Convergence, ID Critics, and Public Theatre

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

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

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

And, predictably, Aci vanishes at this point . . . kairosfocus

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

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 TKI kairosfocus

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

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

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 TKI kairosfocus

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

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

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

F/N: GVCS -- Global Village Construction Set initiative. kairosfocus

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 TKI kairosfocus

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

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 TKI kairosfocus

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

BA: If you want to do an optimality analysis, on DNA, look at what I have cited here, HT Mike Gene. GEM of TKI kairosfocus

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

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 Life bornagain77

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 TKI kairosfocus

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

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

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 TKI kairosfocus

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=en bornagain77

"Sweet and Low" the supernatural sweetener! Joseph

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

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 TKI kairosfocus

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

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

"And then make it a front page post at least once a month." Nah. Let's scare away the people who are only in it for cheap fodder. Worked for Jesus (John 6). tragic mishap

myname,if God picks up a book, or takes a walk in the park, is that supernatural just because he's God? It would only be supernatural if he willingly suspends or bypasses the laws of physics, but I dont see why God cannot willingly work within the physical bounds he created. If he engineered life, he wouldnt need to break the laws of nature to accomplish that any more than we need to break the laws of nature when we engineer computers,space shuttles, ect..... kuartus

myname, Is god supernatural? Beats me. Which god are we talking about here? Zeus? And what does this have to do with ID's central tenets? God and gods are among the possibilities of designers - alongside aliens, demiurges, impersonal telic processes, simulations, etc. If so is the process of god guiding an evolutionary process a natural process or a supernatural process? Assuming we're speaking of a god, it depends on which god we're talking about, and how the guidance manifests. Front-loading? Intervention? And again, what does this have to do with ID's central tenets? Which tenet says that the designer of anything in the universe must be supernatural, much less a god? That life can’t have evolved by purely natural processes. Can't possibly have? ID doesn't make that claim. ID proponents make an (if possibly strong) inference about design being an explanation for some what we see in nature, with the possibility of said inference being weakened or overruled at a future date depending on the data that comes in. And if Craig Venter creates biological artifact X in a laboratory, did X come about through 'natural processes'? Or is Craig Venter an example of the supernatural? Is any powerful intelligence supernatural by default? nullasalus

kairosfocus, Yup, I read those. I guess we will just have to agree to disagree- I say the blind watchmaker definition is incompatible with ID. I am pretty sure Dr Behe agrees. IMHO 9 & 10 need to be rewritten and retitled. Joseph

myname- I don't think that is the proper claim. Do you have a reference? Blind, undirected (chemical) processes, is what I have read. Joseph

I'll take a shot at why the designer must be "other worldly". Is it a true statement of Id theory that biological info cannot come from a undirected non biological source? velikovskys

@nullasalus Is god supernatural? If so is the process of god guiding an evolutionary process a natural process or a supernatural process? By all means, name the claims and tell me how “the only logical consequence” is that the designer is supernatural. That life can't have evolved by purely natural processes. myname

T, This is what happens when “science” becomes captive to one narrow set of conceptions, be they methodological, epistemological, or metaphysical. It becomes politicized, and one has to tread carefully to avoid offending the ruling regime. That's the real take-home message of this, I suppose. The fact that the website requires some kind of ritual sacrifice before even meekly gesturing somewhere in the direction of teleology speaks volumes. Conway Morris, to his credit, is sometimes pretty bold about his views. Really, that's a great article - if more TEs were like that, I'd be cheering them on. I don't know if he was personally involved with that 'aims' entry on the site either. But that makes the whole thing all the more silly, this ritual faux-slaughter of ID before even beginning to discuss direction in evolution. And really, if it's necessary, is it too much to ask that they at least get it right? Who am I kidding. The answer is "yes". And that's just one more reason why my ID sympathies have remained over the years. nullasalus

Joseph: WAC's 9 - 10: ____________ >> 9] “Evolution” Proves that Intelligent Design is Wrong The word “evolution” can mean different things. The simplest meaning is one of natural history of the appearance of different living forms. A stronger meaning implies common descent, in its universal form (all organisms have descended from a single common ancestor) or in partial form (particular groups of organisms have descended from a common ancestor). “Evolution” is often defined as descent with modifications, or simply as changes in the frequencies of alleles in the gene pool of a population. None of those definitions can prove ID wrong, because none are in any way incompatible with it. ID is a theory about the cause of genetic information, not about the modalities or the natural history of its appearance, and is in no way incompatible with many well known patterns of limited modification of that information usually defined as “microevolution.” ID affirms that design is the cause, or at least a main cause, of complex biological information. A theory which would indeed be alternative to ID, and therefore could prove it wrong, is any empirically well-supported “causal theory” which excludes design; in other words any theory that fits well with the evidence and could explain the presence or emergence of complex biological information through chance, necessity, any mix of the two, or any other scenario which does not include design. However, once we rule out “just-so stories” and the like, we will see that there is not today, nor has there ever been, such a theory. Furthermore, the only empirically well-supported source of functionally specific, complex information is: intelligence. To sum it up: no definition of evolution is really incompatible with an ID scenario. Any causal theory of evolution which does not include design is obviously alternative to, and incompatible with, ID. However, while many such theories have indeed been proposed, they are consistently wanting in the necessary degree of empirical support. By contrast, design is an empirically known source of the class of information – complex, specified information (CSI) — exhibited by complex biological systems. 10] The Evidence for Common Descent is Incompatible with Intelligent Design ID is a theory about the cause of complex biological information. Common descent (CD) is a theory about the modalities of implementation of that information. They are two separate theories about two different aspects of the problem, totally independent and totally compatible. In other words, one can affirm CD and ID, CD and Darwinian Evolution, or ID and not CD. However, if one believes in Darwinian Evolution, CD is a necessary implication. CD theory exists in two forms, universal CD and partial CD. No one can deny that there are evidences for the theory of CD (such as ERVs, homologies and so on). That’s probably the reason why many IDists do accept CD. Others do not agree that those evidences are really convincing, or suggest that they may reflect in part common design. But ID theory, proper, has nothing to do with all that. ID affirms that design is the key cause of complex biological information. The implementation of design can well be realized through common descent, that is through implementation of new information in existing biological beings. That can be done gradually or less gradually. All these are modalities of the implementation of information, and not causes of the information itself. ID theory is about causes. >> _____________ I think that this is clear enough. There is such a thing as an intellectual duty of being truthful and fair. If one is just a click or two away form something like this, and insists on a strawmannish distortion, that goes to a failure of intellectual duty. But then, evolutionary materialism, ever since Plato, has been known to be amoral and prone to ruthless, manipulative factions. (And if you doubt me on this in respect of more recent history, kindly cf here.) GEM of TKI kairosfocus

(follow up from my comment #7) From Dembski’s CV:

Contributor, “Prospects for Post-Darwinian Science,” symposium, New College, Oxford, August 2000. Other contributors included Michael Denton, Peter Saunders, Mae-Wan Ho, David Berlinski, Jonathan Wells, Stephen Meyer, and Simon Conway Morris.

http://www.designinference.com/documents/PDF_Current_CV_Dembski.pdf john_a_designer

But on 3# I have to say that IC biological structures have in their definition that they can’t arise by an evolutionary process. So this is really a no-brainer. No, they don't. They're suggested not to arise by Darwinian evolutionary means. Other evolutionary processes can be possible. While it may not be implicit in ID if you put a few ID claims together the only logical consequence is that the designer is supernatural. No, it's not. By all means, name the claims and tell me how "the only logical consequence" is that the designer is supernatural - and make sure these are central tenets while you're at it, rather than individual ID-related claims. Keep in mind, "supernatural" (along with "natural") are words that are nearly bereft of meaning at this point. And in public debates Steven Meyer and others usually admit that they think the intelligent designer is god. They also stress that their conclusions about who or what is responsible for design are distinct from ID, which they claim does not (and really, cannot) identify the designer. So I don’t really understand why on this blog this is such an issue. It's possible you misunderstand ID. nullasalus

I will bite my tongue on #1. But on 3# I have to say that IC biological structures have in their definition that they can't arise by an evolutionary process. So this is really a no-brainer. Okay to #1: While it may not be implicit in ID if you put a few ID claims together the only logical consequence is that the designer is supernatural. And in public debates Steven Meyer and others usually admit that they think the intelligent designer is god. So I don't really understand why on this blog this is such an issue. myname

nullasalus: 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. I remember reading someplace Dr. Dembski saying that in the late 1990’s he along with Michael Denton (and maybe some others) traveled to London where they met Conway Morris. I believe that it was some kind of conference or colloquium on ID, or ID related issues. Therefore, I can’t believe that Conway Morris is that ignorant of ID, which of course, implies that he is either being dishonest or trying to say the right things as not to be ostracized by his peers. However, neither of those positions speak very highly of his integrity as either a scientist or a human being. john_a_designer

Good post, nullasalus. To your list of complaints let me add mine: "Not only that but we understand how each of the component parts became adapted [to] make the complex structure that exists today." Oh, really? So Conway Morris (or whoever wrote that blurb) can give us a stepwise list of changes from land mammal to whale, telling us how each change was adaptive, all the way up to a viable cetacean? I'd be interested in getting the volume and issue numbers of the journals in which Conway Morris (or whoever produced the above text) has published these results. (Maybe they are the same journals in which Ken Miller has published the stepwise path to the flagellum, telling us how each additional part was adaptive.) The bluster of Darwinians knows no end. But as you say, nullasalus, it's likely that Conway Morris is moving, ever so cautiously and tentatively, away from the classic Darwinian formulation of evolution and toward something teleological. But any language that sounds like "design" must be avoided, or Conway Morris will be ostracized from the fraternity by his peers. So how do you talk about teleology, even when the scientific evidence points that way, without being savaged by the biological community? The dance one has to perform is like navigating between Scylla and Charybdis. This is what happens when "science" becomes captive to one narrow set of conceptions, be they methodological, epistemological, or metaphysical. It becomes politicized, and one has to tread carefully to avoid offending the ruling regime. Why not just put everything on the table? Scientists should say: "We're interested in finding out what really happened, and we don't care if the data point to hypotheses that don't meet with the approval of an elite of ageing population geneticists. From this moment on, *all* views are on the table for discussion." Neither Conway Morris nor anyone else should have to apologize for following the evidence wherever it leads. Timaeus

kairosfocus, Thank you but that is a weak argument. For one it needs to have a stronger "title" , ie Intelligent Design Is NOT Anti-Evoution. And then it needs to be the first point. For example- Evolution has several meanings. The meanings of evolution, from Darwinism, Design and Public Education: 1. Change over time; history of nature; any sequence of events in nature 2. Changes in the frequencies of alleles in the gene pool of a population 3. Limited common descent: the idea that particular groups of organisms have descended from a common ancestor. 4. The mechanisms responsible for the change required to produce limited descent with modification, chiefly natural selection acting on random variations or mutations. 5. Universal common descent: the idea that all organisms have descended from a single common ancestor. 6. “Blind watchmaker” thesis: the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms. Make it clear that ID argues only against #6:

Scott refers to me as an intelligent design "creationist," even though I clearly write in my book Darwin's Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think "evolution occurred, but was guided by God." -Dr Behe

Referece Dr Spetner's "Not By Chance" in which he discusses the role of "built-in mechanisms to environmental cues" as part of his "non-random evolutionary hypothesis". Say something about mutations being directed pretty much a computer program directs an output, as spell-checker is so directed- no intervention required- they are under software control. And then make it a front page post at least once a month. Joseph

Joseph: The "post" is already there, and it is permanently linked, top right, this and every UD page: the weak argument correctives, starting from the first several correctives. Been there, literally, for years. We are not dealing with innocent ignorance here, but with willful distortion in service to a rhetorical agenda that has to distort to be persuasive to anyone. Utterly telling. GEM of TKI kairosfocus

The strawman of "remained unchanged" goes back to Charles Darwin- and most likely dates to before that. A few years back (2006?)Bill Nye "the science guy" was on one of the news channels pushing that same strawman. Recently (2010) on MSNBC Olberman was doing he same thing. Perhaps UD needs a post about that- that ID is not anti-evolution- rater ID i anti- the blind watchmaker having sole dominion over evolutionary processes. Joseph

Or better linked: http://www.newyorker.com/reporting/2010/12/13/101213fa_fact_lehrer#ixzz1ITKa7k33 Charlie

Null: Under aim no 1:

First, that evolution is true. Forms of life change over time, or evolve, as successive generations inherit genetic, epigenetic or cultural information that is modified relative to their ancestors. Features of the changing environment in which organisms live favour differential survival of individuals with the most suitable (or ‘adapted’) modifications for living there. This leads to change in species over time, or their extinction if the environment changes too fast for ecologically well-adapted variants to become established.

Taken at strict face value, this is something that many modern young earth creationists would agree with. But if what is meant is unlimited variability and descent with modification forming novel body plans through blind watchmaker random walks and culling of sub-pops on differential reproductive succe4ss, that is very different. And, it runs into the challenge: where is the observational evidence of such body plan origination? If there is none, then why the extravagant assertions of truth? An inference to best current explanation is not to be equated to truth beyond reasonable dispute, and what evidence of observation supports should not be extrapolated to what is controversial and questionable as though the factual evidence for the one established the other as similarly factual. GEM of TKI kairosfocus

The sites second aim is; 'Second, that evolution repeatedly navigates to stunningly similar solutions from very different starting points. Through the surprisingly ubiquitous process of convergent evolution, organisms as distantly related as moths and birds, ciliates and worms, when inhabiting similar environments, have developed similar features as adaptive solutions to life there. This suggests that evolutionary outcomes can be much more predictable than generally thought, and raises interesting questions about how patterns of convergence arise.' ,,, and yet if we get past the 'almighty power of evolution' 'just so' story here we find,,, Implications of Genetic Convergent Evolution for Common Descent - Casey Luskin - Sept. 2010 Excerpt: When building evolutionary trees, evolutionists assume that functional genetic similarity is the result of inheritance from a common ancestor. Except for when it isn't. And when the data doesn't fit their assumptions, evolutionists explain it away as the result of "convergence." Using this methodology, one can explain virtually any dataset. Is there a way to falsify common descent, even in the face of convergent genetic similarity? If convergent genetic evolution is common, how does one know if their tree is based upon homologous sequences or convergent ones? Critics like me see the logic underlying evolutionary trees to be methodologically inconsistent, unpersuasive, and ultimately arbitrary. http://www.evolutionnews.org/2010/09/implications_of_genetic_conver037841.html Origin of Hemoglobins: A Repeated Problem for Biological Evolution - 2010 Excerpt: When analyzed from an evolutionary perspective, it appears as if the hemoglobins originated independently in jawless vertebrates and jawed vertebrates.,,, This result fits awkwardly within the evolutionary framework. It also contradicts the results of the Long-term Experimental Evolution (LTEE; Lenski) study, which demonstrated that microevolutionary biochemical changes are historically contingent. http://www.reasons.org/origin-hemoglobins-repeated-problem-biological-evolution Convergence: Evidence for a Single Creator - Fazale Rana Excerpt: When critically assessed, the evolutionary paradigm is found to be woefully inadequate when accounting for all the facets of biological convergence. On the other hand, biological convergence is readily explained by an origins model that evokes a single Creator (reusing optimal designs). http://www.reasons.org/convergence-evidence-single-creator Perhaps Morris and company should be interested in actually demonstrating that evolution can build ANY molecular machine whatsoever instead of just assuming that it happened as a starting point?!? Articles and Videos on Molecular Motors http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en Michael Behe - Life Reeks Of Design - 2010 - video http://www.metacafe.com/watch/5066181 ,,,in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,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/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology What I find very persuasive, to the suggestion that the universe was designed with life in mind, is that physicists find many processes in a cell operate at the 'near optimal' capacities allowed in any physical system: William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.html Physicists Finding Perfection… in Biology — June 1st, 2009 by Biologic Staff Excerpt: "biological processes tend to be optimal in cases where this can be tested." http://biologicinstitute.org/2009/06/01/physicists-finding-perfection-in-biology/ bornagain77