Scientists’ reaction to ever more of the cell’s complexity in its own environment

_{Denyse O'Leary

October 28, 2021

Cell biology, Intelligent Design, Irreducible Complexity}

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For a few weeks in 2017, Wanda Kukulski found herself binge-watching an unusual kind of film: videos of the insides of cells. They were made using a technique called cryo-electron tomography (cryo-ET) that allows researchers to view the proteins in cells at high resolution. In these videos, she could see all kinds of striking things, such as the inner workings of cells and the compartments inside them, in unprecedented detail. “I was so overwhelmed by the beauty and the complexity that in the evenings I would just watch them like I would watch a documentary,” recalls Kukulski, a biochemist at the University of Bern, Switzerland.
In recent years, imaging techniques such as cryo-ET have started to enable scientists to see biological molecules in their native environments. Unlike older methods that take individual proteins out of their niches to study them, these techniques provide a holistic view of proteins and other molecules together with the cellular landscape. Although they still have limitations — some researchers say that the resolution of cryo-ET, for example, is too low for molecules to be identified with certainty — the techniques are increasing in popularity and sophistication. Researchers who turn to them are not only mesmerized by the beautiful images, but also blown away by some of the secrets that are being revealed — such as the tricks bacteria use to infect cells or how mutated proteins drive neurodegenerative diseases such as Parkinson’s.
Diana Kwon, “The secret lives of cells — as never seen before” at Nature (October 26, 2021)

No wonder panpsychism is catching on, among those who are forbidden to think in terms of design.

Comments

Upright Biped, I am having trouble accessing biosemiosis.org with web.archive.org. Is there another way to look at your work?Origenes_{October 30, 2021
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. …and while you are here Sev, would you also mind addressing this statement you made?
Sev: Once more, in my view, we are able to infer design on two grounds.
The first …
Sev: The phenomenon or entity has not been observed to result from natural processes
Done. No one has observed a natural process that results in encoded memory containing a set of descriptions of the constraints required to decode that memory … It clearly, unambiguously “has not been observed”. His first criterion is satisfied.. The second …
Sev: and (the phenomenon) resembles what human beings design to a degree sufficient to at least raise the possibility of intelligent design.
Done. The “phenomenon” in question is a completely unique physical system that has been described and identified by physics for the past five decades. It is a self-referent system using rate-independent control of a rate-dependent process, preserving its constraints, just exactly as it was predicted to be. The prediction was confirmed by experimental result. All the necessary parts of the system were found, one by one. All of it abundantly recorded in the literature. Nobel Awards were passed out. And the only other instance where this particular type of system can be found and described (by physics) is in human language and mathematics – two universal correlates of intelligence. It doesn’t merely “raise the possibility” of intelligence; the only other examples are immediate correlates of intelligence. So what say you Seversky?
Upright BiPed_{October 30, 2021
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. Seversky, do you want to talk about Barbieri’s two postulates? They are both given on the first page of the paper. Then, the remainder of the paper is provided to support of the postulates. Why don’t you dig into the paper and present here what Barbieri uses to support his second postulate. I’ll wait. - - - - - - - - Ps — you might want to review comment #75.Upright BiPed_{October 30, 2021
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. Good grief Seversky, did you actually read what you posted? This was written several years ago when the different schools of biosemiotics were trying to organize themselves. Tell me where anything in Barbieri’s paper that indicates that 1) the gene system is not a genuine symbol system, or 2) that the only other example of such a physical system is in the use of language. Can you do that?Upright BiPed_{October 30, 2021
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. Oh wow. I did not see this statement earlier, and I think it should be addressed.
One, in fact, (Dr Pattee), criticised ID proponents explicitly.
JVL, if a person says that the gene system is a genuine rate-independent symbol system, do you think HH Pattee would disagree with that statement? If a person says that the only other physical system to operate like the gene system is in the use of language and mathematics, do you think HH Pattee would disagree? Lets cut to the chase, JVL. If a person correctly repeats any of the central observations about the physical requirements of the gene system, which HH Pattee documented over the course of 50 years, do you think he would disagree with any of those observations? Of course not. Are you beginning to understand why your comments above are so obvious in their intent, yet so impotent in their impact on the issues?Upright BiPed_{October 30, 2021
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A Short History of Biosemiotic

Marcello Barbieri

Biosemiotics volume 2, pages221–245 (2009)

[…] Darwinian Biosemiotics According to the Modern Synthesis, life does not require new laws of physics, but does require a new principle of nature because it is based on natural selection, and this is a process that does not exist in the inanimate world. The principle of natural selection is unique to life, and represents something “extra” in respect to the laws of physics. The Modern Synthesis, in short, takes as explanatory principles not the laws of physics alone, but the laws of physics plus the principle of natural selection. Ernst Mayr, one of the architects of the Modern Synthesis, has repeatedly emphasized that biology has necessarily a wider framework than physics: “…The explanatory equipment of the physical sciences is insufficient to explain the interplay between historically acquired information and the responses of the genetic program to the physical world…. This is why it is just as impossible to include biology in physics as it is to include physics in geometry.” (Mayr 1982). The need to add natural selection to the laws of physics, was accepted by Howard Pattee, and this is a step that amounts to an extended version of his theory. Pattee underlined that there is no contrast between physical biosemiotics and natural selection, and we can therefore put them together. In this way, by adding a mechanism of evolution to physical biosemiotics, this becomes evolutionary physical biosemiotics, and since the mechanism in question is natural selection we can rightly call it Darwinian biosemiotics. This view is in complete agreement with the Modern Synthesis because it accepts all its basic concepts, in particular the model that every organism is a duality of genotype and phenotype and the idea that natural selection is the sole mechanism of evolution. Darwinian biosemiotics, in other words, is physical biosemiotics plus the principle of natural selection, and can be regarded as the evolutionary version of physical biosemiotics. In both cases, the Pattee approach introduces semiosis into the Modern Synthesis without changing its defining principles, and represents, to all effects, an updating of the Synthesis itself, an extension that allows it to incorporate the concepts of semiosis and recognize at last the existence of “symbols that control matter” in every cell of the living world. […] Today there are still differences between the schools, but there is also a ‘minimal unity’ in the field because of two basic principles, or postulates, that are accepted by virtually all biosemioticians. (1) The first postulate is Thomas Sebeok’s idea that “life and semioisis are coextensive”. This implies that semiosis appeared at the origin of life, and sharply differentiates biosemiotics from ‘pansemiotics’ and ‘physiosemiotics’, the doctrines that semiosis exists also in inanimate matter and therefore everywhere in the universe. It also differentiates it from the views that semiosis exists only in animals or only in humans beings. (2) The second postulate is the idea that signs, meanings and codes are natural entities. This sharply divides biosemiotics from the doctrine of ‘intelligent design’, and from all other doctrines that maintain that the origin of life on Earth was necessarily the product of a supernatural agency.
Seversky_{October 30, 2021
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As to Seversky's attempted defense of Theobald, in Theobald's response to Ashby Camp, Theobald honestly admitted that he had to incorporate "new material into the original essay that specifically addresses many of Camp’s points, and thus much of his response is now superfluous." What additional material Theobald may have added, I have not the time nor inclination to look into right now. (My bottom dollar bet is that it is, as usual, all bluff and bluster). If Seversky thinks there is a piece of 'slam dunk' 'additional' empirical evidence for Darwinian evolution in Theobald's response to Camp, he is more than invited to present it to me and we will weigh its strengths and weaknesses then. But as it sits now, I am certainly not going to try to read Seversky's mind as to what part of Theobald's 'new' essay he might find particularly compelling. But regardless, the main thrust of Theobald's response to Ashby, (at least the main thrust of the portion that Seversky referenced to me), seems to be that Theobald claimed that Ashby made a number of logical fallacies in his response to Theobald. i.e. Straw man arguments, Red herrings, Self-contradictions, Equivocation , Arguments from authority, etc.. etc.. My first response to that is that, "You've got to be kidding me? A Darwinist appealing to logical fallacies?" :) You just can't make this stuff up. The existence of 'immaterial' logic, in and of itself, refutes Theobald's entire naturalistic/atheistic worldview of Darwinian evolution. To paraphrase Dr. Egnor, "the very logic that Clark (i.e. Theobald) employs to argue for naturalism is outside of any naturalistic frame."
Naturalism and Self-Refutation – Michael Egnor – January 31, 2018 Excerpt: Furthermore, the very framework of Clark’s argument — logic — is neither material nor natural. Logic, after all, doesn’t exist “in the space-time continuum” and isn’t described by physics. What is the location of modus ponens? How much does Gödel’s incompleteness theorem weigh? What is the physics of non-contradiction? How many millimeters long is Clark’s argument for naturalism? Ironically the very logic that Clark employs to argue for naturalism is outside of any naturalistic frame. The strength of Clark’s defense of naturalism is that it is an attempt to present naturalism’s tenets clearly and logically. That is its weakness as well, because it exposes naturalism to scrutiny, and naturalism cannot withstand even minimal scrutiny. Even to define naturalism is to refute it. https://evolutionnews.org/2018/01/naturalism-and-self-refutation/
And as C.S. Lewis put it, "In other words, unless Reason is absolute—all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based."
"Long before I believed Theology to be true I had already decided that the popular scientific picture at any rate was false. One absolutely central inconsistency ruins it…. The whole picture professes to depend on inferences from observed facts. Unless inference is valid, the whole picture disappears. Unless we can be sure that reality in the remotest nebula … obeys the thought laws of the human scientist here and now in his laboratory—in other words, unless Reason is absolute—all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based. The difficulty is to me a fatal one; and the fact that when you put it to many scientists, far from having an answer, they seem not even to understand what the difficulty is, assures me that I have not found a mare’s nest but detected a radical disease in their whole mode of thought from the very beginning. The man who has once understood the situation is compelled henceforth to regard the scientific cosmology as being, in principle, a myth; though no doubt a great many true particulars have been worked into it." - C. S. Lewis
Thus, for Theobald to even appeal to logic, (i.e. logical fallacies), in the first place is for him, apparently unbeknownst to himself, to undermine his entire naturalistic/atheistic worldview of Darwinian evolution in the process. And furthermore, to state the glaringly obvious, if your atheistic/naturalistic worldview can't possibly ground 'immaterial' logic and reasoning in the first place, then your atheistic/naturalistic worldview can't possibly provide a coherent basis for the inductive logic and reasoning that forms the basis of the scientific method itself. i.e. Methodological Naturalism is a simply non-starter' as to firmly grounding the scientific method itself. And indeed, science can get along quite well without any particular reference to Darwinian 'narratives':
"While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.” Adam S. Wilkins, editor of the journal BioEssays, Introduction to "Evolutionary Processes" - (2000). "In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all." Marc Kirschner, founding chair of the Department of Systems Biology at Harvard Medical School, Boston Globe, Oct. 23, 2005 "Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No. I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss. In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.,,, Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology." ?Philip S. Skell - (the late) Emeritus Evan Pugh Professor at Pennsylvania State University, and a member of the National Academy of Sciences. - Why Do We Invoke Darwin? - 2005? Darwin’s Theory of Natural Selection Has Left a Legacy of Confusion over Biological Adaptation Brian Miller - September 20, 2021 Excerpt: Evolutionary biologist Robert Reid stated: "Indeed the language of neo-Darwinism is so careless that the words ‘divine plan’ can be substituted for ‘selection pressure’ in any popular work in the biological literature without the slightest disruption in the logical flow of argument." Robert Reid, Biological Emergences: Evolution by Natural Experiment, PP. 37-38 To fully comprehend the critique, one simply needs to imagine attempting to craft an evolutionary barometer that measures the selection pressure driving one organism to transform into something different (e.g., fish into an amphibian). The fact that no such instrument could be constructed highlights the fictitious nature of such mystical forces. https://evolutionnews.org/2021/09/darwins-theory-of-natural-selection-has-left-a-legacy-of-confusion-over-biological-adaptation/
Moreover and personally, my main gripe with Theobald's list of 29 supposedly 'falsifiable' predictions is the fact that Theobald is making a patently false claim. Darwinian evolution, (at least how Darwinists treat their theory), is notorious for not being falsifiable by empirical testing. No less than Denis Noble, President of International Union of Physiological Sciences, himself has noted that Darwin's theory is 'so flexible as an idea that it can accept even those findings that the originators intended to be excluded by the theory' that it has become, basically, unfalsifiable by empirical observation.
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 https://jeb.biologists.org/content/218/16/2659
And as Dr. Cornelius Hunter points out, Darwinists are notorious for making up ad hoc 'just-so' stories to cover up embarrassing empirical falsifications of their theory,
"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
On the following site, Dr. Hunter lists many predictions of Darwin's theory, predictions that are core to the theory, that have now been falsified by empirical evidence,
Darwin's (failed) Predictions - Cornelius G. Hunter - 2015 This paper evaluates 22 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena, and how they bear on evolutionist’s claims about their theory. *Introduction Why investigate evolution’s false predictions? Responses to common objections *Early evolution predictions The DNA code is not unique The cell’s fundamental molecules are universal *Evolutionary causes predictions Mutations are not adaptive Embryology and common descent Competition is greatest between neighbors *Molecular evolution predictions Protein evolution Histone proteins cannot tolerate much change The molecular clock keeps evolutionary time *Common descent predictions The pentadactyl pattern and common descent Serological tests reveal evolutionary relationships Biology is not lineage specific Similar species share similar genes MicroRNA *Evolutionary phylogenies predictions Genomic features are not sporadically distributed Gene and host phylogenies are congruent Gene phylogenies are congruent The species should form an evolutionary tree *Evolutionary pathways predictions Complex structures evolved from simpler structures Structures do not evolve before there is a need for them Functionally unconstrained DNA is not conserved Nature does not make leaps *Behavior Altruism Cell death *Conclusions What false predictions tell us about evolution https://sites.google.com/site/darwinspredictions/home Why investigate evolution’s false predictions? Excerpt: The predictions examined in this paper were selected according to several criteria. They cover a wide spectrum of evolutionary theory and are fundamental to the theory, reflecting major tenets of evolutionary thought. They were widely held by the consensus rather than reflecting one viewpoint of several competing viewpoints. Each prediction was a natural and fundamental expectation of the theory of evolution, and constituted mainstream evolutionary science. Furthermore, the selected predictions are not vague but rather are specific and can be objectively evaluated. They have been tested and evaluated and the outcome is not controversial or in question. And finally the predictions have implications for evolution’s (in)capacity to explain phenomena, as discussed in the conclusions. https://sites.google.com/site/darwinspredictions/why-investigate-evolution-s-false-predictions
Likewise, over the years of debating Darwinists, I have collected my own list of falsifications to Darwin's theory, falsifications that also go to the core of the theory,,,, and falsifications that Darwinists simply refuse to ever accept as falsifications 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 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 holds there to be an extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. The mutation rate to DNA 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(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 use when they are doing their research falsifies Darwinian evolution. Darwinism vs. Falsification - list and link to defence of each claim https://docs.google.com/document/d/1I6fT6ATY700Bsx2-JSFqL6l-rzXpMcZcZKZfYRS45h4/edit
Thus in conclusion, Seversky may take umbrage to my claim that Theobald's list of 29 'falsifiable' predictions for Darwinian evolution is a patently false claim for Theobald to make. If so, Seversky is more than invited to list any piece of empirical evidence from Theobald's 'new' list that he thinks can stand up to rigid scrutiny. Again, it is my bottom dollar bet that Theobald's entire paper, (as is usual for Darwinists), is nothing but bluff and bluster with no real empirical evidence in it that can stand up to real scrutiny.
1 Thessalonians 5:21 but test all things. Hold fast to the good.
bornagain77_{October 30, 2021
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. For any onlooker, The researcher that JVL refers to in #68 is esteemed physicist Howard Hunt Pattee. Dr Pattee’s specific conclusion is that the gene system is a genuine rate-independent symbol system (just as it was predicted to be in 1948 by John Von Neumann) and that the only other physical system that operates like it is in the use of language (i.e. a universal correlate of intelligence). This is the actual conclusion that JVL wishes to ignore because it helps to confirm the design inference. This is why JVL wishes to change the subject to the irrelevant topic of Dr Pattee’s own personal worldview. Dr Pattee obviously does not say “Because I am a non-theist, everything I wrote for the past 5 decades is untrue and may be ignored”. That is merely what JVL says in his place.Upright BiPed_{October 30, 2021
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.
JVL: I asked the question: do the researchers that Upright Biped linked to agree with their conclusion regarding intelligent design.
Three things: 1) You were told that the author/paper in question did not directly offer any such ultimate conclusions. You were then reminded that the author is a careful researcher who, in his own words, seeks to avoid what he considers “undecidable” questions which are not required in his physical analysis. You were then asked why you thought such a researcher (in such a frame of mind) should be expected to load his papers with undecidable statements. You had no response. 2) In a comment prior to all this, you stated that you were prepared to accept research from any researcher, regardless of their larger worldview — IF — the research is competent and properly conducted. This indicates that you clearly understand and fully appreciate that a researcher’s personal worldview is properly separate from his/her practice of science. However, then as now, when you are faced with evidence and reasoning that you cannot refute, you immediately throw out your prior words and specifically seek to find solace in the personal worldview of the researcher. This is yet another demonstration of the deception that pervades virtually everything you say on this subject. What you count on is no one noticing, but they do. 3) It must be pointed out that you, once again, refuse to engage in a conversation about physical evidence (which you obviously cannot spin away) preferring again to change the subject to issues that do not alter, and do not impact, that evidence. You will continue to avoid the physical evidence at all costs. (The remainder of your comment follows from the deception)Upright BiPed_{October 30, 2021
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I must have pushed one of Seversky's buttons at posts 18 and 19. At 37 and 38 Seversky seems a bit more animated than he usually is. :) First, as to Lenski's claim that he has evidence for Darwinian evolution in his long term evolution experiment with e-coli, (and as to the overall topic of this thread), I think the following reference from a Biomedical engineer is quite relevant, i.e. "Darwinism Flunks Science Criteria (for high confidence evidence), Says Biomedical Engineer". Particularly, he disagrees with Lenski's claim and holds that the evidence is evidence for Intelligent Design, not for Darwinian evolution.
Darwinism Flunks Science Criteria (for high confidence evidence), Says Biomedical Engineer - April 7, 2019 Excerpt: The commonly cited evidence for evolution (e.g., the fossil record, homology, and vestigial organs) do not meet any of the 6 criteria for high-confidence science. For example, the process that produced the life-forms found in the fossil record cannot be repeated, cannot be directly measured, and cannot be studied prospectively. Also, interpretations of the fossil record are replete with bias and are based upon many assumptions (for example, we are asked to assume that a life-form that is not found in a given layer of fossils did not exist at that time, yet we also are asked to assume that absence of transitional fossils in the fossil record does not imply that they did not exist). Finally, the interpretation of the fossil record (i.e., the effort to explain how the life-forms contained in the fossil record came to exist) extrapolates far from the actual evidence (fossilized bones) to try to explain the process responsible for the origination of the life-forms. The very low confidence provided by this type of evidence cannot provide clarity; it can only provide fuel for endless debate. In stark contrast, experimental evolution studies like Richard Lenski’s Long Term Evolution Experiment (LTEE) meet all 6 criteria and provide very high confidence. Experimental evolution can be repeated, can be studied prospectively and directly measured, with minimal bias and assumptions, and the results can be summarized with sober judgement. The evidence from these high-confidence experimental evolution studies simply must be prioritized over the low-confidence evidence. Yet, biology textbooks routinely prioritize the low-confidence evidence over the high-confidence evidence. The high-confidence evidence from experimental evolution studies paint a highly constrained picture of evolution. For example, Lenski’s 70,000 generations of E. coli show that evolution is highly constrained – unable to produce the innovations necessary to change body plans over time or to produce new molecular machinery. The orphan genes that are prevalent in all life-forms cannot be explained by the evolution observed in these studies. When high-confidence evidence is appropriately prioritized over low-confidence evidence, the result is a profound new view of evolution – one that they did not teach you in biology. https://uncommondescent.com/evolution/darwinism-flunks-science-criteria-says-biomedical-engineer/
bornagain77_{October 30, 2021
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Upright Biped @64,
Chuck, just for a change of pace, why don’t you try engaging in the science instead of the politics? Are you not a “trained biologists”? Here is a question I asked you several days ago. Like all the others I’ve asked, you simply walk away. Put your money were your mouth is.
Indeed--same as my experience. Quite frankly, how could Chuckdarwin be a "trained biologist" and not understand how transpiration works? See Chuckdarwin @8 here: https://uncommondescent.com/intelligent-design/at-evolution-news-and-science-today-why-c-s-lewis-doubted-the-creative-power-of-natural-selection/ Where he asserts . . .
Trees get their water and nutrients by transpiration, not by story telling. That is first year botany.
While there are a few websites that seem to generalize the definition of transpiration to include the process of water transport in the xylem by capillary action involving molecular cohesion and adhesion, the majority of sources define transpiration as the loss of water though leaf surfaces and not involving nutrients typically transported by the phloem. -QQuerius_{October 30, 2021
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Upright Biped: JVL continues to pepper people with irrelevant questions, constantly trying to get a fingernail under some grist for the mill. When someone says they think some mutations are guided and some aren't I think it's fair to ask for their criteria. Likewise, so as not to waste people's time, I think it's fair to ask what they would accept as evidence regarding a particular scientific issue. JVL knows all of these things, but will not speak of them. That is not quite correct. I asked you for information regarding such issues and I read some of the material you linked to. And then I asked the question: do the researchers that Upright Biped linked to agree with their conclusion regarding intelligent design. I didn't find any such researcher discussing these issues who explicitly stated they supported ID. Granted that doesn't mean they don't but they didn't say they did. One, in fact, (Dr Pattee), criticised ID proponents explicitly. Upright BiPed wants to interpret my actions as denying what he says are obvious conclusions from biosemetic work. Not being an expert in that subject myself I looked to see what the experts had to say about ID. I didn't find any of them supporting ID and I definitely found one who criticised ID. Upright BiPed and the researchers he cites seem to disagree on the implications of their work. I'm just observing that, I'm not, myself, saying that. I've got not other comment to make in this regard. If Upright BiPed has a problem with the opinion of the experts whose work he cites then he should take it up with them. Not me.JVL_{October 30, 2021
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A propos... Biology transcends the limits of computation Perry Marshall. Prog Biophys Mol Biol. 2021 Oct. Abstract Cognition-sensing and responding to the environment-is the unifying principle behind the genetic code, origin of life, evolution, consciousness, artificial intelligence, and cancer. However, the conventional model of biology seems to mistake cause and effect. According to the reductionist view, the causal chain in biology is chemicals > code > cognition. Despite this prevailing view, there are no examples in the literature to show that the laws of physics and chemistry can produce codes, or that codes produce cognition. Chemicals are just the physical layer of any information system. In contrast, although examples of cognition generating codes and codes controlling chemicals are ubiquitous in biology and technology, cognition remains a mystery. Thus, the central question in biology is: What is the nature and origin of cognition? In order to elucidate this pivotal question, we must cultivate a deeper understanding of information flows. Through this lens, we see that biological cognition is volitional (i.e., deliberate, intentional, or knowing), and while technology is constrained by deductive logic, living things make choices and generate novel information using inductive logic. Information has been called "the hard problem of life" and cannot be fully explained by known physical principles (Walker et al., 2017). The present paper uses information theory (the mathematical foundation of our digital age) and Turing machines (computers) to highlight inaccuracies in prevailing reductionist models of biology, and proposes that the correct causation sequence is cognition > code > chemicals. https://pubmed.ncbi.nlm.nih.gov/33961842/solemn existence_{October 30, 2021
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. JVL continues to pepper people with irrelevant questions, constantly trying to get a fingernail under some grist for the mill. JVL’s questions should be kept in context. JVL was recently asked by a commenter here about the design inference stemming from presence of a genetic code, and his perpetual denial of that inference. Ignoring science and history, JVL responds:
JVL: Let’s see what the evidence says and go with that.
This answer is pure deception. On steroids. What does JVL know about “what the evidence says”. JVL knows that a symbol entails a three-way relationship between a material token (i.e. an arrangement of matter of some kind), a referent, and (in the words of CS Peirce) an “interpretant” to physically establish a relationship between the token and its referent. This is what is physically required of the system. Or, to be more precise, even if abiogenesis is true, this is still what is physically required of the system. All claims must therefore meet the same requirement of being an adequate claim. To be an adequate claim, they must all result in this particular physical system being perpetuated over time. This system can be perpetuated over time by perpetuating the constraints in the system (i.e. the interpretants). This is implied because the descriptions are dependent on the constraints; until the constraints are stable, the sequences of their descriptions cannot specify them. When the constraints are established and the sequences successfully describe them, the system assumes a functional condition known as “semiotic closure”. In other words, the system must be self-referent in order to function. The way in which the constraints are perpetuated by the system is by specifying them in an inheritable memory. That memory must then be placed in the daughter. JVL knows all this. These interdependent requirements are the uniquely identifying physical characteristics of the type of system that enables open-ended replication among living things. It is what Sydney Brenner would tighten his jaw and specifically emphasize as the ”fundamental act” of self-replication — not to mention the fact that these things were specifically (and successfully) predicted by John Von Neumann in 1948, using Alan Turing’s 1936 Machine as a model. JVL knows all this as well. JVL also knows that these characteristics (and more) have been documented in the literature (i.e. the rate-independent control of a rate-dependent process, the spatial-orientation of objects within the tokens to distinguish one referent from another, the requirement of complimentary physical descriptions of the system, and so on), including the fact that the only other material system known to science that meets this physical description is in the use of language and mathematics. JVL knows all of these things, but will not speak of them. Despite complete coherence and a well-documented history, JVL does not consider them. Very frankly, there is no “ Let’s see what the evidence says and go with that.” That sentiment is rhetorically calculated to portray a rationale openness to evidence. It is delivered in order to deflect away from the fact that the exact opposite is taking place. Instead of incorporating the evidence as it actually exists, JVL wants to replace the acknowledgement of that evidence with a different conversation altogether. JVL wants to ignore what is known to be true in favor of what is not known and never seen — which also just so happens to reflect JVL’s personal preferences on the matter. This is an entirely different situation than merely not knowing something; this is nothing less than choosing to disregard what is known because you don’t like it. This is the context that JVL’s participation here must be seen in. It has nothing whatsoever to do with either science or reason. When JVL throws out RNA and stereochemistry, he is not reasoning with evidence, he is digging a trench to jump in and hide from the science.Upright BiPed_{October 30, 2021
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. Seversky says: ”There are still plenty of proponents of design and they still publish books and articles and videos. It just doesn’t add anything to science” Sev, you wrap yourself in the flag of science, and then run as fast as you can from empirical evidence. You deny the design inference simply because you don’t like it. Why do you so obviously avoid this question:
Sev: Once more, in my view, we are able to infer design on two grounds.
The first …
Sev: The phenomenon or entity has not been observed to result from natural processes
Done. No one has observed a natural process that results in encoded memory containing a set of descriptions of the constraints required to decode that memory … It clearly, unambiguously “has not been observed”. His first criterion is satisfied.. The second …
Sev: and (the phenomenon) resembles what human beings design to a degree sufficient to at least raise the possibility of intelligent design.
Done. The “phenomenon” in question is a completely unique physical system that has been described and identified by physics for the past five decades. It is a self-referent system using rate-independent control of a rate-dependent process, preserving its constraints, just exactly as it was predicted to be. The prediction was confirmed by experimental result. All the necessary parts of the system were found, one by one. All of it abundantly recorded in the literature. Nobel Awards were passed out. And the only other instance where this particular type of system can be found and described (by physics) is in human language and mathematics – two universal correlates of intelligence. It doesn’t merely “raise the possibility” of intelligence; the only other examples are immediate correlates of intelligence. So what say you Seversky?
***crickets***Upright BiPed_{October 30, 2021
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. Chuck says “ID spends way more time honing its feigned victimhood and attempts to elbow its way to the table than it does on real science.” Chuck, just for a change of pace, why don’t you try engaging in the science instead of the politics? Are you not a “trained biologists”? Here is a question I asked you several days ago. Like all the others I’ve asked, you simply walk away. Put your money were your mouth is. - - - - - - - - - - - - - - - - - Oct 17th Speaking of predictions, it was predicted that autonomous self-replication would be code-based, and that encoded descriptions of the constraints (required to interpret code) would be among the descriptions encoded. Chuck, is the Genetic Code established by description?Upright BiPed_{October 30, 2021
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<ET: Right. Some unknown process did something. You don’t even have a mechanism capable of producing eukaryotes given starting populations of prokaryotes. And endosymbiosis doesn’t help. You seem mostly hung up with the transition from prokaryotes to eukaryotes. Are you sure you're caught up with the latest research on that? There aren’t any known naturalistic mechanisms capable of producing the diversity of life starting with populations of prokaryotes. That means there aren’t any known naturalistic mechanisms capable of producing the organisms that fossilized. Well, most of them, especially after the introduction of eukaryotes are due to differential survival because of inheritable variations. Clueless. DNA is NOT the genetic code. And you and yours don’t have anything but to deny reality. I didn't say DNA was the genetic code. Others have. And it is moot anyway. But you are ignorant of genetics, biology and science, so it doesn’t matter. I think it matters a great deal that you a) support your views and b) offer an alternative to modern evolutionary theory. You (seem to) think some mutations are guided and some are not. I'd just like to know what some of the criteria are for deciding which is which. If those criteria have already be developed it should be easy to provide a summary of them. The DNA model for universal common descent is a failure. Science has refuted it. It is beyond time to admit the failure and move on. There is no DNA model for universal common descent. There is evidence in genomes that supports universal common descent.JVL_{October 30, 2021
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It is impossible for differential accumulations of genetic change to account for the diversity of life, starting from some populations of prokaryotes. DNA doesn't have the type of power or influence. The thought that when the human genome project was completed they would uncover the instructions for the human body plan, ie the upright biped. They didn't. Nothing even close. And last year's paper, On the Problem of Biological Form, finally let the cat out of the bag. The DNA model for universal common descent is a failure. Science has refuted it. It is beyond time to admit the failure and move on.ET_{October 30, 2021
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JVL:
Just talking about evolution (past a certain level of basic replicator): inheritable variations creating different morphologies are ‘selected’ by natural forces (at first) creating differential survival rates.
Right. Some unknown process did something. You don't even have a mechanism capable of producing eukaryotes given starting populations of prokaryotes. And endosymbiosis doesn't help.
Looking at the genomic, fossil, geo-biologic and morphological evidence it’s all consistent with universal descent via inheritable variation.
There aren't any known naturalistic mechanisms capable of producing the diversity of life starting with populations of prokaryotes. That means there aren't any known naturalistic mechanisms capable of producing the organisms that fossilized.
Except for the contested structure (DNA) there is zero evidence that any kind of designer with the necessary abilities was around Earth at the pertinent time.
Clueless. DNA is NOT the genetic code. And you and yours don't have anything but to deny reality.
PS you still haven’t specified how mutations can be determined to be guided vs unguided. Just a reminder.
Others have. And it is moot anyway. But you are ignorant of genetics, biology and science, so it doesn't matter.ET_{October 30, 2021
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Two things 1. Evolution happened, some of it, a small amount happened through naturalistic means. That's why it is important to explain what one means by the term "evolution." 2. Most evolution could not happen by naturalistic means. The origin of protein coding sequence is one of the main obstacles for evolution to happen this way. If any protein coding sequences happened through natural process, they are rare and the science shows that they cannot happen but in some extremely rare occasions. This is why every evolutionary site/book avoids the question of how macro evolution happened. As one famous evolutionist, Will Provine, said, " for me, the size of the leap of faith that is required to believe in naturalism is small." A completely disingenuous remark. Imagine a scientist accepting a religious person's rationale for their beliefs using a similar phrase. Transcript from famous 1994 debate between Phil Johnson and Provine. http://www.arn.org/docs/orpages/or161/161main.htmjerry_{October 30, 2021
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Origenes: Just let me know The issue is the history of life on Earth. Nothing to be entered into lightly.JVL_{October 30, 2021
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JVL:
Getting into all that would be another huge discussion. I think we’ll just leave it.
Just let me know. Highly relevant would be A Course on Abiogenesis - by James Tour.Origenes_{October 30, 2021
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Origenes: Unfortunately for your position, those precursors you hypothesize would have to be far more complex than anything we humans have ever produced, so these “millions of years” that you mention won’t be of any help at all. Getting into all that would be another huge discussion. I think we'll just leave it. Thank you for the expressed appreciation for my honesty. Like I said: the very least we can do is to be honest. But it should still be noted and appreciated.JVL_{October 30, 2021
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JVL:
Of course no one is saying complex organisms like humans or wombats or orchids arose without millions of years of precursors but I do appreciate you being clear about your criteria.
Unfortunately for your position, those precursors you hypothesize would have to be far more complex than anything we humans have ever produced, so these "millions of years" that you mention won't be of any help at all. — Thank you for the expressed appreciation for my honesty.Origenes_{October 30, 2021
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Origenes: Yes, that is what I am saying. If blind matter cannot spontaneously produce relatively simple devices such as mobile phone or planes, then I see no point in contemplating the possibility that it can produce infinitely more complex systems such as organisms. Okay, thanks for being clear. Of course no one is saying complex organisms like humans or wombats or orchids arose without millions of years of precursors but I do appreciate you being clear about your criteria. Because I agree with you that a box of raw materials cannot spontaneous (i.e. without guidance) assemble into a mobile phone I won't don't really have anything else to say to you about that matter. But, again, I do appreciate you being clear and honest. We can all do that at the very least.JVL_{October 30, 2021
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Jerry: Yes, there is extremely strong evidence it didn’t occur. I guess we'll just have to disagree about that. That’s why ID is the more intellectually superior and intellectually honest position. It certainly is more compelling and convincing for some people! The statement above is an example of the begging the question fallacy. Are you sure? Let's consider the popular notion in the 70s that our human ancestors could not possibly have built complex and large structures like the pyramids therefore they must have had help from aliens. What evidence did the proponents of such ideas present in support? A few bits of misinterpreted art and such but mostly they just said: these structures are too big, too complicated and too difficult to have been made by humans. We ourselves have only recently figured out how to accomplish such feats. When evidence showing how ancient human beings learned how to build such things, what kind of tools they used, villages where the workmen lived and even some written records one could still, I suppose, argue that: well, it doesn't mean there weren't aliens about supervising the process. BUT there is no real evidence there were aliens about at all!! No landing areas, no living quarters, no workshops, no lavatories, no rubbish pits with alien detritus in them. Nothing. Considering what we now know about the physical difficulties of interstellar travel it all begins to sound extremely physically unlikely as well. So, I would say, there is no strong evidence that human beings didn't build the pyramids. That's not begging the question; that's summarising a lot of data.JVL_{October 30, 2021
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JVL:
Regardless, are you essentially saying that a demonstration along the lines of: putting all the raw materials into a box, letting nature take its course and seeing if a phone or plane comes out? I just want to be sure that’s what you are saying.
Yes, that is what I am saying. If blind matter cannot spontaneously produce relatively simple devices such as mobile phone or planes, then I see no point in contemplating the possibility that it can produce infinitely more complex systems such as organisms.Origenes_{October 30, 2021
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ET: Are you daft? That is all you have. No. Just talking about evolution (past a certain level of basic replicator): inheritable variations creating different morphologies are 'selected' by natural forces (at first) creating differential survival rates. The morphologies better able to produce offspring pass their inheritable variations to more offspring than their 'siblings' without those variations. Simple. Science is about EVIDENCE, not narratives. Looking at the genomic, fossil, geo-biologic and morphological evidence it's all consistent with universal descent via inheritable variation. The 'concept' is falsifiable and many steps have been observed and are being tested. There isn’t any evidence that it did or could occur. You lose. Except for the contested structure (DNA) there is zero evidence that any kind of designer with the necessary abilities was around Earth at the pertinent time. A tree fell in the forest, there was no one around to cut it down, therefore it fell due to natural causes. PS you still haven't specified how mutations can be determined to be guided vs unguided. Just a reminder.JVL_{October 30, 2021
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Origenes: For me, to be open to the concept of unguided evolution, first and foremost a tendency by blind matter to spontaneously form simple systems [such as mobile phones & airplanes] has to be demonstrated. After that I may be somewhat open to the idea that blind matter also has the tendency to form inordinately complex systems, such as organisms. I certainly would not consider mobile phones and airplanes as simple systems!! In fact, I bet there are very few, if any, single human beings that could design either of those two on their own. Regardless, are you essentially saying that a demonstration along the lines of: putting all the raw materials into a box, letting nature take its course and seeing if a phone or plane comes out? I just want to be sure that's what you are saying.JVL_{October 30, 2021
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Too funny. Neither seversky nor JVL understand science or what it entails. Some unknown naturalistic processes did something isn’t a real convincing narrative for a mechanistic position. And that is all they have.ET_{October 30, 2021
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