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

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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
April 11, 2023
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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
April 10, 2023
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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
April 10, 2023
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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. -QQuerius
April 10, 2023
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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
April 10, 2023
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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 . . . ?) KFkairosfocus
April 10, 2023
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JVL, you are sidestepping a whole list. That tells us a lot. KFkairosfocus
April 10, 2023
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Mind you, in Tono-Bungay, he does make up for it to some extent, with Marion, Effie, and Beatrice.Alan Fox
April 10, 2023
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...we men, the creatures who inhabit this earth...
Hmm. I think Wells was overlooking something.Alan Fox
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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_Ikn84ZUdcbornagain77
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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AF, have you heard of redemption and life rescue? If not, kindly pay a visit to say the Salvation Army or to Teen Challenge. KFkairosfocus
April 10, 2023
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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. KFkairosfocus
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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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
April 10, 2023
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Seversky at 206, And I've got photos of my alleged great, great, etc. relatives as lemur-like creatures.relatd
April 10, 2023
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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
April 10, 2023
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