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Chance Ratcliff’s video screen and the significance of search spaces

In a comment in the oldies thread on Sunday evening, Chance Ratcliff raised a very instructive case study  for a search space that is well worth being headlined. Let us adjust a bit on the calc of the config space, and reflect:

_____________

CR, 111, Oldies: >> An illustration might be of some help. For {{an 8-bit, 256 level}} gray scale

The proverbial needle in the haystack

The proverbial needle in the haystack

image of 1024 [ --> 2^10] pixels squared, there’s a search space of {{  2^20,  256-level elements giving 256^(2^20) = 4.26 *10^2,525,222}} possible configurations. This [strike . . . ] provides a vast landscape of images over which it is possible to traverse. For example, there are a nearly inestimable amount of configurations that could yield a recognizable rendering of Albert Einstein’s face. Yet it follows that this can only be a tiny proportion of all possible configurations, because where there may be a million ways to render Einstein’s face in a recognizable way, there must also be numerous ways to render any one of billions of other faces. And then we must also be able to render objects which are not faces at all, but any one of numerous other abstract or specific representations — cars, planes, trains, bicycles, motorcycles, cows, horses, donkeys, cats, dogs, planets, galaxies, chairs, tables, houses, skyscrapers, grass, trees, grapes, etc. — each in their personal identities (Saturn or Jupiter, Nero or Spot, Triumph or Harley, Ford Model T or Maserati MC12, etc). The images of all imaginable objects must be able to occupy the same configuration space of 1024×1024 pixels and 256 shades of gray in different configurations which must each differ substantially from Einstein.

Such is likely the case with proteins. After considering the noisy, non-folding sequences, specific biological functions must narrowly exist in the overall search space, because the space must also account for every type of possible function. I don’t think it’s reasonable to presume that ubiquitous functions such as ATP synthase, the ribosome, and the various polymerases are not required for “other” types of life. We don’t know such organisms can exist. It seems likely that, as with images of Einstein that are specific to a singular man, these biological subsystems are specific to a singular phenomenon in the known universe.

Even so, objections to specific functional necessities notwithstanding, traversing the noise is practically prohibitive. Just as generating random permutations in a 1024^2 gray scale image shouldn’t practically be expected to produce a recognizable image of Einstein, neither should random mutations effectively stumble on a functional sequence of amino acids, regardless of whether such a sequence could contribute to function in a constrained and complex operational system. >>

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Just so, the space of configs for 500 bits — think of a string of 500 coins in a row — must contain ALL 72 or so letter ASCII code sequences in English.  That is, just as the screen space has in it every conceivable image that can fit in 1024 * 1024 pixels as  a grayscale image, the 500-element binary string has in it every possible set of 72 letter English language sequences.

So, why don’t we use random walk scans to try to find what is out there, maybe with some sort of detector to lock-in a lucky hit?

Because that would predictably fruitlessly exhaust the atomic and temporal resources of the solar system, because the number of gibberish or noise states so vastly outnumbers the functional ones, that we confront the needle in the haystack search on steroids.

screen_shot

making screens of info the old fashioned way (by intelligent design)

That is the context in which we see why a threshold of 500 bits of complexity for a functionally specific organised entity allows us to identify that FSCO/I is a reliable, inductively backed up sign of design as best causal explanation.

CR’s screen example allows us to understand how even in cases where the is indeed a very large number of functional states, these will in turn be immersed in a vastly larger, unsearchable sea of gibberish or noise.

In simple terms, the number of snowy screen states vastly overwhelms the large but vastly smaller number of functional ones. So much so that we intuitively know that the best way to compose screen fulls of text or pictures or drawings, etc, is by intelligent effort.

In that context, let us look again at Dembski’s 2005 equation and its log-reduced, simplified derivative for practical purposes. First, Dembski 2005 (as was clipped and discussed in my always linked briefing note):

8 –> A more sophisticated (though sometimes controversial) metric has of course been given by Dembski, in a 2005 paper, as follows:

define ϕS as . . . the number of patterns for which [agent] S’s semiotic description of them is at least as simple as S’s semiotic description of [a pattern or target zone] T. [26] . . . . where M is the number of semiotic agents [S's] that within a context of inquiry might also be witnessing events and N is the number of opportunities for such events to happen . . . . [where also] computer scientist Seth Lloyd has shown that 10^120 constitutes the maximal number of bit operations that the known, observable universe could have performed throughout its entire multi-billion year history.[31] . . . [Then] for any context of inquiry in which S might be endeavoring to determine whether an event that conforms to a pattern T happened by chance, M·N will be bounded above by 10^120. We thus define the specified complexity[χ] of T given [chance hypothesis] H [in bits] . . . as  [the negative base-2 log of the conditional probability P(T|H) multiplied by the number of similar cases ϕS(t) and also by the maximum number of binary search-events in our observed universe 10^120]

χ = – log2[10^120 ·ϕS(T)·P(T|H)].

9 –> When 1 >/= χ, the probability of the observed event in the target zone or a similar event is at least 1/2, so the available search resources of the observed cosmos across its estimated lifespan are in principle adequate for an observed event [E] in the target zone to credibly occur by chance. But if χ significantly exceeds 1 bit [i.e. it is past a threshold that as shown below, ranges from about 400 bits to 500 bits -- i.e. configuration spaces of order 10^120 to 10^150], that becomes increasingly implausible. The only credibly known and reliably observed cause for events of this last class is intelligently directed contingency, i.e. design. Given the scope of the Abel plausibility bound for our solar system, where available probabilistic resources

 qΩs = 10^43 Planck-time quantum [not chemical -- much, much slower] events per second x

10^17 s since the big bang  x

10^57 atom-level particles in the solar system

Or,  qΩs = 10^117 possible atomic-level events [--> and perhaps 10^87 "ionic reaction chemical time" events, of 10^-14 or so s],

  . . . that is unsurprising.

10 –> Thus, we have a Chi-metric for CSI/FSCI . . .  providing reasonable grounds for confidently inferring to design . . . [which relies] on finding a reasonable measure for the information in an item on a target or hot zone — aka island of function where the zone is set off observed function — and then comparing this to a reasonable threshold for sufficiently complex that non-foresighted mechanisms (such as blind watchmaker random walks from an initial start point and leading to trial and error), will be maximally unlikely to reach such a zone on the gamut of resources set by our observable cosmos.

This can be simplified, as is done in the IOSE, to give the Chi_500 metric:

χ = – log2[10^120 ·ϕS(T)·P(T|H)].

–> χ is “chi” and ϕ is “phi” . . . .

xxi: So, since 10^120 ~ 2^398, we may “boil down” the Dembski metric using some algebra — i.e. substituting and simplifying the three terms in order — as log(p*q*r) = log(p) + log(q ) + log(r) and log(1/p) = – log (p):

Chi = – log2(2^398 * D2 * p), in bits,  and where also D2 = ϕS(T)
Chi = Ip – (398 + K2), where now: log2 (D2 ) = K
That is, chi is a metric of bits from a zone of interest, beyond a threshold of “sufficient complexity to not plausibly be the result of chance,”  (398 + K2).  So,
(a) since (398 + K2) tends to at most 500 bits on the gamut of our solar system [[our practical universe, for chemical interactions! ( . . . if you want , 1,000 bits would be a limit for the observable cosmos)] and
(b) as we can define and introduce a dummy variable for specificity, S, where
(c) S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T:

Chi =  Ip*S – 500, in bits beyond a “complex enough” threshold

This leads to a situation where this can be used to take advantage of the Durston metric (which reckons with function already so S = 1, and which takes into account redundancy):

xxii: So, we have some reason to suggest that if something, E, is based on specific information describable in a way that does not just quote E and requires at least 500 specific bits to store the specific information, then the most reasonable explanation for the cause of E is that it was designed. The metric may be directly applied to biological cases:

Using Durston’s Fits values — functionally specific bits — from his Table 1, to quantify I, so also  accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:
RecA: 242 AA, 832 fits, Chi: 332 bits beyond
SecY: 342 AA, 688 fits, Chi: 188 bits beyond
Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond

 xxiii: And, this raises the controversial question that biological examples such as DNA — which in a living cell is much more complex than 500 bits — may be designed to carry out particular functions in the cell and the wider organism.

All of this in turn gives a context for the significance of CR’s discussion. END

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63 Responses to Chance Ratcliff’s video screen and the significance of search spaces

  1. F/N I am having posting problems due I think to a local internet out. Please be patient. KF

  2. If I may cite Durston’s new paper:

    (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

    Supporting notes:

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    “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

    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/

  3. 3

    KF, thanks for the headline. I happen to like the image space example because it is intuitive. It’s amazing how quickly probabilistic resources are exhausted, even for much smaller images. The number of possible states in a 32×32 pixel image at 1 bit per pixel is 2^1024 or 1.8E308, which is more than Dembski’s universal probability bound squared. These figures make the number of atoms in the universe appear practically insignificant. :)

    Of course as agents we navigate such spaces with seemingly little effort. Exactly how we accomplish such is still a mystery. However assuming a modest 10,000 word vocabulary as a context, a 100 word paragraph exists in a space of (10^4)^100 configurations, which is 10^400 possible states. Yet we’re quite capable of navigating the meaningful arrangements. This quality of intelligence, while hardly quantifiable, is undoubtedly objectively quite real.

    Thanks again.

  4. CR thanks for the excellent image space example. It is intuitive indeed!


    Bornagain77 #2, you mention Durston’s new paper which is about the RecA protein. Remember the world’s toughest bacterium – Deinococcus radiodurans?
    Excerpt: “When subjected to high levels of radiation, the Deinococcus genome is reduced to fragments,” they write in Proceedings of the National Academy of Sciences. “RecA proteins may play role in finding overlapping fragments and splicing them together.”
    There is this RecA protein again! I’m talking about that magical protein that somehow ‘knows’ the correct sequence of the bacterial DNA and stitches the shattered fragments back together.

  5. ‘I’m talking about that magical protein that somehow ‘knows’ the correct sequence of the bacterial DNA and stitches the shattered fragments back together.’

    Outside the Consensus, cogitation is just one of the lesser known skills of brute matter, Box. You miss an awful of good stuff, being at the margins.

    But what am I saying? Aren’t they, however informally, members of an animist cult, as one of the editors of Nature once suggested, I believe.

  6. Axel #5, you are absolutely right of course. I guess that my puzzlement about these phenomenons just shows my unfamiliarity with basic chemistry ;)

  7. box: There is this RecA protein again! I’m talking about that magical protein that somehow ‘knows’ the correct sequence of the bacterial DNA and stitches the shattered fragments back together.

    How does a restriction enzyme ‘know’ where to cut DNA? How does hemoglobin ‘know’ when to load oxygen and when to unload oxygen? How do DNA primers know where to bond on a stand of DNA? ect. ect.

    Did you read the article? It does contain the answer to how the protein ‘knows’ how to stitch the genome back together

  8. 8

    Box @4, you are very kind! You’re welcome :)

  9. Box thanks for reminding me of that ‘magical’ protein. I will definitely have to put it close to the Durston paper.

  10. Franklin #7: How does a restriction enzyme ‘know’ where to cut DNA? (…) How do DNA primers know where to bond on a stand of DNA? etc. etc.

    Intriguing questions! I will add one more: ‘how does the cell keep the DNA strands from getting hopelessly tangled’?
    Stephen L Talbott: “All we can say currently is that we know some of the players addressing the problem. For example, there are enzymes called “topoisomerases” whose task is to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of genes or regions of the chromosome, and prevent a hopeless mass of knots. Some topoisomerases cut just one strand of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. This alters the supercoiling of the DNA. Other topoisomerases cut both strands, pass a loop of the chromosome through the gap thus created, and then seal the gap again. (Imagine trying this with miles of string crammed into a tennis ball!)“.

    Franklin #7: Did you read the article? It does contain the answer to how the protein ‘knows’ how to stitch the genome back together.

    Surely you are mistaken. There is nothing in the article that even hints at an answer; only vague speculations about elements that could be involved in an unknown mechanism – an unknown repair mechanism that presupposes knowledge of the correct DNA sequence. May I suggest to you that you reread the article on world’s toughest bacterium.

  11. Box, there’s this also:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]“,,,
    http://www.thenewatlantis.com/.....nisms-mean

    The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern – July 2011
    Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,”,,, “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”,,,
    http://www.physorg.com/news/20.....-seen.html

    An Electric Face: A Rendering Worth a Thousand Falsifications – September 2011
    Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”
    http://darwins-god.blogspot.co.....usand.html

    There is simply no coherent answer as to how this is possible from a materialistic perspective. Anyone, franklin especially included, who argues otherwise is being severely disingenuous:

    With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory – November 2011
    Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,,
    http://www.evolutionnews.org/2.....52821.html

  12. Bornagain77 #11: There is simply no coherent answer as to how this is possible from a materialistic perspective. Anyone, franklin especially included, who argues otherwise is being severely disingenuous.

    Bornagain77, once more I have to say that I could not agree more. The utter impossibility of a concept from a materialistic perspective hit me once more when I read about gene regulation by nuclesomes. DNA strands are partially wrapped around many nucleosomes – containing of histones. The position and shape of these histones are a determining factor of gene expression! Some parts of the DNA strands are simply inaccessible for expression because of its spatial position at the spools. What hit me is the realization that this cannot be framed mechanically!

    Stephen L Talbott: Nucleosomes will sometimes move — or be moved (the distinction between actor and acted upon is obscured in the living cell) — rhythmically back and forth between alternative positions in order to enable multiple transcription passes over a gene. (…)
    The histone spool of nucleosomes, for example, is not some rigid thing. It would be far better to think of its “substance,” “surface,” “contact points,” and “physical interactions” as forms assumed by mutually interpenetrating forces in intricate and varied play. (…) The nucleosome is rather like a maestro directing the genetic orchestra, except that the direction is itself orchestrated by the surrounding cellular audience in conversation with the instrumentalists. (…)
    After a few histone tail modifications were found to be rather distinctly associated with active or repressed genes, the forlorn hope arose that we would discover a precise, combinatorial “histone code.” It would provide a kind of fixed, digital key enabling us to predict the consequences of any arrangement of modifications. But this was to ignore the nearly infinite variety of all those other factors that blend their voices in concert with the histone modifications. In the plastic organism, what goes on at the local level is shaped and guided by a larger, coherent context. As Shelley Berger of Philadelphia’s Wistar Institute observes: ”Although [histone] modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin “language” in which different combinations of basic building blocks yield dynamic functional outcomes. (…)
    Each histone tail modification reshapes the physical and electrical structure of the local chromatin, shifting the pattern of interactions among nucleosome, DNA, and associated protein factors. To picture this situation concretely is immediately to realize that it cannot be captured in purely digital terms. (…)
    Berger envisions histone modifications as participating in “an intricate ‘dance’ of associations.” (…)
    Histones can even be removed from a spool altogether, leaving it “incomplete.” And certain proteins can slide spools along the DNA, changing their position. As we have seen already, a shift of position by as little as two or three base pairs can make the difference between gene activation or repression, as can changes in the rotational orientation of the DNA on the face of the histone spool. And the tails — no doubt depending at least in part on the various modifications and protein associations mentioned earlier — can thread themselves through the encircling double helix, perhaps either loosening it from the spool or holding it more firmly in place.

    And this is just a small part of the all important regulation of chemicals in the cell. Like Behe stated: ‘The essence of cellular life is regulation: The cell controls how much and what kinds of chemicals it makes; when it loses control, it dies.’

  13. Although I expect most of you would know this man, I’ve only come across his name, Rupert Sheldrake, a few times – but that’s all, until today. However, I came across this video just now:

    http://www.whydontyoutrythis.c.....R8939.dpbs

    Also, I thought this quote, noteworthy, and would appeal to this happy brotherhood:

    “The day science begins to study non-physical phenomena, it will make more progress in one decade than in all the previous centuries of its existence.”?Nikola Tesla

  14. here are few extra notes on epigenetics that are very antagonistic to the materialistic perspective:

    It is found that even our thoughts and feelings can ‘epigenetically’ control the gene expression of our bodies:

    Genie In Your Genes – video
    http://www.genieinyourgenes.com/ggtrailer.html
    main website
    excerpt: There are over 100 genes in your body that are activated by your thoughts, feelings and experiences
    http://www.genieinyourgenes.com/

    Anxiety May Shorten Your Cell Life – July 12, 2012
    Excerpt: These studies had the advantage of large data sets involving thousands of participants.
    If the correlations remain robust in similar studies, it would indicate that mental states and lifestyle choices can produce epigenetic effects on our genes.
    http://crev.info/2012/07/anxie.....cell-life/

    a few more notes:

    The Mysterious Epigenome. What lies beyond DNA – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

    Non-Random and Targeted Mutations (Epigentics to the level of DNA) – video
    http://www.youtube.com/watch?v=qTChu5vX1VI

    ,,, And then there is the fact that the entire concept of a ‘gene’ as a fundamental unit of inheritance is being swallowed up by the sheer complexity of what is being revealed for what is termed ‘alternative splicing’:

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Astonishing DNA complexity demolishes neo-Darwinism – Alex Williams
    Excerpt: Exons are not gene-specific but are modules that can be joined to many different RNA transcripts. One exon (i.e. a protein-making portion of one gene) can be used in combination with up to 33 different genes located on as many as 14 different chromosomes. This means that one exon can specify one part shared in common by many different proteins.
    http://creation.com/images/pdf.....11-117.pdf

    If that wasn’t bad enough for Darwinists, the ‘top down’ alternative splicing codes for chimps and humans are found to be vastly different,,

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Moreover the genetic similarity for chimps and humans is found, now that more data is coming in, to be nowhere near the 99% mark that Darwinists had originally misled people to believe:

    Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% – by Jeffrey P. Tomkins – February 20, 2013
    Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor.
    http://www.answersingenesis.or.....chromosome

  15. box: Surely you are mistaken.

    Not at all. The article, while not outling the complete mechanistic details (theh are available elsewhere) provides keen insight into how it works. then mention of six to ten copies of the genome, the RecA protein activity in finding overlapping sequences and the ability to stitch together at least one complete copy of the genome in the ‘salvage’ operation. Following that a quick search (about 30 sec) located the mechanistic details of how the protein has several active sites for binding different things, i.e., ssDNA, dsDNA, an ATP hydrolysis site, ect. Fairly complete descriptions are readily available on how the process proceeds.

    It certainly is not ‘magic’ and the chemistry really isn’t all that hard to understand provided you have some foundation in biochemical processes.

    Are you confused about the other questions asked or do you have a firm understanding of how hemoglobin ‘knows’ to bind oxygen and when to unload pxygen or how PCR primers work (let alone the entire PCR process in use in labs all over the world?

  16. box: I will add one more: ‘how does the cell keep the DNA strands from getting hopelessly tangled’?

    Hopefully you recognize that the thread analogy is fairly limited in that threads do not have charged sections which cause threads to ‘stick’ together. Here is another limited analogy for you: why can’t you get two south poles of a magnet to stick together yet a north and south pole can stick together?

  17. Franklin #15 #16, you haven’t even begun to address the problems presented in my posts.

  18. This is truly painful to watch.

    franklin’s answer to everything the past couple of days has been that we are dealing with particles that have “mass and charge.” It’s chemistry all the way down, don’t ya know.

    Clearly having little understanding of what actually goes on in the cell, franklin proposes that the answers lie in the fact that we are dealing with molecules that have mass and charge. Given that this is true of virtually all molecules, the “explanation” of mass and charge is no different from saying that something is a molecule.

    To all the interesting questions, franklin has the answer:

    How do the amino acids come together to form the correct amino acid chain?

    They are molecules!

    How does the chain properly fold into a functional protein?

    It’s a molecule!

    How do the DNA strands keep from getting tangled in the cell?

    The strands are made up of molecules!

    How does an enzyme know how (and when and where) to properly splice DNA?

    It’s a molecule!

    Yes, indeed, how do we get all the amazing structures we have in biology?

    Molecules! With mass and charge!

    Talk about a Johnny-One-Note. Unfortunately, a moment’s reflection for the individual of average intelligence is adequate to teach us that the note being incessantly pounded out is the wrong note.

    When researchers ask perfectly reasonable questions, like how DNA copying, splicing, and winding can occur with fidelity in the cell, to every question we see franklin in the front row, with his hand raised, shouting “Ooh, ooh, I know, I know! They are molecules! They have mass and charge!”

    The proper response is not to indulge his delusion but to reply “Yes, yes, we know they are molecules and that they have mass and charge. Now please go sit in the back corner quietly, while we actually take a close look at the real issues.”

  19. box: Franklin #15 #16, you haven’t even begun to address the problems presented in my posts.

    ‘Problems? I only see confusion and bewilderment on your part in wondering how any of these things work on a biochemical level.

    eric: Clearly having little understanding of what actually goes on in the cell, franklin proposes that the answers lie in the fact that we are dealing with molecules that have mass and charge.

    Can you name one process that is going on in the cell that does not involve molecules that have mass and charge? Or for that matter anything in the activity in the cell which does not involve chemistry/biochemistry?

    eric: How do the amino acids come together to form the correct amino acid chain?

    They are molecules!

    How does the chain properly fold into a functional protein?

    It’s a molecule!>/blockquote>

    eric, it is not just that they are molecules it is what the physical and chemical environment these molecules posses that dictate what they can and cannot react with in the cell and the organisms.

    It is readily apparent to all reading that you have no grasp for how any biochemical process proceeds within the cell. You should really try and fix that deficiency if you want to speak to the details of anything at all that goes on within the cell. From someone who does have a reasonable understanding of biochemical process your posts have a great ‘face palming’ impact for me or anyone with the barest understanding of what is attempted to being discussed. I doubt you can even spot the ridiculous, and ignorant, nature of, what you thought was a stunning insight, on why a organism that lived a million years wouldn’t evolve into another organism. I about peed my pants reading that line of thought!

  20. franklin, I take it that you are a atheist who believes in reductive materialism, in that you believe that everything, all information, all life, and all consciousness, is reducible to a material basis. But I have a little problem with your reductive materialistic scenario. You see franklin it turns out that recent advances in quantum theory have allowed us to reduce material particles to information.

    Here are my references for the claim that “energy and mass both reduce to information”:

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    How Teleportation Will Work -
    Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made.
    http://science.howstuffworks.c.....ation1.htm

    Quantum Teleportation – IBM Research Page
    Excerpt: “it would destroy the original (photon) in the process,,”
    http://researcher.ibm.com/view_project.php?id=2862

    Unconditional Quantum Teleportation – abstract
    Excerpt: This is the first realization of unconditional quantum teleportation where every state entering the device is actually teleported,,
    http://www.sciencemag.org/cont.....6.abstract

    It is also very interesting to note that the quantum state of a photon is actually defined as ‘infinite information’ in its uncollapsed quantum wave state:

    Quantum Computing – Stanford Encyclopedia
    Excerpt: Theoretically, a single qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,,
    http://plato.stanford.edu/entr.....tcomp/#2.1

    Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh
    Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) — Concept 2. is used by Bennett, et al. Recall that they infer that since an infinite amount of information is required to specify a (photon) qubit, an infinite amount of information must be transferred to teleport.

    As well franklin, besides reducing atoms and photons to information, advances in quantum theory have shown that encoded ‘classical’ information such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is a subset of conserved ‘non-local’ (beyond space and time) quantum entanglement/information by the following method:

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    All this is simply not good for a died in the wool reductive materialists like you franklin!

    Moreover franklin, as if the preceding was not bad enough for your preferred atheistic worldview, due to advances in quantum theory the argument for God from consciousness can now be framed like this:

    1. Consciousness either preceded all of material reality or is a ‘epi-phenomena’ (emergent property) of material reality.
    2. If consciousness is a ‘epi-phenomena’ (emergent property) of material reality then consciousness will be found to have no particularly special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.
    3. Consciousness is found to have a special, even central, position within material reality.
    4. Therefore, consciousness is found to precede material reality.

    Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Leggett’s Inequalities, Wheeler’s Delayed Choice; Wigner’s Quantum Symmetries; Quantum Zeno effect)
    https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit

    The Galileo Affair and Life/Consciousness as the true “Center of the Universe”
    https://docs.google.com/document/d/1BHAcvrc913SgnPcDohwkPnN4kMJ9EDX-JJSkjc4AXmA/edit

  21. Franklin #19: ‘Problems? I only see confusion and bewilderment on your part in wondering how any of these things work on a biochemical level.

    Well, this explains a lot. To be clear, how things work on the biochemical level is not the issue at all. May I suggest to you that you change your tone and step up your efforts for understanding if you wish to be taken seriously.

  22. box: Well, this explains a lot. To be clear, how things work on the biochemical level is not the issue at all

    so when you ask “how does RecA ‘know’ how to stitch the genome back together” you’re not asking about the mechanism the protein uses to accomplish this task? What is it then that you are actually asking?

    box: May I suggest to you that you change your tone and step up your efforts for understanding if you wish to be taken seriously.

    What have I misunderstood? Do you think eric is going to be able to describe a cellular process that does not involve biochemistry? Can you meet that task?

  23. Franklin #22: so when you ask “how does RecA ‘know’ how to stitch the genome back together” you’re not asking about the mechanism the protein uses to accomplish this task? What is it then that you are actually asking?

    Franklin, why the quotation marks? You should know very well that you are not quoting me. Moreover your paraphrasing of my ‘question’ misses the point.
    Probably you refer to my following remark:

    Box: #4: I’m talking about that magical protein that somehow ‘knows’ the correct sequence of the bacterial DNA and stitches the shattered fragments back together.

    And this was not a question franklin, because I know it to be a mystery. Cox and Jong-Il Kim are quoted to be not even sure if RecA proteins play a role in this mysterious process. So please don’t you ‘explain’ it to me with chemistry which ‘really isn’t all that hard to understand provided you have some foundation in biochemical processes.’

  24. box: Franklin, why the quotation marks? You should know very well that you are not quoting me. Moreover your paraphrasing of my ‘question’ misses the point.
    Probably you refer to my following remark:

    no I was referring to a remark you made in another thread re:RecA and how does it ‘know’ how to stitch the genome together.

    box:And this was not a question franklin, because I know it to be a mystery.

    you know this how? Did you think I was making it up when I stated that it is known where and how RecA binds ssDNA, dsDNA, ATP, and how the protein interacts with the DNA to put the genome together? This is all known and published research and it is all chemistry.

    There certainly is more ongoing research with this protein but there is a pretty fair body of literature which elevates it quite above the level of ‘mysterious’ except, evidently, to you and likely Eric as well.

    Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7917-21. Epub 2002 Jun 4.
    The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways.
    Kim JI, Cox MM.
    Source
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544, USA.
    Abstract
    The RecA protein of Escherichia coli, and all filament-forming homologues identified to date, promote DNA strand exchange by a common, ordered pathway. A filament is first formed on single-stranded DNA, followed by uptake of the duplex substrate. These proteins are thereby targeted to single-strand gaps and tails where recombinational DNA repair is required. The observed course of DNA strand exchange promoted by the RecA protein from the extremely radioresistant bacterium Deinococcus radiodurans is the exact inverse of this established pathway. This reaction lies at the heart of a remarkably efficient system for the repair of DNA damage.

    yup, sure seems like Kim and Cox think it is a big mystery and possibly not even involved in the process at all…oh wait that would be wrong!

  25. franklin @19:

    Can you name one process that is going on in the cell that does not involve molecules that have mass and charge?

    LOL!

    Talk about missing the whole issue. Do yourself a favor, franklin, and stop digging the hole you’re in.

    Everything around you involves molecules that have mass and charge. Molecules having mass and charge does not explain any functional, complex, specified structure. Not at the macro level and not at the micro level.

    And please stop it with your silly assertions that you understand so much about biochemistry. You obviously have no clue how cellular processes work. If you did, you would realize that there are design principles at work, algorithms for construction, protocols that control your precious particles with mass and charge. It is not chemistry all the way down.

    Take some time to actually think through the issues. At that point your “explanations” based on mass and charge will quickly fade away and you will start to actually home in on some interesting questions.

  26. box, here is another example of a trio of clueless researchers regarding RecA:

    Cell. 2009 Mar 20;136(6):1044-55. doi: 10.1016/j.cell.2009.01.018.
    Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans.
    Slade D, Lindner AB, Paul G, Radman M.
    Source
    Université Paris Descartes, Faculté de Médecine, INSERM U571, Paris, France.
    Abstract
    Deinococcus radiodurans’ extreme resistance to ionizing radiation, desiccation, and DNA-damaging chemicals involves a robust DNA repair that reassembles its shattered genome. The repair process requires diploidy and commences with an extensive exonucleolytic erosion of DNA fragments. Liberated single-stranded overhangs prime strand elongation on overlapping fragments and the elongated complementary strands reestablish chromosomal contiguity by annealing. We explored the interdependence of the DNA recombination and replication processes in the reconstitution of the D. radiodurans genome disintegrated by ionizing radiation. The priming of extensive DNA repair synthesis involves RecA and RadA proteins. DNA polymerase III is essential for the initiation of repair synthesis, whereas efficient elongation requires DNA polymerases I and III. Inactivation of both polymerases leads to degradation of DNA fragments and rapid cell death. The present in vivo characterization of key recombination and replication processes dissects the mechanism of DNA repair in heavily irradiated D. radiodurans.

  27. eric: If you did, you would realize that there are design principles at work, algorithms for construction, protocols that control your precious particles with mass and charge.

    Ok here is your chance, eric, explain to me how these algorithms and construction protocols work. I do expect some detail concerning their interaction with my ‘precious particles with mass and charge’. So far you’ve avoided backing up any of your assertions (e.g., simplest life form where you stated you know what the minimal requirements are) i so hope you don’t disappoint this time as well.

  28. Franklin #24 #26, you miss the point completely, so I can only repeat what I already stated in post #17. I’m done communicating with you because you have nothing to add and have demonstrated a complete misunderstanding of the subject at hand.

  29. franklin, since you know for a fact that life is ‘chemistry all the way down’, and you got all those pesky biochemical details worked out as to how they can generate these extremely sophisticated algorithms controlling these molecules, perhaps you would like to toss your hat into the ring for the million dollar ‘origin of life’ prize:

    Doctor evil – One Million Dollars – video clip
    http://www.youtube.com/watch?v=l91ISfcuzDw

    The Origin-of-Life Prize ®
    The annuity consists of $50,000.00 (U.S.) per year for twenty consecutive years, totalling one million dollars in payments.
    http://lifeorigin.info/

    My hunch franklin is that you will have a bit more trouble proving life can come from chemicals than you think:

    Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information – David L. Abel and Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?”
    http://www.biomedcentral.com/c.....2-2-29.pdf

    First-Ever Blueprint of ‘Minimal Cell’ Is More Complex Than Expected – Nov. 2009
    Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae’s transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
    “At all three levels, we found M. pneumoniae was more complex than we expected,”
    http://www.sciencedaily.com/re.....173027.htm

    To Model the Simplest Microbe in the World, You Need 128 Computers – July 2012
    Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That’s a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,,
    The bioengineers, led by Stanford’s Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What’s fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell’s lifecycle processes.,,,
    ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore’s Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that’s only a fraction of what will eventually be required to consider the simulation realistic.,,,
    http://www.theatlantic.com/tec.....rs/260198/

    Meet Mycoplasma, a parasitic bare-bones bacterium, with 484 genes – schematic representation of integrated enzyme cycles
    http://www.pnas.org/content/103/2/425/F3.large.jpg

    “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong

    ‘The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.”
    Carl Sagan, “Life” in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894

    The Theist holds the Intellectual High-Ground – March 2011
    Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.”
    (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU)

    So where did all that 100 million pages of information in a ‘simple bacteria’ (as measure from the thermodynamic perspective) come from franklin?

    Is There Evidence of Something Beyond Nature? – John Lennox – semiotic information – video
    http://www.youtube.com/watch?v=F6rd4HEdffw

    I have a solid clue for you franklin as to where all that information came from:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made by him; and without him was not any thing made that was made. In him was life; and the life was the light of men.

    Music:

    Tenth Avenue North – You Are More
    http://www.youtube.com/watch?v=IwtcwQwgdsA

  30. ‘box: Franklin #24 #26, you miss the point completely, so I can only repeat what I already stated in post #17. I’m done communicating with you because you have nothing to add and have demonstrated a complete misunderstanding of the subject at hand.

    I asked you to make your point since it apparently wasn’t about the mechanism of action of RecA but I’m a bit surprised that you can’t even admit you were mistaken about Kim, Coz, and RecA.

  31. so franklin, as a reductive materialist, there is nothing at all mysterious as to how the Deinococcus genome can be put back together after being reduced to fragments?

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    Its that all just basic chemistry for you franklin? DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days. Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem as to how to efficiently repair DNA, in a purely ‘material’ fashion, by crunching bits to make the calculation, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA. Indeed proteins and DNA have now been shown to have ‘non-local’ quantum entanglement/information in them that dwarf man’s achievements thus far in the area of entangling particles for quantum computation.

    Testing quantum entanglement in protein
    Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules.
    http://www.quantum-mind.co.uk/.....-c288.html

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini and 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/

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    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/

    Quantum entanglement between the electron clouds of nucleic acids in DNA – Elisabeth Rieper, Janet Anders and Vlatko Vedral – February 2011
    http://arxiv.org/PS_cache/arxi.....4053v2.pdf

    In the following article, Dr. Hameroff expands on the quantum computation aspect of Rieper, Anders and Vedral paper:

    Is DNA a quantum computer? Stuart Hameroff
    Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,,
    http://www.quantumconsciousnes.....puter1.htm

    Moreover franklin, a beyond space time cause must be appealed to to explain quantum entanglement:

    Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012)
    Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed.
    Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,,
    The remaining option is to accept that (quantum) influences must be infinitely fast,,,
    “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,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,
    http://www.sciencedaily.com/re.....142217.htm

    thus franklin, of all the things that may be said of what is happening in the cell, ‘it’s chemistry all the way down’, is not one of them!

  32. ba77: so franklin, as a reductive materialist, there is nothing at all mysterious as to how the Deinococcus genome can be put back together after being reduced to fragments?

    No more ‘mysterious’ than how restriction enzymes function, or how ‘mysterious’ it is that DNA primers ‘know’ where to bind on ssDNA, or how a retrovirus incorporates its genome into the host cell, ect. That you don’t know how these things function doesn’t make it ‘mysterious’ to those who do understand these things.

    ba77: Its that all just basic chemistry for you franklin?

    Absolutely!

  33. Tell you what, franklin. Let’s regroup and come back to some basic issues to see if we can make any progress in the discussion.

    Do you agree that there is a difference between necessary conditions and sufficient conditions?

    Do you acknowledge that if you you take all the individual molecules necessary for a functional cell and put them in a test tube or solution that they will not spontaneously come together by pure chemistry (using their mass and charge) to form a functional cell?

  34. Eric, tell you what I would rather you describe for me the algorithm and construction protocols you claim exist in the cell and I am especially interested in how they interact with my ‘particles that have mass and charge’. You’ve already bailed on suppling the information on the simplest replicator that you claim you posses. If you would do that, IMO, we would then be making progress in the discussion.

  35. franklin, we have to get back to a very fundamental question of causation before anything else in the discussion matters.

    If you want to learn something about cell algorithms, protocols, regulation and so on, spend some time Googling. I fear it may not be helpful, however, because you are under the impression that it is “all just chemistry.” That is as silly as looking at a computer and saying it is “all just electrons.” To be sure, it uses electrons, but the way the electrons are moved, stored, accessed, processed — based on design parameters, inputs, feedbacks, algorithms, protocols, controls — is what makes a computer, not just the physical properties of the particle. The same goes for a cell.

    As to the simplest living cell, my understanding is that the simplest living cell has just under 500 proteins. Some researchers (Morowitz, for example) have speculated that it might be possible to get a viable cell with around 240-250 proteins. That is perhaps optimistic, but we need to at least look at that level of complexity for a functional cell.

    I would note that this is just looking at raw number of proteins, without taking into account construction requirements and blueprints.

    There were three papers published in 2009 that looked into the “minimal cell.” They studied Mycoplasma pneumoniae. Interestingly: “At all three levels, we found M. pneumoniae was more complex than we expected,” says Luis Serrano, co-initiator of the project at EMBL and now head of the Systems Biology Department at CRG.” The news article is here:

    http://www.sciencedaily.com/re.....173027.htm

    —–

    All very interesting. However, we don’t need to get into that level of discussion yet, because you are stuck on a much more basic issue. If you are unable to answer the very basic fundamental questions I posed in #33, then all the discussions in the world about cellular machinery, genetic coding, programming and the like won’t make any difference to your view.

    So I ask again:

    1. Do you agree that there is a difference between necessary conditions and sufficient conditions?

    2. Do you acknowledge that if you take all the individual molecules necessary for a functional cell and put them in a test tube or solution that they will not spontaneously come together by pure chemistry (using their mass and charge) to form a functional cell?

    No books needed, no citations required, no special pleadings allowed.

    Just simple logic.

    Yes or no?

  36. eric: If you want to learn something about cell algorithms, protocols, regulation and so on, spend some time Googlin

    Eric, you made a claim about these algorityms and control protocols that interact with my ‘particles that have mass and charge’. If I go to google and find some info you’ll just claim its the wrong info. To prevent any misunderstanding just give me the information that you have on these claims of yours.

    eric: If you are unable to answer the very basic fundamental questions I posed in #33, then all the discussions in the world about cellular machinery, genetic coding, programming and the like won’t make any difference to your view.

    How about you don’t make any speculations on what I can or cannot answer before you, yourself, provide the information about the claims you have made previously. Personally, I don’t think you can do it and that is why you sent me to google. for all the onlookers prove me wrong!

    As for your questions I am not willing to address them until you’ve provided the information that you state you posses. FYI: once that is done and I answer your questions I will want to know what exactly you propose to place into the test tube for your proposed experiment. Prepare your list and conditions!

    eric: As to the simplest living cell, my understanding is that the simplest living cell has just under 500 proteins

    What makes you think the first replicator was a cell?

  37. Just your basic bluff…NO scientist ‘understands’ how these things function.

    franklin said: No more ‘mysterious’ than how restriction enzymes function, or how ‘mysterious’ it is that DNA primers ‘know’ where to bind on ssDNA, or how a retrovirus incorporates its genome into the host cell, ect. That you don’t know how these things function doesn’t make it ‘mysterious’ to those who do understand these things.

    More bravado! franklin couldn’t begin to provide equations for the chemistry involved. If he could, then we could all go home while franklin builds a cell from scratch.

    franklin’s ploy is banking on the fact that ID will never be able to provide the evidence for information being a separate, functional entity required for living systems.

    The key take away here is….the trend is your friend. The scientific trend is seeking that missing element that organizes matter using physics and chemistry…and information is a viable candidate for that role.

    Eh, let franklin has his fun….how does that saying go?…the one who laughs last laughs the hardest…

    Go on frankin. Bellow, my pedantic fellow…we’ll take it on our chinny, chin, chins….but wait, wait till we get our gas masks on!!!

    ba77: Its that all just basic chemistry for you franklin?

    franklin said: Absolutely!

  38. franklin asks,

    What makes you think the first replicator was a cell?

    Well, for starters we now have very good reason to believe that ‘simple’ bacterial cells suddenly appeared on earth as soon as water appeared on the face of earth. In fact in the oldest sedimentary rocks ever found on earth we find that,,

    The Sudden Appearance Of Photosynthetic Life On Earth – video
    http://www.metacafe.com/watch/4262918

    Yet we have no evidence of prebiotic chemistry before this time,,

    Dr. Hugh Ross – Origin Of Life Paradox (No prebiotic chemical signatures)- video
    http://www.metacafe.com/watch/4012696

    In fact this paper came out the other day which indicates that that complex symbiotic relationships of bacterial life we now see were present from start:

    Iron in Primeval Seas Rusted by Bacteria – Apr. 23, 2013
    Excerpt: The oldest known iron ores were deposited in the Precambrian period and are up to four billion years old (the Earth itself is estimated to be about 4.6 billion years old). ,,,
    This research not only provides the first clear evidence that microorganisms were directly involved in the deposition of Earth’s oldest iron formations; it also indicates that large populations of oxygen-producing cyanobacteria were at work in the shallow areas of the ancient oceans, while deeper water still reached by the light (the photic zone) tended to be populated by anoxyenic or micro-aerophilic iron-oxidizing bacteria which formed the iron deposits.,,,
    http://www.sciencedaily.com/re.....110750.htm

    related note:

    When Did Life First Appear on Earth? – Fazale Rana – December 2010
    Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
    http://www.reasons.org/when-di.....pear-earth

    These following sites have illustrations that shows some of the interdependent, ‘life-enabling’, biogeochemical complexity of different types of bacterial life on Earth.,,,

    Biologically mediated cycles for hydrogen, carbon, nitrogen, oxygen, sulfur, and iron – image of interdependent ‘biogeochemical’ web
    http://www.sciencemag.org/cont......large.jpg

    Microbial Mat Ecology – Image on page 92 (third page down)
    http://www.dsls.usra.edu/biolo.....nit2.2.pdf

    ,,,Please note, that if even one type of bacteria group did not exist in this complex cycle of biogeochemical interdependence, that was illustrated on the third page of the preceding site, then all of the different bacteria would soon die out. This essential biogeochemical interdependence, of the most primitive types of bacteria that we have evidence of on ancient earth, in the oldest sedimentary rocks ever found on earth, make the origin of life ‘problem’ for neo-Darwinists that much worse. For now not only do neo-Darwinists have to explain how the ‘miracle of life’ happened once with the origin of photosynthetic bacteria, but they must now also explain how all these different types bacteria, that photosynthetic bacteria are dependent on, in this irreducibly complex biogeochemical web, miraculously arose just in time to supply the necessary nutrients, in their biogeochemical link in the chain, for photosynthetic bacteria to continue to survive. As well, though not clearly illustrated in the illustration on the preceding site, please note that a long term tectonic cycle, of the turnover the Earth’s crustal rocks, must also be fine-tuned to a certain degree with the bacteria and thus plays a important ‘foundational’ role in the overall ecology of the biogeochemical system that must be accounted for as well.

    Of somewhat related note to ‘terra-forming’, this paper came out recently,,

    Ancient Earth Crust Stored in Deep Mantle – Apr. 24, 2013
    Excerpt: New research,, demonstrates that oceanic volcanic rocks contain samples of recycled crust dating back to the Archean era 2.5 billion years ago.,, This indicates that the sulfur comes from a deep mantle reservoir containing crustal material subducted before the Great Oxidation Event and preserved for over half the age of Earth.
    “These measurements place the first firm age estimates of recycled material in oceanic hotspots,” Hauri said. “They confirm the cycling of sulfur from the atmosphere and oceans into mantle and ultimately back to the surface,” Hauri said.
    http://www.sciencedaily.com/re.....132705.htm

    Moreover franklin, photosynthesis is certainly not ‘just chemistry’ as is testified to by the following research,,

    Unusual Quantum Effect Discovered in Earliest Stages of Photosynthesis – May 2012
    Excerpt: “The behavior we were able to see at these very fast time scales implies a much more sophisticated mixing of electronic states,” Tiede said. “It shows us that high-level biological systems could be tapped into very fundamental physics in a way that didn’t seem likely or even possible.”
    The quantum effects observed in the course of the experiment hint that the natural light-harvesting processes involved in photosynthesis may be more efficient than previously indicated by classical biophysics, said chemist Gary Wiederrecht of Argonne’s Center for Nanoscale Materials. “It leaves us wondering: how did Mother Nature create this incredibly elegant solution?” he said.
    http://www.sciencedaily.com/re.....092932.htm

    Music:

    Hillsong – Mighty to Save – With Subtitles/Lyrics
    http://www.youtube.com/watch?v=-08YZF87OBQ

  39. franklin:’

    What makes you think the first replicator was a cell?

    What makes you think that a replicator that isn’t a cell can become one?

  40. franklin, I would like to point out a drastic inconsistency as to how you proclaim life to be, ‘it’s just chemistry’, and how you actually live your life:

    The Heretic – Who is Thomas Nagel and why are so many of his fellow academics condemning him? – March 2013
    Excerpt: Fortunately, materialism is never translated into life as it’s lived. As colleagues and friends, husbands and mothers, wives and fathers, sons and daughters, materialists never put their money where their mouth is. Nobody thinks his daughter is just molecules in motion and nothing but; nobody thinks the Holocaust was evil, but only in a relative, provisional sense. A materialist who lived his life according to his professed convictions—understanding himself to have no moral agency at all, seeing his friends and enemies and family as genetically determined robots—wouldn’t just be a materialist: He’d be a psychopath. ,,,
    http://www.weeklystandard.com/.....07692.html

    You see franklin you are constantly living your life as if there was much more to life than just chemistry. In fact, by the very fact of you are here on UD, arguing for the truthfulness of your materialistic worldview, you are in fact revealing the fact that we can’t merely be molecules in motion and nothing but molecules in motion:

    Sam Harris’s Free Will: The Medial Pre-Frontal Cortex Did It – Martin Cothran – November 9, 2012
    Excerpt: There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state — including their position on this issue — is the effect of a physical, not logical cause.
    By their own logic, it isn’t logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order.
    http://www.evolutionnews.org/2.....66221.html

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter”.
    J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

    “One absolutely central inconsistency ruins [the popular scientific philosophy of materialism]. The whole picture professes to depend on inferences from observed facts. Unless inference is valid, the whole picture disappears… unless Reason is an absolute, all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based.”
    —C.S. Lewis, Is Theology Poetry (aka the Argument from Reason)

    “If you do not assume the law of non-contradiction, you have nothing to argue about. If you do not assume the principles of sound reason, you have nothing to argue with. If you do not assume libertarian free will, you have no one to argue against. If you do not assume morality to be an objective commodity, you have no reason to argue in the first place.”
    - William J Murray

    Do the New Atheists Own the Market on Reason? – On the terms of the New Atheists, the very concept of rationality becomes nonsensical – By R. Scott Smith, May 03, 2012
    Excerpt: If atheistic evolution by NS were true, we’d be in a beginningless series of interpretations, without any knowledge. Yet, we do know many things. So, naturalism & atheistic evolution by NS are false — non-physical essences exist. But, what’s their best explanation? Being non-physical, it can’t be evolution by NS. Plus, we use our experiences, form concepts and beliefs, and even modify or reject them. Yet, if we’re just physical beings, how could we interact with and use these non-physical things?,, In all, it seems likely the best explanation for these non-physical things is that there exists a Creator after all.
    http://www.patheos.com/Evangel.....#038;max=1

    Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer – video – (Notes in description)
    http://vimeo.com/32145998

    verse and music:

    1 Corinthians 2:9
    However, as it is written: “What no eye has seen, what no ear has heard, and what no human mind has conceived” — the things God has prepared for those who love him–

    Evanescence – The Other Side (Lyric Video)
    http://www.vevo.com/watch/evan.....tantsearch

    Quote and poem,

    “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.”
    William Shakespeare – Hamlet

    There Is More – Poem set to piano – video
    http://www.metacafe.com/watch/4102086/

    There Is More
    Once I saw a very old Godly man who, being very near death, had
    Become deaf, blind and invalid; Yet somehow he glowed happily
    Then it occurred to me…
    There is more to see than the light we see with our eyes
    There is more to behold than to watch setting skies
    There is more to hear than the airwaves of sound
    There is more to stand on than to stand on the ground
    There is more to feel than what we can touch with our skin
    There is more to all things, things that come from deeper within
    Then I saw a miserly old rich man who had angrily driven away his family
    Now he was in a coma, in his mansion, with no one around who loved him
    Then it occurred to me…
    There is more to the hurt of a word than to sticks and stones
    There is more to people than just skin and bones
    There is more to a home than bricks, steel, and lumber
    There is more to waking up than rising from slumber
    There is more to riches than having gold piled high
    There is more to living than just being alive
    Then I saw a Godly young woman full of compassion
    Working with homeless people helping them get off the street
    Then it occurred to me…
    There is more to loving than the warmth of feeling good
    There is more to understanding than a fact being understood
    There is more to work with than the tools of our crafts
    There is more to cleaning up than taking a bath
    There is more to freedom than having no prison walls
    There is more to poverty than having no stuff at all
    Then I saw a bitter old man who angrily didn’t believe in
    Miracles at all and thinks that this cold world is all there is
    Then it occurred to me…
    There is more to being dead than a body in a tomb
    There is more to being born than coming out of a womb
    There is more to heaven than all the stars above
    There is more to Jesus Christ than a distant example of God’s love
    There is more to learning than books teach us in schools
    And there is more to walking with God than keeping TEN rules
    Then I got home at the end of the day
    Went into my room and quietly prayed
    Lord, If there is more than a lesson to my heart You could teach
    Would You teach me to see spiritually to add depth to my reach
    And Lord, If there is more than a gift to this world You might give
    Would You give the miracle that in all hearts Your light would live

  41. In ‘Cell’, 136, march 2009, R.S.Galhardo, Ph.D. and professor S.M. Rosenberg wrote a review about the research of Slade et al. 2009 on world’s toughest bacterium D. radiodurans.

    What are we talking about? – A miracle.

    After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.

    Does science know how the repair mechanism works? – No they do not.

    Some of the prowess for repair displayed by D. radiodurans may result from having more complementary or homologous DNA fragments to engage as repair partners.

    How do the shattered DNA pieces recombine? – Well they just seem to ”find” their complements …

    Initial synthesis is likely to result from the ends of resected single-stranded DNA (ssDNA; Figure 1B) finding their complements in other overlapping fragments (…)

    Do we know for a fact that RecA proteins are involved? – No, we are not sure about that either.

    However, it is difficult to know whether RecA plays this direct role in repair synthesis (..)

    Is there room for different theories? – Sure there is.

    However, an alternative possibility is that the primer strand might simply land on ssDNA and initiate synthesis from there, as in PCR, and this would not require RecA. This hypothetical mechanism involving PCR-like synthesis and recombination could continue until most of the DNA was reconstituted into long double-stranded fragments.

    Do we even understand the difference between D.radiodurans and say E.coli? – No, unfortunately we do not.

    Thus, we do not yet know why D. radiodurans is an extreme-repair champion whereas E. coli is not. The differences in the repair capacities of D. radiodurans and E. coli seem ever more paradoxical.

    Miraculous? – Yes!

    However, if the miracle of extreme repair could be recreated in a tractable model bacterium (…)
    A strain with such abilities would deserve the name Lazarus.

  42. franklin @36:

    You are wasting everyone’s time.

    I will not engage in further discussion on details on this particular topic unless you are willing to commit to some basic first principles that undergird rational discussion. This is not a matter of citing dueling papers, or competing scientific hypotheses, or disagreeing on particular details of chemistry. This is not a matter of whether this or that algorithm or protocol or replicator or cellular system exists. This is a matter of basic logic.

    I will not humor your demand to engage in this or that set of details unless you demonstrate a willingness, and an ability, to comprehend and adhere to basic logical principles of discourse. If you are willing to answer “yes” to the two questions I have posed, I will then have some follow up questions to help us get the discussion back on track. If not, then you will have demonstrated that you do not intend to engage in a logical discussion of the issues.

    In the meantime, I do not intend to waste further time.

  43. Incidentally, just for whomever is still patiently trying to work with franklin, the reason I responded to franklin above about a minimal cell or simplest form of life, is because that is what we were discussing:

    http://www.uncommondescent.com.....ent-453077

    http://www.uncommondescent.com.....ent-453079

    I have never argued that the first replicator was a complete cell, so franklin has misrepresented what I said, or perhaps just misunderstood the nuance. What the simplest self-replicator is and whether it could ever turn into a complete cell are very interesting questions indeed, but they are separate questions from the question of minimum requirements for a functional cell.

  44. eric: I will not engage in further discussion on details on this particular topic unless you are willing to commit to some basic first principles that undergird rational discussion. This is not a matter of citing dueling papers, or competing scientific hypotheses, or disagreeing on particular details of chemistry. This is not a matter of whether this or that algorithm or protocol or replicator or cellular system exists. This is a matter of basic logic.

    eric, you’ve fulfilled my prediction!

    Eric, using the most basic logic it is clear to everyone that you cannot deliver on any of the claims you’ve made. That is why you’ve tried to send me on a ‘snipe hunt’ via google and are desperately trying to change the subject. Why am I not surprised that ID claims about protocols, algorithms, calculations for CSI (or whatever sciency sounding but void of content acronym you’re trying to use today) are nothing but empty rhetoric.

    steve: franklin’s ploy is banking on the fact that ID will never be able to provide the evidence for information being a separate, functional entity required for living systems.

    thanks for the honest admission, steve that you recognize that ID has no evidence for the claims eric (and all IDists) make.

  45. franklin,

    You don’t seem to know what evidence is. Your position definitely cannot deliver on any of its claims- well the one that mutations happen, but all sides say that, so it isn’t really anything for your position.

    By synthesizing all the parts of a cell we should be able to figure out where the information resides.

    Venter already did the DNA. But that is only one component of the cycle.

    Artificial ribosomes don’t function, even though they are identical to natural ribosomes (Church et al. just synthesized the rRNA, not the entire ribosome). So that tells us there is something other than matter, energy what whatever emerges from their interactions.

  46. How can molecules that have mass and charge explain a cell’s function?

    franklin

    Can you name one process that is going on in the cell that does not involve molecules that have mass and charge? Or for that matter anything in the activity in the cell which does not involve chemistry/biochemistry?

    What causes the notes to arrange themselves into a musical composition?

    franklin

    The notes

    How can the notes themselves explain the arrangement?

    Have you ever known a piece of music that did not involve notes?

    This is fun.

  47. franklin you claim there is no evidence “for information being a separate, functional entity required for living systems.” and yet you were shown direct evidence of transcendent quantum information being present within cells here:

    http://www.uncommondescent.com.....ent-453312

  48. stephenb: How can molecules that have mass and charge explain a cell’s function?

    Ah, another IDist who hasn’t the faintest clue of how chemical and biochemical reactions occur and thinks there are mysterious,invisible, and undetectable little fingers moving atoms and molecules around in the cell. You are correct though this is fun but likely not for the reasons you think.

  49. F:

    I think your basic problem is with Crick, not SB or anyone else you may think you can score points off by being sarcastic.

    Let me cite his note to his son, March 19, 1953:

    Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another) . . .

    It is evident that you are bound up in the physico-chemical forces that bind ink to paper and fail to understand that it is the intelligent arrangement in conventional or coded functional ways — from the vast space of possible ways for the same amount of ink to be on the same sheet of paper — that makes the difference.

    With all due respect, you need to think again, starting with going and buying a newspaper.

    (Assuming, you are not one of the evo mat-driven dark triaders we seem to be dealing with too much these days: coldly angry, benumbed, unduly self-important, lacking in remorse for wrongs done, manipulative — highly machiavellian, narcissistic sociopaths. Prone to say and do anything they think they can get away with, to push an agenda. I hope that you are not such. Please.)

    Please, in any case, think again.

    KF

  50. 50

    franklin, as with any system, appeals to its operation will not suffice to account for its origin. The properties of electrons and silicon do not account for the emergence of computer systems — they are necessary but not sufficient. The properties of combustion and mechanical forces do not account for the rise of the combustion engine — they are necessary but not sufficient. The properties of chemistry will not account for the existence of biological systems — they are necessary but not sufficient. No amount of knowledge about biochemical reactions will explain contingent, complex, and specified biological nanotechnology by physical necessity.

    Nobody knows how chemical reactions give rise to information storage, processing, and error correction systems, much less an entire cellular replicator; this is quite probably because they can’t. Simply pointing out that these behaviors require the properties of atoms and molecules in order to function is like suggesting that electric motors require the principles of electromagnetism. Nobody disputes this; but electromagnetism does not explain how motors arise. This is why Eric Anderson has been pressing you about necessary and sufficient conditions. Electricity is necessary for electric motors but is not sufficient to account for them. The properties of chemistry are necessary for biological function but are not sufficient to account for the system itself. Physics is required for mechanical clocks but is not sufficient to account for their existence. It’s the configuration of the biological system that needs to be accounted for. Pointing at what such a system can do once it’s properly in existence does not explain the thing itself, because the mere existence of a thing does not account for its cause.

    Apparently you missed the point of StephenB’s musical notes example. Perhaps you’d suggest that if one is an expert in music theory then one can account for the arrangement of notes in a composition by appeals to the theory itself. Or perhaps you would mock those who suggest that musical compositions require an explanation beyond music theory by joking that “invisible hands” must have been at work. Are you unaware of the distinction between how a system operates and how it comes about?

    ID suggests that intelligence is a necessary cause of biological systems, because biological systems require complex and specified information. To deny that life relies on specified complexity is to suggest that we know how chemical necessity forms the DNA-based coding abstractions of amino acid sequences required for basic biological function and replication, so as to render the notion of specified complexity illusory. However two significant situations exist with regard to biological specification: 1) the types of systems observed in self-replicating organisms have strong parallels to those types of systems that are the result of intelligent design, if they are not outright identical by definition;* 2) no known chemical pathway exists which can form the complex, specified, contingent arrangements of matter required for the simplest, extant, prokaryotic self-replicating organism.**

    Additionally, biological systems construct their components through complex and specific processes which cascade from one step to the next. So not only does “basic chemistry” need to account for the construction of whole systems, but it needs to account for the construction of the processes by which the entire system is itself built. A good example is here: Video: Flagellar Construction. That video isn’t just another one about the flagellar motor, it gives details about what’s required for the motor to be assembled within the context of the whole organism. So again, it’s not just the organisms themselves which need to be accounted for, but the construction processes by which individual organelles are built within the cell, requiring ordered steps, materials construction and transport, signalling systems to trigger the various ordered phases of construction, and so on. To suggest that the origin of such teleological sophistication can be accounted for by basic chemistry is outright hubris. We’re not asking for the biochemical rules by which these systems must operate, we’re asking for elucidation of the principle by which these whole nanotech manufacturing processes are arrived at.

    * Cells require code storage, replication machinery, translation machinery, quality control, chemical synthesis pathways, motors of multiple types, transport and signalling systems, etc.

    ** Because the nature of information is contingent, it is not logically compatible with physical necessity. No known necessity mechanism can produce specified, complex, contingent arrangements of matter such as those we find coded in DNA.

  51. 51

    Our Secret Universe: The Hidden Life of the Cell

    I haven’t seen anything but snippets yet, but it looks like it might be pretty entertaining and informative.

  52. Chance @50:

    Well said.

  53. franklin

    Ah, another IDist who hasn’t the faintest clue of how chemical and biochemical reactions occur and thinks there are mysterious,invisible, and undetectable little fingers moving atoms and molecules around in the cell. You are correct though this is fun but likely not for the reasons you think.

    LOL franklin. Obviously, you missed the point of the musical analogy. The fun part is in watching you pound your chest triumphantly while you continue to blur the essential distinction between a necessary cause and a sufficient cause.

  54. franklin, since you consider yourself an expert on how molecules randomly colliding into each other can give rise to a ‘simple’ cell which defies, due to the complexity inherent therein, human comprehension, I was wondering if you could help with a little problem that has been bugging me. You see franklin, neo-Darwinists claim that ‘random’ variation is their designer substitute. But randomness has a huge problem going against it as to being a replacement for almighty God. To give you a glimpse of this huge problem let me illustrate. I’ve already shown you this fact:

    “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong

    ‘The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.”
    Carl Sagan, “Life” in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894

    And that number was derived in the following manner:

    Moleular Biophysics – Information theory. Relation between information and entropy: – Setlow-Pollard, Ed. Addison Wesley
    Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
    http://www.astroscu.unam.mx/~a.....ecular.htm

    Dr. Morowitz did another calculation working from the thermodynamic perspective with a already existing cell and came up with this number against the cell reassembling itself in ideal conditions:

    DID LIFE START BY CHANCE?
    Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
    http://members.tripod.com/~Black_J/chance.html

    Punctured cell will never reassemble – Jonathan Wells – 2:40 mark of video
    http://www.youtube.com/watch?v=WKoiivfe_mo

    Now franklin, the reason why Dr. Morowitz, and others, were able to calculate that a ‘simple’ bacteria has equivalent of 100 million pages of information in it is because,,,

    “Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…” Siegfried, Dallas Morning News, 5/14/90, [Quotes Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin]

    Now franklin you may object (being the good neo-Darwinist you are) that just because the equations are the same between entropy and information that does not mean that there is any real connection between entropy and information, well you would be wrong in that presupposition:

    Demonic device converts information to energy – 2010
    Excerpt: “This is a beautiful experimental demonstration that information has a thermodynamic content,” says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. “This tells us something new about how the laws of thermodynamics work on the microscopic scale,” says Jarzynski.
    http://www.scientificamerican......rts-inform

    But franklin if there is a real connection between entropy and information then this plays havoc with ‘randomness’ as a designer substitute:

    Thermodynamics – 3.1 Entropy
    Excerpt:
    Entropy – A measure of the amount of randomness or disorder in a system.
    http://www.saskschools.ca/curr.....rgy3_1.htm

    “Gain in entropy always means loss of information, and nothing more.”
    Gilbert Newton Lewis – preeminent Chemist of the first half of last century

    “Bertalanffy (1968) called the relation between irreversible thermodynamics and information theory one of the most fundamental unsolved problems in biology.”
    Charles J. Smith – Biosystems, Vol.1, p259.

    Sometimes Darwinists desperately try to appeal to an ‘open system’ to circumvent the second law’s relentless grip on nature ever producing functional information, but that is simply ludicrous for the second law was derived right here on earth in the first place! Moreover,,

    “there are no known violations of the second law of thermodynamics. Ordinarily the second law is stated for isolated systems, but the second law applies equally well to open systems.”
    John Ross, Chemical and Engineering News, 7 July 1980

    “…the quantity of entropy generated locally cannot be negative irrespective of whether the system is isolated or not.”
    Arnold Sommerfel, Thermodynamics And Statistical Mechanics, p.155

    further notes:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.

    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    Are You Looking for the Simplest and Clearest Argument for Intelligent Design? – Granville Sewell (2nd Law) – video
    http://www.evolutionnews.org/2.....56711.html

    Music and Verse

    Glory Defined Share – Building 429
    http://myktis.com/songs/glory-defined/

    Romans 8:18-21
    I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. The creation waits in eager expectation for the sons of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the glorious freedom of the children of God.

    supplemental note:

    Shining Light on Dark Energy – October 21, 2012
    Excerpt: It (Entropy) explains time; it explains every possible action in the universe;,,
    Even gravity, Vedral argued, can be expressed as a consequence of the law of entropy. ,,,
    The principles of thermodynamics are at their roots all to do with information theory. Information theory is simply an embodiment of how we interact with the universe —,,,
    http://crev.info/2012/10/shini.....rk-energy/

    and yet

    Quantum Zeno effect
    Excerpt: The quantum Zeno effect is,,, an unstable particle, if observed continuously, will never decay.
    - per wikipedia

    This is just fascinating! Why in blue blazes should conscious observation put a freeze on entropic decay, unless consciousness was/is more foundational to reality than entropy is? And seeing as to how entropy is VERY foundational to reality, I think the implications of all this are fairly obvious: i.e. Consciousness precedes material reality!

  55. 55

    Eric @52, thank you. :)

    BA77 @54, The Quantum Zeno effect is pretty amazing. I’ll have to look into it further. It’s a stunning result.

    Stephen @53 and Eric, I was fascinated with the conditional operator, p→q (p implies q), when I first learned what it entailed. Necessary and sufficient causes, modus ponens, modus tollens, the notions of the converse and contrapositive, and the formal fallacies of affirming the consequent and denying the antecedent, all come from the implications of implication. The distinction between necessary and sufficient causes is important for reasoning and arguing, and dealing with the conditional operator is a good way to go about learning it.

    For anyone wanting to get their feet wet with basic logic, this is be a good place to start: Introduction to Logic. It has good examples and exercises, and is generally well-paced.

  56. CR: Another excellent contribution. KF

  57. BA:

    Now I have had the pause to look, great clips.

    I beg to remind F et al that there is an informational approach to thermodynamics, that sees an organic link between entropy and information.

    Here is a clip from my always linked that cites a good remark in Wikipedia:

    we may average the information per symbol in the communication system thusly (giving in terms of -H to make the additive relationships clearer):

    – H = p1 log p1 + p2 log p2 + . . . + pn log pn

    or, H = – SUM [pi log pi] . . . Eqn 5

    H, the average information per symbol transmitted [usually, measured as: bits/symbol], is often termed the Entropy; first, historically, because it resembles one of the expressions for entropy in statistical thermodynamics. As Connor notes: “it is often referred to as the entropy of the source.” [p.81, emphasis added.] Also, while this is a somewhat controversial view in Physics, as is briefly discussed in Appendix 1 below, there is in fact an informational interpretation of thermodynamics that shows that informational and thermodynamic entropy can be linked conceptually as well as in mere mathematical form. Though somewhat controversial even in quite recent years, this is becoming more broadly accepted in physics and information theory, as Wikipedia now discusses [as at April 2011] in its article on Informational Entropy (aka Shannon Information, cf also here):

    At an everyday practical level the links between information entropy and thermodynamic entropy are not close. Physicists and chemists are apt to be more interested in changes in entropy as a system spontaneously evolves away from its initial conditions, in accordance with the second law of thermodynamics, rather than an unchanging probability distribution. And, as the numerical smallness of Boltzmann’s constant kB indicates, the changes in S / kB for even minute amounts of substances in chemical and physical processes represent amounts of entropy which are so large as to be right off the scale compared to anything seen in data compression or signal processing.

    But, at a multidisciplinary level, connections can be made between thermodynamic and informational entropy, although it took many years in the development of the theories of statistical mechanics and information theory to make the relationship fully apparent. In fact, in the view of Jaynes (1957), thermodynamics should be seen as an application of Shannon’s information theory: the thermodynamic entropy is interpreted as being an estimate of the amount of further Shannon information needed to define the detailed microscopic state of the system, that remains uncommunicated by a description solely in terms of the macroscopic variables of classical thermodynamics. For example, adding heat to a system increases its thermodynamic entropy because it increases the number of possible microscopic states that it could be in, thus making any complete state description longer. (See article: maximum entropy thermodynamics.[Also,another article remarks: >>in the words of G. N. Lewis writing about chemical entropy in 1930, "Gain in entropy always means loss of information, and nothing more" . . . in the discrete case using base two logarithms, the reduced Gibbs entropy is equal to the minimum number of yes/no questions that need to be answered in order to fully specify the microstate, given that we know the macrostate.>>])

    Maxwell’s demon can (hypothetically) reduce the thermodynamic entropy of a system by using information about the states of individual molecules; but, as Landauer (from 1961) and co-workers have shown, to function the demon himself must increase thermodynamic entropy in the process, by at least the amount of Shannon information he proposes to first acquire and store; and so the total entropy does not decrease (which resolves the paradox).

    Summarising Harry Robertson’s Statistical Thermophysics (Prentice-Hall International, 1993) — excerpting desperately and adding emphases and explanatory comments, we can see, perhaps, that this should not be so surprising after all. (In effect, since we do not possess detailed knowledge of the states of the vary large number of microscopic particles of thermal systems [typically ~ 10^20 to 10^26; a mole of substance containing ~ 6.023*10^23 particles; i.e. the Avogadro Number], we can only view them in terms of those gross averages we term thermodynamic variables [pressure, temperature, etc], and so we cannot take advantage of knowledge of such individual particle states that would give us a richer harvest of work, etc.)

    For, as he astutely observes on pp. vii – viii:

    . . . the standard assertion that molecular chaos exists is nothing more than a poorly disguised admission of ignorance, or lack of detailed information about the dynamic state of a system . . . . If I am able to perceive order, I may be able to use it to extract work from the system, but if I am unaware of internal correlations, I cannot use them for macroscopic dynamical purposes. On this basis, I shall distinguish heat from work, and thermal energy from other forms . . .

    And, in more details, (pp. 3 – 6, 7, 36, cf Appendix 1 below for a more detailed development of thermodynamics issues and their tie-in with the inference to design; also see recent ArXiv papers by Duncan and Samura here and here):

    . . . It has long been recognized that the assignment of probabilities to a set represents information, and that some probability sets represent more information than others . . . if one of the probabilities say p2 is unity and therefore the others are zero, then we know that the outcome of the experiment . . . will give [event] y2. Thus we have complete information . . . if we have no basis . . . for believing that event yi is more or less likely than any other [we] have the least possible information about the outcome of the experiment . . . . A remarkably simple and clear analysis by Shannon [1948] has provided us with a quantitative measure of the uncertainty, or missing pertinent information, inherent in a set of probabilities [NB: i.e. a probability different from 1 or 0 should be seen as, in part, an index of ignorance] . . .

    I trust this will help to set a context for serious discussion.

    KF

  58. ID cannot explain D. radiodurans repair capabilities. Only Bornagain77 seems to take notice of this fact. The information which resides in the sequence of Deinococcus radiodurans’ DNA is shattered. See my posts #4 and #41 for info and links.
    Somehow D.radiodurans is able to reproduce the 3.2 Mb information out of nowhere. This doesn’t just pose a problem for naturalism, but also for ID. The problem for both positions is that there is no feasible bottom up mechanism / explanation – designed or not.
    If information is only produced by intelligence, what is going on during the repair of D.radiodurans genome?

  59. 59

    Box, interesting. I just read the article you linked. They speculate thus:

    “Scientists have speculated that the physical arrangement of D. radiodurans’ genome could help the organism accomplish its feats of DNA repair. The microbe carries between four and ten copies of its genome, rather than the usual single copy, and the copies appear to be stacked on top of each other.

    The additional genomes may allow the bacterium to recover at least one complete copy of its genome after exposure to radiation. The proteins and pathways involved in suturing a fractured genome back together are now the focus of a number of studies. Initially, the genome sequence shed frustratingly little light on this question.”

    Regardless, I think that further study of D. radiodurans should prove fascinating, and certainly will end up providing key insights into molecular biology. Being able to stitch DNA back together is utterly remarkable. How will it be explained? I have no idea, but this organism is on my radar. Thanks for calling attention to it.

  60. Chance, Box, and lifepsy, I just edited down the Nobel lecture:

    Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video
    http://www.metacafe.com/w/10395212

    Denis Nobel’s concession, from empirical evidence, that many protein domains are not acquired gradually, is not a minor concession for him to make. Perhaps as important a concession as his two other concessions. One being that mutations are not truly random in the Darwinian sense, and two being that no one has yet observed speciation in all of human history. He had me cheering through his thorough dismantling of neo-Darwinism (i.e. the modern synthesis). Yet, his materialistic fudge factor that he invoke towards the end of his lecture (for whatever reason) was to invoke widespread horizontal information flow among a ‘web’ of life instead the usual vertical information flow of the tree of life to try to find an escape hatch for ‘bottom up’ evolution. Yet, alas, as with neo-Darwinism’s bottom up mechanism, it is found to be grossly inadequate for the job.

    Here horizontal information flow shown to be inadequate at the bacteria level:

    The Dictionary of Life | Origins with Dr. Paul A. Nelson – video
    http://www.youtube.com/watch?f.....vCo#t=760s

    Estimating the size of the bacterial pan-genome – Pascal Lapierre and J. Peter Gogarten – 2008
    Excerpt: We have found >139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered.
    http://www.paulyu.org/wp-conte.....genome.pdf

    The essential genome of a bacterium – 2011
    Figure (C): Venn diagram of overlap between Caulobacter and E. coli ORFs (outer circles) as well as their subsets of essential ORFs (inner circles). Less than 38% of essential Caulobacter ORFs are conserved and essential in E. coli. Only essential Caulobacter ORFs present in the STING database were considered, leading to a small disparity in the total number of essential Caulobacter ORFs.
    http://www.ncbi.nlm.nih.gov/pm.....201158.pdf

    And here horizontal information flow is shown to be inadequate at the multicellular level:

    Common Ancestry: Wikipedia vs. the Data – Casey Luskin – October 5, 2012
    Excerpt: In fact, the largest category of genes here is eukaryotic (cells with a nucleus) genes that have no homolog among prokaryotes (cells without a nucleus) — they don’t even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of “a direct correlation with common descent.”,,,
    ,,, if two phylogenetic trees aren’t congruent, the problem isn’t that common descent is wrong, but rather the conflict is simply evidence of HGT.,,, Syvanen, (in “Evolutionary Implications of Horizontal Gene Transfer,” Annual Review of Genetics, Vol. 46:339-356 (2012), invokes widespread HGT (Horizontal Gene Transfer), but he’s uncommonly honest about the data and its implications, offering the radical suggestion that “life might indeed have multiple origins.”,,,
    let’s now look within eukaryotes.,,,
    The biochemical organization of the innate immune systems of plants and animals is strikingly similar — but this is a direct non-correlation with common descent. Thus, evolutionary scientists are forced to call them “unexpectedly similar,” postulating that the similarities were “independently derived.” This data is not explained by Darwinian evolution and common descent. It is explained by common design.
    Somehow, something tells me not to expect any corrections over at Wikipedia.
    http://www.evolutionnews.org/2.....65001.html

    An Enzyme’s Phylogeny Reveals a Striking Case of Convergent Evolution – Jonathan M. – February 11, 2013
    Excerpt: The authors attempt to account for the incongruity by positing that “the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.” They thus attribute the shared genes to horizontal gene transfer (with no offered mechanism), a proposition that has become a catch-all to explain away severe conflicts between evolutionary phylogenies.,,,
    “phylogenetic conflict is common, and frequently the norm rather than the exception”
    (Dávalos et al., 2012).
    Is it possible that the real reason for such striking and widespread phylogenetic discordance is that evolutionary biologists are looking at biology through the wrong lens? Could the reason that there is so much difficulty in correlating organisms to a tree be that no such tree exists?
    http://www.evolutionnews.org/2.....68911.html

  61. CR #59, the following two sentences from the same article seem to be contradictory:

    The additional genomes may allow the bacterium to recover at least one complete copy of its genome after exposure to radiation.

    After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome (..)

    My interpretation of the last quote is that all of the genome including the copies are shattered. How can it be that the DNA is completely shattered by desiccation or radiation but the copies are untouched?

  62. 62

    Box @61, I agree, that is quite problematic. However it may not be intractable from a computational, algorithmic point of view. Assuming that’s the case, how such an algorithmic process would translate to the activity of protein machinery or other activity in that cell I couldn’t even begin to speculate. But the redundancy of information in that genome might be a clue that it’s important to the process, whatever it happens to be.

  63. 63

    Ba77 @60, you might find this interesting. It was linked from that Noble lecture. Here is part one:

    Homage to Darwin (part 1)

    It’s a discussion on OOL with several panelists including Lynn Margulis and Richard Dawkins, and moderated by Denis Noble, with questions asked by the audience. There are three parts, but I’ve only been able to watch part one so far. Here too there are a lot of assumptions made about life’s history tracing back to a simpler “LUCA” but there’s still quite a bit to learn from the material, with some good questions and candid answers.

    I agree with you about the Noble lecture, that invoking biological networks as the “answer” to the problem of origins is not exactly helpful, but I find it much more evidence based than the alternative, and I enjoyed it thoroughly. While these bacterial information networks may do little to account for origins of everything else, it does appear to be a valid observation in the realm of prokaryotes at least. I find no end to amazement about how life works on different levels.

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