Intelligent Design

Barriers to macroevolution: what the proteins say

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KeithS has been requesting scientific evidence of a genuine barrier to macroevolution. The following is a condensed, non-technical summary of Dr. Douglas Axe’s paper, The Case Against a Darwinian Origin of Protein Folds. Since (i) proteins are a pervasive feature of living organisms, (ii) new proteins and new protein folds have been continually appearing throughout the four-billion-year history of life on Earth, and (iii) at least some macroevolutionary events must have involved the generation of new protein folds, it follows that if Dr. Axe’s argument is correct and neo-Darwinian processes are incapable of hitting upon new functional protein folds, then there are indeed genuine barriers to macroevolution, in at least some cases. The argument put forward by Dr. Axe is robustly quantifiable, and it is fair to say that Dr. Axe carefully considers the many objections that might be put forward against his argument. If there is a hole in his logic, then I defy KeithS to find it.

Finally I would like to thank Dr. Axe for putting his paper online and making it available for public discussion. The headings below are my own; the text is entirely taken from his paper.

Abstract

Four decades ago, several scientists suggested that the impossibility of any evolutionary process sampling anything but a miniscule fraction of the possible protein sequences posed a problem for the evolution of new proteins. This potential problem – the sampling problem – was largely ignored, in part because those who raised it had to rely on guesswork to fill some key gaps in their understanding of proteins. The huge advances since that time call for a careful reassessment of the issue they raised. Focusing specifically on the origin of new protein folds, I argue here that the sampling problem remains. The difficulty stems from the fact that new protein functions, when analyzed at the level of new beneficial phenotypes, typically require multiple new protein folds, which in turn require long stretches of new protein sequence. Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure and with direct experimental evidence. If this is correct, the sampling problem is here to stay, and we should be looking well outside the Darwinian framework for an adequate explanation of fold origins.

Why the origin of new protein folds is a “search problem”

[T]he origin of protein folds can be framed with complete generality as a search problem. Briefly, because genes encode proteins, any functional problem that can be solved with a suitable protein can be solved with a suitable gene. Therefore any functional challenge that calls for structural innovation may be thought of as posing a search problem where the search space is the set of possible gene sequences and the target is the subset of genes within that space that are suitable for meeting the challenge… The aim here will be to decide whether Darwinian mechanisms (broadly construed) can reasonably be credited with this success.

If we take 300 residues as a typical chain length for functional proteins, then the corresponding set of amino acid sequence possibilities is unimaginably large, having 20^300 (= 10^390) members… Here the point is simply that biological protein sequences are indeed members of astoundingly large sets of sequence possibilities. And by ‘astoundingly large’ we mean much more numerous than any mutation events we might postulate as having produced them. According to one estimate, the maximum number of distinct physical events that could have occurred within the visible universe, including all particles throughout the time since the Big Bang, is 10^150. Since only a minute fraction of these events had anything to do with producing new protein sequences, we can assert with confidence that there is a vast disparity between the number of distinct protein sequences of normal length that are possible, on the one hand, and the number that might have become actual, on the other. In other words, real events have provided only an exceedingly sparse sampling of the whole set of sequence possibilities.

Axe’s metaphor: Searching for a gemstone in the Sahara Desert

We will refer to this as the problem of sparse sampling, or the sampling problem, with the intent of deciding whether or not it really is a problem for the standard evolutionary model. At the very least it raises the important question of how such sparse sampling would uncover so many highly functional protein sequences. To picture the difficulty, imagine being informed that a valuable gemstone was lost somewhere in the Sahara Desert. Without more specific information, any proposal for finding the missing gem would have to come to terms with the vastness of this desert. If only an infinitesimal fraction of the expanse can feasibly be searched, we would judge the odds of success to be infinitesimally small.

What if there’s more than one gemstone?

Evolutionary searches for functional proteins might seem less hopeless in some respects, though. For one, there is a highly many-to-one mapping of protein sequences onto protein functions. This means that vast numbers of comparably valuable targets (protein sequences that are comparably suitable for any particular function) are there to be found. Therefore, while it is effectively impossible to stumble upon a particular 1-in-10^390 protein sequence by chance, the likelihood of stumbling upon a particular protein function by chance will be m-fold higher, where m represents the multiplicity of sequences capable of performing that function…

Why the search space for a protein has to be very large

On the most basic level, it has become clear that protein chains have to be of a certain length in order to fold into stable three-dimensional structures. This requires several dozen amino acid residues in the simplest structures, with more complex structures requiring much longer chains. In addition to this minimal requirement of stability, most folded protein chains perform their functions in physical association with other folded chains [12]. The complexes formed by these associations may have symmetrical structures made by combining identical proteins or asymmetrical ones made by combining different proteins. In either case the associations involve specific inter-protein contacts with extensive interfaces. The need to stabilize these contacts between proteins therefore adds to their size, over and above the need to stabilize the structures of the individual folded chains…

The ATP synthase provides an opportunity at this point to refine the connection between protein size and the sampling problem. Returning to the lost gemstone metaphor, the gem is a new beneficial function that can be provided by a protein or a set of proteins working together, and the desert is the whole space of sequence possibilities within which successful solutions are to be found. Although some of the component proteins that form the ATP synthase are at the small end of the distribution shown in Figure 1 (see Figure 3 legend), none of these performs a useful function in itself. Rather, the function of ATP production requires the whole suite of protein components acting in a properly assembled complex. Consequently, the desert is most precisely thought of as the space of all DNA sequences long enough to encode that full suite. For our purposes, though, it will suffice to picture the space of protein sequences of a length equaling the combined length of the different protein types used to form the working complex (around 2,000 residues for the ATP synthase; see Figure 3 legend).

Two possible “ways out” for neo-Darwinian evolution: either there are lots of gemstones in the desert, or the gemstones are suitably lined up, making them easy to find if the first one is located

Having shown that the problem of sparse sampling is real – meaning that cellular functions require proteins or suites of proteins that are of necessity far too large for the sequence possibilities to have been sampled appreciably – we now turn to the question of whether it is really a problem for neo-Darwinian evolution. Two possibilities for mitigating the problem need to be considered. One of these has been mentioned already. It is the possibility that the multiplicity of sequences capable of performing the requisite functions, m, might be large enough for working sequences to be found by random searches. The second possibility is that functional protein sequences might bear a relationship to one another that greatly facilitates the search. In the desert metaphor, imagine all the different gems being together in close proximity or perhaps lined up along lines of longitude and latitude. In either of these situations, or in others like them, finding the first gem would greatly facilitate finding the others because of the relationship their positions bear to one another…

Why the first neo-Darwinian solution to the sampling problem won’t work

…[W]e need to quantify a boundary value for m, meaning a value which, if exceeded, would solve the whole sampling problem. To get this we begin by estimating the maximum number of opportunities for spontaneous mutations to produce any species-wide trait, meaning a trait which is fixed in the population through natural selection (selective sweep). Bacterial species are most conducive to this because of their large effective population sizes. So let us assume, generously, that an ancient bacterial population sustained a species consisting of 10^10 individuals [26], passing through 10^4 generations per year. After five billion years, such a species would produce a total of 5×10^23 (=(5×10^9)x(10^4)x(10^10)) cells that happen to avoid the small-scale extinction events that kill most cells irrespective of fitness. These 5×10^23 ‘lucky survivors’ are the cells that are available for spontaneous mutation to accomplish whatever will be accomplished in the species… [A]ny adaptive step that is unlikely to appear in that number of cells is unlikely to have evolved in the entire history of the species.

In real bacterial populations, spontaneous mutations occur in only a small fraction of the lucky survivors (roughly one in 300). As a generous upper limit, we will assume that all lucky survivors happen to receive mutations in portions of the genome that are not constrained by existing functions, making them free to evolve new ones. At most, then, the number of different viable genotypes that could appear within the lucky survivors is equal to their number, which is 5 × 10^23. And again, since many of the genotype differences would not cause distinctly new proteins to be produced, this serves as an upper bound on the number of new protein sequences that a bacterial species may have sampled in search of an adaptive new protein structure.

Let us suppose for a moment, then, that protein sequences that produce new functions by means of new folds are common enough for success to be likely within that number of sampled sequences. Taking a new 300-residue structure as a basis for calculation (I show this to be modest below), we are effectively supposing that the multiplicity factor m introduced in the previous section can be as large as (20^300)/(5×10^23), or 10^366. [Recall that 20^300 is about 10^390 – VJT.] In other words, we are supposing that particular functions requiring a 300-residue structure are realizable through something like 10^366 distinct amino acid sequences. If that were so, what degree of sequence degeneracy would be implied? More specifically, if 1 in 5×10^23 full-length sequences are supposed capable of performing the function in question, then what proportion of the twenty amino acids would have to be suitable on average at any given position? The answer is calculated as the 300th root of 1/(5×10^23), which amounts to about 83%, or 17 of the 20 amino acids. That is, by the current assumption proteins would have to provide the function in question by merely avoiding three or so unacceptable amino acids at each position along their lengths.

No study of real protein functions suggests anything like this degree of indifference to sequence…

The second neo-Darwinian solution: Shortcuts to new folds?

The possibility yet to be examined is that functional protein sequences might bear a relationship to one another that allows spontaneous mutations to discover new functional protein folds much more readily than wholly random sampling would. The simplest way for this to occur would be if all functional sequences, regardless of what their functions are, happen to be much more similar to each other than a pair of random sequences would be. In other words, suppose there were a universal consensus sequence that typified all biological proteins, with functional diversity caused by minor deviations from that consensus. The effect of such a universal correlation between sequence and function would be to concentrate all the useful protein sequences within a tiny region of sequence space, making searches that start in that region much more likely to succeed.

Localized searches of this kind are known to work in some cases… The problem comes when we attempt to generalize this local phenomenon. Although there are definite correlations between the various kinds of functions that proteins perform and the respective fold structures used to perform them, and these structural correlations often imply sequence correlations as well, it is simply not the case that all functional folds or sequences are substantially alike. Consequently, while local searches may explain certain local functional transitions, we are left with the bigger problem of explaining how so many fundamentally new protein structures and functions first appeared.

To get an idea of the scale of this problem, consider that the SCOP classification of protein structures currently has 1,777 different structural categories for protein domains, the basic units of folded protein structure… [N]o model of protein origins can be considered satisfactory without accounting for the origin of this great variety of domain folds.

In fact, although the sampling problem has here been framed in terms of protein chains, it could equally be framed in terms of domains. Since domains are presumed to be the fundamental units of conserved structure in protein evolution [33], the question of whether functional sequences are confined to a small patch of sequence space is best addressed at the domain level. And it turns out that domain sequences are not confined in this way…

It therefore seems inescapable that considerable distances must be traversed through sequence space in order for new protein folds to be found. Consequently, any shortcut to success, if it exists, must work by traversing those distances more effectively rather than by shortening them.

A third neo-Darwinian possibility: proteins are made up of small reusable modules, which a search can easily discover

The only obvious possibility here is that new folds might be assembled by recombining sections of existing folds [40-42]. If modular assembly of this kind works, it would explain how just one or two gene fusion events might produce a new protein that differs substantially from its ‘parents’ in terms of overall sequence and structure. Of course, probabilistic limitations would need to be addressed before this could be deemed a likely explanation (because precise fusion events are much less likely than point mutations), but the first question to ask is whether the assumed modularity is itself plausible.

To examine this further, we begin by considering what this kind of modularity would require. If it is to be of general use for building up new folds, it seems to require that folds be divisible into more or less self-contained structural components that can be recombined in numerous ways, with each combination having a good chance of producing a well-formed composite structure. Two physical criteria would have to be met for this to be true. First, the sequence specificity for forming these components must be internal to the components themselves (making their structures self-contained), and second, the interactions that hold neighboring components together to form composite structures must be generic in the sense of lacking critical dependence on the particulars of the components.

The immediate problem is that the first criterion tends to be met only at the level of a complete fold – a folding domain. Important structural features are certainly discernible at lower levels, the most ubiquitous of these being the regular chain conformations known as the alpha helix and the beta strand (secondary structure being the term for these repetitive patterns in local chain structure). But these only find stable existence in the context of larger fold structures (tertiary structure) that contain them. That is, the smallest unit of protein structure that forms stably and spontaneously is typically a complete globular assembly with multiple, layered elements of secondary structure. Smaller pieces of structure can have some tendency to form on their own, which is important for triggering the overall folding process [43], but the highly co-operative nature of protein folding [44] means that stable structure forms all at once in whole chunks – domains – rather than in small pieces. Consequently, self-contained structural modules only become a reality at the domain level, which makes them unhelpful for explaining new folds at that level…

The binding interfaces by which elements of secondary structure combine to become units of tertiary structure are predominantly sequence dependent, and therefore not generic. This presents a major challenge for the idea of modular assembly of new folds, at least as a general explanation… As we will see next, several studies demonstrate that proteins with substantially different amino acid sequences (roughly 50% amino acid identity or less) fail to show part-for-part structural equivalence even if they are highly similar in terms of overall structure and function. Since the modularity hypothesis assumes a much more demanding sense of structural equivalence (where modules retain their structure even when moved between proteins that differ radically in terms of overall structure and function) the failure of the less demanding sense seems to rule that hypothesis out…

With no discernible shortcut to new protein folds, we conclude that the sampling problem really is a problem for evolutionary accounts of their origins. The final thing to consider is how pervasive this problem is. How often in the history of life would new phenotypes have required new protein folds? Or, narrowing that question, how much structural novelty do metabolic innovations appear to have required in the history of bacteria? Continuing to use protein domains as the basis of analysis, we find that domains tend to be about half the size of complete protein chains (compare Figure 10 to Figure 1), implying that two domains per protein chain is roughly typical. This of course means that the space of sequence possibilities for an average domain, while vast, is nowhere near as vast as the space for an average chain. But as discussed above, the relevant sequence space for evolutionary searches is determined by the combined length of all the new domains needed to produce a new beneficial phenotype…

Summary: the gemstone metaphor revisited

…We have used a picture of gems hidden in a vast desert at various points in our discussion in order to illustrate the challenge. Now that we have estimated the relevant fractions it may be helpful to return to this picture. Imagine that the search for gems is conducted by specifying sample points as mathematically exact geographic coordinate pairs (longitude and latitude). Sampling then consists of determining whether a gemstone rests at any of these specified points. A target the size of a grain of sand amounts to about one part in 10^20 of a search space the size of the Sahara, which is above the feasibility threshold of one part in 5 × 10^23. So under favorable circumstances a Darwinian search would be capable of locating a sand-grain-sized gemstone in a Sahara-sized search space. As mentioned above, the ability to accomplish a search on this scale is clearly of some practical significance.

But as a generator of new protein folds, it turns out to be decidedly insignificant. Extending our desert picture, imagine that the top surface of every grain of sand in the Sahara has a miniature desert of its own resting upon it – one in which the entire Sahara is replicated in minute detail. We may call the sub-microscopic sand in these miniature deserts level-1 sand, referring to the fact that it is one level removed from the real world (where we find level-0 sand). This terminology can be applied to arbitrarily small targets by invoking a succession of levels (along the lines of De Morgan’s memorable recursion of fleas). In terms of this picture, the sampling problem stems from the fact that the targets for locating new protein folds appear to be much smaller than a grain of level-0 sand. For example, the target that must be hit in order to discover one new functional domain fold of typical size is estimated to cover not more than one ten-trillionth of the surface of a single grain of level-1 sand. Under favorable circumstances a Darwinian search will eventually sample the grain of level-0 sand on which the right grain of level-1 sand rests, but even then the odds of sampling that level-1 grain are negligible, to say nothing of the target region on that grain. And the situation rapidly deteriorates when we consider more relevant targets, like beneficial new phenotypes that employ (typically) several new protein structures. In the end, it seems that a search mechanism unable to locate a small patch on a grain of level-14 sand is not apt to provide the explanation of fold origins that we seek.

Clearly, if this conclusion is correct it calls for a serious rethink of how we explain protein origins, and that means a rethink of biological origins as a whole.

————————————————-

FINAL NOTE:

Readers will observe that the foregoing argument made by Dr. Axe has nothing to do with the argument made in his and Dr. Ann Gauger’s subsequent paper, The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway. Even if the argument in that paper were invalid, as KeithS claims, the above argument would still stand as a genuine barrier to macroevolution.

In any case, Dr. Gauger has replied to critics of the latter paper, here, here and here. (Dr. McBride’s comments are available here.) I invite readers to draw their own conclusions.

65 Replies to “Barriers to macroevolution: what the proteins say

  1. 1
    gpuccio says:

    VJ:

    “KeithS has been requesting scientific evidence of a genuine barrier to macroevolution. ”

    Keith would better spend his time, and ours, if he requested of himself scientific evidence of a genuine path to macroevolution of proteins. Should I remind him that a non existing, never observed, never logically supported path is the best “barrier” we can imagine in empirical science?

  2. 2
    bornagain77 says:

    Dr. Torley, another problem that greatly exasperates the problem for proteins is what is termed ‘context dependency’. Dr. Durston puts the problem of context dependency as such,,,

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
    http://powertochange.com/wp-co.....Myers_.pdf

    Moreover, Dr. Gauger informs us that context dependency is found thoughout the protein structure at the level of primary sequence, secondary structure, and tertiary (domain-level) structure.

    “Why Proteins Aren’t Easily Recombined, Part 2? – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

    That protein function is ‘context dependent’ is revealed by the following study. Proteins have now been shown to have a ‘Cruise Control’ mechanism which works to ‘self-correct’ the protein function (and structure) from any random mutations imposed on the proteins.

    Proteins with cruise control provide new perspective:
    “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.”
    http://www.princeton.edu/main/...../60/95O56/

    Thus the entire protein is shown to be involved in safe guarding the specific function(s) of a protein from any random mutations imposed on it. In other words, much contrary to Darwinian thought, proteins are not ‘searching’ for new functions by varying their shape when mutations happen to the individual amino acids, as is presupposed in Darwinian thought, but proteins are instead designed, as a whole, to prevent mutations to its amino acids from having any detrimental effect on its function(s).
    How is it possible for a protein to operate as a cohesive whole despite mutations to individual amino acids? The reason it is possible for a protein to act as a cohesive whole, in a context dependent manner, is because the entire protein structure is found to be quantumly entangled as as ‘a single quantum state’,,,

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini & Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    That the entire protein structure is quantumly entangled as as ‘a single quantum state’ is also revealed by the fact that protein folding is dependent on ‘quantum computation’ in order to find its final folded state.
    First a little background on how extremely difficult it is for ‘random processes’ to explain protein folding. Protein folding, contrary to what Darwinists would prefer to believe beforehand, is simply found not to be amicable to the ‘randomness’ of Darwinists

    The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012
    Excerpt: Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe.
    http://www.evolutionnews.org/2.....65521.html

    In fact, solving the final form of a relatively short and simple protein fold requires several weeks to accomplish, even though several hundred thousand computers have been linked together for the task.

    A Few Hundred Thousand Computers vs. A Single Protein Molecule – video
    https://www.youtube.com/watch?v=lHqi3ih0GrI

    The reason why protein folding is so difficult for super-somputing to solve is that protein folding is similar to the infamous travelling-salesman problem, and travelling-salesman problems are notorious for keeping supercomputers busy for days.

    Confronting Science’s Logical Limits – John L. Casti – 1996
    Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard.
    http://www.cs.virginia.edu/~ro.....Limits.pdf

    Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:

    Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013
    Excerpt: quantum computing is, “in some cases, really, really fast.”
    McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,,
    “This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. “There are degrees of what it can do. If you want it to solve the exact problem it’s built to solve, at the problem sizes I tested, it’s thousands of times faster than anything I’m aware of. If you want it to solve more general problems of that size, I would say it competes — it does as well as some of the best things I’ve looked at. At this point it’s merely above average but shows a promising scaling trajectory.”
    http://www.sciencedaily.com/re.....122828.htm

    Thus, it should not be surprising to learn that protein folding is now found to belong to the ‘spooky’ world of quantum mechanics and that protein folding does not belong to the world of classical mechanics.

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
    To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....f-protein/

  3. 3
    bornagain77 says:

    Another reason why finding quantum entanglement/computation in proteins is so foreign to neo-Darwinian thought, is that one must appeal to a non-local, beyond spece and time, cause in order to explain entanglement, yet neo-Darwinism is based upon the reductive materialistic premise that there are no beyond space and time causes.

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    Closing the last Bell-test loophole for photons – Jun 11, 2013
    Excerpt:– requiring no assumptions or correction of count rates – that confirmed quantum entanglement to nearly 70 standard deviations.,,,
    http://phys.org/news/2013-06-b.....otons.html

    of supplemental note:

    Context dependency is a far more difficult problem for Darwinists to deal with than I have illustrated here, because (and Aristotle would be happy) the ‘form’ of a organism is not reducible to the sequences and DNA and proteins (Jonathan Wells). But ‘form’ is its own independent source of information that provides the primary basis for the overall ‘context’ of an organism.
    To get this very important ‘context dependency’ point across, I highly recommend Wiker & Witt’s book “A Meaningful World” in which they show, using the “Methinks it is like a weasel” phrase of Richard Dawkins, that the “Methinks it is like a weasel” phrase doesn’t makes any sense at all unless the entire context of the play of Hamlet is taken into consideration.

    A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Book Review
    Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part.
    http://www.thinkingchristian.n.....821202417/

    In fact it is interesting to note what the overall context is for “Methinks it is like a weasel” that is used in the Hamlet play. The context in which the phrase is used is to illustrate the spineless nature of one of the characters of the play. To illustrate how easily the spineless character can be led to say anything that Hamlet wants him to say:

    Ham. Do you see yonder cloud that ’s almost in shape of a camel?
    Pol. By the mass, and ’t is like a camel, indeed.
    Ham. Methinks it is like a weasel.
    Pol. It is backed like a weasel.
    Ham. Or like a whale?
    Pol. Very like a whale.
    http://www.bartleby.com/100/138.32.147.html

    After realizing what the context of ‘Methinks it is like a weasel’ actually was, I remember thinking to myself that it was perhaps the worse possible phrase Dawkins could have possibly chosen to try to illustrate his point, since the phrase, when taken into context, actually illustrates that the person saying it (Hamlet) was manipulating the other character into saying a cloud looked like a weasel. Which I am sure is hardly the idea, i.e. deception and manipulation, that Dawkins was trying to convey with his ‘Weasel’ example.

    also of note, Artificial intelligence (AI) does not ‘understand’ context, and is thus a major roadblock in attmpts at AI,,,

    What Is a Mind? More Hype from Big Data – Erik J. Larson – May 6, 2014
    Excerpt: In 1979, University of Pittsburgh philosopher John Haugeland wrote an interesting article in the Journal of Philosophy, “Understanding Natural Language,” about Artificial Intelligence. At that time, philosophy and AI were still paired, if uncomfortably. Haugeland’s article is one of my all time favorite expositions of the deep mystery of how we interpret language. He gave a number of examples of sentences and longer narratives that, because of ambiguities at the lexical (word) level, he said required “holistic interpretation.” That is, the ambiguities weren’t resolvable except by taking a broader context into account. The words by themselves weren’t enough.
    Well, I took the old 1979 examples Haugeland claimed were difficult for MT, and submitted them to Google Translate, as an informal “test” to see if his claims were still valid today.,,,
    ,,,Translation must account for context, so the fact that Google Translate generates the same phrase in radically different contexts is simply Haugeland’s point about machine translation made afresh, in 2014.
    Erik J. Larson – Founder and CEO of a software company in Austin, Texas
    http://www.evolutionnews.org/2.....85251.html

    Verse:

    John 1:1
    In the beginning was the Word, and the Word was with God, and the Word was God.

  4. 4
    kairosfocus says:

    VJT:

    A good, workmanlike job as usual.

    Axe’s argument is a stiff challenge to those who would dismiss the relevance of islands of function in v large config spaces with only v sparse search possible.

    I only note that a more realistic estimate of number of atom-level events would pivot on something about 10^30 times slower than the Planck time sometimes rounded to 10^-45 s but actually like 4 * 10^-44 s, ie a range to 10^-43 s. Namely, fast chem rxn scale events. With 10^80 atoms in the observed cosmos, 10^14 events/s and 10^17 s on a typical timeline, we are looking at more like 10^111 events or thereabouts.

    500 bits have a config space of 3.27*10^150 possibilities and 1,000 bits, 1.07*10^301.

    Such numbers — and dismissals on “big numbers, harrumph” fail — pose sobering search challenges.

    Where, as any base may succeed any other and as any AA may succeed any other, there really is such a large space to search. Especially at OOL but also to source the cell types, tissues, organs and systems to form a new body plan. Genome sizes for that run like 10 – 100+ mn bases.

    I repeat, in the teeth of current caricatures — the only known source of the requisite FSCO/I is design. With, the design inference filter approach being perfectly willing to accept false negatives by assigning the defaults to mechanical necessity and chance contingency, through imposing a stiff hurdle to infer design.

    The payoff is, when design is inferred, the inference is strong.

    KF

  5. 5
    sparc says:

    According to this source Dr. Gauger gave quite an impressive presentation during the “Wistar 2” conference.

  6. 6
    bornagain77 says:

    To further hightlight the insurmountable problem that context dependency (i.e. ‘form’) places on ‘bottom up’ neo-Darwinian explanations for proteins, it is imporatant to note that many proteins, called intrinsically disordered proteins, have no intrinsic shape. taking on different roles in different molecular contexts.

    The Gene Myth, Part II – August 2010
    Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disoredered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy
    http://darwins-god.blogspot.co.....rt-ii.html

    Jonathan Wells notes that about 1/3 of the proteins in our body could be ‘Intrinsically Disordered Proteins’ (IDPs) which take on different roles in different molecular contexts

    podcast – Dr. Jonathan Wells: Biology’s Quiet Revolution – September 17, 2014
    “We are talking about 1/3 of the proteins in our body, (could be Intrinsically Disordered Proteins)” – Jonathan Wells
    http://www.discovery.org/multi.....evolution/

    Moreover, many proteins are found to be multifunctional, taking on more than one one role/function depending on what context they are in. In fact a protein can have two completely opposite functions depending on what context it is in,,,,

    Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought:
    Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.
    http://www.sciencedaily.com/re.....134623.htm

    Explaining how a protein can perform multiple roles – Cell Biology – December 18, 2009
    Excerpt: It’s been known for more than a decade that some cell proteins can carry out multiple functions. For example, it was discovered in 1999 that the protein TyrRS (explained shortly) participated not only in the building of enzymes, but also could function to stimulate the growth of blood vessels. Discovering that the same protein could perform very different roles opened one of the great new chapters in molecular biology.
    http://scitechstory.com/2009/1.....ple-roles/

    Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013
    Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”
    http://darwins-god.blogspot.co.....rs-of.html
    http://www.fasebj.org/content/23/7/2022.full

    At the risk of boring people with my repeated citation of Talbott, In my honest opinion Stephen Talbott, in this following article, does a par excellence job of illustrating just how devasting the problem of context dependency is to neo-Darwinian explanations for how the billion trillion protein molecules of a human body organize into a cohesive whole,,,

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

  7. 7
    bornagain77 says:

    Also of interest to this topic of context dependency is the fact that the strategy of using the ‘top down’ approach of taking context into consideration provides a much more fruitful hueristic for investigating the complexities of molecular biology than the ‘bottom up’ neo-Darwinian approach provides.

    How the Burgeoning Field of Systems Biology Supports Intelligent Design – July 2014
    Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems:
    *”Negative feedback for stable operation.”
    *”Frequency filtering” for extracting a signal from a noisy system.
    *Control and signaling to induce a response.
    *”Information storage” where information is stored for later use. In fact, Snoke observes:
    “This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. ”
    *”Timing and synchronization,” where organisms maintain clocks to ensure that different processes and events happen in the right order.
    *”Addressing,” where signaling molecules are tagged with an address to help them arrive at their intended target.
    *”Hierarchies of function,” where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order.
    *”Redundancy,” as organisms contain backup systems or “fail-safes” if primary essential systems fail.
    *”Adaptation,” where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, “These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way,” and “Only part of the system is allowed to vary randomly, while the rest is highly conserved.”,,,
    Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that “just about everything in the cell does indeed have a role, i.e., that there is very little ‘junk.'” He explains, “Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible,” and quotes additional authorities who assume that biological systems are optimized.,,,
    http://www.evolutionnews.org/2.....87871.html

    “It has become clear in the past ten years that the concept of design is not merely an add-on meta-description of biological systems, of no scientific consequence, but is in fact a driver of science. A whole cohort of young scientists is being trained to “think like engineers” when looking at biological systems, using terms explicitly related to engineering design concepts: design, purpose, optimal tradeoffs for multiple goals, information, control, decision making, etc. This approach is widely seen as a successful, predictive, quantitative theory of biology.”
    David Snoke*, Systems Biology as a Research Program for Intelligent Design – 2014
    http://bio-complexity.org/ojs/.....O-C.2014.3

    podcast: “David Snoke: Systems Biology and Intelligent Design, pt. 1”
    http://intelligentdesign.podom.....9_09-07_00
    podcast: David Snoke: Systems Biology and Intelligent Design, pt. 2
    http://intelligentdesign.podom.....0_01-07_00

    Whereas on the other hand, “Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology”,,,

    “Evolutionary theory contributes little to experimental biology” – Philip Skell

    Excerpt: “Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.,,,
    ,,,Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology.”
    Philip S. Skell – (the late) Emeritus Evan Pugh Professor at Pennsylvania State University, and a member of the National Academy of Sciences.
    http://www.discovery.org/a/2816

    “In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all.”
    Marc Kirschner, Boston Globe, Oct. 23, 2005

    “While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.”
    A.S. Wilkins, editor of the journal BioEssays, Introduction to “Evolutionary Processes” – (2000).

  8. 8
    jerry says:

    Haven’t had time to read OP thoroughly but this is all testable with current technology. New proteins will leave evidence of formation even if it happened millions of years ago.

    As soon as genome sequences become very cheap they will be compared across species and if there are alleles coding for functional proteins/folds in one species but no indication of it in another species then it will say something very different than if there are traces of the allele in related species who supposedly have a common ancestor.

    All coming in about 15-20 years. Too expensive today even though technology is available but that will change.

  9. 9
    bpragmatic says:

    So…Where are the NDE scientists and pertinent scientific data to refute what must be flawed unsupported assertions presented above? Or, forget the NDE “scientists”. Let the usual philosophical “scientifically” uneducated hacks blow the usual rhetoric for obfuscation to substitute as legitimate challenges to serious questions. Surely, there is empirical evidence to clearly refute what everyone knows is “creationist” tripe. Yeah, that is it. If it were not for those stupid creationist’s and their blind adherence to the belief of the “sky fairy”, then the NDE conjecture would surely be completely and unabashedly vindicated without any reservation as the truth that has been clearly established by “empirical science”. Ha Ha! What a bunch of clowns.

  10. 10
    keith s says:

    bpragmatic,

    Don’t forget that UD is actively hostile to open discussion. Most ID critics get banned quickly, and there have been many bannings just within the last week.

    So when you ask “Where are the critics?”, the answer is “They’re out there, but your UD President is afraid to let them speak.”

    It’s pitiful, isn’t it?

    If you’re looking for open discussion, I highly recommend The Skeptical Zone, where open discussion is encouraged and commenters are not censored or banned (except for one sorry example: your own Joe G).

    One caveat: if you go there, you’re likely to discover that most of the “clowns” are smarter and better educated than you are, and that they are very good at refuting ID/creationist nonsense.

    P.S. I’m usually banned quickly at UD, but I seem to be in a sweet spot at the moment. My ‘bomb’ argument is a topic in at least seven threads, and it would look especially ridiculous if UD banned me right now. (It looks ridiculous enough that they’ve banned the others, but perhaps Barry thought it was worth the tradeoff.)

    I’m likely to be banned when the discussion of my argument tapers off.

    When that happens, everyone can find me at The Skeptical Zone.

  11. 11
    Andre says:

    Me me me……. Keith your arguments have been refuted, TSZ is filled with the same people as you…… logically dysfunctional.

  12. 12
    RexTugwell says:

    Keith S, that’s the longest non-answer I’ve read in a long time.

  13. 13
    kairosfocus says:

    KS,

    why the insistent misreperesentation and well-poisoning, as you know or should full well know, UD is open to CIVIL discussion but not to trolling and abusive Internet vandalism . . . a known, habitual problem for far too many objectors to design thought.

    And, for excellent reason there is no such thing as a right to defamation under — false — colours of freedom of expression.

    Where, patently, drumbeat repetition of such a false accusation, as you and others have been doing for years in the teeth of repeated cogent correction, is defamatory and disrespectful to duties of care to truth and fairness.

    I will just note here that your current, ongoing performance on suggested arguments against design theory show serious problems with insistent strawman caricaturing and circular arguments lacking good reference to empirical grounding of blind watchmaker thesis claims regarding OOL and origin of body plans.

    I hardly need to mention that the denial of the obvious and widespread reality of functionally specific complex organisation and associated information backed up by the pretence that relevant info metrics do not exist or that the quantity of info is not calculable or has not been calculated in the teeth of examples starting with PC file sizes and going on from there, does not commend you and others as arguing in good faith and with regard to truth.

    I think you need to take serious stock.

    KF

  14. 14
    Lesia says:

    bornagain77 @6,
    why, no, you’re not boring anyone, your comments are always interesting to read (even if it’s the same thing i’ve read in some other thread – honestly, no irony or sarcasm intended). You’re donig great job bringing all that interesting information to us and repetition only helps comprehend it better. Besides, if Darwinians patiently repeat their nonsense, then it in no way should be bad to post something interesting few times… 🙂

  15. 15
    kairosfocus says:

    F/N: As it seems lost in the onward comments, on the focal topic, I clip 4 above:

    __________

    >> Axe’s argument is a stiff challenge to those who would dismiss the relevance of islands of function in v large config spaces with only v sparse search possible.

    I only note that a more realistic estimate of number of atom-level events would pivot on something about 10^30 times slower than the Planck time sometimes rounded to 10^-45 s but actually like 4 * 10^-44 s, ie a range to 10^-43 s. Namely, fast chem rxn scale events. With 10^80 atoms in the observed cosmos, 10^14 events/s and 10^17 s on a typical timeline, we are looking at more like 10^111 events or thereabouts.

    500 bits have a config space of 3.27*10^150 possibilities and 1,000 bits, 1.07*10^301.

    Such numbers — and dismissals on “big numbers, harrumph” fail — pose sobering search challenges.

    Where, as any base may succeed any other and as any AA may succeed any other, there really is such a large space to search. Especially at OOL but also to source the cell types, tissues, organs and systems to form a new body plan. Genome sizes for that run like 10 – 100+ mn bases.

    I repeat, in the teeth of current caricatures — the only known source of the requisite FSCO/I is design. With, the design inference filter approach being perfectly willing to accept false negatives by assigning the defaults to mechanical necessity and chance contingency, through imposing a stiff hurdle to infer design.

    The payoff is, when design is inferred, the inference is strong. >>
    __________

    BA77 in 6 above raises as well an interesting point on proteins with no intrinsic shape, which Wells suggests may be up to 1/3 in cases. That brings up chaperoned folding and prions as misfolded proteins. Let’s clip BA:

    ____________

    BA77: >> The Gene Myth, Part II – August 2010
    Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disoredered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy
    http://darwins-god.blogspot.co.....rt-ii.html >>
    _____________

    VJT has put a very serious point on the table that is relevant to the islands of function and what Axe aptly terms the sparse search challenge issues.

    Let us see if that will be squarely faced.

    KF

  16. 16
    kairosfocus says:

    PS: Newman’s wider discussion raises various issues:

    http://www.desdeelexilio.com/2.....-a-newman/

  17. 17
    bornagain77 says:

    Lesia @14 thank you, it is nice to know.

  18. 18
    bornagain77 says:

    although the ‘brick wall’ inability of proteins to originate, or to transform into different proteins of a new function, that Dr. Torley has illustrated is certainly a very tight constraint at the molecular level for neo-Darwinian processes to transform one organism into another organism, there is another tight constraint on the unlimited plasticity that is presupposed/imagined for neo-Darwinian processes.,,,

    This tight constraint one has to do with ‘morphological form’ of a body plan which, as I briefly touched on in post 6, is found not to be reducible to the ‘protein parts’ of a body plan.

    ,,,At the body plan, i.e. morphological/form, level we find another tight constraint for the unlimited plasticity envisioned by Darwinists.
    A simple way of illustrating these ‘morphological’ constraints for the plasticity of basic body plans/forms is by envisioning what would happen if you were to have a series of mutations which enlarged, say, a leg bone of a animal. If a corresponding series of mutations did not happen for the muscles, blood vessels , nerves, skin, and etc.. etc.., of the leg,,, as well as for the other legs, the animal would soon lose its symmetry. Here are a few articles which elucidate this principle,,,

    “The real number of variations is lesser than expected,,. There are no blue-eyed Drosophila, no viviparous birds or turtles, no hexapod mammals, etc. Such observations provoke non-Darwinian evolutionary concepts. Darwin tried rather unsuccessfully to solve the problem of the contradictions between his model of random variability and the existence of constraints. He tried to hide this complication citing abundant facts on other phenomena. The authors of the modern versions of Darwinism followed this strategy, allowing the question to persist. …However, he was forced to admit some cases where creating anything humans may wish for was impossible. For example, when the English farmers decided to get cows with thick hams, they soon abandoned this attempt since they perished too frequently during delivery. Evidently such cases provoked an idea on the limitations to variability… [If you have the time, read all of the following paper, which concludes] The problem of the constraints on variation was not solved neither within the framework of the proper Darwin’s theory, nor within the framework of modern Darwinism.”
    (IGOR POPOV, THE PROBLEM OF CONSTRAINTS ON VARIATION, FROM DARWIN TO THE PRESENT, 2009,
    http://www.ludusvitalis.org/te....._popov.pdf

    K´necting The Dots: Modeling Functional Integration In Biological Systems – June 11, 2010
    Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of (embryonic) development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream” (1)
    http://www.uncommondescent.com.....l-systems/

    Newton himself considered this ‘symmetry argument’ for body plans/forms to be a devastating against atheistic arguments,,,

    “Can it be by accident that all birds, beasts, and men have their right side and left side alike shaped, (except in their bowels,) and just two eyes, and no more, on either side of the face; and just two ears on either side of the head, and a nose with two holes; and either two fore- legs, or two wings, or two arms on the shoulders, and two legs on the hips, and no more? Whence arises this uniformity in all their outward shapes but from the counsel and contrivances of an Author? Whence is it that the eyes of all sorts of living creatures are transparent to the very bottom, and the only transparent members in the body, having on the outside a hard transparent skin, and within transparent humours, with a crystalline lens in the middle, and a pupil before the lens, all of them so finely shaped and fitted for vision, that no artist can mend them? Did blind chance know that there was light, and what was its refraction, and fit the eyes of all creatures, after the most curious manner, to make use of it? These, and suchlike considerations, always have, and ever will prevail with mankind, to believe that there is a Being who made all things, and has all things in his power, and who is therefore to be feared.” (Sir Isaac Newton, A Short Scheme of the True Religion)
    Sir Isaac Newton – Of Atheism – video
    https://www.youtube.com/watch?v=XAMCgWV3PVI

    Da Vinci Vitruve Luc Viatour – interactive image
    http://upload.wikimedia.org/wi.....iatour.jpg

    supplemental notes: mutations that could effect body plan morphogenesis, i.e. generate new forms of body plans, are found to be ‘always catastrophically bad’

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” –
    Eric Davidson
    http://www.evolutionnews.org/2.....79811.html

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

  19. 19

    One of keith’s (and other darwinist’s) habits is shifting the burden. Although the terms “microevolution” and “macroevolution” make it sound as if one is a short-form version of the other, Darwinists don’t get to simply assume this and demand that anyone who doubts it prove there is a “barrier” between the two.

    That’s not the IDist’s burden to carry in the first place. It is the Darwinists burden to provide compelling evidence in favor of their assertion that unguided “microevolution” can actually, plausibly accumulate into novel, functional macroevolutionary features.

  20. 20
    Dionisio says:

    KF

    The link you posted at 16 is in Spanish. Thanks.

    🙂

  21. 21
    vjtorley says:

    KeithS,

    I only have a few minutes, but I’d like to say that you are welcome to post scientific criticisms of Dr. Axe’s argument on this thread, if you have any.

    Bornagain77 and Kairosfocus,

    Thank you both for your input, for your comments on my post and for the helpful links. Got to go now.

  22. 22
    gpuccio says:

    keith s:

    “When that happens, everyone can find me at The Skeptical Zone.”

    Thank you for the information. I have no reasons to worry, then! 🙂

  23. 23
    Axel says:

    ‘Should I remind him that a non existing, never observed, never logically supported path is the best “barrier” we can imagine in empirical science?’

    Hilarious, GP!

  24. 24
    Axel says:

    ‘Surely, there is empirical evidence to clearly refute what everyone knows is “creationist” tripe.’ – bpragmatic (i.e. don’t let discursive thought get in the way)

    Well, why don’t you adduce it, bozo? Duh…

  25. 25
    jerry says:

    Surely, there is empirical evidence to clearly refute what everyone knows is “creationist” tripe.

    There has to be evidence in the various genomes that will support or falsify the thesis which Douglas Axe presents. When that is verified or rejected, the debate will probably be over. It should happen in the next 20 years.

    The following is a condensed, non-technical summary of Dr. Douglas Axe’s paper,

    I think we need a more layman’s version of all this. I understand the gist of it but many of the specifics are a little unclear.

  26. 26
    jerry says:

    I’m likely to be banned when the discussion of my argument tapers off.

    Why don’t you point to all the pertinent things said by those who have been banned. I certainly haven’t read all the comments but those that I did were at best childish or irrelevant.

    It is rare that an anti-ID person makes a relevant comment but there are some. Point out where those who have been banned did. But do so in an objective adult way.

    Maybe this should be on another thread since this one is about the origin of proteins.

  27. 27
    Mung says:

    Hasn’t keiths argued that there is only one single objective nested hierarchy of protein evolution that can be produced by unguided evolution?

    And that hierarchy is?

    And the evidence is?

  28. 28
    Mung says:

    keiths:

    UD is actively hostile to open discussion.

    Is that why you so assiduously avoid the open discussion of your ideas here at UD?

    I beg the admins and moderators. Stop censoring the posts by keiths! Allow him to openly discuss his ideas.

  29. 29
    Mung says:

    Perhaps keiths can explain how protein folds fit into a nice objective nested hierarchy that could only have come about by unguided evolution.

    Hoping he doesn’t get banned before he has the chance.

  30. 30
    Box says:

    Mung,

    Surely you understand why Keiths cannot be allowed back in. You must have noticed that his ideas are simply to cogent, valid and convincing.
    IOW letting Keith back in will spell finish for the entire ID-movement.

  31. 31
    Mung says:

    Hi Box,

    I am wondering what the computer algorithm looks like for the function detect_irony.

  32. 32
    tjguy says:

    “KeithS has been requesting scientific evidence of a genuine barrier to macroevolution. ”

    Sorry guys. You should know better than to reference a creationist paper. Creationist papers don’t count.

    Next?

    Sure enough. This is exactly the answer pragmatic gave!

    Surpise, surprise, surprise!

  33. 33
    bpragmatic says:

    Someone above said:

    “So when you ask “Where are the critics?”, the answer is “They’re out there, but your UD President is afraid to let them speak.”

    Man, I do not think I asked “where are the critic?”. I was asking “where Is the scientific evidence” or where is the “empirical evidence?”

    More specifically this is what what asked:

    “Where are the NDE scientists and pertinent scientific data to refute what must be flawed unsupported assertions presented above?”

    why do you want to misrepresent what was really asked? You must have an agenda. And you must believe you are in a battle of a philosophically driven agenda at that. Otherwise you would at least try and answer the honest question with relevant answers. You demonstrate an attitude of contention and not one of deriving truth.

  34. 34
    keith s says:

    bpragmatic:

    Someone above said:

    Someone whose name must not be spoken?

    Man, I do not think I asked “where are the critic?”.

    Yes, you did. You asked:

    Where are the NDE scientists and pertinent scientific data to refute what must be flawed unsupported assertions presented above?

    The overwhelming majority of evolutionary biologists think that ID is a crock, if you haven’t noticed.

    As I wrote above:

    Don’t forget that UD is actively hostile to open discussion. Most ID critics get banned quickly, and there have been many bannings just within the last week.

    So when you ask “Where are the critics?”, the answer is “They’re out there, but your UD President is afraid to let them speak.”

    It’s pitiful, isn’t it?

    bpragmatic:

    You demonstrate an attitude of contention and not one of deriving truth.

    Truth has a much better chance of prevailing in an open discussion. The censorship at UD is antithetical to the pursuit of truth.

  35. 35
    jerry says:

    The censorship at UD is antithetical to the pursuit of truth.

    Absolute nonsense. I have been commenting here for over 9 years and I have not seen one idea censored. What I have seen censored is ill behavior and non stop frivolous remarks like this one.

    Step up and tell us an opinion that has been censored.

  36. 36
    bpragmatic says:

    “Someone whose name must not be spoken?”

    No, I think it is o k Keiths.

    “The overwhelming majority of evolutionary biologists think that ID is a crock, if you haven’t noticed.”

    This proclamation, despite probably being true (that that is what they think), has long since become an absurd “appeal to authority” in my opinion.

    Gpuccio states above:

    “VJ:

    “KeithS has been requesting scientific evidence of a genuine barrier to macroevolution. ”

    Keith would better spend his time, and ours, if he requested of himself scientific evidence of a genuine path to macroevolution of proteins.”

    I think that you would gain much credibility with many, if you were to take that advice. Why not start with scientific responses to the issues raised in “Barriers to Macroevolution: what the proteins say”.

    If you could present viable empirical scientific evidence that addresses the points made in the OP , that would be appreciated.

    Probably no banning if you took that approach.

  37. 37
    centrestream says:

    He Who Shall Not Be Named @13: “as you know or should full well know, UD is open to CIVIL discussion but not to trolling and abusive Internet vandalism . . . a known, habitual problem for far too many objectors to design thought.”

    UD is definitely not open to civil discussion. It is only open to discussion that agrees with you and Barry. I thought that UD might be turning a new leaf when they granted an amnesty, but that barely lasted two weeks. Then I thought that they may at least starting to be fair in their banninations when they banned Joe, but then he was let back in under a technicality.

    You ban people who “refuse to accept your corrections”, but your “corrections” are just a difference of opinion.

    I look forward to a day when UD accepts truly open discussion, but I don’t think that I will ever see it.

  38. 38
    keith s says:

    jerry,

    Absolute nonsense. I have been commenting here for over 9 years and I have not seen one idea censored.

    That’s because you don’t see the ideas that are censored or hear from the critics who are banned.

    Think about it. It’s rather obvious, isn’t it?

  39. 39
    keith s says:

    keiths:

    The overwhelming majority of evolutionary biologists think that ID is a crock, if you haven’t noticed.

    bpragmatic:

    This proclamation, despite probably being true (that that is what they think), has long since become an absurd “appeal to authority” in my opinion.

    I’m not appealing to authority. I’m explaining to you that there are many ID critics out there, plenty of whom would be willing to come here to educate you — if they were allowed to. The problem is that the moderators here are afraid of critics and will ban them in order to protect ID from open discussion.

    I think that you would gain much credibility with many, if you were to take that advice. Why not start with scientific responses to the issues raised in “Barriers to Macroevolution: what the proteins say”.

    If you’ve been following UD lately, you’ll know that I have presented an argument demonstrating that ID is literally trillions of times worse at explaining the evidence when compared to unguided evolution.

    I am happily defending my argument against all comers — anyone who wishes to criticize it is welcome to do so. I’m not asking for anyone to be censored or banned.

    Perhaps you would enjoy taking my challenge. Surely you’re willing to “at least try and answer the honest question[s] with relevant answers”.

    Are you up for it, bpragmatic?

  40. 40
    jerry says:

    Think about it. It’s rather obvious, isn’t it?

    An absolute vacuous statement without any evidence. I suggest you starting naming the censored positions.

  41. 41
    keith s says:

    jerry,

    I suggest you starting naming the censored positions.

    My ONH rgument, for one. You know, the one that has been discussed on at least eight separate threads, and that IDers are still desperately trying to refute after more than two weeks.

    I came up with that argument in 2012. We would have been talking about it two full years ago if it hadn’t been for the censorship at UD.

    And I am far from the only one who has been censored and banned at UD. Look at the embarrassing history of bannings at UD.

  42. 42
    Daniel King says:

    An absolute vacuous statement without any evidence. I suggest you starting naming the censored positions.

    Just passing by and this caught my eye.

    If the comments in question have not been allowed to appear here, how could anyone quote them?

  43. 43
    keith s says:

    Daniel King:

    If the comments in question have not been allowed to appear here, how could anyone quote them?

    That’s what I told him:

    That’s because you don’t see the ideas that are censored or hear from the critics who are banned.

    Think about it. It’s rather obvious, isn’t it?

    The logic is not strong in this one.

  44. 44
    jerry says:

    If the comments in question have not been allowed to appear here, how could anyone quote them

    Another vacuous statement. People have been commenting here for 10 years. A high percentage of them have been anti-ID. Name one position that has been censored.

    We just had an admission that one of the positions has appeared on 8 threads. That is some censorship.

  45. 45
    keith s says:

    jerry,

    We just had an admission that one of the positions has appeared on 8 threads. That is some censorship.

    Logic fail.

    I was censored for two full years before finally being allowed to make my argument here.

    To borrow your words, that is some censorship.

  46. 46
    jerry says:


    Logic fail.

    I was censored for two full years before finally being allowed to make my argument here.

    To borrow your words, that is some censorship.

    I have no idea was system of logic you are using but you certainly were not banned for any ideas on evolution you had. Now with 8 threads somehow related to your idea you are claiming censorship.

    If your ideas were that good, what was preventing someone else from presenting them. Has this happened?

    I did not see any ideas being censored from all the people commenting here during the last few weeks. If there were, there are enough anti-ID people still here who could present them.

    If your ideas were that good, why bother presenting them here? I would think there are much better forums for true genius then this blog.

    As I said, this is all nonsense.

  47. 47
    bpragmatic says:

    keiths:

    The overwhelming majority of evolutionary biologists think that ID is a crock, if you haven’t noticed.

    bpragmatic:

    This proclamation, despite probably being true (that that is what they think), has long since become an absurd “appeal to authority” in my opinion.

    Keiths

    “I’m not appealing to authority. I’m explaining to you that there are many ID critics out there, plenty of whom would be willing to come here to educate you — if they were allowed to. The problem is that the moderators here are afraid of critics and will ban them in order to protect ID from open discussion.”

    Bpragmatic:

    I was just taking your original assertion on what appeared to me to be “face value”. Pardon me for my not making the connection.

    But, back to the point. I would think that anyone that could present actual relevant empirical”evidence that demonstrate(s) scientific evidence of a genuine path to macroevolution of proteins” (per Gpuccio) would be more than welcome here. If not, then that would be a bad thing for the credibility of this forum.

  48. 48
    bpragmatic says:

    Keiths:

    “Perhaps you would enjoy taking my challenge. Surely you’re willing to “at least try and answer the honest question[s] with relevant answers”.

    Are you up for it, bpragmatic?”

    Hello Keith. I did read through your 4 points of challenge. Wasn’t able, with the time available to fully consider what surely must be many assumptions that you are making in order to correlate your examples to the biochemical accumulations of living organisms and ecosystems and related. I hope to be able to have more time in the future to do so. Maybe you can contribute to what surely would not be just my inquisitiveness, but many others.

    Just an basic observation though: You seem to be somewhat confusing what might be called the “physical sciences” with other scientific disciplines such as “chemistry”, “biochemistry”, “organic chemistry” and perhaps other scientific disciplines, (ie quantum mechanics), There are the sciences that deal with the “macro” physical levels and those that deal at a “molecular” and perhaps “submolecular” levels.

    With all due respect,Overall, your assertions seem to rest on a significant degree of ignorance. Having said that, honestly, I haven’t read all of what you have written in this forum to suggest that that is in fact what is the case. Please correct me if wrong.

    I think you may be infusing your personal philosophically driven conclusions (you would be ok with dying and that is the end of it all for you. Meaning of life is what you make it, etc.)with any “impartial”, “scientific” narrative of the nature of reality.

    It might be said that “Too much philosophy is a danger to “real” science”.

  49. 49
    keith s says:

    jerry:

    I did not see any ideas being censored from all the people commenting here during the last few weeks. If there were, there are enough anti-ID people still here who could present them.

    By that logic, it isn’t censorship as long as at least one ID critic remains unbanned, because after all, that one person is available to present all of the ID criticisms.

    Brilliant, jerry.

  50. 50
    keith s says:

    jerry, bpragmatic,

    Have you actually looked at the evidence?

    UD’s hostility to open discussion is a fact, not a mere assertion.

  51. 51
    Quest says:

    keitch s h…y…

    You still have not responded to my challenge… Do you think it is just going to away…?

  52. 52
    jerry says:

    By that logic, it isn’t censorship as long as at least one ID critic remains unbanned, because after all, that one person is available to present all of the ID criticisms.

    Brilliant, jerry.

    But the problem is there has been hundreds of people who have commented here who oppose ID. Point to one criticism that has been censored. It cannot be what you presented because you yourself admit there has been 8 threads.

    Unless you can point to censored ideas, your objections are nonsense.

  53. 53
    bpragmatic says:

    Keiths:

    jerry, bpragmatic,

    Have you actually looked at the evidence?

    UD’s hostility to open discussion is a fact, not a mere assertion.

    Please have patience with me, so as to put it this way Keiths: Personally, I do not care what UD is or is not hostile towards. If this forum went away tomorrow, I really do not care, per se. Ultimately, I know what my motives are, and believe there are many others that share with this. I would like to know what the preponderance of empirical evidence leads to when considering questions regarding the origins of life, the development of the array of current organisms and the ecosystems that exist, the origination, nature and development of any various degrees of conciousness, and what can be determined to be the best explanations for the the emergence of such.

    Personally, and I believe this to be true with many who frequent this site, Ultimately, I have no “axe to grind”. But would like to understand more about the reality of existence.

    If you want to encourage my continued participation in discussions that you seem to be interested in, please respond to points that I made on post 48. Then, with clearer understanding, I can proceed to engage is discussions with you.

  54. 54
    keith s says:

    jerry,

    You are a True Believer. Impervious to evidence.

  55. 55
    keith s says:

    bpragmatic,

    Please have patience with me, so as to put it this way Keiths: Personally, I do not care what UD is or is not hostile towards.

    That’s fine, but remember that you asked the question:

    So…Where are the NDE scientists and pertinent scientific data to refute what must be flawed unsupported assertions presented above? Or, forget the NDE “scientists”. Let the usual philosophical “scientifically” uneducated hacks blow the usual rhetoric…

    You asked the question, and I gave you the answer:

    Don’t forget that UD is actively hostile to open discussion. Most ID critics get banned quickly, and there have been many bannings just within the last week.

    So when you ask “Where are the critics?”, the answer is “They’re out there, but your UD President is afraid to let them speak.”

    It’s pitiful, isn’t it?

    bpragmatic:

    Personally, and I believe this to be true with many who frequent this site, Ultimately, I have no “axe to grind”. But would like to understand more about the reality of existence.

    Give me a break. You definitely have an axe to grind:

    So…Where are the NDE scientists and pertinent scientific data to refute what must be flawed unsupported assertions presented above? Or, forget the NDE “scientists”. Let the usual philosophical “scientifically” uneducated hacks blow the usual rhetoric for obfuscation to substitute as legitimate challenges to serious questions. Surely, there is empirical evidence to clearly refute what everyone knows is “creationist” tripe. Yeah, that is it. If it were not for those stupid creationist’s and their blind adherence to the belief of the “sky fairy”, then the NDE conjecture would surely be completely and unabashedly vindicated without any reservation as the truth that has been clearly established by “empirical science”. Ha Ha! What a bunch of clowns.

    Try to be honest, bpragmatic.

    If you want to encourage my continued participation in discussions that you seem to be interested in, please respond to points that I made on post 48. Then, with clearer understanding, I can proceed to engage is discussions with you.

    Judging from past experience, I’m likely to be banned soon, so I’m focusing on discussions of my “objective nested hierarchy” argument, also known as “The Bomb”, in the time remaining. If you have criticisms to offer, you’re welcome to join in.

  56. 56
    keith s says:

    jerry,

    Rich (who has been banned, of course) would like to direct your attention to this. It’s an OP by former UD moderator DaveScot.

    Barry didn’t like it and deleted the entire thread, including the OP.

    Being a True Believer, you will no doubt find some way of rationalizing the censorship.

  57. 57
    RexTugwell says:

    Keith S, in your “time remaining” here, maybe you can finally answer bpragmatic’s original request for the “pertinent scientific data to refute what must be flawed unsupported assertions presented above” i.e. Dr. Torley’s OP on what the proteins say and stop wasting our time having to read your complaints about cencorship.

  58. 58
    Joe says:

    In order to be an ID critic one must be knowledgeable with respect to ID. That said, UD hasn’t had an ID critic in recent months and perhaps in years.

    Look at the embarrassing history of bannings at UD.

    Embarrassing for the banned,perhaps.

  59. 59
    Joe says:

    keith s:

    You are a True Believer. Impervious to evidence.

    And you are a true believer. Your position doesn’t have any evidence.

  60. 60
    jerry says:

    And you are a true believer. Your position doesn’t have any evidence.

    The evidence provided on censorship was about racism. That is it. Nothing about evolutionary biology. Probably removed in good taste.

  61. 61
    Mung says:

    Mung: Hasn’t keiths argued that there is only one single objective nested hierarchy of protein evolution that can be produced by unguided evolution?

    Perhaps keiths thinks the single unique objective nested hierarchy produced by unguided evolution only applies to macro-evolution and not to the evolution of protein folds.

    Maybe he believes that the evolution of protein folds is guided but macro-evolution is unguided.

    Go figure.

  62. 62
    bpragmatic says:

    Keiths, looks like you have not been banned yet. You said you would stick to your “bomb” of ONH because you thought you had limited time on this forum before you would be banned and you wanted to rest your case on that supposed piece of evidence. Well that was awhile ago. And you are still commenting here. Why not come up with the empirical evidence to put forth that must certainly be easily and readily available to support conjecture that no intelligent guidance is necessary to arrive at living organisms and ecosystems that are currently observable. Oh, and, to put it another way, come up with empirical scientific evidence that chemical processes and physical environments are sufficient to fulfill the accomplishment of such.

    Thanks

  63. 63
    keith s says:

    bpragmatic,

    Keiths, looks like you have not been banned yet.

    Yes. Like I said, I think I’m in a sweet spot right now. It would look ridiculous if UD banned me while my “bomb” is being discussed. But as you know, other critics have been banned.

    You said you would stick to your “bomb” of ONH because you thought you had limited time on this forum before you would be banned and you wanted to rest your case on that supposed piece of evidence.

    No, I said I would focus on the “bomb”. People are running out of counterarguments, though, so I have more time for other topics.

    Well that was awhile ago. And you are still commenting here. Why not come up with the empirical evidence to put forth that must certainly be easily and readily available to support conjecture that no intelligent guidance is necessary to arrive at living organisms and ecosystems that are currently observable.

    That’s what the ONH argument does. It shows that unguided evolution is literally trillions of times better at explaining those things than ID is.

    Oh, and, to put it another way, come up with empirical scientific evidence that chemical processes and physical environments are sufficient to fulfill the accomplishment of such.

    Ditto. It’s either unguided evolution or ID, unless you have a third alternative in mind. I’ve shown that unguided evolution is the superior hypothesis by a factor of trillions.

  64. 64
    Joe says:

    Yes keith s is in a sweet spot.He is the perfect example of our opponents- totally refuted and denying every minute of it.

  65. 65
    bpragmatic says:

    Keiths:

    “Ditto. It’s either unguided evolution or ID, unless you have a third alternative in mind. I’ve shown that unguided evolution is the superior hypothesis by a factor of trillions.”

    You have not shown anything of the sort. You put forth conjecture. Part of your imagination. You can not explain the origination and development of what constitutes the molecular underpiinnings of what an imagination even is.

    This is what really pisses off people who give this stuff a little thought. No science, just unsubstantiated assertions and undisciplined conjecture to promote the philosophical preferences of a few who have unwarranted authority under the guise of “science”. You clowns are a pack of obsolete beggars who need to get out of the way. And quit sucking off the public trough to support your ill begotten philosophy.

    Just some advice. You might want to consider addressing the questions posted at the OP here. If you can do that, maybe you can claim some legitimacy in your assertions.

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