Protein Synthesis . . . what frequent objector AF cannot acknowledge

AF, pardon but you are in obvious self referential denial of patent reality, reflecting no concession hyperskeptical dismissiveness that refutes itself. Your objections are typed by you in English, are effectively, ASCII coded meaningful English text. This is a classic example of Orgel-Wicken functionally specific, complex organisation and/or associated information [FSCO/I] and so too, complex, specified information, CSI, per the NFL p. 144 definition and context that were cited in 105 above. Likewise, we point to computer files with sizes in bits and bytes as ubiquitous examples showing actual quantification, contrary to and exposing your zero concession denialism. A basic reality is, what actually exists such as squares and circles must be coherent in core attributes as opposed to what is impossible of being such as a Euclidean plane square circle. You yourself provide actual cases, FSCO/I is demonstrably real despite your attempts to deny and dismiss. And, ostensive definition by pointing to typical examples and family resemblance, is a valid form of definition, in fact it is antecedent to precising definitions that try to refine the precision of borders of a concept -- how else would we recognise yes the precising statement accurately and reliably says in/out, we trust it. Whatever critics you refer to try to say, whatever errors of discussion Dembski may make, the basic reality is patent and was discussed by Orgel, Wicken and Thaxton 10 - 20 years before WmAD came on the scene. Indeed, it is obvious his thinking is closely connected to ideas in statistical thermodynamics about clusters of microstates and relative statistical weight. This situation of your unjustified denial, therefore is similar to your attempted denial that D/RNA has in it complex, coded algorithms for AA chaining towards proteins. Similarly, with evidence on the table as above, you dismiss and hurl the elephant. Such, also fails. KF kairosfocus

...everyone in the world knows CSI is coherent.

Most people in the world have never heard of CSI nor will they. The few that have given Dembski's CSI time if day divide into two camps. Those, like you and KF, who think CSI is coherent but are unable to show how. Those, like Joe Felsenstein, Jason Rosenhouse and Tom English who argue cogently with supporting evidence, who understand CSI is not a useful concept and certainly not quantifiable. Alan Fox

Jerry, Jerry, Jerry, Do you ever read back to yourself what you have written. You refuse to look at any evidence because you already know there isn't any. That's, well (forgive me) pretty insane. Alan Fox

You simply refuse to look at any evidence showing how CSI is not coherent

But it doesn’t exist. How can someone consider evidence when no one has found any? Your argument is that someone won’t look at nonsense, therefore nonsense exists and is thus, true. Aside: everyone in the world knows CSI is coherent. Every time they speak or write they are endorsing it. jerry

F/N: Some specific values for proteins as put on the table a decade ago:

Using Durston’s Fits values -- functionally specific bits -- from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold: RecA: 242 AA [ --> 6 bits per character capacity for codons, 4.32 for 20 state elements], 832 fits, Chi: 332 bits beyond SecY: 342 AA, 688 fits, Chi: 188 bits beyond Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond

Yes, a decade ago. Meanwhile, of course, toxic distractions notwithstanding, AF et al are unable to show how blind chance and/or mechanical necessity on actual observation give rise to complex coded algorithmic information as we find in D/RNA in the cell. KF kairosfocus

F/N: On style guides https://en.wikipedia.org/wiki/APA_style kairosfocus

AF, as you should acknowledge but predictably will not, complex specified information, CSI, is a generalisation of the Orgel-Wicken FSC[O/]I. FYI, I insert square brackets in follow up to 101 above, where I drew out why I can freely add organisation. Furthermore, such FSCO/I is a matter of readily made observation. The distinction between texts in English in this thread, typical random gibberish drgtjrhjrqa56ui57 and repeated blocks sdsdsdsdsd is manifest. What is further clear is that some lotteries are winnable as they are within available search resources, others are beyond that and that is why Dembski used a 500 bit threshold. As I think that is a bit short for the cosmos as a whole, I specify that to the sol system, our effective universe for atomic interactions and go to 1,000 bits for the observed cosmos. It is not plausible that blind chance and/or mechanical necessity could produce functionally specific text beyond these thresholds. And, manifestly, no case has been observed. I add, and given description languages, discussion on text strings is WLOG. By intelligently directed configuration, routinely, we see cases well beyond, cumulatively, trillions. As for "incoherent" a fact of observation is not possibly incoherent within itself or with the rest of reality. What is obviously happening is facts of observation are being willfully, hyperskeptically, ideologically denied. KF PS, for record, here is Dembski, and of course I have annotated, making sure to use square brackets etc to denote captioning, clarification and the like, including where I gave an exact quote:

[CONCEPT: NFL, p. 148:] “The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology. I submit that what they have in mind is specified complexity [--> cf. p 144 as cited below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . . Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. . . . In virtue of their function [a living organism's subsystems] embody patterns [--> of organisation] that are objectively given [= observable] and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways

[--> through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole. Dembski cites: Wouters, p. 148: "globally in terms of the viability of whole organisms," Behe, p. 148: "minimal function of biochemical systems," Dawkins, pp. 148 - 9: "Complicated things have some quality, specifiable in advance, that is highly unlikely to have been acquired by ran-| dom chance alone. [--> the pipe character FYI denotes a fresh page, dom begins p 149] In the case of living things, the quality that is specified in advance is . . . the ability to propagate genes in reproduction." On p. 149, he roughly cites Orgel's famous remark on specified complexity from 1973, which exactly cited reads: " In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . ." And, p. 149, he highlights Paul Davis in The Fifth Miracle: "Living organisms are mysterious not for their complexity per se, but for their tightly specified complexity."] . . .”

[DEFINITION: p. 144:] [Specified complexity can be more formally defined:] “. . . since a universal probability bound of 1 [chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [the cluster] (T, E) constitutes CSI because T [effectively the target hot zone in the field of possibilities] subsumes E [effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ”

Notice, he explicitly highlights functionality for the biological world. At this point, I no longer expect participants in the voyage of folly mutiny on the good ship academy to be remotely responsible in their mad dash to sail the ship as they please, ignoring the arts of navigation. kairosfocus

AF, stop your policy of false accusation. It simply further exposes you as confessing by projecting. Your attempt to imply that a clearly delineated comment note is suggested to be a part of a citation is irresponsible and blatantly false accusation. You are an educated person and you know better, this is worse than your earlier attempt to pretend that ellipsis is immediately suggestive of out of context twisted citation or misquoting, which was proved false. BTW, that is part of why in the above, on the stele vs DNA, the caption is part of the image. As for, a disciplinary intervention for cause and which is duly annotated is dishonest that simply exposes your lawlessness. The obvious conclusion is you have lost on the merits and are fishing for banning under your latest incarnation, which, predictably, you will claim is censorship. The pattern of irresponsible hostile commentary is clear. KF PS, I again cite Lehninger and heirs, with annotations so the serious person can see for himself what the truth is:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

Notice, a pair of square brackets that begins with an abbreviated citation. That is a caption of sorts that gives source and date as a published document. But authorship here is complicated. This caption therefore then notes further on complexity of authorship, from the second edn 1986 on to this 8th, the actual authorship has passed to literary heirs as Lehninger passed on. At this point, it is obvious that this is not the authors speaking it is citation and commentary, the source of which is obvious from the context of a comment or online post etc. The onward part of the caption is an obvious -- yes, obvious -- note. I even went so far as to add quote marks to the blockquote, and the quote is italicised and bolded in key parts. The quote and emphasis end just before the reference and comment in square brackets begin. The number of cues distinguishing the cite from caption and comment is beyond the call of academic duty. The accusation is not only baseless, it is in the direct teeth of all sorts of evidence to the contrary. I have also sometimes used square brackets, typically with an arrow and if long with further indentation, to comment on key aspects of a citation. Typically a source or link is present so the source itself can be followed up. On rarer occasions I for example rearranged a classic Haldane remark as a skeletal form logical argument to make a point clear. When I did that I specifically, habitually noted what I did. Recently, when I cited Willard and his literary heirs, I used the device of a strike and a substitution of clearer language in the cite, as I am fairly sure Willard is hard to get hands on. I ended up buying the book twice, learning along the way limitations of licencing to use works issued in Kindle format. None of this can responsibly be called dishonest. You have simply further exposed yourself. I do not expect you to do the responsible thing, so I won't even mention it. kairosfocus

I already admonished KF for his dishonest post-editing of other people's comments. Now he's adding daft, misleading remarks into Lehninger that look like quotes. For shame.

We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.

These are your words, not found nor implied in Lehninger. For shame. [--> THREAD OWNER: See the immediately following comment where I correct for record a blatant false and irresponsible accusation based on twisting a remark within a caption into a claim that I falsely put words in the mouths of Lehninger and literary heirs. This annotation is a disciplinary measure in response to defamation. KF] Alan Fox

Oh dear, Jerry. You can't tell me how CSI works yet you assert it is "the same as KFs". You simply refuse to look at any evidence showing how CSI is not coherent. The blatant projection on your part would be disappointing if it mattered. Alan Fox

AF (attn Jerry et al), there is a fairly simple and yet pivotal reason I explicitly refer to functionally specific complex organisation and/or associated information, FSCO/I [as I have constantly explained when I use it for over a decade]. No, it is not that Orgel-Wicken speak to or imply information rich organisation to achieve function. No it isn't just that a watch or a gear or a fishing reel or an oil refinery, or the cellular process-flow metabolic network, or within that network tRNA or a protein or mRNA exhibit such organisation. It is that, as say Autocad exemplifies, description languages exist and demonstrate that a structured pattern of Y/N questions reduces functionally configured organisation to associated information. And manifestly, a structured string of Y/N, two state elements is automatically an information metric in binary . . . two state [Y/N] . . . digits, aka bits, here patently FUNCTIONAL bits, though of course one may make refinements to address redundancy etc, as has been done here at UD and elsewhere. That, too, has been explained many times and once recognised is undeniable and relevant. How easily and snidely these objectors ignore, side step and pretend not to notice that every comment I have ever made at UD links, through my handle, to a discussion that includes a discussion of information, entropy and information, and functional information. How easily they ignore a threshold metric that has actually been discussed here in recent months, that allows us to see how Dembski's 2005 metric reduces to functional information beyond a threshold. So, they superciliously set up and knock over a strawman. How readily, they forget that when Patrick May played at being Mathgrrl here at UD (and ultimately embarrassed himself), a discussion ensued and as an upshot of it I put up a simplified information beyond a threshold metric that uses a two binary state dummy variable to account for functional specificity,

. . . (b) as we can define and introduce a dummy variable for specificity, S, where (c) S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T: Chi = Ip*S – 500, in bits beyond a "complex enough" threshold NB: If S = 0, this locks us at Chi = - 500; and, if Ip is less than 500 bits, Chi will be negative even if S is positive. E.g.: a string of 501 coins tossed at random will have S = 0, but if the coins are arranged to spell out a message in English using the ASCII code [[notice independent specification of a narrow zone of possible configurations, T], Chi will -- unsurprisingly -- be positive. Following the logic of the per aspect necessity vs chance vs design causal factor explanatory filter, the default value of S is 0, i.e. it is assumed that blind chance and/or mechanical necessity are adequate to explain a phenomenon of interest. S goes to 1 when we have objective grounds -- to be explained case by case -- to assign that value.

But in haste to be polarised, dismissive and hyperskeptical, pursuing a no concession policy that overlooks that there is a world of technologists who happen to have direct experience of working with complex multipart systems that require exacting correct configuration to work, there is a closed minded rejection of what should not require more than pointing to a few examples. SUCH CRITICS FAIL TO SEE THAT THEIR NO CONCESSION POLICY EXPOSES THEM FOR THEIR CLOSED MINDEDNESS AND INCOMPETENCE. For, if such are willfully blind on what is so plain to any reasonable person, then their opinions and assertions on the topic obviously come from the self-disqualified. And, with that attitude maintained for literally years, the damage is irreparable. That is part of why I have had to draw the conclusion that we are not dealing with responsible critique but with ideological, deeply polarised hostility that cares little or nothing for the actual merits. If they are willing to turn something as obvious as FSCO/I into a grand dismissive and denigratory song and dance they have locked themselves out of responsible discussion. Period. It is therefore utterly unsurprising that much the same critics refuse to acknowledge that D/RNA has in it complex coded algorithms. Something that has led me to point to Lehninger as is in the OP:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

KF kairosfocus

Well, there’s no fixing that attitude!

Except for evidence. As predicted. No evidence and definitely no logic. Just assertions that it exists someplace.

You could read it, though I doubt you will

You are right, I won’t read it. Why waste my time? I have read several pro natural Evolution books and listened to many videos on the same topic. Never found anything to support the claims in these books. That assertion by me based on evidence has never been disputed by anyone. Just ad hominems. Or polite people make counter assertions that they cannot back up. jerry

The reason is that the evidence and logic don’t exist.

Well, there's no fixing that attitude! Alan Fox

The day you will present evidence and logic will be an amazing day.

Jason Rosenhouse's book has been discussed on this site. You could read it, though I doubt you will. I can link to Felsenstein and English and their critiques of Dembski's CSI. Do you want me to? Alan Fox

Well, my expectations regarding Jerry's video (produced by Jon Bartlett) are confirmed. Jon takes us very methodically (yes, slowly) through some basics. One thing he makes very clear is the -log(base 2)manipulation is simply to make numbers manageable. The sole example is coin tosses. I smile at the final power point:

Therefore if any object exhibits specified complexity, we have sufficient warrant for inferring it is designed.

Interestingly and serendipitously, I came across another video that discusses CSI. The author is sympathetic to "Intelligent Design" and used to be a regular here at Uncommon descent. https://www.youtube.com/watch?v=tA8HzPUdFo0 Alan Fox

Jason Rosenhouse, Joe Felsenstein and Tom English have beaten that horse to death.

Argument by assertion. The day you will present evidence and logic will be an amazing day. The reason is that the evidence and logic don’t exist. So it will be like an universe from nothing. jerry

On CSI or FCSI, Jonathan Bartlett who has a website called the Blyth Institute publishes various things on ID.

Yes, I know (in the blogosphere sense) Jon well. He published a guest post by me (as Aurelio Smith) here some time ago. Unfortunately, all comments as Aurelio Smith, including those in that thread, were deleted.

This video goes into CSI or FCSI in detail.

OK, I have the same aversion to videos as Viola Lee but I'll give it a glance.

Kf’s version is essentially the same. I believe he just says FSCO/I is just a subset of CSI.

Perhaps KF will confirm he is talking about CSI à la Dembski. In which case there is not much else to say. I think Jason Rosenhouse, Joe Felsenstein and Tom English have beaten that horse to death.

So any quibbling with Kf’s definition is just nonsense.

Asking how his FSCO/I works is not quibbling. Avoiding answering a simple direct question is not quibbling, either. It's obfuscating. Alan Fox

On CSI or FCSI, Jonathan Bartlett who has a website called the Blyth Institute publishes various things on ID. This video goes into CSI or FCSI in detail. Kf's version is essentially the same. I believe he just says FSCO/I is just a subset of CSI. So any quibbling with Kf's definition is just nonsense. https://www.youtube.com/watch?v=5CWu_8CTdDY&t=217s jerry

Am away for the day. So later.

RL should always take precedence. But then KF should discount the "O". Now, if you want to talk about Dembski's CSI instead, fine. Bear in mind he's dropped that in favour of "active information". Alan Fox

If you can’t do it, just say so and I’ll stop asking.

Been there done that. I believe the “O” stands for organization. This is Kf’s variation and is not necessary. The other letters are standard. But all has been discussed hundreds of times. Each sentence in what I write is FCSI and can be analyzed probabilistically. Simple and straightforward. Am away for the day. So later. jerry

KF (and Jerry, if he's game) How is FSCO/I calculated? Example? If you can't do it, just say so and I'll stop asking. Alan Fox

AF, you know full well that information can readily be measured in bits, that those bits can be characterised as functional and that this routinely is listed when you display computer files, they are not interested in the gibberish in unallocated store but in specific functionally organised files. Further you know that once AutoCAD etc exist there are descriptive languages that specify 3-d functional entities in strings of bits and so description on bits is WLOG. You are making up an excuse not a valid objection. Repeat, just to object you had to encode text in English, and such is readily different from random gibberish or repeated small strings. All of this was readily accessible all along so you are playing selectively hyperskeptical games. The context is, in D/RNA in the cell, there is coded algorithmic FSCO/I that points to design, which you refuse to allow. KF kairosfocus

PS @ Jerry, No cheating. The thing I wish to see quantified is FSCO/I, which is an acronym for functional specified something stroke information, I think. Not other acronyms, of which FSC is legitimate and does not refer to a quantity. Alan Fox

Explain how you measure it, Jerry. No rush. When you have time, though it would be good if that was in my lifetime. Alan Fox

FSCO/I is only in your fevered imagination, nowhere else. Charitably, let’s call it a model for… something

No, it’s in reality and very obvious. I never knew the entire origin of FSCO/I until recently and it’s overkill. But just because of your ignorance, does not mean it doesn’t exist or isn’t explanatory. Kf is unable to explain a lot of things due to his language style. I definitely disagree with him on certain things but not CSI or FCSI. Only a fool would do that. Aside: the anti ID posters are morphing into versions of ChuckDarwin. All they seem to have is irrelevant snarky remarks. No science, no evidence, no logic, just inanity. They are living proof for ID. jerry

See, this is why I consider you a dishonest propagandist, KF.

...the nature of FSCO/I with multiple part organisation, alignment and coupling naturally leads to islands of function in configuration spaces. KF

FSCO/I is only in your fevered imagination, nowhere else. Charitably, let's call it a model for... something. You are incapable of defining it or giving illustrative examples let alone being able to demonstrate how to calculate any meaningful quantity. Alan Fox

Oh dear. I'm saddened to witness Kairosfocus' blatant dishonesty in pasting in "voice-in-the-ceiling" edits into some of my previous comments. Oh, for shame! God is watching, KF, he sees all. For shame!!! Alan Fox

Sev, BTW, show us an observationally backed, small increment per step path seen to be functional all the way, from a Darwin's pond or the like to a functional self replicating cell. My prediction, you don't have it. Fair comment, the nature of FSCO/I with multiple part organisation, alignment and coupling naturally leads to islands of function in configuration spaces. KF kairosfocus

Sev, no strawman. The worldview level question begging imposition is real. As to alleged or imagined capability of blind chance and mechanical necessity to generate FSCO/I beyond reasonable thresholds, never observed. Next, what we do have in hand is coded algorithms in the cell and antecedent to cell based life. That points to intelligently directed, language using configuration as key causal process. Language comes from minds, so this is the true SETI wow signal. Not some red herring theological imposition . . . by their projections shall ye know them, just basic logic and common sense regarding language. Just, it is unwelcome to those imposing a priori evolutionary materialistic scientism and so to fellow travellers. KF kairosfocus

Kairosfocus/80

JVL, your core problem is that an ideology has been imposed on origins a priori, where blind chance and mechanical necessity has never been observed to create FSCO/I beyond 500 – 1,000 bits. Just so, there is good blind needle in haystack reason to infer it is not plausible, and we do have a known source, design. The real problem is not absence of evidence, it is evidence of an ideologically rejected class of cause. That sort of ideological lock out does not end well. KF

As JVL and others have pointed out, you are attacking a strawman. Nowhere does evolutionary biology claim that complex modern biological phenomena arose improbably from simple, inanimate precursors in a single bound. Your unrecognized and undemonstrated metric of FSCO/I is thus far simply irrelevant. That there is design in the Universe is not in question. We do it. What is also not in question is that we are not capable of designing universes or the life within them and the ID movement has been unable to demonstrate the existence of any extraterrestrial designers that are capable of such work, arguments by analogy or arguments from incredulity notwithstanding. That there may have been, are or will be much more advanced extraterrestrial intelligences out there cannot be ruled out. But that is not the same as claiming that we are warranted in inferring that they do actually exist and that they are responsible for life on Earth. That is not ideological imposition, it is the recognition of the current limits of our knowledge. What would be a theological imposition would be any requirement that science proceeds from the unquestionable assumption of the existence of the Christian God. Seversky

PS, Johnson's reply to Lewontin

For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original -- the context is Lewontin in NYRB] 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.

[--> notice, the power of an undisclosed, question-begging, controlling assumption . . . often put up as if it were a mere reasonable methodological constraint; emphasis added. Let us note how Rational Wiki, so-called, presents it:

"Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific "dead ends" and God of the gaps-type hypotheses." [NB: I am aware that Rational Wiki has backed away, un-announced, from the cat-out-of-the-bag direct phrasing that was in place a few years ago. That historic phrasing is still valid as a summary of what is going on.]

Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to "natural vs [the suspect] supernatural." Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga's reply here and here.] And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And it is not an appeal to ever- diminishing- ignorance to point out that design, rooted in intelligent action, routinely configures systems exhibiting functionally specific, often fine tuned complex organisation and associated information. Nor, that it is the only observed cause of such, nor that the search challenge of our observed cosmos makes it maximally implausible that blind chance and/or mechanical necessity can account for such.]

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.]

kairosfocus

JVL, your core problem is that an ideology has been imposed on origins a priori, where blind chance and mechanical necessity has never been observed to create FSCO/I beyond 500 - 1,000 bits. Just so, there is good blind needle in haystack reason to infer it is not plausible, and we do have a known source, design. The real problem is not absence of evidence, it is evidence of an ideologically rejected class of cause. That sort of ideological lock out does not end well. KF kairosfocus

Kairosfocus: That there is common design does not exclude that there are major innovations that have no actual observational evidence of incremental emergence from antecedent simpler forms. Absence of evidence is not evidence of absence no matter how much you want that to be true. That is why some people say ID is like a God of the gaps method of reasoning: oh, look, there's a transition here that isn't completely clear or documented, must be that some designer bridged that gap. Also, why don't you address what biologists are actually saying instead of creating a false landscape of speculation and arguing against that? JVL

PPS, as you have just used that humble source Wikipedia, are you willing to acknowledge a further point it makes as is in an update to the OP with an embedded onward cite from Lehninger?

In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription [–> algorithmic start, notice, transcribing is generally stepwise], it also guides the nucleotides into position, facilitates attachment and elongation [–> notice direct parallel to stepwise synthesis of AA chains for proteins, cf Lehninger 8th edn p 3346: “RNA polymerase elongates an RNA strand by adding ribonucleotide units to the 3 ?- hydroxyl end, building RNA in the 5 ? --> 3 ? direction”], has intrinsic proofreading and replacement capabilities [–> language, editing], and termination recognition [–> algorithmic halting] capability. In eukaryotes, RNAP can build chains as long as 2.4 million nucleotides.

That is, the assembly of RNA in the cell -- including mRNA and tRNA -- involves an algorithmic, stepwise assembly process with sequential start, steps, halt. "Template" there may be using complementarity of A-T/U and G-C, but it is here used to effect mRNA etc through an algorithmic process. kairosfocus

AF, Dawkins, whatever his scientific CV says, explicitly acknowledged that the living cell embeds a code using molecular nanotech system. Are you willing to now acknowledge that this is in fact the general, evidence based consensus? _______ And, to explain your rhetorical stunt of trying to set that aside? ______ KF PS, as a reminder, Lehninger:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

kairosfocus

JVL, are you arguing that events in a Darwin warm pond or the equivalent exhibit foresight and planning tied thereto? I doubt it. You full well understand what blind chance and/or mechanical necessity [as in natural forces and dynamic-stochastic processes] entail, and where they would have to start from. Further to this, you are trying to wish away the issue of incremental functional all the way transformation. That there is common design does not exclude that there are major innovations that have no actual observational evidence of incremental emergence from antecedent simpler forms. KF kairosfocus

But what actual science has Dawkins done?

From the Wikipedia article that you may have missed: He continued as a research student under Tinbergen's supervision, receiving his Doctor of Philosophy[31] degree by 1966, and remained a research assistant for another year.[32][33] Tinbergen was a pioneer in the study of animal behaviour, particularly in the areas of instinct, learning, and choice;[34] Dawkins's research in this period concerned models of animal decision-making.[35] He was awarded a DSc by Oxford in 1989.[33][32] The numbers in square brackets give the citations, if you are in doubt as to the accuracy of Wikipedia on simple facts. Alan Fox

Kairosfocus: Dere ‘ent enough time . . . to even blind search more than a negligible fraction of the configuration space for 500 – 1,000 bits And no one is saying that a blind search is being done! You keep arguing against that straw man, misinterpreting what the unguided evolutionary theory is saying. That may play well with some ID proponents but it ain't gonna fly with them that knows what the real science is sayin'. Also, there are no islands of function in the biological space. All life forms are related to all other life forms which means there is a developmental path between them. JVL

Dere 'ent enough time . . . to even blind search more than a negligible fraction of the configuration space for 500 - 1,000 bits, with a sol sys of 10^57 atoms or a cosmos, 10^80, for 10^17s. Contrast, 900 bases to code a typical 300 AA protein, 1800 bits info carrying capacity. kairosfocus

You're welcome. relatd

Thanks Relatd. ayearningforpublius

Ayearningforpublius at 69, According to Dawkins, "enough time" is the substitute for God. It replaces God with atheism. You will find here that regardless of the evidence posted for ID, the wall of defenders of evolution must stand. They must repeat "evolution is a fact" every day. But keep this in mind: The truth must be repeated daily to combat the lies being spread among the people. Speak the truth - daily. relatd

For Alan Fox. Thanks for the Wikipedia article on Dawkins. But what actual science has Dawkins done? His book "The Blind Watchmaker" sold many books and contributed much to his fame and fortune. But it was all handwaving. On the other hand, real scientific researchers have taken a good hard look (pun intended) at the eye and provide hands-on scientific analysis as to the making of the eye. Dawkins, on the other hand captivates young naive students with Papier-mâché mountains and bended film strips as his laboratory work. Take a look . . . https://ayearningforpublius.wordpress.com/2015/07/14/the-eye-a-biological-miracle-but-of-what-sort/ Yes, Deep Time — the exotic drape that will cover the collection of eyes and hide from public view the rich imaginations of Richard Dawkins, the lead researcher and Program Manager in this magnificent effort. In the meantime, the soldier needing the replacement eye will have to wait … wait to the limit of deep time, measured in unknown billions of years. Not to worry: “given enough time, and an infinite number of chances, anything is possible" (Dawkins). Why does it matter? The Darwin Lobby is very effective in assuring that their version of reality – this “illusion of science” called Darwinian Evolution is the only game in town … the only version presented to the public and taught to present and future generations. ayearningforpublius

Not only is methodological naturalism the best investigatory methodology of the natural world based on its track record, it is our best defense against those who would attempt to impose their partisan political and religious dogmas on students.

Methodological naturalism is a nonsensical expression. To formulate the definition of the methodological naturalism(and any other definition) you need a mind that is in itself the enemy of naturalism. :lol: Atheists cannot tell what is the chemical formula of the ideas presented in this message. Lieutenant Commander Data

I don't like the ads any more then anyone else but it's the price we have to pay for the content, I suppose. Seversky

@ jvl I understand that fully but this seems excessive they appear in the middle of our commentary. AaronS1978

AaronS1978: When I unlock my phone in to argue on this site I am hit with a GRATUITOUS amount of ads. More ads than any other place that I visit is this necessary? The owners have to pay the bills somehow. While most of the contributors are not paid the hosting and such do cost. I'm sure they would appreciate monetary contributions. JVL

“Wrong you are, matey. I’m neither a strict determinist, nor do I deny free will, in the sense that humans, and not only humans, have the ability to make choices among possible alternatives.“ I have no issues being wrong about that, it is something I like being wrong about AaronS1978

Either way, I’m pretty sure I can guess that your viewpoint is there’s no free will and we are completely guided by the environment and our genetics, meat robots for short with zero control over anything.

Wrong you are, matey. I'm neither a strict determinist, nor do I deny free will, in the sense that humans, and not only humans, have the ability to make choices among possible alternatives. Alan Fox

Haynes not Hanes AaronS1978

By the way off-topic @ the site of uncommon descent I normally block all ads on my phone and I purposely restrict the Internet on my phone so that way I don’t sit there all day wasting time When I unlock my phone in to argue on this site I am hit with a GRATUITOUS amount of ads More ads than any other place that I visit is this necessary? AaronS1978

Seversky, they imposed an historically unjustifiable ideologically tendentious redefinition of science and held parents and children hostage for the accreditation of their high school diplomas. That is an inexcusable outrage and it is going to eventually face a day of accounting. To point out a fact documented and highlighted may be unflattering to the NSTA but no one forced them to put those terrible facts on the ground. Fair comment on manifest fact is not a slur. KF kairosfocus

@ AF “RNA isn’t hypothetical. It is central to cell function across all extant life. The ribosome is a ribozyme.That RNA can both replicate and act as a catalyst (ribozyme) is strong circumstantial evidence for a precursory RNA world.“ I miss type something? The “RNA world hypothesis” is debated and IS HYPOTHETICAL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/ This is just one article in many articles, try Google scholar RNA world hypothesis debate or discussion. Also since you are a wikininja even that junk source of information discusses the challenges. This comment really doesn’t show that you know anything about organic chemistry or about its history Also did you purposely miss quote me? I was discussing the hypothetical RNA world hypothesis, I mean it’s right in the name. Why did you say that I was indicating RNA and its function was hypothetical? Were you doing that on purpose or you an idiot? “Most of the basic facts are not in dispute. When he runs with the ball into the long grass (I love a mixed metaphor) I tend to pick up on” This is a narrative, did not answer my question, answer the question. “DNA is not organic code. DNA stores protein sequences, among other things, as sequences of nucleotides in triplet genetic code or organic code” Again explaining the physical characteristics of organic chemistry does nothing for your argument that’s it’s not code. Why is it not code and try not to go back to “because it’s a combination of organic compounds” you’re wasting peoples time Because it’s some combination of organic compounds does not disqualify it as a form of code “You may be surprised to learn that there is no”hard problem of consciousness” if you are referring to Chalmers. But I guess that is off-topic. Don’t get me started on free will and determinism, either.“ You may be surprised that there is a hard problem of the consciousness and that you’re probably uneducated on it. I excuse your ignorance. You obviously from the “school of thought” of people like Alin Seth where everything can be explained using the IP metaphor and there is no hard problem of the consciousness or you’re one of Alex Rosenberg’s morons living a perpetual world of cognitive dissidents. You are also very likely not up-to-date on any of Aaron Schruger’s work when it comes to the neuroscience of free will or even John Dylan Hanes more current work (anything 2016+) Either way, I’m pretty sure I can guess that your viewpoint is there’s no free will and we are completely guided by the environment and our genetics, meat robots for short with zero control over anything. I also wouldn’t be surprised if you were a big proponent of GWS for the idea of consciousness often purported by Alin Seth So if you are one of the people that believe we’re meat robots then stop wasting everybody’s time, no one can help what they are and what they think. AaronS1978

AF, oh yes you have. Bruce Alberts et al describe string data structure algorithmic code in direct echo of Lehninger. You have been trying to suggest that code is an error of ignorance. Fail. KF PS, More from Alberts et al, p. 7:

the information in the sequence of a messenger RNA molecule is read out in groups of three nucleotides at a time: each triplet of nucleotides, or codon, specifies (codes for) a single amino acid in a corresponding protein. Since the number of distinct triplets that can be formed from four nucleotides is 43, there are 64 possible codons, all of which occur in nature. However, there are only 20 naturally occurring amino acids. That means there are necessarily many cases in which several codons correspond to the same amino acid. This genetic code is read out by a special class of small RNA molecules, the transfer RNAs (tRNAs). Each type of tRNA becomes attached at one end to a specific amino acid, and displays at its other end a specific sequence of three nucleotides—an anticodon— that enables it to recognize, through base-pairing, a particular codon or subset of codons in mRNA. The intricate chemistry that enables these tRNAs to translate a specific sequence of A, C, G, and U nucleotides in an mRNA molecule into a specific sequence of amino acids in a protein molecule occurs on the ribosome, a large multimolecular machine composed of both protein and ribosomal RNA . . . . Special sequences in the DNA serve as punctuation, defining where the information for each protein begins and ends. And individual segments of the long DNA sequence are transcribed into separate mRNA molecules, coding for different proteins. Each such DNA segment represents one gene. A complica- tion is that RNA molecules transcribed from the same DNA segment can often be processed in more than one way, so as to give rise to a set of alternative versions of a protein, especially in more complex cells such as those of plants and animals.

PPS, you seem to overlook aspects of RNA Polymerase, its stepwise sequence action during transcription:

Lehninger 8th edn p 3346: “RNA polymerase elongates an RNA strand by adding ribonucleotide units to the 3 ?- hydroxyl end, building RNA in the 5 ? ? 3 ? direction”

(See u/d's to the OP.) kairosfocus

Kairosfocus/34

PPPS, US NSTA’s educational malpractice:

Calling that "malpractice" is an outrageous slur. Not only is methodological naturalism the best investigatory methodology of the natural world based on its track record, it is our best defense against those who would attempt to impose their partisan political and religious dogmas on students. What could be characterized as "malpractice" is the open advocacy of creationism in science classrooms by 13% of high school biology teachers as reported in a survey of same published in 2011. Not only is such practice unconstitutional, it's also a clear and egregious breach of their ethical and contractual duties as educators. [ED: Sev, ideological, question begging imposition as documented and annotated is educational malpractice. KF] Seversky

https://en.wikipedia.org/wiki/Richard_Dawkins Alan Fox

Dawkins is referenced several times here. Does anyone know if Dawkins is actually a biologist? has he ever done any real research? Or does he just write books and preach in a classroom? ayearningforpublius

So what real evidence to you have that would discredit the concept of DNA being organic code used universally amongst all living organisms on this planet?

DNA is not organic code. DNA stores protein sequences, among other things, as sequences of nucleotides in triplet genetic code or organic code, if you prefer. But otherwise OK. It's certainly almost (but not quite - there are a few important and interesting variations) universal across all known living organisms. In short, I'm not out to discredit DNA as a carrier of information. Alan Fox

...the highly debated RNA world hypothesis can’t say anything it’s a hypothetical organic chemical process, since we like to take things literally.

RNA isn't hypothetical. It is central to cell function across all extant life. The ribosome is a ribozyme.That RNA can both replicate and act as a catalyst (ribozyme) is strong circumstantial evidence for a precursory RNA world. Alan Fox

...for someone who said you are kinda qualified to discuss biochemistry you have yet to put a single real objection using your knowledge to discredit anything KF has posted

Most of the basic facts are not in dispute. When he runs with the ball into the long grass (I love a mixed metaphor) I tend to pick up on it. Alan Fox

This type of fallacy is often used in neuroscience when dealing with the hard problem of the consciousness.

You may be surprised to learn that there is no"hard problem of consciousness" if you are referring to Chalmers. But I guess that is off-topic. Don't get me started on free will and determinism, either. Alan Fox

His conceptions are cemented in the past and are immune to any modern concept of genetics and biochemistry.

Oh, the irony! :) :) :) Alan Fox

THE UNIVERSAl FEATURES OF CELLS ON EARTH 2 All Cells Store Their Hereditary Information in the Same Linear Chemical Code: DNA 2 All Cells Replicate Their Hereditary Information by Templated Polymerization 3 All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form: RNA 4 All Cells Use Proteins as Catalysts 5 All Cells Translate RNA into Protein in the Same Way 6 Each Protein Is Encoded by a Specific Gene 7

I don't dispute any of this, KF. Especially not "templated polymerization"! ;) ETA: all strong indicators of common descent, BTW! Alan Fox

LCD, the biochem of 1953 was decisive and a responsible person would acknowledge seventy years of development summarised in say Lehninger or Alberts and echoed as far down the food chain as Dawkins or Wikipedia. KF kairosfocus

Kairosfocus We are dealing with brazen lying by gaslighting because the significance of coded algorithmic information in the cell is plainly devastating.

The reason could be the old age and not necessary the lying. He knows about the biochemistry of 1950 and about Darwin books (1860-80) and he probably lost connection with modern biochemistry and genetics. His conceptions are cemented in the past and are immune to any modern concept of genetics and biochemistry. Lieutenant Commander Data

F/N: To give you an idea of just how outrageous and irresponsible AF's rhetorical stunt is, here is Alberts et al, Molecular Biology of the Cell, DETAILED TABLE OF CONTENTS, p. xxi; yes, chapter and section titles:

Chapter 1 Cells and Genomes 1 THE UNIVERSAl FEATURES OF CELLS ON EARTH 2 All Cells Store Their Hereditary Information in the Same Linear Chemical Code: DNA 2 All Cells Replicate Their Hereditary Information by Templated Polymerization 3 All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form: RNA 4 All Cells Use Proteins as Catalysts 5 All Cells Translate RNA into Protein in the Same Way 6 Each Protein Is Encoded by a Specific Gene 7 [6rh Edn, 2015]

Sounds familiar? It should. We are dealing with brazen lying by gaslighting because the significance of coded algorithmic information in the cell is plainly devastating. KF kairosfocus

AF, there is no good reason to deny code and algorithms in the cell. Where, such ride on a physical technology, they are not in opposition to it nor are they reducible to it. As you have been claiming all sorts of things, I again remind you of the matter of fact approach in Lehninger

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

You have gone out on a rhetorical limb to pretend it is ignoramuses etc who imagine code is in the cell. Well, Lehninger [now a committee] -- yes, Lehninger -- is one of your ignoramuses. Fail. Gaslighting fail. KF kairosfocus

@AF First, you can encode things in MANY different mediums. Saying it’s a biochemical process does NOTHING for your argument that it is not code. This type of fallacy is often used in neuroscience when dealing with the hard problem of the consciousness Yes we can break “seeing the color red” down to its neural correlates but that does nothing to actually explain why we experience the color red. Using reductionism doesn’t help your point. Second, the highly debated RNA world hypothesis can’t say anything it’s a hypothetical organic chemical process, since we like to take things literally Thirdly, for someone who said you are kinda qualified to discuss biochemistry you have yet to put a single real objection using your knowledge to discredit anything KF has posted You have dismissed out of hand, mocked, or have simply been passive aggressive to everything he has posted but nothing to academically dismiss the argument. You can however excuse his ignorance……. Any lay person would not be able to extrapolate any evidence that you had knowledge in organic chemistry or any school of chemistry. So what real evidence to you have that would discredit the concept of DNA being organic code used universally amongst all living organisms on this planet? AaronS1978

Unless you agree human language is a completely physicochemical set of processes, which of course it is. ;) Alan Fox

...editing in Eukaryotes is a direct language process.

No it isn't. It's a physicochemical process. If you want to insist on an analogy with human language or computer language, go ahead. It adds nothing to the understanding of the process of the origins, evolution or current functions of this biological set of systems. [ED: The doubling down continues, and keeps on going below exactly as the headline to OP predicted . . . KF] Alan Fox

F/N: AmHD:

al·go·rithm (?l?g?-r?th??m) n. A finite set of unambiguous instructions that, given some set of initial conditions, can be performed in a prescribed sequence to achieve a certain goal and that has a recognizable set of end conditions.

That is a finite stepwise sequence from start to halt that completes. This is a matter of instance, not analogy. For record, FYI. KF kairosfocus

F/N: See OP updates on mRNA synthesis and structure. kairosfocus

AF, lying by distraction, doubling down, gaslighting and obfuscation. You full well know there is coded stepwise -- thus algorithmic -- synthesis of AA chains towards proteins using mRNA, as Lehninger et al openly acknowledge, as even Dawkins and Wikipedia admit. KF PS, even the assembly of mRNA has a stepwise aspect and editing in Eukaryotes is a direct language process. kairosfocus

RR at 37, It's not logical. It makes no sense. You should understand that the idea that living things contain codes and switches, for example, that control their life functions is known by those here. They can never promote it or agree with it. The idea of a designer who made living things points to a Creator, to God. That idea must be denied. They have no choice. It would harm atheism if people accepted this. relatd

Millions of positive and negative charges on a magnetic strip have no meaning. Yet the series may carry vast amounts of information. Darwinists would have us believe both the digital stream and the magnetic strip are results of random, non-directed events which exist because "survival of the fittest". Oh, they don't believe that? Except, that is exactly what they believe when the storage and medium are biological. The "thinking" required to believe such nonsense is insanity. Red Reader

You full well know that the pivotal process is where mRNA, bearing a coded algorithm, is used to assemble AA chains towards proteins, as is illustrated in the first figure in the OP.

I know full well that in living cells, messenger RNA is a vital element in protein synthesis, copied from a DNA template, the gene, and via the machinery of the ribosome, is used as a template for the synthesis of a protein. At no stage is there anything algorithmic going on. That is just in your head. [ED: Further doubling down and refusal to attend to correction. Note the gaslighting declaration in the teeth of the general recognition that coded information in D/RNA is used in protein synthesis. Where, Ribosome action involves a start, elongation step by step as an AA chain is assembled and halting using one of three stop codes. Algorithms are goal directed, stepwise finite processes with halting. AF refuses to heed this, in his attempt to dismiss a fact that is fatal to his preferred view. KF] Alan Fox

Seversky at 29, "It’s only very recently that the churches have become a little nervous about an alternative, naturalistic explanation proposed by science that might be credible enough to affect the numbers of bums on pews." That's your concern? The "numbers of bums on pews."? We'll make a Christian out of you yet Seversky. Or would you prefer more atheist converts via science? relatd

PPPS, US NSTA's educational malpractice:

All those involved with science teaching and learning should have a common, accurate view of the nature of science. [--> yes but a question-begging ideological imposition is not an accurate view] Science is characterized by the systematic gathering of information through various forms of direct and indirect observations and the testing of this information by methods including, but not limited to, experimentation [--> correct so far]. The principal product of science is knowledge in the form of naturalistic concepts [--> evolutionary materialistic scientism is imposed] and the laws and theories related to those [--> i.e. ideologically loaded, evolutionary materialistic] concepts . . . . science, along with its methods, explanations and generalizations, must be the sole focus of instruction in science classes to the exclusion of all non-scientific or pseudoscientific methods, explanations, generalizations and products [--> censorship of anything that challenges the imposition; fails to appreciate that scientific methods are studied through logic, epistemology and philosophy of science, which are philosophy not science] . . . . Although no single universal step-by-step scientific method captures the complexity of doing science [--> a good point, but fails to see that this brings to bear many philosophical issues], a number of shared values and perspectives characterize a scientific approach to understanding nature. Among these are a demand for naturalistic explanations [--> outright ideological imposition and censorship that fetters freedom of responsible thought] supported by empirical evidence [--> the imposition controls how evidence is interpreted and that's why blind watchmaker mechanisms never seen to actually cause FSCO/I have default claim to explain it in the world of life] that are, at least in principle, testable against the natural world. Other shared elements include observations, rational argument [--> ideological imposition may hide under a cloak of rationality but is in fact anti-rational], inference, skepticism [--> critical awareness is responsible, selective hyperskepticism backed by ideological censorship is not], peer review [--> a circle of ideologues in agreement has no probative value] and replicability of work . . . . Science, by definition, is limited to naturalistic [= evolutionary materialistic scientism is imposed by definition, locking out an unfettered search for the credibly warranted truth about our world i/l/o observational evidence and linked inductive reasoning] methods and explanations and, as such [--> notice, ideological imposition by question-begging definition], is precluded from using supernatural elements [--> sets up a supernatural vs natural strawman alternative when the proper contrast since Plato in The Laws, Bk X, is natural vs artificial] in the production of scientific knowledge. [US NSTA Board, July 2000, definition of the nature of science for education purposes]

kairosfocus

PPS, Lewontin's cat out of the bag moment:

[Lewontin:] . . . to put a correct [--> Just who here presume to cornering the market on truth and so demand authority to impose?] view of the universe into people's heads

[==> as in, "we" the radically secularist elites have cornered the market on truth, warrant and knowledge, making "our" "consensus" the yardstick of truth . . . where of course "view" is patently short for WORLDVIEW . . . and linked cultural agenda . . . ]

we must first get an incorrect view out [--> as in, if you disagree with "us" of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world [--> "explanations of the world" is yet another synonym for WORLDVIEWS; the despised "demon[ic]" "supernatural" being of course an index of animus towards ethical theism and particularly the Judaeo-Christian faith tradition], the demons that exist only in their imaginations,

[ --> as in, to think in terms of ethical theism is to be delusional, justifying "our" elitist and establishment-controlling interventions of power to "fix" the widespread mental disease]

and to accept a social and intellectual apparatus, Science, as the only begetter of truth

[--> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]

. . . . To Sagan, as to all but a few other scientists [--> "we" are the dominant elites], it is self-evident

[--> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]

that the practices of science provide the surest method of putting us in contact with physical reality [--> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [--> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . . It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] 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 [--> another major begging of the question . . . ] 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 [--> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [--> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is "quote-mined" I invite you to read the fuller annotated citation here.]

kairosfocus

Sev, there is no sound naturalistic alternative. I refer you to the Haldane challenge. KF PS, Haldane

[JBSH, REFACTORED AS SKELETAL, AUGMENTED PROPOSITIONS:] "It seems to me immensely unlikely that mind is a mere by-product of matter. For

if [p:] my mental processes are determined wholly by the motions of atoms in my brain [–> taking in DNA, epigenetics and matters of computer organisation, programming and dynamic-stochastic processes; notice, "my brain," i.e. self referential] ______________________________ [ THEN] [q:] I have no reason to suppose that my beliefs are true. [--> indeed, blindly mechanical computation is not in itself a rational process, the only rationality is the canned rationality of the programmer, where survival-filtered lucky noise is not a credible programmer, note the functionally specific, highly complex organised information rich code and algorithms in D/RNA, i.e. language and goal directed stepwise process . . . an observationally validated adequate source for such is _____ ?] [Corollary 1:] They may be sound chemically, but that does not make them sound logically. And hence [Corollary 2:] I have no reason for supposing my brain to be composed of atoms. [--> grand, self-referential delusion, utterly absurd self-falsifying incoherence] [Implied, Corollary 3: Reason and rationality collapse in a grand delusion, including of course general, philosophical, logical, ontological and moral knowledge; reductio ad absurdum, a FAILED, and FALSE, intellectually futile and bankrupt, ruinously absurd system of thought.]

In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209. Cf. here on (and esp here) on the self-refutation by self-falsifying self referential incoherence and on linked amorality.]

That needs to be cogently answered, on pain of exposing the imposed Lewontinian a priori evolutionary materialistic scientism as outright agit prop educational malpractice. No intellectual scheme of thought can be valid if it self referentially undermines credibility of mind and/or rational, responsible [so, morally governed] freedom. kairosfocus

AF, distraction as usual. You full well know that the pivotal process is where mRNA, bearing a coded algorithm, is used to assemble AA chains towards proteins, as is illustrated in the first figure in the OP. You have been making a rhetorical song and dance to pretend that code and algorithm and perhaps even string data structure are incorrect and ignorant usage of terms and concepts. At length, I took time to cite Lehninger, perhaps the classic text on Biochem, current edn, in 18 above. Lo and behold, your bluffing, rhetorical song and dance collapses:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function."

Your reaction? You try to switch over to templating [used to form complementary D/RNA strands, not stepwise code based assembly of protein AA chains], as though you have not been duly, thoroughly corrected. So, which is it, gross discrediting ignorance on your part, or was it a willfully deceptive irresponsible bluff. Of course, you full well know that coded algorithms make all the difference, being an expression of language and communication systems, with goal directed stepwise processes. In the heart of the cell and antecedent to its metabolism and self replication. Proteins, including enzymes, are proverbially the work horses of the cell. Language, goal-directed stepwise process, involving sophisticated polymer chemistry and molecular nanotech. Transformational. KF kairosfocus

There is not a single discovery in biology/genetics that won't use ID stance(mindset) as a starting point for exploration. Lieutenant Commander Data

Relatd/25

The real problem here is making sure ID is not taught in schools AND does not become popular with the common people.

The irony with that comment is that the Christian version of ID was popular with the common people for thousands of years because it was the only story taught in the schools and churches in Europe for all that time. It's only very recently that the churches have become a little nervous about an alternative, naturalistic explanation proposed by science that might be credible enough to affect the numbers of bums on pews. Seversky

Relatd/23

The Catholic Church can combine scientific information with Theology. Science, as constituted, cannot. • The Church “proclaims that by the light of reason the human intellect can readily and clearly discern purpose and design in the natural world, including the world of living things.” • “Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.”

In other words, we're right, you're wrong and if you disagree it's ideology not science. That about sums it up? Seversky

Atheists will be exposed, will they? Sounds nasty! ;) Alan Fox

The real problem here is making sure ID is not taught in schools ..

What would you teach? I've been asking for some idea of the content of "Intelligent Design" science and haven't got much feedback on substance.

...AND does not become popular with the common people.

Well, there's no chance of that where I live. The US is a very odd place looking on from outside. Alan Fox

AF at 24, Not "works for you". The real problem here is making sure ID is not taught in schools AND does not become popular with the common people. It is easy to see that IF it is taught that it will go beyond the classroom. It will get people thinking about God. It will tell people, someone made all life. That must be stopped. It can't happen. Why? Because the Marxist-Atheists will be exposed. relatd

If it works for you, fine. Alan Fox

AF at 22, The Catholic Church can combine scientific information with Theology. Science, as constituted, cannot. • The Church “proclaims that by the light of reason the human intellect can readily and clearly discern purpose and design in the natural world, including the world of living things.” • “Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.” "Christoph Cardinal Schönborn is archbishop of Vienna and general editor of the Catechism of the Catholic Church." relatd

Could be from the Creator of the Universe. It's one way to imbue creation with a creator. I don't know and I guess there's no way to find out. Alan Fox

AF at 20, "carry information"? Where does that information come from? relatd

Fine, let's refer to the templating process whereby DNA and RNA pair, replicate and copy and carry information as encoding. What difference does that make? [ED: Doubling down on the side tracking distractor while studiously ignoring correction. Sadly familiar techniques. KF] Alan Fox

AF, as further correction, Crick starts with like a code then progresses to IS a code, see the box around key statements. You were corrected but insist on falsehood, that tells us further about your want of credibility, this is stuff right before us. Further, Nobel prizes for the work in question started with Crick and Watson, and went on and on including Monod. You are clearly utterly unreliable. I have already put Lehninger on record, that shows that the consensus as described in OP is indeed the consensus, confirming your basic disregard for facts. KF kairosfocus

F/N: Let me refer to what is perhaps the classic text of Biochem, Lehninger (which I first met on Hall in my Uni in the late 70's), now in 8th Edn by a committee, pp. 194 - 5, as a point of reference:

The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits, but the expression of this information results in a three-dimensional cell. This change from one to three dimensions occurs in two phases. A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . The protein folds into a particular three-dimensional shape, determined by its amino acid sequence and stabilized primarily by noncovalent interactions. Although the ?nal shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function.

Clearly, AF's irresponsible rhetorical bluff attempt fails. We see, that D/RNA is a string data structure that ENCODES through linear sequence of AGCT/U, just as was long since already noted. This is essentially Crick's point in his Mar 19, 1953 letter to his son, as highlighted. Manifestly, the code in question is as tabulated in the OP, with minor variants. The code conveys information through the pattern of the sequence of bases, as was separately noted, i.e. codons, with start, elongation and stop. Obviously, the role of Ribosomes and tRNA with loading enzymes is also as described. Notice, these are not controversial matters, they are a matter of fact summary of core long since warranted points. The Cell A Molecular Approach, 8th Edn, Cooper, adds, p. 122:

Although the sequence of nucleotides in DNA appeared to specify the order of amino acids in proteins, it did not necessarily follow that DNA itself directs protein synthesis. Indeed, this appeared not to be the case, since DNA is located in the nucleus of eukaryotic cells, whereas protein synthesis takes place in the cytoplasm. Some other molecule was therefore needed to convey genetic information from DNA to the sites of protein synthesis (the ribosomes). RNA appeared a likely candidate for such an intermediate because the similarity of its structure to that of DNA suggested that RNA could be synthesized from a DNA template [--> notice where templating happens and from Lehninger where string data structure encoding and expression toward protein synthesis happens] . . . RNA differs from DNA in that it is single-stranded rather than double-stranded, its sugar component is ribose instead of deoxyribose, and it contains the pyrimidine base uracil (U) instead of thymine (T) . . . However, neither the change in sugar nor the substitution of U for T alters base pairing, so the synthesis of RNA can be readily directed by a DNA template. Moreover, since RNA is located primarily in the cytoplasm, it appeared a logical intermediate to convey information from DNA to the ribosomes. These characteristics of RNA suggested a pathway for the flow of genetic information that is known as the central dogma of molecular biology: DNA --> RNA --> Protein

And more. In short, the irresponsible attempt to bluff and hyperskeptically dismiss by AF fails. As should have been obvious. Why did he make such a resort? Because, the consequences of massive coded information in the cell, claims of molecular evolution etc notwithstanding, are devastating to evolutionary materialistic scientism and fellow travellers. As we go on to see other hyperskeptical rhetorical gambits by AF and co, let us bear this track record of ill founded bluffing in mind. KF kairosfocus

AF, the biochem, despite your denials and dismissals, shows the framework in which the genetic code is a code.

Like code, says Crick.

It is all actually tabulated and works in a string data structure using mRNA as the means of numerically controlling the Ribosome.

Poor analogies show your ignorance of the biochemistry. This is curable, KF. There are books that are not too technical that you wouldn't benefit from reading them.

Several Nobel Prizes were won showing that. KF

I don't think so. Alan Fox

AF, the biochem, despite your denials and dismissals, shows the framework in which the genetic code is a code. It is all actually tabulated and works in a string data structure using mRNA as the means of numerically controlling the Ribosome. Several Nobel Prizes were won showing that. KF kairosfocus

Oops. How that got posted four times? Immaterial forces at work? Alan Fox

Yes the biochemistry is well established. I excuse your ignorance as you have never studied the subject at an academic level. Alan Fox

AF, no. The biochemistry is well established and several Nobel Prizes were awarded. It is now literally taught down to primary schools in some measure. Your problem is you refuse to acknowledge the information system architecture that rides on the molecular nanotech. You see string data structures with start, elongate in ways 1 to n, stop and refuse to acknowledge codes in action. Much less algorithms. You snatch at any straw you hope will keep that afloat, such as above not noticing the boxed remark by Crick. You have gone out on a rhetorical limb and it is cracking behind you. KF kairosfocus

RNA world says no to F/N 2 Alan Fox

Well biochemistry is what I'm somewhat qualified to discuss. Anyone else? Alan Fox

See F/N 1 and 2. kairosfocus

But Immaterial mind (mine) creates the sequence and the thoughts flowing into this keyboard.

I suppose we could segue off into philosophy of mind, determinism, philosophical zombies and free will if you want. The OP is about the biochemistry of protein synthesis. Alan Fox

AYP, actually in the 3rd chart Yockey was elaborating the Shannon T/comms framework architecture and applying it to protein synthesis. KF kairosfocus

AF, the usual framework is a layer cake architecture. There is a physical layer but that does not mean there are no informational, software layers. Crick's letter to Michael used fountain pen marks on paper but the text in English does not reduce to the physics of marks on paper. KF kairosfocus

The first diagram from KF reminds me of how messages are sent and received in a distributed but connected communication system. The sender encloses the message between a set of start and stop bits, and the receiver then scans the incoming stream for those start and stop bits and captures the message for downstream use. Analogy! ayearningforpublius

AF, slide down to the box, you will see emphatically, this IS a code. This may be the light bulb moment caught in this letter to his son. KF kairosfocus

AF: And another analogy is this very message I am typing. Every step involves electromechanical interactions once the keys are depressed, and the keystroke is accepted by the computer. But Immaterial mind (mine) creates the sequence and the thoughts flowing into this keyboard. ayearningforpublius

At all stages of the process, notwithstanding that DNA-to-RNA copying is called translation, every step involves physicochemical interactions. [ED: AF full well knows the focus is protein synthesis, which uses the genetic code as a code to effect stepwise assembly of AA chains as a key stage of protein synthesis. He evades the illustrative diagrams in the OP and tries to use the template mechanism as a red herring led away to a strawman. But in fact mRNA creation is ALSO a stepwise algorithmic process as was added to OP on Sept 2. KF] Alan Fox

In Francis Crick's letter to his son, he explains his use of 'code'. This is like a code Not 'this is a code'. It's an analogy. [ED: Kindly see p. 5 of the letter above, AF strategically omits a few lines later where Crick affirms that DNA IS a code using underscore. That sort of misdirection, regrettably, is a typical rhetorical tactic AF uses. KF] Alan Fox

Protein Synthesis . . . what frequent objector AF cannot acknowledge kairosfocus