Sunday, January 29, 2017

The evolution of the citric acid cycle

I just realized that I don't have a post devoted to the evolution of the citric acid cycle. This need to be remedied since I often talk about it. It's a good example of how an apparently irreducibly complex pathway can arise by evolution. It's also a good example to get students to think outside of the box. Undergraduate biochemistry courses usually concentrate on human physiology and too often students transfer that bias to all other species. They assume that what happens in humans is what happens in plants, fungi, protozoa, and bacteria.1

Here's what the standard citric acid cycle looks like (Moran et al., 2011 p. 393).


When the pathway runs in the clockwise direction, the net reaction is oxidation of a two-carbon compound (acetate, shown in green) to two molecules of CO2. The oxidation steps are coupled to reduction of NAD+ or Q and the production of an ATP equivalent at step 5. The substrate, acetyl-CoA, can be though of as a "high energy" molecule and the oxidation steps result in the release of energy that's captured in the synthesis of reducing equivalents (NADH2 and QH2). These reducing equivalents are used in multiple reactions inside the cell. They are usually thought of as the substrates for a series of membrane-associated electron transport reactions that create a proton gradient but that's only part of their fate. The proton gradient is used to drive ATP synthesis so you can think of the reducing equivalents as ATPs where NADH2 is equivalent to 2.5 ATPs and QH2 is equivalent to 1.5 ATPs.

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It's difficult to imagine how a cyclic pathway like this could evolve since in the absence of any one of the enzymes the circle is broken. You might naively think that all of the enzymes had to arise simultaneously.

In fact, we have a pretty good idea how the cyclic pathway evolved from more simple non-cyclic pathways. This is how I describe it in my textbook (Moran et al., 2011 pp. 412-414 © Pearson/Prentice Hall).


13.9 Evolution of the Citric Acid Cycle

The reactions of the citric acid cycle were first discovered in mammals and many of the key enzymes were purified from liver extracts. As we have seen, the citric acid cycle can be viewed as the end stage of glycolysis because it results in the oxidation of acetyl CoA produced as one of the products of glycolysis. However, there are many organisms that do not encounter glucose as a major carbon source and the production of ATP equivalents via glycolysis and the citric acid cycle is not an important source of metabolic energy in such species.

We need to examine the function of the citric acid cycle enzymes in bacteria in order to understand their role in simple single-celled organisms. These roles might allow us to deduce the pathways that could have existed in the primitive cells that eventually gave rise to complex eukaryotes. Fortunately, the sequences of several hundred prokaryotic genomes are now available as a result of the huge technological advances in recombinant DNA technology and DNA sequencing methods.We can now examine the complete complement of metabolic enzymes in many diverse species of bacteria and ask whether they possess the pathways that we have discussed in this chapter. These analyses are greatly aided by developments in the fields of comparative genomics, molecular evolution, and bioinformatics.

Most species of bacteria do not have a complete citric acid cycle. The most common versions of an incomplete cycle include part of the left-hand side. This short linear pathway leads to production of succinate or succinyl CoA or α-ketoglutarate by a reductive process using oxaloacetate as a starting point. This reductive pathway is the reverse of the traditional cycle that functions in the mitochondria of eukaryotes. In addition, many species of bacteria also have enzymes from part of the right-hand side of the citric acid cycle, especially citrate synthase and aconitase. This allows them to synthesize citrate and isocitrate from oxaloacetate and acetyl CoA. The presence of a forked pathway (Figure 13.24) results in the synthesis of all the precursors of amino acids, porphyrins, and fatty acids.

There are hundreds of diverse species of bacteria that can survive and grow in the complete absence of oxygen. Some of these species are obligate anaerobes—for them, oxygen is a lethal poison! Others are facultative anaerobes—they can survive in oxygen free environments as well as oxygen-rich environments. E. coli is one example of a species that can survive in both types of environment. When growing anaerobically, E. coli uses a forked version of the pathway to produce the necessary metabolic precursors and avoid the accumulation of reducing equivalents that cannot be reoxidized by the oxygen requiring electron transport system. Bacteria such as E. coli can grow in environments where acetate is the only source of organic carbon. In this case, they employ the glyoxylate pathway to convert acetate to malate and oxaloacetate for glucose synthesis.


The first living cells arose in an oxygen-free environment over three billion years ago. These primitive cells undoubtedly possessed most of the enzymes that interconverted acetate, pyruvate, citrate, and oxaloacetate, since these enzymes are present in most modern bacteria. The development of the main branches of the forked pathway possibly began with the evolution of malate dehydrogenase from a duplication of the lactate dehydrogenase gene. Aconitase and isocitrate dehydrogenase evolved from enzymes that are used in the synthesis of leucine (isopropylmalate dehydratase and isopropylmalate dehydrogenase, respectively). (Note that the leucine biosynthesis pathway is more ubiquitous and more primitive than the citric acid cycle.)

Extension of the reductive branch continued with the evolution of fumarase from aspartase. Aspartase is a common bacterial enzyme that synthesizes fumarate from L-aspartate. L-aspartate, in turn, is synthesized by amination of oxaloacetate in a reaction catalyzed by aspartate transaminase (Section 17.3). It is likely that primitive cells used the pathway oxaloacetate → aspartate → fumarate to produce fumarate before the evolution of malate dehydrogenase and fumarase. The reduction of fumarate to succinate is catalyzed by fumarate reductase in many bacteria. The evolutionary origin of this complex enzyme is highly speculative but at least one of the subunits is related to another enzyme of amino acid metabolism. Succinate dehydrogenase, the enzyme that preferentially catalyzes the reverse reaction in the citric acid cycle, is likely to have evolved later on from fumarate reductase via a gene duplication event.

The synthesis of α-ketoglutarate can occur in either branch of the forked pathway. The reductive branch uses α-ketoglutarate:ferredoxin oxidoreductase, an enzyme found in many species of bacteria that don’t have a complete citric acid cycle. The reaction catalyzed by this enzyme is not readily reversible. With the evolution of α-ketoglutarate dehydrogenase the two forks can be joined to create a cyclic pathway. It is clear that α-ketoglutarate dehydrogenase and pyruvate dehydrogenase share a common ancestor and it is likely that this was the last enzyme to evolve.

Some bacteria have a complete citric acid cycle but it is used in the reductive direction to fix CO2 in order to build more complex organic molecules. This could have been one of the selective pressures leading to a complete pathway. The cycle requires a terminal electron acceptor to oxidize NADH and QH2 when it operates in the more normal oxidative direction seen in eukaryotes. Originally, this terminal electron acceptor was sulfur or various sulfates, and these reactions still occur in many anaerobic bacterial species. Oxygen levels began to rise about 2.5 billion years ago with the evolution of photosynthesis reactions in cyanobacteria. Some bacteria, notably proteobacteria, exploited the availability of oxygen when the membrane associated electron transport reactions evolved. One species of proteobacteria entered into a symbiotic relationship with a primitive eukaryotic cell about two billion years ago. This led to the evolution of mitochondria and the modern versions of the citric acid cycle and electron transport in eukaryotes. The evolution of the citric acid cycle pathway involved several of the pathway evolution mechanisms discussed in Chapter 10. There is evidence for gene duplication, pathway extension, retro-evolution, pathway reversal, and enzyme theft.




Additional information on other enzymes in this pathway can be found in: On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions.

For more information on succinate dehydrogenase and it's proper substrates and products see: Succinate Dehydrogenase; Succcinate Dehydrogenase and Evolution by Accident.

For more details on the relationship of &appha;-ketoglutarate dehydrogenase and pyruvate dehydrogenase see: Pyruvate Dehydrogenase Evolution.


1. The emphasis on human biochemistry and physiology—partly in order to prepare students for medical school—is what inhibits teaching evolutionary concepts in biochemistry courses.

Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc.

121 comments :

  1. "Some bacteria, notably proteobacteria, exploited the availability of oxygen when the membrane associated electron transport reactions evolved."

    This is a big step. How did this evolve? Is this the origin of ATP synthase?

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    1. Well done, Bill! You found a gap to squeeze your god into.

      So tell me: When can we expect you IDiots to come up with at least a rudimentary explanation of how the citric acid cycle could have been "designed"? Soon, perhaps? We've been waiting 20 years.

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    2. Cole: "Is this the origin of ATP Synthase?"
      No. Not even close. ATP Synthase exists in all cells, and is probably at least half a billion years older than the use of molecular oxygen at the end of the electron transport chain, which exists only in aerobic cells.
      "This is a big step."
      Not all that big. The electron transport chain already existed, as well as the oxidative citric acid cycle that feeds it. All that was needed was to replace one terminal electron acceptor (Fe+++?, SO4--?) with another (O2). At first, the oxygen consuming branch was just an optional destination for electrons, used when the standard acceptor was in short supply. (Larry's use of the word 'exploited' was shrewd.) Eventually, as efficiencies improved and oxygen levels rose, oxygen came to accept all of the flowing electrons, and the enzymes supporting the old standard electron acceptor fell into disuse, and eventually disfunction.

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    3. Hi Jim
      " The electron transport chain already existed"

      The origin of this is what I am claiming is a big step. Using Michael Behe's claim of irreducible complexity may be applied to this.

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    4. Michael Behe's argument from irreducible complexity has been refuted. No need to keep beating that dead horse.

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    5. LS
      "Michael Behe's argument from irreducible complexity has been refuted. No need to keep beating that dead horse."

      Can you support the claim the electron transport chain is not irreducibly complex.

      I do not agree that the argument has been refuted. A counter argument does not mean it is refuted. What experimental evidence can you cite that shows a bacterial flagellum can evolve by your choice of mechanisms.

      There is a reasonable argument that the electron transport chain is evidence of many parts arranged for a purpose, the rapid manufacturing of ATP by the cell. This is evidence of design.

      This is not strong evidence of being the result of a blind process.

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    6. Can you support the claim the electron transport chain is not irreducibly complex.

      I did not make that claim. Behe (or someone else) has to support the claim evolution cannot produce something that appears "irreducibly complex." This is a fundamental error you keep making.

      It's as if I argued "If zebras have stripes, then God does not exist" and you asked me to support that argument. How would you reply if I responded "Can you support your claim that zebras don't have stripes"?

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    7. LS
      "I did not make that claim. Behe (or someone else) has to support the claim evolution cannot produce something that appears "irreducibly complex." This is a fundamental error you keep making."

      I think he needs to support the claim that the complex micro machines like the flagellum and ATP synthase are more strongly supported by the design argument then blind processes.

      As both are observed to be the purposeful arrangement of parts, ATP manufacturing and bacterial mobility, I would argue that design is the better inference.

      Assuming a key component of the citric acid cycle is designed I would then argue that the CAC is a design concept in itself versus the result of a blind process.

      Blind processes and design seem to be the two alternatives on the table.

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    8. As both are observed to be the purposeful arrangement of parts, ATP manufacturing and bacterial mobility, I would argue that design is the better inference.

      This is another failure of logic on your part. "Design" is a process that results in arrangements of parts that serve a purpose, it is true. However, evolution is also a process that does so. So you can't use the appearance of "purpose" alone to demonstrate design.

      It's as if you argued that a tiger must be a zebra, because the tiger has stripes, and zebras have stripes. From the fact that zebras have stripes, it does not follow that everything that has stripes must be a zebra.

      Are you able to follow that? I hope you are.

      By the same token, from the fact that entities consisting of complex arrangements of parts which serve a function are often designed, it does not follow that all such arrangements are the result of design. We know evolution can produce such arrangements, as well.

      Now, if we knew of the existence of intelligent agents that have designed self-reproducing biological structures and systems like the bacterial flagellum or the citric acid cycle, and if these such intelligent beings did not require the prior existence of such biological systems and we knew that such intelligent beings existed on earth millions of years ago when these systems first arose, then there would be an argument to be made that these systems could as easily have been "designed" as evolved. However, I'm not aware of any evidence for the existence of such beings. Are you?

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    9. LS
      "This is another failure of logic on your part. "Design" is a process that results in arrangements of parts that serve a purpose, it is true. However, evolution is also a process that does so. So you can't use the appearance of "purpose" alone to demonstrate design."

      Can you demonstrate evolutions or blind processes ability to create a purposeful arrangement of parts that perform a function?

      " Now, if we knew of the existence of intelligent agents that have designed self-reproducing biological structures and systems like the bacterial flagellum or the citric acid cycle, and if these such intelligent beings did not require the prior existence of such biological systems and we knew that such intelligent beings existed on earth millions of years ago when these systems first arose, then there would be an argument to be made that these systems could as easily have been "designed" as evolved. However, I'm not aware of any evidence for the existence of such beings. Are you?"

      The existence of the purposeful arrangement of parts for a function is evidence of design. The designer is not the argument.

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    10. Cole wrote: "The origin of this [the electron transport chain] is what I am claiming is a big step. Using Michael Behe's claim of irreducible complexity may be applied to this."

      Electron transport is perhaps the worst possible example that an opponent of evolution might choose to make his case. The reason is that there is not just one big complex electron transport chain that is universal in the biosphere and which leaves no clues to how it might have evolved. Instead, there are literally hundreds of different electron transport chains in nature, stretching between a dozen different terminal electron donors and another dozen different terminal electron acceptors. There may or may not be photons involved. The number of protons translocated may vary. The electron donors and acceptors may not even be on the same side of the membrane.

      Looking at any one of these chains, it may seem irreducibly complex. But list them all together and look at the intermediate steps that various chains have in common, and the whole pattern practically screams "Evolution diddit!"

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    11. Hi Jim
      "Looking at any one of these chains, it may seem irreducibly complex. But list them all together and look at the intermediate steps that various chains have in common, and the whole pattern practically screams "Evolution diddit!""

      You appear to be arguing for both differences and commonality. Do you have one that you think you can reconcile its origin to a blind process?

      If you look at all the examples can you knock out an enzyme in the chain and still retain function?

      My experience is that lots of different configurations can be additional
      evidence against evolution especially when more complex features can occur earlier than latter. An example is the Trilobites eye which appeared over 400 million years ago and is very complex

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    12. Can you demonstrate evolutions or blind processes ability to create a purposeful arrangement of parts that perform a function?

      Yes. And it has already been demonstrated to you, many times. Most recently by Jim Menegay. That you are unable or unwilling to understand this evidence is really no one's problem but your own,

      The existence of the purposeful arrangement of parts for a function is evidence of design.

      Or of evolution.

      The designer is not the argument.

      I know, you keep saying that. It doesn't make it any less asinine a attempt to dodge the question. It's very amusing how you IDiots claim to be interested in science, but have not the slightest bit of curiosity regarding the most crucial part of your "theory."

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    13. Can you demonstrate evolutions or blind processes ability to create a purposeful arrangement of parts that perform a function?

      People who use evolutionary algorithms (as a friend of mine who's won a US Defense Department award for best civilian engineering project did in coming up with the aiming algorithm for the "Star Wars" anti-missile defense system; no human designed algorithm had a hope of accounting properly for all the factors involved) are snickering right now, or are just goggle-eyed in amazement that people don't understand the power of evolution.

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    14. I think he needs to support the claim that the complex micro machines like the flagellum and ATP synthase are more strongly supported by the design argument then blind processes.

      The problem with this argument is that there are parts of the process that decidedly are not blind. They are exposed to "extreme vetting" - whether whatever carries them survives and reproduces.

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    15. I'll just point out the blatant hypocrisy of Bill Cole's approach to this question. He demands, not just evidence, but what he calls a "demonstration" that "blind processes" can produce complex functional structures. By which he seems to mean he wants to see a fully formed flagellum suddenly poof into existence from organic chemicals in a test tube.

      But ask him for the even merest scrap of evidence for the existence of his "designer", and waves the question away with "That's not part of the argument."

      Typical.

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    16. Bill Cole,

      "If you look at all the examples can you knock out an enzyme in the chain and still retain function?"

      For many cases, yes, we can knock out a gene and still get a viable cell.

      "The designer is not the argument."

      And that's one of the many problems with ID. In order to consider design, we would have to have a very good case for the existence of designers, their tools, their presence at the appropriate times, some evidence about them. Otherwise they look like any other primitive fantasy when peoples didn't know what a volcano was, or how they formed, and they thought they were gods. Things we have yet to explain, even things we might never be able to explain, are no excuses for imagining that gods-did-it.

      You have to understand how scientists are expected to think. When there's evidence of designers at some time or another, we consider that possibility. Otherwise it's mere wishful thinking.

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    17. PS
      "
      And that's one of the many problems with ID. In order to consider design, we would have to have a very good case for the existence of designers, their tools, their presence at the appropriate times, some evidence about them. Otherwise they look like any other primitive fantasy when peoples didn't know what a volcano was, or how they formed, and they thought they were gods. Things we have yet to explain, even things we might never be able to explain, are no excuses for imagining that gods-did-it."

      I agree that this question is valid and interesting and yet not part of the theory.

      Both design and evolution have limitations. I guess the question is what is the most accurate inference based on whats observed. I see lots of evidence of design inside the cell. I have very little confidence that blind process can explain what we are observing.

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    18. Bill:
      "I see lots of evidence of design inside the cell."

      Like for instance?

      "I have very little confidence that blind process can explain what we are observing."

      Yes, correct. BUT, this has been explained to you many, many times over on this blog what you write above ain't the theory of evolution. I dunno what you're attacking, a windmill like Don Q or Tx love to attack I have to assume from your quote above.

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    19. Ed
      ""I see lots of evidence of design inside the cell."

      Like for instance?"

      The transcription translation mechanism
      The electron transport chain
      The bacterial flagellar motor
      Alternative splicing
      The cell cycle and all its controls

      " Yes, correct. BUT, this has been explained to you many, many times over on this blog what you write above ain't the theory of evolution. I dunno what you're attacking, a windmill like Don Q or Tx love to attack I have to assume from your quote above."

      There are many blind processes(without foresight) in evolutionary theory. Which processes do you think best explains the origin of ATP synthase?

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    20. Ed
      ""I see lots of evidence of design inside the cell."

      Like for instance?"

      The transcription translation mechanism
      The electron transport chain
      The bacterial flagellar motor
      Alternative splicing
      The cell cycle and all its controls


      That is not evidence of design. Those are examples of things you mistakenly believe are "designed." That is not the same thing as evidence.

      Your response is as if someone claimed the Great Pyramids of Giza were built by space aliens, and when you asked them for evidence, they replied, "The Great Pyramids of Giza."

      I suspect you would conclude such a person does not understand what "evidence" actually is, nor how to draw a correct conclusion based on available evidence. So what should we conclude about you?

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    21. and yet not part of the theory

      Because the origins and nature of the Universe aren't part of the theory and science of cosmology, and the origins and nature of the Earth aren't part of the theory and science of geology, just like the origins and nature of the designer aren't part of design theory. Oh, wait....

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    22. LS

      Design: The purposefully arrangement of parts that perform a function.

      "That is not evidence of design. Those are examples of things you mistakenly believe are "designed." That is not the same thing as evidence."

      Your opinion is that I am mistaken in thinking these are evidence of design. How would you support your claim?

      "Your response is as if someone claimed the Great Pyramids of Giza were built by space aliens, and when you asked them for evidence, they replied, "The Great Pyramids of Giza."

      This claim assumes identity of the designer not design. I agree the identity of the designer is interesting but not part of the argument. Your analogy attacks a straw man.

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    23. Bill Cole,

      But you're missing my point. It seems natural to you to assume a designer because you already believe in some supernatural being. It is however nonsense if you're actually dealing in scientific terms, where mythologies are recognized for what they are. Thus, for ID to become something of a sensical scientific proposition, there's a real need for evidence of a designer beyond the claims that "I cannot believe that unguided processes can do this," or "because we see designers doing something that looks like this, designers did it!"

      It gets worse than just that, but I'm just trying to get you to understand why I feel no respect for the "design inference," and why it doesn't make it beyond the fantasy-believers of the DI and other creationist circles. It's evidently based on mythological beliefs, rather than on sound philosophical and scientific understanding.

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    24. No, Bill. You're not following. I probably chose too complicated an analogy for you.

      How about this one: Suppose someone claimed that ducks are cats, and when you asked for evidence to support their claim, they simply replied "Ducks." Would that be a meaningful response? Well, that's the same sort of response you gave to Ed.

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    25. "Your response is as if someone claimed the Great Pyramids of Giza were built by space aliens, and when you asked them for evidence, they replied, "The Great Pyramids of Giza." "

      This is very poor. It is more like someone recognizing that the pyramids were deliberately built, and having some idiot claim that they are the result of natural processes.

      Only one of them is called the Great Pyramid.

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    26. Photo
      "It gets worse than just that, but I'm just trying to get you to understand why I feel no respect for the "design inference," and why it doesn't make it beyond the fantasy-believers of the DI and other creationist circles. It's evidently based on mythological beliefs, rather than on sound philosophical and scientific understanding."

      I think the design inference is a reasonable argument. If you are a card carrying atheist I understand the resistance.

      I think your point is right that it is limited but non the less their is lots of evidence of parts arranged to perform a function and this evidence starts form high level design like the respiratory system where removal of any part(heart, lung liver etc) causes the system to fail to the cycle in the cell that solves the problem of hypoxia where the removal of the beta catenin coding gene would cause the entire cell to shut down.

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    27. I think your point is right that it is limited but non the less their is lots of evidence of parts arranged to perform a function and this evidence starts form high level design like the respiratory system where removal of any part(heart, lung liver etc) causes the system to fail to the cycle in the cell that solves the problem of hypoxia where the removal of the beta catenin coding gene would cause the entire cell to shut down.

      So you think evolution must result in systems in which any part can be removed without affecting its function. Why would you think that?

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    28. If you are really curious about a naturalistic evolution of electron transport, I suggest that you look at the book The Vital Question by Nick Lane. He describes a scenario where the "ETC" got its start near the origin of life via the natural concentration gradient of protons that exists between relatively acidic sea water and the alkaline effluent from alkaline vents. I wont go into details here, except to say that modern cells use the ETC to build a proton gradient, and use that to provide a means to make ATP. But early life would have the proton gradient provided for them in this environment. Life could have started at alkaline vents, and then evolved things like an ETC to be independent of the limiting environment that are the vents.
      So IF you are curious, go look. The 'ETC' does not seem irreducibly complex. Your god is not there.

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    29. Bill,

      so because "There are many blind processes(without foresight) in evolutionary theory." thus ID? Which is the same thing you keep on claiming: "evolution can't do this, thus goddidit."

      So you claim foresight was needed, which actually means for example bacteria have all genes in their genome to beat *every* *single* antibiotic man can ever make. Thus if ID were true, scientists only have to check the bacterial genome to devise antibiotics for which bacteria cant create a defense.
      So how come those fellows @ DI are wasting their time attacking evolution, while instead they could rid the planet of deadly bacteria and disease?
      According to you it's already there in the bacterial genome.

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    30. “But early life would have the proton gradient provided for them in this environment. Life could have started at alkaline vents, and then evolved things like an ETC to be independent of the limiting environment that are the vents.”

      Right.

      ”This essential process depends in turn on ion-pumping proteins that generate these gradients. But this creates a chicken-and-egg problem: cells store energy by means of proteins that make ion gradients, but it takes energy to make the proteins in the first place.”
      http://www.nature.com/news/how-life-emerged-from-deep-sea-rocks-1.12109

      But chicken and egg problems are never really problems.

      ”Lane and Martin think that proto-cells escaped this dilemma because they evolved a sodium-proton antiporter — a simple protein that uses the influx of protons to pump sodium ions out of the cell.”

      So, there you are. See, back then, there was a niche to be filled around the alkaline vents. And things weren’t so formal for proto-cells. Proteins didn’t need to be synthesized. They could just evolve, and then liberate the protos from the stuffy confines of the vents.

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    31. Ed
      Ed
      "
      so because "There are many blind processes(without foresight) in evolutionary theory." thus ID? Which is the same thing you keep on claiming: "evolution can't do this, thus goddidit.""

      God did it is not the design argument.

      The design argument is simply observing evidence for design.

      The DI is a political organization and so is the NCSE. I realize that ID is in many ways a political football but so is evolution as it is currently taught.

      The question is, is there any value in pieces of each of the arguments. I see value in both and limitations in both.

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    32. Bill,

      "Design: The purposefully [sic] arrangement of parts that perform a function."

      If you want to define design in this way, you will have to prove all such arrangements are "purposeful". But first define exactly what you mean by "purposeful".

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    33. Bill Cole said: "I think the design inference is a reasonable argument. If you are a card carrying atheist I understand the resistance."

      But then said: "God did it is not the design argument."

      Hey Bill, who do you think you're fooling, besides yourself?

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    34. The design argument is simply observing evidence for design.

      It is observing *what appears to you* to be evidence. But is it evidence? We see complexity and purposeful-appearing arrangement all around us in Nature even apart from life. Could humans have arranged the orbits of planetary systems to be stable for billions of years without correction (leaving aside our Solar System, since people have said Goddidit about that, too)? But there they are, just stars, balls of rock, and gravity all throughout the observable universe - from every indication, billions and billions of them. You gonna say God hung every last one of those in their positions, even the ones whose presence we're completely unaware of in galaxies billions of light-years away? Or can immense complexity and purposeful-seeming arrangement of parts in fact be accomplished without the intervention of a universal designer/deity?

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    35. tx -

      Thanks for reading or at least scanning through those papers or at least the article about them. What you choose to think about what's said there is up to you. Many scientists disagree with at least some of what's said there. But at least you're informing yourself a bit, even if it's with the attitude that you'll find the stuff you want to criticize.

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    36. Hey Bill,
      you skipped past this bit:
      "So you claim foresight was needed, which actually means for example bacteria have all genes in their genome to beat *every* *single* antibiotic man can ever make. Thus if ID were true, scientists only have to check the bacterial genome to devise antibiotics for which bacteria cant create a defense.

      You claim foresight, like claim many things. If every possible antibiotic man can create is already known by foresight in the bacterial genome, please explain why we aren't finding these sequences? Furthermore, please explain why many antibiotics seem to work fine, in fact are capable of killing bacterial infections, when the bacteria already have a defense against these antibiotics?

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    37. Cole wrote: "The existence of the purposeful arrangement of parts for a function is evidence of design."

      That depends on the purpose. Evolution by natural selection is quite capable of producing a system whose function has a purpose which seems to be enhancing the fitness of the organism containing that system. What WOULD BE evidence of design would be a system with some other purpose.
      For example, if horses were born with stirrups, that would suggest that they exist for the purpose of permitting human riders. Natural selection cannot easily generate this kind of function. The discovery of systems like this which provide a non-reciprocated benefit to something other than their host organism would be strong evidence of design.

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    38. Careful there. There are people out there who are convinced God made animals out of meat so humans could eat them.

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    39. "Natural selection cannot easily generate this kind of function. The discovery of systems like this which provide a non-reciprocated benefit to something other than their host organism would be strong evidence of design."

      Why not non-reciprocated detriment?

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  2. The origin of this is what I am claiming is a big step.

    http://www.nick-lane.net/LAM%20BioEssays.pdf

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  3. I just realized that I don't have a post devoted to the evolution of the citric acid cycle. This need to be remedied since I often talk about it. It's a good example of how an apparently irreducibly complex pathway can arise by evolution. It's also a good example to get students to think outside of the box. Undergraduate biochemistry courses usually concentrate on human physiology and too often students transfer that bias to all other species. They assume that what happens in humans is what happens in plants, fungi, protozoa, and bacteria.1

    Well Larry your speculation has reached another level of nonsense, but that is nothing new when your faith stretches out the logic beyond the breaking point.

    You obviously assume that the cell membrane had already evolved somehow and engulfs all the cell machinery needed for your speculation to even begin. And then your unproven speculation begins with no scientific proof whatsoever. It's pretty much blah, blah, blah and there you go.

    Can anyone imagine what would Larry do to an ID proponent if he even dared to present his argument the way Larry just did?

    I gotta admit I was a bit disappointed when I found out that there is no hell. Well to a degree. But I think some deserve to be in it for at least a few minutes...

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    1. "I gotta admit I was a bit disappointed when I found out that there is no hell. Well to a degree. But I think some deserve to be in it for at least a few minutes..."

      And now we know who among us would feel at home as a member of the inquisition.

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    2. "You obviously assume that the cell membrane had already evolved somehow and engulfs all the cell machinery needed for your speculation to even begin"

      I know it's useless to explain things to you, but here it goes, in order to understand something, we all, all of us, have to assume a background before jumping into explanations.

      For example, if I want to know where humans originated, it does not help considering the question of the origin of life. We have to start with the closer-to-home evidence. We get to our relationship with other apes, lots of evidence in that respect, even more evidence is gathered, the explanation works. OK then, we have a relationship with the rest of the apes.

      Once that's established, it doesn't just disappear because someone then asks, oh, but you haven't even established where apes come from! It is therefore false that we share common ancestry with the rest of the apes! Muahahahaha! Well, no. We have established that relationship beyond reasonable doubt. Asking for the next question won't invalidate the already obtained answer. It's a new question. All right to ask it, all right to try and work on answering it, but, again, that doesn't invalidate what we already have.

      So there we go, we work, we discover that apes are related to other primates, and that it seems like primates is the larger group. Lots of evidence, we also find that the common ancestor seems much more like a monkey than like an ape. Good! But here comes that idiot again, no! muahahahaha, you haven't explained where primates came from, therefore all you did is false! Muahahahaha! Again, no, that's not how it works. We can only work one problem at a time ...

      But creationists are like the idiot in my scenario (which is not imaginary, I have had those "answers" from creationists). They want every detail in the history of life, from the very beginning of life, or from the very beginning of the universe if pushed, and they think that if we cannot give them the whole thing, then we're not even related to the rest of the apes. Ridiculous? yes. I know. Yet, that's exactly how they think.

      So, sure, membranes assumed. Big sin. Therefore everything Larry said must be false. Muahahahahahaha!

      Delete
    3. In fact membranes have not been assumed in several of the published articles. For example, the Nick Lane essay I linked to above has an excellent discussion of issues around formation of the first membranes.

      Delete
  4. @Don and Bill,

    We cannot always ascertain what's true, but we can establish what's false.

    IC, creation-science, most biblical claims regarding genesis, young-Earth, and the foolish idea that the Discovery Institute is a scientific organization have all been FALSIFIED.

    On the other hand, Alternative Facts are the new paradigm amongst the scientific illiterate...no evidence required!!!

    ReplyDelete
    Replies
    1. Terminus Est,

      "IC, creation-science, most biblical claims regarding genesis, young-Earth, and the foolish idea that the Discovery Institute is a scientific organization have all been FALSIFIED."

      No, they have not. Not by any stretch. You're just repeating what you've read, and don't have the capacity to analyze.

      Did you notice the underwhelming response from your fellow storm troopers to your question about how enzymes evolved? Wasn't that thrilling?

      I don't see how you can look the kids you are corrupting in the eyes and not feel sick.

      Delete
    2. "We cannot always ascertain what's true, but we can establish what's false."

      I used to think the "arguments" put forth by the anti-vaccination groups locally (and everywhere) marked those people as the leaders in scientific ignorance and intentional dishonesty. The creationists here take those two characteristics to much higher levels.

      Delete
    3. txpiper,

      Do ya wanna know what's thrilling? Watching young adults use their brains, some for the first time after growing up in their parent's cult, and analyze scientific evidence for themselves (that's not corruption). You do seem irked that your religious ideas don't have the power they once had, over the minds of young people - I guess you could say that we've "drained the swamp" of irrational woo in our public schools.

      But, let's play in your ballpark for a change...if creation-science is correct (now that thought makes me feel sick), and god created Adam and Eve, who in turn gave rise to Cain and Abel (Cain then killed Abel, presumably before Abel could reproduce), how can we/you verify this? Were you there? Does the current variation within the human population support such a recent timeline or small founding population?

      Nevermind, my real question is...with whom did Cain have sex with in order to populate the Earth? Did he impregnate his mother? Did god perform another miracle...after all, they're pretty convenient plot devices, eh?

      I don't see how someone - you appear to have a capable mind; on the surface I can see evidence of some higher education - can read the bible, use it as THE official science textbook and not feel stupid.

      Delete
    4. Terminus Est,

      “Nevermind, my real question is...with whom did Cain have sex with in order to populate the Earth?”

      A sister, but it was Seth. Cain’s descendants were wiped out.
      -
      “I don't see how someone…can read the bible, use it as THE official science textbook and not feel stupid.”

      Genesis is a record (actually a collection of individual records), not a science textbook. There is a technical reason for why you would feel stupid.

      Delete
    5. Genesis is a record (actually a collection of individual records), not a science textbook.

      Yet it enables one to know more geology than a couple of centuries of geologists, more biology than a century and a half of biologists, more nuclear physics than a century of physicists.... How very convenient.

      Delete
    6. A sister, but it was Seth.

      Sorry, but even if that event, so extremely significant but never mentioned for some reason, would have taken place, it is hard to see that sort of inbreeding leading to success of a species. With real biology and evolution you have breeding populations, and you don't run into this sort of elementary, fundamental problem unless the breeding population gets very small. When people are attempting to rescue endangered species with captive breeding programs, for example, these sorts of things require very close attention.

      Delete
    7. Ahhh...now I understand (not really).

      After watching Gervais on Colbert, I'd like to pose another question:

      If a catastrophic event wiped out all humans, save for a small group of inquisitive adolescents boys and girls...all of whom were raised in a non-religious community (bear with me, please).

      If they were to re-populate the Earth, what sort of "books" would we see 2,000 years from now?

      I agree with Gervais...the science books would essentially be the same - cell theory, germ theory, gravity, atomic theory, quantum theory, biological evolution theory (based on population genetics), et. al.

      On the other hand, I find it hard to believe that Christianity, Islam, Judaism, etc., would exist in any form, whatsoever.

      What say you?

      Delete
  5. "It's a good example of how an apparently irreducibly complex pathway can arise by evolution."

    Not according to Michael Behe, he doesn't view this an example of Irreducible Complexity. That's an inadverdant Larry Moran strawman.

    "Unfortunately, the assertion that the TCA cycle is irreducibly complex is Robison's, not mine. In my book (p. 150-151) I clearly state that an A-->B-->C-->D metabolic pathway may have developed in a Darwinian fashion (although this has not been demonstrated rigorously.) I pointedly do not argue about things like the TCA cycle. I do, however, raise questions about the biosynthesis of purines because the end product, AMP, is needed for life and intermediates in the AMP pathway have not been demonstrated to occur in origin of life experiments." -- Michael Behe

    ReplyDelete
    Replies
    1. You are correct. Behe does not claim that the citric acid cycle is irreducibly complex.

      Behe's current definition of irreducible complex is restricted to systems that can't possibly have arisen by evolution (according to Michael Behe). As soon as evolutionary biologists come up with a plausible explanation the system is no longer irreducibly complex.

      It's a classic god of the gaps strategy.

      Delete
    2. "I do, however, raise questions about the biosynthesis of purines because the end product, AMP, is needed for life and intermediates in the AMP pathway have not been demonstrated to occur in origin of life experiments"

      Yes. Clearly a god-of-the-gaps argument.

      Delete
    3. AFAIK, Behe has never publicly acknowledged this, but it is clear that his shifting definition of IC reflects his awareness of its failure as an argument for ID creationism. He had originally hoped that by identifying biological systems that are ID he had devised an argument by which it could be demonstrated these systems could be shown not to have evolved simply by their physical characteristics, without having to refute any putative pathways by which they may have evolved. However, once that argument fell apart when it was demonstrated that versions of the flagellum and the clotting cascade exist that are functional despite missing key components, he was forced to fall back on "god of the gaps" arguments.

      You have to wonder why he even bothered since his target audience, people like txppiper, Bill Cole and Don Quixote, will cheerfully swallow any argument he coughs up, without even bothering to assess whether it is sound.

      Delete
    4. Correction:

      "...by identifying biological systems that are ID..."

      Should read "IC" at the end.

      Delete
    5. As soon as evolutionary biologists come up with a plausible explanation the system is no longer irreducibly complex.

      That didn't happen in Dover, much to the benefit of the attorneys cross examining him and the plaintiffs they were representing. Behe hung on to his irreducible complexity argument like grim death even after it had been demonstrated that a veritable mountain of books and papers showed alternate, shorter, functional biological mechanisms existed than those he asserted were irreducibly complex. He was reduced to claiming that no amount of scientific evidence and proof could ever change his mind, which didn't do much for his credibility as an expert witness for the proposition that ID is scientific.

      Delete
    6. "You are correct. Behe does not claim that the citric acid cycle is irreducibly complex."

      Well I had to dig the Behe quote up because you did argue your point very well that elements Citric Acid Cycle do exist in isolation such as in bacteria. It was obvious, at this time the IC argument looked pretty indefensible, especially in light of what you wrote. For that reason, alone I'm just might buy your textbook.

      I'm currently working through Lehninger's textbook. They cover the citric acid cycle a few hundred pages later than your book does.

      Thanks for your response.

      Delete
    7. Behe argues against evolution by means of blind and mindless processes producing IC and it isn't enough to come up with a plausible pathway.

      Suggest you read his sworn in-court testimony on the subject. It's got nothing about "blind and mindless processes." What it's got is pretty much the definition Dr. Moran gave in his original post. So Dr. Behe apparently disagrees with you.

      Delete
    8. And yet, on another post on this very page, you quote directly the following definition from No Free Lunch:

      A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system’s basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.

      No mention of "blind and mindless" there.

      This is one of the problems with IDiots: Their thinking is so sloppy and so divorced from any empirical base that they are unable to define any of their core concepts in a consistent and coherent manner.

      Delete
  6. Larry
    "Behe's current definition of irreducible complex is restricted to systems that can't possibly have arisen by evolution (according to Michael Behe). As soon as evolutionary biologists come up with a plausible explanation the system is no longer irreducibly complex.

    It's a classic god of the gaps strategy."

    It's a gaps argument or strategy if that was his argument. It is not. The evolutionary biologist has to show that an irreducible complex system can operate to its specific function without all of its parts. You can claim that this is an argument against Neo Darwinism and not modern evolutionary theory but can modern evolutionary theory challenge Behe's claim? Beyond Behe's claim how does modern evolutionary theory explain how the DNA sequences of these complex machines form without making a design inference.

    ReplyDelete
    Replies
    1. The evolutionary biologist has to show that an irreducible complex system can operate to its specific function without all of its parts.

      Please support the position that this is a requirement of evolutionary theory, as opposed to the straw man version of evolution used by you and your fellow ID creationists.

      Evolutionary biologists already predicted that IC systems would result from evolutionary processes before Behe was even born. But you already know that. Why are you pretending you don't?

      Delete
    2. LS
      " Please support the position that this is a requirement of evolutionary theory, as opposed to the straw man version of evolution used by you and your fellow ID creationists."

      The hope of modern evolutionary theory is that functional space is almost equal to sequence space. With 30 proteins needing to fit together is shape and charge and perform a complex function this claim is a big stretch. While modern evolutionary theory helps explain how the large quantity of mutations observed get fixed it does not help explain how mutations find functional sequence space.

      "Evolutionary biologists already predicted that IC systems would result from evolutionary processes before Behe was even born. But you already know that. Why are you pretending you don't?"

      I do understand this prediction but it has come into question because of the discovery of DNA and the vast complexity of the cell. The Royal Society meeting was about the uncertainty of proposed evolutionary mechanisms explaining the diversity of life. The design argument is still on the outside looking in because of its philosophical implications but in its limits it does explain what we are observing.

      Delete
    3. The hope of modern evolutionary theory is that functional space is almost equal to sequence space.

      Please support this claim. Which evolutionary biologist hopes this is the case? Why is it a requirement for evolution to work?

      I do understand this prediction but it has come into question because of the discovery of DNA and the vast complexity of the cell.

      How so? You seem to be moving goal posts from the original "irreducible complexity" argument, BTW. Don't think no one has noticed.

      The Royal Society meeting was about the uncertainty of proposed evolutionary mechanisms explaining the diversity of life.

      No, it was about a bunch of people who don't understand evolutionary theory trying to explain problems that only seem to exist to them because of this lack of understanding. You are well aware of this, since Larry has written extensively on the subject. If you want to engage in a productive discussion, you'd best stop lying.


      The design argument is still on the outside looking in because of its philosophical implications but in its limits it does explain what we are observing.

      No, it's on the outside because it does not even try to produce scientific research to support its beliefs. It can only produce amateurish apologetics, of the sort you are producing here.


      Delete
    4. The same type of research that shows that the "blind and mindless process" known as gravity causes rocks to fall to the ground. You don't get to propose the existence of some form of intelligence guiding physical processes without positive evidence to support this. It's not a position that's true by default. You IDiots have such a hard time grasping this simple concept.

      Delete
    5. LS
      "
      No, it was about a bunch of people who don't understand evolutionary theory trying to explain problems that only seem to exist to them because of this lack of understanding. You are well aware of this, since Larry has written extensively on the subject. If you want to engage in a productive discussion, you'd best stop lying."

      So we have a group of well educated evolutionary biologists and they don't understand the theory?

      Sounds like the theory does not exist.

      Delete
    6. So we have a group of well educated evolutionary biologists and they don't understand the theory?

      How well they have been educated is an open question. I'll leave it to Larry to comment on that further.

      Sounds like the theory does not exist.

      That conclusion does not follow from the fact that a small group of people (many of whom are not biologists) do not understand the theory.

      Could you kindly point me to the textbook where the theory of Intelligent Design is clearly summarized? I would like to learn the details of the process by which proponents of the theory believe e.g. the bacterial flagellum arose. TIA.

      Delete
    7. LS
      "That conclusion does not follow from the fact that a small group of people (many of whom are not biologists) do not understand the theory."

      Can you clearly state the theory in its current form?

      Delete
    8. I suggest reading Doug Futuyma's textbook. Either one. There is no such thing as "the theory". Evolutionary theory is a bundle of complementary theories, all of them well-tested. Reading Futuyma should help repair your personal ignorance. Come to think of it, some of those molecular biologists ought to read Futuyma too.

      Delete
    9. John
      "I suggest reading Doug Futuyma's textbook. Either one. There is no such thing as "the theory". Evolutionary theory is a bundle of complementary theories, "

      Can you clearly state the theories that make up the basket of evolutionary theory?

      Delete
    10. Can you clearly state the theories that make up the basket of evolutionary theory?

      I could, but it would take longer than I'm willing to waste on you. Read Futuyma instead. It's an undergraduate text, so you might even understand it if you're willing to understand at all.

      Delete
    11. So there you go, Bill. Futuyama. There you will find a good description of evolutionary theory.

      So, could you answer my question? Which book(s) provide a similar explanation of the theory of Intelligent Design, including a detailed explanatory framework of the process by which something like the bacterial flagellum was "designed"?

      Delete
    12. John
      "I could, but it would take longer than I'm willing to waste on you. Read Futuyma instead. It's an undergraduate text, so you might even understand it if you're willing to understand at all."

      Amazing that you are not able to simply articulate the theories without wasting a lot of time. Sorry you are taking this position.

      Delete
    13. ”There cannot be evolution without genetic variation in the first place. So there must be mutation and often recombination to generate the different genotypes or the different versions of the genes, known as alleles, which then may or may not make a difference in the ability of an organism to survive and reproduce. You can’t have any evolutionary change whatever without mutation, and perhaps recombination, giving rise to genetic variation. But once you have genetic variation, there are basically two major possibilities…”
      http://www.actionbioscience.org/evolution/futuyma.html

      Having saluted DNA replication errors, Futuyama goes on to talk about drift and selection. Miraculous accidents taken for granted. Standard flyover.

      Delete
    14. Amazing that you are not able to simply articulate the theories without wasting a lot of time. Sorry you are taking this position.

      You misunderstand. John did not say he is unable to do so. He said doing so for your benefit, specifically, would be a waste of time.

      We've been waiting 20 years for someone, anyone, to articulate a theory of "Intelligent Design," in any form whatsoever. By your refusal to answer my question, it is clear we have to keep on waiting.

      Delete
    15. Miraculous accidents taken for granted.

      Not at all, on a couple of levels.

      - First, if you correctly understood probability math, you would learn that these "accidents" are nowhere near miraculous. They are as mathematically unremarkable as the fact that someone will win the Powerball jackpot in the next few weeks, then someone else a few weeks later, and so on, absolutely unremarkably, despite the odds against that being nearly 300 million to 1.

      - Second, these "accidents" are not nearly taken for granted. Which kinds of "accidents" are relatively common, and which are relatively rare, have been studied intensively in good careful scientific work that has been ongoing for decades. (And for which many results have been published that are available to the public, including you.)

      So the "accidents" are neither miraculous nor taken for granted. It's wonderful and awe-inspiring and fascinating, but it is also just the way life on earth works.

      Delete
    16. Can you clearly state the theories that make up the basket of evolutionary theory?

      In the spirit of Rabbi Hillel and his response to the skeptic who asked Hillel to explain the entire Torah to him while he stood on one foot (it is a wonderful story from the Talmud, Bill - do you know it?), I offer the following:

      Chance and necessity. Now go and learn it.

      Delete
    17. txpiper,

      "Miraculous accidents taken for granted. Standard flyover."

      What exactly is miraculous about mutations? Do you think that mutations have to be produced by some magical beings? Do you think that replication errors, for example, just don't happen?

      Delete
    18. To be quite fair, he may have been referring to mutations that turn out to be advantageous, which are rare. On the other hand, the fact that more mutations are disadvantageous than advantageous doesn't say a lot for the presence of an almighty Designer, does it?

      Delete
    19. “What exactly is miraculous about mutations?”

      Oh, gosh. Mutations can do absolutely anything! They can move reptile jawbones towards the inner ear, and turn them into ossicles so mammals can hear better. How about that?! They can even build two ten-layer collections of interconnected brain cells, position them in the back of your eyeballs, and wire them to a neural transduction center so that you have stereoscopic vision to read Doug Futuyama’s tributes to selection and drift! You name it, and mutations can do it. Why, you'd have to be completely stupid to not recognize the awesome authority of DNA replication errors.

      Delete
    20. txpiper says,

      Why, you'd have to be completely stupid to not recognize the awesome authority of DNA replication errors.

      Speaking of stupid, I'm usually quite tolerant of stupid people who post comments on Sandwalk but you are testing my patience.

      If can't make an intelligent contribution to the discussion then please don't make any contribution at all.

      I urge all commenters to respect this simple rule. That includes those who feel the need to reply to trolls.

      Delete
    21. Larry,

      Perhaps it would be a good exercise to let the theory touch the phenotypical ground every once in a while. I listed two out of billions of things. It is not my fault if they are awkward.

      Delete
    22. LS
      "here is no such thing as "the theory". Evolutionary theory is a bundle of complementary theories, all of them well-tested. "

      Do you agree with this statement that there is no "theory of evolution" ?

      Delete
    23. That's not what he said in that quote. Are you: a) too stupid to understand it, b) too dishonest to accurately represent it, or c) both?

      Should your failure to cite a description of the theory of "Intelligent Design" be taken as confirmation that there is no such theory?

      Delete
    24. LS
      That's not what he said in that quote. Are you: a) too stupid to understand it, b) too dishonest to accurately represent it, or c) both?

      I directly copy and pasted from his post. So you don't agree with John?

      Delete
    25. LS
      "Should your failure to cite a description of the theory of "Intelligent Design" be taken as confirmation that there is no such theory?"

      Start with Behe's book Darwin's Black Box.

      Delete
    26. I directly copy and pasted from his post. So you don't agree with John?

      I agree with John. It's your misinterpretation/misrepresentation of his words with which I disagree.

      Start with Behe's book Darwin's Black Box.

      My understanding is that that book only provides misguided and fallacious attempts to refute evolutionary theory. It does not provide a comprehensive theory of Intelligent Design that explains the processes by which e.g. the bacterial flagellum arose, according to proponents of the belief. I would like independent verification that the book actually does contain such a theory before wasting my time reading it. I'm afraid your claim holds very little weight, since you have shown yourself to be prone to misunderstanding or misrepresenting even very simple statements, never mind an entire book.

      Delete
    27. Bill,


      Can you clearly state the theories that make up the basket of intelligent design theory?

      Delete
    28. @judmarc:

      First, if you correctly understood probability math, you would learn that these "accidents" are nowhere near miraculous. They are as mathematically unremarkable as the fact that someone will win the Powerball jackpot in the next few weeks, then someone else a few weeks later, and so on, absolutely unremarkably, despite the odds against that being nearly 300 million to 1.

      Ah, but you see, that's only if you use the old-fashioned atheist evolutionist math. There's a new and improved math now, called "Intelligent Design Creationist Jesus Math", an example of which is given above by Bill Cole, when he writes:

      The hope of modern evolutionary theory is that functional space is almost equal to sequence space.

      So, you see, it actually is a miracle when someone wins the Powerball lottery. According to ID creationist thinking, the number of winning combinations of numbers drawn ("functional space") must "almost equal" the number of possible combinations ("sequence space'). IOW, for anyone to win the lottery, there would have to be just short of 300 million numbers drawn. That people win when only a single number is drawn shows that the lottery is fixed (i.e. "intelligently designed"). Someone should call the cops!

      Delete
  7. When Bill Cole was asked to explain Intelligent Design Creationism he said,

    Start with Behe's book Darwin's Black Box.

    Okay. Let's start there. Here's a quotation from page 5. Do all Intelligent Design Creationsts adhere to this view?

    For the record, I have no reason to doubt that the universe is the billions of years old that the physicists say it is. Further, I find the idea of common descent (that all organisms share a common ancestor) fairly convincing. I greatly respect the work of my colleagues who study the development and behavior of organisms within an evolutionary framework, and I think that evolutionary biologists have contributed enormously to our understanding of the world.

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    Replies
    1. Do all Intelligent Design Creationists agree with what Michael Behe writes on page 227? Is this part of ID Theory?

      The irreducibly complex biochemical systems that I have discussed in this book did not have to be produced recently. It is entirely possible, based simply on an examination of the systems themselves, that they were designed billions of years ago and that they have been passed down to the present by the normal processes of cellular reproduction. Perhaps a speculative scenario will illustrate the point. Suppose that nearly four billion years ago the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not "turned on." In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.) Additionally. suppose the designer placed into the cell some other systems for which we cannot adduce enough evidence to conclude design. The cell containing the designed systems then was left on autopilot to reproduce, mutate, eat and be eaten, bump against rocks, and suffer all the vagaries of life on earth. During this process, pace Ken Miller, pseudogenes might occasionally arise and a complex organ might become nonfunctional.

      Delete
    2. Hi, Larry. Bill Cole says that Behe's book contains a detailed explication of the theory of Intelligent Design, including explanations of the process by which "irreducibly complex" systems like the bacterial flagellum were "designed" and descriptions of the "design" process. Since you are obviously familiar with the book, could you provide a reference to the exact pages where this discussion takes place? Also, if it's not too much to ask, could you list some of the other ID textbooks that contain similar discussions? I'm sure the books by Douglas Axe, Stephen Meyer, Jonathan Wells, Wm. Dembski, etc also have explanations of who or what this "designer" is and the mechanisms by which this "designer" operates. Otherwise, we'd have to conclude that there is actually no such thing as a theory of ID, which would be absurd given the amount of time and energy some people are expending to try get this theory taught in schools and universities.

      TIA.

      Delete
    3. There is no ID textbook, unless you want to count Pandas & People.

      Maybe that was your point? ;-)

      Delete
    4. "Do all Intelligent Design Creationsts adhere to this view?"

      Drawing a distinction between ID proponents and creationists, I am the latter and do not adhere to Behe's views.

      Delete
    5. Maybe that was your point? ;-)

      I'm just giving the ID proponents the opportunity to make the point for themselves. Whatever point that might be. :)

      Delete
    6. Perhaps a speculative scenario will illustrate the point. Suppose that nearly four billion years ago the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not "turned on." In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.)

      If this is the case, how can the nearest descendants of the first cells, our ancestors (since Behe agrees that common ancestry is correct) have fewer "designs that are not turned on" (less "junk" DNA) than their descendants do?

      Delete
    7. Oh, and "junk" doesn't really matter either (even though Behe, when talking about pseudogenes, apparently allows for it?). Our genomes are just a heck of a lot bigger than the ancestors who were supposed to be "front loaded" with all the stuff necessary to come up with us.

      Delete
    8. An interesting thing is that Behe's fellow IDiots do not excoriate him for accepting the existence of junk DNA, as they do when evolutionary biologist mention it. I have a hard time understanding this. If someone denies the existence of junk DNA, Larry is as hard on them regardless of whether they are evolutionist or creationist. It seems creationists base their "scientific" criticism on the person's religious beliefs, as opposed to whether a claim is scientifically valid.

      Delete
    9. Larry
      I believe Behe is right that the design argument is independent of common descent. I also agree with him that it is independent of the junk DNA discussion.

      The design argument does not explain how the design was implemented. It simply assigns intelligent cause to certain observations in nature.

      Delete
    10. The design argument does not explain how the design was implemented. It simply assigns intelligent cause to certain observations in nature.

      On what basis does it do so? Exactly what is an "argument", in your view, and was is its epistemological status as compared to a scientific theory, such as evolution, which provides detailed and specific explanations for phenomena, explanations which are supported by an enormous amount of empirical evidence?

      Here's how it appears to me: If we see a tiger, you might have an "argument" that it is actually a zebra, on the basis that zebras have stripes and the tiger also has stripes. However, I would respond by pointing out the many morphological differences between tigers and zebras that demonstrate that the former belongs to the cat family. And I would even be able to support this with molecular genetic evidence showing that the tiger is more closely related to other cats than to a zebra.

      Your response to this, if you are true to form, would be to say that physical morphology and molecular genetics are "not part of the 'tigers are zebras' argument" and that "It seems more plausible to me that tigers are zebras."

      Personally, I would not find that argument particularly persuasive. Why do you think I should?

      Delete
    11. I will also add, Bill Cole, that (true to form) you did not answer Larry's question. He did not ask your personal opinion. He asked if the consensus of ID creationists agrees with Behe's claims i.e. whether Behe's claims are reflective of the theory of Intelligent Design.

      Delete
    12. Bill,

      "I believe Behe is right that the design argument is independent of common descent. I also agree with him that it is independent of the junk DNA discussion."

      How could ID be independent of common descent? Either life forms are descended from other life forms or they aren't. What does ID claim, and why?

      How could ID be independent of the junk DNA discussion? To the extent that there is junk DNA, the intelligent designer would had to have consciously put it there, right?

      Delete
    13. Bill doesn't seem to realize the admission he is making by saying ID Creationism is "independent" of those observations. The strength of a scientific theory is based on the number and specificity of the observations it can predict and explain. The seeming paradox is that the fact that ID Creationism is not affected by observations regarding the age of the earth or the existence of junk DNA demonstrates its weakness as a scientific hypothesis (assuming it is even a hypothesis in the first place.)

      Evolutionary theory, OTOH, would be very difficult, if not impossible, to reconcile with a 6000 yr old earth. And the discovery of junk DNA is part of the evidence that forced the modification of evolutionary theory to include neutral theory.

      Wheras, if Bill is to be believed (and why wouldn't he be?) ID Creationism is unaffected by whether common descent exists or not, whether junk DNA exists or not, whether the earth is over 4 billion years old or less than 10,000.

      That doesn't show a "theory" that is robust. It shows one whose explanatory and predictive power is zilch.

      Delete
    14. LS
      "Bill doesn't seem to realize the admission he is making by saying ID Creationism is "independent" of those observations. The strength of a scientific theory is based on the number and specificity of the observations it can predict and explain. The seeming paradox is that the fact that ID Creationism is not affected by observations regarding the age of the earth or the existence of junk DNA demonstrates its weakness as a scientific hypothesis (assuming it is even a hypothesis in the first place.)"

      ID is an inference argument. So is universal common descent. They are both claims that have yet to be fully tested. If LUCA turned out to be a super cell with all information required for the diversity of life packed in it, then as Behe says they could both possible be true.

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    15. ID is an inference argument. So is universal common descent. They are both claims that have yet to be fully tested.

      This is your ignorance of science talking again. All science is inference. Inference from data is how claims are tested. Is it necessary to link to Theobald 2010 again?

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    16. ID is an inference argument. So is universal common descent. They are both claims that have yet to be fully tested.

      Why do you keep repeating this lie, Bill Cole? In addition to Theobald, explain how this is not a test of common descent:

      http://www.evolutionarymodel.com/ervs.htm

      There are many other examples.

      OTOH, why has "design" not been tested yet? The Discovery Institute has received millions of dollars over the past 20 years. What have they been doing with all that money?

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    17. LS
      "Why do you keep repeating this lie, Bill Cole? In addition to Theobald, explain how this is not a test of common descent:"

      It is a collection of evidence. The testing of it is a lot more complicated. The strongest evidence is non functional genes being present in multiple species. Non function is however a hypothesis that is not fully tested.

      Design is actually easier to test then universal common descent. Design you have to show one example for UCD you have to show how several of transitions occurred.

      Humans are reliable at picking out functional designs. There is an argument that we can test design through observation.

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    18. John
      From introduction to the scientific method:

      "II. Testing hypotheses

      As just stated, experimental tests may lead either to the confirmation of the hypothesis, or to the ruling out of the hypothesis. The scientific method requires that an hypothesis be ruled out or modified if its predictions are clearly and repeatedly incompatible with experimental tests. Further, no matter how elegant a theory is, its predictions must agree with experimental results if we are to believe that it is a valid description of nature. In physics, as in every experimental science, "experiment is supreme" and experimental verification of hypothetical predictions is absolutely necessary. Experiments may test the theory directly (for example, the observation of a new particle) or may test for consequences derived from the theory using mathematics and logic (the rate of a radioactive decay process requiring the existence of the new particle). Note that the necessity of experiment also implies that a theory must be testable. Theories which cannot be tested, because, for instance, they have no observable ramifications (such as, a particle whose characteristics make it unobservable), do not qualify as scientific theories."

      Can you test common descent without observing a specie transition?

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    19. Sorry, Bill, but this is Sandwalk. It's not Uncommon Descent or some other blog run by intellectually deficient creationists. You can't just make up shit like this distinction between "collection of evidence" and "testing a hypothesis."

      It is possible to use genetic testing to determine whether whether a person is a parent to another parent, and this is considered reliable enough to be used in a court of law. Do you not think this qualifies as "testing"? If you do, please show how it differs from the type of testing that demonstrates common ancestry?

      Humans are reliable at picking out functional designs. There is an argument that we can test design through observation.

      By this standard of "testing" it has been proven that the sun orbits the earth, and not the other way around, because that is how it seems to humans. Is that how you suggest we "test" hypotheses, and no longer use the "collection of evidence"?

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    20. Experiments may test the theory directly (for example, the observation of a new particle) or may test for consequences derived from the theory using mathematics and logic (the rate of a radioactive decay process requiring the existence of the new particle).

      Way to go, Bill. You just shot down your own argument. And I bet you're too stupid to even realize that's what you've done.

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    21. Just bumping this so Bill doesn't lose track of the conversation.

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    22. Can you test common descent without observing a specie transition?

      First, I don't know how many times you've been told this, but "species" is the singular and plural both. "Specie" is money. A little point, but it annoys me.

      Second, yes, just as you can test all manner of things without observing them. Have you ever observed a carbon atom and seen its 6 protons? Have you seen Pluto make an orbit around the sun? Did you even read the examples provided in the bit you quoted? The only problem with the quote is that word "experiment". A better word would be "observations". An experiment is just an arrangement of conditions in order to make particular observations more likely. Repeated observations are the same thing, from the viewpoint of science, as repeated experiments. And a test of a hypothesis is just an examination of its compatibility with repeated observations.

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  8. LS
    "It is possible to use genetic testing to determine whether whether a person is a parent to another parent, and this is considered reliable enough to be used in a court of law. Do you not think this qualifies as "testing"? If you do, please show how it differs from the type of testing that demonstrates common ancestry? "

    This is reliable because we can observe common descent among humans. We can then generate a data set that when the DNA data is compared to it, we can have high confidence of paternity.

    We have not been able to observe common descent like this in nature except among like species. We can generate data but how do we know when a comparison is made that the two species share a common ancestor except as an a priori assumption based on Darwin's inference.

    Another problem with the common descent inference is that cells are designed to minimize variation. Evidence for this is DNA repair and apoptosis. To get the diversity we are observing through reproduction we would need lots of variation.

    From the design argument we know what human functional designs look like. This is the standard for which design in biology is compared. A human will rarely be fooled when comparing functional designs with non functional objects.

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    Replies
    1. "we know what human functional designs look like"

      We also know that complicatedness in human functional designs can be unraveled. With accidental designs, the deeper you dig, the more complexity you find.

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    2. This is reliable because we can observe common descent among humans.

      Ah, yes. The infamous creationist "species barrier." So, remind, when was the research done that finally identified the mysterious force that prevents mutations occurring that would cause a genome to move out of its "kind." Bonus points for identifying what these "kinds" are and how they are differentiated.

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    3. From the design argument we know what human functional designs look like.

      Yes. And it looks almost nothing like things that have arisen thru evolution. Can you identify the homologous genes shared by the internal combustion engine and a pair of scissors? Where is the phylogenetic classification, forming a nested hierarchy, of all the products of human design? Please provide the citation to this crucial piece of ID research. Obviously, this research must have been done. It's just too obvious a question not to be addressed.

      That's not to mention the fact that the "design argument" hasn't even attempted to identify the nature, origin, or mechanisms used by this mythical "designer" operates. You can stamp your feet and whine "That's not part of the argument" all you like. The goal of science is to elucidate and answer the questions raised by a hypothesis. Not just sweep them under the rug and hope they disappear.

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  9. That you SO much for these resources. I am banging my head on glycoslysis, the citric acid cycle the calvin cycle and the stoichiometry of the oxidative phosphorylisation that the NADH, ATP and NADPH energy provides. I can use all the help I get get.

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