We didn't start from scratch building up a Ford piece by piece, mistake by mistake. More likely we started out a bright shiny new Ford with all the bells and whistles in place and along the way, started breaking down, bit by bit. So started all the repair jobs to fix the defects. Still here though, scars and all.

DS said: Look dipstick, I don't know how I can make this any clearer. You have a book on repair of Edsel Fords in every room in the house. Some are missing covers, some have lots of mistakes, some are missing pages, some are missing chapters. None of them are gong to do you any good whatsoever, even if you ever read them. And you are claiming not only that they are not junk, but that the house was built yesterday and nobody put any books in the house since! Gert a clue.

SteveP. said: Ah, but DS, if I have a book on Edsel Fords in every room with some missing pages, and some missing chapters, I could go through all of them and paste together a minimum of one complete book. Remember I have that capability. Redundency solves the problem. Your attempt to knock this analogy down fails. In fact, my scenario is more than likely a truer picture than what you paint. We didn't start from scratch building up a Ford piece by piece, mistake by mistake. More likely we started out a bright shiny new Ford with all the bells and whistles in place and along the way, started breaking down, bit by bit. So started all the repair jobs to fix the defects. Still here though, scars and all.

DS said: Look dipstick, I don't know how I can make this any clearer. You have a book on repair of Edsel Fords in every room in the house. Some are missing covers, some have lots of mistakes, some are missing pages, some are missing chapters. None of them are gong to do you any good whatsoever, even if you ever read them. And you are claiming not only that they are not junk, but that the house was built yesterday and nobody put any books in the house since! Gert a clue.

Steve wrote:

"We didn’t start from scratch building up a Ford piece by piece, mistake by mistake. More likely we started out a bright shiny new Ford with all the bells and whistles in place and along the way, started breaking down, bit by bit. So started all the repair jobs to fix the defects."

So we've gone from the "intelligent genome" hypothesis to the "fall caused it" hypothesis. Do you ever think before you write anything? Sorry to break it to you Stevie, but if you had bothered to ever learn anything about genetics you would know that some of the mistakes happened before there were humans. That's how we know the mistakes were copied. No magic apples, no magic floods, just descent with modification. Deal with it.

DS said: Steve wrote: "We didn’t start from scratch building up a Ford piece by piece, mistake by mistake. More likely we started out a bright shiny new Ford with all the bells and whistles in place and along the way, started breaking down, bit by bit. So started all the repair jobs to fix the defects." So we've gone from the "intelligent genome" hypothesis to the "fall caused it" hypothesis. Do you ever think before you write anything? Sorry to break it to you Stevie, but if you had bothered to ever learn anything about genetics you would know that some of the mistakes happened before there were humans. That's how we know the mistakes were copied. No magic apples, no magic floods, just descent with modification. Deal with it.

ogremk5 said: yep, good old vitamin C for example. Why is it that almost every other mammal on the planet can synthesize their own vitamin C, except for a very small group of primates that just happens to include chimps, humans, and gorillas.

And isn't it curious that all three have exactly the same change, in exactly the same place that results the inability to synthesize vitamin C?

This was a welcome presentation, PZ. Thanks.

Idiot #1 writes: Be careful here Diogenes. You advocate an evolutionary narrative not supported here. Evolution records jack shit...Recording and remembering is an intelligent act of foresight.

Idiot #2 writes: If Man records and remembers, how is it that nature cannot?

Idiot #1 writes: Be careful here Diogenes. You advocate an evolutionary narrative not supported here. Evolution records jack shit. It has no goals, no purpose... Evolution as explained on this board has no way of recording anything. How could it? Its not in the business of planning ahead. Recording and remembering is an intelligent act of foresight…

Idiot #2 writes: If Man designs libraries, how does it follow that nature could not design libraries? If Man records and remembers, how is it that nature cannot? Don’t you think its the height of arrogance to suggest only Man designs but not nature in general... It is nature that ‘evolved’ design. So DNA must in fact be a designed object; the consequence of foresight.

Bette Korber, a staff scientist at the Los Alamos National Laboratory in New Mexico, has "collaborated" with a supercomputer named Nirvana to chart the genetic history of HIV. Looking at the mutations the virus experienced from the mid-1980s to 1999, Korber created a molecular clock to determine the rate at which HIV changes. Using that rate and calculating backward, she and Nirvana dated the last common ancestor of HIV, the virus from which all present variations descended, to 1931. If Korber is right, the virus must have jumped from monkeys to humans before that date and well before Koprowski was trying out his vaccine. Korber published her results in the journal Nature in 2000. While Korber and her computer contributed a time line to the debate, Hahn's team has traipsed through the jungles of Africa picking up chimp feces and urine. Analyzing those samples for genetic traces of SIV, they have found that different subspecies of chimpanzees harbor different variants of SIV, and only one of those variants is the likely ancestor of HIV-1, the virus responsible for infecting more than 60 million people worldwide. "In 1999 we published a paper in Nature that said that not all chimpanzee viruses are the likely source of HIV-1, only those found in West Central Africa are," said Hahn. [Wired Magazine, http://www.wired.com/medtech/health/news/2004/05/63424?currentPage=2]

John said: Several days ago Max Libbrecht from ENCODE stopped by Mike White's blog and posted this: "Max Libbrecht from ENCODE and the ENCODE AMA on reddit here. Since I'm mentioned in the comments, I thought I'd put in that I essentially agree with this article: ENCODE did not debunk the idea of "junk" DNA, contrary to many news outlets. Here is one summary of the true results and their misinterpretation -- there are many others: http://selab.janelia.org/people/eddys/blog/?p=683" You can read his and other comments, especially Diogenes', here: http://www.huffingtonpost.com/michael-white/media-genome-science_b_1881788.html Meanwhile James Shapiro has been claiming how much the ENCODE results vindicate what he and Rick (von) Sternberg proposed back in 2005 here: http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html and here: http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html and finally here: http://www.huffingtonpost.com/james-a-shapiro/mobile-dna-repeats-and-tr_b_1906135.html I have to commend Diogenes for his tenacity in critiquing Shapiro.

If any of you would like to view an argument with a less tedious creationist Junk-killer, who is announcing the 999th. "Death of Junk DNA" at the blog of Ewan Birney (Lead Analysis Coordinator of ENCODE), the argument between this creationist genius vs. the mighty blogger T. Ryan Gregory and my humble self is found here.

SteveP. said: Ogre, of course termites and ant are intelligent. In fact bacteria are intelligent as well. Im sure you have heard of the case where bacteria wait to attack until they have sufficent numbers to be successful- quorum sensing is the term I think.

Its a no brainer, pardon the pun. The question is what makes you think termites are not intelligent?

apokryltaros said: You have not done that, beyond to confuse and conflate instinct and levels of increasing pathogenicity with intelligence, then insult us for being idiots simply because we do not share your crippling pareidolia.

SteveP. said: Well bigdakine, My wife thinks Mahavishnu Orchestra is noise. To me, its an unbelievably sophisticated amalgamation of jazz, rock, funk, new age and classical music. Awesome creativity but still noise to the wife. So contrary to your assertions that ENCODE's work is a problem for ID, rather the trend is in ID's favor. The more we look and think, the more we see through the noise and see the function.

It seems to me the results of the ENCODE study spell even more doom for ID if anything. The fact that much of the “junk” is transcribed means that there is an awful lot of biochemical *noise* in the cell which has no function. Which seems to me an even bigger problem for ID

diogeneslamp0 said: If any of you would like to view an argument with a less tedious creationist Junk-killer, who is announcing the 999th. "Death of Junk DNA" at the blog of Ewan Birney (Lead Analysis Coordinator of ENCODE), the argument between this creationist genius vs. the mighty blogger T. Ryan Gregory and my humble self is found here.

ogremk5 said:

DS said: Steve wrote: "We didn’t start from scratch building up a Ford piece by piece, mistake by mistake. More likely we started out a bright shiny new Ford with all the bells and whistles in place and along the way, started breaking down, bit by bit. So started all the repair jobs to fix the defects." So we've gone from the "intelligent genome" hypothesis to the "fall caused it" hypothesis. Do you ever think before you write anything? Sorry to break it to you Stevie, but if you had bothered to ever learn anything about genetics you would know that some of the mistakes happened before there were humans. That's how we know the mistakes were copied. No magic apples, no magic floods, just descent with modification. Deal with it.

yep, good old vitamin C for example. Why is it that almost every other mammal on the planet can synthesize their own vitamin C, except for a very small group of primates that just happens to include chimps, humans, and gorillas. And isn't it curious that all three have exactly the same change, in exactly the same place that results the inability to synthesize vitamin C? Here's a good place to actually do those "magic" possibility calculations that you creationists are so fond of. What are the odds, that every single animal, in every single species in every one of these groups has exactly the same mutation that results in the loss of vitamin C? Family Tarsiidae: tarsiers Family Callitrichidae: marmosets and tamarins Family Cebidae: capuchins, squirrel monkeys Family Aotidae: night or owl monkeys (douroucoulis) Family Pitheciidae: titis, sakis, uakaris Family Atelidae: howler, spider, and woolly monkeys Family Cercopithecidae: baboons and macaques Family Hylobatidae: lesser apes (gibbons) Family Hominidae: great apes and humans Now, compare that to the odds of a single mutation occurring once and that all these species are descendants of that one.

SteveP. said: Ogre, from your POV you should be able to see that in fact books and cars do replicate themselves. They use humans to replicate. Books are parasites lurking in the human genome wanting to break out and infect other humans. So they come out through human fingertips. Now they are everywhere; infecting countless millions of humans.

ogremk5 said:

SteveP. said: Ah, but DS, if I have a book on Edsel Fords in every room with some missing pages, and some missing chapters, I could go through all of them and paste together a minimum of one complete book. Remember I have that capability. Redundency solves the problem. Your attempt to knock this analogy down fails. In fact, my scenario is more than likely a truer picture than what you paint. We didn't start from scratch building up a Ford piece by piece, mistake by mistake. More likely we started out a bright shiny new Ford with all the bells and whistles in place and along the way, started breaking down, bit by bit. So started all the repair jobs to fix the defects. Still here though, scars and all.

DS said: Look dipstick, I don't know how I can make this any clearer. You have a book on repair of Edsel Fords in every room in the house. Some are missing covers, some have lots of mistakes, some are missing pages, some are missing chapters. None of them are gong to do you any good whatsoever, even if you ever read them. And you are claiming not only that they are not junk, but that the house was built yesterday and nobody put any books in the house since! Gert a clue.

Books and cars DON'T SELF REPRODUCE!!!!!

Well at least he does make termites look intelligent.

SteveP. said: Stanton, quorum sensing is not evidence of intelligence? Mile long ant trails laid down with chemical tracers is not an act of intellignece?

You (pl) are comparing bacteria to yourselves. What is so hypocritical is you (pl) wanting to humble humanity by claiming we aren't better than ants, just different. Then, you turn around and say only humans are intelligent but termites are not.

What? You don't think bacteria analyzed their situation before deciding they needed to wait before making their move?

If making their move was based on physics and chemistry only, then, following Elzinga's logic, how is anything Man does any different? What we do is based on what we need to survive. All physics and chemistry. Its a quantitative difference rather than a qualitative difference.

Anyway, if quorum sensing is not an act of intelligence, then what is it?

And if its not an act of intelligence, then why is radio technology an act of intelligence?

John said: Read looked up my e-mail address online and...blah, blah, blah.

SteveP. said: Anyway, if quorum sensing is not an act of intelligence, then what is it? And if its not an act of intelligence, then why is radio technology an act of intelligence?

SteveP.

For the purposes of our discussion, (and since you have not provided your own definition) we are using the definition of intelligence I have provided. That is: advanced cognitive skills including, planning, creative thought, knowledge of self, and one critical one, the ability to overcome instinct.

By that definition, no insects are intelligent, no bacteria are intelligent. And no, a reaction to an input is not a sign of intelligence, planning, forethought, etc. Sigh.

Once again, we see SteveP. would rather try anything than discuss the actual science of what's going on. He desperately clings to his pathetic little analogy and refuses to actual discuss the concept of ERVs for example.

ERVs instantly destroy the notion that all DNA has a useful function (even if that 'function' is merely an 'action'). Why? Because ERVs are not human DNA. They are viral DNA. If they had any function or action left, it would be to promote the viral DNA in our genomes instead of human DNA. Up to 8% of the human genome is ERVs.

Now, ERVs also completely destroy your notion that I think that DNA can't act as a memory system. Because I, personally, was not infected by thousands of different viruses that inserted some DNA into my genome and then shutdown. I received all those ERVs from my parents who got them from their parents, etc on down the line until we find one of the people who actually was infected with one of the viruses.

In fact, if you claim to support the notion that DNA does store information, then you absolutely must accept all of the conclusions that result from that notion. Such as, the genetic history of an organism can be extracted from the DNA. For example, why human fetuses have gill arches and what those gill arches become in the human body. Why chicken embryos have teeth. And many, many other avatisms that result from genetic information leftover from the organisms ancestors.

Further, all of these things support evolutionary notions. For example, both chicken and human embryos have gill arches. However, no human embryo has ever had (or will ever have) feathers. Evolutionary theory explains that perfectly, ID has no comment on that.

So you can blather on about the magical books that replicate themselves (I note that you don't actually have one) and intelligent termites and bacteria, but it's utterly meaningless to the actual discussion (and reality for that matter).

SteveP. said: OK Stanton I'll play. Define instinct.

Here is a question for you Steve, since you don't know anything about science and are incapable of understanding an analogy. All you seem to want to do is to play word games, demanding definitions from others and refusing to provide them yourself. All right then, how about this, is the human genome irreducibly complex? In other words, using the definition proposed by Dembski, could you remove any part of it and still have it function properly? If the answer is yes, the according to Dembski, it could not have evolved. If the answer is no, it could have evolved. So which is it.

Still waitin for a response on the questions about DNA fingerprinting Steve. Here's a hint, it's the basis of forensics, paternity testing, etc.

A question: if I’ve read this right, then ENCODE has used the broadest possible criterion of ‘chemically active’ to come to it’s 80% figure. Does this mean that the remaining 20% is about as junky as junk can be – it’s literally not doing anything – useful, meaningful or otherwise (apart, possibly, from providing some sort of inert structural support)?

Matt Bright said: if I’ve read this right, then ENCODE has used the broadest possible criterion of ‘chemically active’ to come to it’s 80% figure.

Does this mean that the remaining 20% is about as junky as junk can be – it’s literally not doing anything – useful, meaningful or otherwise (apart, possibly, from providing some sort of inert structural support)?

I note that some comments from John Kwok, that were quite substantial and useful (to me), have been moved to the BW.

Could we see more discernment in which comments get moved to the BW?

Instinct is behaviour that is not learned, nor is it the result of cognition, but occurs in response to specific stimuli. That it is not cognitive is demonstrated when the behaviour is repeated whether that specific stimulus does or does not have survival value in that particular instance, or even is contrary to survival. That it is not learned is demonstrated when it occurs in species where there is no opportunity to learn, yet the behaviour appears spontaneously, fully developed. Spiders, for example, spin webs. Ants follow chemical trails. They don't practice these behaviours, they simply perform them. Further, all defined members of the species follow that behaviour. It must follow that the behaviours are innate and therefore inherited. Exactly how that works is not known in detail, but the principle is clear.

Because it is not cognitive, instinctive behaviour is not a measure of intelligence, no matter how complex the behaviour may be.

All right, Steve. Have a go at that.

Sorry, the second sentence of the above should read:

"That it is not cognitive is demonstrated when the behaviour is repeated whether or not that specific behaviour does or does not have survival value..."

You might as well give up on Steve P. For him, it's teleology all the way down. No facts, no tests, no experiments, no mountains of data will ever convince him otherwise.

SteveP:

In the first place, you have now shifted ground. You were arguing that there is an intelligence behind animal behaviour that the animals possess. I have shown that this is not the case. By removing the action of this now-unspecified intelligence to some unspecified time in the distant past, you have conceded the point, and further conceded that the assertion is void of useful information. What intelligence? When? How?

In the second place, neither of your alternatives, with regard to spiders and their webs, is necessary. Neither is actually indicated. All spiders, and many insects, have the ability to use specialised body fluids that harden in air to make threads. The glands that excrete them, and the fluids themselves, are similar. The structures so produced - coccoons, egg sacs, flying threads, traps, nets, etcetera - are as diverse in form as the purposes to which they are put. An intelligent designer would have had to make separate decisions in each case. Evolution makes no such "decision". The diversity is explained by natural selection, operating blindly.

There never was a spider that created the first spiderweb, any more than there was a prehuman who had the first abstract thought. There never was any cognitive thought by spiders. The physical organs, the behaviours, and the structures they produced, were selected from very basal properties, and gradually emerged and specialised, in a mutual feedback loop, with the ineffective changes ruthlessly culled.

Evolution explains this without reference to intelligence, either in the organisms or external to them. None is required. All that is required is a fundamental property on which natural selection can and must act. An arthropod's chances of surviving injuries are enhanced if its body fluids are self-sealing. Merely a thin place in the exoskeleton of the abdomen would allow sticky body fluids to be spread on, say, a leaf or bark. Small insects could be trapped, providing rewards. Feedback does the rest. Each step in the process improves the fitness of the organism in a specific environment and niche. Complexity emerges from simple natural causes, just as it does with snowflakes.

If an explanation accounts adequately for the observations, no further explanation need be sought. Evolution by (mostly, but not exclusively) natural selection accounts for the observations. There is simply no need to posit an intelligence in addition. None should therefore be posited.

It's as simple as that.

Citrate. E coli. No, this is not intelligence. Most of the e-coli starved. But a chance mutation turned up in one or a very few. This mutation - which Lenski precisely defined and documented - enabled the organism to metabolise citrate in a citrate-rich environment. The mutation occurred entirely by chance, with a probability that could be computed from an accurate understanding of exactly what it entailed.

The organism that expressed the mutation survived and thrived, in that specific environment. However, neither it, nor its descendents, thought or intended anything. Natural selection and random variation were sufficient. There was no other cause, and none was needed. And neither was intelligence.

SteveP, why should we trust you and your worthless word? You have earned a reputation here for being a liar who hates and scoffs at science, and who makes up all sorts of excuses to avoid supporting your inane claims. You refuse to show us or even explain to us how or why you came up with your latest moronic claim, yet you want us to accept it without question.

I only sound repetitive because you keep saying the same stupid things, and keep demanding of us the same stupid demands.

SteveP. said: Actually, ID some have something to say about it. Common design. By the way, your explanation may be very plausible while still being completely wrong, like 3 blind men inspecting an elephant. And conversely, my take may be very implausible but right on the money. Yet, ID gets the short end of the stick as testing and supporting an implausible yet correct position is much harder than supporting a plausible yet wrong explanation.

fnxtr said: You might as well give up on Steve P. For him, it's teleology all the way down. No facts, no tests, no experiments, no mountains of data will ever convince him otherwise.

apokryltaros said: It would be of greater help if SteveP were to somehow realize his own futility and stop trying to convince us of the illusionary worth of his bullshit.

https://www.google.com/accounts/o8/id?id=AItOawkqPIHF5zvWlUzSyYRWDkEN1Z0BiuSxKF0 said:

apokryltaros said: It would be of greater help if SteveP were to somehow realize his own futility and stop trying to convince us of the illusionary worth of his bullshit.

mrg said: Come now, Stanton. He's not trying to convince anyone of anything. He's just baring his arse in your face and giggling.

SteveP. said: Shit Ogre, by your definition, only Man is intelligent.

How does this help anyone? In fact, lots of folk on this board want to make Man out to be just a cut above the rest. But defining Man this way you are putting us on a pedestal. Is that what you want to do?

For the purposes of our discussion, (and since you have not provided your own definition) we are using the definition of intelligence I have provided. That is: advanced cognitive skills including, planning, creative thought, knowledge of self, and one critical one, the ability to overcome instinct. By that definition, no insects are intelligent, no bacteria are intelligent. And no, a reaction to an input is not a sign of intelligence, planning, forethought, etc. Sigh.

But you don't know that.

Its an assumption on your part; an assumption you believe is justified. However, you have not demonstrated that our genome is not making us of the ERVs.

You assume they fought their way into our genome and we have no way to expel them.

Yet we know the extraordinary capabilities cells have of detecting problems in DNA structure and making appropriate repairs.

This knowledge alone destroys your assertion that our genome does not have the capability to recognize foreign DNA and expel it.

Rather, it is quite plausible that cells do recognize the invader and make use of it.

One possible use is assembling a library of viruses for reference purposes. But of course if you think only Man in particular is intelligent, but simple organisms and individual cells could not possible possess intelligence, then you wouldn't consider this line of reasoning.

Thats why ID has the conceptual advantage. Start with the assumption that intelligence is embedded in life and run with it. See where it leads. Testing it is very difficult but like one of adidas' mottos goes - Impossible is nothing.

So my money is on the 80/20 rule. 20% does all the work, but 80% provides the variation/innovation.

Once again, we see SteveP. would rather try anything than discuss the actual science of what’s going on. He desperately clings to his pathetic little analogy and refuses to actual discuss the concept of ERVs for example. ERVs instantly destroy the notion that all DNA has a useful function (even if that ‘function’ is merely an ‘action’). Why? Because ERVs are not human DNA. They are viral DNA. If they had any function or action left, it would be to promote the viral DNA in our genomes instead of human DNA. Up to 8% of the human genome is ERVs.

Actually, ID some have something to say about it. Common design.

By the way, your explanation may be very plausible while still being completely wrong, like 3 blind men inspecting an elephant. And conversely, my take may be very implausible but right on the money. Yet, ID gets the short end of the stick as testing and supporting an implausible yet correct position is much harder than supporting a plausible yet wrong explanation.

In fact, if you claim to support the notion that DNA does store information, then you absolutely must accept all of the conclusions that result from that notion. Such as, the genetic history of an organism can be extracted from the DNA. For example, why human fetuses have gill arches and what those gill arches become in the human body. Why chicken embryos have teeth. And many, many other avatisms that result from genetic information leftover from the organisms ancestors. Further, all of these things support evolutionary notions. For example, both chicken and human embryos have gill arches. However, no human embryo has ever had (or will ever have) feathers. Evolutionary theory explains that perfectly, ID has no comment on that.

Steve wrote:

"But you don’t know that. Its an assumption on your part; an assumption you believe is justified. However, you have not demonstrated that our genome is not making us of the ERVs. You assume they fought their way into our genome and we have no way to expel them. Yet we know the extraordinary capabilities cells have of detecting problems in DNA structure and making appropriate repairs. This knowledge alone destroys your assertion that our genome does not have the capability to recognize foreign DNA and expel it."

This is all completely wrong, but at least it has something to do with the topic of the thread.

First, we know exactly what ERVs are, where they came from, how they got into the cell, how they increase in copy number and why they are deleterious. If Steve wants to know the details he can look them up for himself, but first he is going to have to find out what ERV stands for, apparently he doesn't know. Second, there is no known mechanism be which ERVs can be precisely excised, the cell doesn't recognize them as foreign, that is why they persist for millions of years. They can sometimes be excised by recombination, usually mediated by the insertion sequences, but this is a random process and not very efficient, that is why ERVs tend to increase in copy number and why there are millions of them in the human genome. Third, the insertions sometimes cause disease and death, this means that it is a random accident, no intelligence involved on anyones part. I would suggest that Steve take a course in molecular biology, but what's the point?

Steve is trapped in his own little world of magically thinking. Everything must have intelligence and everything must happen for a reason. Like a three year old trapped in a world of make believe, he simply cannot conceive of the fact that natural laws and random processes happen all around him, degrading his genome and making it possible for spiders to spin webs. He literally can't conceive of the process of random mutation and natural selection. His twisted mind will go through any contortions necessary to deny reality and cling to his fantasy world, where he feels safe and secure.

Look Steve, I suggest you actually read the Lenski papers. The author did NOT conclude that the bacteria were intelligent, quite the opposite in fact. You are free to distort and misinterpret his results any way you want, but you aren't gong to convince anyone who is actually aware of the experiments. There is no rational definition of intelligence that includes bacteria, that's why you haven't provided one. The only one you are fooling is yourself.

Steve wrote:

"Its an assumption on your part; an assumption you believe is justified. However, you have not demonstrated that our genome is not making us of the ERVs."

Actually, it's true, the human genome has made use of some ERVs, eventually. A few have changed into regulatory sequences over millions of years. Of course this does absolutely nothing for the intelligent design hypothesis. What it means is that any sequences can serve as raw material on which random mutation and natural selection can act. No intelligence would generate regulatory sequences this way, it could just produce them from scratch. Why dump millions of useless copies of broken genes into the genome, causing death and disease all the while, just on the off chance that someday some of them might somehow do something useful? Unintelligent design isn't going to get you anywhere.

And don't forget, since they persist through speciation events, specific insertions are strong evidence for common descent. No creationist has any convincing alternative explanation for this evidence. All they can do is make up crap about intelligent spiders and hope nobody notices.

I have a question, and let me use an analogy. Let's say I have an old junky radio. I plug it in and it lights up but all I can hear is static--I can't get any station. According to ENCODE, is it considered functional?

hey Steve, you might want to wander over to Uncommon Descent and explain to them that bacteria and insects are intelligent.

Torley over there is flatly denying that crows are intelligent. Personally, I'd be willing to argue that crows meet the definition of intelligence I used. But since he thinks that crows aren't intelligent, surely bacteria and insects are even less so.

Go set him straight.

DS said: I have no idea why PZ has allowed this dipstick to take over a thread

I'd like to hear what the knowledgeable people have to say about the Wikipedia article Noncoding DNA

tomh said: It's more like replies to SteveP have taken over the thread. People seem to enjoy engaging with him.

The author of the original post is PZ Myers. It is cloned from his own blog and he is obviously not actively moderating this discussion. It seems not to be being moderated enough, and it has degenerated into the favorite total waste of time at PT, troll-chasing.

Joe Felsenstein said: The author of the original post is PZ Myers. It is cloned from his own blog and he is obviously not actively moderating this discussion. It seems not to be being moderated enough, and it has degenerated into the favorite total waste of time at PT, troll-chasing.

Joe Felsenstein said: It seems not to be being moderated enough ...

It is insane that Kwok gets blocked while Steve gets to troll out of control. Steve should be permitted one comment per thread then off to the BW. This idiot ruins every thread here, and the troll feeding is cited by the DI as typical of Darwinist immaturity.

diogeneslamp0 said: I note that some comments from John Kwok, that were quite substantial and useful (to me), have been moved to the BW. Could we see more discernment in which comments get moved to the BW?

Well, I'm a moderate Republican, and I LOVE science.

diogeneslamp0 said: It is insane that Kwok gets blocked while Steve gets to troll out of control. Steve should be permitted one comment per thread then off to the BW. This idiot ruins every thread here, and the troll feeding is cited by the DI as typical of Darwinist immaturity.

dalehusband said:

diogeneslamp0 said: I note that some comments from John Kwok, that were quite substantial and useful (to me), have been moved to the BW. Could we see more discernment in which comments get moved to the BW?

Simple. Any comments made by John Kwok, no matter what they say, are moved to the Bathroom Wall by P Z Myers because of an longstanding grudge between them over politics which has nothing to do with science. Such prejudicial behavior destroyed Myers' credibility long ago. Being a Republican does not mean you are anti-science. He should grow up!

Well, I’m a moderate Republican, and I LOVE science.

diogeneslamp0 said: It is insane that Kwok gets blocked while Steve gets to troll out of control. Steve should be permitted one comment per thread then off to the BW. This idiot ruins every thread here, and the troll feeding is cited by the DI as typical of Darwinist immaturity.

I’m grateful to ogremk5, Dave Luckett and others for patiently taking pains to explain elementary genetics and biology and concepts of natural selection to trolls: There have been breakthrough moments just in the last week when I’ve suddenly learned something about these subjects that was, for me, painfully hard to grasp. Thanks – I go back to Conway Morris, Coyne, Shubin, and all the others with renewed enthusiasm.

At least John Kwok is on the side of science, that much is sure!

BioLogos also had 2 good posts on ENCODE by Dennis Venema.

FL said:

Well, I’m a moderate Republican, and I LOVE science.

I used to be a Democrat, but they STOPPED loving science.

I used to be a Democrat, but they STOPPED loving science.

Karen S. said: Huh? Then explain why most of the people here seem to be Democrats.