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The TSZ and Jerad Thread, III — 900+ and almost 800 comments in, needing a new thread . . .

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Okay, the thread of discussion needs to pick up from here on.

To motivate discussion, let me clip here comment no 795 in the continuation thread, which I have marked up:

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>> 795Jerad October 23, 2012 at 1:18 am

KF (783):

At this point, with all due respect, you look like someone making stuff up to fit your predetermined conclusion.

I know you think so.

[a –> Jerad, I will pause to mark up. I would further with all due respect suggest that I have some warrant for my remark, especially given how glaringly you mishandled the design inference framework in your remark I responded to earlier.]

{Let me add a diagram of the per aspect explanatory filter, using the more elaborated form this time}

The ID Inference Explanatory Filter. Note in particular the sequence of decision nodes

 

You have for sure seen the per apsect design filter and know that the first default explanaiton is that something is caused by law of necessity, for good reason; that is the bulk of the cosmos. You know similarly that highly contingent outcomes have two empirically warrantged causal sources: chance and choice.

You kinow full well that he reason chance is teh default is to give the plain benefit of the doubnt to chance, even at the expense of false negatives.

I suppose. Again, I don’t think of it like that. I take each case and consider it’s context before I think the most likely explanation to be.

[b –> You have already had adequate summary on how scientific investigations evaluate items we cannot directly observe based on traces and causal patterns and signs we can directly establish as reliable, and comparison. This is the exact procedure used in design inference, a pattern that famously traces to Newton’s uniformity principle of reasoning in science.]

I think SETI signals are a good example of really having no idea what’s being looked at.

[c –> There are no, zip, zilch, nada, SETI signals of consequence. And certainly no coded messages. But it is beyond dispute that if such a signal were received, it would be taken very seriously indeed. In the case of dFSCI, we are examining patterns relevant to coded signals. And, we have a highly relevant case in point in the living cell, which points to the origin of life. Which of course is an area that has been highlighted as pivotal on the whole issue of origins, but which is one where you have determined not to tread any more than you have to.]

I suppose, in that case, they do go through something like you’re steps . . . first thing: seeing if the new signals is similar to known and explained stuff.

[d –> If you take off materialist blinkers for the moment and look at what the design filter does, you will see that it is saying, what is it that we are doing in an empirically based, scientific explanation, and how does this relate to the empirical fact that design exists and affects the world leaving evident traces? We see that the first thing that is looked for is natural regularities, tracing to laws of mechanical necessity. Second — and my home discipline pioneered in this in C19 — we look at stochastically distributed patterns of behaviour that credibly trace to chance processes. Then it asks, what happens if we look for distinguishing characteristics of the other cause of high contingency, design? And in so doing, we see that there are indeed empirically reliable signs of design, which have considerable relevance to how we look at among other things, origins. But more broadly, it grounds the intuition that there are markers of design as opposed to chance.]

And you know the stringency of the criterion of specificity (especially functional) JOINED TO complexity beyond 500 or 1,000 bits worth, as a pivot to show cases where the only reasonable, empirically warranted explanation is design.

I still think you’re calling design too early.

[e –> Give a false positive, or show warrant for the dismissal. Remember, just on the solar system scope, we are talking about a result that identifies that by using the entire resources of the solar system for its typically estimated lifespan to date, we could only sample something like 1 straw to a cubical haystack 1,000 light years across. If you think that he sampling theory result that a small but significant random sample will typically capture the bulk of a distribution is unsound, kindly show us why, and how that affects sampling theory in light of the issue of fluctuations. Failing that, I have every epistemic right to suggest that what we are seeing instead is your a priori commitment to not infer design peeking through.]

And, to be honest, the only things I’ve seen the design community call design on is DNA and, in a very different way, the cosmos.

[f –> Not so. What happens is that design is most contentious on these, but in fact the design inference is used all the time in all sorts of fields, often on an intuitive or semi intuitive basis. As just one example, consider how fires are explained as arson vs accident. Similarly, how a particular effect in our bodies is explained as a signature of drug intervention vs chance behaviour or natural mechanism. And of course there is the whole world of hypothesis testing by examining whether we are in the bulk or the far skirt and whether it is reasonable to expect such on the particularities of the situation.]

The real problem, with all respect, as already highlighted is obviously that this filter will point out cell based life as designed. Which — even though you do not have an empirically well warranted causal explanation for otherwise, you do not wish to accept.

I don’t think you’ve made the case yet.

[f –> On the evidence it is plain that there is a controlling a priori commitment at work, so the case will never be perceived as made, as there will always be a selectively hyperskeptical objection that demands an increment of warrant that is calculated or by unreflective assertion, unreasonable to demand, by comparison with essentially similar situations. Notice, how ever so many swallow a timeline model of the past without batting an eye, but strain at a design inference that is much more empirically reliable on the causal patterns and signs that we have. That’s a case of straining at a gnat while swallowing a camel.]

I don’t think the design inference has been rigorously established as an objective measure.

[g –> Dismissive assertion, in a context where “rigorous’ is often a signature of selective hyperskepticism at work, cf, the above. The inference on algorithmic digital code that has been the subject of Nobel Prize awards should be plain enough.]

I think you’ve decided that only intelligence can create stuff like DNA.

[h –> Rubbish, and I do not appreciate your putting words in my mouth or thoughts in my head that do not belong there, to justify a turnabout assertion. You know or full well should know, that — as is true for any significant science — a single well documented case of FSCO/I reliably coming about by blind chance and/or mechanical necessity would suffice to break the empirical reliability of the inference that eh only observed — billions of cases — cause of FSCO/I is design. That you are objecting on projecting question-begging (that is exactly what your assertion means) instead of putting forth clear counter-examples, is strong evidence in itself that the observation is quite correct. That observation is backed by the needle in the haystack analysis that shows why beyond a certain level of complexity joined to the sort of specificity that makes relevant cases come from narrow zones T in large config spaces W, it is utterly unlikely to observe cases E from T based on blind chance and mechanical necessity.]

I haven’t seen any objective way to determine that except to say: it’s over so many bits long so it’s designed.

[i –> Strawman caricature. You know better, a lot better. You full well know that we are looking at complexity AND specificity that confines us to narrow zones T in wide spaces of possibilities W such that the atomic resources of our solar system or the observed cosmos will be swamped by the amount of haystack to be searched. Where you have been given the reasoning on sampling theory as to why we would only expect blind samples comparable to 1 straw to a hay bale 1,000 light years across (as thick as our galaxy) will reliably only pick up the bulk, even if the haystack were superposed on our galaxy near earth. Indeed, just above you had opportunity to see a concrete example of a text string in English and how easily it passes the specificity-complexity criterion.]

And I just don’t think that’s good enough.

[j –> Knocking over a strawman. Kindly, deal with the real issue that has been put to you over and over, in more than adequate details.]

But that inference is based on what we do know, the reliable cause of FSCO/I and the related needle in the haystack analysis. (As was just shown for a concrete case.)

But you don’t know that there was an intelligence around when one needed to be around which means you’re assuming a cause.

[k –> Really! You have repeatedly been advised that we are addressing inference on empirically reliable sign per patterns we investigate in the present. Surely, that we see that reliably, where there is a sign, we have confirmed the presence of the associated cause, is an empirical base of fact that shows something that is at least a good candidate for being a uniform pattern. We back it up with an analysis that shows on well accepted and uncontroversial statistical principles, why this is so. Then we look at cases where we see traces from the past that are comparable to the signs we just confirmed to be reliable indices. Such signs, to any reasonable person not ideologically committed to a contrary position, will count as evidence of similar causes acting in the past. But more tellingly, we can point to other cases such as the reconstructed timeline of the earth’s past where on much weaker correlations between effects and putative causes, those who object to the design inference make highly confident conclusions about the past and in so doing, even go so far as to present them as though they were indisputable facts. The inconsistency is glaringly obvious, save to the true believers in the evo mat scheme.]

And you’re not addressing all the evidence which points to universal common descent with modification.

[l –> I have started form the evidence at the root of the tree of life and find that there is no credible reason to infer that chemistry and physics in some still warm pond or the like will assemble at once or incre4mentally, a gated, encapsulated, metabolising entity using a von Neumann, code based self replicator, based on highly endothermic and information rich macromolecules. So, I see there is no root to the alleged tree of life, on Darwinist premises. I look at the dFSCI in the living cell, a trace form the past, note that it is a case of FSCO/I and on the pattern of causal investigations and inductions already outlined I see I have excellent reason to conclude that the living cell is a work of skilled ART, not blind chance and mechanical necessity. thereafter, ay evidence of common descent or the like is to be viewed in that pivotal light. And I find that common design rather than descent is superior, given the systematic pattern of — too often papered over — islands of molecular function (try protein fold domains) ranging up to suddenness, stasis and the scope of fresh FSCO/I involved in novel body plans and reflected in the 1/4 million plus fossil species, plus mosaic animals etc that point to libraries of reusable parts, and more, give me high confidence that I am seeing a pattern of common design rather than common descent. This is reinforced when I see that ideological a prioris are heavily involved in forcing the Darwinist blind watchmaker thesis model of the past.]

We’re going around in circles here.

[m –> On the contrary, what is coming out loud and clear is the ideological a priori that drives circularity in the evolutionary materialist reconstruction of the deep past of origins. KF]>>

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GP at 796, and following,  is also a good pick-up point:

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>>796

  1. Joe:

    If a string for which we have correctly assesses dFSCI is proved to have historically emerged without any design intervention, that would be a false positive. dFSCI has been correctly assessed, but it does not correspond empirically to a design origin.

    It is important to remind that no such example is empirically known. That’s why we say that dFSCI has 100% specificity as an indicator of design.

    If a few examples of that kind were found, the specificity of the tool would be lower. We could still keep some use for it, but I admit that its relevance for a design inference in such a fundamental issue like the interpretation of biological information woudl be heavily compromised.

  2. If you received an electromagnetic burst from space that occurred at precisely equal intervals and kept to sidereal time would that be a candidate for SCI?

  3. Are homing beacons SCI?

  4. Jerad:

    As you should know, the first default is look for mechanical necessity. The neutron star model of pulsars suffices to explain what we see.

    Homing beacons come in networks — I here look at DECCA, LORAN and the like up to today’s GPS, and are highly complex nodes. They are parts of communication networks with highly complex and functionally specific communication systems. Where encoders, modulators, transmitters, receivers, demodulators and decoders have to be precisely and exactly matched.

    Just take an antenna tower if you don’t want to look at anything more complex.

    KF>>

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I am fairly sure that this discussion, now in excess of 1,500 comments, lets us all see what is really going on in the debate over the design inference. END

Comments
petrushka:
Gpuccio is arguing that because no one has completed the painstaking research to find the history of protein domains, such histories cannot exist.
Mung:
That is incorrect. The painstaking research is in. That’s what allows us to identify the protein superfamilies. It is that same painstaking research which allows us to say that the intermediates are missing.
http://theskepticalzone.com/wp/?p=1450&cpage=6#comment-19021Mung
December 22, 2012
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If biology was asked to avoid these implicitly semiotic terms it would have a hard - and probably impossible - job of explaining function. The theoretical issue at stake here is that in biology empirical facts are always contextually constrained.
It is an accepted truth in biology that structure and function are interdependent, e.g., a biological explanation is incomplete even if you have exhaustively described the production and the structure of a macromolecule in a cell. There is still a missing feature of the explanation - we still need an answer to the question: "what is it for?" Answering this question is part of the functional contextualization that all biological facts require.
Most of the predictive power of biology is lost if semio-functional analysis is excluded.
Towards A Semiotic Biology: Life is the Action of SignsMung
December 21, 2012
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LOL :DGenomicus
December 20, 2012
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Reductionism has the ability to lose sight of our important biological context.
Context? What context? We don't need no stinking context.Mung
December 20, 2012
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Mike Gene criticizes Keefe and Szostak for using evolutionary modelling to concentrate functionality. Not convincing! Mike says “The function uncovered by this paper is very weak ATP-binding”. Sounds like and, in fact, is “what good is half an eye”.
Let's look at this a bit closer. Mike Gene suggests that there are two fundamental flaws with the study which would invalidate Keefe and Szostak's conclusions. Firstly: "The experiment starts out fine. They generate 6 x 10^12 random proteins, incubate with an ATP-agarose affinity matrix, wash off the unbound material, retrieve the bound material, and then use the bound material to start the cycle over again. Basically, they are purifying this random population such that only those sequences that bind ATP remain. After eight rounds of this cycle, the fraction of ATP binders rose from 0.1 to 6.2%. At this point, the researchers decided to take a look at the sequences that were binding and found the binders to be dominated by four distinct families of proteins (none show similarity to each other or any other biological protein). This, however, is not all that impressive, because it basically means that these four classes of ATP-binders bound ATP very weakly (in other words, the binders were about 20 times more likely to exist in an unbound state than bound to ATP). In fact, the researchers themselves noted, "One possible explanation for this low level of ATP-binding is conformational heterogeneity, possibly reflecting inefficient folding of these primordial protein sequences." At this point, the researchers switched gears. They used PCR to introduce point mutations into the binders for 3 consecutive rounds, at a mutagenic rate of 3.7% per amino acid for each round. After these three cycles of mutagenesis [3], the researchers went back to the original procedure. But in my opinion, this is cheating the "entirely stochastic means." When point mutants are introduced, most of the protein sequence is held constant so that we can then sample in the nearby area. Furthermore, because of the nature of the genetic code, the search was no longer truly random." In other words, in the second stage of the study, the researchers were not following a strictly Darwinian model. Now, you say that:
Mike says “The function uncovered by this paper is very weak ATP-binding”. Sounds like and, in fact, is “what good is half an eye”.
Yet you ignore the rest of his paragraph, and for a very good reason. It very succinctly demonstrates that this study is hardly relevant to biological reality: "In biology, a function usually looks like this: X is modified by Y such that X now modifies Z. In other words, there is a consequence entailed by function. Yet there is no consequence in the proteins described in this paper - they simply weakly bind ATP. Reductionism has the ability to lose sight of our important biological context. Of course, at the core, all proteins basically do is bind things. Even enzyme catalysis is about the binding of transitional states. But to view proteins as mere binders is like viewing carpentry as merely nailing boards together. In biology, what matters is not merely binding, but how things bind, where things bind, and when they bind. What matters is the context of binding. And it is not surprising that Nature paper does not describe ATP hydrolysis activity of these proteins. That would entail not just binding ATP, but also the specificity required to position the substrate so that it could bind another network of amino acids that position themselves to stabilize the transitional state. Thus, to bring this paper into a position where it is relevant to "living organisms", we have to go back to the drawing board and demonstrate the following: Starting with a random pool of polypeptides, isolate proteins that both specifically bind and hydrolyze ATP. But even this would not be sufficient, as ATP hydrolysis by itself is not important to biology (in fact, it is simply an energy sink)." And he goes on. You need to confront the actual arguments instead of hand-waving them away.Genomicus
December 20, 2012
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F/N: When we suggest a particular cause of a trace from ther unobserved deep past, it is a minimum requirement, that the suggested cause be observed to be able to cause the effect, for it to be acandidate. Absent such, we are really just dealing with just so stories. FSCO/I has been -- routinely -- observed produced by design, and ONLY been obsereved as produced by design. In addition, we see good reason to observe that it is all but impossible for chance to explain such a contingent object when the info content is beyond 500 - 1,0000 bits. Against that, we are in effect told that [macro-] evolutuion as the explanation for the world of life is a "FACT,' to the point where we are told by a leading spokesman, Dawkins, that if you question such, you are tantamount to being equivalent to a holocaust denier. All in a context where this outrageous ad hominem by invidious association is being used to cover up a basic, blatant fact: we do not see FSCO/I coming from blind chance and mechanical necessity. When things go to this level, it is patent that this is materialist ideology we are dealing with not science. KFkairosfocus
December 20, 2012
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Alan Fox: this is getting repetitive. Indeed! Like in: Points I have repeatedly made and you have repeatedly avoided to comment upon: 1) The Szostak paper is a lie. He finds weak chemical affinities for ATP in a random library (which could never be considered functional in any context) and without analyzing the original sequences in the random library, he enters those sequences into cycles of mutations and intelligent selection for ATP binding. Then he analyzes the final, engineered protein (which, however, is still not functional in any context, but now has strong linking to ATP and some folding), and concludes with the amazing lie that functional sequences can be found in a random library. That darwinists still quote this shameful paper in support of their views is a clear sign of how little they respect truth. 2) The McLaughlin paper, instead, is fair and interesting. But its results are in complete accord with the ID views, and certainly do not support in any way the idea that bridges exist between functional islands. 3) That protein superfamilies are completely isolated at sequence level is a very well known fact. That no functional bridge has ever been found between them is a very well known fact. How do you feel about these facts. Can you honestly say that we know nothing about protein functional space? Do you approve of simply ignoring what is known, because it is not in support of what you desire? However, Merry Christmas and Happy New Year to you from my heart. You are a fair interlocutor, and I appreciate your contributions.gpuccio
December 20, 2012
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Alan Fox:
You know, that is simply a version of “evolutionary theory is wrong about X so ID wins”.
And you know that your position has nothing so you are forced to lash out at ID with your ignorance. Merry Christmas and Happy New Year, indeed...Joe
December 20, 2012
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SF: I forgot, you suggest: "evolutionary theory is wrong about X so ID wins." Strawman, and in the teeth of the often presented summary of inference on observed and reliable signs. The design inference is not simply a dismissal of the claimed powers of evolutionary mechanisms -- BTW, how do such Darwinist mechanisms operate in the warm little pond or the like chemical-physical system BEFORE there is reproducing life (where hypothetical self-replicating molecules do not count) -- but a positive inductive inference on the identified, reliably known cause of FSCO/I. Something that is as common as writing posts in this thread. The insistence on strawman caricatures in the teeth of evidence and reasoning to the contrary inadvertently supports the point that there is no evo mat observational base for spontaneous origin of life, and that there is no base for the chance variation and differential reproductive success based origin of novel body plans, beyond the eye of darwinist faith and huge extrapolation. KFkairosfocus
December 20, 2012
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"Change one letter in a sentence and it usually still means something. Therefore you should get similar results by just typing out random gibberish. Or at least, you can't argue you wouldn't because we haven't studied that yet."englishmaninistanbul
December 20, 2012
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AF: With all due respect, what part of "In the natural proteome, superfamilies are completely separated at sequence level" is it that is so hard to see for what it says? As in, OBSERVED large and unbridged Hamming distances between clusters of somewhat sequence-similar AA chains that occur in nature. Those are observed islands in the space of possible AA sequences, and in significant numbers. The issue being that while one may argue for incremental changes within the island, in the gaps we are looking at large zones with no observed function and no possibility of incremental heightened success or performance to appeal to; thus the isolation challenge surfaces. In addition, the recent paper is about incremental changes in and around such islands of observed function, and with so many cases where one-step changes destroy function, that is revealing already. Where also, this is not a survey of the abundance of function in the space of AA chain possibilities as a whole. In answer you are being dismissive of and resistant to observed facts, which is absolutely telling. KFkairosfocus
December 20, 2012
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We know quite well how rare they are in the space we know. In the natural proteome, superfamilies are completely separated at sequence level. And nobody has ever shown any connection. These are facts, and ignoring them only because they are uncomfortable for your dogmas is not a good scientific attitude at all.
You know, that is simply a version of "evolutionary theory is wrong about X so ID wins". We should wait for further data as this is getting repetitive. Merry Christmas and Happy New Year.Alan Fox
December 20, 2012
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Mike Gene criticizes Keefe and Szostak for using evolutionary modelling to concentrate functionality. Not copnvincing! Mike says "The function uncovered by this paper is very weak ATP-binding". Sounds like and, in fact, is "what good is half an eye".Alan Fox
December 20, 2012
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Keefe and Szostak only looked at ATP binding, so, yes, their approach was limited but it was certainly not worthless.
Yes, but their study was hardly relevant to biological reality. See Mike Gene's critique of that study here: http://web.archive.org/web/20080517131415/http://www.idthink.net/biot/ranprot/index.htmlGenomicus
December 19, 2012
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Alan Fox: They took a protein and varied each amino acid using the twenty coded residues. They found quite a lot of functionality. Let's say things as they are. They explored the space one step distant from the functional protein. Of course they found a lot of functionality. What did you expect? And, even so close to the original protein, for 20 sites even one substitution was essentially fatal to function. And this would be an argument against the "islands of functions" model? Sometimes I really wonder how much darwinists have lost any connection with reality! Keefe and Szostak only looked at ATP binding, so, yes, their approach was limited but it was certainly not worthless. It was simply a lie. They used intelligent selection (various runs of mutagenic PCR followed by selection of ATP binding variants) and considered the results as indicators of what randomness can do. The usual trick. The usual lie. Absolutely unforgivable, in a scientific paper. And your side still uses that lie for its propaganda. You too. It’s a signpost that points away from “islands of function”. It's simply a signpost of what should never be done in a scientific paper. It is a signpost of ideology in science. Nothing else. It would be currently correct to say we don’t know how rare potentialy biologically active proteins are in sequence space We know quite well how rare they are in the space we know. In the natural proteome, superfamilies are completely separated at sequence level. And nobody has ever shown any connection. These are facts, and ignoring them only because they are uncomfortable for your dogmas is not a good scientific attitude at all. but Keefe and Szostak and McLaughlin et al are providing insights. All of them in favor of the ID scenario, when they do not lie. And you forgot Axe and Behe, strangely. More will follow, no doubt. They will, they will. And the truth will become so clear that not even darwinists will be able to deny it.gpuccio
December 19, 2012
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Joe: It seems OT has missed a few points: 1 --> There now are cell based living things, but we are confident on many lines of evidence that the cosmos and planet on which we observe such has not always existed. Therefore there was -- on evidence -- a first cell based living organism. 2 --> Cell based life forms exhibit metabolism and replicate using coded information and molecular nanomachines. This being the only observed form of fully functional biological life, we have good reason to infer on observed life forms and fossils that such have characterised the world of life from its beginning on this planet. Again, on evidence. 3 --> We did not and cannot directly observe the actual origin of cell based life forms, as it is in the unobserved remote past. This constrains all investigations, so it is unfair to imagine or suggest that it applies ot only one approach, to use it to try to dismiss it. 4 --> In scientific reconstructions of unobserved events, we normally examine traces in the present and compare such to known causal factors that we can see may or do leave similar consequences. Where some of these -- say, S -- are characteristic of a given cause of type X, we are entitled to infer that S is a sign of X. For instance, the spectrum of the sun leads us to infer its chemical composiiton, and the same for stars. Similarly, an arson investigation often pivots on signs of arson such as traces of accelerant and fires that propagate in ways characteristic of such. (As just happened here, unfortunately>) 5 --> It so happens that functionally specific complex information and associated organisation, especially symbolically coded info beyond 500 - 1,000 bits is welll known to be a characteristic sign of design as cause. There are billions of cases in point, and there are no credible counter examples, Genetic Algorithms and the like being actually plainly intelligently designed. 6 --> The living cell we observe today, and per reasonable inference, those form the remote past of life, have abundant FSCO/I. This includes digital coded messages well beyond 500 - 1,000 bits. Indeed the estimates for the minimally complex life would point to 100 - 1,000 kbits as reasonable as the minimum. This too is evidence. 7 --> So, we have excellent evidence based reason to infer that the best explanation for the world of cell based life is design. Which is a well known and easily observed mechanism that has created the world of information based technologies we use every day. Indeed, with the work of Venter and others in recent years, we see that known or reasonably developed lab techniques can arguably be a way in which such could have been done. ====== Thus, the "no evidence" talking points being resorted to are obviously selectively hyperskeptical and show what OT would wish to be so rather than what is so. They are a mark of desperation not to see what evidence is manifestly there, to refuse to be consistent in methods of empirical investigation and inference, and to insist that a predetermined ideological materialist conclusion be chosen, never mind that the evidence strongly points in another direction. KFkairosfocus
December 19, 2012
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Progress- omtwo is finally catching on (with a little fix included):
You haven’t a clue about how the first replicator was designed "evolved", if there ever was a first replicator. And if there was a first replicator you have no clue whether it was capable of Intelligent Design blind watchmaker evolution. Given the nature of your evidence-free theory you can pretty much say anything you like, but that doesn’t make it so. If you had evidence which favored your position you would present it. If you believe my pointing out the lack of evidence for your claims is impeding the discussion I could really care less. Without evidence what’s to discuss?
He nails it- his position doesn't have any evidence so he has nothing to discuss....Joe
December 19, 2012
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Alan Fox:
They took a protein and varied each amino acid using the twenty coded residues.
One at a time and never more than one. No one on the ID side said that all proteins were fixed and couldn't toerate variation. But all that is moot because Alan's position cannot account for any proteins. And they sure as heck cannot account for chaperones.Joe
December 19, 2012
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I suppose you would also be surprised to hear that cells self-replicate.
You suppose no such thing. I doubt you could even give a bogus explanation of how such a supposition might arise in your consciousness. That would surprise me. ;)Alan Fox
December 19, 2012
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Alan Fox:
Obvious that cells are self-aware? We must mean different things when we use the word “self-aware”!
I suppose you would also be surprised to hear that cells self-replicate.Mung
December 17, 2012
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I would have thought this rather obvious.
Obvious that cells are self-aware? We must mean different things when we use the word "self-aware"!Alan Fox
December 17, 2012
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Not so. The MacLaughlin paper, as I have said, only tells us how sensitive a protein is to a simple step in a random walk, and is compatible with a very high functional complexity even in a very short protein sequence.
They took a protein and varied each amino acid using the twenty coded residues. They found quite a lot of functionality. What basis is there for prejudging unknown sequences with regard to functionality? None! So we have no reason to think functionality is less widespread elsewhere in unknown protein sequences.
The Szostak paper is, as I have shown many times, only a false argument which shows the limited capabilities of RV + intelligent selection, and as often happens in the darwinist field explicitly lies in its conclusions.
Keefe and Szostak only looked at ATP binding, so, yes, their approach was limited but it was certainly not worthless. It's a signpost that points away from "islands of function".
The “haystack crammed with needles” exists only in your imagination, and is not supported by anything.
It would be currently correct to say we don't know how rare potentialy biologically active proteins are in sequence space but Keefe and Szostak and McLaughlin et al are providing insights. More will follow, no doubt.Alan Fox
December 17, 2012
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Alan Fox:
You think cells are self-aware?
I would have thought this rather obvious.Mung
December 17, 2012
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Alan, what happens to a protein that does not fold correctly?
It sometimes causes CJD (Creutzfeldt–Jakob disease). Alpha-helices to beta-sheets.
Even a dumb cell is smart enough to know that there are islands of function.
You think cells are self-aware???Alan Fox
December 17, 2012
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Alan Fox: But, where this has been done, functionality turns up, as shown in the McLaughlin paper and previously by Jack Szostak. The haystack is crammed with needles! Not so. The MacLaughlin paper, as I have said, only tells us how sensitive a protein is to a simple step in a random walk, and is compatible with a very high functional complexity even in a very short protein sequence. The Szostak paper is, as I have shown many times, only a false argument which shows the limited capabilities of RV + intelligent selection, and as often happens in the darwinist field explicitly lies in its conclusions. The "haystack crammed with needles" exists only in your imagination, and is not supported by anything. I doubt it will remain so. It will not.gpuccio
December 17, 2012
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It’s strange that darwinists always stress so much how difficult it should be to measure the topology of the protein space, while we IDists are so confident that it can and will be done soon.
The fact is predicting the possible functionalities of novel proteins without synthesis and testing is currently beyond our capabilities. I doubt it will remain so. It is about time ID proponents contributed some efforts as you suggest. It would be worth the effort.Alan Fox
December 17, 2012
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gpuccio Thanks for the response. You write:
But when we look, we find functionality. It’s unjustifiable to claim functionality is rare.
Dream on. Indeed, if that were true, it should be very easy to find in the lab those functional, selectable intermediates which would explain the origin of protein domains. And protein engineering should be a piece of cake.
What do you mean by protein engineering? We can synthesize protein sequences routinely. What we can't do is predict the functionality of novel proteins. The only way to establish the functionality of a novel protein is to make it and test it (rather after the fashion of variation and selection ;) ) But, where this has been done, functionality turns up, as shown in the McLaughlin paper and previously by Jack Szostak. The haystack is crammed with needles!Alan Fox
December 17, 2012
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gpuccio,
Statistical coupling analysis (SCA) is a quantitative approach for understanding the information content of protein sequences through a generalization of the principle of evolutionary conservation.
Are you familiar with this technique? Any comments? CheersMung
December 17, 2012
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kf, yes, thanks. I thought of that but hoped we could be casual enough to ignore those details, lol.
Amino acids are covalently bonded together in chains by peptide bonds. If the chain length is short (say less than 30 amino acids) it is called a peptide; longer chains are called polypeptides or proteins.
So let's call it a peptide or polypeptide then. Anyways, the point being, does the cell just let these non-folding non-functional chains accumulate? Or are they so rare as to never be seen? Or are they recycled so the parts can be put to use?Mung
December 17, 2012
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Alan Fox: You really can’t extrapolate like this. We don’t know what is out there. It was Petrushka who proposed the paper (which is indeed interesting). I was only trying to make sense of it. But when we look, we find functionality. It’s unjustifiable to claim functionality is rare. Dream on. Indeed, if that were true, it should be very easy to find in the lab those functional, selectable intermediates which would explain the origin of protein domains. And protein engineering should be a piece of cake. Experiment shows the opposite. No. The honest thing is to to say we don’t know about unknown sequences until we synthesize and try them. No. There are many other approaches. That paper is one of them. I have suggested ways to deepen the research on that line. Axe has worked in other ways. Maybe, in the future, we can develop a method of predicting emergent properties of new proteins. That day has not yet arrived. It's strange that darwinists always stress so much how difficult it should be to measure the topology of the protein space, while we IDists are so confident that it can and will be done soon. What does that say of the subconscious convictions of both?gpuccio
December 17, 2012
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