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Why is the debate over design theory so often so poisonous and polarised?

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To answer this one, we need to go as far back as Aristotle’s The Rhetoric some 2300 years ago.

In this verbal self-defense classic — as in: “you gotta know what can be done, how, if you are to effectively defend yourself . . . ” —  on what has aptly been called the devilish art of persuasion by any means fair or foul, Aristotle (left, courtesy Wiki, public domain)  found this key answer to the question “How do arguments work to persuade us?” in Book I Ch 2:

“Of the modes of persuasion furnished by the spoken word there are three kinds. The first kind depends on the personal character of the speaker [ethos]; the second on putting the audience into a certain frame of mind [pathos]; the third on the proof, or apparent proof, provided by the words of the speech itself [logos]. Persuasion is achieved by the speaker’s personal character when the speech is so spoken as to make us think him credible . . . Secondly, persuasion may come through the hearers, when the speech stirs their emotions. Our judgements when we are pleased and friendly are not the same as when we are pained and hostile . . . Thirdly, persuasion is effected through the speech itself when we have proved a truth or an apparent truth by means of the persuasive arguments suitable to the case in question . . .”

Now, of course, as clever ad men and smart politicians have long since known, the most persuasive form of argument is the appeal to our emotions and underlying perceptions. Unfortunately, how we feel about something or someone is no more reasonable or accurate than the quality of the facts beneath our perceptions.

But, what does this dusty quip by a long since dead philosopher have to do with science and getting rid of creationists and their dishonest attempts to push in the supernatural into science by the back door?

A lot, and indeed that artfully cultivated and widely spread perception that we are dealing with “a war between religion and science” is at the heart of the problem.

For, if clever but willfully deceptive rhetors — Ms Forrest, B, with all due respect; sadly,  this means you — can get away with strawmannising and dismissing design thinkers as “Creationists in cheap tuxedos,” where it has already been firmly fixed in the public mind by other clever rhetors — Mr Dawkins, CR, with all due respect; sadly, this means you — that Creationists are “ignorant, stupid, insane and/or wicked,” and that such are fighting “a war against science” and want to impose “a right-wing theocracy” (presumably  complete with Inquisitions and burnings at the stake) then we can be distracted from the issues on the merits and be lured into burning ad hominem- soaked de-humanised creationist strawmen.

That’s how we come to the way a priori evolutionary materialism is now often presented as if it were the defining essence of science, “science” in this sense being taken for granted as the defining essence of “rationality.”

This last is why, in his 1997 NYRB review of Sagan’s last book, Lewontin notoriously said:

. . . To Sagan, as to all but a few other scientists, it is self-evident that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . .

It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. [From: “Billions and Billions of Demons,” NYRB, January 9, 1997.  Emphases added. (NB: before following red herrings out to strawman rebuttal talking points, kindly, follow the link to see the context.)]

As in:  fallacy of the question-begging materialist assumption and the resulting materialism-indoctrinated, closed mind presented under false colours of science, anyone?

ID thinker, Philip Johnson’s reply that November was therefore richly deserved:

For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose” . . . .
The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

Let’s set a contrast, by proposing a definition of science as it should be at its best, one rooted in classic definitions of science and its method (i.e. those from the days before methodological naturalism was being artfully pushed into such definitions):

science, at its best, is the unfettered — but ethically and intellectually responsible — progressive, {U/D, 06:02: observational evidence-led} pursuit of the truth about our world (i.e. an accurate and reliable description and explanation of it), based on:

a: collecting, recording, indexing, collating and reporting accurate, reliable (and where feasible, repeatable) empirical — real-world, on the ground — observations and measurements,

b: inference to best current — thus, always provisionalabductive explanation of the observed facts,

c: thus producing hypotheses, laws, theories and models, using  logical-mathematical analysis, intuition and creative, rational imagination [including Einstein’s favourite gedankenexperiment, i.e thought experiments],

d: continual empirical testing through further experiments, observations and measurement; and,

e: uncensored but mutually respectful discussion on the merits of fact, alternative assumptions and logic among the informed. (And, especially in wide-ranging areas that cut across traditional dividing lines between fields of study, or on controversial subjects, “the informed” is not to be confused with the eminent members of the guild of scholars and their publicists or popularisers who dominate a particular field at any given time.)

As a result, science enables us to ever more effectively (albeit provisionally) describe, explain, understand, predict and influence or control objects, phenomena and processes in our world.

So, plainly, no authority — even one wearing The Holy Lab Coat — is better than his or her facts, assumptions and reasoning.

As just one instance, why is it that we so often see the contrast, natural vs supernatural, when in fact ever since Plato in The Laws, Bk X, what design thinkers have put on the table is first of all the question of inferring on observable and reliable empirical signs (and this link has a counter to yet another red herring-strawman distractor) to nature vs art?

So also, we must never forget: only an argument that focuses on the merits of the well-warranted material facts — the facts that make a difference to the conclusion —  and on correct reasoning about those facts, can hope to properly warrant a conclusion.  Just so, we must also recognise that when we come to matters of fact and observation, such warrant will always be provisional.  That’s why Physics — the senior science — has undergone two major revolutions within 250 years.

When we deal with origins science issues, a further factor comes in: we are now dealing with the model, reconstructed remote past beyond observation and record. A model past that serves as a worldview foundation for many. And, since evolutionary materialism is inherently relativistic and amoral — it has in it no grounding is that can ground ought (cf. here) — we are thus right back at the force of Plato’s warning in Bk X of The Laws:

[The avant garde philosophers, teachers and artists c. 400 BC] say that the greatest and fairest things are the work of nature and of chance, the lesser of art [ i.e. techne], which, receiving from nature the greater and primeval creations, moulds and fashions all those lesser works which are generally termed artificial . . . They say that fire and water, and earth and air [i.e the classical “material” elements of the cosmos], all exist by nature and chance, and none of them by art, and that as to the bodies which come next in order-earth, and sun, and moon, and stars-they have been created by means of these absolutely inanimate existences. The elements are severally moved by chance and some inherent force according to certain affinities among them-of hot with cold, or of dry with moist, or of soft with hard, and according to all the other accidental admixtures of opposites which have been formed by necessity. After this fashion and in this manner the whole heaven has been created, and all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only . . . .
[T]hese people would say that the Gods exist not by nature, but by art, and by the laws of states, which are different in different places, according to the agreement of those who make them; and that the honourable is one thing by nature and another thing by law, and that the principles of justice have no existence at all in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made. [Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT. (Cf. here for Locke’s views and sources on a very different base for grounding liberty as opposed to license and resulting anarchistic “every man does what is right in his own eyes” chaos leading to tyranny.)] These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might [Evolutionary materialism leads to the promotion of amorality], and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [Evolutionary materialism-motivated amorality “naturally” leads to continual contentions and power struggles; cf. dramatisation here],  these philosophers inviting them to lead a true life according to nature, that is, to live in real dominion over others [[such amoral factions, if they gain power, “naturally” tend towards ruthless tyranny; here, too, Plato hints at the career of Alcibiades], and not in legal subjection to them . . . [Jowett translation. Emphases and explanatory parentheses added.]

To all of this, we must add the baneful and growing influence across our civilisation of the neo-marxist (and yes, he was just that — cf. RFR’s prologue here and a survey of Marxism here)  radical, Saul Alinsky. For instance, in his Rules for Radicals, we may read the following observations, recommendations and thoughts:

“The end is what you want, the means is how you get it. Whenever we think about social change, the question of means and ends arises. The man of action views the issue of means and ends in pragmatic and strategic terms. He has no other problem; he thinks only of his actual resources and the possibilities of various choices of action. He asks of ends only whether they are achievable and worth the cost; of means, only whether they will work. … The real arena is corrupt and bloody.” p.24

“The first step in community organization is community disorganization. The disruption of the present organization is the first step toward community organization. Present arrangements must be disorganized if they are to be displace by new patterns…. All change means disorganization of the old and organization of the new.” p.116

3. “Whenever possible, go outside the expertise of the enemy. Look for ways to increase insecurity, anxiety and uncertainty. (This happens all the time. Watch how many organizations under attack are blind-sided by seemingly irrelevant arguments that they are then forced to address.)

4. “Make the enemy live up to its own book of rules. You can kill them with this, for they can no more obey their own rules than the Christian church can live up to Christianity.”

[Of course, here — even at the rhetorical risk of inviting the onward tactic of deflecting a well-warranted point by using turnabout accusation — I can only speak as one finite, fallible, fallen sinner in recovery through grace to others who may access the same grace: moral struggle is a key characteristic of any serious attempt to walk in virtue. But if you go for the polarising credibility kill of characterising the other side as all hypocrites, in the end, you face the issue of the plank in your own eyes. So, while there is no immoral equivalency, this point cuts just as sharply on both sides of any issue, including this one.  Let us all therefore turn from such destructive, even demonic tactics. Far better is to accept that we all struggle and must try to help one another (even when neighbour love calls for frank correction), instead of playing at dehumanising finger-pointing games compounded by the cruel tactic of incendiary ridicule. He who plays with rhetorical matches may set a fire that blazes beyond his ability to contain.]

5. “Ridicule is man’s most potent weapon. It is almost impossible to counteract ridicule. Also it infuriates the opposition, which then reacts to your advantage.” . . . .

13. Pick the target, freeze it, personalize it, and polarize it. [NB: Notice the evil counsel to find a way to attack the man, not the issue. The easiest way to do that, is to use the trifecta stratagem: distract, distort, demonise.] In conflict tactics there are certain rules that [should be regarded] as universalities. One is that the opposition must be singled out as the target and ‘frozen.’…

“…any target can always say, ‘Why do you center on me when there are others to blame as well?’ When your ‘freeze the target,’ you disregard these [rational but distracting] arguments…. Then, as you zero in and freeze your target and carry out your attack, all the ‘others’ come out of the woodwork very soon. They become visible by their support of the target…’

One acts decisively only in the conviction that all the angels are on one side and all the devils on the other.” (pp. 127 – 134.)

The cynically amoral and polarised rhetorical pattern, sadly, is instantly recognisable from the tactics commonly used to oppose design thought in the public and in the policy making arena.

It even creeps into Faculty Seminar rooms and scientific institutions. But, in the end, if we begin to think and act like this, it will do no one any good.

Far better, is to take the stance of Aristotle, where one studies rhetoric for self-defense, to the intent of exposing evil counsel, and calling the public and policy makers to a better way: building bridges, not walls.

It is high time that the debates over design theory and thought moved on beyond the destructive rhetoric of the trifecta fallacy: red herring subject-changing distractors, led away to caricatured and deceitful strawman misrepresentations of design thought, soaked in ad hominem false accusations and ignited through snide or incendiary rhetoric.

For, if such rhetoric and incivility are unchecked, the temporary advantage of clouding issues, poisoning and polarising the atmosphere will be bought at the bitter price of a breakdown of our character and the foundational mutual respect that is needed if we are to build a future worth having.

Materialists and fellow travellers: victory at any price may be bought at a price so dear as to be ruinous. END

_________

F/N: News, in a new post, highlights a key example of the unfortunate red herring, strawman, ad hominem distortions we discussed above, in this case, from P Z Myers. And, as for the comments section . . .

Comments
KF: It sounds like Herr Hitler didn't understand the science really. But he knew what he wanted and he found justifications for that. I wonder when his personal racist views were formulated, before or after he heard about Darwin. Before or after he looked there for justification. That's the real issue I think: what made him a racist in the first place? Well, thankfully, we are more enlightened. Materialist or Theist, we have to learn to touch people as Dr Bronowski put it whilst standing in the pool at Auschwitz. Too bad Darwin didn't live to learn that much of our own bodies are suffused with bacteria, clearly an 'inferior' creature.ellazimm
June 1, 2011
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EZ: I am not sure if he believed in common descent of the races of man -- that was a debate in that general era, especially in the wider socio-cultural circles that tend to popularise even dead scientific theories that fit with where people want to go. He definitely believed in evolution as a law and as grounding an imperative of predatory behaviour of man viewed as predator: survival of the fittest. And, his view on struggle for access to women is plainly a form of Darwinian sexual selection. His racism was plainly at least in key part rationalised on the perils of diluting the Aryan bloodline by breeding with inferiors. In that general era there was a notion of a superior Aryan race that was responsible for cultural advance. I guess in his mind, Jews were a particular temptation to dilute the race and so must be eliminated. Poles were the roadblock to getting living space in the East. My point was to document, in the face of denials and obfuscations, the roots of social darwinism in Darwin, the social darwinist milieu that was a key influence on the rise, thought and actions of Hitler, and the nazis more generally, and to answer the claim that Hitler's thought was not specifically shaped by Darwinism. In addition, I drew on a case of someone who 40 years before it happened, saw what was coming and tried to warn. I am astonished that the Wells text was in the opening of one of the most famous of all Sci Fi works of all time, and was so roundly ignored. Something has to be driving that sort of moral blindness. GEM of TKIkairosfocus
June 1, 2011
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KF, it is easy to make any case you want by using selective quotes out of context isn it.
The consequence of this racial purity, universally valid in Nature [i.e. this is a natural law], is not only the sharp outward delimitation of the various races, but their uniform character in themselves. The fox is always a fox, the goose a goose, the tiger a tiger, etc., and the difference can lie at most in the varying measure of force, strength, intelligence, dexterity, endurance, etc., of the individual specimens.
In that very quote Hitler indicates he believed in created kinds, and in the rest of the quotes you provide he indicates that mixing these kinds was against nature. Contrast that with Darwins work where he made an argument that the Fox, goose, tiger etc were not seperate created kinds but part of a pattern of diversification. Hitler had an idea of racial purity linked to superiority - the 'fitter' were created that way by a creator. Darwins work explored the idea that 'fitness' was was a product of the creature, in the environment it was in - i.e. not something imposed by a creator. As I have already indicated, I'm not denying that the Nazis drew on ideas about both eugenics, and biblical antisemitism, when constructing their ideas about created kinds and the need to preserve their idea of racial purity. But their ideology is in stark contrast to the theory proposed by Darwin, and only a deliberate and ideologically driven attempt at distortion can turn Darwins theory - describing natural processes - into a set of commandments for how people should treat other people. The theory of evolution does not prescribe how people ought to behave, it describes observations in nature. You are trying to get an ought from an is. Newtons laws of motion do not imply that when someone hits you, you should strike them back with equal force - even though in the act of striking someone this is literally true in the physical sense.DrBot
June 1, 2011
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KF: "The fox is always a fox, the goose a goose, the tiger a tiger, " So Hitler was influenced by Darwinian thought but did not actually believe in common descent?ellazimm
June 1, 2011
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#83 Mung Mung #83  
In the context of a computer and operating system it pretty much always does what it does by virtue of the physical circuits.
Does that make machine code non-arbitrary?
Isn’t the key difference that the machine code was chosen by the designers to do the job? There are a number of other choices they might have made, and they would have had to create a different context so the machine code had the desired effect.  You presumably believe that the DNA – Amino Acid relationship was also chosen – but others believe the relationship and the context developed without design.  So, unless you assume your premise, DNA is not arbitrary in the same sense as machine code.markf
June 1, 2011
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Dr BOT: Your insistence on trying to put up irrelevant objections forces me to cite Hitler, Bk I Ch X of his Mein Kampf [it was accessible in the previously linked], I refuse to give the link. Let me give the key cluster of clips: _______________ Darwin, Descent, ch 6, 1871: >> Man is liable to numerous, slight, and diversified variations, which are induced by the same general causes, are governed and transmitted in accordance with the same general laws, as in the lower animals. Man has multiplied so rapidly, that he has necessarily been exposed to struggle for existence, and consequently to natural selection. He has given rise to many races, some of which differ so much from each other, that they have often been ranked by naturalists as distinct species . . . . At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate, and replace, the savage races throughout the world. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked, will no doubt be exterminated. The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilised state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla. >> H G Wells, War of the Worlds Ch 1, 1897: >> No one would have believed in the last years of the nineteenth century that this world was being watched keenly and closely by intelligences greater than man's and yet as mortal as his own; that as men busied themselves about their various concerns they were scrutinised and studied, perhaps almost as narrowly as a man with a microscope might scrutinise the transient creatures that swarm and multiply in a drop of water . . . No one gave a thought to the older worlds of space as sources of human danger, or thought of them only to dismiss the idea of life upon them as impossible or improbable. It is curious to recall some of the mental habits of those departed days. At most terrestrial men fancied there might be other men upon Mars, perhaps inferior to themselves and ready to welcome a missionary enterprise. Yet across the gulf of space, minds that are to our minds as ours are to those of the beasts that perish, intellects vast and cool and unsympathetic, regarded this earth with envious eyes, and slowly and surely drew their plans against us . . . . looking across space with instruments, and intelligences such as we have scarcely dreamed of, they see, at its nearest distance only 35,000,000 of miles sunward of them, a morning star of hope, our own warmer planet, green with vegetation and grey with water, with a cloudy atmosphere eloquent of fertility, with glimpses through its drifting cloud wisps of broad stretches of populous country and narrow, navy-crowded seas. And we men, the creatures who inhabit this earth, must be to them at least as alien and lowly as are the monkeys and lemurs to us. The intellectual side of man already admits that life is an incessant struggle for existence, and it would seem that this too is the belief of the minds upon Mars. Their world is far gone in its cooling and this world is still crowded with life, but crowded only with what they regard as inferior animals. To carry warfare sunward is, indeed, their only escape from the destruction that, generation after generation, creeps upon them. [Note, he had the Martians land in England, turning the English into the inferior savages to be exterminated, as in use of irony . . . ] And before we judge of them too harshly we must remember what ruthless and utter destruction our own species has wrought, not only upon animals, such as the vanished bison and the dodo, but upon its inferior races. The Tasmanians, in spite of their human likeness, were entirely swept out of existence in a war of extermination waged by European immigrants, in the space of fifty years. Are we such apostles of mercy as to complain if the Martians warred in the same spirit? >> Hitler, Mein Kampf, Bk I ch XI, 1920's: >> Any crossing of two beings not at exactly the same level produces a medium between the level of the two parents . . . Consequently, it will later succumb in the struggle against the higher level. Such mating is contrary to the will of Nature for a higher breeding of all life . . . The stronger must dominate and not blend with the weaker, thus sacrificing his own greatness. Only the born weakling can view this as cruel, but he after all is only a weak and limited man; for if this law did not prevail, any conceivable higher development of organic living beings would be unthinkable. [notice how racism and by direct extension eugenics are inferred from the law of evolution] The consequence of this racial purity, universally valid in Nature [i.e. this is a natural law], is not only the sharp outward delimitation of the various races, but their uniform character in themselves. The fox is always a fox, the goose a goose, the tiger a tiger, etc., and the difference can lie at most in the varying measure of force, strength, intelligence, dexterity, endurance, etc., of the individual specimens. [He deduces fitness from superiority of characteristics, a classic Darwinist view on survival of the fittest, and significantly he shifts to predators, overlooking that predators need prey to survive, but well adapted to the displacement view of races: preservation of favoured races in teh struggle for life, as the subtitle of Origin highlights] But you will never find a fox who in his inner attitude might, for example, show humanitarian tendencies toward geese, as similarly there is no cat with a friendly inclination toward mice [Notice his predatory and displacement views brought together, and for foxes and cats read Aryan Germans; for geese and mice read: Poles, Jews, etc] . . . . In the struggle for daily bread [Nutrition as a determinant of survival of the fittest through Malthusian struggle, nb Origin is explicitly Malthusian] all those who are weak and sickly or less determined succumb [first level of survival of the fittest, food], while the struggle of the males for the female grants the right or opportunity to propagate only to the healthiest. [That is, Darwinian sexual selection.] And struggle is always a means for improving a species’ health and power of resistance and, therefore, a cause of its higher development. [survival of the fittest] If the process were different, all further and higher development would cease and the opposite would occur. [notice the specific evolutionary progress per law of evolutionary ascent emphasis] For, since the inferior always predominates numerically over the best [NB: this is a theme in Darwin's discussion of the Irish, the Scots and the English in Descent], if both had the same possibility of preserving life and propagating, the inferior would multiply so much more rapidly that in the end the best would inevitably be driven into the background, unless a correction of this state of affairs were undertaken. Nature does just this by subjecting the weaker part to such severe living conditions that by them alone the number is limited, and by not permitting the remainder to increase promiscuously, but making a new and ruthless choice according to strength and health [This directly answers to an issue raised in Descent Chs 5 - 7] . . . >> _______________ After this, please do not tell me that Hitler's thought was not decisively shaped by evolutionary, eugenics and Malthusian struggle driven survival of the fittest ideas tracing directly and indirectly to Darwin (cf. here and the article clipped here). I suggest that a major means of this transfer was WW I German propaganda -- decried by Bryan along the lines of my own implied critique -- and his experience in and around Belgium, the precursor to the horrors of the 2nd WW. After all Hitler served in that area for the duration of the war. We need to face the serious implications of the wider chain of thought that has been traced by many others elsewhere, with Haeckel playing a starring role in the transmission and development of scientific racism tied to evolutionary thought and leading onwards to eugenics, the precursor to genocide. Indeed, as a black man, I have to note that some of the key champions of eugenics thought saw it as subtle, slow motion genocide of perceived inferior races and classes. This is the serious point behind the angry graffiti on the walls of Kingston of my childhood: "Birth Control plan to kill black people." GEM of TKIkairosfocus
June 1, 2011
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Onlookers: Notice the great reluctance to accept that the genetic code as implemented in the ribosome, with its start/methionine, extend with AA-x, repeat with next AA, stop algorithmic step by step sequence, is a code based algorithmic process. What sort of cause, on our empirical observation, best explains code driven, algorithmically controlled, step by step assembly line manufacturing processes that create units that are processed onwards to fulfill function? This is of course a self-answering, or "rhetorical" question. (Verbal self-defense in action.) The fact that the chained monomers in nucleic acids are selected to have a complementary fit as the means by which the code is implemented, suddenly, is seen as evidence that the code and the algorithm are all more or less a result of chemistry and physics. But in fact they are constrained by the physical situation, but that is taken advantage of to implement something of a different order, a string based digitally controlled protein manufacturing process. Remember, the onward functionality is remote from the sequence of AAs in the DNA (and in eukaryotes, there is a snipping apart and reassembly of the right proteins). Also, there is a dispatching code that often appears in AA chains, to send the protein to where it is to work. And this is before we get to the real point of the code: the specific possible sequences are very diverse and are set up to find deeply isolated functional fold domains in AA config space. In addition, the tRNA AA taxis and position arm units, carry the AA at the side that is remote from the anticodon that key-lock fits the mRNA codon. In short, the exchange above is plainly misdirected and overlooks the key context. I think this illustrates a subtler issue than is emphasised in the OP above: when there is a contentious and momentous issue at stake, our perceptions are very likely to be inaccurate based on what we "need" to see to support our view. This is one reason why mutually respectful but uncensored constructive dialogue among the informed is so important. GEM of TKIkairosfocus
June 1, 2011
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Elizabeth Liddle @78:
That seems to me an extremely important difference. Leucine is “coded” by CUA via CTA not because of some arbitrary pairing, as in the latin alphabet, for example, but because, in the physical configuration and context of the cell, that is the physical result.
I'd be intereseted in knowing what makes a code arbitrary? Are you familair with the concept of machine code? In the context of a computer and operating system it pretty much always does what it does by virtue of the physical circuits. Does that make machine code non-arbitrary? http://en.wikipedia.org/wiki/Machine_code http://en.wikipedia.org/wiki/Assembly_languageMung
June 1, 2011
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You will note that I am very aware of Darwin’s context, only I refuse to spin it. He is talking about gaps in the record and trying to explain away that embarrassing bit of non-evidence. He then draws out the implications of his theory for extinction of inferior races of human beings and the top level apes — notice the continuum — and having proved his point gets on with the gaps argument without batting an eye.
I guess we will have to agree to disagree but with respect, I don't see how you interpret that passage in the way you do without some spin.
Sorry, you just exposed a major moral hazard. You need to stop and deal with it, even if only in a footnote.
And I'm not really sure what I'm being accused of here?
(onlookers, this appears in the linked, which Dr BOT is not addressing, nor is he seriously addressing the relevant clip from Hitler that directly builds on Darwin’s arguments in Chs 5 – 7 of Descent of Man):
And again, I don't understand. Given that the Nazis considered Darwins books worth burning as false science why would Hitler build on Darwins works, and where is the evidence that he build arguments directly on Darwins published work? It would help to have the quote from Hitler you are referring to.DrBot
May 31, 2011
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#80 UB I hope you don’t mind me butting in on this but this comment caught my eye:
If your response is that it is not the physicality of the individual constituent parts themselves, but is the context and configuration of the system in which they operate (charged tRNA, etc) then you have established that it is indeed arbitrary in regard to the physics of the nucleotides themselves. Why? Because the context can change; a feat which has already be performed experimentally.
Surely virtually every cause effect relationship is dependent on the context? A meteor hits a planet  - the effect will depend on the context – the density of the atmosphere, the nature of the surface, etc .  I cannot think of any effect which is totally determined by the “physicality of the individual constituent parts themselves”markf
May 31, 2011
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EL,
Thanks, but you now seem to be supporting my original point! That the mapping is not arbitrary (as most human codes are).
With all due respect, I said all along that physical objects follow physical laws. If that is all that is needed to support your point, then your point is trivial by virtue of everyone's tacit agreement.
Leucine is “coded” by CUA via CTA not because of some arbitrary pairing, as in the latin alphabet, for example, but because, in the physical configuration and context of the cell, that is the physical result.
This is indistinguishable from suggesting that a light switch is not arbitrary because in the context of an electrical circuit, it has a physical result. If you want to show that the mapping of nucleic acids to amino acids is actually determined by physics, then you are going to have to do a lot more than point to its functionality in order to establish the point of determination. You are not just going to have to demonstrate that cytosine, thymine, and adenine have an inherent physical mapping to leucine, but you are going to have to demonstrate that cytosine, followed by thymine, followed by adenine, in that specific order, creates an inherent physicality which establishes the mapping to leucine. So let me cut to the chase, what are the physical properties (of cytosine, thymine, and adenine) that create the mapping (to leucine). And, in order to not trample any further on KF’s post, let us be specific. For instance, cytosine has a molecular formula of C4H5N3O. Adenine has a molecular formula of C5H5N5, thymine has a formula of C5H6N2O2 and leucine has a formula of C6H13NO2. That is the starting point. What are the observable physical properties of these nucleic acids (presented in the above sequence) which determine that leucine should be added to a polypeptide? If your response is that it is not the physicality of the individual constituent parts themselves, but is the context and configuration of the system in which they operate (charged tRNA, etc) then you have established that it is indeed arbitrary in regard to the physics of the nucleotides themselves. Why? Because the context can change; a feat which has already be performed experimentally. Quite frankly, you are looking at an informational medium containing abstracted information recorded by means of a system of chemical symbols. These symbolic representations are passed through a channel and decoded using the rules established in the translation hardware. All of this is an observed reality, but you keep suggesting it’s an illusion of human making. The observations suggest otherwise. Humans didn’t invent symbols systems and recorded information; we came along later and found it already existed.
I think we are going round in circles! The configuration and context doesn’t “come from” the “information being decoded by the system”. The configuration and context IS the information!
Whoa! Perhaps I am not the person to have this conversation with. I don’t think you could be more mistaken if you deliberately tried. In deference to the topic of the OP (and it's late here) I withdraw. CheersUpright BiPed
May 31, 2011
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"No search for truth will cause unknown concepts to magically jump into existence." Tell it to Wegener, Neil, tell it to Pasteur.Upright BiPed
May 31, 2011
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Upright BiPed: Thanks, but you now seem to be supporting my original point! That the mapping is not arbitrary (as most human codes are). That seems to me an extremely important difference. Leucine is "coded" by CUA via CTA not because of some arbitrary pairing, as in the latin alphabet, for example, but because, in the physical configuration and context of the cell, that is the physical result. But when you say:
And, where do the configuration and the context come from? …from the information being decoded by the system, of course.
I think we are going round in circles! The configuration and context doesn't "come from" the "information being decoded by the system". The configuration and context IS the information! Or as I would prefer to put it (for clarity): the chemical reaction sequence is contingent on local molecular context.Elizabeth Liddle
May 31, 2011
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UB: Good catch. Shows the informational connexion. Gkairosfocus
May 31, 2011
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nullasalus (#69)
And you miss the point: First, that engineers – not scientists – have the primary role in coming up with toasters, etc, and that scientists’ hand in such only comes up insofar as they take on the tasks and attitudes of engineers.
Sorry, but we are still miscommunicating. I agree with you on what is an engineer's job. I was not intending to imply that scientists invented the toaster. I was making a very different point. In designing those things, the electrical engineer use concepts such as electrical current, voltage, resistance, inductance. None of those concepts were even in the language when scientists began studying electricity. The engineer cannot cannot work with concepts that are unknown. No search for truth will cause unknown concepts to magically jump into existence. No amount of abduction to the best inference will cause unknown concepts to jump into existence. It required going beyond the kind of activity that is often said to characterize science.Neil Rickert
May 31, 2011
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Hello again EL, sorry for the delay.
Thanks for your response. I’m a bit surprised by it,tbh. I thought I was referring to something that was pretty self-evident, so I guess I’ve learned something
I am not surprise that you could be surprised – after all, that is the fundamental power of the unquestioned assumption, is it not? :)
It hadn’t actually occurred to me that anyone thought that the reason that CTA maps to leucine is anything other than, well, the fact that CUA, in the contexts of a codon, catalyses a CTA RNA sequence, and thence leucine.
The implementation of the mapping follows chemical law, (as I acknowledged above) but that relationship only exist in the context of the system. It is the system which requires an explanation.
Are you saying that CTA might just as easily catalyse valine? In which case, what stops it doing so?
The elasticity of the genetic code is a matter of ongoing research, in particular are the effects of genetic proofreading machinery. I don’t think you’ll find many researchers on the cutting edge who think the system is beyond manipulation, and certainly not any who think that CTA leads to Leucine in the same way that iron and oxygen lead to iron oxide.
I simply don’t have the evidence you ask for, so, shame on me. But I’d certainly like to know what mechanism you propose “tells” the RNA molecule that if it has a CTA codon,it has to make leucine not something else.
The mechanism is no mystery. Properly charged tRNA results from the chemical configuration of the constituent parts of the translation system. However, I think you are missing the point. There is nothing inherent in the physical properties of the constituent parts that establishes “CTA must have a relationship with Leucine”. CTA has a relationship to Leucine because of the configuration and the the context. And, where do the configuration and the context come from? …from the information being decoded by the system, of course. If you care to do so, you might search for these topics and peruse the offerings. Various papers attack the issue from different angles. You might come across something like the following: Abstract Most organisms, from Escherichia coli to humans, use the ‘universal’ genetic code, which have been unchanged or ‘frozen’ for billions of years. It has been argued that codon reassignment causes mistranslation of genetic information, and must be lethal. In this study, we successfully reassigned the UAG triplet from a stop to a sense codon in the E. coli genome, by eliminating the UAG-recognizing release factor, an essential cellular component, from the bacterium. Only a few genetic modifications of E. coli were needed to circumvent the lethality of codon reassignment; erasing all UAG triplets from the genome was unnecessary. Thus, UAG was assigned unambiguously to a natural or non-natural amino acid, according to the specificity of the UAG-decoding tRNA. The result reveals the unexpected flexibility of the genetic code
And if there’s an answer to “why”, it’s going to lie in the physics and chemistry, and stereochemistry of the CTA bonds. Not in a lookup decoder table.
Correct. Material objects follow physical laws. But physical laws are incapable of explaining all things by virtue of the matter in those things. It must be simply assumed that they do. - - - - - Since this conversation is going off-topic (and I fear KF) I will drop it.Upright BiPed
May 31, 2011
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NR: The record is plain, at minimum you made a major error, because you failed to read what I wrote starting with the original post (a clip from that course draft you dismissed). GEM of TKIkairosfocus
May 31, 2011
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kairosfocus (#70)
Let’s roll the tape, by excerpting above:
Sigh! That's the third or fourth time that you have quoted the same material, each time falsely insinuating that I haven't read it. That's the third or fourth time that you falsely accuse me of a strawman misrepresentation. Enough already. Yes, I get it, that you somehow imagine that there was a strawman misrepresentation. It doesn't follow that there was. In a post last evening on my blog, before you had even posted this thread, I raised some of the same points about why I disagree with the traditional view of science. My comments about science in this thread, like those in my blog post, were not specifically criticizing you. If you still think that my understanding of science is the same as yours, that I actually agree with you but am mischaracterizing your position, then please go read my blog post and see if you agree with it. Maybe even post a comment there.Neil Rickert
May 31, 2011
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Null: You have a point, but I must note that a lot of engineering work is embedded in scientific praxis, e.g in designing and implementing serious experiments in say physics or the like. More to the point however, once we are dealing with cutting edge technologies, scientists, engineers and mathematicians tend to be all over the place in developing the science and applying it. In fact, the best teams for that sort of thing have mixed discipline people in them. Bletchley Park was a great case in point. So was the Manhattan project. As was the MIT Radiation Lab that played such a key role in the development of radar in WW II. There are no hard and fast borders, especially where currently emerging sci and tech are involved. BTW, this is also happening to some extent with ID, e.g. Marks is an Electrical Engineer working with Dembski, a Mathematician and computer scientist. Linked in are Abel a Physicist, and Behe a Biologist-biochemist. Off on the side is Meyer a historian-philosopher of science. And so on. GEM of TKIkairosfocus
May 31, 2011
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Although they are mighty tricky to use when you have a specific goal in mind
They can be tricky to use when you have a specific goal in mind but that that does not mean that they simply are mighty tricky to use when you have a specific goal in mind. GA's can be tricky no matter what, as evidenced by Schneider's attempts to get ev to generate CSI. The hardest part of using a GA is in mapping the problem domain on to a chromosome.Mung
May 31, 2011
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NR: I will do something that I seldom do these days, as it is germane to the basic problem this thread addresses. Now, despite posts being buried by much since earlier today, we can all scroll up to see how you tried to knock over my summary as though it failed to address the aspect of the agenda that leads to applications, even though this is exactly how the extended definition concludes -- the second most emphatic position in a statement. I showed the agenda, in the end by clipping and citing. You now argue that you did not make the objection I replied to. (Hint, cf your reference to "journalism" and your emphases as though I had ONLY said that science seeks truth about our world.) Let's roll the tape, by excerpting above: ______________ KF, 32: >> I am sorry, but science should be understood as an unfettered (but ethically and morally responsible) progressive pursuit of the truth about our cosmos based on observation, experimental testing, measurement where appropriate, explanatory modelling, theorising and analysis, and serious but mutually respectful discussion among the informed. Its main explanatory results will always be provisional, but must at minimum be empirically testable and reliable. That way we can go about serious, open minded exploration, description, explanation, prediction, testing and application. [cf OP] >> NR, 36: >> That is not how I understand science. I see it as far more of a pragmatic enterprise, one that is directed more toward understanding than could be expected of a search for truth. “Search for truth” is a better characterization of journalism than it is of science. >> [And BTW, the whole CSI/FSCI concept is riddled with observationally testable hypotheses and there are specific reports on the results of such testing, just for starters -- yet another misrepresentation that I did not have time to deal with previously. Similarly, I should suggest to you that there are highly significant and close resemblances between engineered and living systems such as codes, algorithms, implementing machines, even position-arm devices with tool tips, and so on.] NR, 49: >> kairosfocus (#39)
If you don’t believe that searching for the truth about our world in light of empirical evidence, observation, experiment, analysis, modelling etc is key to good science, that explains a lot. The name of the game is scientific integrity, and trying to get to and be honest about the accurate truth about the world is a non-negotiable if science is to keep its integrity and in the end its credibility.
You are mischaracterizing what I said. I was not in any way suggesting that scientists do not care about the truth of their statements. In the 18th century, scientists investigated phenomena such as lightning, hair standing on end, sparks when you touch something metal after walking on a carpet. If science were a search for truth, then today we should have extremely accurate descriptions of lightning, hair standing on end, etc. Instead, we have electric toasters, refrigerators, lighting, computers. The goals of science have to be far wider than a “search for truth” to have those achievements. >> OP: >> science, at its best, is the unfettered — but ethically and intellectually responsible — progressive pursuit of the truth about our world (i.e. an accurate and reliable description and explanation of it), based on: a: collecting, recording, indexing, collating and reporting accurate, reliable (and where feasible, repeatable) empirical — real-world, on the ground — observations and measurements, b: inference to best current — thus, always provisional — abductive explanation of the observed facts, c: thus producing hypotheses, laws, theories and models, using logical-mathematical analysis, intuition and creative, rational imagination [including Einstein's favourite gedankenexperiment, i.e thought experiments], d: continual empirical testing through further experiments, observations and measurement; and, e: uncensored but mutually respectful discussion on the merits of fact, alternative assumptions and logic among the informed. (And, especially in wide-ranging areas that cut across traditional dividing lines between fields of study, or on controversial subjects, “the informed” is not to be confused with the eminent members of the guild of scholars and their publicists or popularisers who dominate a particular field at any given time.) As a result, science enables us to ever more effectively (albeit provisionally) describe, explain, understand, predict and influence or control objects, phenomena and processes in our world. >> ______________ The strawmannisation of what I said is quite plain. GEM of TKIkairosfocus
May 31, 2011
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Neil, You miss the point. Engineers would not be developing toasters, etc, were it not for the fact that the goal and achievments of science go far beyond a “search for truth.” And you miss the point: First, that engineers - not scientists - have the primary role in coming up with toasters, etc, and that scientists' hand in such only comes up insofar as they take on the tasks and attitudes of engineers. "Science" is not a person. It is a method, a practice. I could agree that science is not "search for truth" - but insofar as a man wants to build a better mousetrap, his concern is largely that of engineering, not science. If science produces something that engineering can use, it's a happy accident considering the method.nullasalus
May 31, 2011
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kairosfocus (#65)
See how you have set up and knocked over a strawman misrepresentation.
There was no strawman. I expressed my opinion as to how to characterize science, and that clearly disagrees with how you want to characterize science. From the wording that I used, it should have been very clear that I was expressing opinion. I am not insisting that you change your view. It does not bother me that we disagree on such issues. In fact, many people agree with your way of characterizing science. Surely you are not saying that expressing an opinion amounts to a strawman misrepresentation.Neil Rickert
May 31, 2011
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F/N: News, in a new post, highlights a key example of the red herring, strawman, ad hominem distortions we discussed above, from P Z Myers.kairosfocus
May 31, 2011
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F/N: Dr BOT, do you remember the days of Ge ckts that coupled through IR, becoming inadvertently optocoupled ckts? That happened BTW without a GA -- it;s not just GA's that do stuff. The magnetron was a similar case, discovered and developed -- a war winning weapon used in the H2S for bombing and sub hunting -- before the theory for it was properly worked out. Edison saw the photoelectric effect practically before it was explained by Einstein as a big part of his Nobel Prize. A lot of things we take for granted were identified through a breadboard, not a deliberate design. And, originally, a breadboard was literally that.kairosfocus
May 31, 2011
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NR: Kindly take some time to see what I actually said in the OP and have clipped above. See how you have set up and knocked over a strawman misrepresentation. GEM of TKI PS: Null, there is such a thing as a spectrum from pure to applied science to engineering and onward to commercial product development. there is a considerable overlap between science, engineering and mathematics, and so it is not helpful to try to force fit tight borders.kairosfocus
May 31, 2011
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Dr BOT: You will find historians, scientists and philosophers to dispute any conclusion, especially one that points to a serious hole in science and science education, i.e. the ethics gap, as I spoke to in 34. My issue is not based on who said what among the guild of scholars today. I have gone back, and seen for myself, as the key clip from Wells shows. Onlookers, here is the key blog post from the series done nearly three years ago. And, there is more, much more, sickeningly much more. Think about the case of Ota Benga (ask yourself why an obvious human being could ever have been shown in a cage at a zoo as though he were a monkey -- compare that same extract from Darwin), and the trade in museum specimens based on assumed sub-humans, some of whom were killed to make the specimens. You will note that I am very aware of Darwin's context, only I refuse to spin it. He is talking about gaps in the record and trying to explain away that embarrassing bit of non-evidence. He then draws out the implications of his theory for extinction of inferior races of human beings and the top level apes -- notice the continuum -- and having proved his point gets on with the gaps argument without batting an eye. Sorry, you just exposed a major moral hazard. You need to stop and deal with it, even if only in a footnote. Here is Wells (a student of Huxley BTW), who seems to have realised the problem and addressed these issues in at least three novels, War of the Worlds [genocide of inferior races], Time machine [eugenics on steroids, i.e. breeding humans like sheep for the slaughter] and Island of Dr Moreau [the proverbial ethically irresponsible mad scientist]. No-body took him seriously, and made him a prophet. Opening words from War of the Worlds, excerpted (onlookers, this appears in the linked, which Dr BOT is not addressing, nor is he seriously addressing the relevant clip from Hitler that directly builds on Darwin's arguments in Chs 5 - 7 of Descent of Man): ______________ >> No one would have believed in the last years of the nineteenth century that this world was being watched keenly and closely by intelligences greater than man's and yet as mortal as his own; that as men busied themselves about their various concerns they were scrutinised and studied, perhaps almost as narrowly as a man with a microscope might scrutinise the transient creatures that swarm and multiply in a drop of water . . . No one gave a thought to the older worlds of space as sources of human danger, or thought of them only to dismiss the idea of life upon them as impossible or improbable. It is curious to recall some of the mental habits of those departed days. At most terrestrial men fancied there might be other men upon Mars, perhaps inferior to themselves and ready to welcome a missionary enterprise. Yet across the gulf of space, minds that are to our minds as ours are to those of the beasts that perish, intellects vast and cool and unsympathetic, regarded this earth with envious eyes, and slowly and surely drew their plans against us . . . . looking across space with instruments, and intelligences such as we have scarcely dreamed of, they see, at its nearest distance only 35,000,000 of miles sunward of them, a morning star of hope, our own warmer planet, green with vegetation and grey with water, with a cloudy atmosphere eloquent of fertility, with glimpses through its drifting cloud wisps of broad stretches of populous country and narrow, navy-crowded seas. And we men, the creatures who inhabit this earth, must be to them at least as alien and lowly as are the monkeys and lemurs to us. The intellectual side of man already admits that life is an incessant struggle for existence, and it would seem that this too is the belief of the minds upon Mars. Their world is far gone in its cooling and this world is still crowded with life, but crowded only with what they regard as inferior animals. To carry warfare sunward is, indeed, their only escape from the destruction that, generation after generation, creeps upon them. And before we judge of them too harshly we must remember what ruthless and utter destruction our own species has wrought, not only upon animals, such as the vanished bison and the dodo, but upon its inferior races. The Tasmanians, in spite of their human likeness, were entirely swept out of existence in a war of extermination waged by European immigrants, in the space of fifty years. Are we such apostles of mercy as to complain if the Martians warred in the same spirit? >> _______________ That's 1897 folks. Ota Benga was put into a Zoo as if he were a monkey in New York City circa 1910. Mrs O'Leary has put her finger on something serious. GEM of TKIkairosfocus
May 31, 2011
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nullasalus (#54)
Science is not engineering.
You miss the point. Engineers would not be developing toasters, etc, were it not for the fact that the goal and achievments of science go far beyond a "search for truth."Neil Rickert
May 31, 2011
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KF, re war stories. I once worked with a guy who used genetic algorithms on reconfigurable logic circuits. He started by trying to evolve a clock pulse generator, beginning with a population of random configurations, testing each ones output against a fitness function and applying crossover and mutation to produce a new generation (all happening on real hardware rather than a simulation) The process was automated and after a week the evaluation system indicated that a good level of fitness had been reached. When they tested the output all they saw was random noise. A bit more testing and they saw a good quality square wave, but for only a quarter of a second. It was no coincidence that the fitness evaluation period for the GA was a quarter of a second. The GA had evolved exactly what they asked - produce a square wave for 1/4 sec! What was most interesting was that the random noise they saw in the output was actually RF noise. It turns out that the logic gate had evolved to make use of RF noise from the computers nearby - they had inadvertently evolved a radio reciever. Another aspect uncovered on analysis was that one part of the circuit was electrically isolated from the other, yet disabling that part stopped the entire thing from working - it turned out to be using parasitic capacitance between isolated components. I believe in other experiments he also managed to evolve solutions that relied on manufacturing flaws in the circuits - flaws that had no effect on their designed function as logic gates, but which the evolutionary process was able to exploit. A neat offshoot of this work, done by another guy I met at a conference a few years ago were successful attempts to evolve fault tolerant logic gates - he managed to evolve an logic circuit that both performed a logic operation, and would reliable indicate a fault if any part of the circuit stopped working - including the fault checking element. The GA produced a much more effective solution than any human designer had managed. I'm an engineer at heart but I am a big fan of GA's as design tools because they are not constrained in the way that human designer are - they can find and exploit things the designer didn't realize were even there. Although they are mighty tricky to use when you have a specific goal in mind ;)DrBot
May 31, 2011
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kairosfocus, Applied scientists — “I are one” — do bridge the gap between science and engineering. No doubt, but they bridge a gap insofar as there is a gap that needs to be bridged to begin with.nullasalus
May 31, 2011
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