Monday, February 22, 2016

An Intelligent Design Creationist disputes the evolution of citrate utilization in the LTEE ... Lenski responds

Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.

The pathway to this event is complex and requires multiple mutations [see On the unpredictability of evolution and potentiation in Lenski's long-term evolution experiment and Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source].

Intelligent Design Creationists are not happy about this experiment because it not only shows evolution in action but it also illustrates features of the process that ID proponents don't understand; features like drift, neutral alleles, and contingency that expose the ignorance of the average creationist. However, there are a few ID proponents who actually understand evolution so they are forced to come up with other kinds of criticism to soften the impact of the results coming out of the Lenksi lab.

One of those creationists is Scott Minnich1, a professor and researcher at the University of Idaho in Moscow, Idaho (USA). Minnich wants you to believe that the LTEE isn't significant because no new genetic information was created. This is part of a strategy to accept microevolution but deny that macroevolution can be explained by naturalistic processes.

Minnich's lab did some experiments in order to replay the evolution of citrate utilization in E. coli cultures. They found that they could evolve strains that utilized citrate under aerobic conditions but in their hands it took much less time than it took in the LTEE and it was much more likely to occur. (Recall that the Cit+ phenotype only evolved in one of the twelve cultures in the LTEE and it took 30,000 generations.) Here's the Minnich paper and the abstact.
Van Hofwegen, D.J., Hovde, C.J., and Minnich, S.A. (2016) Rapid evolution of citrate utilization by Escherichia coli by direct selection requires citT and dctA. Journal of bacteriology, published online Feb. 1, 2016 [doi: 10.1128/JB.00831-15]

ABSTRACY The isolation of aerobic citrate-utilizing Escherichia coli (Cit+) in long term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit+ mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested with wild-type E. coli B, K12, and three K12 derivatives: E. coli ΔrpoS::kan (impaired for stationary phase survival), E. coli ΔcitT::kan (deleted for the anaerobic citrate/succinate antiporter) and E. coli ΔdctA::kan (deleted for the aerobic succinate transporter). E. coli underwent adaptation to aerobic citrate metabolism that was readily and repeatedly achieved using minimal medium supplemented with citrate (M9C), M9C with 0.005% glycerol, or M9C with 0.0025% glucose. Forty-six independent E. coli Cit+ mutants were isolated from all E. coli derivatives except E. coli ΔcitT::kan. Potentiation/actualization mutations occurred within as few as 12 generations and refinement mutations occurred within 100 generations. Citrate utilization was confirmed using Simmons-, Christensen-, and LeMaster Richards citrate media and quantified by mass spectrometry. E. coli Cit+ mutants grew in clumps and long incompletely divided chains, a phenotype that was reversible in rich media. Genomic DNA sequencing of four E. coli Cit+ mutants revealed the required sequence of mutational events leading to a refined Cit+ mutant. These events showed amplified citT and dctA loci followed by DNA rearrangements consistent with promotor capture events for citT. These mutations were equivalent to the amplification and promoter capture CitT-activating mutations identified in the LTEE.

IMPORTANCE E. coli cannot use citrate aerobically. Long term evolution experiments (LTEE) by Lenski found a single aerobic, citrate-utilizing E. coli after 33,000 generations (15 years). This is interpreted as a speciation event. Here we show why it probably is not. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are the same class of mutations identified by the LTEE. We conclude the rarity of the LTEE mutant was an artifact of the experimental conditions, not a unique evolutionary event. No new genetic information (novel gene function) evolved.
A lot of the work in deciphering the Cit+ phenotype in the LTEE was done by Zachary Blount when he was a graduate student in the Lenksi lab. He is now a post-doc and he and Lenski have teamed up to write a critique of the Van Hofwegan et al. paper. The essay is posted on Lenski's blog at: On the Evolution of Citrate Use.

Blount and Lenski discuss two technical points: the rapidity of the events in the Van Hofwegan et al. paper and the criticism of historical contingency in that paper and in an accompanying commentary by Roth and Maisnier-Patin (2016). Neither criticism is valid.

(Blount has published a nice paper on historical contingency in the LTEE (Blount, 2016). It's relevant to our discussions about replaying the tape of life.)

Blount and Lenski also address the creation of new genetic information. They say,
The claim that “no new genetic information evolved” is based on the fact that the bacteria gained this new ability by rearranging existing structural and regulatory genetic elements. But that’s like saying a new book—say, Darwin’s Origin of Species when it first appeared in 1859—contains no new information, because the text has the same old letters and words that are found in other books.

In an evolutionary context, a genome encodes not just proteins and patterns of expression, but information about the environments where an organism’s ancestors have lived and how to survive and reproduce in those environments by having useful proteins, expressing them under appropriate conditions (but not others), and so on. So when natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria.

That’s how evolution works—it’s not as though new genes and functions somehow appear out of thin air. As the bacterial geneticist and Nobel laureate François Jacob wrote (Science, 1977): “[N]atural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him, whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science.
This is an important point.

Evolution works by modifying pre-existing DNA to create new genes or new regulatory elements from sequences that were already present in the genome.2 Creationists seem to think that new genetic information has to be "poofed" into existence from nothing or it doesn't count as new information. They would like very much to demonstrate that there are real examples of such magic because that would lend support to their claim that goddidit. So far they haven't come up with a single, credible, example of such a gene so they have to be content with denying that evolution can create new genetic information.

It's sad, really.


1. Minnich is a fellow at the Center for Science and Culture (Discovery Institute).

2. There are some exceptions, let's not quibble.

Blount, Z.D. (2016) A case study in evolutionary contingency. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. [doi: 10.1016/j.shpsc.2015.12.007]
Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit+), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit+ trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.

Roth, J., and Maisnier-Patin, S. (2016) Re-interpreting long-term evolution experiments—Is delayed adaptation an example of historical contingency or a consequence of intermittent selection? Journal of bacteriology, JB. 00110-00116. [doi: 10.1128/JB.00110-16]

227 comments :

  1. so new function = new information? I have an old, broken radio that I sometimes use as a door stop in my office. Does that mean new information was acquired since it's being used for something other than what it was initially designed to do? And maybe this is a bad analogy, but the point is, what new was added here? A new gene? (don't think so) A new promoter? (don't think so) What new hardware emerged? What evidence does this give us that "nature-did-it" can conjure up new physical raw material via mutation?

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    1. What evidence does this give us that "nature-did-it" can conjure up new physical raw material via mutation?

      Can you give an example of an evolutionary change that required the creation of "new physical raw material"?

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    2. New physical raw material? That would be any kind of nucleotide insertion or even duplication. Those happen all the time.

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    3. Did the radio mutate a bit to turn it into a more effective door stop? Because that it's what your analogy is missing.

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    4. sez Unknown @ Monday, February 22, 2016 10:51:00 AM
      so new function = new information?
      I don't know. What does this "new information" stuff look like? Can you tell me how "new information" differs from "information" which is not "new"? If you can't tell me that, why are you making noise about "new information" in the first place?

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    5. "Did the radio mutate a bit to turn it into a more effective door stop?"-

      lets say that it is. can it will evolve into something like a car?

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    6. The radio is an inanimate object, so yes, it is a bad analogy. Try again.

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    7. When are you creationist going to understand that biological evolution has no effect on dead objects like pencils or rocks or radios? Are you that fucking dumb that you don't get it or are you ignorant un porpuse? How can a radio mutate you dumb shit? Does it have genes? Is it affected by natural selection? NO.

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    8. "When are you creationist going to understand that biological evolution has no effect on dead objects like pencils or rocks or radios? "

      lets say that it is have a genes and self replicating system. can it evolve into a car for example?

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    9. Sure, why couldn't it? It probably wouldn't, because the number of other things it could evolve into is very large. But the possibility is there.

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    10. hiw actually? only the new engine will need a jump of about several parts. so there is no step wise.

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    11. You're the one making the positive claim, you have to substantiate it. You say it is impossible for a radio to become a car thru stepwise processes, so I presume you have worked out every single pathway that could possibly result from modifying the components of a radio and determined that not a single one of these could function as a car. If you haven't, then you should just STFU with your unsubstantiated claims.

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  2. It's funny. Creationists (including the ID) kind expect POOF and are so deep into the POOF mentality, that they can't understand evolution that doesn't go POOF.

    "You can't expect the human genome to poof into existence, it's too complex, the probability that all those nucleotides would spontaneously arrange that way is a gajillion bajillion to 1."

    Of course it is. But no biologist thinks that the human genome poofed into existence.

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  3. Larry's final point should be emphasized. If the IDiots were correct, the LTEE would have been the perfect opportunity to have demonstrated this. Lenski's team could have come into the lab one morning and found that an entirely new gene had materialized de novo in the genome of one or more of the colonies. This did not occur nor, to my knowledge, has it ever been observed. The IDiots are strangely silent on this (for them) embarrassing finding.

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    1. All the flasks could have been broken and long extinct Dinosaur species could be all over the lab, having been divinely wished into existence.

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  4. Was this critque of Lenski published in a reputable journal?

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    1. Yes the Journal of Bacteriology is a legitimate scientific journal published by the American Society for Microbiology - probably the largest such society in the world. I checked wikipedia to see when they began publishing. It was in 1916 according to that site but it also states that the journal is a medical journal. It is not that, the journal will consider a broad range of microbiology-related manuscripts for publication including, but not limited to, those related to pathogenesis.

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  5. I'm talking about the ability of mutation to build new bodily structures. Nothing new was observed to be created by the lenski experiment; just a duplication of an already exiting gene and promoter. If the claim that new information was created then there should be, at least occasionally, an additional physical (and selectable) structure to prove it... But there never is. You evolutionists have no legitimate creator.

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    1. So you're expecting E. coli to start sprouting legs or wings or something?

      Is it any wonder you guys are called "IDiots"?

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    2. But if it's "new bodily structures" you're concerned about, I'm surprised you're not aware of this example:

      Lizards Undergo Rapid Evolution After Introduction To A New Home

      Goal post shift coming in 3, 2, 1,...

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    3. Unknown face-plants: Nothing new was observed to be created by the lenski experiment; just a duplication of an already exiting gene and promoter.

      Unknown has forgotten that this falsifies the conclusion of Behe and Snoke's paper, which claimed that bacteria can't evolve new functonally coded elements (which means no new genes or non-coding regulatory elements.) The LTEE E.coli got both. To dismiss it because it happened by gene duplication and divergence is to shift the goalposts and redefine "genetic information" for the 999th time. Again, as always trying to evade falsification of ID "information theory" misdefinitions.

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    4. I'm talking about the ability of mutation to build new bodily structures.

      Right, what the E. coli did in the LTEE is analogous to humans developing the ability to eat silicon and breathe helium, which would be nothing new...oh, wait.

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    5. Unknown has forgotten that this falsifies the conclusion of Behe and Snoke's paper, which claimed that bacteria can't evolve new functonally coded elements

      Also worth noting is that the finding in the new paper by Minnich's group contradicts the chief claim of Behe's "The Edge of Evolution", which is that adaptations requiring two or more mutations are so unlikely that they only occur over long timescales with enormous population numbers. Minnich's paper, OTOH, demonstrates that such adaptations arise frequently and easily. Ironically, then, Behe's hypothesis has been contradicted by research conducted by one of his own colleagues at the Discovery Institute.

      One would think this would require a response from Behe. I expect, instead, an eerie silence.

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    6. There's a good discussion on Biologos of Behe's attempts to dismiss the results of the LTEE:

      http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/series/behe-lenski-and-the-edge-of-evolution

      The whole thing is worth reading, but this quote in particular is pertinent to Unknown's claim above:

      (Q)uibbling over whether this mutation constitutes a “genuine gain-of-FCT” mutation is not my purpose here, since the definition is Behe’s to define, and I am not aware of anyone else in the scientific literature who uses Behe’s definitions. That said, I consider it passing strange to claim that a series of events that produced a gene that has a new sequence and functional properties distinct from either of its component parts does not constitute the production of a new “functional coded element.” If nothing else, it is a functional coded element that has not previously existed, cobbled together from parts of other functional coded elements, displaying new, adaptive properties. If according to Behe’s definition that’s not “new” or a “gain” then I guess it’s not, but that seems to me to torture the words “new” and “gain” beyond recognition.

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  6. Here's the big question: does anybody have an explanation why Minnich's experiment got an analogous result much more quickly than Lenski's? I think somebody must have screwed up somewhere.

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    1. For Diogenes. Short answer = different selective environment and, in most cases, different starting genotype: Longer answer from my blog post with Zachary Blount:

      "First, we already demonstrated in replay experiments that, in the right genetic background and by plating on minimal-citrate agar, Cit+ mutants sometimes arose in a matter of weeks (Blount et al. 2008). Second, rapid evolution of citrate utilization—or any evolution of that function—was not a goal of the LTEE. So while it is interesting that Van Hofwegen et al. have identified genetic contexts and ecological conditions that accelerate the emergence of citrate utilization (as did Blount et al., 2008), that in no way undermines the slowness and rarity of the evolution of this function in the context of the LTEE (or, for that matter, the rarity of Cit+ E. coli in nature and in the lab prior to our work)."

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    2. But if Minnich started from a different genotype, how can he think that this tells us about information gains, if any, in the actual LTEE? That's a total non sequitur, right?

      We already discussed the genetic changes in the actual LTEE, so this wouldn't change much.

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    3. For Diogenes again: I'm not sure I'd say "total non sequitur" although they changed media and used different strains in most experiments. Even so, I think they provided some useful microbiological information. Again from our blog post:

      "By and large, the work confirms many of the findings that were reported in our papers cited above:

      (i) the ability to grow on citrate in the presence of oxygen can and does evolve in E. coli (Blount et al., 2008);

      (ii) when aerobic growth on citrate evolves, it does not do so quickly and easily (Blount et al., 2008) but instead takes weeks or longer—more on that below;

      (iii) all strains that have evolved this new ability have physical rearrangements that involve the citT gene and appear also to involve a so-called “promoter capture” whereby a copy of this transporter-encoding gene acquires a new upstream regulatory region (Blount et al., 2012); and

      (iv) genetic context matters—the strain one uses affects the likelihood of evolving the Cit+ function (Blount et al., 2008) and the resulting ability to grow on citrate (Blount et al., 2012; Quandt et al., 2015).

      The problem, then, is not with the experiments and data. Rather, the problem is that the results are wrapped in interpretations that are, in our view, unscientific and unbecoming."

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    4. Richard Lenski,

      Do you agree or disagree with scientists, such as Micheal Behe but not only him, who claim that your experiments do not bring in "anything new" to the evolutionary processes and at the same time the "supposed novelty" in the evolution are the channels that had already existed but JUST WEREN'T USED because of a direct or an indirect result of breaking up other genes and decreasing the fitness of an organism?

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    5. sez Eric @ Monday, February 22, 2016 6:21:00 PM"
      Richard Lenski, Do you agree or disagree with scientists, such as Micheal Behe but not only him, who claim that your experiments do not bring in "anything new" to the evolutionary processes…
      If you want to criticize Lenski's experiment on the grounds that nothing "new" happened, you really ought to, you know, define what you think "new" means in this context. What are the qualities of a "new" whatever-it-is, such that you could actually distinguish a "new" whatever-it-is, from a whatever-it-is that is not "new"?

      These "scientists" you speak of, Eric: They do have an objective, empirically-confirmable definition of "new", don't they? They're not just waving the word "new" around as yet another vaguely-defined anti-evolutionary shibboleth? They can identify the actual differences between wild-type, non-citrate-eating E coli and the citrate-eating E coli of Lenski's experiment, and they can demonstrate—not just assert, but actually demonstratethat there is nothing "new" about any of those differences?

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    6. "Revolving door solution
      E. coli don’t normally feed on citrate because they can’t carry it into their cells. But a mutation in the citrate-eaters allowed them to make an “antiporter” protein, CitT, that allows citrate to cross the membrane and enter the cell. The gene for this protein already existed, but it’s usually switched off when oxygen is present.

      The antiporter is a kind of revolving door. It allows one molecule to be swapped for another. In this case, the citrate is imported into the cell in exchange for one of three smaller, less-valuable molecules: succinate, fumarate or malate."

      "The gene for this protein already existed, but it’s usually switched off when oxygen is present."

      This is what I meant by new; the gene for the protein already existed so how could it be new? How could this pathway be new if bacteria already had the ability to use it?

      If this is all Darwinists have to hang on to, to prove that evolution is a fact, creationists can sleep well at night lol

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    7. Define: New. Give a rigorous measure of "newness".

      For example, if a gene is duplicated and mutations happen in the duplicate, is it then new?

      How many mutations must happen in that gene for it to be "new"? 2%, 10%, 100% ? Why is that new?

      Answer all of these questions and explain why those are the correct answers. Be the first creationist in history to do so.

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    8. The protein for bringing citrate into the cell already existed, but it didn't work in the presence of oxygen. As a result of the mutations, it did work in the presence of oxygen. This was new.

      This isn't a huge change (though the required duplication plus rearrangement of DNA is not trivial), but this is how evolution works. Small and occasionally big changes add up to significant changes (e.g. the ability to use citrate in this environmental set-up).

      The fact that this doesn't match Eric's false idea of what evolution is just totally doesn't matter.

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    9. The duplicated gene and regulatory region have a new function, and are new "functionally coded elements" by the definition of Behe and Snoke, when they claimed that bacteria do not evolve new "functionally coded elements". So Behe's version of "new information" is falsified.

      Now creationists seek to shift the goalposts somewhere else. OK, Behe and Snoke were wrong. Now give us a clear cut, mathematical equation defining the new, v7.0 definition of "information" which you want to use to replace Behe and Snoke's. Just give us an equation for it. If you don't give us an equation for "new information", you have no right to demand we measure or observe it. You won't give us an equation because you need to keep shifting the goalposts to evade falsification.

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    10. Small and occasionally big changes add up to significant changes"-

      can a small chenges in a car will change it into an airplane?

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    11. Rumraket: Define: New. Give a rigorous measure of "newness".

      Thats a good question. Pigliucci writes : I think that evolutionary novelties are a necessarily fuzzy concept, like that of biological species (Pigliucci 2003). Nonetheless, it seems to me that these two deficiencies need to be addressed, which is why I venture to propose an amended definition of evolutionary novelties: Evolutionary novelties are new traits or behaviors, or novel combinations of previously existing traits or behaviors, arising during the evolution of a lineage, and that perform a new function within the ecology of that lineage. This definition does not imply any specific mechanism or long-term evolutionary effect, since the first one is precisely the objective of empirical research in this area and the second one is a matter to be settled based on the historical record. However, my definition (1) makes explicit the fact that often novelties are not absolute discontinuities but can be built on previously existing parts, (2) indicates that they are a phenomenon that affects the evolution of certain lineages without implying that all derived characters are in fact novelties, and (3) requires some kind of ecological function to eventually be coupled with the novelty, although it does not imply a necessary link between novelties and adaptive radiations.

      The problem is, to get a new function is often a long way to to. And in most cases, the intermediate stages do not confer adaptive advantages. Macroevolutionary novelties means the arise of new cells, tissues, organs, and functions. Take the make of blood. How do you go from a unicellular to a multicell organism that has a proto-blood circulatory system ? Blood or hemolymph ( the blood of insects ) needs to be able fullfill several different tasks all at once. If it cannot fullfill immunological protection, the organism dies. Infact, modern blood requires ten different blood cells, all essential. The proto hemopoietic stem cell would have had to arise all at once, and forsee the need of all intermediate cells to get the final ones. That would require thousands, if not millions of muatations all at once. Thats a hard sell.

      http://reasonandscience.heavenforum.org/t2295-hematopoiesis-the-mystery-of-blood-cell-and-vascular-formation

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    12. Yeah yeah El, we all know about your tome of knowledge regarding 'why evolution can't bah blah blah' . But you didn't answer Rum's question, instead you went into preach mode 'why evolution can't do this, can't do that'.

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    13. can a small chenges in a car will change it into an airplane?

      Darwins Black Box page 40:

      http://reasonandscience.heavenforum.org/t2115-the-best-of-darwins-black-box#3760

      So let us attempt to evolve a bicycle into a motorcycle by the gradual accumulation of mutations. Suppose that a factory produced bicycles, but that occasionally there was a mistake in manufacture. Let us further suppose that if the mistake led to an improvement in the bicycle, then the friends and neighbors of the lucky buyer would demand similar bikes, and the factory would retool to make the mutation a permanent feature. So, like biological mutations, successful mechanical mutations would reproduce and spread. If we are to keep our analogy relevant to biology, however, each change can only be a slight modification, duplication, or rearrangement of a preexisting component, and the change must improve the function of the bicycle. So if the factory mistakenly increased the size of a nut or decreased the diameter of a bolt, or added an extra wheel onto the front axle or left off the rear tire, or put a pedal on the handlebars or added extra spokes, and if any of these slight changes improved the bike ride, then the improvement would immediately be noticed by the buying public and the mutated bikes would, in true Darwinian fashion, dominate the market. Given these conditions, can we evolve a bicycle into a motorcycle? We can move in the right direction by making the seat more comfortable in small steps, the wheels bigger, and even (assuming our customers prefer the «biker» look) imitating the overall shape in various ways. But a motorcycle depends on a source of fuel, and a bicycle has nothing that can be slightly modified to become a gasoline tank. And what part of the bicycle could be duplicated to begin building a motor? Even if a lucky accident brought a lawnmower engine from a neighboring factory into the bicycle factory, the motor would have to be mounted on the bike and be connected in the right way to the drive chain. How could this be done step-by-step from bicycle parts? A factory that made bicycles simply could not produce a motorcycle by natural selection acting on variation—by «numerous, successive, slight modifications»—and in fact there is no example in history of a complex change in a product occurring in this manner.
      So far we have examined the question of irreducible complexity as a challenge to step-by-step evolution. But there is another difficulty for Darwin. If the base were made out of paper, for example, the trap would fall apart. If the hammer were too heavy, it would break the spring. If the spring were too loose, it would not move the hammer. If the holding bar were too short, it would not reach the catch. If the catch were too large, it would not release at the proper time. A simple list of components of a mousetrap is necessary, but not sufficient, to make a functioning mousetrap.

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    14. tl;dr version: The living things we observe do not resemble the things that have been created thru intelligent design. Behe scores an own-goal, again.

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    15. Does Behe really believe evolutionary theory states that bicycles and motorcycles evolved from a common ancestor? Of course not. He's not that stupid. However, he knows his fans, such as ElShamah777, are that stupid (if not more so) and so will not see the glaring error in his argument.

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    16. Its obvious that Behe just gave a illustration of the problem.

      Basic rule of thumb in debates with atheists is: When they start calling you names, it means they have nothing left to debate against your argument. It also means: The creationist just won the debate.

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    17. So what "problem" does Behe illustrate with his example? Sure, motorcycles could not exist in their current form if they were derived by modifying existing parts of bicycles, for the simple and obvious reason that that is not how motorcycles were designed.

      IOW, Behe has proven that motorcycles did not evolve from bicycles. Big deal. Who thought they did?

      Now, maybe he could show how that illustration applies to things that have arisen thru evolution. For instance, in comparing humans and chimpanzees, what is the equivalent of the motorcycle's gas tank, which was just added to the human body and with no homologous equivalent in the chimpanzee?

      I suspect I will be waiting a very long time for the answer to this question. The rest of my life, in fact.

      Rule of thumb with creationists: Once their arguments have been debunked, they declare victory and then run off or change the subject.

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    18. ElShamah777 quotes Behe: "and a bicycle has nothing that can be slightly modified to become a gasoline tank."

      The whole frame of a bicycle is a big empty tube that could be used as a gas tank - even better if enlarged and partitioned. Behe is either dense or dishonest or both.

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    19. It usually degenerates to name calling when the rational person gets frustrated from the inability of the other to use simple logic and they don't step out of the argument.

      There's no arguing with creationists. It's a belief system. It has little to do with logic or fact. If creationists held these concepts to be of value, they'd not be creationists for long. Using logic and fact against someone who finds them to be of no value is ineffective.

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    20. @FailSamah77

      That's a nice copy-paste of Pigliucci, but it doesn't relate to the question i ask of Eric, which is about INFORMATION not about FUNCTION. I specifically asked to be given a rigorous definition that could be applied to mutating gene-duplications. Nothing in your copy-paste addresses my question.

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    21. @ Richard Lenski

      I find one of your "mentions" very intriguing:

      (iii) all strains that have evolved this new ability have physical rearrangements that involve the citT gene and appear also to involve a so-called “promoter capture” whereby a copy of this transporter-encoding gene acquires a new upstream regulatory region (Blount et al., 2012); …

      Susan Rosenberg suggested that: “Cells actually decide to turn up their mutation rate when they are poorly adapted to the environment.”

      I wonder if one result of “stress” would be cells inadvertently (as it were) unleashing transposons which would accelerate indel events including translocation and “promoter capture”.

      Am I getting that right?

      Thank you for your patience and indulgence.

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    22. @ Tom Mueller

      In the case of the LTEE population that first evolved the ability to use citrate, the promoter capture did NOT involve any transposable element (Blount et al 2012 Nature). However, in our 19 replay experiments where citrate-utilization re-evolved, transposable elements (specifically, IS3 insertions) were involved in 6 of those cases (Blount et al. 2012 Nature).

      The IS3 present in the ancestral strain has generally been inactive during the LTEE, unlike several other IS elements ( IS1, IS150, and IS186) that have been active (Papadopoulos et al 1999 PNAS; Raeside et al 2014 mBio). We don't know whether IS3's increased activity during the replay experiments was a response to the prolonged starvation during those experiments. In any case, the activity of the other IS elements evidently did not require such prolonged starvation.

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    23. @ Richard Lenski

      Thank you! I am trying to wrap my head around what you say:

      You mention that you ”… already demonstrated in replay experiments that, in the right genetic background and by plating on minimal-citrate agar, Cit+ mutants sometimes arose in a matter of weeks”

      … no differently than “Van Hofwegen et al. have identified genetic contexts and ecological conditions that accelerate the emergence of citrate utilization…”

      Is it possible that Van Hofwegen’s particular strains were particularly unstable from some idiosyncratic genetic POV, due perhaps to enhanced IS activity?

      Meanwhile, do I understand you correctly when concluding that you confirm Susan Rosenberg’s contention that “ “Cells actually decide to turn up their mutation rate when they are poorly adapted to the environment…”?

      … something along the lines, the increased activity of IS elements may be "sufficient" to enhance mutation rates but are not "necessary" (as the Jesuits were wont to phrase it).

      I merely want to confirm I have understood you correctly.

      Again, thank you for your patience and your indulgence.

      Delete
    24. @ Tom Mueller

      "Is it possible that Van Hofwegen’s particular strains were particularly unstable from some idiosyncratic genetic POV, due perhaps to enhanced IS activity?"

      I doubt that's the case, since they used multiple genetic backgrounds including both K-12 and B strains. I would be inclined to look more towards specific alleles in genes that affect growth on different carbon sources, and to environmental factors including the media in which cells were grown before the onset of starvation.

      "Meanwhile, do I understand you correctly when concluding that you confirm Susan Rosenberg’s contention that “ “Cells actually decide to turn up their mutation rate when they are poorly adapted to the environment…”?"

      No, I wouldn't agree with such a blanket statement. In work with John Mittler years ago (1990, Nature 344:173-175) we found evidence that a particular type of mutation involving a Mu element increased greatly during starvation. But there's a lot of potential for idiosyncrasy from case to case, depending on genetic and environmental details. Moreover, whether a cell should even "want" to turn up its mutation rate when it is doing poorly is not at all clear to me --it may make things even worse (since many mutations are deleterious), and a cell might be better off (probability-wise) just waiting for the possibility of improved conditions (Sniegowski & Lenski, 1995, Annual Review of Ecology and Systematics 26:553-578).

      Delete
    25. Yes. It's quite odd how many of the people (not serious scientists) who suggest that organisms were "designed" to start mutating at an accelerated rate when under stress are the same folks who say almost all mutations are deleterious. They don't seem to notice the contradiction.

      Delete
    26. @lutesuite: That's a good one. Another is the contradiction in the arguments that (1) organisms are "front-loaded" to effectuate the future plans of the Designer; (2) the apotheosis of said plans is humanity; and (3) humans have no "junk" DNA.

      Presumably due to (2) our genomes are not front-loaded." If that's so, then why do we have much bigger genomes than many predecessor organisms that presumably had to be front-loaded sufficiently to account for nearly the entirety of the history of life on Earth (bacteria, for example)? Apparently it can't be that much of our genome is unnecessary, see (3).

      Delete
    27. @ Richard Lenski

      thank you... For dotting some "i"s and crossing some "t"s for me. On more than one occasion I have expressed my scepticism of Susan Rosenberg's interpretation.

      Thank you for slaying that Shibboleth


      Delete
    28. judmarc,

      "Another is the contradiction in the arguments that (1) organisms are "front-loaded" to effectuate the future plans of the Designer"

      Some studies are much more supportive of prepared adaptation mechanisms than they are of the natural selection/random errors idea.
      http://www.sciencemag.org/news/2014/05/polar-bear-evolution-was-fast-and-furious

      Delete
    29. Interesting article on evolution of polar bears! I'm amazed at how much we can now learn from DNA sequences. It hasn't been long since every one of the many interesting tidbits would have merited its own publication.

      Bottom line for purposes of this discussion: "the distinct adaptations of polar bears may have evolved in less than 20,500 generations; this is truly exceptional for a large mammal."

      There were several genetic changes involved, affecting lipid metabolism, heart function (in the presence of high cholesterol levels), and hair color. Evolution was (relatively) fast. This change seems compatible with processes of random mutation and selection, considering that the selection pressure was very high, the polar bear population was very small or went through several population bottlenecks, and 20,000 polar bear generations were available for the change.

      Delete
    30. I fear txpiper is functionally illiterate. Here is a quote from the article he cites as an example of creationism in action:

      “It’s a schoolbook example of evolution,” says Eske Willerslev, an evolutionary geneticist at the University of Copenhagen who helped the lead the research.

      LOL!

      Delete
    31. @txpiper -

      You quoted the part of my comment mentioning front-loading. Now care to tell me how that is consistent with *both* (1) bacteria, with relatively small genomes, being front-loaded with the genetic information for all that comes after, including us, and (2) us humans having much bigger genomes than those bacteria (supposedly with no junk), yet nothing to be front-loaded *for*, if we are indeed the "crown of creation."

      So which one is wrong in this set of contradictions, txpiper? Front-loading? No junk DNA? Or that we humans are the apotheosis and object of creation?

      Delete
    32. judmarc,

      “Now care to tell me how that is consistent….”

      Come on. Since when did consistency become important? Good grief, you have all kinds of examples of organisms essentially deadlocked for tens if not hundreds of millions of supposed years, and then whales evolving like thoroughbreds. Here’s my theory: Those artist renderings of animals supposedly leading from Pakicetus to blue whales are no more related to each other than I am to carrots.

      Delete
    33. For an example of the intellectual dishonesty of creationists, we need look no further than txpiper. A confessed Young Earth Creationist, he cites as evidence for his position an article that contains this quote:

      Drawing on that data, Willerslev and his colleagues conclude that polar bears split off from brown bears between 343,000 and 479,000 years ago.

      So in this well-worked out theological model of which you boast, txpiper, does God first create bears then, 400,000 years or so later, create the universe? Where were those bears for all that time, with no universe to hold them?

      Delete
    34. txpiper,

      "Come on. Since when did consistency become important? Good grief, you have all kinds of examples of organisms essentially deadlocked for tens if not hundreds of millions of supposed years, and then whales evolving like thoroughbreds."

      How is this a problem for evolutionary theory?

      "Here’s my theory: Those artist renderings of animals supposedly leading from Pakicetus to blue whales are no more related to each other than I am to carrots."

      That is a hypothesis. Now all you have to do is provide evidence for it. Incidentally, all available evidence so far says you are wrong.

      Delete
    35. "How is this a problem for evolutionary theory?"

      I think we've determined that nothing is ever a problem for evolutionary theory.

      Delete
    36. txpiper,
      "I think we've determined that nothing is ever a problem for evolutionary theory. "

      Stop projecting. Of course certain observations would be a problem for evolution. It's just that your claim that observable morphological change must occur at the same pace in every time a place is absurd, and therefore not a problem for evolutionary theory.

      Now name one falsifiable hypothesis given by any ID/creationist theory.

      Delete
  7. So far they haven't come up with a single, credible, example of such a gene so they have to be content with denying that evolution can create new genetic information.

    Remember, too, that because evolution of new information is impossible, bacterial genomes have to be "front-loaded" with all the information necessary for all the rest of the life on Earth. That's why the genome of E. coli, for example, is so much larger than hum...oh, wait.

    ReplyDelete
  8. Show me the new structures on the lizards and the mutation(s) that caused them. Paper please.

    ReplyDelete
    Replies
    1. The paper is here;

      http://www.pnas.org/content/105/12/4792.full

      Abstract

      Although rapid adaptive changes in morphology on ecological time scales are now well documented in natural populations, the effects of such changes on whole-organism performance capacity and the consequences on ecological dynamics at the population level are often unclear. Here we show how lizards have rapidly evolved differences in head morphology, bite strength, and digestive tract structure after experimental introduction into a novel environment. Despite the short time scale (≈36 years) since this introduction, these changes in morphology and performance parallel those typically documented among species and even families of lizards in both the type and extent of their specialization. Moreover, these changes have occurred side-by-side with dramatic changes in population density and social structure, providing a compelling example of how the invasion of a novel habitat can evolutionarily drive multiple aspects of the phenotype.

      Delete
    2. I'm going to ask one more time for the mutation reference. Which gene(s) mutated? Quote it.

      Delete
    3. As predicted, Unknown shifts the goal posts.

      I know you're stupid, Unknown, but surely you're not so stupid as to deny that mutations can have observable physical effects. Are you?

      Delete
    4. Hey, Unknown, where's the reference to Baby Jesus personally climbing down the throats of each lizard and stretching out the wall of their gut to create a new valve? Surely you have one.

      Delete
    5. So there's a novel structure, and it's heritable, which in the 19th century and most of the 20th century would be the end of the argument.

      I don't know if the whole genome of the lizards was sequenced, but I wouldn't assume the mutation was in a gene. It might be in a regulatory element.

      Delete
    6. Even if it's not a mutation, even if it really is some kind of epigenetic change - that's still a natural process that yields a change of a species, it's still evolution. It's still a falsification of the requirement for supermagicallydivine wishing into existence by crucified middle-easterners from the bronze-age.

      Why are the IDiots so hooked on epigenetics? It's still not ID. If the theory of evolution by mutation, drift and natural selection is false, and instead most evolution is due to epigenetic changes, that's still not ID and still leaves no room for god.

      Delete
    7. If it were an epigenetic change, it would disappear after a few generations, like all epigenetic changes.

      Delete
    8. not sure. it can be the reslut of activision of pseudo trait. its mean a function that lost back again by one mutation.

      Delete
  9. Minnich must be using the Spetnerian metrics of information (http://www.talkorigins.org/faqs/information/spetner.html).

    ReplyDelete
    Replies
    1. Lee "Archaeopteryx was a total fraud" Spetner.

      Delete
  10. Yea that's what I thought. Next time don't make a claim about something mutations can do without being able to back it up. Maybe Dr. Larry can help y'all with this little problem of having no legitimate creator. But I doubt it.

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    Replies
    1. So what is your hypothesis to explain the changes in the lizards? You seem to accept new morphologies and demand the specific genetic changes. I don't know the genetic changes and for the sake of argument let's assume no one knows them. How do you explain the morphological changes? God, if so show me exactly and specifically how it did it. If not god and not evolution what?

      Delete
    2. Why are you even responding to this guy? He's a source of moving goal posts. He's not interested in understanding or talking, just criticizing and antagonizing. There's no point.

      Delete
  11. It rather looks as though Minnich and colleagues have done some solid science and then snuck in some creationist interpretation past naive reviewers. The reference to poorly defined concepts such as "new genetic information" should clearly have been picked up at the review stage.

    ReplyDelete
  12. Probably epigenetic. Might just be plasticity. Or both. Whatever it is, it's a nonrandom response to the environment on behalf of individuals. Too bad for you evos that life is intelligently-perceptive and tends to crank out adaptive variation to blend in and adjust to environmental threats and challenges. But evolutionists generally refuse to do long term experiments on living organisms (over a period of multiple generations), so it's often difficult to know which mechanism is responsible and how changeable organisms really are.

    ReplyDelete
    Replies
    1. In order to fully grasp the dishonesty of creationists, please read this nugget from Unknown:

      evolutionists generally refuse to do long term experiments on living organisms (over a period of multiple generations)

      THIS WAS WRITTEN IN A THREAD ABOUT AN EXPERIMENT THAT LASTED FOR 30,000 GENERATIONS.

      it's often difficult to know which mechanism is responsible

      AND THEY REPEATED THE EXPERIMENT FROM FROZEN CELLS AND SEQUENCED THE GENOMES OF BEFORE AND AFTER STATES

      The argument with creationists is not a debate between equals.

      Delete
    2. Probably epigenetic.

      That's not very specific. Please describe the exact "epigenetic" mechanisms that led to this fixed change in the phenotype of this species. Y'know, just to show you're not a hypocrite when you demand this of those who accept evolution.

      Might just be plasticity.

      Again, exactly what do you mean by this? Please provide the exact process behind this "plasticity."

      Delete
    3. you can ask them, lutesuite.....http://www.bioone.org/doi/abs/10.1670/87-05N.1

      Delete
    4. So you don't know. As I suspected, you were just throwing a word around without understanding it.

      What about "epigenetics"? How did that cause the adaptaton in the wall lizards?

      Delete
    5. > Probably epigenetic

      *facepalm* epigenetic changes are transient and do not last for many generations

      Delete
  13. Long term "controlled" experiments, that is

    ReplyDelete
  14. @Diogenes...THIS WAS WRITTEN IN A THREAD ABOUT AN EXPERIMENT THAT LASTED FOR 30,000 GENERATIONS.

    30.000 generations???!!! Really? And the results? Instead of eating banana's (loss of function) the poor guy is forced to consume nuts.
    So, where's the evolution?

    But c'mon, 30K generations? Compare it with human generations.
    Btw, what happens in a lab, under controlled circumstances, has nothing to do with evolution. It's still a bacteria.

    ReplyDelete
    Replies
    1. Btw, what happens in a lab, under controlled circumstances, has nothing to do with evolution. It's still a bacteria.

      Ah the wit and wisdom of the creationist. And yet, without the slightest comprehesion of scientific matters, he persists in arguing. Aggressively dumb, and proud of it too.

      Delete
    2. Bacteria are a DOMAIN of life. It's like saying "it's still a eukaryote" after seeing fish evolve into tetrapods. What an unbelievably stupid reply.

      Delete
    3. All Lenski's experiments have done is show the awesomeness of intelligent life forms like bacteria.

      They do diddly squat to bring home the darwinian evolutionary bacon.

      There was nothing disconnected between the mutation to metabolize citrate and the bacteria's drive to survive (one of countless observations evo-devo has no clue about).

      So the mutation is clearly not random with respect to need. Not knowing the specifice mutation that will be used to make the metabolic transition in no way invalidates the observation that bacteria are scrambling to find a mutation that will work to maintain their viability.

      Again, Lenski's work if anything validates intelligent design.

      Delete
    4. Steve: The bacteria did not mutate in response to the metabolic challenge. There were variable phenotypes ALREADY within what was originally a clonal population due to the accumulation of RANDOM mutations among the individuals in the starting population and in their subsequent lineages. If the carbon source is switched, some subset of those phenotypic variants are incrementally better at utilizing it and divide more rapidly, eventually purifying the corresponding genotypes; continue for 30,000 generations, adding incremental improvements due to continued selection or drift. The bacteria have no "survival instinct"; the ability to survive is already a variant in the population, and is simply a function of the net effectiveness of all of the associated unintelligent metabolic pathways and biosynthetic processes, which are nothing more than chemical reactions.

      Delete
    5. Brian,

      You, as several other posters here are unwittingly making ID's case.

      The variable phenotypes didn't get there by accident. The accumulation of random mutations is no accident. What do you think excess reproduction is for?? Excess reproduction allows the genome to generate enough random variations, which selection will weed out. The environment will be the final arbiter of which mutation is retained.

      The survival instinct is in the genome's variable reproduction rate as required to produce enough variation that will produce the mutation which will allow for the viability of the colony.

      If bacteria had no survival instinct, they would be no variability in their rate of reproduction. The scarcity of nutrition would have no effect on the bacteria. The colony would simply cease to be in rapid fashion.

      Yet, the bacteria DO react to a scarcity of nutrition.

      The intelligence is not is the metabolic pathways or biosynthetic processes you speak of. The intelligence is in the genome having the embedded ability to reproduce in excess, that said excess producing the required minimum amount of variation that will allow the genome to match any variation in environmental conditions.

      That design has had 3 billion years of success.

      By the way, the genome is so much more than 'mere' biological processes. Tell me, what is responsible for the 'coordination' and 'timing' of said processes. More processes you say? And those processes that control the processes? When and how did they arise and how was the coordination of the coordination arrived at?

      You can only keep the inevitable conclusion at bay so long. But if the genome being designed is too scary for you, then by all means keep deferring.

      Delete
    6. Steve: "You, as several other posters here are unwittingly making ID's case.

      The variable phenotypes didn't get there by accident. The accumulation of random mutations is no accident. What do you think excess reproduction is for?? Excess reproduction allows the genome to generate enough random variations, which selection will weed out. The environment will be the final arbiter of which mutation is retained.

      The survival instinct is in the genome's variable reproduction rate as required to produce enough variation that will produce the mutation which will allow for the viability of the colony.

      If bacteria had no survival instinct, they would be no variability in their rate of reproduction. The scarcity of nutrition would have no effect on the bacteria. The colony would simply cease to be in rapid fashion."

      So, your point is simply that the existence of random mutations, and thus variability and selectability when faced with adaptive challenges, demonstrates the existence of a teleological force. And you are calling this variability the bacteria's "survival instinct". Correct?

      Delete
    7. A "survival instinct" that takes 34k generations to kick in. Now *there's* intelligent design for you, by gosh.

      Delete
  15. Unknown
    Long term "controlled" experiments, that is
    Topgoosz
    Btw, what happens in a lab, under controlled circumstances, has nothing to do with evolution

    So which is it guys? Was the LTE experiment "controlled" or "uncontrolled"?

    ReplyDelete
    Replies
    1. I was referring to multicellular organisms being subjected to environmental changes: not one instance of a multi-generational, controlled experiment has ever been done to test the capacity of an individual organism to respond to the environment by altering its dna, and then possibly passing these alterations down to future generations. Epigenetic studies have been done like this, but none involving mutations. I'd love it if you could prove me wrong.

      Delete
    2. ...not one instance of a multi-generational, controlled experiment has ever been done to test the capacity of an individual organism to respond to the environment by altering its dna, and then possibly passing these alterations down to future generations...

      Well, since such an experiment would not demonstrate evolution, but instead a scenario often proposed by intelligent design creationists, that's decidedly inconvenient for your side, isn't it?

      Before you try to deny the importance of Dr. Lenski's experiment, maybe you could point us to its creationist counterpart. Where is the multigenerational study of unicellular organisms in which the "intelligent designer" was caught in the act of creating new adaptations?

      Delete
    3. Well, since such an experiment would not demonstrate evolution, but instead a scenario often proposed by intelligent design creationists, that's decidedly inconvenient for your side, isn't it?

      Heh, heh. And once again a person (Unknown) full of bluster and argument demonstrates that they understand nothing about the topic, describing evolution perfectly incorrectly, and at the same time shooting the idea of intelligent design in the head.

      Delete
    4. Epigenetic studies not involving mutations? How did they prevent mutations? Did they pray them away?

      Delete
    5. Yeah, Unknown, what happened to Shapiro and his Natural Genetic Engineering? You IDers all love NGE. When have any of you ever done a multi-generation experiment in which a bacteria used Shapiro's alleged NGE to turn into a dolphin?

      And as for your alleged "epigenetics", when have any of you ever done a multi-generation experiment in which a bacteria changed epigenetically into a Tibetan yak?

      Much less will any of you ever look for the hand of the Intelligent Designer.

      Delete
  16. @lutesuit Where is the multigenerational study of unicellular organisms in which the "intelligent designer" was caught in the act of creating new adaptations?

    The most stupid question i've ever heard in my whole entire life. Obvious for clear reasons. To mask your impotency.
    How long will it gonna take before Lenski create a two-celled bacteria? Now that would be something.

    ReplyDelete
    Replies
    1. Multicellularity has also been observed to have evolved in the lab:

      http://www.pnas.org/content/109/5/1595

      Strangely, once again, no gods were needed for this to happen.

      Delete
    2. What the flying fuck is a two-celled bacteria? What is it with these lunatics and their sublime ignorance of the history of life?

      There never was a "two-cell bacteria" and the evolution of multicellular life is not contingent on such an entity having ever existed.

      Delete
    3. Topgoosz,

      I was just thinking the exact same thing.

      Darwinist promote Lenski's experiment results as if the bacteria he has been growing for 25 yours evolved into another species or developed a previously unknown metabolic pathway. Something unique. Or it evolved into a multi-cellular organism perhaps.

      This is not it boys and most knowledgeable creationists don't question natural selection. They question the power of it or what it can accomplish.

      The way I see it, Darwinists have nothing experimental to hang on to to validate their claims about evolution, so they have to exaggerate Lenski's lab results. Because there is nothing else. If there is, it is going to be in my face lol

      Lenski, on the the other hand, does not seem like a guy who after 25 years of experimenting with e-coli bacteria, which apparently equals millions of year of real evolution, is not going to throw in the towel and admit that he has wasted 25 years of his life on nothing and who knows who's money...

      Lenski's experiment will go down the history books as one of the Icons of Evolution very similar to the Miller-Urey Experiment. It has misled many people who trusted those scientists and Lenski's myth has the same vibe; Nonsense

      I'm pretty sure he can live with that lol

      Delete
    4. Topgoosz,

      I was just thinking the exact same thing.


      "Thinking" is not the correct word for whatever it is that goes on in your craniums.

      So are you not going to explain what "two-celled bacteria" are? Could you provide an example of such a beast?

      Delete
  17. Some of the examples in this discussion are embarrassing because they happen too quickly to work well with the idea of undirected processes. It might be prudent to entertain the notion that there could be feedback mechanisms that can result in adaptive responses.

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    Replies
    1. The authors directly state they use directed selection you moron. Obviously you're going to get a faster result when you deliberately select for certain outcomes. By the way, evolution being fast is just making evolution all the more plausible. Please just think for a moment.

      Delete
    2. Mikkel, you're supposed to revere the natural sluggishness.

      "..that [offensive speediness] in no way undermines the slowness and rarity of the evolution of this function in the context of the LTEE (or, for that matter, the rarity of Cit+ E. coli in nature and in the lab prior to our work)." "

      Delete
    3. You're supposed to use your brain to think, not to defecate with.

      Delete
    4. Some consequential genetic changes in bacteria happen very, very rapidly, others take a very, very long time. On some of the early work that James Shapiro co-authored, he and the other scientists observing what was going on began to talk about "directed evolution" because favorable changes were occurring within one generation, and they thought the bacteria must be volitionally directing such changes. Later experiments found the favorable changes were in a particular space of one-nucleotide substitutions that *could* be accomplished in a single generation, and that they happened about as often as would be expected for such substitutions in the context of *random* variation. More complex favorable changes did not occur in a single generation. They, too, occurred in a time frame and with a frequency that would be expected in the context of *random* variation. Eventually all of Shapiro's previous co-authors abandoned the "directed evolution" idea, leaving him to soldier on in the absence of any confirming evidence.

      So what we actually find are an entire range of frequencies of occurrence of changes and generations required for such changes to take place, all at the pace expected in the context of *random* variations.

      Or you could choose to depend on Designer-directed evolution, in which case I'll ask you to give me the *scientific* reason God - err, sorry, the Designer - hates E. coli with such passion he makes them suffer through 35,000 generations before they get to really chow down.

      Delete
    5. Great story Judmarc, do you have a reference?

      Delete
    6. You'd have to look up the early and later papers of a Shapiro co-author. It was a couple of years ago I read these, so I no longer recall full names off the top of my head or have cites at the ready. I think I remember a co-author with the first name Barry...? It was stuff about increased mutation rates in response to negative environmental stimuli (heat shock?). The general topic area name that might respond to a Google search was "directed evolution" or "directed mutation."

      Delete
    7. After a quick Google: Ah, OK, it was Barry G. Hall who originally published pro-"directed" papers, then eventually backed off. Papers critical of the hypothesis were written by Richard Lenski (co-authored with Slatkin and Ayala), and Paul Sniegowski.

      Delete
    8. Cairns and Rosenberg were also early n the 'directed' bandwagon. Rosenberg clung to it for a long time after the genome-wide hypermutation effects were discovered.

      Delete
    9. Thanks all, I knew it under the name 'Cairnsian evolution' or 'Fred' (yes it was called that for a while.)

      Delete
  18. I have a question as to the meaning or value of the concept of information. One can certainly think of information content in genetics, but it seems to me that information content is really not primary; it is the actual biochemistry that is primary and the changes in it and the means by which the change occurs. After all, although information content may be characterizable and interesting, the total information in a type or species of living thing can rise or fall as it evolves. I can understand why Intelligent Design advocates like the concept as it carries the immediate idea of a designer (after all information is something intelligent humans trade) thus using the term information immediately biases the conversation. As well, they get an advantage by obfuscating matters and setting the discussion at arms length the chemistry, I think. But perhaps I am missing something. Is there any real need to discussing information content in genetic systems? It must be obvious, of course, that I am not in the field, just an interested spectator.

    ReplyDelete
    Replies
    1. DGA,

      How would you appraise the sequential, role-specific performance of DNA replication enzymes in strictly chemical terms? There is obviously some kind of cognizance involved if the replication process is interrupted because errors are detected, removed and replaced. The same principle applies to white blood cells producing specific antibodies in response to specific antigens. Information is not just a concept.

      Delete
    2. There is obviously some kind of cognizance involved if the replication process is interrupted because errors are detected, removed and replaced.

      Yes, just like the goop you can fill your tires with must intelligently realize there's an air leak. Or like water molecules must "take cognizance" of the fact that it's 0 degrees C out and intelligently arrange themselves as ice crystals.

      Delete
    3. I have a question as to the meaning or value of the concept of information. One can certainly think of information content in genetics, but it seems to me that information content is really not primary; it is the actual biochemistry that is primary and the changes in it and the means by which the change occurs.

      Hi, DGA. There is actually a scientific answer to this question. It comes from the work of one of the "fathers" of scientific information theory, Claude Shannon. It turns out that information can be equated to concepts from thermodynamics, such as entropy. For example, work on whether information could escape from black holes led to predictions regarding black hole entropy and thermodynamics that have since been confirmed by observations. What this leads to is that the normal, everyday thermodynamics of chemistry and thus biochemistry can be viewed as involving information as validly as they can be seen to involve energy exchange. Understand we're talking rigorous scientific definitions here, not the primitive anthropomorphized spirit-world picture of intelligence, volition or teleology somehow being involved.

      Delete
    4. DGA, I agree that the idea of information, as used by creationists, shifts the conversation into stupid channels. It may not always be technically wrong (see Judmarc) but it's easy to misuse.

      Delete
    5. @judmarc, thanks for the reply. I know that information is a genuine scientific concept tied to thermodynamics by Shannon and so on. I can see my first line might have suggested I was denigrating the concept of information generally, rather than simply questioning its primacy in this area. I do think that IDists do use the term to suggest an intelligence by implication, which is unwarranted and that is why the term shows up in so many of their posts.

      @txpiper, the recognition of one chemical for another is by physical structure, proteins fit their intended targets, and actions proceed once the fit is made, when bonds are strengthened and weakened.

      Generally, I still think that information theory, valid scientifically, takes us step away from the reality of how evolution takes place, biochemically.

      Delete
    6. Information is a red herring.

      Information means-
      ‘a mathematical quantity expressing the probability of occurrence of a particular sequence of symbols, impulses, etc., as contrasted with that of alternative sequences’.

      Information can also mean ‘the answer to a question’.

      If one uses the first definition, then a mindless alteration of sequence will bring about new information. If one is using the second definition, then a mind has to pose a problem for solution for information to come into being.
      (This is the problem of the ‘genetic algorithm’, the programmers ask a question before the trials take place, so it looks like the second definition is being used).

      If one sticks to the first definition, then all the arguments about ‘new information’ become obviously flawed.

      Delete
    7. You are certainly getting to the heart of the matter vis a vis ID/creationism. Semantic fallacies are at the heart of virtually all their superficially difficult questions. In my experience it is more fruitful to first analyze the abuse of language inherent in the question before assuming that said language actually models the real world.

      Delete
    8. Creationists use equivocation when they discuss "information"; they have multiple definitions of it, so that they can evade falsification of their claims that 1. "no natural process can create information" and 2. "life forms contain information."

      Creationists use a very broad definition of information to claim 2 (there's information in biology). But when you point out that by that definition, natural processes can create that stuff (thus violating 1), they immediately switch to a very narrow definition of information, e.g. information is like the Mona Lisa or a Shakespearean sonnet, it encodes human purposes, that satisfies 1 (natural processes can't make it) but fails 2 (you can't find it in biology.) Look out for the "Mona Lisa switch."

      What about real information? Shannon's mutual information is the distance of a probability distribution from a random distribution. E.g. if you had 100 individuals in a population and at one position in the genome, 25% had C, 25% had T, and similarly for G and A, you could say that was no mutual information by Shannon's information. But natural selection will push the population away from the random distribution, so, e.g. if T were the most fit genotype, T could be fixed so you have 100% T and 0% C, G, or A. That's an increase in Shannon's mutual information (not to be confused with entropy) caused by natural selection.

      Kolmogorov-Chaitin information is a different measure, it measures (to oversimplify) how non-repetitive a sequence is (technically, how long must a computer program be to output that sequence?) Random mutation increases Kolmogorov-Chaitin information.

      So suppose that rounds of gene duplication create a repetitive sequence CATCATCAT. That's low Kolmogorov information, because it's repetive. But if a random mutation makes it CATCGTCAT, now it's less repetitive, that's more K-C information.

      If you had a population where all sequences were CATCATCAT, then random mutation can make one of them CATCGTCAT. This would increase the K-C information. However, the population is a tiny bit closer to a random distribution, so RM decreases Shannon's information. If CATCGTCAT is more fit than CATCATCAT, next, natural selection will probably fix it in the population and everyone will have CATCGTCAT. This pushes the Shannon mutual information back up (NS makes the population farther from a random one) while not reducing K-C information.

      So in the end, RM and NS together increase both Shannon and K-C information.

      Delete
    9. Relevant (open access):

      http://rsta.royalsocietypublishing.org/content/374/2063/20150065

      Delete
    10. I should add that that entire issue (with Koonin's paper) of the Royal Society Philosophical Transactions A deals with the nature of biological information. Outstanding papers, just published.

      Delete
    11. Evolutionary adaptation is, at its core, about accumulating information about past environments (where ancestors lived) into the genomes of organisms, where that information promotes survival and reproductive success in their current environment.
      http://wp.me/p3PJBI-6K

      Delete
    12. Diogenes: "So in the end, RM and NS together increase both Shannon and K-C information."

      Which seems consistent with us having lots of genes AND lots of junk.

      Delete
    13. txpiper,

      "The same principle applies to white blood cells producing specific antibodies in response to specific antigens."

      That's not how it works. Antibody producing cells (B-lymphocytes) produce an antibody on their surface which is different for each B-cell lineage, and is made by randomly rearranging gene segments in the antibody gene. There is no forethought in this process or a response to an antigen yet. With all these random variants circulating throughout the body, if a B-cell happens to encounter a foreign antigen it can bind to, it begins to proliferate and eventually produces secreted antibody. Therefore we make antibodies before the antigen is encountered by random rearrangements followed by positive selection for random variants that recognize a foreign antigen.

      At this stage the stimulated B-cell undergoes a process called 'affinity maturation', whereby random DNA mutations are introduced into the antibody binding region, producing a pool of genetic variation. Those variants that bind better to the foreign antigen are better stimulated to proliferate and produce antibody. Thus by a process of random mutation and positive selection, higher affinity antibodies are selected for to improve the immune response.

      Delete
    14. Lenski,

      "Evolutionary adaptation is, at its core, about accumulating information about past environments (where ancestors lived) into the genomes of organisms, where that information promotes survival and reproductive success in their current environment.
      http://wp.me/p3PJBI-6K"


      Accumulating information and creating new information are two very different things.

      How does the evolution, the way you see it, create new information?
      How can evolution progress from e-coli bacterium to the next level of evolution by accumulating the information ONLY?

      Delete
    15. Can you provide a short nucleotide sequence illustrating what new information looks like, and indicate the features that render it inaccessible to mutation/recombination?

      Delete
    16. Eric,

      "How can evolution progress from e-coli bacterium to the next level of evolution by accumulating the information ONLY?"

      5 or 6 genetic changes were sufficient for Yersinia pseudotuberculosis, a fecal-oral bacterial pathogen causing relatively mild disease, to evolve into a hypervirulent, flea-borne illness responsible for some of the worst pandemics of disease in human history (Yersinia pestis).

      This did not require poofing new information into existence, but did involve both the accumulation and 'creation' of new information.

      Delete
    17. judmarc.

      “Or you could choose to depend on Designer-directed evolution…”

      More like a DNA molecule prepared to adapt. This is an interesting article that shows why some people find the standard explanations unsatisfying:

      ”Eye loss in these fish is considered to be a demonstration of an evolutionary concept known as "standing genetic variation," which argues that pools of genetic mutations—some potentially helpful—exist in a given population but are normally kept silent. The manifestations of these mutations, that is, their impact on observable phenotypes, don't emerge until the population encounters stressful conditions.”

      I don’t buy this idea at all, but at least it shows that some researchers still have enough curiosity left to recognize that something is wrong. There’s a good chance she even thinks that there is more to genetic information than chemical reactions.
      http://phys.org/news/2013-12-cavefish-evidence-alternative-mechanism-evolutionary.html



      Chris B,

      Thanks for taking the time to write about that. I did some reading about affinity maturation, and in regards to Somatic Hypermutation, the Wikipedia article says that:

      ”Mutations in the variable, antigen-binding coding sequences (known as complementarity-determining regions (CDR)) of the immunoglobulin genes. The mutation rate is up to 1,000,000 times higher than in cell lines outside the lymphoid system.”

      There are apparently dozens of these genes. Would you suppose their affinity for catching mutations began as an anomaly and was selected for because it was useful?

      Delete
    18. txpiper,

      "There are apparently dozens of these genes. Would you suppose their affinity for catching mutations began as an anomaly and was selected for because it was useful?"

      There are two things going on here. One is the rearrangement of these many genes into various combinations to generate the initial pool of variation, before a foreign antigen is ever encountered. They constitute a random pool of membrane bound antibody that can monitor the body for the presence of foreign antigens. This type of random rearrangement of certain proteins is actually widespread in extant life, present in some bacteria and protozoons as well.

      This is different from affinity maturation, where somatic hypermutation introduces a new pool of genetic variation in the antibody binding region in a random manner. The higher affinity variants are selected for and go on to produce the majority of antibody against a particular foreign protein.

      My point was that random variation followed by selection for more efficient variants is all that is required to make protective antibodies. No forethought or supernatural intervention is required, but let me know if you have any evidence suggesting otherwise.

      Delete
    19. txpiper,

      I don't speak for judmarc, but I wanted to point out that the alternative explanation of physiological adaptations in cavefish you point out is still entirely consistent with natural, evolutionary processes producing change. This isn't a problem for evolutionary theory at all, and in fact provides an example against a common anti-evolution "criticism" that there is not time for these morphological changes to occur. The fact is that genes affecting developmental pathways can indeed result in morphological change and aren't always hopelessly deformed, lethal mutants.

      It doesn't seem to help out ID/creationists much, though, since it is hard to imagine why an intelligent designer would still give the blind cavefish empty eye sockets for no apparent reason.

      Delete
    20. Chris:
      "No forethought or supernatural intervention is required, but let me know if you have any evidence suggesting otherwise."

      You're requesting something from Txpiper, which no creationist has ever done before, provide evidence for his supernatural claims. I've asked the same question a few times last week, but Txpiper can't get past 'evolution can't do blah blah blah'.

      I do sincerely hope he can provide evidence, because this might actually make for some interesting discussions. But, I won't be holding my breath.

      Delete
    21. Good call, Ed, I won't be holding my breath either. And I don't think Eric will ever get back to me about how a few changes resulting in the "accumulation of information" can lead to changes. Once his vague gibberish is met with facts, he wanders off.

      Delete
    22. Eric says: Accumulating information and creating new information are two very different things.

      What evidence is there that any information in any genome was "created" but not "accumulated"? Do you think one is green and one is purple?

      Do you have equations for either that could take a genetic sequence as input? Of course not.

      Delete
  19. Semantic fallacies and all sorts of abuse of logic and language - or just inventing your own, personal version of logic, terms, and concepts. That's the method chosen by the infamous Ray Martinez, phantom of the talk.origins opera.

    ReplyDelete
  20. I dont really see the problem here. Its basically creationist saying. This is yet another instance in which we agree with the theory of evolution. they are simply cornering themselves in a smaller place than before.

    ReplyDelete
    Replies
    1. No, creationists don't agree that evolution is non-teleological in nature.

      Clearly Lenski's bacteria were reacting to the lack of nutrition. Why? If they are like rocks, the citrate should simply have obliterated the bacteria, like wind and water erode the rocks until it becomes sand. The rock had no say in what the wind and water did.

      But the bacteria had an 'opinion'. No, we will not lay down and die. We are not rocks. We have a choice.

      Even a child can understand such a basic distinction between life and non-life.

      Delete
    2. Steve: The bacteria did not "react to the lack of nutrition." This is the part you don't get: There are variable phenotypes ALREADY within what was originally a clonal population due to the accumulation of random mutations among the individuals in the starting population and in their subsequent lineages. When the carbon source is switched, some subset of those phenotypic variants are incrementally better at utlizing it and divide more rapidly, eventually purifyng the corresponding genotypes; repeat for 30,000 generations, adding incremental improvements due to continued selection or drift. The bacteria have no mechanism to alter their genome in a "response" to a metabolic challenge; the ability to do so so a selectable degree is already a variant in the population.

      Delete
    3. But the bacteria had an 'opinion'.

      Even a child can understand such a basic distinction between life and non-life.


      Even as a child I could understand the absurdity of ascribing opinions to bacteria.

      Delete
    4. Hey Steve,
      "But the bacteria had an 'opinion'. We have a choice."

      Ye gods, Steve... Perhaps this ia a nice story to tell to kindergarten kids, to explain how bacteria can make them, the kids, ill. But do you seriously expect people age 6 and higher to believe this?????????? Uhm... you do, don't you? And, you seem to be surprised people when don't believe this? Wow...

      Delete
    5. "But the bacteria had an 'opinion'. No, we will not lay down and die. We are not rocks. We have a choice."

      I have read some truly idiotic things from creationists in my day, but this... just, wow...

      Delete
    6. Hey N. Manning if all you have is ridicule of a figure of speech, then ID is in particulary good hands.

      The point is clear. Bacteria, any child can see, are categorically different from rocks because they REACT to stimulie. And yes they DO in effect make choices.

      Your childish ridicule is a weak rhetorical device I suggest your chuck into your little junk box of failed retorts.

      Delete
    7. Brian, its the other way around. You don't understand what you see.

      The random mutations as you say were ALREADY there. How did they get there? Why were they not eliminated by the genome? Answer. Because they were useful. Precisely because when a situation arises, they have the tools necessary to deal with it. The bacteria are not accumulating mutations for the fun of it or because they don't recognize there is an accumulation (if bacteria can quorum sense, who is to say they cannot recognize changes within their own genome?).

      The accumulation is what is required for the variation and selection process to work. What? Do you think the bacteria only start accumulating mutations just when the threat arose? And if the accumulated mutations are not enough, do you think they don't recognize a need to increase their reproductive rate in order to increase the rate and quantity of mutations that will tilt the probability in their favor?

      I think its your muddled non-teleological thinking that keeps revolutions in biology and artificial intelligence from happening.

      Your thinking is that old school 'its all just chemistry' evolutionary meme that is by and large a sterile idea.

      Science is moving on. I suggest you do the same if you want a more productive career, that is.


      Steve: The bacteria did not "react to the lack of nutrition." This is the part you don't get: There are variable phenotypes ALREADY within what was originally a clonal population due to the accumulation of random mutations among the individuals in the starting population and in their subsequent lineages. When the carbon source is switched, some subset of those phenotypic variants are incrementally better at utlizing it and divide more rapidly, eventually purifyng the corresponding genotypes; repeat for 30,000 generations, adding incremental improvements due to continued selection or drift. The bacteria have no mechanism to alter their genome in a "response" to a metabolic challenge; the ability to do so so a selectable degree is already a variant in the population.

      Delete
    8. Steve: "Science is moving on. I suggest you do the same if you want a more productive career, that is."

      Science is indeed always moving on, Steve, and you are correct that a productive scientific career requires staying on top of that advancement. However, not being able to distinguish science from non-science would be a career killer.

      Delete
  21. Professor Lenski,

    This assumes the pre-existing abililty of life to recognize the concepts of information, promoting, and success. But it makes no sense from the perspective of the vast majority non-teleological step wise change advocates who assert than there is no intelligence at play in any biological change.

    If this is true, you cannot speak of bacteria 'accumulating'information, or that information 'promoting' survival, or of reproductive 'success'.

    In a non-teleological world, how does organic matter acquire a survival instinct? why didn't the bacterial colonies in your experiments simply collapse in the face of citrate. Why did they react at all? Why did they scramble to mutate?

    Darwinian evolutionary concepts are so Orwellian in nature. They defy logic and rational thought.

    Richard Lenski: "Evolutionary adaptation is, at its core, about accumulating information about past environments (where ancestors lived) into the genomes of organisms, where that information promotes survival and reproductive success in their current environment. "

    ReplyDelete
    Replies
    1. Oh, this is going to be good. Pop some popcorn and pull up a chair, everyone....

      Delete
    2. Why did they scramble to mutate?

      That's some scrambling - took only 33,127 generations.

      Delete
    3. I'll put it here too, Steve: The bacteria did not "react" to anything. There are variable phenotypes ALREADY within what was originally a clonal population due to the accumulation of random mutations among the individuals in the starting population and in their subsequent lineages. If the carbon source is switched, some subset of those phenotypic variants are incrementally better at utilizing it and divide more rapidly, eventually purifying the corresponding genotypes; repeat for 30,000 generations, adding incremental improvements due to continued selection or drift. The bacteria have no "survival instinct"; the ability to survive is already a variant in the population.

      Delete
    4. "The bacteria did not "react" to anything....The bacteria have no "survival instinct" "

      "Procaryotes are known to exhibit a variety of types of tactic behavior, i.e., the ability to move (swim) in response to environmental stimuli. For example, during chemotaxis a bacterium can sense the quality and quantity of certain chemicals in its environment and swim towards them (if they are useful nutrients) or away from them (if they are harmful substances)."

      Delete
    5. "That's some scrambling - took only 33,127 generations."

      Yeah, it's not like we're talking about whales.

      Delete
    6. txpiper: No, they did not react in the case of mutations allowing the utilization of citrate. Chemotaxis is a different story, and is indeed a "reaction" in the physiochemical sense. It's a well-characterized molecular mechanism that orients the motility machinery of a cell (this applies to eukaryotic cells as well) such that polarized directional movement toward or away from a concentration gradient of some chemical signal. The biochemical workings are actually pretty well described. Is this what you would classify as a "survival instinct"? Under those terms, any chemical reaction that occurs would be doing so because of its "survival instinct". Don't let the use of anthropomorphic terms like "sense" or "react" throw you.

      Delete
    7. "Yeah, it's not like we're talking about whales."

      Yeah, the evidence for whale evolution is solid.

      Delete
    8. In a non-teleological world, how does organic matter acquire a survival instinct? why didn't the bacterial colonies in your experiments simply collapse in the face of citrate. Why did they react at all? Why did they scramble to mutate?

      You are aware that most of the colonies did not develop the ability to metabolize citrate, right? Why do those colonies lack the "survival instinct"? Why haven't they "collapsed"?

      More pertinent question: Do you have the slightest clue what you're talking about?

      Delete
    9. Under those terms, any chemical reaction that occurs would be doing so because of its "survival instinct". Don't let the use of anthropomorphic terms like "sense" or "react" throw you.

      You've hit the nail on the head here Brian. Anthropomorphic language is causing txpiper to confuse agency with a chemical reaction.

      Even in the human sense, agency is nothing more than a far more complicated series of chemical, electrical and physical interactions.

      I think he wants to believe that all bacteria have a little bit of magic driving them but if we fully understand all of the chemical processes that drive these responses to stimuli then where is the room for magic?

      Delete
    10. @txpiper

      http://rationalwiki.org/wiki/Magical_thinking

      Delete
    11. Aceofspades,

      “Anthropomorphic language is causing txpiper to confuse agency with a chemical reaction.”

      No, I’m not the least bit confused. They use language that accurately reflects what is going on. You’re simply trying to oversimplify and trivialize the processes until they are ideologically manageable. Same story with ‘information’. I once discussed replication errors with a guy who insisted in calling them ‘events’ for the same reason.

      Let’s try this. During the DNA replication process, errors are detected, excised/removed, and replaced. What words or concepts would you substitute that more accurately describe those three activities in terms of chemical reactions?

      Delete
    12. txpiper, why do you call them "errors", especially since you believe that yahoo-yeshoo-holy-spook created and are directing them? Does your so-called 'God' make errors?

      Delete
    13. I call them that because that is what they are. Unfortunately, your education comes from support groups like this, so you don't have a frame of reference to comprehend the answers to your other penetrating inquiries.

      Delete
    14. txpiper,

      "Let’s try this. During the DNA replication process, errors are detected, excised/removed, and replaced. What words or concepts would you substitute that more accurately describe those three activities in terms of chemical reactions?"

      If you understood how DNA is replicated and proofread, you would already have the answer to your question.

      Delete
    15. Chris, if you understand it, then you can make the easy substitutions.

      Delete
    16. txpiper: "Let’s try this. During the DNA replication process, errors are detected, excised/removed, and replaced. What words or concepts would you substitute that more accurately describe those three activities in terms of chemical reactions?"

      Maybe you don't know this, but every one one these steps in the mismatch repair mechanism has been worked out to atomic-level structural and catalytic detail. During each one of the phases you mention, it involves non-covalent interactions between constituent atoms of DNA and free nucleotides and atoms of specific amino acids in the substrate binding and catalytic sites of the enzymes involved (hydrogen bonds, electrostatic interactions, some van der Waals, hydrophobic interactions, etc.), which is known to atomic detail from numerous NMR and crystallographic analyses. It also involves enzyme-mediated catalysis in these complexes involving breakage of phosphodiester bonds in DNA (hydrolysis? I can't remember the catalytic mechanism), and the re-formation of an ester linkage with the replacement nucleotide. The catalytic mechanism, and the atomic-level structure of the substrates in complex with the enzymes are known. The precise rates and equilibrium constants of all of the reactions, as well as pre-steady state data, are well-established from kinetic assays. There are no mysteries. It is all chemistry, governed by the same laws (mass action, etc.) that govern all chemical reactions.

      So, I guess I'm not sure what you're getting at.

      Delete
    17. txpiper said: "I call them that because that is what they are."

      Ah, so you do believe that yahoo, yeshoo, and holy spook make errors.

      "Unfortunately, your education comes from support groups like this, so you don't have a frame of reference to comprehend the answers to your other penetrating inquiries."

      Diversionary gibberish.

      Delete
    18. txpiper,

      "Chris, if you understand it, then you can make the easy substitutions. "

      The substitutions happen, with or without our understanding. Do you understand that?

      I don't know what you mean by "easy" substitutions.

      Delete
    19. Yeah, it's not like we're talking about whales.

      Given 10-15 million years between Pakicetus and whales, txpiper, how many generations is that? And exactly how many differences are there between the two genomes? And exactly how many of these do you say were impossible in that time frame?

      Whoops, forgot - it's a nonsensical question to you, due to your "scientific" view that the Earth is 6000 years old. News flash, txpiper, a lot of the science developed since Galileo is going to look absurd if you shoehorn everything into that view. Another news flash, the past 400 years of science ain't all wrong.

      Delete
    20. Brian,

      See the problem here? Everything is studied in isolation but absolutely none of it can be tied together non-teleologically. If so, if would have been done ages ago.

      Economists have the same problem. Everything is studied ion isolation -using the 'all things being equal' approach- and extrapolate from there. But alsa the real world (with thinking people in it) doesnt work that way.

      By the same token, knowing each individual chemical process by heart will not lead you to any deeper understanding of the genome.

      This is precisely why evolutionary biology has gone and is going nowhere. It refuses to concede the need for a teleological approach to understanding the integrative, interactive, cooperative nature of the myriad of chemical processes taking place, which are all working toward a collective goal.
      ____________________________________________________________

      Brian: "Maybe you don't know this, but every one one these steps in the mismatch repair mechanism has been worked out to atomic-level structural and catalytic detail. During each one of the phases you mention, it involves non-covalent interactions between constituent atoms of DNA and free nucleotides and atoms of specific amino acids in the substrate binding and catalytic sites of the enzymes involved (hydrogen bonds, electrostatic interactions, some van der Waals, hydrophobic interactions, etc.), which is known to atomic detail from numerous NMR and crystallographic analyses. It also involves enzyme-mediated catalysis in these complexes involving breakage of phosphodiester bonds in DNA (hydrolysis? I can't remember the catalytic mechanism), and the re-formation of an ester linkage with the replacement nucleotide. The catalytic mechanism, and the atomic-level structure of the substrates in complex with the enzymes are known. The precise rates and equilibrium constants of all of the reactions, as well as pre-steady state data, are well-established from kinetic assays. There are no mysteries. It is all chemistry, governed by the same laws (mass action, etc.) that govern all chemical reactions."

      Delete
    21. Steve: "See the problem here? Everything is studied in isolation but absolutely none of it can be tied together non-teleologically. If so, if would have been done ages ago."

      No, I don't see the problem. What's an example of something that cannot be tied together noon-teleologically? Finding mechanistic (i.e. non-teleological) connections is pretty much what scientists do (e.g. the connection between the random mutations and evolution), contrary to your assertion. You're question begging. Why do things need to be tied together teleologically? Why is being tied together mechanistically not enough?

      I understand the epistemological arguments against reductionism with respect to emergent properties and unpredictable system level effects, but the things "studied in isolation," as you say, still underlie these processes (albeit with often unpredictable interaction effects).

      Delete
  22. Chris B (and txpiper) - really enjoyed following your discussion. I've learnt something new about how immunity develops. Thanks.

    Steve - too funny. Can't believe anyone who can spell can be that stupid. Giving you the benefit of the doubt - best troll of the thread award: "the bacteria had an opinion". No one saw that coming - anyone else spray coffee on their computer screen?

    ReplyDelete
  23. Oh and thanks Diogenes for the technical insight into how information is accumulated by RM & NS.

    ReplyDelete
  24. I've written to UofI, again, calling for the review and termination of Mr. Minnich for his deception and his utter contempt for real science. The dean of the College of Science forwarded my email to Mr. Minnich who responded with Roth's error filled "analysis", as if that would be satisfactory. I'll be contacting Dr. Roth as well, and I'm still calling for Minnich's removal from a teaching position for his religious nonsense.

    ReplyDelete
    Replies
    1. @Jay

      One of the quickest ways to be banned from Sandwalk is to harass people by writing to their employers (or relatives) demanding that they be fired or reprimanded for something they said.

      It applies to anyone but it's especially egregious, and stupid, when the person is a professor at a university.

      Goodbye.

      Delete
    2. For the record, I agree completely with Larry Moran on this point.

      Delete
  25. I have read Minnich paper and Lenski's rebuttal, and it seems to me that the following is true. Minnich et al. did not find anything new, even the fact that the Cit+ enabling mutations happen more quickly under direct selection had already been found by Lenski's team ( Blount et al. 2008), note the year. The experiments done by Minnich et al. are mere window-dressing to make it sound to laymen as if Minnich et al. have found out something that undermines Lenski's results. Equally important, it gives Minnich a chance to air his opinion in a science journal that rearranging existing parts isn't real evolution and generates no "new" information.

    Minnich isn't doing actual research, just going through the motions/paying scientific dues, to get his foot in the door of a scientific journal so he can add ID buzz phrases into paper which he can then quote later. "See, we did experiments! With science and everything! And it says Lenski found nothing new! It's in a science paper so it must be true!" Just one more way in which ID is a huge waste of everyone's time.

    Thank you for a very interesting post, Prof. Moran.

    ReplyDelete
  26. sez Eric @ Tuesday, February 23, 2016 5:43:00 PM:
    Accumulating information and creating new information are two very different things.

    How does the evolution, the way you see it, create new information?

    Hi there, Eric! I see you've just wheeled out the hoary old mutations can't create new information argument beloved of Creationists.

    Groovy.

    Of course, said argument depends on one's ability to recognize this "new information" stuff when one sees it. So here's a golden opportunity for you, Eric, to demonstrate that you are, in fact, not just repeating a hoary old Creationist argument like a tape recorder—that you actually do understand said argument—that you actually can recognize this "new information" stuff what you see it!

    Here's an arbitrary nucleotide sequence, to which I will give the arbitrary label "Sequence Fred": gcg ccc tgg tcc gcg aac att gta ttg cac tcg cta caa atc aga act aca tat att gta ttg gga cag taa cag cct gct cga tgt acc

    Does Sequence Fred contain any "new information"? If it does, how much "new information" does it contain?

    ReplyDelete
  27. A radio does not become a car. The radio breeds with other radios and over several generations attributes that are s benefit to the baby radios survival are selected for until you have an MO3 player. An IT person traps a wild MP3 player, and listens to it in his car. Eventually the cars radio (a whole different species of radio, which evolved under different conditions) goes unused and the driver plugs the mo3 player into the six jack of the car radio. The resulting child of this mating is a windows phone, and cortana takes over the car like a parasite. Ta da. Now can we get past this poor example?

    ReplyDelete
  28. Aceofspades,

    Were you unable to find suitable replacement language for those three activities that wasn’t too anthropomorphic? I was really looking forward to seeing how you would deal with the excision since that is an actual course reversal.

    =====

    Brian,

    You know a lot, and I appreciate you taking the time to write and about the chemistry behind the replication check and correct process. Perhaps you can explain something not nearly as complex.

    Why is there a reaction if I drop an Alka-Seltzer tablet into glass of water?

    =====

    judmarc,

    “Given 10-15 million years between Pakicetus and whales, txpiper, how many generations is that? And exactly how many differences are there between the two genomes? And exactly how many of these do you say were impossible in that time frame?”

    Okay, let’s try this again. And let’s base it on the thundering evolutionary progress of Lenski’s experiment, whereby after 64,000 generations, one (but just one) of the original twelve populations can now utilize a food source that it already had the genetic wherewithal to use in anaerobic conditions before the experiment began. We’ll call that our progress increment.

    And let’s make it easy and use 15 million years.

    And let’s make it more than generous and assume 1 generation per year.

    If you divide 15,000,000 by 64,000, you get about 235 progress increments. So, I have two questions.

    1) Is that enough steps for countless major systems and subsystems to be altered or generated by DNA replication errors so that Pakicetus is transformed into a fully functional marine mammal?

    2) When you look at an artist’s rendering of Pakicetus, do you actually see a whale?

    ReplyDelete
    Replies
    1. txpiper: "You know a lot, and I appreciate you taking the time to write and about the chemistry behind the replication check and correct process. Perhaps you can explain something not nearly as complex.

      Why is there a reaction if I drop an Alka-Seltzer tablet into glass of water?"

      It seems my answer to your question missed your thickly veiled point, so I'm guessing you're not interested in hearing about solvent systems and chemical kinetics and the like. Why don't you quit being coy and present your alternative?

      Delete
    2. Brian, can you explain the chemical reactions responsible for the Alka-Seltzer tablet solution to your stomach ache?

      The reaction that occurs when the tablet touches water was designed by a teleological entity that sought a solution to a specific problem and understood the use of various chemical reactions and their interaction with other chemical reactions AND what the final result would be- a cessation of uncomfortable acidicy in the gut.

      That is the extremely important part you conveniently left out.

      Why is that?

      Delete
    3. Because it's irrelevant to the fact that the chemical reaction takes place, whether the tablet was designed by humans or appeared by chance.
      The reaction is what it is and will take place regardless.

      Delete
    4. @txpiper
      "Okay, let’s try this again. And let’s base it on the thundering evolutionary progress of Lenski’s experiment, whereby after 64,000 generations, one (but just one) of the original twelve populations can now utilize a food source that it already had the genetic wherewithal to use in anaerobic conditions before the experiment began. We’ll call that our progress increment.

      And let’s make it easy and use 15 million years.

      And let’s make it more than generous and assume 1 generation per year."


      All of these assumptions are based on the false assumption that only one adaptation or change has happened in the Lenski experiment. That's simply false. There has been at least 20 unambigously beneficial mutations, and many many more neutral changes.

      In some of the lineages, over 800 mutations have accumulated in the bacteria. Most of these are very nearly neutral with respect to fitness, but that does not mean they are without phenotypic or morphological effect.

      That means to make the sort of extrapolation you do, from bacterial evolution to the evolution of whales from terrestrial tetrapods, you need to factor in quite a lot of change that doesn't necessarily have an effect on fitness.

      The whole idea that this kind of extrapolation can even be done is idiotic in the first place.

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    5. “Given 10-15 million years between Pakicetus and whales, txpiper, how many generations is that? And exactly how many differences are there between the two genomes? And exactly how many of these do you say were impossible in that time frame?”

      Okay, let’s try this again. And let’s base it on the thundering evolutionary progress of Lenski’s experiment, whereby after 64,000 generations, one (but just one) of the original twelve populations can now utilize a food source that it already had the genetic wherewithal to use in anaerobic conditions before the experiment began. We’ll call that our progress increment.


      So here's what you're not understanding (involuntarily or purposefully) and why you can't make the comparison you're attempting:

      An animal like Pakicetus has something all bacteria lack by definition, a body plan, whereby development of the various parts of the body, ultimately amounting to trillions of cells in an adult, is controlled by regulatory genes. You see just how powerful this is when you consider differences in body plan tendencies that have evolved in humans over much shorter time frames than 15 million years - from ectomorphic tendencies in tropical climates (less volume per surface area, helps get rid of heat) to endomorphic tendencies in colder climates (more volume per surface area, helps retain heat).

      And of course we're talking about "generations" of clones with bacteria, versus sexual reproduction with mammals like Pakicetus.

      So while the LTEE is extremely well conducted and very instructive in any number of ways, trying to use it to establish a timeline for whale evolution has a number of problems.

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    6. Steve: "The reaction that occurs when the tablet touches water was designed by a teleological entity that sought a solution to a specific problem and understood the use of various chemical reactions and their interaction with other chemical reactions AND what the final result would be- a cessation of uncomfortable acidicy in the gut.

      That is the extremely important part you conveniently left out.

      Why is that?"

      No, that's the answer to the question "Why is there Alka Seltzer?". He asked why there is a reaction (presumably he's talking about the production of CO2 gas; maybe not) when you put Alka Seltzer in water. I presumed txpipers question is "Why does sodium bicarbonate dissociate into cabonic acid and hydroxide ion in water, and why does the carbonic acid decompose into carbon dioxide and water?". The solution to the stomach ache is due to the buffering action of the production of the alkaline hydroxide ion when the sodium bicarbonate dissociates. The folks who designed the tablets knew this (hence the teleological origins of Alka Seltzer), but the underlying chemistry is certainly not teleological (which is why I left out the teleology of Alka Selter). What's your point?

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    7. Mikkel, judmarc,

      So you don’t like using the LTEE experiment to gauge the speed of evolution? Above, Dr. Lenski defends “the slowness and rarity of the evolution of this function”. I can appreciate your discomfort, but I don’t understand why you would think that whale evolution should occur any faster. I would tend to think exactly the opposite for all kinds of reasons, not the least of which would be hideous complexity.

      ===

      Brian,

      “He asked why there is a reaction (presumably he's talking about the production of CO2 gas; maybe not) when you put Alka Seltzer in water.”

      Well, recalling that the original issue was about agency, the answer to me is very simple. There is a reaction because I put the tablets in the water.

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    8. txpiper,
      "So you don’t like using the LTEE experiment to gauge the speed of evolution? Above, Dr. Lenski defends “the slowness and rarity of the evolution of this function”. I can appreciate your discomfort, but I don’t understand why you would think that whale evolution should occur any faster. I would tend to think exactly the opposite for all kinds of reasons, not the least of which would be hideous complexity."

      There is no one 'speed of evolution'. Why would you think such a thing?

      You have no ides of the circumstances of whale evolution or how "hideously complex" it was or wasn't. That's pure speculation on your part.

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    9. "Well, recalling that the original issue was about agency, the answer to me is very simple. There is a reaction because I put the tablets in the water.:

      Did you then direct all the chemical reactions that occurred after you put the tablets in the water?

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    10. "Did you then direct all the chemical reactions that occurred after you put the tablets in the water?"

      No, I was just reacting to a signal that told me I have heartburn. I don't always drink Alka-Seltzer, but when I do, it is for a reason. Agency involves purpose. What enzymes do is purposeful.

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    11. "No, I was just reacting to a signal that told me I have heartburn. I don't always drink Alka-Seltzer, but when I do, it is for a reason. Agency involves purpose."

      So all the chemical reactions in the universe have an agency? This is the same thinking that led people to beleive that the Sun was ridden across the sky by a magical chariot while the Earth stood still in the firmament.

      What enzymes do is because of physics. You have zero evidence any purposeful forethought went into any enzyme.

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    12. "So all the chemical reactions in the universe have an agency?"

      The dividing line between chemistry and biochemistry is purpose and function. You could call it mission.
      -
      "You have zero evidence any purposeful forethought went into any enzyme."

      And you have no mechanism to account for their origins or their role. I'll go with the idea that they do what they do because they were designed to do it.

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    13. "And you have no mechanism to account for their origins or their role. I'll go with the idea that they do what they do because they were designed to do it."

      So after all that, your argument is just a god of the gaps argument. How disappointing.

      Delete
  29. txpiper: " The dividing line beteen chemistry and biochemistry is purpose and function. You could call it mission."

    No, biochemistry is just chemistry that happens in cells. It's still chemistry.

    ReplyDelete