Mapping fitness: bacteria, mutations, and Seattle

Posted 27 November 2010 by Steve Matheson

Thinking about fitness landscapes can stimulate detailed discussion and consideration of the meanings and limitations of such metaphors, and my introductory comments did just that. Most notably, Joe Felsenstein pointed us to the various ways these depictions can be employed, and urged everyone to use caution in interpreting them. All too true, but the goal here is modest: I want to discuss the interesting questions that arise when considering the relationship between genotypes and phenotypes, i.e., how a particular genetic makeup influences fitness, whether the genetic makeup in question is simple or complex, and however fitness is conceived. These questions can take further discussion in all sorts of directions, but there are two that I have in mind in this series. First, I want to point to increasing capacity of scientists in their ability to examine these relationships experimentally. Second, I want to highlight the failure of design creationists to address or even to understand such matters.

If you know a little about evolution, you already know that mutation is a major source of genetic novelty. And you've probably heard (or surmised) that the mutation rate in a population or lineage is thought to contribute to something called "evolvability." No mutation means no evolvability. And maybe it's clear that too much mutation is a bad thing, too. And so, the mutation rate itself is a parameter that contributes to fitness, with fitness referring in this case to the ability of a population to adapt or compete over time. There can be, it seems, a fitness landscape for mutation rates, in which we could depict fitness as a function of the mutation rate. Perhaps we could even sketch such a landscape if we could generate genetic variants that differ solely in their mutation rate.

Experiments like this have been done, and the best-known examples come from work on bacteria. Earlier this year, a group at the University of Washington in Seattle, led by Lawrence Loeb, took the analysis a big step further, in work that sought "to characterize the fitness landscape across a broad range of mutation rates." The co-first authors of the report are Ern Loh and Jesse Salk.

Loh et al. introduce their work by noting that previous analyses of the influence of mutation rate on bacterial fitness were informative but limited in scope. These experiments tended to emphasize mutators (variants with higher-than-normal mutation rates) and tended to perform head-to-head competitions between only two variants (mutator vs. normal, for example). And modeling studies of the phenomena would benefit from further validation by experimental data. So the authors set out to measure bacterial fitness in the presence of widely-varying rates of mutation. Their experiment employed two innovations that filled these gaps in previous work:

The panel of variants included not two, or ten, but 66 versions of the DNA copying enzyme (DNA polymerase I). These variants all grow normally when they live alone, but they exhibit mutation rates that span six orders of magnitude, from one thousandth of the normal rate to a thousand times the normal rate. (Because the DNA polymerase is the main copying machine, its fidelity is a major determinant of the error rate and therefore the mutation rate.) This means that unlike all or most previous work in this area, their library included antimutators - variants with a lower-than-normal mutation rate.
The authors staged evolutionary competitions in which all 66 variants were put together and grown for 350 generations. Specifically, they regularly diluted the cultures so that the environment cycled between low density (leading to rapid growth) and high density (leading to nutrient depletion and stasis).

The experiment is, then, relatively simple in concept. Create a pool of variants and then see which ones (if any) will take over when they're in competition with all the others. We'll skip the details of the creation of this library of variants, though it could be fun to discuss in comments. Suffice it to say that because the variants all grow normally when living in isolation, any differences in competition outcome are likely due to the effects of mutation rate on the ability of variants to adapt in the face of competition.

In one excellent graph (from Figure 2 of the paper) shown below, the authors summarize their basic result: in the various competitions, only eight of the 66 variants emerged as winners or co-winners. Those eight variants represent a relatively small subset of what we might call mutation-rate space. Here's how the authors describe the outcome:

The recovered mutants were all moderate mutators, with mutation rates ranging from 3- to 47-fold greater than that of the wild type. Of these, 88% had at least a 10-fold elevated mutation rate. No antimutators were detected in the output population despite constituting 77% of the input population.

Loh et al Fig 2.jpg You can see this from the graph: each colored arrow points to a mutation rate, representing a variant that was one of the winners, and the bar graph above it shows how often that particular variant won. The scale left to right is mutation rate. Variants from normal on down (going left on the scale), all of those antimutators, were losers. Ditto for the super-mutators at the other end of the scale.

Loh et al. went on to show that the winning variants had adapted by putting the winners into head-to-head competition with their ancestors. (Oh the cool things you can do when your experimental organism is E. coli!) In other words, the winning variants had evolved, becoming more "fit" than when they started, by virtue of competing in a crowded jungle of other variants. The winners were different from their ancestors, but also from each other, demonstrating that the winners had acquired new characteristics beyond their higher mutability. The authors conclude that "under conditions where organism fitness is not yet maximized for a particular environment, competitive adaptation may be facilitated by enhanced mutagenesis."

The paper is fun to read and relatively approachable. Check it out.

So back to the two points I wanted to emphasize. First, the authors briefly employ the "fitness landscape" metaphor, simply to indicate that mutation-rate variation (in this case due to engineered genetic variation in DNA polymerase I) is likely to map onto "fitness" (in this case, ability to win an evolutionary competition under a certain set of environmental conditions) in interesting and perhaps surprising ways. Their data add a layer of intriguing complexity to studies and discussions of the roles of mutation and mutability in evolution and evolvability. Second, they did their experiments at the University of Washington School of Medicine. Less than 12 miles away, in Redmond, Washington, is a research institute dedicated to intelligent design. According to Google Maps, it's a 16-minute drive from that institute to the UW School of Medicine. (Or 40 minutes in traffic. Neither of these numbers impresses me, having lived in metropolitan Boston for five years.) Now, some of the researchers at that institute are keenly interested in mutation and evolution in bacteria. Do you suppose those researchers are interacting with the Loeb lab? Attending seminars, exchanging research materials, collaborating, consulting? I would be interested to hear from scientists at either place. If, as I suspect, none of those things has happened, then maybe the folks at that institute in Redmond could, with our encouragement, expand their influence and find new opportunities by contacting their world-class colleagues, right in their own neighborhood. As curious as they claim to be about evolution and mutation, they would be crazy not to. Right?

(Cross-posted at Quintessence of Dust.)

Loh E, Salk JJ, & Loeb LA (2010). Optimization of DNA polymerase mutation rates during bacterial evolution. Proceedings of the National Academy of Sciences of the United States of America, 107 (3), 1154-9 PMID: 20080608

107 Comments

jkc · 27 November 2010

Very interesting paper and an excellent summary. Thanks for keeping us laypeople in the loop.

Just to play devil's advocate and anticipate DI objections: how do the different variants of DNA Polymerase come to be and how did we end up with the ones that are in the medium-mutaton range? And, if the medium mutators were selected for, what caused the mutations that allowed for their to be many different variants of mutators? In other words, where does the (presumably non-infinite) regress end?

DS · 27 November 2010

Thanks Steve. This is certainly interesting stuff.

Now I wonder why the ID crowd hasn't done similar experiments to show that only advantageous mutations poof into existence?

But seriously, if the mutations that increase mutation rate are simple ones and no wild type ever wins such competitions, it makes one wonder why the wild type mutation rate isn't higher? Perhaps selection is more complex in the long term that these relatively short term experiments would seem to imply.

In the future, I'm sure we can look forward to whole genome sequencing in order to determine the exact mutations that imparted the competitive edge to the winning strains. Now that is going to be cool stuff. Kind of blows the "no beneficial mutations" nonsense out of the water though - again.

Steve Matheson · 27 November 2010

jkc, if you're asking about the real world, mutators occur normally in the population, due to genetic variation in the normal machinery. They seem to come to the fore when evolutionary pressure is applied, e.g. during adaptation to environmental changes or during competition. So the answer to your question is that the copying machinery can vary in its fidelity, and fidelity (and therefore mutation rate) can likewise vary depending on the environment.

DS, the idea is that the "wild-type mutation rate" could be the state of the system in what we might call equilibrium, but that during adaptation, mutators can be beneficial by increasing genetic diversity. As the authors mention in their summary statement, we might postulate that once the population is "maximized for a particular environment," then the mutator phenotype is no longer an advantage, and selection can reduce the mutation rate back to "wild-type."

Loh et al. addressed these issues in their discussion. Have a look, and note their references to the extensive literature on these subjects.

MichaelJ · 27 November 2010

The ID crowd will say that these experiments were done by humans and were intelligently designed, therefore Jesus.

Mike Elzinga · 27 November 2010

“Evolvability?” Hoo boy! How is that related to “fitness?”

If I may take the role of Simplicio here, maybe I can ask the stupid questions others may be thinking about (probably not).

Just for simplicity (because I think I get this part), let’s go back to the lattice of frequencies (actually probabilities) and talk in terms of the population for the moment. In other words suppose the following for the set of alleles A_i, a_i where i is the index running over all alleles:

We let p_i be the freq(A_i), and of course, q_i = 1 - p_i = freq(a_i).

Now the set of p_i traces out a set of axes, each from 0 to 1, that form a unit hypercube describing probabilities of all the alleles in the population, however many there are (and assuming for the moment they change independently).

Here is where it gets a bit murky for me. Suppose that at some location within that hypercube there is a fitness peak. Now, in the real world, that peak is not solely determined by the specific set of p_i at that location. The peak is also determined by external environmental conditions (e.g., gravity, temperature, and a host of other specific properties of the environment).

If it were the case the members of the population never competed with each other, then that fitness peak would be labeled by a set of other parameters, but not the p_i. As it is, it is a function of both sets.

Furthermore, is it reasonable to take an entire specific set of p_i and use it as a label for a phenotype? Presumably phenotype depends on environmental factors as well (gravity, chemicals in the environment, conditions in the womb or egg, the state of “switches” determining growth, etc.).

So it appears to me that fitness plots are not plots in quite the same sense as plots in mathematics and physics. There is a “backwards” way in which they can be interpreted in which the location of fitness peak “selects” both a set of environmental factors and a set of alleles in the population as “special.”

It is almost like the “volume” of intersection of a couple of hyper-cubes or hyper-spheres.

Steve Matheson · 27 November 2010

Mike: In this case, fitness refers roughly to reproductive success. The variants that experienced the highest reproductive success have, in this conception, the highest fitness. Their higher fitness seems to result from their ability to accumulate genetic variation, and that's one way to understand "evolvability."

Chris Nedin · 27 November 2010

SM: we might postulate that once the population is “maximized for a particular environment,” then the mutator phenotype is no longer an advantage, and selection can reduce the mutation rate back to “wild-type.”

Where do such marked differences in mutation rate leave molecular clocks? If mutation rates can cycle between short periods of significantly increased intensity, and then (presumably) longer periods at reduced intensity, you end up with a Gould/Eldredge pattern of 'punctuated' rates, rendering elapsed time calculation rather difficult.

Mike Elzinga · 27 November 2010

Steve Matheson said: Mike: In this case, fitness refers roughly to reproductive success. The variants that experienced the highest reproductive success have, in this conception, the highest fitness. Their higher fitness seems to result from their ability to accumulate genetic variation, and that's one way to understand "evolvability."

Yeah, I think I have the fitness part. It is perfectly reasonable - and, in fact, necessary – to find descriptions of complex systems that acknowledge the emergent properties that may dominate the system behavior. If biological systems are not to appear to violate the laws of physics and chemistry, it would be hoped that such terms used to describe biological systems aren’t “built in the air” so to speak. One would hope that such terms would be ultimately expressible in terms of more fundamental concepts as linkages among various levels of complexity become understood. This has been very much the history of chemistry and physics; and there is no reason to think biological systems, despite their complexity, should not be simply a continuation of this evolution in understanding. So in the case of mutations rates contributing to “evolvability,” by allowing organisms to have enough variants to take advantage of a wider range of environments makes sense, provided the proliferation of words doesn’t cloud the issues. In the case of physical/chemical systems in general, binding energies have a lot to do with the way a system responds to external forces. If a system, such as a complex of molecules, exists at temperatures comparable to its binding energy potentials, relatively small perturbations can rearrange bonds (cause mutations?). If the system exists in a bath of other molecules that provide a sort of catalytic background that also assists in rearranging bonds, we would expect to see the same effects as we do with increases in temperature. My own suspicions are that the distances between the descriptions of biological systems and the fundamentals of chemistry and physics are not as great as they might appear at the moment. It’s more a matter of finding the right descriptions and the right relationships. As I think I have mentioned before, the replicating part of biological systems may not be as big a gap as it appears. This process simply replaces a system with surrogates having the requisite variations to adapt to whatever environmental changes occur (provided such changes don’t destroy the system). In a sense, such systems “melt” or “deform” to match changes. But the melting and deformations depend on such systems being near their melting temperatures. Being near melting temperatures or in the presence of catalytic agents simply increases the rates of change and the ranges of opportunities.

raven · 28 November 2010

jkc: how do the different variants of DNA Polymerase come to be and how did we end up with the ones that are in the medium-mutaton range?

SM: (in this case due to engineered genetic variation in DNA polymerase I)

For this paper, the various mutators were engineered into DNA polymerase 1 so the strains only differ by one mutation in one gene. You can select for and find mutator phenotypes in the wild. If one selects for rare mutations such as streptomycin resistance, some of those will also be mutators. IIRC, Lenski in his citrate evolution experiments also picked up a few mutators as well. High levels of selection pressure are all that is needed to select for mutator phenotypes.

Selection of a Mutant of Escherichia coli Which Has High Mutation ... by RB Helling - 1968 - Cited by 24 - Related articles [PubMed]; Newcombe HB, Hawirko R. SPONTANEOUS MUTATION TO STREPTOMYCIN RESISTANCE AND DEPENDENCE IN ESCHERICHIA COLI. J Bacteriol. 1949 May;57(5):565–572. ... www.ncbi.nlm.nih.gov › Journal List › J Bacteriol › v.96(4); Oct 1968

Frank J · 28 November 2010

MichaelJ said: The ID crowd will say that these experiments were done by humans and were intelligently designed, therefore Jesus.

I don't think that the DI's Klinghoffer or Medved would go with that. And none of them publicly objected to Behe's admission (at the Dover trial) that the designer might no longer exist. One might expect their Biblical literalist fans to collectively pass out from that, but they're good at tuning out anything inconvenient as long as it comes from someone willing to tell them other things that feed their cravings. But you're right that they often object that any experiment conducted by humans "smuggles in" design. They may be terrible at research - they know better than to even try any experiment that could shed light on what the designer did, when or how - but they are good at playing "heads I win, tails you lose" word games.

DS · 28 November 2010

Well the mutator variants were definitely designed. However, they can and do occur spontaneously in nature, so eventually this experiment would be carried out in nature. Perhaps more importantly, the environment, and hence the selection pressure, was designed. Apparently this type of selection is not very common in nature, or the wild type mutation rate would probably be higher. However, once again, this type of selection will inevitably occur in nature, so this experiment would occur spontaneously as well.

Experiments, by their very nature, are designed. That's the way science works. Laboratory experiments usually don't tell us much about what has actually occurred in nature, but they usually tell us a great deal about what could occur in nature. In this case it has been demonstrated that variation in polymerase fidelity will produce variation in mutation rates and that some of these variants will more quickly produce adaptive mutations in certain types of environments than the wild type. This alone is sufficient to falsify several common creationist claims. If sequencing reveals that any of these adaptations are the result of multiple mutations, then another creationist claim will be falsified. This would not be at all surprising, since this is essentially the result that Lenski got under different environmental conditions.

No wonder these guys never bother to do any research. Closing gaps doesn't appear to be in their "research agenda".

Frank J · 28 November 2010

No wonder these guys never bother to do any research. Closing gaps doesn’t appear to be in their “research agenda”.
— DS

As you probably know, some of them do some research. But it either supports evolution or at best can be used to spin misleading incredulity arguments. The Behe and Snoke paper apparently qualifies as both. At the risk of giving them too much credit as skilled verbal strategists I see them exploiting both lay people whose who are sympathetic to "underdogs" (especially if they share one's "worldview") and critics. The former generally extrapolate any perceived incredulity of evolution as validating their childhood fairy tale. The latter are forced to defend evolution in greater detail, giving the scammers more evidence and quotes to take out of context to spin more incredulity to the uninformed/misinformed. And if those critics tangent onto religion and politics, it further lets the scammers off the hook from providing any detail about their "theory." But that would involve closing "gaps," or at least trying to. And as you note, they have no intention of doing anything of the sort. If we say that none of them do research, they trot out Behe and Snoke. If we say they avoid peer-review they trot out Meyer's paper. If we object that it was not properly peer-reviewed they whine about being "expelled." If I may repeat one of the best descriptors of their antics that I have ever heard, they like to play "heads I win, tails you lose."

Paul Burnett · 28 November 2010

Mike Elzinga said: It is almost like the “volume” of intersection of a couple of hyper-cubes or hyper-spheres.

Is the fitness map restricted to two dimensions (x,y)? They look like topographic maps - three dimensions represented on a two-dimensional map (x,y,z). Four dimensions doesn't seem out of hte question.

Mike Elzinga · 28 November 2010

Paul Burnett said:
Mike Elzinga said: It is almost like the “volume” of intersection of a couple of hyper-cubes or hyper-spheres.
Is the fitness map restricted to two dimensions (x,y)? They look like topographic maps - three dimensions represented on a two-dimensional map (x,y,z). Four dimensions doesn't seem out of hte question.

No, it isn’t. The x-y plane, if you like, is a simplified picture involving, say, the frequencies (actually probabilities) of two different alleles. That’s what Joe referred to as the lattice on the other thread. The axis perpendicular to this is fitness. This kind of plotting is also encountered in physics in which a 2-D plane is used as a simplified picture for visualization purposes. In relativity, for example, only two spatial dimensions are shown in a horizontal plane while time is shown on a separate axis passing through that plane (it’s a little difficult to visualize more than three dimensions projected onto a two-dimensional piece of paper or chalkboard). From the mathematical perspective, one just adds more numbers to the array of numbers representing a specific point in a higher dimensional space. There are other issues to consider, such as orthogonality; but as far as the plotting is concerned, it is meant to be a representative slice through a higher dimensional space. In statistical mechanics, phase-space diagrams are shown in two dimensions with a position axis and a momentum axis. But these are a slice through something like 10²³ dimensions representing the positions and momenta of all the particles making up a system.

JGB · 28 November 2010

I know the discussion cropped up on a different thread in regards to the vector or scalar nature of fitness. And I think some of the fuzziness in the landscape model points back to that question. If you model genotypes as vectors and the environment as a vector. Fitness naturally comes out as the scalar result of multiplying two vectors. One could then do as Mike suggests and picture the landscape as a slice of the genotype space against the fitness (assuming a constant environment) or alternatively perhaps a slice of the environment space against fitness at a constant genotype.

Mike Elzinga · 28 November 2010

JGB said: I know the discussion cropped up on a different thread in regards to the vector or scalar nature of fitness. And I think some of the fuzziness in the landscape model points back to that question. If you model genotypes as vectors and the environment as a vector. Fitness naturally comes out as the scalar result of multiplying two vectors. One could then do as Mike suggests and picture the landscape as a slice of the genotype space against the fitness (assuming a constant environment) or alternatively perhaps a slice of the environment space against fitness at a constant genotype.

There are a number of ways to “multiply” vectors, including inner (or dot) product, vector (or cross) product, and various kinds of tensor products. The dot product is a scalar, and it requires that the vectors have the same dimensions. In the case you suggest, it is not necessarily the case that the two spaces would have the same dimensions. And, even if they did, the norm of such a product would not necessarily have anything to do with fitness. In fact, the significance of the volume of intersection of two such sets would be a property determined independently, namely, the reproductive success of the organisms possessing the set of alleles in that intersection.

eric · 29 November 2010

If people are interested in this subject they might also like this Op-ed: Evolving the Single Daddy by Olivia Judson (New York Times, 2008). Its not about mutation per se, but it comes to the same conclusion as the Loeb et al. article: while evolution can produce species with very low variability, they get outcompeted. The money quote from the op-ed:

The evolution of traditional, female-only asexuality typically leads to a swift extinction. We know this because although such species frequently evolve, they don’t stay around for long. If you look at the tree of life, female-only asexual groups are all out on the twigs: there are no great asexual lineages equivalent to fish or birds. Instead, the asexual groups are a few species of snail here, a dandelion there. Male-only asexuality is likely to lead to extinction too, but faster.

This is consistent with the results of the Loeb et al. research. Low variability = swift extinction.

Mike Elzinga · 30 November 2010

eric said: This is consistent with the results of the Loeb et al. research. Low variability = swift extinction.

I gather that this does not have to be the case, however. Aren’t there some species (coelacanth, for example; and some sharks) that have maintained pretty much the same phenotype for unusually long periods of time? Of course, that doesn’t necessarily indicate the genotype has remained as constant.

Henry J · 30 November 2010

Aren’t there some species (coelacanth, for example; and some sharks) that have maintained pretty much the same phenotype for unusually long periods of time? Of course, that doesn’t necessarily indicate the genotype has remained as constant.

Also, having the hard parts stay fairly constant for a long period doesn't necessarily mean that all the soft parts did. Or the proteins and other biochemistry, either. Henry J

Kris · 1 December 2010

eric said: If people are interested in this subject they might also like this Op-ed: Evolving the Single Daddy by Olivia Judson (New York Times, 2008). Its not about mutation per se, but it comes to the same conclusion as the Loeb et al. article: while evolution can produce species with very low variability, they get outcompeted. The money quote from the op-ed:
The evolution of traditional, female-only asexuality typically leads to a swift extinction. We know this because although such species frequently evolve, they don’t stay around for long. If you look at the tree of life, female-only asexual groups are all out on the twigs: there are no great asexual lineages equivalent to fish or birds. Instead, the asexual groups are a few species of snail here, a dandelion there. Male-only asexuality is likely to lead to extinction too, but faster.
This is consistent with the results of the Loeb et al. research. Low variability = swift extinction.

http://biology.about.com/od/genetics/ss/Asexual-Reproduction.htm http://www.cosmosmagazine.com/news/1957/fish-goes-without-sex-100000-years http://en.wikipedia.org/wiki/Parthenogenesis http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2010.04869.x/abstract http://www.sciencedaily.com/releases/2010/11/101103111210.htm http://www.sciencedaily.com/releases/2007/05/070523072254.htm

Kris · 1 December 2010

Henry J said:
Aren’t there some species (coelacanth, for example; and some sharks) that have maintained pretty much the same phenotype for unusually long periods of time? Of course, that doesn’t necessarily indicate the genotype has remained as constant.
Also, having the hard parts stay fairly constant for a long period doesn't necessarily mean that all the soft parts did. Or the proteins and other biochemistry, either. Henry J

I think it should also be mentioned that the genotype, soft parts, proteins, and biochemistry could have remained as constant. It's something that would have to be determined for each species, if possible.

Henry J · 1 December 2010

I think it should also be mentioned that the genotype, soft parts, proteins, and biochemistry could have remained as constant. It’s something that would have to be determined for each species, if possible.

In general, I'd think one would need living (or at least recently living) close relatives of the species in question, in order to check aspects that don't generally leave traces in fossils. Henry J

Michael Behe · 7 December 2010

Steve, whatever happened to: "Second, I want to highlight the failure of design creationists to address or even to understand such matters." You sort of left that part out. Try reading what they wrote, here I'll make it easy for you: "Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. This finding has particular significance for models of gene recruitment, since weak new functions are likely to require costly over-expression in order to improve fitness. If reductive, cost-cutting mutations are more abundant than mutations that convert or improve function, recruitment may be unlikely even in cases where a short adaptive path to a new function exists."

Steve Matheson · 7 December 2010

Uh, hi "Michael Behe." Not sure who you're quoting there, but if your goal was to illustrate the failure of design creationists to address or even to understand fitness landscapes and evolutionary trajectories, that silly quote will do very nicely.

Michael Behe · 7 December 2010

what you're failing to understand about the Lenski experiment, Steve, is that the mutations of the E Coli have been shown to be incoherent and disordered, which is exactly what we would expect from NS. Since Lenski started his experiment no new molecular machinations have been built and this, in spite of the fact that it has tracked I forget how many generations, maybe 10^12. 10^12 generations and still nothing of any significance. The only thing that has evolved is just a few broken genes.

Stanton · 7 December 2010

Michael Behe said: what you're failing to understand about the Lenski experiment, Steve, is that the mutations of the E Coli have been shown to be incoherent and disordered, which is exactly what we would expect from NS. Since Lenski started his experiment no new molecular machinations have been built and this, in spite of the fact that it has tracked I forget how many generations, maybe 10^12. 10^12 generations and still nothing of any significance. The only thing that has evolved is just a few broken genes.

Yet, that still doesn't explain why we should assume that Natural Selection doesn't exist, and it still doesn't explain why we should assume that Intelligent Design is supposed to have explanatory power. Also, if the only things that evolved are "a few broken genes," then how does that explain the fact that Lenski directly observed the evolution of citrate-metabolizing Escherichia coli bacteria from Escherichia coli bacteria that could not metabolize citrate? Or does this question raise a "pathetic level of detail" that you, as an Intelligent Design proponent, are hypocritically not obligated to explain?

Michael Behe · 8 December 2010

I started this thread because I wanted to highlight the fact that you failed this promise: "I want to highlight the failure of design creationists to address or even to understand such matters." Why don't you read the article you posted, quote from it, and show where it's wrong? Do you read any ID literature or does cognitive dissonance prevent you from doing that?

"why we should assume that Intelligent Design is supposed to have explanatory power." Dna is information. Chance cannot produce information, intelligence can.

"if the only things that evolved are “a few broken genes,” then how does that explain the fact that Lenski directly observed the evolution of citrate-metabolizing Escherichia coli bacteria from Escherichia coli bacteria that could not metabolize citrate?"
Was this new citrate-metabolization just a case of epigenetics? Was the gene already there and the environment turned it on? Was a completely new gene built that would metabolize citrate? Or was one already-built gene mutated with the result on one amino acid changing? Which gene was it? Which amino acids changed places? I want direct quotes, not hearsay evidence.

Stanton · 8 December 2010

Michael Behe said: I started this thread because I wanted to highlight the fact that you failed this promise:
I want to highlight the failure of design creationists to address or even to understand such matters.
Why don't you read the article you posted, quote from it, and show where it's wrong? Do you read any ID literature or does cognitive dissonance prevent you from doing that?

All "ID literature" ever says is "Evolution is wrong and can't happen because we're too lazy to understand it, therefore GODDIDIT" If you're that concerned, why not quote from the relevant papers, yourself? On the other hand, it's been my personal experience that the sole reason why no Intelligent Design proponent ever quotes the relevant papers is because such things do not exist. And such things will never exist because Intelligent Design proponents are totally incapable and unmotivated to do research.

why we should assume that Intelligent Design is supposed to have explanatory power.
Dna is information. Chance cannot produce information, intelligence can.

And yet, you still have not demonstrate how Intelligent Design allegedly has explanatory power with this non sequitor. So it is experience, not cognitive dissonance like you falsely accuse, that tells me Intelligent Design proponents are incapable of saying anything beyond "GODDIDIT" In fact, from the way you misspell "DNA," it strongly suggests you're an impostor who probably never taken a high school science class.

if the only things that evolved are “a few broken genes,” then how does that explain the fact that Lenski directly observed the evolution of citrate-metabolizing Escherichia coli bacteria from Escherichia coli bacteria that could not metabolize citrate?
Was this new citrate-metabolization just a case of epigenetics? Was the gene already there and the environment turned it on? Was a completely new gene built that would metabolize citrate? Or was one already-built gene mutated with the result on one amino acid changing? Which gene was it? Which amino acids changed places? I want direct quotes, not hearsay evidence.

This rant of yours strongly suggests that you lack the rudimentary brain and will power needed to look up the Wikipedia article about Lenski's experiment, as well as the fact that the only "science" you've ever learned is from mindlessly parroting pro-Creationist sites. Of course, even if I do quote directly, you're just going to pull some inane, nonsensical excuse to simultaneously magically invalidate what I say while magically excusing yourself from providing any actual explanations or even coherent refutations. You have to be aware that the onus is on you and other Intelligent Design proponents to explain exactly how and why Lenski's experiments really show the magical Hand of God magically diddling with the bacteria within, and not Random Mutation + Natural Selection. Going on and on with "Nuhuh nuhuh, not true 'cuz GODDIDIT" is not a viable argument.

DS · 8 December 2010

MB wrote:

“why we should assume that Intelligent Design is supposed to have explanatory power.” Dna is information. Chance cannot produce information, intelligence can.

Ever played poker? The cards are shuffled and dealt randomly. There is information in the combination of cards that you are dealt. That is how they decide who wins.

Random mutation and natural selection produce information. That is how molecular phylogenetics works.

As for the mutations responsible for citrate metabolism, whole genome sequencing will definitively answer this question. If you really wanted the answer, you would be doing this type of experiment yourself. It seems most likely that some type of gene duplication was involved, followed by divergence due to point mutations. That might not turn out to be the exact mechanism involved, but it would explain why the experiment showed a significant effect of historical contingency. It would also conclusively falsify several creationist claims. But then again, we already have plenty of examples of this kind of thing in nature. This would just be a good laboratory demonstration.

Michael Behe · 8 December 2010

Stanton,

I'm afraid dialogue between us is not possible. If one side refuses to answer the other's questions than the two sides cannot learn from each other. I asked you questions about Lenski's experiment which you refused to answer.

Michael Behe · 8 December 2010

DS, thank you for dialoguing with me in a respectful manner. The same respect I accord you, I hope to receive in return.

[quote]
Ever played poker? The cards are shuffled and dealt randomly. There is information in the combination of cards that you are dealt. That is how they decide who wins.
[/quote]
Yes, there is information on a deck of cards. The cards were built by an intelligent source. Moreover, it is intelligence that interprets the information after the hands have been dealt.

[quote]
Random mutation and natural selection produce information. That is how molecular phylogenetics works.
[/quote]
Evidence please.

[quote]
As for the mutations responsible for citrate metabolism, whole genome sequencing will definitively answer this question.
[/quote]
I predict that no new genes will be built.

[quote]
If you really wanted the answer, you would be doing this type of experiment yourself.
[/quote]
I'm too busy working on studying the bacterial flagellum.

[quote]
It seems most likely that some type of gene duplication was involved, followed by divergence due to point mutations. That might not turn out to be the exact mechanism involved, but it would explain why the experiment showed a significant effect of historical contingency.
[/quote]
Since you're speculating about possible results I won't comment. I'll wait for the results.

Stanton · 8 December 2010

Michael Behe's impostor said: Stanton, I'm afraid dialogue between us is not possible. If one side refuses to answer the other's questions than the two sides cannot learn from each other. I asked you questions about Lenski's experiment which you refused to answer.

I'm not the one who lacks the brain and will power to read even the Wikipedia page about Lenski's experiment. What's the matter? Afraid that you'll get smart and get excommunicated? Furthermore, how come you're so reluctant to actually demonstrate the alleged explanatory power of Intelligent Design? We are not having a discussion not because of me, but because of you not wanting to go through even the motions of explaining why Intelligent Design is supposed to be superior to Evolutionary Biology. That is, not wanting to go beyond the non-explanation of "GODDIDIT"

Stanton · 8 December 2010

Michael Behe's impostor said: DS, thank you for dialoguing with me in a respectful manner. The same respect I accord you, I hope to receive in return.

And yet, you're stupid enough to assume that we're stupid enough to not notice you're bullshitting us.

Ever played poker? The cards are shuffled and dealt randomly. There is information in the combination of cards that you are dealt. That is how they decide who wins.
Yes, there is information on a deck of cards. The cards were built by an intelligent source. Moreover, it is intelligence that interprets the information after the hands have been dealt.

In other words, no, you've never had the opportunity to play poker or any other card game. Plus, you've successfully missed the entire point of DS' statement there.

Random mutation and natural selection produce information. That is how molecular phylogenetics works.
Evidence please.

Your request makes me suspect that you have never been able to look at an elementary biology textbook, AND that you have no intention of looking at any evidence, either.

As for the mutations responsible for citrate metabolism, whole genome sequencing will definitively answer this question.
I predict that no new genes will be built.

It's extremely pathetic to make prophecies after the event has occurred. It's even more pathetic when those prophecies turn out completely wrong. And if you had the willpower to read even the Wikipedia page about Lenski's experiment, you would know this.

If you really wanted the answer, you would be doing this type of experiment yourself.
I'm too busy working on studying the bacterial flagellum.

Bullshitting again, I see. I could have sworn that the real Michael Behe had given up bullshitting about bacterial flagella and was last seen making a lying idiot out of himself by making inane and inaccurate navel contemplations about the malarial parasites.

It seems most likely that some type of gene duplication was involved, followed by divergence due to point mutations. That might not turn out to be the exact mechanism involved, but it would explain why the experiment showed a significant effect of historical contingency.
Since you're speculating about possible results I won't comment. I'll wait for the results.

Your wait is over http://myxo.css.msu.edu/ecoli/ Now what sort of bullshit excuse are you going to make? Again, don't be stupid enough to assume we're stupid enough to assume that you were sincere about wanting to wait for actual results. After all, we've dealt with blabbermouth Intelligent Design proponents who never actually had anything to say, before.

DS · 8 December 2010

Michael Behe said: DS, thank you for dialoguing with me in a respectful manner. The same respect I accord you, I hope to receive in return. [quote] Ever played poker? The cards are shuffled and dealt randomly. There is information in the combination of cards that you are dealt. That is how they decide who wins. [/quote] Yes, there is information on a deck of cards. The cards were built by an intelligent source. Moreover, it is intelligence that interprets the information after the hands have been dealt. [quote] Random mutation and natural selection produce information. That is how molecular phylogenetics works. [/quote] Evidence please. [quote] As for the mutations responsible for citrate metabolism, whole genome sequencing will definitively answer this question. [/quote] I predict that no new genes will be built. [quote] If you really wanted the answer, you would be doing this type of experiment yourself. [/quote] I'm too busy working on studying the bacterial flagellum. [quote] It seems most likely that some type of gene duplication was involved, followed by divergence due to point mutations. That might not turn out to be the exact mechanism involved, but it would explain why the experiment showed a significant effect of historical contingency. [/quote] Since you're speculating about possible results I won't comment. I'll wait for the results.

INtelligence did not produce the information in the poker hand, the random deal did that. The information would still be there whether you looked at the hand or not. The information is there even if the cards are dealt by a machine with no intelligence. No intelligence is required to produce the information, only to interpret it. As for molecular phylogenetics, we can determine that the closest living relative to humans is the chimpanzee. This can be determined by the information present in the DNA. The information was produced by random mutations. You get the same nested hierarchy whether you look at nuclear genes, mitochondrial genes or SINE insertions. No intelligence was required in order to produce the information, only to interpret it. Why do you conclude that no new gens were built before looking at the results of the experiment? It seems much more likely that at least one new gene was produced. TIme will tell in this case, but there are many documented instances of this in nature. Indeed, this is a major mechanism of evolution and is one major mechanism for producing new structures and functions. If you really study the evolution of the bacterial flagellum, you would know that the process I mentioned is one mechanism that has produced the genes responsible for the evolution of the many different types of bacterial flagella.. If you are by any chance the "real" Michael Behe, my apologies. I am aware that you have already admitted that you do not read the scientific literature.

DS · 9 December 2010

Information can be produced by random processes. It doesn't take intelligence to produce information, it takes intelligence to interpret information.

That's how astronomy works. There is information in the absorption spectrum of a star. There is information in the red shift of stars. There is information in the periodicity of a pulsar. There is information in the wobble of star.

That's how population genetics works. There is information in the allele frequencies in a population. From this type of data you can estimate population size, mutation rate, migration rate, selection, inbreeding, population substructure, etc.

In the end, it doesn't matter if citrate metabolism evolved due to production of a new gene or not. The adaptation evolved by random mutations which were selected on in the environment. Some of the mutations were beneficial and increased in frequency. This represents an increase in information. That is why they are doing whole genome sequencing. That's the way evolution works.

DS · 9 December 2010

I guess Mikey doesn't include responses to the answers to his questions under the category of "respect".

Michael Behe · 9 December 2010

DS, You're confusing data with information. Data is pure material and is not dependent on sequence, but depends on its location in time and space. For example, you claimed that there is information in "the absorption spectrum of a star, the red shift of stars, in the periodicity of a pulsar, in the wobble of star." Given this understanding you would also conclude that there is information in the CO2 levels of the planet. Our CO2 levels are data not information. Data adheres to certain physical laws which operate according to the rule if x then y, chaos theory aside. For example, if CO2 rises to 500ppm, then this might set off a chain reaction that will inevitably lead to CO2 levels 600ppm. Or let's take the data that there is 4 cm of snow on the ground and the temperature is 3 C. If these conditions are met, then the snow will melt. The snow and the CO2 levels are material and operate according to physical laws. Information does not operate according to physical laws but the rules specified by the intelligent agent that CREATED the information. For example, we humans have CREATED the English language. If your boss writes the information: "your position with this company has been terminated and from now on your presence on company property will be considered trespassing and prosecuted to the full extent of the law," then the intelligent agent (an employee) reading that information will cease to visit that company's property if they are rational. We English speakers have specified what the words position, termination, company, trespassing, property, etc, mean. None of this information depends on the material body that the information is found in, it can be on paper or on a computer screen, so long as the intelligent agent can distinguish the letters. Let us also take the letters o r b and e. These letters carry no information by themselves, but when they are sequenced as robe they mean one thing and when they are sequenced as bore they mean something else. The information carried by those four symbols depends on the sequence specified by its CREATOR. It is the same with amino acid sequences. Sequence amino acids one way, you will get one protein, sequence them another way you will get another protein. Now regarding poker. The information found in cards was CREATED by INTELLIGENT human beings. Chance can only shuffle already existing information, it cannot create new information, because chance cannot specify what a sequence means. You need INTENTION to do that and chance has no intentions. So let's take the poker sequence AAA74, this is a three of aces. Chance just shuffled the information specified by INTELLIGENT humans, it did not CREATE new information.

As for molecular phylogenetics, we can determine that the closest living relative to humans is the chimpanzee. This can be determined by the information present in the DNA.

I agree on common anestry. I do not agree that NS through random mutation is the ONLY means which changes species.

Why do you conclude that no new gens were built before looking at the results of the experiment? It seems much more likely that at least one new gene was produced. TIme will tell in this case, but there are many documented instances of this in nature.

Very few cases, such as the ice fish in the antartic. The vast majority of cases are those in which desperate environmental circumstances arise and those species with broken genes now suddenly have an advantage, such as humans who suffer from sickle cell anemia in their fight against malaria. Or malaria that are unable to digest harmful drugs because their vacuole has broken.

Indeed, this is a major mechanism of evolution and is one major mechanism for producing new structures and functions.

There is a big difference between mutating one or two amino acids and building a brand new gene of 900 amino acids from scratch. I'd like to see the Darwinian explanation for the rise of Titin, a protein with some 27,000 amino acids.

If you are by any chance the “real” Michael Behe, my apologies. I am aware that you have already admitted that you do not read the scientific literature.

The Darwinists time and again resort to insults rather than rational argument.

Stanton · 9 December 2010

Michael Behe's imposter said:
Indeed, this is a major mechanism of evolution and is one major mechanism for producing new structures and functions.
There is a big difference between mutating one or two amino acids and building a brand new gene of 900 amino acids from scratch. I'd like to see the Darwinian explanation for the rise of Titin, a protein with some 27,000 amino acids.

Then explain to us in "pathetic" detail why saying GODDIDIT is supposed to be a superior explanation.

If you are by any chance the “real” Michael Behe, my apologies. I am aware that you have already admitted that you do not read the scientific literature.
The Darwinists time and again resort to insults rather than rational argument.

Stating a fact is not an insult. The real Michael Behe stated that he does not, and refuses to read scientific literature. How is that supposed to be insulting?

Mike Elzinga · 9 December 2010

There don’t appear to be any consistent definitions of “information” in any ID/creationist literature. Nor does there appear to be any definition of information that has anything to do with how Nature works.

Some of the ID/creationist uses of information that suggest it organizes matter are completely at odds with known physics and chemistry. There is no such thing as some kind of top-down “information” that pushes matter around into arrangements that some other physical system called a living organism “recognizes as significant.”

And any possible definition of information that could coordinate states of an observed system with states in an “observer” system requires that there be some correspondence and interaction between the system states and “observer” states that initiates a set of events or responses on the part of the “observer” system.

To say that any physical system contains “information” seems to imply a physical observer for which (or for whom) that particular configuration of the physical system has some “meaning”. And the meaning of “meaning” would suggest it has something to do with prior states in the observer that have predisposed it to respond to that configuration of states in the observed system in some way.

But just because some physical system “likes” some configuration in some other physical system doesn’t mean there is anything out of the ordinary going on. All that might be happening is that one system is settling into a different state that is constrained by its interaction with another system that is in some particular state.

And all that is more concisely and accurately described by the laws of chemistry and physics; laws we understand pretty well.

There is no “ghost in the machine.”

DS · 9 December 2010

Mike,

No one is claiming that any new gene was produced from "scratch". Are you? As for insults, if you aren't the "real" Micheal Behe then you cannot be insulted. If you are the "real" Micheal Behe then you made those comments under oath in a public court of law.

I'm glad that you agree on common descent. Presumably then you agree that there is information in the nested hierarchy of SINE insertion in primate genomes. This information was not produced by any intelligence. It was produced by random transposition events followed by selection. The information did not require an intelligence to produce it, only to interpret it. The information is still there whether or not any intelligence interprets it.

In the end, it doesn’t matter if citrate metabolism evolved due to production of a new gene or not. The adaptation evolved by random mutations which were selected on in the environment. Some of the mutations were beneficial and increased in frequency. This represents an increase in information. That is why they are doing whole genome sequencing. That’s the way evolution works. No intelligence produced the changes but intelligence will be required in order to understand the lessons they can teach us.

Dale Husband · 9 December 2010

Michael Behe said: DS, You're confusing data with information. Data is pure material and is not dependent on sequence, but depends on its location in time and space. For example, you claimed that there is information in "the absorption spectrum of a star, the red shift of stars, in the periodicity of a pulsar, in the wobble of star." Given this understanding you would also conclude that there is information in the CO2 levels of the planet. Our CO2 levels are data not information. Data adheres to certain physical laws which operate according to the rule if x then y, chaos theory aside. For example, if CO2 rises to 500ppm, then this might set off a chain reaction that will inevitably lead to CO2 levels 600ppm. Or let's take the data that there is 4 cm of snow on the ground and the temperature is 3 C. If these conditions are met, then the snow will melt. The snow and the CO2 levels are material and operate according to physical laws. Information does not operate according to physical laws but the rules specified by the intelligent agent that CREATED the information. For example, we humans have CREATED the English language. If your boss writes the information: "your position with this company has been terminated and from now on your presence on company property will be considered trespassing and prosecuted to the full extent of the law," then the intelligent agent (an employee) reading that information will cease to visit that company's property if they are rational. We English speakers have specified what the words position, termination, company, trespassing, property, etc, mean. None of this information depends on the material body that the information is found in, it can be on paper or on a computer screen, so long as the intelligent agent can distinguish the letters. Let us also take the letters o r b and e. These letters carry no information by themselves, but when they are sequenced as robe they mean one thing and when they are sequenced as bore they mean something else. The information carried by those four symbols depends on the sequence specified by its CREATOR. It is the same with amino acid sequences. Sequence amino acids one way, you will get one protein, sequence them another way you will get another protein. Now regarding poker. The information found in cards was CREATED by INTELLIGENT human beings. Chance can only shuffle already existing information, it cannot create new information, because chance cannot specify what a sequence means. You need INTENTION to do that and chance has no intentions. So let's take the poker sequence AAA74, this is a three of aces. Chance just shuffled the information specified by INTELLIGENT humans, it did not CREATE new information.
As for molecular phylogenetics, we can determine that the closest living relative to humans is the chimpanzee. This can be determined by the information present in the DNA.
I agree on common anestry. I do not agree that NS through random mutation is the ONLY means which changes species.
Why do you conclude that no new gens were built before looking at the results of the experiment? It seems much more likely that at least one new gene was produced. TIme will tell in this case, but there are many documented instances of this in nature.
Very few cases, such as the ice fish in the antartic. The vast majority of cases are those in which desperate environmental circumstances arise and those species with broken genes now suddenly have an advantage, such as humans who suffer from sickle cell anemia in their fight against malaria. Or malaria that are unable to digest harmful drugs because their vacuole has broken.
Indeed, this is a major mechanism of evolution and is one major mechanism for producing new structures and functions.
There is a big difference between mutating one or two amino acids and building a brand new gene of 900 amino acids from scratch. I'd like to see the Darwinian explanation for the rise of Titin, a protein with some 27,000 amino acids.
If you are by any chance the “real” Michael Behe, my apologies. I am aware that you have already admitted that you do not read the scientific literature.
The Darwinists time and again resort to insults rather than rational argument.

Mr. Behe, if you think you have been giving us "rational" arguments, instead of empty rhetoric, your stinger is broken. Data is not information? Because YOU say so? LOL! Genes are broken, because YOU say so? ROTFL! Cards were made by humans, therefore intelligence is necessary to produce random sequences of cards? OK, what about replacing the cards with seashells we find on a beach? Or rocks? Or anything not man-made? See how stupid your arguments really are? That's why we insult you!

Michael Behe · 9 December 2010

DS,

I recommend you to read the proceedings of the Wistar Conference 1967. It took a while for biologists to decode which DNA codes for which amino acids and how complex proteins really are. Moreover, it took a while for super computers to calculate large numbers. But finally in 1967 mathematicians were able to look at the math of evolution and they found out that the numbers didn't add up. Mathematicians essentially told biologists in 1967 that there theory was wrong but biologists are too stubborn to listen to their advice and they did this at the Wistar Conference. See Marcel Schutzenberger for quick information. Do the math, 20 different amino acids in a chain of 150, that's 10^138 different combinations. And there are only 10^80 atoms in our universe and 10^17 seconds in our history. "This information was not produced by any intelligence. It was produced by random transposition events followed by selection." Information is immaterial and you need intelligence to interpret it. I have already stated why and you have refused to accept my argument. You will continue to confuse data with information, I will do the opposite. I'm sure you will also continue to deny the mathematics of DNA and amino acids. Darwinism was construed in an era when information theory was not known. It will be information which will lead to the downfall of Darwinism. And I, as the leader of the ID movement, will go down in history as a sort of Galileo and you will go down in history as an oppressive Catholic Church that clung to an old idea and refused to let it go in spite of evidence.

Michael Behe · 9 December 2010

There don’t appear to be any consistent definitions of “information” in any ID/creationist literature. Some of the ID/creationist uses of information that suggest it organizes matter are completely at odds with known physics and chemistry.

The letters TAG code for one codon, after you get about 150 codons you get a protein which folds in a certain way which can then perform usually once specific task, also usually in conjunction with a half dozen other proteins. Most ribosomes are assemblies of about 20 proteins. An intelligence had to know the properties of the amino acids, how the protein would fold, how the other proteins would fold so that it could perform its task. Foresight is required. NS has no foresight. The fact that amino acids have certain properties is information.

And any possible definition of information that could coordinate states of an observed system with states in an “observer” system requires that there be some correspondence and interaction between the system states and “observer” states that initiates a set of events or responses on the part of the “observer” system. To say that any physical system contains “information” seems to imply a physical observer for which (or for whom) that particular configuration of the physical system has some “meaning”. And the meaning of “meaning” would suggest it has something to do with prior states in the observer that have predisposed it to respond to that configuration of states in the observed system in some way. But just because some physical system “likes” some configuration in some other physical system doesn’t mean there is anything out of the ordinary going on. All that might be happening is that one system is settling into a different state that is constrained by its interaction with another system that is in some particular state.

You're going to have to rephrase because I don't get what you're saying.

There is no “ghost in the machine.”

Since this is just an assertion of belief I won't comment.

DS · 9 December 2010

Michael Behe said: DS, I recommend you to read the proceedings of the Wistar Conference 1967. It took a while for biologists to decode which DNA codes for which amino acids and how complex proteins really are. Moreover, it took a while for super computers to calculate large numbers. But finally in 1967 mathematicians were able to look at the math of evolution and they found out that the numbers didn't add up. Mathematicians essentially told biologists in 1967 that there theory was wrong but biologists are too stubborn to listen to their advice and they did this at the Wistar Conference. See Marcel Schutzenberger for quick information. Do the math, 20 different amino acids in a chain of 150, that's 10^138 different combinations. And there are only 10^80 atoms in our universe and 10^17 seconds in our history. "This information was not produced by any intelligence. It was produced by random transposition events followed by selection." Information is immaterial and you need intelligence to interpret it. I have already stated why and you have refused to accept my argument. You will continue to confuse data with information, I will do the opposite. I'm sure you will also continue to deny the mathematics of DNA and amino acids. Darwinism was construed in an era when information theory was not known. It will be information which will lead to the downfall of Darwinism. And I, as the leader of the ID movement, will go down in history as a sort of Galileo and you will go down in history as an oppressive Catholic Church that clung to an old idea and refused to let it go in spite of evidence.

Oh the dreaded probability calculation. That is just so much crap. No one is claiming that any amino acid magically popped into existence from nothing. That is not how evolution works. That is not how any real biologist thinks that evolution works. Get a clue man, you have been duped. Oh no, the dreaded downfall of Darwinism. I'm so scared. By the way, calling something "data" doesn't somehow magically mean that it contains no information. Now, do you admit that there is information in the nested hierarchy of SINE insertions in primate genomes or not? Do you admit that this information was produced by random process completely lacking in intelligence or not? Trying to change the subject isn't going to work.

DS · 9 December 2010

Mikey,

I recommend that you read the following link:

http://www.talkorigins.org/faqs/abioprob/abioprob.html

Seems that mathematicians didn't really disprove evolution after all. I guess that kind of explains why no real scientist has bought their argument in the last fifty years. But then again, the "Galileo" of modern biology would have already known that now wouldn't he? As for the Catholic Church, I'm not the one threatening people with anything as a punishment for what they believe, are you?

Dale Husband · 9 December 2010

Michael Bee the non-stinger said: DS, I recommend you to read the proceedings of the Wistar Conference 1967. It took a while for biologists to decode which DNA codes for which amino acids and how complex proteins really are. Moreover, it took a while for super computers to calculate large numbers. But finally in 1967 mathematicians were able to look at the math of evolution and they found out that the numbers didn't add up. Mathematicians essentially told biologists in 1967 that there theory was wrong but biologists are too stubborn to listen to their advice and they did this at the Wistar Conference. See Marcel Schutzenberger for quick information. Do the math, 20 different amino acids in a chain of 150, that's 10^138 different combinations. And there are only 10^80 atoms in our universe and 10^17 seconds in our history. "This information was not produced by any intelligence. It was produced by random transposition events followed by selection." Information is immaterial and you need intelligence to interpret it. I have already stated why and you have refused to accept my argument. You will continue to confuse data with information, I will do the opposite. I'm sure you will also continue to deny the mathematics of DNA and amino acids. Darwinism was construed in an era when information theory was not known. It will be information which will lead to the downfall of Darwinism. And I, as the leader of the ID movement, will go down in history as a sort of Galileo and you will go down in history as an oppressive Catholic Church that clung to an old idea and refused to let it go in spite of evidence.

I've read that if life started over again on Earth just as it did 4 billion years ago, it would be extremely improbable for anything resembling a human being to emerge. So what? We would still have proteins. There is no reason to assume that only certain proteins are necessary to produce life, intelligent life, or even life forms that may be able to produce and advanced civilization. ANY organism existing on Earth would be more closely related to us than any organism that evolved on another world. One way to prove Intelligent Design would be to find organisms on other worlds that were simular to humans both genetically and physically, but did not descend from any Earth organisms at all, which would be proven from comparisons to other organisms on the same world, which would also be simular to Earth organisms. Convergent evolution alone couldn't explain such a level of simularity, but Intelligent Design would. So your empty rhetoric means nothing, Mr Behe. The proof for ID is empirical, not logical.

Stanton · 9 December 2010

DS said: Mikey, I recommend that you read the following link: http://www.talkorigins.org/faqs/abioprob/abioprob.html

You would have far better success asking a formaldehyde-soaked corpse to clink on that link. Michael Behe's impostor, here, is even less hesitant to educated himself that the original.

Michael Behe · 9 December 2010

Oh the dreaded probability calculation. That is just so much crap.

It's one thing to call something crap, it's quite another to prove it. I would like to hear from you personally why you think the odds are not difficult to overcome

No one is claiming that any amino acid magically popped into existence from nothing. That is not how evolution works. That is not how any real biologist thinks that evolution works.

Here is how a real Darwinist thinks: I don't know how life arose, therefore I know that NS caused it.

Get a clue man, you have been duped.

When Darwinists cannot use argument they resort to insults.

Now, do you admit that there is information in the nested hierarchy of SINE insertions in primate genomes or not? Do you admit that this information was produced by random process completely lacking in intelligence or not? Trying to change the subject isn't going to work.

Of course I admit it. What I found amazingly remarkable is that heaps of the DNA code is repetitive, why would you attribute that to chance? If all of sudden you saw repetitive patterns on Mars you wouldn't attribute that to chance now would you?

Michael Behe · 9 December 2010

Stanton,
The only thing you have proven to me is the exorbitant amount of hatred you Darwinists have been attacking with me ever since my book came out in 1996

DS · 9 December 2010

Mikey;

Here it is from me personally:

It's pure crap.

If you want to know why, the link I provided gives several very good reasons. I have already provided you with one. The calculation has nothing whatsoever to do with the way that evolution is known to work. It's nothing but a red herring. Why do you think that no real biologist has been convinced in fifty years? Are they all stupid? Are they all biased? Are they all anti religion?

Hers is how a real creationist thinks:

I won't be bothered to learn about the evidence or the real mechanisms proposed for evolution, I'll just ridicule my own contrived caricatures, that should fool everyone.

Pointing out that you have been duped is not an insult. Since you refuse to deal with the real theory of evolution, what else is left but to point out that you are sadly mistaken?

Well now that you have admitted that random process can produce information, there is nothing left to discuss. You have admitted that there is no theoretical reason why evolution could not occur. Thanks for playing.

As for repetitive sequences, they can definitely be produced by chance. That's the way DNA replication works, or are you ignorant of that as well? (See that was a deliberate insult). Ever hear of DNA fingerprinting? Ever been to the desert?

DS · 9 December 2010

Hey Mikey, have you read those references on the evolution of the immune system yet? You might be back in court any day now, It would look really bad if you still hadn't read them. You know there are thousands more to catch up on now don't you? Better get busy.

DS · 10 December 2010

Hey MIkey,

If you think your calculations are so great, then you won't mind enlightening everyone as to exactly which evolutionary process they are being used to model. You know, what proposed mechanism is being tested? See, the thing is, I think that calculation had nothing whatsoever to do with evolution. I think it conclusively proves that god cannot exist cause the calculations prove that she couldn't pop out of nothing spontaneously. Unless of course you think that god is less complex than a protein!

Stanton · 10 December 2010

Michael Behe's impostor said: Stanton, The only thing you have proven to me is the exorbitant amount of hatred you Darwinists have been attacking with me ever since my book came out in 1996

I read your original's book: I ultimately found it uninformative, given as how it utterly failed to explain or even describe what Irreducible Complexity is, and utterly failed to explain or describe why Intelligent Design is supposed have explanatory power. "Criticism" does not equal "hatred" I make unpleasant and nasty statements about you because you make very stupid claims that betray profound, willful stupidity, AND you continue to refuse to explain or support your shockingly inane claims, even though you've been repeatedly asked to do so, AND you whine about how you're some sort of Jesus Christ Galileo being lead to the Stakes by the evil Darwinists. In other words, Mr Impostor, if you stop saying stupid things, stop verbally masturbating about your martyr complex, and start explaining how and why Intelligent Design is supposed to be a superior explanation than Evolutionary Biology, I will stop pointing that you are a loudmouthed, arrogant idiot. But since you have repeatedly stated that you are reluctant to do so, well...

Stanton · 10 December 2010

DS said: Hey MIkey, If you think your calculations are so great, then you won't mind enlightening everyone as to exactly which evolutionary process they are being used to model. You know, what proposed mechanism is being tested? See, the thing is, I think that calculation had nothing whatsoever to do with evolution. I think it conclusively proves that god cannot exist cause the calculations prove that she couldn't pop out of nothing spontaneously. Unless of course you think that god is less complex than a protein!

I wonder why Michael Behe's impostor is so reluctant to explain how and why Intelligent Design is supposed to have explanatory power greater than that of Evolutionary Biology?

Michael Behe · 10 December 2010

Well now that you have admitted that random process can produce information, there is nothing left to discuss. As for repetitive sequences, they can definitely be produced by chance.

Do you expect me to be duped by that circular reasoning? This is what you are saying: 1. Random processes can produce information 2. Therefore DNA is made from random processes All you're doing is making an unsupported assertion.

If you think your calculations are so great, then you won’t mind enlightening everyone as to exactly which evolutionary process they are being used to model. You know, what proposed mechanism is being tested?

The amino acid sequences. I'm not sure why you think that was supposed to put me into a corner.

See, the thing is, I think that calculation had nothing whatsoever to do with evolution. I think it conclusively proves that god cannot exist cause the calculations prove that she couldn’t pop out of nothing spontaneously.

Basically what you're saying is: 1. proteins are highly improbable 2. therefore, the designer could not assemble them. You expect me to be persuaded by that?

Mike Elzinga · 10 December 2010

Michael Behe said: The letters TAG code for one codon, after you get about 150 codons you get a protein which folds in a certain way which can then perform usually once specific task, also usually in conjunction with a half dozen other proteins. Most ribosomes are assemblies of about 20 proteins. An intelligence had to know the properties of the amino acids, how the protein would fold, how the other proteins would fold so that it could perform its task. Foresight is required. NS has no foresight.

How do protons, neutrons, and electrons know to form the various kinds of atoms that exist in the periodic table? How do atoms and molecules know to form solids and liquids? How do these atoms and molecules know what properties to give these solids and liquids? In fact, why do solids and liquids have properties not seen in individual atoms and molecules? Are you are suggesting some kind of intelligence has to know the properties of all the solids and liquids ahead of time before atoms can form such things? At what level of complexity in condensed matter systems must this intelligence enter the picture in order for such systems to combine with various parts of themselves and with other systems to form ever more complex systems? Natural selection is not directed at any particular target; so why does “it need foresight?” If what falls out works in doing something, why does anything need to have been planned ahead? Are you only focusing on properties that you think have some significance to you? What about all those billions of other complex systems you don’t notice or care about? Do they not have “significant” properties? What strikes you as significant?

You’re going to have to rephrase because I don’t get what you’re saying.

I said it very carefully and very generally. Study it and think about it. It contains the gist of everything you have missed; and that includes all the misconceptions you inherited from Henry Morris about how matter behaves and interacts.

Since this is just an assertion of belief I won’t comment.

It’s not an assertion of belief; it is an acknowledgement of the fact that there is absolutely no evidence whatsoever anywhere in chemistry or physics that even hints of there being such a thing. And physics has looked at levels of sensitivity far deeper than the easily measurable levels of the fundamental forces and quantum effects known to be operating in atomic and molecular systems at every level of complexity. There is no evidence that anything else is necessary in the assemblies of complex organic systems in which the properties of life emerge. That’s just the way it is at the moment. If you want to postulate another set of particles and fields (or “intelligence”) that are involved in the assemblies of atoms and molecules into macroscopic complex systems, then the ball is in your court to demonstrate experimentally and reproducibly this set of particles and fields (or that “intelligence”). But first you have to work out the epistemology that will produce results in the lab for any experimenter who doesn’t hold to a particular sectarian dogma.

Michael Behe · 10 December 2010

How do protons, neutrons, and electrons know to form the various kinds of atoms that exist in the periodic table? Are you are suggesting some kind of intelligence has to know the properties of all the solids and liquids ahead of time before atoms can form such things?

Of course. Why did you even need to ask that? That should be obvious. Why was this every in doubt?

At what level of complexity in condensed matter systems must this intelligence enter the picture in order for such systems to combine with various parts of themselves and with other systems to form ever more complex systems?

" level of complexity in condensed matter systems" has nothing to do with anything. NS can't produce information, intelligence can. Don't really see the point of the question.

Natural selection is not directed at any particular target; so why does “it need foresight?”

translation and transcription requires about a 100 proteins. They all have to be there at once in order for translation and transcription to work. You need to build those proteins with the foresight that they will eventually work together. NS can't do that.

Are you only focusing on properties that you think have some significance to you?

I'm focused on those responsible for constructing life

physics has looked at levels of sensitivity far deeper than the easily measurable levels of the fundamental forces and quantum effects known to be operating in atomic and molecular systems at every level of complexity.

don't see the relevance

There is no evidence that anything else is necessary in the assemblies of complex organic systems in which the properties of life emerge.

There is evidence, namely, NS can not construct with foresight. There is clear evidence of foresight in the cell. Intelligence is the only thing in our cosmos that has foresight. See above for evidence. Please read my book the Edge of Evolution for more info

raven · 10 December 2010

Behe or his imposter: Stanton, The only thing you have proven to me is the exorbitant amount of hatred you Darwinists have been attacking with me ever since my book came out in 1996

About the time you stopped being a scientist and started lying for jesus. Think there is any connection there? When you attack science, the basis of our modern civilization, you can expect modern civilization in general and scientists in particular to attack back. It's only a matter of personal and national survival.

Do you expect me to be duped by that circular reasoning? This is what you are saying: 1. Random processes can produce information 2. Therefore DNA is made from random processes.

Wow is this stupid or what? Evolution is anything but random. Evolution is random mutation plus natural selection. The result is anything but random. And sure it creates information. This has been shown innumerable times in many different ways. It is just a fact. I guess we have established one other fact. The Behe or Behe wannabe has less that a grade schoolers understanding of evolution. Pretty pathetic for someone who was once a scientist.

raven · 10 December 2010

Behe or his imposter lying: NS can’t produce information, intelligence can. Don’t really see the point of the question.

Evolution can produce information and does so constantly. This has been shown empirically and in computer simulations for decades. Behe or his imposter is simply lying. If this is Behe (who knows, anyone can claim to be anyone on the internet), he seems to be following in the footsteps of Dembski. Dembski is on record as hating secular democracy, modern Western civilization, and science. He now claims on pain of being EXPELLED for heresy that Noah had a boatload full of dinosaurs and the earth is 6,000 years old. IMO, this is simply a descent into profound madness. Intelligent Design is not only a science career killer, but also a science killer (goddidit isn't a scientific explanation and leads nowhere). It also, from my dealings with a few Dishonesty Institute members, watching Dembski spiral downwards, and now looking at something that might be Behe, a sanity killer.

Stanton · 10 December 2010

Michael Behe's impostor said:
There is no evidence that anything else is necessary in the assemblies of complex organic systems in which the properties of life emerge.
There is evidence, namely, NS can not construct with foresight. There is clear evidence of foresight in the cell. Intelligence is the only thing in our cosmos that has foresight. See above for evidence.

Natural Selection never did, nor does it operate with foresight: it operates with the current situations facing that particular generation of offspring. Furthermore, you have not given us any evidence, simply projections of your own monstrous ignorance and stupidity twisted into useless, hollow rhetoric that is incoherent and inane.

Please read my book the Edge of Evolution for more info

Are you aware that Panda's Thumb already reviewed your original's inane book? If anything, The Edge of Evolution is even more inane and more stupid than Darwin's Black Box, what with Behe STILL REFUSING to explain what Intelligent Design is, and STILL REFUSING to identify it. And then he implies that God apparently enjoys seeing people suffer from diseases so much that He would deliberately tinker with the pathogens' genomes to do so. So, yeah, please try to provide some coherent explanations, or please get lost. If you really are Michael Behe, don't you have papers to grade?

DS · 10 December 2010

Mikey wrote:

"translation and transcription requires about a 100 proteins. They all have to be there at once in order for translation and transcription to work. You need to build those proteins with the foresight that they will eventually work together. NS can’t do that."

Evidence please.

Foresight is not what what is required for the production of complex systems. Random mutations and neutral variation, combined with cumulative selection is sufficient. In fact, the evidence shows that this is exactly how the transcription and translation machinery evolved, as well as the intron splicing mechanism, etc. There was a recent article in Science that addressed this very issue. I'm sure you subscribe to Science, right? I'm sure you read the scientific literature, right?

"There is evidence, namely, NS can not construct with foresight. There is clear evidence of foresight in the cell. Intelligence is the only thing in our cosmos that has foresight. See above for evidence."

But you presented no evidence whatsoever, only baseless assertions assuming your conclusion. Look dude, as long as you define "information" as only being produced by intelligence, you aren't going to get anywhere. No real biologist buys your crap. Calling it "data" doesn't magically remove the information.

Now how about answering my question about your probability calculation? Do you still claim that this is a valid argument?

DS · 10 December 2010

Here you go Dr. Behe. I found that article for you.

Gray et. al. (2010) Irremediable Complexity? Science 380(6006):920-921.

From the article:

"Complex cellular machines may have evolved through a rachet-like process called constructive neutral evolution."

Perhaps you should publish a rebuttal article, since you claim to have evidence that this could not possibly be true. I would suggest that you at least read the article, otherwise your next court appearance might be even more embarrassing than the last one.

Mike Elzinga · 10 December 2010

Michael Behe said:
How do protons, neutrons, and electrons know to form the various kinds of atoms that exist in the periodic table? Are you are suggesting some kind of intelligence has to know the properties of all the solids and liquids ahead of time before atoms can form such things?
Of course. Why did you even need to ask that? That should be obvious. Why was this every in doubt?
At what level of complexity in condensed matter systems must this intelligence enter the picture in order for such systems to combine with various parts of themselves and with other systems to form ever more complex systems?
" level of complexity in condensed matter systems" has nothing to do with anything. NS can't produce information, intelligence can. Don't really see the point of the question.

Wow! We seem to have an imposter here. And talk about making assertions of belief. Apparently this guy believes everything in science is an assertion of belief; nevertheless he himself is allowed to make any ad hoc assertions of belief he wants. This guy is a troll.

Michael Behe · 10 December 2010

DS,
As for Gray, did you mean Terry Gray with this paper:
http://www.asa3.org/evolution/irred_compl.html

He wrote

I am not going to claim that I know how complex biochemical systems originated. My opponent is absolutely correct in his claim that little is known for certain and in much detail and that there is very little in the professional literature on this subject. What I will be presenting are broad outlines and hints of an explanation. They are most certainly wrong in the details, but they have convinced me that the "intelligent design" inference from "irreducible complexity" is fundamentally wrong-headed.

I really like his argument: I don't know how biochemical arose, therefore they are not designed. A classic argument from ignorance.

Michael Behe · 10 December 2010

Elzinga,

It is you who makes unsupported assertions not me. I already stated my reason for supporting intelligent design, so I was just restating my thesis. I will state it one more time. 64 DNA codons code for 20 different amino acids. These amino acids have specific properties. These properties are information, just as it is information that water boils at 100 C. When you sequence amino acids into strings of about 400 (in the human) you get proteins which have new properties. The properties of these proteins are information. An intelligent source had to know the content of this information as well as the content of the information of the elements and the molecules because these proteins have been constructed such that their properties have been exploited to form cells, working in conjunction with other proteins.

DS, you asked for evidence that the cell needs about 100 genes to perform translation and transcription. It's here

http://mmbr.asm.org/cgi/content/full/68/3/518#%28i%29_Basic_transcription_machinery. Let me quote from it:

RNA metabolism. RNA metabolism refers to all processes that involve RNA, including transcription, processing, and modification of transcripts; translation; and RNA degradation and its regulation. It is the central and most evolutionarily conserved part of cell physiology. The genes involved in these pathways represent more than 50% of the total number of genes included in our proposed minimal set (107 of 206 genes).

Basic transcription machinery. Five genes that encode components of the basic transcription machinery

Translation. The largest category of preserved genes corresponds to those involved in protein synthesis (78 genes), represented mainly by aminoacyl-tRNA synthases and ribosomal proteins.

we assume that the minimal number of ribosomal proteins required for proper functioning of the ribosome corresponds to the gene set present in M. genitalium, which includes 31 proteins for the large ribosomal subunit and 19 proteins for the small one.

WOW!!! all those genes working together!! what amazing foresight! This is what I tried to tell Ken Miller at Dover but he wouldn't listen to me. The judge made the wrong decision.

William Dembski · 10 December 2010

Great point, Michael. You really know how to show up the Darwinists!

stevaroni · 10 December 2010

Michael Behe said:

Wow! Michael Behe graces us with his presence! How did I miss this thread before? First, Mikey, let me open with my thanks for your efforts to besmirch the formerly good name of my alma mater, Lehigh University - until recently, a quiet college, known mostly for being as a solid, if somewhat boring engineering school, with a football team whose abysmal performance approaches the legendary. But you changed all that. Thanks. Your work was so... um... groundbreaking that the Biology department saw fit to actually publish a disclaimer specifically distancing themselves from you. Probably just professional jealousy. Anyhow...

When you sequence amino acids into strings of about 400 (in the human) you get proteins which have new properties. The properties of these proteins are information. An intelligent source had to know the content of this information as well as the content of the information of the elements and the molecules because these proteins have been constructed such that their properties have been exploited to form cells

When the popcorn-machine lottery tumbler on the TV machine spits out the wining pick-6 numbers every night, it makes strings that have new properties. One property of these strings is unquestionably information. The properties of these strings can be exploited for a purpose - to win gobs of cash. No intelligence whatsoever was necessary to create them, In fact, great care is taken to make sure that they are, in fact, random. And yet, they still work at least a few times each night.

Flint · 10 December 2010

WOW!!! all those genes working together!! what amazing foresight!

I'm reminded a bit of the amazingly complex system of global water circulation. You have basic processes like evaporation and condensation, which results in a process (rainfall) clearly beyond the realm of random accident. And once the rain falls, you have all of these many streams and rivers, What are the odds that those streams will nearly ALL intersect other streams, which in turn intersect others, leading to the formation of wide rivers. Coincidence? Forget it! And this entire system, which defies astronomical odds of happening at random, turns out to be absolutely essential to nearly every organism on earth, which must have been designed to take advantage of it. How could anyone believe all these organisms require water just at random? Clearly, anyone who opens their eyes can see Design, Purpose, and Intelligence wherever they look. It's immediately obvious, to the point where only a dunce or someone willfully blind could fail to see that Design is a property of all things biological, as intrinsic as color or mass.

Ichthyic · 10 December 2010

Great point, Michael. You really know how to show up the Darwinists!

maybe you could make some sort of flash-based fart animation out of it, Bill?

I mean, that would really show up all the "darwinists", right?

the irony you guys generate is scrumptious, but I can't indulge too much for all the high fat and cholesterol.

DS · 10 December 2010

Michael Behe said: DS, As for Gray, did you mean Terry Gray with this paper: http://www.asa3.org/evolution/irred_compl.html He wrote I am not going to claim that I know how complex biochemical systems originated. My opponent is absolutely correct in his claim that little is known for certain and in much detail and that there is very little in the professional literature on this subject. What I will be presenting are broad outlines and hints of an explanation. They are most certainly wrong in the details, but they have convinced me that the "intelligent design" inference from "irreducible complexity" is fundamentally wrong-headed. I really like his argument: I don't know how biochemical arose, therefore they are not designed. A classic argument from ignorance.

No, that was not the paper I was referring to. I provided the reference. Don't you have a a subscription? If you actually read the real paper, you will see that the authors present a plausible model that shows that conceptually, complex systems can arise by small increments. So now, your information argument is demolished, your Irreducible complexity argument is demolished and your bullshit probability argument has been completely demolished, even if you refuse to admit it. Your failure to even attempt to answer my reasonable question speaks volumes about your intellectual integrity. There is ample evidence that gene duplications, followed by divergence due to random mutations, can provide the raw material on which natural selection can act in a cumulative fashion to produce complex systems. No foresight, planning or intelligence is required. If you would just read the relevant literature you would know this. If you refuse to read the literature, then you will be rightly ignored.

DS · 10 December 2010

Mikey wrote:

":DS, you asked for evidence that the cell needs about 100 genes to perform translation and transcription. It’s here"

That's not what i asked for evidence for and you know it. You have provided absolutely no evidence whatsoever that complex systems cannot evolve. All you have done is make the assumption. It is unjustified. Since you have made no attempt to justify it, everyone can see that it is unjustified.

DS · 10 December 2010

Mikey wrote:

"WOW!!! all those genes working together!! what amazing foresight! This is what I tried to tell Ken Miller at Dover but he wouldn’t listen to me. The judge made the wrong decision."

Well Mikey, that should tell you something. An expert was not convinced by your hand waving. An impartial observer was not impressed by your bullshit. Man, either you got nothin, or you really suck at communication. or both. I guess they had the data but not the information, right?

Ichthyic · 10 December 2010

This is what I tried to tell Ken Miller at Dover but he wouldn’t listen to me. The judge made the wrong decision.”

well, maybe you should have told it to the judge instead?

oh, wait, you did.

and he LAUGHED IN YOUR FACE.

much like we are doing now.

Say, do you and Bill have some new predictive dates for the demise of the ToE?

WATERLOOOOOO!!!!

Stanton · 10 December 2010

I noticed Michael Behe's impostor posted again, and also neglected to provide any coherent explanation how and why Intelligent Design is supposed to be a better explanation than Evolutionary Biology.

I wonder why [/facetiousness]

Steve P. · 10 December 2010

Ichthyic said: Say, do you and Bill have some new predictive dates for the demise of the ToE? WATERLOOOOOO!!!!

Er, no one cares about Darwinism; if they ever did. No, Darwinism is not dead. When you are all but invisible though, and just plain ignored, what's the difference? Darwin - Ghost Town!

DS · 10 December 2010

Dr. Behe,

It is indeed a pleasure to have such an extinguished individual gracing the pages of this humble blog. Since you are a real scientist, I am sure that you are well aware of the relevant literature pertaining to your field. However, I realize that you may be too busy to keep up with all of the literature, given your ambitious speaking schedule. Therefore, please allow me to bring your attention to the following references. They show conclusively that the ribosomal protein genes have arisen through a process of gene duplication and mutational divergence. Furthermore, they document the mechanisms whereby new functions are acquired and the mechanisms responsible for the evolution of the regulatory mechanisms affecting the coordinated expression of these genes . As you no doubt are aware, this is a very active field of research. I hope that this short list will aid you in your efforts to address these issues in an intellectually honest fashion, rather than simply denying that any evidence exists. I thank you in advance for your willingness to review these references.

Golden et. al. (1993) Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein, EMBO Journal 12(13):4901-4908.

Zhang (2003) Evolution by gene duplication: an update. Trends in Ecology and Evolution 18(8):293-299.

Komill et. a;. (2007) Functional specificity among ribosomal proteins regulates gene expression. Cell 131:557-571.

Wapinski et. al. (2010) Gene duplication and the evolution of ribosomal protein gene regulation in yeast. PNAS 107(12):5505-5510.

I can also provide references for the evolution of the genetic code and the evolution of intron splicing. It seems you have some catching up to do.

Michael Behe · 10 December 2010

DS, what happened to all of the insults? I kind of liked it better when you threw mud at me, that way I could rest assured that Darwinists had no arguments.

In any case, duplicating an already-built gene is not the same as build a new gene from scratch. Come on, DS, you know better than that.

stevaroni · 10 December 2010

DS said:
Michael Behe said: DS, As for Gray, did you mean Terry Gray with this paper: http://www.asa3.org/evolution/irred_compl.html
No, that was not the paper I was referring to. I provided the reference. Don't you have a a subscription?

Mikey, Mikey, Mikey, I'm sure Lehigh has a subscription. Just amble over to Linderman Library and look it up, bubeleh.

DS · 10 December 2010

Are you some kind of retarded idiot? No one ever claimed that you had to build a "new gene from scratch". In fact, you were specifically told many times exactly what the mechanism was. Now I have provided you with references, they show exactly where new genes come from, it ain't from scratch. I can provide many more references if you demonstrate that you are willing to learn. Are you gong to read them or not? Are you going to become educated or not? Are you just going to continue to attack a hackneyed caricature of evolution or are you going to actually try to learn something? If you want to know why you can't convince anybody of anything, that is exactly the reason. I would advise you to increase your knowledge.

By the way, you made the same ignorant mistake with your bullshit probability calculation. Since you refuse to admit it, I have no choice but to conclude that you are as disingenuous as you are dishonest.

You know man, part of your job as a professor is to read the literature. How else are you going to remain current in the field? How else are you going to teach your students the latest discoveries? You do want to be a good teacher don't you? Given the disposition of your department towards your shenanigans, you wouldn't want to provide them with any excuse to fire your sorry ass now would you?

If you reread nay last post, I think you will discover a few insults in there as well. See the arguments are still valid whether I include the insults or not. Get a clue.

Flint · 10 December 2010

Er, no one cares about Darwinism; if they ever did. No, Darwinism is not dead. When you are all but invisible though, and just plain ignored, what’s the difference? Darwin - Ghost Town!

Well, sort of. While Charles Darwin retains his stature as an historic scientific founder, of course the state of the art has advanced enormously, rendering old Charles an admirable visionary, but as dated as any other noteworthy 19th century scientist. Really, what would you expect? But the important point is that biology is no more "invisible" because Darwin lived long ago, than physics is obsolete because Newton did. Biology is not "Darwinism" any more than physics is "Newtonism". I admit I can't think of a single field in science that's named after any scientist in that field, no matter how instrumental. Relativity is not "Einsteinism", for example. Naming obsolete and limited views after their founders is a religious practice, not a scientific practice. So you'd probably have a hard time finding a biologist who had any clue what you meant by "Darwinism", nor any interest in finding out.

Stanton · 10 December 2010

Michael Behe's imposter said: DS, what happened to all of the insults? I kind of liked it better when you threw mud at me, that way I could rest assured that Darwinists had no arguments. In any case, duplicating an already-built gene is not the same as build a new gene from scratch. Come on, DS, you know better than that.

So how come you're still refusing to provide an explanation of how and why Intelligent Design is supposed to be a superior explanation to Evolutionary Biology?

Ichthyic · 10 December 2010

what happened to all of the insults?

good thing you're too dimwitted to notice he called you "extinguished".

John Kwok · 10 December 2010

William Dembski said: Great point, Michael. You really know how to show up the Darwinists!

Hi Bill, it's been exactly three years since you tried to have Amazon.com censor my harsh, but accurate, review of your book co-authored with Jonathan Wells. As compensation you are required to purchase expensive Leica rangefinder camera equipment worth at least $6,000 - $10,000 (Or make a donation for the amount of $10,000 in support of stucent scientific research at my alma mater Stuyvesant High School, where its current principal pledged in the Fall of 2005 to an alumni audience that Intelligent Design would never be taught there since it isn't scientific.). I raised this point with you in our private e-mail correspondence three years ago, when you told me you knew scores of Texas high school principals who want Intelligent Design, not evolution taught in science classrooms. When I asked you how many teach a rigorous freshmen-only introductory physics class - which I believe Sutyvesant's principal still does - you couldn't answer. Maybe now you can provide me with such an answer, Bill.

John Kwok · 10 December 2010

Michael -

Thanks for stopping by. When we read your book, "The Edge of Evolution" both graduate student Dave Wisker and I independently arrived at the conclusion that you don't understand at all the concept of coevolution. How can you claim that the interaction between the malarial parasite Plasmodium and humanity can be seen as a "failure" of "Darwinism", when instead, it is a superb example of a pharmaceutically driven coevolutionary arms race between this parasite and humanity?

P. S. Ken Miller and I still eagerly await your textbook on Klingon Biochemistry. Since your American publisher, Simon and Schuster, also publishes the "Star Trek" books, I am sure that they would greet a proposal for such a textbook from you with considerable interest.

John Kwok · 10 December 2010

Michael -

Can you explain to us here at Panda's Thumb how Intelligent Design is a superior alternative to the Modern Synthesis Theory of Evolution in accounting for the origins, history and present composition (and structure) of Planet Earth's biodiversity? What testable hypotheses would you propose as suitable tests to demonstrate Intelligent Design's superiority over modern evolutionary theory in this regard?

Stanton · 10 December 2010

John Kwok said: Michael - Thanks for stopping by. When we read your book, "The Edge of Evolution" both graduate student Dave Wisker and I independently arrived at the conclusion that you don't understand at all the concept of coevolution at all

All better now.

Stanton · 10 December 2010

John Kwok said: Michael - Can you explain to us here at Panda's Thumb how Intelligent Design is a superior alternative to the Modern Synthesis Theory of Evolution in accounting for the origins, history and present composition (and structure) of Planet Earth's biodiversity? What testable hypotheses would you propose as suitable tests to demonstrate Intelligent Design's superiority over modern evolutionary theory in this regard?

I don't know whether to consider tag-teaming you about attempting to wring an explanation or excuse out of Behe's imposter, or berate you for stealing my schtick.

John Kwok · 10 December 2010

You have to forgive me, but it's late, so am reposting this with corrections (see below):

John Kwok said:
William Dembski said: Great point, Michael. You really know how to show up the Darwinists!
Hi Bill, it's been exactly three years since you tried to have Amazon.com censor my harsh, but accurate, review of your book co-authored with Jonathan Wells. As compensation you are required to purchase expensive Leica rangefinder camera equipment worth at least $6,000 - $10,000 (Or make a donation for the amount of $10,000 in support of stucent scientific research at my alma mater Stuyvesant High School, where its current principal pledged in the Fall of 2005 to an alumni audience that Intelligent Design would never be taught there since it isn't scientific.). I raised this point with you in our private e-mail correspondence three years ago, when you told me you knew scores of Texas high school principals who want Intelligent Design, not evolution taught in science classrooms. When I asked you how many teach a rigorous freshmen-only introductory physics class - which I believe Sutyvesant's principal still does - you couldn't answer. Maybe now you can provide me with such an answer, Bill.

Hi Bill, it's been exactly three years since you tried to have Amazon.com censor my harsh, but accurate, review of your book co-authored with Jonathan Wells. As compensation you are required to purchase expensive Leica rangefinder camera equipment worth at least $6,000 - $10,000 (Or make a donation for the amount of $10,000 in support of student Intel Science Talent Search scientific research at my alma mater Stuyvesant High School, where its current principal pledged in the Fall of 2005 to an alumni audience that Intelligent Design would never be taught there since it isn't scientific.). I raised this point with you in our private e-mail correspondence three years ago, when you told me you knew scores of Texas high school principals who want Intelligent Design, not evolution, taught in science classrooms. When I asked you how many teach a rigorous freshmen-only introductory physics class - which I believe Stuyvesant's principal still does - you couldn't answer. Maybe now you can provide me with such an answer, Bill.

John Kwok · 10 December 2010

Well Stanton, "The Edge of Evolution" is one long argument against coevolution, but I do endorse your editorial revisement:

Stanton said:
Michael Behe's impostor said: Stanton, I'm afraid dialogue between us is not possible. If one side refuses to answer the other's questions than the two sides cannot learn from each other. I asked you questions about Lenski's experiment which you refused to answer.
I'm not the one who lacks the brain and will power to read even the Wikipedia page about Lenski's experiment. What's the matter? Afraid that you'll get smart and get excommunicated? Furthermore, how come you're so reluctant to actually demonstrate the alleged explanatory power of Intelligent Design? We are not having a discussion not because of me, but because of you not wanting to go through even the motions of explaining why Intelligent Design is supposed to be superior to Evolutionary Biology. That is, not wanting to go beyond the non-explanation of "GODDIDIT"

Stanton · 10 December 2010

John Kwok said: Well Stanton, "The Edge of Evolution" is one long argument against coevolution, but I do endorse your editorial revisement

From what I've read about Behe's inane sequel, well... I don't even consider it to have or be an argument, what with Behe essentially closing his eyes, pressing the points of his index and middle fingers deep into his temples while repeating and rewording the mantra "Couldn't Happen" over and over and over and over again.

386sx · 11 December 2010

William Dembski said: Great point, Michael. You really know how to show up the Darwinists!

Loved your debate with Hitchens and your point about how all the other creation myths except for the Christian one are natural forces just like Darwinism. Those darn naturalistic creation myths. Lol, I had to get a new computer screen. That is classic comedy gold.

John Kwok · 11 December 2010

I was half awake, newly returned from a chamber music recital and post-concert reception, when I saw "Behe" and "Dembski" stop by. I missed your earlier comment:

Stanton said: I noticed Michael Behe's impostor posted again, and also neglected to provide any coherent explanation how and why Intelligent Design is supposed to be a better explanation than Evolutionary Biology. I wonder why [/facetiousness]

John Kwok · 11 December 2010

386sx said:
William Dembski said: Great point, Michael. You really know how to show up the Darwinists!
I think it is utterly fascinating that a dying Christopher Hitchens is still able to make a lot more sense than my "dear" pal Bill Dembski. Think that says a lot about the intellectual caliber of both gentlemen, don't you think? Loved your debate with Hitchens and your point about how all the other creation myths except for the Christian one are natural forces just like Darwinism. Those darn naturalistic creation myths. Lol, I had to get a new computer screen. That is classic comedy gold.

John Kwok · 11 December 2010

Sorry I goofed a bit earlier this morning, so here's the correction:

386sx said:
William Dembski said: Great point, Michael. You really know how to show up the Darwinists!
Loved your debate with Hitchens and your point about how all the other creation myths except for the Christian one are natural forces just like Darwinism. Those darn naturalistic creation myths. Lol, I had to get a new computer screen. That is classic comedy gold.

I think it is utterly fascinating that a dying Christopher Hitchens is still able to make a lot more sense than my “dear” pal Bill Dembski. Think that says a lot about the intellectual caliber of both gentlemen, don’t you think?

John Kwok · 11 December 2010

Hey Bill, I forgot to ask you four questions last night:

William Dembski said: Great point, Michael. You really know how to show up the Darwinists!

Here they are: 1) When are you going to return to the Dover Area School District board the $20,000 you stole from them in agreeing to serve as their lead witness for their defense at the 2005 Kitzmiller vs. Dover Area School Distict trial? 2) When will you apologize to eminent University of Texas ecologist Eric Pianka for falsely accusing him of being a potential bioterrorist to the Federal Department of Homeland Security in 2006? 3) When will you apologize to both Harvard University and to David Bolinsky, President, XVIVO, for "borrowing" the XVIVO-produced cell animation video in 2007, in which you all but admitted that it wasn't merely an act of "borrowing", but rather, larceny? 4) For the fourth time (twice in person after the AMNH Intelligent Design debate back in the Spring of 2002; the third when we corresponded via e-mail back in December 2007; no answers from you were ever forthcoming) can you explain how you would calculate confidence limits for the Explanatory Filter? Since I'm not nearly as smart as you are with regards to statistics, then I would imagine that it should be a trivial exercise for someone such as yourself with a Ph. D. in Mathematics from the University of Chicago and a M. S. in Statistics from the University of Illinois, Chicago.

DS · 11 December 2010

I guess all the insults scared "Dr. Behe" away. I guess he really does use that as his excuse to ignore the substance of the arguments, just like he said.

So, let's recap shall we?

1) Random processes can produce information, it takes intelligence to interpret the information, not to produce it.

2) New genes can be produced by random processes such as gene duplications and mutational divergence. This is a major mechanism by which new structures and functions can evolve, often through a process involving fixation of v=initially neutral variation.

3) New genes do not poof out of nowhere from scratch. That is a creationist misconception and the basis of their irrelevant and inappropriate probability calculations.

Now "Dr. Behe" is free to reject these conclusions, but until he demonstrates that he has read and understood the relevant scientific literature his opinion is essentially worthless. Those of us who are familiar with the scientific evidence, respectfully (or disrespectfully) disagree with "Dr. Behe". SInce he has provided absolutely no evidence, I cannot think of a single reason why anyone should be convinced by his blustering. How does this guy continue to sell books anyway?

fnxtr · 11 December 2010

Dollars to donuts, "Michael Behe" and "William Dembski" have the same ISP.

DS · 11 December 2010

fnxtr said: Dollars to donuts, "Michael Behe" and "William Dembski" have the same ISP.

What's the difference, neither one of him has a clue. Hell, I insulted the guy three times and he thanked me for not insulting him! That was after he proved mathematically that "poof" don't happen. Oh well, if they are the same guy, that should make it easier for him to read the papers. He can just split them up and read two each.

Henry J · 11 December 2010

How does this guy continue to sell books anyway?

Maybe something like this: "BUY MY BOOK!!111!!one!!" ?

Mike Elzinga · 12 December 2010

DS said:
fnxtr said: Dollars to donuts, "Michael Behe" and "William Dembski" have the same ISP.
What's the difference, neither one of him has a clue. Hell, I insulted the guy three times and he thanked me for not insulting him! That was after he proved mathematically that "poof" don't happen. Oh well, if they are the same guy, that should make it easier for him to read the papers. He can just split them up and read two each.

I have never been impressed with any of the ID/creationist “scientists.” Every one of them from ICR, to AiG, to the DI has extremely distorted conceptual understandings of science. And Behe simply showed to the entire world – with his airy dismissal in Dover of piles of research - that he doesn’t even understand what is going on in what is supposed to be his own area of expertise. So it is not surprising that trolls, who show up attempting to pose as Behe or Dembski, would have no clue when they just got nailed. But it really is funny to watch. Troll gets whacked between the eyes, blinks dopily, and says, “Duh, I won!”

mrg · 12 December 2010

Mike Elzinga said: I have never been impressed with any of the ID/creationist “scientists.”

I have. No matter how low I set my expectations, they keep surprising me.

Flint · 12 December 2010

mrg said:
Mike Elzinga said: I have never been impressed with any of the ID/creationist “scientists.”
I have. No matter how low I set my expectations, they keep surprising me.

How so? Put your self in the shoes of a creationist scientist. On the one hand, creationism HAS to be true, since that was indoctinated into you in early childhood and those neural pathways can no longer be altered. But on the other hand, the scientist in you wants to understand how things really work, what the principles are that reality operates by. You're curious to understand your god's methods and handiwork. And one thing you understanding intuitively is, if it requires magic, then it ain't science. So your god had to have used principles science can explain. But subconsciously, you're aware that it's not going to happen. Your theological requirements are flat antithetical to your scientific requirements. Your only possible strategy is to atomize science into a set of tiny, unrelated and disparate claims. And then find some rationalization for rejecting each one individually, without allowing yourself to notice that your rationalizations are themselves mutually exclusive. So what's impressive about creationist scientists, beyond their limitless ability to kid themselves, is the imaginative way they can whitewash sheer idiocy with a sheen of plausibility (if you don't look too closely) while never losing sight of the theological constraints. I actually admire them the way I admire a circus contortionist. They know that what absolutely must be true, absolutely can't be true. They have to find some way to enable themselves to THINK it's true, without shorting out their whole brains.

mrg · 12 December 2010

Flint said: I actually admire them the way I admire a circus contortionist.

Precisely. "I couldn't possibly do such things. It is beyong my imagining how anyone else can do such things themselves." Hmm, I heard the Cirque du Soleil roadshow is coming to town next month, I'll have to check. This time I get the first-class seats.

Dale Husband · 12 December 2010

What the hell are Michael Bee the non-stinger and William Dumbski doing here, anyway? Do we at PT often invade their stupid blog Uncommon Descent (into madness)? If we have done that lately, I do apologize, since we have better things to do with our time.....and so do they!

Stanton · 12 December 2010

Dale Husband said: What the hell are Michael Bee the non-stinger and William Dumbski doing here, anyway? Do we at PT often invade their stupid blog Uncommon Descent (into madness)? If we have done that lately, I do apologize, since we have better things to do with our time.....and so do they!

Quite frankly, if the two idiots' idiot impostors are through humiliating themselves, then we should have this thread put out of its misery.

Steve Matheson · 12 December 2010

Stanton, that's a great idea. Let's all stop feeding the trolls. If you need that kind of entertainment, take Dale's hint and head to UD.

John Kwok · 13 December 2010

Yours is a sentiment I endorse with ample enthusiasm. Kudos to you and Stanton, and to Dale for suggesting Uncommonly Dense:

Steve Matheson said: Stanton, that's a great idea. Let's all stop feeding the trolls. If you need that kind of entertainment, take Dale's hint and head to UD.