Uncommon Descent Serving The Intelligent Design Community

When Darwinism infects popular culture, confusion follows as well as nonsense

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File:Nostradamus prophecies.jpg

Every so often, one reads a sentence that just takes one’s breath away from an otherwise intelligent writer who uses Darwinism to help explain the world: This from Colin Dickey’s “Quack Prophet” (Lapham’s Quarterly):

Whether it’s the Dead Sea Scrolls or Finnegan’s Wake, there’s a long literary history of taking the garbled and the fragmented and looking for lucid meaning beneath. The science writer and professional skeptic Michael Shermer has gone so far as to argue that we’re hard-wired, from an evolutionary perspective, to look for such hidden meanings. “From sensory data flowing in through the senses the brain naturally begins to look for and find patterns, and then infuses those patterns with meaning,” Shermer writes. “We can’t help it. Our brains evolved to connect the dots of our world.” By adjusting the signal-to-noise ratio, Nostradamus introduced enough static into his Prophecies that they could be all things to all readers, poetic Rorschach blots of detail and blur.

Excuse us, but: The Dead Sea Scrolls are a remarkable 1947 find (since augmented) of a group of manuscript fragments and artifacts that everyone knew had lucid meaning, but awaited translation and clarification. You didn’t need to be “hard-wired” to notice any of that. Finnegan’s Wake is a deliberately obscure novel written by Irish novelist James Joyce, pored over by generations of academic dullards – to Joyce’s huge amusement, had he lived to see that entire circus play out. Much of it probably did have some meaning; it was written in English by an already successful novelist. Again, no “hardwiring” required to suppose that, though a certain amount of denseness for spending a lot of time on the problem.

It’s not like seeing patterns in the clouds, which might actually be evidence for Shermer’s thesis if not pressed too far – which it nearly always is.

Conflating the Scrolls and Finnegan’s Wake, spiced up with some Shermerite nonsense about how our brains evolved to … whatever, is an appalling but telling example of cultural Darwinism at work.

Those who don’t believe in meaning corrupt and confound it.

Note: The ostensible subject of the piece is that reliable checkout counter tabloid icon, the “prophet” Nostradamus, who was obscure for an entirely unrelated reason – to avoid falsification. Reminds one of something, no … ?

Comments
Sad, but I need to let you know that per the direct implication of what you have said, you falsely accused me of support for genocide etc.
You LIAR! (slanderer even! ) You really are the most despicable excuse for a human being I have ever had the displeasure of encountering. I find myself hoping that the god of Christianity exists just because it would be comforting to know that at some point you will ultimately be shown the true scale of your hipocracy. I have not engaged in the debate over genocide as the record on this blog will attest, yet you now claim that I am accusing you of supporting genocide - that is a flat out lie KF and you know it. Now do the decent, Christian, thing: withdraw the accusation and apologize - or do I have to get my lawyers involved, I hear that British libel laws can have a long reach ;)DrBot
November 2, 2011
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State 1: A State 2: U State 3: C State 4: G
Thats wrong, it should be: State 1: G State 2: C State 3: A State 4: U ... oh, hang on, no, its: State 1: U State 2: A State 3: C State 4: GDrBot
November 2, 2011
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Pardon a necessary off Topic. Dr Bot: You have now definitively crossed the threshold of incivility. Sad, but I need to let you know that per the direct implication of what you have said, you falsely accused me of support for genocide etc. You now refuse to explain yourself. Your choice; I will make mine. Good day GEM of TKIkairosfocus
November 2, 2011
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Elizabeth Liddle:
Forget the bottom half of the base-pair (because it is entirely predicted by the top half) and just look at the top row. What is it that can take one of the four states? Do look at my post 1.2.2.2.2, it might help.
Fine. Looking now at only the top half: http://en.wikipedia.org/wiki/Base_pair
The corresponding RNA sequence, in which uracil is substituted for thymine where uracil takes its place in the RNA strand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC
State 1: A State 2: U State 3: C State 4: G The top half can each take one of the four possible states.
What you are not addressing is the fact that point mutations are only one of several kinds of mutation, that include insertion, deletion, duplication and recombination.
Irrelevant to the 4 possible molecules of A, U, C, or G from which the mutation is comprised.
What “changes state” when any of these other mutations occur?
The base-pair in any given position in the sequence, changes. But a change of any particluar base-pair, a change in the content of its position in the sequence, doesn't alter the fact that base pair is still comprised from one of four possible molecules: A, U, C, or G (whether you look at the top or bottom half).
Look again at my post 1.2.2.2.2
You still have same four possible molecules: A, U, C, or G, no matter the sequence.Charles
November 2, 2011
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Charles:
Elizabeth Liddle:
Wrong answer. There is only one “allowed state” for the other half of a base pair, given the first half.
http://en.wikipedia.org/wiki/Base_pair
The corresponding RNA sequence, in which uracil is substituted for thymine where uracil takes its place in the RNA strand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC State 1: A ( other half is U) State 2: U ( other half is A) State 3: C ( other half is G) State 4: G ( other half is C)
Four possible states in different permutations (Take care you don’t start arguing combinations, as if position didn’t matter)
States of what?
My question was what thing, what entity, can take one of these four states.
Asked and answered: one half of the base-pair – see above.
No, you aren't getting it. Forget the bottom half of the base-pair (because it is entirely predicted by the top half) and just look at the top row. What is it that can take one of the four states? Do look at my post 1.2.2.2.2, it might help.
DNA is not a “positional” system, but a sequential one.
In a sequence, each component has its position, a position dictated by its relative appearance in the sequence. Point mutations, for example, are the substitution of a different base-pair into a specific position in a sequence of base pairs. But again, you already knew all the above.
Yes, and you know that I know it, because I've mentioned point mutations several times. What you are not addressing is the fact that point mutations are only one of several kinds of mutation, that include insertion, deletion, duplication and recombination. What "changes state" when any of these other mutations occur? Look again at my post 1.2.2.2.2Elizabeth Liddle
November 2, 2011
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William J Murray
I challenge you to respond to the following: If we find what appears to be to some an ancient, abandoned alien space ship on an otherwise deserted and desolate planet, how would one go about establishing, as best explanation, that the object in question was probably designed and built by an intelligent alien species
Your example still assumes aliens built space ships the same way humans do and that we could recognize one just by looking at it. It's just a modern spin on the Paley's Watch argument that was rebutted over a hundred years ago. Your challenge is to detect design in an object that you have no external knowledge of. In the case of biological life, there is no relevant human design that it can be compared to. How about this: suppose we receive trustworthy information that somewhere in the tens of thousands of separate peaks in the Rocky Mountains is a peak that space aliens carved into a statue of their Great Leader. It has a designed function (a shrine) and it's an exact copy so has lots of designed-in information (or CSI or dFSCI or whatever you want to call it). Unfortunately the space aliens all look a lot like craggy granite blocks. How would you go about determining which peak was designed?
No, it doesn’t; it rightfully limits its potential recognition of designed artifacts to those that are similar enough to human design parameters to be rigorously quantified as designed.
How do you rigorously and objectively quantify what 'similar enough' is? Seems to me that's always going to be a subjective call, which is what keeps tripping up IDers. Features that 'look designed' to them don't look designed to the scientific community, those who know of non-designed processes that produce the same features.GinoB
November 2, 2011
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Dr Liddle: That digital MEANS discrete state is by no means idiosyncratic. As even so humble a source as Wikipedia will verify, it is the standard technical usage, for reasons as already identified.
I agree that all digital systems are discrete. I do not accept that all discrete systems are digital. However, let me concede another point: let us regard any discrete information system as digital, regardless of whether it is alphabetic or numeric. And let us regard them as being in "base N" if "N" is the total number of kinds of item used, and if [what is read] at any given time can take one of N "states".
And it seems I need to make a point clear: a 4- discrete- state per- digit string- structure.
And again, what goes wrong, kf is the bit after the "per". There aren't four states per "digit string structure" - "digit string structure" doesn't mean anything. As I said, if [what is being read] is regarded as the thing that takes a state, you may have a point, but [what is being read] during transcription isn't a "digit string structure" but a base pair. And [what is being read] in translation is a codon, which can take one of 64 states. Sure, those states are combinations of three RNA bases, but the three bases aren't read sequentially, they simply act as a molecular unit with specific chemical properties.
Digital string systems do not always change states, indeed ROM (read only memory) is set up precisely NOT to change state but as reference information pre-loaded into the system, and that is what DNA is.
OK - if you are regarding DNA as a database (which I think is a good model btw) then whether you regard it as digital information in base 4 depends on the reading frame in the particular information-transfer process you are interested in. However, once you consider how that information is "pre-loaded into the system", then you are not really talking about a digital information transfer system at all, because you are not talking about a system with a sequential reading frame.
All the peculiarities that you may look at are things that make DNA a particular kind of digital entity, they do not affect the basic empirical fact that it is a discrete-state (thus, digital) info-storing entity. Just as, had it been more like a cam, it would have been an analogue info storing entity. GEM of TKI
Well, as I said, I think you have to be very careful of what it is you are granting a "discrete state". Is it the "state" of what the RNA polymerase is "reading" (4 possible states)? Is it the "state" of what the ribosome is "reading" (64 possible states)? Is it the state of a gene (two possible states, Off and ON)? Or is it the state of the of the locus of a gene (unlimited number of states aka alleles)? Or is it the state of the gene sequences that makes up a genome (billions, over time)? Or is it the state of the phenotype within a population (many states from dead to breeding madly)? Some of these information transfer-systems might be characterisable as being in base N, but some are in an indeterminate base number, and when we consider the origins of the "base 4 digital" DNA information that is "pre-loaded" into the genome, all these different kinds of "digital" systems, in both finite and undefined base systems, come into play. Yes, living things are packed full of information, and maybe you can call some, if not all, of it digital, but the information transfer systems certainly aren't all in "base 4". And perhaps this has been an illuminating conversation, because it makes me realise where you guys might be coming from. Yes, I will concede that there is a "base 4 digital" information transfer process in living things (transcription). But it's only a tiny component in the vast system of information transfer that we see in Life itself, and completely ignores the information transfer systems that evolutionary theory posits as accounting for the origins of that information. So, I grant you your "base 4 digital" information transfer kf :) Now, look at the rest of the system!Elizabeth Liddle
November 2, 2011
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Elizabeth Liddle:
Wrong answer. There is only one “allowed state” for the other half of a base pair, given the first half.
http://en.wikipedia.org/wiki/Base_pair
The corresponding RNA sequence, in which uracil is substituted for thymine where uracil takes its place in the RNA strand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC
State 1: A ( other half is U) State 2: U ( other half is A) State 3: C ( other half is G) State 4: G ( other half is C) Four possible states in different permutations (Take care you don't start arguing combinations, as if position didn't matter)
My question was what thing, what entity, can take one of these four states.
Asked and answered: one half of the base-pair - see above.
DNA is not a “positional” system, but a sequential one.
In a sequence, each component has its position, a position dictated by its relative appearance in the sequence. Point mutations, for example, are the substitution of a different base-pair into a specific position in a sequence of base pairs. But again, you already knew all the above.Charles
November 2, 2011
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Elizabeth Liddle:
Tell me what it is that “changes state” in the DNA sequences I gave as examples in post 1.2.2.2.2
AUGCCGACAGUAGUAGAG What has changed state, if anything?
That a state has to "change" is your misunderstanding. That there are obviously the same 4 possible states remaining (A, U, G, or C) is again your obdurate refusal to count.
As far as I know, nothing reads the promoter sequence sequentially, it’s just a chemical binding between one molecule and a section of another.
Agreed it isn't sequential, it is rather a parallel pattern recognition (implemented in the machinery of chemical bonds), pattern recognition, analogous to "content addressable memory" which now is the 3rd time that has to be pointed out. That is why you get accused of intellectual dishonesty.
But it’s a bit of a stretch, to my mind, and we haven’t reached the “coding” bit yet.
Actually, it has already encompassed your example. The DNA and RNA sequences are "code". Just like an encrypted message is code, just like a set of unexcuted computer instructions on paper is still code. The RNA polymerase binding, its "pattern matching", is code.
And what is, in fact, read at this point? Not the individual bases, it turns out, but the triplets. So now we have moved into “base 64?.
Triplets of bases formed from A, U, G, or C, which is is still base-4. By asserting that is somehow base-64 (4x4x4) just demonstrates again your ignorance. You continue to conflate an abstract numbering system in which general purpose mathematical operations are done with a special purpose 4-state machine which only does some limited logical operations. By analogy, in a 2-state binary system (1, 0), 2x2x2 is a math operation yielding 8 (decimal) which is represented in binary by 1000, or in octal by 10 or in hexadecimal by 8. But underneath it all is the lowly 2-state transistor, which regardless of your confused conflations, didn't become an 8-state transistor by stringing together a triplet of 2-state values. Likewise stringing together a triplet of 4-state base pairs doesn't change the lowly A, U, G, or C molecules into 64-state molecules.
And this really is digital, but it turns out to be in Base 2, and involves the switching on and off of genes so that the right proteins are made at the right time, in the right place, in response to the right chemical signals.
What you mean is really "binary". Binary is base 2, digital is a broader more generic term (humans are base-10 digital - we have 10 digits on our hands), but you're still wrong, as a gene comprised of pairs of adenine thymine guanine and cytosine is still comprised of 4-state base pairs. As previously pointed out, the issue is not the number of permutations, but the number of states from which all possible permutations derive. Turning a gene on or off doesn't change the adenine thymine guanine and cytosine composition from which it was built up. Analogously, turning off a binary memory cell does not add or subtract from the possible states each transitor in the memory cell can take; turning off a binary memory cell doesn't transform it into a unary base.
So there you have a decent counter-argument, courtesy of me.
Hardly decent and hardly a courtesy.
I agree that there is an attenuated sense in which DNA can be considered as being involved in a “base 4 digital” information transfer process but only at the transcription stage where the exposed DNA acts as direct template. At the much more interesting information transfer process of translation, it is digital, but in base 64.
Yet another paper for you to submit to a symposium.
So, I will happily concede that at one level we do indeed have “base 4 digital” information transfer.
Now all you need do is demonstrate how information transfer from strings of base-4 base-pairs to other strings of base-4 base pairs is multiplicative to become 64 and then identify the 64 possible states in each base position (demonstrate not that 4x4x4=64, but that the transformation is multiplicative), and explain how the same base pairs were 4-state before but those same base-pairs become 64-state afterwards.Charles
November 2, 2011
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Elizabeth Liddle:
Please define the “RNA ‘digit’” that can take “four allowed ‘states’”?
My exact words were:
where its value is any of the possible states allowed by the system upon which the string is built. … and similary adenine uracil guanine and cytosine are the four allowed “states” of an RNA “digit”
“possibly allowed” does equate to having “take[n][all] “four states”. Not all permutations exist. But the absence of some permutations does not change the fact that each permutation consists of not more than four possible states. But the answer you need is the “RNA ‘digit’” which can take [one of the] “four allowed ‘states’” would be one half of a base-pair. Each RNA “digit” is paired with another RNA “digit” to form a base-pair and base-pairs are strung together in strands, strands strung together in kilobase pairs,… etc.
Wrong answer. There is only one "allowed state" for the other half of a base pair, given the first half. Yes, the basepairs are strung together in strands, but that's not the answer to my question. My question was what thing, what entity, can take one of these four states. However, I've now answered it myself. The thing that can take one of four states is the base-pair being currently read by the the RNA polymerase during transcription. So you can have your "base 4 digital" for that part of the process. But only that part, because that is the only part that I can see where some entity (in this case "the base pair currently being read) that can take one of four "states". At translation level, it is the codon that is read, and it can take one of 64 states. So yes, digital, but not base 4 any more. Indeed the mRNA may require editing so that it consist of integral triplets.
Um, no you didn’t. And it’s absolutely critical.
Yes I did. And it’s absolutely critical that you stop ignoring the answers you’ve been given. That is intellectual dishonesty. If you don’t understand, then ask. But stop presuming you know what you’re bloviating about. You don’t.
I haven't had answers to my questions IMO. Stop presuming that if someone thinks their question hasn't been answered that it is she who doesn't know what she is talking about. tbh, I thought you were bloviating, but I was too polite to say so. My question was quite simple ("what is it can take one of four states?") and all I got was guff about half a base pair. Or an "RNA digit" which rather assumes the consequent. harrumph.
If you want to claim that a system is in “base 4 digital” then please provide a definition of “base 4 digital” that doesn’t refer to a positional numeral system.
Data processing systems employ logical operators (AND, OR, XOR, Compare, shift, copy, etc.) as well as mathematical. A base-four system merely does this with strings wherein each element (bit or digit) is in 1 of 4 possible states. That in RNA, strings are not found reflecting all possible permutations in no way changes the irrefutable fact that any position will never have anything other than either adenine uracil guanine or cytosine; regardless of the operation, the allowed values of each position will always be adenine uracil guanine or cytosine.
And yet again you miss my point. What does "each position" mean"? DNA is not a "positional" system, but a sequential one. However, as I've said, I concede that if we think in terms of reading frames, at transcription level we can think of it as a base 4 system, and at translational level as a base 64 system. But the only person that has even mentioned reading frames in this thread is me, and it's the only context in which "state" makes any sense, because the actual basepairs don't change state at all within an organism (we hope) and between generations they don't change digitally.
The example I gave, which in your inexperience you twice now have failed to comprehend is content addressable memory. Present memory architectures mostly use two-state address-selected memory with many special applications that use content addressable instead. These same operations have been repeated in tri-state systems. To my knowledge, no one has attempted a 4-state processing system because there are no 4-state devices and regardless the practical limitations on adoption preclude any benefit.
Look I don't know how old you are, but from your manners I'm assuming younger than me. I hope that as you get older you will become less inclined to attribute disagreements to "inexperience" or "asinine" qualities on the part of your interlocutors. I'm shortly entering my 7th decade, and I have a fair bit of "experience" with digital systems of all kinds. And one thing I have learned from experience is that I am not infallible. I recommend the lesson.
But as I mentioned, the operation by which strings of base-pairs are somehow compared and matched, taking note of markers denoting coding vs non-coding regions is essentially a 4-state content-addressing mechanism: The content is found and its address (endpoints) is subsequently used for “unzipping” and encoding (or not).
Ah, at last. Not a model of clarity, but I agree, that the templating of RNA by DNA is sorta base 4 digital. Sorta.
I’m using something that at least finds support in wiki. Where is yours?
You could interpolate from the same article. It lists commonly used numeral systems and gives examples of base-8 and base-16, albeit the implementations are all on binary base-2 machines. But a base-4 numeral system would have values “0, 1, 2, 3? as its four allowed states. A base-4 RNA system has adenine uracil guanine or cytosine as its four allowed states. But again, as RNA is not a machine which employes math and all abstract permutations of numbers, as RNA employs logical operators similar to comparison and XOR and is not an abstract system, you should not expect to find all permutations of adenine uracil guanine or cytosine.
You are confused again. You were almost there for a minute. First of, thank you, yes, RNA is not a system that involves math, although it does involve logical operators. And you are correct, it is not an abstract system. Glad to have established that. But now you've gone and swapped reference frames again. Considered as single items read sequentially, you can consider that "what is read" in a DNA strand (let's denote it X) as having one of four states: AGCT - so sure, let's call that "base 4 digital". But if we consider it that way, any serial sequence is possible, and indeed all possible permutations occur. However, once we consider RNA, and the translation, we are no longer considering a one base reading frame but a three-base reading frame, i.e. "what is read" in an RNA strand (let's denote it Y) can take one of 64 states, so we should call it "base 64 digital". And again, lots of permutations of codons are possible.
Just because you found the subject matter you sought doesn’t equate to having sought the applicable subject matter.
No indeed.
kairosfocus has already, ad nauseum, provided you with cites defining four-state systems.
But what you were both extremely reluctant to do was tell me what, in a cell, can take one of four states. However, I found one: "what is read" in DNA while being templated by RNA polymerase.Elizabeth Liddle
November 2, 2011
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Eugene S:
Elizabeth, That DNA is a code constitutes a scientific fact.
No, it isn't. There aren't any "scientific facts". It's a scientific model. Also a metaphor. Quite a good one, I'd say.
1. DNA carries instructions, consequently information. 2. This information can be represented by strings composed using an alphabet that consists of 4 letters. Not all strings defined on the 4-letter alphabet have an associated biological meaning. Similarly, not all strings of some given length using letters of the English or any other alphabet, have meaning. Nonetheless, the above considerations allow the scientific community to agree that DNA is a code. To dispute that seems really strange.
And I didn't. As I said, I think it is better considered as "4-letter alphabet" code as you just did, not a "base 4 digital" code. However, as you will see from my post above, that when we consider various levels at which information transfer takes place in living things, one of them, I concede, could, at a stretch, be described as "base 4 digital". I have no problem with the idea that information is transferred in living things - indeed I probably consider more kinds of information transfer than most people here, because I also consider the transfer of information form the environment to the population genome, which is the part that ID guys tend to leave out.Elizabeth Liddle
November 2, 2011
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Elizabeth Liddle:
But it remains highly misleading because what most people mean by “base 4 digital” is a positional numeric system,
That would be most people who have neither built machines from 2-state or 3-state devices, nor implemented logical operations as opposed to merely numeric, but have authored highly misleading wiki articles for people who can’t tell the difference.
Tell me what it is that "changes state" in the DNA sequences I gave as examples in post 1.2.2.2.2, which I note that no-one has even quoted yet, despite the fact that I asked some clear questions in it, and repeated them in posts since then. And people accuse me of intellectual dishonesty and of not answering questions. Sheesh. You know what? I'll make your own argument for you, seeing as no-one seems to want to step up to the plate. What I think you mean is that if you start "reading" a gene from one end to the other, what "changes state" is the thing you are currently reading. So what does the cell "read" when it "reads" DNA? Let's look at how translation occurs: First thing that happens is that RNA polymerase binds to a promotor region of DNA. Is this a "digital" process? Not really. Either there's a promoter sequence or there isn't. As far as I know, nothing reads the promoter sequence sequentially, it's just a chemical binding between one molecule and a section of another. If all you had in a testtube was a TATA box section of DNA and some RNA polymerase, they'd bind to each other, in a manner that is not, AFAICT, qualitatively different from the binding of any pair of reactive molecules. However, once the transcription process has been initiated, and the DNA gene "unzipped" and exposed, we do have a sequential "reading" in that the exposed DNA now forms a template for the sequential assembly of an RNA copy (with uracil replacing thymine of course). So maybe you could call this part "digital base 4", as I guess the RNA polymerase "reads" one DNA base at a time and depending on the "state" of the "read" base, "selects" an appropriate RNA base to add to the emerging mRNA strand. But it's a bit of a stretch, to my mind, and we haven't reached the "coding" bit yet. OK. Now we have our messenger RNA molecule. This in turn is "read" sequentially by the translation machinery. So again we could regard "what is read" as the thing that "changes state". And what is, in fact, read at this point? Not the individual bases, it turns out, but the triplets. So now we have moved into "base 64". Depending on the "state" of "what is read" i.e. the codon currently in the system, a specific amino acid is joined to the emerging protein. So, considered as an information transfer system that conveys information from the DNA molecule to the protein-making system, I guess you could call it "digital", except that the important part is in "base 64" not "base 4" (because I'd scarcely call a templating process a "digital" process, even if it is sequential - it's more like an extrusion, really). However, considered as a system that conveys information about how to build a functional organism from parent to child, it isn't digital at all, because there are no "state changes" between parent DNA and child DNA, although there are a lot of changes, and those changes embody information that has come from the environment about what has produced viable organisms in the past, as well as novel information about how to build this particular organism, that may or may not prove advantageous. If it does, it is more likely to be passed on to further generations. Lastly, there is the transfer of information from cell to cell, and from environment to cell, about what to do next, during development, maintenance, and function of the organism. And this really is digital, but it turns out to be in Base 2, and involves the switching on and off of genes so that the right proteins are made at the right time, in the right place, in response to the right chemical signals. So there you have a decent counter-argument, courtesy of me. I agree that there is an attenuated sense in which DNA can be considered as being involved in a "base 4 digital" information transfer process but only at the transcription stage where the exposed DNA acts as direct template. At the much more interesting information transfer process of translation, it is digital, but in base 64. At the information transfer process from parent to offspring, it isn't digital at all, but alphabetic, as is the information transfer process from environment to population genome. And at the cell-to-cell information transfer process it is digital again, but this time in base 2. So, I will happily concede that at one level we do indeed have "base 4 digital" information transfer. I'm glad I was here to help myself. Cheers Lizzie.Elizabeth Liddle
November 2, 2011
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Dr Liddle: Pardon, but the projection of a nefarious motive is out of order.
Thank you for clarifying that you do not consider the point of view that DNA is not in "base 4 digital" as being an attempt to deny that cells contain the "dfCSI" and therefore "signature of design". As I have made it very clear, I think that in many ways cells do behave like digital systems, and in that sense contain "digital functional complex specified information". I just don't think that intentional design is the only explanation for such a system.
Let’s just say that any of my students over the many years who insisted on refusing to accept that a discrete state system is perforce a digital one would have demonstrated that s/he was unteachable.
So are you really insisting that "digital" and "discrete" are synonyms? And has it never occurred to you that when you meet a student who does not agree with you that rather than the student being "unteachable", it might be you? Seriously kf, if you go through life, as you seem to do, assuming that anyone who disagrees with you has simply not understood what you are trying to say, or worse, culpably resists "correction", you are doing yourself a disservice. If we cannot learn from our students we have no business teaching.
Such a student would be unable to understand an A/D converter or a D/A converter and why we use a low pass filter for the latter. Among many other problems.
Not at all. You are making a classic logical error: All cats have tails. This animal has a tail Therefore this animal is a cat. All digital systems are discrete. This system is discrete. Therefore this system is digital. And, in case you are not aware of it, I do a fair bit of signal processing myself. In fact, I had to go and sort out an analog-digital converter box 20 minutes ago.
A better explanation, it seems, frankly, is that for whatever reason, some objectors tot he design inference, are refusing to acknowledge the discrete state thus digital nature of the information stored in DNA and processed using inter alia mRNA and ribosomes, because they would find it harder to make some of their preferred objections.
And there you go again!!! Nobody at all, to my knowledge, has ever denied that polynucleotides consists of discrete nucleotides. Or that they contain information. So you have yet another straw man there, kf, and are soaking it in ad hom: we do not "refuse to acknowledge" that the information in DNA/RNA is digital "because [we] would find it harder to make some of [our] preferred objections", we refuse to do so because discrete is not a synonym for digital and polynucleotides are not in "base 4" in any definition of "base 4" that I for one am aware of. Except that there are "four kinds of base pairs" but that would be to equivocate painfully with the word "base".
Do you not see that if the key-lock DNA worked like a cam bar instead [i.e. was continuous state], that analogue info storage and processing would be info storage and processing, and it would be a simple matter of identifying the bit depth of the equivalent digital info, for analytical purposes?
Pretty well any information can be digitized, kf, so of course. But my point is not that DNA is not discrete, but that it isn't digital. You seem to think those words mean the same thing.
Indeed, have you not understood why it is that I compare Mt Rushmore and Old Man of the Mountain, Nefertiti and a wire-mesh of a dolphin? The analogue info in the facial portraits, is reducible to a nodes and arcs data structure, which can then be digitised to whatever degree of precision is required to process with adequate fidelity.
Just because information can be digitised doesn't mean it is digital information.
In short, the issue analogue/digital is NOT a critical one to the question of inferring design. It is a simple matter of a key scientific value: being reasonable, well warranted and accurate in using concepts to analyse phenomena.
No, it's completely irrelevant, because, as I keep saying, I am not claiming that polynucleotide information is not discrete. It obviously is. I'm saying it's not digital, and not in base 4.
DNA uses a string-structure, 4-stste digital storage system, which is processed step by step in ribosomes to make proteins, i.e is algorithmic. That is accurate description not crude or loose analogy. That this would be a sticking point, is telling on the balance of the case on the merits.
Yes, it's algorithmic. It's just not base 4 digital. Actually, in some ways it's cam-like, but, as DrBot says, that doesn't mean it's not discrete.
And, if it is not clear to you by now that I despise rhetorical stratagems that try to manipulate by playing on misconceptions, perceptions and feelings, instead of taking on issues of fact, concept, assumptions/ premises and logic, with epistemology hovering in the background [even to the fault of being challengingly complex], something is wrong.
No, it isn't clear to me that you "despise rhetorical stratagems that try to manipulate by playing on misconceptions, perceptions and feelings", kairosfocus. To be perfectly honest, I'd say you indulge in such strategems regularly, as in your recent spate of "BLOOD LIBEL!" posts. I think you operate a marked double standard, whereby you feel free to attribute all kinds of dishonest motivations to those who disagree with you, but react in horrified indignation if you perceive (often erroneously, IMO) a slur cast on you yourself, as in the case of Dawkins and Craig. There was no "blood libel" - Dawkins made the perfectly straightforward point that Craig regarded genocide as not evil if commanded by God. Ergo, Craig was condoning genocide, albeit in specific circumstances (although setting a dangerous precedent - didn't the 9/11 hijackers think that they were obeying God's commands?). He did not accuse all Christians of condoning genocide, and your response, was, IMO, a "rhetorical stratagem... that tr[ied] to manipulate by playing on misconceptions, perceptions and feelings". So no, it is not clear to me that you despise such "stratagems", merely that you despise those who, in your view, use them against yourself. Which, most of the time, IMO, they are not doing.
If you need it, here is my view as I picked up for myself and then learned was in Aristotle: arguments persuade by appeal to fact and logic, to authority, or to emotions. Of these the LEAST persuasive, short term, is the only one that actually can warrant: facts and logic. But, long term this is the one that is decisive. Guess why I insist on going for facts and logic, and will point out the distractive, strawman distortion and ad hominem tactics that so often are used to object to design theory and thinkers. No prizes for guessing why. GEM of TKI
Except that your diagnostic capacity is unreliable, kf. You have made a logical error here. While all digital systems are discrete, not all discrete systems are digital. In DNA, there is nothing that "can take one of four states", as in a "base 4 digital" system. Rather, there are sequences made of permutations of four elements. This is not a "straw man distortion" of your argument, but a simple exposure of what seems to me to be a logical error on your part.Elizabeth Liddle
November 2, 2011
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Dr Bot: You have some fairly serious explaining to do on another thread.
No I don't. But I believe you do. I'm getting a bit fed up of the way you preach at and bully others simply because they disagree with you - and quite often people who have considerably more expertise than you. As for digital logic - it is quite clear that you failed to understand my point. The more I see your posts, riddled with grand claims backed up by no evidence and followed up by bullying attacks on others, the more I am inclined to think ... Dunning Kruger. Please put a sock in your uncivilized behavior and try treating others as you expect to be treated. (Except of course you seem to expect others to treat you as an infallible source of knowledge and truth, which is a bit of a problem considering you are so often wrong)DrBot
November 2, 2011
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Elizabeth Liddle:
But it remains highly misleading because what most people mean by “base 4 digital” is a positional numeric system,
That would be most people who have neither built machines from 2-state or 3-state devices, nor implemented logical operations as opposed to merely numeric, but have authored highly misleading wiki articles for people who can't tell the difference.Charles
November 2, 2011
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1.2.2.2.34 Elizabeth, That DNA is a code constitutes a scientific fact. 1. DNA carries instructions, consequently information. 2. This information can be represented by strings composed using an alphabet that consists of 4 letters. Not all strings defined on the 4-letter alphabet have an associated biological meaning. Similarly, not all strings of some given length using letters of the English or any other alphabet, have meaning. Nonetheless, the above considerations allow the scientific community to agree that DNA is a code. To dispute that seems really strange.Eugene S
November 2, 2011
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Dr Liddle: That digital MEANS discrete state is by no means idiosyncratic. As even so humble a source as Wikipedia will verify, it is the standard technical usage, for reasons as already identified. And it seems I need to make a point clear: a 4- discrete- state per- digit string- structure. Digital string systems do not always change states, indeed ROM (read only memory) is set up precisely NOT to change state but as reference information pre-loaded into the system, and that is what DNA is. All the peculiarities that you may look at are things that make DNA a particular kind of digital entity, they do not affect the basic empirical fact that it is a discrete-state (thus, digital) info-storing entity. Just as, had it been more like a cam, it would have been an analogue info storing entity. GEM of TKIkairosfocus
November 2, 2011
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Elizabeth Liddle:
Please define the “RNA ‘digit’” that can take “four allowed ‘states’”?
My exact words were:
where its value is any of the possible states allowed by the system upon which the string is built. ... and similary adenine uracil guanine and cytosine are the four allowed “states” of an RNA “digit”
"possibly allowed" does equate to having "take[n][all] "four states". Not all permutations exist. But the absence of some permutations does not change the fact that each permutation consists of not more than four possible states. But the answer you need is the “RNA ‘digit’” which can take [one of the] “four allowed ‘states’” would be one half of a base-pair. Each RNA "digit" is paired with another RNA "digit" to form a base-pair and base-pairs are strung together in strands, strands strung together in kilobase pairs,... etc.
Um, no you didn’t. And it’s absolutely critical.
Yes I did. And it's absolutely critical that you stop ignoring the answers you've been given. That is intellectual dishonesty. If you don't understand, then ask. But stop presuming you know what you're bloviating about. You don't.
If you want to claim that a system is in “base 4 digital” then please provide a definition of “base 4 digital” that doesn’t refer to a positional numeral system.
Data processing systems employ logical operators (AND, OR, XOR, Compare, shift, copy, etc.) as well as mathematical. A base-four system merely does this with strings wherein each element (bit or digit) is in 1 of 4 possible states. That in RNA, strings are not found reflecting all possible permutations in no way changes the irrefutable fact that any position will never have anything other than either adenine uracil guanine or cytosine; regardless of the operation, the allowed values of each position will always be adenine uracil guanine or cytosine. The example I gave, which in your inexperience you twice now have failed to comprehend is content addressable memory. Present memory architectures mostly use two-state address-selected memory with many special applications that use content addressable instead. These same operations have been repeated in tri-state systems. To my knowledge, no one has attempted a 4-state processing system because there are no 4-state devices and regardless the practical limitations on adoption preclude any benefit. But as I mentioned, the operation by which strings of base-pairs are somehow compared and matched, taking note of markers denoting coding vs non-coding regions is essentially a 4-state content-addressing mechanism: The content is found and its address (endpoints) is subsequently used for "unzipping" and encoding (or not).
I’m using something that at least finds support in wiki. Where is yours?
You could interpolate from the same article. It lists commonly used numeral systems and gives examples of base-8 and base-16, albeit the implementations are all on binary base-2 machines. But a base-4 numeral system would have values "0, 1, 2, 3" as its four allowed states. A base-4 RNA system has adenine uracil guanine or cytosine as its four allowed states. But again, as RNA is not a machine which employes math and all abstract permutations of numbers, as RNA employs logical operators similar to comparison and XOR and is not an abstract system, you should not expect to find all permutations of adenine uracil guanine or cytosine. Just because you found the subject matter you sought doesn't equate to having sought the applicable subject matter. kairosfocus has already, ad nauseum, provided you with cites defining four-state systems.Charles
November 2, 2011
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kairosfocus:
the chemical structure essentially defining a 4-state discrete state per digit string structure.
Per what? This is the problem! There isn't anything to put in that place! Nothing "changes state" so nothing can take "one of four states". And unless something can take "one of four states" you don't have a "base 4 digital" system!!! That's why you and Charles are having difficulty in articulating what it is that changes state!Elizabeth Liddle
November 2, 2011
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Dr Liddle: Pardon, but you are dancing wrong but strong. By pretty direct inspection, we can easily see that DNA is a string structure, using the Sugar-phosphate backbone. In each position, A, G, C, or T/U (for RNA) can fit. Each of these matches to its partner monomer base in a tRNA anticodon or the complementary DNA strand, etc. 4-states per place or digit, discrete state so digital. And that is why it is commonplace to talk about the DNA or Genetic CODE. GEM of TKI
In other words you are saying that "discrete" and "digital" are synonyms. They aren't, in normal English usage. But if we accept your idiosyncratic usage, then sure, if by "digital" you mean "discrete" then DNA, like any molecule, is "digital". And if by "base 4" you mean that "four different elements are permuted in the sequence" then, sure, it's "base 4 digital". In other words, if you redefine both "digital" and "base N" to mean something other than what they normally mean, your claim can be correct. But it remains highly misleading because what most people mean by "base 4 digital" is a positional numeric system, which DNA isn't, or some kind of discrete state-changing system, which it is at gene level (binary), but not at base-pair level. And are you going to take back your implication that my position on this an attempt to deny that cells are "digital" because I fear the ID implications? Because I've made this request several times now. It is completely irrelevant to whether you think I am wrong about base 4 or not.Elizabeth Liddle
November 2, 2011
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Dunsinane:
I think I get the idea now. If we imagine a DNA “variable”, the basic operators we can use on an integer (+, -, /, *, less then, greater than etc.) wouldn’t apply, neither would bitwise operators (|, &). The operations on the variable would be like operations on an array. That is an important point, but it doesn’t mean it’s not base 4. It just means we can’t use arithmetic.
OK, thanks. Well, I guess it all comes down to how we define "base N" systems then :) It's certainly a 4 element system. I just don't see a radix there, so I think describing it as "base 4 digital" is misleading, and certainly building any kind of case on it being "base 4 digital" is building it on sand IMO. But I'll wait and see of Charles (or someone) can come up with a reasonably widely recognised definition of "base N digital" that covers DNA ;) The ones I'm familiar with don't.Elizabeth Liddle
November 2, 2011
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And BTW designing agencies, successsful designing agencies anyway, usually do have the capability to design what it is they are designing.Joseph
November 2, 2011
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All we know about the designers of Stonehenge we got from studying the evidence left behind.
Er…no. We already had considerable knowledge of human capabilities, evidence of local human habitation, previous examples of human stone monument building, etc. that all helped determine Stonehenge was made by humans.
You just confirmed what I said...Joseph
November 2, 2011
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GinoB, We did not know humans designed and built it until we studied what was left behind. And even then we knew they were capable of bulding Stonehenge because, ummm, Stonehenge exists. If Stonehenge didn't exist we wouldn't infer the people of that age had those capabilities- the capabilities to build such a structure. It is as simple as you are. BTW there aren't any previous stone structures like Stonehenge- so your "reference" is misleading at best. The point is an always has been that in the absence of direct observation or designer input, the only possible way to make any determination about the designer(s) or the specific process(es), is by studying the design in question. Saying "humans didit" is as "useless" as saying some unknown agency did it- at least we know an agency did it and we go from there. So we know what the capabilities of the designer(s) and builders were because they left stuff behind for us to examine. It is just unbelievable that you don't understand that.Joseph
November 2, 2011
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Dr Liddle: Pardon, but you are dancing wrong but strong. By pretty direct inspection, we can easily see that DNA is a string structure, using the Sugar-phosphate backbone. In each position, A, G, C, or T/U (for RNA) can fit. Each of these matches to its partner monomer base in a tRNA anticodon or the complementary DNA strand, etc. 4-states per place or digit, discrete state so digital. And that is why it is commonplace to talk about the DNA or Genetic CODE. GEM of TKIkairosfocus
November 2, 2011
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Dr Bot: You have some fairly serious explaining to do on another thread. Be that as it may, I will note here that electronic logic gates generally speaking -- let's leave off Emitter Coupled Logic, a special case formerly used to get out of problems of saturation and cutoff to gain speed -- are amps run between cutoff and saturation, usually with defined thresholds for high and low. The defined ststes and trheholds are what make them digital, for info processing purposes. Those of us who have had to deal with designs, often know that analogue problems can bleed over into the systems. let's just say that I once had a ckt that insisted that a Ceramic disk capacitor could not do power supply glitch decoupling, only Silvered Mica -- about 100 times as expensive -- would do. Well, it was a one off situation, and I saved time; which was more valuable. A USD 2.00 Silvered mica got soldered in. Never mind the sack of 1,000 otherwise perfectly good Cer disks sitting next to me that came in at about 1 c each. Electronic logic systems are BOTH analogue and digital, with the Analogue usually being responsible for the subtler design headaches. Cam bars use smooth follower mechanisms, and Yale locks seem to use essentially infinitely variable 2-part, spring-loaded pins along a cylinder to line up a shear line. That's a threshold, but the way you get there is at least potentially infinitely variable, though I suspect a lot of locks get built by having three pin positions for the key's teeth: high, mid and low. (DNA is similar, but uses a length-match between the two different pairs of bases, the chemical structure essentially defining a 4-state discrete state per digit string structure.) GEM of TKIkairosfocus
November 2, 2011
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Elizabeth Liddle:
A “string of digits” is a string. The elements of a string are not digits (though they may be alphanumeric).
Wrong. Each element of a string is a “digit” where its value is any of the possible states allowed by the system upon which the string is built. In the case of binary systems that is any of two states “up down”, “on off” “0 1?; in trinary systems “up flat down”, “0 1 2?; and similary adenine uracil guanine and cytosine are the four allowed “states” of an RNA “digit”
Please define the "RNA 'digit'" that can take "four allowed 'states'"? Adenine can't take the state of "guanine", can it? So what is this mysterious "RNA 'digit'" that can take "four allowed 'states'"? It is because there is no coherent answer to that question that DNA/RNA is not a "digital" system. In a digital system there are a finite number positions that are always in one state or another. There are is no such finite set of "positions" in a polynucleotide, because sequences are not altered by changing the "state" of positions" (except in the case of single nucleotide substitutions) but by insertion, deletion, duplication - oh, and recombination - all of which move the "positions" around. In other words "position" is an irrelevant concept, and thus there is no "position" that can take one of "four allowed states".
DNA is not a positional numeral system.
As I already stipulated, but you knew that and yet blew right past it.
Yes, you appeared to stipulate it! Which makes your position all the more bizarre. If you agree that DNA is not a positional numeral system, then in what sense is it in "digital base 4"?
Please let me have a definition for “base 4 digital” that refers to systems other than positional numeral systems, or, alternatively, define “position” for me in the context of a DNA base pair, with reference to the examples I gave in 1.2.2.2.2.
Again I already explained that but either in intransigence or inexperience you blew right past that too.
Um, no you didn't. And it's absolutely critical. If you want to claim that a system is in "base 4 digital" then please provide a definition of "base 4 digital" that doesn't refer to a positional numeral system. If it's your own personal definition, that's fine, but then don't come on at me for "dishonesty". I'm using something that at least finds support in wiki. Where is yours?
I doubt if any symposium would accept a paper that made the perfectly obvious point that a system based on strings made up of permutations of four discrete units, and varied by deletion, insertion, duplication and substitution, is not a “base 4 digital” system.
I too doubt your paper would be accepted, because you would be confronted with refutations from reviewers of your premises and novel conceptual conflations.
Please provide your definition (with references) of "base 4 digital" or retract your allegations that mine is "novel".Elizabeth Liddle
November 2, 2011
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No, that is not true. It’s impossible to recognize conscious design without at least some external knowledge of the designer – its capabilities, the material resources it has available, knowledge of other designs it has done.
I challenge you to respond to the following: If we find what appears to be to some an ancient, abandoned alien space ship on an otherwise deserted and desolate planet, how would one go about establishing, as best explanation, that the object in question was probably designed and built by an intelligent alien species? Or are we committed by the definition of science to just keep tyring to find a natural explanation for the object?
ID makes the unwarranted assumption that all design must be like human design,
No, it doesn't; it rightfully limits its potential recognition of designed artifacts to those that are similar enough to human design parameters to be rigorously quantified as designed. Design theorists do not claim that that ID metrics can identify all artifacts of ID, only those that fall within the metric.
then attempts to match unknown items to known human-produced forms with a subjective superficial examination (“Looks designed to me!). This includes coming up with meaningless metrics for measuring complexity, like dFSCI.
Then please tell us how we can make a determination that the object in my example is best explained as being the artifact of some as-yet unknown alien intelligence?
Logically there is no difference between “that fluffy cloud looks like a choo-choo train, so it must be designed!” and “that flagella looks like an outboard motor, so it must be designed!”
Then, in your opinion, if we happen upon what appears to some to be an ancient alien artifact on some desolate world, there's simply no way to attempt to explain it except as naturally occurring artifacts? Unless you are going to claim that human ID is supernatural or unique, there is no scientific difference in examining the effects of vulcanism or erosion on Earth, and then matching those characteristic features with features on other planets and theorizing that non-terrestrial vulcanism and erosion might be responsible for those featurs, and finding the telltale characteristics of human intelligent design and then using that category of characteristics to identify potential cases of non-human ID.William J Murray
November 2, 2011
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I think I get the idea now. If we imagine a DNA "variable", the basic operators we can use on an integer (+, -, /, *, less then, greater than etc.) wouldn't apply, neither would bitwise operators (|, &). The operations on the variable would be like operations on an array. That is an important point, but it doesn't mean it's not base 4. It just means we can't use arithmetic.Dunsinane
November 2, 2011
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Dr Liddle: Pardon, but the projection of a nefarious motive is out of order. Let's just say that any of my students over the many years who insisted on refusing to accept that a discrete state system is perforce a digital one would have demonstrated that s/he was unteachable. Such a student would be unable to understand an A/D converter or a D/A converter and why we use a low pass filter for the latter. Among many other problems. A better explanation, it seems, frankly, is that for whatever reason, some objectors tot he design inference, are refusing to acknowledge the discrete state thus digital nature of the information stored in DNA and processed using inter alia mRNA and ribosomes, because they would find it harder to make some of their preferred objections. Do you not see that if the key-lock DNA worked like a cam bar instead [i.e. was continuous state], that analogue info storage and processing would be info storage and processing, and it would be a simple matter of identifying the bit depth of the equivalent digital info, for analytical purposes? Indeed, have you not understood why it is that I compare Mt Rushmore and Old Man of the Mountain, Nefertiti and a wire-mesh of a dolphin? The analogue info in the facial portraits, is reducible to a nodes and arcs data structure, which can then be digitised to whatever degree of precision is required to process with adequate fidelity. In short, the issue analogue/digital is NOT a critical one to the question of inferring design. It is a simple matter of a key scientific value: being reasonable, well warranted and accurate in using concepts to analyse phenomena. DNA uses a string-structure, 4-stste digital storage system, which is processed step by step in ribosomes to make proteins, i.e is algorithmic. That is accurate description not crude or loose analogy. That this would be a sticking point, is telling on the balance of the case on the merits. And, if it is not clear to you by now that I despise rhetorical stratagems that try to manipulate by playing on misconceptions, perceptions and feelings, instead of taking on issues of fact, concept, assumptions/ premises and logic, with epistemology hovering in the background [even to the fault of being challengingly complex], something is wrong. If you need it, here is my view as I picked up for myself and then learned was in Aristotle: arguments persuade by appeal to fact and logic, to authority, or to emotions. Of these the LEAST persuasive, short term, is the only one that actually can warrant: facts and logic. But, long term this is the one that is decisive. Guess why I insist on going for facts and logic, and will point out the distractive, strawman distortion and ad hominem tactics that so often are used to object to design theory and thinkers. No prizes for guessing why. GEM of TKIkairosfocus
November 2, 2011
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