The ENCODE delusion

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I can take it no more. I wanted to dig deeper into the good stuff done by the ENCODE consortium, and have been working my way through some of the papers (not an easy thing, either: I have a very high workload this term), but then I saw this declaration from the Electronic Frontier Foundation.

On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California's warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

I am sympathetic to the cause the EFF is fighting for: they are opposing casual DNA sampling from arrestees as a violation of privacy, and it is. The forensic DNA tests done by police forces, however, do not involve sequencing the DNA, but only look at the arrangement of known variable stretches of repetitive DNA by looking at just the length of fragments cut by site-specific enzymes; they can indicate familial and even to some degree ethnic relationships, but not, as the EFF further claims, "behavioral tendencies and sexual orientation". Furthermore, the claim that 80% of our genome has critical functional roles is outrageously bad science.

This hurts because I support the legal right to genetic privacy, and the EFF is trying to support it in court with hype and noise; their opposition should be able to easily find swarms of scientists who will demolish that argument, and any scientifically knowledgeable judge should be able to see right through the exaggerations (maybe they're hoping for an ignorant judge?). That conclusion, that 80% of the genome is critical to function, is simply false, and it's the notorious dishonest heart of ENCODE's conclusions.

And then there is this lovely little commercial for ENCODE, narrated by Tim Minchin, and portraying ENCODE as a giant cancer-fighting robot.

Oh, jebus…that was terrible and cringeworthy. Not just the ridiculous exaggerations … the Human Genome Project also claimed that it would provide the answers to all of human disease, as has, to a lesser degree, most every biomedical grant proposal, it seems — but that they invested in some top-notch voice talent and professional animation to promote some fundamentally esoteric science to the general public as a magic bullet…I mean, robot.

Scientists, don't do this. Do make the effort to communicate your work to the public, but don't do it by talking down to them and by portraying your work in a way that is fundamentally dishonest and misleading. If you watch that video, ask yourself afterward: if I hadn't read any of the background on that project, would I have the slightest idea what ENCODE was about from that cartoon? There was no usable information in there at all.

So what is ENCODE, actually? The name stands for Encyclopedia of DNA Elements, and it's the next step beyond the Human Genome Project. The HGP assembled a raw map of the genome, a stream of As and Gs and Cs and Ts, and dumped it in our lap and told us that now we have to figure out what it means. ENCODE attempts to break down that stream, reading it bit by bit, and identifying what each piece does; this part binds to a histone, for instance, or this chunk is acetylated in kidney cells, or this bit is a switch to turn expression of Gene X off or on. It tries to identify which genes are active or inactive in various cell types. It goes beyond the canonical sequence to look at variation between individuals and cell types. It identifies particular genetic sequences associated with Crohn's Disease or Multiple Sclerosis or that are modified in specific kinds of cancers.

ENCODE also looks at other species and does evolutionary comparisons. We can identify sequences that show signs of selection within the mammals, for instance, and ENCODE then maps those sequences onto proposed functions.

You know what? This is really cool and important stuff, and I'm genuinely glad it's being done. It's going to be incredibly useful information. But there are some unfortunate realities that have to be dealt with.

It's also drop-dead boring stuff.

I remember my father showing me a pile of maintenance manuals for some specific aircraft at a Boeing plant when I was a kid; these were terrifyingly detailed, massive books that broke down, bit by bit, exactly what parts were present in each sub-assembly, how to inspect, remove, replace, repair, and maintain a tire on the landing gear, for instance. It's all important and essential, but…you wouldn't read it for fun. When you had a chore to do, you'd pull up the relevant reference and be grateful for it.

That's ENCODE. It's a gigantic project to build a reference manual for the genome, and the papers describing it are godawful tedious exercises in straining to reduce a massive data set to a digestible message using statistics and arrays of multicolored data visualization techniques that will give you massive headaches just looking at them. That is the nature of the beast. It is, by necessity and definition, a huge reference work, not a story. It is the antithesis of that animated cartoon.

I'm uncomfortable with the inappropriate PR. The data density of the results makes reading the work a hard slog…but that's the price you have to pay for the volume of information delivered. But then…disaster: a misstep so severe, it makes me mistrust the entire data set — not only are the papers dense, but I have no confidence in the interpretations of the authors (which, I know, is terribly unfair, because there are hundreds of investigators behind this project, and it's the bizarre interpretations of the lead that taints the whole).

I refer to the third sentence of the abstract of the initial overview paper published in Nature; the first big razzle-dazzle piece of information the leaders of the project want us to take home from the work. That 80%:

These data enabled us to assign biochemical functions for 80% of the genome.

Bullshit.

Read on into the text and you discover how they came to this startling conclusion:

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

That isn't function. That isn't even close. And it's a million light years away from "a critical role in controlling how our cells, tissue and organs behave". All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn't just a loose and liberal definition of "function", it's an utterly useless one.

Now this is all anyone talks about when describing this research: that it has found a 'function' for nearly all of human DNA (not true, and not supported by their data at all) and that it spells the demise of junk DNA, also not true. We know, for example, that over 50% of the human genome has a known origin as transposable elements, and that those sequences are basically parasitic, and has no recognizable effect on the phenotype of the individual.

I don't understand at all what was going through the head of the author of that paper. Here's this awesome body of work he's trying to summarize, he's representing a massive consortium of people, and instead of focusing on the useful, if rather dry, data the work generated, he decides to hang it all on the sensationalist cross of opposing the junk DNA concept and making an extravagant and unwarranted claim of 80 going on 100% functionality for the entire genome.

Well, we can at least get a glimpse of what's going on in that head: Ewan Birney has a blog. It ended up confusing me worse than the paper.

For instance, he has a Q&A in which he discusses some of the controversy.

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

Oh, jeez, straining over definitions—ultimately, what he ends up doing is redefining "functional" to not mean functional at all, but to mean simply anything that their set of biochemical assays can measure. It would have been far more sensible to use a less semantically over-loaded word or phrase (like "specific biochemical activity") than to court confusion by charging into a scientific debate about functionality that he barely seems to comprehend. It would have also conformed to the goals he claims to have wanted to achieve with public education.

ENCODE also had the chance of making our results comprehensible to the general public: those who fund the work (the taxpayers) and those who may benefit from these discoveries in the future. To do this we needed to reach out to journalists and help them create engaging stories for their readers and viewers, not for the readers of Nature or Science. For me, the driving concern was to avoid over-hyping the medical applications, and to emphasize that ENCODE is providing a foundational resource akin to the human genome.

Uh, "giant cancer-fighting robot", anyone? Ewan Birney's name is right there in the credits to that monument to over-hyping the medical applications.

I'll be blunt. I don't think Birney has a clue about the biology. So much of what he has said about this project sounds human-centered and biased towards gross misconceptions about our place in biology. "We are the most complex things we know about," he says, and seems to think that there is a hierarchy of complexity that correlates with the phylogenetic series leading to humans, where, for instance, fugu are irrelevant to the argument because they're not a mammal. This is all nonsense. I would not be at all surprised to learn that the complexity of the teleost genome is significantly greater than that of the tetrapod genome; and there's nothing more complex about our genetics than that of a mouse. I get the impression of an extremely skilled technologist with almost certainly some excellent organizational skills, who is completely out of his depth on the broader conceptual issues of modern biology. And also, someone who is a total media disaster.

But I'm just a guy with a blog.

There is a mountain of material on ENCODE on the web right now — I've come late to the table. Here are a few reading recommendations:

Larry Moran has been on top of it all from day one, and has been cataloging not just the scientific arguments against ENCODE's over-interpretation, but some of the ridiculous enthusiasm for bad science by creationists.

T. Ryan Gregory has also been regularly commenting on the controversy, and has been confronting those who claim junk DNA is dead with the evidence: if organisms use 100% of their genome, why do salamanders have 40 times as much as we do, and fugu eight times less?

Read Sean Eddy for one of the best summaries of junk DNA and how ENCODE hasn't put a dent in it. Telling point: a random DNA sequence inserted into the human genome would meet ENCODE's definition of "functional".

Seth Mnookin has a pithy but thoughtful summary, and John Timmer, as usual, marshals the key evidence and makes a comprehensible overview.

Mike White summarizes the ENCODE projects abject media failure. If one of Birney's goals was to make ENCODE "comprehensible to the general public", I can't imagine a better example of a colossal catastrophe. Not only does the public and media fail to understand what ENCODE was about, but they've instead grasped only the completely erroneous misinterpretation that Birney put front and center in his summary.

You'll be hearing much more about ENCODE in the future, and unfortunately it will be less about the power of the work and more about the sensationalistic and misleading interpretation. The creationists are overjoyed, and regard Birney's bogus claims about the data as a vindication of their belief that every scrap of the genome is flawlessly designed.

123 Comments

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.

This is exactly what ENCODE did according to Ewan Birney’s own blog:

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%

Note that he is blaming readers for choosing 80% rather than realistic estimates based on a solid definition of function:

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.

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.”

https://www.google.com/accounts/o8/[…]vtiF0BBqF10Q 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.”

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.

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.”

Really. Well let’s see.

The human genome contains about 6% simple repetitive DNA, most of which does absolutely nothing. This is in fact the basis of human DNA fingerprinting techniques. DNA transposons constitute about 3%. LTR retrotransposons 8%, LINEs 21%, SINEs 13% and processed pseudogenes 0.4%. So that’s over 50% right there.

Now of course you could always argue that this could be raw material that will eventually become functional, but then I guess you pretty much have to admit that evolution is real to do that.

I posted the following comment at Ewan’s blog. I’m betting he will never answer.

——————————————————–

Birney: “For me, the driving concern was to avoid over-hyping the medical applications…”

Really? You mean like when you helped Nature produce a video cartoon in which ENCODE is presented as a mega-robot that destroys cancer and heart disease by punching it very hard?

Is that what you meant by avoiding over-hyping of medical applications? What, then, WOULD be hype by your definition? Immortality? Free nose jobs for ugly children? The ability to fly? What?

Birney: “With hindsight, we could have used different terminology to convey the concepts…”

True, you could have used accurate terminology.

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

No, no. You told the general public that there was 80% FUNCTION in the genome, FUNCTION not activity, and you told Ed Yong at Discover that would go to 100%. And almost all of the media interpreted function to mean “necessary”, “needed”, “essential”. Was that accurate?

NPR reported John Stamatoyonnopoulis as saying:

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.

Was John Stam telling the truth or lying, Ewan?

This is from the Independent:

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.”

Does the vast majority of the human genome have a vital function by regulating the genes, Ewan?

This is from the New York Times:

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.

Is 80% of human DNA active and needed, Ewan?

This is from the Washington Post:

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”

Is the vast majority of human DNA involved in maintaining individuals’ well being, Ewan?

This is from USA Today:

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.”

Is 80% of human DNA genome “switches” that control genes, Ewan?

Birney: “ENCODE also had the chance of making our results comprehensible to the general public…”

Ewan, did you succeed of fail?

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 is reminiscent of the long hard slog with entropy and the second law in popular literature. I can sympathize.

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

DS said -

“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.

It’s unfortunate that Ewan Birney has to some degree misunderstood or misrepresented the important and powerful results of the ongoing ENCODE project, but as DS implies, even if Ewan Birney’s hype, which is far less dishonest than creationist hype, were all 100% accurate, ID/creationism would still be wrong.

Creationists are like Charles Manson obsessively claiming that one of his fingerprints on one of his victims’ walls doesn’t incriminate him. First of all it isn’t true, and second of all, if it were true the evidence against him would still be overwhelming.

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.

But it doesn’t follow that ID would be “true” if they could get rid of that one death knell. There are many other death knells tolling.

ID is in the somewhat unique position of making no potentially useful predictions or testable claims whatsoever, and yet still being easy to falsify. It’s internally incoherent, and many of its arguments are grounded in patently false analogies.

It’s a childish word game played by a motley crew of wealthy conniving scoundrels and wretched academic failures, each group making far more money by pandering to the fantasies of despicable, deluded, unhappy billionaires, than they could otherwise.

Bacteria have very little “junk” DNA. Certainly, the common strains studied by humans as pathogens or lab organisms tend to have far less than 20% “junk” DNA. Yet efforts to present bacteria as the products of “intelligent design” meet with richly deserved jeering ridicule.

Just because junk DNA makes ID look stupid, does not mean that ID would stop looking stupid if junk DNA went away.

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?

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We here see illustrated the dangers of thinking by analogy.

Mahavishnu Orchestra

They’re not bad, but John McLaughlin did his best work with Miles Davis.

Anyway, Steve P. is of course partly correct that “bad design” can be explained away by resorting to “the mysterious ways of the designer”.

If “bad design” were the ONLY issue that argument would work. It looks subjectively “bad” to us but the designer is so all-powerful and inscrutable that we can’t understand it’s work, and so on.

The thing about ERVs, LINES, SINES, pseudogenes, and other things that are quite reasonably labeled “junk” DNA is that they are not only “bad design” to the human eye.

They are also strong positive evidence for, and well explained by, the theory of evolution.

In placental development in humans and some but not all other placental mammals, an ERV gene is co-opted for an important function. You can’t get more functional than that. It’s “junk” DNA that became functional in a true sense, but the situation is still strong evidence for evolution and poorly explained by ID/creationism. Any sequence of DNA could hypothetically do something, or mutate into something that does something, harmful, neutral or beneficial, from the human perspective, but a good amount of it doesn’t right now - twenty percent at a minimum, even by the incredibly loose definition of “function” being used by Ewan Birney.

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.

That’s exactly the point. You have all this junk you are holding onto. You have copies of all of this junk in every room in your house. You have the junk not because it is useful or ever will be, you have it because of your past history. That is the only way it makes any sense at all. You not only have books on car repair, you have them in every room in your house, including outdated books, books filled with typos, parts of books, books with stuff that doesn’t have anything to do with modern cars but antique cars that you don’t own and can’t afford. And the thing is that you still want people to believe that your house was built from scratch yesterday, without any past history! Someone who built a modern house wouldn’t fill every room with old useless junk, at least not it they were intelligent. Or are you advocating the “intelligent hoarder” hypothesis?

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.

Dave Luckett said:

We here see illustrated the dangers of thinking by analogy.

Exactly: Intelligent Design proponents, like SteveP, also readily demonstrate how they are too arrogant to care/realize that they simultaneously use inaccurate analogies, and use analogies inaccurately.

@SteveP:

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

SteveP has brilliantly explained what evolution is, and its relationship to the genome. Evolution is a long history of experiments. Records are only kept of the successful experiments; the failed experiments are not recorded. The records are, therefore, biased.

Nevertheless the genome is, as SteveP says, “a library of historical environmental records [that helps] in their survival,” thanks to evolution.

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.

Correct again! Yes, that is “the smart play”, as Steve says– but only if evolution is real. An organism may evolve to make crucial use of a tiny fraction of all that junk. See, SteveP is useful for something. He has re-stated Sydney Brenner’s distinction between “garbage” and “Junk DNA.”

It only takes 6-8 bp to make a TF binding site. TF binding sites are so small they evolve in and out, accessible to mutation and selection. Viral DNA (ERV’s) comes with powerful promoters that promote transcription. A genome can evolve to make use of those tiny bits 6 to 8 base pairs at a time.

But unfortunately for us, some of those “experiments” recorded in the genome involve parasitic elements duplicating themselves out of control. The “records” of that make up about half of the genome.

Most of your genome is still junk, and ID is still dead.

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.

Furthermore, SteveP doesn’t remember that, according to Intelligent Design as argued by Behe, if a single component is missing, the whole system stops functioning.

@DS:

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.

Bwa ha ha. But they’re not radios– they’re toy robots that can reproduce themselves, using your car’s machinery to make copies of themselves, so they did. Many many copies of toy robots that once had the ability to reproduce, but are broken now.

ENCODE picked through all those toy robots and found, here and there, a working transistor or an LED light that still works, and they tell the Muggle press, “80% of the genome has function!” In the sense that tiny bits of things that used to be able to reproduce themselves, still have parts that can interact.

Most of your genome is still junk, and ID is still dead.

This comment has been moved to The Bathroom Wall.

@SteveP:

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

How is this a good analogy for transposons? Books can’t copy themselves. Transposons can. Maybe that explains why half your genome is copies of transposons, but half your attic is not books.

Add some ERV’s and pseudogenes, and most of your genome is still junk and ID is still dead.

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?

FL said:

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

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

And that’s another one of your damned lies.

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

Huh? Then explain why most of the people here seem to be Democrats.

Karen S. said:

Huh? Then explain why most of the people here seem to be Democrats.

Simple. They follow, contribute to, and discuss science (at a cost of time and effort) because they hate science. Just like the President of the United States of America hates America.

Beckthink.

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This page contains a single entry by PZ Myers published on September 23, 2012 6:07 PM.

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