(2020-10-02, 04:04 PM)nbtruthman Wrote: [ -> ]Considering the hostility here by some parties toward the Discovery Institute due to its Christian background, I thought it would be instructive to look at a very recent breakthrough in professional publication of an ID-friendly paper in a leading evolutionary biology journal. The authors follow a line of thinking very much based on concepts espoused by the DI, that are firmly founded on good science.
The paper is: "Using statistical methods to model the fine-tuning of molecular machines and systems", https://www.sciencedirect.com/science/ar...9320302071 .
Highlights:
- Statistical methods are appropriate for modelling fine-tuning.
- Fine-tuning is detected in functional proteins, cellular networks etc.
- Constants and initial conditions of nature are deliberately tuned.
- Statistical analysis of fine-tuning model some of the categories of design.
- Fine-tuning and design deserve attention in the scientific community.
This is a major peer-reviewed article on fine-tuning in biology that favorably discusses intelligent design. The Journal of Theoretical Biology is a top peer-reviewed science journal.
The article explicitly cites work by Discovery Institute Fellows such as Stephen Meyer, Günter Bechly, Ann Gauger, Douglas Axe, and Robert J. Marks. The article is co-authored by Steinar Thorvaldsen and Ola Hössjer. Hössjer is a professor of mathematical statistics at Stockholm University who is favorable to intelligent design.
Sure enough, after Darwinists discovered the article, they succeeded in obtaining a “disclaimer” from the journal’s editors, who proclaimed their bias against ID.
But the disclaimer actually made publication of the article all the more significant. It meant that the article survived peer-review and was accepted for publication despite the open hostility of the journal’s top editors.
A short and remarkably inadequate rebuttal was published in Journal of Theoretical Biology (JTB), of the paper by Hossjer and Thorvaldsen that is described above. An excellent rebuttal of this rebuttal has been written and published in Uncommon Descent (at
https://uncommondescent.com/intelligent-...jer-paper/ ). The excuse-for-a-rebuttal itself is also at this link:
Quote:Karsten Pultz writes from Denmark to respond:
The recent rebuttal of Hössjer and Thorvaldsen’s paper in JTB promotes the view that since we have a pool of variation and the mechanism of natural selection, we don’t need to infer that the fine tuning in biological systems came about through intelligent agency.
This is nothing but a “natural selection-of-the-gaps argument”, – we don’t know how fine tuning arose, therefore natural selection (must have done) it.
If the authors of this extremely short rebuttal applied the same rigorous mathematical methods to their view as Thorvaldsen and Hössjer did to theirs, we would all realize which explanation is best supported by the evidence. Choosing an inference to the best explanation can only be done if both sides of this issue are treated the same way.
The problem with the rebuttal is this. The pool of variation which natural selection can act upon is very small. First the overall mutation rate is extremely low; that’s why species are stable. Second, the vast majority of mutations are deleterious, leaving natural selection with not a pool, but a tiny puddle of beneficial variations. Third, recent research done by Michael Behe reveals that those variations are caused by loss of information (broken or damaged genes) and are therefore not adding new functions to an organism, hence not on their way to building complex fine tuned functional systems.
As long as the opponents of ID do not demonstrate, using math, that random mutation and natural selection provide the required probabilistic resources for the fine tuning of biological systems, they have not given us a science-based rebuttal. What they offer is just a “because we say so” rebuttal.
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Regarding JTB’s disclaimer, the call for retraction by Retraction Watch, and the above mentioned rebuttal, it is worth mentioning that three great mathematicians Newton, Maxwell and Planck all adhered to the view that the universe and life were products of intelligent design. I think we can rule out the possibility that there would have been calls for their works to be retracted.
It should also be considered that in his book Der Teil und das Ganze, Werner Heisenberg expresses his own and also Niels Bohrs’ doubt that random mutations could have produced any of the complex biological systems. Heisenberg wrote: "Thus it is still difficult to believe that complex organs like the eye could arise gradually solely through random changes." Bohr adds that while natural selection obviously occurs it is the idea that new species come about by random changes, which is very hard to imagine, even if this is the only way science can explain it.
Taking into account these five giants’ views on intelligent design and evolution, it seems to me that it is not the claims of Hössjer and Thorvaldsen which require extraordinary evidence, it’s the neoDarwinian claims that are extraordinary. Let us therefore see a real rebuttal where the neoDarwinian claims are backed up by the extraordinary (mathematical) evidence scientists like Heisenberg, Bohr— and by the way also von Neumann— would very much have liked to see.
The inadequate and extremely short rebuttal referred to above:
Quote:"We write to rebut the conclusions of a recently published paper in the Journal of Theoretical Biology (Thorvaldsen and Hössjer, 2020). The central claim of this paper is that because biological systems are complex then they must be fine-tuned. This inference is flawed and is not supported by the evidence.
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.... irreducible complexity ignores the idea that evolution and natural selection act on a pool of variation: any number of individuals within the pool will not pass on their genes because their specific complement of protein complexes and cellular networks do not accomplish the necessary functions for life to continue. Hence, neither fine-tuning nor intelligent design is required when sample spaces are viewed through the lens of evolutionary dynamics.
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....These ideas have been repeatedly debunked in the past. In the words of Carl Sagan: “extraordinary claims require extraordinary evidence”, a threshold that is not met in this paper. Large sample spaces do not imply biological systems are ‘fine-tuned’"
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This is mainly argument by simple assertion with no substantiation by data, evidence, seemingly assuming that the reader will accept the authors' authority as a substitute.
I was just thinking today about the "Quantum Fathers" and their views on various facets of reality.
Really shows the decline in academia's intellectual standard that the materialist evangelicals have perpetuated.
I do think it will be interesting to see what the eventual response is to ID, I suspect it will be along the criticisms I've suggested - that the assumption of designer should be done with proximal causation in mind.
I do need to rank the designers of biological "fine tuning", haven't forgotten, just have to read up more on Ufology.
(2020-10-21, 05:55 PM)nbtruthman Wrote: [ -> ]A short and remarkably inadequate rebuttal was published in Journal of Theoretical Biology (JTB), of the paper by Hossjer and Thorvaldsen that is described above
"Remarkably inadequate" is a good description. I'm not even sure that it
qualifies as a rebuttal, since it fails to engage with the actual argument of the paper (which I've just finished reading for the first time), and seems even to misrepresent that argument.
By the way, just from a moderation perspective, would you mind awfully truncating the two articles (the original "rebuttal" and the rebuttal-of-rebuttal) and linking to them, rather than quoting them in full, so as to adhere to our
Guidelines for reproducing external content (in particular guideline #1, unless one of the exemptions there applies)?
Interesting that there is an insect that has actual gears:
This Insect Has The Only Mechanical Gears Ever Found in Nature
Joseph Stromberg
Quote:The gearing is an elegant solution. The researchers’ high-speed videos showed that the creatures, who jump at speeds as high as 8.7 miles per hour, cocked their back legs in a jumping position, then pushed forward, with each moving within 30 microseconds (that’s 30 millionths of a second) of the other.
The finely toothed gears in their legs allow this to happen. “In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t,” Burrows said in a press statement.
The gears are located at the top of the insects’ hind legs (on segments known as trochantera) and include 10 to 12 tapered teeth, each about 80 micrometers wide (or 80 millionths of a meter). In all the Issus hoppers studied, the same number of teeth were present on each hind leg, and the gears locked together neatly. The teeth even have filleted curves at the base, a design incorporated into human-made mechanical gears because it reduces wear over time.
Water can appear to be “fine-tuned” for life
Quote:In their study published in early 2018, Hajime Tanaka, John Russo, and Kenji Akahane—all researchers in the Department of Fundamental Engineering at the University of Tokyo, in Japan—tried to tease apart what makes water unique among liquids. It’s got anomalous properties, like expanding when cooled below 40 degrees Fahrenheit, which explains why lakes freeze downward, from top to bottom, rather than up. Normally frozen solids are more dense than their liquid equivalents, which would mean that frozen chunks would fall to the bottom of a lake instead of staying on top. Water also becomes less viscous compared to other liquids when compressed, and has an uncanny level of surface tension, allowing beings light enough, like insects, to walk or stand atop it. Since it’s these distinctive features among others that power our climate and ecosystems, water can appear to be “fine-tuned” for life.
The researchers, with the benefit of supercomputers, were able to tweak and untune a computational model of water, making it behave like other liquids. “With this procedure,” Russo said, “we have found that what makes water behave anomalously is the presence of a particular arrangement of the water’s molecules, such as the tetrahedral arrangement, where a water molecule is hydrogen-bonded to four molecules located on the vertices of a tetrahedron,” a shape of four triangular planes. “Four of such tetrahedral arrangements can organize themselves in such a way that they share a common water molecule at the center without overlapping,” Russo said. As a result, when water freezes, it creates an open structure, mostly empty space and less dense than the disordered structure of liquid water, which is why water props ice up. Both highly ordered and disordered tetrahedral arrangements give water its “peculiar properties.” The paper’s title spells this out: “Water-like anomalies as a function of tetrahedrality.”
It seems like the "appearance" of fine-tuning, purpose, even consciousness keeps inconveniently showing up where Physicalist types were hoping to find the opposite...
This research is valuable because it is delineating a computational model of bio-information. It still is focused on the physical, with information coming only from physical evolution, rather than including mental evolution, as well.
RNA world has been the hope of a physical answer. This paper is all over its flaws.
https://getpocket.com/explore/item/the-e...ists-argue
Quote:
Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely. In Wills’ view, RNA might have been able to catalyze its own formation, making it “chemically reflexive,” but it lacked what he called “computational reflexivity.”
“A system that uses information the way organisms use genetic information — to synthesize their own components — must contain reflexive information,” Wills said. He defined reflexive information as information that, “when decoded by the system, makes the components that perform exactly that particular decoding.” The RNA of the RNA world hypothesis, he added, is just chemistry because it has no means of controlling its chemistry. “The RNA world doesn’t tell you anything about genetics,” he said.
. “More and more bits of evidence are accumulating,” Lancet said, “that can make an alternative hypothesis be right.” The jury is still out on what actually transpired at life’s origins, but the tide seems to be turning away from a story dedicated solely to RNA.
“We should put only a few of our eggs in the RNA world basket,” Hofmeyr said.
Jordana Cepelewicz is a staff writer at Quanta Magazine who covers biology.
Let's get into it. Here is the real state of affairs in biological evolution.
http://www.science.auckland.ac.nz/people/p-wills
Hint: its not neoDarwinism.
Quote: Origin of genetic coding
There is an enduring problem concerning the way in which information can gain meaning in material systems. The actual occurrence of one specific pattern (when many were originally possible) must become causally connected to a choice among some otherwise unrelated set of outcomes. Genes are nucleic acid sequences (linear patterns) that are causally connected, through sets of biochemical events, to the construction and maintenance of specific organisms. How did this connection arise? The synthesis of proteins with amino acid sequences that are accurately specified by nucleic acid sequences is the most obvious pathway whereby information stored in molecular systems finds meaning. The complicated process of ribosomal translation, the execution of the genetic code, is a primary mechanism whereby genetic information is expressed in functional form. My research focuses on the way in which the machinery necessary for the processes of genetic coding could have evolved through thermodynamically driven stages of self-organization which became progressively more complex, in terms of not only the biochemical machinery involved but also the computational steps necessary.
In my simple worldview, electro-chemistry is the physical structure track of development. And in a parallel track, mental outcomes build informational objects that are the structural basis of organic regulation (meaningful functions).
(2021-01-07, 02:38 PM)stephenw Wrote: [ -> ]This research is valuable because it is delineating a computational model of bio-information. It still is focused on the physical, with information coming only from physical evolution, rather than including mental evolution, as well.
RNA world has been the hope of a physical answer. This paper is all over its flaws.
https://getpocket.com/explore/item/the-e...ists-argue
I don't think this has any chance of revealing a mindless unintelligent mechanism behind evolution. Just
an example (paraphrased for brevity):
Now, 24 years after Behe’s book Darwin's Black Box was published, it is still the case that there simply are no peer reviewed research studies that provide an evolutionary model to explain the origin of the bacterial flagellum, or how it is not irreducibly complex. Despite numerous research studies (mainly into unravelling the details of the mechanism, increasingly revealing that it is an extremely complex irreducibly complex system including the assembly subsystem). If there was, then all the Darwinists would have to do is reference all those studies. Yet that remains the one thing missing in all of the articles and comments.
In just this one example, the problem that the flagellum presents for Darwinists has only gotten much worse, not better, as more scientific evidence has come along.
As exemplified at the 2016 Royal Society conference on the problems of the New Synthesis Darwinist theory, it is not an argument anymore that Darwinist processes can't make complex functional systems; it is an observation that it does not.
(2021-01-10, 06:13 PM)nbtruthman Wrote: [ -> ]In just this one example, the problem that the flagellum presents for Darwinists has only gotten much worse, not better, as more scientific evidence has come along.
Do you mean that there have been peer reviewed papers published regarding evolutionary explanations for other aspects of biology, with the flagellum as among the standout exceptions?