Sunday, September 06, 2015

Constructive Neutral Evolution (CNE)

Constructive Neutral Evolution (CNE) is a term that describes the evolution of complex systems by non-adaptive mechanisms. The idea (and the name) was developed by Arlin Soltzfus in 1999 (Stoltzfus, 1999) but it has antecedents in the literature and in the environment where Stoltzfus did his post-doc (Michael Gray and Ford Doolittle). It has been promoted by a number of prominent evolutionary biologists/population geneticists, notably Michael Lynch in his book The Origins of Genome architecture. Several examples have been described and discussed in the scientific literature and in popular books. For example, there is good reason to think that the evolution of the complex spliceosome that removes introns has evolved by mainly non-adaptive evolution.

Ford Doolittle and Michael Gray are fans of constructive neutral evolution. They and their collaborators wrote a review of the idea in Science (Gray et al., 2010). It has the provocative title "Irremediable Complexity." The same authors (different order) published another review the following year (Lukeš et al., 2011).

It's important to understand this concept because it challenges the idea that the evolution of complexity is adaptive and it sets the stage for challenging the idea that all adaptive structures arose exclusively by natural selection. Almost everyone who writes about constructive neutral evolution understands that it poses a problem for those who cling to adapatationist or selectionist views of evolution. It also helps us understand why the core idea behind irreducible complexity has been refuted.

Let's look at the introduction to the Lukeš et al. paper ...
In a recent Science Perspective, we highlighted a neutral evolutionary theory, called constructive neutral evolution (CNE) by Stoltzfus, emphasizing how such a process could lead to what we term ‘‘irremediable complexity’’: the seemingly gratuitous, indeed bewildering, complexity that typifies many cellular subsystems and molecular machines, particularly in eukaryotes. We offered (in fact reoffered) the CNE paradigm as a counterpoint to purely adaptationist/selectionist schemes that are often favored by biologists, and molecular biologists in particular, to explain the evolution of structural and biochemical complexity. We argued that continued failure to consider CNE alternatives impoverishes evolutionary discourse and, by oversimplification, actually makes us more vulnerable to critiques by antievolutionists, who like to see such complexity as ‘‘irreducible.’’ Here, we expand on this idea by presenting in more detail ‘‘case histories’’ that illustrate how CNE might have operated in the emergence of several complex systems, including RNA editing, the spliceosome, and the ribosome, and how it might be invoked more broadly as an evolutionary paradigm underlying cellular complexity in general.
They have a very nice figure that makes the whole idea quite easy to understand.1

Imagine an enzyme "A" that catalyzes a biochemical reaction as a single polypeptide chain. This enzyme binds protein "B" by accident in one particular species. That is, there is an interaction between A and B through fortuitous mutations on the surface of the two proteins. (Such interactions are common as confirmed by protein interaction databases.) The new heterodimer (two different subunits) doesn't affect the activity of enzyme A. Since this interaction is neutral with respect to survival and reproduction, it could spread through the population by chance.

Over time, enzyme A might acquire additional mutations such that if the subunits were now separated the enzyme would no longer function (red dots). These mutations would be deleterious if there was no A + B complex but in the presence of such a complex the mutations are neutral and they could spread in the population by random genetic drift. Now protein B is necessary to suppress these new mutations making the heterodimer (A + B) irreducibly complex. Note that there was no selection for complexity—it happened by chance.

Further mutations might make the interaction more essential and make the two subunits more dependent on one another. This is a perfectly reasonable scenario for the evolution of irreducible complexity. Anyone who claims that the very existence of irreducibly complexity means that a structure could not have evolved is wrong.

The evolution of modern hemoglobin, composed of two alpha subunits and two beta subunits is an example of a well-known structure that probably evolved in this manner. We already know that a single subunit can function on its own because that's what myoglobin does.

It's important to note that this explanation for the evolution of hemoglobin has not been "proved" even though it seems extremely likely. Creationists will focus on this and claim that irreducible complexity is still a valid objection to naturalistic evolution. Their logic is faulty because the initial claim was that the very existence of irreducible complexity means that it could not possibly have evolved. That means, according to them, that all the intermediate steps had to be functional and evolution by natural selection can't accomplish the goal. In other words, they take the evolved complex (A-B) on the right of the figure above and point out that neither of the subunits has activity on its own therefore they both had to be created simultaneously in order to get activity. Evolution can't do this so gods have to take over.

All that's required is that evolutionary biologists propose a reasonable explanation making it possible for such structures to evolve naturally in a world where gods play no role in evolution. That has been done. The idea that irreducibly complex structures are impossible to evolve has been falsified.2

One of the characteristics of complex eukaryotes is that their enzymes and complexes are almost always a lot more complicated that the prokaryotic versions. It doesn't make sense that eukaryotic ribosomes, for example, have a lot more protein subunits than their bacterial counterparts.

If you understand Constructive Neutral Evolution, you will realize that there doesn't have to be an adaptive explanation for all this extra complexity. It can be easily explained by neutral evolution in small populations. This is especially true of mitochondrial ribosomes ...
When one looks at the ribosomes of mitochondria, however, what emerges is an entirely different picture, one of extraordinary evolutionary plasticity. In keeping with their endosymbiotic origin, mitochondrial ribosomes in some species have strikingly bacteria-like compositions. However, in other lineages, drastic changes to rRNA size and structure, as well as protein composition, have occurred. Most relevant here are cases where a marked reduction in the size of rRNA components has occurred concomitantly with a substantial increase in ribosomal protein complexity. For example, the human mitochondrial ribosome contains rRNA species that are about half the size of their bacterial counterparts, but the number of proteins has increased in both subunits to a complexity closer to that of cytoplasmic ribosomes. Clearly, the human mitochondrial ribosome has lost substantial RNA and gained substantial protein in the course of its evolution from a bacterial progenitor, reversing the usual protein:RNA ratio (33:67) to become protein-rich (69:310). An even more extreme situation is seen in the kinetoplastids. Here, rRNA shrinkage has resulted in Trypanosoma mitochondrial rRNAs of only 610 and 1,150 nucleotides, with additional proteins among a total of 133 (vs.55 in E. coli) evidently compensating for this loss. Notably, the novel mitoribosomal proteins do not have detectable homologs outside of the kinetoplastids, and only a low degree of conservation and/or divergent function within this lineage.

This process appears to have been accompanied by a substantial remodeling of ribosome structure. In the human mitochondrial ribosome, many proteins occupy new positions, and intersubunit bridges consist mainly of protein rather than RNA. Especially notable is the absence of 5S rRNA in the large subunit of the mammalian mitoribosome; instead, proteins occupy the site where this RNA species normally sits, suggesting that a protein element may assume some of the roles of 5S rRNA. An even more extreme situation developed in the RNA-poor mitoribosome of kinetoplastid flagellates, which is more porous than other known ribosomes and where functionally conserved sites, such as the mRNA channel, the transfer RNA passage, and the exit site for nascent polypeptides are occupied by newly acquired ribosomal proteins rather than familiar ones.

In short, a CNE scenario can be used to rationalize not only the emergence of the ribosome as an RNP per se but also its peculiar ‘‘degeneration’’ in certain systems, notably mitochondrial, where constraints on ribosome function are presumably limited only to synthesizing a very small number of proteins.
This view—neutral evolution of complexity—is not just a problem for creationists. Evolutionary biologists and other scientists need to change their way of thinking about evolution in order to adapt to the new emphasis on population genetics and the role of chance in evolution. Too many scientists see life's complexity as a finely tuned Swiss watch rather than a sloppy Rube Goldberg machine that's just good enough.

Here's Lukeš et al. again ... as you read this, think about your own view of complexity. Do you always interpret it as an adaptation for "fine tuning"?
As we pointed out previously, machines of marvelous complexity such as lightharvesting antennae in photosynthesis, RNA and DNA polymerases and their attending initiation, elongation, and termination complexes, apparatuses for import, folding, and degradation of proteins, or the cytoskeleton and its motors, all might have grown to their current form through a process of CNE accretion. The same argument could apply to large and complex regulatory networks, which are often described as being ‘‘finely tuned’’ but might be better interpreted as ‘‘runaway bureaucracy’’ or biological Rube Goldberg machines where what could be a relatively simple task is performed though many steps by an unnecessarily complex machine.

UPDATE: A reader has alerted me to a post by Dan Graur on the same subject (June 11, 2014): Rube Goldberg’s 131st Birthday: Irremediable Complexity by Constructive Neutral Evolution.


1. Not that this is going to be much help to creationists. They are highly resistant to easy ideas.

2. The ideas described here have been around for twenty years and they have been explained repeatedly to many creationists, including all the leading figures in the Intelligent Design Creationist movement.

Gray, M.W., Lukeš, J., Archibald, J.M., Keeling, P.J., and Doolittle, W.F. (2010) "Irremediable complexity?" Science 330: 920-921. [doi: 10.1126/science.1198594]

Lukeš, J., Archibald, J.M., Keeling, P.J., Doolittle, W.F., and Gray, M.W. (2011) "How a neutral evolutionary ratchet can build cellular complexity." IUBMB life 63: 528-537. [PDF]

Stoltzfus, A. (1999) "On the possibility of constructive neutral evolution." J. Mol. Evol. 49: 169-181.

225 comments :

  1. Constructive Neutral Evolution (CNE) is a term that describes the evolution of complex systems by non-adaptive mechanisms.

    By the removal of adaptation or survival of the fittest from evolutionary theory, one creates another question/problem; why would living things evolve? What would be the driving force since evolution has not foresight or foreknowledge?

    Why would evolution happen at all?

    ReplyDelete
    Replies
    1. 1) Neutral evolution is still evolution. How hard is that to understand?

      2) Nobody who emphasizes the importance of neutral mechanisms of evolution is doing so while rejecting the importance of selection. It might look like that because there is internal controversy between panselectionists and evolutionary pluralists within the scientific community. But that does not mean the latter are stupid and are rejecting selection as a mechanism for evolution - the people who misunderstand them to be doing so are.

      Delete
    2. Evolution happens because it can't be avoided. Mutations can't be entirely prevented. Neutral mutations can't be prevented from becoming fixed (at a rate equal to the mutation rate) in any finite population. Evolution is an unavoidable consequence of reproduction.

      Delete
    3. While I'm a fan of the concept of Constructive Neutral Evolution (CNE) and other intellectual contributions by Arlin and the other scholars developing the concept, I don't think that some of the supporting examples of CNEs are valid. Take, for example, the evolution of the splicing and the spliceosome, which are arguably the most complex eukaryal macromolecular machinery.

      As I previously discussed, splicing has evolved as an adaptive defense mechanism system against insertion mutagenesis by a wide range of inserting elements ( http://biorxiv.org/content/biorxiv/early/2013/11/18/000588.full.pdf), which explains its complexity.

      Delete
    4. Claudiu: I don't know much about the spliceosome, but as I understand the argument by supporters of CNE, some examples are considered to be "overly complex" in the sense that some spliceosomes with less subunit complexity work fine and perhaps even more efficiently. Hence, the idea that subunit complexity has arisen through sequential "rescue/suppression" events and not because the additional subunits have improved function. Is this not your sense of the situation then?

      Delete
    5. When it comes to "immune functions" complexity is a fundamental feature, as the system must cope with highly variable and evolving contra-responses from parasitic/pathogenic elements.

      Delete
    6. In a recent post entitled "Jim Lake and the Eocyte tree", I brought forward what I think is the 'Elephant in the Room' of the exciting field of viral origin and evolution:

      If all intracellular parasitic or symbiotic cellular lineages have evolved overall by reductive evolution, why would parasitic or symbiotic viral lineages evolve the opposite way towards larger genomes and higher complexity?

      Unfortunately, the researchers and scholars in the field have yet to address this question, perhaps because it is irrelevant, which I doubt, or possibly because it challenges the prevalent view that viral lineages have evolved towards larger genomes and higher complexity.

      Perhaps Arlin and the other scholars promoting the concept of Constructive Neutral Evolution (CNE) might come up with at least one reasonable CNE scenario for the evolution of viruses from simple to complex in an intracellular environment.

      Delete
    7. If all intracellular parasitic or symbiotic cellular lineages have evolved overall by reductive evolution, why would parasitic or symbiotic viral lineages evolve the opposite way towards larger genomes and higher complexity?

      Well, in the most simplistic of scenarios, endosymbiotic bacteria start out as relatively complex free-living organisms that come to proliferate quite efficiently with the aid of the host, whereas viruses might have started out as little more than replicative bits of nucleic acid that would benefit from an acquired ability to spread from cell to cell. In other words, one shouldn't consider all parasites equal just because they are all parasites.

      Delete
    8. There are tens of thousands of obligate intracellular parasitic cellular species and, apparently, all of them have evolved by reductive evolution from more complex free living species. That's every strong data. Does anyone know of a single obligate intracellular parasitic cellular species that has evolved toward complexity within an intracellular environment?

      If not, we might as well make it the 1st a law of evolution.

      Delete
    9. What these people are saying is that there's more to evolution than selection. Not the selection doesn't happen.

      Delete
    10. John,

      "Evolution happens because it can't be avoided. Mutations can't be entirely prevented. Neutral mutations can't be prevented from becoming fixed (at a rate equal to the mutation rate) in any finite population. Evolution is an unavoidable consequence of reproduction

      Evolution needs reproduction or replication, and reproduction or replication need evolution. What was first John Harshman?

      Delete
    11. and reproduction or replication need evolution

      why?

      Delete
    12. Before moving to new posts, is anybody aware of data indicating that at least some intracellular parasitic cellular species have evolved toward complexity in an intracellular environment?

      Delete
  2. Georgi

    Do you really believe it or ... you have to believe it? I think I know the answer to this question.

    ReplyDelete
    Replies
    1. You might want to try and construct a question that actually makes sense.

      Delete
    2. Yes, he is secretly a IDiot but is too afraid to speak out for fear of losing respect among his peers. lol

      Delete
  3. Very interesting. At times you have disparaged online learning, MOOCs, but, while this blog is not a MOOC, I have been able to learn, at least in some imperfect way, a great deal of evolutionary biochemistry and theory here, so thanks. Also, in the quote from Lukes (can't find the proper symbol for the last letter) should it be "performed through many steps", rather than "performed though many steps"?

    ReplyDelete
  4. "Do you always interpret it as an adaptation for "fine tuning"?"

    More than I should, anyway. It does seem like there must be some natural selection and adaptation going on as it all jostles around and settles down to a well oiled machine. But that is no reason for all the complexity, if that complexity is not really necessary. I think this account of genetic drift and fixation is especially clear and helpful.

    ReplyDelete
  5. "Rube Goldberg" seems to capture what is going on much better than "constructive".

    Sometimes I wonder if there isn't a lot of straw manning going on here. To quote Georgi Marinov from above, nobody who emphasizes the importance of neutral mechanisms of evolution is doing so while rejecting the importance of selection. Conversely, these kinds of posts always read as if there was some significant number of adaptationists who reject the existence of neutral evolution, but I have yet to encounter somebody like that.

    What there appears to be are different foci of the narrative. I am probably as a adaptationist as they come and have, for example, commented here in the past that the stuff that is really interesting about evolution, story wise and especially to the public, is what is adaptive. But I can easily read this post and simply go, yes, of course evolution is a sloppy process where everything survives that is merely good enough.

    I just fail to see how "everything that doesn't work dies" is any less of an adaptive process than "only the very best and most efficient survive".

    ReplyDelete
    Replies
    1. "Conversely, these kinds of posts always read as if there was some significant number of adaptationists who reject the existence of neutral evolution, but I have yet to encounter somebody like that."

      One of my favorite Gould quotes seems apropos:

      "At this point, some evolutionists will protest that we are caricaturing their view of adaptation. After all, do they not admit genetic drift, allometry, and a variety of reasons for nonadaptive evolution? They do, to be sure, but
      we make a different point. In natural history, all possible things happen sometimes; you generally do not support your favored phenomenon by declaring rivals impossible in theory. Rather, you acknowledge
      the rival but circumscribe its domain of action so narrowly that it cannot have any importance in the affairs of nature. Then, you often congratulate yourself for being such an undogmatic and ecumenical chap. We maintain that alternatives to selection for best overall design have generally been relegated to unimportance by this mode of argument."

      While Gould frequently overstates his case, I think he had a point here. In my view there are plenty of biologists (e.g., the more high profile ENCODE folks) who might acknowledge the existence of neutral evolution, but when the rubber meets the road, they all but ignore neutral hypotheses when it comes to explaining the evolution of whatever trait they are interested in. My guess is that this tendency has lessened somewhat among evolutionary biologists over the past few decades, but I'm not so sure that the "panselectionist" view has really lessened in popularity among other sorts of biologists. I, for one, have talked to people who, upon encountering a complex trait, immediately assume that it must be a product of adaptive evolution.

      One very useful application of neutral evolution is as a null model for testing hypotheses regarding molecular evolution. It seems to me that if we want to seriously understand the origin of complex traits, we should at least entertain neutral hypotheses as well adaptive ones, if only to make our adaptive hypotheses more rigorous and testable.

      Delete
    2. Dawkins claimed that any "visible phenotype" cannot be neutral. Arch-selectionists are real and not straw men. Although you can argue what he means by "visible", I suppose.

      Delete
    3. Well, I argue that it is merely a matter of degree. Take leaf shapes, for example. Looking across the outline of oak, beech, maple, elm, ash, etc. leaves I can easily believe that this is mostly a combination of random walk and developmental contingencies. So leaf shape evolves neutrally, right?

      Well, then imagine an oak tree with leaves that are spheres of 10 cm radius. Would that be a physiologically viable solution in a temperate forest? Of course not. So even the shape of this organ must them be under some serious stabilising selection. The same is true for every organ and protein, simply because everything doesn't work dies. We can look at small changes and tell ourselves a neutralist story, but if we imagine something going seriously sproing we must realise that from a slightly more distant perspective it is still adapted (at a minimum to the niche called "not dead").

      Delete
    4. But that's not what someone like Dawkins would accept. To them, the leaft shape that we see today must have been selected for. It isn't enough that it was good enough for the tree to be "not dead" -- it must be better than any other possible shape.

      Delete
    5. @Alex SL

      There are still a huge number of features, of eukaryotes in particular, that are best explained by neutral mechanism. They are mostly at the cellular and molecular level, but some of them are absolutely fundamental to out biology.

      Delete
    6. Leaf shape seems to be adaptive. The warmer it gets the more likely a tree will have evolved entire (unlobed or untoothed leaves). Geologists use this to infer paleoclimates. I think this makes tree species easier for birds ot learn and helps them track trees (tree populations) that are being consumed by prey insects they can feed on. In tropical forests trees are too rare to be worthwhile tracking, and leaves tend to converge on efficiently elliptical. Even if my hypothesis proves wrong, the correlation between leaf shape and climate show leaf-shape is somehow adaptive. If there were no hypotheses, we would never learn anything. In the tropical SE Asia, the leaves of the local maple tree species practically lack lobes. It would put a Canadian to shame.

      Delete
    7. Woody Benson,

      I have deliberately chosen examples that are all from temperate forests to minimise the influence of climate-driven selection.

      The argument of "no hypotheses" is a bit odd; if it turns out that something really is random, then we just have to accept that even if it is a bit unsatisfying.

      Georgi Marinov,

      Unfortunately I fail to see how any of them would not be under stabilising selection. The only counter-example I can come up with is the precise sequence of an intergenic spacer region, but again within limits.

      Jonathan Badger,

      Maybe you are right about Dawkins, I wouldn't know, have only ever read one of his books. I can only say that I have yet to meet somebody who wouldn't accept standard population genetics / neutral theory / etc. People just generally get more excited about a story that goes "this is because it helps the plant to defend itself against herbivores" than about one that goes "this is because of... no particular reason" - and unsurprisingly so!

      Delete
    8. It seems like there is some misunderstanding here.

      Stabilizing selection today (which is by no means necessary to invoke with respect to everything I had in mind in that post) and establishment through neutral mechanisms in the past are very different things.

      Delete
    9. GM,

      My point is I am not sure you can separate these processes neatly into adaptive and neutral. If something establishes through neutral means in the sense of changes that are fitness-irrelevant enough it would still at the same time have experienced selection against all larger changes that are fitness-relevant.

      Note again that I am not saying it all boils down to adaptation, quite the opposite. I am saying that whether we can tell an adaptationist or neutral story depends on how deleterious a mutation we allow into our story, and that neutral and seriously deleterious changes are both happening in every single case. For every cell that would have made the step towards the complicated machinery of the eukaryotic cell there would have been gazillions that died because of a deleterious mutation.

      I just don't see how neutral theory really contradicts an adaptationist view as long as the adaptationist does not insist on Panglossian perfection but recognises that 'good enough' will survive and that evolution muddles around with what material it is given. And every evolutionary biologist who uses coalescent theory or population genetics or who has discussed the laryngeal nerve in their book must recognise that.

      Delete
    10. But I don't separate them. Of course it's not that simple - there is a constant interplay between drift and selection.

      But it is wrong to explain all features in terms of adaptation -- there are features that most likely cannot evolve in certain population genetic environments while they can in others. That is a very important distinction, because it explains a lot that could either not be explained otherwise, or the explanation would be wrong.

      It is also a question of mental discipline -- of always asking yourself "What is the selection coefficient, how does it relate to the state of the population, and does my story make sense given all that?" before telling that story. Of course that becomes more and more difficult the grander the question becomes, but is still very important to keep it in mind.

      Delete
  6. If the best survive differentially, you almost certainly have an accelerated rate of fixation.

    ReplyDelete
  7. Professor Moran,

    Professor Behe has responded to the Lukes paper here:

    http://behe.uncommondescent.com/2011/08/irremediable-complexity/

    I think that in order to advance the debate you need to address Behe's points.

    ReplyDelete
    Replies
    1. Behe parrots the standard creationist objections to anything they don't like. He demands evidence and calculations. He claims that the scenario seems impossible (to him).

      He misses the point. It's a possible scenario for the evolution of an irreducibly complex structure. Even if it's very unlikely (it isn't) it still refutes the argument that evolution of such systems is impossible.

      It always amazes me that creationists demand solid evidence and mathematical calculations for all hypothetical explanations based on evolution but they aren't willing to provide even a brief explanation of how intelligent design works, let alone evidence or calculations. "God did it" seems to be sufficient explanation for every perceived gap.

      Any truly honest creationist has to admit that there are several ways for irreducibly complex systems to evolve by natural means. But once they admit that, they don't have a case. Behe can't admit that the simple scenario described above is even possible because it means that his first book is wrong. He has to show that the scheme shown in the first figure above is impossible. He can't do that.

      Delete
    2. Professor Moran,

      I think you misrepresent Behe's position. But the most interesting thing you just asserted is that it isn't unlikely for such systems to evolve by CNE. Has somebody demonstrated the truth of that claim?

      Delete
    3. Please stop trying to shift the burden of proof. Creationists argue that it is IMPOSSIBLE for irreducibly complex systems to evolve by natural means therefore there must be an intelligent designer. Do you believe that the evolution of irreducibly complex structures is IMPOSSIBLE? If so, has someone demonstrated the truth of that claim?

      I've just described a way to evolve irreducible complexity without the need of an intelligent designer. You have to prove to me that it's impossible, otherwise your argument for the existence of gods collapses.

      Delete
    4. Professor Moran,

      If you want to teach that CNE is the correct scientific answer to how complex systems evolved, then I think you need to provide much more evidence than you have, so far. Otherfwise, CNE remains, at best, a hypothesis.

      It appears that both proponets of CNE and ID claim that neo-Darwinism is an inadequate scientific explanation of the evolution of complex biological systems, If so, I consider that a very significant development. Now we can try to decide whether either of them can adequately explain the evolution of those systems.

      I realize that you like to say that ID claims that God or gods are the designers. Strictly speaking, this isn't the case. If it turned out that ETs designed life on Earth, that would qualify as an example of ID. Most ID proponents believe that God is the designer. But they do not claim that there is empirical evidence demonstrating that God is the designer.

      So the ID argument isn't that God exists. It is that one or more designers does or did exist. And the argument is the same kind of argument that SETI uses: X looks designed. We don't know a non-intelligent way to design X. Therefore, it is reasonable to believe that X was intelligently designed.

      In my opinion, it's not an airtight, rigorous, scientific argument. But until one demonstrates that there is a plausible, probable way to evolve complex biological systems, it is at least a reasonable hypothesis. As reasonable as CNE.

      Delete
    5. CNE is one way complex systems evolve, nobody said that it is THE ONLY way they do.

      However, there is still this curious negative relationship between complexity and effective population size across life -- the more complex things are, the lower their N_e. And vice versa.

      I think it was in one of Michael Lynch's papers on the subject where he said something in the spirit of that if complexity is so beneficial, one has to marvel at the inability of natural selection to promote it in prokaryotes, which have enormous both absolute and effective population sizes, and accordingly selection is most powerful there.

      Our best current explanation for these patterns is that they are precisely due to the greater role that drift plays in lineages with lower N_e, which allows for more CNE to take place. So it goes like this, in most simplified terms:

      prokaryotes --> eukaryotes, which are bigger and have much larger cells, thus lower N_e (and probably, there was quite a bit of CNE in the earliest stages of their evolution too), which opens the door for further complexification, in particular at the level of gene regulatory networks (see PMID: 17878896 if you want to see what exactly I mean), and the evolution of multicellularity (happened dozens of time in eukaryotes, and more than once it proceeded to very high levels of complexity; but very few times in prokaryotes and always very simple -- why?). A positive feedback loop gets established in which increased complexity and physical size lead to lower absolute and effective population sizes (for obvious ecological reasons), which makes it even easier for further complexification to arise, and so on. Of course, selection plays a major role during all that time, but the important thing to understand is that what it is acting on would not have been available had selection always been as efficient as it is in E. coli. Prokaryotes seem to be stuck with being prokaryotes because most unnecessary complexity is quickly weeded out by extremely powerful selection so it cannot accrue and expand.

      Will this ever be proven to the same epistemological standards as physical theories are? Most likely not. We cannot run repeated experiments on such a scale. But it is our best explanation at the moment, and it is a very rich and powerful one.

      Delete
    6. Thanks for the explanation Georgi Marinov. I'll have to look into CNE and the relationship between complexity and N_e size in more detail.

      Delete
    7. Bilbo says,

      It appears that both proponets of CNE and ID claim that neo-Darwinism is an inadequate scientific explanation of the evolution of complex biological systems, If so, I consider that a very significant development.

      It would be significant if the IDiots finally started to realize that the view they've been arguing against for 30 years (neo-Darwinism) is not the standard view of evolution. So far they have proved resistant to learning and education so I'm not holding my breath.

      So the ID argument isn't that God exists.

      Of course it is. You can wiggle and squirm all you want but we all know the truth.

      In my opinion, it's not an airtight, rigorous, scientific argument. But until one demonstrates that there is a plausible, probable way to evolve complex biological systems, it is at least a reasonable hypothesis. As reasonable as CNE.

      Really? What's the probability that a "designer" exists who can do the things you claim? Remember you're answering that question from an atheist not from someone who already believes in gods. It's absurd to say that you have a "reasonable" hypothesis unless you already believe in a supernatural being who could construct the genes for a bacterial flagellum and stick them in a primitive prokaryote some three billion years ago.

      What's your evidence for gods that could do that? Were you there?

      You need to face up to the fact that your argument for an Intelligent Designer only begins to make sense provided you already believe in gods. Otherwise, it makes about as much sense as a fairly tale.

      Delete
    8. Really? What's the probability that a "designer" exists who can do the things you claim? //// 99,999999999999999999999999999999999999999%. What is the probability that natural, non intelligent mechanisms made life emerge ? 0,0000000000000000000000000000000000000000000000000001%

      and thats based on solid scientific evidence.

      Delete
    9. "99,999999999999999999999999999999999999999%."

      How did you get this number?

      Delete
    10. Just to be clear, I know you just pressed 9 until you felt it was enough, you have zero reason to think that number is the correct one.

      "and thats based on solid scientific evidence."

      No, you made it up on the spot. Both numbers you just typed out as you felt it. That makes you both wrong and a liar.

      Delete
    11. What is the probability of the existence of said designer?

      (Noting that it must be more complex than these molecular machines, to be able to design these "way to complex thingys", so the probability of it existing by your logic, would set off my "keyboard error" check on my computer long before we reach a reasonable number of zeros...).

      Or are you another one engaging the the "turtles all the way down" argument?

      Delete
    12. What is the probability of the existence of said designer?

      The funny thing is, design proponents are motivated solely by their faiths (almost always christian) in god. Meanwhile, if anything akin to an intelligent designer did actually exist, it would bear no resemblence to the cartoon gods of human religions, and it wouldn't be anything that requires worship, or that you could pray to, or that would make capricious promises of eternity. The only kind of god that matters to the creationist simply will not exist, even if something like an intelligent designer does. Normally, that would be demoralizing... but such is faith, that it is not.

      Delete
    13. "99,999999999999999999999999999999999999999%."

      How did you get this number?////

      http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible

      The cell is irreducible complex, and hosts a hudge amount of codified, complex, specified information. The probability of useful DNA, RNA, or proteins occurring by chance is extremely small. Calculations vary somewhat but all are extremely small (highly improbable). If one is to assume a hypothetical prebiotic soup to start there are at least three combinational hurdles (requirements) to overcome. Each of these requirements decreases the chance of forming a workable protein. First, all amino acids must form a chemical bond (peptide bond) when joining with other amino acids in the protein chain. Assuming, for example a short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45. The second requirement is that functioning proteins tolerate only left-handed amino acids, yet in abiotic amino acid production the right-handed and left-handed isomers are produced in nearly the same frequency. The probability of building a 150-amino-acid chain at random in which all bonds are peptide bonds and all amino acids are L-form is roughly 1 chance in 10^90. The third requirement for functioning proteins is that the amino acids must link up like letters in a meaningful sentence, i.e. in a functionally specified sequential arrangement. The chance for this happening at random for a 150 amino acid chain is approximately 1 chance in 10^195. It would appear impossible for chance to build even one functional protein considering how small the likelihood is. By way of comparison to get a feeling of just how low this probability is consider that there are only 10^65 atoms in our galaxy.

      Delete
    14. The cell is irreducible complex, and hosts a hudge amount of codified, complex, specified information

      IC & SCI are just creatard gibberish. Go shove your tornado in a junkyard nonsense where the sun don't shine.

      Delete
    15. Of course, you can try to use math to calculate unreasonable chances for the origin of living cells, for evolutionary processes to have proceeded randomly, but such numbers will not be accepted by the believers in the Darwinian faith. A discussion is useless.

      Delete
    16. I ask how he calculates the probability of design (he said it was 99.9999etc.etc. %), and he gives me instead an article that tries to estimate the odds of the origin of life through natural means.

      Right, but that's not what I asked for. I don't care what the odds of a natural origin of life is (and all his math is irrelevant anyway, since nobody believes life formed by proteins magically assembling themselves), I need the other number to compare it to. Natural origins are improbable. Yeah, okay - I can accept that. But what are the odds of design?

      When you make probability estimates you need two numbers to compare to each other. The odds on natural process vs the odds on supernatural design process.

      Try to not just make up a number. What is the supernatural design process number and how do you know?

      Also, he writes that the cance of a natural origin is "0,0000000000000000000000000000000000000000000000000001%", but now he links an article that at last 1 in 10^195th power. So the first number, as I explained, he just made up. He pulled it out of his ass. Ex-recto assertion. The second number, the one from the article, is irrelevant because it doesn't deal with any postulated process.

      You people are unimaginably dumb and deluded. You wouldn't know logic and reason if it sat and smothered it's greasy cunt on your faces.

      Delete
    17. ElShamah777,

      Wouldn't you think that if the chances of having a very specific protein sequence by chance has such a small probability, that therefore evolution is neither about chance alone, nor about very specific protein sequences?

      Wouldn't you think that if evolutionary theory had nothing but chance about it (and very specific protein sequences), then the scientists working on it would be doing something else, as it would be too obvious that evolution could not be an answer to anything?

      If you haven't, then you should. Otherwise you're just been a wishful thinking imbecile. Of course, we don't know who you are, but you come and represent something you might consider important, like you religious beliefs. OK, then have some respect for yourself and for those beliefs and don't be such an obvious idiot.

      Delete
    18. ElShamah777 said,

      "99,999999999999999999999999999999999999999%."

      How did you get this number?////

      http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible

      The cell is irreducible complex..."

      MR. GRASSO!! How are you? I wondered where else you'd turn up. Not satisfied peddling your Behe, Dembsky IC quotes on reddit, facebook and ChristianForums and getting shot down all over the place. Nothing new to say I see.

      Delete
    19. Mikkel Rumraket Rasmussen, normally I like your comments, but please review the last sentence in your 9:21 comment above, consider that it might offend non-target readers (e.g. me) and avoid such language in the future.

      Delete
    20. I need the other number to compare it to. Natural origins are improbable. Yeah, okay - I can accept that. But what are the odds of design? /// A intelligent cause is a POTENT cause, as we know that intelligence is able to produce coded complex specified information, A post of Michael Breck at FB brought it nicely to the point : Michael Breck you should be able to just look at a snowflake under a microscope and conclude that it was formed by a designed process. Crystallization to me... is clear evidence of a Creator. Whether you look at a tree or any mammal or even insect or fish... you should be able to have some intuitive sense that it is not the result of accident or chance... but there is meaning and purpose in the universe. For those who do not see clearly... we have more persuasive arguments. The arrangement of codon triplets in specific order as to be used as a template for coding polypeptide sequences is clearly information. Information always comes from Intelligence. Random processes never put things in any useful order (unless such order is already present in the system). Mechanical working systems themselves are also clearly the result of Intelligence. The nano factory of the living cell that performs processes like protein biosynthesis is clearly the result of Intelligence. When we look at other features in microbiology such as gene regulation of the lactose operon in E. coli we see IF-THEN algorithms based on contingency built into the code: IF lactose is present, and IF glucose is absent THEN synthesize beta-galactosidase and permease. Someone clearly programmed this as they did all of the genetic code. These types of points are often made within a cumulative case argument for general theism once "identifying features in biological systems which are the result of Intelligence" are allowed. This step is actually distinct from theistic implication which comes later in the cumulative case. There are other ways in which we can know there is a Creator or an Originator... just using basic reasoning to honestly admit that you can't have an infinite regress... and that you must at some point have a non-contingent Originator (uncaused) which possesses the quality of "being" itself in order to have any sort of existence now is a good step toward a reasonable theism (but clearly this does not prove the God of Abraham...that is an additional distinct cumulative case argument).

      Delete
    21. ElShamah777 -- nice poetry, but as an argument it has a basic logical flaw. It proposes only two alternatives -- chance vs. intelligent design. However, evolution is very importantly NOT a chance process. Alternatives are generated randomly, and then which alternatives reproduce is determined (partly, importantly) by non-random processes.

      Some of the controversy we face seems to result from not being able to understand that two things can be true at once. CNE and selection. Drift and selection. Random and non-random processes. Even, we humans are animals like any other (and eukaryotes like any other), continuous with the rest of the animal world, and we are unique (on earth at least) and amazing. We live in a universe without purpose or meaning, and we can live lives full of meaning and purpose.

      Delete
    22. Information always comes from Intelligence

      How do you explain Fox news then?

      But in all seriousness, you still have nothing but the same idiotic arguments from ignorance, appeal to common sense, etc, etc.... Gets old pretty fast.

      Any of that could be said of the movement of the planets in the solar system before Newton.

      Crystallization to me... is clear evidence of a Creator

      Ha, science 101, check mate atheists!

      Delete
    23. I'm still waiting for an explanation for how you calculate the probability of a designer designing life. What is the number and how do you get that number?

      Delete
    24. It proposes only two alternatives -- chance vs. intelligent design. However, evolution is very importantly NOT a chance process // mutations happen by chance. But its actually naturalism against creationism. All boils down essentially to these two alternatives.


      Rumraket is now resorting to a strawman demand. Intelligence does not act upon chance and probability. Intelligence works upon will and is goal oriented, which is essentially different . What is chance ? chance is not a thing.

      What naturalism basically says is that over time by chance matter evolved into the entire universe. Jacques Monod won the...this is unthinkable...the Nobel Prize for biology and in his book Chance and Necessity he says this, "Man is alone in the universe's unfeeling immensity out of which he emerged by chance." That's the Nobel winning biologist. Chance alone is the source of every innovation. Chance alone is the source of all creation in the biosphere. He writes, "Pure chance absolutely free but blind is at the very root of the stupendous edifice of evolution." So Monod says it's just chance.


      http://www.gty.org/resources/sermons/90-208

      But let me tell you about chance. Chance doesn't exist, it's nothing...it's nothing. Chance is a word used to explain something else. But chance isn't anything. It's not a force. Chance doesn't make anything happen. Chance doesn't exist. It's only a way to explain something else. Chance didn't make you meet that person, you were going there when she was going there, that's why you met her. Chance didn't have anything to do with it because chance doesn't exist. It's nothing. But in modern evolution its been transformed into a force of causal power. It's been elevated from being nothing to being everything. Chance makes things happen. Chance is the myth that serves to undergird the chaos view of reality.

      I mean, this is so fraught with problems from a rational or philosophical viewpoint you hardly know where to begin. How do you get the initial matter upon which chance operates? Where does that come? You would have to say, "Well, chance made it appear." You know what? This sounds so ridiculous and yet this is the undergirding philosophy behind evolution. It is completely incoherent and irrational. But the new evolutionary paradigm is chance. And it's the opposite of logic.

      You see, when you abandon logic and logic says, "Oh, there's a universe. Hum...somebody made it." What else would logic say? "There's a building, somebody made it. There's a piano, somebody made it. There's a universe, more complex than a building, infinitely more complex than a piano, somebody...somebody who is very, very powerful and very, very intelligent made it."

      You say, "No, no, chance made it." Listen, folks, that's rational suicide, that's not logical.

      Delete
    25. ...and another wasted opportunity to post your magnificent probabilistic model for your imaginary designer. BTW, you couldn't think logically to save your life.

      Delete
    26. El, you forgot to give the source of the second part of your copy-and-paste job, so let me help you:

      http://ravingatheists.com/forum/showthread.php?t=14763

      Even the dumbest creationists I have met come up with some thoughts of their own from time to time. You seem to have the intelligence of a xerox machine.

      Delete
    27. Piotr

      that was my post, Godlovesyou is my nickname. And the original source is the one posted above.

      And, oh well, the fact that rather to address the argument, you argue about my intelligence, says a lot about your attitude.

      Delete
    28. Anyway, the whole point is that they are not your words, and they don't express anything worth addressing. It's a f***ing sermon, not a logical argument. There is a technical term for copying, posting and re-posting such propaganda on different discussion boards and blogs: it's spamming. Why don't you say something from yourself, just to show that you're a human being rather than a spambot?

      Delete
    29. Piotr

      nice dodging of the issues raised..... feel free to point out where the logic fails....... and why you think nothing is a potent cause for complex biological systems, and the software stored in DNA, LOL....

      Delete
    30. ElShamah77,

      You have presented nothing rational from an empirical scientific point of view. Just a bunch of vague claims and misrepresentations of the role of chance, incoherent and self-contradictory.

      If you want to approach reationality, you have to reconcile this, your claim, about reality:

      "Intelligence works upon will and is goal oriented, "

      Explain how this is an explanatory hypothesis for the generation of the diversity of life on planet Earth, and provide evidence to support it.

      Delete
    31. What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex.

      By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning.


      But today, there are many such cases observed in nature.

      High information content machine-like irreducibly complex and interdependent structures, of which photosynthesis, the eye, the human body, nitrogenase, the ribosome, the cell, rubisco, photosystem II, the oxygen evolving complex etc. are prime examples, are commonly found in nature.
      Since Evolution is unable to provide a advantage of adaptation in each evolutionary step, and is unable to select it, 1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.

      Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.
      Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.
      Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and bodyparts, and even of animals and plants, aka moths and flowers, for example.

      Delete
    32. Here you go:

      Nilsson D., Pelger S. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London, Series B 1994; 256:53-58.

      Your problems are many, but that's one; Nilsson & Pelter show that each successive, small step from light-sensitive spot to camera eye is advantageous if by advantageous you mean increased vision. Another is that you can't imagine evolution occurring other than by the stepwise addition of individual, unchanging parts. In fact there are many ways to evolve an irreducibly complex system, and oddly enough the constructive neutral evolution Larry's post is about is one of them. Did you even read it?

      Delete
    33. Hey ElShamah77, if you are going to cut & paste from Behe's book "Darwin's Black Box: The Biochemical Challenge to Evolution." (page 39) you should at least cite your references.

      Delete
    34. ElShamah777 looks upon the words of Behe, and decrees :
      High information content machine-like irreducibly complex and interdependent structures, of which photosynthesis, the eye, the human body, nitrogenase, the ribosome, the cell, rubisco, photosystem II, the oxygen evolving complex etc. are prime examples, are commonly found in nature.

      Since Evolution is unable to provide a advantage of adaptation in each evolutionary step, and is unable to select it, 1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.


      But given the fact that 'irreducibly complex' systems can evolve, and the fact that the 'MAGIC MAN DIDIT !!!' of 'intelligent design' is utterly useless, you have no argument. Your willful incredulity is evidence against nothing.

      Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.


      Information ('specified' and otherwise) is readily generated by any system that has a cycle of selection and variation.

      Irreducible and interdependent systems can evolve - the only reasons you 'think' they harm evolution is because you presume that nature is as rigid and limited as your mind. Observations of REALITY show that a system's 'function' can change over time. And that parts of a system can be added, subtracted and modified. Both observations together pretty much castrate ID - without those two core conceits, ID is reduced to the willfully stupid declaring anything they PERSONALLY can't figure out as 'absolute, irrefutable evidence that a Magical Sky Pixie somehow did something sometime in the past for some reason !!!!'

      Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.

      Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and bodyparts, and even of animals and plants, aka moths and flowers, for example.


      Given that premise #1 is woefully, incredibly WRONG, your conclusion is quite silly.

      Observed evolution of an IC system : atrazine degradation pathway in bacteria. Requires 3 enzymes - AtzA, AtzB and AtzC to fully degrade atrazine - a compound that does not exist naturally. Bacteria EVOLVED the pathway in just a few years via a consortium - one species developed AtzA, another developed AtzB, and a third evolved AtzC.

      Alone, only the bacteria that produced AtzA could grow with with atrazine as a carbon source, but very poorly. The other two - if alone - could not utilize atrazine. Mix all three together, and all grow to high cell densities.

      Thus demonstrating that the atrazine degradation pathway is an example of an evolved 'irreducibly complex' system.

      Even t-URF13 shows ID's core delusion to be wrong - t-URF13 is a multimeric, gated ion channel protein evolved from DNA sequences that never coded for protein (they code for ribosomal RNA components).

      Any example of the use of genetic algorithms to solve a problem demonstrates the FACT that information arises in any system that has cycles of mutation and selection.

      Starting from a string of 70 RANDOM amino acids, an ATP binding protein was quickly evolved via multiple rounds of mutation and selection - in complete and utter defiance of IDiot rantings. This evolved ATP binding protein was a zinc finger - NO KNOWN ATP BINDING PROTEIN USED A ZINC FINGER MOTIF. The reaction exploited a mineral even the researchers had overlooked to gain the information of 'how to be an ATP binding protein'.

      Delete
    35. John

      Nilsson D., Pelger's paper is a JOKE for the gullible like you , who swallow any nonsense without giving a second thought to the proposals.

      http://reasonandscience.heavenforum.org/t1638-eye-brain-is-a-interdependent-and-irreducible-complex-system

      http://www.grisda.org/origins/21039.htm

      "What is one to make of all this? First, comparing the evolution of the eye to shape changes on a computer screen seems rather far-fetched. The entire project seems closer to an exercise in geometry than in biology. Second, the exercise assumes a functional starting point. Thus it has nothing to do with the origin of the biochemical systems of vision or the requisite neural network. Third, Nilsson and Pelger's computer exercise operates as if each 1% change in morphology can be accounted for by a single gene mutation. They do not consider the effects of pleiotropy, genetic background, or developmental processes. Fourth, an important part of the model relies on the special circumstance of a layer of clear cells covering the "retina." This layer somehow assumes the proper shape of a lens. Fifth, as noted by the authors, several features of the eye remain unaccounted for, such as the iris. Basically, the only result achieved was to show that two light-sensitive surfaces that differ in shape by 1% will have different efficiencies in photoreception, and that an uninterrupted series of 1% improvements is possible. The failure of scientists to produce new structures in selection experiments illustrates the implausibility of Nilsson and Pelger's "just so" story."

      Delete
    36. Paul

      But given the fact that 'irreducibly complex' systems can evolve

      IC systems cannot evolve BY DEFINITION. Either they are evolvable, and then they are not ic, or they are ic, then they can't evolve. You can't have it both.

      http://reasonandscience.heavenforum.org/t1468-irreducible-complexity

      3. Michael Behe's "Evolutionary" Definition — "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." (A Response to Critics of Darwin's Black Box, 2002)

      unselected steps means, natural selection can't select these steps. I go as far as to say that all cellular functions are irreducibly complex :

      http://reasonandscience.heavenforum.org/t2179-all-cellular-functions-are-irreducibly-complex

      as most biological systems work and exercise their function like a machine, through several intelocked parts, like a watch, to take Paleys example, as Cornelius Hunter puts it nicely :

      http://reasonandscience.heavenforum.org/t2180-the-spliceosome-and-mrna-processing-in-eukaryotes#4010

      its job ( of the watch ) is to steadily tick away the time. But a look inside reveals a much more intricate dance of parts, from precisely-fitted gears to cable-embraced pulleys and bobbing levers.

      clocks, is full of parts that fit together. That means that both parts are required for the mechanism to work.

      That easily contradicts evolution’s blind action, which can’t even reroute a nerve. How could it luckily evolve two parts together? What is needed is a gradual pathway of functional intermediates. Needless to say proponents of evolution know of no such pathway. That doesn’t mean it doesn’t exist, but it does raise the question of how evolutionists can be so certain that it exists. Particularly when evolution cannot even explain how a single protein could have evolved.

      Delete
    37. Paul

      Information ('specified' and otherwise) is readily generated by any system that has a cycle of selection and variation.//


      In plain english, thats simply NONSENSE.

      http://reasonandscience.heavenforum.org/t1405-the-genetic-code-cannot-arise-through-natural-selection

      http://www.arn.org/docs/booher/scientific-case-for-ID.html

      The probability of useful DNA, RNA, or proteins occurring by chance is extremely small. Calculations vary somewhat but all are extremely small (highly improbable). If one is to assume a hypothetical prebiotic soup to start there are at least three combinational hurdles (requirements) to overcome. Each of these requirements decreases the chance of forming a workable protein. First, all amino acids must form a chemical bond (peptide bond) when joining with other amino acids in the protein chain. Assuming, for example a short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45. The second requirement is that functioning proteins tolerate only left-handed amino acids, yet in abiotic amino acid production the right-handed and left-handed isomers are produced in nearly the same frequency. The probability of building a 150-amino-acid chain at random in which all bonds are peptide bonds and all amino acids are L-form is roughly 1 chance in 10^90. The third requirement for functioning proteins is that the amino acids must link up like letters in a meaningful sentence, i.e. in a functionally specified sequential arrangement. The chance for this happening at random for a 150 amino acid chain is approximately 1 chance in 10^195. It would appear impossible for chance to build even one functional protein considering how small the likelihood is. By way of comparison to get a feeling of just how low this probability is consider that there are only 10^65 atoms in our galaxy..


      For, under such "infinite monkey" circumstances , searches based on random walks from arbitrary initial configurations will be maximally unlikely to find such isolated islands of function. As the crowd-source Wikipedia summarises (in testimony against its ideological interest compelled by the known facts):

      The text of Hamlet contains approximately 130,000 letters. Thus there is a probability of one in 3.4 × 10^183,946 to get the text right at the first trial. The average number of letters that needs to be typed until the text appears is also 3.4 × 10^183,946, or including punctuation, 4.4 × 10^360,783.

      Even if the observable universe were filled with monkeys typing from now until the heat death of the universe, their total probability to produce a single instance of Hamlet would still be less than one in 10^183,800. As Kittel and Kroemer put it, “The probability of Hamlet is therefore zero in any operational sense of an event…”, and the statement that the monkeys must eventually succeed “gives a misleading conclusion about very, very large numbers.” This is from their textbook on thermodynamics, the field whose statistical foundations motivated the first known expositions of typing monkeys.

      Delete
    38. ElShamah: I take that quote as good evidence that whoever wrote it didn't read the actual Nilsson & Pelger paper, just saw something about it on TV.

      Delete
    39. Once again confirming:
      "What we do have here, however, is an excellent case of someone, namely Casey Luskin, inserting the miraculous intervention of a “common designer” where he has gaps in his knowledge. This is exactly the problem with ID/creationism – invoking God into gaps in knowledge is pretty troublesome, but creationists do something even worse. They insert God into gaps in their own knowledge, assuming, usually without even a vaguely serious attempt at a literature search (!!!), that whatever tidbits of biology they happen to have picked up represent the sum total of scientific knowledge on a topic. This is, I think, why they so often stay ignorant, even when, as Luskin did, they have had the whole thing explained to them before."

      http://pandasthumb.org/archives/2009/01/god-of-the-gapsin-your-own-knowledge-luskin-behe-blood-clotting.html

      Delete
    40. Okay so according to Elsamoron, the probability of a natural origin of life is very small. Good, but then how probable is the alternative?

      What is the probability that a designer will design life as we know it? We need to compare the two numbers, otherwise we can't make a decision.

      Delete
    41. If we build a simple machine which flips a fair die half a million times and records the outcome, the probability of that particular outcome is many, many orders of magnitude higher than typing Hamlet correctly, with all the right punctuation marks in all the right places, though the machine is quite dumb compared to Shakespeare's brain, and the HTTTHTHHTTTT... sequence is completely meaningless. The only valid conclusion is that the result would have been unpredictable a priori, not that it can't have happened without a supernatural designer. The event space in such an experiment may be vastly bigger that the number of elementary particles in the universe -- there are no constraints at all on its size (why should there be?).

      Thermodynamics, probability theory, information theory: things that creationists invariably misunderstand and abuse.

      Delete
    42. the probability of that particular outcome is many, many orders of magnitude higher

      Dammit, I mean LOWER. Why doesn't Blogger offer an "Edit" button?

      Delete
    43. Rumraket

      it seems you try to make easy things difficult.

      Which probability is higher : Someone writing Hamlet, or the letters happen to align by accident to form the coded information ?

      Delete
    44. What is the probability that someone writes Hamlet? How would you even calculate that? I'm genuinely interested in an answer. You seem to think you know it, tell me.

      Delete
    45. Here's my probabilistic model for supernatural creation by gods.
      Gods are claimed to be infinite in power.
      Hence, a god can create an infinite number of possible worlds.
      So the probability of this universe being created by a god = 1 / infinity = zero

      Delete
    46. "IC systems cannot evolve BY DEFINITION. Either they are evolvable, and then they are not ic, or they are ic, then they can't evolve."

      That's a tautology, not a logical refutation of evolution. It provides an ever moving goalpost. A freshman debate team member could have pointed that out to you.

      All you are doing here is rephrasing your hypothesis; you aren't providing any evidence for your claims at all. Try again:


      "Intelligence works upon will and is goal oriented, "

      Explain how this is an explanatory hypothesis for the generation of the diversity of life on planet Earth, and provide evidence to support it.

      Delete
    47. What is the probability that someone writes Hamlet? How would you even calculate that? ///
      Its enough that we do know that minds write books, and use coded information. Your pet theory can't.

      Delete
    48. So evolution can't account for literature?. How cute. I don't know what's more hilarious: your retarded arguments or the fact that you don't realise how retarded they are

      Delete
    49. Me : Information ('specified' and otherwise) is readily generated by any system that has a cycle of selection and variation.//

      ElShamah777 mindlessly retorts :
      In plain english, thats simply NONSENSE, then vomits up standard IDiot numerology, 'calculating' the odds of a pre-specified protein falling together all at once purely by chance at 1 in 10^195.

      But the most mind-buggeringly STUPID point is : "the third requirement for functioning proteins is that they amino acids must link up like letters in a meaningful sequence, i.e. in a functionally specified sequential arrangement'.

      The calculation is the height of stupid for several reasons :

      1. The Fallacy of the One True Sequence. You seem to have this stupid idea that there is only ONE amino acid sequence that can perform any given reaction. Examination of REALITY shows that is not so - for vacuolar H+ PPases, the bacterial protein has only 30% identity to eukaryotic V-H+ PPases. Structure is far more conserved than sequence, and even then there are quite a few different structures that can do the same job.

      2. The STUPID idea that it had to fall together, all at once, purely by chance. No sane or rational person that actually understands real world biology believes any modern protein arose that way.

      3. By actual laboratory experiments, the odds of a random peptide 70 amino acids long having a selectable function is actually 1 in 10^9 to 1 in 10^15.

      So your 'calculations' are off by 150+ orders of magnitude.

      For the other post : a system can gain information by repeated CYCLES of variation filtered through selection. That fetid example of monkeys typing Hamlet you presented has no cycles, no variation, no selection.

      I realize that as an IDiot, you have difficulty following any process of more than one step, so I'll try to make this simple enough for even YOU to understand :
      1. Start with a pool of 10^12 phage expressing a string of 70 RANDOM amino acids.
      2. Bind the population to gel immobilized ATP.
      3. Wash off all those that don't bind.
      4. REPLICATE WITH A FEW MUTATIONS THOSE THAT DID BIND.
      5. Got step 2, with more stringent reaction conditions (less time, higher temperature)
      6. Repeat a few dozen times.
      The resulting population will have greatly increased ATP-binding capability. In fact, about 1 in 10^9 of them.

      From "Functional proteins from a random sequence library", Keefe AD, Szostak JW, Nature 410(6829): 715-718, 5 April 2001.
      Now, by IDiotic numerology, the 'odds' of the experiment working are about 1 in 20^70, or 1 in 10^91.

      The population gained 'information' about how to be an ATP-binding protein.

      Delete
    50. for vacuolar H+ PPases, the bacterial protein has only 30% identity to eukaryotic V-H+ PPases. Structure is far more conserved than sequence, and even then there are quite a few different structures that can do the same job./// Convergent evolution is a argument AGAINST evolution, nor FOR it:

      Convergence, another problem for evolution

      http://reasonandscience.heavenforum.org/t2014-convergence-another-problem-for-evolution?highlight=convergence

      Biologists are uncovering numerous examples of organisms that cluster together morphologically (structurally), and yet are genetically distinct. Frogs, lizards, or herbs that appear to be identical are actually different at the genetic level. An evolutionary interpretation of this data, then, demands that the morphologically identical organisms must have evolved independently of one another in a “repeatable” fashion.

      “…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1

      Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York, NY: W.W. Norton & Company, 1989), 51.

      Gould’s metaphor of “replaying life’s tape” asserts that if one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different.2 The very essence of the evolutionary process renders evolutionary outcomes as nonreproducible (or nonrepeatable). Therefore, “repeatable” evolution is inconsistent with the mechanism available to bring about biological change.

      Paleontologist J. William Schopf, one of the world’s leading authorities on early life on Earth, has made this very point in the book Life’s Origin.

      Because biochemical systems comprise many intricately interlinked pieces, any particular full-blown system can only arise once…Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA cell line had the same traits that characterize all its present-day descendents.

      http://www.upenn.edu/pennnews/news/evolution-unpredictable-and-irreversible-penn-biologists-show

      Gould’s famous tape of life would be very different if replayed, even more different than Gould might have imagined.”

      Evolutionary theorist Stephen Jay Gould is famous for describing the evolution of humans and other conscious beings as a chance accident of history. If we could go back millions of years and “run the tape of life again,” he mused, evolution would follow a different path.

      Delete
    51. 2. The STUPID idea that it had to fall together, all at once, purely by chance. No sane or rational person that actually understands real world biology believes any modern protein arose that way.//

      So what mechanism was involved to make the proteins and enzymes and metabolic pathways required for the first living cell to arise ? There was no replication yet........

      Delete
    52. 3. By actual laboratory experiments, the odds of a random peptide 70 amino acids long having a selectable function is actually 1 in 10^9 to 1 in 10^15.//

      and you think that number speaks in favour for naturalistic explanations ?? LOL....

      Delete
    53. a system can gain information by repeated CYCLES of variation filtered through selection. ///

      The more name calling , the more foolish are the concrete counter proposals of the poster. That is YOUR case.

      Lets for a moment grant that your CYCLES of variation filtered through selection would produce a functional protein. SO WHAT ??!!

      For a working biological system to be built, the five following conditions would all have to be met:

      C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.

      C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

      C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

      C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

      C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if sub systems or parts are put together in the right order, they also need to interface correctly.

      ( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

      If your functional protein has no use, and the information is not there to mount it at the right place, in the right manner, in the right sequence, fitting precisely at the right location, and able to interact with other functional proteins, nothing is done. And if you do not have a functional membrane in place, nothing done either.

      Delete
    54. I'm still waiting for an explanation for how you calculate the probability of a designer designing life. What is the number and how do you get that number?

      Okay so according to Elsamah, the probability of a natural origin of life is very small. Good, but then how probable is the alternative?

      What is the probability that a designer will design life as we know it? We need to compare the two numbers, otherwise we can't make a decision.

      What is the probability that someone writes Hamlet? How would you even calculate that? I'm genuinely interested in an answer. You seem to think you know it, tell me.

      Delete
    55. Mikkel,

      "I'm still waiting for an explanation for how you calculate the probability of a designer designing life. What is the number and how do you get that number?"

      Don't hold your breath. Creationists like ElShamah are only interested in setting up straw man versions of evolution to knock down. When they make the argument that convergence is a problem for evolution (when in reality it is once of the clearest evidences for evolution), you can see the level of irrationality you are dealing with. No level of misrepresentation of obfuscation is too low for these folks to maintain their made up religious beliefs.They just need gaps to hide their god in. They thrive on uncertainty. You will never see them provide any empirical evidence for their absurd claims.

      Delete
    56. I'm still waiting for an explanation for how you calculate the probability of a designer designing life.// your previous question was in regard of the probability of a designer producing coded information, as compared to the probability numbers shown in regard of random chance. Well, the probability is ONE. We have empirical evidence that minds can create coded information. As for example, we KNOW Hamlet was written by Shakespeare.......

      Delete
    57. With this creationist logic, the probability of rolling a four in a fair die throw is not 1/6 but 1 or 0 if you "calculate" it after the fact. Indeed, such an a posteriori probability of anything can only be 1 (it happened) or 0 (it didn't happen). Since the origin of life and biological evolution are known to have occurred, their probability is 1. It's a tautology, and not a very insightful one.

      Delete
  8. Ah Mr. Moran, so much to refute in this post!.

    NO one is interested in the mere possibility of evolution but rather its plausibility and probability. So let clear that out first.

    Moran: "All that's required is that evolutionary biologists propose a reasonable explanation making it possible for such structures to evolve naturally in a world where gods play no role in evolution. That has been done. The idea that irreducibly complex structures are impossible to evolve has been falsified.2 " (I added bold)

    Lets take endosymbiosis as a clear example of design that evolutionists need to steal (i mean co-opt) to kickstart their highly implausible explanations.

    You have a single-celled organism around 2 billions years ago, just getting used to its new-found existence. According to evolution it just happened to accumulate just the right neutral mutations that allowed it to start taking up nutrients (note the organism does not yet know that it is destined for multi=cellularity).

    So here it is, just having picked up the habit of taking up nutrients to maintain its cellular integrity. Then all of a sudden another more simplified organism runs across its path. Naturally, the first organism takes it for nutrients it can uptake to maintain its cellular integrity so starts the process of (then) crude digestion.

    But wait!! The single-celled organism has an EPIPHANY!!! It doesnt digest the other organism. The losing organism pleads, the winning organism defers judgement, then they decide to become pals and live as a single unit.

    See, THAT is what Larry Moran wants you to believe. That neutral evolution could explain (with a straight face) that early organisms (devoid of any complex mechanisms we know today are required for many complex operations) just happened to be able to differentiate between a meal and an ally.

    THATis what isso extremely improbable. Not impossible mind you. But EXTREMELY improbable.

    The fact that it did happen does NOT support neutral evolution. It says nature, as the author of Man's intelligence and design capability is also intelligent and designs stuff.

    Its amazing the painful contortions evolutionists in this 21st century will endure to avoid conceding the most straight forward logic, evidence, and observations in order to avoid their dreaded slippery slope scenario.

    Endosymbiosis is clearly a designed object that defies probable (or even plausible) evolutionary explanation.

    And its only one of many such designed objects evolutionists are required to steal (i mean co-opt) to give evolution a veneer of respectability.



    ReplyDelete
    Replies
    1. Let's see if I understand your argument. For any irreducibly complex system you admit that there are possible ways they could have evolved by purely natural processes. However, you claim that those possible explanations are very improbable. You claim that there's a much more likely explanation based on the actions of a supernatual being.

      But no one is interested in the mere possibility of a god or gods that build irreducibly complex systems from time to time. We want to know if that's plausible or probable. Show me your calculations.

      Delete
    2. Steve :
      There are such things as predatory prokaryotes - Bdellovibrio penetrates other bacteria and replicates in the periplasm; Daptobacter penetrates into the cytoplasm and replicates there. So you blubbering 'ENDOSYMBIOSIS BE TOO IMPROBABLE/ IMPOSSIBLE !!!' only makes you look really, really ridiculous.

      And the fact that it would not be a matter of one cell 'deciding' not to digest another (since bacteria don't do phagocytosis), but of the invaders backing off just a little so the 'host' cell survives.

      That and the fact that archaebacteria and eubacteria are equally 'simple'.

      And some bacteria can replicate once every hour (so 2 billion years to 'get used to existing' is utterly silly).

      And both lineages had been able to utilize organics ever since they left the hydrothermal vents (no need to suddenly 'learn' how to).

      But most of you IDiots seem to 'think' that your personal incredulity is of any relevance. And reliance on the False Dichotomy demonstrates arrogance in excess of your ignorance - it is essentially 'since ** I ** can't/won't accept reality-based explanations, the only explanation is 'The Magic Man DIDIT !!'.

      You want people to reject evolution because you feel it does not provide enough detail to please you - and then blindly accept an 'alternative' that not only provides not detail whatsoever, but is unwilling and unable to ever do so.

      "The Magic Man/'Intelligent Designer DIDIT !!!!!!!!11!1!!1!!" is not an explanation - it is a meaningless noise squeezed from the bowels of bewildered IDiots and creationuts every time they encounter anything beyond their willfully limited comprehension.

      Delete
    3. Nice post, but let me point out one thing:

      If endosymbiosis was very prevalent in prokaryotes, in particular endosymbiosis between an archaeal host and bacterial endosymbiont, we would have a bit of a problem, because then we would have to explain why eukaryogenesis happened as far as we know only once (we can speculate all we want about extinct, invisible in the fossil records, lineages, but that's not very useful). Even chloroplasts don't seem so unique as we once thought given Paulinella.

      It is almost fortunate that there are no such known examples...

      Delete
    4. @Steve
      Allow me to demonstrate that you are a hypocrite: You write: "NO one is interested in the mere possibility of evolution but rather its plausibility and probability."

      This principle requires consistent application for all competing explanatory models. What is the plausibility and probability of design? Show your math.

      Given that no such math will be forthcoming from you, I have now demonstrated that you are a hypocrite. You have a hypocritical double-standard with respect to evidence and explanations. While you demand detailed mathematical treatments of the probabilities for evolutionary models, you believe in design on the mere claim.

      Hypocite. All IDcreationists are hypocrites. You all have double standards with respect to evidence. You don't consistently apply your criterion for belief to yourself and the beliefs you already hold. Design gets a pass every time, there are no probability statements, no why or how or where or when, not even an attempt to speculate on these matters or anything. But at the same time you demand ludicrously detailed explanations, complete with probabilistic treatments for the world-histories of every fucking atom involved in the construction of complex traits.

      I will not be proven wrong.

      Delete
    5. @Larry Moran
      "You claim that there's a much more likely explanation based on the actions of a supernatual being."

      Exactly. This is the quintessetial failure of all IDcreationist arguments against evolution. They blather and whine about chance and probability, but offer none themselves. When you dimiss one option because it is "improbable" in favor of another, you have to actually have an idea how probable that alternative is. That means you need at leat two numbers to compare.

      So where's the math on design? What is the probability that a designer will design a flagellum?

      If they can't even supply a number then the option is simply not even on the table.

      Delete
    6. Prof. Moran,

      Well no, I did not admit that there were possible ways organisms could have evolved naturally.

      What I said was that it is clear nature designed the organisms. How could it be otherwise? Humans are products of nature. Nature is the author of our ability to dream up and make stuff.

      To be clear, to say that yes Man clearly designs and makes stuff BUT nature does and cannot design and make stuff is clearly the irrational, illogical position that in fact defies the results of empirical investigation.

      When one investigates nature we find the same design concepts in the genome as we find in human designs. Humans can take a small combustion engine used for lawnmowers and convert to use in a go-cart.
      Nature has and does the same. It reuses designed objects in a myriad of ways.

      Nature is the one that discovered design before we did. Nature is the source of design. Evolutionists just dont want to characterise nature as possessing intelligence in general because its a slippery slope to conceding a disembodied intelligence OUT THERE.

      But to be rational, logical, honest in doing science we must admit that in fact nature does possess intelligence in general as well as in particular (Man). How nature acquired its intelligence is an open question. Neither evolution nor ID can as yet answer this question. So it makes no sense to assert either of these competing ideas solve this particular enigma.

      What we must do however, is admit nature does in fact design. And then go on about the business of asking "how did nature design endosymbiosis? Did nature use quantum effects to control molecular behavior. Did nature use an electrical templates (as we now know is used to design frog faces) as the control mechanism.

      There are plenty, plenty of scientific questions we can ask about nature's design tools. We just need to take the leap and ask again "How did nature design ATP"? How did nature design the flagellum? How does nature reuse already designed objects in other applications? How does nature circumvent the 2nd law to keep organisms from degrading faster that they can replicate? How does nature use mutations to quickly modify organisms' genomes to deal with environmental changes?

      Remember, evolution is not an entity that does stuff. Yet, all evolutionists talk about evoluton as if it in fact we an entity. Why? Because for all intents and purposes, the stuff in nature looks and acts like an entity is at work. Regarless if one want to call it God, or call it something else, we do know that SOMETHING is at work doing stuff.

      It is pointless to deny that nature is doing stuff...purposefully, intelligently.

      That is the (sensible, rational, logical, honest) argument I am making.



      Delete
    7. Steve,

      what is Nature ? Nature is the natural stuff things are made of. Its the physical thing. The question is, how does matter, how do natural things organize into complex biological systems ? There are basically just two answers : Either non intelligent mechanisms were involved, or , in the contrary, intelligent mechanisms caused dead matter to become alive.

      Delete
    8. There you go, no number forthcoming. Steve proven to be a hypocrite with a double standard.

      Delete
    9. BUT nature does and cannot design

      Ever been to the Grand Canyon?

      Delete
    10. NO one is interested in the mere possibility of evolution but rather its plausibility and probability. So let clear that out first.

      To the contrary, Behe's argument (if you understood it, which from your statement above you clearly don't) absolutely depends on there being not even the mere possibility that a given feature of life could have evolved - no possibility whatever. As soon as there is the slightest possibility, Behe's "proof" of design utterly collapses.

      Delete
    11. Steve, Good to have a thorough explanation of your position.

      By the way, no matter what approach you try, you won't find an answer to "How does nature circumvent the 2nd law to keep organisms from degrading faster that they can replicate?" because organisms don't violate the 2nd law of thermodynamics. That law applies to closed systems. The earth is not a closed system with regards to energy. Every day, it is bathed in huge amounts of energy from the sun. Living things grab some of it and use that to maintain their complexity and functions, their lives. Then they release it. Meanwhile, the sun increases in entropy. With regards to energy, living things are like waterwheels, doing their own work without violating the basic downhill movement of the water (or energy). The whole sun/earth/organisms system complies with the second law, as indeed it must.

      If you doubt this, stop partaking of the sun's energy (as trapped in food) and I'm sure you will degrade faster than you can replicate.

      Delete
    12. One of my pet peeves.

      The 2LoT applies to all identifiable systems (albeit perhaps not when the system is larger than a galaxy cluster). Yes the Earth is an open system and the energy crossing the boundary must be considered. But the second law in an appropriate formulation applies to the Earth.

      Delete
    13. IDiots don't understand thermodynamics. They think the 2LoT means a dismantled fishing reel can't re-assemble spontaneously:

      http://www.uncommondescent.com/molecular-animations/piotr-and-ks-dna_jock-vs-et-al-and-compensation-arguments-vs-the-energy-audit-police/

      Delete
    14. Of course the 2nd law of thermodynamics applies to earth (in the earth/sun system). My problem is with creationists who think that the 2nd law prohibits life from evolving. (It doesn't.)

      Delete
    15. "IDiots don't understand thermodynamics. They think the 2LoT means a dismantled fishing reel can't re-assemble spontaneously"

      Looks like professor of misspelling needs some correction.

      It looks like his google searched came up incorrect.

      There is a difference between thermos and dynamite and thermodynamics.

      Everyone can tell how layman can make this kind of a mistake.

      Next time you try to pretend that you know something, make sure you enter the correct spelling in google.

      Delete
    16. liesforthedevil,

      If what you wrote above is an attempt at wit, it's too lame to show any rhyme or reason. I suppose our host will delete your comment soon, so I'm not going to waste more space responding to you. I have no idea what you would like to correct in my two sentences, but if you like proofreading, begin with your own broken English.

      Delete
    17. Elshamah777,

      As I mentioned it makes no difference how nature acquired its intelligence and design capabilities. It makes no difference to scientific research if nature recieved its ability from the Abrahamic God or some other source. What does make a difference are scientists acknowledging the reality that nature does in fact possess intelligence and design capabilities and to do scientific research according to this rational, logical, reasonable assumption. It is only by recognizing design in nature will be be able to investigate just what tools nature is using to control molecules.

      It is the idea that molecules are not controlled by an intelligence but are shuffled around based on physics and chemistry is what is hampering any new potential revolutionary discoveries. The majority of the current crop of biologists are so wedded to this materialistic philosophical disposition simply out of an irrational fear of intelligence in nature.

      We need to change that.


      Elshamah777: "what is Nature ? Nature is the natural stuff things are made of. Its the physical thing. The question is, how does matter, how do natural things organize into complex biological systems ? There are basically just two answers : Either non intelligent mechanisms were involved, or , in the contrary, intelligent mechanisms caused dead matter to become alive."

      Delete
    18. Steve,

      "It is the idea that molecules are not controlled by an intelligence but are shuffled around based on physics and chemistry is what is hampering any new potential revolutionary discoveries."

      All you have to do. Steve, is provide some empirical evidence to support your claim that molecules are controlled by some intelligence. I would start by defining what you mean by control and how you know that control is intelligent.

      Delete
    19. The earth is not part of an open system. This notion seems merely an attempt to make an end run around reality.

      If the earth was part of an open system, if would be able to get energy from different sources at different times. That would constitute open (verses controlled, regulated). Yet, we clearly observe that the earth is actually part of a regular pattern of astronomical activity we call the solar system.

      It is the 2nd law that causes all individual organisms to die off. But life continues on precisely because it has a mechanism to renew itself just in time before the 2nd law does its ultimate damage.

      Without replication the first organisms would have not lasted long, eventually disintegrating due to the 2nd law of Thermodynamics. We know this because we can see all the mechanisms that life uses in order to keep the effects of entropy from destroying the organism. But it eventually loses the battle. That is what we call death. Yet, life goes on because...

      Life replicates.

      So you have to think back to early life, when the 1st cell just happened (according to materialistic evolutionary logic) to acquire a lipid sheath for it's set of components that had been mingles together due (supposely) to simple physics and chemistry.

      But what now? The environment is pressing hard. The entropic scythe is bearing down on that gregarious set of amino acids and hangers-on.

      So how did this congregation stay glued while it figured out just how to replicate itself? It is irrational to assume that first life JUST happened to figure out a way sans intelligence to deal with the entropic reaper.

      Hence, replication is a designed object (not a mundane property of matter).

      Delete
    20. Steve, you propose your own private definition of an open system and your own private concept of entropy different from that used by physicists. What you mistakenly call "the 2nd law" is in fact something completely different -- the Creationist Law of Thermodynamics (CLOT), for which there is no physical justification in this universe. Since you could easily find a sympathetic audience for your ideas among the gullible ignoramuses who populate Uncommon Descent and other similar forums, I don't understand what makes you preach them here, where your Dunning–Krugeresque hubris is obvious to most people.

      Delete
    21. I believe we have found Byers' equal.

      Re: Steve's last post. Oh my, what an epic monument to creationist ignorance when it comes to understanding basic science.

      I wanted to copy and paste one of his ridiculous statements, but there was one in every paragraph, and how could I pick just one?

      Okay just one: Without replication the first organisms would have not lasted long, eventually disintegrating due to the 2nd law of Thermodynamics.

      Sigh. Reading Steve is like watching an eager 7 year old advise a NASA engineer about the "bestest" rocket design.

      Delete
    22. One might expect that after being corrected about the 2nd law of thermodynamics, Steve would think, "I'll check that, if only to prove you wrong." It's not that hard to check, though it would require reading outside the creationist literature. Then if he didn't want to admit he was wrong, he could just be quiet about this small part of his . . . "theory." But no. He doubles down.

      Of course, if he's wrong about the 2nd law (he is), maybe he'd be wrong about other things! Can't let doubt into that house of cards.

      Delete
    23. Steve - the Second Law giveth and the Second Law taketh away. It foldeth thy proteins. It generateth thine ATP. It bindeth thy promoters and repressors. It enableth thy tomatoes to grow. It's not all about 'disorder'.

      Delete
    24. So you have to think back to early life, when the 1st cell just happened (according to materialistic evolutionary logic)...
      But what now? The environment is pressing hard. The entropic scythe is bearing down on that gregarious set of amino acids and hangers-on.


      Hey, maybe thats why I feel stressed out every day, its the entropic scythe!

      But this is so typical of creationists. Whether by magical god-means or by a miscontrued natural process, complex things poof into existence, and like rats in a burning silo, must suddenly scramble to figure out a way to survive and persist.

      Take bwilson's advice Steve. Persist in your denial if you wish, but avoid rationalization of your beliefs, as it does not improve your position.

      Delete
    25. Steve knows less about thermo than most IDiots.

      Different disciplines use slightly different definitions of open systems, but as an ME I know it as any system in which some relevant thing may cross the boundary. It is the opposite of closed, and doesn't even require that something *does* cross the boundary.

      Delete
  9. I think I can confidently say that I'm not terribly surprised by this, though I haven't previously heard of it.

    As I learn more, I've become a huge fan of the idea that evolution isn't even close to survival of the fittest, but survival of the lucky and mostly adequate. Combine that with genetic drift and this becomes almost a given.

    Though, I do still tend to agree with Dawkins that most external physical characteristics, in many species, still tend to be selected rather than drift. But internal morphology or biochemical, not selected at all.

    I almost didn't mention this, but I find it laughable that people still demand we take Michael Behe seriously. "You MUST refute his points." Why? He's an idiot who happens to have tenure and once every 10-12 years or so manages to get a paper published. Big deal.

    ReplyDelete
    Replies
    1. 1) Why do you care?
      2) Why does it matter?

      Are you trying to say that I am not an authority or that my opinion doesn't matter because you think I'm not a published scientist?

      Is what you are saying is you think that Behe is correct because he has a Ph.D., but the thousands of scientists who also have a Ph.D. are wrong because they disagree with him?

      Or are you saying that no one who is not a professor can ever begin to understand a complex topic like evolution? In which case, what are you whining about, you can't understand it either?

      In ANY of those case, you're being illogical by attempting to attack the person instead of the argument. I have a firm basis for my opinions on Behe and Meyer (the liar) and evolution, which I have studied for some time and I've posted those thoughts and explanations on my blog... with references.

      Delete
    2. Beau seems to think that you are saying that Behe should be disregarded solely because he publishes infrequently. Beau does not understand that Behe's ideas fail on their own lack of merit, and that the fact that Behe occasionally manages to get an article published does not mitigate this. The IDiots, OTOH, try to leverage that meager publication history and Behe's tenured position to give Behe's claims more credit than they deserve. They do this because they know there are lots of people like Beau around, who are unable to critically appraise the scientific evidence and so need a preacher or someone like that to tell them what to believe.

      Delete
    3. Lute, you're right i cannot critically appraise anything in science. I can spot irony from a mile away. The intelligence by association syndrome is running deep on this thread.

      Delete
    4. The "intelligence by association syndrome"? What is that, Beau? Does it have anything to do with thinking you can refute a person's claim merely by asking how many scientific publications he has?

      Delete
    5. Suppose he has got a good publication record; what then? Will Beau eat his words and declare Behe defeated and his pseudoscience debunked?

      Delete

    6. Yes it does. Why aren't you asking the man who doubts Behe the same question? It's insane, you guys are truly blinded by your worldview. I've given this blog a lot of time and I've come to the realization many of you are as nuts as Ken Ham. I won't comment here anymore. Good bye, God bless and good luck.

      Delete
    7. Why aren't you asking the man who doubts Behe the same question?

      Because he's a long-term poster with his own blog, and we know him well enough to be pretty certain that he doesn't base his doubts about Behe's credibility on the mere fact of Behe's spotty publication record. Even I, who read more than I comment, know who he is. Having a history at a place generally earns you a certain amount of leeway to make comments without people assuming it's Your Entire Word on the Subject.

      Delete
    8. "Why aren't you asking the man who doubts Behe the same question? "

      Because he didn't use Behe's publication record as his main point for not taking him seriously, rather it was more like a final footnote to a larger post. He's also made two, but you have responded to nothing in his 2nd post.

      Delete
    9. The answer is even simpler, Mikkel. I didn't ask OgreMkV about the "intelligence by association syndrome" because he mentioned nothing about it. Beau has difficulty understanding why I would ask him to clarify a term that he (Beau) used himself, and thinks it unfair that I did not ask some other guy who did not use that term.

      It's too bad Beau is leaving us. He really needs help learning how to think, and there are lots of folks here who could have helped with that. Plus, now I'll never learn what the "intelligence by association syndrome" is. :- (

      Delete
  10. Irreducible complexity has not been disproven as a great criticism of evolution.
    You just introduce, even new, a hypothesis on how to get around IC.
    IfIC is such a good point NEEDING this new hypothesis then its always been a good point and a scientific point. Evolutionists denied both. Now DR Moran mentions some evo biologists and other scientists also need to correct themselves.
    What if they say no? They don't agree? Is this a paradigm shift?

    ID thinkers need to get into the claim this makes IC wrong and so on.
    However it does mean IC is right IF historic ideas of selection on mutations was the evolutionary mechanism promoted. I think this is being said here.

    The word probably was used a lot in the explanation.
    Having a answer for complexity evolving without selection needs and so there it is when needed means the IC argument must have hit a nerve.
    Before telling iD thinkers give up IC you mUST tell evolutionists give up evolving complexity based on selection for adaptive need.
    This would be a notable surrender.
    Otherwise ID can fight those guys and later come around to this new idea.

    ReplyDelete
    Replies
    1. IC is so current that Disney are working on a musical called Behe Poppins, check this out:

      It's...

      Super-Irreducible-Complexialidocious
      Turns out they proved it's unscientific and atrocious
      Had to move the goalpost, damn, these evos are ferocious!
      Super-Irreducible-Complexialidocious

      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!

      Even though it's still an argument from ignorance
      I know you will buy it, fellow Christian sycophants.
      And if I never publish anything that's peer-reviewed
      Well I don't care, I'll be OK, I'm in the DISCOtute!

      Super-Irreducible-Complexialidocious
      Insisting it's creationism is just plain obnoxious
      Home-schooled Cdesign proponentsists are so precocious!
      Super-Irreducible-Complexialidocious

      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!

      I've travelled all around the south and everywhere I went
      I'd use my word and "git er done y'all!" is all they would yell,
      But when I come across one of those god damn darwinists
      I can hear them giggling, taking the piss out of me

      Super-Irreducible-Complexialidocious
      Even Jeebus Christ would think it's something quite atrocious
      But with a crowd that's dumb enough I always sound precocious!
      Super-Irreducible-Complexialidocious

      Dumb diddle diddle diddle I'm Dumb, diddle ay!
      Dumb diddle diddle diddle I'm Dumb, diddle ay!

      You know you couldn't have it more backwards, right Behe?
      Well there's this other thingy a friend came up with,
      but he might have gone full retard, don't you think?

      Just when I thought there's no way someone's dumber in this nation
      Billy Dumbski shows up rambling about "information"
      Can't these fucking IDiots test something in a lab?

      For example,
      Yes?
      One night I paired me crock with me duck...
      But still there ain't no 747 in me junkyard!
      Oh! and a lovely thing I ain't no monkey!

      It's....

      Now-it's-Specific-and-Complexialidocious
      Super-Specific-and-Complexialidocious
      Still-it's-Irreducible-Complexialidocious
      Mostly-Specific-and-Complexialidocious!

      Delete
    2. Byers:"Irreducible complexity has not been disproven as a great criticism of evolution.
      You just introduce, even new, a hypothesis on how to get around IC."


      One immediate problem with your claim is that IC was predicted to occur as a result of evolution in 1918, long before creationists like Behe had thought of claiming it disproved evolution.

      Muller (1918, pp 463-464): "Each new mutant in turn must have derived its survival value from the effect which it produced upon the “reaction system” that had been brought into being by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former."

      Delete
    3. Creationists even have the audacity of claiming that co-option is an ad-hoc, made up argument to counter Behe's IC.
      Obviously they never read "On the Origin of Species"

      https://books.google.es/books?id=q3swUdXxFvMC&pg=PA165&dq=%22We+should+be+extremely+cautious+in+concluding%22&hl=en&sa=X&ved=0CCEQ6AEwAGoVChMIlL6d28nkxwIVyG0UCh2sVwOl#v=onepage&q=%22We%20should%20be%20extremely%20cautious%20in%20concluding%22&f=false

      But it's even more astonishing that they believe that IC is actually an original idea and somehow caught scientists off guard, when actuallt it's the same stupid rehash of paley's watchmaker that they've been recycling for ages

      Delete
    4. Paul Mcbride
      ID IC is a great idea and yes some forward evolutionist realized this was a problem way back in the day.
      So the hypothesis of existing parts being ready for a great complex operation is easily suggested. Its guessing.
      Its unlikely that parts were johnny on the spot even as a option.
      The glory of IC is that reducing the parts to original form and then seeing them evolve in cohesion for complexity is a freat criticism.

      you admit this, as does this thread, by invoking old evolutionists also seeing its important.
      So iD critics on this were right all along in this powerful point EVEN if new hypothesis arrive to deal with it.
      Your side did say IC was not a credible criticism and the authors not credible.
      Sure they were and thoughtful evolutionists realize it needs a hood and great answer.
      Not silly dismissal as will be noted in history books.
      Lets move on and up.
      Give Behe and company full credit. They push their trench forward.

      Delete
    5. Give Behe and company full credit. They push their trench forward

      Full credit for what? For being completely ignorant of the literature? For convincing a bunch of sycophants that IC is relevant in any way when it's not, never was and never will be?

      Delete
    6. Robert, please consider proofing your stream of consciousness. I have very little idea what you mean in your response, other than some patently false take-home message that IC is a problem for evolutionary theory, and that ID deserves all the credit for this.

      Delete
    7. OM
      Its an equation.
      Dr Moran said this new idea was a reply to beat IC. SO I say that means iC needs to be beat. Because its a good idea . YET evolutionists always said it was not a good idea.
      SO I think Behe and company proved they were right about IC as a good criticism aside from whether it was true.
      It is true but thats aside of the bigger point here.
      There should be a general apology or retraction if IC needs AFTER ALL to be refuted and by new ideas. So new evolutionists and other scientists need to correct themselves.

      Delete
  11. I am not a scientist, just one of those stubborn types that insist on the Who, How and When of Intelligent Design.

    I find ID very difficult to understand as anything more than an argument from incredulity, religious faith et cetera.

    Looking at the evidence from geology, paleontology, genetics and probably some more I may not be aware of, the history of life on the planet seems quite well researched and made known in so many ways, unless one just brushes everything off with a strong GODDIT to settle the case. Although that raises too many questions to make any sense from a realistic point of view.

    There is much too much religion attached to claims of ID that makes it inedible to rational people. I miss durable (not to mention testable) justification for claims of ID.

    ReplyDelete
    Replies
    1. YEC embraces iD in SOME Mutual conclusion and cooperation .
      You don't need to be a scientist to understand these things. Whats a scientist?
      Just apply your thinking to the subjects in origins that you like. You can keep up and on these blogs its easier because the boss and others are important teachers. Teachers make it better then others even if others understand the concepts.
      This is a intellectual discussion and religion is not involved . Save in some presumptions.
      NOPE> its down and dirty on the merits of evidence and reasoning from that evidence.
      Remember this is about past and gone processes and results/mostly.
      Its not as easy as physics or biology etc. Which are present results and processes and more easily studied and tested.
      All people are rational. Its just old fashinoed ideas to say people are irrational if they don't agree with you.

      Delete
  12. Robert, how can you be both a YEC and an ID proponent(sist) at the same time?
    Anything goes as long as it is anti science?

    ReplyDelete
    Replies
    1. The tent of ID creationism spreads wide. They rarely, if ever, outright renounce YEC's or other such loons. It's strange, because you'd think the correct age of the universe would be an important question to settle if they wish to investigate the methods by which the "Intelligent Designer" created all life forms.

      The fact that a YEC's money is as good as anyone else's may have something to do with it.

      Delete
    2. lutesuite, I think it's more of a "The enemy of my enemy is my friend" thing, though of course any money involved wouldn't hurt, either.

      Delete
  13. "It's important to understand this concept because it challenges the idea that the evolution of complexity is adaptive and it sets the stage for challenging the idea that all adaptive structures arose exclusively by natural selection."

    Sound like frontloading, like creationism....

    Evolutionism and creationism come together in CNE!



    ReplyDelete
    Replies
    1. "Sound like frontloading, like creationism"

      No, it does not.

      Delete
    2. Sound like frontloading, like creationism....

      Only to the volitionally uninformed. :-)

      Delete
  14. It also helps us understand why the core idea behind irreducible complexity has been refuted. // LOL.... no kidding. The spliceosome is a PRIME EXAMPLE of irreducible complexity and interdependence of the software with the hardware. What emerged first, the Spliceosome, or the epigenetic information to insctruct the small nuclear RNA's where to splice the pre mRNA ??!!

    ReplyDelete
    Replies
    1. You can only say that if you have no understanding of how the spliceosome most likely evolved.

      What came first were group II introns

      Delete
    2. how do you know, and why ? what good are exons and introns for, if the machinery for splicing is not in place?

      Delete
    3. Why do introns have to be good for anything? Did you read the OP? It's about constructive neutral evolution...

      Is it even possible to fail more miserably at getting the point?

      Introns preceded the spliceosome, because they were originally self-splicing. Then with time some of them started losing the ability to self-splice so cells had to rely on trans-activities to excise them. And the spliceosome gradually evolved. Then once there was a spliceosome there was no need for any introns to be self-splicing so they all became spliceosomal. BTW, self-splicing introns still exist so we did not make this up just to save face, and not only that, but their structure is very similar to the structure that the snRNA components of the spliceosome adopt. Food for thought...

      Delete
    4. Introns preceded the spliceosome, because they were originally self-splicing.// so how did they emerge with that feat ? where did the information come from in order for them to be able to do so ? please show evidence for these " constructive neutral evolution " what ever is meant with that, and that introns and exons could arise through it.

      Delete
    5. And the spliceosome gradually evolved. // please provide evidence that this is not another just so claim . As usual.....

      Delete
    6. ElShamah777,

      Out of curiosity, what is your alternative for how the spliceosome came to be?

      Delete
    7. Chris B,

      That a fallacy of no alternative.

      But I am game. Nature designed the splicosome just as it designed humans.

      That's how. We do not know yet HOW nature designed the splicosome. But we can surely investigate it? We can look at quantum mechanics or electrical activity to get a glimpse of how nature can control molecules, give molecules memory and instructions, etc etc etc.

      Intelligent design far from impeding science can provide lots and lots of good questions for scientific study.

      We just need those that control the grant money to get on (logical, rational) board with the freedom to ask "How did nature design the splicosome?.

      Delete
    8. Steve (and ElShamah777),

      "That a fallacy of no alternative. "

      No, it's not a fallacy. It's a simple, logical question. Except you (and ElShamah777) have no answer. Your "intelligent design" alternative is a fairy tale for which you have ZERO evidence. That is all. ID/creationism is a science stopper. It says 'godidit' and nothing more. it offers no rational alternative. Never once have ID/creationist believers ever offered a scientifically testable hypothesis for their absurd claims. Far from providing 'lots of good questions' you only misrepresent and dishonestly attack evolutionary theory. ID/creationism has never presented a scientifically testable alternative. Be the first, Steve. Tell us how it happened, and what your evidence is for it.

      Delete
    9. Okay you IDiot-creationists, let's say, for the sake of discussion, that spliceosomes were/are 'intelligently designed'. Now, let's see you thumpers explain, scientifically and in detail, how, when, where, and why they were/are intelligently designed. Let's see you thumpers explain, scientifically and in detail, how, when, where, and why they were/are created, assembled, distributed, and guided. Let's see you thumpers explain, scientifically and in detail, who intelligently designed/designs, created/creates, assembled/assembles, distributed/distributes, and guided/guides them.

      Let's see you thumpers explain, scientifically and in detail, how, when, where, and why your chosen intelligent-designer-creator-assembler-distributor-guider (i.e. god) came into existence. Let's see you thumpers explain, scientifically and in detail, how and why you chose a particular intelligent-designer-creator-assembler-distributor-guider (i.e. god). Let's see you thumpers support your responses with plenty of scientific, detailed evidence. And last but not least, let's see you explain, in detail, exactly how the acceptance of 'intelligent design' (i.e. your religious beliefs) by all scientists would improve any or all of science.

      And don't spew your usual evasions, distortions, demands, vague assertions, goal post moves, just so stories, sermons, and your usual attacks on evolutionary theory, evolutionists, Darwin, science, scientists, atheists, materialists, or anyone/anything else.

      Delete
    10. "so how did they emerge with that feat ? here did the information come from in order for them to be able to do so ?"

      If they couldn't self-splice to begin with, they would not have propagated at all since they'd probably have killed their hosts. So this ability was not something that had to be somehow "put into them" or had to evolve, it was there all the way from the beginning. It was simply a property they had.

      It doesn't take any special "information" to be put into them. Either the sequence of RNA is self-splicing or it is not. Any given stretch of RNA that evolves to do some new activity does so through mutations.

      Delete
    11. Steve said:

      "We just need those that control the grant money to get on (logical, rational) board with the freedom to ask "How did nature design the splicosome?."

      Scientists already have "the freedom" to ask that question and any other question, and scientists are already studying how nature 'designs' spliceosomes and other things via natural evolutionary processes and events. The thing is, there's a HUGE difference between 'intelligent design' by your imaginary sky daddy and natural evolutionary processes and events that result in things that humans may or do call a 'design'. You obviously believe that "nature" is controlled/guided by your imaginary, so-called god and you're just playing a stupid, dishonest game by using the word "nature" instead of 'God'.

      You complain that grant money isn't being spent on what you want it spent on but nothing is stopping you or anyone else from getting grant money for scientific studies IF you have the qualifications, appropriate means, and something to study that at least has a chance of being realistic, informative, and useful. There's also the fact that billions of dollars are taken in and spent by thumpers to push religious crap and some thumpers even call themselves 'creation scientists', so why don't you or some other IDiots try to get some of that money? You can't blame atheists or evolutionists or materialists or so-called "Darwinists" for holding back that money from you and other IDiot-creationists.

      And how about the discotoot? They've gotten millions of dollars from the theocrat/dominionist/IDiot Howard Ahmanson and other religious donors and they allegedly have a lab where they allegedly study intelligent design, but for some reason they never come up with evidence for intelligent design. Hmm, maybe it's because they spend most of the millions on preaching and pushing IDiot-creationist propaganda, denying evolution, bashing evolutionary theory, evolutionists, science, scientists, Darwin, so-called "Darwinists" and "Darwinism", materialists, etc., paying themselves fat salaries and perks, lobbying politicians to enact laws to force ID wedge agenda crap into schools and everything else, conning religious suckers into giving them more money, renting green screens, pushing students, parents, school boards, faculties, administrators, and others to get on the ID wedge agenda train (wreck), and doing other self-serving autocratic/theocratic garbage that will never produce ANY positive evidence of intelligent design by the imaginary yahoo-allah-yeshoo-holy-ghost-sky-daddy or any other alleged sky daddy.

      Of course if they were to spend all of their money on scientific research they still wouldn't and couldn't produce any evidence for intelligent design by the imaginary yahoo-allah-yeshoo-holy-ghost-sky-daddy or any other alleged sky daddy, and they know it. The discotooters and some other creationist cults (ICR, AIG, etc.) pretend that they're doing lots of scientific research into intelligent design or some other version of 'creation' but they all spend way more money on pushing their autocratic/theocratic agendas than on scientific research because they know that no amount of scientific research will ever verify their religious beliefs and because pushing religious propaganda, conning suckers, denying evolution, bashing evolutionary theory, etc., is very profitable.

      Oh, I almost forgot. Someone correct me if I'm wrong but didn't the Templeton foundation offer grant money to anyone who could propose and/or do credible research into ID (or something like that) but no one even applied for the grant money?

      Delete
    12. We can look at quantum mechanics or electrical activity to get a glimpse of how nature can control molecules, give molecules memory and instructions

      Holy moly.

      Please show the quantum mechanical equations whereby "nature...give[s] molecules memory and instructions."

      Delete
    13. "Quantum mechanics of electrical activity..."

      Alan Sokal, is that you?

      Delete
    14. And how about the discotoot? They've gotten millions of dollars from the theocrat/dominionist/IDiot Howard Ahmanson and other religious donors and they allegedly have a lab where they allegedly study intelligent design, but for some reason they never come up with evidence for intelligent design.

      Ahmanson could only afford a stock photo lab, so that's where they do their stock photo research. When they make a stock photo discovery, they'll publish it in a green-screen journal.

      Delete
  15. Am I right, evolutionists agree, that having a answer for IC, and a important one with legs, means IC was a great criticism all along and it took ID thinkers to insist on it.??
    Or are evolutionists saying IC was always accepted as a good criticism but there was good answers right back?
    It seems to me IC was dismissed and its authors?
    Anyone know the history and status of this criticism??

    ReplyDelete
    Replies
    1. Robert Byers, I don't know the history, but the current status is that what looks like "irreducible complexity" now can evolve. The topic is interesting and leads to new thoughts, but it's not a problem for evolution.

      Delete
    2. We already told you IC is nothing more than a rehash of Paley's watchmaker teleological crap, and that it was debunked even before it was out.
      But the bar is set so low for creatards that anything will fly, as long as it sounds sciency, you perceive it as groundbreaking

      Delete
    3. ALL the cell is irreducible complex. You can't reduce a protein upon a certain threshold, where it cannot exercise its function anymore. Every protein has a minimum size . Heck, even DNA is irreducible complex. Unless all 3 individual parts and the bonds are present, nothing goes. And DNA cannot be the result of evolution. It takes proteins to make proteins. It takes proteins to make membranes. But no membranes, and you cannot keep the machinery to make proteins protected in a enclosed place. Why is that not obvious to proponents of naturalism ?

      Delete
    4. ALL the cell is irreducible complex.

      Then how are you alive?

      For a few thousand dolalrs, we can sequence your genome and that of your parents. You will see a few dozens of a mutations have happened in their germlines on their way of becoming you.

      For a somewhat some larger sum we can also sequence the genomes of a few hundred of your somatic cells. And we will see that each has suffered some mutations on its own too.

      So if "all of the cell is irreducibly" complex, how can it function with even a single mutation?

      Delete
    5. " Why is that not obvious to proponents of naturalism ?"

      Maybe because every attempt at invoking IC (eye, flagellum, blood clotting) and ultimately goddidit has failed? Check this very detailed description how blood clotting works out fine, even with one or more bits missing in the cascade.

      How can it be El?

      There's a really good quote in the post I linked above:
      "This is exactly the problem with ID/creationism – invoking God into gaps in knowledge is pretty troublesome, but creationists do something even worse. They insert God into gaps in their own knowledge, assuming, usually without even a vaguely serious attempt at a literature search (!!!), that whatever tidbits of biology they happen to have picked up represent the sum total of scientific knowledge on a topic. This is, I think, why they so often stay ignorant, even when, as Luskin did, they have had the whole thing explained to them before."

      'nuff said.

      Delete
    6. "You can't reduce a protein upon a certain threshold, where it cannot exercise its function anymore."
      So for the protein to evolve, if you mutate it enough it either does something else, or emerged by chance from already existing DNA regions that happened to transcribe and translate into a functional polypeptide.

      "Every protein has a minimum size"
      Glycine is a catalyst for the polymerization of amino acids. The dipeptide of glycine is even better.

      "Heck, even DNA is irreducible complex. Unless all 3 individual parts and the bonds are present, nothing goes."
      DNA is biochemically synthesized from RNA precursors. Curious fact.

      "And DNA cannot be the result of evolution."
      Prove it.

      "It takes proteins to make proteins."
      Rather, proteins are involved in how proteins are made in cells. That doesn't mean it absolutely requires proteins to already exist for the first proteins to evolve.

      The way things are now does not prove they must have always been so. This is the same stupid mistake you keep making.

      "It takes proteins to make membranes. But no membranes, and you cannot keep the machinery to make proteins protected in a enclosed place."
      So maybe they weren't enclosed in lipid membranes to begin with, maybe they were enclosed in mineral compartments of some sort? We don't know, but that doesn't mean we can't find out or that there is no way it will work without membranes.

      You simply cannot make that inference, it is plainly fallacious. It does not follow from "it works like this now" that "therefore it must have always been so and there is no other way it could have worked". It doesn't follow.

      Delete
    7. "For a few thousand dolalrs, we can sequence your genome and that of your parents. You will see a few dozens of a mutations have happened in their germlines on their way of becoming you. "

      No, this is just non-sense. Due to repetitive elements this cannot be done for a few thausand dollers. DNAseq is extremely biased towards exons. The non-protein coding part is almost entire unaccessable with such techniques.

      Fact of the matter is that this part is the most plastic part of the genome, and we will find the major variaties here (as demonstrated by ENCODE and the 1000G projects).

      Nobody seems to realize that evolution is determined by the non-protein coding part of the genome. miRNA, lncRNA, TEs make up the major part of variation and provide the mechanisms for genetic change, adaptations, novelties, etc. It is all frontloaded.

      Delete
    8. It is all frontloaded.

      How very curious then that it does not exist in the life that came before ("in front of") us. But it exists in us. So I guess the Designer is just using us to get to whatever comes next and you've just proved we're nothing special according to frontloading theory, eh?

      Delete
  16. For some reason this reminds me of the computer scientist that designed an algorithm to allow a computer to program a chip using natural selection.

    In the end the algorithm was extremely efficient but he found it impossible to understand.

    More interestingly though, the final program did not work reliably when it was loaded onto other FPGAs of the same type implying that the algorithm had adapted the program to work with that particular chip with it's unique imperfections.

    One might remark that the chip and the program upon it are interdependent and necessarily rely upon each other to produce the desired result. An outsider looking at the system might say it is irreducibly complex since the chip's flaws appear to be designed to work with that program and the program won't work with any other chip.

    Yet here we have a system of interdependent parts that arose through natural selection without design or outside interference.

    ReplyDelete
    Replies
    1. I remember reading about that and it was fascinating. Does anyone know if it implemented some sort of drift mechanism too?
      I wonder if they run it several times, and if it would yield the same result, a similar one or entirely different solution

      Delete
    2. The genetic simulation would almost certainly have a finite number of individuals in the population. Genetic drift would thus be fully present. Births, deaths, mutations, and genetic segregation events would be simulated using draws from a random number generator.

      A re-run using a different sequence of random numbers would have the potential to arrive at a different result. Whether the result would be substantially different is not easy to say without doing the experiment.

      Delete
    3. Thanks Dr. Fesenstein. Just asked because I also remember a post here by Prof. Moran about evolutionary algorithms, and how those were more like adaptationist algorithms because they didn't implement neutral fixations.
      Keep in mind that I'm no biologist so I apologize in advance if I got it wrong and that doesn't make sense.

      Delete
    4. I wondered if Aceofspade's comment were true, and if so, if I could learn more about it. (As a biologist, I wouldn't be able to describe something like this fully from memory.) So I ran it by my brother, a computer chip designer. His response:

      I would say this is kind of a stretch, . . . . [Something like this] involves knowing a lot about the chip (an FPGA) to start with and having some simple desired result and the ability to try/modify things until one gets there or gets toward there. But -- there are so many issues with this that I'm inclined to almost opt for, *This isn't even wrong.* . . . .

      This comment refers only to the computer chip design issue, not to computer simulations of population genetics.

      Delete
    5. I don't think you can make a general statement about whether GAs implement neutral drift. I know I made a toy GA along the lines of WEASEL, but without a specific target. It drifts indefinitely, and makes words while doing so. It is a very simple program, so I would assume that more sophisticated programs would also allow drift.

      Without drift, you quickly get stuck in a local optimum.

      Delete
    6. At any rate, maybe what was most remarkable was that the final result was, as noted by Aceofspades, an intricate mess of of logical gates, nothing anyone would ever design, but the result was super efficient. That's not to say that it has any relevance with regards to evolutionary biology, no idea.

      I guess it would make more sense to tests evolutionary scenarios using Avida or the likes?

      Delete
    7. What happened in Adrian Thompson's experiment was that his evolved chip (whose task was to dicrimnate tones) was able to exploit the physics of its substrate in a way so crazy that no human designer would even have considered. Unconnected logic cells somehow interacted, presumably via some subtle magnetic flux effects, and this "irreducibly complex" interaction was necessary for the circuit to work.

      Delete
    8. Cool. Glad you were able to find out more about it.

      Delete
    9. Here's Thompson's own description of the experiment:

      http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.50.9691&rep=rep1&type=pdf

      Delete
    10. Wow! look at figures 6 & 7. You mean to tell me it also generated "junk gates"?

      Delete
    11. I see two really impressive things there:

      (1) The circuit, which had no access to a clock but needed some kind of timing device to discriminate between different frequencies, managed to evolve an internal "clock" (not that it's easy to see how it works).

      (2) The discriminator is a hybrid device despite being "in principle" digital. It makes use of the physical properties of the chip and of subtle analogue couplings between some of its parts. The ability of the GA to explore such a rich search space was really unexpected.

      Delete
    12. This should be of interest in neuroscience and in AI research. I have thought for some time that brains are largely analog. I would phrase your statement the other way round. The circuits components are digital, but the circuit is in operation, analog. It is a kind of A/D converter.

      Delete
    13. @bwilson295 I sourced my story, did you not follow the link? Which part of my comment did you think was untrue?

      Delete
    14. Aceofspades, I apologise. I missed that. I only learned about the link later. I've sent it to my chip-making brother.

      Delete
  17. bwison 295 and dazz.
    Well it has been a problem for evolution up until the new hypothesis to explain away IC.
    anyways first things first.
    IC was a criticism by iD folks and, I think, they were dismissed THAT this was not a good criticism even before there was a new hypthesis to deal with it!!
    Something funny going on here eh.
    If its important to have a careful hypothesis to explain how complexity could evole despite its segregated parts then iC was a important criticism until there was this new hypothesis.
    so it WAS a great criticism to the credit of these iD thinkers EVEN if it was wrong.
    This discredits most criticism of iD on IC.
    Second thing is I think iC still is a great criticism and this new hypothesis is no better then the old ones or the dismissal of the IC criticism.
    Am i missing something here?

    ReplyDelete
    Replies
    1. Yes, Robert Byers, you are missing something. Actually, two things. First, "constructive neutral evolution" (1999) came before "irreducible complexity" (2006). So, you are mistaken to characterize CNE as though it were some kind of reactionary attempt to "deal with" IC.

      In general, a minority of evolutionary biologists have been fighting for decades to beat back naive Darwinism and promote a more general view of evolution. CNE is an alternative to views-- including naive Darwinism and creationism-ID-- in which the ultimate explanation for an evolved feature refers to a natural purpose. Both ways of thinking are teleological, opting for the illusory elegance of "design" or "adaptation" over more messy and truthful options that involve a lot of conditions and probabilities.

      Second, the idea that CNE is "no better than" naive Darwinism is absurd. CNE is a genuine attempt to address complexity, to be contrasted with naive Darwinism, and to be considered alongside Kauffman's "The Origins of Order" or Lynch's "The Origins of Genome Complexity".

      Delete
    2. I was going to ask you if you were aware of the creationist idea of "irreducible complexity" in 1999 if you showed up in the thread, as I wasn't around at the time. My understanding was that Behe first wrote about in Darwin's Black Box, which came out in 1996.

      Delete
    3. Behe at Dover:

      Q. Now you testified yesterday that you coined the term irreducible complexity in Darwin's Black Box, which was published in 1996, is that correct?

      A. Yes.

      Q. So that book was published actually three years after Pandas was written, is that accurate?

      A. Yes, that's correct.

      Q. Is it accurate to say then that the concept of irreducible complexity was not fully developed when you had written that section in Pandas on blood clotting in 1993?

      A. Yes, that's right. I was still contemplating the idea.

      Q. Does Pandas, however, discuss the complexity of this system, the blood clotting system?

      A. Yes, it does. It elucidates all the parts of the system.

      Link

      Delete
    4. Georgia

      Behe just made up the term that stuck. I could have very well been "indispensable" or "life-indispensable" which I thought would give more meaning to an average Joe Blow. Irreducible complexity seems to me to be more of an indoor-science-term and even on this blog I find many, many people not fully understanding it.

      BTW: Georigi; how come you never commented on the subject on a cells (say prokaryotic cell) being irreducibly complex? Do you know it is scientific fact and there is nothing you can do about it? Or, you'd rather just not accept any possibilities but materialistic ones...

      Delete
    5. OK, my mistake. Based on the testimony that Piotr quotes, Behe's concept of IR was developed in the 1990s and the term "Irreducible complexity" dates to 1996. However, this does not change the fact that CNE was not in any sense a response to IR. The idea of CNE was developed in the 1990s on the 8th floor of the Sir Charles Tupper building at Dalhousie, soon after I got there in 1991. The ideas from the 1993 by Covello and Gray were already being talked about then.

      This thinking was part of the evolutionary counter-culture that for decades has been responding to the excesses of Darwinism by promoting neutral ideas. It was not a reaction to creationist challenges.

      Delete
  18. Arlin.
    Hmmm.
    This thread presented CNE as a reply to IC. A needed reply that also was to correct general evolutionists on these things.
    You say a minority were already pushing CNE> Well the majority were pushing wrong ideas that IC was correcting!
    It was the general idea things evolved and so the great ID criticism was that they can't at a reduced level in order to build a complexity that is obvious in nature.
    This CNE was new and also can be shown to be wrong.
    First things first.
    IT MUST mean ID was right about the IC concept since CNE is needed now to explain how IC does not prove evolution impossible at such levels .
    BEHE and company were right and the majority of evolutionists were wrong in not seeing or dismissing the needed explanation for how complexity at such levels can evolve.
    I don't know if CNE is a reactionary reply or independent but it was a minority.
    ID was right and evolutionists were wrong.
    In those moronic court cases also.

    ReplyDelete
    Replies
    1. IT MUST mean ID was right about the IC concept since CNE is needed now

      No, your stupidity has no limits. It's been explained to you time and again that there were proposed and observed ways to evolve IC even before Behe was born. Darwin himself discussed co-option in "On the Origin of Species".

      But it doesn't even matter!, because even if there had been no known mechanism to evolve IC, that doesn't make IC true until one is found you idiot. That's why IC is nothing more than a pathetic, useless argument from ignorance.

      Delete
  19. Claudiu, you are creating a false dilemma when you point to reductive evolution (e.g., viruses and intracellular parasites) as though it were a contradiction of CNE.

    Some people who invoke CNE believe that it is the manifestation or the realization of some kind of intrinsic tendency to complexification. If this were the case, then reductive evolution would raise a question, but would not be a contradiction. Local cooling does not contradict global warming, and limited cases of reductive evolution would not contradict an overall tendency toward complexification. This is a false dilemma.

    Furthermore, I personally never said that there is a global tendency toward complexification. From my perspective, CNE is a mode of evolution in which local complexification occurs.

    One also can imagine a mode of Reductive Neutral Evolution in which local simplification occurs. It is simply a matter of the local position of the system relative to the spectrum of mutational possibilities.

    ReplyDelete
    Replies
    1. Arlin,

      To keep the discussion together, here is what I wrote earlier:

      "Claudiu Bandea, Monday, September 07, 2015 12:37:00 PM
      While I'm a fan of the concept of Constructive Neutral Evolution (CNE) and other intellectual contributions by Arlin and the other scholars developing the concept, I don't think that some of the supporting examples of CNEs are valid. Take, for example, the evolution of the splicing and the spliceosome, which are arguably the most complex eukaryal macromolecular machinery.
      As I previously discussed, splicing has evolved as an adaptive defense mechanism system against insertion mutagenesis by a wide range of inserting elements (http://biorxiv.org/content/biorxiv/early/2013/11/18/000588.full.pdf), which explains its complexity."

      As you can see, I specifically challenged one of the examples that you have used to support CNE, namely the evolution of spliceosome, which is arguably the most complex eukaryal macromolecular machinery. Is the challenge valid?

      Regarding the evolution of viruses, I made the point that there is a huge problem with the prevalent hypothesis that viruses evolved towards complexity, whereas, within the same intracellular environment, tens of thousands parasitic cellular species have evolved by reductive evolution. And because the scientists in the field of viral evolution have yet to present a rationale for this discrepancy between the evolution of cellular and viral lineages, I thought that you and some of the other scholars writing on the evolution of complexity might be able offer a plausible explanation. Any ideas?

      Delete
    2. Arlin: "Claudiu, you are creating a false dilemma when you point to reductive evolution (e.g., viruses and intracellular parasites) as though it were a contradiction of CNE"

      Just to make it clear, I'm not saying, or implying, that reductive evolution of viral and cellular lineages was a contradiction of CNE; that would, of course, make no sense.

      Delete
    3. Arlin,

      I'm posting below the comment you left at Dan Graur's blog, ( http://judgestarling.tumblr.com/post/88449119459/rube-goldbergs-131st-birthday-irremediable?soc_src=mail&soc_trk=ma), which some readers might find relevant to the discussion here:

      "Thanks for covering this interesting idea, but I'm not sure why you are crediting this to Lynch, 2007. The basic idea, the name "constructive neutral evolution", the examples of the spliceosome, Neurospora CYT18, RNA editing, etc.-- all of that is found in a paper that I published in 1999 (JME 49: 169; PubMed id #10441669).
      I would not describe CNE as a unidirectional ratchet. In my conception, there also could be a process of reductive neutral evolution. When Lynch argues that genomes become larger and more complex in organisms with small population sizes, he is not necessarily invoking CNE, and I'm not sure what evolutionary principle is supposed to supply the directionality. In the specific case of eukaryotes, one could argue that they are constantly fending off genomic parasites, and so the main effect of reducing N, in practice, is to lower the gates and allow more parasites to invade, increasing the genome size. To my way of thinking, this is not a general principle of increase in complexity, but rather a consequence of an idiosyncratic mutation bias (biased toward additions rather than subtractions). I can imagine a situation where an opposite bias would lead to a pattern in which organisms with smaller N have smaller (not larger) genomes."


      I hope you are willing to address the following points:

      Apparently, Dan gives you credit: "As an alternative to such selectionist thinking, Arlin Stoltzfus in 1999 invoked fixation of neutral or slightly deleterious features as a general and unavoidable source of complexity in taxa with small effective population sizes. Such nonselective processes could account, for instance, for the origins and spread of transposable elements and other contributors to the high DNA content of many eukaryotes. Can you explain?

      You write that CNE can also lead to small genomes (i.e. reduced complexity). How do you think CNE might apply to the evolution of parasitic viral and cellular lineages within an intracellular environment, whose complexity apparently evolved in opposite directions?

      Let's consider that the so called 'junk DNA' (jDNA) in the human genome and that of other species with relatively high C-values is the product of CNE. As you know, the human genome is bombarded with various inserting elements, both in the germ-line as well as in the trillions of somatic cells, throughout the reproductive period. In your opinion, is it reasonable to hypothesize that jDNA protects the genome against insertion mutagenesis, as I previously suggested ( http://biorxiv.org/content/biorxiv/early/2013/11/18/000588.full.pdf)?

      Delete
  20. I think there is a very easy way to resolve the ID issue. Using a very simple way of reasoning, it is also very easy to determine ones' motives whether he/she are really interested in learning if the claim is reasonable that there had to be an Intelligent Designer.

    Step number 1.

    Scientists have discovered on one of the planets far away from the Earth some unusual machines. They don't resemble anything known to men on earth, but there is no doubt they had be designed and assembled by an intelligent designer and maker. However, there is no evidence whatsoever who the designer and the maker of the machines is.

    Let's see what Larry and his gang are going to say about the discovery;

    1. Did it evolve?
    2. Was it design?
    There are only two options to answer the question. I'm 100 % sure that none of Larry's gang will answer the challenge with answering one of those 2 questions.

    The reason is obvious. Too obvious.

    ReplyDelete
    Replies
    1. Scientists have discovered on one of the planets far away from the Earth some unusual machines. They don't resemble anything known to men on earth

      If they don't resemble anything known to men, how do you know they are machines?

      but there is no doubt they had be designed and assembled by an intelligent designer and maker

      Oh my! Septic solved the mystery! There simply is no doubt. Who needs step two? praise the flying spaghetti monster!

      Delete
  21. The awe inspiring spliceosome, the most complex macromolecular machine known, and pre-mRNA processing in eukaryotic cells

    http://reasonandscience.heavenforum.org/t2180-the-spliceosome-the-splicing-code-and-pre-mrna-processing-in-eukaryotic-cells

    Along the way to make proteins in eukaryotic cells, there is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to get the functional product, that is proteins. At the beginning of the process, DNA is transcribed in the RNA polymerase molecular machine, to yield messenger RNA ( mRNA ) , which afterwards must go through post transcriptional modifications. That is CAPPING, ELONGATION, SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION , before it can be EXPORTED FROM THE NUCLEUS TO THE CYTOSOL, and PROTEIN SYNTHESIS INITIATED, (TRANSLATION), and COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING.

    Bacterial mRNAs are synthesized by the RNA polymerase starting and stopping at specific spots on the genome. The situation in eukaryotes is substantially different. In particular, transcription is only the first of several steps needed to produce a mature mRNA molecule. The mature transcript for many genes is encoded in a discontinuous manner in a series of discrete exons, which are separated from each other along the DNA strand by non-coding introns. mRNAs, rRNAs, and tRNAs can all contain introns that must be removed from precursor RNAs to produce functional molecules.The formidable task of identifying and splicing together exons among all the intronic RNA is performed by a large ribonucleoprotein machine, the spliceosome, which is composed of several individual small nuclear ribonucleoproteins, five snRNPs, pronounced ‘snurps’, (U1, U2, U4, U5, and U6) each containing an RNA molecule called an snRNA that is usually 100–300 nucleotides long, plus additional protein factors that recognize specific sequences in the mRNA or promote conformational rearrangements in the spliceosome required for the splicing reaction to progress, and many more additional proteins that come and go during the splicing reaction. It has been described as one of "the most complex macromolecular machines known," "composed of as many as 300 distinct proteins and five RNAs".

    The snRNAs perform many of the spliceosome’s mRNA recognition events. Splice site consensus sequences are recognized by non-snRNP factors; the branch-point sequence is recognized by the branch-point-binding protein (BBP), and the polypyrimidine tract and 3′ splice site are bound by two specific protein components of a splicing complex referred to as U2AF (U2 auxiliary factor), U2AF65 and U2AF35, respectively.

    ReplyDelete