Beating a dead horse (Darwin’s Doubt)

First off I must apologize for doing another post on a subject that’s been done to death around here, but I’ve been meaning to make a post about this for a while but other stuff kept coming up. Anyway, things have quietened down at work where I now only have to maintain some cell cultures, so I have a bit of time duing the christmas holiday.

My post, which is a repost of something I also brought up in a thread on Larry Moran’s sandwalk blog, is about a chapter in Stephen Meyer’s book Darwin’s Doubt and what I can, if I’m being generous, only attribute to extremely shoddy scholarship.

Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:

“Axe had a key insight that animated the development of his experimental program. He wanted to focus on the problem of the origin of new protein folds and the genetic information necessary to produce them as a critical test of the neo-Darwinian mechanism. Proteins comprise at least three distinct levels of structure:4 primary, secondary, and tertiary, the latter corresponding to a protein fold. The specific sequence of amino acids in a protein or polypeptide chain make up its primary structure. The recurring structural motifs such as alpha helices and beta strands that arise from specific sequences of amino acids constitute its secondary structure. The larger folds or “domains” that form from these secondary structures are called tertiary structures (see Fig. 10.2).
Axe knew that as new life-forms arose during the history of life—in events such as the Cambrian explosion—many new proteins must also have arisen. New animals typically have new organs and cell types, and new cell types often call for new proteins to service them. In some cases new proteins, while functionally new, would perform their different functions with essentially the same fold or tertiary structure as earlier proteins. But more often, proteins capable of performing new functions require new folds to perform these functions. That means that explosions of new life-forms must have involved bursts of new protein folds as well.”

In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiates that the cambrian diversification, or indeed any kind of speciation, or the that new cells types or organs, requires new protein folds. ZERO. Not one single reference that supports these claims. At first It reads like what I quote above, lots of claims, no references. Later on he eventually cites the work of Douglas Axe that attepts to address how hard it is to evolve new folds(and that work has it’s own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which eventually Meyers cites), but in Axe’s papers, that claim is not supported by any reference either. It’s simply asserted as fact. In other words, Meyer makes a claim, then cites Axe making the same claim. Neither of them give a reference.

Meyer mentions Ohno:

“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life such as sponges or one-celled organisms. Thus, Axe was convinced that explaining the kind of innovation that occurred during the Cambrian explosion and many other events in the history of life required a mechanism that could produce, at least, distinctly new protein folds.”

No reference is given here either. The claim is simply made initially, so it’s hard to check. Is Meyer and Axe willing to bet that a preceding evolutionary history of, for example, Lysyl oxidase cannot be found in structure and sequence of related molecules? That there ARE no related molecules? Is that his claim? That the Cambrian explosion required tonnes of bona fide Orphan proteins with no preceding history? Where are the references that support this? Did Meyer or Axe look for homologues of Lysyl Oxidase and found none?

It gets much worse, turns out Meyer is making assertions diametrically opposite to what his very very few references say. Remember what Meyer wrote above?

“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures.”

Well, much later in the same chapter, Meyer finally references Ohno:

“Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21”

What is reference 21? It’s “21. Ohno, “The Notion of the Cambrian Pananimalia Genome.”
What does that reference say? Let’s look:

Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.
Assuming the spontaneous mutation rate to be generous 10^-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can’t possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome – possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 10^8 DNA base pairs, which amounts to only 6% of the
mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome.”

The bold is my emphasis. I trust you can see the problem here. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened, that the genes and proteins were already present and had long preceding evolutionary histories.

Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that:

“The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions.”

 

Where does he get this? His ass, that’s where.

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447 thoughts on “Beating a dead horse (Darwin’s Doubt)

  1. Allan Miller,

    Any day now … that is, positive support for ID at the same kind of level that you expect evolution to provide.

    Umm we just ask evolutionism to provide what it says it has, ie a step-by-step process for producing the diversity of life. ID doesn’t make that claim so it doesn’t have to support it.

    That you people fail to understand that basic fact is very telling.

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  2. CharlieM</strong>But without knowing anything about the designer we can still compare designs and judge which involved more intelligence. Take for example the British Comet airliner. Comets underwent a major modification. There were two types of window, one angular with ninety degree corners and the other in which the corners were rounded. Assuming you know nothing of the designers do you think you would be able to determine which is the more intelligent design?

    I think you have identified an important problem here. Even if you know nothing of the designer, you would still need to know the designer’s goals and constraints. If you do not know the RELATIVE advantages of these window shapes, the advantages and disadvantages of each, you couldn’t know which was the more “intelligent”, meaning “most nearly optimal given all of the functional requirements.”

    Way back in another life, I studied highway design. In designing intersections, there are two primary goals — safety and cost. In all cases, these were positively correlated – to increase safety, you must increase cost. The construction cost of each type of intersection was known (or very nearly). But how do you assign a dollar value to deaths or maimings?

    At the time, calculated across all new intersections and statistical measures of accidents (and severity), this averaged out to about 4000 in increased cost per single death avoided, over the typical lifespan of the intersection type and extrapolated traffic volume. Is this number more “intelligent” than 5000? Or3000? The intelligent intersection designer balanced all relevant factors so as to minimize the casualty per dollar ratio. Would you agree?

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  3. Flint,

    Even if you know nothing of the designer, you would still need to know the designer’s goals and constraints.

    Why? Make your case.

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  4. Alan Fox: I’ve forgotten the context (I’m supposing it was while looking at some ancient stone edifice), and I suspect I’m far from the only one to have heard such a remark, but someone once remarked to me that “they knew how to build in the old days”. I thought then that the truth is more nuanced. Most old buildings fall down but some (usually the most soundly constructed) survive and builders learn from past builders and past mistakes.

    I’ve no difficulty in imagining the evolution of solitary insect to family group to full sociality. I can imagine the variation in types and extent of constructions of mounds and tunnels evolving over time by the process of trial and error. The most interesting question for me is how on Earth the extended phenotype of the termite mound is stored genetically and inherited.

    Have you ever asked yourself if maybe there is more to it than genetics?

    The physical environment is a powerful designer. The physical properties of water, weather and the water cycle, the topography of the Earth and the effects of gravity result in rivers and river basins. Water runs downhill and erodes a river course. Who designs that?

    I like to think of the earth with its cycles as a living organism. So there are phenotypes within phenotypes. All of earthly life contributes to the phenotype of the earth, certain communities of organisms make up single phenotypes and the most concentrated, individualized phenotype is the human.

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  5. CharlieM: Have you ever asked yourself if maybe there is more to it than genetics?

    When you ask, do you get an answer?

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  6. petrushka: The looking no further bit is both pathetic and funny. What is it you thing evolutionary biologists do? And what exactly do IDists do after they make their sky fairy inference?

    I’m sure evolutionary biologists do lots of things. But if they start out with preconceived ideas they may not be asking the right questions and so will be looking for answers in the wrong places.

    I’ve never heard of an IDist making a sky fairy inference so I can’t answer your last question.

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  7. CharlieM: I’ve never heard of an IDist making a sky fairy inference so I can’t answer your last question.

    I’m sure you’ve heard of Behe. It doesn’t make any difference what you call the designer. Behe calls it God.

    Your other question:

    If it isn’t genetics, what is it?

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  8. OMagain: And yet every time we pull back the curtain there is never any ‘Intelligent Designer’ there. Do you think it’ll be any different this time?

    Who do you think I’m expecting to be revealed, the Wizard of Oz?

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  9. Alan Fox: I think of the process as environmental design. Aspects of the structure of termite mounds seem quite obviously at an optimum that could have evolved over time, especially the north-south orientation. How would this be incorporated in the germ line of termite populations intrigues me, as I said. (It also intrigues me that it doesn’t seem to intrigue anyone else here )

    How can you be so sure that its incorporated in the germ line?

    Well we do have something in common, being intrigued by termites 🙂

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  10. CharlieM: Who do you think I’m expecting to be revealed, the Wizard of Oz?

    You SEEM to be expecting some sort of quasi-human Intelligent Designer, as opposed to entirely natural processes. You SEEM uncomfortable with the notion that perfectly ordinary chemical and physical processes, plus a selective feedback mechanism, can produce all of life as we know it given enough time.

    You SEEM to be implying that there is some sort of implicit conspiracy, whereby thousands of biologists for a couple of centuries have somehow all managed to ask the same wrong questions, which have somehow resulted in enormous advances in biological knowledge.

    And the implication is that there is a small group of folks asking the right, not pre-conceived, questions, even though those questions produce no research and no progress.

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  11. CharlieM: How can you be so sure that its incorporated in the germ line?

    Because termites today do not seem to have to invent, entirely from scratch, what millions of generations of ancestor termites have developed and refined over the millennia.

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  12. Flint: Because termites today do not seem to have to invent, entirely from scratch, what millions of generations of ancestor termites have developed and refined over the millennia.

    I’m always intrigued when someone comes along who is smarter and more knowledgeable than all the working biologists combined.

    I am holding my breath for the alternative to genetics.

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  13. petrushka: I’m always intrigued when someone comes along who is smarter and more knowledgeable than all the working biologists combined.

    I am holding my breath for the alternative to genetics.

    I submit you’re barking up the wrong tree. These guys do not claim to be smarter or more knowledgeable than all working biologists, they only claim that naturalism or materialism or atheism or some other evil ism has blinded all of mainstream science to obvious alternatives they have taken for granted since before kindergarten.

    They combine “I’m right because you can’t prove me wrong to my satisfaction” with the ever-popular “possible, therefore probable” fallacy, where the probable (and thus possible) can be assumed because, of course, you can’t prove it’s wrong.

    We see this in Donald Trump’s politics – that if he never admits error, he never makes errors (and the people love him for it).

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  14. I like Trump because everyone hates him. Well, everyone who writes for the media. I am always suspicious of politicians who get good press.

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  15. CharlieM: I’ve never heard of an IDist making a sky fairy inference so I can’t answer your last question.

    My own preferred designers of choice are the orbiting teapots.

    Have you ever stopped to think how much magic is involved in evolution?

    Everything was already prepared by the magic preparation council, then a bunch of shuffling went on by the magic shuffling society, and then “poof” “poof’ “poof” all sorts of new animals in the Cambrian. Just no rabbits. Those would enter the magic act later.

    Magical mechanisms indeed.

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  16. petrushka: I’m always intrigued when someone comes along who is smarter and more knowledgeable than all the working biologists combined.

    We don’t have to be smarter than all the biologists, we just have to be smarter than you.

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  17. Mung,

    We don’t have to be smarter than all the biologists, we just have to be smarter than you.

    A hope that is just as forlorn.

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  18. Flint: You SEEM to be expecting some sort of quasi-human Intelligent Designer, as opposed to entirely natural processes.

    And design processes are not entirely natural because … ?

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  19. Flint: You SEEM uncomfortable with the notion that perfectly ordinary chemical and physical processes…

    And you know these physical and chemical processes are “perfectly ordinary” because you learned this in the Church of Darwin?

    And you know that the physical and chemical processes in living things are perfectly ordinary because they are like all the perfectly ordinary physical and chemical processes that occur in the absence of living organisms?

    Such faith. It’s touching.

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  20. keiths:
    Mung,

    A hope that is just as forlorn.

    C’mon, I hear Mung is pretty smart for a Creationist. Every time he leaves TSZ to go to UD he raises the average IQ of both places.

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  21. Mung: My own preferred designers of choice are the orbiting teapots.

    You told us before there is no Intelligent Designer, like there was no Intelligent Designer in the Cambrian. ID is only concerned with the disembodied Intelligent Design. I suppose it’s silly to expect an IDiot to be logically consistent.

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  22. petrushka:
    I like Trump because everyone hates him. Well, everyone who writes for the media. I am always suspicious of politicians who get good press.

    Lots of Republicans love him.

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  23. Mung,

    Everything was already prepared by the magic preparation council, then a bunch of shuffling went on by the magic shuffling society, and then “poof” “poof’ “poof” all sorts of new animals in the Cambrian. Just no rabbits. Those would enter the magic act later.

    Ah, the phoodoo-style lampoon, excellent.

    Physics. Just little things interacting magically with other things.
    Chemistry. Just mix things and see what happens, as if by magic. Sure it’s shuffling electrons, but how do they work?

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  24. CharlieM,

    How can you be so sure that its incorporated in the germ line?

    Do you have a candidate for another mode of inheritance, or a non-inherited mechanism by which the info is transmitted to the new colony?

    (I suspect you may say ‘epigenetics’, but that would need some kind of evidence beyond just waving the word. Genetics is the default assumption, for sound reasons).

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  25. CharlieM: Like “evolution”, “Intelligence” is one of those words that can never be fully described by a definition.

    And it doesn’t strike you as a considerable flaw for a supposedly scientific theory that one of the two key terms making up ID is a word that can’t be fully described by a definition?

    Do you think that every ID proponent would agree with the definition provided at Uncommon Descent?

    I am sure they don’t, which makes discussing Intelligence in the context of ID such a frustrating, and ultimately pointless exercise.

    But without knowing anything about the designer we can still compare designs and judge which involved more intelligence. Take for example the British Comet airliner. Comets underwent a major modification. There were two types of window, one angular with ninety degree corners and the other in which the corners were rounded. Assuming you know nothing of the designers do you think you would be able to determine which is the more intelligent design?

    I think that intelligence is innate throughout the natural world, not just in termite mounds.

    What do you mean by ‘intelligence’? Give us your operational definition so we can jointly determine if termite mounds, and other things, contain it.

    fG

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  26. And it doesn’t strike you as a considerable flaw for a supposedly scientific theory that one of the two key terms making up ID is a word that can’t be fully described by a definition?

    I don’t think ID should be promoted as science:
    http://theskepticalzone.com/wp/id-should-not-be-promoted-as-science-but-instead/

    That said, there are undefined terms in math and physical science. We sometimes call them primitive concepts. Example: if one defines mass in terms of its relation to force, such as:

    F = ma

    either Force or mass becomes a term that is formally undefined. We can measure mass, but it doesn’t mean we have a definition that doesn’t result in circularity.

    The problem with defining intelligence is it is hard to measure short of using stuff like CPU cycles (speed of calculation) as an objective metric. Which piece operating system is more intelligence MS Windows or Linux?

    I leave intelligence as an undefined in ID theory. Again, I don’t promote ID as science.

    That said I don’t think UCA (universal common ancestry) is science, but similarity comparison is. There is too much arbitrariness in deciding convergence, HGT, descent, and mechanical feasibility of transitionals.

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  27. stcordova: That said I don’t think UCA (universal common ancestry) is science, but similarity comparison is

    I take it you again mean comparative genomics are fine, so long as they’re only applied to humans Sal? Not sure if you prefer not to answer this or you missed it when I asked you a few days ago. If it’s the former I won’t insist, but don’t you think common descent is a valid scientific hypothesis, and if the same methods that are proven to work with humans, worked for the rest of the species without exception, that would be strong evidence for CD?

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  28. Alan Fox: So does everyone else, Sal!

    Wrong- Intelligence has been defined wrt ID. Intelligence as it pertains to ID is merely the ability to manipulate nature for a purpose. And guess what? Forensics and archaeology concur.

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  29. [Everyone] leave[s] intelligence as an undefined in ID theory.

    Frankie: Wrong-

    That there is a definition of intelligence to be found in ID literature that makes sense? Do you have a link?

    Intelligence has been defined wrt ID. Intelligence as it pertains to ID is merely the ability to manipulate nature for a purpose.

    An ability to manipulate nature for a purpose? Hmm! So something or someone has to possess that ability. How could intelligence, as you define it, exist except as an ability possessed by some agent?

    And guess what? Forensics and archaeology concur.

    I challenge you to produce any evidence that forensic scientists or archaeologists have given credit to “Intelligent Design” proponents for any useful input into forensics or archaeology.

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  30. Mung: And you know these physical and chemical processes are “perfectly ordinary” because you learned this in the Church of Darwin?

    And you know that the physical and chemical processes in living things are perfectly ordinary because they are like all the perfectly ordinary physical and chemical processes that occur in the absence of living organisms?

    Such faith. It’s touching.

    Once again, we see a vivid illustration of Sagan’s demon-haunted world, where even physics and chemistry are magical processes, and one needs blind faith to believe in them. The notion of a reality NOT being diddled from behind the curtain by some purposeful supernatural entity is incomprehensible. He HAS to be there. HAS to.

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  31. Alan Fox,
    Here Alan, start with the following: Intelligent Design is Not Optimal Design

    How could intelligence, as you define it, exist except as an ability possessed by some agent?

    It isn’t how I define it, Alan. Buy a dictionary. And intelligence requires the respective agency. Did you have a point?

    I challenge you to produce any evidence that forensic scientists or archaeologists have given credit to “Intelligent Design” proponents for any useful input into forensics or archaeology.

    You have it backwards, as usual. ID uses their concepts and techniques.

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  32. Frankie: It isn’t how I define it, Alan.

    You just did:

    Intelligence as it pertains to ID is merely the ability to manipulate nature for a purpose.

    Is that not now your definition?

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  33. Frankie: I challenge you to produce any evidence that forensic scientists or archaeologists have given credit to “Intelligent Design” proponents for any useful input into forensics or archaeology.

    You have it backwards, as usual. ID uses their concepts and techniques.

    To do what?

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  34. newton: Lots of Republicans love him.

    He’s a populist appealing to anger. People are always angry. See “Network”.

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  35. stcordova,

    My sole interest in ID is the claim that it is scientific and we appear to agree on that it is not.

    Everybody defines Intelligence differently. Like above, where Frankie says:

    Intelligence has been defined wrt ID. Intelligence as it pertains to ID is merely the ability to manipulate nature for a purpose.

    This is a totally different definition than the one offered by UD. It would help if the ID proponents could at least agree on their principal terms and concepts. As I said, these discussions are very frustrating if everyone uses their own personal definitions.

    This particular definition by Frankie has a major weakness in itself: it contains the term ‘purpose’ for which again no operational definition nor a metric is given.

    Scientifically speaking it is all jelly.

    fG

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  36. faded_Glory,

    Compared to evolutionism ID is science. ID has a superior falsification criteria and it also has a positive case.

    And if you want definitions of words just buy a dictionary

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  37. Frankie: To determine if design exists or not.

    Let me get this straight. Forensics and archaeology are disciplines that try to decide if design exists?

    Here’s me thinking forensics is more to do with finding scientific clues in a legal investigation, an important aspect of which is to link a crime scene with a suspect or eliminate them from the investigation. And archaeology is using scientific techniques to study artefacts, records and and other remains left by historic and prehistoric peoples.

    But no, they’re just looking for design, according to Frankie.

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  38. Alan Fox,

    Forensics and archaeology are disciplines that try to decide if design exists?

    Archaeologists try to determine if an object is an artifact or not, Alan. Are you saying you don’t know nor understand what they do? They first have to determine an artifact exists before they can study it.

    And forensics uses those clues, the evidence, to determine if a crime has been committed.

    All of that is what ID also does. Follow the clues, ie the evidence, and see if a design inference is warranted (or not).

    But no, they’re just looking for design, according to Frankie

    Except I never said nor even thought such a thing. So you need to retract that and apologize.

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  39. Frankie:
    Alan Fox,

    Archaeologists try to determine if an object is an artifact or not, Alan. Are you saying you don’t know nor understand what they do? They first have to determine an artifact exists before they can study it.

    Good grief. It is not yet possible to study non-existent artefacts. Charitably, I’ll interpret you as meaning an archeologist may need to decide whether a stone flake was struck by a human tool maker or had spalled off a rock face due to frost action.

    And forensics uses those clues, the evidence, to determine if a crime has been committed.

    I think the decision on whether a crime occurred is still left to the courts. Generally, crimes are committed by people, however and the job of forensic scientists is often to link or exclude suspects from an enquiry by providing evidence of events and whether that evidence links or excludes suspects.

    All of that is what ID also does. Follow the clues, ie the evidence, and see if a design inference is warranted (or not).

    The only ID arguments I have seen are of the Sherlock Holmes pattern. ‘Evolution can’t do X so “design” must be the explanation.’ (Without of course expanding further on “design”!)

    Except I never said nor even thought such a thing. So you need to retract that and apologize.

    You typed: “To determine if design exists or not.” in answer to my question: “[Frankie: ID uses their[archaeologists and forensic scientists] concepts and techniques.] To do what?”

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  40. Alan Fox,

    Forensics determines if some intelligent agency was involved- true the Courts can find that although an intelligent agency was involved there wasn’t a crime. Forensic scientists have tools and techniques for doing so. ID’s are the same or very similar.

    Archaeologists need to determine if an object is an artifact or not. They also have tools and techniques for doing so. ID’s are the same or very similar

    The only ID arguments I have seen are of the Sherlock Holmes pattern. ‘Evolution can’t do X so “design” must be the explanation.’ (Without of course expanding further on “design”!)

    Then you haven’t looked. My post about testing ID goes further than that.

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  41. Alan Fox,

    You typed: “To determine if design exists or not.” in answer to my question: “[Frankie: ID uses their[archaeologists and forensic scientists] concepts and techniques.] To do what?”

    And nothing in that says what you said- nothing there says they just look for design.

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