Thanks for jumping into the conversation. I'm glad to interact.

According to my conversations with biologists and geneticists, there are not an equal amount of beneficial vs. deleterious ones. In actuality, the quantity of beneficial mutations is by far in the minority. In a paper by Charles F. Baer, Michael Miyamoto, and Dee Denver: "We know that the vast majority of mutations with observable effects are deleterious."

Also Dr. Sarah Bodbyl Roels says, "It's very, very hard to get a clear picture of what proportion of mutations—writ large, since there are many kinds of mutations with varying effects, dependent of population sizes, environmental conditions, and even linkage dynamics within genomes—are deleterious, beneficial, and 'effectively neutral'."

And they are not totally random. In one sense they're random, but in another sense, they're not. Dr. Denis Alexander, of Oxford University, says mutations "come in clusters and tend to occur at certain points in the genome more than at other points. If they were totally random, they could come in any position, but they're not. They're not randomly generated."

While the vast majority of mutations are deleterious, and another large number are neutral, that paper by Baer, Miyamoto and Denver concludes that beneficial alleles are beneficial to the organism because they pack more punch than the deleterious ones, either because of their fortuitous placement in the genome at a punch-packing segment or because the organism (at the cellular, RNA, protein levels) is able to favor those alleles over the neutral or deleterious ones. The result is better than would ever be expected by chance, leading to the productive evolution of the species.

Dr. Steve Roels says, "The reason is that those beneficial mutations, though rare, are non-randomly favored by natural selection. In essence, natural selection sifts through the pile of mutations, retains favorable ones and throws the rest in the dustbin. At the heart of natural selection is math. ... What the pioneers of evolutionary biology realized was that tiny variations are bubbling up all the time (the average human carries several totally unique mutations). Given that populations are thousands, millions, or even billions of individuals, the chances that beneficial mutations arise and become established, while deleterious mutations are continuously purged from the population, are actually very high."

So let's talk more.

I know I'm over a year late responding to this thread, but I want to explain how there are so many beneficial mutations (and a somewhat equal amount of non-beneficial ones). Mutations are experienced in every living creature at birth, some of those mutations are positive and beneficial for the species, some are negative and harmful for the species. It's important to note that mutations are entirely random. An animal who experiences a non- beneficial mutation will have a greater chance of it dying out (and its offspring by extension). Animals who experience positive mutations will benefit from those mutations and pass their genes onto their offspring. I hope this clears things up.

> The complexity of the brain may allow for choices and agency, but how can these be free choices, choices for which someone can be held morally responsible, if the conscious mind isn't responsible for the system that its choices emerge from

My point is that the conscious mind supersedes the system from which they came. It is capable of emergent qualities inexplicable by the biology of the system.

> What exactly do you mean by 'creating information', and what would such a mutation look like?

Neo-Darwinian theory says that mutation and natural selection have created all biological information essentially and ultimately out of nothing. It says that all genomes must have derived from a simple initial genome that came from a non-genome via a long series of beneficial mutations (positive typographical errors, so to speak) and lots of natural selection (the approval of step-forward organisms and the refusal of deleterious organisms, though all by a non-intelligent and non-purposeful judge). What evolutionary theory speculates is that molecular mutations over time had enough beneficial accidents in the instruction manual, not only increasing information but also providing beneficial information, to evolve more complex, higher information (an advanced genome), better able to survive organisms. What I'm saying is that the research bears out that this has not happened. Instead, we have an overwhelming evidentiary river of deleterious mutations and no evidence of this forward movement necessary for evolution to have done what it claims to have done.

Suppose we have a little red wagon. The first primitive genome encoded the instruction manual for this wonderful wagon. It's job is to make copies of the manual so more identical wagons can be made. But the genome is, as we have learned, incapable of making an identical facsimile. Every time it copies the manual, it changes at least something at random: each manual comes out different, and therefore each wagon comes out different. Each wagon has its own unique instruction manual taped to the bottom of it. When any wagon is junked, its manual is junked with it. New copies of the manual are not based off the original but instead only off the ones with errors. Errors are going to be accumulated over time. This is what geneticists have observed.

But let's introduce a quality-control judge: natural selection. Natural selection is able to destroy the wagons that are inferior. Keep in mind that it is not selecting for good instruction manuals. Natural selection is only looking at the wagons and voting thumbs-up or thumbs-down.

The scribe and the judge work entirely independently. The scribe is essentially blind, extremely near-sighted, reproducing manuals with variations (at the molecular level), and the judge is very far-sighted—he only looks at the whole project, never the details. He evaluates whether the wagon is a go or trash.

The scribe often just makes typing errors, misspelling words, adding words that don't make sense in the sentence, or even deleting words, some of which might be important. He might occasionally recopy even a whole page, but that doesn't add any new information. He may leave out a whole page, to great demise.

The scribe is at the beginning of the assembly line, imperfectly copying instruction manuals. The wagons are built according to the unique manual. The judge is at the end of the line, accepting and tossing. What we must also admit is that the judge and the scribe are never talking to each other. Not only do they not communicate, but they are not intelligent. They are forces, one of accident and one of selection.

What are the odds that these mutations are creating not only new but also beneficial information? The geneticists tell us that the odds are abysmal to nonexistent. Bad duplications might presumably be eliminated and harmless (neutral) duplications might be preserved. But even the harmless duplications will have copying errors in them, with more errors in each iteration of the manual. Some of these errors might possibly create new and useful information. With a little imagination, perhaps we can picture where occasionally a beneficial mutation might just happen and be selected, of course, for reproduction. Scientists, however, have found no such thing. And then have to realistically consider whether through the course of time this little red wagon will develop, by these processes alone, a workable and efficient internal combustion engine, wings, and an on-board computer navigational system. What are the realistic odds that this wagon, through billions of typographical errors, can become the Space Shuttle? Remember, no communication or intelligence is involved in the sequence.

> Then how do you explain evolution by natural selection being so widely accepted in the scientific community as supported by massive amounts of evidence?

I can't explain it. I believe in evolution, but it has to have been guided by an intelligent, interfering personal being to have happened. All I can figure is two possibilities: (1) Scientists can't propose metaphysical solutions. It's outside of the range of science. And once they propose such solutions, they are no longer doing science, but rather philosophy or theology. (2) Scientists are motivated to arrive at an explanation that doesn't include God. (a) There is tremendous peer pressure. (b) Some scientists don't believe in God. And therefore they are a lot of fudge factors, god-of-the-gaps (we don't know the answer yet, but eventually we will so we assume the reality of what is now in the gaps), and just plain old ignoring the gaps to assume a sequence to explain the hypothesis.

I agree that for some complex systems you can't understand the whole thing just by understanding its parts, and the human mind may be one of those. The complexity of the brain may allow for choices and agency, but how can these be free choices, choices for which someone can be held morally responsible, if the conscious mind isn't responsible for the system that its choices emerge from - if it isn't responsible for the evaluation system all of it's supposedly free actions and decisions are based on?
​
> From my reading, there is not one, single, crystal-clear example of a known mutation that unambiguously created information.

What exactly do you mean by 'creating information', and what would such a mutation look like? As I said, if you look at an animal's genes you can find out a lot about the environment in which its ancestors successfully survived and reproduced. I would call that 'information'.
​
> Beneficial mutations occur at a rate less than 1 in a million, so low as to thwart any actual measurement. And a certain percentage of these are unselectable. Everything about the true distribution of mutations argues against their possible role in forward evolution.

The more complex an organism becomes the less likely a mutation is to be beneficial, since it's many genes interact in such an intricate way. But that doesn't apply to less complex organisms, so evolution probably proceeded much faster early on. Also, you can't forget that we're talking about 3-4 billion years of evolution. One beneficial mutation in a million can be quite a lot if you're talking about such a long time involving probably millions of trillions of organisms.
​
> No form of selection can maintain, let alone create, higher genomes. Selection can sometimes work on the genic level, but systematically fails at the genomic level.

Then how do you explain evolution by natural selection being so widely accepted in the scientific community as supported by massive amounts of evidence?

> I'm still waiting for you to provide me with some credible sources for this. From what I know we can't fully explain our mental capabilities yet, using a materialist approach, but that doesn't mean it's impossible to explain it in that way.

Dr. Warren Brown, neurologist of the Lee Travis Research Center, writes that neuronal systems are dynamical enough to give a plausible account of the emergence of high-level causal properties in complete system, but also reveal non-reducible properties and patterns in that system. He says that complex, nonlinear, highly interact aggregates becomes systems that are causal in tier own right through adaptive self-organization. He uses the illustration of an ant colony. Colonies of ants, he says, have causal properties that are not entirely attributable to the capacities and behaviors of individual ants. In the same way, neurons adapt and emerge in complex dynamical systems. (There's a whole lot more he says.) He concludes: "Thinking, deciding, consciousness, memory, language, representation, belief, etc. are large dynamic patterns of brain activity that constrain the ongoing lower-level physiological phenomena whose activity constitute the brain patterns themselves. Therefore the causal properties of patterns are not reducible to the elements. They are emergent."

His summary and conclusion:

* Will (agency) is not about initiation action from inaction, but it the modulation of ongoing action.
* Modulation occurs by comparison of the outcomes of ongoing action with criteria for evaluation.
* As we move up the nervous system more and more complex levels of criteria come into play.
* The anterior frontal lobes evaluate and modulate action with respect to long-term perspectives (past and future).
* Human nervous system is largely a self-organizing complex dynamical system that acts from its own point of view.
* Behavior and thought emerge from complex patterns related to current or imagined environmental situations.
* The very slow physical development of the human brain means it is maximally open to being formed by interaction with the physical and social environment.
* The capacity to simulate action off-line and evaluate the results allows for choice (agency).

He says, "There is an increasingly large domain of resources within the current understanding of neuroscience that support the requirement of human moral agency and free will."

I'm not a neurologist. I can only read and try to digest.

> Setting aside that most mutations don't have any phenotypic consequences, I agree that the majority of the mutations that do have an effect on the phenotype are destructive.

From my reading, there is not one, single, crystal-clear example of a known mutation that unambiguously created information. Muller (1964) showed that many mutations of a genome's nucleotides are unselectable. Kimura (1979) shows that most mutations are negative, even though near neutral.

Beneficial mutations occur at a rate less than 1 in a million, so low as to thwart any actual measurement. And a certain percentage of these are unselectable. Everything about the true distribution of mutations argues against their possible role in forward evolution.

Bergman (2004) reviewed the research and literature on beneficial mutations. Of his 453,732 "mutation" hits," only 186 even mentioned the word "beneficial." Of those 186, the presumed beneficial mutations were only beneficial in a very narrow sense and consistency involved loss of function (loss of information) changes. He was unable to find a single example of a mutation that unambiguously created new information.

Geneticists were working on an estimated rate of deleterious mutation of 0.12 - 0.30 mutations per person per generation (Morton, Crow, and Muller, 1956). Recent findings show that the rate is rather 100 (and possibly as high as 300) per person per generation (Kondrashov 2002). In other words, genetic deterioration is a certainty.

Natural selection doesn't help. Selection capabilities are limited to the final product, not the wording of the instruction manual, so to speak. Nor can natural selection communicate with the mutation process to create a superior manual. Natural selection can only allow or destroy the final product. Crow (1997) says, "The consensus among human geneticists is that, at present, the human race is genetically degenerating due to rapid mutation accumulation and relaxed natural selection pressure." This is not to claim natural selection doesn't work. It does, but only on a limited level. Natural selection has eliminated the worst human mutations, but selection is not a magic wand, nor omniscient, nor even intelligent. No form of selection can maintain, let alone create, higher genomes. Selection can sometimes work on the genic level, but systematically fails at the genomic level.

> Neurologists studying the brain find that our capabilities, ability to create, intuit, infer and adapt are not reducible to any physical explanation. The complexity of the brain's capabilities are far greater than any synapses firing sequence.

I'm still waiting for you to provide me with some credible sources for this. From what I know we can't fully explain our mental capabilities yet, using a materialist approach, but that doesn't mean it's impossible to explain it in that way. And we already made a lot of progress in that direction (again, see the Stanford lecture playlist I linked you). Just like a few hundred years ago people couldn't explain how life could emerge from dead matter, and they concluded there had to be some metaphysical life force - which we now know is not the case. It's a highly complex but 100% physical process.
​
> Random mutations consistently destroy information. "Natural selection" is a blind process.

Setting aside that most mutations don't have any phenotypic consequences, I agree that the majority of the mutations that do have an effect on the phenotype are destructive. But the very few ones that actually lead to an advantage in the organisms fitness, or the "fitness" of the replicators inside it, make for the potential of cumulative complexity and adaptation to the environment. So natural selection is actually a process of gathering information about the environment of a replicator (or a group of replicators "acting" in unison) and how to be successful in it, and it's a process of slowly (and very wastefully) giving rise to non-random strings of DNA, which have non-random consequences. If you don't think this is enough to lead to such highly complex organisms as we see today, it's just a failure to grasp the immense amount of time that has passed, and the diversity of possible chemical reactions.

> To think that random mutations and natural selection, chemicals and neuronic activity could somehow arrive at a working space shuttle is ludicrous.

> The idea that it came about through a process involving no purpose and no intelligence baffles credibility.

What more are these statement than mere intuitions of yours? And why should your intuitions be a trustworthy assessment of what's likely or possible? I could say the same thing about an all-powerful God - it "baffles credibility".
​
> Therefore how can you assert that they are conscious of their actions but those actions don't control them?

How do you know that you're not just experiencing your actions and decisions as being yours, when in fact you are aware of them but don't actually control them?

I have already explained these things. Consciousness is more than the processing of information. The brain is more than the sum of its parts. We are able to do things that defy mechanistic and chemical explanation. Neurologists studying the brain find that our capabilities, ability to create, intuit, infer and adapt are not reducible to any physical explanation. The complexity of the brain's capabilities are far greater than any synapses firing sequence. The primary axiom of evolutionary biology—that humanity is merely the product of random mutations plus natural selection—is an extremely vulnerable theory. To assume evolution from chemicals to reason, when truth is not part of the mutational or selective process, doesn't wash. Random mutations consistently destroy information. "Natural selection" is a blind process. Neither of them claim to create and verify informational data. One human cell contains more information than the Library of Congress. Our phenomena is immeasurably more complex than any known technology. To think that random mutations and natural selection, chemicals and neuronic activity could somehow arrive at a working space shuttle is ludicrous, and yet our brain is geometrically far more complex. The idea that it came about through a process involving no purpose and no intelligence baffles credibility. Our brains are not just senseless but high-level molecular machines. Instead, we are more than just the sum of the parts.

> Is it impossible for a conscious zombie to exist, someone who is conscious of their actions and decisions but doesn't control them? "Why [is this impossible]?"

First of all, we're into the Twilight Zone here, so the analogy is difficult if not impossible to work with. Zombies don't exist. But if they did, how do we know what their state of consciousness is? Therefore how can you assert that they are conscious of their actions but those actions don't control them? And then you try to hold me to that definition and explanation as if it's an argument against what I am saying?

To me it seems that you're just asserting things without explaining why it must be that way.
​
> Perceiving the brain as a computer minimizes and discredits the brain's capability and the unique place of consciousness.

How do you know this? Why should this be the case?

> Physicalism doesn't explain the complexity of the brain's dynamical systems that result in what we call consciousness.

Why not?

> Thinking, deciding, consciousness, memory, language, representation, belief, etc. are large dynamic patterns of brain activity that constrain the ongoing lower-level physiological phenomena whose activity constitute the brain patterns themselves. Therefore the causal properties of patterns are not reducible to the elements.

How do you know this?
​
Yes it is impossible.
Why?

Ah, yes. Now it seems we are resorting to the logical fallacy of "discredit the messenger."

> you start to sound dogmatic ("I will never believe that the brain is just a computer")

It's not that I'm dogmatic but rather that I'm not reductionistic. Perceiving the brain as a computer minimizes and discredits the brain's capability and the unique place of consciousness. Physicalism doesn't explain the complexity of the brain's dynamical systems that result in what we call consciousness.

* We are able to reason our way far deeper and beyond what can be explained by deterministic synaptic connections.
* Even within our own brains we are able to specialize, filter, innovate and adapt. Sometimes completely new systems emerge.
* Thinking, deciding, consciousness, memory, language, representation, belief, etc. are large dynamic patterns of brain activity that constrain the ongoing lower-level physiological phenomena whose activity constitute the brain patterns themselves. Therefore the causal properties of patterns are not reducible to the elements.
* Therefore there is necessarily true self-determination and free will.

> jump to straw men conclusions I already cautioned you against

Please. Let's not descend into insult. Straw men? C'mon. "I just want to caution you not to throw out everything in a purely deterministic world..." I have not thrown out everything but rather shown that it is self-contradictory and self-defeating. It's an untenable position.

> and cite authorities

Arguments citing authority are types of inductive reasoning.

> because you didn't address the argument I gave against free will, and I'd really like you to do that in your next response.

I've addressed it several times. I addressed it that last time you accused me of not addressing it. I devoted a whole post to addressing your argument against free will.

> What I assert is that you cannot ultimately determine your wants and control your decision because it leads to an infinite regress. You shape your wants because you want to shape them, and either you just uncontrollably want to or you decided to want it, which means you want to want it and so on, ad infinitum. How can this be reconciled with free will?

I disagree. Exercising my consciousness is an expression of my self-awareness which is an expression of self-direction, and therefore free will. My decisions that arise from my desires are not cyclical as you assert, but linear. I continually arrive at novel places and confront new desires and decisions. My free will expresses itself in my humanity, as I have explained. Both time and consciousness are linear in a forward direction, so free will is not an infinite regress.

> "any entity/organism that is self-aware must also necessarily be self-directed." Why should this be the case?

Because self-awareness involves reason: weighing situations, evaluating environment, assessing pros and cons, truth and falseness, and making decisions. Self-awareness that is locked into an unalterable path is not self-awareness at all but rather mere mechanistic robotism.

> Is it impossible for a conscious zombie to exist, someone who is conscious of their actions and decisions but doesn't control them?

Yes it is impossible.

> You assume there has to be metaphysical, transcendental truth and reason

I don't assume it a priori—the evidence leads me to it. But if we don't start with the possibility of truth as a first principle, we can't even have a discussion. Everything devolves into "what is," and truth is not part of the picture. But I have already explained this several times. If we can't agree that truth is possible, our discussion is meaningless. If we can agree that truth is possible, then we agree that some sense of transcendental truth must exist for us to define it and reason by it.

> And as I said, our merely physical reason has proven to be pretty damn effective in helping us understand the universe and become a technologically advanced species that's about to fly to Mars in the next decades.

Yes, and I have disagreed with this. Unless we have true free will, science is a sham and there is no such thing as science or reason. Unless we can honestly consider the data, weigh and assess the information, consider hypotheses, and decide which ones conform to reality (i.e., science and reasoning), "mere physical reason" doesn't take us anywhere. But, as I mentioned before, I'm repeating myself and I wonder if we have reached an impasse.

Actually, I think now it's just getting really interesting because (no offense):

1. you start to sound dogmatic ("I will never believe that the brain is just a computer"),
2. jump to straw men conclusions I already cautioned you against (you: "Every criminal could rightfully plead, 'I couldn't help it,' and they would have to be set free"; me, in a previous post: "I just want to caution you not to throw out everything in a purely deterministic world because people tend to overreact in that way. Like for example an admission that free will doesn't exist wouldn't mean we should get rid of our justice system and find everyone not guilty for reasons of insanity. We would just treat people like sentient robots.", meaning we would lock up people for the same reason we keep lions and crocodiles in zoos instead of letting them roam freely through the streets: prevention of violence and crime),
3. and cite authorities ("Francis Gorman says", "Many nontheist scholars disagree with you").

I only think it seems like we reached an impasse because you didn't address the argument I gave against free will, and I'd really like you to do that in your next response. This time you've said, again: "I am the one who shapes my wants. I am the one who decides my direction." What I assert is that you cannot ultimately determine your wants and control your decision because it leads to an infinite regress. You shape your wants because you want to shape them, and either you just uncontrollably want to or you decided to want it, which means you want to want it and so on, ad infinitum. How can this be reconciled with free will?

You also brought up another point, which is that "any entity/organism that is self-aware must also necessarily be self-directed." Why should this be the case? Is it impossible for a conscious zombie to exist, someone who is conscious of their actions and decisions but doesn't control them?

And the third point is that you claim "[my] retort is that what [you] say just isn't the case", whereas I see it as this: You assume there has to be metaphysical, transcendental truth and reason - or at least that everything would be pointless without it - and all I'm saying is that this isn't the case. This gets reflected again in your last sentence: "There is no warrant to assume the brain evolved to come to the right conclusion at least most of the time." What I mean by "right" is sufficiently corresponding to objective reality in such a way that the conclusions aid survival. And as I said, our merely physical reason has proven to be pretty damn effective in helping us understand the universe and become a technologically advanced species that's about to fly to Mars in the next decades.