It doesn't follow that for something to be observed it must be part of physics. If the physical universe is a medium, like our computers, they can transmit information from other entities without the entities themselves being embedded in the computers. It sounds like your argument begs the question by first assuming everything that interacts with us must be physical.

Darwin's mechanisms do not explain anything in evolution. All of his mechanisms select against increased complexity and diversity, so are useless to explain the origin of species as he originally claimed. Darwinian evolution is dead and died a long time ago. Modern evolution is very much non-Darwinian.

> It doesn't follow that for something to be observed it must be part of physics.

It's the other way around. If it can be observed, it interacts with matter. If it interacts with matter, it is within the domain of physics, by definition. I don't understand why you have a problem with this.

Physicists are well aware that we do not understand all the interactions and we do keep discovering more and more interesting phenomena, such as quantum entanglement.

> All of his mechanisms select against increased complexity and diversity, so are useless to explain the origin of species as he originally claimed.

I don't know where this criticism comes from, but it sounds like a straw man. Natural selection may select against "complexity and diversity", but random mutation puts "complexity and diversity" back in the game.

I think you are equivocating between the laws that govern material interaction and things that interact with matter. They are not the same thing. The laws of physics are developed by breaking matter down to its most uniform and granular components, and then characterizing their interaction. An immaterial soul would not be captured by such an analysis, but its interaction with matter could still be empirically identified.

As for evolution, I see where you are coming from. Randomness, like flipping a coin, is always complex and different. However, if there are only a few specific, long coin sequence you are trying to construct, then flipping a coin does not get you there. There are just too many possibilities within a couple hundred coin flips to check within the lifespan of the universe. And, if you have one of these sequences, then randomly flipping some of the coins will destroy the sequence. Just think about what happens if you flip random bits in a computer program. For the most part, unless you get really, really lucky, it will destroy the computer program. So, while a few random mutations may be very lucky and flip the right nucleotides to create new functionality, the vast majority of mutations are destructive, and will kill off the species before there is the chance to evolve new functionality.

> I think you are equivocating between the laws that govern material interaction and things that interact with matter. They are not the same thing. The laws of physics are developed by breaking matter down to its most uniform and granular components, and then characterizing their interaction. An immaterial soul would not be captured by such an analysis, but its interaction with matter could still be empirically identified.

If an "immaterial soul" interacted with matter in an empirically identifiable way, it is part of physics. The forces that interact with matter are themselves not made out of matter. To be precise, matter is only that which has a mass, but there are also particles that don't have mass. Their interactions are nevertheless part of physics and we can measure them at least indirectly. They're not abstract constructs, they're very much part of the physical universe.

In that sense, perhaps the term "materialism" is misleading, because ultimately physics is about forces, not matter. Remember, I'm not using that term for myself.

> However, if there are only a few specific, long coin sequence you are trying to construct, then flipping a coin does not get you there. There are just too many possibilities within a couple hundred coin flips to check within the lifespan of the universe.

There isn't just a single coin though. There's about 10^46 molecules in the ocean[1]. That's a lot of interactions over the span of billions of years.

> And, if you have one of these sequences, then randomly flipping some of the coins will destroy the sequence. Just think about what happens if you flip random bits in a computer program. For the most part, unless you get really, really lucky, it will destroy the computer program.

It depends on the bits flipped. Bits flip all the time[2] and people rarely notice, because they're not necessarily important bits. It also depends on whether the program will abort upon error detection. Without memory protection by the operating system, most programs wouldn't terminate, they'd keep trucking along, perhaps producing some garbage here and there. In fact, the difficult part about memory corruption bugs is that the program often won't terminate until well after the corruption has taken place.

Also, computer programs aren't like organisms exposed to nature. In nature, it's possible that a mutation kills you, but it's far more likely that some physical process or another organism kills you.

> So, while a few random mutations may be very lucky and flip the right nucleotides to create new functionality, the vast majority of mutations are destructive, and will kill off the species before there is the chance to evolve new functionality.

The vast majority of mutations are relatively inconsequential, at least for short-term survival. Our DNA mutates all the time, but also we have evolved error correction, which you probably also will not accept as evolving "by random mutation and selection".

[1]https://www.quora.com/How-many-water-molecules-are-in-the-Ea...

[2]https://en.wikipedia.org/wiki/Cosmic_ray#Effect_on_electroni...

So, it doesn't really seem we are disagreeing, it's just a matter of terminology. You seem to want to call every interacting thing 'physics', which you are free to do, but then I'm not sure what the value of the term is. And, you agree we already empirically measure many immaterial things. So you seem to agree that in theory an immaterial soul is an empirically testable hypothesis, in which case I'm not sure what your objection is.

As for the number of interactions, we have trouble reasoning about large numbers. Billions of years and molecules sound like unimaginably large numbers and of similar magnitude to trillions or decillion, even though the latter are many orders of magnitude greater. DNA sequences can be hundreds of billions of base pairs long. So, if we could only depend on random mutation and natural selection, we'd need 4^10^11 attempts to hit a particular sequence, which is more trials than even a multiverse of universes can offer.

> So, it doesn't really seem we are disagreeing, it's just a matter of terminology. You seem to want to call every interacting thing 'physics', which you are free to do, but then I'm not sure what the value of the term is.

Everything that interacts with matter is in the domain of physics. So if your concept of a "soul" (or whatever makes you a "dualist") can at least in principle be observed, we can count it in. It's then not "beyond this universe".

It would also raise a lot of questions: Are souls "individuals"? If so, does every organism afford a soul? If so, where do new souls come from when the amount of organisms increases? Where do they go if they decrease? Is there really only one soul spanning all organisms? How can we test for any of these things? What are the consequences?

It's perfectly fine to explore such questions, but I am personally not convinced that something like a soul - within or outside the realms of physics - is at all necessary to explain life or intelligence as the phenomena we can already observe. That's what we disagree on.

> DNA sequences can be hundreds of billions of base pairs long.

Perhaps, but the simplest lifeforms alive today have on the order of hundreds of thousands of base pairs.

> So, if we could only depend on random mutation and natural selection, we'd need 4^10^11 attempts to hit a particular sequence, which is more trials than even a multiverse of universes can offer.

Yes, but DNA didn't just form spontaneously, fully assembled. It formed from simpler precursors, which formed from simpler precursors still, all the way down to proteins which formed from the simplest of molecules. Those precursors don't survive because they can not compete with their successors. They could be forming in the oceans right now, but they won't progress because they'll just get eaten.

There have been experiments done reproducing it up to the "protein formation" step. Anything more complex than that is likely going to take too much time to result in a new lifeform - especially one that could survive ex-vitro.

Even staying within materialism, it isn't clear that 'everything is physics'. For example, our computers operate according to the laws of physics, but the physical laws tell us nothing about how they operate. To understand how computers operate, we need to know a lot of extra information besides the physical laws. In other words, physical laws tell us nothing about physical conditions. This is why there are many other scientific disciplines besides physics. So, since this notion of 'everything is physics' doesn't even work within materialism, it is hard to see why it would exclude immaterial entities.

And as you point out, the notion that Darwinian mechanisms can account for evolution of complexity and diversity is pure speculation. Which is why modern evolution theory does not use Darwin's theories. It uses mechanisms that we can see operating in the lab and in bioinformatics, such as bacterial horizontal gene transfer and empirically calculated substitution matrices. And the further that bioinformatic algorithms diverge from Darwin's ideas, the better they perform.

There's a difference between the physical laws (that we know) and the "domain of physics". There's a great deal we don't yet know about physics that's nevertheless within its domain.

Not everything is in the domain of physics. "What is the meaning of life, the universe, and everything?" is not in the domain of physics. However, physics (or its subsets chemistry and biology) can explain how life may have emerged.

Physics can't rule out that a god snapped his godfingers 5000 years ago and made it all appear the way that it does now. It can't rule out an immortal soul. It can't rule out that we're in a simulation, or that unobservable fairies are actually behind all the forces in the universe. For those cases, I like to apply Occam's Razor - not because it's true, but because it's practical.

> And as you point out, the notion that Darwinian mechanisms can account for evolution of complexity and diversity is pure speculation.

Random mutation and natural selection do result in complexity and diversity. This is a fact, not speculation. You can try it at home, on your computer. We do have genetic algorithms working on those exact principles. They're generally not preferable to more informed algorithms, because they're slow, but they do work.

> It uses mechanisms that we can see operating in the lab and in bioinformatics, such as bacterial horizontal gene transfer and empirically calculated substitution matrices. And the further that bioinformatic algorithms diverge from Darwin's ideas, the better they perform.

As we can see from computer simulation, pure selection and mutation is inefficient. If nature can find a shortcut mechanism that "Darwinian evolution" itself does not account for, it's not surprising that it would become a dominating factor. However, what makes you believe that such a mechanism itself could not possibly arise from natural selection and random mutation? Is it the improbability? It's a big universe, you know. We're not even talking about the probability of this happening on all planets, but on any planet in the universe.

I think you are missing my point. Physical phenomena are not reducible to physical laws, and cannot be explained by the laws. You cannot derive a binary adder from the laws of electricity, and that is why computer engineering is not a field of physics, but is its own domain with its own set of laws.

As for Darwin's mechanisms, I'm not speaking from personal incredulity, but from what I see reading bioinformatics textbooks and what leading biologists write, not what we are taught in high school. Darwin's mechanisms are only given lip service, and when the rubber meets the road in practice they are completely ignored.

> I think you are missing my point. Physical phenomena are not reducible to physical laws, and cannot be explained by the laws. You cannot derive a binary adder from the laws of electricity, and that is why computer engineering is not a field of physics, but is its own domain with its own set of laws.

Fair enough, let's just leave it at that.

> As for Darwin's mechanisms, I'm not speaking from personal incredulity, but from what I see reading bioinformatics textbooks and what leading biologists write, not what we are taught in high school. Darwin's mechanisms are only given lip service, and when the rubber meets the road in practice they are completely ignored.

Okay, I've done some googling. Now let me take a shot at reconstructing what happened here. You read that one paper[1] that quite boldly claims that the CRISPR mechanism proves that Lamarckism is real. You stumbled upon it because it appeared to confirm something that you already wanted to believe: "Darwinism is wrong". You otherwise have no background in bioinformatics.

The thing is, that paper doesn't prove Darwin wrong at all - he never ruled out other effects besides random mutation and selection. Darwin just wasn't very fond of Lamarck's work, which wasn't very scientific even by the standards of its time.

The effects of random mutation and selection have been readily reproduced countless times. Lamarckian effects on the other hand have not been observed until epigenetics (a bit of a stretch), HGT (rather uncommon in eukaryotes like us two) or this here CRISPR (more of a bacteria thing). That's despite lots of experiments that have been performed to prove Lamarckism right. If anything, nature has a lot of obvious Darwinism and maybe some not-so-obvious Lamarckism here and there. To quote the paper:

"Neither Lamarck nor Darwin were aware of the mechanisms of emergence and fixation of heritable variation. Therefore, it was relatively easy for Lamarck to entertain the idea that phenotypic variation directly translates into heritable (what we now consider genetic or genomic) changes. We now realize that the strict Lamarckian scenario is extremely demanding in that a molecular mechanism must exist for the effect of a phenotypic change to be channeled into the corresponding modification of the genome (mutation). There seems to be no general mechanisms for such reverse genome engineering and it is not unreasonable to surmise that genomes are actually protected from this type of mutation."

Personally, I actually find the prospect of Lamarckian effects in the evolution of "higher" species exciting and plausible. It's not exactly a proven thing that this is common in nature, as you seem to believe.

Of course using natural selection and random mutation is a pretty dumb method when you can artificially select and selectively mutate instead.

It's why we don't use genetic algorithms when we have a better method. It's really expensive to simulate a "natural environment" and run it for hundreds, thousands, or even millions of generations.

Like I said, if nature found a shortcut - and it has, in the case of HGT or CRISPR - it will use that shortcut. It's just more efficient. The same goes for sexual selection, which Darwin didn't pay special attention to, but which is clearly a very important part of "natural" selection.

In my view, those shortcuts could have developed through Darwinian processes alone, in simpler lifeforms. If you can't conceive of that being possible, that's fine. We can't exactly prove it right through a simulation that is accurate to life on earth.

It's not a disagreement over whether Darwinian processes maybe happened somewhere at some time. The question is what is the primary process driving evolution, and what do we see in the lab. Darwinism isn't there, as far as I can tell. So, why some irrelevant processes are taught as the big guiding mechanisms of evolution is a mystery to me. Darwinism, insofar as it's a major part of evolution, is clearly dead. And with certainty it is dead insofar as it proposed to be #the# fundamental explanation of origin of species, as Darwin originally proposed.

> The question is what is the primary process driving evolution, and what do we see in the lab.

As far as the "state of the art" is concerned, it's still primarily random mutation and natural selection. I highly doubt that Koonin would disagree on this, by the way.

> Darwinism isn't there, as far as I can tell.

What do you mean by "we don't see it in the lab"? Of course you don't see natural selection in the lab, that's oxymoronic.

We can see randomness in the offspring of, say, lab rats. We can selectively breed them to e.g. make them more susceptible to certain diseases. I'd rather call this Mendelian than Darwinian, but the difference is only in how the selection happens.

What happens in nature over billions of years obviously can't happen in a lab. It's obviously not sensible to use natural selection as a tool when you can just artificially select or even directly manipulate the genome.

> So, why some irrelevant processes are taught as the big guiding mechanisms of evolution is a mystery to me. Darwinism, insofar as it's a major part of evolution, is clearly dead. And with certainty it is dead insofar as it proposed to be #the# fundamental explanation of origin of species, as Darwin originally proposed.

It's not irrelevant at all. Again, the fact that you don't observe the effects of natural selection in lab, or that it isn't useful for bioinformatics doesn't make Darwinism irrelevant as an explanation for the origin of species.

Even if we accept that known processes like HGT or CRISPR aren't Darwinian and that it may have accelerated some evolutionary processes in some of our ancestors, they couldn't be the primary driver of evolution because so far we haven't observed it in any "higher" species beyond bacteria.

If you want to speculate that there are more such processes hitherto unknown, that's fine. That doesn't mean a eulogy for Darwinism is warranted at this time.

I'm not sure how to line up what you are saying above, and my observation that bioinformatics algorithms work better the further they are from the RM+NS assumption, plus all the other discrepancies I see between theory and practice in bioinformatics.

Sure, Koonin and others can say RM+NS is primary, but I don't see this in the actual work people do that is quantitative and rigorous vs speculative stories.

Also, I'm not talking about genetic engineering, although the fact we can do genetic engineering vs just randomly jamming nucleotides together in the hopes something happens is also fairly surprising if it was all just RM+NS.