Uncommon Descent Serving The Intelligent Design Community

Paper at Nature Reviews Genetics demands some respect for junk DNA

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

File:DNA simple.svg

Abstract: Pseudogenes are defined as regions of the genome that contain defective copies of genes. They exist across almost all forms of life, and in mammalian genomes are annotated in similar numbers to recognized protein-coding genes. Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution. – Cheetham, S.W., Faulkner, G.J. & Dinger, M.E. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet (2019) doi:10.1038/s41576-019-0196-1 Published: 17 December 2019

The friend who sent us the abstract also quotes from the paywalled paper:

In addition to the untested hypothesis that evolution has left us with a dichotomy between genes and pseudogenes, the term pseudogene itself asserts a paradigm of non-functionality through its taxonomic construction. Pseudogenes are defined as defective and not genes. This point is highlighted because impartial language in science is known to inherently restrict the neutral investigation between conflicting paradigms[119]. In the case of pseudogenes, the term itself is constructed to support the dominant paradigm and therefore limit, consciously or unconsciously, scientific objectivity in their investigation.

It was in fact Darwinism that prevented the role of pseudo genes from being properly recognized.

As another friend puts the matter, “This is an important paper for documenting that not only is pseudogene function is far more prevalent than we often recognize but also that evolutionary “dogma” has prevented investigation into the function of pseudogenes. The paper’s message is that pseudogenes probably have many more functions than we think and only the false view that they are “junk” prevents us from finding them.”

Remember how important pseudogenes (evolution’s huge library of useless junk) once were?

By now, Darwin could paper his study with goodbye notes.

Comments
UB, Thanks for the explanatory answer.OLV
January 21, 2020
January
01
Jan
21
21
2020
09:04 AM
9
09
04
AM
PDT
. Sven, by my count, you have failed to engage in any question asked of you. I'll try once again:
You say: Pattee does not just say it’s questionable. He says they have enormous differences.
1. First, Pattee doesn't say the conclusions of his 50 years of research are "questionable". That was your rhetoric. 2. Do any of these "differences" (you claim as relevant) actually nullify the simultaneous requirements of a linear rate-independent medium and a coordinated set of coding constraints? Do any of them eliminate spatial-orientation as the means to distinguish one referent from another in a common medium? How about the need for semantic closure? Can you answer of these question?Upright BiPed
January 21, 2020
January
01
Jan
21
21
2020
08:04 AM
8
08
04
AM
PDT
.
Is there a known physicochemical association between the GCAT-based 3-letter codons and the corresponding amino acids?
The short answer is: "I've checked the list of Nobel Awards and didn't find any" The longer answer is that there has been a Nobel effort for the past half-century, which has produced little fruit. Materialists* really haven't even convinced themselves of a mechanism. Further, something like a stereochemistry origin wouldn't actually answer the larger issue of semantic closure, which is required in order for any association to stick over time. Semantic closure can only occur when there is a functional relationship between the descriptions (memory) of the interpretive constraints operating in the system and the descriptions of the system itself. The former alters the latter. * I hesitate to add that if you surveyed some of the names appearing on the latest rounds of research and speculation on this issue, names would appear of people that I have had several very pleasant conversations with - people who have actually read things that I have written and been surprisingly complimentary. I have a good amount of humble respect here, and I know both they and their research goals are genuine. The physical and organizational requirements remain what they are.Upright BiPed
January 21, 2020
January
01
Jan
21
21
2020
07:11 AM
7
07
11
AM
PDT
Sven Mil:
This isn’t how you twist Pattee’s work while simultaneously demonstrating your lack of biological knowledge.
YOU are not one to talk about a lack of biological knowledge in others. YOU have yet to post any biological evidence or science that would support anything you have spewed. And THAT is very, very telling.ET
January 21, 2020
January
01
Jan
21
21
2020
05:59 AM
5
05
59
AM
PDT
UB, Is there a known physicochemical association between the GCAT-based 3-letter codons and the corresponding amino acids?OLV
January 21, 2020
January
01
Jan
21
21
2020
12:39 AM
12
12
39
AM
PDT
.
He recognizes that the analogy breaks down and that the essential differences between them are what allow the molecular evolution of the genetic language, while requiring intelligent input for the creation of human language.
You have this backwards. It is not “the essential differences” between human language and genetic language that allows molecular evolution; it is what is common between them (i.e. a rate-independent linear medium, a set of multi-referent coding constraints, extendibility, etc) – it is their open-endedness for crying out loud. The ability of both human and genetic languages to change and evolve is enabled by what they share, not their differences. From a material perspective, both systems must not only be able to physically express a referent, but also any variation of that referent. (”It is this broad expressive power that is the unique and essential feature that allows both open-ended evolution and - after 4 billion years - human speech.” Pattee). However, it appears you are merely lodging an objection because genes can evolve via mutation/error, whereas words change as humans coin new ones or modify old ones. If that is the case, then I don’t know what to tell you. Your point of reference may be rhetorically opportunistic, but it’s physically irrelevant to the system.Upright BiPed
January 20, 2020
January
01
Jan
20
20
2020
10:38 PM
10
10
38
PM
PDT
.
“All metaphors have limits. There are other analogies of genetic and human language (e.g., Sereno 1991), but these similarities should not obscure the enormous differences between genetic and human language. Those differences are why their relation is still a tacit metaphor. The crucial linguistic similarities that account for their great expressive power are few and simple, while the differences in their production, interpretation, and functions are many and complex, as you would expect after 4 billion years of evolution.”
Yep.
“The essential semiotic functions of writing, reading, and interpreting symbols in genetic language and in the brain’s language have different material substrates, different functions, and operate by completely different processes. ”
Yep. And so? No one thinks or assumes anything different, and never have. I think the very first paper I ever read by Pattee, he made the point as clearly and vividly as possible that genetic language and human language are separated by four billion years of evolution, and that it was his goal to study the necessary physical conditions of symbolic control at its primal level. So he did. He didn’t require the vague terminology of semiotics, nor the evolved refinements of linguists. He studied the physical conditions themselves. Okay, no problem. Now what, Sven? Is it your claim that Pattee doesn’t believe the gene is a linear multi-referent symbol system? Are you even able to answer that question? Let us see if you are.Upright BiPed
January 20, 2020
January
01
Jan
20
20
2020
07:40 PM
7
07
40
PM
PDT
Howard Pattee: "All metaphors have limits. There are other analogies of genetic and human language (e.g., Sereno 1991), but these similarities should not obscure the enormous differences between genetic and human language. Those differences are why their relation is still a tacit metaphor. The crucial linguistic similarities that account for their great expressive power are few and simple, while the differences in their production, interpretation, and functions are many and complex, as you would expect after 4 billion years of evolution." Sorry, Pattee does not just say it's questionable. He says they have enormous differences. He goes on "The essential semiotic functions of writing, reading, and interpreting symbols in genetic language and in the brain’s language have different material substrates, different functions, and operate by completely different processes. " And on " I know of only one early discussion between a biologist and a linguist about the significance of genetic and human language similarity. That was between François Jacob (1977) and Roman Jakobson. Jacob’s view was that the analogous structures resulted only from the requirements of analogous functions, i.e., convergent evolution—a view with which I agree because of the enormous differences between the two languages" Pattee openly admits the vast differences between human language and genetic language. He recognizes that the analogy breaks down and that the essential differences between them are what allow the molecular evolution of the genetic language, while requiring intelligent input for the creation of human language. Pattee recognizes where the analogy breaks down and the importance of this fact. You ignore this, assume that the analogy is perfect, and demand that others see it this way. This isn't how you twist Pattee's work while simultaneously demonstrating your lack of biological knowledge.Sven Mil
January 20, 2020
January
01
Jan
20
20
2020
05:57 PM
5
05
57
PM
PDT
.
The only thing on your side is your own personal interpretation
Okay, then you should be able to point to a numbered comment upthread and name the specific things I’ve stated that are wrong. What are they, Sven? Is it where I said that autonomous open-ended self-replication requires the complexity of both a multi-referent medium and a set of physical constraints to interpret it? Is that what you think is just “my personal interpretation”? Or, is it where I asked you if the codon-to-anticodon association is independent of the anticodon-to-amino acid association? Do you think that question merely reflects my personal interpretation as well? Are you able to engage in any of these questions, Sven? Is the codon-to-anticodon association temporally and spatially independent of the anticodon-to-amino acid association, or not? Frankly (and I think most people grasp these things almost intuitively), I believe that if you had actually seen me making these mistakes and mis-interpretations, then you would have simply jumped right in to happily me in public -- directly and forthrightly – not by completely refusing to engage, as you have done here. This continued theme in your argument, where you are going to show my mistakes by keeping them to yourself, is incoherent.
Unlike you, UB, I know the actual molecular biology behind these systems.
Great! So you are the expert, and thus, can answer the question: Is the codon-to-anticodon association independent of the anticodon-to-amino acid association, or not? During protein synthesis, is the specification of a particular amino acid established by the structure of the codon or by the structure of the aaRS?
Pattee himself (as I’m sure you know since you incessantly cite him) admits that the language-cells analogy is quesuitionable
“admits” … “questionable” (!!!) Sven, you may be trying too hard. Pump the brakes and back up just a minute. Take good stock in the defense you are trying to sell here. Pattee is a guy who spent 50 years (very carefully and thoughtfully) writing about the symbolic necessity of the gene system. His life’s work includes such titles as: “The Necessity of Biosemiotics: matter-symbol complementarity”; “Physical and functional conditions for symbols, codes, and languages”; “The physics of autonomous biological information”; “How does a molecule become a message”; “The physical basis of coding and reliability”; “Laws and constraints, symbols, and languages”; “Symbol-structure complementarity”; “The Physics of symbols: bridging the epistemic cut” -- etc., etc., etc. Dozens upon dozens of published papers, all capped off with a final compendium entitled Laws, Languages, and Life, a collection of all his classic papers in a book form. And what you want to do here is to create and position the laughable narrative that -- even Pattee himself knows (admits!) that his whole life’s work is a meaningless analogy – it’s “questionable!” Oh … and how is it that you want to float this grand ruse? You go find a quote (from his response to Umerez) where he notes (as is not unusual for him) some of the differences between the genetic symbol system versus recorded or spoken language … and then you try to sell this as some clear admission that his five decades of science may be conveniently disregarded . It’s as if you actually believe there can be no material distinctions between genuine symbol systems. C'mon, get real.
UB, what does Pattee say about the molecular evolution of this symbol system in biology?
I know exactly what his position is. He believes that both life and evolution are fully dependent on a multi-referent “quiescent” symbol system, a set of interpretive constraints, and a successful process of semantic closure. And if you have read much of Pattee, then you already know the answer to the brunt of your question: He is satisfied that he’s properly defined the systems and conditions; but can provide no answer as to their origin. In other words, he writes as a disciplined scientist, not a salesman.Upright BiPed
January 20, 2020
January
01
Jan
20
20
2020
01:14 PM
1
01
14
PM
PDT
Sven Mil:
Unlike you, UB, I know the actual molecular biology behind these systems.
Very doubtful
I’ll give you a hint; he has no problem seeing potential pathways to the molecular evolution of the gene symbol system.
Even if true, no one cares, duh. Everyone knows that no one can demonstrate such a thing exists. You can't even get biologically relevant molecular replicators.ET
January 20, 2020
January
01
Jan
20
20
2020
09:46 AM
9
09
46
AM
PDT
Sven Mil
I’ll give you a hint; he has no problem seeing potential pathways to the molecular evolution of the gene symbol system.
I was gratified to find that Hoffmeyer and Emmeche (1991) recognize the fundamental symbol-matter problem of connecting discrete symbols with continuous dynamics, although I am not clear how their code-duality solves it. https://paperity.org/p/12962762/response-by-h-h-pattee-to-jon-umerezs-paper-where-does-pattees-how-does-a-molecule-become
"Symbol-matter problem". No, that's not the same as "no problem".Silver Asiatic
January 20, 2020
January
01
Jan
20
20
2020
09:26 AM
9
09
26
AM
PDT
"all the science, history, and literature is on my side" Lol. No. The only thing on your side is your own personal interpretation and twisting of the "field" of biosemiotics, which you then jumble together with your limited understanding of the actual molecular biology. Unlike you, UB, I know the actual molecular biology behind these systems. Pattee himself (as I'm sure you know since you incessantly cite him) admits that the language-cells analogy is quesuitionable and that there are enormous differences between human language and the language of genetics. He says language and genetics, while "intuitively similar in one fundamental aspect, are explicitly dissimilar in many ways." UB, what does Pattee say about the molecular evolution of this symbol system in biology? I'll give you a hint; he has no problem seeing potential pathways to the molecular evolution of the gene symbol system.Sven Mil
January 20, 2020
January
01
Jan
20
20
2020
08:58 AM
8
08
58
AM
PDT
Sven Mil:
These physical interactions can come about via molecular evolution.
So you say but never support. It's as if you think your ignorant spewage is an argument. And just saying an analogy fails is meaningless. You are just upset because your side doesn't have any analogies to call upon. So , Sven, you have no place to talk about someone's trustworthiness when all you are is a pathological liar.ET
January 15, 2020
January
01
Jan
15
15
2020
04:25 AM
4
04
25
AM
PDT
. By the way Sven, you have been trying to impugn me from the very start of this exchange, as anyone can see. Suggesting that I am lying (or worse) as you have here, is not particularly interesting, and is not something that I need to bite off on. The only thing that really matters (in the physical sciences) is what you can actually show and demonstrate. Yet, you keep making claims, but never actually connect the dots to support those claims. On the other hand, all the science, history, and literature is on my side regarding this subject, and I have been fully aware of this all along. There are plenty (dozens) of articles in the literature I could offer that might aide you in bringing your conceptions up to speed. I'll offer you one. If you care to have something more to say than just personal attacks and empty claims, then you can find your way from there. Howard Pattee: The Physics of Symbols; bridging the epistemic cut cheersUpright BiPed
January 14, 2020
January
01
Jan
14
14
2020
11:27 PM
11
11
27
PM
PDT
.
I have never said von Neumann was wrong,
So the gene system is a semantically-closed symbol system? Okay.Upright BiPed
January 14, 2020
January
01
Jan
14
14
2020
10:57 PM
10
10
57
PM
PDT
Once again UB, you are deliberately twisting my words in order to push your own agenda. I have never said von Neumann was wrong, you're just apparently in perpetual strawman-building mode (like many of your friends here). What I have repeatedly said is that the machine analogy breaks down at the molecular level. The analogy works as a description of the basic parts in perfect self-replication, which at the time was quite an accomplishment. Though, perfect self-replication is not what happens in biology. Small variations occur, and biological systems are tolerant of these variations, in fact it is what evolution is built on. Machines are not tolerant of this. I believe von Neumann himself even predicted that biological systems could undergo mutations which would then be inherited and subsequently produce variability in offspring. In fact this is all in the Sydney Brenner series that you, yourself, initially posted here. Of course you have conveniently left that out. (Just another example of your complete lack of trustworthiness) Anyways, back to the problem at hand; which you were so quick to steer away from. The machine analogy (as well as all of your other terrible analogies) breaks down when extrapolating it to the level of molecular biology. The transformation of information in cells occurs through physical interactions. These physical interactions can come about via molecular evolution. All of your analogies require an intelligence to make the initial association and/or make subsequent interpretations of the symbols. The machine analogy fails. All of your analogies fail.Sven Mil
January 14, 2020
January
01
Jan
14
14
2020
10:19 PM
10
10
19
PM
PDT
. Nobel Laureate Sydney Brenner once commented that “what von Neumann got right” is what “Schrödinger got wrong” in his classic paper What Is Life. Prior to von Neumann, Erin Schrödinger had predicted that the cell would include a heritable description of itself, along with the physical means to decode that description. Von Neumann offered a more precise formulation, predicting instead that the cell would contain a heritable description of itself, but with a description of the means to decode it. Brenner insisted this was a fundamental distinction. Given that you’ve come back to imply (once again) that von Neumann was somehow wrong – a bad analogy; that the gene system is not really a genuine symbol system – don’t you think you should tell us what he got wrong? But if that question is one you simply won’t answer, we can always discuss the issues in other terms. After all, the design inference is not dependent on von Neumann’s prediction; it is dependent on the recorded descriptions of the gene system itself – “using the language of physics” as Howard Pattee would say it.Upright BiPed
January 12, 2020
January
01
Jan
12
12
2020
02:28 PM
2
02
28
PM
PDT
"Saved By Junk DNA: Vital Role In The Evolution Of Human Genome" 'Stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome, researchers have now shown. They found that unstable pieces of 'junk' DNA help tuning gene activity and enable organisms to quickly adapt to changes in their environments'. https://www.sciencedaily.com/releases/2009/05/090528203730.htmTruthfreedom
January 12, 2020
January
01
Jan
12
12
2020
10:39 AM
10
10
39
AM
PDT
. Sven, Von Neumann predicted that autonomous self-replication would require (among other things) one arrangement of matter to serve as a set of symbolic representations, and a second set of arrangements that would independently establish what was being specified by those symbols. The system would then use the spatial orientation of objects within the medium to distinguish one referent from another. Allow me to ask you a question. Inside the cell, is the codon-to-anticodon association independent of the anticodon-to-amino acid association? And, isn’t it the spatial orientation of nucleobases within a codon that signifies one amino acid from another? Is this the point where you are going to finally tell us what von Neumann got wrong?Upright BiPed
January 12, 2020
January
01
Jan
12
12
2020
09:38 AM
9
09
38
AM
PDT
Sven Mil:
however in biology, the transformation is entirely carried out by physical interactions.
And with computers it is carried out by electrical interactions. So what? We know that computers did NOT arise via physio-chemical processes. And the same can be said for biological organisms.
Intelligence is not needed to assign amino acid to codon, this can be done via molecular evolution...
Nice question-begging and unsupportable trope. Next time, Sven, present the science as opposed to your wishful thinking.ET
January 12, 2020
January
01
Jan
12
12
2020
09:05 AM
9
09
05
AM
PDT
So you have to dredge up some fledgling field in order to defend yourself UB? Lol. Von Neumann correctly predicted the basic components of cellular replication, as I have said. But your extrapolation of this machine system and forcing its constraints upon molecular biology is what is wrong. Your friend kairos here has already admitted that von neumanns system is only "reasonably comparable," it's not looking good! The difference between biology and all your bad analogies is that intelligence is require to initiate and transform the information of symbol systems in language etc. however in biology, the transformation is entirely carried out by physical interactions. Intelligence is needed to assign cat to a furry creature and interpret the word cat as so. Intelligence is not needed to assign amino acid to codon, this can be done via molecular evolution and is interpreted by a series of molecular interactions. This is why the analogy fails.Sven Mil
January 12, 2020
January
01
Jan
12
12
2020
08:02 AM
8
08
02
AM
PDT
. The answer to the question I posed in comment #94 (are there any visiting critics prepared to acknowledge the physical reality) remains “none thus far”.Upright BiPed
January 8, 2020
January
01
Jan
8
08
2020
09:13 AM
9
09
13
AM
PDT
Maybe Sven Mil is still working on his response.Silver Asiatic
January 8, 2020
January
01
Jan
8
08
2020
06:02 AM
6
06
02
AM
PDT
An immensely enjoyable thread. I don't remember our opponents looking so miserable facing scientific facts.EugeneS
January 8, 2020
January
01
Jan
8
08
2020
04:12 AM
4
04
12
AM
PDT
PS: Menuge on the factors C1 - 5:
For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met: C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function. C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time. C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed. C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant. C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly. ( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)
kairosfocus
January 3, 2020
January
01
Jan
3
03
2020
04:20 AM
4
04
20
AM
PDT
SM, 70:
Irreducible complexity is just a way to shoehorn design into something complex. It amounts to: “look at how complex this is! It must be designed!”
Strawman. An irreducibly complex entity comprises a core of several interacting parts, each necessary for and together jointly sufficient to achieve a result. For simple instance, a fire requires heat, oxidiser, fuel and uninterfered with chain reaction. Knock any one out and it cannot start of keep going. The phenomenon is a commonplace. In the context of biosystems, you need to know that many biological entities are studied through knockout experiments, showing that missing this or that part, the function does not happen. The point is, if something is sufficiently complex and organised in a way that requires a core of enabling elements to be mutually well matched and arranged, then it has to arise all at once, not by increments. Which leads to the islands of function isolated in configuration space effect and thus frustrates searches based on incremental hill climbing in one form or another. That brings back the issue of leaps. And a lot more can be put on the table. KFkairosfocus
January 3, 2020
January
01
Jan
3
03
2020
04:15 AM
4
04
15
AM
PDT
. Sven, Von Neumann considered the ways in which an complex object might replicate itself, centering on the idea that it could replicate through either self-examination or through recorded memory. He went on to predict that replication would most effectively proceed from a description stored in an encoded symbolic memory. He referred to it as a “quiescent” (inert) description, meaning that it would not in some manner become the product of the process, but would be “read” and used to control the process instead, specifying the product. He had some intellectual grounding for this kind of analysis, giving that he had already shown that the act of measurement (the creation of a record) could not be reduced to law without infinite regress, for instance. Further, von Neumann was an admirer of Alan Turing, and supposed that his machine (following Turing) would not only have the faculty to read the description (which is its own specialized physical process) but would also contain a set of physical “constraints” in the system to properly interpret the symbolic description it was reading. All of this would be wrapped up in a coordinated dissipative process that would cause the symbols to be read and the process of construction to be successfully followed, enabling semantic closure to occur (so that the system could persist over time) As we now know, all of these issues and predictions were experimentally demonstrated in the gene system. We have the inert molecule of DNA (physically established as a medium of information by the arrangement of discontinuous association between it and its referents); the encoding system in codons, the faculty of reading, the set of interpretive constraints in aaRS, as well as all the remaining details of copying, control, and coordination that make up the required dissipative process. When you say;
Just because the machine-replication system is irreducibly complex, does not mean the biological system is irreducibly complex.
I would like to know what you think the distinction is? Von Neumann’s analysis was based on the physical and logical necessities of construction from a quiescent symbolic memory. To the best of my knowledge, atoms of matter being involved in biology are not imbued with a special status beyond physical law. Are you suggesting that the reading a symbol made up of the spatial arrangement of iron oxide on a computer tape needs an interpretive constraint in order to properly convey its referent, but the reading a symbol made up of the spatial arrangement of nucleotides in a codon doesn’t? - - - - - - - Isn’t this merely the case that you were unaware of the actual details and recorded scientific history that surrounds (and patently supports) the modern design argument, and did not recognize that you are forced to simply assume your conclusions in order to argue directly against that physical and historical evidence? Isn’t it also true that your personal remarks about me (and others here) are intended to dredge up popular derogatory images of design proponents which have nothing whatsoever to do with the physical and historical information I was conveying to you?Upright BiPed
January 1, 2020
January
01
Jan
1
01
2020
10:54 AM
10
10
54
AM
PDT
SM, kindly, drop the sweeping dismissals and engage substantial facts. For example, D/RNA implements an algorithmic, 4-state digitally coded string data structure used to control the assembly of proteins, which are themselves molecular nanomachines. The coded algorithmic information was recognised from the outset by Crick. This is an expression of language, a signature of intelligence -- if you doubt kindly provide an actually observed creation of similar string based complex functional information beyond 500 - 1,000 bits by blind chance and mechanical necessity. Going beyond, the bacterial flagellum is a rotary motor, coupled to a whip-like tail that provides propulsion. The cell's replication process is reasonably comparable to von Neumann's kinematic self replicator architecture, which served as a case of theoretical prediction. Going beyond, there is a reason why many technologies parallel or outright copy the systems we find in the world of life. for simple example, our hearing is based on a time to frequency domain transformation using excitation of hair cells. And more. However, what is clearly decisive is the digital, algorithmic technology in the heart of the cell. KFkairosfocus
January 1, 2020
January
01
Jan
1
01
2020
09:47 AM
9
09
47
AM
PDT
.
I hate to break it to you, but there is nothing irreducibly complex in all of biology.
You seem very fond of merely repeating your claim without substance. On the one hand you say that Von Neumann was astute and correct when he predicted the irreducibly complex system that enables autonomous open-ended self replication. Then you turn right around and say he was wrong. Tell us. Tell us what he had wrong.Upright BiPed
December 31, 2019
December
12
Dec
31
31
2019
05:23 PM
5
05
23
PM
PDT
.
No, you avoided the question, as you are doing now. Probably because you know that machine-biology analogies are extremely superficial.
I am avoiding nothing, which is why I gave you a summary of specific issues involved - after all, it is the details that most properly frame the issue, and that is why they interest me (and all those curious scientists who study them). On the other hand, it appears very clearly that you would like to continue hammering at the idea of a “false analogy“ without actually entering into any of the details whatsoever. Can you point to any comment recorded on these pages where you have actually examined the empirical details of the thing/system you are attempting to make claims about? I have not seen it. All I see is you merely repeating your conclusion, without providing any of the details that would be required to make your case. This all forces an interesting conundrum for the users of this blog (like me) who have spent a good amount of time over many years reading the primary literature on these systems. On the one hand we have well-respected well-known researchers (biologists and physicists, for instance) writing in respected journals for years upon years — very dutifully engaging the details of these system at the level of physical law and the formulas of energy and motion — stating very clearly (without any ambiguity whatsoever) that they are not expressing mere metaphors, as you are attempting to suggest here. Who is right on this issue Sven? Is it you, who seems unable to provide any of the details that would demonstrate the false analogy that you propose -or- is it the researchers such as H.H. Pattee, M. Barbieri, and many others who have published dozens upon dozens of papers carefully and coherently describing this specific issue over the past five decades?Upright BiPed
December 31, 2019
December
12
Dec
31
31
2019
05:13 PM
5
05
13
PM
PDT
1 2 3 5

Leave a Reply