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Real Time Evolution “Happening Under Our Nose”

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A couple of weeks ago a friend forwarded me a link to this recent article about “ongoing research to record the interaction of environment and evolution” by University of California, Riverside biologist David Reznick. Reznick’s team has been studying adaptive changes in guppies. Reznick’s work focuses on tracking what happens in real-world situations in the wild, rather than the somewhat artificial environments in the lab. As a result, Reznick has gathered some of the more trustworthy and definitive data about changes over time in a real-world environment, largely free from the intervention and interference of the coated lab worker.

The article states:

The new work is part of research that Reznick has been doing since 1978. It involved transplanting guppies from a river with a diverse community of predators into a river with no predators – except for one other fish species, an occasional predator – to record how the guppies would evolve and how they might impact their environment.

In the recent follow-up research, Reznick’s team studied “how male color pattern affected” their differential survival in the environment. Significantly, the team even gathered DNA from the guppies over time to track who their parents were and reconstruct a guppie pedigree to help determine the reproductive success. Without going into all the details, which are interesting in their own right, the key point for my purposes today is that this adaptive change occurred extremely quickly.

Graduate student, Swanne Gordon, noted,

Our research shows that these fish adapted to their new habitats in less than one year, or three to four generations, which is even faster than we previously thought.

Reznick adds,

People think of evolution as historical. They don’t think of it as something that’s happening under our nose. It is a contemporary process. People are skeptical; they don’t believe in evolution because they can’t see it. Here, we see it. We can see if something makes you better able to make babies and live longer.

What Really Happened?

Now normally when my friend forwards a link, I will just review the article, realize it is making claims beyond the data, and move on. But coincidentally, just days earlier I had been reading Chapter 7 of Lee Spetner’s 1998 book, Not by Chance!

Part of Spetner’s argument is that many adaptive changes we see in nature are in fact not examples of a Darwinian process of chance changes + natural selection, but instead the result of specific programming capabilities in the organism to allow it to respond to changes in the environment. Indeed, what caught my eye about the article my friend forwarded is that Spetner had discussed Reznick’s earlier experiments in that very context.

After describing two different predators of the guppies: (i) the cichlid, which prey on large mature guppies; and (ii) the killfish, which prey on small immature guppies, Spetner continues:

Reznick and his team took 200 guppies from the Aripo [river in Trinidad] and put them in a tributary of the river that is home to the killfish but has no cichlids and had no guppies. Changes soon appeared in the newly introduced guppies. The fish population soon changed to what would normally be found in the presence of the killfish, and Reznick found the changes to be heritable.

The full change in the guppy population was observed as soon as the first samples were drawn, which was after only two years. One trait studied, the age of males at maturity, achieved its terminal value in only four years. The evolutionary rate calculated from this observation is some ten million times the rate of evolution induced from observations of the fossil record [Reznick et al. 1997].

Reznick interpreted these changes as the result of natural selection acting on variation already in the population. Could natural selection have acted so fast as to change the entire population in only two years?

Spetner goes on to argue that the adaptive change observed in the guppies is more likely the result of a programmed response to environmental change, and provides several examples of such changes in other species.

Where is the Darwinian Evolution?

Darwinian evolution, as we know, is supposed to work by natural selection weeding out random variation. The Neo-Darwinian model has traditionally gone a step further, suggesting that those random variations are genetic in nature — taking place in the DNA as a copying error here, a misplaced sequence there, an accidental cut-and-paste elsewhere . . .

So the question arises: do the kinds of rapid, adaptive, reversible changes Reznick observed owe their existence to this kind of Darwinian process, or are they the result of a pre-programmed genetic response to environmental changes?

Spetner makes a good argument that we are observing the latter. He goes on to show that even many of the classical examples of Darwinian evolution — you know, the examples of random mutation + natural selection that even most evolutionary skeptics have tended to accept: convergent “evolution” of plants in similar environments, the “evolution” of bacteria to live on lactose or salicin — are not good examples of Darwinian evolution at all. Even that icon of icons, finch beaks in the Galapagos, is likely not a good example of the alleged Neo-Darwinian mechanism of random mutation + natural selection.

All of this prompts me to ask a simple, but pointed, question:

How many good examples are there of Darwinian evolution?

The more research I do the more I come to the same conclusion Spetner did, namely that most adaptive changes are not the result of the random, purposeless changes Darwinian evolution posits as the engine of biological novelty.

Even skeptics of the grand evolutionary claims tend to accept, either specifically or implicitly, that Darwinian evolution can produce all kinds of minor adaptive changes, the so-called microevolutionary changes: variations in finch beaks, insect resistance to insecticides, coloration of peppered moths, and so on. And indeed, the “selection” side of the formula seems to work well, which is simply the somewhat pedestrian observation that if an organism is poorly adapted to its environment it has a poor chance of surviving.

Yet the engine of the novelty, the alleged random variation that is supposed to provide all this adaptive variability on which selection can work its magic, seems stubbornly absent. Even these most common of examples, on closer inspection, do not support the Darwinian claim. Thus the doubts multiply. If Darwinian evolution cannot even claim explanatory credit for things like bacteria being able to metabolize lactose, what can it explain? The more closely we look, the more anemic the Darwinian claim becomes.

Now we could be intellectually lazy and call every adaptive change we observe an example of “evolution.” But the problem with observing a change and claiming that we have observed “evolution” is that (i) we rob the word of explanatory value if it is applied indiscriminately, and (ii) we trick ourselves into thinking we have an explanation for what occurred, when in fact we have have no idea what is happening at the molecular level or the organismal level to produce the change. Claiming that we are witnessing “evolution” in such circumstances becomes then not so much an explanation as a confession of ignorance.

Real Darwinian Evolution

There are no doubt quite a number of legitimate, confirmed examples of random mutation + natural selection producing an important biological effect. For example, I think Behe’s review of malaria/sickle cell trait is a legitimate example of Darwinian evolution in action. And the circumstances of that example are rather telling: (a) large population size, (b) meaningful amount of time, (c) very strong selection pressure, (d) and change that can be caused by one or two single-point mutations.

If we see adaptive change outside of these parameters — small population, short timeframe, an adaptation that requires significant genetic change — we might be better served to suspect that we are witnessing a programmed adaptive response, rather than Darwinian evolution. And rather than being naively impressed with the great power of Darwinian evolution to act more rapidly than anticipated, we should be prompted to look deeper to find what is actually taking place.

Your Turn

In addition to the malaria/sickle cell example, what other examples of legitimate, confirmed Darwinian evolution can you think of?

Comments
Eric Anderson @ 352- Here it is: In 1997 “Not By Chance” by Lee Spetner was published. In it he argued for a “non-random evolutionary hypothesis” which had a mechanism of “built-in responses to environmental cues” at its heart. Some mutations happened just when they were needed. And some happened at just the right place to be effective. And even others, called transposons aka jumping genes, carried within its DNA coding sequence the coding for two of the enzymes required for it to be able to move around.
A transposon has in it sections of DNA that encode two of the enzymes it needs to carry out its job. The cell itself contributes the other necessary enzymes. The motion of these genetic elements about to produce the above mutations has been found to be a complex process and we probably haven't yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and as well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of variation for evolution were point mutations, we could say the variation is random. But if the source of variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events. Dr Lee Spetner "Not By Chance" page 44
Barbara McClintock was laughed at when she elucidated her discovery of jumping genes for the simple reason they have the characteristics of being under some control. The “non-random evolutionary hypothesis” applies to individuals- individuals do evolve, ie change at the genetic level. Enter 2006 and the publication of “Evolution in Four Dimensions” by Eva Jablonka and Marion J. Lamb and the elucidation of epigenetics, ie “built-in responses to environmental cues”. I couldn’t stop thinking about “Not By Chance” wondering if Lee Spetner had read it and if he felt vindicated by it. Organisms are designed with different levels of possible variation. For example there is a possible variation with how the existing genes get expressed and another is changing the actual genes such that it changes the proteins. Change the regulation of the gene or change the gene itself. Lenski’s E. coli changed the regulation of a gene by duplicating it and putting it under control of a promoter that allowed for it to be expressed in an aerobic environment. It was an environmental factor, the presence of O2, which repressed the gene. It was another environmental factor, the presence of citrate, which made getting that gene expressed beneficial. “Evolution in Four Dimensions” is a good book to have around. They describe experiments of microsurgery on Paramecium. A piece of the cortex was cut out, rotated 180 degrees and reinserted. The offspring inherited the change. Lamarck 101. Then came 2011 and the publication of “Evolution: A View from the 21st Century” by James A. Shapiro (a colleague of Dr. McClintock) and even more support for the “non-random evolutionary hypothesis” and “built-in responses to environmental cues”. Again I wondered about Dr Spetner and if he was reading this book too. The book starts out talking about “Sensing, Signaling, and Decision Making in Cell Reproduction” and has a table of “Examples of Targeted Genetic Engineering”. Of course he thinks it all evolved because obviously that is what evolution does or maybe due to coercion from fellow U Chicago Professor Jerry Coyne that is what he had to say to prevent being attacked. But I digress, the book is well worth the read and there is evidence that some mutations happen just when they are needed. They are not random with respect to fitness; it is the organism doing some rearranging to stay fit. In 2014 Lee Spetner’s “the Evolution Revolution”- Why Thinking People are Rethinking the Theory of Evolution” was publisged and although he doesn’t cite “Evolution in Four Dimensions” he does cite Jablonka’s work on epigentics. He does cite both Shapiro’s work and the book “Evolution: A View from the 21st Century”. Moving along Lee Spetner cites several cases in which evolution happened much too rapidly to be accountable for genetic accidents and have all the appearances to have been triggered by the environment: 1- Studies on daisy and daisy-like plants and their seed dispersal mechanisms. On the mainland the seeds are packaged such that the wind can carry them great distances- little white fluff-balls floating endlessly on a warm summer’s breeze. But on a small island that isn’t a good strategy. Once transplanted from mainland to small island they lose that seed-dispersal ability in just a few years – Cody & Overton (1996) “Short Term Evolution of reduced dispersal in Island Plant Populations” Journal of Ecology 84(1): 53-61 2- Rhagoletis pomonella- went from feeding solely on hawthorn, to apples and onto cherries, roses and pears. Studies show the hawthorn and apple flies differ genetically 3- Guppies- Cichlid fish prey on large mature guppies and killifish prey on small immature guppies. When cichlids are their main predator in the environment the guppies mature earlier and have many small offspring which evade the cichlids. When killifish are their main predator the guppies mature late and have fewer but larger offspring which can evade the killifish. He cites several papers that have Reznick as one of or the main contributor 4- Lizards and rapid evolution- Losos (2001) “Evolution: A Lizard’s Tale” Scientific American 284(3): 64-69; Losos and Schoener (1997) “Adaptive differentiation following experimental island colonization in Anolis lizard” Nature 387: 70-73; and other articles by Losos and/ or Schoener 5- Finches- Lee Spetner was here on UD and posted this one See here He reiterates his hypothesis is different in that with his individuals do evolve ----- EA: Posted as a new head post here: https://uncommondescent.com/evolution/spetners-non-random-evolutionary-hypothesis/Virgil Cain
October 25, 2015
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And yet nature forms stars and planets and galaxies and rivers and clouds and storms and crystals, conforming to all sorts of rules.
And yet nature couldn't have formed nature.Virgil Cain
October 23, 2015
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EugeneS: A 6-th year school child can distinguish between the rules of a game and the laws of nature. Rules of a game are a group of principles governing conduct when playing, especially competitively. Laws of nature are observed regularities in the physical world.Zachriel
October 23, 2015
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Zachriel #374, Pathetic. A 6-th year school child can distinguish between the rules of a game and the laws of nature.EugeneS
October 23, 2015
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EugeneS: And I explained why many times: because inanimate nature does not care about rules of behavior. And yet nature forms stars and planets and galaxies and rivers and clouds and storms and crystals, conforming to all sorts of rules. EugeneS: For a snooker ball on a horizontal plane, nature cannot distinguish between different points on the plane: any point is a point of equilibrium for the ball. Sure, and planes and equilibriums and and rolling objects exist in nature. So? You still haven't made an argument. You just reword your claim.Zachriel
October 23, 2015
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Yes, it is my belief. Yes, it seems obvious to me. And I explained why many times: because inanimate nature does not care about rules of behavior. For a snooker ball on a horizontal plane, nature cannot distinguish between different points on the plane: any point is a point of equilibrium for the ball. These equilibrium states are called indifferent, Zachriel. Welcome to secondary school physics. When you integrate the equations of motion, a constant enters the equation. The presence of this constant is another manifestation of the same indifference. However, human intelligence can distinguish between the indifferent equilibrium states. Exactly by imposing rules. E.g. by drawing cells on the snooker table and assigning different utility values to different cells. The consumer unit switch is acted upon by the same physical forces regardless of whether it is ON or OFF. Nature does not care whether electric current flows through the wire. It takes intelligence to build rule-based material systems generating utility. "Fundamental logic can be expressed mechanically with a few simple processes." You always appeal to simplicity. A = A, Zachriel, so what? What processes? How many exactly? How simple? What is 'simple'? What is 'mechanical'? What is 'expressed'? What is 'fundamental'?EugeneS
October 23, 2015
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EugeneS: You still don’t get the issue: physicality cannot be responsible for the logic of rules. Fundamental logic can be expressed mechanically with a few simple processes. EugeneS: The inability to understand the issue is not an argument. It's not an argument, but a claim. It seems obvious to you, so you think merely stating the claim is sufficient, but it's not. It's just rewording of your belief.Zachriel
October 23, 2015
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Zachriel, "Molecules act like something all the time." You deliberately conflate the different meanings. I have reason to believe you are doing it knowingly. "It’s a key feature of extant life, but most researchers believe the translation system evolved from a simpler system. You are attempting to rule out such an evolutionary history a priori, but invoking woo is not an argument." I don't care what somebody believes. The world is full of strange people. If there were stupid researchers who would wish to experimentally disprove the validity of the 2nd law, why should I care even if they were in a majority?! You still don't get the issue: physicality cannot be responsible for the logic of rules. Indeed, physicality itself is logical, due to the laws of nature. It is here that you want to deliberately conflate the definitions. Nonetheless, physicality cannot be responsible for the appearance of logic that is incapsulated in material systems in the form of rules of behaviour on top of the laws of nature. The only thing physicality can do as regards rules, is allow them to be loaded into material systems, which it does. The inability to understand the issue is not an argument. Calling it strange names such as 'emergence' is not an argument either. If you want to consider it a claim, you are free to do so. This claim is based on evidence. And it is as strong as the 2nd law. The logic present in material systems in the form of rules is not an emergent property of matter simply because physicality is indifferent to it. I stand by it. You have no evidence to the contrary. You can choose to remain ignorant. I cannot help, it is your choice. But from your responses I can see you have a lack of understanding. The real problem is that you prevaricate. It blocks you from being able to understand it.EugeneS
October 23, 2015
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It’s a key feature of extant life, but most researchers believe the translation system evolved from a simpler system.
1- There isn't any evidence for a simpler system 2- There isn't any evidence that today's system could evolve via drift and natural selection from a primitive system 3- There isn't any evidence that drift and natural selection can produce a simpler system.Virgil Cain
October 23, 2015
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Upright BiPed: First Off, I was having a little fun That's fine. We took the discussion back to the original claim. Upright BiPed: So I answered you: “there’s not one; that’s the whole point. In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.” That wasn't the claim, but that “You still need a logical, non-physical formal protocol before your molecule can act like something.” Molecules act like something all the time. Upright BiPed: You left out this entire point: In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated. Indeed, we directly answered by saying it could evolve from simpler relationships, which you ignored. Upright BiPed: yawn EugeneS: The fact that there is no single physical link between RNA and polypeptide is one of the key enablers of life. It's a key feature of extant life, but most researchers believe the translation system evolved from a simpler system. You are attempting to rule out such an evolutionary history a priori, but invoking woo is not an argument.Zachriel
October 23, 2015
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Zachriel, Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”? I am sure UB is right. You have not got a clue what the problem is. That is the whole difference! In chemical reactions or physical interactions, there is no protocol in the same sense as there is one in the RNA translation system. The whole point is that there is physical discontituity between RNA codons coming in and the polypeptide coming out. If there was a single deterministic law-like necessary physical link between the RNA and the polypeptide, there could only be produced at best a single identical regular low-information polypeptide sequence every time regardless. In reality, a single cell produces of the order of 400 different proteins. It is this discontinuity between the trigger (data) and the effect (the processor processing the data) that enables information processing in any physical system not necessarily RNA translation. Without it, there would be produced only redundant low-informational regular structures like crystal lattice that are entirely due to the laws of nature (minimum potential energy). The rules of translation are categorically not the same as the laws of nature. The fact that there is no single physical link between RNA and polypeptide is one of the key enablers of life. The physical discontinuity makes it possible to front-load a protocol into the physical system and make it a physical system executing rules. Rules are logical relations between the trigger(s) and the effect(s) of the trigger. It is only in this type of material systems that information transfer becomes at all possible. The rules of RNA translation are irreducible to the laws of nature in exactly the same way as the phonemes of a human language are irreducible to sound waves the vocal chords produce. Likewise the rules of chess are irreducible to the laws of the motion of chessmen. I think you have a gap in understanding here you need to close yourself.EugeneS
October 23, 2015
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Such a system can evolve from simpler relationships.
yawnUpright BiPed
October 22, 2015
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The claim was “You still need a logical, non-physical formal protocol before your molecule can act like something.” So water molecules can’t act “wet” unless there’s a logical, non-physical formal protocol.
You’ve lost your place. Let me help:
UB: Eugene, for all your efforts, you’ll be comforted to know in Zachriel’s world, oxygen represents rust in the presence of iron. Zachriel: Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”?
First Off, I was having a little fun with you repeatedly saying RNA can act as memory and catalyst and always pushing research that involves an entirely different physical event than the translation of DNA into protein. In their key physical features, these two processes have absolutely nothing in common, and one has no means to produce the kinds of effects that the other produces. Your favored scenario has neither representations nor the translation of representations. Hence, the little comment about oxygen representing rust to iron. But then you asked me to tell you where there’s a protocol in the formation of rust. So I answered you: “there’s not one; that’s the whole point. In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.” And then you avoided that answer in your last response. You left out this entire point: In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated. That was the clarification that you asked for, but I supposed you’ve read Joyce, as I have, and you’re already aware that the product of that system is entirely determined by the properties of the RNA you are calling “memory”, and this is most likely why you made that silly comment about water being wet. Either that, or you actually don’t have any idea what the issues are. Either way, it doesn’t really matter. This is particularly true if all you can do is repeat the mantra “RNA can act as a memory and a catalyst”. It’s irrelevant to the process - in fact, it’s the very limitation that translation does away with. You can’t prescribe a protein from the dynamic properties of nucleotides. That's why the cell doesn't do it that way.Upright BiPed
October 22, 2015
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Upright BiPed: there's not one; That's the whole point. The claim was "You still need a logical, non-physical formal protocol before your molecule can act like something." So water molecules can't act "wet" unless there's a logical, non-physical formal protocol. Upright BiPed: In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated. Such a system can evolve from simpler relationships.Zachriel
October 22, 2015
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OT: I wonder who sent in the questions that led to this episode of ID the Future. ID Inquiry: Jonathan Wells on Codes in BiologyMung
October 22, 2015
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Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”?
Zach, there's not one; that's the whole point. In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated. Welcome to 1958.Upright BiPed
October 22, 2015
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Eugene,
Zachriel has not got a clue.
One would not need to look any further than #360 to see that.Upright BiPed
October 22, 2015
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Oxygen acts on iron to create rust.
Oxygen alone is not sufficient to cause rust.Virgil Cain
October 22, 2015
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Upright BiPed: oxygen represernts rust in the presence of iron. Good example. Oxygen acts on iron to create rust. What is the "logical non-physical formal protocol"?Zachriel
October 22, 2015
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UB, Zachriel has not got a clue. Clouds are talking to rivers, rivers talking to stones. The pansemiotic world of Zachriel :) ESEugeneS
October 22, 2015
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Eugene, for all your efforts, you'll be comforted to know in Zachriel's world, oxygen represernts rust in the presence of iron. :) cheers...Upright BiPed
October 22, 2015
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EugeneS: No reference to any paper makes sense if you assume what you purport to prove. A hypothesis is a tentative assumption used to deduce empirical implications. The hypothesis was RNA World. The implication was that ribosomes would be ribozymes. Confirmation of this supports, but does not 'prove' the hypothesis. However, it is far from a trivial result. EugeneS: You still need a logical non-physical formal protocol before your molecule “can act like” something. Air molecules act to fill the available space. Are you hung up on semantics? Upright BiPed: it’s so much easier to just say “RNA can be both a memory and a catalyst” and be done with the details. He’ll not tell you what property of a representation he thinks makes it a representation. In the case of a replicating molecule, the memory is of the evolved sequence that is capable of replication, which is passed to new generations, with variation.Zachriel
October 22, 2015
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Hi UB, Yes, I guess that's true, understandably.EugeneS
October 22, 2015
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Hi Eugene, Zachriel is not going to acknowledge the distinction in the physics of the system. People do what profits them; it's so much easier to just say "RNA can be both a memory and a catalyst" and be done with the details. He'll not tell you what property of a representation he thinks makes it a representation. He has no reason to.Upright BiPed
October 22, 2015
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Eric Anderson- That was for wd400 and it pertained to the definitional issue. My apologies for any confusion. I have access to both of Spetner's books, as well as Shapiro's, which he cites, and "Evolution in Four Dimensions", which he also cites. But yes, I could write something and present it. Give me a week or so to put something together.Virgil Cain
October 22, 2015
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Zachriel, No reference to any paper makes sense if you assume what you purport to prove. You still need a logical non-physical formal protocol before your molecule "can act like" something. Ignorance of this fact or lack of understanding of this fact is no justification.EugeneS
October 22, 2015
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Virgil Cain @340:
Do you really think that some Intelligent Designer designed living organisms, with all that they require, including a just-so planet, and not design them with the ability to adapt? Really?
I hope you weren't directing that comment at me. It should be clear from both the OP, where I brought up the point you are making in the first place, and my comments to wd400 throughout, that I think there is evidence for non-random genetic changes. I was just trying to make sure wd400 disagreed and that we weren't dealing with a definitional issue. It is silly -- one more piece of Darwinian baggage hampering the understanding of biology -- that every genetic change would be called a "mutation." But when that is all the anemic Darwinian paradigm has to bring to the table, then unfortunately every square peg gets pounded into a round hole. Fine. We can deal with the poor terminology and correct the past shortsightedness of evolutionary terminology by just talking about different categories of "mutations": those that are random with respect to fitness and those that aren't. Whatever. We can deal with the nonsensical terminology. What I was trying to pin down, and what we have confirmed, is that wd400 denies the existence of anything other than random-with-respect-to-fitness genetic changes. As I mentioned to him, I was hoping to get a chance later to do a post on that. You have been active in the discussion and seem to have access to Spetner's latest book. Would you be willing to do a guest post on the evidence for non-random genetic changes? Doesn't have to be a long essay. Just a couple of the examples he cites with some references. Let me know. Thanks,Eric Anderson
October 22, 2015
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We know that RNA can act as both memory and processor, and that such a molecule can evolve.
LoL! Intelligently designed RNAs can perform a self-sustained replication only in the presence of other intelligently designed, shorter RNAs. And nothing new evolved.Virgil Cain
October 22, 2015
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EugeneS: Before one can say “can act” there must be a protocol establishing the relation between the symbol and what it denotes! We know that RNA can act as both memory and processor, and that such a molecule can evolve. See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014.Zachriel
October 22, 2015
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No, unfortunately, it does not. Before one can say "can act" there must be a protocol establishing the relation between the symbol and what it denotes! That is the whole issue.EugeneS
October 22, 2015
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