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Otangelo Grasso on the difficulties of reasoning with atheists

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Conversation in Clubhouse ( a conversation app ) with an atheist:

Please answer with yes or no.

Are computers always designed?

Yes

Is hardware, and software, always designed?

Yes

Are machines always designed?

Yes

Are factories always designed?

Yes

Are transistors always designed?

Yes

Are energy turbines always designed?

Yes

Are codes always designed?

Yes

Good. All this, we see analogously, but also literally in the cell.

Neurons are literally computers

DNA is the hardware, and the sequence of DNA nucleotides is the software

Proteins are molecular machines

Cells are chemical factories

Neurons are transistors

ATP synthase is an energy turbine.

The genetic code is a real code

Is it logical to infer that therefore, these things were also designed?

Atheist answer: No. The first mentioned things, we know humans design them. The secondly mentioned things in nature, we don’t know how they came to be.

It’s sometimes so frustrating to have a conversation with atheists…. Others deny and claim the things mentioned in nature are not analogous to human made artifacts.

Once you back up the claim:

The Cell is a super computer
https://reasonandscience.catsboard.com/t2712-the-cell-is-a-super-computer

1. A transistor can be considered an artificial Neuron. Every living cell within us is a hybrid analog–digital supercomputer. The brain is like 100 billion computers working together.
2. Biological cells are programmed to be experts at taking inputs, running them through a complicated series of logic gates through circuit-like operations and producing the desired programmed output.
3. The origin of programs, logic gates, and complex circuits to obtain a purposeful specific outcome is always tracked back to intelligent implementation.  

The hardware and software of the cell, evidence of design
https://reasonandscience.catsboard.com/t2221-the-hardware-and-software-of-the-cell-evidence-of-design

Paul Davies: the Fifth Miracle page 62: Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it.

Molecular machines in biology
https://reasonandscience.catsboard.com/t1289-molecular-machines-in-biology

1. Machines are always designed.
2. Proteins are machines.
3. Therefore, proteins were designed.

The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument

1. Blueprints, instructional information and master plans, and the making of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  
2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks.
3. The Blueprint and instructional information stored in DNA and epigenetics, which directs the making of biological cells and organisms – the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

Inside the neuron
https://reasonandscience.catsboard.com/t2292-neurons-remarkable-evidence-of-design#7201

HIDDEN IN PLAIN SIGHT 9 The Physics Of Consciousness Andrew Thomas:
The similarity between transistors and neurons is elucidated when we consider how most transistors are used nowadays. The vast majority of transistors are micro-miniaturised onto a semiconductor substrate to form an integrated circuit (“silicon chip”). The latest fabrication techniques allow extraordinary densities of up to 25 million transistors on a square millimetre of silicon. This actually results in an individual transistor size which is rather smaller than a neuron, but it is clear that the principle of packing microscopic transistors onto an integrated circuit resembles the packing of microscopic neurons in a brain.

The irreducibly complex ATP Synthase nanomachine, amazing evidence of design
https://reasonandscience.catsboard.com/t1439-the-irreducibly-complex-atp-synthase-nanomachine-amazing-evidence-of-design

1. ATP synthase is a molecular energy-generating nano-turbine ( It produces energy in the form of Adenine triphosphate ATP. Once charged, ATP can be “plugged into” a wide variety of molecular machines to perform a wide variety of functions). It consists of two very different subunits that have to be externally and stably tethered together, just the right distance apart. The two major subunits (F0 & F1) are connected together by an external tether, and just the right distance apart. This tether doesn’t have anything to do with the functionality of either subunit but without it ATP synthase would not be able to perform its function. One of the subunits has to be embedded in the cell membrane so that an energy gradient can be formed ( The proton energy gradient is like the water in a dam, feeding a water turbine to generate energy). The second subunit has to be stably tethered to the membrane the proper distance away.
2. This is an irreducibly complex system, where a minimal number of at least five functional parts of ATP synthase must work together in an interlocked way, in a joint venture to bear function. The challenge is particularly onerous because these components are highly complex in all of life and are interdependent to provide energy for life. Individually, the subunits have no function whatsoever ( Not even in different setups). Besides ATP synthase, the membrane is essential to pump protons across the membrane. This setup cannot be the product of evolution, because it had to be fully operational and functional to start life ( The origin of life has nothing to do with evolution). No life form without ATP synthase is known.
3. We know by experience that complex machines made of various interlocked subparts with specific functions are always created by intelligent minds.  Therefore, ATP synthase is definitely evidence of a powerful intelligent creator, who knew how to create power-generating turbines.

The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin

1. Creating a translation dictionary, for example of English to Chinese, requires always a translator, that understands both languages. 
2. The meaning of words of one language that are assigned to words of another language that mean the same requires the agreement of meaning in order to establish translation.
3. That is analogous to what we see in biology, where the ribosome translates the words of the genetic language composed of 64 codon words to the language of proteins, composed of 20 amino acids. 
4. The origin of such complex communication systems is best explained by an intelligent designer.

John Frederick William Herschel: A Preliminary Discourse on the Study of Natural Philosophy, page 149, 1830
If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.Flagellum, Behe’s prime example of irreducible complexity
https://reasonandscience.catsboard.com/t1528-the-flagellum-behe-s-prime-example-of-irreducible-complexity

The irreducible complexity of the flagellum
1. The flagellum has 36 different proteins essential for the function of the flagellum. Every protein is a complex structure of average 300 amino acids
2. All proteins are required and one has no function without another just like a piston of a car engine has no use without the other engine parts. 
3. Evolutionary biologists are unable to give any explanation on how all these proteins could have evolved in a gradual fashion to form the flagellum 
4. Therefore, the only option is set up by an intelligent designer. 

They will still deny it…..

Comments
Ba77 at 120, Here is the formula: Raise a magic curtain. That way, no one can see what goes on behind it. Wait millions of years. Then a rabbit appears.relatd
October 13, 2022
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Moreover, as if that was not already bad enough for Darwinists, In the following article Larry Moran, (who denies even being a “Darwinist” anymore since he no longer believes Natural Selection to be the driving force behind evolution), quotes Austin Hughes who states, ‘Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.’
Austin Hughes and Neutral Theory – Laurence A. Moran – June 19, 2017 Excerpt: Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance. http://sandwalk.blogspot.com/2017/06/austin-hughes-and-neutral-theory.html
Thus, with Natural selection being tossed by the wayside by the mathematics of population genetics, (and by empirical evidence I might add), as the supposed explanation for the ‘appearance of design’ that we see in life, Darwinists did not accept such a devastating finding from population genetics as an outright falsification for their theory, as they should have done, but are instead now reduced to arguing that the ‘wonderful design’ that we see pervasively throughout life is, basically, the result of pure chance with natural selection now playing a very negligible role if any role at all. To call such a move on the part of Darwinists, (or whatever Moran calls himself), disingenuous would be a severe understatement. Even Richard Dawkins himself finds the claim that chance alone, all by its lonesome, can explain the 'well designed' things we see in biology to be 'absolutely inconceivable'. Specifically, in the following video Dawkins states that it “cannot come about by chance. It’s absolutely inconceivable that you could get anything as complicated or well designed as a modern bird or a human or a hedgehog coming about by chance.’
4:30 minute mark: “It cannot come about by chance. It’s absolutely inconceivable that you could get anything as complicated or well designed as a modern bird or a human or a hedgehog coming about by chance. That’s absolutely out.,,, It’s out of the question.,,, So where (does the appearance of design)) it come from? The process of gradual evolution by natural selection.” Richard Dawkins – From a Frog to a Prince – video https://youtu.be/ClleN8ysimg?t=267
For crying out loud, the entire purpose behind ‘Natural Selection’ in the first place was to supposedly “explain away” the overwhelming ‘appearance of design’ we see in life without any reference to a real Designer, i.e. without any reference to God. And as Ernst Mayr himself explained, “Every aspect of the “wonderful design” so admired by the natural theologians could be explained by natural selection.”
“The theory of evolution by natural selection explains the adaptedness and diversity of the world solely materialistically. It no longer requires God as creator or designer (although one is certainly still free to believe in God even if one accepts evolution). Darwin pointed out that creation, as described in the Bible and the origin accounts of other cultures, was contradicted by almost any aspect of the natural world. Every aspect of the “wonderful design” so admired by the natural theologians could be explained by natural selection.” – Ernst Mayr – “Darwin’s Influence on Modern Thought” in Scientific American, July, 2000 https://sciphilos.info/docs_pages/docs_Mayr_Dawin_css.html
And as Francisco J. Ayala put it, natural selection supposedly accounted for “Design without designer”, i.e. “The adaptive features of organisms could now be explained,, as the result of natural processes, without recourse to an Intelligent Designer.,,,”
Darwin’s greatest discovery: Design without designer – Francisco J. Ayala – May 15, 2007 Excerpt: With Darwin’s discovery of natural selection, the origin and adaptations of organisms were brought into the realm of science. The adaptive features of organisms could now be explained, like the phenomena of the inanimate world, as the result of natural processes, without recourse to an Intelligent Designer.,,, Darwin’s theory of natural selection accounts for the “design” of organisms, and for their wondrous diversity, as the result of natural processes, the gradual accumulation of spontaneously arisen variations (mutations) sorted out by natural selection. https://www.pnas.org/content/104/suppl_1/8567
And as Richard Dawkins himself staled in “The Blind Watchmaker”, “Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.”
“Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.” – Richard Dawkins – “The Blind Watchmaker” – 1986 – page 21
Thus contrary to what Darwinists, (or whatever Moran calls himself), may believe, with the tossing of Natural Selection to the wayside as the explanation for the ‘wonderful design’ we see in life, the explanation for the ‘appearance of design’ we see in life does not automatically become, ‘Well, golly gee whiz, chance, all by its lonesome, must have done it all by itself”, as Darwinists are apparently intent on believing with Neutral theory, but instead the explanation for the ‘wonderful design’ we see in life reverts back to what it originally was in the first place before Darwin came along with Natural Selection. As Richard Sternberg explains, “Darwinism provided an explanation for the appearance of design, and argued that there is no Designer — or, if you will, the designer is natural selection. If that’s out of the way — if that (natural selection) just does not explain the evidence — then the flip side of that is, well, things appear designed because they are designed.”
“Darwinism provided an explanation for the appearance of design, and argued that there is no Designer — or, if you will, the designer is natural selection. If that’s out of the way — if that (natural selection) just does not explain the evidence — then the flip side of that is, well, things appear designed because they are designed.” Richard Sternberg – Living Waters documentary Whale Evolution vs. Population Genetics – Richard Sternberg and Paul Nelson – (excerpt from Living Waters video) https://www.youtube.com/watch?v=0csd3M4bc0Q
Moreover, (since Darwinists have now basically appealed to ‘chance’, all by its lonesome, to supposedly explain the ‘wonderful design’ we see in life, minus any major role for natural selection), it is also worth pointing out that ‘chance’ is not an actual cause of anything but is only a place holder for ignorance. Charles Darwin himself admitted as much.
“I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation.” Charles Darwin – Origin – Chapter V As What Is Chance? – Nicholas Nurston Excerpt: “The vague word ‘chance’ is used as a substitute for a more precise word such as ’cause’. “To personify ‘chance’ as if we were talking about a causal agent,” notes biophysicist Donald M. MacKay, “is to make an illegitimate switch from a scientific to a quasi-religious mythological concept.” Similarly, Robert C. Sproul points out: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’” Others who reasoned in this fashion, Nobel laureate Jacques Monod, for one, used this chance equals cause line of reasoning. “Pure chance, absolutely free but blind, (is) at the root of the stupendous edifice of evolution,”… https://books.google.com/books?id=bQ5OAAAAQBAJ&pg=PT25&lpg=PT25
The word ‘chance’, as it is used by Darwinists, is not an appeal to any known mathematical probability, or to any known cause in physics, but is, in reality, simply a placeholder for ignorance. As Wolfgang Pauli himself explained, “(Darwinists) become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’"
Pauli’s ideas on mind and matter in the context of contemporary science – Harald Atmanspacher Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) https://pdfs.semanticscholar.org/234f/4989e039089fed5ac47c7d1a19b656c602e2.pdf
The following article by Stephen Talbott is very good at illustrating just how synonymous the words ‘chance’ and ‘miracle’ actually are in the Darwinists appeal to ‘chance’ as a cause.
Evolution and the Illusion of Randomness – Talbott – Fall 2011 Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.” In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.” This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness
Thus in conclusion, with the casting aside of natural selection as being a major player in evolution, and with their claim, via Neutral theory, "that the majority of evolutionary change is due to chance", Darwinists, (or whatever Moran calls himself), are basically reduced to arguing for miracles minus any miracle maker. In short, Darwinists are trying to pull a miraculous 'design' rabbit out of a hat without any rabbit or even a 'miracle making' hat to do so.
John 3:2 The same came to Jesus by night, and said unto him, Rabbi, we know that thou art a teacher come from God: for no man can do these miracles that thou doest, except God be with him.
bornagain77
October 12, 2022
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It is interesting to note exactly why Dan Graur, (and Larry Moran), have argued that "if Encode is right, evolution is wrong,"
Next Phase of ENCODE Finds MORE Functional Information in Genome “Junk” - August 4, 2020 Excerpt: The first publications from the ENCODE project (Encyclopedia of DNA Elements) made a big splash at Evolution News in 2013, and around the world, because it undermined the “junk DNA” myth and simultaneously fulfilled an ID prediction: that non-coding parts of the genome would prove functional. Junk-DNA proponents like Dan Graur were upset at the time, admitting as Jonathan Wells reported, “If ENCODE is right, evolution is wrong.” Well, ModENCODE (ENCODE for model organisms) found “unprecedented complexity” in the fruit fly genome in 2014, then “ENCODE 2” followed up with more discoveries of function. Now, ENCODE 3 has just finished submitting its reports, with record numbers of DNA annotations listed, and ENCODE 4 is gearing up. Nothing like a little overkill to drive the point home: “… then evolution is wrong.” Look at how much constructive science is being done with the assumption that DNA elements are there for a purpose. https://evolutionnews.org/2020/08/next-phase-of-encode-finds-more-functional-information-in-genome-junk/
The main reason why Dan Graur, (and Larry Moran), have been forced to argue that the genome must contain a large percentage of useless junk DNA is not because of any compelling scientific evidence, (indeed, as the reference I cited makes clear, they steadfastly ignore the onslaught of scientific evidence to the contrary), but is because it is forced upon them by the mathematics of population genetics, particularly by the 'genetic load' argument.
Five Things You Should Know if You Want to Participate in the Junk DNA Debate - Larry Moran 1. Genetic Load Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk. https://sandwalk.blogspot.com/2013/07/five-things-you-should-know-if-you-want.html
And here is Kimura’s genetic load argument for neutral theory,
Molecular evolution and neutral theory – Summary Excerpt: Kimura argued that the high rate of evolution, and the high degree of variability of proteins, would, if caused by natural selection, impose a high genetic load. Neutral drift, (where evolution is decoupled from Natural Selection), however, can drive high rates of evolution, and maintain high levels of variability, without imposing a genetic load. per Blackwell publishing
As Dr. Robert Carter explains, “Based on the work of J.B.S. Haldane5 and others, who showed that natural selection cannot possibly select for millions of new mutations over the course of human evolution, Kimura6 developed the idea of “neutral evolution” (i.e. Kimura’s genetic load argument for the neutral theory), If “Haldane’s Dilemma”7 were correct, then the majority of DNA must be non-functional.”,,, “Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done.”
The slow, painful death of junk DNA – Robert W. Carter – 2009 Background Based on the work of J.B.S. Haldane5 and others, who showed that natural selection cannot possibly select for millions of new mutations over the course of human evolution, Kimura6 developed the idea of “neutral evolution”. If “Haldane’s Dilemma”7 were correct, then the majority of DNA must be non-functional. It should be free to mutate over time without needing to be shaped by natural selection. In this way, natural selection could act on the important bits and neutral evolution could act randomly on the rest. Since natural selection will not act on neutral traits, which do not affect survival or reproduction, neutral evolution can proceed through random drift without any inherent “cost of selection”.8 The term “junk DNA” originated with Ohno,9 who based his idea squarely on the idea of neutral evolution. To Ohno and other scientists of his time, the vast spaces (introns)between protein-coding genes were (exons) just useless DNA whose only function was to separate genes along a chromosome. Junk DNA is a necessary mathematical extrapolation. It was invented to solve a theoretical evolutionary dilemma. Without it, evolution runs into insurmountable mathematical difficulties. Junk DNA necessary for evolution Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. https://creation.com/images/pdfs/tj/j23_3/j23_3_12-13.pdf
In fact, in the following article Moran claims that, because of Genetic Load/Neutral Theory, upwards to 90% of our genome must be junk.
Revisiting the genetic load argument with Dan Graur – Larry Moran – July 14, 2017 Excerpt: I’ve discussed genetic load several times on this blog (e.g. Genetic Load, Neutral Theory, and Junk DNA) but a recent paper by Dan Graur provides a good opportunity to explain it once more. The basic idea of Genetic Load is that a population can only tolerate a finite number of deleterious mutations before going extinct. The theory is sound but many of the variables are not known with precision.,,, Let’s look at the first line in this table. The deleterious mutation rate is calculated using the lowest possible mutation rate and the smallest percentage of deleterious mutations (4%). Under these conditions, the human population could survive with a fertility value of 1.8 as long as less than 25% of the genome is functional (i.e. 75% junk) (red circle). That’s the UPPER LIMIT on the functional fraction of the human genome. But that limit is quite unreasonable. It’s more reasonable to assume about 100 new mutations per generation with about 10% deleterious. Using these assumptions, only 10% of the genome could be functional with a fertility value of 1.8 (green circle). Whatever the exact percentage of junk DNA it’s clear that the available data and population genetics point to a genome that’s mostly junk DNA. http://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Dr. Moran’s belief that 90% of the human genome must be junk just strikes me as being a patently absurd claim right off the bat,,,, but anyways to continue on, I hold Moran’s calculation to be fundamentally flawed in regards to empirical evidence that we now have in hand. Specifically, I hold Moran’s 10% estimate for deleterious mutations, that he used in his calculation in the preceding paper, to be far too conservative, and thus the percentage of junk DNA, according to Moran’s own calculation, should actually be much higher than the 90% estimate for Junk DNA that he derived. As John Sanford explained in his book “Genetic Entropy” and as he elucidated in the following paper, the unselectable ‘near neutral’ mutations, which Dr Moran erroneously classified as being perfectly neutral in his calculation, should, in reality, all be classified as ‘slightly deleterious mutations’. Slightly deleterious mutations which will "accumulate steadily, causing eventual extinction."
Can Purifying Natural Selection Preserve Biological Information? – May 2013 – Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010 Kimura’s Distribution - http://dl0.creation.com/articles/p091/c09164/9164-diagram-3c-lge-white.jpg Correct Distribution - http://dl0.creation.com/articles/p091/c09164/9164-diagram-3d-lge-white.jpg also see: Mathematician and Geneticist Team Up to Correct Fisher’s Theorem - Dec. 22, 2017 Supplemental Information – Fisher’s informal corollary (really just a thought experiment), was convoluted. The essence of Fisher’s corollary was that the effect of both good and bad mutations should be more or less equal – so their net effect should be more-or less neutral. However, the actual evidence available to Fisher at that time already indicated that mutations were overwhelmingly deleterious. Fisher acknowledged that most observed mutations were clearly deleterious – but he imagined that this special class of highly deleterious mutations would easily be selected away, and so could be ignored. He reasoned that this might leave behind a different class of invisible mutations that all had a very low-impact on fitness – which would have a nearly equal chance of being either good or bad. This line of reasoning was entirely speculative and is contrary to what we now know. Ironically, such “nearly-neutral” mutations are now known to also be nearly-invisible to natural selection – precluding their role in any possible fitness increase. Moreover, mutations are overwhelmingly deleterious – even the low impact mutations. This means that the net effect of such “nearly-neutral” mutations, which are all invisible to selection, must be negative, and must contribute significantly to genetic decline. Furthermore, it is now known that the mutations that contribute most to genetic decline are the deleterious mutations that are intermediate in effect – not easily selected away, yet impactful enough to cause serious decline. https://crev.info/2017/12/geneticist-corrects-fishers-theorem/
In short, when realistic rates of 'slightly deleterious' mutations are taken into consideration then we should have 100% junk DNA instead of "just" the 90% junk DNA that Moran erroneously claimed in his calculation.bornagain77
October 12, 2022
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Relatd: I never wrote that.
Except that those are your exact words from 108. Verbatim.Sir Giles
October 12, 2022
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SG at 116, I never wrote that. Among the non-coding regions of DNA, there are some that are linked to disease while others are linked to function in the coding regions. That is all being sorted out. Your strange assumption ignores people who live into their 80s or 90s with little or no sign of serious illness. World life expectancy is increasing. Partly due to early diagnosis and treatment. https://www.macrotrends.net/countries/WLD/world/life-expectancyrelatd
October 12, 2022
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Relatd: Nonsense. At the Mayo Clinic and elsewhere, guess what? The ASSUMPTION made by brainwashed Biologists had to be discarded to make actual progress in identifying the sources of human disease. How are they doing that? By looking at Junk DNA. By studying it. Not throwing it out as ‘leftovers from our long [alleged] period of Evolution.’ By studying it as opposed to ‘it doesn’t code for proteins so it’s useless.’ Those so-called non-coding regions are yielding vital information about human disease, The “natural” approach discarded them – without looking.
So, your argument is that the function of 90+% of human DNA is to cause disease. Not exactly a ringing endorsement for intelligent design. Unless, of course, the purpose of the design is suffering.Sir Giles
October 12, 2022
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Will that stop any of the Darwinists here? Of course not. Their orders are clear: Promote Darwinism forever. Just ignore any challenge, any facts, that might interfere with the promotion or turn any criticism into an additional story about evolution, if possible. Post as if no detractors ever wrote anything at all. This may convince a few that Darwinism has some merit. Any evidence that indicates it does not never stops the repetition, every day, forever... What a tangled web... of nonsense.relatd
October 12, 2022
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Martin,
If 95% of our DNA would be functional, Darwinists would say – what is so surprising ? Of course all of our DNA is functional and only a small percentage is junk … it can’t be otherwise … because natural selection removes anything what is not useful/functional … If 95% of our DNA would be non-functional, then, Darwinists would say – look, this is an ultimate proof that evolution is true, how else could you explain that 95 % of it is a junk ? Clearly, it is an artifact of millions of years of evolution … an ultimate proof ….
To wit,
Post-ENCODE Posturing: Rewriting History Won’t Erase Bad Evolutionary Predictions Casey Luskin - November 10, 2015 Excerpt: As recently as 2009, Dawkins adopted the incredible position that “the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.”10 In September 2012, however, Dawkins changed his tune dramatically. Just one week after ENCODE’s results were published, in a debate against Britain’s chief rabbi, Dawkins declared that ENCODE’s results are precisely what “Darwinism” (in Dawkins’s own words) predicts: "There are some creationists who are jumping on [ENCODE] because they think it’s awkward for Darwinism. Quite the contrary, of course, it is exactly what a Darwinist would hope for — to find usefulness in the living world."11 https://evolutionnews.org/2015/11/post-encode_pos/
Such 'turn on a dime waffling' beautifully illustrates the unfalsifiable, "Heads I win, tails you lose', pseudoscientific mentality of Darwinian atheists. Or as Matti Leisola put it, "It (Darwinism) produces exquisitely fine-tuned designs except when it produces (loads of) junk"
"Evolution is slow and gradual except when it is fast. It is dynamic and creates huge changes over time, except when it keeps everything the same for millions of years. It explains both extreme complexity and elegant simplicity. It tells us how birds learned to fly and how some lost that ability. Evolution made cheetahs fast and turtles slow. Some creatures are made big and others small, some gloriously beautiful and some boringly gray. It forced fish to walk and walking animals to return to the sea. It diverges except when it converges. It produces exquisitely fine-tuned designs except when it produces junk. Evolution is random and without direction except when it moves toward a target. Life under evolution is a cruel battlefield, except when it demonstrates altruism. Evolution explains virtues and vice, love and hate, religion and atheism and it does all this with a growing number of ancillary hypotheses…It explains everything without explaining anything well." — Matti Leisola, bioengineer (former Dean of Chemistry and Material Sciences at Helsinki University of Technology)
Or as Dr. Cornelius Hunter put it, "Being an evolutionist means there is no bad news.",,,
"Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought." ~ Cornelius Hunter
There is simply no empirical finding that Darwinists will ever accept as a falsification of their 'theory'.
1. Darwin’s theory holds mutations to the genome to be random. The vast majority of mutations to the genome are not random but are now found to be ‘directed’. 2. Darwin’s theory holds that Natural Selection is the ‘designer substitute’ that produces the ‘appearance’ and/or illusion of design. Natural Selection, especially for multicellular organisms, is found to be grossly inadequate as the ‘designer substitute. 3. Darwin’s theory holds that mutations to DNA will eventually change the basic biological form of any given species into a new form of a brand new species. Yet, biological form is found to be irreducible to mutations to DNA, nor is biological form reducible to any other material particulars in biology one may wish to invoke. 4. Darwin’s theory, (via Fisher’s Theorem in population genetics), assumed there to be an equal proportion of good and bad mutations to DNA which were, ultimately, responsible for all the diversity and complexity of life we see on earth. Yet, the ratio of detrimental to beneficial mutations is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever. 5. Charles Darwin himself held that the gradual unfolding of life would (someday) be self-evident in the fossil record. Yet, from the Cambrian Explosion onward, the fossil record is consistently characterized by the sudden appearance of a group/kind in the fossil record, (i.e. disparity), then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. Moreover, Fossils are found in the “wrong place” all the time (either too early, or too late). 6. Darwin’s theory, due to the randomness postulate, holds that patterns will not repeat themselves in supposedly widely divergent species. Yet thousands of instances of what is ironically called ‘convergent evolution’, on both the morphological and genetic level, falsifies the Darwinian belief that patterns will not repeat themselves in widely divergent species. 7. Charles Darwin himself stated that “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Yet as Doug Axe pointed out, “Basically every gene and every new protein fold, there is nothing of significance that we can show that can be had in that gradualistic way. It’s all a mirage. None of it happens that way.” 8. Charles Darwin himself stated that “If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.” Yet as Wolf-Ekkehard Lönnig pointed out, “in thousands of plant species often entirely new organs have been formed for the exclusive good of more than 132,930 other species, these ‘ugly facts’ have annihilated Darwin’s theory as well as modern versions of it.” 9. Charles Darwin himself stated that, ““The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God. Yet ‘our conscious selves’ are certainly not explainable by ‘chance’ (nor is consciousness explainable by any possible reductive materialistic explanation in general), i.e. ‘the hard problem of consciousness’. 10. Besides the mathematics of probability consistently showing that Darwinian evolution is impossible, the mathematics of population genetics itself has now shown Darwinian evolution to be impossible. Moreover, ‘immaterial’ mathematics itself, which undergirds all of science, engineering and technology, is held by most mathematicians to exist in some timeless, unchanging, immaterial, Platonic realm. Yet, the reductive materialism that Darwinian theory is based upon denies the existence of the immaterial realm that mathematics exists in. i.e. Darwinian evolution actually denies the objective reality of the one thing, i.e. mathematics, that it most needs in order to be considered scientific in the first place! 11. Donald Hoffman has, via population genetics, shown that if Darwin’s materialistic theory were true then all our observations of reality would be illusory. Yet the scientific method itself is based on reliable observation. Moreover, Quantum Mechanics itself has now shown that conscious observation must come before material reality, i.e. falsification of ‘realism’ proves that our conscious observations are reliable!. 12. The reductive materialism that undergirds Darwinian thought holds that immaterial information is merely ’emergent’ from a material basis. Yet immaterial Information, via experimental realization of the “Maxwell’s Demon” thought experiment, is now found to be its own distinctive physical entity that, although it can interact in a ‘top down’ manner with matter and energy, is separate from matter and energy. 13. Darwinists hold that Darwin’s theory is true. Yet ‘Truth’ itself is an abstract property of an immaterial mind that is irreducible to the reductive materialistic explanations of Darwinian evolution. i.e. Assuming reductive materialism and/or Naturalism as the starting philosophical position of science actually precludes ‘the truth’ from ever being reached by science! 14. Darwinists, due to their underlying naturalistic philosophy, insist that teleology (i.e. goal directed purpose) does not exist. Yet it is impossible for Biologists to do biological research without constantly invoking words that directly imply teleology. i.e. The very words that Biologists themselves are forced to use when they are doing their research falsifies Darwinian evolution.
Indeed, as Denis Noble pointed out, there simply is no falsification criteria to be found within Darwinism,
Central tenets of neo-Darwinism broken. Response to ‘Neo-Darwinism is just fine’ – 2015 Excerpt: “If, as the commentator seems to imply, we make neo-Darwinism so flexible as an idea that it can accept even those findings that the originators intended to be excluded by the theory it is then incumbent on modern neo-Darwinists to specify what would now falsify the theory. If nothing can do this then it is not a scientific theory.” – Denis Noble - President of International Union of Physiological Sciences https://jeb.biologists.org/content/218/16/2659
And as such, and as Popper himself pointed out, since Darwinism is unfalsifiable by empirical observation then that means that "it does not speak about reality.”
“In so far as a scientific statement speaks about reality, it must be falsifiable: and in so far as it is not falsifiable, it does not speak about reality.” - Karl R. Popper, The Logic of Scientific Discovery
Whereas, on the other hand, ID is easily falsifiable. There is even a 10 million dollar prize being offered for the first person who can falsify ID by showing unguided material processes producing a code,
An incentive prize ten times the size of the Nobel – believed to be the largest single award ever in basic science – is being offered to the person or team solving the largest mystery in history: how genetic code inside cells got there, and how cells intentionally self-organize, communicate, then purposely adapt. https://www.prnewswire.com/in/news-releases/evolution-2-0-prize-unprecedented-10-million-offered-to-replicate-cellular-evolution-875038146.html The challenge https://www.herox.com/evolution2.0
Verse:
1 Thessalonians 5:21 Test all things; hold fast what is good.
bornagain77
October 12, 2022
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Maybe define what is meant by "junk" in the first place?Seversky
October 12, 2022
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Relatd: https://www.discovery.org/b/the-myth-of-junk-dna/ Oh wow, two paragraphs of summary and then lots of positive reviews. There's real science eh? I tell you what: why don't you predict how much of the human genome is 'junk', i.e. what percentage could be completely eliminated without any loss of viability. Go on, have a guess . . . I'll give you at least a 5% buffer.JVL
October 12, 2022
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https://www.discovery.org/b/the-myth-of-junk-dna/relatd
October 12, 2022
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Relatd: How are they doing that? By looking at Junk DNA. By studying it. Not throwing it out as ‘leftovers from our long [alleged] period of Evolution.’ By studying it as opposed to ‘it doesn’t code for proteins so it’s useless.’ Oh dear, that's quite a rant. Shall we look at a bit more of what the paper actually says?
Cutting-edge analytical approaches are combined with large-scale clinical and genomic data to discover genes related to disease and clinical outcomes. The division's studies cover a broad range of common and rare diseases including cancer, neuropsychiatric diseases, cardiovascular disease and others using a variety of study designs to better understand how genetic variants influence disease within and across populations. Through biomedical discovery, these studies help predict who has an increased risk of disease. These studies also facilitate treatment development, leading to better diagnosis and treatment of patients. The division actively pursues studies aimed at deciphering the contribution of common and rare genetic variants, measured using genotyping and sequencing technologies. To facilitate such studies, division researchers develop novel statistical methods for genetic data analysis, including methods to study pleiotropic genetic effects, polygenic risk prediction, gene-environment interaction analysis, sex chromosome analysis and data integration including mediation analyses to link inherited variation with intermediate risk factors leading to disease.
So, in fact, there was no 'brainwashing' to overcome. It's pure statistics.
Modern technologies in genomics allow for high-throughput variant discovery, measuring expression of all genes and determining epigenomic alterations across the entire human genome. Studies are conducted to map gene expression and the associated epigenomic influence across multiple diseases, cancers and tissues at the single-cell level. Recent advances have enabled application of technologies such as assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to single cells. Expression and epigenome maps based on single-cell analyses enable the deciphering of functions of noncoding regions in a cell-specific way, which is the foundation for revealing how variants contribute to disease pathogenesis, cancer development and progression.
Again, they looked at the whole genome. They weren't brainwashed or forced to reconsider. These are just good scientists doing good science. As one would expect. And, if you think about it for even five seconds, you realise that diseases are probably more likely to arise in areas of the genome that have fewer selection pressures than the essential coding regions 'cause changes there can kill the organism before some diseases arise.JVL
October 12, 2022
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Here's another one of Bornagain77's copy-and-paste snippets:
Logical Reversibility of Computation* – C. H. Bennett – 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/co.....ett73.html
Follow the link, look at the last paragraph . . . a lot of which has been left off. Here's the whole last paragraph (emphasis added by me):
The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation. respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible. In the cellular environment the reaction is driven in the intended forward direction of RNA synthesis by other reactions. which maintain a low concentration of free pyrophosphate, relative to the concentrations of nucleotide pyrophosphates [8]. A high pyrophosphate concentration would drive the reaction backward. and the enzyme would carry out a sequence-specific degradation of the RNA. comparing each nucleotide with the corresponding DNA nucleotide before splitting it off. This process, which may be termed logically reversible erasure of RNA, does not normally occur in biological systems - instead, RNA is degraded by other enzymes. such as polynucleotide phosphorylase [9], in a logically irreversible manner (i.e.. without checking its sequence against DNA). Polynucleotide phosphorylase catalyzes the reaction of RNA with free phosphate (maintained at high concentration) to form nucleotide phosphate monomers. Like the polymerase reaction. this reaction is thermodynamically reversible: however, because of its logical irreversibility, a fourfold greater phosphate concentration is needed to drive it forward than would be required for a logically reversible phosphorolytic degradation. The extra driving force is necessary to suppress the undesired synthesis of nonsense RNA by random polymerization. In biological systems. apparently, the speed and flexibility of irreversible erasure outweigh its extra cost in free energy kT ln 4 per nucleotide in this case). Indeed, throughout the genetic apparatus, energy is dissipated at a rate of roughly 5 to 50 kT per step. while this is ten orders of magnitude lower than in an electronic computer. it is considerably higher than what would theoretically be possible if biochemical systems did not need to run at speeds close to the kinetic maximum-presumably to escape the harmful effects of radiation, uncatalyzed reactions, and competition from other organisms.
Does that change the impression given? I'll leave it to you to decide. But, again, did Bornagain77 actually read the work cited or just copy-and-paste something?JVL
October 12, 2022
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Nonsense. At the Mayo Clinic and elsewhere, guess what? The ASSUMPTION made by brainwashed Biologists had to be discarded to make actual progress in identifying the sources of human disease. How are they doing that? By looking at Junk DNA. By studying it. Not throwing it out as ‘leftovers from our long [alleged] period of Evolution.’ By studying it as opposed to ‘it doesn’t code for proteins so it’s useless.’ Those so-called non-coding regions are yielding vital information about human disease, The “natural” approach discarded them – without looking. Source: https://www.mayo.edu/research/departments-divisions/computational-biology/focus-areas A few excerpts: "Because most genetic variants occur in noncoding regions of the genome, their effects remain poorly understood." "Modern technologies in genomics allow for high-throughput variant discovery, measuring expression of all genes and determining epigenomic alterations across the entire human genome." "Expression and epigenome maps based on single-cell analyses enable the deciphering of functions of noncoding regions in a cell-specific way, which is the foundation for revealing how variants contribute to disease pathogenesis, cancer development and progression."relatd
October 12, 2022
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Here's another one of Bornagain77's pasted 'quotes' and link:
Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon – Charles H. Bennett – September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/s.....980300039X
If you follow the link you get to: https://www.sciencedirect.com/science/article/abs/pii/S135521980300039X Which is actually just a brief summary of the paper and that summary DOES NOT contain the quote he cites. Which means, again, that Bornagain77 did not actually follow the link and read the material linked to. He just lifted the quote and link from someone else. AND that's aside from the fact that it's hard to figure out what the paper and the quote have to do with the point Bornagain77 is trying to make.JVL
October 12, 2022
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Bornagain77: So apparently JVL does not think that ‘over half’ of the genome being useless garbage will effect the thermodynamic efficiency of the cell. The fact that reactions are performed efficiently has nothing to do with whether or not those reactions are necessary!! You really are showing your ignorance. I think I will check some of you other links to see if they too contradict what you say they say. o that about does it for me. I have much better things to do today than chase a unreasonable, and unscientific, troll’s tail around in a circle. Oh dear, you got caught being ignorant of something you claimed said one thing when it said the exact opposite!! So now you're running away. Figures.JVL
October 12, 2022
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I just want to make clear the big OOPS that Bornagain77 made. Here's the quote he reproduced:
“Transcriptomics studies show the pervasive transcription of virtually the entire human genome”(Clark et al. 2011; Hangauer et al. 2013). https://academic.oup.com/gbe/article/12/11/2183/5906514
But, if you follow the link provided you get: Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage Daniel Dowling, Jonathan F Schmitz, Erich Bornberg-Bauer Genome Biology and Evolution, Volume 12, Issue 11, November 2020, Pages 2183–2195, https://academic.oup.com/gbe/article/12/11/2183/5906514 Which contains the quotes I posted above. Clearly Bornagain77 is just copy-and-pasting stuff he hasn't read or understood. I wonder how many of his copy-and-pasted links and quotes are inaccurate and, in fact, contrary to his assertions? Does anyone care to check?JVL
October 12, 2022
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BA @101 Talking about "dead weight' (junk DNA). Junk DNA perfectly illustrates how absurd Darwinism is. If 95% of our DNA would be functional, Darwinists would say - what is so surprising ? Of course all of our DNA is functional and only a small percentage is junk ... it can't be otherwise ... because natural selection removes anything what is not useful/functional ... If 95% of our DNA would be non-functional, then, Darwinists would say - look, this is an ultimate proof that evolution is true, how else could you explain that 95 % of it is a junk ? Clearly, it is an artifact of millions of years of evolution ... an ultimate proof .... It is like in some mental hospital ....martin_r
October 12, 2022
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So apparently JVL does not think that 'over half' of the genome being useless garbage will effect the thermodynamic efficiency of the cell. So that about does it for me. I have much better things to do today than chase a unreasonable, and unscientific, troll's tail around in a circle.
Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20 Logical Reversibility of Computation* - C. H. Bennett - 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html The astonishing efficiency of life - November 17, 2017 by Jenna Marshall Excerpt: All life on earth performs computations – and all computations require energy. From single-celled amoeba to multicellular organisms like humans, one of the most basic biological computations common across life is translation: processing information from a genome and writing that into proteins. Translation, it turns out, is highly efficient. In a new paper published in the journal Philosophical Transactions of the Royal Society A, SFI researchers explore the thermodynamic efficiency of translation.,,, To discover just how efficient translation is, the researchers started with Landauer's Bound. This is a principle of thermodynamics establishing the minimum amount of energy that any physical process needs to perform a computation. "What we found is that biological translation is roughly 20 times less efficient than the absolute lower physical bound," says lead author Christopher Kempes, an SFI Omidyar Fellow. "And that's about 100,000 times more efficient than a computer." https://phys.org/news/2017-11-astonishing-efficiency-life.html The thermodynamic efficiency of computations made in cells across the range of life. - 2017 Dec. Excerpt: Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. https://www.ncbi.nlm.nih.gov/pubmed/29133443/
bornagain77
October 12, 2022
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Bornagain77: JVL, so measuring the thermodynamic efficiency of a human cell is not ‘scientific’ enough for you to tell you how much useless ‘garbage’ the cell is forced to carry? The story (not a scientific paper) says: "In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power." And what does that have to do with "how much (useless) 'garbage' the cell is forced to carry"? Please be specific. AND I didn't say you didn't copy-and-paste scientific stuff; I'm just saying I don't think you actually understand what it is you are copy-and-pasting. Here's a reason why: From the other paper you linked to: (which you mis-labelled, I'm going on the actual link) Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage
Analyses of the human genome and annotated protein-coding genes suggest that several dozen human-proteins arose de novo and indicate that de novo proteins are added to the genome at a slow and stable rate (Knowles and McLysaght 2009; Wu et al. 2011; Guerzoni and McLysaght 2016).
And
Evidence from ribosome-profiling experiments indicates that many taxon-restricted sequences bind to ribosomes and are translated into proteins which evolve neutrally (Wilson and Masel 2011; Schmitz et al. 2018; Ruiz-Orera et al. 2018). Thus, eukaryotic genomes are likely home to a shifting population of novel transcripts containing ORFs with members regularly being gained and lost.
Which makes it look like you never even read the introduction to the paper you linked to. But wait, there's more!!
It seems likely that novel ORFs may remain in the human genome for millions of years before being selected for specific functions. Indeed, data in great apes show the existence of hundreds of novel multi-exon transcripts evolving neutrally, indicating that young de novo may evolve gene-like properties prior to acquiring biological functions (Ruiz-Orera et al. 2015). In our data, which included single exon transcribed ORFs, pairwise ? values show that the majority of primate-restricted ORFs are evolving neutrally.
From the last paragraph:
Our results support previous findings which indicate that each species is host to a myriad of novel transcribed sequences. Fine-scale analyses, using closely related taxa, have allowed for the study of the evolution of protein properties in insects (Heames et al. 2020) and fish (Schmitz et al. 2020) but, until now, not mammals. Our use of recently diverged primate taxa allows us to trace the fine-scale evolution of expressed ORFs over recent time scales in a mammalian order. We find that novel ORFs are frequently formed and transcribed from intergenic and intronic regions. Properties of these transcribed ORFs, such as ISD, aggregation propensity, and proximity to annotated genes; do not change with increasing level suggesting that their chance of survival over time and long term retention are largely stochastic rather than driven by selection.
Too funny. Thank you for providing documentation that runs counter to your claims. Clearly, not only do you not understand the science but you don't even read the stuff you link to. How sad is that?JVL
October 12, 2022
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JVL, so measuring the thermodynamic efficiency of a human cell is not 'scientific' enough for you to tell you how much useless 'dead weight' the cell is forced to carry? And you accuse me of not 'understanding the science'? :)bornagain77
October 12, 2022
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Bornagain77: Really? Yes really. Look, instead of just copy-and-pasting lots of things other people said why don't you pick an actual bit of research and show where you think the researchers made a mistake or misinterpreted their results. Can you do that? Do you want me to pick a paper for you to consider? Can you actually demonstrate an understanding of the science involved and critique it based on its actual merits? Yes or no? Why not try this paper: Kinetic Analysis Suggests Evolution of Ribosome Specificity in Modern Elongation Factor-Tus from “Generalist” Ancestors https://pdfs.semanticscholar.org/702f/df512beb219f7fcd739656eefef4da8d683d.pdfJVL
October 12, 2022
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Relatd: Really? Based on what? I’ve seen the so-called evidence. It’s junk. Well, lots and lots and lots and lots of highly educated people disagree with you. And they can explain why they think the evidence is compelling. And that explanation does not require the supposition of some alien being or intelligence that we have no hard and fast physical evidence of. Evolution is fast except when it isn’t. Evolution makes a lot of changes except when it doesn’t. For someone who claims to have looked at the evidence you are strangely ignorant of the explanations for such things. I'm beginning to think you haven't actually looked at the evidence. OR you didn't understand it. OR you chose to ignore or disbelieve it. Look, you are bringing up the same old tropes that have been addressed over and over and over again on this blog and otherwise. You can chose to disagree with the arguments but you can't say they don't exist. Why don't you try and address the actual arguments and reasonings made (which are easy to find) instead of just saying it's all junk. Try and exhibit some actual scientific reasoning. You know, like real scientists do. WHY, exactly do you think it's junk. Discuss research, point out places you think mistakes were made, discuss particular places or points where you think misinterpretations were made. Can you do that sort of thing? Most important: address the actual work that has been done. Here's a starting point: pick a paper or book and spell out particular places where you think the author(s) made a mistake and give reasons and evidence why you think they are mistakes. Can you do that?JVL
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AF: "The fact remains that over half the human genome serves no positive purpose for humans." Really? All that 'junk DNA', "over half", must place a fairly large energetic burden on the cell? Especially since "Transcriptomics studies show the pervasive transcription of virtually the entire human genome"
"Transcriptomics studies show the pervasive transcription of virtually the entire human genome"(Clark et al. 2011; Hangauer et al. 2013). https://academic.oup.com/gbe/article/12/11/2183/5906514
And yet, despite transcribing all that supposedly useless junk DNA into useless transcriptions, the human cell somehow manages to be amazingly energetically efficient.
Cell-inspired electronics – February 25, 2010 Excerpt: “A single cell in the human body is approximately 10,000 times more energy-efficient than any nanoscale digital transistor, the fundamental building block of electronic chips. In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” http://phys.org/news/2010-02-cell-inspired-electronics.html
Something definitely is not adding up in terms of the amazing energetic/thermodynamic efficiency found in the human cell and the Darwinian claim that massive amounts of junk DNA exist in the human genome. As they use to say on Sesame Street, "can you guess what does not belong in this picture?"bornagain77
October 12, 2022
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JVL at 96, Really? Based on what? I've seen the so-called evidence. It's junk. Evolution is nothing more than a storytelling device. And trust me, I understand storytelling. I know exactly how it works. Examples: Evolution is fast except when it isn't. Evolution makes a lot of changes except when it doesn't. With that type of storytelling in hand, I could write a story about ancient peoples going to the Moon on the backs of large dogs. Those dogs went extinct and now we have to use rockets.relatd
October 12, 2022
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10:21 AM
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Relatd: None of it was compelling then and it’s not compelling now. Maybe a) you didn't understand it or b) you have compelling reasons for disbelieving it. Regardless, many highly educated people who have spent years studying the pertinent science and evidence and data and research do find it compelling. It's not a popularity contest but you just saying:it's not compelling compared to the lengthy explanations of why it's compelling from the scientists . . . well . . . your opinion isn't very compelling.JVL
October 12, 2022
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10:06 AM
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JVL at 94, For many years, on sites other than this one, defenders of evolution threw tons of data my way because I didn't "understand" evolution. None of it was compelling then and it's not compelling now. I mean if people say, "You really should look at this," I'll look. I study a lot of science and technology and you know what? Evolution is sinking like the Titanic.relatd
October 12, 2022
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10:02 AM
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Relatd: If you work for the Ministry of Propaganda and your instructions are “to defend evolution in any way you can,” what do you do? Paranoia runs deep, into your life it will creep. Plus it means you don't actually have to discuss or even know anything about the science. Convenient.JVL
October 12, 2022
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Jerry at 85, "The answer is that they have no evidence and they know it. So they play games using one fallacy after the other. But why do they do it?" Why? If you work for the Ministry of Propaganda and your instructions are "to defend evolution in any way you can," what do you do?relatd
October 12, 2022
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Jerry: But yet can not produce any evidence for what he espouses. And you know that because? You've read all his blog posts over the last decade or more? Oh, wait, I forget. You're not interested in having a conversation or discussion. Stupid me; I wasted my time responding to you when you don't care. I've got to remember that.JVL
October 12, 2022
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