L&FP, 71: The island of function, fitness peak trap

_{kairosfocus

April 3, 2023

Fine tuning, Logic and Reason, specified complexity}

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We have been using a 3-D printer-constructor formalism, and now we can use it to see how hill climbing leads to local trapping.

Again, the core formalism:

Now, let us modify by allowing some sort of local random mutation to d(E) case by case within an n-run, now seen as a generation, so E1 to En are all incrementally different, and in effect are a ring around E in a fitness landscape. From this, we can see a survival filter that on average selects for superior performance. This leads, naturally to hill-climbing, perhaps even to several related peaks in a chain on an island of function. But now, we see:

Algorithmic hill-climbing first requires a hill . . .

Here, we see that hill climbing leads to peak trapping, as at A B or C, any change trend is downhill. Ruggedness of a fitness landscape counts, and not for the notion that hill climbing explains evolutionary advance.

No, it gets more complicated, once we realise that complex, information rich functionally specific organisation is a fine tuning phenomenon. That is, we now have the challenge of island hopping across seas of non function:

So, absent injection of active information . . . contrivance . . . there is a “natural, blind, needle in haystack search”challenge to create novel body plans. Where, if “natural selection” is acceptable, plainly so is “natural . . . search.”

This of course feeds back to getting TO the beaches of an island of function. So, we have the natural search problem in focus, once FSCO/I and fine tuned organisation are recognised.

For this, there has been much distraction and dismissiveness over the years [often, pretending hyperskeptically that FSCO/I is ill conceived], but no cogent answer, nor is there any good reason to believe in a vast continent of incrementally accessible functional forms from a last universal unicellular common ancestral form, traversing the tree of life believed to be ancestrally formed. Indeed, this brings to the surface the systematic pattern of gaps, sudden appearances and disappearances that are the trade secret of paleontology.

So, local trapping and need to arrive at shorelines of function by blind “natural . . . search” are significant challenges. Where, intentional injection of active information by intelligently directed configuration, absent ideological imposition, is a very good explanation for, say, the subtleties of a Dragonfly’s wing, including up to 25% speed improvement from flutter-reducing stigma on the leading edge of the wing . . . as obvious a case of subtle fine tuning as one may wish for:

And, so forth. END

Comments

Hnorman42: As far as an example of an island of function goes, I think the flagellum is a good example. And that counterfactual world where we have all those possible configurations of a flagellum — the ones that don’t work because they’re missing a part or lack proper adjustment — that’s the sea of nonfunction. The question is: could the flagellum have arisen via small, discrete, naturally occurring steps from a previous existing structure. If there is such a path then the flagellum is not an 'island' of function; it has a connection with other functioning structures. Obviously there will always be variations that 'break' the structure. That's true for just about any biological structure you can think of. But just because some, if not most, variations break something doesn't mean there is no functional, viable path to other functional biological structures. As a metaphor, the flagellum might be an isthmus or promontory but not an island. JVL

Hnorman42 @237 Good example. The bacterial flagellar motor is very ancient (perhaps even present at the root of all bacteria) and appeared without any known precursors. https://evolutionnews.org/2021/05/study-challenges-evolutionary-relationship-between-flagellum-and-type-iii-secretory-system/ Origenes

JVL @194 Quoting you here:
Life forms that create offspring are all connected by paths of viability or function. There are no islands of function because all life is connected.
I'm having trouble following that but I think it might be something important for seeing the difference between our perspectives here. As far as an example of an island of function goes, I think the flagellum is a good example. And that counterfactual world where we have all those possible configurations of a flagellum -- the ones that don't work because they're missing a part or lack proper adjustment -- that's the sea of nonfunction. hnorman42

Chuckdarwin @195,
The term “favored races” in Origins doesn’t mean human races. Generally, it means healthy procreative lines.
When Charles Darwin wrote about “races” in the Origin of the Species and The Descent of Man, he meant races. Literally. He did not exclude humans as some sort of special exception. Yes, Darwin’s The Descent of Man spells out the racism inherent in his theory far more explicitly than his first book did. For example, what do you think he meant by the following?
“. . . western nations of Europe . . . now so immeasurably surpass their former savage progenitors and stand at the summit of civilization.”
Furthermore, Darwin predicted that the evolutionary gap between “civilized man” and his nearest evolutionary ancestors will widen until the gap between the western nations of Europe and the “savage races” will approach that of . . .
“. . . some ape as low as a baboon, instead of as at present between the negro or Australian and the gorilla.”
He writes about how white Europeans will “exterminate and replace” the world’s “savage races,” similar to how the great apes will become extinct. I’m appalled that you would diminish the impact of his predictions and his justification of the genocide of brown people as “while seemingly harsh in parts, nonetheless pretty accurately describes the course of human development.” Equally appalling is your assertion in agreement that “Displacement of indigenous cultures is inevitable, and the process of displacing indigenous cultures began long before Darwin lived.” No, I don't think it's either inevitable or justifiable.
The most obvious example is the Spanish and Portuguese “conquest” of Meso- and South America which occurred with the full backing and sponsorship of the Church.
No, your history is deeply flawed. Watch the movie, The Mission sometime. While not entirely historically accurate, it nevertheless portrays the difference between the Spanish treatment of indigenous people of Brazil with that of the Portuguese genocide. Unlike The U.S. and Canada, the Catholic church for all of its significant flaws, was able to encourage intermarriage among European migrants to Latin America and the indigenous population rather than rape, genocide, the equivalent of apartheid as was typical of European migrants in the territories of the U.S. and Canada. Later, when Portugal had a race problem, the Catholic Church encouraged intermarriage as the solution. Thank you at least for stepping up to the plate, unlike some others here. -Q Querius

Kairosfocus: you are sidestepping a whole list. That tells us a lot. Give me a specific, biological island of function if you've got one. That's all I'm asking. JVL

F/N: For those utterly unfamiliar with the quite general Goldilocks zone issue, just rightness of design of complex systems [thus, fine tuning and islands of function amidst seas of non function], perhaps this exercise in design of an ornithopter will help: part 1: https://www.youtube.com/watch?v=nPx_fwZuL3Q part 2: https://www.youtube.com/watch?v=XqPB6HIMAJk part 3: https://www.youtube.com/watch?v=o0TaEe_VMYQ That is TYPICAL. (Guess why they talk about rocket science . . . ?) KF kairosfocus

JVL, you are sidestepping a whole list. That tells us a lot. KF kairosfocus

Mind you, in Tono-Bungay, he does make up for it to some extent, with Marion, Effie, and Beatrice. Alan Fox

...we men, the creatures who inhabit this earth...
Hmm. I think Wells was overlooking something. Alan Fox

Bornagain77: already addressed at 207 and 208. Basically every protein and/or protein fold,. Okay, so does that mean every species? Every genus? Give us a specific biological example. JVL

JVL, already addressed at 207 and 208. Basically every protein and/or protein fold,. Of course you will deny it because you are scientifically dishonest. But unbiased readers can judge for themselves who is being scientifically forthright and who is being a liar. bornagain77

Bornagain77: Shoot buddy, perhaps you just need to kick back and have a few Bud Lites? ? You can probably find a few cans of it in a trash can near you. ? Perhaps you'd like to address the scientific question I have brought forward: can you identify a biological specific island of function? JVL

Name calling JVL? Just because you are shown to be, scientifically speaking, a liar over and over and over again,,,, is no excuse for you to get so upset and start hurling insults. :) Shoot buddy, perhaps you just need to kick back and have a few Bud Lites and chill out? :) You can probably find a few cans of it in a trash can near you. :) https://www.youtube.com/watch?v=5_Ikn84ZUdc bornagain77

Bornagain77: JVL feigns moral outrage You are a jerk, that's is clear. From any perspective. I might be concerned with JVL’s moral outrage if he had a objective moral basis in which to judge whether anything is evil or good in this universe.. Well fine, let's concentrate on the science then. Can you provide a specific biological example of an island of function? JVL

LOL, JVL feigns moral outrage whilst ignoring, scientifically speaking, he is found to be a liar over, and over, and over, and over, and over, etc.. etc.., again. Aside from his blatant hypocrisy in failing to pull the beam of scientific dishonesty from his own eye,, I might be concerned with JVL's moral outrage if he had any objective moral basis in which to judge whether anything is evil or good in this universe..
"The universe that we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil, no good, nothing but pitiless indifference.” - Dawkins
bornagain77

Kairosfocus: apparently, you have forgotten or side stepped ever so many islands of function put on the table, over many years. And not just from me, as was already pointed out. Fine. Just reiterate them and you'll have addressed my query. All I'm asking is for you to give a specific biological island of function. JVL

AF, have you heard of redemption and life rescue? If not, kindly pay a visit to say the Salvation Army or to Teen Challenge. KF kairosfocus

JVL, apparently, you have forgotten or side stepped ever so many islands of function put on the table, over many years. And not just from me, as was already pointed out. As proteins are the workhorse molecules of life, that protein fold domains are isolated in AA sequence space is already enough. This means the first island is OoL. And that for every significant body plan innovation there will be another as proteins are needed for tissues, organs and systems. Where, of course, biological systems are not magically exempt from requisites of complex configuration of parts based function. As one result, every irreducibly complex entity or structure in life forms will be another -- just so exaptations etc notwithstanding. The fossil record, dominated by gaps, sudden appearances and stasis of core form, provides another set, most notably the cambrian fossil revolution that we have seen every failed effort to evade. The fine tuned requisites of flight in its many styles (contrast Dragonflies, moths, birds, bats etc) and even including some plants, becomes another. And so forth, where the predictable objections and attempted dismissals will lack empirical support. KF kairosfocus

Relatd: Unless you have a Gallup Poll in hand, I suspect you don’t know what anyone else supports. It's a matter of what is written and stated in peer-reviewed journals NOT polls. There are those who firmly believe that life began by opening a package of ingredients and dropping it into a liquid of some kind. Not many, if any, believe that. Anyway, amusing as this is let's get back to the science shall we? Can you give a specific example of a biological island of function? JVL

JVL at 217, Unless you have a Gallup Poll in hand, I suspect you don't know what anyone else supports. There is a major Conference for Origin of Life researchers coming up. There are those who firmly believe that life began by opening a package of ingredients and dropping it into a liquid of some kind. Once the proper "formula" is >> discovered << then scientists will - presumably - just start making life. There is no evidence that this is possible. relatd

Given the level of respect and dignity you show to those you disagree with I choose not to respond to your comments which have, I note, been addressed over and over and over and over and over again in the past. Not only are you snide and nasty but you never actually try and understand opposing arguments.
Yes, it's odd that Phil, according to himself, has experienced homelessness, alcoholism, drug addiction and yet ends up here, writing the stuff he writes. It is very odd. Alan Fox

CR at 216, Please don't try your hand at physics. As far as is known. there is the macro, atomic-scale version and the sub-atomic or quantum version. As far as the latter, since observers, meaning humans, primarily experience the macro or atomic version, the quantum functions are far less easily grasped. If all possible quantum functions could be enlarged to the scale humans experience every day, and observed, some of the more unusual aspects could be more easily understood. But human interaction is a built-in interaction that goes beyond a purely mechanistic explanation. relatd

Relatd: I am the first life. The first single-celled organism. I ‘woke up’ one day in a large, warm pod. Somehow, I know what food is. Somehow, I have the internal machinery to digest it. Somehow – and don’t ask – I can reproduce. No one supports that scenario. But if you want to attack something that no one is actually supporting, please, waste your time. Oh, by the way, can you provide an example of a specific biological island of function? No one else seems to be able to do so. JVL

Random variation painstakingly produces what is in principle viable organisms, and next some environment kills most of it.
Huh? Organisms are immortal, and the environment kills them? Production happens over time. When we look at the environment from the perspective of a constructor, mutations are not completely random, but random to any problem to solve.
Only organisms that happened to have the right tools survive.
More survival of the fittest? This has already been addressed. Many organisms may survive. And do so for reasons that are not heritable. Those reasons will not end up making it to the next generation. Tools do not spring up at once in some massive event of mutations.
This is widely hailed as a good thing for evolution, many even go so far as to say that it is a ‘creative’ act. I have great difficulty understanding what this appraisal is based on.
First, it’s an explanation of how the world works, in reality, no some kind of product review on Amazon. Second, I’ve already explained how it’s similar in #135. You have great difficult because evolution is not an authoritative source.
In my view, random variation does all the heavy lifting, and the environment “allows” some of the organisms that random variation painstakingly has managed to come up with to live.
Again, see above. You’ve already presented your view. I’m referring to the reformulation of natural selection as defined in the paper. For example, suggesting the environment allows some organisms “to live” is very vague, while the paper is far more specific. For example, you wrote….
IOW the environment does not kill off everything. Well, thank you very much Mr. Environment!
All organisms eventually die, even if due to old age, unless your some species of tortoises, jellyfish etc. So, this doesn’t come close to actually reflecting the paper. The environment doesn’t kill everything off but x. It’s about genes that are most fit to make it into the next generation. A member of a population might live its entire normal lifespan, yet still have its genes not make it into the next generation. It could become more fit that other species, but unless that fitness is heritable, then it will not make it into the next generation. It might even make itself into the next generation, but the environment might be such that other members of the population have some advantage, which allows it to better utilize resources, nesting spots, etc. For example, mutations could cause a member of an island bird species to have harder lives, due to nesting earlier in the season. Nesting earlier, it could obtain the best nesting locations, which would prevent other members of the species from nesting there later in the season, in which they would have easier lives. Eventually, the entire population can become less fit and have harder lives due to nesting earlier. If the mutations to nest earlier continue, the species could eventually go extinct. It all depends on how detrimental the tendency to nest earlier is on the species as a whole.
In my view, it is completely wrong to call the environment “the constructor” of organisms in this story. Unlike random variation, it did not produce anything. Not killing off everything is a far cry from being the ‘constructor’ of what you allow to live.
First, see above. Second, constructor, as used above, refers to, well, constructor theory.
Constructor theory is a new fundamental theory of physics. First, it provides a paradigm to express the other laws of physics, to be expressed solely as statements about which transformations are possible, which are impossible and why. Guesses at those laws - e.g., current physical theories such as general relativity and quantum mechanics - it calls subsidiary theories. In addition, it also proposes new laws - principles - constraining the subsidiary theories. Here it suffices to know that the principles are obeyed by all known laws of physics, nor do they themselves contain the design of biological adaptations (see [16], [17]). The properties of a physical system M are attributes, defined as sets of states of M. We say that M (say, a collection of atoms) has the attribute X (say, being a car, or a self-reproducer) if it is in any of the states in X. (5)The model is intended to be faithful only insofar the logic is concerned. Most realistic details of these processes are irrelevant to their logic, so they shall be neglected. Constructor theory’s main elements are tasks. A task T is the abstract specification of a transformation [diagram] as a set of input/output pairs of attributes {xi}, {yi} of the substrates (the physical systems being transformed).?Tasks form an algebra under parallel and serial composition, and are com- posable into networks to form other tasks. A physical system with some attribute C is a constructor, capable of performing the task T if: • whenever presented with the substrates with any of the legitimate input attributes of T, C delivers it with the corresponding output attribute, as follows: • C retains the ability to do so again. A task is impossible if it is forbidden by the laws of physics (e.g., building a perpetual motion machine); otherwise, it is possible.?Under our laws of physics, only approximate constructors exist, e.g. catalysts or robots. They have non-zero error rates and deteriorate with use. Hence, that a task is possible means that the laws of physics impose no limit, short of perfection, on how accurately it could be performed, nor on how well objects capable of approximately performing it could retain their ability to do so. The term “constructor” is a placeholder for the (infinite) sequence of approximations to the ideal behavior of a constructor.
This is a core principle of constructor theory. it’s allows us to explain in a more fundamental way possible than the current conception of physics. So, it would be even more fundamental than, say, quantum mechanics. IOW, at a more fundamental level, we can model the environment a constructor that transforms a substrate. And, in the context of the paper, the transformation start with generic resources, as opposed to having the design of replicators being present in the laws of physics.
Unlike random variation, it did not produce anything. Not killing off everything is a far cry from being the ‘constructor’ of what you allow to live.
As indicated above, constructors must retain the ability to transform the substrate again. So, it’s an iterative process. Nor is it just mutation. It also includes horizontal gene transfer, etc.
This seems to be what Darwin is hinting at:
This is more of “Darwin says x” which isn’t relevant. Rather, it’s a red herring.
However, evolution has no foresight, so putting all chips on specie A is a gamble and not a reliable one. In my example, who is to say that the eliminated species B, C, and D are “bad”, and that specie A is “good”, in the context of finding biological information?
First, yes. Evolution has no foresight. This explains aspects of species, like how specific nerves go around parts of our hearts in primates, etc. It has far less reach and is non explanatory in nature. Second, B, C and D could be better adapted for other environments. Which explains the diversity of life in various regions, etc. critical rationalist

JVL at 213, 'You - Ba77 - have been so rude!' Now that the chastisement has been meted out, let's go back to the old 'opposing arguments.' Pardon my bluntness: You're wrong. Full stop. Opposing arguments are fine as long as they are substantive. In this case, one side is right and the other is wrong. Oh sure, opposing comments will continue because that is the mission of the opposers. 'By any means necessary' and so on. I get it. relatd

Ba77, I am the first life. The first single-celled organism. I 'woke up' one day in a large, warm pod. Somehow, I know what food is. Somehow, I have the internal machinery to digest it. Somehow - and don't ask - I can reproduce. Well, before you know it, my warm pond is full of kids and they start eating, then those kids have more kids and they start eating. One day, all of the available food has been eaten. Everyone died. Our lifeless bodies sink to the bottom. And there's no life on Earth. relatd

Bornagain77: But let’s presuppose that most of us are not transvestites who woke up with a few Bud-Lites for breakfast,,, Given the level of respect and dignity you show to those you disagree with I choose not to respond to your comments which have, I note, been addressed over and over and over and over and over again in the past. Not only are you snide and nasty but you never actually try and understand opposing arguments. JVL

Sandy: Funny! You mentioned the very definition of island of function(bolded in your first quoted message) . I know what is meant by a biological island of function but no one has been able to provide a specific example. Yet. Can you? JVL

Seversky at 206, And I've got photos of my alleged great, great, etc. relatives as lemur-like creatures. relatd

Kairosfocus: complex functional performance based on integrated configuration is readily seen to depend on precise matching, orientation, arranging and coupling of parts, which naturally results in fine tuning, thus islands of function. Well then, it should be easy for you to give an example of a biological island of function. But, strangely, you have been unable to do that. You tell us how say a dragonfly’s flight capacity per empirically warranted incremental steps, came about — and not with handwaving or just so stories. I never claimed I could outline a step-by-step process that gave dragonflies the ability to fly (starting from where would be the first question though). However, you claimed that there are biological islands function but you can't even give an example of such a thing. Instead of trying to change the subject perhaps you'd like to support your own claims first. JVL

Asauber/204
They should repudiate the racism within Darwin’s theory and the repudiate the entire theory because it’s a fraud.
I thought Darwin's personal racist/misogynistic views and any implied racism in Descent - such as they are - have been repudiated. No, the theory is imperfect but it's not a fraud. Seversky

JVL goes on
Life forms that create offspring are all connected by paths of viability or function. There are no islands of function because all life is connected.
JVL simply has no scientific proof for any of those claims. Shoot, proteins themselves are now shown to NOT be "connected by paths of viability or function".
Right of Reply: Our Response to Jerry Coyne - September 29, 2019 by Günter Bechly, Brian Miller and David Berlinski Excerpt: David Gelernter observed that amino acid sequences that correspond to functional proteins are remarkably rare among the “space” of all possible combinations of amino acid sequences of a given length. Protein scientists call this set of all possible amino acid sequences or combinations “amino acid sequence space” or “combinatorial sequence space.” Gelernter made reference to this concept in his review of Meyer and Berlinski’s books. He also referenced the careful experimental work by Douglas Axe who used a technique known as site-directed mutagenesis to assess the rarity of protein folds in sequence space while he was working at Cambridge University from 1990-2003. Axe showed that the ratio of sequences in sequence space that will produce protein folds to sequences that won’t is prohibitively and vanishingly small. Indeed, in an authoritative paper published in the Journal of Molecular Biology Axe estimated that ratio at 1 in 10^74. From that information about the rarity of protein folds in sequence space, Gelernter—like Axe, Meyer and Berlinski—has drawn the rational conclusion: finding a novel protein fold by a random search is implausible in the extreme. Not so, Coyne argued. Proteins do not evolve from random sequences. They evolve by means of gene duplication. By starting from an established protein structure, protein evolution had a head start. This is not an irrational position, but it is anachronistic. Indeed, Harvard mathematical biologist Martin Nowak has shown that random searches in sequence space that start from known functional sequences are no more likely to enter regions in sequence space with new protein folds than searches that start from random sequences. The reason for this is clear: random searches are overwhelmingly more likely to go off into a non-folding, non-functional abyss than they are to find a novel protein fold. Why? Because such novel folds are so extraordinarily rare in sequence space. Moreover, as Meyer explained in Darwin’s Doubt, as mutations accumulate in functional sequences, they will inevitably destroy function long before they stumble across a new protein fold. Again, this follows from the extreme rarity (as well as the isolation) of protein folds in sequence space. Recent work by Weizmann Institute protein scientist Dan Tawfik has reinforced this conclusion. Tawfik’s work shows that as mutations to functional protein sequences accumulate, the folds of those proteins become progressively more thermodynamically and structurally unstable. Typically, 15 or fewer mutations will completely destroy the stability of known protein folds of average size. Yet, generating (or finding) a new protein fold requires far more amino acid sequence changes than that. Finally, calculations based on Tawfik’s work confirm and extend the applicability of Axe’s original measure of the rarity of protein folds. These calculations confirm that the measure of rarity that Axe determined for the protein he studied is actually representative of the rarity for large classes of other globular proteins. Not surprisingly, Dan Tawfik has described the origination of a truly novel protein or fold as “something like close to a miracle.” Tawfik is on Coyne’s side: He is mainstream. https://quillette.com/2019/09/29/right-of-reply-our-response-to-jerry-coyne/ "Enzyme Families -- Shared Evolutionary History or Shared Design?" - Ann Gauger - December 4, 2014 Excerpt: If enzymes can't be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,, Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That's longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. We have now addressed two objections raised by our critics: that we didn't test the right mutation(s), and that we didn't use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF's entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine. Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It's because modern enzymes can't be coopted to anything except trivial changes in function. In other words, they don't evolve! That is precisely the point we are making. http://www.evolutionnews.org/2014/12/a_new_paper_fro091701.html
Much less do Darwinists have any scientific evidence that all 'life is connected' in a continuous Darwinian fashion. Both genetics and the fossil record demonstrate a highly discontinuous pattern. As Dr. Cornelius Hunter, (PhD – Biophysics), put the genetic situation, “the dependency graph (intelligent design) model is astronomically superior compared to the (universal) common descent model.”
New Paper by Winston Ewert Demonstrates Superiority of Design Model - Cornelius Hunter - July 20, 2018 Excerpt: Ewert’s three types of data are: (i) sample computer software, (ii) simulated species data generated from evolutionary/common descent computer algorithms, and (iii) actual, real species data. Ewert’s three models are: (i) a null model which entails no relationships between any species, (ii) an evolutionary/common descent model, and (iii) a dependency graph model. Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree. Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process. Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model. Where It Counts Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous. Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent. Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other. We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand. Ten thousand is a big number. But it gets worse, much worse. Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division. The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set, given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division. Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth? Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros. That’s the ratio of how probable the data are on these two models! By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage over that of common descent. 10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence. This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits. But It Gets Worse The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450. In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450. We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data. https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/
And as far as the fossil record in concerned, it gets worse for Darwinists,
Günter Bechly video: Fossil Discontinuities: A Refutation of Darwinism and Confirmation of Intelligent Design – 2018 https://www.youtube.com/watch?v=M7w5QGqcnNs The fossil record is dominated by abrupt appearances of new body plans and new groups of organisms. This conflicts with the gradualistic prediction of Darwinian Evolution. Here 18 explosive origins in the history of life are described, demonstrating that the famous Cambrian Explosion is far from being the exception to the rule. Also the fossil record establishes only very brief windows of time for the origin of complex new features, which creates a ubiquitous waiting time problem for the origin and fixation of the required coordinated mutations. This refutes the viability of the Neo-Darwinian evolutionary process as the single conceivable naturalistic or mechanistic explanation for biological origins, and thus confirms Intelligent Design as the only reasonable alternative.
Needless to say, this type of scientific evidence is NOT what Darwin predicted for the fossil record. Thus in conclusion, JVL may be satisfied with a theory that "You can be drunk, addled, or stupid and still understand", but for those of us who are not transvestites who had a few Bud-Lites for breakfast, but who are interested in the actual science behind JVL's claims instead, we find that JVL's claims fall completely apart with even minimal scientific scrutiny. To put it mildly, finding Darwin's theory to be, basically, a flimsy 'house of cards' that collapses in on itself with minimal scientific scrutiny is NOT good for a supposedly scientific theory that claims to be the be all/end all scientific explanation for all life on earth.
1 Thessalonians 5:21 but test all things. Hold fast to what is good.
bornagain77

JVL's comment at 194 reminds me that "You can be drunk, addled, or stupid and still understand" the basics behind Darwin's theory,
"You might think that a theory so profound would be laden with intimidating mathematical formulas and at least as difficult to master as Newton’s Mechanics or Einstein's Relativity. But such is not the case. Darwinism is the most accessible “scientific” theory ever proposed. It needs no math, no mastery of biology, no depth of understanding on any level. The dullest person can understand the basic story line: “Some mistakes are good. When enough good mistakes accumulate you get a new species. If you let the mistakes run long enough, you get every complicated living thing descending from one simple living thing in the beginning. There is no need for God in this process. In fact there is no need for God at all. So the Bible, which claims that God is important, is wrong. You can be drunk, addled, or stupid and still understand this. And the real beauty of it is that when you first glimpse this revelation with its “aha!” moment, you feel like an Einstein yourself. You feel superior, far superior, to those religious nuts who still believe in God. Without having paid any dues whatsoever, you breathe the same rarified air as the smartest people who have ever lived."? – Laszlo Bencze - 2014
But let's presuppose that most of us are not transvestites who woke up with a few Bud-Lites for breakfast,,,
Kid Rock vs. Bud Lite https://www.youtube.com/shorts/st1VPPGUvpU
,,, But let's instead presuppose that most of us are interested in the actual science behind JVL's claims,,,
JVL: Umm, remember: starting with a viable, functional life form,,
Right off the bat we have a huge scientific problem. Where is the scientific rule that says that Darwinists get to start with the 'miracle' of life as a starting point? i.e. If you can't explain where life came from in the first place, well then, so much for your claim that you are offering an adequate scientific explanation for all the diversity of life on earth. And it is for good reason that Darwinists want to assume the 'miracle' of life as a starting point. Darwinists simply have no realistic scientific clue how life could possibly come about by naturalistic processes.
“There is no such thing as a simple cell. Every cell is is amazingly complex. This has been calculated. I’ve not done the calculation this was done by biophysicists.,, They have figured this out. They give the pieces that are needed to build a simple cell. So it’s about 15 different pieces you would need to build for there to be a simple cellular life. Of those 15 pieces zero, ZERO, have been made by origin of Life researchers. Even in their Laboratories. Even with all their equipment. I’m not talking about under a rock or in some pool by the side of the ocean. I’m talking in the pristine Laboratories building up these molecules and making any of those 15 pieces.,,, You have to have each one of these pieces none of them, ZERO of them, have been made.” – James Tour – Origin of Life: Controversial Chemist Shakes up Scientific Community | Problems with Primordial Soup - 2023 https://youtu.be/ZugOrSD7YL4?t=1393
In fact, it is not just that ZERO of the 15 pieces that were calculated to be necessary for ‘simple’ life have ever been made in pristine laboratories, and as Dr Tour stated elsewhere, even if you were somehow able to make all of the different pieces that are required for life, still no one would have any realistic clue as to how to put all those different pieces together.
(July 2019) “We have no idea how to put this structure (a simple cell) together.,, So, not only do we not know how to make the basic components, we do not know how to build the structure even if we were given the basic components. So the gedanken (thought) experiment is this. Even if I gave you all the components. Even if I gave you all the amino acids. All the protein structures from those amino acids that you wanted. All the lipids in the purity that you wanted. The DNA. The RNA. Even in the sequence you wanted. I’ve even given you the code. And all the nucleic acids. So now I say, “Can you now assemble a cell, not in a prebiotic cesspool but in your nice laboratory?”. And the answer is a resounding NO! And if anybody claims otherwise they do not know this area (of research).” – James Tour: The Origin of Life Has Not Been Explained – 4:20 minute mark (The more we know, the worse the problem gets for materialists) https://youtu.be/r4sP1E1Jd_Y?t=255
JVL goes on,
variation arises.
And here is another huge scientific problem for Darwinists. Darwinists assumed that any variation that arises in a genome was/is by a completely random, unguided, processes. Yet that assumption is now scientifically proven to be false.
"Physiology Is Rocking the Foundations of Evolutionary Biology": Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism - Casey Luskin March 31, 2015 Excerpt: Noble doesn't mince words: "In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved." Noble then recounts those assumptions: (1) that "genetic change is random," (2) that "genetic change is gradual," (3) that "following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population," and (4) that "inheritance of acquired characteristics is impossible." He then cites examples that refute each of those assumptions,,, He then proposes a new and radical model of biology called the "Integrative Synthesis," where genes don't run the show and all parts of an organism -- the genome, the cell, the body plan, everything -- is integrated. http://www.evolutionnews.org/2015/03/physiology_is_r094821.html How life changes itself: the Read-Write (RW) genome. – 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611
As Jonathan Wells stated, and directly contrary to a core presupposition of Darwinian theory, "I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism."
Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html
JVL goes on,,
Some of that variation is not viable/non-functional and doesn’t create offspring with the same variation. Some of the variation is viable enough to survive and pass on its characteristics.
JVL is assuming that some non-trivial percentage of random variations/mutations will be beneficial. But it is now known that almost all, in not all, of mutations to DNA are degradative.
When Darwin’s Foundations Are Crumbling, What Will the (Darwinian) Faithful Do? Excerpt: Here’s a summation of the evolutionary picture that has emerged, according to Behe (in his new book "Darwin Devolves": • The large majority of mutations are degradatory, meaning they’re mutations in which the gene is broken or blunted. Genetic information has been lost, not gained. • Sometimes the degradation helps an organism survive. • When the degradation confers a survival advantage, the mutation spreads throughout the population by natural selection. ,,,, Behe sums up his main argument like this: “beneficial degradative mutations will rapidly, relentlessly, unavoidably, outcompete beneficial constructive mutations at every time and population scale.”1 The only Darwinian examples of evolution that have been observed have followed this pattern and resulted in evolutionary dead ends. Darwin devolves.,,,, https://salvomag.com/article/salvo49/darwinism-dissembled Critic ignores reality of Genetic Entropy - Dr John Sanford - 7 March 2013 Excerpt: Where are the beneficial mutations in man? It is very well documented that there are thousands of deleterious Mendelian mutations accumulating in the human gene pool, even though there is strong selection against such mutations. Yet such easily recognized deleterious mutations are just the tip of the iceberg. The vast majority of deleterious mutations will not display any clear phenotype at all. There is a very high rate of visible birth defects, all of which appear deleterious. Again, this is just the tip of the iceberg. Why are no beneficial birth anomalies being seen? This is not just a matter of identifying positive changes. If there are so many beneficial mutations happening in the human population, selection should very effectively amplify them. They should be popping up virtually everywhere. They should be much more common than genetic pathologies. Where are they? European adult lactose tolerance appears to be due to a broken lactase promoter [see Can’t drink milk? You’re ‘normal’! Ed.]. African resistance to malaria is due to a broken hemoglobin protein [see Sickle-cell disease. Also, immunity of an estimated 20% of western Europeans to HIV infection is due to a broken chemokine receptor—see CCR5-delta32: a very beneficial mutation. Ed.] Beneficials happen, but generally they are loss-of-function mutations, and even then they are very rare! http://creation.com/genetic-entropy
The hypothetical 'beneficial' mutations that Darwinists needed to make their hypothesis viable as a scientific theory, and as far as empirical science is concerned, simply don't exist! bornagain77

Relatd/203
Prrrrfffssttt tttt! Oh, yes, the book was meant to be read by apes.
That's right and it is read by apes. Seversky

CD, actually, there is a well known history of Darwinism in Europe that is relevant, amply documented and hotly denied because of its import. As for Las Casas, he was no lone voice, but the point is that effectively unaccountable power is corrupting. A lesson we all need and it is why I point to first duties of natural law per Cicero et al as a point of departure for sound reform; which is yet again desperately needed. Meanwhile the configuration space dynamics that point to fine tuning and islands of function -- as well as to the statistical form of the second law -- are hotly resisted. Revealing. KF PS, Here is H G Wells, who tried to warn at turn of C20, literally in the opening words of War of the Worlds:
No one would have believed in the last years of the nineteenth century that this world was being watched keenly and closely by intelligences greater than man's and yet as mortal as his own; that as men busied themselves about their various concerns they were scrutinised and studied, perhaps almost as narrowly as a man with a microscope might scrutinise the transient creatures that swarm and multiply in a drop of water . . . No one gave a thought to the older worlds of space as sources of human danger, or thought of them only to dismiss the idea of life upon them as impossible or improbable. It is curious to recall some of the mental habits of those departed days. At most terrestrial men fancied there might be other men upon Mars, perhaps inferior to themselves and ready to welcome a missionary enterprise. Yet across the gulf of space, minds that are to our minds as ours are to those of the beasts that perish, intellects vast and cool and unsympathetic, regarded this earth with envious eyes, and slowly and surely drew their plans against us . . . . looking across space with instruments, and intelligences such as we have scarcely dreamed of, they see, at its nearest distance only 35,000,000 of miles sunward of them, a morning star of hope, our own warmer planet, green with vegetation and grey with water, with a cloudy atmosphere eloquent of fertility, with glimpses through its drifting cloud wisps of broad stretches of populous country and narrow, navy-crowded seas. And we men, the creatures who inhabit this earth, must be to them at least as alien and lowly as are the monkeys and lemurs to us. The intellectual side of man already admits that life is an incessant struggle for existence, and it would seem that this too is the belief of the minds upon Mars. Their world is far gone in its cooling and this world is still crowded with life, but crowded only with what they regard as inferior animals. To carry warfare sunward is, indeed, their only escape from the destruction that, generation after generation, creeps upon them. And before we judge of them too harshly we must remember what ruthless and utter destruction our own species has wrought, not only upon animals, such as the vanished bison and the dodo, but upon its inferior races. The Tasmanians, in spite of their human likeness, were entirely swept out of existence in a war of extermination waged by European immigrants, in the space of fifty years. Are we such apostles of mercy as to complain if the Martians warred in the same spirit?
The moral hazard is real, as the history of Eugenics, euthanasia and worse has shown. The last century made a prophet out of Wells. kairosfocus

"Are you asking them to repudiate the racism within Darwin’s theory or to repudiate the entire theory because it is racist?" PM1, They should repudiate the racism within Darwin's theory and the repudiate the entire theory because it's a fraud. Andrew asauber

CD at 195, 'The term “favored races” in Origins doesn’t mean human races.' Prrrrfffssttt tttt! Oh, yes, the book was meant to be read by apes. relatd

@185
Inquiring minds want to watch the usual ad hominems and evasions as previously demonstrated as there’s no hope that these trolls will ever repudiate the racism in Darwin’s theory.
Are you asking them to repudiate the racism within Darwin's theory or to repudiate the entire theory because it is racist? PyrrhoManiac1

KF/198 Mein Kampf? That's where your brain takes you? Or a lone priest who grows a conscience after reaping the benefits of the Spanish killing, subjugation and enslavement of thousands of Native Americans all with the blessing of the Vatican? One who could never quite articulate an understandable policy re slavery? When you have to resort to extremes to make your point, you've already lost the argument. Or, better, you don't even understand the argument..... chuckdarwin

JVL Umm, remember: starting with a viable, functional life form, variation arises. Some of that variation is not viable/non-functional and doesn’t create offspring with the same variation. Some of the variation is viable enough to survive and pass on its characteristics.
Who said that atheists don't believe in magic*?
But, if anyone thinks there are islands of function then please provide a specific example. So far no one has been able to do so but I live in hope.
:)Funny! You mentioned the very definition of island of function(bolded in your first quoted message) . Definition of an atheist: believing in magic* but thinking about himself that ( ) have the mind of a scientist. magic* = atheistic belief that matter have creative powers. Not a single scientific evidence. Sandy

Querius/193
Seversky @191, Remember this quote?
Data is not information, information is not knowledge, knowledge is not understanding, understanding is not wisdom. -Clifford Stoll

That's nice but it tells us what they aren't but not what they are. Seversky

CD, maybe you might consider Schicklegruber:
Any crossing of two beings not at exactly the same level produces a medium between the level of the two parents . . . Consequently, it will later succumb in the struggle against the higher level. Such mating is contrary to the will of Nature for a higher breeding of all life . . . The stronger must dominate and not blend with the weaker, thus sacrificing his own greatness. Only the born weakling can view this as cruel, but he after all is only a weak and limited man; for if this law did not prevail, any conceivable higher development of organic living beings [--> i.e. evolution] would be unthinkable. The consequence of this racial purity, universally valid in Nature, is not only the sharp outward delimitation of the various races, but their uniform character in themselves. The fox is always a fox, the goose a goose, the tiger a tiger, etc., and the difference can lie at most in the varying measure of force, strength, intelligence, dexterity, endurance, etc., of the individual specimens. But you will never find a fox who in his inner attitude might, for example, show humanitarian tendencies toward geese, as similarly there is no cat with a friendly inclination toward mice [--> Jewish or Polish or Russian geese and mice, take due notice] . . . . In the struggle for daily bread all those who are weak and sickly or less determined succumb, while the struggle of the males for the female grants the right or opportunity to propagate only to the healthiest. [That is, Darwinian sexual selection.] And struggle is always a means for improving a species’ health and power of resistance and, therefore, a cause of its higher development. If the process were different, all further and higher development would cease and the opposite would occur. For, since the inferior always predominates numerically over the best [NB: this is a theme in Darwin's discussion of the Irish, the Scots and the English etc in chs 5 - 7 of Descent of Man], if both had the same possibility of preserving life and propagating, the inferior would multiply so much more rapidly that in the end the best would inevitably be driven into the background, unless a correction of this state of affairs were undertaken. Nature does just this by subjecting the weaker part to such severe living conditions that by them alone the number is limited, and by not permitting the remainder to increase promiscuously, but making a new and ruthless choice according to strength and health . . . [Mein Kampf, Bk I, Ch XI]
(And Darwin, and even Wells' warning.) KF PS, you might want to study the history of the first priest ordained in the New World, Las Casas. kairosfocus

JVL, complex functional performance based on integrated configuration is readily seen to depend on precise matching, orientation, arranging and coupling of parts, which naturally results in fine tuning, thus islands of function. You tell us how say a dragonfly's flight capacity per empirically warranted incremental steps, came about -- and not with handwaving or just so stories. KF kairosfocus

CR, rubbish. Darwin highlights NS in the title of Origin and here gave an explanation. I cited him as historical anchor point of meaning, drawing out basic issues. I cannot but notice that where I reapeatedly drew up a summary in terms of causal chains, you have been unresponsive. The bottomline is obvious, as at 125:
1: chance variation [CV] + differential reproductive success [DRS] –> Descent with unlimited modification [DWUM], where 1a: CV + ({fitness slope [FS] –> statistically biased reproductive success [SBRS]} –> DRS) –> DWUM (hence, continent of incrementally accessible viable forms, CIAF, and DRS is seen to be a result) 1b: CIAF + GT –> Branching tree body plan level macroevolution [BTME] 2: DWUM + geologic time [GT] –> Branching tree body plan evolution [BTME] 3: BTME + GT –> world of life, fossil and living [WoL]
Notice, I draw out the implicit assumptions and summarise what is happening, culling out of less successful forms, thus the NS is a subtraction of information not the source, which is left to chance variation. The inadequacy of this claimed or implied source is manifest. Especially, given requisites of the sort of fine tuned complex functional integration that say goes into a dragonfly. And if you doubt that, talk with a helicopter or drone designer. KF kairosfocus

Querius/185 The term "favored races" in Origins doesn't mean human races. Generally, it means healthy procreative lines. For example, Darwin discusses "superior races" of various plants. There is very little discussion of humans in the Origin. So, in the context of the Origin, it doesn't make sense to ask, "what exactly are these “favored races” among humans?" I would think your beef would more be with The Descent of Man, which, while seemingly harsh in parts, nonetheless pretty accurately describes the course of human development. Displacement of indigenous cultures is inevitable, and the process of displacing indigenous cultures began long before Darwin lived. The most obvious example is the Spanish and Portuguese "conquest" of Meso- and South America which occurred with the full backing and sponsorship of the Church. chuckdarwin

Hnorman42: It’s those seas of nonfunction that’s the problem. Natural selection depends on feedback and there is no feedback when there is no function. Umm, remember: starting with a viable, functional life form, variation arises. Some of that variation is not viable/non-functional and doesn't create offspring with the same variation. Some of the variation is viable enough to survive and pass on its characteristics. Life forms that create offspring are all connected by paths of viability or function. There are no islands of function because all life is connected. But, if anyone thinks there are islands of function then please provide a specific example. So far no one has been able to do so but I live in hope. JVL

Seversky @191, Remember this quote?
Data is not information, information is not knowledge, knowledge is not understanding, understanding is not wisdom. -Clifford Stoll
-Q Querius

. . . as there’s no hope that these trolls will ever repudiate the racism in Darwin’s theory.
Q.E.D. @187 Repeating my challenge ad nauseum from @185:
Querius: In Charles Darwin’s book, “On the Origin of the Species By Means of Natural Selection or the Preservation of the Favoured Races in the Struggle for Life,” what exactly are these “favoured races” among humans?

Querius: Also, in the link that Alan Fox provided, maybe someone could elaborate on what Wikipedia meant by
Darwin did feel that the “savage races” of man would be subverted by the “civilised races” at some point in the near future, as stated in the human races section below. He did show a certain disdain for “savages”, professing that he felt more akin to certain altruistic tendencies in monkeys than he did to “a savage who delights to torture his enemies”. However, Darwin is not advocating genocide, but clinically predicting, by analogy to the ways that “more fit” varieties in a species displace other varieties, the likelihood that indigenous peoples will eventually die out from their contact with “civilization”, or become absorbed into it completely.
-Q Querius

What are the differences between "knowledge", "information", "data" and "complexity"? They are not simple, monolithic concepts as is often implied here. UD published an OP by William Dembski a few years back in which he referred to a list of upwards of 40 usages for "information" and "complexity" compiled by Seth Lloyd, who wrote the following
The world has grown more complex recently, and the number of ways of measuring complexity has grown even faster. This multiplication of measures has been taken by some to indicate confusion in the field of complex systems. In fact, the many measures of complexity represent variations on a few underlying themes. Here is an (incomplete) list of measures of complexity grouped into the corresponding themes. An historical analog to the problem of measuring complexity is the problem of describing electromagnetism before Maxwell's equations. In the case of electromagnetism, quantities such as electric and magnetic forces that arose in different experimental contexts were originally regarded as fundamentally different. Eventually it became clear that electricity and magnetism were in fact closely related aspects of the same fundamental quantity, the electromagnetic field. Similarly, contemporary researchers in architecture, biology, computer science, dynamical systems, engineering, finance, game theory, etc., have defined different measures of complexity for each field. Because these researchers were asking the same questions about the complexity of their different subjects of research, however, the answers that they came up with for how to measure complexity bear a considerable similarity to eachother. Three questions that researchers frequently ask to quantify the complexity of the thing (house, bacterium, problem, process, investment scheme) under study are 1. How hard is it to describe? 2. How hard is it to create? 3. What is its degree of organization? Here is a list of some measures of complexity grouped according to the question that they try to answer. Measures within a group are typically closely related quantities.
Seversky

@KF
F.N: Origin of Species, Ch 4:
This is yet another example of Darwin says x. Which is an appeal to sources, not ideas. When I present a constructor theoretic reformulation of natural selection, KF quotes Darwin. Go figure. Of course, KF. Natural selection must be what Darwin said it 160+ was and that is frozen in time. It's like KF and company think science merely the task of correctly defining words. critical rationalist

Recently I summarized the islands of function idea as being a metaphor for specified complexity. "There's just a lot more ways for matter to be put together that don't yield a complex function than there are those that do." (Approximate self quote - I hope I don't accuse myself of quote mining). I was pointing out that the metaphor was for something that was common to both sides - the existence of complex specified information. That's the problem that both Darwinists and ID'ers are trying to explain. Turns out on inspection that I was missing half the point. Islands of function represents a good metaphor for complex functional information but it also highlights the basic problem that natural selection has with it. It's those seas of nonfunction that's the problem. Natural selection depends on feedback and there is no feedback when there is no function. hnorman42

As they've been told ad nauseam Seversky

Inquiring minds want to watch the usual ad hominems and evasions as previously demonstrated as there’s no hope that these trolls will ever repudiate the racism in Darwin’s theory.
That's ad hominem, Querius. :) Alan Fox

Ah, UD back up again. For how long, I wonder. Alan Fox

And still ignoring Darwinian racism? In Charles Darwin's book, “On the Origin of the Species By Means of Natural Selection or the Preservation of the Favoured Races in the Struggle for Life," what exactly are these "favoured races" among humans? Also, in the link that Alan Fox provided, maybe someone could elaborate on what Wikipedia meant by
Darwin did feel that the "savage races" of man would be subverted by the "civilised races" at some point in the near future, as stated in the human races section below. He did show a certain disdain for "savages", professing that he felt more akin to certain altruistic tendencies in monkeys than he did to "a savage who delights to torture his enemies". However, Darwin is not advocating genocide, but clinically predicting, by analogy to the ways that "more fit" varieties in a species displace other varieties, the likelihood that indigenous peoples will eventually die out from their contact with "civilization", or become absorbed into it completely.
Inquiring minds want to watch the usual ad hominems and evasions as previously demonstrated as there's no hope that these trolls will ever repudiate the racism in Darwin's theory. -Q Querius

@ Chuck, thanks. Well folks, I really thought UD was a goner this time. Apologies for #176 and #177. Site froze on me from then until now. Alan Fox

@ Chuck, thanks. Well folks, I really thought UD was a goner this time. Alan Fox

Good people everywhere, listen to Sandy. Whenever I write about random variation, natural selection, and the going extinct of more than 99% of all species, it is only to show that the Darwinian concept is internally incoherent — not because I hold it to be real. Origenes

People there is no such thing like natural selection because selection is made by information from living creatures and information is not natural , is supernatural. If were natural then we would observe everywhere around us how chemistry creates information spontaneously . There is no such thing except in the dreams of a materialist atheist. Sandy

AF/174 Well played. Unfortunately, Larry Moran is anathema on this website. Why? Because he's a real scientist. And, maybe also because he's Canadian :-) chuckdarwin

CR @120, Chuckdarwin
Selection emerges from the interaction between the replicators and the environment with finite resources.
So, natural selection has only a partial role at the onset of life. In the beginning stages, there is only selection in the form of a challenging environment. Random variation painstakingly produces what is in principle viable organisms, and next some environment kills most of it. Only organisms that happened to have the right tools survive. This is widely hailed as a good thing for evolution, many even go so far as to say that it is a ‘creative’ act. I have great difficulty understanding what this appraisal is based on.
CR: … natural selection as an approximate construction, whose substrates are populations of replicators and whose (...) constructor is the environment.
In my view, random variation does all the heavy lifting, and the environment “allows” some of the organisms that random variation painstakingly has managed to come up with to live. IOW the environment does not kill off everything. Well, thank you very much Mr. Environment! That is a big relief. In my view, it is completely wrong to call the environment “the constructor” of organisms in this story. Unlike random variation, it did not produce anything. Not killing off everything is a far cry from being the ‘constructor’ of what you allow to live.
In challenging environments, a vehicle with many functionalities is needed to meet this requirement.
Indeed. A challenging environment kills off just about everything. In my view, the requirements of the environment hamper random variation in its sheer impossible job. The more challenging the environment, [the more natural selection], the more difficult the task of random variation becomes. Conversely, the less natural selection, the easier the task of random variation becomes.
Chuckdarwin: Evolution doesn’t benefit from extinction; competitor organisms benefit in terms of an empty niche.
Suppose a niche is occupied by 4 different species A, B, C, and D. Suppose that due to natural selection only specie A survives and fills the niche. The consequence is that random variation operates only on the genome of specie A, but with quadrupled effort! So, more search space is penetrated WRT specie A. Now I admit that this can turn out to be a good thing for evolution. It could be the case that the genomes of B, C, and D were evolutionary dead-ends anyway, that neither of them contained unique valuable biological information, and that, in short, nothing of importance is lost. And it could also be the case that the surviving specie A turns out to be supremely evolvable and that from specie A many biological novelties ensues. This seems to be what Darwin is hinting at:
… natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good
However, evolution has no foresight, so putting all chips on specie A is a gamble and not a reliable one. In my example, who is to say that the eliminated species B, C, and D are “bad”, and that specie A is “good”, in the context of finding biological information? Origenes

CR, Chuckdarwin
Selection emerges from the interaction between the replicators and the environment with finite resources.
So, natural selection has only a partial role at the onset of life. In the beginning stages, there is only selection in the form of a challenging environment. Random variation painstakingly produces what is in principle viable organisms, and next some environment kills most of it. Only organisms that happened to have the right tools survive. This is widely hailed as a good thing for evolution, many even go so far as to say that it is a ‘creative’ act. I have great difficulty understanding what this appraisal is based on.
CR: … natural selection as an approximate construction, whose substrates are populations of replicators and whose (...) constructor is the environment.
In my view, random variation does all the heavy lifting, and the environment “allows” some of the organisms that random variation painstakingly has managed to come up with to live. IOW the environment does not kill off everything. Well, thank you very much Mr. Environment! That is a big relief. In my view, it is completely wrong to call the environment “the constructor” of organisms in this story. Unlike random variation, it did not produce anything. Not killing off everything is a far cry from being the ‘constructor’ of what you allow to live.
In challenging environments, a vehicle with many functionalities is needed to meet this requirement.
Indeed. A challenging environment kills off just about everything. In my view, the requirements of the environment hamper random variation in its sheer impossible job. The more challenging the environment, [the more natural selection], the more difficult the task of random variation becomes. Conversely, the less natural selection, the easier the task of random variation becomes.
Chuckdarwin: Evolution doesn’t benefit from extinction; competitor organisms benefit in terms of an empty niche.
Suppose a niche is occupied by 4 different species A, B, C, and D. Suppose that due to natural selection only specie A survives and fills the niche. The consequence is that random variation operates only on the genome of specie A, but with quadrupled effort! So, more search space is penetrated WRT specie A. Now I admit that this can turn out to be a good thing for evolution. It could be the case that the genomes of B, C, and D were evolutionary dead-ends anyway, that neither of them contained unique valuable biological information, and that, in short, nothing of importance is lost. And it could also be the case that the surviving specie A turns out to be supremely evolvable and that from specie A many biological novelties ensues. This seems to be what Darwin is hinting at:
… natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good
However, evolution has no foresight, so putting all chips on specie A is a gamble and not a reliable one. In my example, who is to say that the eliminated species B, C, and D are “bad”, and that specie A is “good”, in the context of finding biological information?
Origenes

Quite frankly, I don’t believe you’ve read anything by your patron saint [Charles Robert Darwin], either. But then he’s written a lot of embarrassing things as Alan Fox pointed out earlier. I merely offered a more reliable source as a précis of what is in Descent of Man so TL~DR folks can get an idea without relying on Querius' dubious interpretations.
Alan Fox

Quite frankly, I don’t believe you’ve read anything by your patron saint[Charles Robert Darwin], either. But then he’s written a lot of embarrassing things as Alan Fox pointed out earlier. I merely offered a more reliable source as a précis of what is in Descent of Man so TL~ DR folks can get an idea without relying on Querius' dubious interpretations.
Alan Fox

All of this has been gone over long since.
Unfortunately, scientific research turns up new evidence continually. A science denier's job is never done. Alan Fox

I see Stephen Meyer has been mentioned. Darwin's Doubt should have been titled "Meyer's Mistakes". https://sandwalk.blogspot.com/2014/07/idiot-book-by-stephen-meyer-cant-be.html?m=1 And I'm being generous. Alan Fox

Kairosfocus: please read on, start from molecular to sub phylum, noting on gaps, sudden appearances and stasis. Can you give me a specific example of a biological island of function or not? You've been championing the concept for years and years. If you can't give an example how do you know they exist? JVL

JVL, please read on, start from molecular to sub phylum, noting on gaps, sudden appearances and stasis. All of this has been gone over long since. KF kairosfocus

Chuckdarwin @168,
You don’t have to read Behe’s books when you’ve got a direct quote by him from . . .
I guess you think you save a lot of time by not having to read a book by Behe when you have all those quotes you can mine. Quite frankly, I don't believe you've read anything by your patron saint, either. But then he's written a lot of embarrassing things as Alan Fox pointed out earlier. -Q Querius

JVL @165,
Origenes: Or maybe you could try to articulate a simple, concise, and accurate definition of Intelligent Design. We can go from there.
Origenes did not post the challenge. You got us confused.
Querius: It does not involve “the assumption that a designer brought all that complexity about” JVL: Well it does though since you have no other evidence that there was a designer around at . . .
No, it doesn’t. You’ve also got ID confused with creationism. They’re not at all the same. No wonder half your comments don’t make any sense. -Q Querius

Querius/163 The interview was conducted by Peter Robinson of the right leaning Hoover Institute. He has conducted prior softball interviews with Discovery Institute personnel. This is the second or third time that Meyer has been involved. Friendly venue, no pressure, nothing out of context. As Joe Friday used to say, “nothing but the facts.” chuckdarwin

Querius/163 You don’t have to read Behe’s books when you’ve got a direct quote by him from a softball interview that natural selection results in speciation. Like I said before— crystalline……. chuckdarwin

More for Jerry to ignore https://discourse.peacefulscience.org/t/behe-responding-to-the-polar-bears-fat/4530 Alan Fox

Oh, the overwhelming evidence problem all over again.
https://thehumanevolutionblog.com/2019/02/12/behe-polar-bears/ Alan Fox

Origenes: Or maybe you could try to articulate a simple, concise, and accurate definition of Intelligent Design. We can go from there. I did have a go. Or maybe you've forgotten already. Try reading my previous comment again. It does not involve “the assumption that a designer brought all that complexity about” Well it does though since you have no other evidence that there was a designer around at . . . what time exactly? Who did what exactly? You have to make that assumption because you can't do otherwise without other evidence. If you've got some good physical evidence of the purported designer then please let us know. JVL

JVL @162, Or maybe you could try to articulate a simple, concise, and accurate definition of Intelligent Design. We can go from there. Hint: It does not involve "the assumption that a designer brought all that complexity about" as you wrote in @158 and then subsequently denied in @162. LOL -Q Querius

Jerry @161, Having read Michael Behe's books, it quickly becomes apparent that the trolls and sock puppets here have not! Seems like all they do is occasionally look at a link to some random debunking website for a plausible but completely misinformed opinion. -Q Querius

Querius: ID takes no position on the designer. Try again. I didn't say it did. Perhaps you should pay more attention. But obviously, cluelessness is no impediment to Darwin trolls and sock puppets spreading their ignorance on the subject as widely as possible. Amusing that your latest attack criteria is your perception that those who disagree with you don't seem to be interested in specifying your position. Perhaps you'd like to specify your position and then let us ask questions in case any of your statements aren't completely clear. Meanwhile Jerry continues to avoid explaining his stated position that islands of function are fundamental concepts. You'd think someone who complains that few people can be bothered to understand the real concepts would want to explain them to someone who specifically asks. But maybe it's not about actually having a dialogue or explaining positions. Maybe it's about something else. JVL

Too many links to choose from.
Oh, the overwhelming evidence problem all over again. What a fantastic endorsement of Behe by our resident fount of evidence and logic. jerry

JVL @159,
It’s not really up to us to define ID is it?
Oh, so you identify as a Darwinist troll or sock puppet? No, I don't think you can. ID takes no position on the designer. Try again. But obviously, cluelessness is no impediment to Darwin trolls and sock puppets spreading their ignorance on the subject as widely as possible. -Q Querius

Hnorman @42,
Dawkins’ weasel simulation is still relevant because he gave us a very strong analogy as to what natural selection needs to be able to do to have creative power. It needs to be able to weed out things that don’t conform to a complex future goal.
Exactly. According to doctrinal Darwinism, there is NO goal. Not “Methinks it is like a weasel,” nor “To be or not to be, that is the question,” nor anything else. Whatever survives . . . survives, which is why Darwinism has such an abysmal record of accurately predicting anything with any reliability. It also explains why hardly a week goes by without some newly published paper reports a discovery that threatens to "rewrite what we know about evolution." -Q Querius

Querius: And the Darwinian trolls and their sock puppets STILL cannot provide a simple, concise, and accurate definition of the subject of their attacks, Intelligent Design. It's not really up to us to define ID is it? This blog has a definition in the About section (as I recall). I've always thought that ID was the assertion that, considering the complexity of existing life forms, the assumption that a designer brought all that complexity about is a better explanation than unguided natural processes especially given our experience that functionally complex structures seem to always be the product of an intelligence. But that's just me. JVL

Chuckdarwin @136, 140,
Evolution doesn’t benefit from extinction; competitor organisms benefit in terms of an empty niche.
Are you joking? How do you think niches become empty according to doctrinal Darwinism? And do competitor organisms actually need a niche to be empty according to doctrinal Darwinism? Obviously, you have no idea of what Michael Behe actually wrote. And what’s a simple, concise, and accurate definition of Intelligent Design? -Q Querius

...brown to polar bear speciation is one of the best understood examples of speciation studied...
Nathan Lents and others had a field day with Behe over this. Too many links to choose from. Alan Fox

Asauber @133,
What’s the Selection criteria, and where is it accessed, and did Nature adhere to the criteria when the selection was made? Demonstrate.
As we all know, selection criteria can only be demonstrated in retrospective. The three gods-of-the-gaps of Darwinism are then typically invoked: MUSTA, MIGHTA, and EMERGED. LOL -Q Querius

...brown to polar bear speciation is one of the best understood examples of speciation studied...
Nathan Lents and others had a field fay with Behe over this. Alan Fox

Jerry @130,
It is a tautology and some give it magical powers when it is just what happens. But no one understands it because they miss what it is.
Yes, I agree. It’s more like the survival of the luckiest. Or more cynically, the survival of the survivors. Obviously, when the environment changes dramatically, organisms either adapt (epigenetics), migrate, or die, but this is not evolution. As one science fiction writer proposed, organisms are bred for luck! Maybe those "luck" genes are preserved in “junk DNA.” LOL -Q Querius

Sandy @126,
99% extincted species (like 99% identical DNA with chimp, like 99% consensus, etc.)it’s a lie . Check how many species are in fossil strata, how many are still living today even if “experts” are giving different names for the same species living today that are found in fossil strata.
Good point! I’ve noticed that too. Another thing that’s often missing is just how many modern-looking plants and animals are found in the same fossil strata as their supposedly less-evolved ancestors. -Q Querius

In @118, we read
Differences in “body plans” can be seen as changes in growth inhibitor and promotor <sic> concentrations in critical regions and at critical times within the developing embryo.
Or, just as unsupported by any operationally relevant data, differences in “body plans” can be seen as the inhibitors and promoters of the Easter bunny or other science fantasy. So what was inhibited in the “body plan” of a sea star that resulted in the “body plan” a chihuahua? And the Darwinian trolls and their sock puppets STILL cannot provide a simple, concise, and accurate definition of the subject of their attacks, Intelligent Design. LOL -Q Querius

As Alan Fox happily provided us with a link in @117 to one of Charles Darwin’s more egregious examples of racism, here’s a quote (with emphasis added) that I’d like to see the Darwin trolls and sock puppets finally repudiate:
With savages, the weak in body or mind are soon eliminated; and those that survive commonly exhibit a vigorous state of health. We civilised men, on the other hand, do our utmost to check the process of elimination; we build asylums for the imbecile, the maimed, and the sick; we institute poor-laws; and our medical men exert their utmost skill to save the life of every one to the last moment. There is reason to believe that vaccination has preserved thousands, who from a weak constitution would formerly have succumbed to small-pox. Thus the weak members of civilised societies propagate their kind. No one who has attended to the breeding of domestic animals will doubt that this must be highly injurious to the race of man.
Oh, lovely! Do these weak members of society now live on the streets as homeless people in your opinion? Is their skin color adapted to a more primitive environment? Please, do enlighten us. -Q Querius

CR, knowledge grows through warrant. When something is adequately warranted as credibly true, so reliable, people are willing to bet the farm on it, it is now knowledge. KF So, apparently, science is about correctly defining words? You’ve just repeated a definition, as opposed to addressing ideas, which is exactly my point. This adds nothing to my comment, as it does not conflict with it. Evolution cannot be the source because it’s not justified, even in some weak sense. This discussion will continue go nowhere because you’ve basically defined it that way. critical rationalist

Jerry: Meanwhile, Chuck is in the on deck circle waiting for his chance to knock it out of the park. And we are waiting for you to defend your notion that islands of function are fundamental. Are you going to do that by, at the very least, providing a clear biological example of an island of function? Or are you going to pretend you didn't say it was a fundamental concept? Your call. JVL

discussion of selection of versus selection
this is a perfect example of multiple processes leading to an end result. The magic word “selection” is used. And since it happened by natural process they are examples of natural selection. The population which is the focus of change does not exist in a vacuum. See https://uncommondescent.com/origin-of-life/paul-davies-on-the-gap-between-life-and-non-life/#comment-775881 So as a population is changing so are possibly thousands of other entities in the ecology. And each is providing feedback to the other entities of the ecology.
horizontal gene transfer or random drift
These are just two of the many processes that can go on in a population and an ecology. The question becomes can the processes lead to any substantial change? This is what gets ignored when one uses the term, “natural selection.” Just what is happening, what are the processes causing change and how do they play out over time. Aside: If climbing Mt Improbable were physically possible and combinatorial problems not an issue, would it still be possible? The process has to take place in an ecology with its thousands of other entities. Meanwhile, Chuck is in the on deck circle waiting for his chance to knock it out of the park. jerry

Jerry! Hello Jerry. Why won't you give me an example of a biological island of function? You aren't afraid of answering the question are you Jerry? JVL

Kairosfocus: did you notice, where I then gave biological cases, showing that core body plans starting with the cell then moving on to basic body plan designs, define such islands, even, protein fold domains in AA space? So, again, at what biological level do islands of function exist? And can you give a particular example? Do you struggle, similarly, with say how fiveness and fourness apply to limbs for vertebrates as a dominant pattern, reflecting the universal validity of core math? No, I don't struggle with that because of the basic physics AND the way pairs of limbs tend to be represented in DNA. Or, with how an unsupported plant or animal will fall under gravity? What is the point of this point? Or with how chemistry is applicable to biological processes at molecular level? Well, obviously. Which is Alan Fox's point regarding RNA-world. JVL

A couple of thoughts on natural selection - Dawkins' weasel simulation is still relevant because he gave us a very strong analogy as to what natural selection needs to be able to do to have creative power. It needs to be able to weed out things that don't conform to a complex future goal. And if natural selection can't do it, then we need to know how horizontal gene transfer or random drift can. Fodor and Piattelli-Palmarini's book "What Darwin Got Wrong" I think was talking about the same thing with their discussion of selection of versus selection for. I found this book extremely opaque though and I would appreciate any light that anyone can provide. hnorman42

While Chuck is collecting the details, here is something else for him. What is a species? That’s especially important for a book entitled “On the Origin of Species” and any understanding of it. No need to overthink this. Just a simple definition we all can agree on. And don’t leave out those poor neglected grizzlies. You should be an expert since you live in grizzly country. jerry

I doubt much that you are really interested
We are all ears, Chuck! It will be a first for you, presenting details that matter. I thought your expertise lied elsewhere. Let's go Chuck! jerry

CR, knowledge grows through warrant. When something is adequately warranted as credibly true, so reliable, people are willing to bet the farm on it, it is now knowledge. KF kairosfocus

I'm not hanging my hat on anything. Behe's statement is crystalline. We can get into details (however, I doubt much that you are really interested); brown to polar bear speciation is one of the best understood examples of speciation studied...... chuckdarwin

JVL, did you notice, where I then gave biological cases, showing that core body plans starting with the cell then moving on to basic body plan designs, define such islands, even, protein fold domains in AA space? Besides, what part of bio forms show many cases of FSCO/I thus come under general patterns of configuration spaces is so hard to see as directly relevant? Do you struggle, similarly, with say how fiveness and fourness apply to limbs for vertebrates as a dominant pattern, reflecting the universal validity of core math? Or, with how an unsupported plant or animal will fall under gravity? Or with how chemistry is applicable to biological processes at molecular level? Etc? KF kairosfocus

Next thing, Behe will come out as a full-fledged Neo-Darwinist
Most definitely, yes. All that means is that Behe accepts genetics. As does all of ID. I personally was advocating NDE back in 2006 and said ID subsumes NDE. But NDE is not Evolution. It makes some really extravagant unsupported claims which the science does not support. Chuckdarwin is now an ID advocate. He cannot help it. From 2006
In a way ID subsumes neo Darwinism, presuming it is an explanation for some limited life form changes and may in fact account for some more wide ranging phenomena but absolutely can not account for much of the complexity of life itself. You have to look for something beyond neo Darwinism for that.” Any way that is my take on ID and Neo Darwinism. According to my taxonomy scheme, NDE is part of ID but only represents one of the many mechanisms that have produced life and all its varieties. And NDE may turn out only to be responsible for minor changes to life forms while the major changes originated by some other means. One of those mechanisms is definitely an input by an intelligence. So the better logic and science backs ID. NDE is a charade (as an explanation for Evolution) even if it in fact explains cichlids which I am willing to grant.
jerry

"eventually a new species." CD, If you are hanging your hat on arbitrary classification, you somehow missed what's in the rest of the paragraph prior. Andrew asauber

Origene/122 asks: "If so, how exactly does evolution benefit from this removal?" Evolution doesn't benefit from extinction; competitor organisms benefit in terms of an empty niche. This from a February 2023 interview of Behe, Meyer and Lennox (link graciously provided by Jerry):
Michael Behe: That's exactly right, because if you posit that natural selection produced all of life, then it has to have produced not only trivia but the profound molecular machines that are found in the cell, the genetic code, the wings of a bird and much more, and we don't see that. And yet, [natural selection] can work on DNA. For example, it can break genes. A random mutation can break a gene and say, cause a brown bear to lose its coloration and become a white polar bear, and eventually a new species. (emphasis added)
Eventually a new species. Wow. "Breaking genes" is not completely accurate--but that's for another day. This on top of his previous admission during the Kitzmiller trial that he accepted common descent. Next thing, Behe will come out as a full-fledged Neo-Darwinist.... https://www.hoover.org/research/design-behe-lennox-and-meyer-evidence-creator chuckdarwin

@Ori
Now here is my question: in what sense was that helpful and/or creative?
Knowledge grows via conjecture and criticism, in some form or another. It's not founded on anything in the sense you seem to think. In the case of people, we first start with a problem. From there, we conjecture explanatory theories about how the world works, in reality, with the explicit intent of solving that problem. Then we criticize those theories and adopt the one that has best withstood criticism. This doesn't mean our conjectures has been positively justified, etc. It just means we currently lack good criticism of it. Being people, we are universal explainers. We can conceive of problems. Only people can create explanatory knowledge. At some point, some observation or new criticism is conceived of and the process starts again. it's iterative. We make progress, fallibly. In the case of the biosphere, evolution is not a person. As such, It cannot conceive of problems like we do. Nor can it create explanations, which reach, designed to solve them. However, this doesn't mean there is no progress to be made. In neo-Darwinsim, Conjecture takes the form of mutations and criticism takes the form of natural selection. Namely the genes that are most fit to get into the next generation. The process is iterative, as above, so mutations are not random, they are random to any specific problem to solve. Again, only people are universal explainers that can conceive of problems. So, we would predict that the knowledge in living things would not be explanatory in nature. We would not find explanatory concepts like love, loyalty, rivalry, etc. Rather we would find non-explanatory knowledge. People can create both explanatory and non-explanatory knowledge. Evolution can only create non-explanatory knowledge. For example, there is nothing in a tiger that knows about how having stripes impacts its food supply. As such, this knowledge is non-explanatory. But this doesn't mean there is no knowledge, or that it does not grow. critical rationalist

So, according to you, natural selection is “a myriad of processes”? Is that your profound insight, Jerry? Is that the reason why you continually proclaim that “no one here understands natural selection”?
Natural selection is just what happens that’s stable, no matter the cause. It definitely is not a process. It is the stable end result of a number of processes. (Maybe hundreds). As such it is a meaningless term and has no explanatory power. It says what happened, happened. Duh? It takes away from examining the processes. It is this which must be the basis of any undertaking of Evolution. Those who espouse naturalized Evolution desperately want to avoid any examination of these processes especially at the genetic level or some other sub-cellular level because maybe there aren’t any that lead anywhere. I mentioned what evolutionary biologists were saying. There used to be a couple of them on UD who defined the process. But no one now addresses it. Instead we just get rhetoric. Aside: All the processes that cause stable changes are definitely supported by science and endorsed by ID. They are just under the science of genetics. It is the small stable changes accumulating to something entirely different that is not supported by any science/evidence or logic. Changes do happen but they are/must be limited. jerry

There is an easy way to expose Natural Selection to be a fraud. What's the Selection criteria, and where is it accessed, and did Nature adhere to the criteria when the selection was made? Demonstrate. Andrew asauber

Jerry @130
Whatever ends up as stable is natural selection.
A stable biological form **is** natural selection? I do not understand. Do you perhaps mean to say that a stable biological form is the result of natural selection?
How or why something becomes stable is due a myriad of processes.
So, according to you, natural selection is "a myriad of processes"? Is that your profound insight, Jerry? Is that the reason why you continually proclaim that "no one here understands natural selection"? Origenes

I have great difficulty understanding how natural selection assists unguided evolution. Perhaps you can explain its creative power to me.
Of course you have great difficulty, Ori. It's the same difficulty you have with knowledge either being justified, even if in some weak sense, or being worthless, in that there can be no knowledge. So, this comes as no surprise. After all, according to you, knowledge can only come from authoritative sources. Right? And natural selection is not an authoritative source. So, obviously, it couldn't possible be the source of the knowledge in living things. This is why you, KF etc. keep beating the drum that natural selection is just random, despite having been corrected over and over and over again. So, no. It's really not that complicated. Evolution conflicts with your epistemological view on knowledge. critical rationalist

I rest my case. No one here understands natural selection. Well, there may be one or two. And certainly Darwin didn’t. But he can be excused since so little was known then. Whatever ends up as stable is natural selection. It is a tautology and some give it magical powers when it is just what happens. But no one understands it because they miss what it is. How or why something becomes stable is due a myriad of processes. Sighting fitness is just a begging of the question. This concept readily applies to combinations of living entities and non living things which we call ecologies. It can also apply solely to combinations of non living things. So should we define the latter as ecologies too? Probably. As far as islands of function, this is just stable combinations that appear to have no natural predecessor. It could be stable combinations of genes/proteins. But it could apply to non life entities also. Basically, it was explained in #5 Much ado about nothing. But that is the objective of UD, the generation of irrelevant OPs and meaningless comments. Pixels is the goal no matter how. The more, the better. jerry

"It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and add-ing up all that are good;" If anyone out there thinks this poem has any scientific value, you really are living in a fantasy world. Andrew asauber

Kairosfocus: That is, biological cases are a subset of a far more general pattern. That's not helping identify biological islands of function though. Let's try another way: Is each species on a separate island of function? Or is it at the genus level? Or something else? JVL

Origenes, or, there is a nest of superior younglings, but a grass fire roasted them, or the nest fell over a cliff, or predators got them, or there was a meteor impact event etc. The notion that NS is not random is here exposed, in reality DRS is a stochastic effect that is deemed to lead to hill climbing due to a stable enough upward slope. While I am at it there will predictably be stuff over how environment changes move fitness slopes, FYI, islands can be movable too, esp barrier islands. The essential point remains. KF kairosfocus

Origenes Next natural selection whimsically freezes the organisms to death, just like it did with more than 99% of all species, and as a result, deserts remain virtually devoid of life.
99% extincted species (like 99% identical DNA with chimp, like 99% consensus, etc.)it's a lie . Check how many species are in fossil strata ,how many are still living today even if "experts" are giving different names for the same species living today that are found in fossil strata .
Kairosfocus 1: NS, so called is highlighted over the chance variation required to furnish changes, as is seen from the title, a telling shift of emphasis. 2: We see here hill climbing incrementalism, joined to geologic time. 3: We see the assumption of improvement [hence, hill-climbing on a fitness slope] 4: We see the attempt to deride and dismiss a common phenomenon long noticed by breeders, that variation tends to have limits . . . which are evidence of multiple interacting genetic traits that give a normal range, which can be selected out leading to breeds that have less variability than a typical wild population. 5: The word used for that dismissal is tellingly familiar: assumption. 6: We notice, the implicit suppression of the implication of a familiar pattern, functionally specific, complex organisation requiring many well matched, properly oriented and arranged parts, with correct coupling. This naturally tightly constrains feasible arrangements i.e. we see tuning and islands of function as a natural consequence. 7: The implicit continent of being fitness landscape implicit in Darwin, is a questionable underlying assumption. Ironically
Your Bullet(Bomb) points are excellent. Sandy

JVL, 119: >>Please give a biologically focused definition of islands of function and provide a couple of biological examples.>> No need, strictly, we have a general systems phenomenon here, that there are far more ways to clump parts p1, p2 . . . pn at random than in functionally specific ways. Further, the matching of parts is a further big challenge [as you should know from auto maintenance], and beyond such the scattering of parts is far, far more vast a sea of obviously non functional possibilities. That is, biological cases are a subset of a far more general pattern. In biology we can see that protein fold domains form scattered islands in AA sequence space, as GP pointed out vigorously years ago. That alone establishes the onward matter, as proteins are the workhorse molecules of life. But the pattern goes on to the overwhelmingly deleterious nature of mutations [why are we so afraid of radioactivity . . . (but then physicists glow in the dark)], and to the trade secret of paleontology that many are indoctrinated not to see: sudden appearances, stasis of core form, disappearance. The Cambrian revolution of fossil forms is the most notorious case. What is in reality required, is that there be presented good observational warrant as to why biological forms are allegedly exceptional and for 160 years such has not been forthcoming, headlines about missing links found [then un-found again] notwithstanding. Remember, Darwin hoped that future fossil explorations would close enough gaps. But after 160 years, 1/4 million fossil species globally, millions of specimens in the lab and billions in the ground, the pattern of gaps has been confirmed. Hence, the rise and fading away of punctuated equilibria etc. CR, 120: >>Is there some reason why you keep referring to “survival of the fittest”? >> As you know, the obvious one, for many decades this has been a dominant term used by Darwinists. Hence the classic challenge, survival of the fittest does not explain their arrival, which gets us to an expanded version of my causal chain model summarising Darwinist thought on origin of body plans -- far more than species -- above:
1: chance variation [CV] + differential reproductive success [DRS] –> Descent with unlimited modification [DWUM], where 1a: CV + ({fitness slope [FS] --> statistically biased reproductive success [SBRS]} --> DRS) --> DWUM (hence, continent of incrementally accessible viable forms, CIAF, and DRS is seen to be a result) 1b: CIAF + GT --> Branching tree body plan level macroevolution [BTME] 2: DWUM + geologic time [GT] –> Branching tree body plan evolution [BTME] 3: BTME + GT –> world of life, fossil and living [WoL]
But more to the point, Natural selection so called is an effect, DRS. This is what leads to fitness peak trapping. As to, we don't care what Darwin thought, that is an evasion of what I supplied. Level 1, what the Natural Selection in the title of Origin meant and how it is cashed out per implied fitness landscape. Level 2, I have put up a summary of more modern thought, which is seen to be organically traceable to Darwin, with addition of genetic mutations etc. (I did not bother to talk about the minor point, sexual selection.) AF, 121: >> I would emphasize that “fitness” is shorthand for “comparative reproductive success” in the niche environment occupied by the population>> That is, differential reproductive success [on a fitness slope]. Origenes, 122: >>I have great difficulty understanding how natural selection assists unguided evolution. Perhaps you can explain its creative power to me.>> Darwinist, global incrementalism across an imagined continent of viable forms. Of course, no one has shown good empirically based reason to reject the fine tuning implications of complex, highly integrated functional organisation. KF kairosfocus

Darwin: It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and add-ing up all that are good; ...
Let's assume some organisms that possess a unique intricate system that can deal with extreme heat and drought. These organisms are highly evolvable so that entire desserts could be enriched by ensuing species. However, these organisms cannot cope with extreme cold. Next natural selection whimsically freezes the organisms to death, just like it did with more than 99% of all species, and as a result, deserts remain virtually devoid of life. Now here is my question: in what sense was that helpful and/or creative? Origenes

F.N: Origin of Species, Ch 4:
. . . It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and add- ing up all that are good; silently and insensibly working, whenever and wherever opportunity offers, at the improve- ment of each organic being in relation to its organic and in- organic conditions of life. We see nothing of these slow changes in progress, until the hand of time has marked the lapse of ages, and then so imperfect is our view into long- past geological ages, that we see only that the forms of life are now different from what they formerly were. In order that any great amount of modification should be effected in a species, a variety when once formed must again, perhaps after a long interval of time, vary or present indi- vidual differences of the same favourable nature as before ; and these must be again preserved, and so onwards step by step. Seeing that individual differences of the same kind perpetually recur, this can hardly be considered as an unwar- rantable assumption. But whether it is true, we can judge only by seeing how far the hypothesis accords with and ex- plains the general phenomena of nature. On the other hand, the ordinary belief that the amount of possible variation is a strictly limited quantity is likewise a simple assumption.
We find here: 1: NS, so called is highlighted over the chance variation required to furnish changes, as is seen from the title, a telling shift of emphasis. 2: We see here hill climbing incrementalism, joined to geologic time. 3: We see the assumption of improvement [hence, hill-climbing on a fitness slope] 4: We see the attempt to deride and dismiss a common phenomenon long noticed by breeders, that variation tends to have limits . . . which are evidence of multiple interacting genetic traits that give a normal range, which can be selected out leading to breeds that have less variability than a typical wild population. 5: The word used for that dismissal is tellingly familiar: assumption. 6: We notice, the implicit suppression of the implication of a familiar pattern, functionally specific, complex organisation requiring many well matched, properly oriented and arranged parts, with correct coupling. This naturally tightly constrains feasible arrangements i.e. we see tuning and islands of function as a natural consequence. 7: The implicit continent of being fitness landscape implicit in Darwin, is a questionable underlying assumption. Ironically. KF kairosfocus

Kairosfocus I have great difficulty understanding how natural selection assists unguided evolution. Perhaps you can explain its creative power to me. Could it be said that natural selection removes transitional forms and y doing so "creates" species?
Wiki: More than 99% of all species that ever lived on Earth, amounting to over five billion species,[1] are estimated to have died out.
If so, how exactly does evolution benefit from this removal? Origenes

A organism can become more fit in some aspect, however if that aspect is not heritable, it is not passed down to future generations. This is not a tautology.
No indeed. I would emphasize that "fitness" is shorthand for "comparative reproductive success" in the niche environment occupied by the population. Dawkins talked about selection at the gene level, but neither gene selection nor group selection are accepted currently. It is phenotypes that are selected, individuals within populations, not genes or groups. Differential selection of phenotypes results in change of allele frequencies over time. Alan Fox

@KF Is there some reason why you keep referring to “survival of the fittest”? For example, in the paper I referenced, this is addressed directly. It is the survival of the fittest genes. You know, Dawkins’ The Selfish Gene. What’s particularly amazing about constructor theory is that it is a generational of catalysts to information to even quantum computation. This allows us to model natural selection in such a way that the environment is a highly approximate constructor.
3.3 Natural selection is permitted under no-design laws These conclusions imply that an accurate self-reproducer - together with an accurate replicator - is permitted under no-design laws that allow for information media. So, under such laws, it can be constructed from generic resources only, given enough knowledge: it could continue to exist, say, had a chemical lab created it. However, one must also address the question: can accurate self-reproducers arise from generic resources only, under such laws? Note that what the prevailing conception would aim to prove is that the emergence of accurate self-reproducers follows (with some probability) given certain initial conditions and laws of motion. This approach, informing the search for viable models for the origin of life, [25], is suitable to solve scientific problems such as predicting the existence of life elsewhere in the universe - e.g., by providing bounds to how probable the emergence of those self-reproducers is on an earth-like planet. Here I am addressing a different problem: whether accurate self-reproducers are possible under no-design laws. This is a theoretical (indeed, constructor-theoretic) question and can be addressed without resorting to predictions. Indeed, the theory of evolution provides a positive answer to that question, provided that two further points are established. I shall argue for them in what follows. The first point is that the logic of evolution by natural selection is compatible with no-design laws because - in short - selection and variation are non-specific to its end products. This can be seen by modeling the logic of natural selection as an approximate construction, whose substrates are populations of replicators and whose (highly approximate) constructor is the environment. This occurs over a much longer time-scale than that of self- reproduction, whereby replicators - constructors on the shorter scale - become now substrates. Evolution relies upon populations being changed by variation and selection over the time-scale spanning many generations. Crucially, the mutations in the replicators, caused by the environment, are non-specific, (as in section 3.1), to the “end product” of evolution (as Dawkins put it, not “systematically directed to improvement” [27]). This constructor-theoretic characterization of mutations replaces the less precise locution “random mutations” (as opposed to non-random selection, [5]). These mutations are all transmitted to the successfully created individuals of the next generation, by heredity - irrespective of their being harmful, neutral or beneficial in that particular environment. Selection emerges from the interaction between the replicators and the environment with finite resources. It may lead to equilibrium, given enough time and energy. If so, the surviving replicators are near a local maximum of effectiveness at being replicated in that environment. Thus, the environment is passive and blind in this selection process. Since it retains its ability to cause non-specific variation and passive selection again, it qualifies as a naturally-occuring approximation to a constructor. Crucially, it is a crude approximation to a constructor: crude enough that it could have arisen by chance and requires no explanation. Its actions - variations and selection - require no design in laws of physics, as they proceed by non-specific, elementary steps. So the logic of evolution by natural selection is compatible with no-design laws of physics. The second point is that natural selection, to get started, does not require accurate self-reproducers with high-fidelity replicators. Indeed, the minimal requirement for natural selection is that each kind of replicator produce at least one viable offspring, on average, per lifetime - so that the different kinds of replicators last long enough to be “selected” by the environment. In challenging environments, a vehicle with many functionalities is needed to meet this requirement. But in unchallenging ones (i.e. sufficiently unchanging and resource-rich), the requirement is easily met by highly inaccurate self-reproducers that not only have no appearance of design, but are so inaccurate that they can have arisen spontaneously from generic resources under no-design laws - as proposed, for instance, by the current theories of the origin of life [11, 31]. For example, template replicators, such as short RNA strands [32], or similar “naked” replicators (replicating with poor copying fidelity without a vehicle) would suffice to get natural selection started. Since they bear no design, they require no further explanation - any more than simple inorganic catalysts do.(11) I conclude that the theory of evolution is compatible with no-design laws of physics, that allow, in addition to enough time and energy, information media. These requirements do not contain the design of biological adaptations. Hence, under such laws, the theory of evolution fully explains the appearance of design in living organisms, without their being intentionally designed.
Arguments along the lines that Darwin thought x, are irrelevant, including whether he thought natural selection reflects the survival of the fittest organisms. Rather, it’s the genes most fit to make it into the next generation. A organism can become more fit in some aspect, however if that aspect is not heritable, it is not passed down to future generations. And vice versa. This is not a tautology. Of course, this has been pointed out to you ad nauseam, but the referenced paper makes it possible to model natural selection significantly more clearly. critical rationalist

Kairosfocus: Fine tuning with zones of adequate function in the configuration space of clumped or scattered possibilities for such parts, merits the description, islands of function. Please give a biologically focused definition of islands of function and provide a couple of biological examples. JVL

...there is some mysterious superpower that creates novel body plans out of the info source, incremental lucky noise.
There does seem to be some connection between how embryological development proceeds and the rules of topology. Differences in "body plans" can be seen as changes in growth inhibitor and promotor concentrations in critical regions and at critical times within the developing embryo. Alan Fox

When are you going to admit to the racism implicit in Darwin’s theory?
Implicit? https://en.m.wikipedia.org/wiki/The_Descent_of_Man,_and_Selection_in_Relation_to_Sex For us TL~DR. Alan Fox

Jerry, "natural selection/survival of the fittest" readily gets into tautologies similar to the Gostak distims the Doshes, a notorious Sci Fi tale. Many times, others and even the undersigned have pointed out the framework, but of course the rhetorical pretence is that there is some mysterious superpower that creates novel body plans out of the info source, incremental lucky noise. I summarise, noting the predictable zero concessions policy (as seen above as objectors dissemble about the force of Lehninger et al who emphatically brought out the coded info in DNA, even printing a side by side image of DNA and a Cuneiform stele as parallel cases of coded textual information):
chance variation [CV] + differential reproductive success [DRS] --> Descent with unlimited modification [DWUM] DWUM + geologic time [GT] --> Branching tree body plan evolution [BTME] BTME + GT --> world of life, fossil and living [WoL]
Implicit in this is the fitness landscape framework, which leads to peak trapping as noted in OP. Of course, DRS is the operational description of what is too often reified as natural selection. Further, the indoctrinated in the above dogmas of evolutionary materialism and/or fellow travellers will predictably refuse to acknowledge the massively evident fact that from cell based life to us, life forms exhibit multiple integrated systems and networks involving complex, functionally specific, information-rich organisation and thus associated information. This directly requires many correct and well matched components, correctly arranged and oriented, with correct coupling to achieve relevant function. Even text in objecting comments is an example of such FSCO/I, much less cell based life. Such further implies fine tuning to get such things to work. Fine tuning with zones of adequate function in the configuration space of clumped or scattered possibilities for such parts, merits the description, islands of function. Deeply isolated in the configuration spaces. Where, as the OP shows using the 3-DPC as a formalism, compact description d(E) is informationally equivalent to E and provides a metric of the K-complexity, i.e. information quantity. Beyond 500 - 1,000 bits, the sol system or observed cosmos scale resources cannot plausibly rise above negligible blind watchmaker natural search by random walk. In this context, it is obvious that a means of adaptation to niches in islands of function has been grossly, fallaciously extrapolated into a mechanism presented as explaining body plans. And, such has been institutionally imposed, too often, ruthlessly, as a reigning orthodoxy. The refusal to acknowledge the relevance of Orgel-Wicken FSCO/I, therefore, is a back handed admission of the cogency of the point. KF kairosfocus

Up late tonight. Just get back from your Passover dinner?
I'm on Central European Time, seven hours ahead if the time displayed at UD. There will be an Easter celebration this weekend in our village that I'll be attending. The highlight will be "omelettes de Pâques", some flavoured with wild asparagus followed by sweet ones with eau de vie. Then there'll be dancing and worse! Alan Fox

ChuckDarwin @84,
Second, your characterization of evolutionary theory as “infallible, racist, colonialist and genocidal” is a complete overreach. Evolutionary theory is not a prescriptive public policy as you chose to characterize it; it is a scientific theory. Nothing more, nothing less…….
Except for all that eugenics stuff that your patron saint wrote in The Descent of Man and even featured in the extended title of his other book, “On the Origin of the Species By Means of Natural Selection or the Preservation of the Favoured Races in the Struggle for Life. Yeah, some scientific theory all right. Not to mention the Darwin-encouraged German genocide of Africans in Namibia, the massacres of aboriginal people in Australia, the apparently ongoing Canadian genocide against indigenous peoples, and many others. When are you going to admit to the racism implicit in Darwin's theory? -Q Querius

Gee Jerry, why are you still avoiding answering my questions about islands of function? For someone who says no one is trying to understand the real issues and since you said islands of functions were important then why are you not trying to explain them to me? JVL

Alan, Up late tonight. Just get back from your Passover dinner? jerry

Origenes: Sure. And thanks to Dr. James Tour we now know that it was all a bunch of nonsense. So, you do admit that tentative explanations have been presented to you? If you are always just going to believe Dr Tour over anyone else then stop asking for anyone else to come up with another explanation. Stop pretending that you want to have a discussion. Stop playing whatever game you are playing. If a YouTube video is your idea of science then just stop. JVL

JVL
People have posted many, many, many times about such things.
Sure. And thanks to Dr. James Tour we now know that it was all a bunch of nonsense. See e.g. https://www.youtube.com/watch?v=WKLgQzWhO4Q Origenes

It was an absolute massacre.
Oh, I don't know, Upright Biped and BA77 were quite tenacious for a while. Alan Fox

Origenes: Unfortunately, there are no explanations whatsoever coming from your position, not even tentative ones. That is just not true. People have posted many, many, many times about such things. If you're going to just ignore information that is given to you then stop requesting it. JVL

JVL on OOL:
... there are (tentative) explanations ...
Unfortunately, there are no explanations whatsoever coming from your position, not even tentative ones. BTW you just missed out on a discussion about RNA-world. It was an absolute massacre. https://uncommondescent.com/intelligent-design/a-review-of-nicholas-spencers-magisteria-the-entangled-histories-of-science-and-religion/#comment-779307 Origenes

"the Behe, Meyers and Maddox discussion" Thanks, for the link, Jerry. That was a good listen. Andrew asauber

Asauber: Evolution has problems before we even go back to OOL… I know you think so. And you disagree with the consensus. That's fine. As long as you don't deny there is research, there are (tentative) explanations, work is being done, no one is avoiding the issue. Can you at least do those things? JVL

Jerry: From reading the comments of the anti ID people here, it is clear that they do not understand what they are believing. They never propose any evidence for their beliefs when the ID people are constantly providing evidence and logic for their beliefs. Okay, then help me understand the evidence for islands of function. Define them for me in a pertinent biological context and give me some clear examples. JVL

A couple of months ago I proposed a discussion of just what natural selection is. See https://uncommondescent.com/origin-of-life/paul-davies-on-the-gap-between-life-and-non-life/#comment-775881 No one was interested as people continually discuss Evolution where different states end up being stable without any understanding of just what that means or how they got there. The obvious conclusion is that don’t care. People just want to rant, make disparaging comments or pronounce something else irrelevant. jerry

Jerry/100 Thanks…. chuckdarwin

JVL, Evolution has problems before we even go back to OOL... Andrew asauber

Do you have a link to the Behe, Meyers and Maddox discussion?
https://www.hoover.org/research/design-behe-lennox-and-meyer-evidence-creator There is a transcript there if one doesn’t want to listen. jerry

Seversky/92 or perhaps The Island of Dr. Moreau--either one seems perfect...... chuckdarwin

If anyone is interested and from past comments here, no one seems to be, the basis for naturalized Evolution was explained here over 16-17 years ago by Allen MacNeill. Allen was essentially a proponent of punctuated equilibrium and in the course of following up on his reading recommendations I learned what that meant. It is not what nearly everyone thinks it means. From reading the comments of the anti ID people here, it is clear that they do not understand what they are believing. They never propose any evidence for their beliefs when the ID people are constantly providing evidence and logic for their beliefs. Aside: All the issues of Evolution could be settled with the right research project but no one is interested. But even if Evolution is based on naturalized processes, that in no way invalidates ID. Aside2: Separating Evolution from OOL is a bogus issue. Darwin did it because he had no idea what life is or consisted of. But both had to go through a very similar process with probably thousands if not millions of steps. It is just that the natural Evolution adherents propose that all of the steps in Evolution are made of life and non life changes. While OOL is based strictly on non life changes. So separating them is a little arbitrary. jerry

Asauber: Well… the reason Evolution doesn’t address how life arose is because it can’t. It can’t even explain the biology of right now. It’s a fairy story for atheists and similar lost sheep. But biology researchers ARE addressing the question of how life arose. They are doing work, They are trying to find out. What is your point? That one branch of biology isn't answering the questions from another branch of biology? Really? Does that even make sense? When you, yourself, won't commit on who the designer was from an ID point of view. Perhaps you'd like to provide a clearer picture of when design was implemented. At least. Can you do that? JVL

"how life arose" Well... the reason Evolution doesn't address how life arose is because it can't. It can't even explain the biology of right now. It's a fairy story for atheists and similar lost sheep. Andrew asauber

Relatd: A lot of time and money is being spent on Origin of Life research. I’m not behind it. But the research exists, the work is being done. BUT, again, how the first 'species' arose doesn't tell you how the others were derived from it. ID, as science, does not identify a designer but that is what the word Intelligent in ID points to. Of course, aliens is a poorly though through idea, since the next question is: So who made the aliens? I agree. But, again, ID tends to support a double standard: ID doesn't have to specify who created life but unguided evolution does have to specify how life arose or the whole idea is bogus. That's disingenuous. You're asking for more that you can and are willing to provide. JVL

JVL at 93, A lot of time and money is being spent on Origin of Life research. I'm not behind it. ID, as science, does not identify a designer but that is what the word Intelligent in ID points to. Of course, aliens is a poorly though through idea, since the next question is: So who made the aliens? relatd

Realtd: So, a running automobile engine that can upgrade itself was just found in a field somewhere? What a strange thing to say. ID proponents continually make the claim that ID has no opinion on who the designer is/was (when clearly God vs Aliens is hugely different and has massive implications as far as when and how design was implemented) but they keep insisting that a theory which addresses how new species arise from existing species HAS TO address how life arose. A bit of a double standard surely. JVL

I wonder if the island archipelago of the Republic of San Serriffe is one of the "islands of function" ? Seversky

"With regard to evolution, how life arose is irrelevant." So, a running automobile engine that can upgrade itself was just found in a field somewhere? relatd

Hey Jerry. How come you haven't answered my questions about islands of function? You did say they were important so I asked you to define the term (in a useful biological context I hope) and give an example. For some reason you have avoided addressing those questions. I'd love it if Kairosfocus answered the same questions. I'm particularly interested in an example of a biological island of function. There is no basis for what is being taught. That is obvious. Strange you should say that. When I look at an Evolution textbook I find pages and pages and pages of references to research and publications backing up what is being said. Now, perhaps, you'd like to address all those references and show why all of them are inaccurate or fallacious. Would you like to do that? JVL

Jerry Do you have a link to the Behe, Meyers and Maddox discussion? Thanks.... chuckdarwin

My apologies for the formatting of my comment at 86. I noticed the mess right after I posted it but when I tried to correct it, UD was down. Ford Prefect

What is currently being taught in most schools is based on fairly current research.
Nonsense. There is no basis for what is being taught. That is obvious. jerry

Kairosfocus writes:
AF, you continue to skip the core issues as were again highlighted, 1: differential reproductive success is necessarily a subtracter of information rather than a source;
It is both. You should read up on meiosis, inversions, duplications, etc. that occur during reproduction.
the claimed source is incremental chance variation, which means
So? “The source of genetic variation in a population is mutation. Mutation rates in humans have been estimated to be on the order of 10?4 to 10?6 per gene per generation. The rate of nucleotide substitutions is estimated to be 1 in 108 per generation, implying that 30 nucleotide mutations would be expected in each human gamete.” <blockquote<2: hill climbing and issues such as peak trapping and need to cross to other hills are not properly solved, Strawman mischaracterization if his evolution works. Your cherished “islands of function” are more like wave crests in a storm tossed sea than static islands in an calm sea. If you are going to use an analogy to prove a point it is best to use one that is not so easily debunked.
especially given the fine tuning implications of FSCO/I (thus of islands of function deeply isolated in configuration spaces dominated by seas of non function).
See above.
3: The root issue, OoL has to be bridged to access the tree, and it remains the case that there is no adequate, observationally warranted means to go from a Darwin pond or the like to cell based life by blind dynamic-stochastic forces.
Evolution does not make any claims on OoL. With regard to evolution, how life arose is irrelevant. <blockquote<4: Life, being full of FSCO/I, is full of known, reliable signs of design. Except that nobody has been able to adequately explain what FSCO/I is and how to quantify it. What is the FSCO/I of an arrowhead vs a stone? What is the FSCO/I of Mount Rushmore vs a mountaintop? What is the FSCO/I of a flagellum?
5: This includes something you spent months trying to dismiss, the Nobel Prize winning research that shows coded, algorithmic string data structure information in DNA and mRNA, used to assemble AA chains towards proteins. I put it to you this is alphanumeric, structure describing text that also is algorithmic, showing start and finite step by step instructions with halt; and, it is thus of clearly linguistic character.
Another argument based on the poor use of an analogy. “Code” when referring to DNA simply refers to the fact that known triplets of nucleotides have affinities to known amino acids. “Analogous” to how certain characters in a human code are placeholders for other characters. It takes a special pathology to intentionally mischaracterization a biologist’s use of the term to argue that this is proof of intentional design.
6: So, we do not actually have an empirically warranted blind watchmaker account of either origin of cell based life or of body plans, but we also know that such life is full of organisation and explicit information manifesting strong signs of design.
Neither side has an empirically warranted account of OoL. But one side is conducting research to try to narrow the possibilities down. Which side do you think that us?
7: Where there is clear evidence from eminent scientists of ideological imposition on the science, making it and education based on it severely biased.
What is currently being taught in most schools is based on fairly current research. (Unfortunately there is always a delay in updating curriculum) and the teachings have changed over time as new evidence is found. If you want your children to be taught that the universe and life are designed, there is already a constitutionally protected venue for that. Ford Prefect

Well, that’s not true.
most definitely true. I’ve read the books and have a couple in my Kindle list.
Darwin’s On the Origin of Species set out the mechanism of natural selection,
Natural selection is not a mechanism. It’s a tautology. Whatever happens is by definition natural selection. This is evidence that you have no idea what you believe.
Do you live in a cave
No, but I understand what is behind what you believe even if you don’t. Aside: In a recent interview, Behe, Meyers and Maddox demonstrated that they don’t understand what the theory of Evolution is about. So commenters here should not feel lonely. They did demonstrate why naturalized Evolution can’t happen according to the reasons given by its adherents. Especially those who endorse Darwin’s ideas. jerry

Querius/78
I wasn’t surprised at all when I ran across the apparently obligatory equivocation in the original text about their assertion of the impact of their findings on the infallible (and racist, colonialist, and genocidal) Theory of Evolution.
A couple observations: First, given the title of the original Nature publication there's clearly no "equivocation" as to where these results fit within the evolutionary model. It is explicit in the title of the article: "Mutation bias reflects natural selection." Can't get more explicit than that. Second, your characterization of evolutionary theory as "infallible, racist, colonialist and genocidal" is a complete overreach. Evolutionary theory is not a prescriptive public policy as you chose to characterize it; it is a scientific theory. Nothing more, nothing less....... chuckdarwin

In short, oh you ignoramus fails, fails in a way that exposes the ideological agenda at work and implies that this is so powerful that AF feels compelled to gaslight at any cost. Here, this is what exposed him as of negative credibility.
Time for a fishing break, I think. Alan Fox

KF, neither I nor Nick Lane have any issue with Lehninger. It's your interpretation that is at fault Alan Fox

AF, insubstantial, for the moment, no 1. I am sure we both know that proverbially survival of the fittest does not explain arrival of the fittest. Or, going to the actual title of Origin, " On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life." How are favoured preserved, oh, by the failure thus subtraction, of the less favoured. Thus, that so-called natural selection is a subtraction of genetic information is manifest on its face; survival of the fittest -- let's skip the question begging in that for now -- means extinction, non-survival of the alleged less fit. That leaves chance variation, mutations etc as the chance driven, claimed writer of required information. That you are unwilling to admit this is a backhanded admission that you know this suggested means is grossly inadequate. KF PS, I beg to remind onlookers, as AF will never acknowledge, what expert biochemists Lehninger et al had to say:
"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]
See https://uncommondescent.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/ In short, oh you ignoramus fails, fails in a way that exposes the ideological agenda at work and implies that this is so powerful that AF feels compelled to gaslight at any cost. Here, this is what exposed him as of negative credibility. kairosfocus

KF's core issues: 1: Nonsense. Reproductive success fills the gap left by reproductive failure. 2. Poor analogy. You mistake map for territory. 3. Currently a mystery. But not one that concerns evolutionary theory. 4. FSCO/I exists only in your imagination. There's nothing to address. 5. Your lack of knowledge in biochemistry prevents you making sense. 6. More poor analogy. 7. Eminence does not outweigh facts and evidence. You'd maybe do better to argue against evolution as it is rather than your own straw-man. Alan Fox

AF, you continue to skip the core issues as were again highlighted, 1: differential reproductive success is necessarily a subtracter of information rather than a source; the claimed source is incremental chance variation, which means 2: hill climbing and issues such as peak trapping and need to cross to other hills are not properly solved, especially given the fine tuning implications of FSCO/I (thus of islands of function deeply isolated in configuration spaces dominated by seas of non function). 3: The root issue, OoL has to be bridged to access the tree, and it remains the case that there is no adequate, observationally warranted means to go from a Darwin pond or the like to cell based life by blind dynamic-stochastic forces. 4: Life, being full of FSCO/I, is full of known, reliable signs of design. 5: This includes something you spent months trying to dismiss, the Nobel Prize winning research that shows coded, algorithmic string data structure information in DNA and mRNA, used to assemble AA chains towards proteins. I put it to you this is alphanumeric, structure describing text that also is algorithmic, showing start and finite step by step instructions with halt; and, it is thus of clearly linguistic character. 6: So, we do not actually have an empirically warranted blind watchmaker account of either origin of cell based life or of body plans, but we also know that such life is full of organisation and explicit information manifesting strong signs of design. Where, 7: there is clear evidence from eminent scientists of ideological imposition on the science, making it and education based on it severely biased. KF kairosfocus

Nothing important happens here.
That appears to be getting truer by the day.
Get your Nobel at another site. Better yet, write a textbook on Evolution. It would be the first one to show how Evolution worked.
Well, that's not true. Darwin's On the Origin of Species set out the mechanism of natural selection, even though Darwin knew nothing of genomes, and opened the floodgates for evolutionary biology and molecular phylogenetics. Do you live in a cave, Jerry? Alan Fox

PPS, the key questions are begged: >>Neo-Darwinian evolutionary theory>> 1: Which appeals to chance variation and differential reproductive success leading to micro and macro level descent with modification 2: Here, the root question is set aside, OoL. >>explains>> 3: Has no empirically founded adequate explanation for origin of body plans >> how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed.>> 4: Yes, this is a designer substitute framework but one lacking adequate means to the claimed end. 5: Where as differential reproductive success is a summary of culling out, we see a subtractor of biological information here, not an adder. 6: The only actual hoped for adder of information is chance variation, grossly inadequate for reasons already highlighted. >>The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection.>> 7: Not gene replication itself but mutations, accidental changes 8: Natural selection, is differential reproductive success, a subtraction process. 9: So we are left with chance variation as proposed adder, grossly inadequate for the scale required. 10: Also, the root of the tree, the biggest question, is left out, OoL. 11: Fail. kairosfocus

Chuckdarwin @71, From your quote:
potentially explaining differences in the distribution of fitness effects of new mutations among species.
Really? "Potentially explaining"? Or maybe not explaining. The Easter bunny might "potentially explain" quantum mechanics as well. This isn't science. It's science fantasy. I wasn't surprised at all when I ran across the apparently obligatory equivocation in the original text about their assertion of the impact of their findings on the infallible (and racist, colonialist, and genocidal) Theory of Evolution. -Q Querius

CR, designers exist as an observable in a going concern world, in fact you are a designer of the text of your objection. Design and designers are therefore, necessarily, possible -- and are common, this is not a vanishingly rare esoteric matter. On observation of trillions of cases, the research question, are there signs of design is firmly empirically answerable, yes. The real problem for many objectors, is, such signs are found in the cosmos and in the world of cell based life, which opens up issues of designers inconvenient for their ideological preferences, as say Lewontin, Crick, Mahner, US NSTA and Monod showed. As for oh where did designers come from in a chain, or how did they get their capability, that is both irrelevant and answered for record. Contingent being designers with intelligence, skill and purpose can be seen, and can be seen building capability. Venter et al are showing early stages of molecular nanotech and there is no reason to doubt that technical capability will continue to grow. At more basic level, beavers design dams to match stream flow conditions. As for roots of design, you have been given outline on failure of infinite regress claims and of the possibility of necessary being reality root, which is a logic of being issue. None of such onward questions changes the validity of inference to design on reliable sign. KF PS, I pointed out precisely what I have pointed to as random in real or suggested dynamic-stochastic systems, and I have pointed out that from Plato on we have known of chance, necessity and art. In context I pointed to darwin pond or the like and the forces those looking for no design solutions have, chem, phys, thermo-d. Going to origin of body plans chance variation and differential reproductive success -- which has from Darwin on a huge chance component -- similarly is materially appealing to chance. And is natural SELECTION is valid so is natural SEARCH by random walk, kairosfocus

@KF
CR, what part of chance variation is not random?
What part have you left out from my comment? Was that random?
Evolution is not random. Mutations are random to any problem to be solved.

Do you also intend that C-Chem, cell based, aqueous medium, genes, proteins etc using life is written into the laws of physics, chemistry and thermodynamics?
No, it's not. This exact question was address in the constructor theory of life. We do not need the design of replicators to be present in the laws of physics.
Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection. In this paper I show that for those processes to be possible without the design of biological adaptations being encoded in the laws of physics, those laws must have certain other properties. The theory of what these properties are is not part of evolution theory proper, and has not been developed, yet without it the neo-Darwinian theory does not fully achieve its purpose of explaining the appearance of design. To this end I apply Constructor Theory's new mode of explanation to provide an exact formulation of the appearance of design, of no-design laws, and of the logic of self-reproduction and natural selection, within fundamental physics. I conclude that self-reproduction, replication and natural selection are possible under no-design laws, the only non-trivial condition being that they allow digital information to be physically instantiated. This has an exact characterisation in the constructor theory of information. I also show that under no-design laws an accurate replicator requires the existence of a "vehicle" constituting, together with the replicator, a self-reproducer.

In contrast, actual gene-replication is an impressively accurate physical trans- formation, albeit imperfect. But even more striking is that living cells can self-reproduce to high accuracy in a variety of environments, reconstruct- ing the vehicle afresh, under the control of the genes, in all the intricate details necessary for gene replication. This is prima facie problematic un- der no-design laws: how can those processes be so accurate, without their design being encoded in the laws of physics? This is why some physicists - notably, Wigner and Bohm, [12], [13] - have even claimed that accurate self-reproduction of an organism with the appearance of design requires the laws of motion to be “tailored” for the purpose – i.e., they must contain its design [12]. These claims, stemming from the tradition of incredulity that living entities can be scientifically explained, [14], highlight a problem. The theory of evolution must be supplemented by a theory that those physical processes upon which it relies are provably compatible with no-design laws of physics. No such theory has been proposed; and those claims have not been properly refuted. Indeed, the central problem here – i.e., whether and under what circum- stances accurate self-reproduction and replication are compatible with no- design laws – is awkward to formulate in the prevailing conception of fun- damental physics, which expresses everything in terms of predictions given some initial conditions and laws of motion. This mode of explanation can only approximately express emergent notions such as the appearance of design, no-design laws, etc. Von Neumann, who attempted to investigate self-reproduction within this framework, got as far as discovering its essential (replicator-vehicle) logic, [9]. However his use of the prevailing conception forced his analysis to be in terms of predictions: thus he attempted without success to provide the design of an actual self-reproducer in terms of atoms and microscopic interaction. He finally produced a viable toy model, [15], within cellular automata, but at the cost of severing the connections with actual physics. That model is thus inadequate to address the current problem - whether self-reproduction is compatible with the actual laws of physics un-augmented by any design of adaptations. The prevailing conception also forces a misleading formulation of the prob- lem, as: what initial conditions and laws of motion must (or must probably) produce accurate replicators and self-reproducers (with some probability)? But what is disputed is whether such entities are possible under no-design laws. More generally, it cannot express the very explanation provided by evolution- ary theory – that living organisms can have come about without intentionally being designed. It would have aimed at proving that they must occur, given certain initial conditions and dynamical laws. To overcome these problems I resort to a newly proposed theory of physics, constructor theory. [16, 17, 18]. It provides a new mode of explanation, expressing all laws as statements about which transformations are possible, which are impossible and why. This brings counterfactual statements into fundamental physics, which is key to the solution. The explanation provided by the theory of evolution is already constructor-theoretic: it is possible that the appearance of design has been brought about without intentionally being designed; so is our problem: are the physical processes essential to the theory of evolution - i.e., self- reproduction, replication and natural selection - possible under no-design laws? I shall show that they are (in section 2-3) provided that those laws of physics allow the existence of media that can instantiate (digital) information (plus enough time and energy). Information has an exact physical characterisation in the constructor theory of information [17]. I also show that under no-design laws an accurate self-reproducer requires an accurate (i.e., high-fidelity) replicator, and vice versa. Thus, the replicator- vehicle logic von Neumann envisaged is here shown to be necessary for accu- rate self-reproduction to be possible under such laws. This provides physical foundations for the relation between “metabolism” and replication (as de- fined by Dyson, [10]). In addition, that vehicles are necessary to high-quality replicators under our laws of physics (despite replicators being the conceptual pillar of evolutionary theory), informs the current debate about the necessity of organisms. The latter was recently doubted by Dawkins [19]: “ Just as life did not have to become multicellular [...] so living materials did not have to become packaged into discrete, individual organisms [..] behaving as unitary, purposeful agents. The only thing that is really fundamental to Darwinian life is self-replicating, coded information - genes, in the terminology of life on this planet.”. Constructor Theory’s mode of explanation also delivers an exact physical expression of the notions of the appearance of design, no-design laws, and of the logic of self-reproduction and natural selection. Finally, Wigner’s argument implies that accurate self-reproduction is incom- patible particularly with quantum theory, thus challenging its universality - a claim that others, with different motivations, have also made [20, 21, 22]. I shall demonstrate (in section 4) a quantum-mechanical (kinematical) model of the logic of self-reproduction, updating von Neumann’s, thus rebutting those claims. This, incidentally, clarifies how self-reproduction differs from cloning a quantum state (which has occasionally caused some confusion [20]). It also vindicates that self-reproduction - and even (possibly artificial) self- reproducers employing quantum coherence - are compatible with quantum theory.
Of course, I've posted a link to this before. What gives? critical rationalist

Kairosfocus: kindly look at the OP and the previous two. Your attempted stipulation is out of order My question, valid question, was not directed at you was it? It's fair to ask other readers of this blog if they understand and can explain one of your posts. If no one steps up to back you up then what should we conclude? JVL

CR, the causal origin of a given designer is irrelevant to the fact of recognizability of design per reliable sign.
It seems that you didn't seem to think that through very well. If the reliable recognizability of design is irrelevant of origin, then the origin of the designer of bacterium is irrelevant as well. Design recognizability would reliable in the case of the designer of bacterium, etc. critical rationalist

Querius/64 If you read beyond the headline, a couple interesting things stand out regarding the research to which you link. First, from the Baker article:
The new finding does not disprove or discredit the theory of evolution, and the researchers said randomness still plays a big role in mutations. But the study does show that these genetic alterations are more complex than scientists previously believed.
Second, from the original paper published in Nature, entitled: Mutation bias reflects natural selection in Arabidopsis thaliana (emphasis added in part):
Since mutational biases are a product of evolution, they could differ between organisms, potentially explaining differences in the distribution of fitness effects of new mutations among species. (emphasis added)
What was under consideration in the report was the occurrence and persistence of non-random "mutational biases." For our purposes, the important language from the report is that mutational biases are a product of evolution. This brings us full circle to the observation that these findings do "not disprove or discredit the theory of evolution." chuckdarwin

JVL, kindly look at the OP and the previous two. Your attempted stipulation is out of order, KF kairosfocus

The boost from molecular phylogenetics has revolutionized evolutionary biology.
If anything it has destroyed naturalized Evolution. Great for genetics.
And I’m happy to dispute the idea that evolution is bankrupt.
You are living proof that it is.
if Uncommon Descent keeps going
UD has little if anything to do with ID. Nothing important happens here. Get your Nobel at another site. Better yet, write a textbook on Evolution. It would be the first one to show how Evolution worked. jerry

d(E) plus 3-DPC + [n = 1] –> E Can anyone, other than Kairosfocus explains what this means and how it is pertinent? JVL

Jerry: And the gibberish will be answered as if it is meaningful with something that’s convoluted. What about people like you who make statements about how it's all about islands of function but then refuse to answer some basic questions about islands of function? IF you're interested in having a real substantial dialogue that is. Are you? JVL

AF, specifically, here, first principles of information and of how organisation has implicit information. Which leads to fine tuning of configuration to achieve relevant function. Where, d(E) plus 3-DPC + [n = 1] --> E This has several extensions and applications, being conceptually related to Turing Machines and automated manufacturing systems. KF kairosfocus

As I said no one wants to explore just what Evolution means and why it is bankrupt. Both sides are afraid.
This isn't right, though. The boost from molecular phylogenetics has revolutionized evolutionary biology. And I'm happy to dispute the idea that evolution is bankrupt. Subject to time available, if I'm spared and if Uncommon Descent keeps going. Alan Fox

Kairosfocus @55,
Jerry, blind, random walk natural search is a reasonable term for the dynamic stochastic, blind processes being invoked.
Just thinking about a random walk and Darwinism in terms of the Turing test, I have to agree with you. Functionally, they are identical and indistinguishable. What might be interesting is to map mutational changes to see whether they are actually random or not. If I remember correctly, some mutations are more likely than others. So unlike the sock puppets here, I looked it up and here's what I found: New study provides first evidence of non-random mutations in DNA "This goes against one of the key assumptions of the theory of evolution." By Harry Baker published January 14, 2022 https://www.livescience.com/non-random-dna-mutations Imagine that . . . LOL -Q Querius

Logic and First Principles? Right! Thanks, Jerry. BTW, you are correct in stating that the process of evolution is not a search. Alan Fox

Jerry, incoherent claims that have proved persuasive for some, are being shown to be incoherent, e.g. Xenophanes, and before him [in threads, not in history] Popper. KF kairosfocus

So we get convoluted basically incoherent diatribes or platitudes.
I should have said
So we get convoluted basically incoherent diatribes or platitudes or gibberish
And the gibberish will be answered as if it is meaningful with something that’s convoluted. QED jerry

CR, the causal origin of a given designer is irrelevant to the fact of recognisability of design per reliable sign. So, first invited error is corrected. Second, imagine Venter were to have a breakthrough and built a bacterium from scratch, that would show that he and team were highly intelligent, had adequate technology and funding etc to carry out a goal they chose, build a bacterium from scratch. Venter is a contingent designer, showing that contingent designers are possible. You were already corrected by pointing to the other class of possible beings, but obviously side stepped it. Dawkins committed a similar error. There is no implied infinite regress of contingent designers, just as the observed cosmos does not imply a transfinite past of causally successive causal temporal thermodynamically constrained stages. Indeed, per the logic that shows transfinite traverse by finite steps is an infeasible supertask, we instead know that there was a hard beginning, not from non being nor from circular retrocausation, those are absurd. We are left with necessary being at the root of reality, with capability to cause a cosmos. For simple case, try to imagine a distinct possible world without two-ness thus the number two in it, or one where twoness came into being after a time where it was not, or ceased from being while the world carried on, the absurdities speak for themselves. KF kairosfocus

@KF So, how was the functionality of the designer of bacterium reached? After all, It functions by designing organisms. critical rationalist

@ Seversky
Although this is mostly a question of semantics.
Science is not the quest to correctly define worlds. Words are shortcuts for ideas. Also, progress often takes the form of unifications. critical rationalist

what “L&FP” stand for
Logic and First Principles I stand by my assertion
There is no such thing as a search in Evolution
As I said no one wants to explore just what Evolution means and why it is bankrupt. Both sides are afraid. If it is natural, there is nothing to be afraid of for either side. But the evidence overwhelmingly says it cannot be natural. It’s actually a side show. So we get convoluted basically incoherent diatribes or platitudes. jerry

Kairosfocus, Could you just clarify what "L&FP" stand for? Alan Fox

Jerry, blind, random walk natural search is a reasonable term for the dynamic stochastic, blind processes being invoked. The underlying context of genetic and wider evolutionary search algorithms is well known, and it is obvious that fine tuned, multiple part configuration based function will come as deeply isolated islands in a configuration space. For, as random text generation exercises easily demonstrate [a case in point of d(E)] gibberish will dominate the field. The switch in rhetoric simply backhandedly reveals that the evolutionary algorithms push of years past, predictably, failed but they are not going to frankly admit to that. As for one tornado in a junkyard, the search challenge issue is that sol system or cosmos level atomic resources and time cannot get to plausible blind natural search once we have spaces of 500 - 1,000 bits of complexity. KF PS, here is Wiki as confessing on monkeys at keyboards, which i/l/o the formalism is WLOG, but tellingly reveals that blind random walk search is a significant focus, current rhetorical pretence otherwise notwithstanding:
[Wikipedia confesses regarding the infinite monkeys theorem:] The theorem concerns a thought experiment which cannot be fully carried out in practice, since it is predicted to require prohibitive amounts of time and resources. Nonetheless, it has inspired efforts in finite random text generation. One computer program run by Dan Oliver of Scottsdale, Arizona, according to an article in The New Yorker, came up with a result on August 4, 2004: After the group had worked for 42,162,500,000 billion billion monkey-years, one of the "monkeys" typed,
"VALENTINE. Cease toIdor:eFLP0FRjWK78aXzVOwm)-‘;8.t"
The first 19 letters of this sequence can be found in "The Two Gentlemen of Verona". Other teams have reproduced 18 characters from "Timon of Athens", 17 from "Troilus and Cressida", and 16 from "Richard II".[26] A website entitled The Monkey Shakespeare Simulator, launched on July 1, 2003, contained a Java applet that simulated a large population of monkeys typing randomly, with the stated intention of seeing how long it takes the virtual monkeys to produce a complete Shakespearean play from beginning to end. For example, it produced this partial line from Henry IV, Part 2, reporting that it took "2,737,850 million billion billion billion monkey-years" to reach 24 matching characters:
RUMOUR. Open your ears; 9r"5j5&?OWTY Z0d...
[ACC: Dec 17, 2019. NB: Where, also, as this is a digital age, we will readily see that we can compose a description language and then create a string of yes/no questions to specify any reasonable object -- as say AutoCAD etc do. Thus, our seemingly simplistic discussion on bit strings *-*-*- . . . is in fact without loss of generality [WLOG].] [Comment: 16 - 24 ASCII characters is far short of the relevant thresholds, at best, a factor of about 1 in 10^100. Yes, the article goes on to note that "instead of simply generating random characters one restricts the generator to a meaningful vocabulary and conservatively following grammar rules, like using a context-free grammar, then a random document generated this way can even fool some humans." But, that is simply implicitly conceding that design makes a big difference to what can be done. ]
PPS, at a more serious level, Walker and Davies are relevant to OoL and to multiverse, fluctuation models etc:
In physics, particularly in statistical mechanics, we base many of our calculations on the assumption of metric transitivity, which asserts that a system’s trajectory will eventually [--> given "enough time and search resources"] explore the entirety of its state space – thus everything that is phys-ically possible will eventually happen. It should then be trivially true that one could choose an arbitrary “final state” (e.g., a living organism) and “explain” it by evolving the system backwards in time choosing an appropriate state at some ’start’ time t_0 (fine-tuning the initial state). In the case of a chaotic system the initial state must be specified to arbitrarily high precision. But this account amounts to no more than saying that the world is as it is because it was as it was, and our current narrative therefore scarcely constitutes an explanation in the true scientific sense. We are left in a bit of a conundrum with respect to the problem of specifying the initial conditions necessary to explain our world. A key point is that if we require specialness in our initial state (such that we observe the current state of the world and not any other state) metric transitivity cannot hold true, as it blurs any dependency on initial conditions – that is, it makes little sense for us to single out any particular state as special by calling it the ’initial’ state. If we instead relax the assumption of metric transitivity (which seems more realistic for many real world physical systems – including life), then our phase space will consist of isolated pocket regions and it is not necessarily possible to get to any other physically possible state (see e.g. Fig. 1 for a cellular automata example).
[--> or, there may not be "enough" time and/or resources for the relevant exploration, i.e. we see the 500 - 1,000 bit complexity threshold at work vs 10^57 - 10^80 atoms with fast rxn rates at about 10^-13 to 10^-15 s leading to inability to explore more than a vanishingly small fraction on the gamut of Sol system or observed cosmos . . . the only actually, credibly observed cosmos]
Thus the initial state must be tuned to be in the region of phase space in which we find ourselves [--> notice, fine tuning], and there are regions of the configuration space our physical universe would be excluded from accessing, even if those states may be equally consistent and permissible under the microscopic laws of physics (starting from a different initial state). Thus according to the standard picture, we require special initial conditions to explain the complexity of the world, but also have a sense that we should not be on a particularly special trajectory to get here (or anywhere else) as it would be a sign of fine–tuning of the initial conditions. [ --> notice, the "loading"] Stated most simply, a potential problem with the way we currently formulate physics is that you can’t necessarily get everywhere from anywhere (see Walker [31] for discussion). ["The “Hard Problem” of Life," June 23, 2016, a discussion by Sara Imari Walker and Paul C.W. Davies at Arxiv.]
more on the anthropic principle from Lewis and Barnes https://uncommondescent.com/intelligent-design/hitchhikers-guide-authors-puddle-argument-against-fine-tuning-and-a-response/#comment-729507 kairosfocus

JVL (attn, Seversky et al), as I noted, if you can speak of "natural SELECTION" you can speak of "natural, blind watchmaker, random walk SEARCH," so this is not a strawman; you are putting up a needlkess rhetorical obstacle and you must know better. For, we both know there are three main causal factor categories [long since established in the days of Plato and discussed by Newton but refined since], blindly mechanical necessity, equally blind chance, intelligent purposeful action; which of course can all be at work in a situation. Thus, we have dynamic-stochastic systems and models, we have agent action including design. In the case of origin of life theorising, the chemistry and physics of a Darwin pond etc will be thermodynamically constrained and dynamic-stochastic. The natural search challenge applies and as Tour has laid out in telling detail, there is no empirically warranted blind watchmaker path to life. There is no cogent, empirically warranted evolutionary materialistic solution. Likewise, for origin of body plans, mechanisims invoked include blind chance variations [especially mutations] and differential reproductive success, which is at least partly random but is generally presented as allowing incremental hill climbing. Which is precisely why peak trapping and the challenge to cross seas of non function, thence finding shores of function are all highly relevant. Where, we both know protein fold domains are deeply isolated in AA sequence space, more broadly configuration spaces are dominated by gibberish [ i.e. d(E) will naturally come as islands], and at body plan, macroevolutionary level the trade secret of anthropology is that fossil forms show systematic gaps and sudden appearances. It is the smoothly branching and growing tree of life model that is a simplistic icon. For cosmology, fine tuning is a serious challenge. So, resort to long since cogently answered objections simply exposes that the evolutionary cupboard is bare. KF kairosfocus

Seversky @52,
Correct me if I’m wrong, but no evolutionary biologist has ever argued that a single tornado passing through a junkyard of aircraft parts could ever assemble a Boeing 747.
So, which is more complex: a Boeing 747 or a living cell? Within 3 billion years, could ANY human machine be randomly assembled from undirected evolutionary processes including random mutation (removal or addition) and natural selection (i.e. pitilessly indifference to the survival or extinction of any machine that might emerge) over that period of time? -Q Querius

Correct me if I'm wrong, but no evolutionary biologist has ever argued that a single tornado passing through a junkyard of aircraft parts could ever assemble a Boeing 747. There was no disagreement between them and a certain physicist. As far as I'm aware, no evolutionary biologist has ever claimed that a complex modern organism, organ or protein - something that requires upwards of 500 bits of information to specify - is likely to be found on a single-pass search through the universe of all possible configurations within the current lifetime of our Universe. All agree that it would be so improbable as to be effectively impossible. Understanding this, evolutionary biologists all the way back to Darwin have argued that, if life arose from inanimate precursors, it would most likely have been through a process of tiny, incremental steps occurring over vast periods of time. When you criticize the improbability of the "tornado in a junkyard" or FSCO/I scenarios you are attacking positions that no evolutionary biologist holds or is concerned with defending. They are strawmen. What appears to be the problem is that people with a teleological mindset find it difficult to grasp that evolution is not searching for pre-determined targets and it is pitilessly indifferent to the survival or extinction of any organisms that might emerge, including us. If we want to survive and thrive we might do well to find a common purpose for ourselves rather than rely on some other intelligence (including artificial) to do it for us. Seversky

Sandy/45 Edited for clarity ...
How dare you contest intelligent design creationism. “God did it" is dogma so doesn’t matter if there is no scientific evidence. Creationist belief must be true and is true …because I want to be true … I need it to be true!
Seversky

Sandy @45,
How dare you to contest materialist teology. “Creative” Darwin’s pond is a dogma so doesn’t matter if there are no scientific evidences , materialist dogma must be true and is true …because I want to be true.
Direct hit! Your observation is supported by a conspicuous lack of ANY substantive scientific information within the flood of vacuous comments by a certain persistent Darwinist and ALL his sock puppets! -Q Querius

Jerry: It would be easy to explore just what it means but no one here is interested in understanding. Strangely enough I asked you a couple of questions a few posts back, so I could better understand your view. But you ignored them. JVL

There is no such thing as a search in Evolution. The use of the term is a metaphor for variations changing part of the genome and the new organism’s position in protein space is then slightly different. It would be easy to explore just what it means but no one here is interested in understanding. They want to attack each other over meaningless and irrelevant issues. By doing so each side has indicated how little they know. But we already know they know very little. jerry

Do you ever trace IP addresses?
I have a website and used to look at the data of those visiting the site. It didn’t list email addresses but did identify the location of the server. Of course I wasn’t interested in who they were just where my web traffic was coming from. But for UD, there does seem to be a conflation of like minded people in short time spans periodically over the last few years. My guess they are friends or internet buddies. jerry

Sandy: How dare you to contest materialist teology. “Creative” Darwin’s pond is a dogma so doesn’t matter if there are no scientific evidences , materialist dogma must be true and is true …because I want to be true. Nice screed. But, do you have an actual scientific argument to present opposing unguided evolutionary theory? JVL

Kairosfocus darwin pond
How dare you to contest materialist teology. "Creative" Darwin's pond is a dogma so doesn't matter if there are no scientific evidences , materialist dogma must be true and is true ...because I want to be true. :) Sandy

JVL@42, I couldn’t have said it better. If you can’t soundly argue against the evidence for a scientific theory, redefine the theory in a way you can dispute. Ford Prefect

Does someone want to take a stab at translating comment 41? KF lost me at AF..... chuckdarwin

Kairosfocus: system resources will be grossly inadequate to carry out plausible search It's time to stop this straw man attack against what unguided evolutionary theory is saying. There is no need to do some kind of search in a configuration space. Start with a very simple, very basic replicator, much shorter than you 500 bits. Allow it to replicate with occasional errors (including duplication of some sections of the heritable material) and introduce a non-random weeding process. There is no search. There are no islands of function because there is a path from every life form to every other life form. All of this has long since been shown, the denialism we see is just a back handed admission of no empirically backed answer. This has NOT been shown. It's your assumption of how life forms came about. You're not even arguing against the main tenets of unguided evolutionary theory. You're arguing against some perverted version of it that you have created in your mind. A version that no one is backing or supporting. At least have the basic human decency to actually address what the real arguments are. JVL

AF (& attn bCR and CD, also AF's FP et al), after months of denial of the empirically grounded, Nobel Prize winning work, that established the presence of symbolic, algorithmic code in DNA and mRNA, you are of negative credibility. This OP builds on a formalism that identifies per Kolmogorov-Chaitin complexity, a compact description d(E) is informationally equivalent to a functionally specific, complex, organised entity E, by way of, having produced a description d(E) a 3-D Printer-Constructor can create a fresh copy. Once d(E) is compact, comparable to Kolmogorov minimum length, length of d(E), esp. in bits, is an estimator of the associated information in organised entity E. Of course, in cases such as AA chain assembly code toward building proteins, information is already explicitly present. Functionally specific, complex organisation and/or associated information is valid, period. Further to this, complex, configuration based function depending on correct arrangement, orientation and coupling of parts will take up a narrow zone in a space of possible configurations, thus FSCO/I is naturally associated with fine tuning. Thus the metaphor, islands of function in a much larger sea of non function is patently valid. While, arguably incremental hill climbing by random walk and selection of superior function can happen within such an island, peak trapping is an obvious challenge. Which is what the OP for cause highlights. Further, starting at the equivalent of a darwin pond, the dominant natural blind search challenge will be to find shorelines of function. Where at 500 bits complexity, Sol system resources will be grossly inadequate to carry out plausible search, and it is worse for cosmos scale resources with 1,000 bits. All of this has long since been shown, the denialism we see is just a back handed admission of no empirically backed answer. KF kairosfocus

Kairowfocus @9,
FP is one of a circle of personas tracing to a common email.
That's disgusting. So, I presume that Ford Prefect arranges interesting conversations with his sock puppets. Is there a limit on how many UD accounts can use the same email? Do you ever trace IP addresses? -Q Querius

Another comment that show’s he hasn’t a clue about what he believes. Says one thing then essentially denies it a few comments later.
QED! :) Alan Fox

Andrew at 19, He could always post on cooking sites. :) relatd

CR, what part of chance variation is not random? Do you also intend that C-Chem, cell based, aqueous medium, genes, proteins etc using life is written into the laws of physics, chemistry and thermodynamics? Recall, the root of the tree of life is the first question. Beyond, the complex integrated functional organisation and information for body plans has to be accounted for. These are full of Orgel-Wicken FSCO/I and the only actually empirically warranted source is intelligently directed configuration. Where, the OP poses an onward challenge, peak trapping even on hill climbing within a fitness -- functional superiority/inferiority -- landscape, so called. KF kairosfocus

And much more.
no, actually much less. Another comment that show’s he hasn’t a clue about what he believes. Says one thing then essentially denies it a few comments later. People on both sides just mouth things here and never think them through. jerry

I see there's a mangled comment of mine upthread. Too late to edit now. It was to Jerry so it is probably not worth rewriting Alan Fox

Naturalized Evolution has to leave a trail in the genome. There is no trail. Why?
Of course there is. Since cheap and rapid gene sequencing, comparison of genes across species has enabled molecular phylogenetics to construct trees of relatedness that match trees produced solely by comparative anatomy. And much more. Alan Fox

Contact restored! I lost it after my previous post. Seversky

Jerry: it’s islands of function. So, give an example of an island of function in biology. Then we'll have a better idea of what you're talking about. Also, a strict definition of an island of function would be useful. Naturalized Evolution has to leave a trail in the genome. There is no trail. What kind of trail are you looking for? Not like a list of changes in a Word document surely. JVL

All is easily determined. Neither side understands the issues and how to test. Instead they both make irrelevant comments. Been presented number of times. Both sides ignore. Never even ask questions or comment except Ann Gauger once who understood the issues. Clue: Naturalized Evolution has to leave a trail in the genome. There is no trail. Why? jerry

Hint: it’s islands of function. And the question always has been whether these islands are attainable. How do I know of the ignorance? By the comment on gene duplication. An incredibly stupid comment.
Jerry, you're the Greek Chorus. Genes and genomes do gend up getting Alan Fox

FP, again, ducking, start from a Darwin pond or the like and get around the fine tuning of complex, configuration based function. The insubstantiality of your dismissiveness speaks volumes. KF kairosfocus

Needle in a haystack, FSCO/I and islands of function are all based on mischaracterizations of how evolution works. GIGO. Ford Prefect

AF, first, we start in a darwin pond or the like, and you have no viable path to complex function, this extends to origin of body plans. The telling sign is we do not see the linked massive documentation and Nobel Prizes. Tour is right. KF kairosfocus

"Uncommon Descent, its history and evolution, fascinates me from a sociological perspective." AF, Ah. Well, you also like to participate. Obviously. Do you think you are conducting an experiment with your stinky cheese? Andrew asauber

FSCO/I and “islands of function” are essentially variations on the Hoyle’s Fallacy theme…
Needle in a haystack, too. Alan Fox

It also seems to me that FSCO/I and "islands of function" are essentially variations on the Hoyle's Fallacy theme... Seversky

Does that mean you’re going to spend your days on something else you aren’t interested in instead?
Uncommon Descent, its history and evolution, fascinates me from a sociological perspective. Alan Fox

It’s real enough…… :-) chuckdarwin

Testing, testing, testing ... How do you get a dead horse to an island of function? You're going to need a pretty big canoe I'd have thought. Knowledge is subjective in that it requires the existence of a "knower", otherwise we're talking about "information" or "data". Although this is mostly a question of semantics. And is the surfboard real? Seversky

KF/10 "CD, the challenge is to get to shorelines of function. KF" I don't know about anyone else, but I'm already there, at the beach on the island of function. Surf's up... chuckdarwin

"I can foresee an even more noticeable waning of interest in ID." AF, Does that mean you're going to spend your days on something else you aren't interested in instead? Andrew asauber

with the chance of stumbling on novel functionality.
Obviously way behind on what’s behind what he believes. This comment alone points to ignorance. First, what the islands of functionality actually means as one stupid comment after the other gets made. Second, what’s behind naturalized Evolution. On the latter, Alan Fox just demonstrated he is completely unaware of the theory for naturalized Evolution. Hint: it’s islands of function. And the question always has been whether these islands are attainable. How do I know of the ignorance? By the comment on gene duplication. An incredibly stupid comment. Aside: neither side of the debate know what they are talking about. Aside2: We also get nonsense comments on natural selection illustrating commenters haven’t a clue what they are talking about. jerry

@KF Evolution is not random. Mutations are random to any problem to be solved. Active information can be more fundamentally be expressed a information that plays a causal role in being retained when embedded in a storage medium. Knowledge is objective. It can exist and grow outside knowing subjects. living things are vehicles for genes, which are replicators. Natural selection prefers genes that make their way into the next generation. This does not necessary mean the vehicle (living thing) cannot become less fit in the process. Again, this is part of von-Neumann's replicator-vehicle model of replication. You know, the thing you keep reminding us of. Apparently, living things are von-Neumann's replicators, but only when it's convenient for you? It has consequences, except when it doesn't. That is to say when the consequences of it having consequences suit your purpose. critical rationalist

I used to enjoy Denyse's eclectic science news posts. They were often how I would first hear of new developments. Eric was quite good in following that tradition. If all UD is going to have as new OPs is L & FPs from KF, I can foresee an even more noticeable waning of interest in ID. Alan Fox

And what has happened to Eric Hedin/Caspian/News? From posting OPs at least daily to nothing since 23rd March. Are you OK, Eric? Alan Fox

The main issue in the Evolution debate has always been the origin of proteins.
Gene duplication happens. A lot. Whole genome duplications even. Duplication introduces redundancy. An extra copy of a gene, being redundant, is not under purifying selection, allowing neutral mutations to accrue with the chance of stumbling on novel functionality. Alan Fox

...the challenge is to get to shorelines of function.
The real challenge is to work out what KF is thinking of. What is analogous to a "shoreline" in evolutionary biology. Anyone have a clue? Alan Fox

Good grief, by the way. ;) Set up a poor analogy as a straw-man and attack! The niche environment is not a fixed landscape. Aspects of the niche can change slowly, rapidly, instantaneously. Alan Fox

L & FP? What do the letters stand for. Alan Fox

CD, the challenge is to get to shorelines of function. KF kairosfocus

FP is one of a circle of personas tracing to a common email; I note this because of his doubling down on snideness despite warnings in previous threads. It is thus, sadly, unsurprising to see personalities and mocking dismissiveness in reaction to something as commonplace as that you had better put together your car transmission parts correctly or it will not work. Similarly, arbitrary random chains of ASCII characters vastly outnumber those that make grammatically correct meaningful English text or those that with slight correction would do so. The same, for computer software. The same for DNA, which expresses coded algorithmic genetic information, and can be repurposed for archival store [including a documented case of 16 GB for Wikipedia's content in English]. These are examples, of course, of the fine tuning required to set systems to operating points. More to the point, the OP above expresses an operational-in-principle process by which we can come to understand such fine tuning and related phenomena such as peak trapping. None of these are incoherent or ill founded, just, they do not feed into the dominant, too often domineering evolutionary materialistic scientism narrative and/or those of its fellow travellers. Fine tuning in a configuration space [so, islands of function amidst seas of non function as is illustrated in the OP] is real, is a common place and obviously runs counter to a preferred narrative. Notice, dismissiveness not substantial correction on demonstration of continents of incrementally accessible, complex function. KF kairosfocus

Our daughter was conceived on the island of function. After, and maybe during, several nights on the island of sexual pleasure. Followed by time on the islands of fear, terror, worry, apprehension, delight, pride and joy. Interspersed, thankfully, with countless additional evenings on the island of sexual pleasure. And hopefully there will be many more evenings on the island of sexual pleasure. I really can’t under-emphasize the importance of spending as much time as you can on the island of sexual pleasure. But I digress. My experience is that there is an island for everything. But, like KF’s islands of function, they are poorly articulated analogies based on weak assumptions. Ford Prefect

Life is a beach on the island of function……. :-) chuckdarwin

The great and powerful OZ speaks:
FP, the “corrections” have been grossly wrong.
Watch out for that little dog. He may pull aside your curtain. Ford Prefect

The main issue in the Evolution debate has always been the origin of proteins. One unlikely way that a new functional protein comes into existence is the possibility that a current protein/gene sequence is modified by the numerous variation processes. This requires that the functional protein is nearby in protein space or that a frame shift throws the new protein into a faraway position that is functional or near a functional protein. Thus, the search analogy. Highly unlikely to happen. Aside: Darwinian Evolution is extremely silent on how new proteins arise from what is essentially genetics. jerry

Kairosfocus @1, Seems to me that Michael Behe made a similar point in one of his books. Darwinism seems to be based primarily on morphology rather than genetic tracing. This sets up the fitness peak trap. I'd also note that the presumed fitness advantage is believed to be very slight according to Haldane and his successors. -Q Querius

FP, the "corrections" have been grossly wrong as for FSCO/I, many parts, properly oriented and arranged need to be coupled to yield function. That is classic Goldilocks just right fine tuning. Start with the text of your objections as a case in point, noting on the 3-DP/C formalism that discussion on strings is WLOG. KF kairosfocus

You have been corrected on your islands of function analogy on numerous occasions, yet you continue to beat this dead horse. Ford Prefect

L&FP, 71: The island of function, fitness peak trap kairosfocus

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