Saturday, June 28, 2014

Fish Have a Toolbox and Several Other Findings

Aristotle Couldn’t Have Said it Better



Electric organs in fish have challenged evolution ever since Darwin and a new study published today peered even deeper into the problem, down to the genetic level. First let’s see what Darwin had to say (from the section entitled “Special Difficulties of the Theory of Natural Selection,” pages 150-1 of the Sixth Edition of the Origin of Species):

Although we must be extremely cautious in concluding that any organ could not have been produced by successive, small, transitional gradations, yet undoubtedly serious cases of difficulty occur.

Notice how Darwin has subtly shifted the burden of proof to those who aren’t so sure the species spontaneously arose. They must prove that an organ could not have evolved. And when evolutionists call for such proofs, they set the bar very high. Even vague speculation must somehow be falsified. Don’t believe me? Read on and see how Darwin defends his shifting of the burden of proof:

The electric organs of fishes offer another case of special difficulty; for it is impossible to conceive by what steps these wondrous organs have been produced. But this is not surprising, for we do not even know of what use they are. In the Gymnotus and Torpedo they no doubt serve as powerful means of defence, and perhaps for securing prey; yet in the Ray, as observed by Matteucci, an analogous organ in the tail manifests but little electricity, even when the animal is greatly irritated; so little, that it can hardly be of any use for the above purposes. Moreover, in the Ray, besides the organ just referred to, there is, as Dr. R. M'Donnell has shown, another organ near the head, not known to be electrical, but which appears to be the real homologue of the electric battery in the Torpedo. It is generally admitted that there exists between these organs and ordinary muscle a close analogy, in intimate structure, in the distribution of the nerves, and in the manner in which they are acted on by various reagents. It should, also, be especially observed that muscular contraction is accompanied by an electrical discharge; and, as Dr. Radcliffe insists, "in the electrical apparatus of the torpedo during rest, there would seem to be a charge in every respect like that which is met with in muscle and nerve during rest, and the discharge of the torpedo, instead of being peculiar, may be only another form of the discharge which attends upon the action of muscle and motor nerve." Beyond this we cannot at present go in the way of explanation; but as we know so little about the uses of these organs, and as we know nothing about the habits and structure of the progenitors of the existing electric fishes, it would be extremely bold to maintain that no serviceable transitions are possible by which these organs might have been gradually developed.

So we shouldn’t conclude that complex organs could not evolve because very little was understood about them. In other words, it is an argument from ignorance. We don’t understand them, therefore we can’t doubt that they could have evolved. Never mind that, beyond hand waving, Darwin had no idea how such organs could possibly have spontaneously arisen, let alone even how such organs worked or much of anything else about them.

But there was another problem. These electric organs appeared in a wide variety of fish, not following the expected common descent pattern:

These organs appear at first to offer another and far more serious difficulty; for they occur in about a dozen kinds of fish, of which several are widely remote in their affinities. When the same organ is found in several members of the same class, especially if in members having very different habits of life, we may generally attribute its presence to inheritance from a common ancestor; and its absence in some of the members to loss through disuse or natural selection. So that, if the electric organs had been inherited from some one ancient progenitor, we might have expected that all electric fishes would have been specially related to each other; but this is far from the case. Nor does geology at all lead to the belief that most fishes formerly possessed electric organs, which their modified descendants have now lost. 

Darwin argues the problem disappears because the electric organs in the different fish are not very similar, and so are not homologous (i.e., deriving from a common ancestor):

But when we look at the subject more closely, we find in the several fishes provided with electric organs, that these are situated in different parts of the body,—that they differ in construction, as in the arrangement of the plates, and, according to Pacini, in the process or means by which the electricity is excited—and lastly, in being supplied with nerves proceeding from different sources, and this is perhaps the most important of all the differences. Hence in the several fishes furnished with electric organs, these cannot be considered as homologous, but only as analogous in function. Consequently there is no reason to suppose that they have been inherited from a common progenitor; for had this been the case they would have closely resembled each other in all respects. Thus the difficulty of an organ, apparently the same, arising in several remotely allied species, disappears, leaving only the lesser yet still great difficulty; namely, by what graduated steps these organs have been developed in each separate group of fishes.

So to summarize Darwin argued that while he couldn’t provide an explanation for how these electric organs could have evolved, their evolution could not be disproven because we don’t know anything about them. And furthermore, the fact that the organs did not appear according to the common descent pattern was not a problem because they were not homologous and therefore arose independently rather than from a common ancestor.

Aside from the obvious fallacy in Darwin’s argument (lack of falsification means little and in any case Darwin had set the bar so high it was impossible anyway), he apparently was unaware that he had just shot himself in the foot. For his second argument, that the failure to fulfill a common descent pattern was not a problem because the organs arose independently, meant his first problem was that much more difficult. For now Darwin needed to explain not merely how an electric organ could have spontaneously arisen, but how this could have occurred many times over, in different ways. One miracle would not be enough.

Fast Forward

That was then and this is now. How have the past century and a half dealt with Darwin’s defense of the evolution of electric organs?

Not well.

One might think that given all this time, and the enormous mountain of data scientists have since gathered on electric organs in fish, that by now evolutionists would have a fairly detailed and convincing, step-by-step, explanation of how these incredible devices arose by themselves. How can evolution provide the capability for a fish to generate a 600 Volt pulse to stun its prey? How can evolution provide the capability for a fish passively to track tiny prey using an array of ultra sensitive electromagnetic sensors and neural processing?

Amazingly, for a theory that is supposed to be a fact beyond all reasonable doubt, held in question only by the lowly, the ignorant and the biased, there are no answers to these questions. Evolutionists still do not have detailed and convincing, step-by-step, explanation of how these incredible devices arose by themselves. In fact, beyond Darwin-like speculation, evolutionists do not have any explanation, period.

So Darwin’s first argument, that the theory is saved by our ignorance, no longer holds. We now understand these organs in far more detail than even Darwin could have imagined. And it hasn’t helped. We can no longer hide behind our ignorance.

Now, today’s study nullifies Darwin’s second argument. As we saw above, Darwin argued that the designs of the different electric organs were sufficiently different that they must have arisen independently, and so they would not form a common descent pattern.

But the new study, which peers deeper into the data, down to the genetic level, finds no such differences. As one report explained, the new study “provides evidence to support the idea that the six electric fish lineages, all of which evolved independently, used essentially the same genes and developmental and cellular pathways to make an electric organ.” Here is how one evolutionist described the first problem:

What is amazing is that the electric organ arose independently six times in the course of evolutionary history.

And as another evolutionist explained, “The surprising result of our study is that electric fish seem to use the same ‘genetic toolbox’ to build their electric organ,” despite the fact that they evolved independently.

A genetic toolbox? This is a common teleological phrase evolutionists use to refer to regulatory DNA. The idea that fish would use a genetic toolbox hides the absurdity of the evolutionary narrative. There is a reason why Aristotelianism persisted for almost two thousand years.

24 comments:

  1. When I heard this reported on the radio my first thought was to wonder how long it would be before it appeared here - et voila!.

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  2. Absurdity?

    But good ideas are good regardless of where they came from, right? Or perhaps you judge ideas according to their source?

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  3. Aristotelianism lives on today as a property of ID's designer. It's "Design" needs to be explained.

    For example, how did the designer know exactly what genes would result in the right proteins that would result in the electric origins of fish? Or did he simply will them into existence?

    If the latter, that would be the spontaneous creation of knowledge since fish build copies of themselves, including those very electric organs, using the instructions in their genes. And, according to Cornelius, spontaneous origins is absurd.

    So, it would seem that the designer is either itself complex entity, because it contains the knowledge of what genes would results in just the right proteins, which would result in just the right biological adaptations, or that same knowledge was spontaneously created.

    Which is it? Better yet, which option am I not considering?

    Anybody?

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  4. 1. Darwin hypothesized that electric organs in fish are due to convergent evolution, adapted from muscle.
    2. Scientists determine electric organs in fish are due to convergent evolution, and how they adapted from muscle.
    3. Mapou: This fully falsifies Darwinian evolution.

    Darwin falsified Darwin 150 years ago!

    -
    xposted from AtBC

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    1. Scientists determine electric organs in fish are due to convergent evolution, and how they adapted from muscle.
      Funny, I must have missed this world shaking proof.

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  5. Darwin: Hence in the several fishes furnished with electric organs, these cannot be considered as homologous, but only as analogous in function.

    As Darwin was aware, muscular neurons are homologous, even if they are in different anatomical structures. Anatomic structures don't become homologous just because the cellular structures are.

    Darwin: It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation.

    And this basic rule still applies.

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    1. Good ideas, including electric organs, are good regardless of their source. Evolution converges on them because they are good ideas. They solve problems.

      This is in contrast to assumption that ideas have to come from an authoritative source.

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    2. You guys are freaking morons. This is scary.

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  6. Thanks Dr. H.
    Many good points:
    1) Darwin shifts the burden of proof to those who do not accept his theory: "Prove to me there are not 100 blue faeries hovering somewhere above the South Pacific Ocean; and if you can't prove it, then you are either uneducated (don't understand the theory) or you are a creationist."
    2) when the only argument for evolution of highly complex electric organs with no common ancestor is that they MUST have evolved independently six times without small incremental changes, it really is past time to consider a new explanation for their existence.
    3) the concept of a "genetic toolbox" is a teleological argument employed to keep a explicitly non-teleological theory from sinking; kind of like trying to keep the Titanic afloat with those little plastic armbands kids wear in swimming pools.

    I even appreciate Scott's willingness to help prove your point about teleological arguments: Scott wrote: "Good ideas, including electric organs, are good regardless of their source. Evolution converges on them because they are good ideas. They solve problems." Thanks Scott.

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    1. One wonders what it would take to falsify the theory.

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    2. Marcus One wonders what it would take to falsify the theory.

      You're all highly knowledgeable about science in general and evolution in particular, CH especially. What would you look for as a falsification?

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    3. Ian:

      Falsification of evolution is tricky. Darwin presented a criterion ("If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.") but it wasn't a very good one because it is so difficult. How can one prove a universal negative dealing with a theory that is so flexible? Indeed the passage in which that criterion appears is a good demonstration of that flexibility.

      To this day there are myriad biological structures for which we do not know how they evolved, and we have no detailed description of a series of numerous, successive, slight modifications, leading to the structure. But such ignorance does no harm to evolution.

      Behe's work is a good example. For instance, he took the example of protein-protein binding surfaces and showed how traditional evolution does not have the resources to evolve them. But again, no harm.

      It seems Darwin's criterion is either too difficult to demonstrate, or if one does demonstrate it, we just set it aside, assuming that a solution will come some day. One way or another, the theory is protected.

      continued ...

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    4. Ian:

      Darwin presented another criterion, regarding utilitarianism which was at the foundation of evolution:

      "The foregoing remarks lead me to say a few words on the protest lately made by some naturalists, against the utilitarian doctrine that every detail of structure has been produced for the good of its possessor. They believe that very many structures have been created for beauty in the eyes of man, or for mere variety. This doctrine, if true, would be absolutely fatal to my theory. "

      This criterion reveals some of the underlying metaphysics. But the criterion is not very good because it is not scientific (something Darwin later mentions).

      Popper criticized evolution for not being falsifiable at one point, and David Penny tried to address that in an influential 1982 paper. Penny presented an example (protein sequence comparisons) he said would have falsified evolution, had the results come out differently. But 30 years later the results did come out differently. Evolution would be false according to that 1982 paper. But now Penny has changed the criterion. So his 1982 falsifiability criterion was not genuine. You can read about it here:

      http://darwins-god.blogspot.com/2011/07/david-pennys-reversal-and-why.html

      continued ...

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    5. Ian:

      So I think evolutionists have presented some flawed ideas for how evolution could be falsified. But it is, nonetheless, falsifiable. It would be false if creationism or design were demonstrated to be true, or highly likely. This is what evolutionists consistently ask for when challenged: "If you have a better theory then we'll drop evolution."

      This makes sense, because evolution is proved by contrastive thinking. It is the failure of creationism and design that proved evolution, and so it requires a proof of creationism or design to falsify evolution.

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    6. Cornelius Hunter: To this day there are myriad biological structures for which we do not know how they evolved, and we have no detailed description of a series of numerous, successive, slight modifications, leading to the structure.

      We don't have to know everything to know some things. There is ample evidence of transitions, including the evolution of complex structures.

      Cornelius Hunter: For instance, he took the example of protein-protein binding surfaces and showed how traditional evolution does not have the resources to evolve them. But again, no harm.

      If he had, it would require either revising or discarding the current theory of evolution, however, he never showed such a thing. That's why his claims have never had any effect on evolutionary theory.

      Cornelius Hunter: Evolution would be false according to that 1982 paper.

      The hypothesis would have been falsified, and that would mean either revising or discarding the then current theory of evolution.

      Cornelius Hunter: The new answer is horizontal gene transfer, which evolution is supposed to have created against all odds so that evolution could happen.

      As we can directly observe horizontal gene transfer, it's not such as leap to think that it worked in the past. For most taxa, the phylogenetic tree is not difficult to discern, even if there are some genes that don't match the tree.

      Cornelius Hunter: So I think evolutionists have presented some flawed ideas for how evolution could be falsified.

      Evolutionary theory makes all sorts of predictions, and they are tested every day, with no reference to creationism.

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    7. Zachriel:

      however, he never showed such a thing ...

      Can you explain what you mean here? Why do you say that?

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    8. Cornelius Hunter: For instance, he took the example of protein-protein binding surfaces and showed how traditional evolution does not have the resources to evolve them. But again, no harm.

      There are many problems with Behe & Snoke 2004, among them:

      * "Traditional evolution" includes recombination, including sexual recombination, which Behe fails to incorporate into his model.

      * As proteins are generally tolerant of many mutations, there will usually be a large variety of different versions of the same protein even before duplication, some of which may have the potentiating mutation.

      * The potentiating mutation may be functionally neutral or even have some advantage.

      * Most protein-protein binding evolved early in the history of life, when the supposed rarity of 10^-20 is not a significant hurdle.

      * Potentiating mutations have been observed. See Blount et al., Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 2008.

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    9. Z:

      As proteins are generally tolerant of many mutations, there will usually be ...

      Well for starters that is false.

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    10. Cornelius Hunter: Well for starters that is false.

      Axe et al., A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease, Biochemistry 1998: "Exhaustive-substitution studies, where many amino acid replacements are individually tested at all positions in a natural protein, have proven to be very valuable in probing the relationship between sequence and function. The broad picture that has emerged from studies of this sort is one of functional tolerance of substitution."

      Guo et al., Protein tolerance to random amino acid change, PNAS 2004: "the probability that a random amino acid replacement will lead to a protein's functional inactivation ... was found to be 34% ± 6%."

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    11. Z:

      No, you are confusing single residue replacement with multiple residue replacement. Your original point, in attempting to refute Behe's uncontroversial point that protein-protein binding is a hard problem for evolution, was that proteins typically can sustain a significant number of (multiple) substitutions. This is not generally true. When I pointed this out to you, you responded with citations stating that typically, only about a third of residues, if altered, affect the protein function significantly. So *single* substitutions can occur at most locations. That is true, but it does not imply that a protein can sustain very many multiple substitutions. There's quite a bit if data on that, showing that function rapidly falls off with only a few substitutions.

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    12. Cornelius Hunter: No, you are confusing single residue replacement with multiple residue replacement.

      The model in Behe 2004 is *one* or more potentiating mutations followed by an enabling mutation. Behe assume potentiating mutations are nearly always detrimental, when most of the time, they are nearly neutral, and sometimes beneficial.

      Behe: The majority of nonneutral point mutations to the gene will yield a null allele (again, by which we mean a gene coding for a nonfunctional protein) because most mutations that alter the amino acid sequence of a protein effectively eliminate function.

      As we have already shown, single mutations are commonly not detrimental to function. Behe cites Reidhaar-Olson, who say "At some positions only one or two residues are functionally acceptable; at other positions a wide range of residues and residue types are tolerated." He also cites Bowie 1989: "The identities of approximately one-third of the residues in Arc repressor are functionally important, about one-half are structurally important, and the remainder are unimportant for either structure or function." Lim &
      Sauer: "The random alteration of hydrophobic core positions in the N-terminal domain of lambda-repressor, both individually and in combination, shows that there are many ways of repacking the core of the protein." And so on.

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    13. Sorry for the delay. I discussed this here:

      http://darwins-god.blogspot.com/2014/07/heres-that-protein-protein-interaction.html

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  7. Glenn: I even appreciate Scott's willingness to help prove your point about teleological arguments:...

    If you think I've proved Cornelius' point, then it would seem my comment has gone over your head.

    "Purpose", in teleological arguments, refers to something endowed by a source. Yet, I said that good ideas are good, regardless of their source. So, your response seems to indicate you cannot recognize this philosophical assumption, even after I pointed it out to you.

    For example, I'm a computer scientist, not a cancer researcher. Despite this fact, let's hypothetically assume I decide to create a drug for the purpose of curing cancer. I then order laboratory mice that have cancer and administer my drug. Given the above, it would come as no surprise that my drug doesn't actually serve the purpose of curing cancer, despite the fact that I developed it for that specific purpose.

    IOW, any treatment that was actually successful would be successful because it embodied the "knowledge" of how cancerous cells multiply, how they can be identified and how cell death can be induced in just those cells, while excluding healthy cells. IOW, curing cancer occurs when the right transformations of matter occurs, which is independent of anyone's purpose. Ideas are jugged by their contents, not the source.

    To use another example, let say an actual researcher decided to find away to extend human life. As such, she might develop a drug protocol specifically for that purpose, then order middle aged mice for testing. Since all ideas start out as conjectures, she might find that her protocol doesn't actually extend the life of her test mice beyond their normal lifespan. But, for the sake of illustration, let's assume it does actually extend their life by a year. However, a year after ordering them, the mice supply company called and apologies for what must be the obvious mixup that occurred. It ends up, the mice she received weren't actually healthy middle aged mice but actually had been given cancer for testing as in the previous hypothetic experiment. They assumed her mice should be dead long ago, but in our hypothetical experiment, they were not! It ends up, the researchers protocol ended up curing the cancer in those mice, which was not her original purpose. This is an unexpected consequence.

    Again, curing cancer occurs when the right transformations of matter occurs. That's independent of anyone's desire, including whether or not any researcher's treatment was developed for that specific purpose. To reiterate, we judge ideas by their contents, not their source.

    On the other hand, your response to my comment suggests you think the exact opposite. For my comment to be teleological, you must assume an idea solves a problem due to having been endowed that purpose, not it's contents. Some authoritative source wanted it to work that way, so it did. But, as I've illustrated above, that doesn't survive rational criticism.

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