Junk_DNA_Design

Junk DNA, the ENCODE Project, and Intelligent Design: Facts, Hype, and Spin

Contents:

SUMMARY

PART 1.  HUMAN GENOME AND “JUNK” DNA

  Genes, Pseudogenes, and Regulatory Regions

  Other Parts of the Genome: Repetitive Sequences and Self-Replicating Elements

PART 2. THE ENCODE PROJECT AND ITS RECENT RESULTS

  The ENCODE Project

  The ENCODE Project Did NOT Show That 80% of Human DNA Has Genetic Function

  Publicity Hype Around ENCODE Results

  Scientists Repudiate ENCODE Hype

  Spokesman Ewan Birney Attempts to Defend ENCODE’s Hype

PART 3. THE INTELLIGENT DESIGN SPIN

  The Intelligent Design Movement

  Common Deceits in ID’s Treatment of Junk DNA

  Intelligent Design Spins the Encode Results

  The Psychology of Intelligent Design

  The Fundamental Error Behind Intelligent Design

  A Way Out of the Box for Intelligent Design

SUMMARY

The researchers of ENCODE Project, the successor to the Human Genome Project, have been working to identify regions of functionality throughout the human DNA.  Medical benefits are expected from this increased understanding.  The ENCODE results to date were released in early September in the coordinated publication of 30 academic papers, accompanied by news conferences and press releases. ENCODE spokesmen claimed they had found “biochemical functionality” in some 80% of the genome; this was presented   as a shocking discovery which overturned the alleged consensus that nearly all DNA (outside of the 1-2% that was known to code for proteins) was functionless “junk.” Intelligent Design proponents immediately hailed these results as support for design, and as evidence for the failure of “Darwinism”.

The reality is:

(1) The type of “biochemical functionality” used here for the 80% figure does not at all translate to having any real effect on the organism.  ENCODE researchers did identify some regions of genuine genetic functionality, but these amounted to only 8% of the genome, not 80%.

(2) The term “junk DNA” has been thrown around a lot, but with widely differing shades of meaning. This can cause confusion. Genetics researchers have been aware for decades of the functionality of non-coding DNA. The reason that the huge ENCODE project was conceived and funded was because everyone already believed that there was lots of function there to be discovered. So it was no surprise when they found the function that they were looking for.

(3) No one can tell in advance which DNA an inscrutable Intelligent Designer would choose to place into a genome, so no scientific finding here can ever count for or against Intelligent Design.  The naturalistic alternative (that the human genome developed from earlier primates) fits the physical evidence just fine.

Below we cover in some detail the facts of the human genome and of the ENCODE accomplishments, the hype from ENCODE spokesmen, and the spin by Intelligent Design proponents.  By not thinking carefully about its presuppositions, the Intelligent Design movement has condemned itself to a fruitless and (in practice) deceitful policy of trying to undermine evolution. We suggest an alternative approach which engages the valid concerns of believers in Intelligent Design, while stepping away from the god-of-the-gaps abyss.

PART 1.  HUMAN GENOME AND “JUNK” DNA

Genes, Pseudogenes, and Regulatory Regions

Most readers here will know already that the information used to form the cells in your body is encoded in a long strand of DNA. Human DNA has just over 3 billion base pairs. Each of these positions is occupied by one of four possible nucleotides, which can be denoted A, T, C, and G.

Most of the human body is composed of proteins. Segments of DNA which code for the synthesis of protein are called “genes.” About 20,000 genes have been identified in the human genome. In plants and animals, the region for a gene is often spread out over a long stretch of DNA, where only a few, relatively short patches (“exons”) actually code for the protein. In between the exons, there are long regions of non-coding DNA, called “introns.”  For the great majority of protein-coding genes, the length of intron sequences is 10- to 100-times the length of exon sequences, as indicate in the sketch below. In humans, the exons (i.e. the actual protein-coding DNA) comprise about 1.5% of the genome, while 25-40% of the genome is commonly attributed to introns.

In the process of expressing the gene as a protein, the whole gene (exons and introns) is first transcribed by RNA polymerase into a complementary strand of RNA. In plants and animals, this is “pre-messenger RNA”, which subsequently is processed to snip out all the introns and splice together just the exons. This final messenger RNA is then used as a template to assemble the specific sequence of amino acids that make up the expressed protein. Thus, there is no a priori reason to expect any genetic function within the introns. This does not mean there cannot be some genetic function within an intron; various regulatory sequences and other functionalities have been identified, but they typically make up only a small fraction of the whole intron.

Another component of the genome is “pseudogenes.” These are  sequences which can be identified as having been functional genes at an earlier time in evolutionary history, but which have been disabled by some mutation.

One such pseudogene is the GULO gene, which codes for a key enzyme used in the production of vitamin C (L-ascorbic acid). In most animals, this gene is functional, so they can synthesize vitamin C from other compounds and hence are not dependent on taking in vitamin C in their food. In most primates (including humans), along with a few other animals, this gene has been crippled, so they need vitamin C in their diet.

This non-functional pseudogene sits in human DNA at the position in the genome where a functional version of the gene lies in other species. Thus, it appears that this pseudogene is a relic of an earlier functional GULO gene that suffered mutations that inactivated it. This pseudogene lies at the same position in chimpanzee, macaque and orangutan DNA, and all share a common crippling mutation with the human sequence. This is consistent with the idea that this mutation occurred in a common primate ancestor of humans and these three species.

Most pseudogenes derive from genes which have been duplicated, after which one copy of the gene becomes inactive. Scientists estimate that about 100 genes are duplicated every one million years in the human genome.    While pseudogenes by definition do not directly code for proteins, in some cases they can impact genetic expression. Also, since they were at one time functional genes, pseudogenes, or parts of them, can mutate to become active for coding again. This is one evolutionary source of new genes.

The GENCODE arm of ENCODE (see below) has annotated some 11,216 pseudogenes, and estimated there is a total of 12,700-14,100 pseudogenes in the human genome.   For 9,400 pseudogenes, the parent gene (i.e. gene which was duplicated to form the pseudogene) was identified with high confidence.  873 pseudogenes were identified as being transcribed into RNA in at least one type of tissue. The researchers estimated for that for the human genome as a whole, 9% of the pseudogenes are actively transcribed. As discussed below, transcription is an indicator but not a proof of actual genetic activity.

Comparison with the genomes of other species can indicate which areas of DNA are being “conserved”, i.e. under selection to not accumulate so many mutations. This is a strong indicator of genetic function. GENCODE identified 1019 pseudogenes (i.e.  11% of the 11,200 indentified pseudogenes) as being under such evolutionary constraint.  Of these 1019 conserved pseudogenes, 195 (18%) were transcribed, which is further evidence of genetic function. Depending on how to interpret the overlap between these two categories (transcribed and conserved), we can say that the GENCODE results indicate that about 10-20% of human pseudogenes likely have some genetic function, though the specific functionalities largely remain to be discovered.

Regulatory sequences can play a critical role in the expression of the protein or proteins from that gene.  There are usually several regulatory elements associated per gene. Some of these may interact with each other as well as with directly with the gene. These relatively short elements can reside within introns, or in regions between genes. These regulatory regions can comprise around 10-20% of the genome, and may derive from sections of DNA (e.g. pseudogenes or repetitive sequences) that were originally appeared in the genome as a result of unrelated duplication/insertion events.  Many other functional elements, such as those producing noncoding RNAs (e.g. microRNAs) have been identified in recent decades with the availability of improved DNA analysis techniques, but they only amount to a few percent of the genome.

Other Parts of the Genome: Repetitive Sequences and Self-Replicating Elements

About 8% of the human genome consists of repetitive DNA sequences, termed tandem DNA arrays or tandem repeats. The repeated sequences may be of variable lengths, from two nucleotides to tens of nucleotides (“microsatellites” and “minisatellites”). Because of their relatively high rates of mutation, these sequences are highly variable, even among closely related individuals, and so are used for genealogical DNA testing and forensic DNA analysis.

The biggest portion (about half) of the human genome is comprised of mobile genetic elements, also known as transposable genetic elements, transposons, or (inaccurately) “jumping genes”.  These are DNA sequences that can replicate and insert copies of themselves at other locations within a host genome. Some of these sequences represent endogenous retroviruses, DNA copies of viral sequences that have become permanently integrated into the genome and are now passed on to succeeding generations. Long Interspersed Elements (LINEs) are common class of tranposon. Because LINEs move by copying themselves, they enlarge the genome. The human genome, for example, contains about 500,000 LINEs, which is roughly 17% of the genome.

Short Interspersed Elements (SINEs) can move with or without duplication. With about 1,500,000 copies, SINEs make up about 11% of the human genome. The most common SINE in humans is an “Alu element”, which consists of about 300 base pairs. The human genome acquires one new Alu insert in approximately every 200 births. LINEs and SINEs are typically non-coding for proteins, but over time they can accumulate mutations which enable parts of them to serve as exons or as regulatory elements.  They can have deleterious effects (e.g. cancer) if they happen to land in a genetically functional portion of the DNA.

LINEs and SINEs are also known as “ancient repetitive elements” (AREs), since their insertion into mammalian DNA in many cases dates back millions of years. For instance, we can see many similar AREs located in the same places in the mouse and the human genomes. The straightforward interpretation of this observation is that these AREs landed in those spots in a common ancestor to today’s mice and humans.

The Nature of “Junk” DNA

By the late 1960s, biologists had come to realize that the amount of DNA in animal genomes was much larger than needed to simply encode proteins. For instance, biologist Ryan Gregory discusses a 1972 paper by David Comings, which anticipated much that was confirmed in later experiments. Comings noted several reasons to believe that much of human DNA is non-functional, including:

 (1) Some organisms have an unreasonable excess of DNA, clearly more than they require. (2) Reasonable estimates of the number of genes necessary to run a eukaryote seem significantly less than the amount of DNA available. (3) The mutational load would be too great to allow survival if all the DNA most eukaryotes carry was composed of essential genes.

Comings is not saying, “We haven’t identified function for most of the genome, and therefore we conclude it is functionless.” Rather, he is stating positive reasons to believe that there is substantial non-functional DNA in animal genomes. For instance, regarding his point (1): Onions have a genome 5 times larger, and salamanders 4 times larger, than humans, while the pufferfish has a genome 10 times smaller than humans. Most of these differences in genome size are due to differing loads of repetitive elements (like LINEs and SINEs), which will normally (there are exceptions) not show function. These considerations do not 100% prove that some of the genome is non-functional, but the insertion of largely non-functional repetitive elements over millions of years of evolution is a parsimonious explanation for the observed differences in genome sizes.

Regarding his point (3): Each human birth adds about 100 mutations to the genome.  You have approximately 400 mutations compared to your great-great-grandparents.  Since the vast majority of mutations are harmful, you likely would not be alive except for the fact that most of those mutations have landed in more or less nonfunctional places in your DNA.

To continue with Comings:

These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.

The observation that up to 25% of the genome of fetal mice is transcribed into rapidly labeled RNA, despite the fact that probably less than half this much of the genome serves a useful function, indicates that much of the junk DNA must be transcribed. It is thus not too surprising that much of this is rapidly broken down within the nucleus. There are several possible reasons why it is transcribed: (1) it may serve some unknown, obscure purpose; (2) it may play a role in gene regulation; or (3) the promoters which allow its transcription may remain sufficiently intact to allow RNA transcription long after the structural genes have become degenerate.

Comings here estimates that up to 20% of human DNA may be functional (which, interestingly, is the same figure arrived at in 2012 by ENCODE). He notes that much of the genome can be transcribed into RNA, although being transcribed does not necessarily imply function. He allows that there may be as-yet unknown purposes for non-coding transcripts, and particularly suggests gene regulation as a target. Since this was way back in 1972, five years before it was even known that genes are interrupted by introns, it would be unfair to demand too much precision of Comings. Nevertheless, this paper demonstrates that mainstream scientists were well aware that non-coding DNA, loosely called “junk DNA”, could have important functionality.

The existence of regulatory regions and other functional spots in non-coding DNA was known even before Comings published these paragraphs. For instance, a 1965 Nobel Prize went to Jacques Monod and co-workers for their discovery of regulatory elements.  King and Wilson in a 1975 Science article noted that the proteins of chimps and humans were nearly identical, deducing that the morphological differences between the two species must derive more from regulation of gene expression than from differences in their coding DNA.

Gregory further observes:

Those who complain about a supposed unilateral neglect of potential functions for non-coding DNA simply have been reading the wrong literature. In fact, quite a lengthy list of proposed functions for non-coding DNA could be compiled (for an early version, see Bostock 1971). Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordinating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

A key source of confusion is that “junk DNA” can mean different things. Practicing researchers have nearly always used the term in the sense of “partly or largely non-functional; with its functional elements dispersed and incompletely understood”, as is evident in the Comings quote above.  Occasionally researchers use “junk DNA” to mean “completely non-functional,” but the context will show that they are distinguishing such non-functional, non-coding DNA from functional, non-coding DNA.

Nevertheless, starting around 1990, one can find a small but steady stream of publications by misinformed and/or publicity-seeking scientists claiming that, “The scientific consensus before [fill in the date] was that essentially all non-coding DNA is useless junk….. But NOW we have overturned this consensus with our dramatic discovery of [fill in the blank]”.   As Gregory notes:

By 1989 or 1990, we start to see claims that noncoding sequences were “long dismissed” as mere “junk” or “parasites”, and that biologists finally are beginning to recognize that it is interesting. We have heard this line, more or less unaltered, ever since. This statement is usually not backed up with any reference to the literature, it is more of a “general sense” sort of claim… or authors who make the statement will cite Ohno (1972), and possibly also Doolittle and Sapienza (1980) and Orgel and Crick (1980), even though these original publications did not in any way dismiss possible functions for some noncoding elements.

The “junk” that is in my basement is a reasonable analogy: there is a lot of it, and only a small portion is demonstrated to be useful in a given year. But it does have some actual and potential usefulness. If it were positively known to be completely valueless to my household, it would no longer be called “junk” but “trash”, and would be discarded. Similarly, an automobile “junkyard” retains many cars, with the expectation that some parts from some cars will be found useful. If a vehicle is determined to be totally useless, it is not considered “junk”, but rather “scrap”, and gets melted down.

PART 2. THE ENCODE PROJECT AND ITS RECENT RESULTS

The ENCODE Project

The Human Genome Project provided the first complete sequencing of the human genome. An initial rough draft of the human genome was available in 2000.  By 2001 a working draft had been completed and published, followed by the final sequencing mapping of the human genome in 2003. The complete (3 billion base pair) sequence for one individual was mapped out, and 20,000-25,000 genes were identified. However, this turned out to be less useful than originally anticipated, since the function of the vast majority of all those DNA sequences remained unknown.

The Encyclopedia of DNA Elements (ENCODE) project was intended to fill in our understanding of DNA function. ENCODE was launched by US National Human Genome Research Institute (NHGRI) in 2003. Its goal is to find all functional elements in the human genome. In 2007, ENCODE published pilot results on analysis of 1% of the genome.   Wikipedia summarizes its recent accomplishments:

On 5 September 2012, initial results of the project were released in a coordinated set of 30 papers published in the journals Nature (6 publications), Genome Biology (18 papers) and Genome Research (6 papers).These publications combine to show that approximately 20% of noncoding DNA in the human genome is functional while an additional 60% is transcribed with no known function. Much of this functional non-coding DNA is involved in the regulation of the expression of coding genes. Furthermore the expression of each coding gene is controlled by multiple regulatory sites located both near and distant from the gene. These results demonstrate that gene regulation is far more complex than previously believed.

The flagship paper in Nature is here, while this site provides links to twelve difference themes or “threads” in the ENCODE results.    With years of intellectual toil, backed by massive computer processing, the ENCODE team of over 400 scientists identified genetic function in 8% of the genome for the cell types they examined. They extrapolated that this figure would climb to 20% for the full range of tissues in the human body. While this is fine work, it is no surprise that ENCODE identified much additional function in the genome.  We already knew that non-coding DNA had many different functions in many locations.  The reason ENCODE went to all that effort is because they, along with the whole biological research community, fully expected to find such function. That is precisely why their funding agency spent nearly $300 million on this effort, including $125 million for technology development.

Various lines of evidence have led biologists to believe that around half of the mutations that get fixed in animals are beneficial to the organism, while the rest are more or less neutral. We expect, then, that some functional regions would be strongly conserved from generation to generation, while a large portion of functional DNA might be more subject to minor mutations without harming the organism.  This is confirmed in the ENCODE results.  Analysis of ENCODE results by Ward and Kellis indicates about 9% of the of the human genome is being conserved, i.e. is under negative (purifying) selection. This is around half of the 20% of the genome which was estimated by ENCODE to have genetic functionality.

The ENCODE Project Did NOT Show That 80% of Human DNA Has Genetic Function

To understand what follows (the hype and the spin), we need to describe what the ENCODE scientists did and did not accomplish.  Basically, they looked for regions of human DNA which could be transcribed to RNA, or bind to various chemicals. These regions, comprising some 80% of the genome, were deemed to have “biochemical function.” The key point to take away is that this sort of “function” is a probably necessary, but definitely not sufficient indicator of actual genetic function. By “genetic function” we mean “having some real effect on the organism”.

The fact that a chunk of DNA can be transcribed into RNA in no way shows that it really does anything. For instance, nearly all introns in the genome are transcribed, so they count as “biochemically functional” by the ENODE definition. But as we noted above, the intron sections are chopped out of the RNA before it is shipped off to a ribosome to make the protein. This is why the introns can often sustain massive mutations with no discernible effect on the organism. Introns were already known to comprise 25-40% 0f the genome, so nearly half the “80% biochemically active” DNA that ENOCODE identified was merely mapping the intron regions which were already known to exist.

Molecular biology researcher Sean Eddy emphasizes this point:

If you made a piece of junk for yourself — a completely random DNA sequence! — and dropped it into the middle of a human gene, what would happen to it? It would be transcribed, because the transcription apparatus for that gene would rip right through your junk DNA. ENCODE would call the RNA transcript of your random DNA junk “functional”, by their technical definition. And if even it weren’t transcribed, that would be because it acted as a different kind of functional element (your random DNA could accidentally create a transcriptional terminator).

Eddy also notes that transposable elements (e.g. SINEs, LINEs), which make up about half of the human genome, would also show up as having “biochemical function” with ENCODE:

As far as questions of “junk DNA” are concerned, ENCODE’s definition isn’t relevant at all. … Are transposable elements transcribed as RNA? Do they bind to DNA-binding proteins? Is their chromatin marked? Yes, yes, and yes, of course they are – because at least at one point in their history, transposons are “alive” for themselves (they have genes, they replicate), and even when they die, they’ve still landed in and around genes that are transcribed and regulated, and the transcription system runs right through them.

Biologist Michael White, in a comment under this post, made the same point:

It’s easy to refute the main claims in the ENCODE news stories without invoking evolution at all, from biochemical arguments. What happens to transposable elements? They promote their own transcription. What do transcription factors recognize? Short, degenerate sequences that crop up all over the genome.   Synthesize 1000 random DNA sequences (as I did this summer), and stick them in front of a reporter gene. What happens is exactly what any self-respecting molecular biologist should expect – many drive transcription, are bound, get marked etc.

In response to the 2007 ENCODE publications, biology professor Larry Moran   observed :

Most of us who teach transcription take pains to point out to our students that RNA polymerase binds non-specifically to DNA and that much of this binding will result in spurious transcription at a very low frequency. This is exactly what we expect from a knowledge of transcription initiation…The ENCODE data shows that most of the genome is “transcribed” at a frequency of once every few generations (or days) and this is exactly what we expect from spurious transcription. The RNAs are non-functional accidents due to the sloppiness of the process.

Thus, the “80%” number reported by ENCODE is nearly meaningless in establishing genetic function.  The amount of the non-coding DNA for which ENCODE actually found actual indicators of function was only 8% for tissue types they examined.  Adding to that the 1-2% known coding DNA, and making various assumptions, ENCODE extrapolated to a possible 20% of the genome having genetic function.

Publicity Hype Around ENCODE Results

So far, this is unremarkable. The ENCODE team found what they, and essentially all other biologists, expected to find.  The plot twist comes in how the ENCODE spokesmen described these results to the press, and how the press took the story and ran with it. They emphasized the 80% figure (biochemical activity, which proves almost nothing of itself), not the 8% (actual genetic function identified) or even the 20% (extrapolation of the 8%). The press was duped into thinking that ENCODE had discovered genetic function in 80% (not 8% or 20%) of the genome. The language used in the lead ENCODE article in Nature would support this impression; there it was stated that ENCODE had assigned “biochemical functions” (not merely “biochemical activity”) for 80% of the genome.

The initial press release by NIH (the parent of NHGRI)  contained this quote from Eric D. Green, director of the NHGRI:  “During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong.”

This statement by Green is misleading at best.  Yes, “researchers” predicted (correctly) that “only a few percent of the human genome sequence encoded proteins.”  And, yes, “researchers” did sometimes refer to the rest as “junk.” But by “junk” they did NOT mean “non-functional.” I would challenge Green to cite a single active genetics researcher after 1980 who claimed there was no function in the genome outside of coding exons.    The references cited above, and the steady stream of papers on non-coding DNA over the past 30+ years show that nearly all “researchers” believed it had significant functionality, well before the dazzling light of ENCODE broke over the darkling field of genomics. Green’s statement is transparently self-serving hype. Nevertheless, it served its purpose by misleading the press as to the significance of the ENCODE results.

Scientists Repudiate ENCODE Hype

As a scientist, and knowing hundreds of other scientists, I can say that most scientists sincerely care about accuracy and truth. Thus, it was no surprise that scientists were irritated by the misrepresentation of ENCODE’s results, and have spoken out in protest. The quotes above from Eddy and White are indicative of this response.  White also wrote (“A Genome-Sized Media Failure”) of the ENCODE announcement:

This was a fantastic opportunity for scientists and science journalists to explain to the public some of the exciting and important research findings in genome biology that are changing how we think about health, disease, and our evolutionary past. But we blew it, in a big way…..The Washington Post headline read, “‘Junk DNA’ concept debunked by new analysis of human genome.” The New York Times wrote that “The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as ‘junk’ but that turn out to play critical roles in controlling how cells, organs and other tissues behave.”   Influenced by misleading press releases and statements by scientists, story after story suggested that debunking junk DNA was the main result of the ENCODE studies. These stories failed us all in three major ways: they distorted the science done before ENCODE, they obscured the real significance of the ENCODE project, and most crucially, they mislead the public on how science really works..….ENCODE, in what was a genuine, technological tour-de-force, measured dozens of different kinds of biochemical landmarks, which can be suggestive of important functions, but do not by themselves demonstrate that a region of the genome is doing something useful for us. This distinction was obscured by the press releases put out by ENCODE, and largely lost on most of the reporters who covered the story. Missing from press releases and news reports was a description of what non-functional DNA looks like: it carries many of the same biochemical landmarks as functional DNA. The widely reported claim of debunked junk DNA is simply wrong.

The Comments on White’s article include references to at least seven ENCODE scientists who have gone on record disputing the notion that ENCODE has “debunked junk DNA.”   Also, Berkeley biologist Michael Eisen wrote:

The issues all stem, ultimately, from the press releases issued by the ENCODE team, one of which begins:

“The hundreds of researchers working on the ENCODE project have revealed that much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work – and mutations in these regions might lead to human disease. The new information delivered by ENCODE is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected.”

The problems start before the first line ends. As the authors undoubtedly know, nobody actually thinks that non-coding DNA is ‘junk’ any more. It’s an idea that pretty much only appears in the popular press, and then only when someone announces that they have debunked it. Which is fairly often. And has been for at least the past decade. So it is more than just intellectually lazy to start the story of ENCODE this way. It is dishonest – nobody can credibly claim this to be a finding of ENCODE. Indeed it was a clear sense of the importance of non-coding DNA that led to the ENCODE project in the first place. And yet, each of the dozens of news stories I read on this topic parroted this absurd talking point – falsely crediting ENCODE with overturning an idea that didn’t need to be overturned.

But the deeper problem with the PR, and the main paper to some extent, is the way that they slip and slide around the extent and nature of the functions they have “discovered”. The pullquote from the press release is that the human genome is a “massive control panel with millions of switches regulating the activity of our genes”. So let’s untangle this a bit. It is true that the paper describes millions of sequences bound by transcription factors or prone to digestion by DNase. And it is true that many bona fide regulatory sequences will have these properties. But as even the authors admit, only some fraction of these sequences will actually turn out to be involved in gene regulation. So it is simply false to claim that the papers have identified millions of switches.

Polypompholyx hits all the key points in a short article which includes a good chart of the contents of the human genome. He notes, ” Having ‘specific biological activity’ doesn’t mean the same as having ‘important biological activity’. Although there is precedent for viral sequences being co-opted for interesting new roles in the cell, these poachers-turned-gamekeepers appear to be a vanishingly small fraction of your genome.” Ryan Gregory here lists over a dozen other articles likewise decrying the misinformation around the ENCODE results.

Gregory  reprints comments from two graduate students who contributed to ENCODE. One of these students wrote:

ENCODE has not demonstrated function for ANYTHING because we published no functional studies. The only thing ENCODE has done is to find new regions on the genome that are correlated, in terms of their chemical signature (i.e. chromatin state of “openness”, transcription factor occupancy, etc.), with other regions that have been proven functional by site-directed experiments. Correlated, no more and no less. … The 80% figure is almost certainly not even real chemical signatures. If you notice, 80% of the genome is the percent of the genome that is mappable so right now, I think the 80% figure simply means that if you sequence any complex genome-wide dataset deeply enough, you will eventually return the entire genome….Heck, all of it could still be “junk” by ENCODE results alone (and NOW when I say “junk”, what I mean is that they don’t have a direct effect on gene expression)… it’s unclear what many of these assays mean in terms of physical reality…. EVEN IF we believed that most of the regions we identify are real (i.e. there is occupancy there), as is likely the case for the more conservative 20% of the genome, that only means that that chemical signature is there — it DOESN’T mean that this has anything to do with function.

Dan Gauer et al. piled on a few months later with a 40-page shredding of the claim of 80% functionality, claiming to “detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome.”  Even initial ENCODE-hype-defender John Stamatoyannopoulos has backed away from the “80% functional” claim, now putting the number at more like 40%.

Spokesman Ewan Birney Attempts to Defend ENCODE’s Hype

Ewan Birney, lead analysis coordinator for the ENCODE project, addressed some of these complaints in a post on his own blog.  Birney notes that the notion of “function” is ambiguous. Fair enough. He then writes, “Pragmatically, in ENCODE, we define our criteria as ‘specific biochemical activity’ ”.  As we showed in detail above, that is indeed an accurate description of what ENCODE found in 80% of the genome. But – – – if all they meant was “specific biochemical activity” why did Birney and his colleagues describe it to the press as “biochemical function”?  There is a big difference in connotation between “activity” and “function”.

Why not clearly state that ENCODE had detected “specific biochemical activity” (Birney’s words in his own blog) of uncertain significance in 80% of the genome, of which 20% was estimated to have genuine genetic function?   Birney’s answer to this question is breathtaking:

…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 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.

So there you have it – – the ENCODE promoters believed that their readers were too stupid or lazy to understand the difference between 20% actual function, and 80% mere chemical activity, so they went with the bigger number for bigger “impact.” I commend Birney for his candor here, but it would have been much better to have been that candid in the publications and press releases.  (Side comment:  Eisen notes above that Birney’s “4 million switches” claim is bogus.)

Birney in his blog post admits that the bulk of what ENCODE tagged as having “biochemical activity” may have no real genetic function:

As I’ve pointed out in presentations, you shouldn’t be surprised by the 80% figure. After all, 60% of the genome with the new detailed manually reviewed (GenCode) annotation is either exonic or intronic, and a number of our assays (such as PolyA- RNA, and H3K36me3/H3K79me2) are expected to mark all active transcription. So seeing an additional 20% over this expected 60% is not so surprising.

Here Birney is stating what we have pointed out above, that a large fraction of the genome will get tagged simply because it consists of introns, not because it has genetic function. (He uses a figure of 60% for combined exons plus introns; that is higher than I have seen elsewhere, but doesn’t change the overall point here.)

PART 3. THE INTELLIGENT DESIGN SPIN

The Intelligent Design Movement

The “Intelligent Design” (ID) movement began around 1990, centered mainly around Michael Behe, Stephen Meyer, William Dembski, and attorney Phillip Johnson. The Design Institute in Seattle is the current epicenter.  ID advocates oppose evolution because they see it as driving unbelief and moral decay.

While the evidence for evolution is compelling for almost everyone who actually engages it, to fully appreciate that evidence may take more scientific training than possessed by the average college graduate.   Many Christians remain skeptical of macro-evolution because they don’t like its ethical implications, because it seems to contradict the Bible, and because present evolutionary theory cannot offer a detailed explanation for all the data.  (See here  and here for my approach to reconciling discrepancies between science and the Genesis narrative.)

ID attempts to offer intellectual respectability for disbelief in evolution.  ID advocates try to show that natural processes cannot account for the complexities of today’s life-forms.  Meyer, Dembski, Behe and others have PhD’s and are conversant with the academic literature.  Typically ID advocates accept the geological evidence for an old earth, although they avoid mention of that when speaking to non-scientist, mainly young-earth creationist audiences.

ID proponents engage in the following tactics:

(A) Ignore or belittle the vast explanatory and predictive power of the theory of evolution (i.e. the concept that today’s life-forms have developed over eons from earlier, different organisms).

(B) Call attention to issues where scientists cannot yet provide complete explanations or where scientists disagree. (It is not hard to find such issues; the reason we scientists still have jobs is because much remains to be discovered).  Also call attention to poorly-worded or erroneous claims by (sometimes obnoxious) advocates for evolution.

(C) Ignore or belittle the explanations or clarifications offered by mainstream scientists regarding the issues in (B).

(D) Avoid offering any concrete, testable alternative to the scientific narrative of changes occurring from generation to generation by natural processes such as mutations and natural selection.

Let’s  unpack (D) a bit.  ID proponents demand that evolutionary scientists provide a complete, detailed, unchanging explanation of everything in biological history; if anything less than that is forthcoming, ID proponents proclaim that “Darwinism is tottering” or “Evolution is a sinking ship” or some such metaphor.  Very well. Let’s apply the same standard to ID: let ID proponents  propose some alternative narrative to explain the appearance of today’s organisms, and let them show how every observation of current biology and inferences from fossils fit perfectly in this narrative.

ID advocates avoid offering such alternatives, since they know full well they cannot defend them.  As an example, Meyer and others have claimed that natural processes cannot account for the relatively rapid proliferation of life-forms in the early Cambrian period, and so they invoke an Intelligent Agent.  OK – so what (even in the most general terms) did this Agent actually do to create the trilobites and their cousins? Did the Agent create, ex nihilo, two species every thousand years for 10 million years in the early Cambrian? Or did the Agent work with the species that existed immediately before the Cambrian, but miraculously rearranged some specific chunks of DNA to get certain big new features? Or what? Merely to say “The early Cambrian life-forms were designed” or “The early Cambrian life-forms reflect the action of an intelligent agent” are effectively content-less statements. All they mean is “Aha, we have found a gap that scientists have not yet filled in; we can’t fill it either, but we claim it for our Agent-of-the-gaps.”

ID proponents try to wiggle out from this by saying, “We are not arguing from ignorance; rather, we are positively detecting design, in the form of specified complexity.” Some of the fallacies in ID’s formulation of specified complexity are discussed here. The supposed instances of specified complexity are defined so as to always fall within the current knowledge gaps.  Thus, in practice ID is nothing more than a sophisticated version of the standard god-of-the-gaps ploy: if science cannot yet explain something, then we can claim that it God did it. (ID substitutes the term “Intelligent Agent” for “God”, but nobody is fooled by this.)

Common Deceits in ID’s Treatment of Junk DNA

ID advocates have a well-established pattern of misrepresenting what most scientists have believed about non-coding DNA, in order to set up a “straw man” to be knocked down. Seven main deceits in their publications are as follows:

{1} State or imply that mainstream biologists up until recently have believed that essentially all non-coding DNA was functionless.

{2} Instead of using the clear term “non-coding DNA”, use “junk DNA” to milk its ambiguity in an attempt to support {1}.

{3} State or imply that biologists believed most non-coding DNA is functionless merely because no function had yet been discovered (“argument from ignorance”); suppress the well-known positive reasons discussed above that indicate that much of human DNA has no genetic functionality (e.g. the vastly differing genome sizes among similar organisms which correlates with increased loads of self-replicating elements).

{4} Claim that the alleged consensus in {1}, that non-coding DNA had no function, has held back research in this area.

{5} Claim that evolutionists rely on the mere existence of (supposedly) functionless DNA as a chief argument for naturalistic evolution as opposed to the intervention of an Intelligent Agent.

{6} Claim that Intelligent Design predicts that essentially all of the genome will have function.

{7} Imply that recent scientific papers show that most of the genome is indeed functional, thus vindicating ID against “Darwinism.”

Some comments on these deceits: The discussion above has already shown {1}, {3}, and {4} to be outright falsehoods.  Regarding Deceit {5}, ID advocates can mine some quotes (often taken out of context) that seem to support this claim, but this claim, too, is false. The main reason that both theistic and atheistic evolutionists believe that the form of the genome is best explained by natural processes is not merely because much of it appears functionless, but because the functionless parts look like they got there via natural, largely-understood processes like gene duplication, hopping of transposable elements, and mutations. We can trace, and even predict and verify, all sorts of details in the genomes of different species that are understandable in the framework of common ancestry. There is just no need to invoke the supra-natural.

Whether a given SINE has a regulatory function or not, it still gives every appearance of being where it is by dint of its well-known propensity for duplication and insertion.  If the 1,500,000 SINES in the human genome did not derive from ordinary duplication events in our primate ancestors, how did they get there? ID advocates cleverly avoid proposing an alternative narrative or mechanism.

According to Deceit {6}, if a genome is designed by an intelligent agent, it logically follows that the genome will be essentially all functional. That also is false. We do not know what some unnamed Agent (or even a specifically Judeo-Christian God) might choose to put into a genome. Said Agent might well have an aesthetic sensibility that delights in extravagant numbers of unnecessary LINEs and SINEs. ID advocates really paint themselves into a corner with this claim, since any DNA chunk which can be shown to be functionless (e.g. the  busted vitamin C gene shared by humans and apes, or the 20% of the genome that failed to register even ENCODE’s loosest definition of chemical activity)  would then count against ID.

Finally, Deceit {7}, the claim that recent scientific papers show that most of the human genome is functional, is also clearly false. What ID proponents do is present long laundry lists of functions that have been found in pseudogenes or in AREs like LINEs and SINEs. That gives lay readers the impression that most these of elements are functional. What ID advocates carefully withhold from their readers is that demonstrated genetically functional pseudogenes or SINEs are only a small fraction of the total pseudogenes or SINEs. For instance, we noted above how only 10-20% of human pseudogenes were tagged by GENCODE as possibly having genetic function.  That leaves room for lots of functionality to be discovered among these 1000-2000 tagged pseudogenes, but that does not mean that most pseudogenes are functional.

Some Examples of Treatment of Junk DNA by Intelligent Design

ID proponents and their opponents have fired many salvos back and forth on the internet regarding junk DNA. I’ll sample just a few articles, and key them to Deceits {1}-{7} listed above. From Luskin in 2008:

Darwinists have long made an argument from ignorance, where our lack of present knowledge of the function for a given biological structure is taken as evidence that there is no function and the structure is merely a vestige of evolutionary history. Darwinists have commonly made this mistake with many types of “junk” DNA, now known to have function. In contrast, intelligent agents design objects for a purpose, and therefore intelligent design predicts that biological structures will have function. [Note: This short paragraph packs in Deceits {1}, {2}, {3}, {5}, {6}, and {7} from our list above]

In 2011, the Discovery Institute published The Myth of Junk DNA, by Institute fellow Jonathan Wells. This book is based on the deceits enumerated here, and has been thoroughly reviewed by Larry Moran.

Casey Luskin wrote an article, entitled  “New Scientific Research Papers
Published Since Myth of Junk DNA Confirm Jonathan Wells’ Thesis“,  in support of Wells’ book. The article leads off:

In The Myth of Junk DNA, Jonathan Wells predicted that “assuming that any feature of an organism has no function discourages further investigation. In this respect, the myth of junk DNA has become a science stopper.” (p. 107). Recently published literature has overwhelmingly confirmed Wells’ thesis, and evolutionary scientists who cling to the myth of junk DNA are being refuted by continual research publications.

Luskin’s article cites some recent articles that note some functions of non-coding DNA, and concludes, “The presumption that noncoding DNA is ‘junk’ hinders biological and medical research from moving forward.”   Here we see Deceits {1}, {2}, and {7}, with a special emphasis on Deceit {4} (the claim that the concept of junk DNA has discouraged research).

In a related article, Luskin starts with:

Materialists have a longstanding love affair with the notion that life is a poorly constructed kluge. For decades, they have argued that since only about 2 to 3 percent of human DNA codes for proteins, most noncoding DNA is useless genetic junk.

As their argument goes, no designer would put such genetic garbage in our genomes, and therefore so-called junk DNA refutes intelligent design (ID). Random evolutionary mutations, on the other hand, might be expected to produce a genome full of what Francis Collins called “genetic flotsam and jetsam.”

Here we see Deceits {1}, {2}, {3}, and also {5} (the claim that evolutionists rely on the mere existence of functionless DNA as an argument for naturalistic evolution). The article goes on to quote Jonathan Wells listing some functions found in non-coding DNA, and noting “New functions for non-protein-coding DNA are being reported every week.” But the article never informs us that all these newly discovered functions amount to only a few percent of the genome (Deceit {7}).

In 2010, ID advocate Robert Crowther penned a piece entitled Francis Collins, Evolution and “Darwin of the Gaps”. The text here summarizes an embedded video clip of ID spokesmen like Jonathan Wells and Richard Sternberg making accusations against Francis Collins and his theistic evolution book The Language of God. Here is the text of Crowther’s article:

Much of Collins’s case for Darwinian evolution is based on so-called “junk DNA.” This is the part of the genome that does not appear to code for the production of proteins. In mammals, the vast majority of DNA has been dismissed as “junk.”

Junk DNA, according to Darwinists like Collins, gives evidence of common descent—the idea that all life, including human life, branches off from a common evolutionary tree. As life evolved, according to this view, garbled, useless genetic information accumulated and has remained fixed—like dirt swept under a carpet—even as mammals, for example, diversified from a common ancestor.

But the argument from junk DNA—also called “ancient repetitive elements” (AREs)— depends on the premise that no function will ever be discovered for AREs. Collins’s faith in Darwinian theory would be severely hamstrung if the premise were shown to be wrong. It is a faith based on gaps in scientific knowledge. Hence, “Darwin of the gaps.”

We note here the appearance of Deceits {1}, {2}, {3}, {5} and (in the video, which flashes literature citations of functions found in non-coding DNA) Deceit {7}. The level of dishonesty deepens if we compare the statements above to what Collins actually wrote in The Language of God. In describing the state of knowledge in the early 1980’s, he acknowledges (p.111) that when it was found that “there were long stretches of DNA in between genes that did not seem to be doing much”, some people “referred to these as ‘junk DNA’.”  Collins himself, however, does not endorse any blanket dismissal of non-coding DNA, writing that “a certain level of hubris was required for anyone to call any part of the genome ‘junk,’ given our level of ignorance.”

Crowther’s text above would have us believe that Collins is banking on ancient repetitive elements (AREs) like LINEs and SINEs having absolutely no function (“…depends on the premise that no function will ever be discovered for AREs”). Even for ID, that is a whopper. The following excerpt from The Language of God (pp.136-137) shows that Collins was well aware that some AREs may have regulatory functions; he is NOT pointing merely to functionlessness, but also to the fact that the positioning and truncation of these AREs show a clear evolutionary history:

When one aligns sections of the mouse and human genomes, anchored by the appearance of gene counterparts that occur in the same order, one can usually indentify AREs in approximately the same location in these two genomes….Of course, some may argue that these are actually functional elements placed there by the Creator for a good reason, and our discounting of them as “junk DNA” just betrays our current level of ignorance. But…there are AREs throughout the human and mouse genome that were truncated when they landed, removing any possibility of their functioning. In many instances, one can identify a decapitated and utterly defunct ARE in parallel positions in the human and mouse genomes.

Unless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable.

The ID folks (Wells, Sternberg, Crowther) who are critiquing The Language of God have presumably read the book, and would especially pay attention to polemical passages like that one. They are without excuse, then, for misrepresenting Collins’s views.

Intelligent Design Spins the Encode Results

Predictably, ID proponents cast the September, 2012 ENCODE results as supporting their viewpoint. Given the initial media misrepresentation, it is hard to blame them for their gleeful early articles on the subject, with titles like Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” and Why ENCODE Is a Significant Defeat for Darwinism.

However, once the truth came out about the ENCODE hype, the continued ID gloating over the ENCODE results has become simple dishonesty. ID advocates have obviously read the criticisms of the hype, but have responded by (a) belittling and attacking the motivation of the professional biologists who are correcting the hype, and (b) concealing from their readers that these biologists are obviously correct in noting that the biochemical activity found in 80% of the genome by ENCODE does not translate to actual genetic functionality.

Below are excerpts of three representative articles by Discovery Institute authors:

What a Darwin Advocate’s Response to the ENCODE Project Tells Us about the Darwin Debate (Casey Luskin, Sept 10, 2012)

University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of “biochemical functions for 80% of the genome.” Other Darwin-defenders are trying to dismiss this paper as mere “hype”.

Yes that’s right — we’re supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it’s “hype.” (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet Darwin-activists are welcome to disagree and protest these conclusions, but it’s clear that the consensus of molecular biologists — people who actually study how the genome works — now believe that the idea of “junk DNA” is essentially wrong.

This shows that Luskin has read Moran’s criticisms of the ENCODE hype – but Luskin spends the rest of the article attacking Moran’s motives instead of addressing Moran’s substantive points. Here are excerpts from another Luskin article (Sept 27, 2012), Why the Case for Junk DNA 2.0 Still Fails :

Confronted with the ENCODE results that attribute “function” to at least 80% of the genome, some Darwinist bloggers and critics of intelligent design have established a defensive perimeter around the precious idea of Junk DNA. It truly is that critically important to them. Their favored critique of ENCODE — call it the case for Junk DNA 2.0 — is that ENCODE’s definition of functionality is wrong. “Well, maybe it’s technically functional,” they say, “but it really isn’t.”

…. We already know of several non-biochemical functions of non-protein-coding DNA: providing a structural basis for centromeres (which in living cells are not just functional, but absolutely essential); providing spacers to regulate the timing of protein production; and focusing light in rod cells in the retinas of nocturnal mammals. …So if anything, ENCODE uses too narrow a definition of function — by limiting it to “biochemical” function. For this reason, the functionality reported by ENCODE surely underestimates the total.

Luskin here waves around some legitimate non-biochemical functions (e.g. scaffolding) found in small sections of non-protein coding DNA in order to evade the elephant in the room, which is that ENCODE’s watered-down definition of “function” has little connection to  any real effects on the organism.

And lastly, Why All the Fuss Over Some Junk? by Jonathan Wells (Sept. 25, 2012):

When the ENCODE Project (ENCyclopedia Of DNA Elements) announced recently that more human DNA is functional than biologists previously knew, most people congratulated the several hundred scientists who had worked for five years to produce their results. A few Darwinists, however, lit up the blogosphere with angry denunciations — including Larry Moran, Nick Matzke, P.Z. Myers, and T. Ryan Gregory.

Wells is a master of the half-truth. He, along with Luskin above, tries to characterize the protest against the ENCODE hype as the work of a few rogue “Darwinists” on the internet. He conveniently omits the fact that similar objections have been voiced in publications like Scientific American, Forbes, and New Scientist (see list here).   As far as motivations, Wells fails to note that these “Darwinists” are hard-working, practicing researchers who take time out of their busy lives to try to correct the falsehoods they see being promulgated in their areas of expertise. This contrasts with Wells and Luskin, who are paid by the Discovery Institute to write their pieces against evolution.

Wells gives the tiniest lip service to the legitimate concerns over the ENCODE hype, but immediately returns to attack mode for the rest of the article:

…Moran, Matzke, Myers and Gregory (and a few other critics) argue that RNA transcription is too broad an assay, because some RNAs might not serve any function. Possibly, but why set the blogosphere ablaze over it?

Wells then mines several quotes, especially from 1980 Nature papers by Doolittle and Sapienza and by Orgel and Crick, which make it seem like scientists of that day completely dismissed functionality for non-coding DAN. As Wells puts it, “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.’ ”

Deceitfully, Wells does not show the other lines in both of these articles showing that the authors fully acknowledged  functionality in some non-coding DNA, including the repetitive elements that were the subject of these papers. For instance, Orgel and Crick in that 1980 article wrote, “It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another.” Which turns out to be exactly right.

Orgel, Crick and Sapienza wrote in another 1980 Nature article, “In our recent experience most people will agree, after discussion, that ignorant DNA, parasitic DNA, symbiotic DNA (that is, parasitic DNA which has become useful to the organism) and ‘dead’ DNA of one sort or another are all likely to be present in the chromosomes of higher organisms. Where people differ is in their estimates of the relative amounts. We feel that this can only be decided by experiment.” Again, this is correct.

Wells does not tell his readers that, through the 1970s, the dominant viewpoint in biology was that most or all of what was in a genome must be there because it had beneficial function, helping the organism to adapt in some way to its environment. This viewpoint was generally hostile to the notion of fixed near-neutral mutations and to enduring non-functional DNA.  In the face of this “adaptionist” orthodoxy, it was a controversial step for Doolittle and Sapienza and for Orgel and Crick to propose that some of the repetitive elements could maintain their presence merely by their ability to self-duplicate, not because these elements served a beneficial function to the host organism.  Thus, the real “myth of junk DNA” is that there was ever a time in the last 40 years when most scientists thought that non-coding DNA was completely functionless.

The Psychology of Intelligent Design

We have elucidated the misrepresentation and deceit practiced by Intelligent Design proponents in the matter of non-coding DNA and the recent ENCODE results.  Earlier we found a similar pattern of deceptive half-truths in Casey Luskin’s treatment of human, chimp, gorilla, orangutan genomes. The question then arises, what is going on with these people? Are they conscienceless liars? Paid-off propagandists?

From my limited interactions with them, I believe that the employees of the Design Institute hold their views as sincerely as do their opponents.  Humans have a well-documented propensity towards confirmation bias, which is the tendency to acknowledge and remember only the information which accords with a previously-formed opinion.  This tendency becomes more pronounced with emotionally-loaded issues. We have discussed elsewhere the inability of young-earth creationists to admit the basic facts of geology into their minds.   Anne Rice put it dramatically in The Vampire Lestat:

 Very few beings really seek knowledge in this world. Mortal or immortal, few really ask. On the contrary, they try to wring from the unknown the answers they have already shaped in their own minds – justifications, confirmations, forms of consolation without which they can’t go on. To really ask is to open the door to the whirlwind. The answer may annihilate the question and the questioner.

This describes all of us, to one degree or another, in various spheres of life. In politics, for instance, a political liberal or conservative can typically discern policy failures in the other party, but not in his or her own. Few theists really come to grips with the problem of horrendous suffering in a world ostensibly governed by a loving God. Atheists may gloss over the paradoxes (for a materialistic worldview) of consciousness, of abstract meanings, and of knowing their loved ones to be so much more than just bags of organic molecules.

What, then, drives the fellows of the Discovery Institute into their state of crippled perception regarding fossils and genomics? We are not left guessing, since their foundational “Wedge” document has been made available on the internet. This manifesto starts off:

The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built. Its influence can be detected in most, if not all, of the West’s greatest achievements, including representative democracy, human rights, free enterprise, and progress in the arts and sciences.

Yet a little over a century ago, this cardinal idea came under wholesale attack by intellectuals drawing on the discoveries of modern science. Debunking the traditional conceptions of both God and man, thinkers such as Charles Darwin, Karl Marx, and Sigmund Freud portrayed humans not as moral and spiritual beings, but as animals or machines who inhabited a universe ruled by purely impersonal forces and whose behavior and very thoughts were dictated by the unbending forces of biology, chemistry, and environment. This materialistic conception of reality eventually infected virtually every area of our culture, from politics and economics to literature and art.

The cultural consequences of this triumph of materialism were devastating. Materialists denied the existence of objective moral standards, claiming that environment dictates our behavior and beliefs. Such moral relativism was uncritically adopted by much of the social sciences, and it still undergirds much of modern economics, political science, psychology and sociology.

Materialists also undermined personal responsibility by asserting that human thoughts and behaviors are dictated by our biology and environment. The results can be seen in modern approaches to criminal justice, product liability, and welfare. In the materialist scheme of things, everyone is a victim and no one can be held accountable for his or her actions.

Finally, materialism spawned a virulent strain of utopianism. Thinking they could engineer the perfect society through the application of scientific knowledge, materialist reformers advocated coercive government programs that falsely promised to create heaven on earth.

Discovery Institute’s Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies.

All of these points are debatable, but this is not a foolish or cavalier starting point. It is certainly worth pondering the origins of the modern “victim mentality” and of the calculated massacres of tens of millions of human beings under atheistic regimes in the twentieth century.

The Fundamental Error Behind Intelligent Design

We will just focus on one point in the Wedge document: it assumes that the non-supernatural formation of human beings from other species, and ultimately from inorganic chemicals, is not compatible with humans having a spiritual nature or being in the image of God. If common descent threatens the notion that humans have spiritual and moral nature, then common descent must be jettisoned.

This conviction (i.e. that a natural origin for the human species is incompatible with a spiritual nature) drives the whole Intelligent Design enterprise to its denial of evolution. This conviction, however, has no logical basis. This can be demonstrated by contemplation of embryonic development, where it can be shown that all humans today are assembled from molecules, according to the ordinary rules of chemistry.

I got my start some 87 years ago, as one of about a million egg cells formed inside my mother’s ovaries, while she was still in her mother’s uterus. Thirty years later, one of those eggs, containing half of my DNA, traveled from her ovary toward her uterus.  About the same time,  a certain sperm cell, containing the other half of my DNA, formed in my father’s testes. After that sperm’s DNA was joined to the DNA in the now-fertilized egg, the egg divided into two, then four, then eight cells. Soon the cells formed a hollow sphere. After three weeks, my heart started beating even though there was hardly any central nervous system; it would be three more weeks before my brain waves would be detectable.  After about nine months of development, all rigorously progressing by the laws of physics, I was born into the outside world. It would be another several years before I could make anything resembling a moral decision.

Now a key question: when did I receive my spiritual nature? As an unfertilized egg in 1925? As a fertilized but still microscopic, single-celled egg in 1955? No, that can’t be right, because fertilized eggs are known to split to form twin babies, each (presumably) with its own soul. Did I receive a spiritual nature when I was a hollow cluster of cells ? When primitive brain waves could be detected?

A related question: how did I receive my spiritual nature? It seems clear that it did not simply ride in on my parents’ DNA.  If there was some Original Blessed DNA bequeathed to the First Humans many thousands of years ago, that has surely been shredded since then by the 100 added mutations per generation.  But if God supernaturally bequeaths a spiritual nature to a physical clump of cells or to a newborn baby, it cannot matter whether the DNA in those cells was created ab initio in 4000 B.C. , or whether this DNA developed from other primate species. Thus, whether homo sapiens sapiens developed from other primates through the regularities of chemistry, or whether there was some grand or subtle supernatural intervention involved, has no logical bearing on how each human today receives or possesses a spiritual and moral aspect.

A Way Out of the Box for Intelligent Design

Atheistic thinkers have asserted that if human bodies and brains come into existence and assume their final forms via normal material processes, then there is no room for God or transcendent ethics. Instead of challenging this metaphysical assertion, the ID founders unwittingly bought into it. This is what has stampeded them into desperately trying to find some “gaps” in evolution that would allow scope for an Intelligent Agent to do something (though IDers cannot seem to specify what that “something” is).

The fact this effort to discredit evolution involves consistent deception and misrepresentation should lead theists to reconsider this god-of-the-gaps strategy. It may be more fruitful to take a step back and consider the Intelligent Design of the entire universe, including the out-workings of all of its initial conditions.  Physicist Howard van Till has described this perspective as the “fully-gifted creation”, where God graciously endowed the universe from the start with all the properties needed to form stars, planets, and life.  Christians who believe that God is providentially at work in their day-to-day, non-miraculous lives, and who take seriously “the plan of him who works out everything in conformity with the purpose of his will” (Eph 1:11), should have no problem with this.

One final suggestion, directed again to any conservative Christian who has managed to read this far: if you yearn to be able to point to some physical manifestation of God’s activity, consider doing it the New Testament way.  While Paul did make an effort (e.g. Acts 17) to communicate to the philosophers of his day in their terms, his typical modus operandi was to present the gospel message and back it up with a gracious, sacrificial lifestyle and with miraculous healings.  Here are a couple of links that suggest such healings still occur today: legs growing out , deaf boy healed , and a medical journal study on healing of blindness and deafness.

Instead of picking unwinnable fights with evolutionists, consider praying for them in person, with faith and compassion. This is risky, since our prayers are not always answered as we wish. But sometimes they are; one tumor that vanishes could go a long way in building a hearing for your message of a caring God whose existence lies beyond the observable universe.

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8 Responses to Junk_DNA_Design

  1. Pingback: Do the Recent ENCODE Results on the Human Genome Support Intelligent Design? | Letters to Creationists

  2. Pingback: Response to John Sanford’s Defense of Genetic Entropy, March 2013 | Letters to Creationists

  3. John says:

    “As discussed below, transcription is an indicator but not a proof of actual genetic activity.”

    I think the ENCODE project is showing that it’s not even an indicator!

  4. JimV says:

    Thanks for all the work you have done on this and other fact-finding posts. (I just found this blog on a link from Nick Matzke today and have read several posts.) A blogger named Todd Wood has done some similar work from a similar perspective; and of course, Ken Miller.It gives me hope for humanity.

  5. themayan says:

    There will always be denialist when old entrenched ideas are refuted by newly discovered data. Encode is not the only one discovering more and more function in this so called junk DNA. The real problem with these findings is that the data is incongruent with the the modern synthesis. Just maybe, its the theory that needs revising and not the data. See (Altenburg 16.

    Below is Dan Graur critique of ENCODE and is an example of the crux of the controversy.

    Dan Graur… 
”playing fast and loose with the term “function,” by divorcing genomic analysis from its evolutionary context and ignoring a century of population genetics theory”….

    Dan maybe its time to update these 80 year old constructs. As this paper below which is one of many indicates……

    The new biology: beyond the Modern Synthesis
    Michael R Rose1* and Todd H Oakley2

    “The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the “Modern Synthesis” which provided the foundations for most biological research during that century. The foundations of that “Modernist” biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century.”

    It seems another big criticism of the paper by the likes of Graur, PZ Myers and T. Ryan Gregory is in how the the word function is used, as its definition of function is used broadly, but it also seems kind of silly to not expect such a broad definition when the findings themselves are so broad. And again just because the findings seem incongruent to how we view selection based on the modern synthesis (and or what Stewart Newman refers to as these old entrenched dogmas) it does not mean the theory should trump scientific revelation & the discovery of new and empirical data. Maybe it’s the theory that needs changing. One very well known scientist once told me. Scientist don’t change their minds, they just die.

    As Ewan Birney stated. ‘We may not understand what all of it is doing but we believe it is doing something important’

    ENCODE is not alone in this, as more and more functionality is being discovered all the time

    Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation-How ‘junk DNA’ can control cell development
    1 AUGUST, 2013 all the time.
    How ‘junk DNA’ can control cell development

    “Researchers from the Gene and Stem Cell Therapy Program at Sydney’s Centenary Institute have confirmed that, far from being “junk”, the 97 per cent of human DNA that does not encode instructions for making proteins can play a significant role in controlling cell development”

    “Indeed, researchers like John Mattick of Queensland University, Australia think that the idea of junk DNA is junk science:
    Researchers the world over are confirming that non-coding DNA holds critical clues to a vast range of diseases; breast cancer, HIV, Crohn’s disease, Alzheimer’s, heart disease, ovarian and skin cancer … the list is growing daily. A leading figure in world genetics, Prof. John Mattick, recently claimed that, ‘the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology’ [Genius of Junk (DNA), Catalyst, Thursday, 10 July 2003].”

    Junk DNA’ Can Sense Viral Infection: Promising Tool in the Battle Between Pathogen and Host
    ScienceDaily (Apr. 24, 2012) — “Once considered unimportant “junk DNA,” scientists have learned that non-coding RNA (ncRNA) — RNA molecules that do not translate into proteins — play a crucial role in cellular function. Mutations in ncRNA ”

    Citation: Pray, L. (2008) Transposons, or jumping genes: Not junk DNA? Nature Education 1(1)
    “For decades, scientists dismissed transposable elements, also known as transposons or “jumping genes”, as useless “junk DNA”. But are they really?”

    Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116.

    A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells
    Nature Structural & Molecular Biology 20, 440–446 (2013) doi:10.1038/nsmb.2516

    Junk’ DNA Has Important Role, Researchers Find
    May 21, 2009 — Scientists have called it “junk DNA.” They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature force the genome to carry so much excess baggage?

    Comparative and Functional GenomicsVolume 2012 (2012), Article ID 424526, 4 pagesdoi:10.1155/2012/424526

    Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called “genomic fossils” and treated as “junk DNA” several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Pseudogene transcripts may also form small interfering RNA or decrease cellular miRNA concentration. Thus, pseudogenes regulate tumor suppressors and oncogenes.

    Gill Bejerano, PhD, assistant professor of developmental biology ‘Junk’ DNA now looks like powerful regulator, researcher finds
    April 23, 2007
    Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study by researchers at the Stanford University School of Medicine and the University of California-Santa Cruz. The scientists propose that this redeemed DNA plays a role in controlling when genes turn on and off.

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