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What Are the Top Ten Problems with Darwinian Evolution?

A few months back I gave my top three criticisms of Darwinian evolution that I think should be taught in public schools. But the problems with Darwinian evolution run much deeper. Here are my top ten problems with biological and chemical evolution:

  1. Lack of a viable mechanism for producing high levels of complex and specified information. Related to this are problems with the Darwinian mechanism producing irreducibly complex features, and the problems of non-functional or deleterious intermediate stages. (For details see: "The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information," "Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones's Straw Tests of Irreducible Complexity for the Bacterial Flagellum," "Opening Darwin's Black Box," or "Can Random Mutations Create New Complex Features? A Response to TalkOrigins");

  2. The failure of the fossil record to provide support for Darwinian evolution. (For details, see "Punctuated Equilibrium and Patterns from the Fossil Record" or "Intelligent Design Has Scientific Merit in Paleontology");

  3. The failure of molecular biology to provide evidence for a grand "tree of life." (For details, see: "A Primer on the Tree of Life");

  4. Natural selection is an extremely inefficient method of spreading traits in populations unless a trait has an extremely high selection coefficient;

  5. The problem that convergent evolution appears rampant -- at both the genetic and morphological levels, even though under Darwinian theory this is highly unlikely. (For details, see "Convergent Genetic Evolution: 'Surprising' Under Unguided Evolution, Expected Under Intelligent Design" and "Dolphins and Porpoises and...Bats? Oh My! Evolution's Convergence Problem");

  6. The failure of chemistry to explain the origin of the genetic code. (For details, see "The origin of life remains a mystery" or "Problems with the Natural Chemical 'Origin of Life'");

  7. The failure of developmental biology to explain why vertebrate embryos diverge from the beginning of development. (For details, see: "Evolving views of embryology," "A Reply to Carl Zimmer on Embryology and Developmental Biology," "Current Textbooks Misuse Embryology to Argue for Evolution");

  8. The failure of neo-Darwinian evolution to explain the biogeographical distribution of many species. (For details, see "Sea Monkey Hypotheses Refute the NCSE's Biogeography Objections to Explore Evolution" or "Sea Monkeys Are the Tip of the Iceberg: More Biogeographical Conundrums for Neo-Darwinism");

  9. A long history of inaccurate predictions inspired by neo-Darwinism regarding vestigial organs or so-called "junk" DNA. (For details, ] see: "Intelligent Design and the Death of the 'Junk-DNA' Neo-Darwinian Paradigm," "The Latest Proof of Evolution: The Appendix Has No Important Function," or "Does Darrel Falk's Junk DNA Argument for Common Descent Commit 'One of the Biggest Mistakes in the History of Molecular Biology'?);

  10. Humans show many behavioral and cognitive traits and abilities that offer no apparent survival advantage (e.g. music, art, religion, ability to ponder the nature of the universe).

Of course, even these "top ten" still just scratch the surface. What would you add?


31 Comments

Diogenes claims that Casey Luskin and Jonathan Wells are guilty of two falsehoods regarding “junk DNA.”

Alleged Falsehood 1. Molecular biologists believed ‘non-coding DNA = non-functional DNA.’
Alleged Falsehood 2. Most of the human genome is experimentally known at present to be functional.

With regards to alleged falsehood 1, this is a demonstrable misrepresentation. Let's take a look at what Jonathan Wells has to say in his "The Myth of Junk DNA.”

From chapter 2:

"Yet by 1970 biologists already knew that much of our DNA does not encode proteins. Although some suggested that non-protein-coding DNA might help to regulate the production of proteins from DNA templates, the dominant view was that non-protein-coding regions had no function.

In 1972, biologist Susumu Ohno (at the City of Hope National Medical Center in Los Angeles) published an article wondering why there is "so much 'junk' DNA in our genome." The same year, his City of Hope colleague David Comings wrote that only about 20% of the human genome appears to be used; the remaining 80% seemed to be "junk" -- though Comings did not necessarily think it was entirely useless."

As to alleged falsehood 2, this is also a demonstrable misrepresentation. As Jonathan Wells has stated on this blog [source: http://www.evolutionnews.org/2011/10/post_32051651.html],

"I never claim that functions have been found for most non-protein-coding DNA, though as I stated above the list grows longer every week. It is the trend, more than the current total, that should worry any defender of junk DNA."

Steve Hunter asks,

>>>"If an intelligent agent has been repeatedly active in the history of life on this planet, why can’t the methods of science be used to figure out that agent’s identity and mechanisms?"<<<

Regardless, one doesn't need to demonstrate a modus operandi of design in order to legitimately detect the products of intelligent agency. Indeed, you make that judgement all the time. The SETI researchers in the movie “Contact” were justified in inferring design from the series of prime numbers even though it wasn't immediately possible to tell the nature and identity of the architect of those signals. Those questions are, therefore, by nature secondary. Addressing them requires a different sort of evidence and is not a requisite for detecting design.

It is also worth noting that the causal interaction between mind and matter is still very much a grey area. The tools used by a human engineer fall into the category of secondary causation. Mind by its nature is immaterial, and it interacts with the material brain – how it does this we don't know, but that doesn't imply that the inference to design is not warranted. We have uniform-and-repeated experience of the kinds of effects produced by intelligent agents, even if we don't fully understand how intelligence works and how it interacts with the material world.

Finally, as for whether it is possible to shed light on the designer's identity, I don't think science is equipped to address that question at present, especially if we are dealing with a supernatural intelligence like a deity (science can only deal with the natural world). But I believe that other disciplines, such as metaphysics, are equipped to tackle this question.

Jonathan

I'm definitely adding this ENV post to my collection of things to pass on to anyone who wants a crash course on this debate.

As an addition within #4, I would add that selection also has trouble eliminating deleterious mutations if they start off as neutral but become harmful as they accumulate. By the time the aggregate effect of otherwise neutral mutations become negative, it's too late to eliminate them one by one.

This lack of foresight is a bigger problem for organisms with larger genomes, as highlighted in the book "Genetic Entropy."

On number 10, from a non-biologist. Religion, song, ritual, higher levels of thought absolutely contribute to the survival of our species. Over thousands of years they promote common social norms that engender cooperation. They have bound us together to seek common goals. Many people forget that many species are successful because of cooperation and not as much competition.
My guess is as follows. People react at such a gut level with contempt to contrary convictions and free thinking that goes against societal norms because it could represent a threat to survival of the community. Free thinkers are routinely cast out and shunned because they don't follow the crowd. If you are going to survive and thrive, you would rather be with the crowd.
Higher levels of thought were useful in this way, and we all know that there is no indisputable evidence of supernatural origin. Thomas Huxley said, 'I am conscious that I have no explanation why I am conscious' but that doesn't mean we have to use creationism as a backstop that excludes further research.

There is something about this back and forth that I do not understand. You claim that the existence of an intelligent designer is a matter for scientific inquiry, but that the identity and mechanism of that designer/builder is beyond the reach of science.

By the time Captain Cook saw the huge stone figures on Easter Island, the history had been lost even to the people who were there. It was immediately apparent that these were designed and crafted by intelligent agents. Since then, scientific inquiry has revealed a great deal about the people responsible and how they did it.

If an intelligent agent has been repeatedly active in the history of life on this planet, why can’t the methods of science be used to figure out that agent’s identity and mechanisms?

Dear Casey,

I'm afraid you have misunderstood what Diogenes said in your response to him. Molecular biologists have never stated that all non-coding DNA is junk. They have stated that there are excellent reasons to believe that a large amount of non-coding DNA is junk.

These two statements are not the same.

As Diogenes quite correctly points out, function in non-coding DNA has been known since before the term junk DNA was coined. It is therefore quite fallacious to assume an equivalence -- even though a majority of non-coding DNA is probably junk. I hope that important distinction is clear.

So, junk DNA is not simply non-coding DNA. It is non-functional DNA. A better term might be putative junk, because a few % may eventually turn out to be functional. Incidentally, some have suggested the term junk DNA be rejected wholesale (e.g. Ryan Gregory). This is not because they do not believe that a majority of human genome is functionless, but because the term originated with a specific meaning (pseudogene), which does not accurately describe the majority of the human (or indeed any mammalian) genome.

Also, you bring up Dawkins but in fact Dawkins' definition of selfish DNA is not junk DNA. He refers to the active transposable elements that make up a miniscule proportion of our genome. The vast majority are the broken remains of the past duplications, that have lost the ability to copy themselves or be copied back into our genome. Dawkins is an ultradarwinist who actually would be one of the last people to actually argue for junk DNA. Ultradarwinists have a position far closer to ID than do typical evolutionary biologists - they expect overwhelming function in the genome.

I suspect you do not understand the positive arguments for junk DNA. You did not cover them in your book chapter on junk DNA, which I would have expected in a book that puports to make a scientific case for a certain position. Do you understand what those positive arguments are and why they pose a problem to the ID predictions of very high levels of functionality in the genome?

Luskin’s “response” to me was a generic form letter Luskin always sends out, a robo-response that in fact presented NO EVIDENCE to defend his and Jonathan Wells’ false claims about scientists and junk DNA.

So when Luskin says “you” and “your” in his “response” to me, he does not mean me, nor anything I actually wrote, but a generic “ID opponent” that Luskin invented in his imagination at least a year ago, when his “response” was first written.

You can see Luskin send out the identical form letter one year ago, to the blogger John Farrell at Forbes (see: http://www.forbes.com/sites/johnfarrell/2011/05/20/the-myth-of-the-myth-of-junk-dna/2/?commentId=comment_blogAndPostId/blog/comment/1186-2878-153; click to expand the second comment.) Luskin’s fake “response” is just a form letter he repeatedly sends out to anyone on the internet who dares breathe disobedience of Jonathan Wells’ vast legendarium.

Here’s what Luskin wrote to Farrell, one year ago. Compare it to what he “wrote” to me:

“…your [Farrell’s] post is logically incoherent because it tries to make 2 contradictory points, both of which are wrong:
(A) [blah blah]
(B) [blah blah blah]
Your [Farrell’s] point (A) is an attempt to rewrite history, which is a predictable response to the overwhelming mass of evidence Jonathan Wells compiles in his book…
…Your [Farrell’s] attempt to rewrite history and claim that evolutionary scientists largely haven’t “asserted [the genome was full of] was functionless ‘junk’” is also refuted by the following quotes, two from textbooks and another from Scientific American…”
(See: http://www.forbes.com/sites/johnfarrell/2011/05/20/the-myth-of-the-myth-of-junk-dna/2/?commentId=comment_blogAndPostId/blog/comment/1186-2878-153; click to expand the second comment.)

I asked Casey Luskin four specific questions about junk DNA, and he evaded the three questions that required quantitative scientific answers. Luskin and Jonathan Wells cannot honestly answer my first 3 scientific questions without admitting that they have stated outright falsehoods about junk DNA. So instead he baldly misrepresents my points by dumping a robo-response that grossly caricatures “me” [and Farrell, and God knows who else].

To review: I proved by evidence that Jonathan Wells and Casey Luskin have falsely claimed two things:

Falsehood 1. Molecular biologists believed ‘non-coding DNA = non-functional DNA.’

Falsehood 2. Most of the human genome is experimentally known at present to be functional.

Start with Falsehood 1. As I pointed out before, Jacques Monod won a Nobel Prize for showing in the 1960’s that genetic regulatory elements are in non-coding DNA. Also, Jack Szostak in 2009 won a Nobel Prize for showing in the 1980’s the important functions of telomeric DNA.

But Luskin tells me, or Farrell, or somebody: “Junk DNA fell in spite of--not because of--Darwinian thinking.”

That’s funny Casey, the Nobel committee apparently knew that non-coding DNA could be functional, when they handed out two Nobels for evolutionists discovering novel functions in it. No molecular biologists protested that; rather, they employed and built on these discoveries.

So far the score is two Nobels for the “Neo-Darwinists” finding function in non-coding DNA. Now Casey, I could ask you how many Nobel Prizes ID proponents have won for discovering novel functions in non-coding DNA. But you’d claim the Nobel committee discriminates against the Discovery Institute just because they have no discoveries.

T. Ryan Gregory’s blog proves, by combing research articles from the era, that the peer-reviewed scientific literature from the early 1970s to the mid-1990s provides NO evidence that scientists failed to consider functions for non-coding DNA. The phrase "Long dismissed as junk…" was a concoction invented by journalists in the mid-1990’s to sex up the newspapers. It was never accurate, and Wells and Luskin have no evidence to show it was ever true.

Now on to Casey’s absurd straw-man misrepresentation of what I, or Farrell, or somebody, or everybody, wrote.

What I really wrote: “the absurd falsehood that molecular biologists believed non-coding DNA was non-functional 'junk.'"

What Luskin says I, or Farrell, wrote: “Your [mine or Farrell’s?] attempt to rewrite history and claim that evolutionary scientists largely haven’t “asserted [the genome was full of] was functionless ‘junk’” is also refuted by the following quotes…”

What I actually wrote is crystal clear, unambiguous, and has not been disproven by any experimental evidence presented by Luskin nor Wells. But Luskin deliberately inverts my crystal clear words. Because of Luskin’s, um, lack of reading comprehension, let me make this Doctor Suess simple (please bear with me, adult readers.) Consider the following two statements.

#1 (True): Non-functional DNA is a subset of non-coding DNA.

#2 (False): Non-coding DNA is a subset of non-functional DNA.

I trust adult readers understand #1 does not imply #2. Wells’ and Luskin’s trick is to quote scientists talking about #1 and then they tell their readers that molecular biologists believed #2, which is their scurrilous lie.

To use an analogy: suppose scientists say “All bats are mammals.” Wells and Luskin want to smear all scientists and make them look dumb. So they tell their readers that scientists think “All mammals are bats”, which is absurd.

Their evidence being, quotes wherein scientists use the word “junk” and “non-coding” in the same sentence. No, that is not proof that molecular biologists believed #2.

Luckily for me, Luskin has put all his eggs in one basket, so I can set about merrily stomping all his eggs, every one! Let’s start with his quotes about transposons:

Start with Luskin’s ref #1, Michael Lynch, Trends Ecol. and Evol. (2001), apparently miscopied; perhaps Luskin misplaced his friend in a time of need, the ellipsis: "Approximately half of the human genome consists of sequences that are [transposon-related], and a large fraction of the remaining noncoding DNA might be a product of such activity…"

Lynch says #1: non-functional DNA is a a subset of non-coding DNA.

But Luskin says Lynch says #2: non-coding DNA is a subset of non-functional DNA.

STOMP! This does not prove Wells’ and Luskin’s claim that scientists believed non-coding DNA was non-functional DNA.

Luskin’s ref #5: Voet and Voet (1995): "…a possibility that must be seriously entertained is that much repetitive DNA [in eukaryotic genomes] serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that… has disseminated itself throughout the genome…"

Just like John Avise (below), the Voets say “REPETITIVE DNA” and do not say “non-coding DNA.” At no point do the Voets say non-coding DNA is non-functional DNA, which is Wells’ and Luskin’s scurrilous lie. And the Voet’s quotes are still accurate today. STOMP!

Wells’ quote of John C. Avise, 2010: Avise said “noncoding REPETITIVE sequences.” But Wells and Luskin said NON-CODING DNA, suppressing "repetitive." Moreover, Avise’s specific fraction for how much DNA is non-functional—at least 50%-- is still true AFAWK, and Avise’s statements about a few pseudogenes having function, but most not, is still correct today. STOMP!

Wells’ quote of Avise from PNAS, undated: "the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes."

Again, Avise says “repetitive” but Wells and Luskin leave that out. Avise’s quote is again accurate, both as regards fraction of non-functional DNA and the existence of pseudogenes that are indeed non-functional “decomposing corpses.” STOMP!

Luskin’s ref #4, David Clark (2005): "Other stretches of parasitic DNA [defective transposons] are stuck permanently where they are and are probably the remains of once mobile gene creatures. They have degenerated into junk DNA. Much of the large human genome is comprised of these types of junk DNA that are no longer active."

At no point does Clark say that non-coding DNA is non-functional DNA, which is Wells and Luskin’s scurrilous lie. And Clark’s quote is still accurate today. STOMP!

Wells’ quotes of W. Ford Doolittle, Sapienza, Orgel and Crick’s (all 1980) also address transposons, and do not anywhere assert that non-coding DNA is a subset of, or equivalent to, non-functional DNA, which is the scurrilous lie that Luskin asserted without evidence. STOMP! STOMP!

Moving on, next some not-just-transposon quotes.

Wells’ quote of Dawkins (1976): “The amount of DNA in organisms… is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. …If the 'purpose' of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing [supervising building bodies]. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing.”

Dawkins directly contradicts the myth-history of Wells and Luskin. According to Wells and Luskin, the “Neo-Darwinist” assumptions are a “science stopper” preventing research into non-coding DNA. But Dawkins actually said scientists are frantically trying to find functions in apparently non-functional DNA. And they did: Szostak the evolutionist later got a Nobel Prize for doing just that.

Again, Dawkins (not a molecular biologist) never says non-coding DNA is non-functional, which is the scurrilous lie Luskin and Wells cannot defend. Dawkins says DNA which does not "supervise building bodies" is non-functional, which is correct. STOMP!

Luskin’s ref #3, Ken Miller (1994): "…the human genome is littered with pseudogenes, gene fragments, "orphaned" genes, "junk" DNA, and so many repeated copies of pointless DNA sequences… a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by [evolution]…"

At no point does Miller say that non-coding DNA is non-functional DNA, which is Wells and Luskin’s scurrilous lie. And Miller’s quote is still accurate. STOMP!

And next, two quotes about pseudogenes.

Luskin’s ref #10: Francisco Ayala et al., Ann. Rev. Gen. (2003). "pseudogenes that have been suitably investigated often exhibit functional roles.”

Again, this does not say molecular biologists ever believed that non-coding DNA is non-functional, which is the scurrilous lie that Luskin and Wells cannot defend. Moreover, Luskin does not tell his readers that Ayala et al.’s 2003 paper considers mere transcription to be indicative of function. As I addressed previously, that assumption must be questioned in light of von Bakel et al.’s work of 2010, cited previously.

Moreover, Ayala counts a pseudogene as "functional" if a part of it forms a regulatory element. As I said last time, if a regulatory element forms 10 base pairs out of a 1000 bp pseudogene, even then, 99.8% or 99.9% of the nucleotides in the pseudogene are still not biochemically constrained. They are STILL JUNK, AFAWK.

Luskin’s ref #9: Pink et al., "RNA" (2011): "However, recent results are challenging this moniker [junk DNA]; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins… Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway.”

Again, this does not say molecular biologists ever believed that non-coding DNA is non-functional, which is the scurrilous lie that Luskin and Wells cannot defend. Moreover, if a pseudogene regulates its paralog via RNAi [interfering RNAs], the snippet of RNAi is typically shorter than the pseudogene. The article also discusses microRNAs, which are also small.

As I addressed previously, most of the nucleotides in that pseudogene are still not biochemically constrained, even if a fraction of it becomes a microRNA or RNAi. Moreover, most pseudogenes do not form either microRNA’s nor RNAi’s. So most nucleotides in pseudogenes are still not biochemically constrained, and are STILL JUNK, AFAWK.

Below Luskin gives us two quotes from popular magazines, not peer-reviewed scientific literature, which do not support his and Wells’ claims.

What next, Casey? People Magazine? Tiger Beat?

Luskin’s ref #6, Philip Yam, from Scientific American (1995): “In fact, the vast majority of genetic material in organisms from bacteria to mammals consists of noncoding DNA ... In humans, about 97 percent of the genome is junk.”

Yam says one sentence about “non-coding” and the next sentence about “junk.” Yam does not say that non-coding DNA is non-functional junk. Not a peer-reviewed research article, and Yam is writing about a physicist, not about a molecular biologist. STOMP!

Luskin’s ref #8, Wayt T. Gibbs, again from Scientific American (2003): it allegedly says introns "were immediately assumed to be evolutionary junk." and "The failure to recognize the importance of introns may well go down as one of the biggest mistakes in the history of molecular biology."

Again, no molecular biologist said that non-coding DNA is a subset of non-functional DNA, which is the scurrilous lie that Luskin and Wells cannot defend. And again, not a peer-reviewed research article.

Luskin’s ref #2: Historian Michael Shermer (2006) is not a molecular biologist, and does not say that non-coding DNA is a subset of, nor equivalent to, non-functional DNA, which is Wells’ and Luskin’s scurrilous lie that they cannot defend. And who cares what historians think?

And now a couple of News & Views type articles, not peer-reviewed research articles.

Luskin’s ref #11, Erika Check Hayden, Nature (March 2010):“Biology’s new glimpse at a universe of non-coding DNA — what used to be called ‘junk’ DNA — has been fascinating and befuddling.”

Luskin describes this bizarrely: “So there you have it. According to Nature, non-coding DNA “used to be called ‘junk’ DNA”, but we now know that many of these noncoding elements have regulatory functions…”

But Hayden says no such thing; Luskin quote-mined the phrase "used to be called ‘junk’ DNA" and stuck his own ideas in front. Hayden means that non-functional DNA "junk" is a subset of non-coding DNA, whereas Wells and Luskin twist it into non-coding DNA being a subset of non-functional DNA.

But Hayden says that scientists have known non-coding DNA regions are functional and essential for decades; she writes: "In 1961, French biologists François Jacob and Jacques Monod proposed the idea that 'regulator' proteins bind to DNA to control the expression of genes... In 1990, several labs found that p53 binds directly to DNA to control transcription, supporting the traditional Jacob–Monod model of gene regulation."

The author’s online bio describes her as a journalist who "earned her undergraduate degree in biology from Stanford…", not a molecular biologist. This is a “News & Views” type article, not a research article.

Hayden also bases her statements on the ENCODE project, but those conclusions must be questioned as Hayden wrote this one month before publication of the von Bakel et. al. paper in 2010.

Luskin’s ref #7, Luskin writes about Wojciech Makalowski (2003); Luskin: "The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." Fortunately some rogue scientists conducted research--"at the risk of being ridiculed"--that led to the overturning of the junk DNA paradigm."

Luskin merely quote mines sentence FRAGMENTS of sentences, not whole sentences, but Makalowski does not say that non-coding DNA is non-functional DNA, which is the scurrilous lie that Luskin and Wells cannot defend. The article is about Alu elements that get inserted into protein-coding genes, thus forming parts of proteins, and becoming functional when they become part of coding regions. It is not about function in non-coding regions.

Moreover, Makalowski’s article is a “Perspective” article, not a peer-reviewed research article.

Now I have refuted of every one of Luskin’s quotes. No evidence that any molecular biologist ever said that non-coding DNA is a subset of, or equivalent to, non-functional DNA.

Readers, please visit T. Ryan Gregory’s blog, who shows, by citing *REAL* peer-reviewed research articles *FROM THE HISTORICAL ERA IN QUESTION*, from the early 1970s to the mid-1990s, that there is NO evidence that scientists failed to consider functions for non-coding DNA.

Casey, please answer the following questions, which you evaded last time:

1. What fraction of all nucleotides in the human genome are now experimentally known to be functional—not just transcribed—but biochemically constrained as to sequence?

2. Under ID theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from ID?

3. Under evolutionary theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from evolution?

And let the evading begin!

How about this: the philosophical problem of science tackling an explanation for particular, unrepeatable, historical events? Science is not equipped to handle such questions.

Dear Steve,

You wrote, "Every example of design that you point to involves living humans with living brains and living corporeal bodies capable of executing their designs...Design by itself produces nothing in the physical world."

Both true, but neither was the point. The point was that in the case of helicopters or other known instances of human creation, design is a required and integral step. I wouldn't call it a "mechanism," but the word is less important than that neither a helicopter nor a brief sentence occurs without some devising. Out of the architect who designs a building, the inventor who automates the production of materials, and the construction workers who put it together, who gets paid the most, who gets paid the least, and why? All contribute necessary functions, so why deny the vital causative role of the architect?

Even Richard Dawkins readily concedes that living things have the appearance of having been designed. All instances of apparent design fall into two categories: There are those known to have been designed and those of unobserved origin in which cases we can only infer the cause. Even if the latter is debatable then where is the evidence for apparent design without design?

I also appreciate the refreshingly polite discussion.

While I agree with the original post and much of Casey's reply to FrankJ, I think a few points need a response.

Admittedly Casey starts his reply to FrankJ by pointing out that he's not talking about any particular form of creationism, but he then makes a few sweeping claims about creationism. He says that "One general problem with creationism is that it often claims we can scientifically prove a supernatural, divine creator." I would respond that this claim is either wrong (as a generalisation), or at the very least needs overstated and in need of clarification. (I'm responding from the point of view of a biblical creationist (YEC), not a progressive creationist or other form of OEC.)
Biblical creationists generally /don't/ claim to be able to scientifically prove a supernatural creator. However, they will point out that proposing that the Intelligent Designer was someone other than God doesn't really solve anything. Yes, we could, in theory, have been created by intelligent aliens. But who created /them/? Or /their/ creator? Eventually, you need to have a transcendent Being (God). (This should not give comfort to those who wish to claim that ID really does propose Yahweh, as other designers are still logically possible.)

Biblical creationists might also try and derive some attributes of the designer, such as being an economiser of design, from the science.

But with small exceptions such as those, biblical creationists do /not/ try and scientifically prove a supernatural creator.

Actually, for what it's worth, I'll make another point about Casey's throwaway list of other potential creators. He said that "that same empirical data does not inform us whether the intelligence ... is Yahweh, Allah, Buddha, Yoda, or some other type of intelligent agency."
As a creationist, one argument I /would/ make is that there are very few realistic candidates on offer. His list includes one that is indisputably fictional (Yoda), one that is not claimed to be anything other than human (Buddha), and two that are, at one level, actually different names for the same being (Yahweh and Allah). Casey didn't mention them, but the Greek gods were simply not that powerful. The point is that there are actually very few qualified candidates for the role that are seriously proposed. (Again, that does not refute ID's claim that it doesn't identify the designer.)

Casey also wrote that "So ID respects the limits of science whereas creationism doesn’t." This is false. Creationists talk a great deal about the limits of science, pointing out, for example, that much of evolution is about unique (one-off) past events, and are therefore outside the capabilities of science to really investigate. They admit that creation is not itself scientifically testable, but quickly add that the same applies to various evolutionary claims, such as the origin of life.

The main matter on which creationists and ID proponents disagree is which evidence is admissible. ID proponents want to only consider scientific evidence. And in a purely-scientific exercise, this is quite legitimate. Biblical creationists also want to admit documented eyewitness history from a reliable source, i.e. the Bible. This is not /scientific/ evidence (and therefore not appropriate for a scientific discipline like ID), but it is evidence nevertheless, and for unique past events, can be /better/ evidence than scientific evidence.

So I agree that ID is not creationism. But I disagree on some of the claimed faults of creationism.

Dear Diogenes,

Thanks for the comment—you have stated quite well the logically incoherent and historically inaccurate position of ID-critics on junk DNA. In particular, you try to make two contradictory points, both of which are wrong:

(A) On the one hand, you try to rewrite history by arguing that evolutionary biologists never argued that the genome was full of junk ("Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional 'junk.'")

(B) On the other hand, you then claim the genome is full of junk DNA. (“As for junk, it is between 65 to 91.3%.”)

Do you not see how the fact that you’re making argument (B) makes it really hard for me to believe your argument (A)?

In any case, your point (A) is an attempt to rewrite history, which is a predictable response to the overwhelming mass of evidence Jonathan Wells compiles in his book showing that evolutionary scientists have predicted that much of the genome is junk. Contra your claims, many of these scientists essentially equated noncoding DNA with junk. As Jonathan Wells documents:

“In 2010, University of California Distinguished Professor of Ecology & Evolutionary Biology John C. Avise published a book titled Inside the Human Genome: A Case for Non-Intelligent Design, in which he wrote that ‘noncoding repetitive sequences--' junk DNA'--comprise the vast bulk (at least 50%, and probably much more) of the human genome.’ Avise argued that pseudogenes, in particular, are evidence against intelligent design. For example, ‘pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered along the chromosomes like useless molecular cadavers.’ To be sure, ‘several instances are known or suspected in which a pseudogene formerly assumed to be genomic ' junk' was later deemed to have a functional role in cells. But such cases are almost certainly exceptions rather than the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic tinkering for which nonsentient evolutionary processes are notorious.”

“Avise also published an article in Proceedings of the National Academy of Sciences USA titled ‘Footprints of nonsentient design inside the human genome,’ in which he repeated the same argument. ‘Several outlandish features of the human genome,’ he wrote, ‘defy notions of ID by a caring cognitive agent,’ but they are ‘consistent with the notion of nonsentient contrivance by evolutionary forces.’ For example, ‘the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes.’”

(Jonathan Wells, The Myth of Junk DNA, pp. 26-27 (2011).)

Wells provides many other examples of evolutionary scientists who predicted that most of the noncoding DNA in the genome would be junk. Here are just a couple he cites:

“’The amount of DNA in organisms,’ Dawkins wrote in 1976, ‘is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the 'purpose' of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

“In 1980, two papers appeared back to back in the journal Nature: ‘Selfish genes, the phenotype paradigm and genome evolution,’ by W. Ford Doolittle and Carmen Sapienza, and ‘Selfish DNA: The ultimate parasite,’ by Leslie Orgel and Francis Crick. The first paper argued that many organisms contain ‘DNAs whose only 'function' is survival within genomes,’ and that ‘the search for other explanations may prove, if not intellectually sterile, ultimately futile.’15 The second argued similarly that ‘much DNA in higher organisms is little better than junk,’ and its accumulation in the course of evolution ‘can be compared to the spread of a not-too-harmful parasite within its host.’ Since it is unlikely that such DNA has a function, Orgel and Crick concluded, ‘it would be folly in such cases to hunt obsessively for one.’”

(Jonathan Wells, The Myth of Junk DNA, p. 20 (2011).)

And of course Wells cites multiple scientists who have used junk DNA as an argument against intelligent design. We already saw that Avise did this. Here are some other examples from my own notes:

"Our debris-laden genome Approximately half of the human genome consists of sequences that are obviously associated with transposable-element activity, and a large fraction of the remaining noncoding DNA might be a product of such activity but too divergent to be recognized as such. So much for intelligent design."[1]

"Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution."[2]

"In fact, the human genome is littered with pseudogenes, gene fragments, "orphaned" genes, "junk" DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection to innovate, to test, and to discard what fails in favor of what succeeds. The organisms that remain alive today, ourselves included, are evolution's great successes."[3]

Your attempt to rewrite history and claim that evolutionary scientists largely haven't asserted the genome was full of was functionless 'junk' is also refuted by the following quotes, two from textbooks and another from Scientific American:

"Some of these integrated DNA segments are able to move around from site to site within host DNA molecules and are known as transposable elements or transposons. Other stretches of parasitic DNA are stuck permanently where they are and are probably the remains of once mobile gene creatures. They have degenerated into junk DNA. Much of the large human genome is comprised of these types of junk DNA that are no longer active."[4]

"Considering both the enormous amount of repetitive DNA in most eukaryotic genomes and the dearth of confirmatory evidence for any of the above proposals, a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome through some sort of transpositional process."[5]

"These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution. ... In fact, the vast majority of genetic material in organisms from bacteria to mammals consists of noncoding DNA ... In humans, about 97 percent of the genome is junk."[6]

Many additional examples could be given. It's very convenient for some scientists to argue, in 2012, that the genome isn't full of useless junk. Good for them--they know to jump off a sinking ship when they see one. But that doesn't change the fact that for decades, evolutionary scientists presumed that non-coding DNA was largely junk. Your comment is attempting to rewrite history.

But of course, Wells' book cites numerous papers which have found function for junk-DNA. In fact, his 170 page book has over 600 references--and that barely scratches the surface of the volume of literature which has found function for junk DNA.

In fact, the junk-DNA mindset, which was born and bred from the Darwinian paradigm, even stifled research into the function for junk DNA. The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." Fortunately some rogue scientists conducted research--"at the risk of being ridiculed"--that led to the overturning of the junk DNA paradigm.[7]

In 2003, Scientific American reported that one type of non-coding DNA called introns "were immediately assumed to be evolutionary junk." According to the article, "The failure to recognize the importance of introns may well go down as one of the biggest mistakes in the history of molecular biology."[8]

Junk DNA fell in spite of--not because of--Darwinian thinking.

Your point (B), that the genome is full of nonetheless junk-DNA, is simply wrong on the facts. To understand why, you should read Jonathan Wells' book.

Much of the evidence he cites also is even finding function for pseudogenes. As a recent 2011 paper in the journal RNA states:

Pseudogenes have long been labeled as "junk" DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys. The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.[9]

Now I’m not claiming that all 20,000 pseudogenes are known to have function. So you are putting words in my mouth. Nor am I claiming that we know the function of all genetic elements. Hardly--we’ve just begun to scratch the surface of how the genome works. There's still a lot we don't understand. But I am claiming that for years, Darwinian scientists claimed that non-coding DNA was largely junk, and that we’ve discovered massive amounts of function for non-coding DNA, and that the trendline is strongly in favor of function, rather than non-function, for DNA that we’re studying. For example, when we carefully study pseudogenes, they often turn out to have function. As one paper he cites from Annual Review of Genetics states: "pseudogenes that have been suitably investigated often exhibit functional roles."[10]

There are a lot of dubious claims in your comment. The fact that something is transcribed isn’t 100% proof that it’s functional, but it’s highly suggestive since it’s a waste of cellular resources to transcribe something that isn’t being used. Non-protein-coding RNAs have a myriad of functions in the cell. So you’re simply showing that junk-DNA thinking is alive and well.

You ask me how I sleep at night for saying “many types of ‘junk’ DNA, now known to have function”. Specifically, you state:

"The science community may never forgive you for making up that story about how molecular biologists believe that ‘non-coding DNA = non-functional DNA.’ Casey, how do you sleep at night?"

I sleep very well (and in fact I hoep to be sleeping in just a couple minutes here) because I am simply following what the literature says. Nature refutes your assertion. If you post the entire quote of a quote you only partly quoted, it shows that many biologists equated non-coding DNA with "junk" DNA. Here's what Nature said:

“Biology’s new glimpse at a universe of non-coding DNA — what used to be called ‘junk’ DNA — has been fascinating and befuddling. Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA2. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear.”[11]

So there you have it. According to Nature, non-coding DNA “used to be called ‘junk’ DNA”, but we now know that many of these noncoding elements have regulatory functions. This also refutes your outlandish claim that "there are no types of junk DNA now known to have a function.”

You claim that only some 8.3% of the genome is confirmed to have function, and you assume that if it’s repetitive DNA, then it isn’t functional. But a paper that we just reported on last week notes that one study looking at noncoding DNA in the mouse genome found that most of some 11% of its genome is conserved. See:

http://www.evolutionnews.org/2012/07/new_scientist_c062001.html

That's just one paper--and there are literally hundreds out there finding vast levels of functionality for non-coding DNA.

You make all kinds of nasty moral insinuations against me--accusations which fall apart when we examine the scientific literature.

I'm not here to attack you personally; I am just following what the literature says. I think you would do well do tone down your rhetoric and familiarize yourself with the literature.

Jonathan Wells’ book "The Myth of Junk DNA" would be a great place to start—you’ll learn that there are numerous studies which have found function for repetitive-DNA, and many other types of DNA you call "junk". Yes, there's still a lot we don't understand. But your junk-of-the-gaps argument is getting weaker and weaker with time.

Thanks and all the best.

Sincerely,

Casey Luskin

References Cited:
[1.] Michael Lynch, "The molecular natural history of the human genome," Trends in Ecology & Evolution, Vol. 16(8): 420-422 (August, 2001).
[2.] Michael Shermer, Why Darwin Matters: The Case Against Intelligent Design, p. 75 (Times Books 2006).
[3.] Kenneth R. Miller, "Life's Grand Design," Technology Review, Vol 97(2): 24-32 (February / March 1994).
[4.] David P. Clark, Molecular Biology: Understanding the Genetic Revolution, pp. 84-85 (Academic Press, 2005).
[5]. Donald Voet and Judith G. Voet, Biochemistry, p. 1138 (John Wiley & Sons, 2nd Edition, 1995).
[6.] Philip Yam, "Talking Trash," Scientific American, Vol. 272(3)W:24 (March 1995).
[7.] Wojciech Makalowski, "Not Junk After All," Science, Vol. 300(5623) (May 23, 2003)
[8.] Wayt T. Gibbs, "The Unseen Genome: Gems among the Junk," Scientific American (Nov., 2003) (quoting John Mattick, internal quotations omitted).
[9.] Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul Francisco Carter, "Pseudogenes: Pseudo-functional or key regulators in health and disease?," RNA, Vol. 17:792-798 (2011).
[10.] Evgeniy S. Balakirev, and Francisco J. Ayala, Pseudogenes, "Are They "Junk" or Functional DNA?," Annual Review of Genetics, Vol. 37:123-51 (2003)
[11.] “Life is Complicated,” Nature, Vol. 464:664-667 (April 1, 2010)


Dark matter? Quantum theory?

Do we throw those out of consideration by the same standard since the former cannot be studied directly and the latter has no tangible mechanism?

Daer Frank J,

Thanks for the reply. I'm not sure how "DI" defines creationism--but I know that leading authorities on all sides of this debate have observed that the central claim of creationism is that a "supernatural creator" created life. This isn't a DI-definition: The U.S. Supreme Court, National Academy of Sciences, Eugenie Scott, National Science Teachers Association, Phillip Johnson, Robert Pennock, William Dembski, Barbara Forrest, Paul Gross, and many others have all defined creationism like this. So while many people (including you) might believe in a "supernatural creator," it's not a scientific conclusion. So I think we're in agreement here.

I provided you with principled, logical reasons for why ID lacks this central, defining characteristic of creationism. This demonstrates that ID is substantively different from creationism in one of the most important ways possible.

Finally, I'm not calling anyone a "Darwinist" here (even though evolutionists themselves use this term -- see http://www.discovery.org/f/628 )-- and I also don't think the term "evolution-denier" is appropriate, since ID proponents acknolwedge that life has changed over time.

Thanks for writing.

sincerely,

Casey

Dear Steve,

Thanks for the reply, but I think we've responded to your arguments, and you haven't responded to ours. There's no reason to presume that the designer, whether "corporeal" or not, would have any trouble implementing the designs in the natural world. So I don't think you've made an argument here. Thanks.

Casey


I dare you (or anyone else on any side of this discussion) to define positive evidence.

As for Casey’s #9, “Junk DNA”: the ID movement has a long history of misrepresenting genetics, both cutting edge research and the history of science, and that is the case with Luskin’s and Jonathan Well’s gross misrepresentations about molecular biology, junk DNA, and the history thereof. Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional “junk.” Utterly false. Molecular biologists believed (and still believe) that non-functional DNA is “junk”, not non-coding. The mythology that molecular biologists believed ‘non-coding = non-functional’ is a figment of the creationist imagination, aggressively promoted.

Every molecular biology grad student since the 1970’s has known—and had to know—that regulatory elements are in non-coding regions. Jacques Monod was awarded the Nobel Prize in 1965 for showing that regulatory elements are in non-coding DNA, so the Nobel Committee had to know. Every mol. bio. grad student knows that he has to control induction of genes he clones in, and control of induction means binding (or non-binding) to regulatory elements in non-coding regions.

For a lawyer like Luskin to accuse molecular biologists of thinking that ‘non-coding = non-functional’ is like telling the police that their job requires catching criminals. It is like a sports fan telling quarterbacks that goals are made by getting the football in the end zone. It is fantastically insulting. The scientific community will never forgive ID proponents for inventing the ‘non-coding = non-functional’ myth.

Secondly, scientists did not predict that most DNA would be junk (most of it is still junk, today, AFAWK) because of “neo-Darwinism.” No sir: scientists believe bacteria are a product of evolution, and everyone knew they have no junk DNA. No scientist would say, as Luskin and Jonathan Wells would caricature, “Bacteria are the products of ‘blind chance’ and ‘accidents’, so they must have lots of junk DNA.” Any scientist would choke on that, because they know bacteria don’t have junk DNA.

As has been repeated endlessly, in the 1960’s there were opposing schools of thought who added to evolutionary theory very different assumptions about the strength of selection and the cost/benefit ratio of a high mutation rate. The “adaptationists” thought selection was strong, and the costs of a high mutation rate were low, the benefits high. The “neutralists” thought selection was weak, and the benefits of natural selection not strong enough to outweigh the huge number of possible neutral mutations. “Adaptationists” would expect little or no junk DNA, “neutralists” would allow for junk DNA (not require it). “Junk DNA” does not follow from ID’s gross cartoon of “neo-Darwinism,” but rather from evolutionary theory plus 1970's observations that genes and regulatory elements together make up a small part of the genome, plus assumptions about cost/benefit ratios.

Fast forward to the present: the neutralists were right, at least about complex animals and plants; most nucleotides in the human genome are not biochemically constrained by any functional constraint. Mostly still junk. For bacteria, which have no junk DNA, the adaptationists were right. Some amoeba and dinoflagellates have more DNA than humans; some plants have 50 times more DNA than humans. This is because the cost/benefit ratio for DNA duplication is different for bacteria vs. for complex organisms.

Thirdly, the human genome is mostly still junk. Most nucleotides in the human genome are still not biochemically constrained as to sequence, and no ID proponent has ever offered any evidence to contradict this. Jonathan Wells and Luskin have used innuendo and vague terminology to state, or to imply, that most DNA in the human genome is functional. This is false, AFAWK.

These innuenodoes and false statements from ID proponents fall into three categories.

Category #1: I’ll call “vaguediction.” This includes the use of weasel words to give a false impression of how much DNA is known to be functional—for instance, “much.”
Jonathan Wells: “The arguments by Dawkins, [Ken] Miller, Shermer, [Sean] Collins, [etc.] rest on the premise that most non-coding DNA is junk... [But] Much of the DNA they claim to be "junk" actually performs important functions in living cells.” [Well, The Myth of Junk DNA, p. 27. Note the first part of this sentence dishonestly portrays molecular biologists as believing ‘non-coding DNA = non-functional DNA.’]

William Dembski: “If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.”—[First Things, 86, 21-27]

What does “much” mean in the sentences above (note Mr. Luskin has made “much” statements many times)? “Much” is deliberately vague in order to be non-falsifiable. By “much” do they mean ten million nucleotides? Ten million might impress non-scientists, but it’s 0.3% of the genome. Does it mean 90% of the nucleotides in the genome? If that’s what they mean, it’s a factually false claim.

This vague terminology--“much”-- impresses non-scientists, but it is not a prediction, and scientists find it infuriating. Does “much” refer to an absolute count of nucleotides (in millions) or a relative fraction of the genome? Thousands? Millions? Billions? What the heck does it mean?

If these “much” statements of ID proponents have a definite meaning, they are factually false. If they have no definite meaning, they are not predictions and simply misleading.

Category #2 is to claim that entire classes of junk DNA are all functional, every last nucleotide of every last one, if an example can be found in which a small fraction of an instance of that type of junk DNA is functional.

Casey Luskin: “Darwinists have commonly made this mistake with many types of "junk" DNA, now known to have function.”

This is false: in fact there are no types of junk DNA now known to have a function; if by “have a function” we mean that most or all of their nucleotides are biochemically constrained.

Here is an example of the trick they pull. There are about 20,000 pseudogenes in the human genome, and a typical pseudogene may be 1,000 nucleotides. If 10 of those nucleotides (0.1% of one pseudogene out of 20,000) have been co-opted as, say, a regulatory element, then ID proponents like Jonathan Wells and Luskin trumpet that that whole pseudogene is now functional (because 0.1% of its nucleotides are constrained) and by extension, that that “type” of junk DNA is now proven to be “functional”, implying that all 20,000 pseudogenes are functional. In this way, ID proponents like Jonathan Wells and Luskin mislead their readers into thinking that 20-30 million nucleotides are now “functional”, because of the discovery of a few dozen functional nucleotides.

They then repeat the trick for other classes of junk DNA, like defective transposons, Alus, etc. Presto! The whole genome is functional!

Category #3 is for ID proponents to make quantitative statements that are simply false. For example, in the OP above, Mr. Luskin linked to this ENV posting which supposedly has evidence about false predictions of “Neo-Darwinism.” Here we find a rare quantitative (but obviously false) statement:
“But the [tiling array] study goes further, indicating for the first time that the vast majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of previously invisible tasks.”

(Uh, for the first, and last, time.) At least that’s quantitative, but what’s wrong with it? It’s from a 2007 newspaper article, not a scientific publication, five years out of date and not correct when it was published. The claims that most of the genome is functional are all based on experiments using tiling arrays that allegedly showed almost all the genome was transcribed into RNA, though most of it at an extremely low level.

However, the idea that ‘transcribed’ means ‘functional’ is a big assumption (the article uses the phrase “toiling away”), and at any rate, more recent research contradicts the 2007 claim. In 2010 research using a more accurate method, RNA-seq, showed that the tiling array data was unreliable and overestimated transcription, possibly due to cross-hybridization (in addition the RNA transcription apparatus is not perfectly specific and may make mistakes on rare occasions, still detectable by tiling arrays.) What’s worse, much of the transcribed regions are not evolutionarily conserved and/or are repetitive. Very hard to believe all that could be functional.

See: van Bakel, H., Nislow, C., Blencowe, B. and Hughes, T. (2010) Most "Dark Matter" Transcripts Are Associated With Known Genes. PLoS Biology 8: e1000371 [doi:10.1371/journal.pbio.1000371]

Larry Moran predicted results like this before the van Bakel study was published. No ID proponent predicted this. Another falsified prediction of ID.

So what fraction of nucleotides in the human genome are known to be functional?
Larry Moran summarizes what we really know about junk DNA. As of May, 2011, we know at least 8.7% of the human genome is essential or functional. As for junk, it is between 65 to 91.3%.

The ID proponents mostly avoid Moran's arguments, and cannot contradict him. Here is an ID proponent at ENV trying but failing to refute Moran's points. Read that post carefully-- the poster, Jonathan M, cannot factually state that most of the genome has been experimentally shown to be functional.

Casey, please answer the following questions:

1. What fraction of all nucleotides in the human genome are now experimentally known to be functional—not just transcribed—but biochemically constrained as to sequence?

2. Under ID theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from ID?

3. Under evolutionary theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from evolution?

4. The science community may never forgive you for making up that story about how molecular biologists believe that ‘non-coding DNA = non-functional DNA.’ Casey, how do you sleep at night?

Please note: I am having trouble with hyperlinks in this commenting system; my hyperlinks may not work.

It's not just "Darwin's adherents" who think that, but Michael Behe too, and many other "Darwin doubters," including an apparent majority of the signatories of the "dissent" statement. And some of "Darwin's adherents" do not think that a single free-living organism was ancestral to all subsequent life.

The “chicken and egg problem” is something that Darwin’s hypothesis of random processes does not explain.

In regards to the origin of life and that first cell which, according to Darwin’s adherents, all life descended: how did all of the necessary components come together by random, undirected processes and reproduce themselves? Specifically, to replicate a protein (which every cell needs to do continually and correctly to sustain life), requires ribosomes (consisting themselves of about 50 proteins).

Where did the 50 proteins of the first ribosomes come from and how did they aggregate to form that ribosome? Plus, how did the instructions for building these ribosomes proteins get encoded in the first DNA along with instructions for the myriad of other proteins needed just for translation and transcription? These other proteins include the following (or the whole thing doesn’t work): proteins to unravel DNA, build the mRNA, edit the mRNA, transport the mRNA to the ribosomes, to meet up with the tRNA, to build a protein molecule which may need folding in a structure that we have no idea how it does its job, do error checking to see if the protein is correct, and then transport the new protein to where it was needed in the cell. All of these proteins have specific structures and specific functions and if even one of them was missing, the first cell would not replicate a single protein much less reproduce.

Casey,

Thanks for the reply. As you know, “creationism” has several definitions, so I should be clear in that I mean as the DI defines it, which seems to correspond to the YEC and OEC promoted by AiG and RTB, respectively. I should add that I do not criticize ID for not identifying the designer. Like you, Michael Behe and Ken Miller, I think it’s God, but don’t think that’s a scientific conclusion. I’m much more interested in the “what happened when” part. As you know, evolution and creationism make many such claims, as do some individuals in the ID movement. So it only makes sense that ID criticize all claims that it finds unconvincing, whether they come from “Darwinists” or evolution-deniers. That would add some support to ID’s claim of being scientific. And it would put an end to the claims of “ID is too creationism” that at least one “Darwinist” finds annoying.

I acknowledge that I did not address the challenges directly. In a forum like this, brevity is a necessity and this list does not lend itself to brevity in reply. I am convinced, as an example, that the fossil record comports quite well with the idea of evolution. But asserting such a thing would require the support of an essay of equal length to your supporting essays.

I admit, as well, that my response was along the lines of: What’s good for the goose, etc. You claim a lack of mechanism. I am doing the same. Every example of design that you point to involves living humans with living brains and living corporeal bodies capable of executing their designs. The genetic engineers you refer to have human brains and human-devised tools that allow them to physically modify DNA molecules. The mechanism and the nature of the designer are inexorably linked. A half a billion years or so ago, without humans and their genetics labs, what or who and how?

Again, even the best-imagined helicopter will not get off the ground until at least one is actually built. Design by itself produces nothing in the physical world.

The respectful discussion is appreciated.

If the physical implementation of a design is its mechanism, then the mechanism of a written paragraph is not a thought and the arrangement of words to express it. It is the movement of a graphite pencil across paper.

How does that absurd logic hold up to scrutiny? An animal can scribble on a paper but cannot conceive or write a paragraph. And that specific implementation is easily replaced by a pen, a typewrite, dictation, or sign language. One can arrange a selection of words and never write or speak them.

For a design to be fully realized it does require some means of implementation. But just like a written paragraph, the implementation is almost always preceded by an abstract design. (If it takes a moment to think of an exception, that's probably because it's an exception.)

If abstract intelligent design is nearly always required before implementation of what has been designed, and the implementation can be varied, then why would we choose to discard the one required factor that such implementations have in common?

To further illustrate the absurdity of arguing that implementation is a "mechanism" but design is not, consider: If I imagine a helicopter, draw schematics for it, and then manufacturer one thousand of them, does it follow that the entire process of creating a helicopter has been repeated on thousand times? Or would we conclude that the process consisted of a single design and one thousand implementations? Again, how or why does one factor out the design?

In response to Steve Hunter, thanks Steve for participating in this thread, and good questions.

You wrote that “Regarding item #1: Design by itself produces nothing in the physical world.”

Actually, item #1 here is intended merely as a critique of evolutionary mechanisms, not as an argument for design. I already explained this in response to a comment from J Preston.

That said, I do believe that natural selection and random mutation cannot produce high levels of complex and specified information (CSI). Some of the experimental research backing this claim is discussed here:

Can Random Mutations Create New Complex Features? A Response to TalkOrigins
http://www.evolutionnews.org/2012/06/can_random_muta061221.html

All of this only establishes that random mutation and natural selection cannot produce high CSI. But what about the claim that design is a better explanation for high CSI? Well, as I explain at:

Responding to the Challenge that Intelligent Design Lacks a "Mechanism"
http://www.evolutionnews.org/2012/05/responding_to_t059941.html

we regularly observe intelligent agents producing designs in the natural world. As I wrote:

"Intelligent agency, therefore, is a mechanism which we can observe and understand in the world around us, and from those observations we know it alone is capable of producing high CSI. But the skeptic wasn't satisfied with this argument. He insisted what ID lacks is a mechanism that, at the direction of an intelligent agent, could be capable of instantiating information, or design, in the real world. As we spoke after the talk, I asked him, 'Why should it be so hard to believe that intelligent agents can implement their designs in the real world? After all, we see intelligent agents manipulating the information in DNA all the time.' As the skeptic was a philosopher, he was apparently unaware of the burgeoning field of genetic engineering, where biologists manipulate the information in DNA to produce new biological functions. Unfortunately, this hardened ID critic was probably still not convinced after I explained that it's easy to believe intelligent agents might have ways of implementing their designs in the natural world -- since we see it happening, reported in the scientific literature on a regular basis. This new research discussed in Nature News shows exactly how intelligent agents can manipulate information in DNA to create new structures and functions. There is no reason, in principle, why an intelligent agency must lack a mechanism for implementing designs in the natural world."

Steve Hunter then wrote: “For an idea in the unknown designer’s mind to manifest, actual atoms must be manipulated in the physical world. This manipulation would be the mechanism of ID. None has been suggested.”

I reply: Really? I just suggested a mechanism here. There are many possible ways for an intelligent agent to implement its designs in the physical world. This is hardly a problem for intelligent design.

Steve Hunter then writes: “I suspect the reason is that what isn’t being admitted is that the designer is God and the mechanism is miracle - a tough sell as science.”

I reply: Well, since ID doesn’t conclude the designer is God and doesn’t conclude that the mechanism had to be a miracle, ID isn’t trying to “sell” these claims as science.

As I explained to Frank J, yes, I do believe the designer is God. But I’m not claiming this is a conclusion of ID; this is my personal religious belief. And I’ve offered principled reasons why a scientific investigation doesn’t allow us to conclude the designer is God. As I wrote in response to Frank J:

This is not merely a rhetorical argument, but rather is a principled one. The empirical data, such as the information-rich, integrated complexity of the flagellar machine, may indicate that the flagellum arose by intelligent design. But that same empirical data does not inform us whether the intelligence that designed the flagellum is Yahweh, Allah, Buddha, Yoda, or some other type of intelligent agency. There is no known way to use such empirical data to determine the nature or identity of the designer, and since ID is based solely upon empirical data, the scientific theory of ID must remain silent on such questions.

You can’t on the one-hand criticize ID for not identifying the designer, and then on the other hand criticize ID for allegedly identifying the designer as God. Both criticisms can’t be true—and you’ve made an incoherent set of criticisms against ID.

In reality, ID has a fully consistent and coherent position:

- ID aims to take a scientific approach, which means it limits its claims to what we can learn through scientific methods.
- The scientific method reveals that life uses an information-rich, language-based code which contains high CSI. In our experience, high CSI comes only from intelligence. As a result, ID infers that intelligence is the best explanation for the origin of that information.
- All ID can detect is intelligent causation; were it to go further and identify the intelligent cause responsible, it would go beyond what the scientific data can tell us. As a result, ID doesn’t try to identify the intelligent cause. It only infers that an intelligent cause was at work.
- Nonetheless, ID proponents are fully open about their personal beliefs about the identity of the designer. Like many ID proponents, I believe the designer is God. But we make it clear that this is a personal religious belief and not a conclusion of ID.
- In fact, some ID proponents don’t believe the designer is God. This shows ID is not united around some particular belief about the identity of the designer, but rather around the scientific claim that we can empirically detect the prior action of intelligent causes in nature.

That position is entirely coherent. But criticizing ID for not identifying the designer, and then also critique ID for identifying the designer is not a coherent position.

It’s amazing how all I did was point out some scientific criticisms of evolution, and all evolutionists want to talk about is how the designer is really God. It kind of tells you about the level of this debate, and who’s got what on their minds.

In reply to “Frank J,” there are many different types of "creationism" so you'd have to be more specific to define what you mean by that term. One general problem with creationism is that it often claims we can scientifically prove a supernatural, divine creator.

I think that the scientific evidence allows us to infer an intelligent cause was at work, but to go further and identify whether that cause was natural or supernatural goes beyond what a scientific investigation can tell us. So one problem I have with certain types of creationism is that it makes sweeping conclusions about the designer--which it claims are scientific--but which go beyond what the data can tell us.

Now I personally do believe the designer is God--but I never claim that's a scientific conclusion of ID; that's my personal religious belief, not part of ID. But creationism claims that's a scientific conclusion, and in that respect I'd say ID has a major disagreement with creationism.

This is not merely a rhetorical argument, but rather is a principled one. The empirical data, such as the information-rich, integrated complexity of the flagellar machine, may indicate that the flagellum arose by intelligent design. But that same empirical data does not inform us whether the intelligence that designed the flagellum is Yahweh, Allah, Buddha, Yoda, or some other type of intelligent agency. There is no known way to use such empirical data to determine the nature or identity of the designer, and since ID is based solely upon empirical data, the scientific theory of ID must remain silent on such questions.

So ID respects the limits of science whereas creationism doesn’t.

This is discussed in much more detail at:

ID Does Not Address Religious Claims About the Supernatural
http://www.discovery.org/a/7501

In any case, Frank J's comment asked us about problems with creationism. It's interesting to note how critics keep trying to change the subject rather than addressing scientific problems with neo-Darwinism.

Regarding item #1: Design by itself produces nothing in the physical world. For an idea in the unknown designer’s mind to manifest, actual atoms must be manipulated in the physical world. This manipulation would be the mechanism of ID. None has been suggested. I suspect the reason is that what isn’t being admitted is that the designer is God and the mechanism is miracle - a tough sell as science.

Since ID is not creationism, will you tell us the top 10 problems with creationism?jzfe

Has Darwinian evolution been fully explained? To ask the question another way, do scientists really know at a sufficiently detailed level how evoluton really works such that they can claim that it does work?

An evolutionary event, as I will call it, has to supply the sufficient and necessary information required to build an organism in space and time.

Dr. Stephen Meyer has said that there is evidence that a genetic mutation does not affect the body plan. If so, then all the mutations in the world cannot effect a new body plan.

There are many "design" problems to be solved when building something as complex as a living organism. Until science has some basic understanding of what it takes to build a body, with its hierarchy of cells, tissues, and organs, I don't think it is legitimate to claim that there is a theory of evolution.

I have just been discussing darwinian evolution on UD and was given an example of 'transitional fossils that prove gradualism'.

http://en.wikipedia.org/wiki/File:Ceratopsian_skulls.jpg

Woud any one care to comment on this.

This sarcastic comment by J Preston provides something of a teachable moment for ENV readers. The fact that sometimes we discuss scientific challenges to neo-Darwinian evolution in no way negates the fact that there also exists a positive case for ID.

The purpose of this article here was NOT to discuss the positive case for design. Rather, the purpose here was to raise some scientific data that challenges neo-Darwinian evolution. I'm not claiming that this article here makes a positive case for design; it doesn't, and that's a different topic. But if readers would like to see more about the positive case for design, you might enjoy articles like:

http://www.evolutionnews.org/2011/03/a_closer_look_at_one_scientist045311.html

http://www.evolutionnews.org/2012/04/revisiting_the058771.html

http://www.evolutionnews.org/2011/10/of_molecules_and_straw_men_a_r051601.html

http://www.discovery.org/f/986

http://www.evolutionnews.org/2010/03/a_response_to_questions_from_a032501.html

http://www.evolutionnews.org/2010/11/does_intelligent_design_help_s040781.html

Surely evolutionists have better, classier arguments then sarcasmic and snark. Don't they, J Preston?

I would add the problem of irreducible complexity, although it is probably covered by one of the above mentioned problems.

But specifically, the PROBLEM OF THE EVOLUTION OF SEX.

It seems incredible to me that both the male and female reproductive system could simultaneously evolve and not only that but do so in the same geographical location. How can a half evolved reproductive system benefit the organism? How can an asexual organism maintain it's ability to reproduce while simultaneously changing into either a male or female for sexual reproduction? What possible selection pressure could there be to drive this change which would clearly involve an almost unbelievable number of mutations. We don't even know if such a genetic pathway even exists.

The evolution of sex seems to be another show stopper for new-darwinism.

I really like this post because, just like so many others, it offers a positive, testable case for Intelligent Design.

I would add the 'hard problem' of consciousness:

Notes:

Mind and Cosmos - Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False - Thomas Nagel - November 2012 (projected publication date)
Excerpt: If materialism cannot accommodate consciousness and other mind-related aspects of reality, then we must abandon a purely materialist understanding of nature in general, extending to biology, evolutionary theory, and cosmology. Since minds are features of biological systems that have developed through evolution, the standard materialist version of evolutionary biology is fundamentally incomplete. And the cosmological history that led to the origin of life and the coming into existence of the conditions for evolution cannot be a merely materialist history.
http://ukcatalogue.oup.com/product/9780199919758.do

Darwinian Psychologist David Barash Admits the Seeming Insolubility of Science's "Hardest Problem"
Excerpt: 'But the hard problem of consciousness is so hard that I can't even imagine what kind of empirical findings would satisfactorily solve it. In fact, I don't even know what kind of discovery would get us to first base, not to mention a home run.'
David Barash - Materialist/Atheist Darwinian Psychologist
http://www.evolutionnews.org/2011/11/post_33052491.html

Neuroscientist: “The Most Seamless Illusions Ever Created” - April 2012
Excerpt: We have so much confidence in our materialist assumptions (which are assumptions, not facts) that something like free will is denied in principle. Maybe it doesn’t exist, but I don’t really know that. Either way, it doesn’t matter because if free will and consciousness are just an illusion, they are the most seamless illusions ever created. Film maker James Cameron wishes he had special effects that good.
Matthew D. Lieberman - neuroscientist - materialist - UCLA professor
http://darwins-god.blogspot.com/2012/04/neuroscientist-most-seamless-illusions.html

“No, I regard consciousness as fundamental. I regard matter as derivative from consciousness. We cannot get behind consciousness. Everything that we talk about, everything that we regard as existing, postulates consciousness.”
(Max Planck, as cited in de Purucker, Gottfried. 1940. The Esoteric Tradition. California: Theosophical University Press, ch. 13).

“Consciousness cannot be accounted for in physical terms. For consciousness is absolutely fundamental. It cannot be accounted for in terms of anything else.”
(Schroedinger, Erwin. 1984. “General Scientific and Popular Papers,” in Collected Papers, Vol. 4. Vienna: Austrian Academy of Sciences. Friedr. Vieweg & Sohn, Braunschweig/Wiesbaden. p. 334.)

"It will remain remarkable, in whatever way our future concepts may develop, that the very study of the external world led to the scientific conclusion that the content of the consciousness is the ultimate universal reality" -
Eugene Wigner - (Remarks on the Mind-Body Question, Eugene Wigner, in Wheeler and Zurek, p.169) - received Nobel Prize in 1963 for 'Quantum Symmetries')
http://www.informationphilosopher.com/solutions/scientists/wigner/