Monday, March 3, 2014

Here’s Darwin’s Solution for Convergent Evolution: Like Two Inventors “Independently Hit on the Very Same Invention”

Bad Analogy

One of the powerful arguments for evolution is that the species and the various biological organs and structures fall into the expected common descent pattern. We may not understand how they could have evolved and what transitional forms led to what we observe, but if they were created would they not show discontinuities from species to species? Darwin captures all of these ideas in this famous passage from Origins:

Although in many cases it is most difficult to conjecture by what transitions an organ could have arrived at its present state; yet, considering that the proportion of living and known forms to the extinct and unknown is very small, I have been astonished how rarely an organ can be named, towards which no transitional grade is known to lead. The truth of this remark is indeed shown by that old canon in natural history of "Natura non facit saltum." We meet with this admission in the writings of almost every experienced naturalist; or, as Milne Edwards has well expressed it, nature is prodigal in variety, but niggard in innovation. Why, on the theory of Creation, should this be so? Why should all the parts and organs of many independent beings, each supposed to have been separately created for its proper place in nature, be so invariably linked together by graduated steps? Why should not Nature have taken a leap from structure to structure? On the theory of natural selection, we can clearly understand why she should not; for natural selection can act only by taking advantage of slight successive variations; she can never take a leap, but must advance by the shortest and slowest steps. [Charles Darwin, Origin of Species, 1st ed., 1859, Ch. 6, p. 194]

Here Darwin makes a compelling argument for his theory. Isn’t it a bit suspicious that all those “parts and organs” from so many different species fall into a common descent pattern with small, gradual steps of change between them? Why would they be created that way by an all-powerful designer?

You can imagine how many readers have been swayed by this passage and others like it in Origins. There’s only one problem: This is all wrong.

The species and their “parts and organs” do not fall into such a pattern. Similar species have very different parts, and distant species have very similar parts. These cases are not exceptions but rather are rampant in the biological world and evolutionists maintain their common descent narrative to this day only by careful filtering of the data. Even in Darwin’s day there were hints of this problem and in one of those often overlooked foibles Darwin addressed this just before the passage above:

The electric organs offer another and even more serious difficulty; for they occur in only about a dozen fishes, of which several are widely remote in their affinities. Generally when the same organ appears in several members of the same class, especially if in members having very different habits of life, we may attribute its presence to inheritance from a common ancestor; and its absence in some of the members to its loss through disuse or natural selection. But if the electric organs had been inherited from one ancient progenitor thus provided, we might have expected that all electric fishes would have been specially related to each other. Nor does geology at all lead to the belief that formerly most fishes had electric organs, which most of their modified descendants have lost. The presence of luminous organs in a few insects, belonging to different families and orders, offers a parallel case of difficulty. Other cases could be given; for instance in plants, the very curious contrivance of a mass of pollen-grains, borne on a foot-stalk with a sticky gland at the end, is the same in Orchis and Asclepias,—genera almost as remote as possible amongst flowering plants. In all these cases of two very distinct species furnished with apparently the same anomalous organ, it should be observed that, although the general appearance and function of the organ may be the same, yet some fundamental difference can generally be detected. I am inclined to believe that in nearly the same way as two men have sometimes independently hit on the very same invention, so natural selection, working for the good of each being and taking advantage of analogous variations, has sometimes modified in very nearly the same manner two parts in two organic beings, which owe but little of their structure in common to inheritance from the same ancestor. [Charles Darwin, Origin of Species, 1st ed., 1859, Ch. 6, p. 193]

Here Darwin notes that there are several examples of similar organs in more distant species, indicating that they must have evolved independently. These are the sorts of similarities that would have been ascribed to evolution’s common descent, as in the powerful passage quoted above, if they had appeared in sister species. But these similarities do not appear in sister species—they appear in more distant species. So Darwin produced a new explanation: they evolved independently just as “two men have sometimes independently hit on the very same invention,” such as Leibniz and Newton independently developing calculus. Such personification of evolution and natural selection was common in Origins, and remains common in today’s literature. Aristotelianism never really died, it just changed names.

This has the virtue of not having to explain how low entropy, high Kolmogorov complexity designs which are astronomically unlikely to have spontaneously arisen (yes, that is what evolution says) even once could have evolved, err, multiple times independently.

And so there you have it. Evolution can explain common descent patterns and .NOT. common descent patterns. This is an example of the great flexibility of evolutionary theory. It doesn’t matter what the pattern is, evolution can explain it. And if a theory can explain both X and not X, then the scientist must not claim X (or not X) as evidence for his theory.

But this isn’t about science. Look at the first passage quoted above. Halfway down Darwin makes the argument compelling. Sure there are species that don’t fit the common descent pattern, but the important point is that the species would not have been created this way. X is powerful evidence, not because evolution can explain it but because creation cannot explain it. Evolution must be true—our religion demands it.

Religion drives science, and it matters.

453 comments:

  1. Why do you think high Kolmogorov complexity is something that is unlikely and needs explanation, especially when we have sources of true randomness in nature? If you sample the parity of cosmic rays every minute, you'll get a string of bits with high Kolmogorov complexity almost surely. It seems you're just throwing out random terms without understanding them.

    Where is the calculation to back up the claim of "astronomically unlikely to have spontaneously arisen"? I don't want some vague appeal or claim based on uniform probability; let's see a real calculation based on the actual history of the events to justify your claim.

    Note that I'm not claiming that we can do this for all events in evolutionary history. Rather, I think one should be a little more circumspect about probability claims when in fact nobody knows how to do those calculations currently.

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    1. What we see in the past is critically incomplete. This is acknowledged with biologic sciences, and by Darwinist themselves. Though it's usually in the form of a qualifier buried in a paper. Besides, probability is used within biology and population genetics all the times. Without a mechanism to explain how Darwinian macro-evolution could occur it remains another just so story.

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    2. eklektos: What we see in the past is critically incomplete. This is acknowledged with biologic sciences

      There are millions of data-points supporting the nested hierarchy.

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    3. You didn't answer either of my questions. Neither has Cornelius himself.

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    4. Professor Shallit:

      Why do you think high Kolmogorov complexity is something that is unlikely and needs explanation, especially when we have sources of true randomness in nature? If you sample the parity of cosmic rays every minute, you'll get a string of bits with high Kolmogorov complexity almost surely. It seems you're just throwing out random terms without understanding them.

      I’m glad you distinguish between cosmic rays and a biological species, or organ such as electromagnetic organs which the fish uses to map out its environment, track prey, and even stun prey.


      Where is the calculation to back up the claim of "astronomically unlikely to have spontaneously arisen"? I don't want some vague appeal or claim based on uniform probability; let's see a real calculation based on the actual history of the events to justify your claim.

      It is amazing how much detail evolutionists suddenly demand when the tables are turned. If only they maintained such a scientific attitude when it is their theory. Anyway, here is a place to start:

      http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html

      No it isn’t for fish or electric organs. It is merely for a single protein, which clearly falsifies the evolutionary expectation. And you need a great many of them for a fish or an electric organ.


      Note that I'm not claiming that we can do this for all events in evolutionary history. Rather, I think one should be a little more circumspect about probability claims when in fact nobody knows how to do those calculations currently.

      If nobody know this then how do you know evolution is a fact?

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    5. Cornelius Hunter: Anyway, here is a place to start:
      http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html


      Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001: "In conclusion, we suggest that functional proteins are suffciently common in protein sequence space (roughly 1 in 1011) that they may be discovered by entirely stochastic means, such as presumably operated when proteins were first used by living organisms."

      While random assembly is not how most proteins originated, the results do give us some idea of the density of functional proteins in sequence space.

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    6. A snowflake has a very high Kolmogorov complexity, and it forms randomly.

      But it doesn't digest proteins. Does it?

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    7. Zach:

      Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001 ... the results do give us some idea of the density of functional proteins in sequence space.

      Yes, and they are consistent with the other studies I mentioned here:

      http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html

      Of course the Keefe study was much simpler and less informative, as it merely detected weak binding. But the different studies are all consistently revealing another failure of evolutionary theory.

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    8. Zachriel,

      All you've done is quote again what I gave a detailed explanation about. And I also demonstrated several reasons that study was inadequate. You have not touched upon the science except to offer broad generalities which are without content.

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    9. Jeffrey,

      Biologic systems are not just ordered, nor just complex, but contain specified complexity. A Mandelbrot set is ordered, but it is simply repeating a pattern. It contains no information beyond the repetition of a pattern. You're comparing apples and oranges. And when I address actual scientific problems all I get is jargon. Give me a mechanism which works. Shouldn't be that hard to do. Be specific. And don't shift the ground.

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    10. Cornelius Hunter: Of course the Keefe study was much simpler and less informative, as it merely detected weak binding. But the different studies are all consistently revealing another failure of evolutionary theory.

      Huh? It shows that functional proteins are common in sequence space, no sparser than 10^-11, and that's with random sequences. If we start with existing proteins, the density is on the order of 10^-5 to 10^-7.

      eklektos: A Mandelbrot set is ordered, but it is simply repeating a pattern.

      A Mandelbrot set doesn't repeat, but it does rhyme.

      eklektos: Give me a mechanism which works.

      Bifurcating descent, variation and natural selection. You're welcome.

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    11. Zach:

      Huh? It shows that functional proteins are common in sequence space, no sparser than 10^-11, and that's with random sequences.

      Oh gosh no, you need to learn about proteins. The Keefe study did not deal with functional proteins, it merely detected weak binding. Those are two very different things. 10^-11 for functional proteins would contradict what we know by about 60 orders of magnitude!

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    12. Cornelius Hunter: The Keefe study did not deal with functional proteins

      So you're saying that Keefe & Szostak don't know what constitutes a functional protein, when they say "Functional proteins from a random-sequence library"? Binding is one of the primary functions of proteins, and is specific to the substrate.

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    13. Zach:

      So you're saying that Keefe & Szostak don't know what constitutes a functional protein, when they say "Functional proteins from a random-sequence library"?

      Yes, indeed. It is a good example of evolutionary over reach. From the Abstract:

      Starting from a library of 6 times 1012 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP. This selection yielded four new ATP-binding proteins that appear to be unrelated to each other or to anything found in the current databases of biological proteins. The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries.

      It is another example of how evolutionary theory abuses the science. Only by 60 orders of magnitude ...

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    14. Cornelius Hunter (quoting): "we selected functional proteins"

      Yup. That's what they said.

      Cornelius Hunter: Yes, indeed.

      Very interesting claim, that a recognized expert on telemeres, and who constructed the first artificial yeast chromosome, doesn't know what constitutes a functional protein.

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    15. Zach:

      Very interesting claim, that a recognized expert on telemeres, and who constructed the first artificial yeast chromosome, doesn't know what constitutes a functional protein.

      It is an obvious example of over reach, as I said.

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    16. Cornelius Hunter: It is an obvious example of over reach, as I said.

      Heh. So now not only does Szostak not know a functional protein when he sees one, but it's obvious. You didn't, however, provide an argument. Binding, along with joining and cleaving, are basic protein functions.

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    17. Zach:

      Heh. So now not only does Szostak not know a functional protein when he sees one, but it's obvious.

      Sorry, but this is science. If Henry Ford cited a wheel as an example of a functional automobile, then we'd have problem.

      You didn't, however, provide an argument.

      Actually I've provided plenty of arguments. The one I didn't give is the one you should have already known if you're going to make such claims, and that is that binding to a molecule is not a big deal. Proteins actually need to, um, do something.

      In the case of ATP binding, a protein enzyme would remove the third phosphate group via hydrolysis, and channel the resulting energy to make an unfavorable reaction occur. That's orders of magnitude more complex than merely ATP binding and so it's no surprise there are 60+ orders of magnitude between the result from this paper and those from various other studies that actually, um, *did* the work you are claiming this paper did.

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    18. Cornelius Hunter: If Henry Ford cited a wheel as an example of a functional automobile, then we'd have problem.

      But he didn't. Ford knew the difference. We might think Szostak might be wrong on the fringes of knowledge, but it strains credulity that he wouldn't know a functional protein when he saw one.

      Cornelius Hunter: The one I didn't give is the one you should have already known if you're going to make such claims, and that is that binding to a molecule is not a big deal.

      The "not a big deal" metric.

      Cornelius Hunter: In the case of ATP binding,

      Cytochrome c accepts an electron from the b-c1 complex and transfers it to the cytochrome oxidase complex, an essential function.

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    19. Zach:

      it strains credulity that he wouldn't know a functional protein when he saw one.

      But then again, there it is, right there in black and white: "we selected functional proteins ..." Of course this isn't a matter of a scientist not knowing what a functional protein is, it is a matter of how results are presented when it is dogmatically maintained that the biological world must have arisen spontaneously. Religion drives science and it matters; and here we have a good example.

      Cytochrome c accepts an electron from the b-c1 complex and transfers it to the cytochrome oxidase complex, an essential function.

      Very good. And guess what else: you're going to need >10^70 sequences to find one of those. But that's science.

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    20. Cornelius Hunter: But then again, there it is, right there in black and white: "we selected functional proteins ..."

      That's right. They took random sequences and found some that were functional proteins.

      Cornelius Hunter: Of course this isn't a matter of a scientist not knowing what a functional protein is, it is a matter of how results are presented when it is dogmatically maintained that the biological world must have arisen spontaneously.

      The hypothesis came from research in abiogenesis, but the data stands on its own.

      Cornelius Hunter: Very good.

      The question concerned the definition of protein function. Szostak found functional proteins in random sequences.

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    21. Zach:

      That's right. They took random sequences and found some that were functional proteins.

      We were making progress but now you are playing games with the semantics. We can either use the words "functional protein" as it is normally understood by molecular biologists, or we can dilute it to mean something as simple as weak binding. I don't care, but either way the results are the results. They find a sequence that does ATP binding in roughly a million-million sequences. That is consistent with several other studies that show that sequences that actually do something the cell needs are about 60 orders of magnitude more unlikely. The science is in and it's no surprise.

      We are now beyond a mere misunderstanding and your resistance to the science is telling. We are now in the Monte Python How-much-for-an-argument stage. You're an evolutionist and there is a lot at stake here for you. Evolution can't be wrong, by definition.

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    22. Cornelius Hunter: We can either use the words "functional protein" as it is normally understood by molecular biologists

      That's the very point. Szostak is a professor of genetics and of chemical biology. Keefe & Szostak was published in the journal Nature. Szostak used the term as it is usually understood by molecular biologists.

      Keefe & Szostak started with random sequences. If you start with snippets of existing proteins, the density of functional proteins is much higher.

      Cornelius Hunter: They find a sequence that does ATP binding in roughly a million-million sequences. That is consistent with several other studies that show that sequences that actually do something the cell needs are about 60 orders of magnitude more unlikely. The science is in and it's no surprise.

      No, because once you have function, the protein is then subject to selection and further adaptation.

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    23. Zach:

      That's the very point. Szostak is a professor of genetics and of chemical biology. Keefe & Szostak was published in the journal Nature. Szostak used the term as it is usually understood by molecular biologists.

      I agree. Top journal, top school, top professor. But no, mere ATP binding does not a functional protein make. Not as the term is normally understood. And certainly not in any meaningful sense. This phony terminology is the influence of evolutionary thinking.

      No, because once you have function, the protein is then subject to selection and further adaptation.

      No, that has already all been accounted for. You either don't understand the science, or you're not up on the literature. You need ~10^70 tries, not 10^12 tries and then RM+NS gets you the rest of the way.

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    24. Cornelius Hunter: Top journal, top school, top professor. But no, mere ATP binding does not a functional protein make.

      You said to use the term as normally understood by molecular biologists.

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    25. Cornelius Hunter: Top journal, top school, top professor. But no, mere ATP binding does not a functional protein make.

      Z: You said to use the term as normally understood by molecular biologists.

      J: Yeah, don't you get it Dr. Hunter? The difference between ~10^70 tries and 10^12 tries has no relevance to the probability of naturalistic abiogenesis+UCA. When you're a fideist, science just IS what the subsidized members of the consensus believe. It has no other defining characteristics.

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    26. Jeff: The difference between ~10^70 tries and 10^12 tries has no relevance to the probability of naturalistic abiogenesis+UCA.

      The claim is that proteins are relatively dense in sequence space, and that highly optimized proteins are evolved from these primitive versions.

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    27. Zachriel said

      "That's the very point. Szostak is a professor of genetics and of chemical biology. Keefe & Szostak was published in the journal Nature. Szostak used the term as it is usually understood by molecular biologists. "

      Isn´t this an argument by authority? We have to believe what experts says no matter we do not understand it or we have another understanding of the problem?

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    28. Zac, here's the level of "binding" we're talking about;
      https://www.youtube.com/watch?v=U_mZGTB5uKg

      It's part of this protein complex that runs very similarly to a Mazda engine;
      https://www.youtube.com/watch?v=J8lhPt6V-yM&list=PL7B32AE4CCCA67E1E

      Do you see why I said his study is like claiming, I can find out how common the solution of gasoline burning cars are in evolutionary sequence space by throwing gasoline on the cars and seeing which cars it sticks to? To be sure gasoline must stick...

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    29. Blas: Isn´t this an argument by authority?

      The meaning of terms is determined by usage. In this case, we are using the standard Cornelius Hunter set when said we should "use the words 'functional protein' as it is normally understood by molecular biologists". Szostak is a molecular biologists. The paper was published by the journal Nature. The same terminology can be found in many other papers. Binding is a common protein function, such as single-stranded DNA-binding proteins. Furthermore, ATP binding is a function, one that the researchers chose for testing. It's not meant to be the be-all and end-all of biology.

      John: I can find out how common the solution of gasoline burning cars are in evolutionary sequence space by throwing gasoline on the cars and seeing which cars it sticks to?

      The difference is that the shape of the molecule has to be specific to the substrate, which is why most sequences won't bind.

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    30. Z: The claim is that proteins are relatively dense in sequence space, and that highly optimized proteins are evolved from these primitive versions.

      J: Science isn't a collection of mere claims. CH directed you to http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html. Can you address it?

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    31. Well gosh, it said functional in the title. Get real.
      A. He didn't fold the protein. B. He paid no attention to the sidechains. C. He didn't demonstrate it could perform any function. D. Other more recent comprehensive studies disagree with him. E. His credentials don't make him correct F. You're full of hot air.

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    32. Z: The difference is that the shape of the molecule has to be specific to the substrate, which is why most sequences won't bind.

      I just don't see what hope "binding" is giving you. I mean, yes, when we look at ATP, it does "bind" to the molecules it powers. But then saying eureka is like saying one of the materials in my car has been found to stick to gasoline more readily because of it's molecular shape. You can clearly see that is absurd. Why change your mind when an evolutionary scientist says he's shown the first step along the path to the solution evolution found?

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    33. Jeff: Science isn't a collection of mere claims.

      Science is a methodology for matching theory (a body of interrelated claims) to observation.

      Jeff: CH directed you to http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html

      The claim is directly contradicted by experiment. The experiment has been replicated many times and in many different ways. For instance, with a restricted amino acid library. See Doi et al., High solubility of random-sequence proteins consisting of five kinds of primitive amino acids, Protein Engineering, Design and Selection 2005.

      eklektos: Well gosh, it said functional in the title.

      That's what they said in the journal Nature.

      eklektos: A. He didn't fold the protein.

      The researchers found foldable proteins in a random sequence library.

      eklektos: B. He paid no attention to the sidechains.

      The actual structure may be of interest, but is not directly relevant as to density of functional proteins in the random sequence library.

      eklektos: C. He didn't demonstrate it could perform any function.

      They were searching for proteins that would bind to ATP.

      eklektos: D. Other more recent comprehensive studies disagree with him.

      It was a direct experiment that has been replicated many times.

      eklektos: E. His credentials don't make him correct

      No, they don't, but it's reasonable to assume that Szostak, the editors of Nature, and the many other scientists who are working in the field of protein engineering, would know what constitutes a functional protein.

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    34. John: But then saying eureka is like saying one of the materials in my car has been found to stick to gasoline more readily because of it's molecular shape.

      Protein binding is a lot more specific. The 3-dimensional structure of the protein has to conform to the 3-dimensional structure of the substrate.

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    35. Jeff: CH directed you to http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html

      We responded on that thread to the particulars of the post, but our comment has yet to appear.

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    36. ,Zachriel,

      I'm sorry, both Cornelius and I showed they didn't. But you didn't deal with our arguments, you appealed to authority. This is quite common. I gave specific reasons why their claims were wrong. This is not actually about science which is a recurring theme. As Dr. Hunter said, it's about religion.

      The researchers found foldable proteins in a random sequence library.

      What part of could fold don't you understand?

      The actual structure may be of interest, but is not directly relevant as to density of functional proteins in the random sequence library.

      You are dodging the issue. You said functional proteins are common in sequence space
      Not just any old protein. And 1 out of 10^11 is not common by any standard. And the number is wrong to begin with. And this all goes back to that AXE study which I'd bet you still haven't read, have "we".

      They were searching for proteins that would bind to ATP

      You said Functional proteins are common in sequence space. He didn't demonstrate the protein was functional, would fold, or had the right side chains. Change the amino acids you change the side chains. So it could fold is not will fold. So it doesn't make your point.

      You're boring me.

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    37. eklektos: But you didn't deal with our arguments, you appealed to authority.

      Um, Cornelius Hunter said to use the definition used by molecular biologists. That's what we did. In particular, ATP-binding is a common natural function.

      eklektos: I gave specific reasons why their claims were wrong.

      And we responded to each of your points.

      eklektos: What part of could fold don't you understand?

      The proteins formed a three-dimensional fold.

      eklektos: And 1 out of 10^11 is not common by any standard.

      A mole is 6 * 10^23. So, yes, it does depend on the standard. Also, 10^-11 is a minimum density, as that is the density of just a single function.

      eklektos: And this all goes back to that AXE study which I'd bet you still haven't read, have "we".

      We did and we have, and replied on the appropriate thread.
      http://darwins-god.blogspot.com/2013/10/failure-how-evolutionists-react.html

      eklektos: He didn't demonstrate the protein was functional,

      ATP binding is a common function in nature, which is why they chose it.

      eklektos: would fold, or had the right side chains

      The whole point of evolution is that you don't have to know the structure, you just have to select for function. But the sequences did fold into the active conformation.

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    38. Zacriel: Protein binding is a lot more specific. The 3-dimensional structure of the protein has to conform to the 3-dimensional structure of the substrate.

      Why is the ability to simply "bind" so compelling a thing for you? Again did you watch the video? There's much more going on than simply sticking together.

      Zacriel: ATP binding is a common function in nature, which is why they chose it.

      Binding to water is also common, and ice is everywhere. But when gasoline binds to oxygen withing a specific chamber inside the engine of my car, do you see why that looks more designed? Then why not when ATP "binds" to ATP synthase to power this motor vs just any chemical reaction it might make? It really seems like you're trying to not understand.

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    39. John: Why is the ability to simply "bind" so compelling a thing for you?

      It's not. Cornelius Hunter introduced the question of protein function on this thread. As for binding, it's just a common, naturally occurring function suitable for the experiment.

      John: But when gasoline binds to oxygen ...

      Protein binding is a lot more specific. The 3-dimensional structure of the protein has to conform to the 3-dimensional structure of the substrate.

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  2. CH,

    Spot on. Darwinism has no explanation for how such structures could arise once, much less twice independently. They simply argue against a designer in the fashion we saw in earlier posts, "well, I wouldn't have done it that way". As if a designer would be bound by their notion of how to do it.

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    1. eklektos: As if a designer would be bound by their notion of how to do it.

      I agree, so you believe the appeal to common design or human design is a fallacy . Analogies to human design would also be rejected on the same basis. So unless someone could prove experimently non design,design inferences should be avoided.

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    2. I don't see how that follows. That only leaves open the Darwinian explanation, however bad. Because it effectively eliminates all other explanations unless they are materialistic. If it's designed it's designed. Claims about the nature of the designer is outside the realm of science. But it provides a definite stopping point within the realm of science, which is exactly why it's opposed so stringently. Note the savant Dawkins postulating that if it can't be explained within the realm of natural origins of Darwinian evolution then aliens must have done it and they evolved. So on back to infinite regression. What they fear is explanatory power for human origins leaving the realm of science. Which they've as much as said when they let their guard down. I find that curious.
      .

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    3. eklektos: Darwinism has no explanation for how such structures could arise once, much less twice independently.

      Of course it does. Divergence from common ancestors and natural selection.

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    4. Zachriel,

      Sounds nice, give me the mechanism. Explain how you can overcome extraordinary odds, not once but twice, often more, when they are divergent lines and the starting point doesn't supply the genetic material.

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    5. eklektosClaims about the nature of the designer is outside the realm of science.

      Really? I would have thought the nature of any putative designer would be of great interest to any scientific research program into intelligent design.

      Unless, that is, you believe you know who and what this designer really is and so define he, she or it as to place them conveniently beyond the reach of human science.

      eklektos But it provides a definite stopping point within the realm of science...

      Only in your rather singular notion of science. For the rest of us, evidence of the handiwork of alien designers would be certain to arouse intense curiosity about them.

      eklektos Note the savant Dawkins postulating that if it can't be explained within the realm of natural origins of Darwinian evolution then aliens must have done it and they evolved.

      If we didn't do it and there is no God then all we are left with is a natural process like evolution or aliens or a combination of both.

      eklektos So on back to infinite regression

      Which is a problem, why exactly?

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    6. Ian,

      What if it's not aliens. What if there is no natural explanation? I know, you can't bear to contemplate that. So we'll try to solve an insoluble problem forever. Meanwhile we could constructively use the resources. But endlessly searching for an answer that doesn't exist with a paradigm that doesn't work is far better right?

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    7. eklektos: Sounds nice, give me the mechanism.

      Um, we just did. Divergence from common ancestors and natural selection.

      eklektos: Explain how you can overcome extraordinary odds, not once but twice, often more, when they are divergent lines and the starting point doesn't supply the genetic material.

      What odds? That organisms have a range of variation that is subject to selection? Or that there is a source of novel variation?

      eklektos: What if there is no natural explanation?

      People never thought we could know what stars are made of. (Hint: it's not quintessence.)

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    8. Zachriel,

      "Um, we just did. Divergence from common ancestors and natural selection."

      Um, that would be a process, not a mechanism. Much like writing is a process, but the hand and the pen are the mechanisms.

      Delete
    9. mechanism, natural or established process by which something takes place or is brought about
      http://www.oxforddictionaries.com/us/definition/american_english/mechanism

      Delete
    10. Zachriel,

      "mechanism, natural or established process by which something takes place or is brought about"

      I can accept that definition, though it is a secondary definition which applies a concrete essence (such is the nature of the standard definition of mechanism), to something which is essentially abstract in nature. However, I think that leaves you with the responsibility of defining and describing what it is that would drive such processes.

      Also, as neither divergence from a common ancestor or natural selection has actually been observed as operating or having operated in the past, designating them as the mechanism driving evolution is tenuous at best.

      Delete
    11. eklektos:I don't see how that follows. That only leaves open the Darwinian explanation, however bad.

      At this point yes, but before Einstein it was generally thought that Newton would never be replaced.

      Because it effectively eliminates all other explanations unless they are materialistic.

      Since organisms are made of matter at some level a materialistic explanations are necessary, even if one believes in immaterial causes of life. The immaterial would have to interact with the material.

      If it's designed it's designed. Claims about the nature of the designer is outside the realm of science

      Depends on who the designer is. Science studies design all the time, those created by nature and those created by man. But unless material tools can measure the immaterial then science is helpless.


      But it provides a definite stopping point within the realm of science, which is exactly why it's opposed so stringently

      Theistic evolutionists refute that theory

      My guess a big reason that ID is opposed,by those who consider worth the the effort,is because it is considered a bad pseudo scientific theory which portrays scientists as liars or inept. Sort of a sports talk version of science.

      Note the savant Dawkins postulating that if it can't be explained within the realm of natural origins of Darwinian evolution then aliens must have done it and they evolved

      Expelled? Stein: "what do you think is the possibility that there then, intelligent design might turn out to be the answer to some issue in genetics ...or evolution?"

      He said is was a possibility, which is more open minded about intelligent design than IDists are about evolution. And since aliens are presumedly not immaterial beings, they could be studied like the designers of the pyramids.

      So on back to infinite regression. What they fear is explanatory power for human origins leaving the realm of science.

      I agree and that is why ID is not science. Ultimately the Designer must be God.

      Which they've as much as said when they let their guard down. I find that curious.

      I agree, with the exception of who "they" are.

      Delete
    12. Nic: Also, as neither divergence from a common ancestor or natural selection has actually been observed as operating or having operated in the past, designating them as the mechanism driving evolution is tenuous at best.

      Natural selection can be directly observed. It even has its own unit of measure, darwins and haldanes. See Weiner, Beak of the Finch, Knopf 1994.

      Common descent is generally inferred from the nested hierarchy, but speciation has been observed, such as by polyploidism in plants. The nested hierarchy linked to common descent can also be observed in specific genes, such as the y-chromosome of Genghis Khan.

      Delete
    13. velikovsky,

      At this point yes, but before Einstein it was generally thought that Newton would never be replaced.

      Seriously? You're argument is that we should use a bad theory till it can be replaced with a good one?? Newton wasn't replaced. We use Newtonian mechanics to this day. Einstein refined Newton, he didn't replace him.

      The immaterial would have to interact with the material.

      I have no problem with physical descriptions of operation. I have a problem with materialistic creation myths and religion posing as science. Besides, what makes you think the immaterial if it exists is precluded from interacting with the material?

      But unless material tools can measure the immaterial then science is helpless.

      Kinda my point don't you think? If it's not ontologically necessary then there may be limits.

      Theistic evolutionists refute that theory

      That assumes theistic evolutionist are correct about their science and their theology. It also assumes their motives are neutral, but nobody is neutral.

      He said is was a possibility, which is more open minded about intelligent design than IDists are about evolution.

      Assumes moral neutrality, which doesn't exist. Dawkins knows there is no God, and he hates Him.

      I agree and that is why ID is not science. Ultimately the Designer must be God.

      Or God is the uncaused cause. Which is why He is outside the material. The Universe had a beginning no matter who's right. You're problem is you think you can use material explanations for the immaterial, and if you can't it can't exist or be known.

      I agree, with the exception of who "they" are

      Richard Lewontin for one. Although he got pilloried for it. Though shalt have other gods before Darwin.




      Delete
    14. Nic,

      Natural selection is unquestionable. But it is insufficient to explain origins. It is necessary cause for Darwinism, but it is an insufficient cause for Darwinism to be true. As are all the other "proofs" Darwinist claim. None of them are sufficient.

      Delete
    15. eklektos: You're argument is that we should use a bad theory till it can be replaced with a good one??

      All theories are wrong. Some theories are useful.

      eklektos: Natural selection is unquestionable. But it is insufficient to explain origins.

      Small changes led from reptilian jaw bones to mammalian ossicles, each step providing a selectable advantage in hearing while maintaining and in some ways improving jaw function.

      Delete
    16. Nic,

      For a discussion of natural selection from us looney creationist see:

      http://www.answersingenesis.org/articles/arj/v6/n1/does-natural-selection-exist

      Delete
    17. eklektos:Seriously? You're argument is that we should use a bad theory till it can be replaced with a good one??

      So far you have shown it as incomplete and unpersuasive to you. But thousands of scientists are collecting data to lessen that problem.

      Newton wasn't replaced. We use Newtonian mechanics to this day. Einstein refined Newton, he didn't replace him..

      True, it is a good description of motion, but it is not a explanatory as Einstein model. But that model fails at certain levels so it is not completely correct as well. But until something better arrives, it is the most useful. A broken hammer is better than no hammer

      eklektos:have no problem with physical descriptions of operation. I have a problem with materialistic creation myths and religion posing as science.

      Science can only explain the physical with the physical with any predictability and regularity. Anyone who claims it proves that all there is is physical,is incorrect.

      Besides, what makes you think the immaterial if it exists is precluded from interacting with the material?

      I don't,I have no idea what the immaterial is capable of exactly ,but if it exists as a causal agent at sometime it must interact with the material world.

      Delete
    18. Zachriel,

      Nice claim. Show me a sequence. Not nodes of imaginary animals connected to actual animals.
      And do it without using parsimony(which is connecting animals into "nested hierarchies" based on the fewest assumed evolutionary steps.). Until you can do that, including the simultaneous systems to make an ear work. Until you can you're just full of hot air and cherry picking your data, studies, sentences within studies, etc.

      Delete
    19. eklektos: Show me a sequence.

      http://daphne.palomar.edu/ccarpenter/jaws1.gif

      Delete
    20. That's not a sequence. Sorry. It's a just so story. Show me migration happened. Show me where the supporting systems developed. Sho me a real sequence. Not connect the dots with a just so story and mythological animals.

      Delete
    21. Velikovsky,

      So far you have shown it as incomplete and unpersuasive to you. But thousands of scientists are collecting data to lessen that problem

      There showing it's far less probable than it was just ten years ago. They are merely strengthening my resolve. Plus they keep demonstrating the inherent dishonesty in the whole process. I'm actually interested in the truth. Now I realize there are a good many religious people who aren't honest. I don't see that. I don't think we honor God by being dishonest. Which is why I corrected Nic about natural selection. But natural selection is inadequate to explain macro evolution. All it has demonstrated is variations within a species that can be acted upon by ecologic pressures. If the population remains under the same pressure for a long enough period it will lose genetic information. It may also lose the ability to breed with the original population due to this loss. So we haven't advanced beyond animal husbandry.

      A broken hammer is better than no hammer

      There's nothing useful from a scientific perspective in Darwinism. It's only it's religious usefulness that keeps it around.

      Science can only explain the physical with the physical with any predictability and regularity. Anyone who claims it proves that all there is is physical,is incorrect.

      There's no actual science to Darwinism. It's only function is as a creation myth. There's no advances in any field that are driven by a belief in Darwinism. It's nothing but just so stories about the past. And it's used all the time to make moral and metaphysical claims.

      I don't,I have no idea what the immaterial is capable of exactly ,but if it exists as a causal agent at sometime it must interact with the material world.

      Yes, we call that agent God. And He revealed Himself. However asking Him to prove himself is pointless. I Am is a statement of fact. It's not negotiating. You can Infer Him, if you give up fairy tale creation myths. But that won't get you there. His revelation must be personal. I know. :)


      Delete
    22. eklektos: That's not a sequence.

      Handwaving.

      Delete
    23. Zachriel,

      Artificial sequence if you prefer. Till you can show something other than arranging fossils to suit your creation myth you're the one handwaving.

      Delete
    24. eklektos: There's no advances in any field that are driven by a belief in Darwinism.

      The Theory of Evolution is the central unifying theory of biology. It's used in everything from genetics to ecology. It's used to make vaccines. It's used to find mineral resources.

      eklektos: Artificial sequence if you prefer.

      They're ordered by time.

      Delete
    25. eklektos:Assumes moral neutrality, which doesn't exist. Dawkins knows there is no God, and he hates Him.

      Could you elaborate on this a bit,I don't follow your reasoning?

      Or God is the uncaused cause. Which is why He is outside the material.

      That is what I said, if everything requires a cause,then you need another something that doesn't.

      The Universe had a beginning no matter who's right.

      This universe theoretically did,though there was never a time when it did not exist according to the same theory.

      You're problem is you think you can use material explanations for the immaterial, and if you can't it can't exist or be known.

      Unless you addressing someone else,you need to read what I write. I don't believe that at all. It seems possibly that something radically different could exist, I expect it does.

      But that is not your position,you claim to know things about it . You are free to but your belief is not based on science by definition.

      Richard Lewontin for one. Although he got pilloried for it. Though shalt have other gods before Darwin.

      Except Darwin is commonly acknowledged to be mistaken in several ways,is Einstein considered a God as well? Robert Plant?

      That argument that science is religion seems to me to trivialize religion into nothing more than a hobby, that religion is a materialistic obsession.

      Delete
    26. The Theory of Evolution is the central unifying theory of biology. It's used in everything from genetics to ecology. It's used to make vaccines. It's used to find mineral resources.

      Nice story.

      They're ordered by time.

      Assumed time. Plus that's ad hoc. Their placement in time, even if correct, doesn't prove what you claim.

      Delete
    27. eklektos: Nice story.

      True story.

      eklektos: Their placement in time, even if correct, doesn't prove what you claim.

      Sure it does. You claimed it was an "artificial sequence", when, in fact, they are ordered by time, not to mention fitting all the other transitions both within the lineage and in the entirety of life.

      Delete
    28. True story.

      There's no proof that evolutionary beliefs are responsible for modern medicine, or anything else. Most molecular biology books don't even mention Darwinism, and those that do mention it as an afterthought.

      Sure it does. You claimed it was an "artificial sequence", when, in fact, they are ordered by time, not to mention fitting all the other transitions both within the lineage and in the entirety of life.

      Migrating bones, if they migrated at all, don't make an ear. All you've got is fossils and your typical Ad Hoc reasoning. And out of sequence time in the case of Yanoconodon. This is exactly why Darwinism is not science. It's totally unfalsifiable because any data contrary to the religion is co-opted to become part of the religion. "We" are full of hot air.

      Delete
  3. "Why, on the theory of Creation, should this be so? Why should all the parts and organs of many independent beings, each supposed to have been separately created for its proper place in nature, be so invariably linked together by graduated steps?"

    If Darwin had read Lyell as closely as Meyer, he might have searched for a "cause now in operation" that explains perfectly why parts of things that have been created separately for its proper place are linked together by graduated steps. That's the way a mind designs parts of things. Or was this not obvious until the industrial revolution? Good thing we didn't have to wait for a Darwinian industrial "evolution".

    ReplyDelete
  4. Cornelius Hunter: So Darwin produced a new explanation: they evolved independently just as “two men have sometimes independently hit on the very same invention,” such as Leibniz and Newton independently developing calculus.

    Darwin: "although the general appearance and function of the organ may be the same, yet some fundamental difference can generally be detected."

    In other words, even though trout and dolphins both have hydrodynamic shapes, if we look closely, we should be able to tell their independent origins. And we can.

    ReplyDelete
    Replies
    1. Yes, obviously the trout and dolphin have independent origins, and didn't both descend from a fish.

      The point, that evolutionists have such a hard time grappling with, is that convergence (of both general function and specific morphological and molecular traits) is data that contradicts the claim of the existence of a nested hierarchy that predictably follows from common descent.

      There is no objective nested hierarchy of common descent. The data must be constantly accommodated into CD with all sorts of ad-hoc rationalizations.

      Delete
    2. lifepsy: obviously the trout and dolphin have independent origins, and didn't both descend from a fish.

      Both descended from a common Gnathostomata ancestor, what would probably be considered a fish.

      lifepsy: The point, that evolutionists have such a hard time grappling with, is that convergence (of both general function and specific morphological and molecular traits) is data that contradicts the claim of the existence of a nested hierarchy that predictably follows from common descent.

      Convergence is part of Darwin's original theory. It's important evidence supporting natural selection. Not sure why you think it's a problem.

      lifepsy: There is no objective nested hierarchy of common descent.

      The nested hierarchy is strongly supported. Do you really think dolphins group best with trout rather than land mammals?

      Delete
    3. Zachriel: The nested hierarchy is strongly supported.

      Of course there is a nested hierarchy. Just not one that reflects Common Descent for the reasons already mentioned. As an evolutionist, you are constantly reduced to subjective rationalizations and special pleading to claim otherwise.

      Delete
    4. Zachriel: The nested hierarchy is strongly supported. Do you really think dolphins group best with trout rather than land mammals?

      Here's just one of your problems. When you say something "groups", you are undoubtedly hallucinating evolutionary lineages into a nested hierarchy model. But a "mammal" isn't an ancestral group. It's only a conceptual type describing the presence of certain traits. It says nothing about evolutionary lineages.

      When you claim "Whales are nested within mammals." All you're really saying is that whales nest within whales. Common ancestry is a totally unnecessary assumption that you tag onto a nested hierarchy as theoretical baggage.

      Likewise, both whales and trout "group" within vertebrates. A vertebrate of course, like a mammal, is simply a trait type and says nothing about shared ancestry.

      Any notion of an actual pattern of common descent is contradicted by close examination of character traits. Thus the constant need to invoke subjective rationalizations and special pleading arguments to accommodate both X and -X into the theory. This is why Common Descent only accommodates the data, but does not explain or predict anything.

      Delete
    5. lifepsy: Of course there is a nested hierarchy. Just not one that reflects Common Descent for the reasons already mentioned.

      lifepsy: evolutionists have such a hard time grappling with, is that convergence

      Convergence is part of Darwin's original theory. It's important evidence supporting natural selection. Not sure why you think it's a problem.

      lifepsy: you are constantly reduced to subjective rationalizations and special pleading to claim otherwise.

      Natural selection is hardly special pleading, and has been an integral part of the theory since it was first proposed.

      lifepsy: When you say something "groups", you are undoubtedly hallucinating evolutionary lineages into a nested hierarchy model.

      Nope. We're grouping based on traits regardless of explanatory framework.

      lifepsy: When you claim "Whales are nested within mammals." All you're really saying is that whales nest within whales.

      No. We're saying whales nest within mammals because of shared traits; everything from the skeleton to the reproductive system to the blood.

      lifepsy: Likewise, both whales and trout "group" within vertebrates. A vertebrate of course, like a mammal, is simply a trait type and says nothing about shared ancestry.

      That's right. The natural groupings occur without regard to explanatory framework. Common descent is an inference, which entails testable implications.

      lifepsy: Any notion of an actual pattern of common descent is contradicted by close examination of character traits.

      Which you haven't bothered with providing.

      Delete
    6. lifepsy: When you claim "Whales are nested within mammals."

      We mean they share more traits with mammals (mice, wolves, zebras, lions) than with trout; such as hair follicles, auditory ossicles, mammary glands, single-boned lower jaw attaching directly to the skull, endothermic, four-chambered heart with bellows lungs, neocortex. Indeed, just a close look at the flipper, which would seemingly be closest to a trout, reveals it to be closer to other mammals, complete with radius, ulna, carpals, metacarpals, phalanges, not to mention red blood cells lacking nuclei, and platelets. Molecular characteristics also supports the grouping.

      Delete
    7. Zachriel, just showing you don't even understand what you're arguing listing off mammalian traits. Whales grouping with those traits is entirely independent of common descent hypothesis.

      Guess what, Zach, if whales were minus any number of those traits, it would just be something evolution did. If whales shared more traits with trout, then they wouldn't be classified as mammals, but nested within fish type groups closer to sharks. Any remaining "whale-ness" traits would be rescued with "convergent evolution".

      You really haven't thought this through, have you?

      Zachriel: Common descent is an inference, which entails testable implications.

      Laughable. No it doesn't, and you've never been able to show that it does. You just keep harping on your silly baseless mantras.

      Delete
    8. Zachriel: We're grouping based on traits regardless of explanatory framework.

      lifepsy: Whales grouping with those traits is entirely independent of common descent hypothesis.

      Um, yeah.

      lifepsy: if whales were minus any number of those traits, it would just be something evolution did.

      Do whales group best with rabbits or with trout?

      Delete
    9. Sigh, why do I even bother trying to extract a rational argument from you?

      Zachriel, as usual, when challenged on it, you're totally incapable of defending your vague mantras of nested hierarchies being explained by common descent.

      Delete
    10. lifepsy: as usual

      You don't have an argument. In case you forgot, we agreed that the nested hierarchy is independent of any explanatory framework.

      lifepsy: if whales were minus any number of those traits, it would just be something evolution did.

      Do whales group best with rabbits or with trout?

      Are centaurs and griffins plausible natural organisms? Why or why not?

      Delete
    11. Zachriel

      "Do whales group best with rabbits or with trout?"

      Best is bad scientific term, what do you mean specifically for "best" in this case?

      Delete
    12. lifepsyGuess what, Zach, if whales were minus any number of those traits, it would just be something evolution did.

      It they had gills it might be a problem, any examples?

      If whales shared more traits with trout, then they wouldn't be classified as mammals, but nested within fish type groups closer to sharks.

      True, since animals are classified according to their traits.

      Any remaining "whale-ness" traits would be rescued with "convergent evolution".

      So you're saying because evolution cannot explain a Centaur ,evolution is false.

      Delete
    13. Zachriel: Do whales group best with rabbits or with trout?

      Blas: Best is bad scientific term, what do you mean specifically for "best" in this case?

      The most parsimonious grouping based on the panoply of traits. Hint: It's not even close.

      Delete
    14. Zachriel,

      Parsimonious in Hegginian cladistics means fewest evolutionary steps. It's not a magic word.

      Delete
    15. eklektos: Parsimonious in Hegginian cladistics means fewest evolutionary steps.

      We have been discussing phenetics, not cladistics. Of course there are differences within phenetics and cladistics, due to differently methodologies or as new data becomes available. However, the overall nested hierarchy is largely the same.

      Delete
    16. Yes, assumed evolutionary lineages.

      Delete
    17. eklektos: Yes, assumed evolutionary lineages.

      No. What we have been discussing is phenetics, which is independent of any explanatory framework, including evolution.

      Delete
    18. Zachriel,

      Horse manure. You've been claiming it proves Darwinism all along. Nice attempt at bait and switch though. The lineages you are claiming are all based on Darwinian assumptions. So you're just being dishonest.

      Delete
  5. Cornelius Hunter: Sure there are species that don’t fit the common descent pattern, but the important point is that the species would not have been created this way.

    Actually, you're pointing to a function, not a structure, nor a species.

    ReplyDelete
    Replies
    1. Function, structure, and species. All regularly violate predicted patterns of common descent.

      Delete
    2. lifepsy: Function, structure, and species. All regularly violate predicted patterns of common descent.

      The pattern of common descent is strongly supported across most taxa. Not sure why you would say otherwise.

      Delete
    3. Zachriel: The pattern of common descent is strongly supported across most taxa.

      Not at all. As an evolutionist you simply invoke special pleading to explain away contradictory data.

      Zachriel: Not sure why you would say otherwise.

      Because, unlike yourself, I've actually studied the matter and have transcended simple mantras that you seem constrained to.

      Delete
    4. lifepsy: As an evolutionist you simply invoke special pleading to explain away contradictory data.

      Natural selection is hardly special pleading, and has been an integral part of the theory since it was first proposed.

      lifepsy: Because, unlike yourself, I've actually studied the matter and have transcended simple mantras that you seem constrained to.

      Sorry. Thought it might have had something to do with the evidence.

      Delete
    5. Zachriel: Natural selection is hardly special pleading

      Natural Selection is the definition of special pleading. It explains nothing. Equivalent with "evolution dunnit". With such blind credulity it's no wonder you embrace such a vacuous non-falsifiable model like common descent.

      Delete
    6. lifepsy: Natural Selection is the definition of special pleading. It explains nothing.

      Handwaving. The relationship between the environment and morphology (natural selection) can now be directly observed.

      Delete
    7. Zachriel,

      "The relationship between the environment and morphology (natural selection) can now be directly observed."

      In what way? Don't misunderstand, I can accept natural selection to a degree, but the simple truth is the concept is not without its problems.

      The whole case for it basically boils down to 'that which survives, survives.' You in fact cannot build a case which clearly demonstrates that the fittest indeed survives, as that which survives is simply declared to be the fittest based solely on the fact it has survived. Too many other factors can be in play which renders such a conclusion tenuous.

      Delete
    8. Nic: In what way?

      Directly. You just have to be patient. Price et al., Recurrent patterns of natural selection in a population of Darwin's finches, Nature 1984.

      Nic: The whole case for it basically boils down to 'that which survives, survives.'

      No. Natural selection posits a correlation with the environment. See Grant & Grant, Unpredictable Evolution in a 30-Year Study of Darwin's Finches, Science 2002.

      Nic: Too many other factors can be in play which renders such a conclusion tenuous.

      Which is why Darwin could only posit natural selection. However, if you are very patient, and get to know every individual in a population, and their children, and their children's children, and take lots and lots of notes, then you can demonstrate a correlation between the environment and heritable traits.
      http://explore-evolution.unl.edu/grant.html

      Delete
    9. Nic, otherwise known as the SHL. (Stuff Happens Law)

      It's funny how many prominent evolutionary researchers doing actual analyses in the life sciences have no problem admitting the obvious tautological nature of attributing the origin of a biological feature to natural selection.....

      Yet the common net-Evo like Zachriel believes he is actually explaining something when he says a morphological trait evolved because it helped the organism survive. And to top it off he will accuse you of hand-waving for pointing his fallacy of reasoning out to him... truly a bizarro world that evolutionists inhabit.

      Delete
    10. nic:The whole case for it basically boils down to 'that which survives, survives.'

      Sorry to interrupt bit your synopsis leaves out a key feature. Perhaps better might be" that which survives has a higher rate of reproduction than that which does not survive"

      Delete
    11. lifepsy: It's funny how many prominent evolutionary researchers doing actual analyses in the life sciences have no problem admitting the obvious tautological nature of attributing the origin of a biological feature to natural selection.

      You might want to cite the actual argument.

      Population geneticists will often assume natural selection is occurring when a population undergoes change beyond what can reasonably assumed to be due to stochastic mechanisms.

      On the other hand, you will notice that we provided a study that predicts phenotypic evolution from environmental changes, so your objection falls flat.

      Delete
    12. nic:The whole case for it basically boils down to 'that which survives, survives.'

      There is a book called The Selfish Gene. You might have heard about it. It elaborates on how, in biological Darwinism, individual genes are replicators. They play a causal role in being copied into the next generation.

      So, in some cases, as a result of being copied the organism becomes less fit.

      For example, a mutation that would cause a bird to nest earlier in the season could result in it getting copied due obtaining better nesting locations, while at the same time making the birds life more difficult due to having their young in colder weather.

      You've got the unit wrong. It's not at the level of an organism, or even the genome as a whole. You're confused about they very theory you're trying to criticize.

      Delete
    13. Scott,

      " individual genes are replicators. They play a causal role in being copied into the next generation."

      Genes replicate, evolution has nothing to do with it.

      "So, in some cases, as a result of being copied the organism becomes less fit."

      Actually that happens each time. It has been known for a long time the genome is deteriorating with time.

      "For example, a mutation that would cause a bird to nest earlier in the season could result in it getting copied due obtaining better nesting locations, while at the same time making the birds life more difficult due to having their young in colder weather."

      Nice story.

      "You've got the unit wrong. It's not at the level of an organism, or even the genome as a whole. You're confused about they very theory you're trying to criticize."

      Where did I ever say it occurred at the organism level? This is nothing more than you making assumptions, again.









      Delete
    14. nic: Actually that happens each time. It has been known for a long time the genome is deteriorating with time.

      No, that is not "known".

      Delete
  6. OK, let's come back to the Anthony D. Keefe & Jack W. Szostak Study.

    http://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf

    Let's notice a few thing. first lets notice the size of the protein involved.

    In vitro selection and amplification of mRNA-displayed proteins. The DNA library
    encodes proteins with 80 contiguous random amino acids.


    So it's a very small polypeptide. So the probability given is for a tiny protein. Think not?

    Let's look at the protein chains involved in transport in various single celled organisms:.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC94969/

    Pay attention to Table 1. Notice the smallest average residue, (amino acid chain), is for the Archaea major intrinsic protein (transport channel) at 246, not 80. Notice the size of most of them is far larger. So is 80 residues a good choice to determine the probability of a functional protein arising? Not really. This is very small number. This is what is used to arive at the 10^11 number. Now the Axe study used a modest protein chain composed of 153 residues. That's still less than the smallest average residue involved in the transport system of a Archaea. Hence the probability of 10^77. And as we see that's a very small protein. Smaller than the smallest protein used in the transport system of the simplest one celled organisms. Now let's got to table 2.

    The smallest average residue is for the Major intrinsic protein of a plant at 268 residues. Most are over 500. The animal residue with the smallest average residue is Major intrinsic protein at 315. Most are well over 500 residues. So was Douglas Axe inflating his numbers? No, he was probably far to conservative. The more realistic polypeptide of 300 residues yields a result of 10^151 to 10^104. That's older than the universe by a good bit.

    So we see the likelihood of a de novo, (from scratch), protein sufficiently large to perform a function is astronomically high. Further when you look at a polypeptide fold you must consider the side chains. Wrong side chains and the polypeptide won't from a stable fold. Then you consider that many structures are composed of smaller folds, which must form a tertiary fold. Now in the Keefe/Szostak study they never folded the protein, they just looked at the bonds and assumed it would fold:

    We selected for proteins that could bind a small molecule target with
    high affinity and specificity as a way of identifying amino-acid
    sequences that could form a three-dimensional folded state with a
    well-defined binding site and therefore exhibit an arbitrary specific
    function.


    But we have no reason to suppose it actually would simply from looking at the bonds, or to believe the bonds would be particularly strong, plus side chains aren't eve mentioned.. This is why the Axe study is untouched. Until a better explanation is forth coming I see little reason to accept Darwinian claims.

    So are we now beginning to see the magnitude of the problem?

    ReplyDelete
  7. Even if functional proteins were not all that rare, to evolve one protein form another involves a number of changes in the amino acid sequence. So untill all the changes happen a uselless floppy protein will be produced. Do we know of any actual examples of useless proteins being produced in organisms currently? Why shouldn't we see the process in happeing now? I would imagine that that producuing useless proteins woudl eb metabolically expensive.

    ReplyDelete
    Replies
    1. natschuster: Even if functional proteins were not all that rare, to evolve one protein form another involves a number of changes in the amino acid sequence.

      There are various mechanisms, including mutation, frameshifts and shuffling.

      Mutation
      Negoro et al., Nylon-oligomer Degrading Enzyme/Substrate Complex: Catalytic Mechanism of 6-Aminohexanoate-dimer Hydrolase, Journal of Molecular Biology 2007.

      Frame-shift
      Okamura et al., Frequent appearance of novel protein-coding sequences by frameshift translation, Genomics 2006.

      Riechmann & Winter, Novel folded protein domains generated by combinatorial shuffling of polypeptide segments, Proceedings of the National Academy of Sciences 2000.

      Delete
    2. Mutation:

      Protein truncation. No new information. No new structure.

      Frame-shift: See here

      http://onlinelibrary.wiley.com/doi/10.1002/cplx.20365/abstract

      Also addresses nylonase eating bacteria.

      Last study is both out of date and a mere 70 residues. Barely a polypeptide. Authors had this to say:

      .We do not know how frequently such recombinations would take place in nature, because these would be expected to depend on many factors, including the number of segments and the distance between each pair of segments on a chromosome and the presence of small regions of homology.

      Further this study does not address the boundaries which is surely a factor in forming tertiary folds. So all in all it doesn't answer the question of a fold that can be incorporated in a tertiary fold to build a novel structure.

      For a more recent study:

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714538/pdf/nihms-62844.pdf




      Delete
    3. eklektos: Protein truncation.

      None of your comments rebut that new proteins can evolve from old proteins.

      eklektos: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714538/pdf/nihms-62844.pdf

      "We have described an experimental system by which secondary structure elements are combinatorially assembled into a library that contains soluble proteins with significant secondary structure."

      Graziano et al. supports that new proteins can be created by recombining non-homologous regions.

      Delete
    4. Yea, there's no counter argument to that...

      Delete
    5. Zachriel,

      Oh, and they didn't fold any of them. In fact they said:

      The selected clones should therefore not be considered viewed as “native-like” proteins but rather “molten globule-like”46 perhaps as an intermediary stage (This is pure conjecture, not proof of anything.) in the evolution from a random assembly of secondary structural elements towards a compact stable protein.

      So no, it doesn't support anything. Perhaps is not did. Always look for the disclaimer! You would have known this if you'd read the loony creationist paper. So far your 0 for? Lost count.

      Delete
    6. eklektos: they didn't fold any of them

      They folded, but didn't have stable tertiary structures. They were interested in studying folds to see if there were novel folds not found in nature.

      Delete
  8. eklektos: So the probability given is for a tiny protein.

    Longer proteins can evolve from smaller proteins as long as the precusors are functional. Your original contention was that novel functional proteins couldn't arise. In fact, they occur in randomized libraries.

    ReplyDelete
    Replies
    1. Zachriel, evolution theory is waaay beyond that.

      Your camp is now saying that whole protein-coding genes (Orphan genes) can become functional all at once (from a previous state of non-function), without having to accumulate incrementally selected variations from ancestors.

      So... No, according to your theory, precursors do not even need to be functional. Is this hypothesis based on data? Of course not. It's based on being the only ad-hoc explanation that saves the theory after finding so many protein-coding genes with no signal of common ancestry between any other taxonomical groups.

      You waved goodbye to potential falsifiability in molecular biology a long time ago. Evolution theory has nothing resembling such criteria. It's storytelling.

      Delete
    2. lifepsy: Your camp is now saying that whole protein-coding genes (Orphan genes) can become functional all at once (from a previous state of non-function), without having to accumulate incrementally selected variations from ancestors.

      That's one way new proteins occur. However, the new function is almost certainly going to be weak, but rounds of selection will tend to improve function.

      lifepsy: No, according to your theory, precursors do not even need to be functional.

      New proteins are normally made up of components of older proteins, or are mutations of older proteins.

      lifepsy: Is this hypothesis based on data?

      Yes. If you use a random sequence library, new proteins have a minimum density of 10^-11.

      Delete
    3. Zachriel: New proteins are normally made up of components of older proteins, or are mutations of older proteins.

      Except when they're not, of course. (e.g. Orphans)

      I think the subject of potential falsifiability just flew about a mile over your head.

      Delete
    4. lifepsy: Except when they're not, of course.

      Which is why we said "normally". However, we have seen that exon shuffling can generate novel proteins.

      Delete
  9. Zachriel,

    give me a mechanism whereby shorter proteins can evolve into longer ones. And remember, a flagellar motor is a luxury compared to a transport system which is not. And before you say exon shuffling define exactly what you mean by exon shuffling. Are you talking about shuffling folds or sections of folds?

    ReplyDelete
    Replies
    1. eklektos: give me a mechanism whereby shorter proteins can evolve into longer ones... And before you say exon shuffling define exactly what you mean by exon shuffling.

      You can read about exon shuffling here:
      http://en.wikipedia.org/wiki/Exon_shuffling

      eklektos: Are you talking about shuffling folds or sections of folds?

      In metazoa, domains are preferentially shuffled due to the arrangement of introns. However, for our purposes, it can be any section of a gene. Density of new proteins is on the order of 10^-5 to 10^-7.

      Delete
  10. I'm confused. On one hand, we hear the supposed astronomical probability of finding just the right protein that will result in just the right biological features supposedly makes biological darwinism astronomical unlikely.

    On the other hand, why wouldn’t this same supposed astronomical probability of finding just the right protein make a designer finding just the right protein astronomically unlikely as well? It’s unclear why it a problem for evolution, but not a designer.

    IOW, why don’t you start out by explaining how a designer would just so happen to know just the right proteins that would result in just the right biological features, then point out how biological Darwinism doesn’t fit that explanation.

    ReplyDelete
    Replies
    1. Scott,

      "IOW, why don’t you start out by explaining how a designer would just so happen to know just the right proteins that would result in just the right biological features, then point out how biological Darwinism doesn’t fit that explanation."

      Wow! Could it possibly have something to do with the fact that a designer, by definition, possesses intelligence, forethought and intent, while blind, purposeless, goalless and mindless evolution does not? Just maybe that would have something to do with the difference, don't you think?

      Delete
    2. Nic: Just maybe that would have something to do with [possesses intelligence, forethought and intent], don't you think?

      What do I think? I asked you, Nic.

      Apparently, you think it’s obvious. So, humor me. How does possessing intelligence, forethought and intent translate into possessing the knowledge of just the right protein out of an astronomical number that would result in just the right biological feature? How does it that work, in practice?

      For example, when Darwin formed his theory, we didn't even know genes or proteins even existed. Did we not posses intelligence, forethought and intent? 150 years later, we know a lot more than we did then, yet we're just scratching the surface. Do we not posses intelligence, forethought and intent today?

      IOW, it’s seems that there is some additional assumption that you haven’t yet disclosed, by which you connect the dots, which you think is obvious. What might that be?

      Delete
    3. Scott,

      "What do I think? I asked you, Nic."

      Really, when?

      "Apparently, you think it’s obvious. So, humor me. How does possessing intelligence, forethought and intent translate into possessing the knowledge of just the right protein out of an astronomical number that would result in just the right biological feature? How does it that work, in practice?"

      You're right, I do think it's obvious for the simple fact that a mind which would be able to create a protein to begin with would be able to use their creation to build further features. Does that not make sense?

      It would appear you're vision of a designer is that of a being who came along and found a bunch of proteins floating around and while he did not really understand them decided he would use them to create more complicated features.

      Due to your stunted concept of this designer you naturally assume he would not have the knowledge or understanding necessary to accomplish his ends.

      You're problem is you think of a finite designer, while I lean more to the omnipotent, infinite type.

      "IOW, it’s seems that there is some additional assumption that you haven’t yet disclosed, by which you connect the dots, which you think is obvious. What might that be?"

      Well I must say if you think I have not disclosed my position I would have to conclude you're very slow on the uptake. I would hazard to guess everyone else reading what I have posted would not be confused as to where I'm coming from, whether they agree with me or not.

      Delete
    4. Nic: Well I must say if you think I have not disclosed my position I would have to conclude you're very slow on the uptake. I would hazard to guess everyone else reading what I have posted would not be confused as to where I'm coming from, whether they agree with me or not.

      You claim positing a designer solves the problem. But you merely end up with a variation on the very same problem.

      All you've done is claim the knowledge in organisms was previously located in a designer. But that doesn't explain the origin of that same knowledge which is supposedly just the right gene out of an astronomical number. You're still left with the same problem: the origin of that knowledge.

      That's why I asked for an explanation of how intelligence, forethought and intent actually translate into possessing the knowledge of just the right protein. Merely claiming it's "obvious" dodges the question. That would be like saying "it's obvious how evolution works", which I'm not.

      IOW, you've merely pushed the food around on your plain and claimed you ate it. Yet it's still right there staring you in the face.

      And I'm slow on the uptake?

      Delete
    5. Scott,

      "Still waiting."

      For what?

      "All you've done is claim the knowledge in organisms was previously located in a designer. But that doesn't explain the origin of that same knowledge which is supposedly just the right gene out of an astronomical number. You're still left with the same problem: the origin of that knowledge."

      Are you serious? Please tell me I'm wrong. You're not making the 'who designed the designer' argument are you? I wouldn't be surprised as you seem to be a Dawkins groupie.

      "And I'm slow on the uptake?"

      Yep, as evidenced by your comment to eklektos vis a vis the lack of afarenis feet.

      eklektos: There has been no afarenis skeleton found with feet."

      Scott: IOW, when we take into account the rest of our best explanations for how organisms compete and survive, the idea that afarenis lacked feet does not survive criticism."

      That's just classic. Sorry, it took me a while to stop laughing at that one.

      Delete
    6. Nic,

      Be patient with Scott, he's still emerging. :)

      Delete
  11. [continued]

    For example…

    eklektos: Claims about the nature of the designer is outside the realm of science.

    So, apparently, you have a designer that just so happens to know exactly which protein out of a supposed astronomical number would result in just the right features, yet you lack an explanation as to how it came to posses this knowledge.

    ReplyDelete
    Replies
    1. No, it's designed. You can't interrogate the designer. You can't scientifically explain the designer. All you can say within the realm of science is natural explanations don't work. Hence it must be designed. I know that it bothers you. But if Darwinism is wrong all you're doing is wasting resources on a fruitless endeavor.

      Delete
    2. eklektos: No, it's designed. You can't interrogate the designer. You can't scientifically explain the designer.

      Ok, for the sake of argument, let's assume that statement is true for some reason you have yet to elaborate on. How do you that biological Darwinism doesn't "work" in a way that mimics how this supposed designer would have done, when you're the one claiming we can't know said designer works in the first place?

      Are you saying that it's impossible for biological Darwinism to mimic this supposed designer, in principle? As such, it's a fruitless endeavor?

      Delete
    3. Scott,

      Mimic implies intentionality. Nature has no intentions. You're anthropomorphizing.

      Delete
  12. I asked earlier if it was ontologically necessary that science explain human origins. The one response I got was no. If it's not ontologically necessary then why the fight over ID? Because despite the claims to the contrary the Darwinists feel it is absolutely ontologically necessary. Because the alternative is horrifying to them.

    ReplyDelete
    Replies
    1. We can solve some problems using incomplete theories that contain errors to some degree. So, not it's not necessary to solve absolutely any problem.

      But, in the same sense, we do not need to have a working theory of abiogenesis to have a working theory of evolution, even when evolution is incomplete and contains errors to some degree.

      eklektos: Because despite the claims to the contrary the Darwinists feel it is absolutely ontologically necessary. Because the alternative is horrifying to them.

      Despite being a Darwinist, I don't think we can ever have one single theory to explain everything. Rather, I think problems will always lead to even better problems, which will lead to even better problems, etc.

      Billions of years from now (assuming we create the necessary knowledge in time to survive that long), people (in whatever form they take at the time) will still have problems. They will just be far removed from the problems we have as people today, which we have yet to even conceive of.

      So, apparently, I'm not a Darwinist?

      Delete
    2. eklektos: Because the alternative is horrifying to them.

      I'm confused. If Darwinism means we just die, wouldn't that be more horrifying than the alternative you propose? IOW, if anyone would be horrified by the prospect of the alternative being true, wouldn't it be you?

      But Evolutionary theory isn't abiogenesis. As such, the theory is only interested in the origin of biological features. So, this is merely hand waving based on, well, a misconception of disingenuous presentation of the theory itself.

      I'd point out the theistic idea of eternal punishment isn't tied to ID or even a supernatural designer. It's a specific theological assumption which is not necessarily implied in any of your arguments.

      For example, I'd point out our biosphere could be equally (poorly) explained as the result of an all powerful, perfectly good God and his equally powerful evil twin brother; both of which are diametrically opposed opposed to each other's goals.

      And we're the one's that are dogmatic and not open minded?

      Delete
  13. Where are these graduated steps? In nature. Anyways a common design would make common looks for common needs?
    Anyways other mechanisms are a option for details? Darwin is persuading himself of his idea by simply eliminating other ideas. Thats not science. Its about imagination limitation.
    A creator could have other options going on though not noticed.
    like human colour differences.
    convergence is unlikly if evolution was true.
    Do people know how convergence is claimed for such alike but unrelated critters?
    Its absurd what they must say.
    marsupials just being a example.

    ReplyDelete
    Replies
    1. Robert Byers: Where are these graduated steps?

      Good question, and a primary area of interest for Darwin. The graduated steps are found not only in fossils, but also in extant life.

      Delete
    2. The steps are not found in fossils. What is found are fossils of types of creatures. The steps are speculation. No steps are fossilized unles you can show me.
      finding differences in extant/fossil life is not scientific biological evidence for evolution. its just evidence of different types.
      Other mechanisms are a option .
      still they are not proven evidence however persuasive to someone who wants to see it.
      science only please.

      Delete
    3. Robert Byers: No steps are fossilized unles you can show me.

      There's a clear progression from the simplest chordates to birds. But let's take a closer look.

      Increasing skull size:
      http://www.evolution-textbook.org/content/free/figures/25_EVOW_Art/11_EVOW_CH25.jpg

      Here's dinosauria:
      http://www.gavinrymill.com/dinosaurs/Cladogram/CladogramComplete.jpg

      Equine foot
      http://chem.tufts.edu/science/evolution/horse_series_icon.gif

      Reptile-mammal jaw
      http://daphne.palomar.edu/ccarpenter/jaws1.gif

      Robert Byers: finding differences in extant/fossil life is not scientific biological evidence for evolution.

      If evolution posits a transitional process, and we find transitional organisms, it is evidence supporting evolution.

      Delete
    4. None of this shows what you say it shows. It only shows what it shows. Different types of something.
      Again it shows NO evolutionary connection between them. All one has to do is have another option for these fossils looks. Therefore its nOT biological scientific evidence.
      Where? Where is the biology?
      You didn't confirm a prediction of transitions by biological change.
      All you did was show types of something(s)
      You showed no biology but only a guess about biology in geology stratas.
      I await if you have any biological scientific evidence to allow evolution to be a theory.
      This is science. Not mere guessing however one thinks its reasonable as a guess.

      Delete
    5. Robert Byers: Different types of something.

      They show incremental change, "steps".

      Robert Byers: Again it shows NO evolutionary connection between them.

      You asked for "steps". We showed you steps.

      Delete
    6. Zachreil,

      you showed us fossils and claimed steps.

      Delete
  14. Now all of the interactions I've seen here are straight out of the talkorigins, Eugene Clark, et al playbook. They pick hills to die on and then use disingenuous debate tactics. Afarensis being an example. If the found a mummified Homo skeleton in the hadar formation they would still explain it away. If the genetic numbers don't work toss out some generalized jargon and which they don't really understand. If the fossil record doesn't fit their "theory" make statements like "The fossil record strongly supports evolution" even if it's totally incomplete. You don't really get arguments, you get assertions. They citation bluff. But they don't really understand or frequently even read the citations they post. Darwinism is a religion. Cornelius is right it does matter. I pray for their repentance because I know what awaits them. I also pray for those who are authentically my brethren who think they can make peace with this whole materialistic enterprise. Because they have emptied the Gospel of content. If death is natural then God either lied or didn't speak. This is the conclusion these people want Christians to draw. It's been remarkably successful. In the end however their victory will be pyrrhic. It ain't going to be pretty. So ramble away. I won't even be watching. God bless those who continue the battle. Amen.

    ReplyDelete
    Replies
    1. eklektos: "The fossil record strongly supports evolution" even if it's totally incomplete.

      Of course the fossil record is incomplete. But it is complete enough to know that mammals didn't occur in the Precambrian and that mega-dinosauria died out millions of years ago.

      eklektos: I pray for their repentance because I know what awaits them.

      Oh gee whiz. No one is doomed to hell because they subscribe to a well-supported scientific theory.

      Delete
    2. God says in Romans they suppress the self-evident truth and puff themselves up with vain imaginations. Those who profess themselves wise, become fools. I can't think of a better description of people who readily accept and promote the superstitious idea that humans and a blade of grass mystically arose from a common ancestor. Evolution is religion on steroids. It's a wall people put up between themselves and the Creator to try and shield themselves from the light of truth in their hearts.

      Delete
    3. eklektos:I can't think of a better description of people who readily accept and promote the superstitious idea that humans and a blade of grass mystically arose from a common ancestor.

      It seems a foolish man that dictates to God the way He can act, that believes God could not choose to create in any way He wished, that he can comprehend the infinite with his finite mind.

      Delete
    4. Pardon for the incorrect attribution eklektos,my finite mind did not get enough sleep last night

      Delete
    5. Velikovskys, I don't follow the unknown gods that darwinian mystics and theistic evolutionists follow. I follow the Word of God, Jesus Christ.

      Delete
    6. In other words, the objections to the theory of evolution are not founded on the alleged inadequacies of the science but on conflicts with religious beliefs, in particular, literalist readings of the Bible.

      What you seem unable to comprehend is that there are those of us who feel no need of a god or anything else to 'worship' and who are able to live fulfilling lives without comforting mythologies (well, except maybe for Star Trek) as a prop.

      Delete
    7. lipesy:Velikovskys, I don't follow the unknown gods that darwinian mystics and theistic evolutionists follow. I follow the Word of God, Jesus Christ.

      What was his view on Darwinian evolution?

      Delete
    8. Zachriel,

      Oh gee whiz. I didn't sat that.

      Delete
    9. Ian: and who are able to live fulfilling lives without comforting mythologies (well, except maybe for Star Trek) as a prop.

      Yes Yoda was very smart

      Delete
    10. Ian,

      'In other words, the objections to the theory of evolution are not founded on the alleged inadequacies of the science but on conflicts with religious beliefs, in particular, literalist readings of the Bible."

      The inadequacies of evolutionary theory are not alleged, they are very real indeed. In fact they are terminal.

      "What you seem unable to comprehend is that there are those of us who feel no need of a god or anything else to 'worship' and who are able to live fulfilling lives without comforting mythologies (well, except maybe for Star Trek) as a prop.'

      Speaking only for myself I can very much comprehend that there are those who feel no need of a 'god' or anything else to worship, as I was there for many years myself. I can understand your ability to believe you can lead fulfilling lives apart from any form of conventional religious belief.

      However, what you don't comprehend is that you are simply living on borrowed capital. Your moral positions are borrowed from faith systems of various kinds and your comforting mythologies are all too real, they simply exist in a different form. And you do indeed 'worship' at a variety of alters. Some worship the self. Others may worship science or nature. Whatever it may be, you do indeed worship and adhere to comforting mythologies. Perhaps the biggest mythology you adhere to and to which you are totally blind, is that you truly believe what I just said is completely untrue. C'est la vie.

      Delete
    11. nic The inadequacies of evolutionary theory are not alleged, they are very real indeed. In fact they are terminal.

      The overwhelming majority of the world's evolutionary biologists beg to differ. Now, either they are all engaged in a mass conspiracy or prey to some vast delusion or you are wrong.

      nic However, what you don't comprehend is that you are simply living on borrowed capital.

      I'm not really sure what you mean by that. Would you care to elaborate?

      nic Your moral positions are borrowed from faith systems of various kinds and your comforting mythologies are all too real, they simply exist in a different form.

      Borrowing "moral positions" from other sources - although I prefer to say "adopting" - is a time-honored tradition. There is evidence of the Golden Rule pre-dating Christianity, for example. There are few enough good ideas. We should hang on to whatever we can find.

      nic And you do indeed 'worship' at a variety of alters. Some worship the self. Others may worship science or nature.

      To me, "worship" implies an uncritical adherence and almost fawning obeisance. That may be true of a few defenders of science - people are a mixed bunch after all - but not of the majority. Science is fallible, as are all human enterprises, and we tend not to worship imperfection. If anywhere, I find the spirit of science expressed in a comment made by Winston Churchill about war, namely that there was no certain way to win one, all you could do was to keep trying.

      nic Whatever it may be, you do indeed worship and adhere to comforting mythologies.

      Doubt and uncertainty, an awareness of one's own impermanence and mortality are not exactly comforting beliefs.

      Delete
    12. Ian,

      They're certainly deluded.

      Delete
    13. Ian.

      "The overwhelming majority of the world's evolutionary biologists beg to differ. Now, either they are all engaged in a mass conspiracy or prey to some vast delusion or you are wrong."

      So what? The vast majority of 16th century scientists supported geocentrism, so obviously majority opinion does not count for much in the face of facts. And please don't try to bring up the red herring of the church persecuting Galileo.

      As for mass conspiracy and mass delusion, or I am wrong, this is simply the result of your narrow thinking. What the vast majority of biologists today do adhere to is a particular set of presuppositions. Those presuppositions leave them no alternative but to believe evolution to be a fact.

      "I'm not really sure what you mean by that. Would you care to elaborate?"

      Your moral compass comes from the teachings of one religion or another. You simply do not acknowledge that as your source, in other words, borrowed capital.

      "Borrowing "moral positions" from other sources - although I prefer to say "adopting" - is a time-honored tradition. There is evidence of the Golden Rule pre-dating Christianity, for example. There are few enough good ideas. We should hang on to whatever we can find."

      Thank you, you just confirmed my statement.

      "To me, "worship" implies an uncritical adherence and almost fawning obeisance."

      That does not mean you don't worship anything. Worship is a very personalized activity. You may worship in a way you don't define as worshipful, ut you do engage in it.

      Delete
  15. Zachriel said

    "Of course the fossil record is incomplete. But it is complete enough to know that mammals didn't occur in the Precambrian."

    Please Zachriel could you explain how the fossil record make that?

    ReplyDelete
    Replies
    1. Blas: could you explain how the fossil record make that?

      Not only are there no mammals found in the Precambrian, but no land vertebrates, no amniotes, no gnathostomes. Instead, we have a progression, from the first vertebrates to gnathostomes to lobed fishes to amniotes to land vertebrates to mammals to placentals to hominines to hominids. While there may be some uncertainty about the first appearance of each of these groups, the pattern is clear. There were no mammals in the Precambrian because they would predate any plausible ancestor.

      Could centaurs and griffins be natural creatures that just died out?


      Delete
    2. Ah, the final refuge of the evolutionist: "no mammals in cambrian", etc.

      Of course the lower paleozoic rock layers are characterized by largely benthic ecosystems. So there is really no reason to expect either land vertebrates, or pelagic aquatic mammals to be found there.

      Evolutionists, for some odd reason, insist that they should be found there if Evolution isn't true.

      Zachriel does not realize that if a different fossil pattern had been uncovered (throughout the 18th,19th, 20th centuries) Evolution theory would have adjusted itself accordingly to fit the data. (e.g. Thomas Huxley once proposed mammals evolved from amphibians due to anatomical similarities)

      The obvious implication being that Evolution does not predict or explain the fossil record, it merely accommodates the data like everything else.

      Zachriel: While there may be some uncertainty about the first appearance of each of these groups...

      Understatement of the century, Zach.

      Zachriel: the pattern is clear

      Clearly non-evolutionary, yes.

      Delete
    3. lifepsy: Ah, the final refuge of the evolutionist: "no mammals in cambrian", etc.

      It's not just no mammals in the Precambrian, but a clear succession over time.

      lifepsy: Of course the lower paleozoic rock layers are characterized by largely benthic ecosystems.

      Why would that be?

      Delete
    4. "Not only are there no mammals found in the Precambrian, but no land vertebrates, no amniotes, no gnathostomes."

      Absence of evidence it is not evidence of absence.

      "Instead, we have a progression, from the first vertebrates to gnathostomes to lobed fishes to amniotes to land vertebrates to mammals to placentals to hominines to hominids."

      But the some theory that try to explain this "obvious" progression states that many intemediate forms are not fossilized because the fossil record is incomplete.
      And according that progression in the fossil record we understood that many life forms become extint , by they are her with us now.
      Also according that progressio titaalik should be the ancestor of tetrapods, and then we found that just a "blink of an eye" of 15 My before a full walking tetrapod lived on the land.

      " While there may be some uncertainty about the first appearance of each of these groups, the pattern is clear. There were no mammals in the Precambrian because they would predate any plausible ancestor."

      This is turning an explanation in evidence. If evolution were true we can explain the "clear" pattern. Then the fossil record it is not "strong support" for ToE, fossil record is one of the possible explanations of the fossil recors. If you want we can discuss if ToE is the most parsimonious explanation of the fossil record.
      Until darwinist recognize this simply point of logic the discussio is worthless.

      "Could centaurs and griffins be natural creatures that just died out?"

      There is evidence in the fossil record that they didn`t exist?

      Delete
    5. Zachriel: Why would that be?

      Uh, because that's what we find: benthic ecosystems buried and fossilized.

      There is certainly no evidence of Paleozoic creatures "evolving" the morphological systems that we find them with. Just the same pattern of suddenly appearing highly differentiated creatures.

      As an evolutionist, do you ever get tired of constantly fighting the data?

      Delete
    6. Blas: Absence of evidence it is not evidence of absence.

      We have lots of evidence.

      Blas: But the some theory that try to explain this "obvious" progression states that many intemediate forms are not fossilized because the fossil record is incomplete.

      Take all the life in the history of Earth, randomly sample it over time, weight the sampling towards organisms with larger bones, and according to environmental conditions.

      What would you see? The more samples, the more complete your picture. You might be able to interpolate and search for fossils to fill those gaps. But as time goes on, the pattern becomes clear. There's an historical progression.

      Blas: And according that progression in the fossil record we understood that many life forms become extint , by they are her with us now.

      There's nothing that says an organism has to go extinct. However, you're probably thinking of organisms such as the coelacanth, often called a living fossil, but the modern coelacanth is not the same species as from millions of years ago.

      Blas: Also according that progressio titaalik should be the ancestor of tetrapods, and then we found that just a "blink of an eye" of 15 My before a full walking tetrapod lived on the land.

      Titaalik is a transitional, a close relative, but not a direct ancestor of modern tetrapods.

      Blas: If evolution were true we can explain the "clear" pattern.

      The fossil record is consistent with evolution.

      Blas: Then the fossil record it is not "strong support" for ToE, fossil record is one of the possible explanations of the fossil recors.

      When predictions about the fossil record are repeatedly verified, then it is considered strong support.

      Blas: If you want we can discuss if ToE is the most parsimonious explanation of the fossil record.

      Be happy to.

      Zachriel: Could centaurs and griffins be natural creatures that just died out?

      Blas: There is evidence in the fossil record that they didn`t exist?

      Consider that scientists predicted a 'fishapod'. They journeyed to the Canadian arctic to find strata of the appropriate age, spent years looking, and found a fishapod.

      Per evolutionary theory, centaurs and griffins have no plausible ancestors. Their existence would contradict what we know about biology. But virtually no one spends any time looking for centaurs, even if they don't 'believe' in evolution. On the other hand, centaurs and griffins do have the earmarks of *design*!

      Delete
    7. lifepsy: Uh, because that's what we find: benthic ecosystems buried and fossilized.

      There was dry land in the Cambrian. Fossil life there is primarily composed of microbial mats.

      In any case, so we agree, there were no land mammals in the lower Paleozoic.

      Delete
  16. When exons are shuffled to make new proteins, don't you also have to change the system for cutting out the introns, and splicing the exons, as well? How lse will the new proteins be formed. Isn't intron excision a very precise process?

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    1. natschuster: When exons are shuffled to make new proteins, don't you also have to change the system for cutting out the introns, and splicing the exons, as well?

      Genomes are not completely static, but include mobile genetic elements, such as transposons.

      Delete
    2. But can you change a part to make a new protein without changing the things that work with that part, like the enzymes that cut and paste the exons. Is exon reshuffling a really viable explanation for new proteins.

      Delete
    3. natschuster: But can you change a part to make a new protein without changing the things that work with that part, like the enzymes that cut and paste the exons.

      A single gene sequence can and are made into more than one protein. Here's an animation to show you the process:
      http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter16/animation_-_exon_shuffling.html

      Delete
    4. But that is only possible because of a very complex cut and paste system, isn't it? So you can't change they genes without changing the whole system, can you?

      Delete
    5. natschuster: So you can't change they genes without changing the whole system, can you?

      First, the proteins can be changed without changing the whole system by changes in the splicing order. Genes can also be changed when they are copied to other parts of the genome.

      Delete
  17. Oh look, chimps and humans genomes are only 70% similar. Once again the impartial scientist didn't tell the whole story. What a shock!

    http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome

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    1. eklektos: http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome

      The "paper" simply discusses actual research. See The Chimpanzee Sequencing and Analysis Consortium, Initial sequence of the chimpanzee genome and comparison with the human genome 2005. The key is once again in the title of the paper; Initial sequence. The entire genome had not yet been compared. Even before sequencing was available, simple DNA reannealing experiments showed that the DNA similarity is more than 98%.

      Delete
    2. Zachriel,

      What has been compared is not 99%, 98%, 97% etc. And I read the referenced papers.

      Delete
    3. Zachriel,

      Also as the paper points out that figure was arrived at by cherry picking the data.

      Delete
  18. Supposed Ape/Human fusion site:

    http://www.answersingenesis.org/articles/arj/v6/n1/human-chromosome-fusion
    Once again we see that close examination of the claims does not bear the supposed fusion. And attempts to get around the discrepancies are not based on anything actually observed.

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    Replies
    1. eklektos: Once again we see that close examination of the claims does not bear the supposed fusion.

      The gene is part of a family that always appear on the ends of chromosomes, so it's not unusual. Did you think evolutionary theory predicted that evolution would stop when humans first evolved?

      Costa et al., DDX11L: a novel transcript family emerging from human subtelomeric regions, BMC Genomics 2009.

      Delete
    2. Didn't read it, did you? You're such a fraud. Citation Bluffing won't get it.

      Delete
    3. eklektos: Citation Bluffing won't get it.

      "Our data provide an additional clue to the duplication and the evolution of the human subtelomeres, confirming the high degree of plasticity of these regions, continuously involved in processes of genomic rearrangements and novel gene creation."

      The data doesn't go away because you don't want to look at it.

      Delete
    4. Zachriel,

      The data doesn't go away because you don't want to look at it.

      Your quote isn't data.

      Delete
    5. eklektos: Your quote isn't data.

      The paper has the data, which shows that DDX11L is a rearrangement of the primate DDX11, and then copied to subtelomeric locations. They point to these regions as creators of novel genes due to their plasticity.

      Delete
    6. Zachreil,

      No, the data is the existence of the genes and their make up. The rest is story telling. It assumes a rearrangement. A carefully crafted display of the supposed rearrangement. Obviously you didn't read the counter argument. Which is hardly surprising.

      Delete
    7. eklektos: It assumes a rearrangement.

      They showed that exon shuffling and common ancestry are sufficient to explain the evidence.

      Delete
    8. They showed it by genetic sequencing.

      Delete
  19. I find this statement by Zachriel quite telling:

    All theories are wrong. Some theories are useful.

    So what is the "usefulness" of Darwinian evolution? I leave you to ponder that.

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    1. eklektos: I find this statement by Zachriel quite telling: "All theories are wrong. Some theories are useful."

      It's a rephrasing of George Box's statement about models. Theories are essentially models.

      eklektos: So what is the "usefulness" of Darwinian evolution?

      It explains and predicts a vast amount of data, from molecular to geological.

      Delete
    2. It explains and predicts a vast amount of data, from molecular to geological.

      Darwinism explains molecules and geology? You should tell the physicist and geologist that. I'd like to see it when you do.

      Delete
    3. eklektos: Darwinism explains molecules and geology?

      We said it explains a vast amount of data, from molecular (such as genes) to geological (such as fossils found in the geological strata).

      Delete
    4. Zachriel,

      It assumes a lot of data fits your model. It actually explains nothing. Particularly as contradictory data and counter arguments are routinely ignored. Just like you did with the Keefe/Szostak paper.

      Delete
    5. eklektos: It actually explains nothing.

      And yet geologists successfully use the model to predict where to find minerals. Lucky guess?

      Delete
  20. CH: This has the virtue of not having to explain how low entropy, high Kolmogorov complexity designs which are astronomically unlikely to have spontaneously arisen (yes, that is what evolution says) even once could have evolved, err, multiple times independently.

    As I mentioned to Nic, There is a book called “The Selfish Gene”. You might have heard of it.

    Genes are biological replicators in that they play a causal role in being copied in the next generation. The resulting design plays a part in that causal role. That’s the underlying explanation behind biological Darwinism. Nor is it random as you keep implying.

    Just as good ideas are good regardless of their source, the advantage a gene has in being being copied is an advantage regardless of it’s source or where it emerges in a particular tree.

    So, your claim that “two men have sometimes independently hit on the very same invention,” is a bad analogy either reveals ignorance of evolutionary theory or a disingenuous presentation.

    CH: And so there you have it. Evolution can explain common descent patterns and .NOT. common descent patterns. This is an example of the great flexibility of evolutionary theory. It doesn’t matter what the pattern is, evolution can explain it. And if a theory can explain both X and not X, then the scientist must not claim X (or not X) as evidence for his theory.

    See above. Common decent is based on genes as replicators. That’s the explanation behind the “evolutionary pattern”. Darwinism is not merely a prophecy divined 150 to be observed or not observed. It is a explanation about how the world works, in reality.

    IOW, implicit in your “argument” that evolution isn’t “science” is a specific definition of science which you never actually argue.

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  21. CH: You can imagine how many readers have been swayed by this passage and others like it in Origins. There’s only one problem: This is all wrong.

    Apparently, Cornelius has some rather creative license with the terms “all” and “wrong”.

    For example, Darwin knew of exceptions, including hybridization, which is reflected in the quote. Nor is it the case that no organs follow the “common decent pattern”. So, the claim that the quote is “All wrong” is, well, false.

    So, this is yet another example of the kind of hand waving we see around here on a regular basis.

    Furthermore, when theories start out as conjectures, we expect them to be incomplete and contain errors to some degree. “Theory X is incomplete and has errors to some degree” is a poor criticism because it’s applicable to all theories. As such, it cannot be used in a critical way.

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  22. I’m glad you distinguish between cosmic rays and a biological species, or organ such as electromagnetic organs which the fish uses to map out its environment, track prey, and even stun prey.

    You were the one who brought up Kolmogorov complexity, despite clearly not understanding it. I am glad that you implicitly admit that your argument has little to do with it.

    It is amazing how much detail evolutionists suddenly demand when the tables are turned.

    The "tu quoque" fallacy. I am not actually demanding any detail; I am just wondering where you get you claims about probability. Your calculations are irrelevant, since you are basing it on a random generation model, which is not what actually happens.

    If nobody know this then how do you know evolution is a fact?

    Because our arguments are not based on bogus probability calculations, any more than models of stellar formation are based on bogus probability arguments. There are many different and converging lines of evidence for evolution; evidence that has sufficed to convince nearly every biologist. The only significant holdouts are those committed to a particular religious view.

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    1. Professor Shallit:

      You were the one who brought up Kolmogorov complexity, despite clearly not understanding it.

      Missed me!!


      I am not actually demanding any detail.

      Well here is what you asked for: Where is the calculation to back up the claim of "astronomically unlikely to have spontaneously arisen"?

      Sorry, but down here we call that “detail.”


      Your calculations are irrelevant, since you are basing it on a random generation model, which is not what actually happens.

      So, a “random generation model” is not what happens huh? Are the mutations guided then? Does the DNA sequence somehow know where to look in hyperspace to overcome the curse of dimensionality and find nature’s proteins? That would be quite a claim. And it would put you squarely outside the evolution camp. More likely you are thinking that natural selection provides directionality. Selection provides a non random filter so nature moves in meaningful directions—the same, non scientific, warmed-over Aristotelianism once again. Well sorry but my calculations do account for that. If you actually read the post you would know that (hopefully). Also, they are not my calculations—they come from four different groups, using different methods, all coming to similar conclusions. You’re ignoring peer-reviewed research because it contradicts your theory.


      Because our arguments are not based on bogus probability calculations, any more than models of stellar formation are based on bogus probability arguments. There are many different and converging lines of evidence for evolution; evidence that has sufficed to convince nearly every biologist. The only significant holdouts are those committed to a particular religious view.

      Actually you have it all backwards. First, the probability calculations are not bogus. That would be quite a conspiracy. Second, those converging lines of evidence? They are “converging” only in the sense that they present enormous problems for your claim that the species arose spontaneously. If you took a scientific look at the evidence you would easily see that. And third it is the arguments for evolution that are “religious.” The problems are from science.

      Delete
    2. CH: So, a “random generation model” is not what happens huh? Are the mutations guided then? Does the DNA sequence somehow know where to look in hyperspace to overcome the curse of dimensionality and find nature’s proteins? That would be quite a claim. And it would put you squarely outside the evolution camp.

      Is there some particular reason why you keep presenting this dichotomy? Or is you strategy to simply ignore alternatives that to not suit your agenda? Specifically, when I ask you what form this guidance would have taken, given uncontroversial aspects about biology, you become mysteriously silent.

      Concrete biological adaptations are literally that: the result of transformations that adapt resources into copies of those organisms. This is opposed to other transformations that would result in other organisms or no organism at all. Apparently, you do not find this controversial as you just appealed to this in your post. So, it seems we are in agreement that organisms know how to build copies of themselves. And they do so because they contain the necessary knowledge of what transformations are required to actually bring that about.

      Therefore, the origin of those concrete biological features is the origin of that knowledge.

      Biological Darwinism is the theory that this knowledge genuinely grows, as opposed to having always existed, via a form of conjecture and criticism. Specifically, conjecture, in the form of genetic variation that is random *to any specific problem to solve*, and criticism, in the form of natural selection. Biological Darwinism mimics design because it falls under the umbrella of our current, best explanation for the universal growth of knowledge.

      IOW, biological complexity emerges from variation and selection. In the process, it genuinely creates the knowledge of how to build concrete biological adaptations. That’s evolutionary theory, which is not random.

      This only put us “squarely outside the evolution camp” if you assume that knowledge in specific spheres comes from authoritative sources. Do you deny this is a key fact of your religious belief?

      CH: More likely you are thinking that natural selection provides directionality. Selection provides a non random filter so nature moves in meaningful directions—the same, non scientific, warmed-over Aristotelianism once again.

      See above. You have conflated the absence of an explanation, and therefore being Aristotelianism, with dogmatically rejecting an explanation because, for example, it conflicts with one’s theological commitments.

      Again, why don’t you start out by explaining how knowledge grows, then point out how biological darwinism doesn’t fit that description. Please be specific.

      Delete
    3. Scott,

      Coded instructions within DNA and epigenetic systems is not knowledge. People know things, biologic systems do not. You're making a fundamental error.

      Delete
    4. CH: First, the probability calculations are not bogus. That would be quite a conspiracy.

      No, it wouldn’t. We’ve been over this before. This claim assumes there is only one kind of unknowability. Apparently, this is yet another example where you simply ignore alternatives that do not suit your agenda.

      While you are correct in that no one can choose what our ideas imply, probability calculations are only valid in specific cases. One of which is if all of the possible outcomes are known, which was the context of the calculations you are appealing to. Specifically, it was attempting to find the probability between a specific number of paths from an existing starting point inside an existing explanatory framework: evolutionary theory. As such, the possible outcomes were known.

      However, is not applicable in respect to evolution, the theory itself.

      While you might hold theological commitments to the contrary, evolutionary theory doesn’t assume that life as we know it was pre-selected. Nor does it assume that the particular ways of solving problems in biology were pre-selected. As such, you have confused calculating the probability of a particular outcome in an existing theory, with calculating the probability that a theory is true.

      IOW, you have confused the probability of a feature evolving a specific way, with the probability of it having evolved at all. These are two different things.

      This is why I keep asking you to explain how it’s possible to extrapolate observations without first putting them into some kind of explanatory framework.

      CH: Second, those converging lines of evidence? They are “converging” only in the sense that they present enormous problems for your claim that the species arose spontaneously.

      The growth of knowledge is not spontaneous. It grows because it is possible to be objectively found in error by natural selection.

      On the other hand, if your designer is simple and does itself need to be explained, then how do you explain how organisms it supposedly created ended up containing the knowledge of exactly which genes would results in just the right proteins, which would result in just the right features? Apparently, that knowledge spontaneously appeared when said designer created them.

      Alternatively, saying this knowledge always existed in a designer doesn’t actually solve the problem at hand. It too would be complex, serve a purpose (designing organisms) and contain knowledge, to be explained as well, etc.

      A designer that “just was” complete with the knowledge of exactly which genes would results in just the right proteins, which would result in just the right features, already present, serves no explanatory purpose. This is because one could more economical claim that organisms “just appeared” complete with the knowledge of exactly which genes would results in just the right proteins, which would result in just the right features, already present.

      This merely pushes the problem into some inexplicable realm. Of course, if one holds the theological commitment that the origin of biological complexity in our biosphere is inexplicable, then it would come as no surprise as to why they would find it an “acceptable” solution.

      CH: If you took a scientific look at the evidence you would easily see that.

      One could merely follow the evidence only if it were possible to extrapolate observations without first putting them into an explanatory framework. So, which philosophy of science are you referring to?

      CH: And third it is the arguments for evolution that are “religious.” The problems are from science.

      This assumes it’s impossible to criticize another person’s religious claims without actual holding those believes themselves. Why is this impossible in the case of God? Do I have to believe in Superman to criticize the claim that a female injured by standard rounds of ammunition was Superman? No, I don’t. So, why is God any different? Why is this not special pleading?

      Delete
    5. This is an interesting quote:

      Evolutionists are at times very candid about the state of human evolution, such as Johanson’s admission that “nobody really places a great deal of faith in any human [evolution] tree now" (from interview with Johanson quoted in Morell [1995, p. 546] emphasis his).

      Read the paper on frauds and forgeries here:

      http://www.answersingenesis.org/articles/arj/v2/n1/controversy-in-anthropology

      Delete
  23. For those looking to understand why Popper was wrong see here:

    http://www.reasonpapers.com/pdf/24/rp_24_1.pdf

    and here:

    http://www.stephenjaygould.org/ctrl/gardner_popper.html

    Popper was as off base as Ann Rand. There is no "metaphysical" materialism because it violates the law of non-contradiction. The term "metaphysical" means a reality outside the physical(what you can sense with your five senses).

    ReplyDelete