ICR: Full Blown Reality Denial

A recent article at the PhysOrg website describes a creationist’s worst nightmare: Genomics analysis demonstrates natural selection at work.

Here’s a link to the paper in Nature, Genomic analysis of a key innovation in an experimental Escherichia coli population. You can’t read it without a subscription, so we’ll give you a few excerpts from PhysOrg, with bold font added by us:

A team of researchers at Michigan State University has documented the step-by-step process in which organisms evolve new functions. The results … are revealed through an in-depth, genomics-based analysis that decodes how E. coli bacteria figured out how to supplement a traditional diet of glucose with an extra course of citrate.

This is neat, but it’s relatively technical stuff that we usually don’t discuss — unless the creationists step in to amuse us with their colossal goofiness, as they have now done. But first, a bit more from PhysOrg:

Normal E. coli can’t digest citrate when oxygen is present. In fact, it’s a distinct hallmark of E. coli. They can’t eat citrate because E. coli don’t express the right protein to absorb citrate molecules.

To decipher the responsible mutations, Blount worked with Richard Lenski, MSU Hannah Distinguished Professor of Microbiology and Molecular Genetics. Lenski’s long-term experiment, cultivating cultures of fast-growing E. coli, was launched in 1988 and has allowed him and his teammates to study more than more than 56,000 generations of bacterial evolution.

The experiment demonstrates natural selection at work. And because samples are frozen and available for later study, when something new emerges scientists can go back to earlier generations to look for the steps that happened along the way.

[...]

In the Nature paper, Blount and his teammates analyzed 29 genomes from different generations to find the mutational pieces of the puzzle. They uncovered a three-step process in which the bacteria developed this new ability.

Three steps over 56,000 generations? Okay, let’s read on:

The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events.

The Nature paper explains that there was a duplication of a segment of DNA, the sort of thing that results from a copying error, one of which then mutated into something with a new function. Although creationists are always wailing that evolution can’t generate new “information,” that’s how it happens. We’ve described this sort of thing before (see How One Gene Becomes Two Different Genes). One last excerpt from PhysOrg:

“It wasn’t a typical mutation at all, where just one base-pair, one letter, in the genome is changed,” he [Lenski] said. “Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed.”

Okay, now let’s get the creationist reaction. This is at the website of the granddaddy of all creationist outfits — the Institute for Creation Research (ICR). They’re the fountainhead of young-earth creationist wisdom. Their new article is Bacterial ‘Evolution’ Is Actually Design in Action. Here are some excerpts, with bold font added by us and their links and scripture references omitted. First they mention the new research, and then they ask:

Some say this confirms evolution in action but what if the bacteria were designed to modify themselves? That might disappoint evolution enthusiasts.

Oooooooh! That’s a brilliant question, and one that hadn’t occurred to us. What would we do without these creation scientists? Then they ask this probing question:

Did the strain of E. coli that acquired the new ability to import citrate — called Cit+ — construct new functional, biochemical machinery by chance-base mutations?

To answer that question, they refer to the work of a brilliant creation scientist:

In 2010, biochemist Michael Behe reviewed 12 new phenotypes, which are outward expressions of genetic coding, that Lenski’s E. coli displayed from 1994 to 2008. Behe categorized the known genetics producing each new bacterial phenotypes as either losing, shuffling, or gaining what he called “functional coded elements,” which include genes and gene promoters. All the known changes in the bacteria were either a loss or reorganization of pre-existing functional coded elements. None of the new phenotypes came from a gain of functional coded elements, and yet this is what molecules-to-man evolution requires.

BWAHAHAHAHAHA! Michael Behe. He’s referring to work done before the publication of the new research. ICR quotes more from Behe:

At that time, the mechanism underlying the citrate-eating phenotype was unknown. Behe wrote, “If the [Cit+] phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT [Functional Coded elemenT] mutation.”

Well, that’s exactly what happened, so even Behe should acknowledge that the new research is noteworthy — although we have no current statement from him. But what does ICR say? They never disappoint us. Get this:

So, the big question is: Did E. coli evolve into a Cit+ strain by natural selection? Or did mutations construct new and functional coded elements to its DNA? If so, it would be the first in recorded biological history. If not, then it would be just another loss or modification of a pre-existing piece.

The answer to ICR’s “big question” is “Yes,” and it’s not the first time in biological history that this has been observed. After a tortured description of the new research, ICR says:

So, the bacteria solved the problem of accessing an alternative food source by generating extra copies of the critical gene and by placing those copies under the control of an appropriate promoter. Does any of this resemble natural, undirected Darwinian evolution? Not at all. This amazing mechanism invented no new functional coded elements. It merely modified pre-existing elements.

Stunning. Absolutely stunning. A classic example of reality denial. Here’s the end of their article:

Therefore, not only did the Cit+ bacteria not evolve in the molecules-to-man direction, but they showed what could only be ingenious DNA rearrangement mechanisms. What mainstream headlines portrayed as evidence for evolution is actually the opposite.

Thus endeth our lesson in creation science. And what did we learn today? We have learned that if you don’t like reality, just close your eyes, stick your fingers in your ears (or wherever you like), refuse to listen, and repeat your dogma. It defeats the evolutionists every time.

Copyright © 2012. The Sensuous Curmudgeon. All rights reserved.

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16 responses to “ICR: Full Blown Reality Denial

  1. Charles Deetz ;)

    Love the euphemism: “design in action” … sounds like evolution to me!

  2. This amazing mechanism invented no new functional coded elements. It merely modified pre-existing elements.

    Well, yeah, that’s what evolution is.

    This seems to be another case of creationists mixing up their own brand of special creation with evoluton. Looking for saltation or the ab initio development of functions, whole cloth, in a single generation, and then declaring evolution dead when they don’t find evidence for their own mechanism.

  3. Geez Louise! What do they require for evidence? Maybe that the bacteria will mutate into a teenager and ask to borrow the car keys??

    Don’t answer that – I have a terrible feeling I might be right.

  4. ICR implies that the bacteria detected the citrate in the population, determined that to eat the citrate a rearrangement of their DNA was in order, did that, and now can eat the citrate.

    Therefore, not only did the Cit+ bacteria not evolve in the molecules-to-man direction, but they showed what could only be ingenious DNA rearrangement mechanisms.

    So bacteria have a mechanisms that just kicks in and shuffles it’s DNA when necessary.

    My question is, if this is the case, why did it take 33,000 generations just to begin to take in citrate, and more generations to refine the process? Why, if the DNA change mechanism is inherent in bacteria, did only a few develop this ability (possibly only one initially), and not all of them? What indicator can you identify that distinguishes duplication of a segment of DNA due to a copying error, from a deliberate duplication of the same segment of DNA do to the mysterious mechanism that you propose?

  5. We have learned that if you don’t like reality, just close your eyes, stick your fingers in your ears (or wherever you like), refuse to listen, and repeat your dogma.

    The administration didn’t know the truth about Benghazi.
    The administration didn’t know the truth about Benghazi.
    The administration didn’t know the truth about Benghazi.
    The administration didn’t know the truth about Benghazi…

  6. NeonNoodle says: “The administration didn’t know the truth about Benghazi.”

    I believe it, because as the Discoveroids say about near-death experiences, it’s the most parsimonious explanation — the simplest scientific explanation. The troubles over there were the result of a movie review.

  7. Charles Deetz ;)

    SC says “The troubles over there were the result of a movie review.”

    Actually an interesting metaphor. Was the violence a reaction to a strong input, or a unprovoked planned attack? Seems the same type of person that sees the conspiracy in Benghazi is the type that sees bacteria planning what it wants to eat. They are smart enough to perceive “the facts” that the rest of us can’t.

  8. Ceteris Paribus

    re Benghazi: The complexity of preventing all attacks at all of the hundreds (thousands?) of hot spots in which the US is now operating military or consular bases insures that there will be no simple way to discern a Black Swan event from a conspiracy.

    But back to bacteria. The article says “One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed.” Yup that’s design. Same old ploy used by a couple of frat boys to exploit a naive underage female that come to their party.

    Y

  9. @C.P. re: Benghazi:
    Agreed, but what’s at issue isn’t the attack, but the cover-up.
    Now back to the bacteria discussion, already in progress…

  10. Actually, Hillary has known about Lenski’s experiment for years although she pretended not to and gave the wrong information to Ann Rice who then blabbed a bunch of bunk. So, there you have it. Bengazi + Lenski = Conspiracy.

    The facts are clear. You can agree with me or be un-American. Hey, it’s a free country (for now), your choice.

  11. Once again, Doc Bill, you’ve made me snort Mt Dew into my nose.

    Fortunately, this time the keyboard and monitor were spared.

  12. I don’t see that it matters much whether the embassy attack was planned by “terrorists” which is possibly one of the most over used of words or if it was just a bunch of local hotheads. Either way it exemplifies what happens when religiosity (and the abuse of power that can flourish in a theocratic state) reaches the extreme. Its exactly the type of issue that readers of this blog fear. I for one don’t really care what the president or his oppenent call it.

    As to the E. Coli study. This is one of the most ambitious and informative studies aver undertaken in evolutionary and microbiology. How sad that the folks at ICR can’t acknowledge truth when it stares them in the face.

  13. Curmudgeon, of course those blokes don’t fathom the step-wise procedures of evolution, but others don’t appreciate them either.
    I didn’t try to spam. I had a memory loss about the blogs.
    I wanted to let others know about Kangas’s work so as to stir up debate .
    I’ll recommend this site elsewhere.

  14. And the fact that through it all – E. coli remains E. coli.

    Lenski’s research has revealed the bacterium’s amazing ability to adapt to
    nutritional stress. Is this really cause for Darwiniacs to celebrate the
    particles-to-people philosophy?

    No.

    If this is such a plus for vertical evolution then why have bacteria always been bacteria, protozoa always Protozoa, etc? Why does the fossil record only show abrupt appearance and stasis? If what was described was a new macroevolutionary mechanism, then the results of this “mechanism” should be seen in the sedimentary rocks.

    It is not.

  15. Okay, SamIAm. That’s enough.

  16. This from the ICR article– appears to be outright falsehood.

    ICR: The recent results showed that the bacteria made extra copies of citT and a neighboring sequence—a process called gene amplification… But oxygen deactivates citT…

    But the bacteria solved this problem when the amplification event also moved the gene sequence to a different place in the bacterial chromosome, where a different but pre-existing promoter could regulate it.

    I believe this is wrong– the promoter was ALSO duplicated, so the duplicate of the gene was stitched with a DUPLICATE of a promoter, whose original used to promote a different gene. I believe Venema mentioned this in his article at BioLogos.

    Venema: …the actualization mutation was indeed a change of regulation of the anoxic citrate / succinate transporter, and it arose through a gain-of-FCT mutation. The mutation turned out to be a side-by-side duplication of the citrate / succinate transporter gene, as well as portions of two genes on either side of it. This imprecise duplication placed a partial fusion of these flanking genes next door to one of the copies of the citrate / succinate transporter gene. This brought the copy under the control of promoter sequences derived from of one of its neighbors, a gene that is active when oxygen is present. The resulting product was a copy of the citrate / succinate transporter gene that was now very weakly expressed in aerobic conditions. Since this is an example of a mutation that duplicates a gene and simultaneously creates a new regulatory element for it (causing significant sequence divergence), this is a clear-cut example of a gain-of-FCT mutation.

    [Venema vs. Behe at Biologos]

    This seems to contradict ICR.

    Oh, and note that all through the ICR article, the witch-doctor keeps speaking of the bacteria as if it is intelligent and has will and plans and detects citrate and re-arranges its own DNA.

    ICR: …the bacteria made extra copies of citT and a neighboring sequence… But the bacteria solved this problem… So, the bacteria solved the problem of accessing an alternative food source by generating extra copies of the critical gene and by placing those copies under the control of an appropriate promoter…

    Smart bug. They now talk of bacteria as if they are super-intelligent. No creation “scientist” has performed nor could perform genetic manipulations to “solve” problems this hard, but bacteria are said to “solve” these problems, so creationists now attribute to bacteria an intelligence far greater than their own.

    Of course the bacteria cannot rearrange its DNA unless 1.) it has a pre-existed design or plan, and 2.) if it could detect citrate in its environment. But it can’t detect citrate because it can’t uptake citrate until after the random mutation happens. If the creationists were right, then bacteria can’t uptake citrate until after it detects citrate (thousand of generations after, actually) and then re-designs itself– but the bacteria can’t detect citrate until it can uptake citrate. A chicken-and-egg problem.