While I was gone… (aka. Having compound eyes isn’t all it’s cracked up to be)

Really, truly, I didn’t mean it. Life gets busy, you know? Er, I mean, the Men-in-Black arrested me and wiped my memory; my cat ate my laptop; the Tasmanians invaded; the Internet in Australia was shut off for two weeks; I was turned into a horrible Drosophila ananassae/Homo sapiens hybrid in a freak lab accident involving PCR, a papercut and a dodgy pipette: mix and match your favourite (far more exciting) excuses for my absence.

Anyway, the point is, I was gone for a while. But the Internet stops for no undergraduate student, so here are a few things that happened over the last two weeks that I probably would have told you about if I’d had a chance to blog.

Everyone’s favourite wedge-bending ID proponent, David Klinghoffer, sparred (and is still sparring, at the time of writing) with my friend Josh Rosenau over the silly topic of whether or not the National Center for Science Education (NCSE) has murky connections to the world of 9/11 conspiracy theories. Josh (not writing in an official capacity for the NCSE over at his ScienceBlogs blog) does seem to have the upper hand here, but I could just be biased by the fact that I agree with all of his points. That’s what “biased” means, right? Anyway, check the tussle out – David’s posts are amusing, if unsettling: the Discovery Institute really went that far? Really?

To get the taste of conspiracy and allegation out of your mouth, you should also visit the 39th edition of the Carnival of Evolution, which was posted two weeks ago at The End of the Pier Show. Some excellent science blogging in there, and if you read this blog then I know you’re into evolutionary biology in some way at least, so don’t miss it.

In music news, St. Vincent released her new album, Strange Mercy, a few days ago in the UK and the US (for some reason it’s been out in Australia for a bit longer, which goes against everything I’ve experienced with regards to cinema and video games), and NPR has given everyone the opportunity to listen to the entire album for free. I know, it’s awesome. Oh, and so is the album. (I especially like the solo in the middle of Northern Lights – just the right amount of chaos.) If you’ve liked what I’ve previously shown of it, make sure you listen to the whole thing (and maybe even buy it, so, you know, the artist gets some money).

A pro-ID blog that recently came to my attention, called The Genome’s Tale, published a fascinating post recently about the ID concept of “front-loading”. Why is it fascinating? Well, they seem to be a little confused about what front-loading (a mechanism the putative Designer could have used when “designing” life) is supposed to be: is it a philosophical idea or a scientific hypothesis? Take a look at these two quotes:

A pressing question flung at intelligent design proponents is the question of what mechanisms the intelligent designer used. Many intelligent design proponents respond by arguing that this is a philosophical, not a scientific issue. And they are right. However, it is also true that we are beginning to unravel the clues to the origin of the highly sophisticated parts of life – features of life that point to teleology. With the slow but steady unveiling of the origin of those features of life come a number of clues that hint at some possible mechanisms used to design life. The most robust of the possible mechanisms, in my opinion, is the hypothesis of front-loading…

So, it’s philosophical? But…

The front-loading hypothesis is a possible mechanism for teleological design in biology. Several of the predictions of the front-loading hypothesis have been confirmed, but we must keep in mind that, at the moment, that mechanism is a hypothesis. Further work needs to be done in this area to strengthen the case for front-loading as a teleological mechanism.

Seems to me like they’re describing a scientifically testable concept, aka. a hypothesis – a word used many times through out the post. Whether or not they’re interpreting the idea correctly as a hypothesis could be analysed another time, I suppose, but I just find it weird that they are defining “mechanisms of design” as a philosophical area and then claiming to be able to investigate it scientifically. More evidence that the ideas of the ID movement are rather half-baked.

In other news, I’ve been reading lots of papers recently about the evolution of bacterial catabolic pathways for nitroaromatic compounds (eg. 2-nitrotoluene, 2,4,6-trinitrotoluene (TNT), etc.), so I’m thinking I should write about that soon, given how little proper science ever gets discussed on here. It’s all fascinating research and just goes to show how powerful evolution can be, even over the span of a century or so.

52 thoughts on “While I was gone… (aka. Having compound eyes isn’t all it’s cracked up to be)

  1. Jack Scanlan:

    You write that "they seem to be a little confused about what front-loading (a mechanism the putative Designer could have used when “designing” life) is supposed to be: is it a philosophical idea or a scientific hypothesis?"

    The specific idea of front-loading is a hypothesis (and I agree that it might not quite be a hypothesis yet, but I'll leave that discussion for a later day), not a philosophical concept. However, the overall discussion of what mechanism the designer(s) used to design life is somewhat philosophical. But it can also be scientific. I think your problem is that you are seeing everything in either black or in white. The question of what mechanisms were used to design certain features of life can be both a philosophical enterprise and a scientific endeavor. There is no contradiction there, in the humble opinion of yours truly.

  2. Well, silly me. I just re-read what I wrote on my blog, and I think some clarification is in order:

    I wrote that,

    "Many intelligent design proponents respond by arguing that this is a philosophical, not a scientific issue. And they are right."

    I *should* have written that,
    "Many intelligent design proponents respond by arguing that this is a philosophical issue. And they are right."

  3. I know this concept of frontloading as "exaptation", "cooption", or "preadaptation". All well established and conventional terms/concepts within evolutionary biology. For example, feathers originally evolved for heat regulation but were then co-opted for flying. There are many more such examples and there is no need to introduce a new term that implies a frontloader (designer).

  4. yeah…feathers just "came about" for heat then adapted for flight. And many more "examples" in the minds of naturalistic evolutionists at least. Sorry, but these are absolutely anything but "well established" (demanded by the theory of course), but absent in explanatory validity or empirical science. Certainly no need for a "designer," especially since design is the hallmark of feathers (and all of biology for that matter).

  5. @footlose: There is certainly enough evidence showing that the first feathered creatures were not birds that flew actively. Likewise with the gas bladder of fish that eventually became lungs of land dwelling animals. There are intermediates (lungfish or example). That is by all means better established than fancifully assuming a frontloader or designer without teh slightest shred of evidence for it. You just need to search for the keywords 'exaptation' or 'preadaptation' instead of frontloading in order to get more examples..

  6. What you and others deem as evidence is very sketchy at best or entirely absent at worst (the later most probable with my experience). At the very least one has to use massive inference skills ( imagination) to conclude most all of these ancient scenarios. You posit that there is not a shred of evidence for a designer. Do you also reject that biology is void of design characteristics? Of course not, so why is inference to chance events as causation so much better an explanation than a designer, aside from the obvious rejection due to a philosophical commitment to materialism a priori? It's certainly not due to empirical evidence. But of course the complexity of life that clearly looks like it was designed is due to chance, time, and a natural filter. Yeah, design possibly implying a designer is such a crazy stretch:)

  7. Of course the evidence is sketchy. But the inference of evolution is not due to an a priory commitment to materialism. Newton for example was a devout Christian not an insane materialist. Science developed itself by way of hypothesis -> prediction -> testing -> new hypothesis. Thus scientists started some centuries ago with the biblical story and found it does not live up to the evidence. The world is too old, the fossils are anomalies, etc. Too many ad hoc assumptions to be ascribed to the creator. Instead, the sketchy evidence that was available fell naturally in its place in an evolutionary account. That's why it was preferred. Now, IDiots come along, bable about a world conspiracy of materialistic naturalism propose intelligent design and want to overthrow the current paradigm. Such revolutionary change never was in science. Even Darwin had predecessors.

    • "Science developed itself by way of hypothesis -> prediction -> testing -> new hypothesis."

      Exactly! So this is where evolution is exposed as the pseudo science that it is:
      Hypothesis: evolution
      Prediction: none
      Testing: absolutely not
      New hypothesis: sure, whenever needed to support the first hypothesis.

      One example that comes to mind is the evolution of the eye. Evolutionists would say they propose a scientific explanation and that IDers present a philosophical one. OK. so lets look at the "scientific" explanation.

      Start the hypothetical explanation from a light sensitive spot, then an indented light sensitive spot, etc. – the evolutionists know the spiel. The prediction is that a modern complex eye will evolve in gradual steps like this. When it comes time for testing the hypothesis (the heart of the whole scientific process, that really makes it scientific) evolutionists fail utterly. They can't test the mechanism because it is proposed only on the basis of their ideological presupposition. In the name of a scientific explanation, we can only ideological presupposition.

      Then they will point to different types of eyes in Nature and say that the variety of eyes confirms their presupposition, so the test has been done by Nature. But observation of Nature only displays a variety of eyes, it doesn't explicitly show their evolution. The same display of variety can be equally explained as being caused by design. So evolution or design are both equally possible explanations, the only difference is that evolution is a mechanistic explanation and design is non mechanistic. But neither are scientific because they fail to meet the criteria of the scientific process.

  8. No, the display of variety cannot be equally explained by design, because you need several acts of creation or design, where evolution needs only one process. So, the explanations are not euqal. Evolution is better:

    "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." (Darwin 1859)

    There is no grandeur in the view of life being designed by a designer, yet it screws up every time it tries.

    Secondly, testing is not necessarily experimental. The hypothesis and its alternarive are "things evolve" vs. "nope, they don't" (you don't even have to specify the aternative). If the testing is not experimental, then it can be comparative for example. Go to look for eyes in nature and ask whether they conform to an evolutionary series or not. You don't need any fossils for that, because species can have traits in ancestral or derived expressions. If the traits that do exist can be mapped on a tree-like phylogeny, then that is evidence for evolution. We cannot reject the hypothesis of evolution then, but the alternative becomes less likely. As that repeated for over a century, evolution has become a certainty and the alternative untenable. Unfortunately, biologists were expressing this upgradign of evolution from the status of hypothesis by calling it a theory. And we all know how IDiots abused that word.

    • hey joe–

      Your wrote:"No, the display of variety cannot be equally explained by design, because you need several acts of creation or design, where evolution needs only one process."

      Let's take the first part of this sentence: "No, the display of variety cannot be equally explained by design, because you need several acts of creation or design…. " No doubt creation accounts generally presume a serial process of creation — from the more general and abstract to the more solid and concrete. The process is explained in such a way as to give the impression of an unfolding of an implicit potential being into more and more explicit being.But it cannot be that the environment is not created along with the creatures that inhabit the environment, and that the environment must include all that any particular creatures needs for its survival along with other creatures. So it is not that each creature is created individually. They manifest accordingly in the evolving process of creation from potential to actual.

      Evolution as modern science misconstrues it, is not an unfolding of a potential that already pre-exists, but a de novo production of what is not there to begin with – from the nothing of what is eventually produced. This defies logic and reason. Creation is a deductive process, a top down process, whereas evolution tries to present a bottom up explanation.

      You can ask computer experts about the top down process in writing software programs. You can't reach the objective goal of a complex program writing it using the bottom up approach. Any programmer worth his salt in the real world will tell you that.

      So creation is a single process we can call subjective evolution from subtle to gross, and modern science tries to reach the subjective subtle reality of mind etc, by objective evolution. That is the correct comparison that needs to be considered.

      As for your second remark regarding testing, you simply repeated the fallacy that I mentioned in my previous comment. You said, " Go to look for eyes in nature and ask whether they conform to an evolutionary series or not." The fact that a series of eyes in living creatures can be placed in an order of increasing complexity, is not proof that they evolved. Serial alignment says absolutely about whether they evolved from one another or not. Creation of the world with all its complex creatures as merely a manifestation of what is implicitly in the mind of God can include many creatures similar to and slightly different from one another. It can come about in one act of creation. It does not need evolution to produce the seriality that is imposed on the world by human imagination only after the fact of creation.

      • correction: should have been "Serial alignment says absolutely nothing about whether they evolved from one another or not."

      • Umm… I've been programming computers since grade 3 (and I'm about half way through my PhD), and quite often, I do 'bottom-up' programming, especially to develop algorithms based on intuitions. Of course, that is irrelevant to evolution, but you brought it up. The primary de novo production in evolution (i.e. the one that occurs fastest, and is thus to our knowledge the most de novo creative) is genetic mutation.

        As to testing evolutionary hypotheses, you are right about one aspect of the matter, namely that materialistic presuppositions have been most productive in developing hypotheses that are in principle testable and plausible – such hypotheses must stand or fall against the evidence (yet to be collected, if ever – our understanding of genetics and epigenetics is as of yet too limited, to my understanding). As such, hypotheses development is rather comparable to reverse engineering – what factors for which we have evidence could come together with good probability to cause such a structure to develop, in stages, so that we don't need statistical leaps of faith? That brings us to serial alignment.

        A simple test to falsify a given evolutionary serial alignment (though hardly sufficient to falsify evolution generally) is to extract genetic material from a sample said to lie in the alignment, and see that the genes lie within a number of mutations from those before or after. Should that genetic material not be recoverable, a secondary falsification is possible – does radiodating of the sample place it between samples that it appeared to evolve from and which evolved from it? Notice again that in both cases evolution is not being proved – it is posited as a link between two or three fossils, and by falsifying the link, we show that they didn't evolve from each other. At the same time, because of the mathematical nature of the process, we can often infer other relations between the samples, e.g. (recent) common ancestor. If the sets {recent common ancestor} and {X plausibly evolved from Y} are empty, evolution as a hypothesis has a problem, but from my vantage, I'd say its successful. And again, you bring in proof – your opposition to scientific method won't win you adherents here – we don't prove things, but rather disprove them, and keep what remains.

        Of course, for eyes, the tissue doesn't survive for us to inspect, and we cannot always infer eyes from skeletal remains, much less know their structure. So why use an evolutionary hypothesis? One, it can rely on understood processes, e.g. genetic mutation, occasional epigenetic changes and their impact on subsequent natural selection of genetic mutations, and so forth.Two, we can provisionally falsify hypotheses of a given hypothetical genetic trace of the hypothesized evolution of e.g. the focussing eye by showing that such an eye wouldn't work an an intermediate species that relied on sight (some species with eyes are blind), and so forth. Three, we can create plausible scenarios (e.g. transparent material with non-unity refractive index, required for focussing, and body-internal cells that are sensitive to light) and try to falsify an eye arising (e.g. if the curvature for focussing cannot begin to be realised, or the cells can never be directly in the light from the transparent membrane). Again, we don't try to prove – we create materialistic explanations that can in principle (should they be wrong) be disproven.

        So now I'll come full circle with that programming issue. When a professional programmer (i.e. one who programs for a living, and thus is usually not very creative, but rather uses proven algorithms to quickly develop a software) writes a program, (s)he will usually write top-down. An academic or hobby programmer (and people who are professional programmers at work will often be hobby programmers in their spare time) will rather try to develop new algorithms (be creative in the traditional sense), and those will have various short-comings that can be improved incrementally (or more rarely with a "complete" overhaul – though that relies on the experience gained from the previous attempts, and is as such not a true overhaul), and tested, much in the fashion proposed for evolution, with genetics and epigenetic structures serving (along with the ecological situation) as the memory, and the ecological situation serving as the testing ground.

        • saskydisc – you should stick to programming. You obviously don't know anything about biology beyond the dull repetitive mythological dreams of Darwin's delusions. You are still in the biological dark ages talking about "genes" and radiodating. The last 50 years of biological research mean nothing to the true believers because it completely demolishes their faith in a meaningless mechanistic world of their own making.

          I tried to inform you in another comment that "genes" are an ambiguous concept. In his recent book, Shapiro uses the word "genes" in quotes throughout the book. He writes:

          "Throughout the book, the term “gene” appears in quotation marks
          to indicate its hypothetical nature. This term has no rigorous and
          consistent definition. It has been used to designate countless different
          features of genome organization. In other words, the use of
          “gene” gives the false impression of specifying a definite entity
          when, in fact, it can mean any number of different genomic components."

          So your whole genetic comparison spiel is simply a display of your fundamentalist Darwinian brainwashing, which you very loyally and proudly proclaim as if to rally your militant atheist comrades who are becoming increasingly dejected and depressed about the victory over their ideology by the actual discoveries of science. Darwinian evolution is dead. ID has won. Cells are now known to actively and intelligently control their own biochemical functions non-mechanistically, i.e. sentiently — which Shapiro and others call natural engineering.

          And as far as your day dreams about evolutionary lineages are concerned, Koonin's "Logic of Chance" is yet another book you are obviously unfamiliar with that nicely summarizes some of the mythological Darwinian delusions that are being regularly exposed about the "tree of life."

          It turns out that Darwin will be known as one of the most damaging figures in the history of science for misleading biologists and holding back the proper scientific understanding of biology for 150 years. The damage to the spiritual lives of those who have been suckered in by the thoughtless teaching of his materialistic ideology in the schools is yet to be fully exposed.

          In the words of one Bengali poet: "Wake up sleeping souls! Wake up! How long will you sleep in the lap of the witch of [Darwinian] illusion?"

          • Let it be that the word has had many different meanings to different authors. I'm restraining myself to genes as codon sequences marked by promoter sequences and consensus sequences, that code for various proteins, that by a further interplay of DNA-derived proteins and other biomolecules, and epigenetics, lead to the development of the organism.
            http://en.wikipedia.org/wiki/Promoter_%28biology%
            http://en.wikipedia.org/wiki/Consensus_sequence
            http://en.wikipedia.org/wiki/Enhancer_%28genetics

            So why don't you actually quote a damning passage from Koonin (as far as I can tell, a leader in bioinformatics, so this should be good, or absent) and/or cite a damning paper from the last 50 years of biological research, that actually makes your claim?

            But of course, your entire spiel is nonsense, because I didn't rely on genes as distinct entities in my argument above – even if the interplay between DNA and final form were far more complicated than indicated, my argument relies only on DNA (genetic material, the genome, whatever) being the fastest mutating aspect of a population. It could well turn out that 'gene' is incoherent, and genetic material (DNA in particular) retains its coherence.

            • saskydisc – Have you been living under a rock, or perhaps in a hole, like one of the rats in the sunken ship of Darwinian evolution. You really don't know what happened to the TOL? Too late now. You're going down with the ship. Clinging to straws of this viewpoint or that viewpoint about genes only seals your fate along with other evolutionists, since it clearly shows the ideological nature (viewpoints) that evolution has always been. No longer is the FACT of evolution, now its the viewpoint.

              You seem like a big boy who can read the literature for himself, yet you want me to spoon feed you quotes from the literature. We can do that. Open wide:

              "Bushes in the tree of life" Rokas, A. and Carroll, S.B.
              PLoS Biology, 2006, 4(11): e352, 1899-1904

              "Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection. However, recent analyses of some key clades in life's history have produced bushes and not resolved trees. The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted."

              HGT events have created a cobweb of life (2005)
              "Comparing Gene Trees and Genome Trees: A Cobweb of Life?" PLoS Biol 3(10): e347

              2009 January 21 New Scientist
              "Darwin was Wrong/Cutting down the tree of life." by Graham Lawton
              "Charles Darwin's tree of life, which shows how species are related, is 'wrong' and 'misleading'."

              22 Jan 2009 Telegraph:
              "Researchers say although for much of the past 150 years biology has largely concerned itself with filling in the details of the tree it is now obsolete and needs to be discarded."
              Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: "For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality."
              Dr John Dupré, a philosopher of biology at Exeter University, said: "If there is a tree of life it's a small irregular structure growing out of the web of life."

              Craig Venter says of Darwin's Tree of Life: "I think the tree of life is an artifact of some early scientific studies that aren't really holding up." http://www.youtube.com/watch?v=zqaXVqmcDVI

              "W Ford Doolittle [biologist at Dalhousie University in Canada] is not alone in thinking that the truth looks less like a nicely trained apple tree, and more like an old gooseberry bush in need of a prune." (25 January 2009 The Guardian)

              August 2011 "Logic of Chance" Eugene V Koonin: "The genomics revolution,… effectively overturned the central metaphor of evolutionary biology (and, arguably, of all biology), the Tree of Life (TOL), by showing that evolutionary trajectories of individual genes are irreconcilably different."

              Biol Direct. 2011; 6: 32.
              "How stands the Tree of Life a century and a half after The Origin?"
              Maureen A O'Malley1 and Eugene V Koonin
              "We examine the Tree of Life (TOL) as an evolutionary hypothesis and a heuristic. The original TOL hypothesis has failed but a new "statistical TOL hypothesis" is promising. The TOL heuristic usefully organizes data without positing fundamental evolutionary truth."

              MY COMMENT
              The tree of life has gone from a fact to a hypothesis to a heuristic. Just the opposite of what we would expect for the scientific method.

              • Well, thank you for the information. It is very interesting – I've just read the New Scientist article, and I'll read the others after work. Yet I again have to wonder how much you've thought about it – if species can hybridize, does that not increase by almost two orders of magnitude the gross rate of successful mutation? And plainly stated, does the information that you cite not militate even more strongly against your position? To me, this is exceptionally interesting both on a biological and psychological level. On the biological level, quite a bit of what I cited above as falsifications of a given evolutionary event no longer need to be (a plausible scenario is now needed for horizontal gene transfer, i.e. the transferring species must be present, otherwise we can again have falsification). On a psychological level, you have allied yourself with opponents of one of Darwin's ideas, whose evidence lies in strong opposition to your own.

      • Will, another thing struck me. A few days ago, on this very blog, you were abusing biologists as logical positivists, yet now you engage in proof (verification) talk – who is the logical positivist here?

  9. Evolution is observable only in terms of small scale variation (which fits perfectly with design/creation/frontloading arguments). Evolution beyond that is pure fantasy, a desperate hope to cling to a philosophy in spite of the data. Keep telling yourself evolution is a certainty for as long as you'd like, it won't make the statement the least bit more truthful. When the data is judged solely on merit and the "alternative" theory admissible to the debate, the facade of naturalistic evolution crumbles with a weak wind. Evolution barely even reaches the realm of a weak theory…methinks it's more like a outdated idea so desperate and elastic that it will claim ANY evidence as supportive, no matter how counter-intuitive it may be. Will's example of this above is totally accurate.

    • And I take it that that is why people who have the self-discipline to check their own work rigorously, who spend years studying both other people's work and nature itself, who go to great efforts to disprove others' evolutionary theories, are themselves so supportive of it. Or not.

      So let's take that 'alternative' theory seriously. It can come in two flavours that are of interest. Either the designer goofed up occasionally (and/or did something deliberately spiteful on occasion), or didn't. The second variant is readily disproved, at least within the normal theological underpinnings of its main adherents, for if the creator were omnipotent, many kludges could be avoided, yet appear to be necessary based on genetics. (Christians tend to waffle on this point, whereas Muslims are logically consistent – god can be evil, logically inconsistent, fail to be constrained by the limits of genetics and epigenetics, etc.., i.e. true omnipotence.) A Muslim could at least consistently hold to the former design hypothesis, on the grounds that the god (let's be frank – that is the implied designer) didn't choose to violate the physical constraints.

      And what exactly is the testing basis for deeming a theory 'weak'?

      • The old goofy designer up argument. Where is your easily obtainable proof that the designer (which I imagine you don't believe in) screwed up? I love how people equate the idea of God to a the flying spaghetti monster and then go on to tell how he screwed up so much in his design (not necessarily you). The Christian point (and yes many waffle because they don't know their bibles) is easily shown in scripture: Creation was perfect until sin entered the world…from that point man and creatures from the genetic level to entire organism has been suffering. Nobody doubts malformations happen in nature.
        The basis for calling a theory weak is not "testable", but a general observation of evolution compared to most other scientific theories. The only other theory that I can view in the same category (lack of evidence and poor arguments) is anthropic global warming (although that will never draw the passion of evolution, because of course if macroevolution is true it makes no use of God…I don't buy the fence straddling stances…either man created God or God created man, period).

        • Well, I'll give you an A for creativity, but kludges are everywhere:
          http://www.talkorigins.org/faqs/comdesc/section2….
          Note – these are genetic kludges to get rid of features that are no longer useful (tails in humans, hind limbs in whales and dolphins), but that occasionally fail to suppress the no-longer useful features.
          http://therestdoctor.wordpress.com/2011/03/02/you
          Actually a great argument – a designed system would not generally have redundancy, as it would aim for efficiency.
          http://www.enotes.com/topic/Kludge#In_evolutionar
          Inverted retinas give blind spots, so the brain must step in and interpolate.
          http://www.daylightatheism.org/2008/03/the-scars-
          I'll add that the bones in feet are the nastiest kludges – we tend to injure our feet because they are ill-formed for walking – far better designs (not necessarily achievable by evolution) are possible.

          Of course, your interpretation of sin is extremely novel, and relies on human knowledge of genetics.

          • Likewise, I will give you an A for predictability, for I have read and considered most what you linked to. "Kludges" as you call them are so because that is how an evolutionary mindset interprets them against the poor argument of perfect design. With all of the above, you incorrectly assume to know what design would work best. We live in a day and age of unmatched technology, correct? How about this: when you can build a better eye, arm, foot….heck, when you/scientists can even come close to building a cell (please don't link to Varner-not close to qualifying)…maybe I and others would begin consider this bad design stance. I linked a couple of videos on what I call amazing design and you probably see only as "kludges"… http://www.youtube.com/watch#!v=AuLR0kzfwBU&fhttp://www.youtube.com/watch?v=PeTriGTENoc http://www.hhmi.org/biointeractive/immunology/tce

            Would you honestly view these and not see ridiculous amounts of information needed to build these beautiful and amazing designs? Attribute it to time, chance, and selection if you will…you have much greater faith than myself.

            • Part 1.

              Let's consider the question seriously. Why do humans have such pitiful mitochondria? Other animals have larger mitochondria. If larger mitochondria in humans have their own problems, why would individuals with smaller mitochondria in a population not have better health on average, thus being more likely to procreate successfully?

              Or let's take eyes. Engineers can create far more sensitive (minimum signal) devices than any natural eyes, albeit with less dynamic range. Any population (i.e. a species) that uses sight can adapt with mutation and selection for more sensitivity or more dynamic range, etc. But here I think I see your assumptions:

              If an organism is a kludge, a better organism can be designed. In other words, kludges are not optima.

              That assumption might be valid (at least for some organisms, on some level), or might not. Evolutionary theory says it must be close to a local optimal solution in that small modifications should be deleterious if no corresponding change in the ecology occurs first. Perhaps a better eye could be designed (or evolved) within the limitations of the mammalian epigenetic and genetic framework, or perhaps not.

              Because a healthy organ works well in a healthy individual, and is complex, it must have been designed and be optimal, i.e. because it is not practical and perhaps not even neurally possible for a human brain to design something better, it must have been designed.

              This might sound like a caricature, but it does capture much of your argument. But here something interesting happens – consider the developing foetus – as the brain develops, the nerve dendrites are attracted chemically to various parts of the thus far extant brain – the final position of a given dendrite of a given neuron is not fixed, and the number of neurons will vary by individual. To some extent, the random variation described would lead to random variations in outcome (e.g. visual processing), yet most individuals can see quite well. This is a property of neural networks. Now you could claim that this is evidence of good design – hold that thought. It is also an argument for the plausibility of evolution – because neural networks can adjust/compensate for variations in their exact construction, they can lead to very workable outcomes in moderately pathological developmental situations, and a mis-wiring is not overly problematic, so that mutations are survivable. And this is a mathematical property of neural networks, which is why they are employed (as mathematical formalisms and associated electronic implementations) by engineers:
              http://www.dspguide.com/ch26.htm

              In any individual, a substantial number of cells are mutated, including in the brain, and for smaller mutations in the germ line, the effect isn't sufficient to destroy the germ-line, which brings us to Gould – intermediate populations (inter-recognized-species, e.g. during separations of populations, when the separating population is small) may suffer deleterious effects from their mutations, but if the mutations last long enough, reproductive separation may commence, and other mutations may counteract the initial harm. My ethnic group (Afrikaners) has a prevalence of such mutations precisely because of reproductive isolation (after the development of racial ideology in the late 1700s, after we had incorporated substantial non-European ancestry ironically…), and they are deleterious (e.g. Schizophrenia, diabetes, porphyria), yet they don't prevent us from reproducing – which is one requirement over a longer time-scale for speciation in evolution, i.e. something which if absent precludes speciation (another opportunity for falsification).

            • Part 2.

              So let's consider a less ambitious designer. It only designs a neural network in a multicellular organism (an animal). Why can this organism not evolve, given the generous nature of neural networks? An individual with a mis-wired eye will generally be able to see properly, because the brain can adjust itself so well. And why can neural networks not evolve? Why can non-neural chemical signals (given the hordes of these chemical signals) not on occasion give an electric cascade, especially considering that animal cells depend to a substantial degree on varying the concentrations of sodium and calcium ions?

              As to designing a cell, that is impractical, and would be either very foolish or very unoriginal – the biological system is based on the chemically most "promiscuous" element, namely carbon – it is unlikely that a substitute would work, so we can either build cells with a known technology (living systems) and thus be unoriginal, or develop cells that would reproduce to take carbon biomass away from the biosphere, and thus be foolish – and I don't use the word lightly – if successful. But certainly, the technology is (thankfully, IMAO) not there yet.

              But this brings us to the issue of information – a designer would need huge information for all time and initially evaluated, whereas evolution (within a eukaryote framework) requires only one piece of information to be evaluated at a given time, namely whether the organism reproduces successfully (and thus impacts the population that constitutes its species) – intelligent design would require huge calculation, somehow not involving increasing entropy in violation of understood physics, which again brings us to theology – which I'm skipping (I'm a falsification bigot :P ).

              So let's get back to that thought about design and neural networks' (and other cell types') redundancy (note that many human designs are also forgiving). It is equally an argument for evolution, i.e. it can be used to make evolution and design look plausible. Of course, we only look at what is plausible, and as such the exercise has some value. But for scientific advance, a necessary step is to attempt falsification. Let me grant for the sake of argument that your argument above makes design a plausible scenario. How do we falsify whether a given aspect was designed, whether taking into account or ignoring our neural capacities? If you can supply a standard that would falsify a large number of cases, yet leave others unfalsified, your theories would meet a baseline criteria for serious scientific consideration.

              Anyhow, we can probably continue the argument tomorrow if you want.

              • Creation is not a scientific proposal. You are created by God Who does not care whether you can scientifically prove or disprove or disapprove of your created status. God is a FACT, but not a thing or being apart from creation. Neither is God identical with the creation. God is both immanent and transcendent and beyond both those conceptions, absolute. God has his own being that is in and for God, and that includes the whole of created and uncreated (eternal) being.

                You are an infinitesimal (vanishingly small) moment of God. Life has been given to you and in the same ad hoc way can be taken from you, and you have absolutely no say in either case. So you can make all the vainglorious proclamations, declarations and orations you want. It means absolutely nothing if you have not understood your own insignificant position in relation to God.

                Get over yourself., man. You sound more like an overinflated frog than an intelligent human being. Your infinitesimal viewpoint and the the total necessity by which Nature produces itself are two entirely different realities. That total necessity or absolute Reason is not accessible to you. What seems imperfect or unreasonable to you is not the concern of Nature or that of Whom whose nature it is. Everything has its necessity, but the infinite is unknown and unknowable to the finite, unless the infinite chooses to make itself known. Adopt an honest appraisal of yourself and you might be able to understand things properly.

              • The issue of information is not a problem for an almighty creator…but it is a HUGE problem for naturalistic evolution. Not sure of your point with violation of physics and entropy for a SUPERnatural God, however entropy typically seems to be a problem for evolutionary scenarios. Your argument for eukaryotic evolution and information addresses precisely nothing. Sure, a change in information can bring about a change in the organism (although the type of change required for macroevolution—specified, complex new information that would be responsible for a novel function- is uniformly absent in all of science). Moreover, the problem of information in the first place is an even bigger issue for naturalistic explanations. Where does information come from? As a computer programmer, you know the answer… and it makes it even more astonishing that you would even consider the prospect of naturalistic evolution. You realize the digital-style code of DNA is amazingly more complex than any human computer code, correct? Taking design and information a step further, have you ever considered the magnitude of fine-tuning in the universe? As a programmer and soon-to-be PhD (by the way congrats), I find it very curious as to how you think all of these physical principles came to be out of "nothingness" and became so fine-tuned when they literally could have fallen in any range? At least to me, it seems that basic logic has left the realm of 21st century naturalistic science. Here's a quick reference(not super-scientific): http://www.2001principle.net/2005.htm
                You describe yourself as a falsification bigot, however your own theory fails miserably to meet the demands of strict scientific criteria. You seem to want to have it both ways. What is the strict scientific criteria for evolutionary theory? There is none…it is dogma. And any possible bit of data that can be discovered "somehow" fits into the theory…it essentially explains nothing because it has become a tautology that explains everything (and against every grain of common sense in my opinion). When one gives up the presupposition of naturalistic explanations as exclusive, design becomes overwhelmingly apparent to the point of absurdity. Of course most scientists need to remain committed to materialism, squashing the idea of design as a mere illusion while holding fast to the treasured philosophy. I guess that is why Crick said "Biologists must constantly keep in mind that what they see was not designed, but rather evolved."

                • Thanks.

                  I read your website, and truthfully, I found myself amused, especially on the cognitive dissonance pages (I'll get to the fine-tuning next). Actually, although I do quite a bit of algorithm development, my background is electronic noise, so I'll use an example from my own experience. When I was learning about 1/f noise, I was told that the measured variance of the noise is always finite, in contradiction to the simplest form of the theory. I thus demanded that there must be a lower cut-off frequency below which the 1/f tendency flattens. Later I found papers that showed (using a variation on the standard theory) that said that the variance one observes is a function of the observation period. With the insight that the observation period determines the variance, I used the standard theory coupled with a representation of observation (linear filters), and calculated the variance – not ground-breaking (my supervisor threw me in so I had to 'learn swimming' without a substantial background, so I repeatedly reinvented the wheel – he didn't specialize in the subject either) but illustrative of the problem – and this is how science progresses: Someone makes a scientific contribution, but later insists on theory over observation (often, one makes a scientific contribution just by seeing when a theory reproduces observation and when not, as the algebraic forms may hint at an underlying pattern). Then a next generation ignores the previous contributor and his/her errors. Einstein famously argued against continental drift (way outside his field, but not remarkably different from his constant universe). That is the strength of science – substantial error can be shown – cognitive dissonance and self-deception usually doesn't last more than 40 years.

                  As for fine-tuning, on the one hand, I'm skeptical, but on the other, as long as it isn't falsified, by all means, play with the idea – this is as close as I've seen creationist ideas get to falsification – physics should soon be in great flux (neutrinos were always the bastard children of the standard model, and assigning them mass leads to conservation of mass issues, if memory serves. If they in fact can move faster than the speed of light, it is all the more interesting. Maybe new physical theories will have the same sensitivity issues, maybe not – so fine-tuning is intermediate in that any falsification is dependent on the prevailing physical understanding.

                  I don't per se believe that existence came out of nothingness – I merely have no hypothesis that can be subjected to any degree of testing, so I don't spend my energy speculating on it.

                  As to information and life, I have two observations. First, the earth/biosphere is a heat engine of sorts, with a source temperature of 5800K and a sink temperature of 3K – not exactly thermodynamic equilibrium. Life, like any other chemical process, needs thermodynamic disequilibrium. Second, you don't specify the criteria that evolution fails to meet. Actually, it was will on this blog yesterday morning that 'will' gave one rapid mechanism of information sharing across species (horizontal gene transfer) – without it, each species must separately come up with an initial functional variant of a gene which can then undergo successive improvement. Yet here (s)he's supplied us with an understanding that the genetic novelty of nature is actually almost 33 times less than appears on the surface based on a naive understanding of genetics. I'm confused why you consider that strange as an argument for evolution – when a scientific theory meets many falsification opportunities, and a certain structure continually survives these falsification tests despite becoming apparently ever more constrained by evidence, we usually consider the theory an enormous success. And now nature doesn't even need as much novelty! All that is needed for the majority of reproductive success is that the occasional (rare) hybrid be a reproductive success (unlike the majority of hybrids).

                  So let's take the occasional creativity that (we evolutionists claim) does occur in nature. Gene duplication is an obvious route – a second copy of a gene can often be modified without overly deleterious effect, and can lead to novel functionality after sufficient drift. One requirement is that natural selection on the duplicate not be too strong during the drift, but that begs the question what determines natural selection. To first approximation, the duplicate gene must not (in at least most of its variants in the population) be sufficiently harmful as to impact reproductive success over the number generations required to develop a new (helpful) functionality.

                  EDIT: fine-tuned -> falsified (too early in the morning)

                  • "Gene duplication is an obvious route" — FALSIFIED!

                    Complexity, Volume 16, Issue 6, pages 17–31, July/August 2011
                    Is gene duplication a viable explanation for the origination of biological information and complexity? by Joseph Esfandiar Hannon Bozorgm

                    "…although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms."

                    • You are confused – reread your own quote – if I'm to take your quote seriously, it played a role, but not was not the only contributor. You've (whether for lack of understanding or whatever other reason) provided us with a mechanism that greatly reduces the underlying novelty of nature compared to what we naively observe – one that reduces the required novelty by an apparent 33 times – I'm at home, so I cannot read that article right now, but I'm curious to what shortfall he finds relative to the observed novelty..

  10. You again have answered nothing about the creation of new, functional information, probably because there is no materialistic answer for it. Gene transfer I get, however you need to look at it for what it is, which is not the formation of a novel gene from a non-existent source (required by evolution). You pretty much illuminate your stance with the following: "And now nature doesn't even need as much novelty! All that is needed for the majority of evolution is that the occasional (rare) hybrid be a reproductive success (unlike the majority of hybrids)" Really? Nature doesn't need much novelty? All that is needed is that occasional, rare hybrid? You can't be serious….what an extreme leap of faith. Too bad science and experimentation totally blow that claim out of the water (see 50 + years of purposefully mutating Drosophila for starters) If you honestly believe the information you posted about HGT , I think you either grossly overestimate the significance of HGT, or have a poor understanding of what is needed to get mud to turn into Mozart. How about a few basic links, since the fine-tuning website amused you so:
    1. How and where does information come from? Here may be some help.. .http://www.youtube.com/watch?v=XexHxgxTbWY
    2. Is ID scientific or falsifiable? Again, a few pages.. http://www.arn.org/docs/behe/mb_philosophicalobjehttp://www.youtube.com/watch?v=hy0_Mn1s1xo

    Everyday I get reminded of the pure strength and blind hope that evolutionists have in their religion of naturalism, worshipping at the alter of time and chance, believing anything as long as it shuts the door on the Creator of the universe. I will leave you with a favorite quote of mine …
    "For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountain of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries."…agnostic Robert Jastrow

    • Notice that that conclusion is what I draw from the data provided: 97% of the apparent novelty (in terms of genes) are coming from hybridization, if I'm to take will's one reference above seriously. So still a good bit of novelty, but much less than what appears on the surface, i.e. the total genome. Of course, you delete the actual novelty, and I omitted the post-borrowing evolution, but evolution once the gene is obtained is much simpler than getting the whole gene first. In terms of identifiable genes, using the definition I posted earlier, the originality does seem reduced by 33 times – is your complaint with my interpretation of will's reference?

      • The problem I am asking about is how does the information get there in the first place, not how information can change or be borrowed. Evolutionists love to speak about the discoveries the have found on the 100th floor of the "building of life," however the general rule is to assume the first 99 floors to either already be in place (as illustrated with your example) or ignore that aspect altogether. The hard part for materialism is providing a logical pathway for functional, digital-style information to be generated, let alone providing scientific evidence for it (there is absolutely none…this is the extreme step of imagination/faith that a naturalist must take…which is fine, so long as they allow ID scientists to play by the same rules, which they typically don't. I'd argue ID scientists actually follow the pure evidence more clearer to the end point). I'd also argue that with observation and real life examples, we humans can readily detect design by intelligent agents. We can do it with technology, engineering, literature, etc…..why does it suddenly become so illogical to follow the same line of thinking when dealing with cells and life? (after all, their technology and engineering obliterates anything man has ever done). I believe the reason is that design detection leads to the end point of a designer, and the idea of a designer/God being someone's creator puts that person as the creation, under the rule of God, and most men/women just don't want to be in that position. It is human nature(sin) to want to be your own god, so a naturalistic philosophy/explanation is not only appealing to the masses, it is justified against the mere possibility of the alternative, no matter what the evidence or logic may suggest.

        • But the origin of the new information has hardly been hidden – mutation with selection is an entirely plausible origin for a substantial portion of the novelty. First you have mutation that yields little selective advantage (otherwise selection would obliterate the new information) then some combination must occur to exert selective pressure, e.g. a combination of one additional mutation that gains selective advantage, and/or an ecological change that makes the existing and/or novel mutations suddenly advantageous. So you have two sources of information – ecology and random variation (noise, if you will) – and possibly more that remains to be discovered (whether by myself or by biologists generally – I'm not trained as a biologist, but rely instead on my statistics background and limited biological understanding).

          As to functional digital information, DNA has been understood for 60-odd years, so I'm a bit confused. Do you mean how DNA came to be? DNA clearly relies on a number of bio-molecules. If one wants to persue the matter, there is substantial study into abiogenesis, though at this point from my vantage not enough is understood – perhaps in ten or twenty years, we can have substantially falsifiable hypotheses. Or is your question why DNA is digital? That is simple – four amino acids code information, and the information is redundant by always pairing so that information mistakes can be repaired to some degree – much like electronic communication (parity bits, etc., albeit not with double encoding of bits/halving of bandwidth).

          As to the rest of your argument, present the evidence. The evidence for design just isn't being offered – what you and will have offered that has been of substance has totally undercut your own arguments. Some of it is presumably due to a lack of scientific training – will's latest being a case in point – if gene duplication is insufficient to explain the existing variety, i.e.

          {Existing variation} is greater than {variation possible due to gene duplication}

          then somehow gene duplication as a source of variation is falsified? This is indeed a novel argument, but it doesn't sound at all coherent. Why wouldn't there be other sources of variation? I don't blame you for lacking scientific training (I blame the left, which historically provided scientific education to the poor, but has since become a back-scratching/back-biting club for middle-class people), but it does show in your arguments. At the same time, I'm glad that you guys are reading the literature – at least you can know what the arguments are about.

          Actually, the only evidence that could meaningfully point to design is kludges (any real designer makes trade-offs, has limited information, etc.), but that doesn't distinguish design from evolution, thus that Crick quote – but then again, because we can see the kludges now, it is no longer as awesome (in the original sense of the word) – a very fallible designer, who cannot frequently select anything but local optima is theologically implausible, yet required to take ID seriously.

          As for your theological argument, meh. I was devout long enough. Were my purpose to 'poke god in the eye,' I'd have gone to the trouble long ago – truthfully, my behaviour hasn't changed much since becoming an atheist (14 months now…). And what I usually find is that devotion of the variety that you promote with that sentence is usually promoted for individuals to profit from, be it with power or with money. Most of the decent religious people I know tend to stay far away from organized mass religious activity – thus the quietism of most Ukrainian Christians vs loud-mouth fraudsters like Sunday Adelaja (who defrauded both Ukrainians and Nigerians). One of my last experiences before leaving was attending a 'non-denominational' church (part of the evangelical movement), and before the service, there was a prayer meeting. In retrospect, I can now only pity the earnestness of the one individual who was trying to show his devotion by doing the 'talking in tongues' bit, but did it without the flair of the gangster mass pastors – 'boom shaka shaka' softly repeated – yet at the time it thoroughly nauseated me. In fairness to the pastor, it was a small church, and he actually tried to help the people around him – much as I did and continue to do – mainly with tutoring in the scientific subjects that I specialised in. I could say more, but I've already derailed the thread.

          • You still fail to understand the problem of original, novel biological information. Let's make this simple: you state mutation with selection is a plausible origin for novel information. Wrong. That is not what is being questioned. Mutation would have to have information to mutate IN THE FIRST PLACE. Where does that come from? Nobody questions what you keep bringing up, but you never address original information and its source. Secondly, mutations don't add entirely new functional codes to the genome (not copying or sharing). Also, it seems you are stuck with this horizontal gene transfer and seem to think this somehow explains the VERTICAL novel functionality that the beloved theory demands, and it flat out does nothing of the sort, and this is the real problem…how does macroevolution happen? What does HGT demonstrate about the missing macroevolutionary events? Horizontal sharing really answers none of the big problems for evolution, and it certainly doesn't answer the origin of information. At best it explains sharing (although it isn't magic…cellular apparati are needed to accomplish this, which brings about other questions). So then you come to your conclusion that all information is generated from ecology and random variation (Noise?…must be your background…but this is biology). Again, there is a monumental lack of evidence for your claim (and don't come back to HGT or say that Will proved your point). Sorry, but your interpretation of what I am presenting or questioning does not undercut my own argument…perhaps you have misunderstood what is being argued or perhaps it makes you feel you your point is somehow more validated. You then simply amaze me (not really, I once was blinded by naturalism as well…what a fanciful world it is:) by stating kludges are the best example of design that exists. The Crick quote had zero to do with your kludge crutch…he simply was stating that everything in biology DOES appear like it was designed, but the naturalist must keep reminding himself that the magic wand of evolution was the designer…..because DESIGN is apparent everywhere….not because kludges appear everywhere. In other words, ignore what appears to be true, and stay committed to the naturalistic philosophy IN SPITE of what you see in all of biology. It is difficult to discuss real biology with you…you examples and background don't make it very easy. Here are some references dealing with evidence, scientific method, etc, per your request. http://www.uncommondescent.com/intelligent-designhttp://www.arn.org/docs/behe/mb_idfrombiochemistrhttp://www.uncommondescent.com/faq/
            Lastly, your comments on my theology are out of this world. Where and how do you extract information from text? How you extract my asserted theological argument (which I never presented one) as one in which I promote profit of power or money???? You have obviously a poor understanding of true biblical theology, not to mention comprehention of my comments. Are you referencing the pitiful prosperity gospel? I cannot help what may be presented as a biblical theological stance in the Ukraine, but it sounds incredibly off base, it it's unfortunate that you have turned from that misfortune to a greater one.

            • Part 2.
              Back to the flagellum: I'll illustrate one plausible evolutionary pathway for the arisal of flagella. Evolution of the cell wall for protection against harsh environmental conditions may lead to hair-like proteins or other cellular meso-scale structures to absorb momentum, instead of the cell wall at one point having to absorb that impact, and therefore suffer local failure. These structures might even initially arise precisely to harm other cells (i.e. a few of them on the predator, several of them on the prey). I'm relying on Newtonian mechanical considerations for this scenario. Once these structures become prevalent, i.e. first the poking and then the protection, optimum configurations within the limits of the genomes involved will be reached quickly (on a geological time-scale). Genetic drift can commence.

              Once genetic drift hits upon getting those structures to move (advantage – more nutrients by setting up currents), that invention can become dominant, and genetic drift can recommence. Notice that life is getting crowded. Eukaryotes might at this point become prevalent, and they are super-prey, but that isn't absolutely necessary – this could happen before – but for the next step of my argument, a plausible mechanism of resource concentration helps – maybe biofilms develop. So whether by biofilms or by eukaryotes, life suddenly isn't as crowded, but resources are being hogged.

              So we have bacteria that have limited access to resources (probably partial population collapse), have somewhat motive hairs (my example), and face a lack of resources. Now the survivors may hit upon somewhat more complex hairs, but losing hairs on one side will allow slightly more directed motion – actually, the gene would probably have to become more complex, but not overly so. With hairs only on one side, and a bit more complexity to achieve a semi-consistent thrust, we've reached the top of a hill – the gene contains many redundancies, and natural selection (e.g. based on resource availability) can start cutting codons out, simplify the unwieldy hairs, down to a point of irreducible complexity.

              So inferring design from irreducible complexity, nay, specified irreducible complexity, would give the wrong result. From a modern understanding of Ockham's razor, with the understanding that irreducible complexity is neither in itself evidence of design nor a designer, design incorporates an unnecessary hypothesis (designer).

              As to the second link, the evolutionary pattern (from a distance) that Darwin gives is entirely plausible. To get to irreducible complexity via evolution, you need some redundancy first. So let's take a redundant biological system: metabolism of glucose. Almost every cell in your body can use it. Your liver can also use it, and store some of it for later (post-meal) use. Most other sugars are not usable, and the liver is the only organism that can convert other usable sugars into fat and animal glucose. But truthfully, we don't begin to understand to what extent we are redundant, and to what extent earlier species were genetically redundant.

            • Part 3.
              Regarding the third reference: Point 1. Evolution as a plausible mechanism for arisal of a given feature is not a falsification of design. That something could evolve doesn't mean that it did – it could still have been designed. ID is not falsifiable.

              point 4: And regular science beat the ID-ers to the punch – so the ID crowd hit upon function of non-coding DNA in 1986, and regular science figured it out in 1978 (toward the bottom, just before the comments): http://pandasthumb.org/archives/2007/01/junk-dna-

              As to point 15, will (whether by accident or intent) demolished many arguments that constrain evolution to occurring in one gene line, so inventions in one gene line can materialistically crop up in another, and apparently does so relatively frequently. Oh well. Science corrected its own mistake.

              As to point 16, now he's bringing in non-falsifiable hypotheses again. See point one above.

              As to point 18, to the extent that it is intelligible – so if early scientists were stuck on some unfalsifiable premise, that has since been set aside, we are to be for ever bound by it? That is a bizarre claim.

              As to point 19, to the extent that supernatural claims involve nature, all science can do is provide a materialistic alternative, or fail to do so (based on the degree of natural understanding and the plausibility of the claims) – to whine 'political correctness' is rather rich.

              As to point 27, the abuses in the actual probabilities used, e.g. as I noted in my previous comments, suggests that Dembski deliberately engaged in fraud. Tell me why, after right-handed amino acids became dominant, and organisms that produced right-handed amino acids ceased to exist (presumably early on), why the probability of producing left-handed amino acids would be anything but one? I've still not received any response, and frankly, the only honest response that I can see is that Dembski lied.

              Regarding point 34, that the parasite failed to evolve is not exactly surprising considering that people who are treated for malaria will generally use mosquito nets and other mosquito repellents, i.e. do precisely what is necessary to prevent such a mutation from spreading. Own goal?

              EDITED to add – re point 34 – and of course, chirping crickets regarding Gould – the evolutionary advantage is small – no population separation of the parasite, and the parasite is hardly under control. Parasite and other pathogen evolution generally occur when populations are pushed close to extinction, e.g. hospitals. If you want to set up a comparable example for parasite evolution, set up a hospital, keep infected individuals around, treat them, have carrier mosquitos bite them, and then bite healthy individuals already using quinone or what-have-you.

            • Part 1.
              Where to start? I'lll work from the bottom up. Here's your own theological argument, for your edification, above:
              I believe the reason is that design detection leads to the end point of a designer, and the idea of a designer/God being someone's creator puts that person as the creation, under the rule of God, and most men/women just don't want to be in that position. It is human nature(sin) to want to be your own god, so a naturalistic philosophy/explanation is not only appealing to the masses, it is justified against the mere possibility of the alternative, no matter what the evidence or logic may suggest.
              When people start suggesting that rebellion against some diety is the motivation of people with whom they disagree, profit seems from my perspective (and even from the perspective of many of the theists I've known over the years) to be the motivation.

              Where does information come from? Noise, yes. Actually, this is kind of funny, as copying errors abound – most of the mutations occur far away from the germ cells (sperms, ova), and thus don't even make it to the next generation. Call them copying errors, call them noise, whatever. My amusement arises from will's argument about quantum physics (which underlies chemistry, and thus DNA) – interpret cellular reproduction on the DNA level as collapsing of wave functions (usually, the errors are on higher levels, where semi-classical and classical methods explain the errors/noise/information, as your prefer), and sometimes it is stray radiation (all those K-40s disintegrating – this time one can actually blame Schroedinger rather directly) – all of this is aside from HGT. In fact, such errors are so common that the cell has means to repair most of them – without these means, we probably wouldn't be stable species, and life as we know it (macroorganisms) would become rather implausible. So here's a reference:
              http://www.nature.com/scitable/topicpage/dna-repl

              Your interpretation of Crick suggests that you've never done engineering design.

              As for your first link, it contains a reference that contains the following gibberish:
              Since Dawkins explicitly accepts CSI as a reliable criterion of design detection, and since he already believes in the existence of "godlike" extraterrestrial beings, one would predict that were he to concede the existence of empirical evidence within the natural world that triggers a design inference, he would likely affirm that the intelligence in question was extraterrestrial, thereby retaining his philosophical assumption that design inferences can only be temporarily correct explanations that must be susceptible to a reductive, naturalistic explanation in the final analysis

              Dawkins doesn't believe in panspermia. He merely seriously considered panspermia-based arguments: http://www.sciforums.com/showthread.php?t=79815

              That said, the flow-diagram is remarkable. Let's take it seriously. We are studying some organism, and we get to "Is this aspect contingent?" Suddenly, we are at the mercy of the achievements of falsification-based science – has falsification-based science developed any understanding of the process? Let's say that it hasn't, or at least that the ID-scholar isn't aware of any such finding.

              So the ID-scholar reaches "Is this complex specified?" I assume, based on the erroneous little article cited at the top, that they mean irreducible complexity. So let's take the bacterial flagellum. The ID-scholar decides that it was designed. Is this conclusion falsifiable? Can such an entity (the flagellum) arise by evolution? Sure, for the latter, as I'll illustrate below, but as will become apparent, it doesn't falsify design – perhaps one could get a more open-minded ID-scholar to revisit the process (flow diagram) and start over, to conclude that in fact the flagellum was evolved, but it wasn't on the basis of falsification, which is why I find this whole methodology an abuse of science.

              [Jack - how come my comment disappeared?]

              • Your analysis of my "theological" argument is laughable, but hey, if you think you see "profit" as the implied message somewhere in there, more power to ya (also,
                "for my edification?"…and from the previous post on my "lack of scientific training"…you need to get off that high horse of imagined intellectual superiority on which you ride so poorly, and possibly stick to computer programming rather than arguing about evolution, at least your examples seem to fit there, because you obviously have no idea how far they are misplaced in real world biology).
                I have not the time nor enduring patience (don't let the ego read into a submission here:) to read the same unfounded positions stated…most of which as predictable as the sunrise…and not have the ability to get you to see that biology and the naturalistic problems in question: #1 exist, and #2 are not equitable to computer analysis, background noise, and an unconnected potpourri of misused/interpreted examples you have provided. I will leave you (at least for now, as my time will be constrained) with a very interesting blog debate which clearly discuss the points I have mentioned above from proponents of both sides of the debate. My hope is that you would join in (many other good debates as well) and challenge them with you vast knowledge of falsification and generic, packaged rebuttals. Good luck with everything (that's kind of like "saying it all" to a naturalist, eh?)
                http://www.uncommondescent.com/intelligent-design

                • As to your link, I read it, and found it rather amusing. So to test a slow probabilistic model, we need high speed integration! Yes, verily, finite element analysis (which is highly dependent on assumptions made) is needed to test evolutionary hypotheses! (I could agree that such analysis could in principle be used, but numerical stability is not exactly a problem in most evolutionary studies, as we are not evaluating integrals or differential equations in most cases…) OK, enough playing of intellectual superiority (that was fun – perhaps I should do it more often)…

                  not equitable to computer analysis Because evolution looks so much like a probabilistic subset problem?

                  But enough mockery from me. I just wanted to make myself guilty of your accusations. As to your invitation, it doesn't interest me – I'm sure that any new fraud from Dembski et alia will with time be posted here with "supporting evidence," and that when the material that is abused as evidence gets posted, I'll have an opportunity to learn something about nature generally (e.g. the scientific literature cited in support of the argument), and to learn about human psychology specifically. Or stated another way, I'm still utterly interested to understand how you justify Dembski's ID falsification argument to yourself, and would like to know whether you attempted to think through it, especially that bit about a when a natural process exists to explain a biological situation, that it somehow falsifies ID…

                  Actually, are you by any chance a disciple of Andrew Schafly? Your grammar suggests that you aren't Andrew himself, but that smiley after a thinly veiled accusation of the is an unregistered trademark of his, to my understanding. Also, many of your other behaviors are suggestive of his influence.

                  I think I want to say one more thing about regurgitation. It strikes me that you have regurgitated what is on that website, without thinking it through – I've limited myself to my own thoughts, but felt it worthwhile to subject you to your methods for this last post.

                  As to submission, I guess I always found the concept repulsive. What I had hoped to do was to engage your mind in your own beliefs – ID to me is a strange belief set that relies on frauds – but I don't care to get submission – the pleasure is in the arguing. I'll let you have the last word (if you don't come up with an insult, I might continue the discussion, but I'll leave that to you).

                  • The link was provided for you to read the logged debate between contributors, not so much the article itself (although again I would have to question your interpretation based off of your previous arguments). From your response, I'd bet you have not done that. I liken you to Liddles ideas possibly, although she (not meant to be a knock) makes a much cleaner and direct argument grounded in actual biology (I find it wrong, however). Do you find everything that negates your arguments "amusing?" By the way, I have no idea who Andrew Shafly is. Please read the dialogue between the contributing scientists if you are interested in learning anything I was talking about. If you cannot see the merit in the arguments (both pro and con) presented, I can be of no help to our conversation, because you would either be very unintelligent (I don''t believe this is the case) or you would be far worse…in a absolute state of denial and out of touch with reality. I have presented my own beliefs. If you choose to argue them that is fine, but that is rather slippery of you to ask to engage my mind, suggesting my only tactic is to link. You asked for sources or evidence. I know you can do better than this, at least I'd hope so. And I have no desire to cast the last insult…I was merely responding to some of your haughty prose. I'd rather a logical debate, like the one linked, but that doesn't seem to be the modus operandi here.
                    Wanna know what I think? I think design is obvious in nature. I used to think that darwinian evolution explained it all…and I never entertained the thought that there were possible problems with the theory (sound familiar yet?) and I argued some same points you have, but with biological coherency. I began to read questions raised by the ID movement and thought for fun I would earnestly answer them. And I began to realize my stance was weak regarding anything beyond macroevolutionary explanation…the rest was a philosophical commitment to my naturalist beliefs. When I began to HONESTLY look at the evidence (DNA protein relation , novel fcsi, abiogenesis improbabilities, lack of evidence for macroevolution, design detection in other sciences), I was pissed off quite frankly, because it was real, it was detailed, is was science, and it was truth (perhaps my first experience) …My previous "science" was indeed all hopeful thinking on my part, creating straw men arguments for me to tear back down, thinking I somehow "proved" something. Disregarding any challenge as religious or absurd, before looking into the merit of it. And then I transitioned into looking at what is there and coming to the most logical conclusion (very odd you referenced Ockam's razor for your argument…I'd stay away from that if I were you considering your stance). The conclusion was this, and it is obvious if you let go of the darwinian presupposition that so grasps your very core, that design need not be explained by time and accidents that cannot explain it. Natural selection is not a creative force. Mutation simply cannot do the job. Ecology?…sheesh. Prebiotic evolution…I've read children's books with more science. Design can be studied for what it is…we no longer have to try to put a square peg through a round hole because philosophy demands it, unless of course one feels the need to reject the alternative at all costs. Ditch the philosophical commitment and allow the evidence to speak for itself…believe it or not, science can still (and does in any other field besides evolution…forensics for example) operate very successfully, much more so than it does in this "field of dreams" called darwinian evolution. My conclusion was that I was believing in a dogmatic naturalistic religion that was linked to very poor, if not deceptive science. There's some insight into my mind…with no links and no smileys. ID was entirely too obvious to resist, and evolution was like the emperor that indeed had no clothes.

                    • You want me to address the debate, OK:
                      Which is it? Differential reproduction or adaptation? How do you know whether differential reproduction has anything to do with the environment at all? It’s circular. Differential reproduction results from a better fit to the environment, and a better fit to the environment is determined by differential reproduction.
                      Umm, more like a better fit into the environment leads to differential reproduction, so we take it as a null hypothesis that differential reproduction (of a genetically identifiable subset of a population) is indicative of a better fit into the environment, at least over sufficient time-scales. Here's the challenge: Show a better hypothesis, namely one that can at least be 1. plausible (if not falsifiable), and 2. explain the data more rigorously, without relying overly on supernatural claims. Over shorter periods, random variations in reproduction can at least temporarily provide opposite results, but (and perhaps this is a failure of my imagination) I cannot begin to imagine what else would provide such trends. At any rate, beyond the trivial assumption used, our understanding is as of yet too simple to provide any falsifiable hypotheses.

                      Much of the rest of the threads rely on misunderstandings of thermodynamics and the like, before getting into simulations of evolution. I can see no helpful purpose in getting a relative ignoramus like myself (as compared to Dr Bot and Liddle) involved there, other than to distract attention based on my relative ignorance.

                      As for science and materialism, frankly, you haven't made a single argument that actually has used my physical understanding (obtained during an engineering education) against my beliefs. The funny thing about that is that my colleagues frequently do.

                      I've just finished reading the entire thread to date – I learned a thing or two from the materialists, but the rest was incoherent – though that may have something to do with the fact that I should have gone to bed hours ago.

                      But you are at a bit of a disadvantage – an elderly relative of mine was a fascist sympathiser during the war, and he'd also try to stir disgust in me, while hopping from one argument to another without answering (except with a casual dismissal) my arguments. That's why you get a bit of a rise from me, but not much more. That is also why I take the effort to read your (plural) references when I have the time (or when I make the time, against my better judgment as to my responsibilities). That's why I spent 15 odd minutes on that paragraph above, and why I did likewise with some of the paragraphs on the evolutionary models – I try to be empathetic, but when I detect nonsense, I get annoyed.

                      Oh, and the bullying tactics that you guys use might work on teenagers, but on emotionally secure (and many emotionally insecure) adults they don't go too far. I include here bandwagon arguments, but far more significantly, the notion that we just didn't put the effort in to challenge ourselves and face the evidence. Let me assure you that I grappled with materialism for a decade before becoming an atheist. Ditto for my politics, my ethics, and so forth. And ditto for evolution – this relates to the paper cited by will above (Bozorgmehr) – his argument, as will uses it, relies on an assumption that duplication is the only materialistic basis for novelty. Considering the case of HGT, it seems at any rate unlikely that the gene will be optimised for its new host, and might occasionally end up with radically new functionality, as the situation of the new host is radically different. Moreover, Bozorgmehr is more careful in his latest, as he doesn't seem to claim anymore that duplication is unable to produce new information (by whatever definition). If these are your arguments, what am I missing? Even granting that duplication and HGT cannot produce new information, how does that preclude mechanisms yet to be discovered? In other words, why stop looking?

                      So even granting your premises, I plainly fail to reach your conclusions.

                    • Judging by your previous comments and these final ones, I was not intending nor expecting you to reach my conclusions. I was simply briefly sharing my changed stance. How could I possibly expect you to change your stance when you fail to even see or acknowledge the shortcomings of a purely naturalistic answer that can produce man from molecules? I have not offered many super-detailed arguments, and the reason is simple: you fail to grasp the simple ones. It's like beating my head against the wall, all the while hearing some of the most nonsensical rebuttals I have ever experienced with an evolutionist in return. Now it's bullying tactics? Before theology for profit? I am truly astonished. Best wishes…

                      " Since what may be known about God is plain to them, because God has made it plain to them. For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that people are without excuse.
                      For although they knew God, they neither glorified him as God nor gave thanks to him, but their thinking became futile and their foolish hearts were darkened. Although they claimed to be wise, they became fools"
                      Romans 1:19-22

  11. Jack – my one comment keeps on disappearing. Why?

  12. saskydisc — You wrote:

    "But the origin of the new information has hardly been hidden – mutation with selection is an entirely plausible origin for a substantial portion of the novelty. " FALSIFIED! (as will be explained below).

    And you wrote:

    "So you have two sources of information – ecology and random variation (noise, if you will) – and possibly more that remains to be discovered (whether by myself or by biologists generally – I'm not trained as a biologist, but rely instead on my statistics background and limited biological understanding). "

    YES. This is the problem – "limited biological understanding." Your background in satistics is not sufficient to argue the details of evolutionary biology with those who keep up with the latest 21st Century research in the field. You are still arguing from primitive 19-20th century biology, which was based on pure reductionist, mechanist mental speculations, thanks to good ol' Darwin and his followers. These fellows hijacked science to foster their own mental concoctions in the name of "falsifiability" when the main principle of science is actual verification of their speculations with testing. Falsifiability doesn't mean a thing without actually testiing imaginatively concocted narratives of couldda-wouldda-shouldda.

    If someone claims the Sun is 239 million miles from the Earth, it is a falsifiable statement. Is it therefore scientific? What evidence is it based on? Has it been tested and verified? These elements are essential for a scientific claim. Otherwise every Tom, Dick Dawkins and Charlie Darwin can make a claim of being scientific and intelligent people are supposed to accept that! I think not.

    And NO ! Ecology and random variation are not the "sources" of information. Ecology has never been considered a "source" of information, even in the primatave old-school biology, but certainly a cause for modifying an organisms constitution. This is called adaption. THere is a certain capacity for adaption in an organism's inherent nature, but it comes primarily from the information in the organism, not the ecology. And secondly, random variation has been discarded as a means for generating new information in an organism. Do you have such a short term memory problem that you haven't recalled the numerous times this has been presented on this page?

    (Based on experimentally observational evidence, not mental speculation) 21st Century Evolution – J. Shapiro (2011):

    "It is difficult (if not impossible) to find a genome change operator
    that is truly random in its action within the DNA of the cell where it
    works. All careful studies of mutagenesis find statistically significant
    nonrandom patterns of change, and genome sequence studies confirm
    distinct biases in location of different mobile genetic elements."

    "The advent of molecular genetics and genome sequencing was a
    major step forward in evolutionary science. Examining the DNA
    record made it possible to subject traditional evolution theories to
    rigorous empirical testing. Do the sequences of contemporary
    genomes fit the predictions of change by “numerous, successive,
    slight variations,” as Darwin stated, or do they contain evidence of
    other, more abrupt processes, as numerous other thinkers had
    asserted? The data are overwhelmingly in
    favor of the saltationist school that postulated major genomic changes
    at key moments in evolution….Contrary to
    the views of Linnaeus and Darwin, nature does indeed make leaps,
    and we now have molecular evidence of how some leaps occurred…
    The systems view of proteins implies that they evolve by natural
    genetic engineering rather than by localized mutation."

    To make this clear, the modern concept of biological organisms is experimentally based on a SYSTEMS view, not the agglomeration of randomly mutating chemical of pre-21st century biologists' speculations.

    "…we have witnessed a paradigm shift in scientific thinking from an
    atomistic, mechanical, reductionist viewpoint to a systems perspective
    that incorporates cell circuitry and molecular networks into a
    more integrated view of cellular and organismal activities, based in
    large measure on information processing. Current “systems” thinking
    attributes primary functional significance to the collective properties
    of molecular networks rather than to the individual properties of
    component molecules."

    "Despite widespread philosophical
    prejudices, cells are now reasonably seen to operate
    teleologically: their goals are survival, growth, and reproduction. In
    multicellular organisms, cells have elaborate control regimes to
    ensure that they fit into the overall morphology and physiology."

    NOte: RANDOM MUTATIONS do not dominate biological organisms because they are highly regulated by the organism's own teleological needs via a deep hierarchy of controls.

    -continued

    • -continued

      "A shift from thinking
      about gradual selection of localized random changes to sudden
      genome restructuring by sensory network-influenced cell systems is a
      major conceptual change. It replaces the “invisible hands” of geological
      time and natural selection with cognitive networks and cellular
      functions for self-modification. The emphasis is systemic rather than
      atomistic and information-based rather than stochastic."

      The life sciences revolution is transforming our world as profoundly as the industrial
      and information revolutions did in the last two centuries. Needless to say, you have a lot to learn.

      BTW _

      Regarding the gene duplication issue. When I gave a reference refuting your purely speculative claim (without even a hint of basing it on any evidence) that gene duplication provided an "obvious route" to new information, you replied to me: "You are confused – reread your own quote – if I'm to take your quote seriously, it played a role, but not was not the only contributor."

      NO! That is not the conclusion from the cited paper. NOt only do you have limited understanding of biology, you also seem to have limited ability to understand period. Hopefully, serious study in your discipline will sharpen your abilities, otherwise your credibility as a statistician will be in jeapardy.

      The proper conclusion should obviously be that gene duplication may be a minor contributor to novel information, but the true generator of information is not to be found there. This means that the question of new information is not answered by your supposition. This is the conclusion. NOt that you have "derailed" the argument by any stretch of the imagination – except in your own 'modest' appraisal of yourself. Rather it would be more accurate to say you have been completely off the rails all this time. Debating your limited, outdated misconceptions of modern biology is really a waste of time for me, but hopefully you may be benefited by the education you recieve from it.

      • Part 1.
        Well, I'm reading that reference (last I only took you at your word), and I'll say that the sentence before reference 9 already seems damning to your project. Ditto before reference 23, 24 and 25. The paragraph after reference 25 seems like a strawman – the issue is not whether selection is relaxed for the trait served by the original gene but whether natural selection inhibits drift in the remainder of the daughter genes. The time scales involved suggests that the argument is not well thought-out. Reading further down makes the purpose of his strawman obvious – natural selection against precisely the damages to the opening reading frame and the like doesn't end as long as the gene encodes some sub-function of the encoding gene (negatively selected against), yet this is partially relevant to novel functions.

        The paragraph containing reference 26 is actually even more harmful to your cause – large populations rarely have innovations – we are back to Gould and population bottlenecks.

        His definition of gain in exonic information, "The qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome" is zero, almost by definition – suggesting either that the fellow didn't understand what he was doing, or selected a journal that wouldn't have the relevant reviewers. His definition is also irrelevant to the processes described in said paragraphs. Every system that grows experiences more failures during growth than during stasis, be it crystals (thermodynamic defects), economies, populations, or anything else, and a standard model that often reproduces the failure statistics is Poisson's process, which allows improving signal to noise ratio as the growth increases. Your author insists on infinite signal to noise ratio for any beneficial mutation – by that standard, even well-established genes would not be detected when established, as they have substantial uncertainty in effect, even when only due to failures of the organism.

        Another strawman shows up in the last paragraph of section 2.2 – why should strong selection be present? Let's concede, for argument's sake, that strong selection (of the function encoded in the daughter genes) would inhibit drift. Why not make the argument general? Shouldn't he focus on the weak selection case, precisely in the opening provided by a population bottleneck?

        The first paragraph of section 2.3 contains yet another strawman, namely that an adaptive mutation need not point to a new functionality (however defined – something he hasn't touched upon – what does he posit as the line between mere adaption and novel function?). Next he seems to claim that an adaptive mutation can never be a novel function – although the text is ambiguous.

      • Part 2.
        Section 2.3.i:
        As has been previously mentioned, there is an appreciably relaxed regime of selection in paralogous genes because only one need maintain the original function(s). As such, the rate of nonsynonymous
        substitutions may be much higher, not on account of adaptive evolution, but because purifying selection is far less stringent than it is for singletons.

        So in paralogous genes, we can have genetic drift, which is necessary, because single mutations are generally not beneficial, and multiple modifications are necessary before their combined presence becomes positively selective – incidentally, his SDIC-CDIC merger is precisely such an example. And again, Gould, as any large population, even without negative selection, will tend to overwhelm genetic inventions to slow drift to a crawl.

        Then we get on to his SDIC growing into CDIC by deletion. Is it his purpose to claim that once the distinction between the genes becomes tenuous, that further deletion (making distinction between the genes less secure, i.e. more likely not to occur, and thus more likely to confer the advantageous trait) is neutrally selected? It might fit with his definition above, but then he's only separating the novel information generation and uncertainty reduction, the former occurring first with a great increase in uncertainty and the latter occurring second after the information is established, thus again raises questions about his honesty, or at least the clarity of his thought – by his definition, positive selection is defined into non-existence, and he uses empirical data to define positive selection out of the empirical data. But the paper indicates that he isn't even committed to this goal.

        He then engages in further apparent deceit: presumably on the basis of the one gene studied (he gives no indication of analysis, either his own or anyone else's) he estimates an average of 50 million generations for evolution of novel functionality to arise in fruit flies – what genes' evolution did he study to make this conclusion? The paper doesn't say. The only vaguely coherent statement in that regard comes two sentences later, but even then the connection is tenuous.

        His citation of Ohno and Negoro is even more bizarre – here we have a new functionality, developed chemically from the building blocks of older functionalities, yet somehow (perhaps having to do with the loss of other functionality, in that author's mind ??) there is no new information! It strikes me that he is confusing new information with an increase in information in one population – never mind that the total information in the ecology has increased! And it remains to be shown that (by his utterly restrictive definition of what constitutes a hydrolase) any other hydrolases exist, or at least that 'specify' hydrolysis activity (the terminology again echoes Dembski, which again suggests that this journal was selected on the basis of the absence of biologists competent to evaluate his claims) of any biopolymers, e.g. lignin, cellulose, etc. In fact, his argument can only make sense using Dembski's definition, but even that might not be sufficient (we speak of cellulase activity, though one enzyme might successfully attack several biopolymers) – and notably, after a period after invention too short to substantially reduce the complexity of the hydrolase to irreducible complexity.

        Next he gives some examples of human genes that were duplicated without the development of novel function – perhaps this serves the purpose of showing that failure to evolve substantially new features after gene duplication is common – what is needed, however, is to show that gene duplication cannot create new information – something the paper singularly fails to do.

        In 3.5.i, why would the disintegration occur any faster than other non-encoding DNA, especially non-regulatory non-encoding DNA? And fast enough to occur without subsequent inventions to inhibit the development of some function? Care to show any evidence for such? Further, granting for argument's sake (I'm not in a position to evaluate Cheng's claims) that Cheng's model doesn't work, why/how does that preclude other such processes?

        JEH Bozorgmehr is notably more careful in topical journals: http://www.sciencedirect.com/science/article/pii/

        But so far, he's only published three papers that I could find, and none of them have been substantially reviewed – in fact, I've not found a single citation on google scholar, which isn't surprising as they've only been published in the last two years.

    • You wrote, "Falsifiability doesn't mean a thing without actually testiing imaginatively concocted narratives of couldda-wouldda-shouldda.
      And that's why evolutionary hypotheses are continually tested.

      These fellows hijacked science to foster their own mental concoctions in the name of "falsifiability" when the main principle of science is actual verification of their speculations with testing.
      So you do subscribe to one of the main tenants of logical positivism. If your argument were merely that a substantial attempt should be made to falsify a falsifiable theory prior to its (provisional) acceptance, that would be reasonable. But we have to my knowledge no means to verify a theory – at most, it can predict an outcome correctly, but this doesn't preclude future erroneous predictions.

      You make a claim to the effect that ecology cannot carry information. Why not?

      All careful studies of mutagenesis find statistically significant nonrandom patterns of change, and genome sequence studies confirm distinct biases in location of different mobile genetic elements. I'm aware that DNA tends to mutate at highly repetitive portions, but as I don't have the book, and the local library doesn't have it either, I'm not in a position to check what he means beyond that.

      What is the structure of his argument in favor of teleology, and what evidence does he use to suggest it? Does he do so on a falsification basis?

      • "…evolutionary hypotheses are continually tested."

        Sure, if you're living in the world of pure imagination, as you obviously are. So where is the test verifying the hypothesis of the evolution of the eye from a light sensitive spot? Where is the test verifying the hypothesis of the evolution of a reptile to a bird? Where is the test verifying the hypothesis of a type three secretory and transport system to a bacterial flagellum? It is all only in your dreams! — Well, WAKE UP! It's time to come back to reality!

        Yes, science is based on logical positivism. That means that it can only give a limited perspective of reality, but within its limited framework evolution is not supported by the scientific method. This is the point. Not only that "it can predict an outcome correctly" but that it is verified within the limits of the scientific method by actual experimental testing. Such testing for verification has NOT been done for any major evolutionary hypotheses.So the hypothesis of evolution has never been verified scientifically within the scope of logical positivism.

        Within the scope of the quotes given above, it should be very easy to understand the meaning of "All careful studies of mutagenesis find statistically significant nonrandom patterns of change.." The point repeatedly made in those quotes is that CELLS ARE SENTIENT SYSTEMS. Random mutations play no role in the overall normal functioning of a living cell due to the fact that it REGULATES its own internal biochemistry.Any mutations are cognitively corrected.

        To understand the arguments and experimental evidence that have led to these conclusions requires reading his recent book and the enormous body of literature that has already been produced by the eminent scientists working in this field. But you have to calm down, take a deep breath, and stop the incessant obsessive logorrhea you have poured out on this page. Your new-found belief in atheism is about to become undone. All you have to do is thank God and REAL science for such a blessing.

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