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Logic & first principles, 1: Analogy, Induction and the power of the principle of identity (with application to the genetic code)


One of the commonest objections we meet when we discuss design inferences — especially concerning the genetic code, is that a claim is “just an analogy” (with implied conclusion that analogies are weak or fallacious). This then extends to inductive arguments used. This common error must be corrected and (as will be shown) the principle of distinct identity helps us to do so.

Before we show that, let us pause to note from the Stanford Enc of Phil, just to counter-weight the tendency of many objectors to be quickly dismissive of anything said by “one of those IDiots” without bothering to actually address the substantial issue at stake:

>>An analogy is a comparison between two objects, or systems of objects, that highlights respects in which they are thought to be similar. Analogical reasoning is any type of thinking that relies upon an analogy. An analogical argument is an explicit representation of a form of analogical reasoning that cites accepted similarities between two systems to support the conclusion that some further similarity exists. In general (but not always), such arguments belong in the category of inductive reasoning, since their conclusions do not follow with certainty but are only supported with varying degrees of strength. Here, ‘inductive reasoning’ is used in a broad sense that includes all inferential processes that “expand knowledge in the face of uncertainty” (Holland et al. 1986: 1), including abductive inference.

Analogical reasoning is fundamental to human thought and, arguably, to some nonhuman animals as well. Historically, analogical reasoning has played an important, but sometimes mysterious, role in a wide range of problem-solving contexts. The explicit use of analogical arguments, since antiquity, has been a distinctive feature of scientific, philosophical and legal reasoning. This article focuses primarily on the nature, evaluation and justification of analogical arguments. Related topics include metaphor, models in science, and precedent and analogy in legal reasoning . . . >>

Notice, analogical reasoning “is fundamental to human thought” and analogical arguments reason from certain material and acknowledged similarities (say, g1, g2 . . . gn) between objects of interest, say P and Q to further similarities gp, gp+1 . . . gp+k. Also, observe that analogical argument is here a form of inductive reasoning in the modern sense; by which evidence supports and at critical mass warrants a conclusion as knowledge, but does not entail it with logical necessity.

How can this ever work reliably?

By being an application of  the principle of identity.

Where, a given thing, P, is itself in light of core defining characteristics. Where that distinctiveness also embraces commonalities. That is, we see that if P and Q come from a common genus or archetype G, they will share certain common characteristics that belong to entities of type G. Indeed, in computing we here speak of inheritance. Men, mice and whales are all mammals and nurture their young with milk, also being warm-blooded etc. Some mammals lay eggs and some are marsupials, but all are vertebrates, as are fish. Fish and guava trees are based on cells and cells use a common genetic code that has about two dozen dialects. All of these are contingent embodied beings, and are part of a common physical cosmos.

This at once points to how an analogy can be strong (or weak).

For, if G has in it common characteristics {g1, g2 . . . gn, | gp, gp+1 . . . gp+k} then if P and Q instantiate G, despite unique differences they must have to be distinct objects, we can reasonably infer that they will both have the onward characteristics gp, gp+1 . . . gp+k. Of course, this is not a deductive demonstration, at first level it is an invitation to explore and test until we are reasonably, responsibly confident that the inference is reliable. That is the sense in which Darwin reasoned from artificial selection by breeding to natural selection. It works, the onward debate is the limits of selection.

With this in mind, we can take a fresh approach to looking at the implications of the genetic code:

The Genetic Code in action


Where also:

The Genetic code uses three-letter codons to specify the sequence of AA’s in proteins and specifying start/stop, and using six bits per AA

So that:

Protein Synthesis (HT: Wiki Media)

Where we may see, with Yockey, the wider communication system involved:

Yockey’s analysis of protein synthesis as a code-based communication process

Comparing, a version of Shannon’s archetype:

A communication system

. . . and reckoning with the possibility of layering of protocols:

Now, many codes are based on s-t-r-i-n-g data structures (which are foundational to data structures in computing), in which elements from an alphabet are chained to create unique words and messages which are then integrated into a meaningful framework that describes or states or instructs. Text in English and computer code are classic examples. Where, too, such are in fact manifestations of language (and intelligence).

Thus, we see, famously, from Crick in his March 19, 1953 letter to his son Michael, on p. 5:

Crick’s letter

What is the challenge, here?

Simple: the genetic code is at the heart of the cell’s functionality, and is thus antecedent to and an enabling causal factor for cell based life. That code implies a code/protocol based communication system (as Yockey expands) and is inherently linguistic. Language is a characteristic of intelligence and so we manifestly have an epistemic right to infer from the DNA code to intelligence and design as causal to cell based life.

Dismissive arguments on analogy notwithstanding. END

KF, Good OP. PavelU sounds like a professional “bluff” seller. I’d rather ignore his vacuous comments. They lack substance. jawa
Good work, KF. StephenB
KF: Very good article, thank you! :) gpuccio
AS, begging the question and imposing an ideology all dressed up in a lab coat. KF kairosfocus
KF remember the first law of Darwinian evolution “the appearance of design in nature is an illusion” Therefore any attempt that you make to justify your point of view is rebuttled by the fact that you are stuck in the illusion. It always bothers me that you have to except that, why do I have to except the appearance of design in nature is an illusion? As I feel that the statement itself is an opinion to begin with, simply to support Darwinism AaronS1978
Wikipedia, testifying against interest: >>In communications and information processing, code is a system of rules to convert information—such as a letter, word, sound, image, or gesture—into another form or representation, sometimes shortened or secret, for communication through a communication channel or storage in a storage medium. An early example is the invention of language, which enabled a person, through speech, to communicate what he or she saw, heard, felt, or thought to others. But speech limits the range of communication to the distance a voice can carry, and limits the audience to those present when the speech is uttered. The invention of writing, which converted spoken language into visual symbols, extended the range of communication across space and time. The process of encoding converts information from a source into symbols for communication or storage. Decoding is the reverse process, converting code symbols back into a form that the recipient understand, such as English or Spanish. One reason for coding is to enable communication in places where ordinary plain language, spoken or written, is difficult or impossible. For example, semaphore, where the configuration of flags held by a signaler or the arms of a semaphore tower encodes parts of the message, typically individual letters and numbers. Another person standing a great distance away can interpret the flags and reproduce the words sent. >> >>Genetic code Main article: Genetic code Biological organisms contain genetic material that is used to control their function and development. This is DNA, which contains units named genes from which messenger RNA is derived. This in turn produces proteins through a genetic code in which a series of triplets (codons) of four possible nucleotides can be translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein molecule; a type of codon called a stop codon signals the end of the sequence. >> KF kairosfocus
Merriam-Webster: >> Definition of code (Entry 1 of 2) 1 : a systematic statement of a body of law especially : one given statutory force 2 : a system of principles or rules moral code 3a : a system of signals or symbols for communication b : a system of symbols (such as letters or numbers) used to represent assigned and often secret meanings c : coded language : a word or phrase chosen in place of another word or phrase in order to communicate an attitude or meaning without stating it explicitly The strategy also appealed to blue-collar workers in the Northeast and Northwest who were opposed to "forced bussing." This was expressed in code as favoring "law and order" and opposing "crime in the streets."— Elizabeth Drew —usually used with for I hear the word "development" a lot in public speech; politicians and activists use it as code for a lot of things—jobs, health care, a change in leadership.— Sallie TisdaleThis quarter-century of Republican momentum was reversed finally by Bill Clinton, who called himself a "New Democrat," code for "not a liberal."— Joshua Muravchik 4 : genetic code 5 : instructions for a computer (as within a piece of software) writing code for a new app>> KF kairosfocus
The term “genetic code” is misleading, because it’s not a code really. I'm interested in hearing your thoughts on how we decide whether the genetic code is a code. First, it's called, the genetic code. Lots of people think it's a code. People who deny it's a code appear to be fringe cases, very much in the minority. If we appeal to definitions, which definitions of "code" are we willing to take seriously?
PPPS: This discussion on whether the genetic code is indeed a code will also be helpful as background: https://uncommondesc.wpengine.com/intelligent-design/is-the-genetic-code-a-real-code/ It is helpful to clip Chaitin in his life as software talk as cited by VJT:
. . . the point is that now there is a well-known analogy between the software in the natural world and the software that we create in technology. But what I’m saying is, it’s not just an analogy. You can actually take advantage of that, to develop a mathematical theory of biology, at some fundamental level… Here’s basically the idea. We all know about computer programming languages, and they’re relatively recent, right? Fifty or sixty years, maybe, I don’t know. So … this is artificial digital software – artificial because it’s man-made: we came up with it. Now there is natural digital software, meanwhile, … by which I mean DNA, and this is much, much older – three or four billion years. And the interesting thing about this software is that it’s been there all along, in every cell, in every living being on this planet, except that we didn’t realize that … there was software there until we invented software on our own, and after that, we could see that we were surrounded by software… So this is the main idea, I think: I’m sort of postulating that DNA is a universal programming language. I see no reason to suppose that it’s less powerful than that. So it’s sort of a shocking thing that we have this very very old software around… So here’s the way I’m looking at biology now, in this viewpoint. Life is evolving software . . .
Observe, how analogy comes up (it is fundamental to how we think), leading to the recognition that we see current technology as reflecting an archetype, which -- lo and behold -- was long since instantiated in the living cell. This takes us back to my OP's focus, how analogies and inductive arguments work when they are cogent rather than weak, fallacious or ad hoc. kairosfocus
PPS: The molecular challenge faced by onward blind watchmaker macro-evolution is discussed here at UD: https://uncommondesc.wpengine.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/ kairosfocus
PS: PU, in addition, there is a problem with the process logic. By definition, evolution requires reproducing, competing populations that show differential reproductive success. In turn, that requires metabolism to ingest and process materials to prepare for replication; requiring sets of protein based machines that are coded for genetically. Replication itself requires genetic coded information. So, there is a pull oneself up by one's bootstraps problem. Speculative prebiotic genes first and metabolism first models are highly speculative, lack actual empirical observation and fail to account for tightly integrated, complex systems using highly informational molecules. Those molecules are highly endothermic and prone to disruption in an uncontrolled environment, pointing to encapsulation and smart gating. That points back to the proteins and genetic machinery required for such encapsulation. Then, in a prebiotic environment, chemicals would come in racemic forms and this would wreak havoc with the fold-to-fit-and-function key-lock fit geometry at work. Spontaneous generation of such systems is appeal to probabilistic miracle, in short. kairosfocus
PU, that literature turns out to be speculation, little more than just-so stories dressed up in lab coats. And so far, what you have done is to hurl an elephant, i.e. make a rhetorical bluff. Time to call it. If you have spontaneous origin of codes, algorithms and execution machines empirically actually observed (without undue experimenter interference) you have something to say; just tell us who won the Nobel Prizes for the experiments. I will not hold my breath waiting. Meanwhile, we have abundant observations of such systems coming about by engineering and we know how codes come about by design also. There are whole industries that show this, including those that engineer genes. KF kairosfocus
Not long ago one of your readers posted in another discussion a comment with a list of recent research papers that strongly support the argument for natural origin and evolution of that what you mistakenly call "genetic code". No counterargument was posted as far as I recall. PavelU
Pavel Generally speaking, where one thing represents another by some rules we recognize the code. Would you give a link to one of the "abundant literature" articles? Eugen
PU, because you say so? Because FYI, because you can identify a physical layer in a comms sys does not reduce higher layers to that one. Crick, from the outset said different, as can be seen above in his handwriting. FYI, you are looking at [1] a machine language, [2] four state per element [3] string data structure that [5] lays out algorithms for [6] assembling proteins, through [7] the work of molecular nanomachines operating as parts of [8] an encapsulated, smart gated metabolising, self-replicating automaton. I can show empirical warrant for 1 - 8, which abundantly vindicates the point that we are dealing with codes, purpose (algorithms are goal-directed), thus language and planning. As for claimed evolutionary narratives they consistently turn out to be highly speculative and ideologically framed by institutionally imposed a priori materialism and/or fellow traveller movements. What would be required is to demonstrate empirically how some Darwin's pond or the like spontaneously throws up something closely parallel, without undue experimenter interference. Which is a looooong way off. We can readily speak of intelligent engineering of genes, something that is now more or less commonplace though at a relatively primitive level compared to what we see in the living cell. KF kairosfocus
The term "genetic code" is misleading, because it's not a code really. It just looks like a code. There's abundant literature out there explaining with much detail the evolutionary origin of that "code" that makes the ID crowd so excited. It's all pure chemistry and physics. Perhaps there are few areas still missing some details in the explanations. Those are the gaps the ID party uses to support their baseless arguments. PavelU
Great article Kairos I doubt our evolutionist readers will say much about it but it's good to remind them from time to time. I'm reading recently about spliceosome, that seems to be the most complex cellular machine as far as I can tell. Eugen
Logic & first principles: Analogy, Induction and the power of the principle of identity (with application to the genetic code) kairosfocus

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