The Grievance Brigades
The most traditional branches of Western learning have been replaced by disciplines designed to serve radical political ends.
By SOHRAB AHMARI
The Victims' Revolution
(Broadside, 378 pages, $25.99)
Torah Issues
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
1.
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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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
sciences.
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.
2.
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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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.
1
Human
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
reason.
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.)
2
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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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
refrigerator.)
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
disagreements.
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.
3.
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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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
reliable.
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
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17:38designer.
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.
1
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). ↩
1.
2
This is often the
result of sin, though not necessarily the sin of the unbeliever; see Plantinga,
Warranted Christian
Belief, p. 214. ↩
2.
Copyri
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.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."(The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, Vol. 489:57-74 (September 6, 2012) (emphasis added))
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."
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 functionalLater 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.
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"
There also is a sort of DNA wiring system that is almost inconceivably intricate.Over at Discover Magazine, Tom Gingeras, a senior scientist affiliated with ENCODE, states that "Almost every nucleotide is associated with a function":"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.
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.
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.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.(Jonathan Wells, The Myth of Junk DNA, pp. 9-10 (Discovery Institute Press, 2011).)