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ENCODE and “Junk DNA,” Part 1: All Good Concepts are Fuzzy

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September 24, 2012 Tags: Genetics
ENCODE and “Junk DNA,” Part 1: All Good Concepts are Fuzzy
Pioneering geneticist Gregor Mendel (1822 –1884) conducted research on heritable traits in pea plants.

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Note: The ENCODE project has recently taken the scientific world by storm by declaring that 80% of the human genome is functional. This has led the media and various science/faith groups to declare that in light of ENCODE’s results, the concept of “junk DNA” is dead. In this series, we explore the science and rhetoric surrounding ENCODE in search of a more meaningful understanding of biological function.

Fuzzy, but useful

One of the challenges for my students learning biology is summed up in one of my favorite sayings (that I’m sure some students are tired of hearing from me): “All the good concepts are fuzzy.” Take a basic concept like “living” versus “non-living,” for example. Obviously this is a fundamental concept for a biologist, since “biology” means the study of living things. Even here, though, we find that a precise definition of what is “alive” is a hard thing to nail down. While things like humans, dogs and cats obviously qualify (though some days with early lectures I might have my doubts for humans), there are other entities out there that blur the boundary between life and non-life. Viruses, for example, have many of the features of living things, but lack some others. Transposons are less life-like even than viruses, and there are even transposon-like entities that parasitize viruses. Life and non-life are useful concepts, but the precise boundary between them is fuzzy.

More technology = greater fuzz

Often, an increase in technological ability exacerbates the “fuzziness” issue. One example in genetics (that we will later see to be highly relevant to understanding the results of ENCODE) is the concept of “dominant” versus “recessive” for different versions of a given gene. If you recall anything at all about genetics from high school, you might remember learning about Gregor Mendel crossing pea plants that differed in certain characteristics (purple versus white flowers, for example). Mendel deduced that the “particles” that controlled a certain trait (what we would later call “genes”) came in pairs, and that the presence of one type of particle (e.g. the one for purple flowers) could mask the presence of another (in this case the one for white flowers). He deduced that one gene version (what we now call an allele) was dominant over the other one, which in turn was recessive. For Mendel, one determined a dominant / recessive relationship by examining the appearance of a plant with both alleles: whichever allele determined the appearance was the dominant one.

Advances in technology would later do two things to Mendel’s model. First, they would provide deeper insights to what was actually going on at the biochemical level. Secondly, those deeper insights would cause the concept of “dominant” or “recessive” to become more fuzzy. I’ll illustrate what I mean with a (hypothetical, but representative) example.

When Mendel did his work he was limited to what he could observe with the naked eye. Now we have the ability to examine the effects of alleles at much deeper levels than Mendel could. Let’s say, for the sake of the discussion, that the gene Mendel was working with made an enzyme that produced purple pigment. The “purple” allele of the gene (let’s represent it with the symbol “P”) made a fully functioning enzyme: its DNA is copied into mRNA, and that mRNA is used to code for the protein enzyme that does the work of making pigment. The “white” allele (let’s call it “p”), on the other hand, turns out to have a mutation in the protein coding portion of the gene. This single mutation has two effects: it stops translation early, resulting in a protein that is too short and cannot work as an enzyme. The mutation also has an effect on the stability of the mRNA: the mRNA produced by the white allele degrades more readily, resulting in a lower steady-state amount of the mRNA in the cell.

With this background in mind, suppose a scientist performs a series of different tests on a plant that has one purple allele and one white allele (i.e. is “Pp”):

If the scientist looks at the flower color of the Pp plant, she would conclude (as did Mendel) that the p allele is recessive to the P allele, since the Pp plant is as purple as a plant with two purple alleles (PP). This arises because one P allele can produce enough enzyme for complete flower pigmentation.

If the scientist compares the amount of mRNA for this gene between PP, Pp and pp plants, she would notice three different outcomes. PP would have the most, Pp would have less, and pp would have the least. For this test the Pp plant is intermediate between the PP and pp plants. The scientist would conclude that neither the P nor p allele is completely dominant over / recessive to the other (an effect known as “incomplete dominance”).

If the scientist did a test to compare the physical size of the protein enzyme in PP, Pp and pp plants, she would again notice three outcomes. PP plants would have only full-sized enzymes, pp plants would have only small enzyme fragments, and Pp plants would have both distinct sizes, full-sized and small. In this case, the Pp plant shows both character traits (full-sized and small) at the same time. The scientist would conclude that the P and p alleles are both dominant, since both alleles display their version of the trait with neither masking the other in any way (an effect known as “co-dominance”.)

So, is the P allele dominant, incompletely dominant, or co-dominant with respect to the p allele? The answer is “yes” – all three apply, but it depends specifically on the details that the new technology is revealing. Which answer is the most meaningful one? Well, it depends on the specific question the researcher is asking. Now that we have the ability to sequence DNA, we can directly observe the nature of all alleles in any given organism, and the presence of other alleles does not interfere with this observation. In effect, modern molecular biology has made all alleles “co-dominant” since all alleles display their “version of the trait” (i.e. their sequence) when they are sequenced. If one was so inclined, one could argue that “recessiveness” is an outdated concept, and that eventually we will determine through sequencing technology that all alleles are co-dominant. While this would be technically true, it would be very misleading. The p allele remains “recessive” in biologically meaningful ways: it is a loss of an enzyme function, and its complete loss has an effect on the appearance of the organism. Plants that have one of each allele (Pp) have the same enzyme content as PP plants. Anyone who would argue that “recessiveness” was no longer a feature of alleles in light of the new sequencing technology would have to address these issues in a meaningful way, since the evidence for “recessiveness” did not simply evaporate when we learned how to sequence genomes. By any measure, Mendel’s ideas of dominance and recessiveness are still useful concepts.

The relevance to ENCODE

So, how does this all relate to the ENCODE project? It hinges on another very useful, and therefore fuzzy term: “function.” Like “life” and “dominant”, “function” is a useful idea in biology, but much hinges on precisely how it is defined, and the technology used to assess its presence or absence.

The ENCODE definition of “function” is a useful one for the purposes of the large undertaking that this project represents. Specifically, ENCODE was seeking for biochemical activity in the genome: the interaction of chromatin proteins with DNA, regions of DNA that are made into RNA, and so on. This is all well and good, for we now have new tools available that allow us to test for these effects – we have new technology that can shed new insights on what is going on in the genome.

What these results don’t do, however, is cause the prior lines of evidence relating to non-functional DNA to suddenly disappear. As we saw with the dominance issue, the results from new techniques will need to be integrated into a more complete understanding of the data. We must also have a wider understanding of the strengths and weaknesses of various techniques to answer certain specific kinds of questions.

As a way to illustrate these issues for the ENCODE project, let’s consider the hypothetical example we used to explore the dominance issue. The ENCODE definition of “function” includes any detectable biological activity such as the presence of an mRNA transcript. In our example, both the “P” allele (that produces a working protein enzyme) and the “p” allele (which does not) both produce an mRNA transcript. As such, the ENCODE project would indentify both alleles as equally functional. In fact, the ENCODE definition of “detectable biological activity” as “function” would not be able to distinguish between these two alleles in any meaningful way, despite the fact that they have real, biological, and obviously functional differences. This is not to criticize the working definition of function adopted by ENCODE, but merely to demonstrate that this definition, while useful in some contexts, has limitations.

These limitations should stand as a caution to any group that wishes to adopt the ENCODE definition as the only viable definition of biological function. To consider our example again, I suspect that many of those opposed to evolution would bristle at the suggestion that the p allele was equally functional to the P allele, given than it represents a clear loss of function in keeping with common Young Earth Creationist, Old Earth Creationist, and Intelligent Design definitions of loss-of-function alleles, and the propensity of these groups to insist that such mutations destroy functional information. Yet what we have seen from these groups, by and large, is a robust embrace of ENCODE and its view of function. I suspect that these groups, in their excitement over the media frenzy declaring the idea of “junk DNA” to be dead, have not yet had time to carefully think through the implications of that embrace.

In Part 2 of this series on Wednesday, we’ll explore other working definitions of “function,” look at other lines of evidence that are better suited to distinguishing between biologically functional and non-functional sequences, and revisit some examples from my previous series on “junk DNA” in light of ENCODE.

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Roger A. Sawtelle - #73054

September 24th 2012


I quite agree, fuzzy concepts are (generally) good concepts, although they have been resisted (so I understand) by the scientific community.

Non-fuzzy concepts, which thing are black or white, right or wrong is based on Western dualism.  Fuzzy concepts recognize the reality of the inbetween, the gray if you will.

Fuzzy concepts are not dualistic or monistic, they are relational and are further evidence that traditional Western thinking is no longer functional for understanding ourselves and the universe we live in. 

HornSpiel - #73059

September 24th 2012

Long ago I learned about thesis, antithesis and synthesis. This is not something new. It seems to me that Western science and philosophy has always progressed by confronting established truths with fresh contradictory evidence.

Dennis’ brilliant article gets to the heart of the controversy over non-functional DNA  by helping us understand the concept of biological genetic function.

What these results don’t do, however, is cause the prior lines of evidence relating to non-functional DNA to suddenly disappear… [they] will need to be integrated into a more complete understanding of the data.

A new more complex understanding or definition of “function” must now be crafted. As evolutionary biologists move on with clearer insight into reality, ID apologists will be left criticizing an abandoned understanding.

ID theorists do I think have some intellectually legitimate insights like the existence of some biological function for all parts of the genome, or teh concept of information accumulation in the genome. However, I would expect that these will be eventually synthesized into standard evolutionary theory. They certainly won’t overthrow it completely. Even Relativity and Quantum Mechanics didn’t do that to Newtonian physics. And ID has not shown anything as radical as those endeavors. For example they do not really challenge the paradigm of common descent, or genetic variation and inheritance.

Of course ID is not really about evolution per se but about changing the definition and basis of science. They think they can do this through scientific evidence, but this is not possible since it is an attack on its philosophical foundations. Either they will fail, or in succeeding, completely destroy science as it has been practiced since the Enlightenment. Creationology will replace evolution in the ID scientific revolution.

Roger A. Sawtelle - #73061

September 24th 2012


It is my observation backed by Thomas Kuhn that Relativity and Quantum physics did overthrow Newtonian physics, so that is not a good example.

If you take ID as a narrow point of view that God directly guides or intervenes in evolution, I would agree that this is unlikely to happen and is unnecessary to our understanding of God and evolution.

On the other hand if you take ID as a broad point of view that evolution is a structured rationally understandable process with a definite goal, which is also not accepted by today’s science,  I think that this kind of ID is correct. 

Evolution is not mechanistic as Darwin thought.  It is relational, which is a very different model for the way the world works.  


HornSpiel - #73077

September 25th 2012

Certainly Relativity and Quantum physics overthrew philosophical speculation based on Newtonian physics such as Determinism or Mechanism. Certaily Darwin, as you mention, was working under the influence of these ideas. However Newtonian physics was still good enough to plot the course of spacecraft to the moon. That is what I meant by saying it did not overthrow it completely.

I do not disagree with  the statement “evolution is a structured, rationally understandable process.” That structured processes are what science studies. The structures are described as laws and or theories. Scientists are rational being who are able to discern and discribe these structures interm,s of the language of science.

Nor do I necessarily disagree with “evolution has a definite goal.” That however is a faith stament, a belief that God has a definite goal and works those out “in all things.” I do not believe that “definite goal” can be articulated in scientific terms or that science would be better off if it were modified to say it should or could.

Finally I might ask, does relational as you use it carry the implications of rationality and self-determination? To me relations occur between persons. The social sciences are relational, physics is not.

Eddie - #73063

September 24th 2012


You asked me a question of clarification on the other ENCODE thread.  I responded there (#72999), two days ago, but didn’t hear back from you whether my explanation was satisfactory.  If you get time, please drop me a note there.   I put some time and effort into my reply, and I’d like to know whether it did any good.


Roger A. Sawtelle - #73079

September 25th 2012


Have you overlooked the fract that the most important scientific advance of the last century was Einstein’s Theory of Relativity which established the fact that physics and the whole universe is based on the relationship between Mass and Energy? 

It was Einstein and his theory that has replaced the mechanistic Newtonian with the relational Einsteinian one, although people’s minds have been slow to catch up with the science. 

How is it good that science claims that life has no meaning or purpose?  Maybe science cannot establish what it is, but that is not the same as saying there is no meaning or purpose. 

Evolution does have a goal which is to populate the earth.  If it has a demonstrable goal, how can one say it doesn’t?   

HornSpiel - #73120

September 26th 2012

most important scientific advance

This is a values statement not a scientific statement. If it is “most important” in some sense, I’d suggest it is in the area of philosophy. Quantum mechanics, for example, is far more important in the economic sphere as it is the basis of electronics. So who’s to say which, or either of these is most important? Unfortunately the example is a distraction from the point I was trying to make.

science claims that life has no meaning or purpose

No, some scientists claim this based on a faulty extrapolation of scientific method into philosophy. On the question of meaning or purpose, Science is properly silent.

Evolution does have a goal which is to populate the earth

Are you sure? Why do you limit it to earth? Can you really claim to be able to articulate the goal of an amorphous process comprising trillions of organisms? Can this process articulated as a theory really have a goal?

Sentient beings can have goals. Are you not anthropomorphizing Evolution?

Roger A. Sawtelle - #73132

September 27th 2012


You seem to think that philosophy has nothing to do with science.  The philosophy of science which is very important and must not be brushed aside.

This is a values statement not a scientific statement.

Does science have no value?  Of course it has value.  The value or purpose of science is to understand our universe, our world.  Certainly the discovery of quantum physics is very important in this process, as is Einstein’s Theory, but you completely avoided my question by picking on an irrelevant issue.

  Sentient beings can have goals. Are you not anthropomorphizing Evolution?

The basic issue as I see it is you and others have given materialists control over the philosophy of science.  You are following a line of reasoning laid down by Jacques Monod in Chance and Necessity, which sounds good, but on close examination is dead wrong.

The issue is not anthropomorphizing nature, but rationalizing it.  Monod claims that nature is not rational and thus things cannot have a purpose because nature cannot think.  Thus the only purpose and meaning found in nature is caused by human thought, because life and reality according to this way of thinking is without rational order, meaning and purpose.

The problem with this point of view is that the basis of science is that the universe does have rational, comprehensible order and if this is true than Monod is full of BS.  So the question Is the universe rationally ordered?  The answer has to be Yes if science has any meaning.

If the universe is rationally ordered, from whence does that rational order come?  The Christian answer is the Logos of God, which is exactly what Scientism does not want to accept or even consider.

There is separation of science, philosophy, and theology, but it is not absolute.  When we accept the separation as absolute, we make theology irrelevant.  The nexus between all three is the Logos and that is what Christians must insist upon because it is true.      





HornSpiel - #73299

October 2nd 2012


You seem to think that philosophy has nothing to do with science. 

Not at all. It is extremely importnat. The philosophy of science (PoS) is what we are discussing. Different philosophies will expect different things of science. A PoS that allows final causes is quite different from one that does not.

Does science have no value?  Of course it has value

I am saying science cannot prove values. Scientists need values in order to do science but those values don’t come from science but from their moral, religious and/or philisophical backgrounds. Therefore I maintian your statement about the most important scientific advance of the 20th century, although relevant to scientists and the discussion of science,  is not scientific.

You completely avoided my question by picking on an irrelevant issue.

Well I guess I am not sure what the question was. Let me try and guess You stated

It was Einstein and his theory that has replaced the mechanistic Newtonian with the relational Einsteinian one, although people’s minds have been slow to catch up with the science. 

I take it your point is that modern physics replaced a mechanistic scentific view with a relational one. It appears to me you are also relating mechanistic with materialistic, and relational with relativistic. So are you are saying the scientific paradigm of (methodological) naturalism more or less still the same since the 19th c. needs to be overthrown with a relational understanding of science that incorporates science with theology and philosophy?

My difficulty is really understanding your ideas.  I asked you above “Does relational, as you use it, carry the implications of rationality and self-determination? To me relations occur between persons.”

My point is I simply have no idea how relational applies to formulating scientific theories or designing scientific research programs. I understand that doing science is a relational enterprise. Relationships with other scientists and those who might be affected (potentially the whole world) must be taken into account in order to do science morally. But to put it another way: How would your realtional point of view help scientists do better science. What avenues of research might they explore that they would otherwise overlook? How would it inform their theories?

You say

Evolution is not mechanistic as Darwin thought.  It is relational, which is a very different model for the way the world works.

That is why we have the social sciences. They are based on the fact that relationships between organisms, from cells to societies, exist. I would say:

“Evolution is not just mechanistic as Darwin thought.  It is also relational, which is another very different and useful model for looking at the way the world works.”

Observations about evolution proceeding through the cooperation between organisms in biological relationships that transcend mechanistic explaination can certainly be useful. But that does not negate other obervations, say, about the cellular machinery responsible for building proteins from the genetic code in a cell. A detailed description of the material and efficient causes of that process are what are important.  

I believe it is important to realize even our best theories are simply approximations that only touch the surface of the reality God has created. People sometimes take scientific statements as comprehensively True, or that Scientists intend them to be taken that way. The current paradigm is useful for may purposes. But it should not be taken as a description of ultimate reality. Genesis One and John One are much more useful for that. 


Roger A. Sawtelle - #73304

October 3rd 2012


This discussion and your questions get down to the nub of our inquiry, which is good, but is the most difficult to discuss because they involve basic assumptions, which we all have and are difficult to objectively evaluate.

First let me give you some background which is important to me and might be helpful to you.  I see that our world, the Western intellectual world, is in the grips of an intense power struggle.  On one side is Scientism which has embraced the monistic Physicalist world view.  Physicalism is updated materialism, it includes energy as well as matter as the only reality in the universe. 

This means that God is non-existent or irrelevant.  It also means that the universe is irrational and meaningless, because order, thinking, rationality, and purpose are not physical.  You can research Physicalism on the web and through books like Science and Nonbelief by Taner Edis and The Atheists Guide to Reality by Alex Rosenberg.

You refered to the difference between the physical or natural sciences and the social sciences being relationships.  First of all let me say that there is some truth in that, BUT the thinking among scientists is that this difference is a flaw in scientific thinking. 

Their goal is to make ALL science subject to physical natural laws of physics.  I have found that scientists in fields other than physics feel that somehow they are in someway inferior to physicists so they have already been convinced at some level that Scientism is right.

It is my observation that physicalists are working to take over evolution and neuroscience in order to use them as stepping stones to reduce the biological and social sciences into sub-fields within physical science.  This is where the battleground is now.

The primary barrier in the way of this movement is that scientists are finding that nature is not as mechanistic as we had assumed.  Einstein’s theory is part of this, as is quantum theory and even evolution and ecological science.  All of these advances in scientific thinking run contrary to Newtonian mechanistic thinking which has been adopted by materialism/physicalism. 

The difference is that now the universe does not appear to be purely Simple at its core, but both complex and one at its core.  The goal of naturalistic science was to reduce nature to its simple basic particle (the God Particle,) which supposedly would allow humans to know and control the whole of Creation.  I think we see that this is a myth.  Reality is not simple, reality is not monistic, reality is complex.

The weakness of physicalism is that science does not support it.  Its strength is that it is a theory.  The traditional alternative to monism is dualism and current science does not support it either.  I have found no one who is able and willing to support it except to say it is traditional and it is not monism.  So the danger is that Scientism might win out by default.  

Therefore we, that is humanity need a new understanding of how the universe works.  This does not mean that the old one was completely wrong, but insufficient.  As a Christian I do not expect this to come from science nor do I sxpect it will come from philosophy which has also lost its way. 

I do not understand why you do not think that John 1 cannot or does not allow humanity to better understand the reality of our universe in light of the Ultimate Reality of God, particularly since Jesus Christ is both fully God and fully Human and humans are natural beings. 

Jesus Christ is God With Us and God For Us.  Jesus Christ demonstrates that God is first and foremost Love, that is Relational.  Even if nature were mechanistic and it has some of these characteristics, since a mechanism is relational, just not as complex and involved as an organism. 

Note: It just occured to me that now humans are making our mechanisms semi-organic because we are incorporating computers in them thus giving ordinary machines the ability to think at a low level, so our experience of what a mechanism is in the process of changing.  


Roger A. Sawtelle - #73305

October 3rd 2012

Part 2

Thus relational describes nature from its simplest chemical interaction to forgiveness. It is the one constant in the three basic characteristics of reality, the physical, the rational, and the purposeful.

The issue is not our understanding of science vs our understanding of God or our understanding of philosophy, but how the three can work together. The only way this can work for the Christian is to allow Jesus Christ to be the Logos as John 1 says He is. How can any Christian argue against that? If Jesus Christ is not the Logos, then we have a real and serious problem with our faith.

HornSpiel - #73326

October 3rd 2012

So what I hear is:

There is a problem with modern science in that it tends towards reductionism. It trys not only to to describe everything in terms of only the physical,  which is matter/energy, but claims that that is all there is. Ultimate reality is purely physical. This is what monism is. Its goal is to know and be able control the whole of Creation.

The agenda of Scientism or Physicalists  is to promote the notion that God is non-existent or irrelevant and that the universe is irrational and meaningless. They believe that because order, thinking, rationality, and purpose are not physical, they are meaningless fictions, illusions or delusions.

However  modern science is discovering that the universe appears to be appears to be fundamentally incompatible with the goal of monism. It is too complex for that. 

The traditional alternative to monism is dualism—Mind and Matter—or rationality and physicality. No one really supports that notion now because the scientific evidence does not support it either. (Really? Why not?)

Your answer is a three part model of reality, triplism, which posits three fundamental foundations of reality, Material(physicality), Mental(rationality) and Relational(purposefulness). The basis of this model is not science or philosophy, but Christian theology. It is based on our understanding of the nature of God, particularly revealed through Jesus Christ the Logos. He revealed that God is Love—a relationship, which we can expect to be reflected in the nature of creation.

I agree that Scientism does tend toward reductionism. I also agree that relativity, quantum mechanics and the evolution of life—particularly of the human person—pose great difficulties for reductionism in terms of explaining everything. I am not sure about the philosophical implications of that complexity though. 

You say of physicalism that

...this means that God is non-existent or irrelevant.  It also means that the universe is irrational and meaningless…

This sounds like a pretty good description of how the physical sciences are practiced. Methodological naturalism says that for scientific descriptions “God is non-existent or irrelevant” and that physical processes are best described without reference to any rationality or purpose. As you know I have no problem with this, as long as these descriptions are not touted as describing Ultimate Reality. 

The battle should be to expose the reductionist philosophical agenda. it is actually quite simple. One can agree with their descriptions of physical reality (e.g. people are machines) but then insist we are not just machines—we are far more than machines.

They may want to try and reduce other sciences to pure physical materialism.  There are three possible results: they fail because Reality won’t let them, or they succeed (for a time) by suppressing contrary thinking, or they are right. However I think the most likely result is they don’t succeed but uncover lots of interesting and useful results in the attempt. So for that reason I really don’t want to block their research programs, just their undue philosophizing.

Let me correct you: I do think that John 1 does allow humanity to better understand the reality of our universe in light of the Ultimate Reality of God. I just don’t see that it applies to the practice of the physical sciences because their proper focus of study is the physical aspect of the universe.

Of course there are fuzzy boundaries between the physical  and social sciences, neuroscience being a good example. However I do not think trying to change the philosophical foundations of science is the best way of gaining perspective on this. Far better is to be a Christian in the field and do a good job research and applying the results. For example see the recent blog posts here http://biologos.org/blog/shaping-the-human-soul-part-1 and here  http://biologos.org/blog/shaping-the-human-soul-part-2.

Roger A. Sawtelle - #73331

October 4th 2012


First, let me make something very clear.  I am in no way suggesting that any research be blocked in any field by anyone.  On the other hand I might suggest that there be new more fruitful areas of research that should be pursued.  Most people are aware that the work of Lynn Margolis was rejected by the biological establishment for a long time, until they had to accept it before her recent death.

In a real sense it seems that HornSpiel and I are in basic agreement, although he probably does not accept the my exact formulation of the situation.  We disagree as to how the respond to this situation.  If I may say so it seems that he ascribes basically to Stephen Jay Gould’s NOMA, Non-Overlapping Magistera. 

While NOMA has its points, I do not think that it is a theologically or practically viable strategy.  I think that history needs to be our guide here.

After the ancient Hellenistic world accepted Christianity, two very important things happened.  First a number of false teachings emerged that resulted in the formulation of the Trinity that established the intellectual foundation for Christainity.  For me was the most important and positive.

Second, thinkers began the process of integrating Christianity with the Greek philosophical tradition.  In the West this would seem to have been completed with the work of Thomas Aquinas.  While this was a great and important intellectual feat, it raises serious problems as to how to separate Biblical truth from philosophical truth when philosophical truth, like all human truths, prove to be faulty and inadequate.

The primary point I want to make here is that the great intellectual Fathers and Mothers of the Church were called to formulate the Faith in an intellectual manner to give the Church and the people a sound intellectual basis for life and living.

I feel called to continue that work, not that I think that I am the intellectual equal of Augustine & Co.  However they have shown the way and Jesus is the Way, so this task is decidedly easier than during their time. What I hear HornSpiel and others saying is that we really don’t need to bother with this.  Somehow the world will find its own way without the help of the Church.

Jesus came for the world, not the church.  God’s people, the Jews, or at least the leadership the the Jews with a few important exceptions reject Jesus as the Messiah.  I think that the Church needs to do more than just deny or attack Scientism.  In a real sense we have spent a long time denying and attacking Darwinism and what has it brought us and the world.

It is time we offered a positive intellectual alternative to both Darwinism and Scientism, rather then negative attacks.  Gnosticism taught that the physical was separate from the spiritual.  Christianity rejected Gnosticism a long time ago on sound spiritual and intellectual grounds.  Let us not fall for that old myth today.                        

HornSpiel - #73341

October 4th 2012


I think I chose my words poorly. I was not intending to imply that you wanted to block science in any way. I should have said perhaps that I do not feel the way that Physicalists say science should be done needs to be changed. It is the same way Christian scientists should be doing it.

I am not sure about your NOMA comment. I subscribe the the idea that Theology and Science, when properly practiced and understood, provide complementary descriptions of reality. This is the position advocated by Richard Bube in his little book Putting It All Together.

One of the alternate, incorrect ways of relating science and theology Bube describes is concordism—that is, trying to correlate theological statements with scientific ones. Although there are natural convergences between science and theology (e.g. Creation and the Big Bang), concordism tries to force correlations rather than allowing them to arise naturally.

What I sense in your triplistic agenda is a concordist approach to the philosophic basis of science. There is nothing wrong with pointing out areas where science seems to reenforce or benefit from a Mind-Body-Relationship paradigm. This is probably most useful in social sciences like psychology and counseling. However it seems to be forcing the issue when Relationship is applied to physical interations like the strong force binding together the nucleons of an atom.

Sorry for keeping this thread going so long. It may be time to abandon it. If you want to make one more response here that’s fine. I will wait for another opportunity to resume this (to me) stimulating conversation.

Roger A. Sawtelle - #73351

October 4th 2012


I have no problem discussing important problems with you.

Now let me try to explain my understanding of the relationship between theology and science. I expect I would agree with Bube about complementarity, but maybe not entirely.

Let me clarify. It seems to me that science is actually based on Biblical theology, for instance it has often said that without the doctrine of the Creation, not creationism, modern science would be impossible. I think that without the idea that God rules humanity through moral law which is found in the Bible is necessary to the concept that God rules nature by natural law.

My theology and my view of science is based on the concept of model. I do not know if you have read Thomas S. Kuhn’s The Structure of Scientific Revolutions. His point was that Einstein’s Theory was not just an adjustment in some equations, but a very different way of understanding how the universe works, a different model of the structure of nature.

This reinforced an idea set forth in a book coauthored by Peter Berger, the Social Structure of Reality, which claimed that changes in social structure, the way we experience and visualize society, affects the was we see nature. I think the point was that non-hierarchical democracy has brought a non-hierarchical view of nature.

The point is that a relational model found in one aspect of life can be and often is transfered to another aspect of life. The conflict/competition model of life found in Darwinian evolution has been used to justify and inspire libertarianism. On the other hand we believe that the model of the life, death, and resurrection of Jesus Christ has inspired many Christians.

Now Scientism has a model of reality which is intellectually false. I expect that you have not read Jacques Monod’s book Chance and Necessity, which is often quoted as the justification for methodological naturalism and his logic and facts are bogus. Human beings owe science and each other to critically examine what scientists believe.

Now I have made it clear in my book Darwin’s Myth that science, theology, and philosophy, the three legs of Western thought must complement each other. The problem is philosophy is dead, science based on naturalism is a lie, and theology based on out of date philosophy is stricken. I want to be clear that the faith is not wrong, but mode of thinking found in both absolutistic creationism and relativistic liberalism is deeply flawed. Fortunately we live by faith and not by knowledge or sight.

We have science, philosophy, and theology, which are complementary, but we need an overarching Model to bring them together and this is where monism, dualism, and triune thought come in. There has always been a conflict between monism and dualism, which I describe in my book, The GOD Who RELATES.

Western thought is generally dualist, but really a compromise between the two. Is the dialectic of thesis, antithesis, synthesis, dualistic or tristic?

The controling Model of Reality is the Trinity, the Christian Model of God. This is not concordance. This is based on a detailed analysis of science, philosophy, and theology. Concordism tries to reconcile Genesis 1 and science. That is an interesting intellectual exercise, which does reveal some interesting facts. However this Model points to the fact that a rational God created a rational universe as a rational home for rational human beings.

Rational relationships are the foundation of human life. Without the reality of of a rational God there is no intellectual basis for the existence of a rational universe or rational human beings. They all must exist or none of them exists.

Physicalism is now making the claim that the universe is not rational and people do not think and have free will. Philosophy is now making the claim that life is not rational and without meaning followed by atheists. That is why we need a new philosophy and philosophy of science, beside the need to put theology back on a solid philosophical basis.

Relationships are some of the simplest and most obvious things imaginable, up-down, right-left, old-new, dark-light, rich-poor, smart-stupid, good-bad. That is how we recognize things and people, by how they are different and how they are similar. If everything were the same, no differences, no relationships, and no knowledge. If every thing were radically different sao there were no similarities, no connections between things, then again there would be no real knowledge, just a jumble of names. That is why all things are relational.

It really doesn’t do the Church much good if we sit in our colleges and cathedrals while the world goes up in flames, because we are part of the world, whether we like it or not.

Roger A. Sawtelle - #76048

January 18th 2013


I agree.  The problem is IMHO is that as our understanding of the world has deepened, our theology, in as much as it has been based on philosophy, has not. 


Metal Gear - #77465

March 14th 2013

What  technicolored research, this has been very helpful on my independent study, I feel like I understood a little bit more now. http://chordsworld.com/gotye-somebody-that-i-used-to-know-chords/

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