New distinctions help accommodate researchers to the usefulness of “junk DNA”

_{Denyse O'Leary

July 21, 2022

'Junk DNA', Intelligent Design}

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Abstract: It is often thought that non-junk or coding DNA is more significant than other cellular elements, including so-called junk DNA. This is for two main reasons: (1) because coding DNA is often targeted by historical or current selection, it is considered functionally special and (2) because its mode of action is uniquely specific amongst the other actual difference makers in the cell, it is considered causally special. Here, we challenge both these presumptions. With respect to function, we argue that there is previously unappreciated reason to think that junk DNA is significant, since it can alter the cellular environment, and those alterations can influence how organism-level selection operates. With respect to causality, we argue that there is again reason to think that junk DNA is significant, since it too (like coding DNA) is remarkably causally specific (in Waters’, in J Philos 104:551–579, 2007 sense). As a result, something is missing from the received view of significance in molecular biology—a view which emphasizes specificity and neglects something we term ‘reach’. With the special case of junk DNA in mind, we explore how to model and understand the causal specificity, reach, and corresponding efficacy of difference makers in biology. The account contains implications for how evolution shapes the genome, as well as advances our understanding of multi-level selection.
Havstad, J.C., Palazzo, A.F. Not functional yet a difference maker: junk DNA as a case study. Biol Philos 37, 29 (2022). https://doi.org/10.1007/s10539-022-09854-1 The paper requires a fee or subscription.

At least this group, unlike evolutionary biologist Dan Graur, is willing to “do politeness” on the topic.

You may also wish to read: Jumping genes … a new clue to octopus intelligence? Despite being very different, the human brain and the octopus brain share the same sort of jumping genes. Formerly thought of as “junk DNA,” their mobility may help explain unique problem-solving abilities. “I literally jumped on the chair…” one researcher said.

Comments

Sev states: "You may also want to look at an extensive series of posts on “The Function Wars” on Laurence Moran’s blog Sandwalk" And what possible 'function wars' could Moran possibly be talking about? Is it the 'war' that Darwinian processes have in explaining the origin of even a single 'functional' protein fold?,,,
Estimating the prevalence of protein sequences adopting functional enzyme folds - Douglas D Axe Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences. https://pubmed.ncbi.nlm.nih.gov/15321723/
,, Or is it the 'war' that Darwinists have with any teleological language that implies purpose, and/or function, in the first place?,,,
tel·e·ol·o·gy noun PHILOSOPHY the explanation of phenomena in terms of the purpose they serve rather than of the cause by which they arise. THEOLOGY the doctrine of design and purpose in the material world. “Teleology is like a mistress to a biologist: he cannot live without her but he’s unwilling to be seen with her in public.” - J. B. S. Haldane
Darwinists, although they deny that life is teleological, (goal oriented purpose and/or function), simply can't stop using words that directly imply teleology, i.e. purpose, and/or function. As the following article points out, “teleological concepts cannot be abstracted away from biological explanations without loss of meaning and explanatory power, life is inherently teleological.”
Metaphor and Meaning in the Teleological Language of Biology Annie L. Crawford – August 2020 Abstract: Excerpt: However, most discussions regarding the legitimacy of teleological language in biology fail to consider the nature of language itself. Since conceptual language is intrinsically metaphorical, teleological language can be dismissed as decorative if and only if it can be replaced with alternative metaphors without loss of essential meaning. I conclude that, since teleological concepts cannot be abstracted away from biological explanations without loss of meaning and explanatory power, life is inherently teleological. https://uncommondescent.com/philosophy/biologists-cant-stop-using-purpose-driven-language-because-life-really-is-designed/
In other words, the very words that Darwinists are forced to use when they are doing their research falsifies Darwinian evolution. As Stephen Talbott points out, it is impossible to describe the complexities of biological life without illegitimately using language that avoids all implication of agency, cognition, and purposiveness (i.e. teleology). Talbott even challenges readers to “take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness 1.”
The ‘Mental Cell’: Let’s Loosen Up Biological Thinking! – Stephen L. Talbott – September 9, 2014 Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”. Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness 1. One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself. http://natureinstitute.org/txt/st/org/comm/ar/2014/mental_cell_23.htm
Denis Noble also states that “it is virtually impossible to speak of living beings for any length of time without using teleological and normative language”.
“the most striking thing about living things, in comparison with non-living systems, is their teleological organization—meaning the way in which all of the local physical and chemical interactions cohere in such a way as to maintain the overall system in existence. Moreover, it is virtually impossible to speak of living beings for any length of time without using teleological and normative language—words like “goal,” “purpose,” “meaning,” “correct/incorrect,” “success/failure,” etc.” – Denis Noble – Emeritus Professor of Cardiovascular Physiology in the Department of Physiology, Anatomy, and Genetics of the Medical Sciences Division of the University of Oxford. http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/
This working biologist agrees with Talbott and Noble’s assessment and states, “in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology–we simply cannot avoid them.”
Life, Purpose, Mind: Where the Machine Metaphor Fails – Ann Gauger – June 2011 Excerpt: I’m a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, ,,, I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology–we simply cannot avoid them. Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn’t troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another. But for those who will consider the evidence that is so obvious throughout biology, I suggest it’s high time we moved on." – Matthew http://www.evolutionnews.org/2011/06/life_purpose_mind_where_the_ma046991.html#comment-8858161
Again, and to emphasize the point, the very words that Darwinists themselves are forced to use when they are doing their biological research, and writing their papers, falsifies Darwinian evolution and validates Intelligent Design: Verse:
Matthew 12:37 For by your words you will be acquitted, and by your words you will be condemned.”
bornagain77_{July 22, 2022
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Couldn't think of anything to say yourself? Sev? Two points, 1. The authors have down-played “junk” to “so-called junk” 2. They argue that it is “causally specific” - and accordingly hint a case for giving it a proper name or classification. This tactic is described as “Glenties” whereby after realisation of a blunder a series of small steps brings the perpetrators of the blunder in a circle around to the opposite position.Belfast_{July 21, 2022
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You may also want to look at an extensive series of posts on "The Function Wars" on Laurence Moran's blog SandwalkSeversky_{July 21, 2022
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