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

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March 24, 2011 Tags: Design
The Origin of Biological Information, Part 2: E. Coli vs. ID

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

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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Rich - #55822

March 27th 2011

Gregory (continuing reply to 55806):

“It would be the same *if* Rich claimed the idea of ‘methodological naturalism’ is not a u.s.american idea. That perspective is simply unsustainable once one widens their view of it to include people, not just treating it an an ‘objective’ idea. MN was coined in USA (which doesn’t mean others can’t/don’t use it, but we know the context of origin).”

Gregory, I agree with you, and with Steve Fuller, that the way that “methodological naturalism” is used in the evolution debates—and possibly even the phrase “methodological naturalism” itself— has a social origin, in the need of atheists like Eugenie Scott to find out a way to exclude design from the study of origins without being accused of a religious position herself (i.e., atheism).  So her gang comes up with this clever distinction between “methodological naturalism” and “metaphysical naturalism,” which allows them to have all the benefits of atheism without falling afoul of the First Amendment.  Steve Fuller has nailed this one down beautifully.

Nonetheless, whatever the *motivation* for the distinction, the most important question is whether the distinction is sound.  While we might naturally suspect that any distinction supported by Eugenie Scott is likely to be specious and politically motivated, that does not prove that the distinction is invalid or seriously misleading.  In order to prove the latter, we have to do what Steve Fuller does—research into the history, philosophy and sociology of science, and try to show the artificial and ad hoc character of the notion, and how it falsifies both the history and the current reality of scientific practice.

Thus, while I agree with you on the sociological point, it makes no difference as to how I proceed.  The sociological insight explains *why* Eugenie and her gang promote a specious distinction.  It does not prove that the distinction is specious.  That requires a separate argument. 

Gregory - #55832

March 27th 2011

“her gang comes up with this clever distinction between “methodological naturalism” and “metaphysical naturalism” - Rich

Are you suggesting that Eugenie Scott (&/or ‘her gang’) coined the distinction between MN & MN or that she got it from someone else?

MN is about more than just ‘exclude design.’ It means natural-physical scientists study natural-physical things using the ‘proper’ tools. If you don’t want to use those tools, then don’t claim to be ‘doing science.’ Only ‘design-centric’ people highlight ‘exclude design’ as a leading definition of ‘methological naturalism.’

The sociological point is more important than most points you are making, Rich. It displays a bias in naturalism that can be properly *cleansed* from some academic realms. Your problem would become massively smaller if you likewise lent credence by actually speaking to the points I am making against ‘universalistic evolutionism.’

You’re playing a ‘defense-only’ game. Where’s your offense using ID? I don’t think you could hit 2 free throws out of 50 promoting ‘intelligent design in biology’ with ‘neutral’ scientists based on what you think is ‘intelligent design theory’ now.

Steve Wilkinson - #55828

March 27th 2011

Steve Wilkinson - #55829

March 27th 2011

Or see Nancey Murphy’s “Theology in the Age of Scientific Reasoning” She flakes out a bit by the end, IMO, but the book as a whole is pretty good on the topic.

Rich - #55835

March 27th 2011

Well, Gregory, I can see that continuing to discuss things point-by-point with you is going nowhere, because you in most cases fail to see the point, and even when you do see it, you just ignore it and repeat your previous arguments, as if I haven’t already granted you the validity of sociological analysis, in its proper place (which is not in determining the validity of philosophical or scientific arguments).
I’ve heard you praise Steve Fuller before, but it’s obvious, based on your reply, that you don’t agree with his remarks about methodological naturalism (in one case directed specifically against the NCSE, by the way).  Too bad, because that’s one of his great contributions to the debate, in my view.

Regarding this:

”[Do you] actually think that your ‘intellectual history’ of biology prepares you to defend Meyer’s biological mistakes against specific questions from biologists?”

I have not undertaken to defend any of Meyer’s alleged mistakes against biologists.  I think they should point out every mistake he makes.  What they should *not* do is (a) issue *innuendo* that he has made mistakes, while refusing to specify the mistakes (as one cranky poster here did a number of times, until just recently, when he summoned up enough courage to directly accuse Meyer of specific errors); (b) imply that Meyer’s arguments about the origin of life are invalid because his arguments about Darwinian evolution are invalid.  These are general points about honest argument that one does not need to be a biologist to grasp.

About social sciences:  it is not that I do not care about the social sciences.  It is that they are *irrelevant to the evaluation of the arguments in Meyer’s book*.  And you may have noticed that, while you have been bringing up social science for over a year now, about 95% of the commenters on this site have shown even less interest in your points than I have.  So why pick on me?  What did I do to earn the role of scapegoat for the sins of all the others here?

Gregory, did it ever occur to you that when you post on a web site which is dedicated to the relation between faith and science, particularly *biological* science (BIO-logos, get it?), and are repeatedly disappointed that people don’t want to talk about *social* science, that perhaps it is *your expectations* that are unreasonable, not everyone else’s unwillingness to discuss subjects in which they have neither interest nor competence?  Has it never occurred to you that maybe you are in the wrong discussion group for your interests?

Rich - #55837

March 27th 2011


Just a couple more points, about your misrepresentation of my views on the Bible:

“literal (something like ‘real,’ but much less powerful in 21c.) vs. figurative (read: ‘not real’) = Rich’s dichotomy”

False.  You could not possibly have read my debates with Martin carefully if you think this.  I stressed that the truths of the Bible are not less true than historical facts, but more true than historical facts.  I said over and over again that Martin and the atheists share a modern understanding of truth as “fact,” and that both of them therefore drag the Bible down to the level of a mundane book, rather than one bursting forth with supramundane Reality. 

But Gregory, you are hardly a credible defender of a historical Adam and Eve.  You fully accept biological evolution over billions of years, without batting an eye.  This means that Genesis, taken literally, is *wrong*.  Yet you suddenly want to insist, in the case of Adam and Eve, that Genesis, taken literally, is *right*.  What gives *you* the right to pick and choose what’s literally true and what’s not—the right you are denying to *me*?

The other thing that is not credible in your position on this point, is that you constantly scold me, a non-biologist, for standing up against the biologists here;  when you, also a non-biologist, do exactly the same thing.  Dennis Venema and Denis Lamoureux, biologists both, have told you that, based on the known laws of genetics, Adam and Eve *can’t* have been the parents of the whole human race!  So are they right when they contradict me based on their biological expertise, but wrong when they contradict you, based on that same expertise?  And does a sociologist have the right to simply veto biological science if it doesn’t suit his theology?

These are all hard questions, Gregory, that you fail to ask yourself.  If I didn’t know better, I’d say you weren’t being “reflexive” enough.

Jon Garvey - #55845

March 28th 2011

@Rich - #55837

Just a quick interjection to suggest that I find Gregory’s (frequent) reminders about the compartmentalisation of disciplines, despite the “evolutionalisation” of many inappropriately, as helpful as your (also frequent) reminders that ID writers are being misrepresented.

To me Biologos is about bringing into the same arena two fields that for various reasons people want to keep separate. It would be a shame if that only resulted in a new, pigeon-holed minority called “TE/EC”. To remind each other that God’s Second Book is full of other essential knowledge that we ignore at our peril, and that this includes insights from TE, even Creationism, Social Psychology, philosophy etc is helpful. It’s also potentially world-changing: a community that fully keeps those things in mind is both intellectually broader than usually found, and more humane/less tribal than is much seen either in the Church, in Science, and on blogs.

Seems to me you two agree on much, differ mainly in argumentation style (or maybe resemble each other two much) and contribute greatly to the wider debate.

Exits, stage left.

penman - #55850

March 28th 2011

Rich - #55719, Gregory - #55722

“And the tragedy of it is that at the leading edge of evolutionary
theory—and I’m not talking about ID writers, I’m talking about
anti-ID, secular, atheist professors of evolutionary biology at leading
universities around the world— Darwinian mechanisms are undergoing a
serious performance review, and are in some cases the target of some
heavy artillery.” (Rich)

I’m just reading a piece by Conway Morris, “Evolution & the Inevitability of
Intelligent Life”. His basic argument (I can’t follow the biological details) is
that nature has been “rigged” by “underlying organisational principles” to
produce humanlike intelligence via the emergence of eukaryotes, the nervous
system, & primitive intelligence (in that order). It looks very much like
he’s probing for mechanisms other than (or maybe alongside?) random genetic
mutation to produce the biomaterial on which natural selection works. There’s a
really fascinating section on primitive intelligence in a slime mould.

Anyway, the thrust of Conway Morris’s piece is to suggest deeper
principles of organisational capacity built into the substructures of nature. 

Rich - #55856

March 28th 2011

Jon Garvey:

Yes, I think Gregory and I do agree on a lot.  But for some reason, he frequently emphasizes where we disagree with great intensity, and rarely celebrates the places where we agree.  I sometimes feel that if I say “black” Gregory will reflexively (no pun intended) say “white,” just to show he is not going to take any “IDM nonsense.”  I find I’m constantly defending myself from side-attacks about the alleged religious and social motivation of ID proponents, when I’m talking to a third person about something else entirely.

I’m very much in favor of interrelating all relevant subjects when dealing with any topic.  As a physician you know that even a correct diagnosis and prescription often does not help the patient, if social factors work against the treatment (e.g., the patient may be too poor to afford a home-care nurse twice a day to clean a wound, or the patient may speak a foreign language and not be able to read labels, etc.)  Obviously, in addition to scientific knowledge, doctors need a basic social knowledge of the patients they are treating.  So I’m not at all against sociological insight, wherever it is relevant.

However, this particular thread is not about the practice of medicine, and it’s not about the sociology of religion or science and society or the like.  It’s a thread written by a geneticist, dedicated to scientific criticism of a specific book.  The subject-matter of the critique includes information theory, biochemistry, etc.  The relevant knowledge to contribute to this particular discussion is:  (a) knowledge of Meyer’s book—what Meyer actually argues; (b) knowledge of information theory, biochemistry, etc.—the things Dennis brings to bear on Meyer’s argument.

Dennis is not claiming that Meyer’s arguments are wrong because Meyer is illegitimately sneaking Christian theology into his science.  Dennis is not claiming that Meyer’s arguments should be discounted because he is part of the “ID movement” which is really all about religion rather than science.  Dennis is claiming that Meyer’s arguments are bad scientific arguments, and he rests his entire case on that.  So on *this* thread, Gregory could participate most constructively by reading Meyer’s book and then trying to follow Dennis’s arguments.

But Gregory has already said bluntly that he has no intention of reading Meyer’s book.  Why, then, join this thread at all?  Why not save his perfectly valid insights (about the need to bring various disciplines together) for another thread, where they are directly relevant to what’s being discussed?  The misapplication of evolutionary theory to social science doesn’t need to be brought up on every single thread here, nor does the subject of the lack of “reflexivity” in scientists always have to be introduced, any more than a physician has to bring sociological insights to bear on every sore throat or dislocated shoulder he deals with on a particular day.  These things only need to be brought up where the subject indicates their relevance.

Rich - #55859

March 28th 2011


The more I hear about Conway Morris, the more I think he is very close to Michael Denton in his general conclusions, though he may be very different regarding many of the details.  He also may have things in common with the ideas of Mike Gene.  I think that “teleological evolution” in one form or another is likely to become more and more acceptable over the next couple of decades, as the older generation of biologists, which is resolutely anti-teleological, dies off, and younger minds, who aren’t locked into the Modern Synthesis, start to dominate the field.

It also strikes me (though this isn’t a reason for accepting a new scientific model of evolution) that such a shift will make creation/evolution discussions much more harmonious.  I’ve read Darwin carefully, and I’ve read Denton carefully, and to me it’s intuitively obvious that Denton’s view is much more easily assimilable to traditional Creation doctrine than Darwin’s is.  One shouldn’t adopt a teleological model of evolution for that reason, but if such models prove over time to be sound scientifically, and if orthodoxy in creation doctrine (re divine sovereignty and planning) comes as a free bonus, there is no law against being happy about the convergence of science and theology.

penman - #55861

March 28th 2011

Rich - #55859

Let’s hope Conway Morris’s 2007 Gifford Lectures find their way into print soon. Since the Giffords are all about natural theology, his series could shed a lot of light on how his evolutionary thinking relates to his theism.

John - #55868

March 28th 2011

John:  “No, Bilbo, you’re missing the point. Where’s the need for the 
mutations to occur?” 

Bilbo: “I thought we agreed that we were talking about the need for genetic variations to become fixed in the population.”

Yes. After doing the simple multiplication, does it involve needing the mutations to occur? Every time Behe goes on about “waiting for mutations,” he’s deceiving himself, his readers, or both.

John:  “How long what would take? Longer than what?”

Bilbo: “Longer than for two alleles to become fixed in the population.”

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

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

I don’t believe you.

John:  “This is about your intellectual discomfort.” 
Bilbo: “Nope.”

And the answer to the multiplication is…? 

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?”

In translation, absolutely. That’s one of my points.

John:  “Or does your imagination conveniently fail you at this point?”
Bilbo: “Nope.”

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? 

John - #55874

March 28th 2011


“I have not undertaken to defend any of Meyer’s alleged mistakes against biologists.  I think they should point out every mistake he makes.”

In fact, you are defending Meyer by describing falsehoods as “mistakes” when you have no evidence that they were unintentional, while there is substantial evidence that they were intentional.

“What they should *not* do is (a) issue *innuendo* that he has made mistakes,...”

I haven’t characterized anything in Meyer’s book as a mistake. You are defending him by making additional false claims.

“... while refusing to specify the mistakes (as one cranky poster here did a number of times, until just recently, when he summoned up enough courage to directly accuse Meyer of specific errors);...”

It’s to test your reflexiveness, Rich. Also, I have never accused Meyer of “errors.” I am accusing him of MULTIPLE false claims about the most important evidence relating to an entire chapter of his book.

John - #55875

March 28th 2011

“...(b) imply that Meyer’s arguments about the origin of life are invalid because his arguments about Darwinian evolution are invalid.”

Huh? Meyer’s CONCLUSIONS about the origin of life are invalid because they are not based on the evidence.

“These are general points about honest argument that one does not need to be a biologist to grasp.”

So now that we agree that “Peptidyl transferase is a protein…” is objectively false, how do you explain Meyer’s multiple reinforcements of it? Start with these:

“These mRNAs would need to be able to direct protein synthesis using, at first, the transitional ribozyme-based protein-synthesis machinery [completely false, as the MODERN protein-synthesis machinery is ribozyme-based] and then, later, the permanent and predominantly protein-based protein-synthesis machinery [false for the same reason]. In short, the evolving RNA world would need to develop a coding and translation system based entirely on RNA and also generate the information necessary to build the proteins that later would be needed to replace it [completely false, as the translation machinery right now is based on RNA].”

That’s three “mistakes” in a single paragraph, and it’s just a coincidence that they reinforce his earlier “mistake”?

RedHatRob - #55899

March 28th 2011

Curious that no one has addressed the critique of Dr. Georgia Purdom - that the ability to utilize citrate already existed in e. coli, under low-oxygen conditions. The article here documents a mutation that allows it to utilize citrate transport under broader conditions. Not exactly the “addition of information.” Also important to note that the 12 lines of e. coli have LOST significant abilities as well. Hardly fits the adjective “fitness improvement.”

John VanZwieten - #55949

March 29th 2011

Interesting how the “truth of God’s word” tells Dr. Purdom that the E. coli are “adapting” whereas “man’s reasoning” is what leads Dr. Lenski to see “evolution.”

Keep in mind that population “fitness gains” are always with respect to their environment.  There’s no “universal fitness” score.

It is still uncertain what changed in the E. coli that allows it to utilize citrate in oxygen environment, though cooption of an existing transport protein is suspected.

Halvorz - #55912

March 28th 2011

Question for John: 

Maybe I’m missing something, but it seems to me like you’re looking at this experiment in terms of sexual reproduction, which is not applicable.  Each nucleotide in the genome of the parental strain has been substituted 6250 times, or thereabouts, and consequently, it’s likely that practically every non-lethal point mutation currently exists in the population. But it’s an asexual strain, so all those mutations are never going to get to party together, so to speak (assuming there’s no transformation going on, of course- I wonder if spontaneous transformation absolutely never occurs in the experimental conditions…). Anyway, that implies that if multiple mutations need to occur, they must occur sequentially in the same lineage (or simultaneously in the same cell). The existing variation in the population helps you up the first step, but the second step is not simply a matter of letting the proper alleles reach fixation- the second step (and third, etc.) step must be a new mutation (new to the cell in question- it undoubtedly already exists somewhere else in the population) in a cell containing one of the necessary mutations.

Or maybe I’m missing your point. Quite likely in fact, I can get my mind all turned around trying to think about population genetics.
Argon - #55956

March 29th 2011

Re: RedHatRob - #55899

Yes, citrate utilisation can be found in other strains. But Dr. Georgia Purdom goes a bit far with the claim that there is no new information: “Since E. coli already possess the ability to transport and utilize citrate under certain conditions, it is conceivable that they could adapt and gain the ability to utilize citrate under broader conditions.

This does not require the addition of new genetic information or functional systems (there are no known “additive” mechanisms). Instead degenerative events are likely to have occurred resulting in the loss of regulation and/or specificity. It is possible that the first mutations or potentiating mutations (at generation 20,000) were either slightly beneficial or neutral in their effect.”

The underlined part is legitimate. The latter half…

It seems odd to suggest that the strains had the ‘information’ necessary to use citrate at the start of the experiment but somehow couldn’t manage to grow on the substrate until after many generations and probably several additional mutations accumulated. With the statement that “there are no known ‘additive’ mechanisms” I’m fear Dr. Purdom is using the Spetnerian metric of information (named after Lee Spetner*) wherein any change in the original sequence or activity of an enzyme is scored as a loss of information (perhaps relative to the original). It’s interesting that other E. coli strains capable of utilizing citrate under aerobic conditions happen to carry a plasmid (an addition set of genes) from some other bacteria. This is not the case in Lenski’s isolates: It is a new acquisition.


Argon - #55963

March 29th 2011

Side thoughts:
To get citrate utilization on aerobic conditions I wonder if overexpressing citT is completely sufficient. There are several other changes that could improve utilization…

Citrate synthase has to be inhibited because otherwise citrate lysase sets up a futile cycle that mostly burns through ATP.

There is some information in the literature that the CitT transporter could be a citrate/succinate translocator. So, to get a citrate molecule in you’ve got to spit out a succinate molecule. That causes a problem if the full TCA cycle is operating because then you’ll get no net acquisition of carbon. The TCA cycle just burns off two CO2 molecules and the resulting succinate molecule gets exported to bring in another citrate molecule. That’s a purely catabolic reaction: It creates energy but no net biomass.

Now, if the glyoxylate bypass (aka. glyoxylate cycle), could be induced then the cell can save the two carbons normally lost as CO2 in the TCA cycle *and* split off a succinate molecule that can be used to import another citrate. This is an anabolic pathway.

Under anaerobic conditions (and during growth on some carbon sources), the TCA cycle is split at alpha-ketoglutarate dehydrogenase. The glyoxylate bypass is inducible under these conditions and also during growth on carbon sources the enter metabolism in two-carbon units, e.g. acetate and fatty acids. The bypass is also repressed during growth on glucose but in the chemostat, there’s very little free glucose around.

So, to get a picture on what’s happening metabolically in the mutant lines, I guess I’d check if the glyoxylate bypass was induced. That would give some idea about the operational mode of the TCA cycle. One might also see if other pathways are induced such as those normally expressed in anaerobic conditions to see if a regulatory system is being hijacked for other uses. It would also be interesting to see whether glucose is preferentially used in glucose + citrate media.

Gregory - #56006

March 29th 2011

“he frequently emphasizes where we disagree with great intensity, and rarely celebrates the places where we agree.” - Rich

Obviously, we do not agree on A&E. This is the first time I recall you stating yourself on A&E b/c you don’t seem to participate in those threads. Look above to note that I agreed with you & others that D. Venema should focus more on OoL in Meyer’s contribution.

The main issue is not whether I am “a credible defender of a historical Adam and Eve.” The point is that this *is* the consistent position of the Catholic & Orthodox churches & fragmented Protestants give much less ‘power’ of authority. Rome & Friends are credible defenders, so your ‘credibility’ challenge should be aimed at them instead of me.

I am not asking you to make a sociological analysis. This is what John does when he demands everyone to ‘test the evidence’ for themselves *in biology*. Not enough time in the day for that. I am asking you to *recognize* the difference that what I am saying @ sociology of science (SoS) makes to *this* conversation (don’t stoop to asking me if i know where i stand, please) - science, philosophy & religion. When I hear people speak @ ‘science’ who know SoS vs. those who know nothing about it, the difference is considerable. I am not simply defending the ‘misrepresented’ or ‘misunderstood’.

Rich, please understand this (i have said it before, now i’ll say it more clearly): I am not ‘attacking’ anyone by highlighting religious and social motivations for ‘intelligent design’ theory, including coinage & usage. These are *facts*, in so far as they are verifiable sociologically. People in this ‘debate’ do show their colours, one way or another. You seem to accuse me of ‘ad homs’ w/out understanding why. I am not attacking your person, but your particularly prioritized display of ideas.

You wrote: “I’m constantly defending myself from side-attacks about the alleged religious and social motivation of ID proponents.”

Not from me. Do not accuse me of this again, please. Thank you.

I am identifying motivations, quite fairly within the social & religious contexts, while you say their existence is irrelevant to ‘doing science’. This is indeed a significant difference between us. But I cannot roll back 30 yrs of SoS to a time when motivations were not counted (they still of course counted=mattered then too) given what we know today. I am not an ostrich, head in sand here.

“it is not that I do not care about the social sciences.  It is that they are *irrelevant to the evaluation of the arguments in Meyer’s book*.” - Rich

Meyer himself is not irrelevant to Meyer’s book. Does that open the reflexive envelope for you?

Gregory - #56009

March 29th 2011

“You fully accept biological evolution over billions of years, without batting an eye.  This means that Genesis, taken literally, is *wrong*.” - Rich

No, Genesis is not *wrong*. There is nothing *wrong* with reading ‘billions of years’ in the ‘language’ of Genesis (in translation, in my case). When I read Genesis I see nothing there that necessitates a ‘young earth’ there. But that is an impersonal, not a personal question like A&E.

Since Rich holds the view that “truths of the Bible are not less true than historical facts, but more true than historical facts,” there should be no problem for him to accept his own ‘common humanity’ with those two biblically-named persons.

Again, I don’t mean to beat a dead horse, but I just don’t think the term ‘literally’ is helpful here. I am not a ‘biblical literalist’ (nor is Rich). But I am speaking about the ‘real, historical’ existence of two persons *named* Adam & Eve (a name cannot ‘evolve’ into being in a vacuum of indecision - we decide to name our children). If I understand it properly, this is in keeping with the main teachings of all three Abrahamic religions.

Finally, yes, i do agree with Steve Fuller’s critique of MN &/vs. MN (now if i were you i would tell you to read more carefully, since you thought otherwise. but why take such a condescending approach?). You continue to pasionately defend ‘design,’ even people who have a ‘fetish’ with ‘design,’ which, as I said, is not MN’s main point of exclusion (though Fuller’s full-frontal attack on Darwinism & neo-Darwinism is noted) within the much larger topic of ‘scientific methodology’. This apparently obscures you from seeing the greater relevance of Fuller’s critique, in light of the biological challenge to social sciences.

Perhaps both Steve & I see the topic of ‘design’ as being/belonging much smaller in both natural-physical sciences & human-social sciences than you do, Rich. You sound almost as exaggerative sometimes as Michael Behe:

“Intelligent design theory has implications for virtually all humane studies”!

Really? Does he mean *all* or just all with his virtual implicationism?

Would Meyer exaggerate about the ‘importance’ of his theories @ intelligent design on OoL research (whatever that ‘means’) today? Maybe Rich will give us some positives about Meyer’s approach in the book? That would race ahead of Venema to the (supposedly) more important parts, i.e. not dealing with biological evolution only, but rather with OoL.

Wow us please, Rich, with your positive review of Meyer’s book.

Bilbo - #56016

March 29th 2011

John:  “Yes. After doing the simple multiplication, does it involve needing the mutations to occur? Every time Behe goes on about “waiting for mutations,” he’s deceiving himself, his readers, or both.”

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.

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

No, as I explained above.

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.”

Why not?

John:  “This is about your intellectual discomfort.” 
Bilbo: “Nope.”

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

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

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.”

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

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? “

Possibly.  We need more information, like the answer to my question above.

Rich - #56022

March 29th 2011

Gregory (56006):

I *agree* with you that 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. 

However, the question arises whether the teaching of historical Christianity is necessitated by the Adam and Eve story as we have it in Genesis.  In other words, it is possible that the tradition misread the text.

Were it not for Paul’s parallel between Christ and Adam, and his allusion to the serpent, I doubt that the Garden story would have played a major role in Christianity at all.  The Garden story was not deemed important by most Old Testament writers; it is hardly ever mentioned or alluded to by them.  In the Gospels the allusions to it are very few, and incidental.

On another of your points:  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.

And if you say, well, the days aren’t meant literally, and the sequence of creation isn’t meant literally, but Adam and Eve’s being the parents of the whole human race, that’s meant literally;  on what grounds would you make that distinction?  Unless you are going to engage in Biblical scholarship, you can’t make such a distinction stick.  You need textual evidence.  So you are in a very difficult place.  

Do you in fact believe that a primordial human couple were the ancestors of all the humans that have ever been?  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.  So if you are going to challenge that, you are going to have to greatly expand your criticism of Biologos and take on the biologists.  Are you going to do that?  Tell Dennis and Darrel that their biological inferences are wrong?  I’d certainly be impressed with your courage if you did.  But the moment you do, expect the commenters here to start treating you the way they treat ID proponents. 

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