> > I've thought about this for a few days, but I'm not sure I'm fully on board:
> > 
> > We agree that evolution requires these things:
> > 1. An organism capable of change
> > 2. A change must happen (by whatever mechanism we've discussed)
> > 3. Natural Selection must be applied to it. 
> > 
> > We already have discussed and agreed that 1 & 2 have three categories: Good changes, Neutral changes, and bad changes. Natural selection operates on both Good and bad, and ignores neutral. So when we're discussing speciation it seems clear that at this level it's a two step process, and in terms of speciation, step 3 is the most important.
> 
> I agree. Natural selection decides if a new species stays around, but the new species must contain adaptive mechanisms (epigenetic) that can move quickly against challenges..-Alright... um... I thought the question was "what is the most important part of evolution?" If we agree that NS is the step that makes the decision and has the largest weight in the process--I completely fail to see why even the title of this thread makes any sense?-Going back to the article you began this post with, we have a guy giving philosophical commentary on the original work "Origin of the Species." Combining the title of the thread, with the content of the article--when we have an agreement that natural selection is the most important part of speciation--I fail to see what, if any, controversy this raises.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"


>But the mechanisms that give rise to change, which are also a lynchpin of evolution, cannot be attributed to an automatic process, and are considered by some theist scientists like David to be too complex to have come into being of their own accord.
> 
> *** I see from David's latest post that in fact he agrees with me that NS and the other mechanisms are equally important. Presumably his agreement was only to what you wrote about the function of NS.-In my view the Darwin mechanism of random mutation and natural selection following is entirely a passive process. Random means 'lucky' if it is a good change in the genome, but it may be neutral in effect or bad for the species, each variety of change about 1/3rd of the outcomes. The 'good' changes start out as recessive genes and with the guidance of natural selection to challenges in nature eventually become dominant. Natural selection responds to random challenges, making natural selection an active process only after random changes in nature, both climatological and biological, preditors, etc. In conclusion, NS becomes an active participant in the speciation process only after a long series of random events, and contingent changes. NS seals the fate of the new species, and at this juncture assumes a major role. All the other mechanisms in the genetic cascade of epigenetic controls are more active in initial responses to natural challenges, for they are actively changing the genome in the adaptations that are necessary for surviorship. In the end all are equal in importance. Use this analogy: locking the barn door after the horse escapes does not fit, but capturing the escaped horse and then putting him back in the barn and locking the door is the correct analogy. NS locks the door. Several equal parts, no single linch-pin.

MATT:
> We agree that evolution requires these things:
> 1. An organism capable of change
> 2. A change must happen (by whatever mechanism we've discussed)
> 3. Natural Selection must be applied to it. 
> We already have discussed and agreed that 1 & 2 have three categories: Good changes, Neutral changes, and bad changes. Natural selection operates on both Good and bad, and ignores neutral. So when we're discussing speciation it seems clear that at this level it's a two step process, and in terms of speciation, step 3 is the most important.
> 
> David agrees***, but adds that "the new species must contain adaptive mechanisms (epigenetic) that can move quickly against challenges."
> 
> My objection was to your describing NS as THE lynchpin of evolution. By definition, you cannot have new species without innovation, and so your steps 1 and 2 are indispensable to the process. The reason why I object to the downgrading of steps 1 and 2 is, as I said in my earlier post, that it distracts attention from the enormous complexity of the mechanisms involved in innovation (mutations and adaptations). That is why some materialist scientists try to make NS synonymous with evolution, and even go so far as to claim that it "explains the whole of life", (The God Delusion, p. 116), which is patently absurd: it does not explain the origin of life or of the mechanisms that produce the changes that take place before nature can make its selection. Natural selection requires no intelligent guidance ... it is an automatic process. But the mechanisms that give rise to change, which are also a lynchpin of evolution, cannot be attributed to an automatic process, -But they ARE automatic processes; one of the properties of life is "self-replicating." An amoeba doesn't have to think to replicate--nor does any other process have to be consciously aware in order to function--save for some human and animal brains. (I've often said that the best arguments for God arise in consciousness.) I think you're aiming at something like "spontaneous process" but if you really believe that, then David's right: take your hands off the fence and step back!

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

The moral of the story is, that a seemingly minor change (dropping a number in the thousandths place resulted in a completely different scenario. 
> 
> Theory; I don't see where I offered one. The mathematics described by chaos has only been known now for about 40 years.-I know that and I've read the lay books on it. You use chaos theory to support the idea that chance mutation and Natural Selection (CM&NS) can create very complex organs. That is a theory in itself. 
> 
> Your claim I responded to can be boiled directly to this:
> 
> "In no instance of life has there been an episode where an organ was able to be derived from simpler components." -Not true. Somehow, 'no' liver became a very simple liver in the first arthropod ancestor in the Cambrian. Later the lobster had a somewhat more complex liver, and eventuqally there is ours with secretory, digestive and clearance mechanisms. Same with kidneys. But not itty step by itty step. The fossil records show leaps, punctuations a la Gould.
> 
> My issue with your absolutism comes from the fact that you seem to really think that we have in our possession, a great deal of knowledge--bordering on the fantastical. 
> 1. You claim that because the universe is so finely-tuned (back from the big bang) that this requires intelligence. -Why not? chance vs. intelligence. I'll pick intelligence every time. How do you know, what is the clue, that it is all chance? Your absoluteism againt mine.
 
> a.) This is problematic from a scientific perspective. A claim like this only holds water if we had good knowledge of where, exactly, our universe actually fits within the grander scope of things--because the two leading theories in physics mandate that a grander framework exists.-Really? Mandate? Not string theory and not multiverse theory. The only thing we know is this universe exists.-> For this proper (in every meaning of the word) to be more than a conjecture--which, in lack of knowledge is exactly where this claim stands--we really do need our 'theory of everything.' Fine tuning doesn't have to wait.- We can all see it. It is the underlying cause for its appearance that is the issue. Chance or intelligence. Do you have a third choice?
> 
> b.) We lack a general model of intelligence; if we can't reason better about intelligence (and to assert we know more here than I claim contradicts modern psychology) than we don't have a good basis to be able to state with certainty, that our universe requires it.- I am intelligent, you are intelligent. It is like pornography. I know it when I see it. What definition are you straining for?
> 
> c.) Philosophically, we have been searching with modern tools and techniques, for an extremely short time; we're just now beginning the job of first enumerating, and then deciphering biological complexity. -Exactly. Give science 50 years uncovering all the asecrets in the genome and Darwin will be dead. I have full faith in that statement.
> 
> 2. It is not possible in any way that evolution can be a passive process. 
> 
> a.) My first objection here is one purely of pragmatism; in what way are you justified in making this kind of claim? What level of play do you allow here if you're not being an absolutist? -It is easy to make that an absolutist statement. Chance mutation is passive. According to Darwin any 'advance' comes from chance genome changes. Nothing about that part alone mandates progress, however that is defined in evolution. Now NS accepts what it is given and there are survivers, and not always the best ones. Perhaps the lucky iones. 
> 
> b.) Again, you seem to be overly willing to make judgments, knowing full well that such judgments are subject to 'the evidence,' which is always "of the minute," and more importantly--subjectively interpreted. What's a better explanation for a whale's vestigial limbs are still there if there's no room for incremental processes? Give me a better explanation. -I don't have to. there was step-wize progress, but the fossil record says in jumps. How do you define increment?
> 
> c.) (Running out of space.) Epigenetics described at present at wikipedia sticks to the point that they are what describes organismal changes that don't translate to DNA. How does your proposed process work then, as evolution requires the transferral of genetic material from parent to progeny? -Wiki is wrong. Just peek in my book at Reznick's guppies. Inherited changes. More recent work (Reznick is still at it but the guppies are so 1990, to use valley-girl speak) expands greatly on the inheritability of epigenetics. And not just through methylation. -I think you have a much greater knowledge of math and philosophy than I, but somehow you seem to accept the changing scene as tied to the minute. Patterns of development are very obvious to me. Over 10 years ago I expected all of this epigenetic manipulation within cells to fit immediate needs, and in organisms for quick change against sudden dangers. Its in the book. to me it is obvious. I am not tied to this minute. I can logically extrapolate.

David: None!!! You have given me my UI, and the only difference I see is I say the UI gave DNA and epigenetics the power to do this so all He need do is sit and watch.
> 
> The difference for me that I see in this scenario is UI is the scenario (creation) and not a UI siting back creating and watching the scenario you've given.-For me the UI is within and without this univrse. Thus the creator is creation. I'm still with Aristotle. There MUST be a first cause. Matt will object.


> Of the two, I find the second far more convincing, as it covers the various gaps I listed at the end of my post of 18 November at 13.18. Your scenario leaves unexplained the need for all the extinct species, for all the long periods of stasis, and indeed for evolution itself, because if man was the goal right from the start, all the intervening stages were clearly superfluous. (What was the point of all those dead dinosaurs?) Since "we can only imagine His reasoning, based on what we see as factual information", what do you imagine was His reason for the delay and the wastefulness covering so many billion years?-Once again you are falling into the trap of reaoning for God's reasoning, if He reasons, but you do it like a human. That doesn't work. One has to analyze backwards: we know what happened, not exactly how, but since it happened (we are here with our giant brains) what are the possible scenarios?
> 
> The reason why I'm pushing this argument is that like yourself, I believe evolution happened, but if it was organized by a UI, I cannot for the life of me see why it would deliberately choose such a messy, wasteful, roundabout way of achieving its purpose. The mess seems to me far more consistent with a process that has not been planned beforehand.-Answered above

Of the two, I find the second far more convincing, as it covers the various gaps I listed at the end of my post of 18 November at 13.18. Your scenario leaves unexplained the need for all the extinct species, for all the long periods of stasis, and indeed for evolution itself, because if man was the goal right from the start, all the intervening stages were clearly superfluous. (What was the point of all those dead dinosaurs?) Since "we can only imagine His reasoning, based on what we see as factual information", what do you imagine was His reason for the delay and the wastefulness covering so many billion years?
> 
> The reason why I'm pushing this argument is that like yourself, I believe evolution happened, but if it was organized by a UI, I cannot for the life of me see why it would deliberately choose such a messy, wasteful, roundabout way of achieving its purpose. The mess seems to me far more consistent with a process that has not been planned beforehand. However, interestingly, your choice of Option 1 fits in far better with the atheist scenario: you and they start with a single mechanism, and the rest follows on of its own accord: an automatic, unbroken, unguided, self-regulating, messy, wasteful and roundabout progression from bacteria to human brain.-As I have said several times in other posts, if humans were the final goal, then answer to that question is so blindingly obvious that it is most often overlooked. It was done that way because it had to be done that way in order for humanity to survive. The basic sustenance of our bodies is dependent on all other life, which is dependent upon the earth, which is dependent on the solar system and all its many planets, which is dependent on the galaxy and all its many solar systems, which is dependent on the universe and all its many galaxies. Early life was an absolute necessity for preparing an inhospitable lump of rock, lava, and water into a livable planet. There had to be soil for plants, which would have required millions upon millions of years of microbial preparation for even the most tenacious of plants to have survived. There would have had to be vast quantities of plant life to sustain the first land creatures, which were every bit as vital for preparing the earth as their microbial predecessors. And most importantly, it had to become a system that could survive without constant micromanagement of every little detail.

Another aspect of this view is that we have no idea how or when H. erectus appeared. the gap from arthropithicous (Lucy) is enormous:

https://evolutionnews.org/2018/06/on-hominid-fossils-and-universal-common-ancestry-deni...

"The focus is on the fact that the fossils that we do have don’t form an evolutionary sequence from apelike precursors to humanlike fossils.

***

"We have ample fossils of australopithecines, and Homo erectus, and Neanderthals, and now we have numerous bones of Homo naledi, and there are many others.

***

"From its first appearance, Homo erectus was very human-like, and differed markedly from prior hominins which were not human-like. Yet Homo erectus appears abruptly, without apparent evolutionary precursors. An article in Nature explains:

“'The origins of the widespread, polymorphic, Early Pleistocene H. erectus lineage remain elusive. The marked contrasts between any potential ancestor (Homo habilis or other) and the earliest known H. erectus might signal an abrupt evolutionary emergence some time before its first known appearance in Africa at -1.78 Myr [million years ago]. Uncertainties surrounding the taxon’s appearance in Eurasia and southeast Asia make it impossible to establish accurately the time or place of origin for H. erectus . … Whatever its time and place of origin, and direction of spread, this species dispersed widely, and possibly abruptly, before 1.5 Myr.”

"That article was written in 2002, but the problem remains. A 2016 paper admits, “Although the transition from Australopithecus to Homo is usually thought of as a momentous transformation, the fossil record bearing on the origin and earliest evolution of Homo is virtually undocumented.” While that paper argues that the evolutionary distance between Australopithecus and Homo is small, it nonetheless concedes that ”By almost all accounts, the earliest populations of the Homo lineage emerged from a still unknown ancestral species in Africa at some point between approximately 3 and approximately 2 million years ago.”

***

"The problem is that most hominin fossils can’t be organized in a manner that leads to an evolutionary lineage, especially one that bridges the gap between the apelike australopithecines and the humanlike members of Homo."

Comment: This, in a way, is as a dramatic gap as the Cambrian explosion. Lucy is quite ape like with long arms and a tiny head with 400+ cc of brain. Erectus approaches modern brain size at just under 1,000 cc, and a much larger body with shorter arms.

DAVID’s comment: The whole article reviews the history of the efforts to get epigenetics recognized. Neo-Darwinists fight tooth and nail against a change in approach to evolution. They want to study only external influences, not internal changes originated by organisms themselves.

dhw: Your comment is as significant as the article. Whether your God devised the whole system or not, it is becoming increasingly clear that evolution is a process in which organisms themselves originate change, and they do so at least partly (I would say mainly) through intelligent organismal responses to the challenges or opportunities presented by external influences. The external influences may well be governed by chance, but the responses are not.

DAVID: The key is recognizing the importance of internal responses. Darwin only noted the external and competition, only a small part of the story.

The key is recognizing the importance of all the factors involved. The aim is not to denigrate Darwin but to try and get as near as we can to a convincing explanation of how evolution happened. Your recognition that internal changes are “originated by organisms themselves” offers very gratifying support to the proposal I have summarized above. Thank you.

DAVID:A new paper by a Darwin scientist appears in Nature and is commented upon by the author in this entry. It estimates the new genes required for a Cambrian jump:
https://theconversation.com/we-reconstructed-the-genome-of-the-first-animal-95900

DAVID’s comment: this fits our discussion. The genes appeared within the animals to create the Cambrian gap. The Darwin scientist is puzzled because this is a jump without chance and without action by natural selection. Direction by God fits. Be sure to look at the ladder diagram to fully appreciate this.

dhw: Is anyone really surprised that new species contain new genes? We all know that the Cambrian is a puzzle – Darwin also recognized it – but I see no reason why it should not fit the scenario outlined above, in which organisms themselves respond to environmental change by originating their own changes. Your God may have invented the mechanisms that enabled them to do so. He may even have directed the environmental changes that offered these new opportunities. Who knows?

Agreed.