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.
Well this all seems fine and well but two things.
First I’ll beat everyone to and save “I can see how this would be an issue for evolution” my problem exactly nothing is
Secondly and far more important in my eyes, wouldn’t it actually be bad if Pseudo genes had not only function but explanatory power to explain everything that makes is human
Giving rise to the second coming of genetic determinism
I for one would be happy with junk DNA if that was the case but am I overstepping my bounds by saying that genetic the terminus could start using pseudo-genes to explain everything a gene for this a gene for that type Mentality
What do you think
AaronS
I was going to say something about the false claims by evolutionary theory on pseudogenes — and doesn’t that falsify the theory? But as you stated, nothing can be a problem for evolution, including a direct contradiction of predicted outcomes.
On the other thing, yes there’s a huge source of DNA that can support all kinds of speculations and supposedly everything we do, say, think, imagine, hope for or dream of is controlled by one gene or another.
Evolution means never having to say you were mistaken.
For evolution, we make sure that every observation will support the theory, even before we make the observation.
Evolution makes everything turn out for the best, even our own failed predictions.
Evolution causes us to believe whatever it says, so there are no losers. Everybody gets a trophy.
I’m not sure how to interpret this. When I went through university we were told that junk DNA would eventually be selected against. Now we are being told that any evidence against junk DNA is proof against evolution. And, on the other hand, people like ET claim that junk DNA is proof of the fall and to be expected. My head is spinning.
Ed George @ 3
Evolutionists claimed that our genome being 99% junk proved we weren’t created because why would a creator load our genome with junk. This argument is being eroded as more and more function is found in that “junk”. However as a YEC I would also say that the genome could contain some junk. Genetic entropy since creation could well have corrupted some of the genome. Perhaps, for instance, we could once synthesise vitamin C but lost that along the way..
Silver Asiatic
I was being facetious, And it was also supposed to be “I can’t see” Which is what we often see, nothing is a problem for the theory. Which if anybody knows me that’s my main gripe with the theory
Ed George exactly!
Now this is what I know for certain that the original interpretation is that we needed pseudo genes and junk DNA as part of our biological continual. It was essential to support the theory because junk DNA showed the biological history of the creature as it evolves
So there has to be nonfunctional DNA a.k.a. junk DNA and pseudo-genes
No proponents of ID would like to find function and lots of function in junk DNA because then it would better support the concept of irreducible complexity and design
That’s my understanding of this
However in my comment I wanted to bring up the double edge sword of genetic determinism if that were the case and what we would make of that
I don’t know about “people like ET”, but this ET says that the existence of histone octamers is evidence against junk DNA. Why? What happened, these biological spools just happened and the DNA just happened to start winding itself around them as they appeared?
That said, broken genes are evidence for blind watchmaker evolution, ie accumulations of genetic accidents, errors and mistakes. But not even that means they are junk. The fact is the current paradigm is preventing from finding the best explanation behind the meaning of the genome.
as to:
This is yet more evidence that the ‘narrative gloss’ of Darwinian evolution is an impediment to science
Darwinian evolution, far from being a science that bears fruit for humanity,,,
,,, Darwinian eolution, far from being a science that bears fruit for humanity,,, Darwinian evolution is a useless and unfalsifiable pseudoscience that is parasitic on science as well as being a severe impediment to the progress of science. As well as being very ‘unfruitful’ for man in particular.
Biology simply does not need Darwinian presuppositions
In short, Darwinian evolution is useless and harmful to both biological science and human society. And these harmful influences of Darwinian evolution are not limited to just the periphery of biological science and society. For prime example
And as cruel as Muslims have been in their barbarity, still It would be hard to fathom a more unfruitful worldview than Darwinian Atheism has been for man thus far.
Whereas on the other hand Christianity is found to be very fruitful,
Indeed, it was the Christian worldview alone (out of all the worldviews) that gave rise to modern science itself,
Verse:
ET
The blind watchmaker cannot make a mistake because he does not have a purpose or goal in mind.
Chemicals cannot produce errors. They do not want or need to survive. A living organism has no greater benefit or value than any collection of inert chemicals does. The fact that we can distinguish Junk DNA from functional DNA is evidence of Design, since everything the blind watchmaker creates should be Junk. The blind watchmaker has no need or interest in functional DNA.
An intelligently designed process can have errors or mistakes because it has a goal in producing organisms that live. In that view, life has value and mutations could be a problem.
We can speak of “defects” in a design. But as more function is discovered for Junk DNA it may be entirely necessary and useful in the cell. Otherwise, even in evolutionary terms, why would it be preserved?
Lol.
This comment section is a perfect example of people “having no knowledge of biology but trying to talk about the details of, and explain, biology.”
Silver Asiatic- Given the proof-reading and error-correction mechanisms say that there will be accidents, errors and mistakes that need to be corrected.
LoL! Sven thinks its cowardly accusations mean something./
ET
True, but error-correction mechanisms in themselves are evidence against evolution since all the diversity on earth was created by errors, so why correct them? Error correction frustrates the supposed creative power of mutations.
Sven Mil
You put that in quotation marks. Is that something an important person said? I mean, you’re certainly important – so you’re quoting yourself?
Yes, SA. My original point was that blind watchmaker evolution breaks things. That is what it does.
Sure.
And here’s another great quote
“the existence of histone octamers is evidence against junk DNA”
You can’t make this stuff up.
ET
By trial and error, the blind watchmaker creates and breaks things, so Junk DNA is just the untidy workshop where all of the broken parts are left over. These broken parts are preserved generation after generation, along with all of the functional parts.
I’d think the trial and error process would be more efficient by now and there should be a continual decrease in coding errors and broken genes. There should be less reason to preserve the junk over a few million years or so also.
My point was that the watchmaker is blind and unintelligent. He doesn’t care about anything, and doesn’t even think he’s a watchmaker.
Changing the analogy, he’s a bull in a china shop. There’s a lot of broken glass on the floor.
But the claim is that the bull actually built the china shop and all of the glassware. Some of it got broken and he doesn’t bother to clean it up.
Sven Mil
It seems like you’re assuming that you have a good explanation for all of this, and that everybody should believe the evolutionary propaganda and not require any actual evidence.
But instead of just scoffing and ridicule, why not defend your worldview?
A blind, unintelligent, mindless effect (it’s not even a process). That’s what you’ve got to work with.
LoL! Sven Mil the cowardly quote-miner. Please share with us the evidence-free special pleading on how blind and mindless processes produced those spooling histone octamers. Or admit that you are just an ignorant and cowardly troll.
SA, the blind watchmaker can only create a mess.
ET – exactly.
Now I want to see how Sven Mil explains how the blind watchmaker created genetic code.
Sven Mil what was the purpose of your comment other to be a jerk? It was near purposeless short of being rude and imply you know better then everyone else. If you do, you can just as easily say it’s not correct, present the reason why, and then we can discuss.
These papers seem to answer all the important questions about the origin and evolution of the chromatin histone octamers:
The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms 2010
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins 2019
PavelU,
Thanks for citing those two papers.
I won’t look at the first paper you cited, because it’s too old for my taste. 🙂
However, I looked at the second paper you cited -which is very recent- and found some interesting text you may want to review:
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins
Perhaps your claim that this paper seems to answer important questions could be taken as valid up to certain point, but note that the paper does not explain how the chromatin histone octamers originated or evolved. it just describes their observations and obviously sprinkle the expected “evolutionary” jargon over the text just to make sure it’s acceptable to the censorship.
i would respectfully suggest you spend more time doing some serious homework reading carefully the papers you want to cite before you post your comments. You’re welcome to cite papers and ask questions about them, but try to refrain from making unsupported claims that make you look very bad in this public forum. My friendly advice.
Be aware that the biology research literature is huge and it keeps growing, but it’s mainly describing what they observe, answering outstanding questions while posing new ones. That seems the result of the reductionist bottom-up research approach that is generally taken, which seems like a reverse engineering work. Such a path usually generates more questions than it can answer. Specially when it deals with a complex system that was designed top-down.
Important issues raised here:
When asked to ‘put up or shut up’, i.e. to engage with the arguments of his opponents in any kind of serious way (wherein a potential for really hilarious wit lies, ironically), just silence. But we must be grateful for small mercies.
I’d be careful in what you say, he might get a reply saying he wouldn’t want to waste his time with such idiots, we wouldn’t understand anyways
When someone explains how “the existence of histone octamers is evidence against junk DNA,” then I’ll be willing to chat with you geniuses about biology.
Goodluck!
Watch out Sven, with that attitude someone with little intellect might accuse you of being Acartia, or Spearshake, or Occam. Whoever they may be. 🙂
Sven Mil
Spoken like a true troll 😉 Almost exactly what I predicted
Sven:
Already have. The existence of histone octamers prove that the length of DNA was expected. It is evidence that said length was intelligently designed. That is because the alternative, that those octamers just happened and just happened to be able to spool that length of DNA an organize it so that it is useful, is beyond absurd. And it is untestable claptrap.
Now that the evidence points to an intelligent design origin for said octamers, the evidence that most of the DNA is junk goes out the window. There is obviously a design reason why the DNA is that long. And to ID that reason is for the storage of immaterial information.
From a couple years ago:
Junk DNA is bein g discussed over on the skeptical zone. In the discussion Larry Moran made the claim that 90% of the human genome is junk and he could get a human to develop using just his chosen 10%. He says the junk has accumulated over the illions of generations since eukaryotes arose.
However there is a problem with that. The problem are the histone octamers used as spools which DNA is wound around to package it in the nucleus. Without the added 90% junk they wouldn’t be required. But with all of that junk it wouldn’t be possible to package it within the nucleus without the histone octamer spools.
So how did blind and mindless processes figure this out and create the spools to solve the problem? Whoops, the problem isn’t just the spools, the spools are active as the DNA moves around them to get exposed and align with other sequences on other histone spools. How did blind and mindless processes pull that off? No one can say. Sven never will
ET
Don’t waste your time with Sven Mil
Acartia Eddie:
LoL! You, “Ed George”, have already admitted to being “William Spearshake”. So perhaps you need to get a grip on that leaking brain of yours.
Thanks AaronS. I understand that Sven is a waste of time. Now we can prove it. 😎
“The existence of histone octamers prove that the length of DNA was expected.”
That’s what you came up with?
Lol this is what you guys call “science?”
And there it is he simply dismisses it, says you’re stupid and walks away
It’s a waste of time he’s just being a troll
Sven, Sven the egg laying hen. Likes to accuse but never defend.
Sven, your continual quote-mining proves that you are just another insipid troll. Good luck with that.
Let’s start with the closest thing to “science-y” that you’ve come up with:
“Without the added 90% junk they wouldn’t be required.”
Do you have any evidence for this claim or did you just pull it out of your derrière?
No Sven, let’s start with your quote-mining cowardice and obvious scientific illiteracy. And let’s continue with the fact that there isn’t any viable scientific alternative to ID.
Plucked it from your derrière. Got it.
At least now we know not to believe a word you say when it comes to anything science.
Like I said, UD’s motto:
“People with no knowledge of biology, trying to talk about and explain biology”
Yes, Sven was plucked from someone’s derrière. Sven is proud to display its ignorance and belligerence. Sven is a prime example of “People with no knowledge of biology, trying to talk about and explain biology”.
Nice own goal, loser
The existence of histone octamers prove that the length of DNA was expected. It is evidence that said length was intelligently designed. That is because the alternative, that those octamers just happened and just happened to be able to spool that length of DNA an organize it so that it is useful, is beyond absurd. And it is untestable claptrap.
Now that the evidence points to an intelligent design origin for said octamers, the evidence that most of the DNA is junk goes out the window. There is obviously a design reason why the DNA is that long. And to ID that reason is for the storage of immaterial information.
Sven is too cowardly to deal with that.
Without the added 90% junk they wouldn’t be required.
That would be because the longest chromosome would be smaller than the largest bacterial genome, for which there aren’t any histone octamer spools required. But then again, unguided/ blind watchmaker evolution cannot account for the existence of chromosomes. So Sven is a failure before it even gets started. 😛
Everything you have said is either made-up, flat-out wrong, or both.
Assuming you’re referring to the human genome, because you aren’t aware of the vast diversity of eukaryotic genome sizes, you are flat out wrong. The largest human chromosome is ~250 million bases, 10% of which is still much larger than the largest bacterial genome (~13million bases).
Also you do know that bacteria compact their genome by other means right?
Not to mention that eukaryotes use other methods to compact their genome, which are similar or identical to that of bacteria. (Google polyamines)
You and your friends here are absolutely clueless.
Sven, don’t confuse ET with facts. At least not this close to Christmas.
Wow. Sven, that bacteria compact their genomes in other ways has absolutely no bearing on the histone octamer spools. You don’t have a mechanism capable of accounting for those bacteria nor how blind and mindless processes produced the method they use to compact their genomes.
That said, yes our longest chromosome is 250 million. But given the hypothesis that junk DNA is the cause for the size we would expect that chromosome to contain more than 90% junk. The 90% figure pertains to the entire genome. It is not that each chromosome would be 90% smaller. And even then you still don’t have a mechanism that can account for the histone octamer spools. And you still cannot account for the existence of chromosomes.
Also- But then again, unguided/ blind watchmaker evolution cannot account for the existence of chromosomes. That happens to be a fact. So your charge of Everything you have said is either made-up, flat-out wrong, or both. is just a cowardly false accusation.
You don’t have a mechanism capable of producing eukaryotes. That is another fact that you will ignore
Earth to Acartia Eddie- No one will ever confuse you with facts. It doesn’t matter the time of year.
ET, it is too painful to watch you try to talk about biology.
I can’t do it anymore.
You are so clueless and you appear to not even know it.
Or maybe you just don’t want to know. Maybe living in a world of your own made-up facts is how you like it.
Seems to be the theme here at UD.
Take care now.
ET, it is too painful to watch you try to talk about biology.
I can’t do it anymore.
You are so clueless and you appear to not even know it.
Or maybe you just don’t want to know. Maybe living in a world of your own made-up facts is how you like it.
Seems to be the theme here at UD.
Take care now.
Translation: Sven Mil is a scientifically illiterate coward who couldn’t defend anything if its life depended on it. And that is a theme here @ UD- evos and the anti-ID mob think their false accusations and asinine innuendos are meaningful discourse.
Thank you for enforcing that.
ET seriously don’t engage, he is a troll, he will add NOTHING, you will learn nothing, he will supply no knowledge or dialogue of worth, he will simply say you and everyone else is stupid and clueless and he KNOWS better, the only thing he has supplied that has ANY knowledge of worth was genome size, which a simple google search supplies this superior knowledge. He ends EVERY statement with belittlements, which serve to goad you, and forge a false narrative that he is smart, he states everyone has a pattern of being clueless on UD, this only serves to write the narrative that everyone here is stupid, illegitimating anyone else without knowing if they where smarter or not
He is a troll, honestly don’t waste your time, you are the only one putting an argument up of your position, he just says you and your friends are dumb I win. He will provide NOTHING ELSE.
Let it be and don’t troll back
Sven@34
What is your counter argument?
OK Aaron, I fed the troll for breakfast. My bad.
Ed George
Anyone in particular here who has “little intellect” you’re referring to here?
I think you were concerned about insults being handed out.
Sven
You’ve posted several times on this thread and contributed very little.
The challenge is to explain the evolutionary development of the process in question.
You don’t seem to be aware of the problem. The spooling mechanism of compacting is what you cannot explain.
AaronS1978@50, although I don’t condone Sev’s behaviour, I think you will agree that if there is anyone here who deserves to be treated this way it is ET.
Ed George
Oh I know, now I don’t agree with any trolly behavior no matter the side, that’s why I said let it be and don’t troll back.
Speaking of which what is the deal with Acartia Eddie? This is obviously a troll why is it necessary to call Ed George this?
But in this case, I saw exactly what Sven Mil was doing, and as Admiral Akbar would say “IT’S A TRAP!!”
Acartia Eddie:
Sven is treating me like it is a clueless infant. I guess that shows me…
AaronS:
Ed George admitted to being William Spearshake. Acartia bogart admitted to being William Spearshake. Acartia is on record saying it is not interested in any fair, honest and open discussion.
AaronS1978
Beats me. ET obviously has some obsession with this Acartia person. I have repeatedly told him that I am not this person. To no effect. Which is why I don’t respond to him any more. He obviously has some serious psychological issues. I prefer not to be his therapist.
Ed George admitted to being William Spearshake. Acartia bogart admitted to being William Spearshake. Acartia is on record saying it is not interested in any fair, honest and open discussion.
Those are the facts.
.
Sven, the last time you dipped your toe in these waters, you took particular issue with Michael Behe’s concept of irreducible complexity. I responded to your comments, thinking that a cat like you would surely jump at the opportunity to make your case. But you didn’t.
This was my response:
You are more than welcome to support your attack on IC. By all means, tell us how you can specify something among alternatives (as every cell on earth does – the defining characteristic of life) without irreducible complexity. If you don’t mind, be sure to point out Von Neumann’s mistakes.
To save some time, you might want to start out with the requirement of a transcribable memory. The living cell physically establishes its memory through the use of discontinuous association (that’s what makes it work) and it uses spatial orientation to enable multiple referents. All of this has to be simultaneously coordinated in the constraints of the system, allowing it to persist over time. But please don’t let me steal your thunder, you go ahead.
UB, most recently, in order to prove a point, you off-handedly reffered to von Neumann as a both a “non-biologist” and “a computer scientist,” when in fact (as I’m sure you know) he was one of the most intelligent human beings to ever walk the planet.
Now what does that say about you?
Well despite the apparent triviality, I believe that given your history here at UD, it indicates that you will say anything in an attempt to push your agenda forward and quite frankly you have lost all respect of someone familiar with the history of science.
It be really awesome if you stopped attacking his character and actually answer his question
>>>>>> Sven: “UB, most recently, in order to prove a point, you off-handedly reffered to von Neumann as a both a “non-biologist” and “a computer scientist,” when in fact (as I’m sure you know) he was one of the most intelligent human beings to ever walk the planet. Now what does that say about you?”
Apparently it says that I am someone who actually knows that Von Neumann was not a biologist, but was a computer scientist. (!)
Does this mean you won’t be defending the claims you make here? Will you not be telling us what von Neumann got wrong?
Here’s another interesting paper on chromatin regulation:
Distinct functions and temporal regulation of methylated histone H3 during early embryogenesis
No, it says that you are perfectly willing to be deceptive, equivocating, and potentially worse in order to push your own personal agenda.
Only insipid trolls and liberals think it is enough to spew accusations. Has anyone else noticed that is all Sven can muster and bluster?
What are the odds that Sven will never produce any evidence to support its attack on upright biped? There isn’t a bookie that would touch that one. Unless they could find someone dumb enough to think Sven will actually ante up.
Sven Mil any time you want to present anything show that they are wrong would be amazing
Again attacking someone’s character unjustly doesn’t make you right, it makes you a jerk and a troll
Good grief Sven. That was entirely incoherent.
When you do that sort of thing, do you not think it shows?
Call it whatever you want, but the nonsense you spout is no better than BA’s quantum mechanics schtick.
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!”
So, is that what you think von Neumann got wrong – you believe that autonomous open-ended self-replication doesn’t really need the complexity of both a medium of information and a set of constraints to successfully interpret it?
Am I the only one who notices the similarity between the debating styles of Sven and ET?
Sven, do you also believe that Turing (the inspiration to von Neumann) was wrong as well? Was Brenner, (who hailed von Neumann’s prediction) wrong too?
Let me ask you a question, when Crick predicted that there would be a set of “adapters” (his famous “Adapter Hypothesis”) found working in the gene system, was that a wild-assed guess on his part, or do you think it was a logical deduction? If its the latter, then why would you think so?
Well that’s a gross misunderstanding of your irreducible complexity, but you’re not even close
Irreducible complexity isn’t about the system just being complex, it’s the fact that all parts in the system HAD to evolve at once and be in the system for the system to work and be naturally selected in the first place, if it’s missing a part the system as a whole flops and stops working, there is no gradual pave way for it to evolve, it either has all its parts or it doesn’t work.
von Neumann was the first to give a correct description of cellular reproduction. I have never said anything in opposition to that.
more evidences supporting ID:
Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos
Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing
Ed, what do you think the effective difference between Sven’s name-calling/refusal to engage physical evidence, and your obfuscation/refusal to engage physical evidence?
>>>>>>>> Sven: “von Neumann was the first to give a correct description of cellular reproduction. I have never said anything in opposition to that.”
Are you aware that von Neumann’s description included an irreducibly complex symbol system and a set of interpretive constraints as the fundamental physical condition of the system?
Have you actually ever read his paper? Truthfully, have you?
Acartia Eddie:
Only you [insert any given evoTARD] could. Unlike Sven I provide the evidence and references to support what I say.
But we have noticed that you and Sven have the same quote-mining and cowardly accusation- style.
ID on steroids? 🙂
A nuclear licence to silence transposons
Sven Mil:
No, it’s an accurate description of certain structures and systems. IC is only an instance of design once necessity and chance are eliminated.
It remains that all it takes to refute any design inference with respect to any given IC structure or system, is to show how spontaneous or stochastic processes, produced it. And we all know why that upsets you.
ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination
And you think von Nuemann’s system is a perfect analogy to biological systems?
Holy crap- Is it really too difficult for Sven to actually make a coherent argument? Or is flailing about the best you have?
>>>>>>>>Sven: And you think von Nuemann’s system is a perfect analogy to biological systems?
Perfect? Are you asking me if von Neumann predicted aminoacyl synthetase by name? Let’s be direct. Von Neumann’s prediction included construction, copying, control, open-ended potential, a quiescent symbolic description, a set of state transformations (interpretive constraints) to interpret the symbols, and semantic closure. All of these have been very famously documented in the scientific literature. These fundamentals are not even in question, and have been described just as I have presented them here by acclaimed scientists over decades. Which of these would you like to take issue with? Please be specific.
ID unleashed!
mTORC1/AMPK responses define a core gene set for developmental cell fate switching
More evidences supporting ID:
Gene Regulatory Logic of Sonic Hedgehog Morphogen Patterning of the Vertebrate Neural Tube
Morphogen Tissue Patterning
Transcriptional Networks and Cellular Decision Making
The Early Life of an Embryo: from Fertilization to the Midblastula Transition
@ET
No no the resemblance is the Unnecessary name calling you actually engage and put your reasons down
Sven Mil suggest makes predictable smart ass remarks and implies everyone that doesn’t agree with him is stupid, which speaks waves about his character.
At the very beginning of this he said nobody knew what they were talking about and then provided no reason why they were wrong
And still hasn’t but he likes to attack your character a lot
AaronS- A person like Sven and Acartia Eddie cannot attack anyone’s character and expect sane people to listen. And I make astute observations, as opposed to name calling.
Sven
It’s like any biological information circuit. Symbol. Sender. Medium. Translation. Receiver.
It’s irreducibly complex. It’s not a question of trying to shoehorn design in.
You have a show how mindless random effects preserve the function with parts of the process missing.
Im asking if you think von Neumann’s automaton system of machines and tape are a perfect analogy to biological systems.
Is it possible that this system is irreducibly complex only when constrained by the principles of computers/machines?
Biology and computers play by very different rules.
Sven Mil:
Basic biological reproduction is irreducibly complex: Peering into Darwin’s Black Box:
The cell division processes required for bacterial life
But that is moot as you need to go from biologically relevant replicating molecules to producing coded systems from the ground up. Too bad Spiegelman’s Monster says that ain’t happening.
They also play by different codes. Rules and codes that, by all evidence and knowledge, were intelligently designed.
.
Sorry for the long holiday delay. Merry Christmas and Happy New Year to all.
I think I’ve already answered this question, and even clarified with a short summary of some of the critical conditions involved. You are welcome to make whatever point you have in mind.
These systems are irreducibly complex because they have to be. They have to perform the real-world task of freely specifying things among alternatives, and they must accomplish this task (dynamic freedom) under real-world physical conditions (invariant law). A system of discontinuous association is the means to accomplish this task, and the type of physical arrangement that makes discontinuous association possible is irreducibly complex.
That is, each individual object to be specified by the system requires one arrangement of matter to serve as a token of memory and a second arrangement of matter to independently establish what is being specified by the token. This organization forms Peirce’s famous triadic relationship (object-symbol-interpretant) and is not only found at the very heart of von Neumann’s prediction, but was experimentally confirmed and described in the gene system as well (amino acid-codon-aaRS).
It is interesting that you say that. One of the defining issues is that they both have rules that they play by (i.e. there are no rules in physics … laws are universal, time-dependent, and reversible; rules are local, time-independent, and irreversible).
Let me say a couple of things about the desire to separate protein synthesis from genuine semiosis (as exemplified by von Neumann’s prediction of open-ended self-replication).
The attempt will fail.
These conditions have been subject to a great deal of interest over decades and generations. The intellectual feelers from this issue spread out into a wide range of disciplines, questions, and areas of interest. Consequently, the material conditions involved here (and there are many of them) have been very (very) carefully recorded in the scientific literature, particularly since the discovery of DNA. The issue here is not “Is protein synthesis a semiotic process?” That question has already been answered, fully and completely. What we refer to as “protein synthesis” was predicted to be enabled by a genuine symbol system, and subsequently, a genuine symbol system was found inside the cell and has been thoroughly described as such. The question today, at least for me, is “Are there any ID critics visiting UD, claiming to be led by the virtues of empirical science, who are prepared to acknowledge the reality?”
No, you avoided the question, as you are doing now. Probably because you know that machine-biology analogies are extremely superficial.
Von Neumann’s automaton system was an accurate prediction of the basic components and their general functions, which was an incredible feat at the time, but it is not useful beyond that.
Biological systems are not anything like machines or computers. Just because the machine-replication system is irreducibly complex, does not mean the biological system is irreducibly complex.
I hate to break it to you, but there is nothing irreducibly complex in all of biology.
The only way you can portray things in biology as irreducibly complex is by drawing poor analogies which always breakdown at the molecular level. I believe you know this, but as I have said, you will say anything to support your own ideas and worldview.
Sven Mil:
Except when there are, right? Information processing and coded systems. Rotary engines.
True. The fact that biological systems and structures meet the definition of irreducible complexity is a hint, though.
And yet a very long list of IC in biology exists. You don’t even have a mechanism capable of producing biologically relevant molecular replicators. And you expect us to believe that nature produced coded systems from the bottom up? Meaning the codes emerged only once the system was up and running.
Talk about saying anything…
Sven
That’s a good step forward.
Now, we’re talking about an information processing network.
It’s irreducibly complex. Code, sender, translation, receiver, confirmation.
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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?
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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.
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. KF
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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;
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?
SM, 70:
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.
KF
PS: Menuge on the factors C1 – 5:
An immensely enjoyable thread. I don’t remember our opponents looking so miserable facing scientific facts.
Maybe Sven Mil is still working on his response.
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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”.
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:
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.
Nice question-begging and unsupportable trope.
Next time, Sven, present the science as opposed to your wishful thinking.
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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?
“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.htm
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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.
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.
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So the gene system is a semantically-closed symbol system? Okay.
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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
cheers
Sven Mil:
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.
“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
“Symbol-matter problem”. No, that’s not the same as “no problem”.
Sven Mil:
Very doubtful
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.
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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.
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?
“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.
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.
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.
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Yep.
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.
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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.
UB,
Is there a known physicochemical association between the GCAT-based 3-letter codons and the corresponding amino acids?
Sven Mil:
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.
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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.
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Sven, by my count, you have failed to engage in any question asked of you. I’ll try once again:
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?
UB,
Thanks for the explanatory answer.