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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
F/N: I suggest the tangential issues above can be better discussed here on.kairosfocus
June 3, 2011
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F/N: Re Dr BOT at 9, Kindly cf. my analysis on willful deception by persistent misrepresentation through drumbeat repetition of a demonstrably false and/or misleading talking point here (and the context of that here [cf here and most recently here on how precisely what was claimed not to be so, was so, over and over again and was brought to attention repeatedly]) in the foot note thread. There is a point where it is necessary to highlight what a subtle rhetorical pattern of behaviour has become tantamount to. Notice:
AT NO POINT OVER THE PAST THREE MONTHS HAS MG TAKEN TIME TO ACTUALLY RESPOND SPECIFICALLY TO THE MANY TIMES THE ISSUES SHE HAS RAISED HAVE BEEN RESPONDED TO ON The MERITS, INCLUDING WHEN SHE MADE THE BLUNDER OF DISMISSING A LOG REDUCTION AS A PROBABILITY CALCULATION AND WHEN SHE IMPROPERLY SUGGESTED THAT OUR RESPONSES AND REQUEST FOR HER RESPONSE IN DETAILS WERE TANTAMOUNT TO THE INQUISITION'S FORCING GALILEO TO RECANT BY SHOWING HIM THUMBSCREWS.
I strongly suspect as well that the places where what I pointed out at length reluctantly and with reasoning was twisted into a turnabout accusation that I was making groundless accusations, did not engage the matters on the merits as I just linked. In short, this is an example of how the trifecta trick of distraction, distortion and demonisation is multiplied and compounded through the turnabout tactic. I refuse to allow such twisted caricatures to stand uncorrected; now those who repeat such distortions are responsible before the corrective record. If they choose to ignore it or play at further distractions & distortions and denigration, they are being willfully deceptive. Period. The only solution, in short, is to insistently focus on the actual merits on the facts, correcting fallacies of distraction and distortion and pointing out the implied moral responsibility that is being ducked. Those who willfully ignore such correction of distraction and distortion thereby become willfully deceptive, which is tantamount to -- but subtler than -- the outright blatant L-word case. (Oh, how easy it is to slip into the L-word condition by dehumanising and disrespecting an opposed person and ignoring or distorting what he has to say, even when one has been corrected. That, I am afraid, is demonstrably -- cf the linked above -- what has happened again and again over the past three months on the part of MG and others as can be seen at MF's blog and in related threads here. Notice how, consistently, several responders at UD have at length been forced to observe on the outright refusal to give serious responses, not even the basic request for even a summary to VJT. Do you see why we have been reluctantly forced to conclude that there was a willful unresponsivenenss and demanding disrespectful attitude at work?) Sometimes, there is a neighbourly duty of frank counsel:
Leviticus 19:15-18 New International Version 1984 (NIV1984) 15 “‘Do not pervert justice; do not show partiality to the poor or favoritism to the great, but judge your neighbor fairly. 16 “‘Do not go about spreading slander among your people. “‘Do not do anything that endangers your neighbor’s life. I am the LORD. 17 “‘Do not hate your brother in your heart. Rebuke your neighbor frankly so you will not share in his guilt. 18 “‘Do not seek revenge or bear a grudge against one of your people, but love your neighbor as yourself. I am the LORD.
(And, onlookers, despite the details linked above and in the context of those links, I fully expect that this too will be made an occasion for turnabout accusations, further compounding the polarisation problem. Only when, by repeated cases exposed, the pattern of mischief on the part of the rhetorical objectors to design thought has become evident to a critical mass, will there be a reconsideration by many taken in by the destructive talking points. That critical mass grows one courageous person at a time, So, please stand up and say out loud: stop the willful distractions, distortions and denigration. [And of course, even this will predictably be used to try for the turnabout accusation.]) Do you see how the problem being highlighted in this thread is potentially deadly to our civilisation? Here is wise king Solomon:
Proverbs 6:16-19 New International Version 1984 (NIV1984) 16 There are six things the LORD hates, seven that are detestable to him: 17 haughty eyes, a lying tongue, hands that shed innocent blood, 18 a heart that devises wicked schemes, feet that are quick to rush into evil, 19 a false witness who pours out lies and a man who stirs up dissension among brothers.
(And, onlookers, even this will be predictably turned into further occasion for distraction, distortion and denigration.) We better wake up to see what is going on before it is too late. Remember, we are dealing with people who will not even accept that the definition of ID is what it is, and who willfully ignore the corrections in the Weak Argument Correctives, both of which are top right this and every UD page. To see what is really going on, scroll up and see how my invitation to examine and mark up the IOSE course was responded to. That reaction, sorry to say, is TYPICAL. I trust that the corrosive, destructive nature of Alinsky's tactics is fully apparent and that there will now be a willingness to turn from them. Oh, how right was James:
James 3:5 . . . the tongue is a small part of the body, but it makes great boasts. Consider what a great forest is set on fire by a small spark. 6 The tongue also is a fire, a world of evil among the parts of the body. It corrupts the whole person, sets the whole course of his life on fire, and is itself set on fire by hell . . .
GEM of TKIkairosfocus
June 3, 2011
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I responded to some further remarks in another thread on "outing tactics" here.kairosfocus
June 3, 2011
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KF: Okay! I'm certainly guilty. I just respond to questions and pose new ones without considering the thread. Sorry, sorry, sorry.ellazimm
June 2, 2011
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INTERVENTION: Pardon, but this thread is now beginning to drift way off topic. I suggest that much of the discussion today should be continued in other threads, if the discussion above cannot be tied into the thread's theme by participants. GEM of TKIkairosfocus
June 2, 2011
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Mung: I'm with markf . . "If it can be anlayzed and described mathematically, perhaps that will tell us whether it’s a code and in what sense it’s a code and what sort of code it may be." We know how the three-base codons are translated into amino acids or read as stop and start, etc; that's the code! And combinations of amino acids make proteins which we also know. What's really interesting and not clear is why certain genes are or are not expressed at various times. For example: how the the same genome in most cells in a human's body know when to make a muscle cell or a bone cells or a neuron? It must have to do with the chemical balance in the cell at the time. So it's a code whose expression is affected by the surrounding chemistry and . . . . Have you heard about the experiments going on for growing new hearts? Fascinating. Take a heart, get rid of all the cells but leave the cartilage like stuff that holds it together (I'm using all the wrong words, my apologies), seed the framework with a stem cell from the person who needs a new heart and one grows onto the framework!! They'll be tons and tons of problems of course but how cool is that? AND how does the stem cell know to make muscles when it's not even in the body????? Fascinating.ellazimm
June 2, 2011
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#143 Mung What I meant was you can't just "analyze" something mathematically. How do you analyze a rabbit mathematically! You need a question you are trying to answer which you can then model mathematically. e.g. how does the population of rabbits change over time, or how does the weight of rabbits vary with age?markf
June 2, 2011
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Analyzed mathematically to what end?
Science. Knowledge. Understanding. If it can be anlayzed and described mathematically, perhaps that will tell us wqhether it's a code and in what sense it's a code and what sort of code it may be. We might even be able to compare it to other codes or other possible codes.Mung
June 2, 2011
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#140 and #141 Mung "You critics no doubt also believe the genetic code was selected, you just don’t think it was selected by an intelligent agent." OK. I will go with that. "Nothing remarkable at all about nature just by chance stumbling upon the only possible genetic code. And you don’t see why something like that smacks of ID. OK." I think this turns on what we mean by "possible". I thought you meant the only code that could possibly be created. I guess you mean the only one (of many possible codes) that could sustain life?markf
June 2, 2011
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I don’t see anything particularly ID about saying something is the only possible outcome...
Sigh. Nothing remarkable at all about nature just by chance stumbling upon the only possible genetic code. And you don't see why something like that smacks of ID. OK.Mung
June 2, 2011
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markf:
I don’t understand this. To me “choose” entails an intelligent agent i.e. someone to do the choosing, and I don’t think the genetic code was chosen.
But to select something doesn't entail an intelligent agent? So either nature is an intelligent agent or the term natural selection is any oxymoron. correct?
You critics no doubt also believe the genetic code was selected, you just don’t think it was selected by an intelligent agent.
All better now?Mung
June 2, 2011
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"Conventional" The first time I can remember hearing that word used to describe the genetic code was in the book The Design Matrix by Mike Gene. I was intrigued by the use of the word, so I contacted Mr Gene and asked him to expand and clarify his use of the word in context. Thanks for reminding me KF.Upright BiPed
June 2, 2011
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F/N 2: "Arbitrary" is not the best word choice for speaking of the rules for using symbols in a code; even though arbitrary is indeed used fairly commonly in engineering etc to speak of values set by decision, not constrained by materials and forces of nature. I believe a better term is "conventional," as in "Conforming to established practice or accepted standards" [AmHD].kairosfocus
June 2, 2011
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F/N: That there are indeed dialects of the genetic code (and the shift from DNA to RNA forms is the first such!), with variant forms and even ways to stick in extra amino acids beyond the usual twenty, tells us that the code is not driven by laws of mechanical necessity. That should have been evident, from the high contingency involved in a code; after all, a linguistic entity. (And yes, I am saying that language plainly was antecedent to C-chemistry, cell based life as we observe it on earth.) There are two and only two known causes of highly contingent outcomes: chance contingency or choice contingency. We have here a code of symbols and rules, with dialects, universal connectors and sockets and various clever tricks (like the wobble base pairing in the anticodon). It is used in an algorithmic context to control the automated assembly line production of proteins -- proteins which are BTW also intimately involved in the operation of the factory (making for a chicken-egg situation). That brings us right back to the key issue: what is the empirically known, best supported cause of codes, algorithms and assembly lines? [ANS: Obvious, intelligence.] Is there any direct observational evidence of such things coming to be (including the chicken-egg causal loop we just identified) by chance contingency? [ANS: No, and we know on thermodynamic reasoning [config spaces], that such functionally specific, complex, organised and information rich systems will be maximally isolated in configuration space.] These questions point, strongly to the most credible causal explanation, to the point of obviousness. Obviousness, save to those who are so committed to a priori materialism (or are fellow travellers) that Lewontin's observation applies:
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.
I dare to say: this is mind-closing ideology, not science. At least if science is to be understood as having the integrity of being committed to an open-minded observational evidence-led assessment of possibilities, towards learning and warranting the truth about our cosmos, including its origins. Perhaps it is time we all paused and looked at this video. GEM of TKIkairosfocus
June 2, 2011
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Mung #132
You critics no doubt also believe the genetic code was chosen, you just don’t think it was chosen by an intelligent agent.
I don’t understand this.  To me “choose” entails an intelligent agent i.e. someone to do the choosing, and I don’t think the genetic code was chosen.
Why the genetic code that we have, and not some other genetic code?
I don’t know why this particular genetic code. That is a question for evolutionary biologists and, as far as I know, they haven’t come up with the answer yet.
One possible answer is that it’s because this is the only possible genetic code.
“possible” is a modal word – there are different kinds of possibility depending on the context.  This is a trap that comes up with amazing frequency in these debates.
But that smacks of ID as well.
I don’t see anything particularly ID about saying something is the only possible outcome (whatever kind of possibility we are talking about).  Is every occurrence of something that is the only possible outcome to count as evidence for ID?
Arbitrary: Based on random choice or personal whim, rather than any reason or system.
You don’t believe the genetic code is arbitrary?
No – precisely because I don’t think there is any choice or personal whim involved.
Consider also whether the genetic code can be and has been analyzed mathematically.
Analyzed mathematically to what end?markf
June 2, 2011
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Mung: "Why the genetic code that we have, and not some other genetic code? One possible answer is that it’s because this is the only possible genetic code." From Wikipedia: "Despite the minor variations that exist, the genetic code used by all known forms of life is nearly universal. However, there are a huge number of possible genetic codes. If amino acids are randomly associated with triplet codons, there will be 1.5 x 10^84 possible genetic codes. Phylogenetic analysis of transfer RNA suggests that tRNA molecules evolved before the present set of aminoacyl-tRNA synthetases. Theoretically, the genetic code could be completely random (a "frozen accident"), completely non-random (optimal) or a combination of random and nonrandom. There are enough data to refute the first possibility. For a start, a quick view on the table of the genetic code shows a clustering of amino acid assignments. Furthermore, amino acids that share the same biosynthetic pathway tend to have the same first base in their codons, and amino acids with similar physical properties tend to have similar codons." The article goes on to discuss various arguments/themes in the discussion of the origination of the genetic code.ellazimm
June 2, 2011
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F/N: Perhaps I should show the number of ways information rather than chemistry is controlling what is going on: 1 --> DNA (and RNA) chains on a standard sugar-phosphate coupling, the 3 - 5 coupling, and chaining any to any. Wiki, testifying against interest, on DNA:
"The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information . . . . DNA consists of . . . polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds . . . Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription."
2 --> And, on Chaining:
The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages.[10] In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality, and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N-9 for purines) and the 1' carbon of the pentose sugar ring.
3 --> RNA is similar:
Like DNA, RNA is made up of a long chain of components called nucleotides. Each nucleotide consists of a nucleobase (sometimes called a nitrogenous base), a ribose sugar, and a phosphate group. The sequence of nucleotides allows RNA to encode genetic information. For example, some viruses use RNA instead of DNA as their genetic material, and all organisms use messenger RNA (mRNA) to carry the genetic information that directs the synthesis of proteins . . . . The chemical structure of RNA is very similar to that of DNA, with two differences – (a) RNA contains the sugar ribose while DNA contains the slightly different sugar deoxyribose (a type of ribose that lacks one oxygen atom), and (b) RNA has the nucleobase uracil while DNA contains thymine (uracil and thymine have similar base-pairing properties). Unlike DNA, most RNA molecules are single-stranded. Single-stranded RNA molecules adopt very complex three-dimensional structures, since they are not restricted to the repetitive double-helical form of double-stranded DNA. RNA is made within living cells by RNA polymerases, enzymes that act to copy a DNA or RNA template into a new RNA strand through processes known as transcription or RNA replication, respectively.
4 --> Proteins, of course, chain amino acids, which have a standard structure: H2N - CHR - COOH (where R is the side-branch functional group), and they are chained by the peptide bond, again the acids may chain any to any. 5 --> In the case of tRNA, at the 3' end, there is a CCA "universal coupler" that ties to the COOH of the AA. The correct AA is transferred by a key-lock fitted enzyme, but the coupling itself is standard (and implies that he amine end is the one that clicks on to the elongating AA chain). 6 --> At each stage we see that we are dealing with standard couplers and chains, so that there s a maximum flexibility. Itis information imposed on the chemistry and expressed in key-lock shape patterns that controls the functional roles. 7 --> DNA stores the genetic info in codes (a code, BTW, which is optimised for robustness against likely single point variations in AAs) based on a 64 state triple base system that translates to AAs and to start/stop procedures, elongation being an implied instruction once the new codon is in the chain. 8 --> MRNA, ribosomes and tRNA, with support enzymes etc, are the keys to the protein assembly process. mRNA is transcribed (and may be edited) based on DNA, and is communicated tot he ribosome, where it is used as a step by step discrete state controller. 9 --> As a rule AUG is the first codon, implying both start and load methionine. tRNAs loaded with the AAs then add in sequence, per the codon control. 10 --> The standard CCA -COOH coupler would mean that the chemistry of the bond to the AA does not control which AA is loaded. That is done by the corresponding aminoacyl tRNA synthetase (an enzyme that fits the tRNA and transfers the right AA based on the specific tertiary config, i.e. the tertiary bent arm folded form of the nucleic acid chain). 11 --> The tertiary functional form results from folding the chain into a cloverleaf secondary form, then further folding into the L-arm. 12 --> The anticodon is at one end, and the coupled AA at the other,so, again this is informationally controlled, not physically controlled. 13 --> The correct tRNA, with its elongation support molecule, loads to the next available codon, with key-lock fitting based on codon-anticodon complementarity, controlling the match. 14 --> This is a digital code control point. _________ In short, we can see how the protein assembly process is informationally controlled based on the code in the DNA. To function, the protein is folded and sent to the use site, based on further information (often coded into an end of the AA chain). Protein assembly is in effect carried out through an automated nanofactory based on discrete state asynchronous control. GEM of TKIkairosfocus
June 2, 2011
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Dr Liddle: Perhaps this animation will help clarify. Notice the way tRNA folds up its polymer string to give the position-arm device that carries the AA. (This one will help see how it is charged up. Notice how the common CCA tail "charging" end -- in effect a universal connector-socket for tRNAs -- bonds to the COOH end of the AA [AA's have a COOH end and a NH2 end], and the particular AA loaded is based on a key-lock fit to the charging enzyme, the relevant aminoacyl tRNA synthetase. The charged tRNA then adds the AA to the elongating protein based on key-lock fit to the codon triplet.) We can see the way information controls the actual step by step processing that makes a protein. GEM of TKIkairosfocus
June 1, 2011
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markf @86:
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.
If only I were assuming the premise. But alas. You critics no doubt also believe the genetic code was chosen, you just don't think it was chosen by an intelligent agent. Question: Why the genetic code that we have, and not some other genetic code? One possible answer is that it's because this is the only possible genetic code. But that smacks of ID as well. What's a critic to do? Arbitrary: Based on random choice or personal whim, rather than any reason or system. You don't believe the genetic code is arbitrary? Consider also whether the genetic code can be and has been analyzed mathematically.Mung
June 1, 2011
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…my (admittedly non-expert) understanding of biochemistry, CTA (or rather CUA) “codes” for leucine because the stereochemistry of the CUA base sequence “stamps out” leucine…
Dr Liddle, like before, you may want to revisit this assumption. A stereochemical basis for the genetic codes is riddled with intractable issues, and always has been. In fact, that is one of its more enduring problems; one scenario seems to provide evidence for something resembling affinities in one instance, but not for others, while another scenario provides some evidence here, but not there. The next competing model suggests an entirely different direction, and on and on the speculation goes. That someone could flatly suggest that stereochemistry has provided the answer, or an answer, or even a sufficient answer, is simply overstating the research by several orders of magnitude. Take the time to open-mindly read the work of perhaps, Yarus and Knight on the current summary of the evidence. You will find deep issues of inconsistency, which they themselves highlight. Further, their own models are forced to make grand assumptions about the distant past which are beyond replication, and they openly acknowledge the observed indirect nature of modern translation. I am not knocking their work, or that of their intellectual competitors. To the contrary I am suggesting it as central reading material – but with an open mind. Let it reveal what is actually known. And also, let it highlight what is simply speculation, and what is speculation based upon assumption. I would suggest that what you will find is enlightening to an open mind. It is the working end result of a prior assumption that the code simply cannot be the result of agency input. In other words, knowing full well that a mind is the only verifiable source of an encoded abstraction, their work represents the pinnacle of an intellectual effort to produce an explanation - without that mind.Upright BiPed
June 1, 2011
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Thanks, kairosfocus. Well, I agree it is "informational" but then I think that contingencies ARE "informational". I don't think that makes them not "physical", nor, more to the point, do I think that means that they have to have been "intelligently" coded in. I simply don't think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery. More tomorrow!Elizabeth Liddle
June 1, 2011
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Dr Liddle: I have just a moment. The tRNA chain is based on a backbone that is independent of whether you have G/C/A/U in any position. The folded tRNA of course has the anticodon in a given position as three sequential bases, but that has nothing to do necessarily with what else is in the 70 - 90 bases in the chain. The chain is however -- informationally! -- sequenced so that for a given anticodon triplet, the rest of the tRNA as folded will lock to the "RIGHT" aa. Worse, for some AAs there are up to was it five or six anticodon triplets that are set up to fold to lock to the SAME AA. That is an informational configuration [much like the one for proteins to fold and function], not a matter of a sequence forced by natural law. There is no law that forces tRNA bases into a particular sequence. There is an informed sequencing, not the equivalent of crystallisation. GEM of TKIkairosfocus
June 1, 2011
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We have a lot of common ground here, kairosfocus (and, btw, I am still musing on your other OP - I haven't forgotten! I won't do it justice, but at least I want to do my best, and I was up very late last night with a deadline). However, I guess I'm not seeing your point - or rather, I'm reading your post, and the wiki extract, and seeing it support mine! But I'm more than prepared to entertain the possibility that I'm missing your point (and presumably you think I am). So let me take one sentence from your post. You say:
That correlation is plainly not a forced outcome by natural law: there is no physical reason why when an anticodon is at the required point in the chain, the folded tRNA will necessarily support the particular AA.
In what sense is the correlation "plainly not a forced outcome by natural law"? By what means are you suggesting that "when an anticodon is at the required point in the chain, the folded tRNA will necessarily support the particular AA" if not "forced...by natural law"? I do accept that the natural law in question may be a contingent one, but lots of natural laws are subject to contingencies. This is not a rhetorical or trick question, btw - I am delighted to have reached what seems to be the ground floor of an argument that is often conducted from different floors in different buildings simultaneously"Elizabeth Liddle
June 1, 2011
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EL: The point about machine code is that it is at the level of the actual register units of a machine, and addresses the messy details of making a machine carry out instructions. So, code elements physically interface, and there is a closeness to hardware that is not engaged in higher level languages. I get the feeling you are hung up on the point that there is a physical, key-lock interface used, more like a digitalised cam than the more abstract states of electronic registers. But in fact the organisation of the system is still implementing a code. The states do not vary smoothly, so it is discrete state, or digital. The tRNA's key lock fit and do so for one of 64 possible combinations, conveying the appropriate AA's on opposite ends of the molecule as folded. That correlation is plainly not a forced outcome by natural law: there is no physical reason why when an anticodon is at the required point in the chain, the folded tRNA will necessarily support the particular AA. For, remember the chaining of tRNA is also contingent. And, there are varieties of tRNA to support 20 or so AA's and a diversity of codons. Observe Wiki on tRNA:
Transfer RNA (tRNA) is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the four-letter genetic code in messenger RNA (mRNA) with the twenty-letter code of amino acids in proteins [1]. The role of tRNA as an adaptor is best understood by considering its three-dimensional structure. One end of the tRNA carries the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. On the other end of its three-dimensional structure, each tRNA is covalently attached to the amino acid that corresponds to the anticodon sequence. This covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl-tRNA synthetases. Each type of tRNA molecule can be attached to only one type of amino acid, but because the genetic code contains multiple codons that specify the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid. During protein synthesis, tRNAs are delivered to the ribosome by proteins called elongation factors (EF-Tu in bacteria, eEF-1 in eukaryotes), which aid in decoding the mRNA codon sequence. Once delivered, a tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly-delivered tRNA, a reaction catalyzed by the ribosome.
Observe the way in which the algorithmic step by step process is aided along by helper molecules, and how we have a many tRNA to one AA pattern (related to the redundancies in a 64 state code matching to a 20 state one, with some other codes being sued for "stop." GEM of TKIkairosfocus
June 1, 2011
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Mung: I think what we have in the cell is only a "code" by certain definitions. There is, I was trying to suggest, a nearly-clean cleavage line between codes that involve arbitrary pairings between signifier and signified (as between graphemes and phonemes in an alphabetic system) and what I might call "codes" in which the "signified" is directly related to the properties of the "signifier". That was the point I was trying to make when I talked about the moveable type "coding" for the printed letter B as opposed to the printed letter B coding (no scarequotes) for the phoneme "buh". I'm not quite sure why you don't think that's a valid "analogy" - although it wasn't, strictly, meant as an analogy, but as an examplar of two kinds of "code" at the fairly extreme ends of the arbitrariness spectrum. And my position is that the way that CTA "codes" for leucine is much closer to the moveable-type-codes-for-the-letter-B end of the spectrum than the letter-B-codes-for-the-phoneme-"buh" end of the spectrum. And the reason I hold to that is that from my (admittedly non-expert) understanding of biochemistry, CTA (or rather CUA) "codes" for leucine because the stereochemistry of the CUA base sequence "stamps out" leucine, not, say, thionine. Not because there is a codebook somewhere that says that CUA "means" leucine. Now you may not agree that I have carved nature at the right joint here, but can you see the argument I am making? As for encryption - I'm not sure what your question is, exactly, but I suggest that it is way easier to decode a code in which the signified is indicated (as in "index"!) by the morphology of the signified (as in hieroglyphic systems) than codes in which the pairing of signifier and signified is arbitrary, and requires a lookup table or a key. Does that help? To clarify what I am trying to say, if not persuade?Elizabeth Liddle
June 1, 2011
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ellazimm:
junkdnaforlife: Are you saying that Christianity is preferable to atheism because it killed fewer people? Interesting. This arithmetic of virtue.
This is just nasty. He wasn't saying any such thing and you know it.
Are you saying you’d rather be ruled by the Westboro Baptist Church than atheists?
I'd take the Westboro nuts over atheists any day. What are there, like 8 of them? I think we could safely ignore any edict they might issue without fear of reprisal.Mung
June 1, 2011
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Elizabeth @94:
But I submit that at the level of the codon, the system has so few “options” that “arbitrary” (literally “concerning judgement”) is not a useful description.
Sorry that this got spread over two posts. What options does the CPU have in my computer analogy? I'd say none. Yet we still call it machine code, and for good reason. Are you saying the machine code isn't arbitrary because the CPU has no choice in it's execution of the code? Or are you arguing that what we have in the cell is not actually a code? IOW, there is no "genetic code."Mung
June 1, 2011
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Why is the debate over design theory so often so poisonous and polarised?
Sure, blame it on Hitler . He's dead, and not here to defend himself.Mung
June 1, 2011
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Elizabeth Liddle @94:
And what I am arguing is that CTA “codes” for leucine in the same manner as the piece of moveable type “codes” for the printed letter “B”, not as in the way the symbol “B” (usually) codes for the plosive voiced fricative sound “buh”.
Why do you think that's even a valid analogy? Not all languages are alphabetical. You probably know that. And I'm not sure that what you are talking about even qualifies as a code. I'll have to think more. Didn't kf post a definition somewhere? I thought my machine code example was right on target. By the way, say your want to encrypt something. What are the chances of your code being broken if we follow your line of reasoning?Mung
June 1, 2011
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PS: Mr Mark F, I suggest you will find my remarks at 104 relevant.kairosfocus
June 1, 2011
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