Thursday, September 13, 2012

  • The Wall Street Journal

The Grievance Brigades

The most traditional branches of Western learning have been replaced by disciplines designed to serve radical political ends.

In 1994, Clarabel Ventura was arrested for scalding her 4-year-old son's hand. "The boy—who police say was forced to put his hands in a pot of boiling liquid several weeks ago—was left in a locked room on a mattress soaked with his own blood, urine and feces," the Boston Globe reported. Ventura had spent her life on welfare and in public housing, and the graphic details of the case fed into the larger welfare-reform debate raging at the time. While reasonable Americans could disagree about what the incident said about our welfare system, both sides in the debate condemned Ventura's abuse of her children.
This brute of a mother appeared in a different light when I read about her in "Legal Skills in Social Context," a first-year diversity course required at my law school. The curriculum treated the story as an instance of the press misrepresenting the urban poor. An article by one of my professors called for "a clear reinterpretation of these lives which does not exclude Ventura and takes into account the institutionalized violence created by a racist, patriarchal and misogynist system." Reporters should "contextualize the experiences of 'unsuccessful mothers,'" the professor suggested. Instead they were "reinforcing the 'other' " and "perpetuating the concept of individual moral fault."
Welcome to the upside-down world of the academy. As Bruce Bawer shows in "The Victims' Revolution," such experiences are the norm in American higher education today. The corrosive relativism that Allan Bloom worried about 25 years ago in "The Closing of the American Mind" has now consolidated its grip on campus.

The Victims' Revolution

By Bruce Bawer
(Broadside, 378 pages, $25.99)
What all these "studies" have in common, Mr. Bawer argues, is a "tendency to reduce the rich drama of the human story to a series of dreary, repetitious lessons about groups, power, and oppression," with "little or no intrinsic connection" to the arts or the wider cultural experience that the study of humanities has traditionally illuminated. All of them assume "that our thoughts about human behavior, our statements about the nature of man, and in fact all ideas of whatever kind are nothing more or less than assertions of power."
Mr. Bawer introduces readers to each of these disciplines, carefully tracing their intellectual origins and interviewing leading scholars. In some of the book's most hilarious passages, the author tours identity-studies conferences, where young professors and graduate students present cutting-edge "research." "Environmental racism is the disrespect of our Mother Earth" was the theme of one presentation at a Chicano Studies conference. "When you [non-Chicanos] started your Industrial Revolution, you started poisoning our Mother Earth, our air and our water. We took care of them for centuries." (The presentation, Mr. Bawer points out, was aided by PowerPoint.)
This fact alarmed critics at the time, such as the legendary civil-rights activist Bayard Rustin. "Is Black Studies an educational program or a forum for ideological indoctrination?" he asked in a 1969 essay questioning the value of Black Studies. "Is it a means to achieve psychological identity and strength, or is it intended to provide a false and sheltered sense of security, the fragility of which would be revealed by even the slightest exposure to reality?"
The skepticism of men like Rustin did little to halt the march of the identity-studies enterprise on campus, where today it serves two major functions. The first is palliative. Rather than confront students with genuine moral and intellectual challenges, identity studies provide them with validation and therapy. For students (and professors) who choose these fields, Mr. Bawer writes, it's all about "personal pain, personal confession, personal grievance." Much of contemporary Women Studies, for example, is devoted to denouncing objective knowledge and rationality as so much "masculinist" oppression. One Women's Studies textbook quoted by Mr. Bawer warns scholars and students away from men's "separate knowing," with its pesky insistence on "mastery of relevant knowledge and methodology."
The second, related function of identity studies is to provide careers for a bulging professoriate. The labyrinthine, illiterate prose so popular among the professors, Mr. Bawer says, masks the fact that most of them don't have very much to say beyond regurgitating catechisms about race, gender and class. The author provides numerous examples of such writing. My own personal favorite is from an article by Ian Barnard, a Queer Theory scholar at California State University, Northridge: "The queer in queer race is thus doubly queer both insofar as it queers queer and destabilizes the (dis)connection between queer and race."
Readers might be tempted to dismiss the danger posed by "scholarship" that yields such nonsense. But identity-studies concepts have filtered down from the ivory tower into our civic and political life. They rear their ugly heads, for example, when students of American law are taught that individual moral fault is a myth to transcend. Such ideas are, as the author writes, "a betrayal, in the profoundest sense, of the promise of America."
Mr. Ahmari is an assistant books editor at the Journal.

A Philosopher Defends Religion

SEPTEMBER 27, 2012

Thomas Nagel

Where the Conflict Really Lies: Science, Religion, and Naturalism

by Alvin Plantinga

Oxford University Press, 359 pp., $27.95                                                 

Sijmen Hendriks

Alvin Plantinga, Utrecht, the Netherlands, 1995


The gulf in outlook between atheists and adherents of the monotheistic religions is profound. We

are fortunate to live under a constitutional system and a code of manners that by and large keep it

from disturbing the social peace; usually the parties ignore each other. But sometimes the conflict

surfaces and heats up into a public debate. The present is such a time.

One of the things atheists tend to believe is that modern science is on their side, whereas theism is in

conflict with science: that, for example, belief in miracles is inconsistent with the scientific

conception of natural law; faith as a basis of belief is inconsistent with the scientific conception of

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1 van 6 8-9-2012 17:38knowledge; belief that God created man in his own image is inconsistent with scientific explanations

provided by the theory of evolution. In his absorbing new book, Where the Conflict Really Lies,

Alvin Plantinga, a distinguished analytic philosopher known for his contributions to metaphysics

and theory of knowledge as well as to the philosophy of religion, turns this alleged opposition on its

head. His overall claim is that “there is superficial conflict but deep concord between science and

theistic religion, but superficial concord and deep conflict between science and naturalism.” By

naturalism he means the view that the world describable by the natural sciences is all that exists, and

that there is no such person as God, or anything like God.

Plantinga’s religion is the real thing, not just an intellectual deism that gives God nothing to do in

the world. He himself is an evangelical Protestant, but he conducts his argument with respect to a

version of Christianity that is the “rough intersection of the great Christian creeds”—ranging from

the Apostle’s Creed to the Anglican Thirty-Nine Articles—according to which God is a person who

not only created and maintains the universe and its laws, but also intervenes specially in the world,

with the miracles related in the Bible and in other ways. It is of great interest to be presented with a

lucid and sophisticated account of how someone who holds these beliefs understands them to

harmonize with and indeed to provide crucial support for the methods and results of the natural


Plantinga discusses many topics in the course of the book, but his most important claims are

epistemological. He holds, first, that the theistic conception of the relation between God, the natural

world, and ourselves makes it reasonable for us to regard our perceptual and rational faculties as

reliable. It is therefore reasonable to believe that the scientific theories they allow us to create do

describe reality. He holds, second, that the naturalistic conception of the world, and of ourselves as

products of unguided Darwinian evolution, makes it unreasonable for us to believe that our

cognitive faculties are reliable, and therefore unreasonable to believe any theories they may lead us

to form, including the theory of evolution. In other words, belief in naturalism combined with belief

in evolution is self-defeating. However, Plantinga thinks we can reasonably believe that we are the

products of evolution provided that we also believe, contrary to naturalism, that the process was in

some way guided by God.


I shall return to the claim about naturalism below, but let me first say more about the theistic

conception. Plantinga contends, as others have, that it is no accident that the scientific revolution

occurred in Christian Europe and nowhere else. Its great figures, such as Copernicus and Newton,

believed that God had created a law-governed natural order and created humans in his image, with

faculties that allowed them to discover that order by using perception and reason. That use of

perception and reason is what defines the empirical sciences. But what about the theistic belief

itself? It is obviously not a scientific result. How can it be congruent with a scientific understanding

of nature?

Here we must turn to Plantinga’s general theory of knowledge, which is crucial to understanding his

position. Any theory of human knowledge must give an account of what he calls “warrant,” i.e., the

conditions that a true belief must meet in order to constitute knowledge. Sometimes we know

something to be true on the basis of evidence provided by other beliefs, or because we see that it is

entailed by our other beliefs. But not every belief can depend on other beliefs. The buck has to stop

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2 van 6 8-9-2012 17:38somewhere, and according to Plantinga this happens when we form beliefs in one of the ways that

he calls “basic.”

The basic belief-forming capacities include perception, memory, rational intuition (about logic and

arithmetic), induction, and some more specialized faculties, such as the ability to detect the mental

states of others. When you look in the refrigerator and see that it contains several bottles of beer,

you form that belief immediately without inferring it from any other belief, e.g., a belief about the

pattern of shapes and colors in your visual field. When someone asks you whether you have had

lunch yet, you can answer immediately because you remember having had lunch, and the memory

is a belief not based on any other belief, or on perception, or on logical reasoning.

Beliefs that are formed in the basic way are not infallible: they may have to be given up in the face

of contrary evidence. But they do not have to be supported by other evidence in order to be

warranted—otherwise knowledge could never get started. And the general reliability of each of

these unmediated types of belief-formation cannot be shown by appealing to any of the others:

Rational intuition enables us to know the truths of mathematics and logic, but it can’t tell us

whether or not perception is reliable. Nor can we show by rational intuition and perception

that memory is reliable, nor (of course) by perception and memory that rational intuition is.

But what then is the warrant for beliefs formed in one of these basic ways? Plantinga holds that the

main condition is that they must result from the proper functioning of a faculty that is in fact

generally reliable. We cannot prove without circularity that the faculties of perception, memory, or

reason are generally reliable, but if they are, then the true beliefs we form when they are functioning

properly constitute knowledge unless they are put in doubt by counterevidence.



knowledge is therefore dependent on facts about our relation to the world that we cannot prove

from scratch: we can’t prove the existence of the physical world, or the reality of the past, or the

existence of logical and mathematical truth; but if our faculties do in fact connect with these aspects

of reality, then we can know about them, according to Plantinga’s theory.

For example, if our perceptual beliefs are in general caused by the impact on our senses of objects

and events in the environment corresponding to what is believed, and if memories are in general

caused by traces in the brain laid down by events in the past corresponding to what those memories

represent, then perception and memory are reliable faculties, which can give us knowledge even

though we cannot prove they are reliable.

So far we are in the territory of traditional epistemology; but what about faith? Faith, according to

Plantinga, is another basic way of forming beliefs, distinct from but not in competition with reason,

perception, memory, and the others. However, it is

a wholly different kettle of fish: according to the Christian tradition (including both Thomas

Aquinas and John Calvin), faith is a special gift from God, not part of our ordinary epistemic

equipment. Faith is a source of belief, a source that goes beyond the faculties included in


God endows human beings with a sensus divinitatis that ordinarily leads them to believe in him.

(In atheists the sensus divinitatis is either blocked or not functioning properly.)


 In addition, God

acts in the world more selectively by “enabling Christians to see the truth of the central teachings of

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3 van 6 8-9-2012 17:38the Gospel.”

If all this is true, then by Plantinga’s standard of reliability and proper function, faith is a kind of

cause that provides a warrant for theistic belief, even though it is a gift, and not a universal human

faculty. (Plantinga recognizes that rational arguments have also been offered for the existence of

God, but he thinks it is not necessary to rely on these, any more than it is necessary to rely on

rational proofs of the existence of the external world to know just by looking that there is beer in the


It is illuminating to have the starkness of the opposition between Plantinga’s theism and the secular

outlook so clearly explained. My instinctively atheistic perspective implies that if I ever found

myself flooded with the conviction that what the Nicene Creed says is true, the most likely

explanation would be that I was losing my mind, not that I was being granted the gift of faith. From

Plantinga’s point of view, by contrast, I suffer from a kind of spiritual blindness from which I am

unwilling to be cured. This is a huge epistemological gulf, and it cannot be overcome by the

cooperative employment of the cognitive faculties that we share, as is the hope with scientific


Faith adds beliefs to the theist’s base of available evidence that are absent from the atheist’s, and

unavailable to him without God’s special action. These differences make different beliefs reasonable

given the same shared evidence. An atheist familiar with biology and medicine has no reason to

believe the biblical story of the resurrection. But a Christian who believes it by faith should not,

according to Plantinga, be dissuaded by general biological evidence. Plantinga compares the

difference in justified beliefs to a case where you are accused of a crime on the basis of very

convincing evidence, but you know that you didn’t do it. For you, the immediate evidence of your

memory is not defeated by the public evidence against you, even though your memory is not

available to others. Likewise, the Christian’s faith in the truth of the gospels, though unavailable to

the atheist, is not defeated by the secular evidence against the possibility of resurrection.

Of course sometimes contrary evidence may be strong enough to persuade you that your memory

is deceiving you. Something analogous can occasionally happen with beliefs based on faith, but it

will typically take the form, according to Plantinga, of a change in interpretation of what the Bible

means. This tradition of interpreting scripture in light of scientific knowledge goes back to

Augustine, who applied it to the “days” of creation. But Plantinga even suggests in a footnote that

those whose faith includes, as his does not, the conviction that the biblical chronology of creation is

to be taken literally can for that reason regard the evidence to the contrary as systematically

misleading. One would think that this is a consequence of his epistemological views that he would

hope to avoid.


We all have to recognize that we have not created our own minds, and must rely on the way they

work. Theists and naturalists differ radically over what justifies such reliance. Plantinga is certainly

right that if one believes it, the theistic conception explains beautifully why science is possible: the

fit between the natural order and our minds is produced intentionally by God. He is also right to

maintain that naturalism has a much harder time accounting for that fit. Once the question is raised,

atheists have to consider whether their view of how we got here makes it at all probable that our

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4 van 6 8-9-2012 17:38cognitive faculties should enable us to discover the laws of nature.

Plantinga argues that on the naturalist view of evolution, interpreted materialistically, there would be

no reason to think that our beliefs have any relation to the truth. On that view beliefs are states of

the brain, and natural selection favors brain mechanisms solely on the basis of their contribution, via

behavior, to survival and reproduction. The content of our beliefs, and hence their truth or

falsehood, is irrelevant to their survival value. “Natural selection is interested, not in truth, but in

appropriate behavior.”

Plantinga’s version of this argument suffers from lack of attention to naturalist theories of mental

content—i.e., theories about what makes a particular brain state the belief that it is, in virtue of

which it can be true or false. Most naturalists would hold that there is an intimate connection

between the content of a belief and its role in controlling an organism’s behavioral interaction with

the world. To oversimplify: they might hold, for example, that a state of someone’s brain constitutes

the belief that there is a dangerous animal in front of him if it is a state generally caused by

encounters with bears, rattlesnakes, etc., and that generally causes flight or other defensive behavior.

This is the basis for the widespread conviction that evolutionary naturalism makes it probable that

our perceptual beliefs, and those formed by basic deductive and inductive inference, are in general


Still, when our faculties lead us to beliefs vastly removed from those our distant ancestors needed to

survive—as in the recent production and assessment of evidence for the existence of the Higgs

boson—Plantinga’s skeptical argument remains powerful. Christians, says Plantinga, can “take

modern science to be a magnificent display of the image of God in us human beings.” Can

naturalists say anything to match this, or must they regard it as an unexplained mystery?

Most of Plantinga’s book is taken up with systematic discussion, deploying his epistemology, of

more specific claims about how science conflicts with, or supports, religion. He addresses Richard

Dawkins’s claim that evolution reveals a world without design; Michael Behe’s claim that on the

contrary it reveals the working of intelligent design; the claim that the laws of physics are

incompatible with miracles; the claim of evolutionary and social psychologists that the functional

explanation of moral and religious beliefs shows that there are no objective moral or religious truths;

the idea that historical biblical criticism makes it unreasonable to regard the Bible as the word of

God; and the idea that the fine-tuning of the basic physical constants, whose precise values make

life possible, is evidence of a creator. He touches on the problem of evil, and though he offers

possible responses, he also remarks, “Suppose God does have a good reason for permitting sin and

evil, pain and suffering: why think we would be the first to know what it is?”

About evolution, Plantinga argues persuasively that the most that can be shown (by Dawkins, for

example) on the basis of the available evidence together with some highly speculative further

assumptions is that we cannot rule out the possibility that the living world was produced by

unguided evolution and hence without design. He believes the alternative hypothesis of guided

evolution, with God causing appropriate mutations and fostering their survival, would make the

actual result much more probable. On the other hand, though he believes Michael Behe offers a

serious challenge to the prevailing naturalist picture of evolution, he does not think Behe’s

arguments for intelligent design are conclusive, and he notes that in any case they don’t support

Christian belief, and perhaps not even theism, because Behe intentionally says so little about the

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Plantinga holds that miracles are not incompatible with the laws of physics, because those laws

determine only what happens in closed systems, without external intervention, and the proposition

that the physical universe is a closed system is not itself a law of physics, but a naturalist

assumption. Newton did not believe it: he even believed that God intervened to keep the planets in

their orbits. Plantinga has a lengthy discussion of the relation of miracles to quantum theory: its

probabilistic character, he believes, may allow not only miracles but human free will. And he

considers the different interpretations that have been given to the fine-tuning of the physical

constants, concluding that the support it offers for theism is modest, because of the difficulty of

assigning probabilities to the alternatives. All these discussions make a serious effort to engage with

the data of current science. The arguments are often ingenious and, given Plantinga’s premises, the

overall view is thorough and consistent.

The interest of this book, especially for secular readers, is its presentation from the inside of the

point of view of a philosophically subtle and scientifically informed theist—an outlook with which

many of them will not be familiar. Plantinga writes clearly and accessibly, and sometimes acidly—in

response to aggressive critics of religion like Dawkins and Daniel Dennett. His comprehensive stand

is a valuable contribution to this debate.

I say this as someone who cannot imagine believing what he believes. But even those who cannot

accept the theist alternative should admit that Plantinga’s criticisms of naturalism are directed at the

deepest problem with that view—how it can account for the appearance, through the operation of

the laws of physics and chemistry, of conscious beings like ourselves, capable of discovering those

laws and understanding the universe that they govern. Defenders of naturalism have not ignored

this problem, but I believe that so far, even with the aid of evolutionary theory, they have not

proposed a credible solution. Perhaps theism and materialist naturalism are not the only alternatives.


The details are complicated, and are set out in Plantinga’s three-volume magnum opus, Warrant:

The Current Debate and Warrant and Proper Function (both Oxford University Press, 1993) and

Warranted Christian Belief (Oxford University Press, 2000).  



This is often the result of sin, though not necessarily the sin of the unbeliever; see Plantinga,

Warranted Christian Belief, p. 214.  




Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome"

A groundbreaking paper in Nature reports the results of the Encyclopedia of DNA Elements (ENCODE) project, which has detected evidence of function for the "vast majority" of the human genome. Titled "An integrated encyclopedia of DNA elements in the human genome," the paper finds an "unprecedented number of functional elements," where "a surprisingly large amount of the human genome" appears functional. Based upon current knowledge, the paper concludes that at least 80% of the human genome is now known to be functional:
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.
(The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, Vol. 489:57-74 (September 6, 2012) (emphasis added))
In the past we've frequently read about studies reporting function for many thousands of base pairs (see here or here for a few of many examples), but it's often hard to get a sense of just how much of the genome has had function detected for it. Through the collaboration of hundreds of researchers, the ENCODE project determined that "The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type." As discussed further below, Tom Gingeras, a senior scientist with the ENCODE project, contends in an interview that "[a]lmost every nucleotide is associated with a function."
"Surprisingly Large" Amount of the Human Genome is Functional
The ENCODE paper divides up functional genomic elements into major categories: RNA transcribed regions, protein-coding regions, transcription-factor-binding sites, chromatin structure, and DNA methylation sites. After analyzing all of these different kinds of genomic elements, the project found:
Accounting for all these elements, a surprisingly large amount of the human genome, 80.4%, is covered by at least one ENCODE-identified element. The broadest element class represents the different RNA types, covering 62% of the genome (although the majority is inside of introns or near genes). Regions highly enriched for histone modifications form the next largest class (56.1%). Excluding RNA elements and broad histone elements, 44.2% of the genome is covered. Smaller proportions of the genome are occupied by regions of open chromatin (15.2%) or sites of transcription factor binding (8.1%), with 19.4% covered by at least one DHS or transcription factor ChIP-seq peak across all cell lines. (internal citations removed)
In addition to finding 863 pseudogenes that are "transcribed and associated with active chromatin," the paper reports that nearly all of the genome is found near a functional DNA element: "A total of 99% of the known bases in the genome are within 1.7 kb of any ENCODE element."
"Non-Conserved" No Longer Implies "Non-Functional"
As we've discussed here on ENV before, molecular biologists often infer function for non-coding DNA by finding the sequence is "conserved" or "constrained" (i.e. similar) across diverse species, implying there is some kind of selectable function preventing it from accumulating mutations. But if a sequence is not conserved or constrained (i.e. it's different) across different species, does that imply it's not functional? The ENCODE paper asked this question, and found the answer is "no":
Primate-specific elements as well as elements without detectable mammalian constraint show, in aggregate, evidence of negative selection; thus, some of them are expected to be functional
Later the paper found that within primates, unconserved sequences may be very important for determining body form:
There are also a large number of elements without mammalian constraint, between 17% and 90% for transcription-factor binding regions as well as DHSs and FAIRE regions. Previous studies could not determine whether these sequences are either biochemically active, but with little overall impact on the organism, or under lineage specific selection. By isolating sequences preferentially inserted into the primate lineage, which is only feasible given the genome-wide scale of this data, we are able to examine this issue specifically. ... [A]n appreciable proportion of the unconstrained elements are lineage-specific elements required for organismal function, consistent with long-standing views of recent evolution, and the remainder are probably "neutral" elements that are not currently under selection but may still affect cellular or larger scale phenotypes without an effect on fitness. (internal citations omitted)
And of course, if a genetic element affects "cellular or larger scale phenotypes," then clearly those elements have function as well.
Findings are "Unprecedented"
The paper concludes that researchers have uncovered an "unprecedented number of functional elements":
The unprecedented number of functional elements identified in this study provides a valuable resource to the scientific community as well as significantly enhances our understanding of the human genome.
They also make the obvious conclusion that much more of the genome appears to be involved in regulation processes than producing biochemically active proteins:
Interestingly, even using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function.
And of course, the implications of this study for fighting disease are profound:
The broad coverage of ENCODE annotations enhances our understanding of common diseases with a genetic component, rare genetic diseases, and cancer, as shown by our ability to link otherwise anonymous associations to a functional element.
Junk DNA Will Be "Consigned to the History Books"
The news media have picked up on this story, with headlines like "Breakthrough study overturns theory of 'junk DNA' in genome" (UK Guardian) or "Bits of Mystery DNA, Far From 'Junk,' Play Crucial Role" (NY Times). These articles frankly acknowledge the implications for the old "junk DNA" notion:
  • "Long stretches of DNA previously dismissed as "junk" are in fact crucial to the way our genome works, an international team of scientists said on Wednesday. ... For years, the vast stretches of DNA between our 20,000 or so protein-coding genes -- more than 98% of the genetic sequence inside each of our cells -- was written off as "junk" DNA. Already falling out of favor in recent years, this concept will now, with Encode's work, be consigned to the history books." (Alok Jha, "Breakthrough study overturns theory of 'junk DNA' in genome," UK Guardian (September 5, 2012))
  • "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. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches. ... Human DNA is 'a lot more active than we expected, and there are a lot more things happening than we expected,' said Ewan Birney of the European Molecular Biology Laboratory-European Bioinformatics Institute, a lead researcher on the project." (Gina Kolata, "Bits of Mystery DNA, Far From 'Junk,' Play Crucial Role,"New York Times (September 5, 2012))
The NY Times further commented on the complexity of what we're finding:
There also is a sort of DNA wiring system that is almost inconceivably intricate.
"It is like opening a wiring closet and seeing a hairball of wires," said Mark Gerstein, an Encode researcher from Yale. "We tried to unravel this hairball and make it interpretable."
There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand -- about 10 feet of DNA stuffed into a microscopic nucleus of a cell -- that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure -- the hairball -- Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.
Over at Discover Magazine, Tom Gingeras, a senior scientist affiliated with ENCODE, states that "Almost every nucleotide is associated with a function":
According to ENCODE's analysis, 80 percent of the genome has a "biochemical function". More on exactly what this means later, but the key point is: It's not "junk". Scientists have long recognised that some non-coding DNA probably has a function, and many solid examples have recently come to light. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. "Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more," says Tom Gingeras, one of the study's many senior scientists.
The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
And what's in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project's Lead Analysis Coordinator and self-described "cat-herder-in-chief". He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. "It's likely that 80 percent will go to 100 percent," says Birney. "We don't really have any large chunks of redundant DNA. This metaphor of junk isn't that useful."
We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let's simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA. ENCODE researchers use words like "surprising" or "unprecedented." They talk about of how "human DNA is a lot more active than we expected." But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.
This important paper also represents a stunning vindication of Jonathan Wells's book The Myth of Junk DNA. He wrote there:
Far from consisting mainly of junk that provides evidence against intelligent design, our genome is increasingly revealing itself to be a multidimensional, integrated system in which non-protein-coding DNA performs a wide variety of functions. If anything, it provides evidence for intelligent design. Even apart from possible implications for intelligent design, however, the demise of the myth of junk DNA promises to stimulate more research into the mysteries of the genome. These are exciting times for scientists willing to follow the evidence wherever it leads.
(Jonathan Wells, The Myth of Junk DNA, pp. 9-10 (Discovery Institute Press, 2011).)
While undoubtedly a few holdouts will continue to defend "junk DNA" thinking for philosophical or theological reasons, this paper should put most arguments in favor of junk DNA to rest.