Uncommon Descent Serving The Intelligent Design Community

Convergence, ID Critics, and Public Theatre

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The Map of Life is a new website, funded in part by the Templeton Organization, devoted to highlighting and discussing the role of convergence in evolution. Simon Conway Morris, whose thoughts on evolution I’m actually very interested in, has a role in the site – and it promises to be a place of interest for those people (ID proponents and TEs both) who see convergence as evidence that evolution may not be as “blind” as many people typically assume.

But I’m actually not interested in the the convergence question at the moment. Instead I’m interested in the site’s stated “aims”. The second aim is to promote discussion about convergence in evolution, and whether or not evolution may be more predictable than previously thought. The first aim is to A) promote the truth of evolution, and B) criticize ID in one of the most mangled, confused ways I’ve seen recently.

More on that below.

Here’s the relevant portion:

Of note, the science of evolutionary biology is NOT consistent with the central tenet of the “intelligent design” (ID) movement that suggests, contrary to all scientific evidence, that amongst other things organisms were supernaturally created and have remained unchanged since the time of their creation. There is also NO evidence for biological structures being supposedly “irreducibly complex”, arising by non-evolutionary “processes”. Indeed, convergence points in exactly the opposite direction because supposedly “irreducibly complex” structures, such as the bacterial flagellar motor, evolved independently at least twice. Not only that but we understand how each of the component parts became adapted make the complex structure that exists today. The existence of change over time in living things is clearly manifest in the fossil record, and is supported by information from the molecules, form and behaviour of organisms alive today.

Where to begin.

1) If it’s the central tenet of the ID movement that organisms were supernaturally created, then I missed the memo. Last I checked, the main ID proponents typically stress that ID absolutely does not claim that the designer, or designs, were “supernatural” in nature.

2) Nor have I seen this tenet that claims said organisms “have remained unchanged since the time of their creation”. I’m sure the writer of this part means a lack of change on the species level, rather than asserting that the very first penguin-like creatures are still waddling around somewhere. But again, where is it a “central tenet” of ID that populations of organisms remain the same? Mind you, I’m sure there are some ID advocates who believe that species don’t change, and so on. I’m also sure there are some evolutionary biologists who think evolutionary psychology is nonsense. It does not therefore become a central tenet of evolutionary biology that evolutionary psychology is bunk.

3) No evidence for IC biological structures arising by non-evolutionary processes? Really? First, last I checked ID proponents didn’t need to eschew evolutionary processes – though said processes would not be entirely unguided or Darwinian ones. Second, I’ve long wondered… if Craig Venter makes an IC structure in a cell, would that count as an IC structure coming about through a non-evolutionary force? Would it count as evidence of some kind, however qualified, for ID? But that’s an aside more than anything.

Now, I’m on record as being skeptical of ID as science (and I’m likewise skeptical of no-design claims being science as well.) But really, one thing I get tired of – and which I encounter quite often – is this blatant mangling of what ID proponents are saying, or what they are committed to. I suppose I should be glad the site doesn’t outright connect ID with a belief in a young earth, since that’s one of the usual talking points I bump into.

Anyway, I’m griping, but I have a suspicion of why ID is taken out and whipped in the “aims” section of the website: Because the second aim – which at least implies thinking about teleology, direction, and maybe even purpose in evolution – is really the “first” aim. But to even hint that perhaps evolution is a purposeful thing – or, even more distantly hinted, perhaps a tool itself employed by a designer – is to invite potential panic, and guilt-by-association with some ID thought crime.

So some theatre is required. ID is denounced, loyalty to the great Defenders of Science is established, and everyone can get on – however carefully – with the business of maybe, kinda, sorta asking if the Blind Watchmaker may have been able to see a little after all.

Comments
Gordon, I'll take all the above verbage as an admission that you, nor can anyone else provide an example of the explainatory filter being used on any biological system. Which, of course, just so happens to be the case with the ID metric CSI. FYI: the only matter you not-so-adequately addressed is your admission of ignorance on poultry production and genetic manipulations used in the aquaculture industry around the world. Other than that you appear to be confused that human fabrications, i.e., internet blogs, somehow represent self-replicating biological entities.Acipenser
April 8, 2011
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Onlookers: The above shows the problem. How does Aci know that I have posted anything in this thread,and it is not the Internet throwing up noise fits? ANS: he is implicitly applying a filter on functional specificity and complexity, so he infers that it is not plausible that posts are noise rather than intelligent action. (The various metrics simply work to quantify this. And, A is apparently unaware of the work of Durston et al who have quantified FSC metrics for 35 protein families, or the Evo Informatics Lab, who are working out the issue of the impact of active information on evolutionary searches. He is also not aware that something so basic as the file sizes we see for ever so many documents are measures of functionally specific information. Most importantly, he is again trying to duck the challenge to show how on undirected chance plus blind necessity, we have empirical evidence of the creation of such FSCI. Without positive evidence of that the materialistic scenarios for origin of life and of body plans are so much empty speculation. ) GEM of TKI PS: Aci, you have indeed reappeared, but only to show how your dodging the important things to focus on trivia, is inadvertently revealing. Having already adequately spoken to such secondary matters [for the astute reader aware of problems with regulation in 3rd world environments, e.g. think of recent scandals on Chinese products . . . ], I need not prolong exchanges on what was from the outset a side issue raised for distractive effect.kairosfocus
April 8, 2011
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karfo: First, I think you will see that I am not using “80? year old references. But, events with close relatives that were 30+ years ago, are in fact relevant to the issue. The only fact presented is that you ARE using 80+ yr old references. You've made nothing but unfounded assertions with no corresponding facts supporting any of your allegations. karfo:And, no I am not going to give more details [especially on the web] on the health problems faced by a close relative; I have no need to prove my point to you by violating someone’s privacy. Let’s just say, we had no reason to doubt at the time, and dietary adjustments did in fact make a positive difference. With no details (without mentioning any names, addresses ect0 I can only assume that there is now doubt about the veracity of the diagnosis. That there are chemical compounds that demostrate estrogenic, androgenic, anti-estrogenic, or anti-androgenic effects is not in question. Your erronious assertions of the use of growth hormones in poultry production is, however, the point in question. The International Poultry Council (of which Jamaica is a member) mission it to specifically address the ignorance which continues to be propogated by people like you concerning poultry production. That you choose to put forward these statements steeped in ignorance rather than actually doing some research is something that all onlookers can easily observe. Kafo:I do and did acknowledge a misreading above, on GM salmon. Turns out the phrasing was that the “injections” were of genetic nature. As I have corrected with references. Of course you had to ackowledge your ignorance because I forced you to do some actual research on the issue in order to back up your claims. You obviously found out how wrong those statements you made were. I see you also brought up the use of the explanitory filter. How about giving us a single worked example of how this metric is used in ID research or is it a concept like CSI that has no rigor and is thus yet another useless metric of ID non-research? Also, as you can see I have not vanished.Acipenser
April 8, 2011
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And, predictably, Aci vanishes at this point . . .kairosfocus
April 8, 2011
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PS: Your remark above: "Perhaps you really don’t know everything about everything . . ." is sadly revealing; the inference (given the wider context of discussion) is plainly the classic Dawkinsian dismissal of those who reject evolutionary materialism: ignorant, stupid, insane or wicked. Let's pick a specific, key point: is or is not functionally specific, complex, Wicken wiring diagram organisation and related information, an empirically reliable sign of intelligent action, justifying the use of an explanatory filter that uses it in one form or another. For, that is the central point I have been making, and it is the one that I suspect is the real target of the peripheral pecking. Why not deal with it, on the merits.kairosfocus
April 5, 2011
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Aci: First, I think you will see that I am not using "80" year old references. But, events with close relatives that were 30+ years ago, are in fact relevant to the issue. And, no I am not going to give more details [especially on the web] on the health problems faced by a close relative; I have no need to prove my point to you by violating someone's privacy. Let's just say, we had no reason to doubt at the time, and dietary adjustments did in fact make a positive difference. In citing HuffPo, I am pointing out that this issue is linked to the problem of the gap between 1st and 3rd world countries. Such is multiplied by the point that there are a great many chemicals that have estrogen like effects that are technically not estrogens, and which have become fairly pervasive in relevant environments. Smart money is to be cautious on what is or is not being done by corner-cutters in less effectively regulated, 3rd world environments. (If I were to tell you on how agricultural herbicides and pesticides etc are sometimes used in such environments, you would not believe me. Let's just say that our corner shops routinely sell over the counter household insect spray bombs that are for good reason banned in the USA. Few people know that after spraying one such, they are supposed to go and BATHE, never mind that it is written on the label.) Thus, my underscoring of MAY. I do and did acknowledge a misreading above, on GM salmon. Turns out the phrasing was that the "injections" were of genetic nature. As I have corrected with references. Now, we have moved off topic, so it would be better to allow the thread to get back on focus. GEM of TKIkairosfocus
April 5, 2011
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kafo:In my part of the world, a close relative had actual health challenges — medically diagnosed after considerable effort to identify the cause — that traced to the hormones that were in the chicken he had consumed. kafo: So, this leaves us with the balance that in recent decades, especially in first world countries with effective enforcement, this practice has apparently stopped, or at least been restricted from poultry. Though, there are concerns that chickens in at least some cases are eating foods that have in them similarly functioning substances. But also, the remarks point out that he practice has been a real one, and there is a widespread concern that it has continued in one way or another, one based on a reality, not mere conspiracy mongering. no enforcement necessary when the breed gentics is all that is needed and was developed long ago (in the 1930's 60 1960's). FYI: your own citations demosntrate the ignorance of the consuming public and the lack of any demonstrable effects from consumption of any meat product (e.g., beef)treated with growth hormones. They also indicate the importance of digestion processes in the exposure scenarion. I'd question the diagnosis. But tell me what did they find, i.e., chemical compound and concentration. Your own citations (between 80-40 years old) state this: a considerable amount of consumer research” that found a widespread misperception that chickens were commonly fed steroids and hormones as growth stimulants. Tyson’s “hormone-free” campaign ran for about 18 months, he said. Broadcast and print versions of the ads already have ended, and the message will be removed from Tyson’s Web site shortly, Nicholson said a campaign designed to increase market shares based on the ignorance of the consuemr is ahrdly evidence for the use of growth hormones in chickens. It's not needed and is not cost efficient when genetics alone has demonstrated the ability to meet market demands for decades. kafo: and you cite this as well: The above hormones are not as useful in increasing weight gain of poultry or hogs. No, kidding. the growth rate is in their genes and these breeds need noting more than a nutritionally complete ration. and further your citation, kafo, states the following: Studies done so far do not provide evidence to state that hormone residues in meat or dairy products cause any human health effects. kafo: And, as I noted — as the main point — in my brief comment that you hopped on, it seems that an attempt is reportedly being made to use hormones put into salmon eggs that result in accelerated growth. This, as I pointed out, is not properly genetic engineering. you should check your sources for accuracy before hanging your hat on them. Creating and/or presenting false charicatures soaked in whatever umbrage you wish to muster is meaningless if the original premise is without merit. Your hufpo quote reminds me of the claims tha polio vaccines are designed to cause sterility in men and thus should be rejected. Perhaps you really don't know everything about everything and sometimes you make erronious statements and then resort to 80-40 yr old references to support your archaic opinions. I just put that in to beg a caution on your part and your claims. and we haven't even started talking about the salmon egg claims......do you ahve a reference for those claims?Acipenser
April 5, 2011
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PS: The somewhat alarmist article I was alluding to above, in part reads:
While not on anyone's dinner table just yet, genetically engineered salmon are just a pen stroke away. GE salmon are being developed by a U.S. company called Aqua Bounty Farms and are preferred for their ability to grow two to four times faster than other farmed salmon: "The goal of producing faster growing Atlantic Salmon for the commercial food market is well on its way at Aqua Bounty Farms, a research facility located in Fortune, Prince Edward Island, Canada. This experimental hatchery has been injecting growth hormone genes into fertilized salmonid eggs to produce fast growing salmon, trout and Arctic char." Research at Aqua Bounty Farms, Aqua Bounty Farms webpage . . . .
And pardon, they are indeed reportedly genetically manipulating through injecting growth hormone genes. Wiki's summary is:
Genetically modified salmon is an Atlantic salmon, modified by adding a growth hormone regulating gene from a Pacific Chinook salmon and a promoter from an ocean pout to the Atlantic's 40,000 genes. These genes enable it to eat year-round, instead of only during spring and summer. The purpose of the modifications is to increase the speed at which the fish grows, without affecting its ultimate size or other qualities. The fish grows to market size in 16 to 18 months rather than three years.
Goals . . . My own thought is that something like genetically engineering energy canes turned into fuel is one thing [though probably not without potential danger of interfering genetically with ordinary sugar cane], manipulating food we directly consume is another. Some fairly serious testing is indicated, and we would be wise to be cautious.kairosfocus
April 5, 2011
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Aci: Perhaps things are/have long been like that in your part of the world. In my part of the world, a close relative had actual health challenges -- medically diagnosed after considerable effort to identify the cause -- that traced to the hormones that were in the chicken he had consumed. This was back to the 70's; consistent with the clips below. More recently, we can find this news article from the USA:
DES MOINES, Iowa -- Tyson Foods Inc. (TSN) said a controversial advertising campaign proclaiming its chickens as hormone-free will stop at the end of this month. The campaign so stirred up two rivals that they complained to the Better Business Bureau's National Advertising Division. Perdue Farms Inc. and Gold 'n Plump Poultry Inc. contended that the ads were misleading, since federal regulations prohibit any commercial grower from adding hormones or steroids to chicken products. Someone also apparently complained to the Federal Trade Commission, which contacted the Springdale, Ark., poultry giant to ask about the claim, a Tyson spokesman said Thursday . . . . Tyson spokesman Ed Nicholson said "the reason we didn't get involved in this whole process is because we knew (the campaign) was ending" soon. That fact was communicated to the FTC to answer its concerns, he said. Nicholson said he was unaware of any inquiry from the USDA. The advertising followed what Nicholson said was "a considerable amount of consumer research" that found a widespread misperception that chickens were commonly fed steroids and hormones as growth stimulants. Tyson's "hormone-free" campaign ran for about 18 months, he said. Broadcast and print versions of the ads already have ended, and the message will be removed from Tyson's Web site shortly, Nicholson said.
Another article about the use of hormones in food, from Cornell U, observes:
The female sex hormone estrogen was also shown to affect growth rates in cattle and poultry in the 1930s. Once the chemistry of estrogen was understood, it became possible to make the hormone synthetically in large amounts. Synthetic estrogens started being used to increase the size of cattle and chickens in the early 1950s. DES was one of the first synthetic estrogens made and used commercially in the US to fatten chickens. DES was also used as a drug in human medicine. DES was found to cause cancer and its use in food production was phased out in the late 1970s . . . . There are six different kinds of steroid hormones that are currently approved by FDA for use in food production in the US: estradiol, progesterone, testosterone, zeranol, trenbolone acetate, and melengestrol acetate. Estradiol and progesterone are natural female sex hormones; testosterone is the natural male sex hormone; zeranol, trenbolone acetate and melengesterol acetate are synthetic growth promoters (hormone-like chemicals that can make animals grow faster). Currently, federal regulations allow these hormones to be used on growing cattle and sheep, but not on poultry (chickens, turkeys, ducks) or hogs (pigs). The above hormones are not as useful in increasing weight gain of poultry or hogs. As mentioned earlier, FDA allows the use of the protein hormone rbGH to increase milk production in dairy cattle. This protein hormone is not used on beef cattle.
So, this leaves us with the balance that in recent decades, especially in first world countries with effective enforcement, this practice has apparently stopped, or at least been restricted from poultry. Though, there are concerns that chickens in at least some cases are eating foods that have in them similarly functioning substances. But also, the remarks point out that he practice has been a real one, and there is a widespread concern that it has continued in one way or another, one based on a reality, not mere conspiracy mongering. And, as I noted -- as the main point -- in my brief comment that you hopped on, it seems that an attempt is reportedly being made to use hormones put into salmon eggs that result in accelerated growth. This, as I pointed out, is not properly genetic engineering. I therefore take your point that my "are" is probably wrong for first world, well regulated environments. I am -- on a fair degree of experience with corner-cutting tactics -- not so sure for third world, less effectively regulated environments; but one hopes that things are at least catching up there. The better sort of farmer or manufacturer in third world situations will be fairly up to date and conscientious, but . . . here is Bolivian Pres Evo Morales as reported a year ago by Huffpo:
TIQUIPAYA, Bolivia — Bolivian President Evo Morales said Tuesday that men should stay away from chicken if they want to maintain their hair and virility. Morales told an environmental conference that chicken producers inject the birds with female hormones "and because of that, men who consume them have problems being men." He also suggested eating too much chicken for too long could make men go bald. Morales' warning may be out of date: Chicken producers in Europe, the United States and many other countries say they abandoned the use of hormones in poultry several decades ago and many if not most Western nations ban them outright . . .
Let us note that "may," in the context of the third, not the first, world. I also know you are fairly quick to find points to snipe at me [as you have done in previous threads], but I would beg to put up a caution. For, perhaps your knowledge of your own situation does not apply to all situations; especially in jurisdictions where things are not so tightly regulated as in first world countries. GEM of TKIkairosfocus
April 5, 2011
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kafo: Chickens are pumped up on hormones, too; for decades. That is what has cut the time to marketable size to such a short run these days. is there some real genetic engineering being done to salmon? From this statement I can only conclude that you know aboslutely nothing about rearing and producing chickens for market. Commercial broilers, Cornish Cross, are not fed growth hormones. It is all in their genetics. I raise hundreds of these each year and market size (dressed wt. 4-5 lbs) are reached between 6-7 weeks post-hatch fed only a diet of grains and an adequate ration of protein to meet their metabolic demands. is it really too much to ask that before making declaritive statements about somethng that you actually make the effort to determine if those claims are valid. The same goes for the broad-breasted varities of turkeys compared to their heritage breed cousins. Genetics and selection....no artificial hormones required. FYI: injecting growth hormone into an egg will do nothing if there is no receptor to bind the hormone. You should actually take a look and see what aquaculturists actually do in their production of fish. There is abundant information avialable on the various methods used in aquaculture, e.g., gynogenisis and use of methods that induce tetraploidy and polyploidy.Acipenser
April 5, 2011
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F/N: I see a case of growth hormone being injected into salmon eggs and leading to faster growing fish. It is being denounced as GENETIC engineering, but that seems to be incorrect. Chickens are pumped up on hormones, too; for decades. That is what has cut the time to marketable size to such a short run these days. is there some real genetic engineering being done to salmon?kairosfocus
April 5, 2011
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As has been repeatedly said, the design of biological systems on earth requires nothing more than intelligences with sufficiently sophisticated molecular nanotechnology; a few tech generations beyond Venter. (And just what is GE doing to salmon?) Funny you should mention the salmon... Got a post up now spurred on by those fish.nullasalus
April 5, 2011
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F/N: GVCS -- Global Village Construction Set initiative.kairosfocus
April 5, 2011
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Null: When it comes to the likes of NCSE and especially Barbara Forrest, the issue is not even a debate. We are dealing with rank dishonesty and smear tactics. Unfortunately, this Plato's Cave shadow shows outfit dressed in the holy lab coat, is given high credibility in the minds of many, and they are confused. However, since the UD correctives have been standing there for literally years, I think those who come here and post comments have a duty of care to do simple investigations before thoughtlessly repeating destructive smears. As has been repeatedly said, the design of biological systems on earth requires nothing more than intelligences with sufficiently sophisticated molecular nanotechnology; a few tech generations beyond Venter. (And just what is GE doing to salmon?) However, there is another context of inference to design that has far more serious import and far more direct worldview reference; the observed cosmos which credibly had a beginning at a finite distance in the past, and exhibits fine tuning that supports a cosmos with C-chemistry, cell based intelligent life. the best candidate for that is a necessary being with the skill, power and knowledge base as well as the intent to create a cosmos such as the one in which we live; even through the usual multiverse detour. Once that is on the table, I think it rebalances the issues on the biological inference to design, as it would make good sense that the architect of a cosmos set up in ever so many ways for life like we enjoy, was set up in order to go on to make such life. How tweredun, however, is an open issue, and ID is a theory of cause based on reliable signs, not of mechanisms. There's more than one way to skin a cat, and there may indeed have been a blend of techniques used. Actually, I am much less interested in that, than in how we can do it too, by reverse engineering the strategies of living systems. My preferred forward engineering projects are:
1: an advanced version of the "global village construction set"/Industrial civ 2.0 initiative [for sustainable development on a modular scale using ICTs and mechatronics to transform technology on an open source plus value added model, 2: developing a version of the von Neumann self-replicator [the self-replicating general purpose fab], then 3: Solar system and onward galactic colonisation using a further developed and refined version of the above for space deployment
GEM of TKIkairosfocus
April 5, 2011
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kf, One driver of the error you are seeing is the failure to understand that there are two relevant contrasts to “natural.” I.e., not only the “natural vs supernatural” so often used in NCSE style talking points but the contrast “nature vs art” that traces back 2,300+ years to Plato in The Laws Bk X. I'm sure there's numerous reasons for the confusion (well, "confusion"), that included. * Repeated claims that ID is about the supernatural and denying all evolution, made by either dishonest or misinformed people. * People noting that many/most ID proponents are religious or see a connection between ID and their belief in God, and then deciding what ID 'must' be about. * Those who reflexively assume any sufficiently powerful designer must be supernatural by definition, with no justification. (Anyone who thinks you need to be the God of Abraham to manipulate genetics really needs to see what GE is doing with salmon nowadays.) I'm not going to say the blame lies entirely on the part of ID critics. ID does have a fairly explicit association with religious thought. Then again, Darwinism also has a fairly explicit association with atheism.nullasalus
April 5, 2011
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BA: A digital, algorithmic information processing machine will require a code that is symbolic in nature. And, such an algorithm will normally process any one input on circumstances and/or prior events as stored in some way. That is, current responsiveness depends on prior situations and current environment. That means that no one input will always have the same outputs regardless of what has already happened or the environment. (Think of the implications of a DO-WHILE or DO-UNTIL loop with a preset and decremented counter and/or a circumstances test.) That ability to respond based on stored information and sensed circumstances, is crucial to best performance of such a machine. And, indeed, the way DNA is manipulated in a growing organism as tissues and organs form and as cell types specialise, is a case in point. GEM of TKIkairosfocus
April 5, 2011
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kf, Thanks, but I already know the DNA code is optimal. What I specifically want to know is if a optimal code is necessary for a optimal machine. Must a 'abstract' convention be implemented onto a material substrate in the successful operation of a molecular machine? i.e. Does a molecular machine 'translate' a set variety of inputs into set variety of outputs? ,,, It would seem to me that this must be a true statement.bornagain77
April 5, 2011
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BA: If you want to do an optimality analysis, on DNA, look at what I have cited here, HT Mike Gene. GEM of TKIkairosfocus
April 5, 2011
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PS: I forgot. Dr S is spotting that noise is coming from thermal sources, and would disrupt the specificity and functional complexity of the coded actions. So, he is picking half of the issue up. The other half is that we are dealing with functionally specific complex activity in DNA etc, and that this is based on codes. The empirically known source of such FSCI is, of course, intelligence. The signal to noise ratio of info theory is an implicit inference to design, i.e the meaningful, coded message is artificial.kairosfocus
April 5, 2011
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kf, That makes me wonder if anything is useful in the paper. kf, I would like to use this statement as evidence if I can,,, (optimal) 70% efficiency of bistate molecular machines - Schneider Excerpt: since the (optimal) efficiency (of molecular machines) is directly related to the channel capacity [see equation (7)], they must also be operating close to the maximum possible capacity. As Shannon pointed out (27) to do so they must not only have codes, but they also must be using nearly optimal codes. http://www.ccrnp.ncifcrf.gov/~toms/paper/emmgeo/emmgeo.pdf ,,, i.e. kf, is the optimal efficiency we observe for molecular machines tied directly to a distinct 'optimal' code for each unique machine, as per Shannon?,,, kf, Is this following statement applicable for each unique molecular machine? “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Lifebornagain77
April 5, 2011
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BA: the first key error with the Schneider paper is that he does not understand that the cell is not harvesting energy from heat. So, the strict Carnot theorem on heat engines [where you have no specific knowledge of molecular states] does not apply. It is easy to build a transformer that is 98% efficient. Similarly, to define the number of "independent parts" as though it were a bandwidth, is dubious. bandwidth has to do with range of frequencies involved in a communication, and is connected to how fast information can move. IIRC, something like 100 AA/s can be assembled in a ribosome, implying a bit rate of up to 100* 3 * 2 = 600 bit/s. Not a particularly fast rate; but obviously an effective one. And not a rate that is going to force bandwidth headaches. Of course the rate is probably set by the known slowish rate of organic reactions, in a context where elevated temperatures are not welcome, and where there are existing functionally specific catalysts, i.e. enzymes. Then, we see:
Rhodopsin, for example, has two biologically important physical states: not having seen a photon and having seen one. If these states were not stable and distinct, the molecule would rapidly switch between them because of thermal impacts, giving an animal the impression that there is light when in the dark. These animals will be eliminated by natural selection, leaving only those who have evolved sufficiently distinct states.
This massively begs the question of getting to the system in which rhodopsin exists and functions in a highly complex network of interactions. The envisioned simplistic case of a molecule that was within the ~ 1/40 eV level of thermal interactions at typical temps, is a strawman. No such entity has been observed and the idea of a complex entity with just one blunder being eliminated in a competition with the presumed "right" version, is nonsense. besides, say blind cave fish -- which I gather often have genes for eyes -- apparently do survive in the context of sighted comparable species in an aquarium. Then, this caps off the edifice of begged questions:
if EcoRI in the bacterium Escherichia coli were to bind to incorrect positions on the DNA other than GAATTC, the genomic DNA would be destroyed because only that sequence is protected from EcoRI digestion by the corresponding DNA methylase (33). The extreme precision of restriction enzymes (34–38) and the thermal stability of rhodopsin (39) are well known but the underlying fundamental reason has not been widely appreciated. Shannon's channel capacity theorem, as applied to molecules (23), guarantees that by appropriate coding it is possible for a molecular machine to evolve distinct states, and once it has done so, it can operate at its capacity with as few errors as is necessary for survival.
Of course the question of where codes are uniformly seen to come from, is begged. And thst a code with sufficiently distinct symbols is required for it to work is a necessary but not a sufficient condition for a code to exist. Nor does Shannon's bandwidth result magically guarantee anything about the actual codes in the channel, save providing an upper bound on what a noisy channel can do. Pardon, but I am a lot less than impressed. GEM of TKIkairosfocus
April 5, 2011
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kf, I was very interested to see that Dr. Schneider discovered that molecular machines had to operate close to their 'information processing maximum' (channel capacity), but I was very disappointed to see him so readily discard the central tenet of information theory, channel capacity, when he saw that it conflicted with Darwinian theory. Heaven forbid that he would actually ever doubt evolution!,,, kairos with your engineering background, perhaps you can help me, and look the paper over, and draw out the proof he developed for a 'distinct code' for each 'optimal' molecular machine. That 'distinct code' proof, minus Schneider's unwarranted story telling, will be useful as evidence.bornagain77
April 5, 2011
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PS: it is a necessary condition for a code that we have sufficiently distinct things or states that can be used to represent information. But, that was a fact known immemorial in the days of St Paul:
1 Cor 14:7 Even in the case of lifeless things that make sounds, such as the flute or harp, how will anyone know what tune is being played unless there is a distinction in the notes? 8 Again, if the trumpet does not sound a clear call, who will get ready for battle? 9 So it is with you. Unless you speak intelligible words with your tongue, how will anyone know what you are saying? You will just be speaking into the air. 10 Undoubtedly there are all sorts of languages in the world, yet none of them is without meaning . . .
It seems the goodly doctor has confused a necessary condition that must be met [and which has long been known as such], with a sufficient one. The only known sufficient source of a code system is a mind.kairosfocus
April 5, 2011
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BA: And, how do molecules create codes, symbolic rule-based representations of other things? I.e. enfolding intentionality? Does Dr Schneider intend to imply that molecules have mental capabilities? If so, on what evidence, does he suggest this? GEM of TKIkairosfocus
April 5, 2011
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It seems someone forgot to notify the Nobel committee of Tom Schneider's work on the 'convergence' of 'optimal' molecular machines: (optimal) 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence Excerpt: The concept of multiple distinct molecular states represented by spheres allowed us to steal the key prize of information theory for use in molecular biology, namely the channel capacity theorem (23). Restating the channel capacity theorem as a ‘molecular machine capacity theorem’, we see that because they are able to change and adapt through Darwinian evolution, biological states of molecules may become as distinct as necessary to reduce error to a level acceptable for robust survival. The molecular machine capacity theorem implies that if a system is to approach capacity it must do so by creating appropriate codes (27). So the discovery reported in this paper of (optimal) 70% efficiencies leads to the additional discovery that molecular states not only can (by the molecular machine capacity theorem) but actually do evolve codes to become as distinct as necessary for survival. http://www.ccrnp.ncifcrf.gov/~toms/paper/emmgeo/emmgeo.pdf Perhaps Schneider will think I'm just a stick in the mud in his march to a Nobel prize, but perhaps, since he now firmly believes it possible to violate the 'law' of Shannon's channel capacity with the evolution of molecular machines, he could actually demonstrate the evolution of ANY 'optimal' molecular machine whatsoever so as to actually prove that what he believes to be true, for violating the central tenet of communication theory, can be done? notes; ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life Shannon Information - Channel Capacity - Perry Marshall - video http://www.metacafe.com/watch/5457552/ Though the DNA code is found to be optimal from a error minimization standpoint, it is also now found that the fidelity of the genetic code, of how a specific amino acid is spelled, is far greater than had at first been thought: Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010 Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,, http://www.creationsafaris.com/crev201009.htm#20100919a The coding system used for living beings is optimal from an engineering standpoint. Werner Gitt - In The Beginning Was Information - p. 95 Collective evolution and the genetic code - 2006: Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving. http://www.pnas.org/content/103/28/10696.full quote from Schneider's paper; 'The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity),' http://www.ccrnp.ncifcrf.gov/~toms/paper/emmgeo/ List of Molecular Motors - Machines https://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=enbornagain77
April 5, 2011
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"Sweet and Low" the supernatural sweetener!Joseph
April 5, 2011
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myname:
What else is he saying than that this high gene duplication rate can’t have occured naturally? This is then by definition supernaturally.
How about ARTIFICIALLY?Joseph
April 5, 2011
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Null: One driver of the error you are seeing is the failure to understand that there are two relevant contrasts to "natural." I.e., not only the "natural vs supernatural" so often used in NCSE style talking points but the contrast "nature vs art" that traces back 2,300+ years to Plato in The Laws Bk X. In the second sense, natural forces trace to mechanical necessity giving rise to natural regularities, and also to chance circumstances that give rise to stochastic contingencies dominated by probability distributions. By contrast, we have choice contingency [i.e. art or design], giving rise to purposefully directed, functionally specific, complex Wicken wiring diagram organisation and associated information: FSCO/I. In turn, that is why there is such a stout rhetorical resistance to the FSCI/CSI concept, and the associated explanatory filter. For, once it is acknowledged that the contrast nature vs art is relevant, and that there are reliable signs that point to aspects of objects, processes and phenomena being driven by chance, necessity or design, the debate on the scientific credibility of design theory is over. GEM of TKIkairosfocus
April 5, 2011
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myname, What else is he saying than that this high gene duplication rate can’t have occured naturally? This is then by definition supernaturally. Luskin is apparently making the claim that the processes being referred to to explain a given biological event are inadequate. Where, exactly, are you getting "this couldn't have occurred naturally" and "therefore it took place supernaturally" from this? Think of a mainstream scientific debate. If one scientist tells the other "What you conjecture to happen is very unlikely given what we know about the processes you cite", do you process that as "He's saying it can't happen naturally - so it must have been supernatural!"? And if not there, why here? Again, is Craig Venter a supernatural being in your view? Is all design necessarily "supernatural"? How do speed up gene duplication by purely natural processes? Good question. Numerous possibilities I imagine, including design - it depends on the context you're speaking of. Are you really taking the position that whenever known natural explanations are taken to be inadequate this or that, it's automatically a claim that natural processes (whether design, or current unknown alternatives) are utterly incapable of being responsible, and it must be supernatural?nullasalus
April 5, 2011
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http://www.evolutionnews.org/2011/01/a_fishy_story_about_antifreeze043141.html
Even if one invokes the magic wand of "positive selection," this gene was apparently duplicating at a rate far higher than the average gene duplication rate. It should have taken some 3 billion years just to accomplish the last step of this little story, which took place in far less than 50 million years, as these repeated duplications are the very last step of the story. In other words, in the last stage alone it seems that this paper requires far too much genetic evolutionary change too quickly.
What else is he saying than that this high gene duplication rate can't have occured naturally? This is then by definition supernaturally. How do speed up gene duplication by purely natural processes?myname
April 5, 2011
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