This Week in Intelligent Design – 27/04/11

Intelligent design news from the 21st of April to the 27th of April, 2011.

The Discovery Institute has been extremely relaxed with its posting over the last week – partially explaining why this is slightly late, there was no massive compulsion on my part to hastily set the record straight on certain blog posts before other new items swallowed the spotlight – and whether this is an external representation of the internal busyness of the organisation, I’m not sure. Perhaps Casey Luskin was too busy doing proper science-attorney things too blog much this week.

But it doesn’t really matter, there’s enough meat for me to sink my metaphorical blogging teeth into. Also, I remember the last time there was a slump in blogging output from the Discovery Institute: I predicted wonderful things were about to happen, but I was wrong. So, I’ll try not to read anything into it.

This week’s TWiID covers pseudogenes and “Darwinian assumptions”, enzyme evolution and ID, and the traditional religious bias of the Discovery Institute.

———

Taking his usual stand against evolutionary biology, Casey Luskin wrote this post about pseudogenes as a sort of news-advertising crossover for Jonathan Wells’ new book, The Myth of Junk DNA. Of course, he was also trying to make a point, not just try to sell books, which is what I want to focus on:

Evolutionists have long cited pseudogenes as a type of “junk” DNA that demonstrates an unguided evolutionary origin of the genome. Richard Dawkins typifies this view:

Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.

(Richard Dawkins, “The Information Challenge,” The Skeptic, Vol. 18 (4) (December, 1998). For a full rebuttal, see here.)

Sounding much like Dawkins, Francis Collins and Karl Giberson discuss pseudogenes to argue that is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes.” (Karl W. Giberson and Francis S. Collins, The Language of Science and Faith: Straight Answers to Genuine Questions, p. 43 (InterVarsity Press, 2011).)

But are pseudogenes actually “nonfunctional … faulty duplicates … that do nothing” (Dawkins) or “broken DNA” (Giberson and Collins)? Consider the abstract of a new review article in the decidedly non-pro-ID journal RNA which sounds decidedly different from atheistic evolutionist Dawkins and theistic evolutionists Giberson and Collins:

Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys. The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.

(Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul Francisco Carter, “Pseudogenes: Pseudo-functional or key regulators in health and disease?,” RNA, Vol. 17:792-798 (2011).)

Casey then focuses on this paper as support that the “Darwinian view” of pseudogenes is wrong and is, in fact, hindering research into the potential functions of pseudogenes. But what he’s failing to realise is that Pink et al.’s paper was published without any ID assumptions or reservations about evolutionary theory. While it’s true that an outlook like Dawkins’s (for the sake of rhetoric in his case, probably), if shared by all evolutionary biologists, would lead to a reduction in imaginative research, that’s simply not the case. Scientists have known for a long time that non-coding DNA can have functions independent of transcription (eg. producing protein or polypeptide products via ribosomes), and when you think about it, pseudogenes are an excellent candidate for evolutionary innovation: they already have sequences that are pretty much promoters, allowing them to undergo transcriptional regulation, and their transcription products are many orders of magnitude more likely to contain sequences that can interact in a useful way with cellular systems, due to them being, at one point in time, functional (if only in another sense).

So evolutionary biology, properly interpreted and thought about, doesn’t hinder biological research. Perhaps if Casey wants to really attack the notion of properly non-functional DNA sequences, he should go after the long stretches of repeats found in many genomes. To the best of my knowledge, evolution predicts that these sequences are unlikely to have any major role in biological processes – but, of course, there’s always the potential, however small or unlikely, for something to evolve out of seemingly nothing.

———

The next post, by the shadowy Evolution News & Views account, is all about Douglas Axe and Ann Gauger’s latest piece of research published in the online, pro-ID journal BIO-Complexity. You might have heard about it: Axe and Gauger took two similar proteins and tried to find out how many amino acid changes would be required to convert one to the function of the other. Their results were simultaneously interesting, not surprising and misinterpreted by the ID community:

New research published in Bio-Complexity calls into question some fundamental assumptions of neo-Darwinian theory and enzyme evolution.

[…]

Doug Axe and Ann Gauger from Biologic Institute recently published a paper that addresses this pervasive assumption about the ease of enzyme conversion:

Here, we explore this question by asking how many mutations are needed to achieve a genuine functional conversion in a case where the necessary structural change is known to be small relative to the change commonly attributed to paralogous divergence.

As the authors report, they focused “not on minor functional adjustments, like shifts in substrate profiles, but rather on true innovations — the jumps to new chemistry that must have happened but which seem to defy gradualistic explanation.” Their aim was not to establish ancestry between two particular enzymes, but to identify a functional innovation that should be relatively straightforward within a superfamily and then evaluate how evolutionarily feasible this modest innovation would be.

[…]

They began by looking at a large “superfamily” known as the pyridoxal-5′-phosphate (PLP) dependent transferases. This is a well-characterized family of enzymes that share a common fold (shape) but catalyze distinctly different reactions. They identified a pair within that superfamily with very close structural similarity but no functional overlap. Kbl2 is involved in threonine (a type of amino acid) metabolism, and BioF2 is part of the biotin biosynthesis pathway. They then used a three-stage process to identify the sequences mostly likely to confer a functional change.

[…]

Gauger and Axe estimate that seven or more mutations would be required to convert Kbl to BioF function.

[…]

The second implication from this failure to convert functionality is the question of whether a neo-Darwinian process of step-by-step conversion from one enzyme to another is actually feasible. The two enzymes in this study were very similar enzymes, yet even with generous estimates for mutation rate, gene duplication rate, and no fitness cost for carrying the extra gene, there does not seem to be enough time for mutations of this sort to occur:

To summarise: they found that more than seven mutations would be required to functionally convert Kbl to BioF, and this is evidence against evolutionary mechanisms because the intermediates would not be functional for either Kbl or BioF function, forcing the hypothetical gene duplicate to evolve neutrally, and seven mutations is far outside the number (they say) that can be achieved by neutral drift alone.

Okay. There are some problems here.

Firstly, while BioF and Kbl are within the same superfamily, meaning that they share sequence and structural similarity, there is no evidence to infer an ancestral relationship between an earlier form of Kbl and modern BioF, which is essentially what this experiment was testing. If the data suggested that, then this paper would be making a very valid point, but since nobody thinks that BioF evolved from a Kbl precursor, it’s making a useless statement.

Secondly, even if BioF and Kbl had the proper phylogenetic relationship, testing for functional evolution from modern Kbl to modern BioF is inappropriate: as I mentioned, BioF would have evolved, most likely, from an ancestral form of Kbl, which could have had substantial differences in sequence from modern Kbl. Going from one modern enzyme to another does not model the evolutionary process at all accurately.

Thirdly, and finally for now, their method of experimental evolution did not model what would have actually happened in nature. While proteins can be, in computer simulations, converted from one function to another through numerous simultaneous amino acid changes, this obviously happens somewhat infrequently in nature, and a substantial amount of protein evolution occurs gradually via point mutations. However, mutations that affect function are not the only ones possible – thermodynamic stability and protein folding are also very important in the evolution of proteins, so mutations that affect these aspects are also selected for. In the absence of stability compensation mutations to conserve functionality, yes, multiple simultaneous mutations may be hypothetically required to jump from one enzymatic function to another. And the fact that this paper didn’t go into these important mutations is telling about how they wanted the evolutionary process to look as implausible as possible.

So, there are three substantial criticisms of Axe and Gauger’s paper. I’m sure there are plenty more out there, but quite frankly, they’re unnecessary for labeling it bad research. BIO-Complexity had yet to impress the scientific community that it has anything substantial to offer the world of evolutionary biology.

———

The final post for this week is by Gailon Totheroh, all about Michael Dowd and “evolutionary Christianity”. I’m mentioning this post not because it has anything particularly interesting to say about Dowd’s views, but because it reveals the religious cards that the Discovery Institute holds, sitting so carelessly with their backs toward a mirror. Of course, everyone knows that the ID movement is religious in root and general nature, but you’d think that the DI would be more discrete about their bias towards “traditional religion” – ie. Catholicism, orthodox Judaism and evangelical Protestantism:

Who is Michael Dowd? He calls himself an evangelist. Not surprisingly, he can be found in churches preaching. But Dowd’s gospel is not one where sin is rebellion against God, but rejection of Darwin.

Likewise, salvation doesn’t come from Jesus on a Roman crucifix, but merely embracing the emergent Universe. Thus, we should Thank God for Evolution, the title of his 2008 magnus opus. Subtitled “The Marriage of Science and Religion,” the popular book-endorsed by no less than six Nobel Laureates-unfolds a central theme that standard Darwinism is scientifically accurate andreligiously inspiring.

With faith-evolution controversies running unabated, Dowd’s Darwin-for-all-occasions may seem a hard sell. Yet Dowd’s effusive friendliness and seeming openness are swaying many his direction. His sales technique even wins over atheists and Christian evangelicals.

Still, Dowd is a mover-and- shaker who doesn’t move everybody to awe. The unwilling might include those who question Neo-Darwinism in whole or part, those who are uncomfortable with religion, and conservative adherents of traditional religions.

Oh no, you wouldn’t want to upset those conservative adherents of traditional religion, those people that make up such an overwhelming majority of DI fellows and associates. Bad idea.

Despite his co-option of theological language, there is little left of traditional monotheism, let alone traditional Christianity, in Dowd’s worldview. Indeed, the “supernatural” itself doesn’t exist according Dowd; it’s merely an invention of the Western mind. “Evidence suggests that the only place that the so-called supernatural realm has ever existed has been in the minds and hearts (and speech) of human beings–and only quite recently.” Accordingy, the God of the Bible is no more real than the Greek gods Poseidon or Helios, and the Bible itself is a jumble of “old mythic stories” that provides no real guidance for the challenges we face today: “Ours is a time of space telescopes, electron microscopes, supercomputers, and the worldwide web. It is also a time of smart bombs, collapsing economies, and exploding oil platforms. This is not a time for parsing the lessons given to a few goatherds, tentmakers, and camel drivers.” (emphasis added [by Gailon])

Ouch. It seems like the ID movement gets very defensive about people attacking the concept of the supernatural, yet when pressed, they often claim that ID is not necessarily supernatural (and I agree). It just goes to show you what biases they’re working from.

———

Rapid fire ID news!

35 thoughts on “This Week in Intelligent Design – 27/04/11

  1. Interesting stuff. One query though: I'm intrigued by your view that ID does not necessarily have to be supernatural. It seems to me that it inherently must be since, at least as I understand it, the essence of ID is that purely natural processes are insufficient to explain the complexity of life and hence there must be a designer at work to interfere with and supplement the natural processes.

    I suppose one could, like my local parish priest, take "ID" as meaning no more than the (very common) belief that the rationality of the laws of nature suggests a creator and perhaps a purpose for creation. But surely that is just traditional Christian belief, not ID in the sense that the proponents of ID as a "theory" intend it. According to them, surely, ID specifically claims the development of life requires intervention, over and above the natural laws of nature as we understand them, by a designer – miracles, in effect. Is that not by definition "supernatural", i.e. beyond/ above/outside nature?

    P.S. The DI are totally out of touch if they think traditional Catholics and mainstream Protestants deny evolution. Of course they don't, cf. Clergy Letter Project, the 2008 Vatican-supported congress on evolution, etc., etc. Orthodox Jews I don't know, though I'd be surprised if they go for evolution denial. My impression is those religions with a professional hierarchy, educated theologians and a body of theological doctrine behind them all realise the futility of denying science. It's the back-to-basics, interpret-the-bible-in-your-own-living-room types who who at risk of getting tangled up in this nonsense.

    • The essential idea of ID is that life was designed by an intelligence. Whether or not that intelligence is supernatural or not is up to the ID proponent. One could conceive of an advanced alien civilisation hypothetically seeding this planet with life (either as the LUCA, the modern array of biological diversity or somewhere in between, it doesn't really matter for this question) – this falls under the blanket term of ID.

      I tend to use "intelligent design creationism" as the subset of ID that is explicitly supernatural and theistic. The Discovery Institute and their related organisations are pretty much ID creationism proponents, even though they slip out of the natural/supernatural language when it suits their purposes – eg. when they want to appear scientific – but it comes back as soon as they're trying to gain support from religious organisations or talking "atheistic Darwinists".

      • Hi Jack,

        You usually avoid answering this question, maybe because you think probability is God, and therefore it can do anything – even the impossible. But I will state it again.

        Microbes and bacteria are among the most successful and prolific reproducers in the world. Even if it is assumed that life began from a similar primordial form (which Darwin several times refers to as that "into which life was first breathed" – implying Genesis) the question is never broached as to why so many complex forms such as giraffes, elephants, dinosaurs, woodpeckers, etc. which are so much more difficult to develop, maintain and reproduce than bacteria.

        Considering the principle of least action – http://en.wikipedia.org/wiki/Principle_of_least_a… – which we know is the central principle for the whole of physical mechanics, natural processes of material nature can not be the only factor in producing such energetically difficult to attain and maintain complexity. Dawkins' idea of step by step micro processes for climbing Mt Improbable, doesn't explain why Mt Improbable would be created to begin with. Yet, neo-Darwinists are completely silent on this salient point.

        And, BTW, there is nothing wrong with an onto-theological foundation of science. The fact that some materialists have hegemonic domination in science does not define science for those who do not have that prejudice. Scientific knowledge is not defined by vox populi (popular opinions or beliefs) or the US government or its courts. Science has and always will have its firm basis in Reason.

        • Here is a brief paper which you may find interesting. The main thesis is that marginal thermostability could be an artifact population genetics (rather than an adaptive trait). Basically the application to your point is that population genetics does not guarantee that life will find the minima of any function. Because of this it should be expected that life would not evolve uniformly towards any particular minima (such as reproductive strength) and instead we should predict that many forms with "mariginal reproductive fitness" should exist. Since these conclusions are basically completely mathematical (given a few assumptions about the selective advantage) the thesis should hold for any property we assume evolution is attempting to optimize.
          http://onlinelibrary.wiley.com/doi/10.1002/prot.2

          • Are you saying that the well known existence of the marginal theormostability of proteins has anything to do with the question I asked? The paper you referenced presents mere computational results. The unrealistic assumptions and truncated iterations hardly have much to do with actual in vivo processes. Primarily in Goldstein's simulations, binding strength of various mutants is completely ignored in order to simplify the calculations, plus numerous other factors which would nullify in real life situations much of what he concludes.

            Furthermore, proteins are assembled based on a specific DNA template. All proteins would therefore be associated with that particular sequence. How does that explain the production of the novel DNA sequences that are found in the varying species of life?

            Hand waving the real problem of explaining variation of species by pointing to such minimalist evidence exhibits the weakness of molecular evolution to provide an explanation of the wonders we observe in nature. Interesting or not, the marginal stability of proteins is hardly sufficient to answer the genuine questions of those who do not blindly accept the ideology of evolution. In this instance, those who have faith in creation have hardly been challenged by the faith of the evolution ideologues.

            Again, I repeat what I said above that the acceptance of creation does not in any way affect the ability of anyone to engage in scientific pursuits without adhering to a dogmatic evolutionary ideology.

            • "Again, I repeat what I said above that the acceptance of creation does not in any way affect the ability of anyone to engage in scientific pursuits without adhering to a dogmatic evolutionary ideology."

              You sit there and tell me that elephants can't reproduce and require too much "maintenance" and then you think you can make this statement without the slightest hint of irony? Your process is simple. You don't even pretend to not be following your own dogma? You just said that things we can observe in reality are impossible by your own understanding, and since we see them that must mean that you're right.

        • "why so many complex forms such as giraffes, elephants, dinosaurs, woodpeckers, etc. which are so much more difficult to develop, maintain and reproduce than bacteria."

          They seem to reproduce fine by me. Maintain? Are you suggesting that giraffes require mechanics to change their oil? Do woodpeckers have to stop off to have their beaks rotated every couple of thousand miles? This is bizarre. You make this statement that animals which are demonstrably successful cannot be successful, but since they are their existence must be proof of existence of supernatural forces. Two assumptions in a row to support your preconception, based on the idea that what you see cannot be and since you still see it it must support your dogma rather than contradict it.

          You cite the principle of least action, but your citation gives zero reference to any applications of the concept to biology, and yet you turn around and declare that it proves that nothing should be complex, and again you say "difficult to maintain".

          You've got a whole mess of unsupported assumptions to deal with here. You get to demonstrate the modern life forms you see are difficult to attain, difficult to maintain (simply defining what you mean by maintain would be a start), and as to difficult to reproduce.. well, again, the animals don't really seem to have any problem there. You might have noticed nature is full of them, and they keep on reproducing, so I think we can drop that one outright.

          "Science has and always will have its firm basis in Reason."

          I'm not sure that word means what you think it means. Because to me, see.. reason says that when I make observations that contradict my assumptions I question the assumptions. When you do you decide it must be proof of your assumptions, and since they're contradicted the only explanation must be the invocation of the supernatural. In other words no matter what you observe your conclusions remain static.

          Your history here is of making claims that are trivially refutable. You claim that evolution is impossible when we can watch it happen. You claim that large animals shouldn't be able to reproduce although they're demonstrably able to do so. You seem to feel that an elephant requires regular maintenance, I don't really know where to begin dealing with that one except to refer to the almost complete lack of elephant mechanics in the wild and note that it doesn't stop their existing and indeed thriving, at least in the absence of human intervention.

          I'll refer again to the fact that although you claim to be a scientist, you seem unable to understand how a scientist thinks. You can only argue by invoking famous people or, in this case, principles, but you can't actually apply the concepts. You mention the principle of least action as if it were a talisman, you think that you invoke it and then that's it. That's not it. Okay, you've invoked a mathematical principle, now you get to produce the mathematics that say that an elephant shouldn't be able to reproduce. I wish you luck with that endeavor, but since, again, we can see that elephants are able to reproduce if you produce a mathematical proof that says they can't you'd be wrong.

          • You missed the entire argument Nomad,. Why quote only part of what I said, and then take the excerpt out of context?

            I'll just assume you're naive and not malicious — perhaps still evolving. Wish you a bright future!

            • That's a good creationist, play the martyr card when your bizarre statements are pointed out and dodge the questions entirely. For extra irony points you do this immediately after you accused the owner of this blog of dodging your questions. Apparently you see yourself as more of a question asker than a question answerer? That is entirely consistent with the past behavior I've witnessed from creationists, but it's not particularly effective or impressive.

              Your question implied that there was something impractical about complex life forms, that for some reason all there should be are microscopic, unicellular life forms because they're somehow better able to function. You see around you a tremendous variety of complex life which continues to function without regard for the problems you seem to feel that the life should be facing, yet you do not question this assumption.

              And I'll note a complete failure to attempt to justify your citation of the principle of least action. You have no idea what it really means or how it applies to biology, do you? You thought that all you had to do was mention it and claim it supports you and that that's all there is to it. Your argument seems to be basically that the principle of least action means that complex life can't happen. But I'd extend that to saying that no life should happen. Hey, why not?

              Both of those arguments however are demonstrably false. Complex life happens. Simple life happens. The principle therefore does not mean what you think it means.

              You're still operating from your fixed dogma. You assume that evolution cannot happen, therefore you operate under the assumption that complex life cannot have evolved. Therefore, your argument goes, the presence of complex life is evidence of the supernatural. Your assumptions are false, therefore your conclusions are false. Garbage in, garbage out. You don't get to cite your assumptions as evidence especially when your assumptions disagree with observed reality.

              So now questions have been asked of you. I'll ask that either you retract your ever so bold accusation of the blog owner ignoring your questions or else suggest that you put your money where your mouth is and get to defending your claims. You have some whoppers to either defend or retract, trying to bluff them away by calling quote mining without actually explaining any sort of missing context isn't going to cut it. It is of course entirely possible that I misunderstood your argument, the one that I'm understanding is so bizarre that I'd hope that you meant something else. Which means it's time to try to explain yourself better. So you didn't mean that elephants require regular overhauls or that woodpeckers actually have trouble making babies. Okay, then what did you mean? Let's try to make a statement that's not directly falsified by observable reality and work from there.

              And I'm still demanding either an explanation or a retraction of your invoking the principle of least action. I still think in that case you think it was a simple matter of bringing up something that looks impressive and hoping that it'll suffice, counting on not having to actually apply it to the subject at hand. If it means what you seem to think it means then complex life itself should be impossible, and since it demonstrably isn't you're in trouble in this area. You've invoked a mathematical principle, so you get to actually bring some equations to the table or else this line of arguing is dead in the water.

              • Hi Nomad,

                Don't be so impudent. We are freely engaging in discussion here. Not by your demand.

                Since you really do seem unable to grasp the concept here., maybe this will help. Somehow I doubt you will be able to follow it – but let's try to make it as simple as possible, but not simpler.

                1. Let's say it takes a bacterium (Eo) amount of energy to reproduce. Now, in order for a bacterium to evolve over billions of years to become a bear, for example, would take a lot of energy, call it (Ee). Now the energy of evolution, Ee, that is needed to transform from bacterium to bear is a lot greater than the energy for a bacterium to reproduce itself, which is E0. If we write this as an inequality we have Eo <<< Ee . This means that Eo is MUCH less than Ee.

                2. According to the principle of least action, a mechanical system (one obeying the laws of physics and chemistry) will tend to minimize the amount of energy it uses to go from one state to another. In our example, we have to go from the state of being a bacterium to the state of being a bear. (Now remember, the end result of all this evolution is simply to create a system or organism that can survive or reproduce.)

                3. It is easier for a bacterium to reproduce using energy Eo, and enourmously more energy for it to evolve using energy Ee and then reproduce as a bear. Thus we would expect from the principle of least action that the bacterium would be perfectly happy to stay as a bacterium and reproduce to its heart's content. Why would it go through the whole process of evolution simply to do what it is already doing – surviving very nicely by reproducing.

                IMPORTANT: Now try to understand that the important factor in this is Ee, the energy it takes to EVOLVE from a bacterium to a bear. This is an enourmous amount of energy. The question I am asking is WHY would the bacterium take such a strenuous path to become a bear simply to reproduce, when it can already do that very nicely and easily as a bacterium. In other words, there is no energetic benefit for a bacterium to become a bear. Simple.

                • Well, I have a bit of a thermodynamics background (from my electrical engineering education), so I'll point out the obvious problems with what you are saying:
                  1. The bacterium doesn't make the transition in one step to being a bear (I'm not sufficiently versed in contemporary evolutionary biology to state whether bacteria are the relevant type of potential ancestor), but rather in millions of steps, and the energy requirement for one step (heading closer to bear, or remaining bacteria or whatever the 'current' state at any point) is the relevant consideration. Anti-evolution crusaders often go for evolution in one step – funny that.
                  2. The ratio of the number of offspring that become closer (e.g. to being a bear) at any one step to those who remain the same is equal to
                  exp((E_{evolutionary reproduction}-E_{stasis reproduction})/kT)
                  where exp is the natural base exponential function (i.e. exp(x)=2.718281828^x), k is Boltzmann's constant, and T is the absolute temperature, in Kelvin., and the energies are for one reproduction, i.e. one brood or offspring). Let N be the average number of generations to occur before an evolutionary change in the right direction occurs in one of the offspring (we need only one descendant moving in the right direction for asexual reproduction – sexual reproduction and evolution being more properly the domain of Gould et alia – another necessary invention, but here I'm tracing toward sexual reproduction, rather than the final state which you are discussing). Then we can calculate N as simply being the inverse of the thermodynamic probability calculated above. Certainly, this is a simplification, but hopefully useful.

                  By pretending that evolution occurs in one step (that is a very fair reproduction of your argument in thermodynamic terms), you make evolution disappear. Nice try, but no cigar. We can measure the average number of genetic changes per reproduction in a lab – that collapses your argument. If you don't get it, I suggest studying the calculus, and then thermodynamics.

                  • Of course we are clearly talking about "evolution" here, and the idea that bacteria can go in one step from bacteria to bears is ludicrous. Why would you even bring this up? I notice this is used in many arguments regarding this issue. Why? No one understands evolution in that contorted way. So we will simply ignore that part of your response, and wonder what other simplistic things you might have to say afterwards.

                    Then yo bring up the ratio of the Energy of reproduction of evolved organism to the Energy of reproduction for original unevolved organisms. Beacause you take Ee for the evolved reproduction to be greater than that of the unvevolved Eo you evaluate the difference as Ee – Eo for obvious reasons. The Boltzman constant is obviously constant, and we will assume T is also constant. The exponential form is merely to account for the probable distribution, and that we will also assume is constant. So that the only concern is with the difference of energies.

                    The point remains, in one step or billions upon billions of steps, Ee is greater than Eo at each step. Why would we expect a tendency in evolutionary development toward greater energy requirement for the task of reproduction that is going on at lower energy expenditure?

                    The usual response that evolutionists give is that energy is coming from the Sun, and that's where the extra energy of evolution is coming from. Does anyone believe we really evolve because of the Sun? I never heard Darwin or neo-darwinists propose such a thing. Anyhow, why would such an assumption be invalid from a thermodynamic viewpoint?

                    To answer this question we have to consider the fact that the Sun's energy is undirected. We can understand the problem here if we think of Brownian motion. A particle that is bombarded on all sides will follow a random walk. It doesn't go in any particular direction. This is what we would expect from undirected energy acting on an organism also. No particular direction for evolution.

                    I suggest that anyone who believes in evolution is as simplistic as you seem to be. No problem with that. However, those who have a better fund of knowledge cannot accept such beliefs that the whole diverse system of Nature is the result of such naive processes. I would certainly prefer belief in God to such nonsense.

                    • Why do I bring it up that the evolution must occur in little steps? Because then the thermodynamics makes your argument ludicrous – the energy difference (Ee-Eo per step) must come down to less than 10kT, which makes the probability of getting closer to some final state finite (this approach ignores population dynamics, which might enhance or reduce such a probability). In one big step, your argument would work, i.e. the probability would become negligible, whereas in small steps, one just needs many steps.

                      On the assumption that the probability, that one offspring (in the bacterial case) will be genetically identical to its parent, is very large (close to 1), the probability of moving closer to some defined end state is almost exp((Eo-Ee)/kT) – do I need to explain why, or can you figure it out? Have you ever done any semiconductor physics, and had to calculate the populations of the valence and conduction bands? It is the same kind of problem. I'm going to take a guess that you cannot, and work through a sample calculation:

                      Let there be twenty kinds of invention with low energy (Ee-Eo for the invention at one reproduction less than 10kT) at a given stage of evolution; one or more of these inventions might be evolving toward a bear (i.e. toward animal life, as this model isn't relevant to sexual reproduction). Let
                      En=Ee_n-Eo_n,
                      and
                      PSP_n (pseudoprobability n) = exp(En/kT).
                      Then the probability that stasis occurs (no mutation) is

                      p_n = PSP_n/(1 sum_{1}^{20} PSP_n)

                      in LaTeX notation. If the sum in the denominator is small (much less than one), then p_n\simeq PSP_n (p_n almost equals PSP_n). Notice that your argument amounts to a thermodynamic denial of the possibility of mutation.

                      Direction is given by population dynamics (survival of the fittest/entering new niches/punctuated equilibrium aka in sexual reproduction, increasing the odds that genetic inventions survive, etc.). The energy for the process comes from the sun, but that is a trivial observation, and not what gives direction to evolution (although that process which gives direction to evolution, namely population dynamics, requires energy, trivially – except now, the system is so far from ergodicity and thermodynamic equilibrium that other approximations should be used).

                      Gaseous molecules do random walks, yet that doesn't prevent them from working through pipes, no matter what the configuration of the pipes (though different pipe configurations will have different flow rates for the same difference in head). To further the analogy, consider piping with moveable walls, where a difference in pressure can reconfigure the piping – that is the population dynamics affecting the outcome.

                      Edited to add:
                      The Brownian motion has another problem – it is usually considered at close to thermodynamic equilibrium – not exactly the case for living systems, which are quite far from thermodynamic equilibrium, and can radically change their own environments. Your argument would disallow internal combustion engines, but I suspect that you don't understand that either.

                    • OK. You're clearly being ridiculous here. Right? Population dynamics provides an analysis of changes in popuations. to say, "Direction is given by population dynamics" is clearly grasping at straws. The factors that are the cause of changes in population are at the foundation of population dynamics.

                      To say that natural selection is the cause of such changes has often been rightly criticized as failing to provide HOW favorable mutants have arisen in the first place – which is at the root of any supposed evolutionary direction.

                      But this is only presupposed and has never been demonstrated in any in vitro or in vivo experiment or observation of Nature. (See Lenski) Furthermore, genetics confirms that DNA and genome are stabilized by their own inherent self correcting nature. You have to really push against the grain to think that evolution occurs in such systems.

                      And this is where the energy gradient comes in. Species are like quantum states of Nature, or quantum states of consciousness. There is no linear or mechanical transition from one to the next. This is your classical Vicotorian Darwinianism at work, when the world has long since entered a new age of quantum biology. I think you need to update your knowledge base.

                    • What gives rise to favourable mutants? Same thing that gives rise to unfavourable mutants – random mutations, whether caused by thermal fluctuations, or by radiation, etc. If this is a problem, I suggest an introductory text on logic – try chapters one and three (and attempt the problems) of "Logic and Discrete Mathematics: A Computer Science Perspective" by Grassman and Tremblay.

                      No one who supports evolution claims that the arisal of mutants comes from natural selection – I challenge you to show one such person. Evolution claims that mutants are accepted or rejected for further reproduction by natural selection, etc. So, the interaction between members of a population, and the interactions of members of different populations, is what decides whether a given mutation (invention) survives in a population. Restated, population dynamics (not an analysis, your false claim notwithstanding) determines whether a mutation survives in the long run. As such, your statement that HOW favourable mutants arise in the first place is (somehow) the source of the direction of evolution, is plainly false. Mutations create functional and (mainly) dysfunctional changes, and nature works with what is functional, and with what dominates (in sexual reproduction, which brings us back to Gould, and that is another form of population dynamics).

                      So again, favourable mutations come from the same source as unfavourable mutations. But I'll give you this much – you state your false premises openly, rather than smuggling them in.

                      And I'm baffled by your notion that thermodynamics doesn't apply to quantum systems – it is very strong, though implicit, in the above (last) paragraph of yours – I take it you've never heard of Bose-Einstein and Fermi-Dirac statistics.

                    • I replied to your ineffectual posturing in my reply to your response in "complex specified correspondence. I suppose you never heard of this, or of that, or… Well, I am sure you never heard of humility and sound reasoning.

                      I try to present my arguments in down to earth common sense reasoning that anyone can understand. I am not interested in impressing anyone with my credentials or technical lingo. As a scientist I know how they are cheating the public, taking their money and going on with their endless speculations to keep their pockets full. They and the people who fund them are all cheaters, whose only interest is to keep as much of the population entranced by "science" as possible, because its big money, and people in a materialistic culture are sure to consume its technological gadgets as the only interest in their worldly oriented lifestyle. Soon such a culture will devour itself.

                      To put this matter of the controversy over selection/fitness to rest, here is an interesting admission from the good scientists at Oxford University:

                      "The idea that organisms maximise their fitness as a result of natural selection is extremely important in many areas of biology. The explanatory apparatus of most whole organism, behavioural ecology, work would make no sense without it. However, the logical basis for the idea is in considerable doubt. The mainstream of mathematical population geneticists since about 1964 has emphatically rejected the claim that fitness is maximised. …There has been essentially no formal consideration of the kind of optimisation that emerges so naturally from verbal arguments such as those of Darwin (1859) and Dawkins (1976).

                      …mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is."

                    • Well, if it makes you happy, my own research is funded by a private corporation.

                      Anyhow, by your implicit argument above, Newton and Leibnitz (and the Arab mathematicians before them who did exploratory work on polynomial integrals) shouldn't have bothered developing the fundamental theorem of calculus, because they didn't have Bolzano's limits. You want to prevent science, by demanding the impossible – physics research was not constrained by the standard you set (everything exceedingly well-defined) – why should biology be?

                • Okay, so let's look at this argument, Will.

                  Your argument, roughly restated, appears to be that the principle of least action means that because it's simpler for a single celled animal to remain single celled it will do so, the fact that it takes more energy to gain additional complexity means that will not happen.

                  So how do you explain a single celled embryo becoming a large multi cellular creature? A bear starts out as such an embryo. Is that bear embryo violating your principle? Let's start here, and explain why your principle applies to a paramecium but not a bear embryo.

                  We can then proceed from there. You're invoking a lot of unsupported assumptions in the rest of this argument, but we can deal with that once we're clear how an embryo can do what you say is impossible, but evolution cannot.

                  • Nomad or Mad, I am not sure. But your sincere simplicity always makes me smile.

                    The argument is not about single cells remaining single cells or becoming multiple cells. It is about energy. Bacteria reproduce by a mitotic process. The energy to do that and maintain themselves is a certain value, we are calling Eo. To change or evolve into another type of critter (whatever you consider different from and more complex than the original bacteria) will require greater energy than Eo, let's say, Ee.

                    Why would it take that harder path when the easier one is readily available to it, if its only drive is to survive? It is easier energetically for a bacteria to remain a bacteria, even under the most extreme conditions than to become another critter. And we readily observe this in Nature. It is not just an ideological prejudice.A population of bacteria, despite all the adaptive changes they may undergo – not by any new innovations – but from the available variety within a population, remain bacteria. All your so-called speciation references do not change this fact.

                    The drive/energy for multicellular species to develop from a singe egg or zygote is a very interesting phenomenon. We notice that the direction of development is very specific and increasingly complex from what seems a relatively homogeneous beginning stage to its highly differentiated adulthood. Not only is energy required for this, but a highly directed energy must be involved.

                    That direction can't come from the DNA or genome because the differentiated functions of the adult all contain cells with the same DNA, genome in them. Muscles, brain, bone, hear, liver, skin, lungs – you name it – all with the same DNA but totally different from one another!

                    So what is directing the whole affair? And from where is that directed energy coming? Science has no answers to these questions. They are still "working on it." Their belief is that chemistry did it. The explanation of where mind comes from they also leave until some latter unspecified time in the future.

                    Well, people for centuries have known that there is something else besides chemicals and physics in Nature. The materialist scientists still have to catch up with them.

                    • I've already given you a reference on biofilms, but for the record, I will do so here again:
                      Nikolaev, Microbiology 76(2), 2007

                      Notice that bacteria of one type (single species biofilm) can have different cells of the same species conglomerate to form a structure, and different cells in this structure perform different functions – bacteria have the ability to form multi-cellular organisms. Reply once you've read the reference, and understood its claims and data, not before.

                    • Bacterial colonies have long been known in biology. Have you never seen them growing in a petri dish?

                      Funny thing though. Multicellular organisms don't form by aggregation, They form by differentiation from a single zygote. So what do bacterial colonies have to do with that? Maybe if you remove the biofilm of Darwinism from your eyes you might stop conglomerating all data around evolutionary dogmatism.

                    • Aggregation versus differentiation? I see a distinction without a difference – the bacteria in the single-type biofilm can all come from a common ancestor – in the paper (which you appear not to have read), the bacterial cells differentiate, and perform different (categories of) functions. A successful mutation or set of mutations could have led to egg/seed formation/sexual reproduction. The zygote (and any of its organs) is as much an agglomeration as the biofilm – there are pathways for nutrients, specializations for different cells, etc, and as in the single cell type biofilm, all the cells can come from one recent (seeding) ancestor. You are making a distinction where one doesn't exist.

                    • So finally we arrive at the crux of this matter:

                      "Why would it take that harder path when the easier one is readily available to it, if its only drive is to survive? It is easier energetically for a bacteria to remain a bacteria"

                      You've constructed a cartoon caricature of reality in which the only selective pressure in existence is that the living thing must consume as little energy as possible. In your view of the world the fitness landscape is a simple 2 dimensional graph, fitness on one axis and "total energy consumption until reproduction" on the other. You're arguing that anything that leads an organism to consume more energy until it reproduces would be selected against, possibly by natural selection itself, possibly by your oversimplification of a mathematical principle.

                      You've shown that you have trouble understanding the concept of a fitness landscape, but surely you have to understand that there are more selection pressures than simply "whatever consumes the least total energy is most fit".

                      Even a moment's contemplation should show you that this is wrong. I mean.. let's take a Cheetah. Look at all those muscles and the enormous lungs and heart. Those things consume a lot of energy. Let's shrink all that down so it's a much more efficient animal. It won't be able to run as fast but in your world the only thing that matters is energy consumption, so therefore the slow low energy cheetah is the most fit.

                      Do you think this would actually work?

                      Let's go to the single celled world. Let's take a bacteria. Now let's say the bacteria gets the ability to make a new enzyme that lets it utilize a new source of food. The bacteria has to spend more energy making this new enzyme, but it gains a new food source. Does your "total energy consumption is the only thing that matters" view work here? Does the new enzyme producing bacteria get selected against even though it got access to a new food source?

                      It is generally true that the living thing that can do the same thing as another living thing but do it with less energy will tend to be more fit. But you're ignoring that living things use energy for specific purposes. And you're also, glaringly, forgetting that things tend to happen to a living thing between it's birth and the time it reproduces. The living thing has to deal with the environment in which it lives. A living thing that fails to deal with the environment will not be around long enough to reproduce, no matter how energy efficient it may be. Dealing with the environment takes energy.

                      There are responses that could be made to the rest of this comment of yours, but until we get this comparatively simple misunderstanding cleared up none of the conclusions you draw or arguments you make are going to make the slightest bit of sense.

        • "Considering the principle of least action – http://en.wikipedia.org/wiki/Principle_of_least_a…. – which we know is the central principle for the whole of physical mechanics"

          Does this statement mean you no longer think the scientific method is invalid?

          "And, BTW, there is nothing wrong with an onto-theological foundation of science. The fact that some materialists have hegemonic domination in science does not define science for those who do not have that prejudice"

          Sorry, I don't follow. Could you explain what a "hegemonic domination in science" means? And can you state your definition of science? I am having trouble imagining a non-materialistic definition.

        • I'll give you a bonus question answer as well, while you ponder if there's any possible way you can salvage claiming that it's too difficult for giraffes to reproduce.

          You asked why mount improbable would be created to begin with. Let's rephrase that to take out the telology, shall we? Why should mount improbable exist?

          There's two ways I can interpret such a question. Both are basically you inquiring about fitness landscapes, but one way is asking why it should be possible for one organism should be more fit than another. But.. if I really have to answer that then we have a lot of basic information to cover.

          Another way to look at it is asking why a fitness landscape has to exist at all, why does life have to be possible at all.

          Well, it certainly doesn't. The surface of the sun hasn't got a mount improbable, so there you go. As far as I can tell the surface of the sun has no fitness landscape at all, no configuration in which life is at all fit. But if you have an environment where life is possible I don't see how you can escape "mount improbable" existing. That's like asking why a planet has to have a surface topography. Being a three dimensional object it can't really escape having it. Similarly a life bearing environment is going to have a fitness landscape. To ask why such a thing should exist is kind of bewildering. You can't just be an evolution denialist to think that, you kind of have to be a basic ecology and biology denialist. I mean that's like asking why it has to be that a cheetah would be less fit in a deep sea environment than a giant squid.

          To claim that neo darwinsts are silent on this salient point is.. shall we say, questionable, at best. I'll say again, you demonstrate a complete lack of understanding of the subject you pretend to debate. Why does the fitness landscape exist? How could it not exist so long as life exists at all? I challenge you to describe a single environment in which life exists but a fitness landscape does not, or rather wherein the fitness landscape is perfectly flat with no peaks, with no selective effect whatsoever. I'd give you a hint as to what you'd require to have such an environment, but at this point you don't deserve such assistance. You claim to be a scientist, you claim to have an understanding of this concept, this should be first principles to you.

          You will of course not attempt to do this, as you have failed to engage in any productive discussion whatsoever, because you're not really here for that. You're here to drop what you think are gotchas, you think you have unanswerable questions, and when they're answered you're stuck. So I'll see you on the next blog post where you show up smugly asking what you think are such clever questions.

          But again, I stress… you just claimed that it's too difficult for an elephant to reproduce and so the only life forms that should exist should be single celled creatures. Honestly, you need to re-examine your founding principles if this is where you've been lead.

      • Capt. Haddock

        Thanks, I was forgetting the alien deus-ex-machina option within ID. That would indeed be a natural explanation.

        Having to take this into account does make a succinct explanation of why ID is not science more cumbersome, admittedly. But I think the basic point remains that resorting calling on outside intervention to account for a phenomenon is just saying "we give up", scientifically speaking. Uniquely in the history of science since the Renaissance, ID tries to elevate "we give up" to the status of a scientific theory. Individual scientists often do give up of course, but there will always be more who continue will the search for explanations that don't call on outside intervention. So obviously ID will never be accepted as a scientific theory.

        But as we all know, it's really a political and religious concept in disguise and it can stay alive in those spheres, so long as there is enough bad education in the Bible Belt of the United States.

        • flawedprefect

          But then do we welcome and worship our new alien overlords? Where do they stand on gay marriage? Did they give us a purpose? Will we live eternally with them when we die? Also: who designed those designers? Did they evolve on their own, use their emergent intellect to design life which led to us, or were they designed by yet another alien race… etc etc etc…

          The alien thing is such a bullshit explanation when it comes to ID. Totally agree: ID is the "we give up" explanation, or the argument from ignorance: I can't work out how it happened, or worse: I don't WANT to put my mind to working out how it happened, I'm gonna give up, and say God did it. Sometimes, it stems from "This explanation is good enough for me, and I don't want to be challenged".

          There are different motivations for denying the fact of evolution, none of which I've seen stemming from "I've examined all the evidence gathered thus far, and think it can be better explained in this way" to the satisfaction of the larger scientific community.

  2. The "full rebuttal" of Dawkins' "The Information Challenge" is entertaining.

    "Dawkins' article has other problems. He writes that "most of the capacity of the genome of any animal is not used to store useful information." This is another good example demonstrating how Neo-Darwinism led may scientists to wrongly believe that non-coding DNA was largely junk. Dawkins' statement is directly refuted by the findings of recent studies, which the Washington Post reported that scientists have now found that "the vast majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of previously invisible tasks." That strikes a fatal blow to Dawkins' argument" — http://www.discovery.org/a/4278

    I find it amusing that whenever a new scientific discovery is made that attributes some sort of previously-unknown function to noncoding DNA, creationists assert that this invalidates the evidence for evolution and/or the scientific method, even though both of these are required in the research they cite.

  3. Pierce R. Butler

    Last I heard, about 45% of human DNA consisted of non-functional retrotransposons called SINES and LINES, considered bits of viruses which persist because they mesh well with the processes of genetic replication. So, either this has been disproved, or somebody at WaPo has gotten too wrapped up in electoral politics to grasp the specific meaning of "vast majority".

    Wikipedia suggests "recent research suggests that in some rare cases both LINEs and SINEs were incorporated into novel genes, so as to evolve new functionality." (Emphasis added.) Does Discovery.org endorse that conclusion, even with its last three words?

  4. Reports of the death of junk DNA have been considerably exaggerated, as Mark Twain might say, at least if the most recent reports of his death hadn't been spot on. Look, folks. Fugu have a tenth the human genome but about the same number of genes. I suggest that means at least 90% of the human genome is junk. If fugu don't need it, chances are you don't need it either.

    That's not to say all non-coding DNA is junk. That's never been argued, by anyone. Some non-coding DNA has a regulatory function. But guess what: there's a test for functional DNA, which is that it's conserved over evolutionary time. By that test, there's only about as much functional non-coding DNA as there is gene, somewhere around 5% conserved DNA all told. As for the rest, if it's so great, why isn't it maintained?

    I'm willing to suggest that even such a respected scientific journal as the Washington Post might conceivably have misinterpreted recent results.

  5. Is not one of the ID arguments that mutations cannot create functional changes in the DNA?

    I wonder what this then means: http://www.sciencedaily.com/releases/2011/04/1104

    So, either mutations can very well create functional changes, or whatever entity created is still very much involved.
    And if this entity is the same as the God figure of the christian persuasion, he actually fights us humans at every step of the way.

  6. Someone should ask the ID proponents to find the function of every single non-coding DNA before this part of their hypothesis is accepted……… Payback for their need to find every fossil in the chain of life :)

  7. http://www.cracked.com/article_19161_the-6-creepi
    (please feel free to remove this post if it is out of bounds)

  8. When are you going to comment on Evonews drawing attention to Oxford's hiring of mathematicians to shore up Darwinism?

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