Keep denying the facts and they'll deny you right back.

Denying ENCODE Data Won't Change the Emerging Facts of Biology

Casey Luskin July 15, 2015 3:20 AM 

Editor's note: This is Part 2 of a 4-part series on ENCODE that Casey Luskin has been publishing this year in Salvo Magazine. Parts 1, 2, and 3 have already been published. Part 4 will be published later this year. Part 1 can be found here atENV.

As we've already seen, the ENCODE project found that 80 percent of the human genome is biochemically functional -- with 100 percent functionality in sight -- overturning the concept of junk DNA. Fearing the demise of a cherished argument, evolutionists immediately retaliated in their customary style -- by becoming emotional and attacking the messengers. Even top journals like Science and Nature recognized the "anger," "rudeness," "intemperate griping,"¹ and "vitriolic . . . hyperbole and mockery"² of ENCODE's critics.

But what were the substantive responses to ENCODE from hard-line evolution-defenders, and do their arguments hold up? Let's examine their top objection.

Arguing That It's Still Junk

The most common counterpoint has been that the ENCODE consortium may have detected "biochemical activity" for most of our genome, but that's very different from demonstrating that the activity has some necessary or important biochemical "function."

According to the central dogma of biology, DNA is transcribed into RNA, and then RNA is translated into protein. ENCODE found that the vast majority of our DNA is making RNA. But what if the process stops there and the RNA isn't doing anything useful? What if it's not junk DNA, but junk RNA?

Under this view, "all this extra transcription may simply be noise, irrelevant to function."³ Or, as outspoken ENCODE critic Dan Graur argues, "transcription is fundamentally a stochastic [random] process," and ENCODE researchers are falling prey to the "human propensity to see meaningful patterns in random data."⁴

Aside from the fact that, even from an evolutionary viewpoint, it would seem colossally wasteful to expend cellular resources creating enormous amounts of RNA from over two-thirds of our genome if that RNA wasn't doing something beneficial, this rejoinder is factually false.

Transcription Isn't Random

ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.

"By studying the trans-cellular patterning of biochemical signatures," writes John Stamatoyannopoulos, a leading ENCODE researcher at the University of Washington, "we gain telling insights into elements responsible for cell-selective regulation of transcript expression, the combinatorial patterns of transcription factors (TFs) that occupy them, and their likely genic targets." ⁵

In other words, we find meaningful patterns of RNA production throughout the genome, creating an orchestrated army of bio-molecules that correlate with the activity of transcription factors--proteins that turn genes on and off. This suggests that our genome's biochemical activity is not just doing something, but doing something very important. And it's not hard to speculate what sort of tasks these RNAs might be doing, for RNA molecules can have all kinds of biochemical functions--including enzymatic properties and gene regulatory functions--whether or not they are translated into proteins.

The fact that DNA transcription is immense--and nonrandom--was confirmed in a 2013 paper that studied RNA transcripts in yeast. It found that while the yeast genome contains only about 6,000 genes, there were over 1.8 million unique RNA transcripts, which were "arranged in a remarkably complex, overlapping pattern across the genome."⁶

RNA Transcripts Specify Development

Clearly RNAs in yeast are encoding many protein sequences. Yeast, however, is only a single-celled organism; in multicellular organisms like animals, RNAs can have additional important functions. They can regulate gene expression and participate in RNA editing and RNA splicing--processes in which different pieces of RNA are stitched together and modified to create new RNA transcripts that in turn can yield additional types of proteins. Such RNA functions have been understood for some time. But a new revelation from ENCODE is that RNAs help specify how cells develop into a particular type.

Animals are composed of many different types of cells. Humans, for example, have nerve cells, blood cells, bone cells, skin cells, and so on. Different kinds of cells combine to form tissues, tissues interact to form organs, and organs coordinate to form an animal's body plan. The distribution of different types of cells is thus foundational to an organism's body plan. But what determines the specific type into which a given cell will develop?

ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases.⁷ Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue--specific transcription in human cells."⁸

Stamatoyannopoulos further finds that repetitive DNA (often called "transposable elements"), which comprises over 50 percent of our genome, is active only in specific cell types. This non-random transcription of repetitive DNA into RNA suggests that transposable elements have functions whose importance are on par with other gene regulation mechanisms:

In marked contrast to the prevailing wisdom, ENCODE chromatin and transcription studies now suggest that a large number of transposable elements encode highly cell type-selective regulatory DNA that controls not only their own cell-selective transcription, but also those of neighboring genes. Far from an evolutionary dustbin, transposable elements appear to be active and lively members of the genomic regulatory community, deserving of the same level of scrutiny applied to other genic or regulatory features.⁹

Opponents of ENCODE further assert that "there is currently no evidence that the majority of highly repetitive elements are functional."¹⁰ But the vast majority of our genome--including repetitive DNA--is transcribed into RNA in nonrandom, cell-type-specific ways. That is evidence of some important function.

Individual RNA molecules then form networks in a cell, interacting with DNA, proteins, and other RNAs to control which genes are turned on and off, and which genes are expressed as proteins, thereby playing a crucial role in determining the cell's type. As Stamatoyannopoulos puts it, this complex system exudes function:

More of the human genome sequence appears to be used for some reproducible, biochemically defined activity than was previously imagined. Contrary to the initial expectations of many, the overwhelming majority of these activities appear to be state-specific--either restricted to specific cell types or lineages, or evokable in response to a stimulus. . . . [B]iochemical signatures of many ENCODE-defined elements exhibit complex trans-cellular patterns of activity. . . . Together, these observations suggest that the genome may, in fact, be extensively multiply encoded--i.e., that the same DNA element gives rise to different activities in different cell types.¹¹

These consistent and predictable cell-type-specific patterns of RNA expression show that mass genomic transcription of DNA into RNA is not random, but has important functional purposes.

No Accident

Finally, transcription doesn't just happen by accident. It can't start without special stretches of DNA, called promoter sequences, which bind to special enzymes called transcription factors (TFs). And just any enzyme won't do--TFs must be able to recognize the specific DNA promoter sequence that they're keyed to unlock for transcription. Without that precise biochemical correspondence, transcription can't occur.

Once the right TFs bind to a promoter sequence, a molecular machine called RNA polymerase can then find the right place on the DNA to start converting the genomic message into a strand of RNA. The fact that the vast majority of the genome is transcribed suggests that these specified molecules--DNA promoter sequences and TFs--exist and are carefully matched throughout the genome.

If all that RNA is junk, why do these innumerable specified molecules exist throughout our cells?

Faulty Default Assumptions

For ENCODE-critics, however, none of this is enough. Their evolutionary mindset is wedded to the notion that organisms are poorly cobbled, junk-filled kluges. "If you don't know a function," Dan Graur argues, "assume as a null hypothesis that it doesn't have function."¹² His default assumption was dubious to begin with, but ENCODE provides empirical evidence that it is false. As a Nature summary puts it:

Results from the ENCODE project show that most of these [non-coding] stretches of DNA harbour regions that bind proteins and RNA molecules, bringing these into positions from which they cooperate with each other to regulate the function and level of expression of protein-coding genes.¹³

Despite their bluster, critics have been unable to disprove what a leading ENCODE researcher stated in 2014: "There is not a single place in the genome that doesn't have something that you might think could be controlling something else."¹⁴ If we're willing to follow ENCODE's experimental evidence where it leads, unhindered by evolutionary assumptions, evidence of important genomic function is everywhere.

References:

[1.] Yudhijit Bhattacharjee, "The Vigilante," Science, 343:1306-1309 (March 21, 2014).

[2.] "ENCODE debate revived online," Nature, 509:137 (May 8, 2014).

[3.] Philip Ball, "Celebrate the Unknowns," Nature, 496:419-420 (April 25, 2013). See also Alexander Palazzo and T. Ryan Gregory, "The Case for Junk DNA," PLOS Genetics, 10(5):e1004351 (May 2014); W. Ford Doolittle, "Is junk DNA bunk? A critique of ENCODE," Proceedings of the National Academy of Sciences, 110(14):5294-5300 (April 2, 2013); Graur et al., "On the Immortality of Television Sets: 'Function' in the human genome according to the evolution-free gospel of ENCODE," Genome Biology and Evolution, 5(3):578-590 (2013); and Deng-Ke Niu and Li Jiang, "Can ENCODE tell us how much junk DNA we carry in our genome?" Biochemical and Biophysical Research Communications, 430:1340-1343 (2013).

[4.] Graur et al., "On the Immortality of Television Sets."

[5.] John Stamatoyannopoulos, "What does our genome encode?" Genome Research, 22:1602-1611 (2012).

[6.] Pelechano et al., "Extensive transcriptional heterogeneity revealed by isoform profiling," Nature, 497:127-131 (May 2, 2013).

[7.] Stamatoyannopoulos, "What does our genome encode?"

[8.] John Mattick and Marcel Dinger, "The extent of functionality in the human genome," The HUGO Journal, 7:2 (2013).

[9.] Stamatoyannopoulos, "What does our genome encode?"

[10.] Palazzo and Gregory, "The Case for Junk DNA."

[11.] Stamatoyannopoulos, "What does our genome encode?"

[12.] Bhattacharjee, "The Vigilante."

[13.] Ines Barroso, "Non-coding but functional," Nature, 489:54 (Sept. 6, 2012).

[14.] Bhattacharjee, "The Vigilante."

A line in the sand XVII

Denver court rules against Little Sisters of the Poor contraception coverage case.

A federal appeals court in Denver ruled on Tuesday against a group of Colorado nuns who challenged a provision in the Affordable Care Act that requires employers to provide insurance policies covering contraception.  

Though religious groups are already exempt from covering contraceptives, the plaintiffs – the Little Sisters of the Poor as well as four Christian colleges in Oklahoma – argued the exemption doesn’t go far enough because they must sign away the coverage to another party, making them feel as though they had a hand in providing contraceptives.he 10th Circuit Court of Appeals disagreed.

The court ruled that because the Little Sisters of the Poor had the option of signing a form that would transfer covering contraceptives to a third-party, they failed to show that the ObamaCare mandate placed a burden on their right to exercise freedom of religion.

Following the ruling, Sister Loraine Marie Maguire said “we simply cannot choose between our care for the elderly poor and our faith.”

Maguire added that forcing the Little Sister of the Poor to make that choice “violates our nation’s commitment to ensuring that people from diverse faiths can freely follow God’s calling in their lives.”

Mark Rienzi, senior counsel for the Becket Fund for Religious Liberty and the lead attorney for the nuns, said there have been “untold millions of people” who have gotten contraceptives without involving nuns and that there was “no reason the government cannot run its programs without hijacking the Little Sisters and their health plan.”

"Although we recognize and respect the sincerity of plaintiffs' beliefs and arguments, we conclude the accommodation scheme ... does not substantially burden their religious exercise," the three-judge panel wrote.

The same court ruled last year that for-profit companies can join the exempted religious organizations and not provide the contraceptives. The U.S. Supreme Court later agreed with the 10th Circuit in the case brought by the Hobby Lobby arts-and-crafts chain.

The birth-control rule has been among the most divisive aspects of the health care overhaul. Some advocates for women praise the mandate, but some religious groups have decried it as an attack on religious freedom.

The Denver nuns run more than two dozen nursing homes for impoverished seniors.

Two years ago the U.S. Supreme Court offered the nuns a short-term reprieve on the exemption pending their appeal.

In addition to the Denver nuns, the law was challenged by Southern Nazarene University, Oklahoma Baptist University, Mid-America University and Oklahoma Wesleyan University. Also challenging the waiver process is a group called Reaching Souls International, an evangelist Oklahoma organization that does Christian mission work overseas.

The birth-control exemption was extended to other religious nonprofits while the case was being heard. Those included Wyoming Catholic College in Casper, Wyoming.

The three-judge panel included one judge who also ruled in the Hobby Lobby decision. The judges drew a distinction between the two cases, noting that the religious nonprofits have an exemption process that wasn't available to Hobby Lobby.

While Hobby Lobby faced the prospect of fines for not providing coverage, the judges noted, the nonprofits must only file for an exemption, making the burden less substantial.

The judges called the health law's accommodation for religious objectors adequate.

"The accommodation relieves plaintiffs from complying with the mandate and guarantees they will not have to provide, pay for, or facilitate contraceptive coverage," the judges wrote.

The group that brought the lawsuit on behalf of the nuns and religious schools, the Becket Fund for Religious Liberty, said in a statement that it would appeal the decision to the U.S. Supreme Court.

"There is no reason the government cannot run its programs without hijacking the Little Sisters and their health plan," Becket Fund lawyer Mark Rienzi said in a statement.

The Associated Press contributed to this report. 

Darwinism vs the real world III

Understanding Cardiovascular Function: How the Body Controls the Heart

Howard Glicksman July 14, 2015 3:23 AM

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News & Views is delighted to present this series, "The Designed Body." Dr. Glicksman practices palliative medicine for a hospice organization.

Blood circulating throughout the body supplies the cells with what they need to live. But blood is made up of matter and therefore is subject to the laws of nature. These laws state that since blood has mass, energy must be used to move it against the forces of inertia, friction, and gravity.

The last article in this series showed that the heart is a muscular pump that provides the power needed to circulate the blood. It has a right and left side, each with an upper chamber called an atrium, and a lower chamber, called a ventricle. Between the atrium and the ventricle, and the ventricle and its outflow tract are "V"-shaped one-way valves. These ensure that the blood flows in the right direction.

The right side pumps blood through the main pulmonary artery to the lungs, while the left side pumps through the aorta to the rest of the body. The heart also has a natural pacemaker, the sino-atrial node, which automatically stimulates it to contract and controls how often it beats. The electrical signal conducted from the sino-atrial node triggers Na⁺ ions to flood into the heart muscle cells, and Ca⁺⁺ ions as well. Together they cause depolarization and heart muscle contraction, the strength of which is dependent on the degree of Ca⁺⁺ ion entry.

But being able to survive in the world is a dynamic process. Experience teaches that when we work and play hard our heart has to pump faster and harder to give us the energy we need. This functional ability of the heart would have been the difference between our earliest ancestors eating, or being eaten.

Evolutionary biologists seem to assume that life takes place in a vacuum and that just because different organisms have similar structures, those structures must have come into existence through the interaction of chance and the laws of nature alone. In contrast, our experience of human invention shows that when we encounter a mechanism that takes control in overcoming the laws of nature to remain functional, it is more plausible to infer the work of an intelligent designer.

A car moving up a hill must have a mechanism in place, like a driver or cruise control, to provide enough gas to its engine so it can overcome the forces of inertia, friction, and gravity to go over the top and continue on its way. So too, the body must be able to take control of its heart function. Let's see how it does that.

When the body is at complete rest, it is like a car that is idling. The car needs a minimum amount of energy just to keep the pistons in the engine moving while the oil lubricates the moving parts and the anti-freeze circulates to keep everything cool. The same can be said of the body. Even though its muscles are relaxed and its gastrointestinal system is at rest, it still needs a minimum amount of energy to maintain adequate brain, heart, lung, kidney, and liver function.

When the driver wants to speed up, she steps on the accelerator, which immediately directs more gas and air into the engine, releasing more energy, and the car moves faster right away. So too, when you decide to be more active, your heart speeds up and beats harder to provide your muscles with the energy they need. Without this ability to respond immediately to the body's energy needs, the survival of our earliest ancestors would have been impossible.

Gland cells and hormones take several minutes to take effective action, but nerve cells can send signals at about one-third the speed of sound and release neurohormones that take action immediately. The Autonomic Nervous System(ANS), centrally located mainly in the hypothalamus, is the mechanism by which heart function is controlled to match the energy needs of the body. These unconscious actions are involuntary and take place automatically.

At rest, the heart is dominated by the parasympathetic division of the ANS -- the rest and digest component. The parasympathetic nerves send out a neurohormone called acetylcholine which attaches to specific cholinergicreceptors in the heart. One of the effects of acetylcholine is to slow down the entry of Na⁺ and Ca⁺⁺ ions into the pacemaker and heart muscle cells. This helps to reduce the heart rate and the force of muscle contraction. When the body becomes more active and/or more anxious and excited, it is thesympathetic division of the ANS -- the flight or fight component -- that takes over to make sure the blood supply to the tissues is adequate. Here's how it works.

As you may recall my saying in previous articles, the first thing you need to take control in such a situation is a sensor that can detect what needs to be controlled. An increase in physical activity is caused by an increase in skeletal muscle contraction. And an increase in skeletal muscle contraction causes a local build-up of certain chemical by-products from the increase in metabolic activity. The body has sensors in the skeletal muscle that can detect its rate of contraction and these chemicals as well.

The second thing you need to take control is something to integrate the data by comparing it with a standard, decide what must be done, and then send out orders. The hypothalamus takes the data from these sensors and from other areas of the brain, and modulates the release of a neurohormone callednorepinephrine from the sympathetic nerves and epinephrine from the sympathetic stimulated adrenal glands.

The third thing you need to take control is an effector that can do something about the situation. Norepinephrine and epinephrine attach to specificadrenergic receptors in the heart, which increases the entry of Na⁺ and Ca⁺⁺ions into the cells of the sino-atrial node, the conducting system and heart muscle cells. This causes the heart rate and the force of muscle contraction to increase. In addition, these neurohormones attach to specific adrenergic receptors in the blood vessels to increase the blood flowing back to the right side of the heart from the veins. The combination of these effects brings about a significant increase in the amount of blood the heart pumps to the tissues.

Now that you understand how the body takes control of its heart function, it is important to consider how all of this works in real life. For, when it comes to the laws of nature, real numbers have real consequences. Just as a car's performance depends on its engine size and efficiency, so too, medical science knows that to stay alive the body's heart function must meet certain objective parameters.

Evolutionary biologists imagine how irreducibly complex organs and their control mechanisms might have come into being. But in real life, when dealing with the laws of nature, if the numbers don't add up just right, the body is as good as dead. Next time we'll look at how this applies to heart function and survival.

When it comes to DNA Darwinists prefer Junk

Trash Be Gone: Why Are Biologists Lashing Out Against Empirically Verified Research Results?

Casey Luskin July 13, 2015 3:03 AM 

Editor's note: This is Part 1 of a 4-part series on ENCODE that Casey Luskin has been publishing this year in Salvo Magazine. Parts 1, 2, and 3 have already been published there. Part 4 will be published later this year.

Is the vast majority of the human genome useless junk or crucial for cellular function? Scientists are split over this question, with evolutionary biologists principally holding the former viewpoint, and molecular biologists the latter.

In our era of advanced biological research, one would think this an easily resolvable question, but when a powerful evolutionary paradigm is threatened by the findings of molecular biology, don't expect the establishment to quickly concede defeat. Indeed, the entire debate over neo-Darwinian evolution and intelligent design (ID) may turn on the outcome of this question.

Flotsam and Jetsam No More

For those who follow the debate over origins, the demise of junk DNA is old news. My very first Operation ID column, in the Fall 2008 issue of Salvo, recounted how Francis Collins argued in The Language of God that our genome is full of "genetic flotsam and jetsam" (i.e., trash), making it "virtually inescapable"¹ that we share common ancestry with mice. But as I explained then, numerous functions had been discovered for noncoding DNA, and more have been found since, forcing a revolution in biological thinking. In a sign of the times, a 2010 Nature article heralded this new era of genomics, noting that "biology's new glimpse at a universe of non-coding DNA--what used to be called 'junk' DNA--has been fascinating and befuddling."² Many other scientific papers reporting functions for "junk" DNA have made similar remarks.

But no publication shook this debate so much as a 2012 Nature paper that finally put junk DNA to rest--or so it seemed. This bombshell paper presented the results of the ENCODE (Encyclopedia of DNA Elements) Project, a years-long research consortium involving over 400 international scientists studying noncoding DNA in the human genome. Along with 30 other groundbreaking papers, the lead ENCODE article found that the "vast majority" of the human genome shows biochemical function: "These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions."³

Ewan Birney, ENCODE's lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, "it's likely that 80 percent will go to 100 percent."⁴ Another senior ENCODE researcher noted that "almost every nucleotide is associated with a function."⁵ A headline in Science declared, "ENCODE project writes eulogy for junk DNA."⁶

Bad News for Darwinism

This report was a game-changer in the debate over Darwinian evolution and intelligent design because, since the mid-1990s, ID theorists had been predicting that noncoding DNA would turn out to have function, and ID critics had been arguing that junk DNA drove a stake through the heart of ID.

For example, back in 1994, pro-ID scientist Forrest Mims submitted a letter toScience warning against assuming that "junk" DNA was "useless."⁷ Sciencewouldn't print the letter, but that same year, anti-ID biologist Kenneth Miller published an article in a different journal making the opposite conclusion, namely that "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."⁸

Contrast Miller's assertion with a conclusion of Discover Magazine 18 years later in light of ENCODE's 2012 breakthrough report: "The key point is: It's not 'junk.'"⁹

Evolutionists Strike Back

Darwin defenders weren't going to take ENCODE's data sitting down. But this time, they found themselves in an unaccustomed position. Many Darwinians take great assurance in knowing they stand in the scientific majority, which enables them to appeal to the consensus and dismiss challengers as "deniers." But in the post-ENCODE world, Darwin defenders have found themselveschallenging the consensus of an international body of leading molecular biologists who have discovered that the vast majority of human DNA has biochemical function.

How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm--and by personally attacking those who challenge their position.

For instance, multiple initial rebuttals from evolution defenders called ENCODE "hype"¹⁰ and castigated researchers and science journalists for acting "irresponsibly" in favorably reporting on its findings.¹¹ In a post titled "The ENCODE Delusion," PZ Myers dismissed ENCODE's central claim that 80 percent of the genome has biochemical functions as "bull****," maintaining that evidence of biochemical activity in DNA and RNA "isn't function. That isn't even close." He called the ENCODE researchers themselves "fundamentally dishonest," and scoffed at Evan Birney, saying, "I don't think Birney has a clue about the -biology."¹²

Another Darwin-defending biologist, Nick Matzke, allowed that the ENCODE researchers weren't stupid, just ignorant: "I'm beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative [i.e., evolutionary] biology."¹³ But University of Toronto biochemist and pro-evolution blogger Laurence Moran wouldn't even grant that the ENCODE researchers were intelligent: "I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists,"¹⁴ he ranted.

Moran further lamented that "the creationists are going to love this," and he feared that ENCODE's results were "going to make my life very complicated,"¹⁵since "it's going to take a lot of effort to undo the damage caused by [ENCODE]."¹⁶

The vast majority of those defending ENCODE, however, are not pro-ID and have no motive to aid and abet "the creationists." They're driven by the empirical data. For example, University of Chicago geneticist James Shapiro praised ENCODE's results while simultaneously disavowing ID. He found that "the old idea of the genome as a string of genes interspersed with unimportant noncoding DNA is no longer tenable," since "ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information."¹⁷

Shapiro wrote papers in the mid-2000s predicting function for "junk" DNA, and he explained that his co-author was an ID proponent who held views he didn't share:

In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function."

These articles with Rick are important . . . for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.

The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e., repeated) signals that make it possible to access the stored information when and where it will be useful.¹⁸

Clearly, some ID critics are embracing ENCODE's results. But most remain steadfastly resistant, most likely because ENCODE threatens to overturn some of the most prominent scientific arguments for an unguided evolutionary origin of the human genome.

What If ENCODE Is Right?

Earlier in 2014, Science reported on the arguments made by another leading evolutionary critic of ENCODE, University of Houston biologist Dan Graur. According to Science, "Graur's atheism inflamed his anger at ENCODE."¹⁹ It's not surprising that Graur would become emotional over ENCODE given his blunt framing of the issue in a talk he gave in 2013:

If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary processcannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then Evolution is wrong.²⁰

Graur's framing of the issue just might be correct. But to appreciate why ENCODE's critics are wrong, wait for the next installment in this series.

References:

[1.] Francis Collins, The Language of God: A Scientist Presents Evidence for Belief (Free Press, 2006), 136-137.

[2.] Erika Check Hayden, "Life Is Complicated," Nature, 464:664-667 (April 1, 2010) (emphasis added).

[3.] The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, 489:57-74 (Sept. 6, 2012).

[4.] Ewan Birney, quoted in Ed Yong, "ENCODE: the rough guide to the human genome," Discover Magazine (Sept. 5, 2012): http://tinyurl.com/knr9co7.

[5.] Tom Gingeras, quoted in Yong, ibid.

[6.] Elizabeth Pennisi, "ENCODE Project Writes Eulogy for Junk DNA," Science, 337:1159-1161 (Sept. 7, 2012).

[7.] Forrest Mims, "Rejected Letter to the Editor to Science" (Dec. 1, 1994):forrestmims.org/publications.html.

[8.] Kenneth Miller, "Life's Grand Design," Technology Review, 97(2):24-32 (February/March 1994).

[9.] Yong, note 4.

[10.] Nick Matzke, "ENCODE hype? From now on I'll just reply: #oniontest," Panda's Thumb (Sept. 5, 2012): http://tinyurl.com/nmxeu4t; Laurence Moran, "The ENCODE Data Dump and the Responsibility of Science Journalists," Sandwalk (Sept. 6, 2012): http://tinyurl.com/k7eup3n.

[11.] Moran, ibid.

[12.] PZ Myers, "The ENCODE delusion," Panda's Thumb (Sept. 23, 2012):http://tinyurl.com/moefwye.

[13.] Matzke, note 10.

[14.] Laurence Moran, "Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012," Sandwalk (Jan. 4, 2013):http://tinyurl.com/p8dc6yp.

[15.] Laurence Moran, "ENCODE Leader Says that 80% of Our Genome Is Functional," Sandwalk (Sept. 5, 2012): http://tinyurl.com/m96r5un.

[16.] Moran, note 10.

[17.] James Shapiro, "Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin'," Huffington Post (Sept. 12, 2012):http://tinyurl.com/pmxowlu.

[18.] Ibid.

[19.] Yudhit Bhattercharjee, "The Vigilante," Science, 343:1306-1309 (March 21, 2014).

[20.] Dan Graur, "How to Assemble a Human Genome?" (December 2013):http://tinyurl.com/mpmxkyw (emphases in original).