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Is There “Junk” in Your Genome? Part 3

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February 3, 2012 Tags: Genetics
Is There “Junk” in Your Genome? Part 3

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

One of the challenges for discussing evolution within evangelical Christian circles is that there is widespread confusion about how evolution actually works. In this (intermittent) series, I discuss aspects of evolution that are commonly misunderstood in the Christian community. In this third of several posts on “junk DNA”, we explore how a specific form of pseudogenes called “processed pseudogenes” arise within genomes.

“Pseudogenes” (literally “false genes”) are generally viewed as sequences in genomes that, though they have high sequence similarity to “real” genes, do not have a function. Historically they were found before the advent of whole-genome sequencing as alternate forms of genes that lacked certain features. Some pseudogenes have characteristics that indicate they are derived from “real” genes – a class of pseudogenes called processed pseudogenes. In this post we’ll discuss the mechanism by which processed pseudogenes arise, and then discuss how a small fraction of them pick up functions and become “real” themselves.

Some assembly required

Processed pseudogenes arise from gene sequences that are transcribed into RNA, and spliced together to form “messenger RNA”, or mRNA, which is what the cell uses to guide protein translation. While I discussed how genes work in the last post in this series, let’s briefly revisit the topic with a view to certain details that we’ll need to understand how processed pseudogenes come to be.

Genes are segments of DNA on chromosomes housed in the nucleus of the cell. In order to make a specific protein encoded by the gene, a “working copy” of the sequence is transcribed into RNA, which for our purposes you can think of as a single-stranded version of DNA (DNA being double-stranded, of course). This RNA copy is then processed to remove sequences that interrupt the protein sequence code. These sequences are called introns, and they are spliced out of the RNA to produce what is called “messenger RNA” or “mRNA” – since it is now ready to carry the protein sequence code, or “message” out to the place where the protein will actually be constructed (outside the nucleus, in the cytoplasm).

While mRNA is a single-stranded molecule, an enzyme called reverse transcriptase is capable of re-creating a double-stranded DNA copy of it. This enzyme function is not a normal cellular function, since the point of producing mRNA in the first place is to make protein, not DNA. Cells don’t need to make DNA copies of RNA transcripts.

So, why is there reverse transcriptase present in cells at all? The answer, as it turns out, is that this enzyme is part of a type of transposon found in many organisms. We discussed transposons in a previous post in this series. In brief, transposons are self-replicating DNA segments that copy themselves and spread within genomes – a sort of minimalist DNA parasite. One class of transposons called retrotransposons copy themselves into RNA and then back into DNA using reverse transcriptase – so this enzyme is present in cells as a result. On occasion, reverse transcriptase makes a DNA copy of a host cell mRNA instead of its intended target (the transposon RNA):

This DNA copy of the mRNA may, at a low frequency, re-enter the nucleus and insert itself into a chromosome. The result is a sequence that is highly similar to the original gene, but lacking several key components: introns are missing, obviously, but also the original “parent gene” chromosomal DNA regulatory sequences. Processed pseudogenes, when inserted, have no function the cell requires – indeed, the cell was getting along just fine without it before it inserted. Accordingly, the vast majority of processed pseudogenes in genomes are not under natural selection, but may mutate freely without consequence.

Seeking the living among the dead

For a tiny fraction of processed pseudogenes, however, this may not be the end of the story. As we saw previously for transposon insertions, in rare cases the arrival of new DNA sequence at a chromosomal location might alter a cellular function and then be selected for on that basis. So to in this example, with an added twist: the fact that the processed pseudogene and its “parent gene” share a great deal of sequence in common raises the possibility that they could interact as RNA copies. If the processed pseudogene lands in a chromosome location that has regulatory sequences nearby, it might be transcribed into RNA as a result. If this happens, the interactions between the two RNA molecules may alter the regulation of the parent gene. If this new interaction has a selectable benefit, the processed pseudogene in effect has become a new gene in its own right and future mutation and selection may hone this nascent function over time.

As we mentioned previously, the fact that transposons can be converted into functional sequences does not “confer” functionality on all transposons. Nor does the (very interesting) finding that “the dead may rise” from pseudogene to gene indicate that all processed pseudogenes are likewise functional or about to become so. Rather, both examples illustrate that new biological information can be obtained through the natural processes of mutation (in this case, duplication and insertion of DNA sequence to a new location in the genome) and subsequent selection.

In the next installment of this series, we’ll examine one final form of non-functional DNA present in genomes, and one that is of great discomfort to antievolutionary views: unitary pseudogenes.

For further reading:

Esnault, C., Maestre, J., and Heidmann, T. (2000). Human LINE retrotransposons generate processed pseudogenes. Nature Genetics (24); 363 – 367.
Zheng, D., and Gerstein, M.B. (2007). The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends in Genetics (23); 219 – 224.

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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Crude - #67555

February 3rd 2012

Dennis, a quick couple of questions.

In your view, is evolution an entirely unguided process? Or was it guided by God, even if not in a way science is capable of detecting?

Atheists (well, let’s say most atheists) believe that evolution is a process which accomplishes what it does without guidance or input from any divine mind - the outcomes being neither foreseen or preordained. Do you disagree with that view, and if so, how?

I think it would add to your critiques if your views on as much were made clear - though perhaps you’ve stated them elsewhere.
Dennis Venema - #67556

February 3rd 2012

Hi Crude, 

Can you define “guided” for me, as you see it?
Crude - #67563

February 3rd 2012

Actually, I’d like you to tell me how you see evolution as guided, if at all, regardless of my reply.

Still, I’ll define it as much as I can. Broadly and for the purposes of this question, guided as in “God knew what the results of evolution would be before they took place, perhaps at the moment of creation. And that God likewise had the ability to choose different outcomes either at that beginning or during the process.”

If one believes God is omniscient and omnipotent, that would be unavoidable. Or were the outcomes of evolution largely surprising to God in your view - He didn’t know rats would evolve, much less humans?
Dennis Venema - #67564

February 3rd 2012

I’m not trying to be coy here, but much turns on precise definitions. 

One more question of clarification - if God is omnipotent and omniscient, is there anything at all in the entire cosmos that is, in your view, “unguided”? 
Crude - #67565

February 3rd 2012

No problem at all.

In an ultimate sense? Perhaps not.
Merv - #67566

February 3rd 2012

Why should foreknowledge (omniscience) necessarily imply guidance (omnipotence)? —they are, after all, two distinct words and concepts.   I can re-watch a movie with complete foreknowledge of everything that will happen and yet without having had any influence whatsoever in making it happen as it did.  (foreknowledge without guidance).  I’m not suggesting that those concepts aren’t both melded in God—I do think he’s both.  But one should also distinguish between omnipotence and strong predestiny—i.e.  not only *can* God do everything, He *does* do everything.  And there is a significant difference there too which I, in turn, would dodge answering until terms were better defined or the necessary caveats in place.  All the same, Dennis, I think Crude may be letting you off the hook too soon.  Why not guided or unguided even with omniscience in place?  Isn’t the old question of how God threw or set the dice still a live one on the table for us all?


Crude - #67567

February 3rd 2012


I’m not letting Dennis off the hook. I’m still waiting for his answer.

I didn’t say that omniscience implies omnipotence, and I think it’s far too loose to equate ‘guidance’ with ‘omnipotence’. (Say God exists, but is not omnipotent. The question of guidance in evolution is still live given that alone, since limited power can do the trick.) What I said was that if God is taken to be both omniscient and omnipotent, then guidance in evolution falls out as a conclusion. Given omniscience, God knew what the outcome of evolution would be. Given omnipotence, God set the universe (and thus evolution) into motion.

I said from the start I’m fine with Dennis explaining what, if any, power he sees God as having over evolution. 
Uncle Bonobo - #67571

February 3rd 2012


Do you think that God controls the weather?

Was Katrina guided or unguided?

Crude - #67572

February 3rd 2012

I think God is omnipotent and omniscient. That should pretty much answer all questions on that front.

Now please - I entered this thread asking a fair question. So far, I’ve gotten no responses. I’ve answered multiple questions in reply. I think it’s understandable that I’d be tired of being the one answering them given what prompted this, and given patience on my part.
Uncle Bonobo - #67574

February 3rd 2012

“I think God is omnipotent and omniscient. That should pretty much answer all questions on that front.”

I agree. God guides evolution in the same manner and to the same extent He guides the weather.

That answers your question as well.

Crude - #67577

February 3rd 2012

It’s a shame, then, that I didn’t ask you the question, nor am I really interested in your answer. But if you wanted a completely disinterested “that’s nice” from me, by all means, it’s yours.

“That’s nice.”
Uncle Bonobo - #67599

February 4th 2012

Your courtesy and intellectual integrity is noted.

dont_blame_me_blame_evolution - #67575

February 3rd 2012



I can re-watch a movie with complete foreknowledge of everything that will happen and yet without having had any influence whatsoever in making it happen as it did.”


I was thinking the exact same thing when I read your words! (Now, don’t tell me you were thinking “Saving Private Ryan”. That would be too weird!)



dont_blame_me_blame_evolution - #67576

February 3rd 2012

Dennis Venema,

“if God is omnipotent and omniscient, is there anything at all in the entire cosmos that is, in your view, “unguided”?


As I understand it, traditional Christian teaching says that God does not put, or in any way guide, anyone into hell; yet He always knew that’s where certain people will end up.

Based on this, the answer to your question would be Yes.

Secondly, IF you think everything is God-guided, even so-called stochastic processes, would you recommend striking “stochastic” and “random” from the dictionary, or at least from your vocabulary?


Jon Garvey - #67578

February 4th 2012


A good  question too often ducked in TE circles. It seems to me than on this question hinges whether theistic evolution is a coherent philosophical and theological position, or just materialist science with a comforting personal pietism nailed on.

It worries me that on another recent thread of nearly 150 posts, hardly anyone was willing to commit to an answer.

Crude - #67580

February 4th 2012


Well, I’m glad someone else thinks it’s a worthy question. I look forward to Dennis’ answer.

I think it’s clear that TE *is* a coherent philosophical and theological position, for what it’s worth. See Plantinga’s recent book for a pretty stark position on the subject. I can think of some other TEs - not on Biologos - who make similar commitments. But I’d like to know Dennis’ position.
Darrel Falk - #67588

February 4th 2012

Dear Crude,

I can’t speak for Dennis, and I appreciate the fact that he followed up with questions of his own—the hallmark of any good professor as he or she draws out the best of those who are gathered around.

So as one of those “gathered around,” I would like to add my view, which is pretty specific.  Clearly God has used the process of natural selection to accomplish God’s purposes in creation.  All that happens in the natural world happens through the natural laws which are a reflection and manifestation of God’s activity.  If God stepped aside from the universe even for an infinitesimally small micro-second, all would cease to exist.  God, as an example then, not only created the “Law of Gravity,” the Law itself is a manifestation of the regular ongoing activity of God’s Spirit in the universe.

 The same is true of natural selection. Natural selection is a manifestation of God’s continuous regular and ongoing activity in the universe. How can God guide what God is already doing?  “All things came into being through him, and without him not one thing came into being”  (John 1:3).

Having said all that, the heart of your question still remains.  We believe that God does intervene in our lives and that God has intervened in human history in ways that are different in some manner than God’s customary way of acting in the universe.  We believe in the resurrection, for example,....hardly a customary way of working.  We believe that Jesus performed miracles—he made the blind man see, and his touch made the leper well.  We also believe that God through God’s Spirit enters into relationship with us, a  personal relationship which is grounded in love.  

It is difficult (perhaps impossible) to study this type of divine activity in the same manner as one studies that which keeps the universe going. Your question, if I may restate it, is, has God’s creative activity in the universe as a whole required this second type of activity.  Has God worked in super-natural ways in the history of life, or has God chosen to work only through his customary activity—that which can be studied through science?  The answer to that question remains a mystery.  Scripture, at least as I see it, is silent on the issue.  It tells us God created—that God spoke it into existence.  But does it tell us that God stopped his customary way of working on occasion to carry out a miracle?  I think Scripture is silent on this.  Was God’s “non-regular” way of working necessary to drive life in the direction God wanted it to go?  We don’t know. Neither Scripture nor science, provide a clear basis for answering those questions, so how would we know?  

The fact is though that it makes little difference. God does enter into relationship with us and does interact with us in a manner that is over and above that described through the natural laws.  God has used miracles to accomplish God’s purposes in human history and God will someday make a new heaven and a new earth, one where tears will be no more and mortality itself will be “swallowed by life.” (II Corinthians 5:4)
beaglelady - #67590

February 4th 2012

I’d say that God’s interaction with us is continuous.  Like the city, God never sleeps.  

Darrel Falk - #67593

February 4th 2012

“If I take the wings of the morning and settle at the farthest limits of the sea, even there you hand shall lead me, and your right hand shall hold me fast.  If I say, ‘Surely the darkness shall cover me, and the light around become night,’ even the darkness is not dark to you; the night is as bright as the day, for darkness is as light to you.”

Jon Garvey - #67594

February 4th 2012


I can’t answer for Crude, any more than you can for Dennis. But I don’t think “supernatural” was what he was asking about. He clarified:

Still, I’ll define it as much as I can. Broadly and for the purposes of
this question, guided as in “God knew what the results of evolution
would be before they took place, perhaps at the moment of creation. And
that God likewise had the ability to choose different outcomes either at
that beginning or during the process.”

That seems to me to cover more than “God initiated natural laws and is the ground of existence”, but also possibilities such as cosmological fine tuning, genetic front-loading, the overseeing of contingency (which is NOT law-driven or it would come under Monod’s “necessity”); all these quite apart from any question of “supernatural intervention”. The essence is “By whatever means, does God determine the specific outcomes of evolution?” Or, as he continues in the same post, “Was he surprised at any stage?”

The answer to that determines whether one can meaningfully talk about “junk DNA” etc, and also defines a difference from naturalistic evolutionists, many of whom are happy for people to believe in God as long as his existence makes no actual difference to anything and evolution can still be said to be “undirected”.

Your quote from Ps 139, of course, raises the same kind of questions, and would suggest that, in the human sphere at least, you yourself maintain God’s actual control, for the psalmist goes on to say, “All the days ordained for me were written in your book before one of them came to be.”

Darrel Falk - #67600

February 4th 2012

Theologians within orthodox Christianity differ greatly on the meaning of the phrase “all the days ordained for me were written…”   There is one thing however, on which we can all agree—-God’s Presence is always with us and we are never removed from his love.

HornSpiel - #67606

February 4th 2012

“Was he surprised at any stage?” 

One of the great pleasures of creativity , in my experience, is being surprised at the outcome. One steps back and says “Did I make that? I only had a vague idea of what I wanted when I started, but now I am amazed with the outcome.”  One can never experience that with out realizing an idea.

Perhaps God’s creative process is something like that, and we experience God’s “surprise,” if we may call it that, as love.

Jon Garvey - #67610

February 4th 2012

Yeah, Hornspiel - but you and I are creatures. We don’t live in eternity, and we don’t make Universes. And much of our creative surprise - maybe better to say joy - is because it’s a gift of God’s grace when our small efforts actually turn out good.

So it’s actually, to be as charitable as possible, fudging the issue vaguely to equate “surprise” with “love”, without being willing as well to affirm that, non-figuratively, “God foresees” or else “God does not foresee.” Or to be unwilling to say whether or not “God assigns every created being its useful function in his cosmic temple” (which is at least a major part of the universal message of Genesis 1). Both these attributes of God are at the heart of every major strand of historic Christianity, not to mention the other Abrahamic faiths.

Therefore Crude was being not in the least out of line to ask, on a site dedicated to reconciling science to Christian faith, how these doctrines are handled. So far, unfortunately, the answer seems to be “cagily”.

Crude - #67609

February 4th 2012


Thank you for your reply.

I agree with Jon Garvey, though, that your reworded question was not a question I was asking, so the answer wasn’t to a question I was curious of. I generally don’t think the “supernatural” or “natural” distinction is very helpful, but there’s another reason it’s not my concern here: because, on the surface, it’s entirely possible for the evolutionary process to be “natural” (let’s put aside particular questions of Adam and Eve for now, but even there natural biological precursors are entirely acceptable in my view, even if not the whole story) yet for God to have known, foreseen, and determined the results outside of time.

So no, I’m not asking “Did God use miracles?” I’m asking what power over and knowledge of evolution did and does God have, if any, in the views of Dennis - and yourself now, of course. Yes, I’m aware that orthodox theologians tend to have differing views on certain quotes from scripture. On the other hand, orthodox theologians tend to hold that God is omniscient and omnipotent - and what would fall out from that is A) God knew what the results of evolution would be, and B) He determined those results, even if we set the question of humanity off to one side. Again, I’ll note that B does not mean that God intervened “supernaturally” to keep things ‘on track’ (nor, I suppose, does it rule it out) - so the idea of miracles in the course of evolution can be put aside for my question. Affirm that God works miracles at times, or affirm that God never worked miracles in evolutionary history, and my question still remains.

So, I ask you the same question I’m waiting for Dennis to reply to: In your view, what knowledge of and power over evolution did God have? Was He surprised by the results of evolution - did He not know mice would evolve, for example?

I’ll add on another question, if you don’t mind. I believe that God did use evolution to create - and that means God knew what evolution would result in, and that He (in an ultimate sense) determined what would evolve. Again, let’s use mice as the example: my statement doesn’t mean ‘God had to tinker around millions of years ago to ensure that mice would evolve’, though it doesn’t rule out miraculous interventions. Let’s go further: this belief I hold is not something I think can be scientifically demonstrated or tested. It’s a theological and philosophical view. God used evolution, knowing and intending what would result - from amoebas to mice.

Is my belief entirely compatible with science and with Biologos’ mission, in your view? I want to stress again: not “does/can science show this?”, which I don’t believe is possible, anymore than it’s possible for science to show the truth of the resurrection in the laboratory. But is it compatible?

I ask this, of course, in addition to the question I asked earlier, both of Dennis and (now) yourself.
Merv - #67614

February 4th 2012

Sorry that I’m not Dennis or Darrel, but while you’re waiting for their reply, let me at least give the obvious answer (which you seem to have given yourself already, and which seems to me to be a necessary conclusion from what Darrel has already written).

You ask:  “what knowledge of and power over evolution did God have?”
Answer:  everything—both knowledge and power.  God did it all.  God knew it all.   (I still maintain ‘free will’, though.  Yeah I know—it’s a mess.)

You ask:  “Was He
surprised by the results of evolution?”   
Answer:  No.

The reason I give (my) answers here is because I want to hear your followup (the ‘so what ...’) that comes from this.  I think I got some of it from what you wrote earlier:  Do you maintain that given my answers I should strike the word ‘random’ from my vocabulary?  If so, I would have to ask you:  why?  ...since that word has nothing to do with God’s perspective and everything to do with yours and mine. 


Crude - #67615

February 4th 2012


Thank you for your reply. I look forward to Darrel’s and Dennis’, yes.

No, I don’t think the word ‘random’ has to be struck from the vocabulary, more or less for the reasons you give. Plantinga actually touches on this very question in his latest book, but even before reading that I was entirely comfortable with the word ‘random’, properly qualified.

I’m not sure why you seem to have thought I believed otherwise. So long as the proper meaning of the word is communicated, the word itself is no concern.
Darrel Falk - #67623

February 4th 2012

Dear Crude,

 “Is my belief entirely compatible with science and with BioLogos’ mission?”

Yes, absolutely.

I do think that God began creation with us in mind, but I also believe that God delights, really delights in all of creation.  Regarding your question about whether God knew of and intended for the existence of each individual species in advance I’ll leave that question for you to think about.  I am a Wesleyan.  We Wesleyans think about matters like that a little differently than Calvinists—but we lock arms in love anyway!!

Crude - #67627

February 4th 2012


Well, I didn’t bring up Calvinism. In fact, I’m echoing ideas that Stephen Barr, a fellow Catholic, once spoke of. I suppose Calvinists and Catholics can agree on some points. Then again, I doubt you’d say that Wesleyanism is incompatible with the idea that God guided evolution and knew its outcomes, in and of itself.

You say you’ll choose not to answer my question. But I have to wonder why? So you think about things differently. That’s fine - it’s not like I’m imposing some purity test here. Your answer is whatever it is. 

But I need to be frank here: Biologos’ mission, as I understand it, involves dealing with the question of how evolution and Christian faith interact. A central question - maybe the central question - when it comes to evolution and Christian faith involves many people, often but not always atheists, insisting that evolution is unguided in a radical sense: that not even God knew whether or not mice would evolve, to say nothing of man. 

Do you really think this is a question that can just be put aside without answer? Biologos isn’t dedicated to ‘locking arms in love’ alone. Biologos does not ‘lock arms in love’ with YECs/OECs or ID proponents and leave aside questions of creation as something that can just go without discussion or commitment.

I want to put this in perspective. You are, I believe, the highest up on the totem pole here (so to speak) at Biologos. I asked Dennis Venema for his views about God’s knowledge, power, and guidance of evolution - touching on the heartblood of Biologos’ mission. While I’m waiting for that answer still, I also asked you. You’ve said, expressly, you’ll not answer the question.

Let me repeat that in (too-wordy) headline form: Executive Director of Biologos Refuses to State Belief on Whether God Knew Outcomes of, Guided, or Had Power Over Evolution of Life.

Are you honestly going to tell me this is just unimportant? “Oh hey, maybe God did know. Or maybe He didn’t! Maybe everything in evolution was a complete surprise to Him. That doesn’t matter, we can all get along.”? Or that it’s important, but not so important that an answer to such a question actually matters?

You don’t answer to me, of course. But I think this is important enough that I’m going to ask again your views on God’s knowledge, power, and guidance of evolution.

And I’ll even ask a followup question. You said that my belief is entirely compatible with science and Biologos’ mission. Of course, some (I have some atheists in mind here particularly) would say my views, as stated, are not compatible with science. That the idea that God knows, has power over, and intended the results of evolution - even without ‘tinkering’ miracles - is incompatible with science.

Should I take it then that Biologos’ position is that such critics are not only wrong, but also get science wrong in the process - and thus they are advancing non-scientific views of their own (indeed, that insofar as they claim science can determine God’s guidance or activity in evolution, that they are abusing and misusing science)?

Thank you for your reply in advance.
Darrel Falk - #67637

February 4th 2012

Dear Crude,

Sorry if I wasn’t clear enough.  I think God began creation with humans in mind.  However, I also want to be clear that God delights in all of creation, You push for an answer that takes it further than that, by asking a significant  philosophical and theological question I am not qualified to address.  Your question.needs to be answered by a philosopher not by me, a biologist.  Your question also illustrates the need for a project that I think BioLogos is about to sponsor.  We need protestant, conservative protestant, theologians and philosophers addressing questions like this in a manner that is much more sophisticated than I, an amateur could do.  I fully expect this will happen soon.

Regarding your question about whether the position you have espoused is inconsistent with science, I want to emphasize that it is not.  Science is silent on these sorts of issues.  We have written fairly extensively on this site about how certain scientists use their scientific credibility to advance their philosophical agendas.   Have you seen, for example, Ian Hutchinson’s series on “Monopolizing Knowledge?”

Finally, I would like to affirm your comment about Stephen Barr.  We protestants have much to learn from Catholics who have thought about some of these issues pretty carefully.  Stephen Barr, a physicist, who is able to speak and write at a broad philosophical and theological level,  is a perfect example of that.

The bottom line, Crude, is that BioLogos is initiating the conversation for conservative protestants.  We don’t have all the answers, but we’re thinking together…and that’s a start.
beaglelady - #67639

February 4th 2012

So Darrel, you admit don’t know everything there is to know about God and His ways?  That sounds like humility to me.  Quite unlike the fundies.  

Jon Garvey - #67660

February 5th 2012

“Fundie” (n): contraction of “fundamentalist”.

The full meaning of the term, therefore, can be given by something like ‘stupid sumbitch whose theological opinions are considerably to the right of mine’. (Alvin Plantinga)

As he explains:

its cognitive content can expand and contract on
demand; its content seems to depend on who is using it. In the mouths of certain
liberal theologians, for example, it tends to denote any who accept traditional
Christianity, including Augustine, Aquinas, Luther, Calvin, and Barth; in the
mouths of devout secularists like Richard Dawkins or Daniel Dennett, it tends to
denote anyone who believes there is such a person as God. The explanation is
that the term has a certain indexical

element: its cognitive content is given by the phrase ‘considerably to the
right, theologically speaking, of me and my enlightened friends.’

Crude - #67642

February 4th 2012


Thank you for the reply.

I really didn’t know Biologos was a project aimed largely at protestants. I assumed it was broader than that, especially since views of Catholics (like Behe) and from Catholics (like Beckwith) have come up here before. But it’s no surprise you know more about the purpose of Biologos than what I can glean from my now-and-then reading.

I forget if I’ve seen Hutchinson’s series, but I’ll have a look at it on your recommendation.

I’m not going to press you any further for your views - they’re yours to give or not. But I’d like to mention a few things about where I’m coming from here. Maybe you’ll be able to at least partly appreciate my perspective.

You affirmed God’s continuous action in the world in unspecified ways in your view, and certainly Christ’s resurrection. I’ve even seen you (I *think*) argue that it’s entirely possible that there was a real Fall, a real Adam and Eve, even if it took place in the context of evolution, with Adam and Eve arising out of a population of biological precursors. I certainly agree.

You didn’t need to consult “conservative protestant, theologians and philosophers” and beg off due to considering yourself to be an amateur. You have your view, and you gave it, despite those being pretty deep philosophical and theological topics. And why not? Tack on “I’m an amateur, I still have things to learn, but this is where I stand based on what I know, and my views don’t reflect all of us at Biologos” if your worry is you’ll be accused of treating yourself as an expert or speaking beyond your expertise.

And that leads me into my second concern. I’m glad you acknowledge it’s entirely compatible with science to take the position that I outlined - one of believing God did know the results of evolution, that evolution was (again, even if this is a subject science can’t decide on) guided and planned and purposeful. You know there are people who insist otherwise, and claim that believing evolution is purposeful, or guided, or directed as I stated is incompatible with science, or that science commits one to the view that evolution is devoid of purpose, guidance, and cannot be the ultimate outcome of God’s action and foreknowledge. This is screamed loudly in books, at conferences, on blogs, etc. And the result - at least one intended result - is to try and belittle religious believers, particularly religious scientists, into shutting up about their views out of worry they’ll be criticized.

You mention ‘initiating the conversation’. I don’t think there’s going to be much of a conversation if everyone starts out saying “Well, I’m an amateur, I better not say where I stand on this, shouldn’t you ask an expert?” If people withhold their opinions, they shouldn’t be doing so out of worry that they’ll be mocked by people who are, frankly, abusing science. That’s one reason why I asked what I did.

That leads me to my final concern. I’m a TE myself, with strong thomist leanings - universals, Adam and Eve, evolution, etc. You’re familiar with it all, I think. I appreciate the difference between science and non-science. I also know that some people who yell “theistic evolution is just creationism, it’s unscientific and science shows evolution is unguided and without purpose!” don’t always do so due to mere misunderstandings, but with the intention of silencing people. Trying to ostracize them, or hoping to make sure they keep their mouths shut. I don’t know Biologos’ mission clearly - look at me, I didn’t even know it was aimed at protestants, much less conservative protestants, to such a degree - but I would hope that Biologos considers it a priority to fight that kind of pressure. *Especially* regarding theistic evolutionists, and particularly if they believe that evolution is/was guided, purposeful, and foreseen, since that’s precisely where the bulk of the attacks come, and where the abuse of science is the most prevalent with critics of that type of theistic evolution.

As I said, I won’t press you for any more replies you don’t want to give - I’ll wait for Dennis’ promised reply and see what comes of that. But hopefully you understand my concern now. I’m encouraged by your frank acceptance of my type of view as compatible with science and Biologos’ mission both. And maybe you can see why I thought it was important to hear your view on these matters. I’m no mindreader, so I don’t know whether or why you keep your views on this matter to yourself, amateur or no. But I want TEs to feel able to frankly state and discuss their own views. I think that’s when the conversation will really begin.
beaglelady - #67586

February 4th 2012

Does God work harder on mutations after people are exposed to radiation? 

Jon Garvey - #67596

February 4th 2012

The evidence shows that radiation damage induces cellular mechanisms of DNA-repair and specific mutagenesis (Weigle mutagenesis), so the cells themselves are working harder.

So the question becomes whether God oversees cellular mechanisms. Jesus does say the very hairs on our head are numbered (and they tend to fall out after irradiation). I’d hate to think he only numbers them when we’re at the hairdressers.

The bigger question, to cite Darrel’s psalm, is whether “all the days ordained for me except the one where I got a belt of radiation were written in your book before one of them came to be.” If not, it’s not a very comforting passage after all.

beaglelady - #67601

February 4th 2012

The bigger question? Why not just the question? 

Jon Garvey - #67604

February 4th 2012

Why not just the answer?

beaglelady - #67611

February 4th 2012

Sure, the answer to my question in 67596

HornSpiel - #67607

February 4th 2012

Understanding this pseudogene thing isn’t rocket science…its more like a Rube Goldberg machine. Quite a ride. Thanks for posting this Dennis

dont_blame_me_blame_evolution - #67624

February 4th 2012

Darrel Falk,

“Has God worked in super-natural ways in the history of life, or has God chosen to work only through his customary activity—that which can be studied through science? The answer to that question remains a mystery… Was God’s “non-regular” way of working necessary to drive life in the direction God wanted it to go? We don’t know. Neither Scripture nor science, provide a clear basis for answering those questions, so how would we know?”

So, bottom-line, as far as the degree of God’s involvement in origins, it’s not a matter of science or Scripture.

It all comes down to faith. Correct?

If correct, would you say that, to a significant and perhaps complete extent, we’re just wasting our time at this website?


Darrel Falk - #67626

February 4th 2012

Dear “Don’t blame me…”

“So, bottom-line, as far as the degree of God’s involvement in origins, it’s not a matter of science or Scripture ”

You missed my point…when we speak of God’s natural way of working (that which is  “regular” and thereby subject to scientific investigation), this does not imply that God is less involved than when God works through supernatural means (that which can be thought of as a singularity).   God’s activity never ceases regardless of whether it can be effectively studied by scientific means.  God’s activity is most certainly not confined to those times when a miracle occurs and the activity associated with a miracle is not greater just because it is a singularity.

Regarding whether we come to believe only on the basis of pure faith uninformed by knowledge, please see our series by Rick Kennedy and Ian Hutchinson.  
dont_blame_me_blame_evolution - #67629

February 4th 2012

Darrel Falk,

I don’t think I missed your point at all.

You said that neither science nor Scripture provides a clear basis for knowing whether God used “natural” or “supernatural” means in “the history of life” (i.e. evolution).

So, again, in your view, science can’t answer the question, and Scripture can’t answer the question.

It’s simply a matter of faith.


Darrel Falk - #67633

February 4th 2012

Dear Don’t…

Faith in what?  Both totally involve our Creator and both, as I see it, are equally consistent with Scripture and science.  Which of the two should I take on faith and why?

dont_blame_me_blame_evolution - #67640

February 4th 2012

Darrel Falk,


“Faith in what? Both totally involve our Creator and both, as I see it, are equally consistent with Scripture and science. Which of the two should I take on faith and why?”

I’m sorry. I was trying my best to be clear.

First, let me clarify that by “faith”, in this context, I meant a belief that is completely independent of science or Scripture. For example, if Joe tells you his favorite color is blue, you might then have faith that his favorite color is indeed blue. Or you might have faith that you actually DID have such and such a dream last night.

Now, let me try restating what I think you have said:


If one believes God “supernaturally” intervened throughout the course of evolution (i.e. trillions of biological miracles), then that’s simply a choice of faith, not a matter of science or Scripture. Or


If one believes God did NOT “supernaturally” intervene throughout the course of evolution but instead just got it started then kept hands-off thus allowing only “natural” processes to run their course, then that’s simply a choice of faith, not a matter of science or Scripture.

BECAUSE, as you said, “Neither Scripture nor science, provide a clear basis for answering those questions.”

I hope that’s clear.



Darrel Falk - #67661

February 5th 2012

Dear Don’t…

You’ve still missed my point.  What if Joe didn’t ” tell you his favorite color was blue?”  And what if you don’t remember a single dream from the night before?

If that  is the case, you’re probably best not to guess what Joe’s favorite color is, correct?  And you’re probably best not to start guessing about what dream you had the night before, when you really don’t have a clue.

Since the natural activity of God (God’s customary way) is every bit as much the activity of God as the supernatural activity of God (God’s singularities), then we’re left not knowing the extent to which singularities (God’s supernatural activity) played a role in creation.   God doesn’t tell us through Scripture and God doesn’t tell us through science.  It is all due to God’s activity though!  It is even self-evident that it is due to God’s activity (see Romans 1:19,20).  But the extent to which God has chosen to work through his non-customary means is up in the air and may always be.  By using the tools of science(which are a gift of God—see Mark Mann’s wonderful current series on this—especially the one that will be posted tomorrow), we know that much of creation was carried out through God’s customary (natural) way of working.  It seems unlikely though that we’ll ever know for sure whether God chose to work supernaturally as well. 

 Just like the only way you’d ever know if Joe’s favorite color is blue is if he told you.  So also, the only way we’d ever know if singularities were required was if God told us.  So far, as I see it, God hasn’t told us….not in either of his two books.  You may see that differently, but that’s how I see it, anyway.
dont_blame_me_blame_evolution - #67652

February 5th 2012

The above article notes beneficial, or at worst inconsequential, effects of genetic mutations:

Accordingly, the vast majority of processed pseudogenes in genomes are not under natural selection, but may mutate freely without consequence.”

If this new interaction has a selectable benefit, the processed pseudogene in effect has become a new gene in its own right and future mutation and selection may hone this nascent function over time.”

new biological information can be obtained through the natural processes of mutation (in this case, duplication and insertion of DNA sequence to a new location in the genome) and subsequent selection.”

I just saw a book on Amazon relating to this. It’s by a Cornell professor who is saying that genetic mutations are usually harmful and never lead to an increase in genetic information. He also says the human genome, because of ever-accumulating mutations, is slowly but inexorably degrading!


dont_blame_me_blame_evolution - #67653

February 5th 2012

Uncle Bonobo - #67684

February 5th 2012

Amazon sells books by many other young earth creationist authors. None of them are scientific.  

Joe Francis - #67665

February 5th 2012


As always I appreciate your work. Mobile genetic elements which transfer pseudogenes appear to a rapid way to change genomes.  As a YEC I am interested in this as you know.  How do the mechanisms you explain here:
1 influence the dating of human genome change and the diversity we see in the human genome?....i.e.,  could insertion of pseudogenes increase genome diversity and correspondingly decrease the number of founding couples needed for human evolution.

2 support the idea of irreducible complexity in the HGT found in microbes….for instance a Nature article a few years ago showed that HGT transfer was most likely the way that microbes received new genetic information because point mutations could not supply all the genes necessary for operon function, i.e. all the genes were required to be transfered because most functions of microbes were controlled by operons…in a sense this article verified that many microbial systems were IC. 

perhaps my examples do not apply…am I comparing apples and oranges here?

Thanks again,


dont_blame_me_blame_evolution - #67675

February 5th 2012

Darrel Falk,

I started reading your comment  #67661 and thought you were joking.

But I guess you weren’t.

I was unclear, justifiably I think, on what your position was. For your comment #67661 seemed to conflict with # 67588.

In #67661 you’re saying that neither science nor Scripture can confirm whether God “supernaturally” intervened in evolution. This is different from at least part of #67588 where you seemed to indicate that neither science nor Scripture can confirm anything at all about God’s “involvement” in evolution: “Has God worked in super-natural ways in the history of life, or has God chosen to work only through his customary activity—that which can be studied through science? The answer to that question remains a mystery.”

I guess #67661 is your true position?

In either case, I think you WOULD say that Scripture is silent on the specifics of the degree of God’s involvement?

Finally, I assume you were talking about evolution when you said “we know that much of creation was carried out through God’s customary (natural) way of working.” But who is “we” and what do “we” “know”?

The “we” certainly isn’t everyone in the U.S. nor everyone in the Gallup poll (see bottom page 2 of “Behold the Man” blog).

And certainly we don’t objectively “know” evolution is true, in a “scientific proof” sense. Otherwise, no controversy would still exist over the validity of evolution theory. And we probably wouldn’t be blogging here.

Actually, please skip the “know” part of the question. But who is “we”?


dont_blame_me_blame_evolution - #67683

February 5th 2012


I was wondering about BioLogos’ mission statement: “The BioLogos Foundation explores, promotes and celebrates the integration of science and Christian faith.”


Science and Christian faith?

As far as Science, does BioLogos have blogs about NASA projects, cancer treatments, stem cell research, or any number of other scientific/medical pursuits?


Any besides particular research involving the word evolution?


As far as Christian faith, do you consider evangelicals or Catholics to be un-Christian? You said “We need protestant, conservative protestant, theologians and philosophers addressing questions like this… The bottom line is that BioLogos is initiating the conversation for conservative protestants.


Should the BioLogos mission statement be revised to “The BioLogos Foundation explores, promotes and celebrates the integration of Evolution and conservative Protestantism”?


Dennis Venema - #67689

February 5th 2012

Hi Crude,

I said from the start I’m fine with Dennis explaining what, if any, power he sees God as having over evolution. 

Well, If that’s what you’re truly asking, then it’s an easy answer. I believe God created and continues to sustain the entirety of the cosmos, moment by moment. We observe that sustaining both in what we would call natural mechanisms and supernatural events - both have their source in God, and both are means of His providence. 

Crude - #67718

February 6th 2012


Thank you for your reply.

Since you asked a few questions to clarify what I was asking, I hope you don’t mind me asking a few to clarify your answer.

You say “I believe God created and continues to sustain the entirety of the cosmos, moment by moment.” And I assume you hold God to be omniscient and omnipotent - you certainly haven’t denied as much. You also mention that God uses both natural mechanisms and supernatural events, so (like me) you see no requirement that God uses a miracle.

So then, you believe God knew what evolution would result in, in advance of His beginning the process. And of course, He had and has complete power over that process - He chose what would result. So you’d hold evolution to be - ultimately, and not necessarily in a way that requires intervening miracles - guided and purposeful.

Do I have you correct?
Crude - #67735

February 7th 2012

By the way, Dennis. I’d like to also ask you the same question Darrel Falk answered - I really appreciate his (the ED of this site, I’m flattered!) input, and loved his answer.

Do you regard it as entirely compatible with science to regard evolution as guided and purposeful - and that God knew what the results of evolution would be, and intended those results to come about, in advance of them doing so?

Thanks again, I really appreciate your willingness to answer questions like these!
Dennis Venema - #67748

February 7th 2012

Hi Crude, 

For me these questions are a subset of the larger free will / predestination question. I hold that God ordains and sustains all things, and that he is all-powerful. I also feel that he values freedom greatly - I am not a Calvinist. I believe God has given humans free will, and I also believe that he has given his creation freedom within the bounds he has set for it through natural law. How God balances his sovereignty with his delight in freedom is something I do not claim to fully understand. I tend to be ok with a little mystery. 
Crude - #67758

February 7th 2012


Thank you for your reply.

Yes, there’s nothing wrong with mystery. Still, Biologos - understandably - puts limits on mystery. I’m sure you do not defend saying, “Well, earth is 6000 years old and all creatures were created fully formed rather than in a way involving common descent. How? Well, that’s a mystery.” or anything similar. 

On the other hand, Darrel Falk would presumably agree that it’s entirely acceptable and scientifically valid to say (even if his own view may differ), “Evolution is guided and purposeful, and God knew exactly what creatures would originate from evolution. He knew what would result. Exactly how He did this, we cannot say for certain.” Not all mysteries are created equal.

Still, one could imagine that guidance and purpose is not binary. God could, for example, foreknow and pre-ordain that mammals should be created through evolution - say, He knew in advance this would take place - though perhaps He allowed some freedom such that He did not ‘build in’ a guarantee of lemurs in the process. Or, God could have foreknown and pre-ordained that some creatures would appear, but not others. Say, God made certain cats were created, but mice? Perhaps they weren’t so certain, for whatever reason.

Granted, this seems to displace either omniscience or omnipotence (or both), but hey, let’s keep all the options on the table.

So I’d ask you to what extent do you believe and feel that evolution was guided and purposeful, and which ends were pre-ordained? Mind you, I am not asking for what you know beyond a shadow of a doubt. Just what you believe, even if you call yourself an amateur. Did God know and preordain it all, up to the introduction of man? Did God know and preordain some things - (mammals and bipeds shall appear) but not others (platypus? what the..)?

And, you may have missed it before, so I’d like to ask this again: Do regard it as entirely compatible with science to regard evolution as guided and purposeful - and that God knew what the results of evolution would be, and intended those results to come about, in advance of them doing so?

Of course, saying ‘Yes’ does not commit you to the belief that this, in fact, happened - only that it’s entirely compatible. See Falk’s great answer for an example of this. And thanks for answering these questions.
Jon Garvey - #67736

February 7th 2012

On the subject of the original post, this article seems very relevant: http://rnajournal.cshlp.org/content/17/5/792.abstract Unfor.tunately only the abstract is available free online.

It does show again the risk of the “Junk of the Gaps” argument, and raise the question (once more) of whether it is more valid to look at pseudogenes as rubbish that, fortuitously, finds an extensive range of functions; or rather as a functional element that either fortuitously loses function - or perhaps, whose function is at a more sophisticated level than that of mere coding genes.

Incidentally, as Mike Gene points out in his blog, since transposons do no significant harm and may be even occasionally co-opted to function, they cannot correctly be said to be parasitic, where the relationship to the host is definitionally harmful. Symbiosis might be a better term since both “parties” benefit - but if one still wishes to downplay function, “commensal” would be a less-loaded and more correct term.

Mike, incidentally, is not happy with the view that transposons are “alien” elements at all.

vince - #67752

February 7th 2012

In my family we used to have a family joke “which one is the doctor?” My grandma would invariably come into a movie or TV show in the middle and ask to be brougth up to date way after it was too late.  In one, she asked the above question, and we all decided it was the perfect example of this behavior. So whenever someone got involved in a discussion in the middle, one of us would ask “which one’s the doctor?”  I feel like Grandma in this discussion as I just joined Biologos and this is the first thread I have read. Is it OK to butt in? I will offer the briefest comment and then you can throw me out or invite me back.  It has to do with “mystery” and I have always pondered whether that meant something we can never know, by its nature, or something that might somehow be solved or at least approached more closely given more effort to find and think about information.  I belive that the mystery of free will is something we can know more about, but perhaps never totally decode, just as we might be able to accelerate an object eventually to near light speed but never quite get there - like the “Library”

beaglelady - #67757

February 7th 2012

Hi Vince,

Welcome aboard!!!  Of course it’s okay to butt in, but you also might like to check out the “Questions” and “Resources” links on the menu to get up to speed. Maybe you have already done so.  Trouble is, there is a lot of material!

I think you are right that we will never fully understand certain mysteries of the faith, such as free will.   This is not to be confused with a scientific mystery (ignorance), which is open to investigation. 

Chip - #67755

February 7th 2012

Crude asks: 

Do you regard it as entirely compatible with science to regard evolution as guided and purposeful…?

If Dennis and others are going to make the case for evolution-as-providence, they’ll have to explain it to mainstream science, who answer Crude’s question with an unqualified no: 

[Darwin’s] alternative to intelligent design was design by the completely mindless process of natural selection, according to which organisms possessing variations that enhance survival or reproduction replace those less suitably endowed, which therefore survive or reproduce in lesser degree. This process cannot have a goal, any more than erosion has the goal of forming canyons, for the future cannot cause material events in the present. Thus the concepts of goals or purposes have no place in biology (or any other of the natural sciences), except in studies of human behavior.

-Douglas Futuyma, Evolution, p. 282, my emphasis

Chip - #67756

February 7th 2012

Sorry—eEmphasis didn’t come through the editor, but you get the idea—Futuyma was pretty clear even without my italics…

Crude - #67759

February 7th 2012

Actually, I think Douglas Futuyma’s statement is a little more complicated. Probably moreso than he himself thought or intended.

A mind can endow a process - even create a process - with a goal, that the process itself, examined without the mind, will not have.

Let’s use Futuyma’s example of erosion. Erosion as erosion can’t be said to have a goal (thomists would argue that it does have a final cause, but let’s put that aside.) Abstracted away, erosion is merely a description of a process that neither has a goal nor lacks it. But does that mean I can’t use erosion to form a canyon? Of course not. If I have the time, the knowledge, and the power, I can use erosion to form canyons and whatever else I please.

Now move to evolution. Again, a description of the evolutionary process makes no reference to a mind. But of course evolution can be used towards an end - one would use artificial selection and/or non-random variation.

So if a scientist (‘science’ says nothing) were to say that evolution-as-providence is off the table ‘according to science’, they’d be wrong. No matter how mainstream their view.
Chip - #67774

February 8th 2012

I guess I introduced Futuyma to act as a sort of foil against the clintonesque answers provided by Biologos  to your initial question.  Sure, water can be channeled or put under pressure by an intelligent agent to achieve a certain end.  But if you use erosion to form a canyon, are you not explicitly guiding it?  Of course you are.  There is a huge difference between that, and simply turning on the faucet and leaving natural law to its own devices.     

To return to your original question, if evolution was God’s means of creating, then it has to have been guided (even if the guidance is done in some subtle way that can’t necessarily be detected).  Without guidance and engagement at some level, in some way, “let us make man in our image” becomes “Hmm, look what happened,” which is not at all consistent with any flavor of Christian theology I’m familiar with, all references to mysteries notwithstanding. 

Crude - #67776

February 8th 2012


I agree with you about the huge difference. And yes, at least in some way you’re absolutely guiding it in the example I gave. My only real point was that ‘mainstream science’, as you quoted it, wasn’t science. Even if some scientists don’t realize it.

I’m grateful to Dennis and Darrel both for their giving some answers to my questions. But at the same time, I think that direct answers are important. Really, the example you gave here was perfect because it indicates precisely one major problem with how modern evolutionary thought is communicated - people get the impression (and they get it because they are told this, sometimes by scientists) that evolution is unguided, and that the idea of evolution being guided an ultimate sense, in any way, is not compatible with science. That’s wrong. And the way to combat that is not to appeal to mystery, but (like Darrel did, to his credit) point out that it’s wrong.

That still leaves the question of individual faith to it (Someone could in principle agree that it’s entirely scientifically possible that evolution is guided, while not thinking this was the case themselves for whatever philosophical or theological reasons), but it’s a step in the right direction.
Jon Garvey - #67766

February 8th 2012

In Biblical terms a “mystery” is something once hidden, now revealed. But we’re using it here as “apparent inconsistency,” eg “how God balances delight in freedom with sovereignty”.

The question is partly who sets up such mysteries. For example, the Bible clearly talks about human freedom and accountability, yet equally clearly about God’s sovereign ordering of events including human actions. Reformed thinkers accept that as a mystery, with the resolution presumably somewhere in the interface between God’s dwelling in eternity and infinity and ours in the flesh. In the end, though, if God says directly that he sees them as compatible, and we don’t, then accepting the mystery is a necessary part of humble faith.

The idea of “the freedom of creation” is different. It’s hard to argue from Scripture, and seems to have arisen only recently from speculation about what God’s nature ought to be, by projecting the idea of human liberty on to inanimate things. Logically it runs into problems in that unless one has a vitalistic view of nature, it’s not clear how non-sentient rocks and particles would want, or use, “freedom”.

Yet the “mystery” that this hypothesis sets up for God’s sovereignty is a starkly logical one: if he does not direct nature’s ends by natural law, does not intervene by miracles  and does not oversee the outcome of stochastic events the “mystery” is simply that one has arbitrarily removed all conceivable (and historically Christian) means for his activity and tacked on “yet he’s sovereign anyway.”

For accepting mystery to be a virtue one needs to be pretty damned sure that both sides of the mystery are actually true. Otherwise it may just be just muddled thinking.

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