The Origin of Biological Information, Part 2: E. Coli vs. ID

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March 24, 2011 Tags: Design

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

The Origin of Biological Information, Part 2: E. Coli vs. ID
If your heart is right, then every creature is a mirror of life to you and a book of holy learning, for there is no creature - no matter how tiny or how lowly - that does not reveal God’s goodness.

Thomas a Kempis - Of the Imitation of Christ (c.1420)

In the first post in this series , we explored the claim made by Stephen Meyer, a leader in the Intelligent Design Movement (IDM), that “specified, complex information” cannot arise through natural means. This is crucial to Meyer’s argument, since any natural mechanism that can be shown to produce information would render his argument that information only arises from intelligent sources null and void.

A second member of the IDM who frequently makes this argument is Douglas Axe, a researcher at the Biologic Institute. Axe’s specialty is in protein structure / function relationships, and he has published a few papers in this area in the mainstream scientific literature. Axe’s work also forms the basis for Meyer’s arguments in this area in his book Signature in the Cell. I met Axe a few years ago when I gave a presentation at Baylor, and again last year in Austin for the Vibrant Dance conference (for whatever reason, it seems we only cross paths in Texas). Axe was present in the audience for a discussion session I shared with Richard Sternberg, and we had a significant amount of back-and-forth. As such, I am familiar with his line of argument, and it matches what we saw previously in Signature (as one might expect, since Meyer bases his work on Axe).

Perhaps the best summary of Axe’s argument is his quote I highlighted previously (begins approx. 15:19):

“Basically every gene, every new protein fold… there is nothing of significance that we can show [that] can be had in that gradualistic way. It’s all a mirage. None of it happens that way.”

One of the interesting features of the IDM is that though it has not yet brought forward strong hypotheses with which to test ID, it frequently makes testable predictions about natural processes. Specifically, Axe’s hypothesis is that mutation and natural selection will be unable to produce anything significant in a gradual way.

Has natural selection been Axed?

The ideal way to test this hypothesis, of course, would be to follow a population of organisms over thousands of generations and track any genetic changes that occur to see if they result in any new functions. Even better would be the ability to determine the precise molecular mutations that brought about these changes, and compare the offspring side-by-side with their ancestors. An experiment with this level of detail might sound too good to be true, but one of exactly this sort has been going on since the late 1980s, studying the bacterium, E. Coli. It’s called the Long Term Evolution Experiment (LTEE), and it’s the brainchild of Dr Richard Lenski at Michigan State University.

The LTEE started in 1988 with twelve populations of E. Coli all derived from one ancestral cell. The design of the experiment is straightforward: each day, each of the twelve cultures grow in 10ml of liquid medium with glucose as the limiting resource. In this medium, the bacteria compete to replicate for about seven generations and then stop dividing once the food runs out. After 24 hours, 1/10th of a ml of each culture is transferred to 9.9 ml of fresh food, and the cycle repeats itself. Every so often, the remaining 9.9 ml of leftover bacterial culture is frozen down to preserve a sample of the population at that point in time – with the proper treatment, bacteria can survive for decades in suspended animation. Early in the experiment this was done every 100 generations, and later this was shifted to every 500 generations. A significant feature of the LTEE is that these frozen ancestors can be brought to life again for comparison with their evolved descendants: in essence, the freezers in the Lenski lab are a nearly perfect “living fossil record” of the experiment.

It is important to note several things about the LTEE. First, there is no artificial selection taking place. The environment for the bacteria is kept constant: the same food, the same temperature and the same dilution routine are maintained each day. Second, the bacteria in the experiment are asexual: this means that genetic recombination, a hugely important source of genetic variation in sexual organisms, is absent. New genetic combinations in the LTEE must arise solely by mutation. Third, the bacterial populations that started the experiment are unlike any natural population, since they are all identical clones of each other. (In other words, genetic variation in the original 12 cultures was essentially zero). While natural populations have genetic variation to draw on, these twelve cultures started from scratch.

Since its inception, the twelve cultures have gone their separate ways for over 50,000 generations. Early on, the cultures quickly adapted to their new environment, with variants in each population arising and outcompeting others. In order to confirm that the new variants indeed represented increases in function (and thus, an increase in “information”) the evolved variants were tested head-to-head against their revivified ancestors. Numerous papers from the Lenski group have documented these changes in great detail. What was remarkable about the early work from the Lenski group was that tracking the 12 cultures showed that evolution in the different populations was both contingent and convergent: similar, but not identical, mutations appeared in many of the lines, and the different populations had similar, but not identical, increases in fitness relative to the ancestral populations. In the details, evolution was contingent, but overall, the pattern was convergent. As Lenski puts it:

To my surprise, evolution was pretty repeatable. All 12 populations improved quickly early on, then more slowly as the generations ticked by. Despite substantial fitness gains compared to the common ancestor, the performance of the evolved lines relative to each other hardly diverged. As we looked for other changes—and the “we” grew as outstanding students and collaborators put their brains and hands to work on this experiment—the generations flew by. We observed changes in the size and shape of the bacterial cells, in their food preferences, and in their genes. Although the lineages certainly diverged in many details, I was struck by the parallel trajectories of their evolution, with similar changes in so many phenotypic traits and even gene sequences that we examined.

In other words, there were many possible genetic states of higher fitness available to the original strain, and random mutation and natural selection had explored several paths, all leading to a higher amount of “specified information” – information that specifies increased reproduction and survival in the original environment. All this was by demonstrably natural mechanisms, with a complete history of the relevant mutations, the relative advantages they conferred, and the dynamics of how those variants spread through a population. The LTEE is at once a very simple experiment, and an incredibly detailed window into the inner workings of evolution.

And so the work continued, day in and day out, for years – until one day, a completely new biological function showed up in one of the cultures.

One of the defining features of E. Coli is that it is unable to use citrate as a food source. The food used to culture the strains, however, has a large amount of citrate in it – a potential food source that remained beyond the reach of the evolving strains. For tens of thousands of generations, no variants arose that could make use of this potential resource – even though every possible single DNA letter mutation (and every possible double mutation combination) had been “tested” at some point along the way. There seemed no way to for the populations to generate “specified information” to use citrate as a food source – they couldn’t “get there from here.” Then one day, the fateful change occurred in one of the 12 populations. Lenski puts it this way:

Although glucose is the only sugar in their environment, another source of energy, a compound called citrate, was also there all along as part of an old microbiological recipe. One of the defining features of E. coli as a species is that it can’t grow on citrate because it’s unable to transport citrate into the cell. For 15 years, billions of mutations were tested in every population, but none produced a cell that could exploit this opening. It was as though the bacteria ate dinner and went straight to bed, without realizing a dessert was there waiting for them.

But in 2003, a mutant tasted the forbidden fruit. And it was good, very good.

Details, details

Tracking down the nature of this dramatic change led to some interesting findings. The ability to use citrate as a food source did not arise in a single step, but rather as a series of steps, some of which are separated by thousands of generations:

  1. The first step is a mutation that arose at around generation 20,000. This mutation on its own does not allow the bacteria to use citrate, but without this mutation in place, later generations cannot evolve the ability to use citrate. Lenski and colleagues were careful to determine that this mutation is not simply a mutation that increases the background mutation rate. In other words, a portion of what later becomes “specified information for using citrate” arises thousands of generations before citrate is ever used.

  2. The earliest mutants that can use citrate as a food source do so very, very poorly – once they use up the available glucose, they take a long time to switch over to using citrate. These “early adopters” are a tiny fraction of the overall population. The “specified information for using citrate” at this stage is pretty poor.

  3. Once the (poor) ability to use citrate shows up, other mutations arise that greatly improve this new ability. Soon, bacteria that use citrate dominate the population. The “specified information for using citrate” has now been honed by further mutation and natural selection.

  4. Despite the “takeover”, a fraction of the population unable to use citrate persists as a minority. These cells eke out a living by being “glucose specialists” – they are better at using up glucose rapidly and then going into stasis before the slightly slower citrate-eaters catch up. So, new “specified information to get the glucose quickly before those pesky citrate-eaters do” allows these bacteria to survive. As such, the two lineages in this population have partitioned the available resources and now occupy two different ecological niches in the same environment. As such, they are well on their way to becoming different bacterial species.

Don’t tell the bacteria

The significance of these experiments for the Intelligent Design Movement is clear. Complex, specified information can indeed arise through natural mechanisms; it does not need to arise all at once, but rather accrue over thousands of generations; independent mutations that do not confer a specific advantage can later combine with other mutations to produce new functions; new functions can be quite inefficient when they arise and then be honed through further mutations and selection; and the entire process can occur without ever reducing the fitness of a specific lineage within a population. Moreover, these findings have been demonstrated with a full historical record of the genetic changes involved for the entire population they occurred in, as well as full knowledge of their fitness at every step along the way.

In other words, what the IDM claims is impossible, these “tiny and lowly” organisms have simply been doing – and it only took 15 years in a single lab in Michigan. Imagine what could happen over 3,500,000,000 years over millions of square miles of the earth’s surface.

In the next post in this series, we will look at an example of new information and function arising during vertebrate evolution: the elegant work of the Thornton lab on steroid hormones and their protein receptors.


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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R Hampton - #56026

March 29th 2011

Before you answer, remember that the best modern science, the same
population genetics reasoning that supposedly proves the truth of
Darwinian evolution, allegedly proves that an original pair is
impossible.


Catholics are not the only Christians who believe the soul is immediately and directly created by God, and by evolution nor sexual reproduction. Therefore population genetics can not disprove that God ensouled only two of the first genetically human beings. Since science can not determine if living people have souls - let alone fossilized Cro-Magnons or Neanderthals - the point is moot.


Rich - #56027

March 29th 2011

Gregory (56006):

I understand that you are not attacking me in the sense of trying to hurt me personally (though sometimes your language is so aggressive, I wonder).  Nonetheless, dialogically speaking, your posts addressed to me tend to be “attack” posts in their literary style.  And they tend to be “attack” posts in this sense:  even though I’ve repeatedly granted the value of sociology in the study of the motivation of ID proponents, you continue to press and press, as if I haven’t granted you enough.  Apparently I will not be able to satisfy you unless I say that the motives of the ID proponents are such that their science is contaminated by wishful thinking and can be discounted.

I won’t do that.  Their (natural) science should be confronted by (natural) science, not by social science in the form of sociology.  The sociology belongs in the analysis of ID’s place in the constellation of culture-war camps, not in the analysis of their math or biochemistry. 

You want to talk about the sociology of the culture wars; I want to talk about the validity of arguments for design.  You are trying to badger me to have a conversation that I’m not interested in having.  Generally speaking, that is considered to be bad manners.   

I don’t badger you, Gregory, into reading up on molecular biology
and information theory.  If you don’t want to learn enough science to understand the arguments of Meyer and Behe, that’s fine with me—as long as you don’t pretend to understand their arguments well enough to reject them.     

Let it go, Gregory.  I’ve already granted that your questions are perfectly valid in their place.  But they have nothing to tell me about the questions I’m interested in.  And they have nothing to do with the technical arguments Dennis is making on this thread. 

Best wishes.


Gregory - #56032

March 30th 2011

“a number of statements have been made by Biologos columnists about Adam and Eve that are out of line with the teaching of historical Christianity.” - Rich

Yes, every time someone suggests that A&E were not ‘real, historical’ people they are “out of line with the teaching of historical Christianity.” You acknowledge this, do you not Rich? Of course you don’t want to, but…

The Old Testament writers you mention: did they most often accept a ‘real, historical A&E,’ even if they didn’t write much about it?

Here is the same question for you, Rich, that made Benoit in France resist coming back to answer it:

“Does D. Venema (or D. Lamoureux) *anywhere* write that genetics/genomics has *proven* a non-real, historical Adam and Eve?”

This question requires no sophistry in Rich’s answer. Yes or No. The question is in simple English.

If he hasn’t read (, corresponded or spoken with) Venema & thus doesn’t know, will anyone who has read (etc.) Venema please answer to this question?

You are surely capable of responding directly to this question, are you not, Rich? I think Benoit Hebert mis-evaluates Venema because he thinks Venema (& thus, the current field of genomics) claims to have *proven* two persons A&E *could not* have existed, when Venema has not (yet) made that claim.

Has he or not? This is asked openly & honestly to a BioLogos community seeking the truth. It would be nice simply to know the current state of Venema’s claims (rather than just if he disagrees with how Meyer approaches/mis-understands evolutionary biology.

I didn’t say ‘primordial human couple’ & besides, this is a diversion in the thread. We’ve discussed this directly on other threads. Be welcome to show up next time.

As fo me, that’s enough with A&E here.


Rich - #56038

March 30th 2011

Me (55718):

“First, Meyer and Behe don’t agree on common decent [sic].”

I never said they did.  And it’s irrelevant to the point I’m making.  Did you not understand my analogy to the Republican Party?

“It is convenient that they belong to a movement where the only commonality is to claim that Darwin’s theory is anti-theistic.”

The main concern of ID as a theory is not that Darwin’s theory is anti-theistic.  The main concern of ID as a theory is that Darwin’s mechanism of evolution is ludicrously improbable and lacks empirical support, and that design seems to be a necessary element in any explanation of the integrated complexity of living forms.  All ID proponents agree on these two things.

Of course, individual ID proponents may well be concerned about the religious implications of Darwin’s version of evolution, and may even write diatribes against Darwin when they write popular columns and books on theology and ethics.  But you don’t see such discussions in Behe’s books, in Dembski’s *No Free Lunch*, etc.

“Most IDers seem incapable of understanding that Darwin’s idea of natural processes occurring to bring about the diversity of life on earth does not mean that the sovereignty of God is weakened.”

It depends on where you put the emphasis.  “Natural processes” in themselves do not weaken the sovereignty of God.  But “Darwin’s idea” of the *sort* of natural processes certainly does, and indeed was intended to, as his remarks on theodicy show.

I have to break off this sub-thread now.


Gregory - #56039

March 30th 2011

It isn’t about me asking you to ‘value sociology’ & I make no plea that you be open to learning. Likewise, it isn’t about ‘granting me enough’. It is about trying to better understand & to seek truths, which means sometimes involving viewpoints we’ve set aside, never known or long forgotten. Be open to enriching yourself, as I have been by your discussions in fields less or unfamiliar to me.

“Their (natural) science should be confronted by (natural) science, not by social science in the form of sociology.  The sociology belongs in the analysis of ID’s place in the constellation of culture-war camps, not in the analysis of their math or biochemistry.” - Rich

I don’t speak much of ‘culture wars’ & that need not be forefront (though certainly not absent) in a sociological analysis of the IDM. ‘Culture war’ is mainly a USA thing & I don’t live in USA. Likewise, I don’t cite the four horseys very often, which seems to be par 4 the course with c-warriors. So, that one might stick more on yourself than on me. 

Of course I agree with the ‘sovereignty of the spheres’ (Kuyper) wrt maths, biochem, sociology etc. All scientific/scholarly fields have their boundaries & limitations within which they define their subjects/objects of study. My argument is broader than sociology & overlaps with HPS. It seems to me that Meyer’s conclusion is a philosophical or ideological one, rather than a natural-physical scientific one. At least, in the things of Meyer I’ve read & from hearing him speak, this is my current view. It has not been impressed on me that Meyer is making a significant ‘natural science’ contribution (e.g. his controversial paper, which I read).

You argue *for design* because you are a reflexive human being, not b/c you, Rich, believe in it for ‘scientific’ reasons. You have said something like this at BioLogos before (of course, w/out using ‘reflexive’). It is not a ‘natural science’ of ‘design’ that you would promote, which is what Meyer is trying to propose in ‘changing the definition of natural science.’

It is indeed a reflexive way of expressing yourself (when your generations were told that is taboo!) that both he & you intuitively seek (perhaps) & also lack. However, teachings to aid your expression can be found in HSSs, which offer a more powerful explanation of ‘intelligent design’ than *anything* yet offered in the IDM. Otoh, I’m glad you don’t have this tool. Otoh, I wonder what a guy like Mike Gene could actually do with his new way of speaking for both NPSs & HSSs about the socially & culturally-influenced ‘conclusions’ that folks like D. Venema have reached.

Oh, was this just a thread about Meyer’s book, biochemistry & information theory (which Rich is in little position to speak about with any authority because he hasn’t read Shannon, let alone Kolmogorov)?

intellectual honesty compels me to confess that I have not read Shannon’s work on information theory.” – Rich


It seems to me, Rich, that you perceive my words as ‘attacks’ only because they wound your position quite accurately & fairly. I consider it good sport, not aggresive. Touche, when it is made! That is, when I point out what ID lacks in explanatory power (e.g. who, what, when, where), you don’t want to talk about ID’s (lack of) content, only the misrepresentation of IDists from opponents (i.e. the ‘go read’ argument). When I challenge with clear cross-examinations any ID content that you occasionally defend, using the ‘knives of reason’, it becomes safer to say ‘you’re missing the point’ to me, rather than to admit ID weaknesses (which presumably you do also care about).

Yes, my arguments are, ‘dialogically speaking,’ sometimes aimed to undermine your defenses. I find they often succeed in that I have *never* seen you offer a positive definition of ‘intelligent design’ on a public discussion board. Have you?

The weak explanatory power of saying ‘biological information *simply was* originated by/with intelligence/mind’ is not strengthened by saying ‘IDists are misrepresented.’ & that is enough with ID-talk for me on this thread.

“The truth knocks on your door, and you say ‘Go away, I’m looking for the truth.’ So it goes away. Puzzling.” - R. Pirsig


penman - #56057

March 30th 2011

Rich & Gregory
“If evolution over billions of years is true, Genesis *is* wrong, if it
is meant to be taken in the way that Martin Rizley and all YECs take it,
i.e., as a literal transcript of the order of events, and as occurring
on six days (evening and morning).  Now, you affirm (or by your silence
here consent to) the proposition that evolution over billions of years
has taken place, and therefore, if Martin could prove that Genesis was
meant to be taken literally, you would have to say that Genesis was
wrong” (Rich).

I’d have to agree with Gregory that this is a matter of how Genesis is to be interpreted, although Rich’s phrasing suggests he might not actually disagree. Yes, if a YEC interpretation of Genesis is correct, then Genesis is wrong. The earth isn’t young. And if some form of evolution isn’t true, we may as well give up even trying to do science: the data has obviously been rigged to deceive us.

But I don’t wish to identify Genesis with a particular interpretation thereof. The YEC gloss is only one. Other views have been expounded & defended by competent biblical scholars. I take the “framework” view, not because I’m desperate to harmonize Genesis with science (when driven by that motive in the past, I adopted the day-age view), but because I’ve become convinced it’s the best or least problematic reading of the text itself. A very competent older treatment is in Henri Blocher’s “In The Beginning”. Lee Irons is a more recent advocate of no mean intelligence who writes accessibly; his expositions can be readily found on the web (he’s an Old Earth Creationist).

And of course the framework view has its roots in Augustine, who manifestly wasn’t motivated by the wish to reconcile Genesis with modern geology.

Further, I think there’s a sound, respectable argument for taking Adam seriously - yes, Romans 5 would figure strongly there, but so would a good spread of other passages. (I’ve opined before that I see nothing in scripture requiring Adam to be the single biological father of all humanity, only the representative covenant-head: the very point of the Adam-Christ parallel in Rom.5. Christ isn’t the biological father of the New Humanity.)

But I accept that insofar as Genesis paints cosmological pictures, it’s using the popular images of the day, which are not physically correct. That doesn’t trouble me overmuch; I can’t remotely believe that “science” falls within the magisterial intent, the teaching purpose, of scripture. And I’ve always thought that scripture’s veracity has to be correlated carefully with its magisterial intent.


Rich - #56090

March 30th 2011

penman (56057):

Yes, you are right that I am trying to agree with Gregory about Genesis, at least in part.  But he does not recognize it.  He also does not recognize that in his posts he is practicing “selective literalism.”  And this selective literalism is bringing him into conflict not with me, but with Drs. Venema, Lamoureux, and Alexander.

As I understand the argument that the biologist-TEs here are making, it is this:  The mathematics of inheritance shows that (a) if we are determined to hold to a *recent* ancestry of all modern human beings, we cannot back-project to an original couple, or to any group smaller than a breeding population of maybe a thousand individuals (and even in this case, that population would have to be dated tens of thousands of years earlier than Bishop Ussher’s genealogy allows); (b) if we are determined to have an original couple (Adam and Eve, or Harry and Sally, or Gronk and Shad, or whatever) as the ancestors of all living human beings, we have to go back on the order of 5 to 9 million years, i.e., to the pre-hominid primates; in other words, Adam and Eve would have to be a sub-human couple, an animal couple. 

Now, as I understand Gregory’s posts (which I may not, because he tends to write in short, elliptical, rhetorical flourishes rather than extended expository prose), Gregory is indignant at the TE-biologists here for denying what he calls the traditional Catholic, Orthodox, and Protestant understanding of Adam and Eve.  That traditional understanding made Adam and Eve not merely the spiritual original of all modern human beings, in the sense of being the first to possess the image of God, but the physical ancestors of all human beings.  So, if he is being consistent, Gregory must be affirming that Adam and Eve are the first biological parents of all human beings now living, and of all human beings who have ever lived. 

But this is precisely what the arguments of Dennis Venema etc. do not allow.  If you want the first biological parents, you’ve got some pre-human apelike or monkeylike pair of animals, who could not possibly have been in the image of God or have understood a commandment well enough to disobey it and “fall.”  Or if you are determined to have a meaningfully human biological ancestry for all persons now living, you can’t get back to an original couple, but only to a breeding population; our genes come not from a single pair, but from this population. 

It is this problem which led Denis Alexander to write his series of columns, offering various ways in which one might retain some notion of Adam and Eve, within the factual constraints imposed by biological science.  But Gregory seems to reject the whole premise that there is any problem.  As far as I can tell from his comments, he thinks that if TE-biology denies a biological Adam and Eve, then TE-biology is both unorthodox and false.

So on the one hand Gregory is dumping Genesis literalism (Genesis 1), but on the other hand he is affirming it (the Adam and Eve aspect of Genesis 2).  But that affirmation brings him into conflict with the very evolutionary science that he claims to accept.  I would like to know on what grounds he practices such selective literalism.  It seems to me that Martin Rizley’s rigorous literalist position is more consistent.  And in any case, this selective literalism has landed Gregory in a halfway house which is equally unacceptable to YECs and TEs.  I count on his “reflexive thinking” to enable him to eventually grasp the situation he has put himself into.


R Hampton - #56104

March 30th 2011

That traditional understanding made Adam and Eve not merely the
spiritual original of all modern human beings, in the sense of being the
first to possess the image of God, but the physical ancestors of
all human beings.  So, if he is being consistent, Gregory must be
affirming that Adam and Eve are the first biological parents of all
human beings now living, and of all human beings who have ever lived.

The Catholic Church has moved on, Rich. Yes, there can be more than two biological parents (some of us have Neanderthal genes in our genome) and yet still have two and only two spiritual parents.

70. With respect to the immediate creation of the human soul, Catholic theology
affirms that particular actions of God bring about effects that transcend the
capacity of created causes acting according to their natures. The appeal to
divine causality to account for genuinely causal as distinct from merely
explanatory gaps does not insert divine agency to fill in the “gaps” in
human scientific understanding (thus giving rise to the so-called “God of the
gaps”).  The structures of the world can be seen as open to non-disruptive
divine action in directly causing events in the world.  Catholic theology
affirms that that the emergence of the first members of the human species
(whether as individuals or in populations)
represents an event that is not
susceptible of a purely natural explanation and which can appropriately be
attributed to divine intervention.  Acting indirectly through causal chains
operating from the beginning of cosmic history, God prepared the way for what
Pope John Paul II has called “an ontological leap…the moment of transition to
the spiritual.”
  While science can study these causal chains, it falls to
theology to locate this account of the special creation of the human soul within
the overarching plan of the triune God to share the communion of trinitarian
life with human persons who are created out of nothing in the image and
likeness of God, and who, in his name and according to his plan, exercise a
creative stewardship and sovereignty over the physical universe.   

http://www.vatican.va/roman_curia/congregations/cfaith/cti_documents/rc_con_cfaith_doc_20040723_communion-stewardship_en.html



John - #56108

March 30th 2011

Bilbo:

“No.  Whether one wants to call it “waiting for mutations” or “waiting for alleles to become fixed in the population,” if we need too many, there seems to be a problem for neo-Darwinism.”

My dear Bilbo, perhaps you should read the first few pages of Behe’s book! He makes it very explicit that he accepts selection and is limiting his thesis to the role of [random] mutation. It’s therefore very important to determine whether he is actually doing that.


John:  “Does that involve waiting for them to appear in the population? IOW, isn’t Behe’s whole book about misdirection?”

Bilbo: “No, as I explained above.”

I don’t see an explanation, just a denial. 

John:  “Or falsify one, but you can’t bring yourself to consider that.”
Bilbo: “Yes, I am willing to consider that.”
John: “I don’t believe you.”

Bilbo: “Why not?”

Because you’re desperately misrepresenting Behe’s thesis to protect the tribe.

John:  “And the answer to the multiplication is…? “

Bilbo: “Irrelevant, since the only point you were making is that we should be calling it “alleles fixed in the population,” not “mutations.””

It’s relevant to assess Behe’s claim that there is waiting for mutations involved. We already know that selection can’t do many things, so if we’re waiting for selection, we aren’t waiting for mutations. 


John - #56109

March 30th 2011

John:  “No, and the stop mechanism accomodates that. Can you also imagine that since proteins have different functions, they may need to START with different residues?”



Bilbo: “Good point.  Does the start codon prevent that from happening?”



John: “In translation, absolutely. That’s one of my points.”



Bilbo: “Ah, finally, something relevant.  So does this create a problem for the folding of the protein?”



Yes, very often. 



John: “So wouldn’t a system in which start codon(s) did not code for any residue be far more intelligently designed than the one we have now? “



Bilbo: “Possibly.  We need more information, like the answer to my question above.”



You have your answer.


Rich - #56112

March 30th 2011

R Hampton (56104):

Take it up with Gregory.  It was his argument I was paraphrasing.

If only it had been someone else here who had provided me with such a great straight line about “Neanderthal genes”!  I would have been strongly tempted to break my policy of silence, given such a Huxleyan moment.


R Hampton - #56113

March 30th 2011

So on the one hand Gregory is dumping Genesis literalism (Genesis 1),
but on the other hand he is affirming it (the Adam and Eve aspect of
Genesis 2).  But that affirmation brings him into conflict with the very
evolutionary science that he claims to accept.


That two spiritual parents existed does not negate a scientific claim of an initial population of biological parents. There need be no conflict with evolutionary science as you argue here. So I understand Gregory’s position as a rejection of a wooden Biblical literalism but not of Biblical truth.


Gregory - #56115

March 30th 2011

“I am trying to agree with Gregory about Genesis, at least in part.”

The ‘in part’ is the obvious catch.

“So I understand Gregory’s position as a rejection of a wooden Biblical literalism but not of Biblical truth.” - R Hampton

Yes, R Hampton is correct and Rich is attempting to twist my views (intentionally or unintentionally is unclear).

As I said, done with A&E for me here. This has been covered on other threads & others have responded better than I could to Rich’s anti-real, historical A&E hypothesis & chosen points of argument.

As if I could stomach a biologist & a condescending ‘intellectual historian’ ganging up to dictate to me how I should study, understand & speak about anthropos, ‘human beings’, which we all agree (even if it has little to do with biology or population genetics) were ‘made in God’s image!’


Bilbo - #56118

March 30th 2011

John: 
“Or falsify one, but you can’t bring yourself to consider that.”
Bilbo:
“Yes, I am willing to consider that.”
John: “I don’t believe you.”

Bilbo:
“Why not?”

John:  “<i>Because you’re desperately misrepresenting Behe’s thesis to protect the tribe.</i>”

No, I’m translating Behe’s thesis into your insistence on talking about genetic variations or alleles.  When Behe says that a certain two mutations appear together every 10^20 organisms, that would mean that we should expect to find those two genetic variations or alleles in every 10^20 organism, unless they have become fixed in the population.

John:  “No, and the stop mechanism accomodates that. Can you also imagine that since proteins have different functions, they may need to START with different residues?”

Bilbo: “Good point.  Does the start codon prevent that from happening?”

John: “In translation, absolutely. That’s one of my points.”


Bilbo: “Ah, finally, something relevant.  So does this create a problem for the folding of the protein?”


John:  “Yes, very often.”

John: “So wouldn’t a system in which start codon(s) did not code for any residue be far more intelligently designed than the one we have now? “

Bilbo: “Possibly.  We need more information, like the answer to my question above.”

John:  “You have your answer.”

In that case I would say that you have presented a strong challenge to the ID hypothesis, which should weaken it somewhat.  Of course, if we find a good ID explanation for the start codon, then we have additional evidence for the the ID hypothesis.  In other words, you and I have engaged in trying to either falsify or verify ID.  Sounds a lot like science to me.


John - #56123

March 30th 2011

“As I understand the argument that the biologist-TEs here are making,…”


Note that Rich presents this as just an “argument,” not evidence. Groups of people always have to be labeled, because Rich loves the tribalism that Jesus Christ taught us to resist.

”… it is this:  The mathematics of inheritance shows…”

Note that the evidence shows this, not some abstract mathematics. But Rich does his best to avoid mentioning evidence. When he does, he invariably gets burned.

“But this is precisely what the arguments of Dennis Venema etc. do not allow.”

Again, note that there’s no mention of the evidence Dennis Venema presented, because Rich can’t explain it to save his life (or to save his soul). So the scientific question is, does the evidence allow it?Rich frames everything as opposing tribes armed with nothing but rhetorical arguments. Rich desperately wants readers to think that it’s all rhetoric on both sides, because his own side is all rhetoric.

John - #56127

March 30th 2011

“No, I’m translating Behe’s thesis into your insistence on talking about genetic variations or alleles.”

Bilbo, you’re doing nothing of the sort.

“When Behe says that a certain two mutations appear together every 10^20 organisms,…”

And he quote-mines a review that is referring to the fixation of mutant alleles, he is deceiving his audience.

”... that would mean that we should expect to find those two genetic variations or alleles in every 10^20 organism, unless they have become fixed in the population.”

Yes, and he’s wrong, which you can see by doing the math that you’re afraid to do. Behe makes the same sophomoric mistake or misrepresentation again and again.

“In that case I would say that you have presented a strong challenge to the ID hypothesis, which should weaken it somewhat.”

Shouldn’t a hypothesis be consistent with all the extant data to have any validity at all?

“Of course, if we find a good ID explanation for the start codon, then we have additional evidence for the the ID hypothesis.”

That’s truly insane. Explanations aren’t evidence. 

“In other words, you and I have engaged in trying to either falsify or verify ID.  Sounds a lot like science to me.”

I don’t see that you have done anything of the sort. Remember, it’s easy to generate testable ID hypotheses, but no one on your side has sufficient faith in any of them to test their empirical predictions.


Rich - #56160

March 31st 2011

Gregory 56115):

“So I understand Gregory’s position as a rejection of a wooden Biblical literalism but not of Biblical truth.” - R Hampton

“Yes, R Hampton is correct and Rich is attempting to twist my views (intentionally or unintentionally is unclear).”—Gregory

Gregory, for me to attempt to twist your views, I would have to understand them first. But your writing is often so fragmentary, scattershot, and unclear, that I can’t be sure what you mean.  I’m doing the best I can (not to twist your views, but) to determine what you mean.

I thought you had asked for my opinion what Dennis Venema believed about Adam and Eve as biological first parents of the race. I’ve given you my understanding. I may have got his argument wrong, so if you think that, you’ll have to ask him instead.

I’m working on the assumption that you have understood what the three Den(n)ises are saying: Adam and Eve cannot have been the common parents of the entire human race; thus, the traditional Christian reading of Genesis 2-3 is no longer tenable. And I notice you’ve been indignant about that conclusion, on several threads, over the last several months.

Since the three Den(n)ises (or at least two of them) are willing to grant that an Adam and Eve who were spiritual heads of the race—the first fully human beings, who possessed the image of God, disobeyed, and fell —could have existed (though much longer than 6,000 years ago), you can’t be indignant about that. It follows that what upsets you is that Adam and Eve can’t be the common ancestors of the whole race, and that you are holding out for the view that they are. Well, if they are, then something is wrong with science of population genetics that Dennis Venema is using. And it’s the same science he uses to validate Darwinian evolution. So what are you saying, that the science is correct regarding dinosaurs and hedgehogs, but wrong regarding man? I don’t think Dennis will agree with you.

The blunt questions you have to ask and answer for yourself are: “Do I believe that there existed a first human couple who were the genetic parents of all human beings who have ever lived?” and “Is such a belief essential to a belief in the Fall, as understood by Paul and later Christian tradition?” If your answer is “yes” to both questions, then you have no choice, on the issue of Adam and Eve, but to side with Martin against Dennis, and that means setting yourself against the current consensus of population geneticists and anthropologists. Are you willing to do that?


Rich - #56165

March 31st 2011

Gregory (56115):

You wrote:

“As if I could stomach a biologist & a condescending ‘intellectual historian’ ganging up to dictate to me how I should study, understand & speak about anthropos, ‘human beings’, which we all agree (even if it has little to do with biology or population genetics) were ‘made in God’s image!’”

Gregory, I have not seen even one person here saying anything at all about how you should “study, understand & speak about anthropos.” Can you show me where anyone has done this?

You are a sociologist. Everyone here is quite content to let a sociologist study human beings sociologically. Nobody has told you to stop doing sociology or any other form of social science. You are imagining things.

In the meantime, Dennis Venema wants to study human beings genetically, and I want to study them philosophically, and through the medium of religious writings, including Genesis. I presume that you are not telling Dennis or myself that we have no right to study human beings in these alternate ways, and that we should stop doing so?

It is difficult for me—and I suspect for most readers here—to understand what you are asking for. That biologists should broaden their minds by reading a little sociology? Well, I’m all in favor of that, and maybe the biologists here are, too. But are you also demanding that, if a conflict comes up, regarding the interpretation of man, between genetics and sociology, they defer to sociology?

Are you saying that I should be aware of the sociological dimensions of the ID debate? I already am, and I was long before I ever heard of you. I’m well aware of the divisions of American Protestantism and the cultural tensions in the USA over creation and evolution. I’m fully aware that there are a lot of fundamentalists who back ID not out of any genuine theoretical interest but because the think they can use it as a club to beat off evolution. I’m fully aware that Discovery receives funding from fundamentalists (as I hope you are aware that Biologos receives funding from a foundation endowed by a religious liberal). The sociological dimension of all this has not escaped me.

Or are you saying that Stephen Meyer’s latest book is filled with religious prejudices, and that my job in reading it is to “deconstruct” it, showing how all his allegedly objective arguments are merely expressions of his Christian will to power? If so, then lend me your expertise; walk me through the book, chapter by chapter, showing how all his scientific and philosophical arguments are really impositions of his world-view. I’m willing to learn. Really I am. All you have to do is start talking about what’s in the book.


penman - #56176

March 31st 2011

I don’t want to get caught in the Gregory-Rich crossfire, but…

It’s true that in the past history of interpretation (pre-modern-geology & biology), those who accepted a historical Adam saw him as the biological father of all “imago dei” humanity. They also identified imago dei humanity with all existing humanity.

So it’s also true that on this point, folk like me should admit that we’re taking a different path of interpretation, when we see Adam as the federal head of imago dei humanity but not its biological father.

But I’d argue that we’re not sacrificing anything essential in the catholic tradition. We’ve retained everything that matters: a historical Adam, a representative head of the race, a historical fall, & the Adamic sin as the primal source of humanity’s problems which rectified in Christ. I’d further argue that the view of Adam as biological father of all humanity was in effect a *scientific* opinion, which shares in the flux of all scientific opinions (like geocentrism). It isn’t actually an exegetical necessity.

The one area where the leading TE/ECs to whom I’m closest seem to differ from me is in not seeing physical death but only spiritual death as a consequence of the Primal Sin. I’d have to argue that physical deatrh is a consequence of the Fall, in the sense propounded (e.g.) by Athanasius. Imago dei humanity - homo divinus - was given the potential for immortality, to be actualized through obedience. Disobedience meant the loss of that potentiality. So whereas the *capacity* for death wasn’t the result of the Fall (but part of mere nature), the *inevitability* of death flowed from the Fall. In Adam we were already *capable* of dying; but through sin, we are *doomed* to die. There’s a difference.

There, just thought I’d clear the morning air…


Gregory - #56236

March 31st 2011

Thank you for your morning fresh air, penman!


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