Jonathan M who seems to have become a regular blogger for the Discovery Institute has noticed this blog once again (From the Darwinist Blogosphere, Stephen Meyer’s Trip to London Elicits a Typical Reaction) in a posting at the bizarrely named Evolution News website – no comments permitted there, it would seem. The BCSE believes Jonathan M to be Jonathan MacLatchie (sometimes his name is given as McLatchie), an undergraduate student in forensic science [UPDATE: Jonathan is now taking a Masters degree in Evolutionary Biology & Systematics at the University of Glasgow (!) ] who appears to have absorbed a typical strategy beloved of Intelligent Design creationists: of devising neologisms that don’t correspond to normally used science terminology, and combined this with ignorance of biology. P. Z. Myers was exposed to some of his ‘thinking’ while visiting Glasgow.

Jonathan begins with a quite mind-bending outline of DNA structure in regard to its genetic role.

For one thing, the point that Meyer makes about the bonding in DNA is that “there are no chemical bonds between the bases along the longitudinal axis in the center of the helix. Yet it is precisely along this axis of the DNA molecule that the genetic information is stored” (SITC, p. 242). It is this fundamental property of DNA that allows DNA to carry the information it does. The bases of DNA do not align in the sequential arrangement they do because of physical necessity or chemical affinity. The arrangement, on the contrary, is arbitrary — any arrangement is possible, but only some arrangements convey functional specificity.

This paragraph just baffles me. I presume this quotation is referring to adjacent bases along each DNA strand, rather that the base pairs themselves. I’m not clear why this ‘fundamental property’ bothers Jonathan M – he seems to have a major comprehension failure at this point.

Meyer’s argument also does not say that “x is complex; therefore, x is designed,” nor does Meyer commit the “god-of-the-gaps” fallacy. On the contrary, Meyer argues — based on the standard historical (abductive) scientific method — that there is only one known cause, one category of explanation, that is known by virtue of our uniform and repeated experience to be able to produce large volumes of highly complex (improbable) and functionally specific information. Thus, in the absence of viable competing explanations, it follows that the most likely explanation for this phenomenon is that it too arose by virtue of an intelligent cause.

Oh, for goodness’ sake, this ( “x is complex; therefore, x is designed,”) is exactly what Meyer is saying. He cannot envisage a mechanism giving rise to the genetic code, so he invokes a supernatural entity. And, yes, we have clearly demonstrable mechanisms by which genetic information can grow in both quantity and complexity. I even see this happening in the lab in experimental timescales.  Jonathan is ignorantly regurgitating ID creationist neologisms, to invoke a supernatural entity.

Jonathan takes a contributor to the CIS forum, Simon, to task, accusing him of not reading the ID creationist literature (I suspect that Simon, or “Simon” as Jonathan rather disparagingly refers to him, is somewhat better qualified to understand the science than he is, judging from his profile at the CIS forum):

“Simon” also cites polyploidy as a means by which specified complexity can arise. But Signature in the Cell is concerned with the origin of such specified complexity in the first life, and polyploidy concerns genome duplication in eukaryotes. Moreover, even in eukaryotes, polyploidy only appears to have a major effect within plants — so its relevance to the origin of the first life is dubious.

This is Jonathan wiffly-waffling around a subject he doesn’t seem to have a strong grasp of. It’s often stated in ID creationist circles (such as the C4ID) that there is no known source of ‘information’ other than from an intelligent mind. This is clearly nonsense, as Simon knows: gene and genome duplication provides the raw material for whole families of diverged genes to arise. What is ‘specified complexity”? Is it the genetic code itself? The mere existence of heritable material? Is this the same as Meyer’s undefined “specified information”?

Jonathan – your statement on polyploidy is naive. Genes duplicate. Sections of chromosome duplicate. Chromosomes can fuse and duplicate, genomes can duplicate. It’s not all about polyploidy. But once there is genetic redundancy due to duplication, novel gene functions can evolve. There are good examples of this in the scientific literature.

On Intelligent Design creationism’s testable predictions, as presented by Jonathan:

For example, it predicts the presence of complex and functionally specific information in the cell; it predicts the already-alluded-to rarity of functional protein folds in amino acid sequence space; it predicts certain patterns in the history of life (e.g., the saltationist nature of the fossil record; morphological disparity preceding diversity, etc.); it predicts that design purposes will be discovered for systems that are currently thought to be functionless (such as the discoveries of the past decade or two which have uncovered a myriad of functions for so-called “junk DNA”). In astronomy, it predicts that, as science progresses, the number of instances of fine tuning in the laws and constants of physics will increase and not decrease over time. And it makes many other predictions as well.

OK, here is why I think this is just so much nonsense:

“it predicts the presence of complex and functionally specific information in the cell” – This is a quite bizarre claim. The Intelligent Design variant of creationism arose in the 1990s. At that time, the presence of large amounts of genetic ‘information’ in cells was well-known. In what way is the presence of information a sensible prediction? And as far as I can tell, this whole ‘complex and functionally specific information’ remains remarkably ill-defined (see for example this demolition by Myers), and in particular is inconsistent with conventional information theory. If we’re now going to think of the origins of life and the genetic systems we see around us today, all ID creationists are saying is that they cannot understand how it happened, and in their religiously motivated world-view prefer to fall back on supernatural intervention rather than taking a genuinely scientific approach to the problem. How is complex and functionally specific information defined?

“it predicts the already-alluded-to rarity of functional protein folds in amino acid sequence space”. This is quite interesting, particularly given Axe’s background as a post-doc in Alan Fersht’s lab in Cambridge. But as far as I can see, this boils down to the usual incredulity argument. For Axe, with a pedigree of working in a prestigious lab in Cambridge, I would have thought a more prestigious outlet for this review might have been possible. As it is, he’s reduced to publishing in the Biologic Institute house journal, with the not-so-impressive archive of 7 papers over its two years of existence, all authored by members of the editorial board (all of whom appear to be creationists of one variety or another).

“it predicts certain patterns in the history of life (e.g., the saltationist nature of the fossil record”; morphological disparity preceding diversity, etc.). This sounds almost as though Jonathan is proposing a rather more interventionist kind of creationism than I normally understand is represented by Intelligent Design creationism: that intervention by a Designer (who, let’s face it, for the Discovery Institute is really the Judeo-Christian god, not Zeus, or Odin, or any other mythological entity) has been repeatedly intervening in the appearance of life-forms on Earth.  Of course, the links between Intelligent Design creationism (which publicly denies that the designer/creator is God) and other forms of creationism, notably those of the Young Earth persuasion have been pretty clearly documented.  Indeed the main figures in C4ID have clear links to biblical literalism and young earth creationism.

“it predicts that design purposes will be discovered for systems that are currently thought to be functionless (such as the discoveries of the past decade or two which have uncovered a myriad of functions for so-called “junk DNA”)” OK, so here Jonathan says that a prediction from Intelligent Design creationism is that design purposes will be found. This is frankly astonishing. How can purpose be ascribed to an unidentified ‘Designer’? How can we divine purpose? What purpose would Jonathan ascribe to his Designer/god’s intent to create the so-called Junk DNA? Where in his Bible does he see the culturally primitive scribes mention DNA when they are transcribing the word of the Designer/god?. This supposed prediction also invokes visions of the stultifying effect of dogma. It may well be that at church/temple/mosque/synagogue pronouncements can be made in the expectation that the word of the deity (as relayed by the priesthood) will be unchanging, but in a world of science, evidence counts. Not the ID creationist kind of negative evidence (“it seems improbable to me; I can’t understand why this is so”), but real, experimentally derived, evidence. Accordingly, the collective understanding of genome structure and function changes as evidence accumulates. As an undergraduate in genetics, one of the great mysteries was the so-called ‘c-value paradox’ – why did genomes vary so greatly in size, even between apparently closely related species?  As techniques and technologies advanced, a clearer and clearer picture of genome composition has been revealed. And, yes, some DNA has been referred to as ‘junk’. But as evidence is uncovered, some of this stuff does have a function. Not always a genetic function. And a lot of this is semantics. DNA sequences could have a ‘function’ related to their propagation (I’m thinking here of P-elements in Drosophila), but not a function that has a role in the biology of the organism.

“In astronomy, it predicts that, as science progresses, the number of instances of fine tuning in the laws and constants of physics will increase and not decrease over time. And it makes many other predictions as well.” The fine-tuning argument has always seemed to me to be somewhat tautologous. Had the constants been different, we would not be here to look at the Universe and its physical constants. We have a sample size of 1. Exactly 1. Who knows if physical constants could have been different. I certainly don’t (I’m not a physicist). I doubt that Jonathan does either, except it’s another of those claims that creationists parrot.

I would have thought the stand-out prediction of Intelligent Design creationism would be the unequivocal demonstration of the existence of that Designer/creator.

On the subject of Meyer’s book, I am at least displaying honesty when, as Jonathan observes, I say I didn’t read his book. Which is why I didn’t review the book, and I didn’t review the talk. Actually, one reason for thinking of attending the lecture would have been to get a copy of Signature in the Cell. But balancing the cost (not value) of the book (£8.99 at Amazon) with the travel costs to and from the venue (several times more than the cost of the book) I decided that wasn’t a good deal. I suppose the cost of travel may explain why Jonathan didn’t attend Meyer’s lecture either, and has chosen as I have done to make comment on Meyer’s other outputs. Besides, science isn’t usually advanced through popular science publications (which for example tend not to appear in University libraries). Usually, the popsci books follow genuine scientific advances published in bona fide science journals. Peer-reviewed journals. Genuinely peer-reviewed publications from Meyer are quite thin on the ground.

Jonathan refers to a list of supposedly peer-reviewed ID publications. I note the prominence of BIO-Complexity, the Biologic Institute’s house journal. With its seven papers in two years, it is hardly prolific and might be best regarded as vanity publishing. I have looked at two sevenths of its published output, and neither is a research paper.

Finally, I’m not a Professor, at least in the British sense of academia.

And finally, finally, I expressly did not review Meyer’s book, even though Alastair Noble claims I did in a comment in this blog.

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56 comments

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  1. Upright BiPed’s avatar

    Mr Suanders, your biggest problem is that you allow yourself to use the word "information" in regard to the genome, yet you haven't done the work of incorporating the observed physcial aspects of information into your materialist's paradigm. The reasons for this are simple, your paraidgm simply falls apart under the observations.

    I welcome you to review a post where this was explained to Larry Moran and Dr Elizabeth Liddle. Perhaps you can come up with a more compelling response, but I am inclined to think you will simply ignore the observations.
    http://www.uncommondescent.com/junk-dna/biochemis

    Reply

    1. GrumpyBob’s avatar

      Larry Moran is correct on 'junk' DNA.
      Your comment makes little sense.

      Reply

    2. derwood’s avatar

      Same old ID monger – paragraph after paragraph of bafflegab and distractions, never getting to the point. Analogies are not evidence. Pity that analogies are all the ID types seem to be bale to muster.

      Reply

    3. Upright BiPed’s avatar

      So the way to handle contrary evidence is to ignore it without addressing it? Is that how you were taught to adress empirical obsverations?

      Tell me, what part of the analysis makes no "sense" to you, the part about one physical thing representing another physical is reuired to be separate from it, or the part about there must be some object to physically establish the relationship that otherwise wouldn't exist? Perhaps you'd like to offer an alternative analysis of the physicality of information transfer?

      I am all ears if you have the acumen, but "that don't make no sense" just will not cut it against observable evidence..

      Come on Mr. Saunders, your work explicitly depends on these things performing their tasks as observed, are you one of those part-time empiricist who only cares about observable physicality when it doesn't threaten their worlview?

      Reply

      1. derwood’s avatar

        Projecting, are we? You UD/ENV types are pretty good at that.

        Reply

      2. Jacob’s avatar

        "Oh, for goodness’ sake, this ( “x is complex; therefore, x is designed,”) is exactly what Meyer is saying."

        I don't think that's what he is saying at all. Think about your favorite 'neologism' – "specified complexity". Think about a self-replicating molecule – say, the sort of RNA strand required at the outset of an 'RNA world' scenario. The complexity of such a molecule can be described by Shannon information theory. The specification is identified by the RNA world scenario itself – the molecule must perform the function of self-replication.

        If RNA sequences that give rise to the function of self-replication are sufficiently rare, such that a 'chance' assemblage is extremely unlikely given the probabilistic resources available… then 'chance' is not a credible explanation for the appearance of such a molecule, even given an environment in which such an occurrence is possible.

        It is the complexity AND the rarity of the specification that, in this scenario, is crucial to Meyers IBE argument. That is why your comment doesn't fit.

        Reply

        1. GrumpyBob’s avatar

          Probability arguments seem to assume all the pieces of a replicating system need to spontaneously appear in a fully functional state in one step. I doubt this needs to be the case.
          Meyer's specified complexity concept only exists in the peculiar world of Intelligent Design creationism.
          In the case of information theory, I refer you to http://recursed.blogspot.com/2009/10/stephen-meye
          where Meyer's mis-usage of information theory is outlined.

          Reply

          1. Jacob’s avatar

            I'm not sure that they do. Regardless of the real-life merits or problems inherent to a particular environment – oceanic thermal vent, warm pool with supply of pummice, etc… – an estimate of probabalistic resources should, for the sake of argument, assume that there is an ideal environment where an RNA can be formed, remain stable and add to its sequence over time. But it should not be assumed that the RNA waits for 'the right' elements in this sequence to come along, since there is no theoretical selective filter which might favour the RNA molecules closest to a sequence whith self-replication function.

            I read the objections raised by Shallit. Much could be said, but he seems to deliberately misunderstand Meyer, raising meaningless technical quibbles so that he can avoid engaging his arguments. It's so rare to see someone really engage and debate an ID argument.

            Reply

            1. GrumpyBob’s avatar

              To be honest, I would trust the opinions of a researcher in information theory over those of a geologist with a philosophy PhD and a strong religious bias in favour of a creator.

              Reply

              1. Jacob’s avatar

                That's fair enough. The point at which I choose to trust an expert opinion varies according to a) the importance of the issue in question. b) my intellectual limits. In this case, I'm not prepared to trust either Meyer or Shallit. The issue in question is important. Both are discussing the matter in a comprehensible manner.

                I had another look at the Shallit blog, I still think his points of contention are trivial, contrary. He's looking for reasons to rule out Meyers argument without really engaging it, and I think he fails to find any good reasons.

              2. GrumpyBob’s avatar

                Virtually all of the major ID proponents are not making their assertions that there is a Designer/Creator from a scientific evaluation of the evidence, but rather from a presupposition of the truth of Christianity. This is true of Meyer (his first degree was from a theological college). I recently read a rather interesting account of the roots of ID as a devious (and ultimately unsuccessful) strategy to inveigle creationism – which is self-evidently not science – into US school science lessons. Meyer appears to have played a major role in that attempted deception, as his authorship of the Wedge Document shows.
                Fundamentally, a failure to understand some aspect of evolution does not constitute evidence for ID creationism. And the same goes for understanding the origins of life. To take Meyer's approach of redefining information theory to make the origin of life without supernatural intervention seem implausible is not an intellectually satisfying way forward. The scientific way forward is to propose hypotheses which can be tested.
                I am continually struck by the sheer volume of research in the biological sciences (sensu lato) which is consistent with the picture of life as explained by evolutionary theory, is consistent with evolutionary theory and which supports evolutionary theory. Particularly in contrast with the tiny quantity and low quality of ID publications, few of which (if any) have really been peer-reviewed.

              3. Jacob’s avatar

                These generalities are all very well as a starting point, but in a search for the truth the details matter. Just one measly paper, authored by a thoroughly ideologically deviant individual, could redefine an entire mountain of peer-reviewed research. The ideologies and weight-of-opinion are relevant – informative, one might say – but any argument stands or falls in its own right.

                It is certainly not Meyer's 'redefining of information theory' that makes a chance origin of life implausible.

              4. GrumpyBob’s avatar

                I think you need to be careful with equating 'improbable' with 'implausible'. Particularly from the perspective that we are only able to take a view on origins of life because life *did* originate.

                I'm not clear what your point of "one measly paper" is. Of course, occasionally scientific fields can be overturned, but it's very rare that such a paradigm shift results from a publication from an individual outside the field, or from an otherwise "ideologically deviant" individual (one sees these claims from a number of quarters, not just from the creationist scene). I also think you are mistaken if you think that there is ideology involved in scientific progress – I'd characterise it as conservatism. In all these matters, remember that extraordinary claims need extraordinary evidence. And to provoke a wholesale shift from one theoretical framework to another would require a considerable body of evidence.

                Meyer, as a religiously motivated individual with no biological experience or expertise (and particularly molecular biological), is an individual who is most unlikely to make a compelling origins case. In particular to ascribe the origins of life to a supernatural entity for which there is no evidence (merely Meyer's inference from his own lack of understanding/imagination) is not going to lead to an overpowering paradigm shift.

                I've been asking around about the body of biological/biomedical published and peer-reviewed work – one estimate suggests in the order of a million items annually, all consistent with or supporting evolutionary biology. Contrast that with the scale of the ID creationist literature, little of which is properly peer-reviewed. It's really going to take something more than a book from a christian philosopher of science to overturn the whole scientific edifice.

              5. Jacob’s avatar

                Let me pick out your comment – "remember that extraordinary claims need extraordinary evidence". The claim that the appearance of life was a deliberate act – by design – has extrordinary implications. But is this claim, in itself, extraordinary? I would suggest not. Consider Dawkins' well known comment in 'The Blind Watchmaker' -"Biology is the study of complicated things that give the appearance of having been designed for a purpose."

                From this perpective, it is the evolutionary claim that is extraordinary. That is one reason why the consonancies you see to between the vast body of "research in the biological sciences" and "the picture of life as explained by evolutionary theory" leaves some – such as myself – unmoved. Something extraordinary is required.

                A good start would be a lab-observed, (not infered), evolutionary development such as a protein-protein binding site involving numerous neutral mutations, the emergence of a novel function in a virus from coherent gain-of-function mutations, something like that. That's not an unreasonable request, in view of the claims evolutionary theory makes.

              6. Jacob’s avatar

                Excuse me taking two bites at your previous comment, but I also want to affirm my use of the word 'implausible', regarding an undirected origin of life.

                'psiloiordinary' makes a comment below, asking if I'd attribute a winning lottery ticket to design. Let me run with that example… Suppose a certain lottery is set up, such that there is a 1-in-a-million chance of guessing the right numbers. On average, a million people play each month, so on average one person wins every month. The lottery is a construct wherebye winning lottery tickets are a possible outcome, and chance is a sufficient explanation for these tickets when there are reasonable probabilistic resources on hand – i.e. enough people playing.

                But suppose only ten people played the lottery each month, yet there is still, on average, one winner every month. Would chance still be an adequate explanation? Of course not. It would be a possible explanation, but the probabilistic resources would be so vastly insufficient that we would all assume the lottery was being fixed. The lottery would be suspended. The police would investigate. If charges were brought, the prosecution would make clear that a chance explanation was completely implausible.

                If a chance explanation for the origin of life is possible, it is also implausible. All Meyer has done is run the numbers and work through the scientific process. Unless new information comes to light, it looks like a fix.

              7. GrumpyBob’s avatar

                Suppose there is a lottery in which there is a one in a million chance of winning the million pounds. This lottery is conducted by drawing a million tickets and allocating them to one million individuals. Further suppose that the only outcome for the winner is that they are sent a cheque for a million pounds, with no other indication of the lottery.

                The winning individual knows something's happened, but the other 999,999 remain unaware.
                Similarly, it doesn't seem to me to be important that someone (Meyer, for example) says that the origins of life (he concentrates on the genetic code) is so improbable that it couldn't have happened by natural causes. Had life not begun, we wouldn't be here to worry about it. In discussing the origins of the Universe or the Earth, or life on Earth, we are constrained by having a sample size of 1.

                Now, I'm not a chemist, so have to look at the literature around proposals for the origins of the genetic code with that in mind – I can see scientists constructing experiments to look at possibilities. I am not a physicist, so I really cannot discuss in detail the physics of the big bang. But here's the difference between me and an ID creationist: Meyer is neither, but still feels competent to push ideas contrary to those with the requisite expertise.

              8. GrumpyBob’s avatar

                Jacob – apologies, but my two responses seem to have gone in the wrong order – this is a reply to the first of your latest two!

                A few quick observations. Within the framework of evolutionary theory, the 'appearance of design' originating through natural processes (including but not exclusively natural selection) is not in my view an extraordinary claim. And in any case, the quantity of supporting evidence is overwhelming, and indeed extraordinary in scale. I don't know what your professional/educational background is (that's not intended as an insult), but for me as an academic involved in biological research, the scale of this evidence is really huge.
                One contrary view, the YEC view, is wholly unsupported by anything other than one collation of religious texts which are of marginal utility from a historical perspective and no utility from a scientific perspective. Additionally, there is no evidence of a supernatural entity capable of what a YEC supporter proposes.
                A similar proposition of a 'Designer' (ID-speak for the christian god) can be thought of similarly. These are the truly extraordinary claims: that there is a vastly powerful entity out there, that can do things that no other entity can do (incidentally, this is an entity that presumably did not itself need to be created). Frankly, arguing for such an entity on the back of personal disbelief or a failure to understand a biological process (for which coherent natural origins are well-supported by evidence) seems to me to be ridiculous.
                There are, I think examples of evolution of the kind of evolutionary changes you are after: often these are seen when comparing DNA sequences in closely related species. I believe there's a case in HIV of viral changes you are after (though I'm not a virologist, and your concept of a 'coherent gain-of-function' mutation is unclear.
                Within Drosophila fruit fly species, the origins of novel genes have been documented (for example by gene duplication or gene fusion – another example of increasing genetic information).

              9. Jacob’s avatar

                I think it has been claimed that HIV, in the last few decades, has 'explored' all possible combinations of up to 6 point mutations. If that is so, that's a massive sequence space that has been explored.

                I'm not convinced that there are evolutionary 'pathways' to complex new features or innovations. HIV studies, Lenski's e-coli experiments, etc. are therfore of considerable interest.

                Yes, my concept of 'coherent gain-of-function' mutations is… loose. I am simply requesting an impressive piece of evidence to back up evolutionary claims. What would you highlight as the most persuasive example or inference to an evolutionary mechanism at work? (note – it is not the mechanisms that I doubt, but rather what they are capable of accomplishing).

              10. GrumpyBob’s avatar

                I think HIV is a classic example of evolutionary radiation and it has 'explored' a greater range of sequence diversity than your comment suggests.

                I also think 'evolutionary pathways' is a poor expression – it suggests routes are plotted out from state A to state B in advance, which is not the case. Evolutionary change is not directed.

                I don't really think it's my job to provide evolutionary examples (after all something I find impressive is not necessarily something you'd find impressive). If you've not done so already, I'd recommend Coyne's 'Why Evolution is True'.

                I would say that the diversity of life around is is a persuasive example: wherever we've looked, evolutionary biology has given clear natural explanations for that diversity. It's also why i named this blog 'Wonderful Life'.

                Ultimately, the onus rests with those who prefer a supernatural explanation to provide definitive proof of the existence and action of their supernatural entity. One doesn't achieve this by essentially saying one cannot comprehend how something can have arisen by natural means.

              11. Jacob’s avatar

                I don't expect to find definitive proof for a "supernatural entity" through science. There are other ways of comprehending the world, some innate, others reasoned (but not scientifically). It is these other ways that I find more compelling in this regard. I think that a materialist explanation for the origin of life and and an evolutionary explanation for its diversity – if true – would render any concept of God either meaningless or false. And equally, if life is created I think this should be detectable, if not provable.

                If science does detect real design in the natural world, just because that line of reasoning reaches a scientific 'dead-end' doesn't mean that it should be rejected. I am quite prepared to pick up other 'intellectual tools' – excuse me if that sounds pompous – and continue the journey where science has stopped.

                I have not read a coherent theoretical explanation for the first life, nor have I seen evidence of evolutionary pathways between one form (or even one protein) in nature, and another. Therefore I don't see that there IS a 'natural' explanation for life.

              12. Jacob’s avatar

                I have no doubt that Jerry Coyne's book is persuasive to this end. I may read it. But these books are always like being sung to by Kaa (jungle book) – vestigial limbs, bad design, transitional fossils, recapitulation, biogeography, 'ssss sss sss sss sss'. The trouble with this kind of evidence is that, just as there are examples that fit an evolutionary picture nicely, there are also examples that don't fit it. Over time, scientists have worked hard to explain features of the natural world that seem to contradict the evolutionary account. These explanations make evolution more plausible, but do very little to prove that it is true. Your countless “evolutionary explanations for the diversity of life” may only show that evolution has, over time, become a theory very well fitted to what it purports to explain.
                For me, I need evidence that evolutionary pathways exist at the molecular and genomic level. No pathways, no evolution.

              13. GrumpyBob’s avatar

                Apologies, the comment system seems a bit random in where it places comments.

                Jacob, do you somehow believe that the entire international biological/biomedical research community (involving individuals of many faiths and of none) are collectively deluding themselves into accepting the reality of the evolutionary explanations of the diversity of life?

                The evidence of around a million publications annually is consistent with if not directly addressing evolutionary theory.

                If you don't have a background in biology or a related science, do you have a chance in comprehending this evidence? The evidence is there. Really.

              14. GrumpyBob’s avatar

                I suppose that if one proved the existence of a supernatural entity, it would cease being supernatural :-)

                One of the things about science is that questions always remain. It's one of the things that makes it attractive. But just because the scientific approach hasn't (yet) figured out how life did begin (insofar as I actually can) doesn't mean that it can't or that we should give up and fall into the arms of a designer.

                I can understand the difficulties in understanding the origins of life. But, really, there is a HUGE mount of evidence for evolution as the explanation for life's diversity. To take as an example, one can (by comparing DNA sequences – and therefore protein sequences – of different extant taxa) infer phylogenetic relationships between sequences. We can see homology in protein sequence and function, by a number of experimental approaches.

                I don't know anything about you or your education in biology (this is not meant as an insult), so I don't really know where to go here other than observing that there IS a heck of a lot of data that underpins evolutionary biology as a discipline. This is why researcher almost universally accept evolution as the explanation of life's diversity.

              15. Jacob’s avatar

                I accept that the overwhelming majority opinion, within the biological sciences, is that life has developed and diversified by undirected processes. No doubt you have surmised, correctly, that I do not have any professional or educational background in the sciences. (More information than you need: Manual laborer, working in London). I very rarely participate in any discussion on the internet, having done so here I appreciate you engaging the points I've raised. Let me conclude with a final point. I would answer your question, "If you don't have a background in biology or a related science, do you have a chance in comprehending this evidence?"

                I would say that I should be able to comprehend the evidence, given that I am an able-minded person who takes a keen interest in this important subject. It is incumbent upon the scientists to collate and explicate their research so that it is accessible to the informed public. In other words my failure, if that is what it is, is their failure.

              16. Jacob’s avatar

                Ti finish with one example: Behe's 'The Edge of Evolution' was beautifully communicated (Insofar as it stayed with science, before drifting elsewhere in the latter part). The questions he posed therein, and attempted to address, were exactly the questions I was asking of evolution at the time. Regardless of the truth of his argument, in arguing thus he spoke for people like me. So I have taken great interest in studying the criticisms from the scientific community of this work, and of his paper in the Quarterly Review of Biology http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper….. Reading the criticisms and Behe's responses, I remain convinced by Behe. If this is because of a lack of knowledge on my part, it is not for want of trying to educate myself on the subject.

                Science seems to be big on assurances regarding the weight of evidence for evolution, but short on convincing responses to the questions asked of it. I find that the evidence for evolution is like the end of the rainbow – it is always just over the next hill. I read what books and papers I can. I'll only believe in the pot of gold when I see it.

              17. Jacob’s avatar

                Oh, I meant to say that "homology in protein sequence and function" would be expected from common design as well as common descent. But common design has no problem with analogous proteins in seperate phylogenies, that have no common ancestral protein. (Surely 'horizontal transfer' of genomic material is impossible?) Ok, the last word really is yours now!

              18. psiloiordinary’s avatar

                Specificity and rarity? Like a lottery winning ticket – that shows design doesn't it?

                Reply

                1. Jacob’s avatar

                  Winning lottery tickets turn up as often as we expect them to, given the probabilistic resources. Think about it.

                  Reply

                2. Upright BiPed’s avatar

                  NOTE: I have posted a repsonse to this blogpost elsewhere because the comments on this blog are too restricted in length to be of any use.

                  That response begins…

                  "Mr Sauders, all competitiveness aside, I do hope you'll choose to return and revise your remarks regarding the semiotic argument for design. I am certainly willing to admit that I wish this for entirely self-serving reasons. The problem is this; I can't find a opponent who can successfully attack the argument on its merits. Like any empirical argument of substance, it is based upon a limited number of premises which are fully supported by observable evidence. The use of terms follow their widely-understood textbook definitions, the argument makes no violations of fact, and has no internal contradictions. To the contrary, since the argument discusses the inter-related physical entailments of recorded information, each individual observation coherently supports the others. Here are some of the observations of information transfer which you may wish to attack: …"

                  link: http://www.uncommondescent.com/intelligent-design

                  Reply

                  1. GrumpyBob’s avatar

                    I think that restrictions on comment length are well-advised, having looked at this comment.

                    Reply

                  2. GrumpyBob’s avatar

                    Jonathan McLatchie linked two copies of his latest outburst via trackback – I deleted one of those in favour of the blog site at which you can see a wider range of his blogging activities.

                    Reply

                  3. Jeffrey Shallit’s avatar

                    Much could be said, but he seems to deliberately misunderstand Meyer, raising meaningless technical quibbles so that he can avoid engaging his arguments.

                    I categorically reject this. Meyer is the one who doesn’t understand information theory, and he makes basic errors in his book. There is no generally-agreed-upon definition of “functional information” and, contrary to Meyer’s claims, information theorists do not discuss it. It is one of a number of made-up creationist concepts, along with things like “baramin”.

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                    1. GrumpyBob’s avatar

                      The argument (as relayed through Jonathan M and Alastair Noble) seems to be muddied by using variable definitions – some of which are neologisms so beloved of ID creationists. As well as 'functional information' and 'baramin' we could add 'irreducible complexity' (which seems to mean 'beyond an ID creationist's comprehension').

                      Over at Pharyngula (http://tinyurl.com/3xdm5lo) PZ pointed out the tautologous nature of Meyer's specified information (never actually defined by Meyer)

                      Reply

                    2. Jacob’s avatar

                      "There is no generally-agreed-upon definition of "functional information""

                      Right. Meyers calls his book 'one long argument', because it proceeds by a series of logical steps, each carefully argued and demonstrated by example. Where he discusses 'functional information', as you say it's an open topic. Meyer explains his reasoning to the reader – (his argument certainly doesn't rest upon claims about what information theorists discuss) – so I would have liked to see you show where his reasoning supposedly fails, rather than focus on whether or not he misrepresents the 'discussions' of information theorists.

                      As a general point, if I may, to rebut an argument you want top get to the central point and dismantle THAT. If the basic assumptions that the argument rests upon are wrong, show that they are wrong and show why the argument would then fail without these assumptions.

                      I think you fail to do this. You get tangled up in side issues, and suggest that you have discredited Meyer and therefore discredited his argument. That doesn't work.

                      Reply

                      1. Jacob’s avatar

                        http://recursed.blogspot.com/2007/09/on-design.ht… – "as a mathematician and computer scientist I have no particular expertise on the general topic of "inferring design". It's just not something we do;"

                        All the more reason not to rule out an argument that attemps to infer design, by appealing to the norms of a field that doesn't attempt to detect design.

                        Reply

                        1. GrumpyBob’s avatar

                          No. If Meyer mangles information theory to make a point about the origin of life, then his inference becomes rather flaky. In common with many ID creationists, this is an attempt to look authoritative. Unfortunately Meyer tries to operate outside his area expertise.

                          Reply

                        2. GrumpyBob’s avatar

                          I have no interest in discrediting Meyer. I merely think his argument from incredulity does not hold water. The central issue here is that Meyer believes that the genetic system is so unlikely (on the basis of mangled information theory) that a magic being must have directed it. Meyer's argument really is no advance over Paley's watchmaker.

                          In contrast, I say we don't yet have a clear picture of the origins of life (and may never have), but that many investigators are seeking to clarify the chemical processes. I know which approach is more logical: the 'let's try and find out' approach over the 'let's give up and praise the designer' approach of Meyer.

                          Incidentally, from your reading of Signature in the Cell, would you say Meyer believes the genetic system we ended up with is the only possible genetic mechanism that might have arisen?

                          At no point in my blog have I addressed the content of Meyer's book – remember I haven't read it. I prefer to engage with the published literature, where science is discussed and issues resolved by professional scientists with the relevant expertise. There is precious little peer-reviewed literature on intelligent design.

                          Reply

                          1. Jacob’s avatar

                            I don't think he addreses that question. Presumably it would be possible – in time – for humans to design an alternate genetic system. But could such an alternate system be discovered by chance/evolutionary mechanisms? That would appear to be a point on which we disagee.

                            Reply

                            1. GrumpyBob’s avatar

                              Interestingly, I went to a research seminar in which (as far as I recall) the lab had added an additional codon, and engineered a tRNA to match, which enabled the incorporation of an unnatural amino acid within a living system. It's not straightforward. http://tinyurl.com/c4zm7uj

                            2. Upright BiPed’s avatar

                              Robert, are you still deleting comments as a method of controlling the debate?

                              Reply

                              1. GrumpyBob’s avatar

                                No, merely insults that don't represent a contribution.

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                              2. derwood’s avatar

                                How rich, coming from someone that writes on a site known to ban and restrict comments in a very heavy handed and biased manner. But hey – these folks have heroes to worship and protect, so they do what they do.

                                Reply

                              3. Upright BiPed’s avatar

                                Ahhh, so now you would like to rewrite the events so as to place yourself on the firm grounds of decorum at the point where you started deleting comments. But, there is a problem with that.

                                You were presented an argument for the puposes of discussing genomic information transfer and its observable dynamic properties. That argument leads to some potential conclusions which are in conflict with your personal worldview. Your response, therefore, was to immediately disengage the argument, leaving a disparaging remark about its content (which you entirely avoided).

                                I then reminded you that "mockery was an political response, not a scientific one” and therefore your remarks “could not suffice as a valid response to the observations of physical evidence”.

                                And THAT is the comment you deleted.

                                So clearly, it is not decorum that caused you to delete my comments, its was something, let us say – less genuine. And besides, I see from your comments (as is typically the case) that you have no problem flinging insults.

                                The question of course, is do you have the intellectual sovereingty to address the evidence against you?

                                Reply

                                1. GrumpyBob’s avatar

                                  Upright BiPed – your comments here tend towards the incomprehensible, please could you proof-read before posting in the future. I also do not follow your links off to the more risible reaches of the ID creationist blogosphere.

                                  Genomic information transfer? Transfer between what? Species? Individuals? Generations?
                                  Observable Dynamic properties? You'd better clarify what you mean there, too.

                                  There is a major problem with discussing just about anything with ID creationists: their propensity for inventing impressive sounding neologisms, rather than using the terminology in common use by scientific researchers. One good example is Meyer's specified information (as deconstructed by PZ over at Pharyngula).

                                  Reply

                                2. GrumpyBob’s avatar

                                  Upright BiPed – If you're unable to actually participate in any meaningful discussion, why should I refrain from removing your comments?
                                  Perhaps you could start by indicating what your background in the biological sciences is. To what level have you studied biology?

                                  Reply

                                  1. derwood’s avatar

                                    From my previous interactions with him, he seems to be little more than an acolyte of David Abel, CV padder:
                                    http://davidlabel.blogspot.com/

                                    Reply

                                  2. GinoB’s avatar

                                    There's something hilariously ironic about Upright BiPed, a regular poster at Uncommon Descent – the 'delete opposing views' capital of the web- whining about comments being deleted.

                                    Reply

                                    1. derwood’s avatar

                                      Hilarious, isn't it?

                                      Reply

                                      1. GrumpyBob’s avatar

                                        Upright BiPed really is a strangely persistent individual.

                                        Reply

                                      2. Upright BiPed’s avatar

                                        You say: "Genomic information transfer? Transfer between what? Species? Individuals? Generations? Observable Dynamic properties? You'd better clarify what you mean there, too. "

                                        At the very start of this thread you offered a quick negative judgment on an argument, but now you indicate that you refuse to read it, yet at the same time, want me to clarify it for you? That seems a little odd, does it not?

                                        Reply

                                      3. Upright BiPed’s avatar

                                        I understand that some people, when communicating on the internet, prefer not to come into contact with anything that challenges their comfortable ideology (often referred to as "living in an echo chamber"). In any case, you have now responded to me 5 times, and have typed out a little over 1200 characters. Each of those responses has generally been designed to isolate yourself from having to engage the physical evidence. I suggest, as a mere token to the idea of an inquisitive scientist, perhaps you could give yourself a pep talk.

                                        Reply

                                      4. Upright BiPed’s avatar

                                        In the first comment on this thread I gave you a link to a single modest posting which contained the entire summary argument, as given to Larry Moran (Prof Biochemistry, U Toronto) and Dr Elizabeth Liddle (Neuroscientist, UK). All of the words used are standard Queen's English, and used in their traditional context. I would estimate it is no more than a 7-8 minute read. However, if you maintain that you cannot be bothered to read the argument, then there should be no need in me clarifying it for you. And, we can simply leave it at that. Your avoidance will have been successful.
                                        http://www.uncommondescent.com/junk-dna/biochemis

                                        Reply

                                        1. GrumpyBob’s avatar

                                          I'm afraid I am too busy to spend too much time over at the ridiculous uncommon descent blog. I have read much of the correspondence regarding Larry Moran's views on 'junk DNA', and I have to say my views are pretty much aligned with his.

                                          To what level have you studied biology, and in which of the biological sciences?

                                          Reply

                                        2. Upright BiPed’s avatar

                                          Robert, the argument (and the evidence behind it) has absolutely nothing whatsoever to do with junk DNA, or Larry Moran's views on junk DNA, or your views on Larry's views on junk DNA.

                                          Your response has been (and will remain being) nothing but avoidance of the issue. The questioned raised earlier, as to whether or not you have the intellectual sovereingty to confront the physical evidence, has now been answered.

                                          You don't.

                                          Reply

                                          1. GrumpyBob’s avatar

                                            Upright BiPed – goodbye.

                                            Reply

                                          2. GrumpyBob’s avatar

                                            In response to some of the comments here, and also because of the paucity of work from Meyer in the peer reviewed journals, I am presently reading 'Signature in the Cell'. A review will appear in this blog in due course. I am presently about a third of the way through the text. It is the Kindle version, and I'm not very impressed by how Harper have set this thing up. No hyperlinks to the notes and the Bibliography is incomplete (nothing from A through to Dembski).

                                            Reply

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