Sunday, January 04, 2015

Is that really all they've got?

Last week I alerted you to seven of the top ten evolution stories according to IDiots [Is that all they've got?. Now it's time for the top three stories .... hang on to your hats.

#3. #3 of Our Top Ten Evolution Stories of 2014: Cosmos Finale Takes One Last Shot at the Privileged Planet Thesis

#2. #2 of Our Top Ten Evolution Stories of 2014: Now with More Doubt! Meyer's Landmark Is Back in a New Edition, Replying to the Critics

And the number one proof of Intelligent Design Creationism in 2014 is ....

#1. Happy New Year! Our #1 Evolution Story of 2014: New Paper from Biologic Institute, "Shared Evolutionary History or Shared Design?"

At this rate real, science will probably survive through most of 2015.


25 comments :

  1. Meyer may have responded to his critics (he didn't), but more importantly he didn't deal with all the quotemining and ignoring of relevant research in his book.

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  2. In Gauger's piece there is actually very little said about "shared design". If they did try to explain it as a scientific hypothesis, it would immediately become obvious that it is not a scientific hypothesis. Creationists who are not willing to accept common descent as true often raise "shared design" as their alternative. But what does it predict? Only that the Designer will do whatever the designer wants to do. So shared design predicts that elephants will be big and gray, and go around the savannah munching on bushes and trees.

    Unfortunately for them, it just as easily predicts that elephants will be small and pink, and fly from flower to flower, pollinating them. If that's what the Designer wants.

    The only way to make Shared Design scientific would be to have some predictions as to what the Designer wants, and what the Designer's powers are and are not. But that is the discussion that ID types and creationists refuse to have. The Designer's powers? Infinite. When and and where is the Designer active? Everywhere and at all times. What does the Designer want to do? We mere mortals cannot speculate on that.(*)

    So nothing can be ruled out, or made unlikely. And the Common Design hypothesis thereby can be made to predict, not only everything that we see, but also everything that we don't observe.

    In other words, the way they use it, it is no scientific hypothesis at all.

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    * Footnote: except when they see junk DNA. Then the ID types and creationists insist that junk DNA would not be Good Design, and they furiously insist that it can't be junk. This has the merit of at least having them make a prediction. Elsewhere they insist that one cannot make Good Design predictions. Consistency is not one of their obsessions.

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    1. Joe:

      Not even junk DNA. Lots of IDiots agree that god might have made junk DNA if he felt like it and that its absence is not a prediction of ID. But that doesn't keep them from triumphantly embracing ENCODE; consistency certainly isn't among their virtues, and neither is intellectual rigor.

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    2. Joe: "So nothing can be ruled out, or made unlikely. And the Common Design hypothesis thereby can be made to predict, not only everything that we see, but also everything that we don't observe."

      But design "theory" can't predict things like antibiotic resistance without falling back on religion (ie., it is just god testing us).

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    3. I'd disagree that 'Common Design' (as typically used, eg by "Professor" Casey Luskin) predicts everything and anything. What they are trying to assert is that the observed commonalities need not be arrived at solely by descent relationships, but that 'like organisms would naturally be expected to have like DNA'. Where this rather falls down is in handling 'alikeness' in the DNA of organisms that are clearly very different - for example, Common Design does not really get to the heart of why pig, deer, whale and hippo DNA should be more 'alike' within than outside that grouping, ditto elephants, aardvarks and manatees. And why nonfunctional changes should follow the same pattern, Heaven alone knows.

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    4. JF
      Oh no! Naughty. iD is about scientific methodology.
      All that is seen in nature is what is seen.
      Evolution looks at like eyes and says THAT PROVES common descent from a original single eye thing.
      ID/YEC says its a option that shared(common ) design is the reason foe like eyes in segregated biological entities AND says its not proof of common descent. Its just a first simple conclusion that didn't allow/imagine a common design option.
      You say CD can predict any biological result but so can we say about CDE.
      everybody is just speculating on why things in biology are so alike at this/that level.

      This is more then meely another option for biological origions, including a creator, including a rejection of evolution BUT its also a smarter investigation of methodology behind evolutionary conclusions.
      its a forensics of methodology concerning evolution "science' and not just another option.
      Nothing to do with elephants. Yes with elephant eyes and sight mechanisms. other stuff too.

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  3. I have to disagree with you here, Larry. They've won. Thery've shown that intelligent designers (them) couldn't change the specificity of the enzymes they studied. Therefore the original specificity must have been done by an intelligent designer. Something like that, anyway.

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  4. I was struck by this little bullet point in #3: "Science is great, but it's not the only way to discover truth." No attempt was made to justify that claim or to explain the other way(s). But I wonder what it/they is/are.

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    1. Hi John

      I will go out on a limb here:

      Buddha’s philosophy was neither atheist nor theist – his thinking was “non-theist”

      Like Buddha, Freud and Jung had some very remarkable insights that can only really be addressed in a subjective i.e. decidedly non-empirical manner.

      I, for one particularly appreciate Buddha’s reaction to human suffering.

      OK, let’s call what I am talking about non-objective/non-empirical introspection, but please do not call it “faith”.

      That said, the Buddha (and others) had something to offer the rest of us worthy of consideration.

      My Canadian 5 cents worth (we no longer have pennies in Canada)

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    2. Hey Tom,

      How is what you are describing different from just making stuff up ?

      How can you describe the "non-objective/non-empirical" insights of Buddha, Freud and Jung as "remarkable" without recourse to some objective standard ?

      And just what are these insights and how how are they remarkable ?

      Are they remarkable because they help assuage your fear of darkness and death ?

      Nice if they do but so what ?

      Please justify and explain.

      And while you are at it perhaps you could explain why whenever someone trots forth anther way of knowing things they never ever provide concrete examples ?

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    3. Buddha's, Freud's, and Jung's insights may well be remarkable in many ways, but how can we find out if they're true? We're asking here about another way of discovering truth, not another way of devising conjectures.

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    4. Hi John,

      I think we are speaking at cross-purposes here and you are reading more into what I said than I had intended. I specifically invoked Buddhism's non-theistic stance permitting "non-conjecture" as it were.

      I am impressed more, with Buddhism's attitudinal approach to life along the lines perhaps, of John Milton's:

      "The mind is its own place and in itself, can make a Heaven of Hell, a Hell of Heaven."

      I still submit therein lies much of value worthy of consideration.

      As Socrates once opined

      "The unexamined life is not worth living."

      That's all.

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    5. Sorry, I thought your comment was directed at "Science is great, but it's not the only way to discover truth." If it wasn't an attempted response, never mind. But then I have no idea why you commented or what your point was.

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    6. Hi John

      My point was really not significant.

      The thrust of my argument is that there are philosophical standpoints other than reductionist materialism that are completely compatible with modern science and that in fact many scientists can and do subscribe to such alternate POVs.

      In other words, the so-called distinction between "rationalism and superstition " is often expressed as a false dichotomy!

      But I really do not want to open that can of worms again as the subject has been thoroughly rehashed enough on previous threads.

      But while you are here - I would be most grateful for any assistance you could provide on http://tinyurl.com/qg7bbjc

      As an aging Biologist - I really could use some expert intervention.

      Thanks in advance for even considering my belated request,

      Best regards

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  5. Shared evo history or shared design is a serious threat to evolutionary biology foundations. they never suggested another option for like looks and convinced themselves, sincerely, like looks proved like evolutionary pathways of descent to the present etc.

    the cosmos show was hilarious its its real, or possibly a second priority, agenda to convince kids/adults that creationism was wrong and a threat to scientific progress and motherhood and America.
    show after show, as I heard not watching, documented this agenda with slipping in some jab at creationism.
    they really document what the establish/the money thinks is a serious threat to old time conclusions in origin subjects.
    Nothing to do with the cosmos or results from sciency folks and work but a social/political (cartoon) to fight rising creationism.
    This show is already a forgotten thing of education but remembered for unjuust and lame accusations and motivations.
    NOW for a CREATIONIST Cosmos. We couldn't do worse!!

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  6. Please forgive my rude interruption of this thread.

    I would be very grateful if any and all could return to a previous thread and comment on my query found here:

    http://tinyurl.com/qg7bbjc


    Thanks in advance from an aging Biology desperately attempting to stay current.

    ... not to mention ongoing gratitude from his students.

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  7. "A New Paper from Biologic Institute: "Enzyme Families -- Shared Evolutionary History or Shared Design?"
    I am pleased to announce the publication of a new paper from Biologic Institute, a research organization devoted to investigating the limits of unguided evolution and advancing the development of a new paradigm for biology based on intelligent design. This paper, "Enzyme Families -- Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family," is the closing chapter of our long-term study of bacterial enzymes to determine if they can be coopted to new functions. The answer to this question is important for the evolution debate. If enzymes can't be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.
    Published in the journal BIO-Complexity, the work was done by Marci Reeves, Doug Axe, and myself.
    In a previous paper we described the difficulty of coopting the enzyme Kbl to perform the function of BioF. The two enzymes are very similar in structure (see below) but have different reaction chemistries and different functions in the cell. We wanted to know if a mutated Kbl could replace missing BioF function. After changing nearly every amino acid in Kbl's active site (where its chemistry is carried out) to look like BioF, Kbl never was able to make the switch to BioF's function.
    (A) BioF dimer; (B) Kbl dimer; (C) backbones of the two enzymes aligned against each other; (D) the amino acid side chains in the active site(s) of each enzyme that carries out each reaction -- BioF is blue and Kbl is green. The red and orange are the reaction products still in the active site(s).
    In this paper we expanded the story to include nine of the most closely related enzymes to BioF, including one that is supposed to be able to carry out both BioF's and Kbl's chemistry. Using random mutagenesis we tested every single-base mutation in those nine genes. None of them was within one mutation of cooption. We went on to test for cooption the two most likely enzymes by generating two-base combinations of mutations. After testing 70 percent of all possible two-base mutations for each enzyme, or about 40 million cells each, that also failed.
    What does this mean? In an evolutionary scenario, to get an enzyme to switch functions the first step is to make a spare copy that can be mutated without destroying a function the cell needs. Second, the cell has to overproduce the mutating enzyme, because any newly emerging enzyme will be very bad at the job at first. To compensate there will need to be lots of enzyme around. Third, there is the problem of finding the right combination of mutations by random search.
    Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 1015 years. That's longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    We have now addressed two objections raised by our critics: that we didn't test the right mutation(s), and that we didn't use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF's entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine.
    Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It's because modern enzymes can't be coopted to anything except trivial changes in function. In other words, they don't evolve!
    That is precisely the point we are making."

    I can't seem to find any refutation of this work.

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    1. Perhaps I'm confused, and perhaps you made this clearer in the paper than you do in your summary, but I have questions about your calculations. You have tested point mutations. You write, "the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 1015 years." (1015 must be computer garble for "10 to the 15th"; that's not the problem.)

      Are you using the same "mutation rate" for gene duplications as for point mutations? Is that appropriate? Polyploidy leads immediately to duplication of every gene in the genome. One copy is free to drift and change, to function differently or to loose all function. This seems important since the consequences of polyploidy last in all the descendents of an event of polyploidy, though they're thinned out with time as one of the two copies of a gene may becomes non-functional. This isn't trivial; it is likely that there were two rounds of polyploidy in the early evolution of vertebrates, a majority of vascular plants are recognisably polyploid, and it seems likely that there was at least one polyploid event in the early evolution of all vascular plants. How does one calculate the probability that a gene will be present in two or more related copies (duplicated) against that background of polyploidy? Surely the number is not equal to the point mutation rate.

      Second, based on recent discussion here of the potential effectiveness of low values for the selection coefficient, it's not clear to me that it's appropriate to to treat a mutation for overproduction the same way as a point mutation changing function. If a point mutation leads to a small beneficial effect in one copy of a duplicated gene, that mutated version will tend to stick around and increase, and mutations for increased production will tend to accumulate AFTER the modified gene begins to be useful.

      (There are other problems here, e.g. with not using the ancestral, less specific version of the enzyme, but I've tended to write too much here lately and should stop.)

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    2. Barbara, I think that, apart from the last line, 'johnny' is quoting Ann Gauger wholesale. I think his principal objective is to watch somneone dance.

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    3. What do you mean by refutation? What is exactly what should be refuted? Why would you ignore the literature showing success in changing other enzymes' specificities from one substrate to another and concentrate in a badly designed "experiment" like the one you show? How much do you actually understand about catalysis in general and enzyme-mediated catalysis in particular? I ask because that understanding leads to much better understanding about how enzymes can/could be co-opted for other functions. How much do you understand about selection coefficients? I ask because that could help you understand why the stats are misapplied by creationists. How much do you understand about biochemistry? I ask because enzyme specificities are measured in terms of preferences, rather than perfect discrimination (in other words, all enzymes show at least some degree of promiscuity for well understood and basic chemical and physical reasons). How much do you understand about recombination? I ask because under rounds of selection, evolution is tremendously accelerated by recombination of selected favourable mutations.

      The people who "designed" the experiment you quote, seem to have designed it for failure to test something that evolution does not do: radically change enzymatic catalytic specificities in one go. Or maybe they are just too ignorant about the scientific method, and of the appropriate background necessary to properly investigate these issues. Evolutionary changes tend to be less spectacular (with some exceptions), and as changes occur, other changes become available to evolved subpopulations. The reason why ignoring ancestral forms is a problem is because the history of changes, of preferred substrates as proteins diverged, might have the key to how these two enzymes evolved their particular preferences. Did your authors show any work about the probable evolution of these proteins by including other members of the family? if not why would they ignore the data? If there's no data, why not choose enzymes with better data that could help them think how their evolution could have happened?

      Take a good look at possible flaws in that study before coming up with claims about refutations.

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    4. Allen Miller: Yes, you're right. I should have had breakfast before I wrote. Sorry I responded.

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    5. I can't seem to find any refutation of this work.

      How hard did you look, Johnny?

      http://sandwalk.blogspot.ca/2014/12/a-creationist-argument-against.html

      http://sandwalk.blogspot.ca/2014/12/ann-gauger-keeps-digging.html

      http://sandwalk.blogspot.ca/2014/12/ann-gauger-moves-goalposts.html

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