I notice Blu already made a point-by-point reply, but there's not much I can do about that.
On evolution and naturalism, and why I think they are separate:
Evolution, to be more specific the modern ToE, tells us the mechanism through which life exists in its current form. While the explanation does not require a supernatural agent, it does not prevent one from existing either, and as such there are millions of people who both accept the ToE and hold supernatural beliefs. Theistic evolutionists being the obvious example, but also people who don't believe in any kind of deity but hold other supernatural beliefs. And, though there are much more rare, people who accept naturalism but reject the ToE also exist.
Ultimately, evolution is a theory, and naturalism is a philosophy. That many people believe the first within the frame of the second does not invalidate the existence of those that don't.
You stated that the only reason people accept evolution is because they wish to reject God. Ignoring the fact that it is generally inadvisable to try to tell people why they believe what they do, this simply does not correspond with reality. Plenty of people believe in both. Maybe they are wrong. I'm sure we both agree they are, if for different reasons. But their existence still shows that people can accept evolution for reasons completely different than the one you stated.
On which definition of evolution we are using:
If you want to discuss evolution as a word in its broadest definition, then we can do that. If you want to discuss every scientific theory that deals with the concept of evolution, then we can do that. But virtually all of your arguments refer specifically to the ToE in biology, which is the common usage of the term. And I'd rather we made the discussion more specific, because otherwise the posts will otherwise get even longer. In any case, we can discuss all of it or only some specific aspects. I already stated my preference, but it's up to you.
In an effort to explain why I think we should discuss these subjects separately: There is no "over-arching theory of evolution", at least not in the scientific sense. There are multiple, independent theories, which you seem to link in the greater concept of naturalism, but as discussed above they are separate concepts.
The ToE in biology can hold true even if you disprove stellar formation, or the Big Bang, or abiogenesis. They work through different mechanisms and different evidence is used for them. To put it in another way, even in a world where abiogenesis is impossible it is possible that, whichever way life got there in the first place, it evolved according to the ToE. And vice-versa, maybe life was actually designed but stars formed the way astrophysics tells us they did.
So, in the end, do you wish for us to discuss everything that could ever have been said to the evolve in any meaning of the term, or your specific idea of evolution as some sort of greater scientific theory, or evolution specifically referring to the ToE in biology?
On time and causality:
Uncaused events at the quantum level have been observed. See for example radioactive decay.
As for my general point about time, well, of course we haven't observed time starting. Humans didn't exist back then. However it is simply not true that something cannot come from nothing. Zero-point energy being a common example.
Your statement that "there really is nothing there" is incorrect, there never was a point in time where nothing existed. Time began with existence. But even if it was, physics shows that something can and does come from nothing. Counter-intuitive as that might be.
On star formation:
I mentioned that there were protons and heat in the early universe, and you asked me where they came from. Heat is energy. Protons are matter. Matter and energy began to exist right there with everything else. It makes no sense to ask where they came from, because there was no "where" before that happened. (there was no "before that happened", either).
As for like charges repelling, that's where electrons come in, in terms of molecular bonds, and the strong nuclear force, in terms of nuclei.
Also, you seem to misrepresent my position on neutron radiation. You start with Fe for it, since it's the heaviest element that allows exothermic fusion. Why bother starting with H? And of course it's possible, it's been done.
On the Big Bang and conservation of angular momentum:
The Big Bang didn't create one single object from which all the others broke off. It formed matter, which clustered later, not in one single object
As for collisions, I was talking about planets. Venus is speculated to rotate "backwards" because one such collision. Galaxies could collide with each other, but in any case it's irrelevant because as pointed above, they didn't break off from a single object. Galaxy spin is complicated, there are even galaxies which have arms rotating in different directions.
On life and inorganic materials:
You were oversimplifying the process, which is why I pointed out the middle step. Organic materials can and do from from inorganic ones. We have observed this many times. And pointing out what the process might have looked like is an important part of showing a working model for that process.
As for abiogenesis, cells didn't arise spontaneously, much less modern cells. Nobody expects a modern cell to arise from mixing its basic constituents, because there were simpler cells before them, and simpler self-replicating systems before those. Evolution is a complex process.
And please explain what point I missed in your Pasteur example. The experiments don't disprove abiogenesis in general, only a very specific kind of it that no serious biologist accepts nowadays.
The definition I posted is that of the scientific term, that's what makes it the actual definition. As for your definition of kind as "Probably the best way to define it is that they cannot reproduce with another kind". Well, see my link on the London Underground mosquito. Here if you missed it the first time. C. molestus and C. pipiens are now distinct kinds as per your definition, yet C. molestus is a new species (as shown by the fact its native environment is the London Underground). One kind from another kind, as per your definition.
On new information arising:
Nylon-eating Flavobacterium and citrate-using E. coli. Nylon digestion is definitely a new trait, as nylon-eating bacteria die outside nylon-rich environments, and those are, obviously, no older than nylon itself.
Citrate-using E.coli were observed in the Lenski experiment which documented decades worth of bacteria generation, and noticed that cit+ mutants arise from cit- populations and quickly thrive. The ability to digest citrate wasn't present in previous generations, and is present now. Thus, new trait.
I don't quite get your claim that a biased conclusion was reached in the Lenski experiment. What would you conclude?
And a beneficial mutation need not be universally beneficial. Some beneficial mutations are only so within specific environments, but that doesn't disprove the fact they exist and are new, useful information.
On the geological column:
I'm curious how you say that information contradicting it isn't published, which goes against that fact you somehow know about it. You seem to be spinning this huge conspiracy to hide evidence against evolution.
When I asked you to provide evidence against the geological column, I was referring to it as a concept, that is, showing fossils that don't match it. You then attempted to provide such examples due to another question, so I just wanted to clarify what I meant there. As for your specific examples:
The Meister prints were disproved by your own source. There wasn't any evidence of human involvement beyond prints that seemed to belong to sandals, which later turned out not to. This is stated in the website you cited, mind you.
"Polystrate trees" can be caused by one of two things, most commonly growth in situ. Occasionally, rapid deposits can be caused by floods or levee breaks which result in uprooted tree fossils. How this invalidates the geological column, I'm not sure.
I'm having a bit of trouble opening some of your links, mostly because my internet is unreliable right now, so there might be something I haven't covered. If so, I apologise, and I'll be happy to do so if you point it out.
On Tiktaalik and Archaeopteryx:
Arcaheopteryx has clear theropodian traits which aren't found in modern birds. Such as, say, teeth and bony tails.
Tiktaalik has basic tetrapod structures, such as wrists and fingers. Also, primitive lungs.
Those make them transitional fossils.
The sorry state of science education is not an argument against evolution.
I ignored it because it's not used by serious biologists, and thus it's misleading to treat it as an argument for evolution. I mean, I have thousands of examples of failed Creationist arguments, but what's the point on arguing them if nobody in this thread buys them?
On vestigial organs:
All I did was point out you were using an incorrect definition of the term, thus your argument was flawed. I never claimed that vestigial organs by themselves prove anything, only that you were misrepresenting a scientific term.
And I don't see how it's "starting with the presupposition that Evolution is true." I never said "less useful that they once were", only "less useful than they are in other species". That doesn't require evolution to be true.
On human chromosome 2:
You can't just say "similar design" and assume that explains everything. Why would humans be designed with fused chromosomes? Why add telomere sequences in the middle, when they only have a use at the end?
By the way, while we are on topic, what are your views on junk DNA?
Was there any actual point to your example? I already showed how it's not the same kind of similarity we see between humans and other great apes, but I'm not sure if you retracted it or not.
I don't see how the differences between humans and chimps are irreconcilable. Adding differences is a great part of what evolution does. And, since you seem sceptical of my claim that a change in 3 nucelotides can do nothing depending on where, here. Removing tens of thousands of base pairs has a grand result of nothing at all.
There are huge advantages in selection in the biggest differences between humans and chimps, like brain capability and erect posture. Regardless, neutral or slightly harmful mutations can be preserved too, not just beneficial ones. Many beneficial mutations are the result of combinations of neutral ones.
On chromosome number:
Evolution does not predict more complexity being equal to more chromosomes, that would be ID. Evolution predicts loads of useless information cluttering the genome to varying extent, which means that a fern can have hundreds of chromosomes filled with very sparse relevant genes. Which just so happens to be what we see.
If, however, DNA was the result of design, we wouldn't see the amount of useless genetic material we see, since the designer would have no reason to put it there. Except maybe as a joke.
Simply put, a retrovirus is one that adds its genetic material to a cell's DNA. An endogenous retrovirus is one whose genetic material is in a germinal line cell and gets passed on to future generations. Basically, they are useless additions to our DNA. (if you think having a virus' genetic material inside our own fits some sort of design purpose for God, I'm open to hearing it)
We can use ERV to trace ancestry. Imagine organisms A and B both have ERV X, Y, and Z in their genome, C has X and Y, and D has X, then we can deduce that A and B's common ancestor is more recent than the Y and Z ERV additions, and that their common ancestor with C is more recent than the Y addition, and that their general common ancestor is more recent that the X addition. This is obviously very simplified. Then we can compare dozens of ERV additions and match the trees we build to each other, and also similar analyses using other mutations to our DNA that might serve a use, or not. What we see is that these trees always match up. This wouldn't happen if DNA was designed, unless our designer specifically distributed similar bits of DNA in such a way that they would always form matching phylogenetic trees in a common ancestry model. Why would a designer do this, unless it wished to trick us into believing in common ancestry?
The whole point, which you ignored, is that population growth isn't a simple geometric progression. Again, look up the Toba event (or genetic bottlenecks). YI've seen the video, and it fails because human population growth rates are complicated. They depend on resource availability and catastrophic events. This has been known since Malthus, who incidentally both predated and influenced the ToE.
The maths might work out using the naive P=Po.e^rt formula, but the assumptions its based on are unsupported by the evidence. Such as the fact that a 0.456% growth rate is not observed.
On Irreducible complexity:
Irreducible complexity is fallacious because it ignores the possibility of a different functional structure losing parts to become another type of functional structure. But, in any case, let's assume it might be true. If so, there should be structures with no possible evolutionary pathway, right? Can you show examples of them?
We don't naturally recognise design, we are hardwired to assume it. We are right about it in cases where we know how the design or similar structures came, which happens to be often because we live in a human-designed environment. Like I said, selection bias. However, to say we are always right when we assume design is petitio principii.
The whole point I was trying to raise and which you ignored is that we know a mechanism that can add information, but it only applies to some specific systems. Namely, imperfect self-replicators within a limited resource environment. AKA life. We say it can't happen that way for computers and books because they aren't self-replicators, and we don't know any mechanism that can apply to them. Life is not a computer or a book, so we treat it differently.
I acknowledge design when it's known. I already explained how our tendency to assume design is a bias evolved into our brains, I don't see how this is some sort of admission that it is always correct. If anything, it shows why it's not.
On evolution being a scientific theory:
I don't get how it surprises you that I believe evolution is a scientific theory, when that happens to be the position taken by the overwhelming majority of scientists. I'd really like to see what makes you claim that "Scientists don’t even say it’s a scientific theory". You can find more biologists named Steve that accept the ToE than scientists in general that don't.
You ignore that empathy is a useful adaptation, and that evolution is not a moral guideline. What evolution says shouldn't happen is nothing at all. There are no "shoulds" in it. It only aims to tell us what happened, not how we should behave.
Evolution progresses by "mistakes", if such a term makes any sense in this context. Empathy was a "mistake" in the sense it wasn't immediately useful, but then it didn't need to be. It only needed to be not terribly harmful. Then, when the trait spread, it became useful. And that's where the story ends, it didn't kill us, so it lasted, it became useful, so it was selected for. Nothing about that disagrees with evolution. And once it became useful, there's no need to "correct" it. Right now, it's very useful, so we keep it. We even try to enhance it, through other, non-evolutionary mechanisms.
Simply, you keep trying to make evolution to say that we should kill the less fit by some arbitrary standard, when what it does say is that those that are less adapted die. Again, no shoulds or oughts there. Just what happens. Whether that is good or not is up to each person's moral compass.
On the brain:
The universe can be chaotic in some places and organised in others. That is in fact what we observe.
There was a random element involved in origin of the brain, true. However, there were organising principles involved in it, too. So it's not entirely random.
When I said that the brain works, well I knew I should have elaborated on that, but I didn't want to get into the philosophy of the matter. In any case...
There are two basic possibilities here, either we live in a world that bears a certain resemblance to our perceptions, or we don't and our senses and reasoning don't apply to the "real world" out there.
If the first, then it doesn't matter how the brain came to be, as our perceptions of the world still match up and are useful. This is what I believe to be the case. But, there's also the other possibility.
If perception doesn't match the real world, my experience so far with them still points towards the fact it follows internally consistent rules, as understood by my thought processes, which again may or may not match the real world. Thus, I can still use my reasoning within the universe I perceive, because regardless of what the outside universe is and how flawed my reasoning is there, the only one that affects me is the one I perceive.
To sum it up, there's the Real Universe (RU), and the Perceptive Universe (PU). If they match, great, no problem. If they don't, then I only need to pay attention to the latter, and my reasoning still works there.
So, the brain works within the frame that is relevant to me, regardless of how it relates to a hypothetical outside frame. Which is why I use it.
As a side comment, this doesn't quite fit anywhere else, so I'll cover it here:
I'd rather you didn't address me as "brother", if you don't mind. It's.. inaccurate, in every sense. Babies recognising good and evil means nothing other than what I already said, namely, there is an inborn notion of right and wrong, in that we know the concepts exist and can use them. Inherent Knowledge implies objective truth, and as such does not apply to morality. Otherwise, all moral systems would be the same.Oh brother, you couldn’t be more wrong. Even little babies recognize it to some extent. But this is an entirely separate topic that I don’t want to get into here. C.S. Lewis’s Mere Christianity does a pretty good job of explaining this one.Current wrote: There's no such thing as inherent knowledge of good and evil. There is the inborn notion of it, but inherent knowledge implies its objective and universal. It's not.