There's some monkey business in the news. A blogger, hoping to prove the old adage that an infinite number of monkeys banging away at typewriters would eventually reproduce the works off Shakespeare, is using an array of servers processing millions of bits of information to "randomly" accomplish the same end. The experiment has already yielded "A Lover's Complaint."

http://tinyurl.com/3ze38st

So why did I put the word "randomly" in quotes? Because, as even the (above-linked) news story points out, the program works by identifying the desired words and checking them off the list. So while each single word is indeed produced randomly, the accumulation of words into coherent strings of text is actually guided by the design of the program.

It is not surprising that a random process can yield individual words, but that's a far cry from establishing that randomness can generate really complex systems. This point is neatly made in a comment by "Alina.Bolero" appended to the linked article:

"I know infinite probability is awfully hard to grasp, but when you start multiplying infinite improbabilities, things really do become that [much] more improbable.

"While I get the feeling that the intent of this experiment was to show that complex order can come from chaos, if you wait long enough, it has actually done a much better job of showing that the best way to create order from randomness is to apply intelligence to the system in order to create the desired outcome."

Comments

[Matt Rouge]

Yes, it's perfectly pointless. From the article:

Dr Ian Steward, emeritus professor of mathematics at Warwick University, said that for the monkeys to type up the complete works in the correct order without mistakes would take much longer than the age of the universe.

"Much" here meaning nearly infinite orders of magnitude more!

[j9]

"Ford, there's an infinite number of monkeys outside who want to talk to us about this script for Hamlet they've worked out."

Hitchhiker's Guide to the Galaxy

[Paul]

J9 - great book and film,

[Topher Cooper]

Anybody else ancient enough to remember Bob Newhart's old "Button Down" routine? -- "To be or not to be, that is the grxlpr"

In principal I agree with the basic idea expressed here -- this experiment is not the classic "infinite monkeys" thought experiment ...

but: a) it is not entirely off-base; b) the additional comments are off base.

It was never clear exactly what was meant by "reproduce all the works of Shakespeare". In a single contiguous sequence of letters? Or each play contiguous? Each act? Each speech? Each sentence? Marginal notes? Childhood exercises? Editions? What order of works if contiguous?

In the thought experiment, these issues were irrelevant, because the point was to illustrate the mathematical theorem that in an infinite sequence (or in this case an infinite set of infinite sequences) all possible sequences will occur after a finite (though indefinitely long) time with a probability one.

If we drop the contiguous requirement and allow it to be in short sequences then this experiment actually does fulfill the requirements.

What I agree with is that significant amounts of structure cannot arise out of randomness alone. That is, of course, one of the fundamental tenants of evolutionary theory. Randomness only provides what can best be described metaphorically as "creativity" or less metaphorically as "novelty".

What is needed to turn creativity into organization is (metaphorically) discipline. One requires a ratchet mechanism. Organization can only come from organization which is contained in that ratchet.

But that organization does not require intelligence. If you believe that that is the case, then you must also believe that the "Devil's Causeway" was actually built by the Devil, that a tornado must be a jinn, and that a dropped rock falls to the ground because an invisible daemon pulls it there.

What is required is not intelligence but a state of low entropy (or high neg-entropy), and the universe that we observe has very, very low entropy and it is a mathematical certainty that that implicit order will become, mechanically, explicit order given the chance.

By definition, any experiment will include intelligence but that is just a detail in this experiment. The template (the works of Shakespeare) is just an arbitrary sequence of characters as far as the experiment is concerned. That it is a sequence that has "meaning" to us beyond the experimental context is irrelevant. The mechanism is just an arbitrary physical mechanism that excludes sequences that fail to match the template as far as the experiment is concerned. That it happens to have been constructed for "a purpose" is irrelevant. We see all around us plenty of natural -- many not biological -- examples of both.

This demonstrates the immense power of the mechanisms of evolution. A random system that would by itself require many, many times the age of the universe, using all the resources of the universe to accomplish a task, can, given an essentially simple selection mechanism accomplish the same task in a few weeks with an infinitesimal amount of the universe's resources. This soundly refutes (once again) those who argue that evolutionary mechanisms are too weak to create anything highly organized.

Topher

[Michael Prescott]

Macroevolution requires a large number of simultaneous or nearly simultaneous changes, but random mutations can account for only one or two beneficial changes (at most) in a generation. According to neo-Drawinism, changes that have no immediate utility should be lost almost at once, since they do not confer any additional survival value.

The experiment shows that very simple order (a single word, corresponding to a microevolutionary change) can be achieved through a random process, but in order to produce a more complex order (macroevolution), some kind of teleology is necessary. In this case teleology is built into the program, which is designed to select only the desired words and then hold them in reserve while more words are identified. This would be the equivalent of evolution holding on to useless traits for many generations until enough microevolutionary changes have occurred to render the previously useless traits valuable. But without teleology, there is no reason for the species to hold on to currently useless traits, even if they might be valuable in the future.

Since teleology is anathema to orthodox neo-Darwinists, they get no help from this experiment.

[Roger Knights]

"Anybody else ancient enough to remember Bob Newhart's old "Button Down" routine? -- "To be or not to be, that is the grxlpr""

To be and not to be
That is the answer

[Topher Cooper]

"Macroevolution requires a large number of simultaneous or nearly simultaneous changes..."

This is very simply untrue. Macroevolution requires small incremental changes. The supposed demonstrations otherwise are flawed, and simply assume that some arbitrarily selected "end point" was necessarily reached in a direct line, and supposes that since a broken egg cannot be put back together again it could not have possibly been formed in the first place.

[Topher Cooper]

"According to neo-Drawinism, changes that have no immediate utility should be lost almost at once, since they do not confer any additional survival value."

Actually, simplified versions of neo-Darwinism say that useless traits will neither diminish nor increase in frequency within the population. More detailed versions, recognize that traits near each other on the genome tend to be inherited together and thus neutral, or even slightly deletrious traits can be carried on the coat-tails, so to speak, of more positive traits and thus may increase in the population for a fair amount of time.

In fact the genome is dominated by useless genes that serve absolutely no purpose. Cases have been observed where such previously useless genes have undergone mutation or recombination and suddenly start serving a function. For example, the development of the third color receptor in primates came about through changes in redundant copies of one of the two existing kinds of color receptors. This process has been shown to have also resulted in a fourth color receptor in a few human beings. Whether or not this will be spread within the population will depend on whether people gain any reproductive advantage from their slightly increased ability to make fine color distinctions, and also on luck.

[Topher Cooper]

"But without teleology, there is no reason for the species to hold on to currently useless traits"

However, "purpose" is irrelevant except for teleological explanations, so the lack of a purpose is not relevant to evolution.

It is a routine, unmistakable observed fact that useless genes (which may or may not correspond to traits) are routinely and massively preserved for millions of years. This isn't an assumption of neo-Darwinism but an observe fact.

Also you appear to be completely neglecting that a trait can be beneficial for one purpose, and then, with other changes in environment or genetics become part of another beneficial trait. Things like sweat glands becoming mammary glands, and breasts become secondary sexual characteristics that are part of mating. No need for breasts to spontaneously appear fully formed.

[Topher Cooper]

"The experiment shows that very simple order (a single word, corresponding to a microevolutionary change) can be achieved through a random process, but in order to produce a more complex order (macroevolution), some kind of teleology is necessary"

Well if "some sort of teleology" includes any selection process, then it does demonstrate it, otherwise not. The relevant characteristic of the process is not "purpose" (i.e., teleology) but only information (in the purely mechanical sense, i.e., the inverse of entropy).

Obviously, by definition, an experiment serves a purpose and so the selection in any experiment will be teleological, but that the selection process serves a purpose is irrelevant to the results. There is nothing about this experiment that makes its purpose relevant to the outcome.

A purpose is only required of the process if one assumes that the result serves a purpose. Teleology is a self-justifying assumption.

Every spring, throughout New England, rocks emerge from fields. A more or less random mixture of soil and rocks spontaneously reorganizes itself so that the larger rocks move upward. This occurs because of a mechanical ratcheting process without any purpose required. So no, Michael, that the raisins are at the bottom of your cereal box, and the peanuts are at the bottom of your Cracker Jacks box does not prove that there is a nasty intelligence putting them there for the purpose of frustrating you.

[Michael Prescott]

"So no, Michael, that the raisins are at the bottom of your cereal box, and the peanuts are at the bottom of your Cracker Jacks box does not prove that there is a nasty intelligence putting them there for the purpose of frustrating you."

Such an idiotic straw-man argument doesn't deserve a serious response. Unless you actually think the problems of macroevolution are comparable to the Cracker Jack example.

You asseverate that a great deal of genetic material is useless, when in fact no one knows what its function may be. Many guesses have been proposed for possible uses of so-called junk DNA.

If macroevolution doesn't require numerous small changes occurring simultaneously or in close succession, Stephen Jay Gould wouldn't have felt obliged to develop his theory of punctuated equilibria. If macroevolution happens slowly, over vast stretches of time, we are hard pressed to explain the Cambrian Explosion and the many sudden jumps in the fossil record.

Neo-Darwinism is the last of the three great 19th century myths. Marxism and Freudianism have already been largely laid to rest. Neo-Darwinism will follow eventually, and then inquiring minds will turn to the real problems of evolution (which surely does occur, by some mechanism) and maybe find some answers.

But, Topher, I doubt those answers will be found at the bottom of a Cracker Jack box.

[XXII]

I'm not intersted in adressing all the points that Topher Raises, but I would like to point out that it doesnt follow from the notion that some organization might require intelligence that 'you believe that the "Devil's Causeway" was actually built by the Devil, that a tornado must be a jinn, and that a dropped rock falls to the ground because an invisible daemon pulls it there."

It seems, by and large, as a strawmen, whose purpose doesnt seem quite clear to me. Otherwise the comment raises some interesting questions, but the portrayal of the issue in that particular point seems to bring into question the cohesion of the arguement.

In the cases suggested 'intelligence' is equated to 'mind'. It is entirely possible that a brute fact of our universe is that everything is inherently mindful, and that albeit its low complexity, this mindful behaviour is sufficient to act as a self-organizing principle.

In this sense there is no clear distinction between inert and organic matter, dumb aggregates and intelligent compounds. It seems entirely possible that this organizing principle becomes actually efficient when certain patterns are achieved, so that it is able to exert changes in the direction of its own development.

Moreover, it is possible that the arbitrary solitude which minds are condemned to is a hasty one, and that although remaining indendent, embodied minds are meshed within a larger scheme of mindful behaviour that elicits simultaneous changes over large distances, which could account for some of the issues Michael raises.

[sbu]

In fact the genome is dominated by useless genes that serve absolutely no purpose.

Says who? :) We think we know so much but in fact we know very little.

[Matt Rouge]

"No need for breasts to spontaneously appear fully formed."

Oh but there *is* a need!

[jshgfcre98ijyds]

Someone please remind me ... what is the empirical evidence that the mechanism of evolution was natural selection. And what is the empirical evidence that the mutations that occured during evolution were due to chance?

Thanks

[Michael Prescott]

Matt Rouge, thread-winner!

[Roger Knights]

"Neo-Darwinism is the last of the three great 19th century myths. Marxism and Freudianism have already been largely laid to rest."

#4: Keynsianism #5: Climatism (catastrophic manmade global warming)

[Topher Cooper]

Re: Jinn and Cracker Box

The argument was made that order cannot arise out of random processes without "teleology" (purpose). Sorting by size by random, anisotropic movements (rocks in soil, raisins in cereal, and peanuts in cracker-jacks), coherent storm systems, the regularity of the Devil's causeway, and (according to QM) the falling of a rock (or any other mechanical movement) are counterexamples outside the realm biological evolution.

And yes, simply saying that something must be going on beyond this (other than a matter of linear scaling) does not mean that, in fact, something more than this is going on.

Mathematically, its the same, except that the process applied many billions of times more produces billions of times more organization.

Calling something an "idiotic straw man" doesn't make its relevance disappear. Your argument is that coherent processes are incapable of shaping random processes to form complex structures (except that you ignore the primacy of the coherent processes in production of the complexity, and just talk about the random processes) unless those coherent processes have a purposeful goal in mind.

This claim is, of course, "idiotic" -- trivially demonstrably untrue. So you draw a line in the sand and insist that while complex systems can clearly form without purpose, there is a unstated mechanism that limits how complex such structures can be.

[Barbara]

"Mathematically, its the same, except that the process applied many billions of times more produces billions of times more organization.Calling something an "idiotic straw man" doesn't make its relevance disappear."

It's fair to say that maths is idiotic if it wasn't invented by an intelligent mind. What or who invented entropy? Did it idiotically invent itself?

As for djinns, I haven't seen one, but I've seen fire spirits. They live on my compost heap and heat it up.

[Topher Cooper]

"If macroevolution doesn't require numerous small changes occurring simultaneously or in close succession, Stephen Jay Gould wouldn't have felt obliged to develop his theory of punctuated equilibria. If macroevolution happens slowly, over vast stretches of time, we are hard pressed to explain the Cambrian Explosion and the many sudden jumps in the fossil record."

Evolution, macro or otherwise, requires many small changes, generally occurring sequentially. Mutations are common. The average human being has around thirty point mutations -- base pairs inherited from neither parent. There are many more non-point mutations, however -- duplications, truncations, transposition, reversals, etc. Plus sex introduces many novel combinations that are not actually mutations but function, evolutionarily in a similar fashion.

For some reason, punctuated equilibrium was controversial in biology. The reaction in the evolutionary computation (EC) community was pretty much a resounding "Well, duh!". When a group of organisms are in a region of the fitness function that is relatively flat, there is little selection and the system will be close to an equilibrium state. Eventually, however, either through slow progression or through changes over time in the fitness function, a point on the fitness landscape will be reached where there is a steep slope, at which point, small steps in genetic terms are strongly selected and you will get rapid change. If this slope leads to a region of complex topology (lots of peaks and valleys -- unfilled niches) you will get a sudden explosion of diversity.

Since Eldredge and Gould proposed the idea tests have been mixed. Their assertion that evolution occurs through punctuated equilibrium has been thoroughly disproved. However, that biological evolution sometimes follows this pattern has been thoroughly demonstrated -- as would be predicted by EC.

So PE, even if it was strictly true, does not mean that evolution requires multiple, near simultaneous, major and individually meaningless mutations. It means that, as has been demonstrated independently of the controversy since, the base mutation rate is much higher than was generally thought at the time but that selection pressures are much more variable than was generally supposed.

Are biologists still emotionally amazed by the rate of diversification during the Precambrian explosion? Yes, just as computer scientists are frequently amazed by the effectiveness of some algorithms or heuristics. Does this give any support to the idea that their must be some purposeful guidance to explain it? No more than that I should conclude from the fact that I can use my phone to handle a difficult problem like speech recognition that it must contain an intelligent spirit.

In fact, the Precambrian explosion argues fairly strongly in favor of evolution rather than purpose, since most of the diverse body plans created in it ended up being tossed aside and discarded, having no long-term effects and therefore serving no particular purpose. Of course, you could suppose that the hypothesized teleological actors were not particularly intelligent or given to planning, and simply experimented randomly. But then, of course, there is no real difference between that and evolution except for an ineffective, unknowable purpose operating.

[Topher Cooper]

"In fact the genome is dominated by useless genes that serve absolutely no purpose."

Says who? :) We think we know so much but in fact we know very little.

I was not speaking of the stretches of DNA that are truly mysterious. Those are not, in any sense now understood, genes. I had in mind the large amount of DNA that represent duplicated, thus redundant, thus useless genes, many of which have had either themselves or their activation sequences so damaged (since they are redundant, their is no selective pressure weeding out such damage) that they do not produce a protein of any kind.

In fact, as was implicit in what I was saying, while they do not have a purpose, they do seem to have a function -- but only if evolution is operating. The form a reservoir of the raw stuff of evolution -- genetic diversity -- available with just a further mutation to provide for a need under circumstances of rapid change and challenge. A redundant red color receptor gene shifts to peak in the green and there is a sudden large leap in color acuity.

[Topher Cooper]

For what it is worth, the term "macro-evolution" is being stretched rather thin here. Mostly, macroevolution (in the loose sense) is precisely the same qualitatively as "microevolution" -- there is just more of it.

Biologists distinguish macroevolution as a particular area of study as changes taking place at or above the species level. The change in scope at times requires a different way of looking at the way the same underlying processes manifest.

It does not particularly refer to large changes in organisms, but to changes in large, genetically diverse populations.
Mostly its about different tools needed to deal with a broader, but not fundamentally distinct, perspective.

The one exception to this is the qualitatively distinct phenomenon of speciation, that marks the lower bound of macroevolution. Thirty years their were lots of theories around about how the seemingly abrupt species boundaries could develop, but neither the analytic tools necessary to show that any of them were particularly mathematically plausible nor the experimental tools necessary to show that they actually occurred. Creationists liked to jump from "we don't know how" to "there is no way" as a way of "debunking" evolutionary theory.

Today, however, a) the whole concept of a species is not as clear-cut as used to be thought; b) analytic tools have been developed that show that while some of the proposals do not work, a number of others have been shown to be mathematically sound -- which essentially means that in the right, quite natural and uncontrived, circumstances, speciation will unavoidably occur; c) it has really sunk in that there is no need for there to be a single theory -- a single set of circumstances that will cause a species to develop; d) new experimental and observational techniques have been developed so that these mechanisms have, in fact, been observed taking place (especially, of course, because of time scales, in single celled life such as bacteria).

This is still a hot area of research, new mechanisms are being regularly proposed and finer nuances added to the analysis of the older ones. But the claim that because it was unclear how evolution could produce speciation that it was therefore clear that evolutionary processes could not do so can no longer be supported even in a weak sense.

Given the conditions observed in the biosphere, it is impossible that highly complex systems would not develop over time and that this would include the development of distinct species.

[Michael Prescott]

"#4: Keynsianism #5: Climatism (catastrophic manmade global warming)"

Yeah, but those aren't 19th century myths. I'm not even sure Keynsianism is a myth. Properly applied, within limits, it may do more good than harm. Needless to say, it wasn't properly applied in the stimulus bill.

"No more than that I should conclude from the fact that I can use my phone to handle a difficult problem like speech recognition that it must contain an intelligent spirit."

Your phone was intelligently designed, Topher.

"The argument was made that order cannot arise out of random processes without 'teleology' (purpose)"

Another straw man. Obviously certain kinds of order do arise out of random processes. For instance, the Shakespeare experiment does generate individual words. But there comes a point where the order is simply too complex to be generated by any random process, because the process would take much longer than the time available. Creating even a single protein purely by chance would take far longer than the age of the Earth, even if the entire planet were packed with amino acids. A cell requires hundreds (at least) of proteins. It also requires the information coded in DNA or at least RNA. That information is massively complex, equivalent to the contents of the Encyclopedia Britannica. We are told it arose by chance, yet it would take much longer than the age of the universe for this to happen. DNA is useless without proteins to carry out its instructions, yet those instructions tell how to make proteins. How did the proteins arise without the instructions necessary to make them? Proteins are necessary to activate DNA, but activated DNA is necessary to make proteins. Which came first, the chicken or the egg?

These are hard problems. They can't be handwaved away with silly pseudo-arguments about the Devil's Causeway. Oh, and by the way - how do we distinguish between the Devil's Causeway and, say, the giant stone heads on Easter Island? If the causeway was formed by natural forces, couldn't the heads have been made that way too? Yet no one believes this. Why? Because while the causeway does not, in fact, show any significant signs of intelligent planning, the stone heads do. The likelihood of a series of humanoid stone heads being formed by chance is so small that no one would credit chance as an explanation. The likelihood of the first living cell arising by chance is much smaller.

[Roger Knights]

I'm not even sure Keynsianism is a myth. Properly applied, within limits, it may do more good than harm. Needless to say, it wasn't properly applied in the stimulus bill.

I'm thinking of it in its exaggerated version, which is the version pushed by Krugman, the Fed, and much of the economics profession. Here's a critique by David Stockman today of how central bankers' "enabled" politicians to run up a huge debt load on the country; the thinking behind this was Keynsian (stimulus will expand the economy and we'll outgrow the debt burden):

http://www.zerohedge.com/news/david-stockman-blame-fed

The EU's central banks, politicians, and eurocrats colluded similarly.

[jshgfcre98ijyds]

The theoretical argument against Keynsianism is that it is more efficient for individuals to spend money than the government. Any layer of government bureaucracy deciding how money should be spent is going to have some mistakes and inefficiencies if not outright favoritism, cronyism, and graft.

Left alone, ie with minimal government regulation and low taxes, people will put money to work either buying and selling as individuals, or investing in companies or lending it to companies, or to banks that lend money. Unless people are hoarding cash under their mattresses, I don't see how letting the government decide how money should be spent is going to help the economy.

Infrastructure projects like dams and interstate highways might be beneficial to society and the economy but not necessarily as a means of moderating the boom and bust cycle.

Some people tend to think corporations are corrupt. I think there is some truth in that and you need some level of government to control the worst tendencies in individuals and corporations that lead to abuse of the environment, customers, workers, competitors, and suppliers. But ultimately all wealth comes from corporations. Corporations hire workers. If everyone worked for the government, no one would be creating wealth to pay taxes to fund the government.

Some people think the government is corrupt, and I think there is some truth in that. Power corrupts. You need a free press and intelligent voters to control the tendencies for people in government to abuse their power. I don't think the partisan press does a very a good job policing its favored politicians or reporting fairly on its disfavored politicians. Thank goodness for the internet with all its flaws and nonsense there are outlets that can publish the truth.

[Topher Cooper]

"No more than that I should conclude from the fact that I can use my phone to handle a difficult problem like speech recognition that it must contain an intelligent spirit."

Your phone was intelligently designed, Topher.

Of course, and that is not at all relevant to the point I was making. I have, on and off, been working in the field of artificial speech recognition since 1970. I understand how it works. I keep up with the latest developments. But I find it amazing that my colleagues have done so much on such a small platform. My sense of amazement comes not from an ignorance of how it could possibly be done, but out of knowledge of the techniques and how well the refinements, extensions and completely novel algorithms built on the work we did on the first working continuous speech recognition system works.

Similarly, interpreting biologists amazement at the Burgess Shale fossils as some kind of evidence that their theories are wrong is totally off base.

[jshgfcre98ijyds]

While I'm rambling off topic... I'll just add that the current economic downturn seems most likely due to the housing crisis. There is some debate as to whether that crisis was caused by wall street corruption or government misregulation. Ultimately it seems to me that the wall street will push the envelope in search of profits but the details of that envelope are the result of government regulations. So I see the cause as ultimately as due to government misregulation.

However I think there is a lot of blame to go around including congressmen who thought demands to fix fanny mae before this crisis happened were due to racists who didn't like to forcing banks to lend to minorites, and wall street rating agencies who misrated mortgage backed securities, wall street firms that marketed those securities, mortgage brokers who encouraged mortgage applicants to lie on their mortgage applications, and ordinary people who bought a houses far more expensive than they could afford or who kept drawing money out of their house through refinancing and who later defaulted when faced with loss of personal income due to a job loss or when the ponzy scheme of continual refinancing was busted up when home prices fell.

[Topher Cooper]

Another straw man.

I think not -- it is a demonstration of the hollowness of your argument. I did go on to say that the argument was so transparently false that for anti-evolutionists to support it, they had to elaborate the original blanket claim that order could never arise out of randomness, to one that argued that there was an unspecified limit on complexity -- but we should take their word for it, life exceeds it.

Obviously certain kinds of order do arise out of random processes. For instance, the Shakespeare experiment does generate individual words.

Read the experiment again. Short sequences (not words) are the fundamental unit of selection, but what will undoubtedly (i.e., with probability 1) result if the experiment runs to completion will be the complete works of Shakespeare.

But there comes a point where the order is simply too complex to be generated by any random process, because the process would take much longer than the time available.

Now who is presenting straw men -- and straw men that have already been labeled as such in this thread.

Hey! I can disprove elementary celestial mechanics. QM shows that all trajectories are the result of the averaging out of an infinite number of random possible paths. Therefore any possible trajectory is a result of a "random process". It would clearly take far more time than the age of the universe for the Earth, wandering randomly, to have made even one nearly perfectly elliptical orbit around the sun much less the millions of such orbits claimed. Therefore, the concept of the Earth revolving around the Sun is nonsense.

In fact, both the modern theory of mechanics and the theory of evolution are not about random processes. They are about random processes constrained by deterministic processes and that is a whole different thing.

It is, however, a fundamental tenet of evolution that there are severe limits to how much change can occur from the random processes without the direction supplied by selection. Over and over again, we find that living things are constrained by just this limit. The vertebrate retina, for example, does not gain sensitivity and accuity by inverting itself and reworking its circulation, as is predicted by evolution, but in contradiction to design (without adding large assumptions of some mysterious problem with a more rational design).

Creating even a single protein purely by chance would take far longer than the age of the Earth, even if the entire planet were packed with amino acids.

We are entirely in agreement here. Since this does not have anything to do with what is claimed by evolution by selection, it is again a straw man.

A cell requires hundreds (at least) of proteins.

As usual we have drifted from what is generally referred to as the Theory of (biological) Evolution, which is as thoroughly proven as celestial mechanics, and speculations about prebiotic evolution, which seems likely but has not been established. If you wish to believe that the first cells were dropped into Earth's ocean by a passing alien spaceship clearing out its toilet tank then I cannot argue with you.

Second, modern cells require hundreds of proteins, but there is no particular reason to assume that primitive life required hundreds of proteins, or anything resembling proteins at all, or were in the form of cells (though it seems a likely requirement, and, given the tendency for some kinds of molecules to form hollow spheres spontaneously, not difficult to account for).

It also requires the information coded in DNA or at least RNA.

Again that is true for modern life but it may not be necessary for early life. Keep in mind though, that we are not discussing neo-Darwinism here.
That information is massively complex, equivalent to the contents of the Encyclopedia Britannica.

That is the case in modern cellular life, but it is an assumption that this is a fundamental requirement for life (especially when there isn't anything more efficient to compete with). A near counter-example is found in viruses. They are very much simpler than cells, are biological systems, subject to mutation and selection, although its questionable that they can be considered living. They could, however, bear some resemblance to early living things operating within the primordial soup.

We are told it arose by chance,

Perhaps, but not by anyone who supports evolution by selection.

yet it would take much longer than the age of the universe for this to happen. DNA is useless without proteins to carry out its instructions,

True but RNA is not, and it is not all that unlikely that there are other, even simpler self-replicating molecular systems.

yet those instructions tell how to make proteins. How did the proteins arise without the instructions necessary to make them? Proteins are necessary to activate DNA, but activated DNA is necessary to make proteins. Which came first, the chicken or the egg?

Obviously the egg unless you means specifically a chicken egg in which case the answer is neither.

You seem to think that the opposite of "random" is "purposeful" but that is an error. The opposite of "random" is "deterministic". Evolution is not a random process, but it is an arbitrary (i.e., non-purposeful) one.

[XXII]

I wonder, though, if allowing for consciousness to be an active agent in Evolution does not equally allow purposeful, rather than strictly deterministic, agency.

If your stance on consciousness isnt that of an epiphenomenalist, a physicalist, or any other stance that assumes consciousness to be determined by the physical properties of the system (brain), then it is atleast possible to admit some degree of purposefulness, albeit not of the class that is suggested by Creationists.

Personally, I do not think that consciousness can be reduced to any mathematical or physical description, and thus it cannot be said to respond to any given deterministic process. This means that consciousness has exerted some kind of agency that is beyond the ones admitted by classical and QM descriptions of physical events and processes.

I do feel that maybe, Topher, you are confusing Michael's Stance as that of a Creationist? Im not sure at all that is what he is suggesting.

[Topher Cooper]

Nope, based on this and previous discussions I do not believe that Michael is a Creationist either under that name or under its more modern redubbing "Intelligent Design"

The Creationists are motivated by religion, primarily fundamentalist Christian though they now have learned to hide the fact using code words to avoid saying that they mean the Christian god when they talk about intelligence.

I do not believe that Michael is a Creationist -- someone who believes that the biosphere was created in essentially its present state in a single act of creation. He does, however, use the arguments based on misunderstandings, question begging, and lots of vigorous assertions that the Creationists have promulgated to support his own belief that evolution needed to be constantly pushed along for the biosphere to develop.

[Barbara]

Topher's use of the word "deterministic" in my view is deliberately obscurantist. The question remains: determined by who?

To imply that the laws of creation simply came about by chance ex nihilo is an act of faith - it cannot be proven.

Why shouldn't the universe be purposeful? I agree with Michael.

[XXII]

Well, but isn't evolution pushing itself along the way too? That's what the rest of my comment was about. If you allow conciousness to be, in the ontological picture, irreducible to physical properties and consequently to physical description, so that its properties are categorically distinct, you might have grounds to argue for purposeful rather than merely deterministic processes in Evolution.

Furthermore, I do think that saying that Intelligent Design is just Creationism under a new guise is nonsense. Those who have professed that some degree of intelligence takes part in Evolution, amongst other processes in Nature, are quite diverse and certainly do not adhere to the tenets of Creationists. Whitehead would be an example.

[J9]

Wish I was smart enough to follow all this. I will refer back to the "to be or not to be comment". Being the mathematician I am, my license plate says 2CALCUL8, with the hope that someone will ponder "or not to calculate". I subscribe to the Platonistic view that math cannot be an art, it isn't made up to explain the universe, but discovered. There are often Debates at Universities that math should belong to the humanities. It almost makes me laugh, but my own department head agrees.

[Michael Prescott]

Topher, I brought up abiogenesis to clarify what I mean by a degree of order that cannot arise by chance.

If you think proteins and DNA (or RNA) can arise by chance, you're in disagreement with the statisticians who've studied the problem. If you think they arose by some constrained process, you'd need to explain what the constraints are. What natural process channels amino acids into the very specific sequences that constitute proteins? No such process is known, so insisting that there must be one is simply promissory materialism.

"Hey! I can disprove elementary celestial mechanics. QM shows that all trajectories are the result of the averaging out of an infinite number of random possible paths. Therefore any possible trajectory is a result of a 'random process'. It would clearly take far more time than the age of the universe for the Earth, wandering randomly, to have made even one nearly perfectly elliptical orbit around the sun much less the millions of such orbits claimed. Therefore, the concept of the Earth revolving around the Sun is nonsense."

The trajectory of any single particle is random, but masses of particles have a predictable trajectory, as determined by classical physics. Therefore the issue of "not enough time" doesn't come up, since a large mass like the Earth would never deviate significantly from its averaged-out orbit; it would exhibit that orbit the very first time, and every time. What this has to do with proteins or DNA or, well, anything, really, is unclear. Unless you're saying there is some chemical equivalent of the Newtonian laws of motion that channels the sequencing of amino acids into proteins? Some natural law(s) that gives rise to self-organizing systems? Prove this, and you'll be a Nobel laureate. For now it's more promissory materialism (though I don't rule out the possibility that it could be proved someday - I'm just not willing to give materialism the benefit of the doubt).

[Topher Cooper]

Furthermore, I do think that saying that Intelligent Design is just Creationism under a new guise is nonsense.

Historically, when the Creationists lost their legal battle to openly teach religion as science, they changed the names of institutions, edited their tracts to no longer explicitly use the word God, and to replace the phrase "Creation Science" and variants with "Intelligent Design" and variants. Much of the literature is word for word identical except for those attempts to hide the agenda.

The arguments are still identical -- the same vehement assertions without evidence, the same misrepresentations of what evolution is, the same quotes out of context, the same assumptions about unsolved problems (many of which have been solved in the meantime) being necessarily unsolvable problems, etc.

The core institutions, most of the key people, most of funding, most of the literature, are exactly the same as the Creationists, simply rebranded in order to deceive (which is OK because its OK to deceive as long as it serves God's Truth).

There are many people, a few prominent who have been taken in by this sham, or don't think it important (which is not unreasonable) who cannot be described as Creationists. I explicitly said that I firmly believe Michael to be among them.

But, to quote the common but recently stupidly controversial saying, "If you put lipstick on a pig...". Like any institution Creationism has changed, but at its core it is the same despite the name change.

[Topher Cooper]

Why shouldn't the universe be purposeful?

No reason why it shouldn't be, nor, more relevantly, why it couldn't be. In fact, I have a lot of sympathy with the idea.

I only have problem with misrepresentation of the facts in order to try to argue that it must be.

I am a parapsychologist (though not in a position to be terribly active at the moment) and am more than moderately open to the idea that consciousness may manifest physically in the universe in ways that are not conventionally understood. But I'm looking for evidence not heartfelt assertions that it must be so.

[XXII]

But Topher, the point isnt wether you can subsume the tenets of Creationism under the tag of Intelligent Design, in so far as the latter term is concieved within an Insitutional framework. Strictly speaking, Intelligent Design doesnt entail, logically or otherwise, the ontological or metaphysical premises that characterize Creationism.

It may be the case that Creationists, as individuals or as an insitution, have embraced such title for their workings, but this has little bearing on the actual failure or sucess of Intelligent Design theories, as a class, in describing acurately the nature of reality.

As I said, many theorists that are fundamentally distinct from Creationism have admitted some degree of purposefulness and 'intelligence' (not to be confused with an human-like mind) in Nature. Some of them learned, dilligent and knowledgeable persons.

To dismiss these explanations with a casual hand waive, grounding such dismissal on the basis of 'guilt-by-association' premise seems unecessary. Maybe you are trying to advocate a political position in the Creationism vs. Evolutionist debate (quite crass terms, to be honest), a prupose to which the dismissal has practical value (as Sam Harris' discourse on 'Religion').

In any case, I just want to note that it seems like a poor tactic and there are stronger grounds in which to argue against the institutionalized position of Creationists, without having to dispose of the notion of ID altogether as a metaphysical model.

Finally, you haven't adressed the points im making about consciousness and purpose in the course of evolution.

[Topher Cooper]

If you think proteins and DNA (or RNA) can arise by chance, you're in disagreement with the statisticians who've studied the problem.

I don't know anything about these statisticians nor why the formation of a chemical is a statistical issue. Rest assured, I do not think that RNA, DNA or carbon-dioxide arises by chance. Nor does anyone else I am aware of.

If you think they arose by some constrained process, you'd need to explain what the constraints are.

Primarily quantum electrodynamics. You do realize that short RNA sequences have been found as the product of conditions that not only could have been, but almost certainly were present on the early, prebiotic Earth?

What natural process channels amino acids into the very specific sequences that constitute proteins?

Actually, virtually any random RNA or DNA sequence represents a protein, and RNA in the presence of amino acids can, by itself, assemble them into proteins. A protein is simply a polymer of amino acids, and amino acids will polymerize spontaneously (though slowly without a catalyst, and completely randomly without a template), so even RNA is not necessary.

But to address the intent of the question, I don't know what process (teleological or otherwise) did channel things into the specific self sustaining and self replicating chemical system we now see. We do know that given the right initial chemical system, selection will inevitably channel things into a more efficient and complex system, but I don't know that this occurred, nor what particular chemical system and physical conditions started it if it did. There is no strong reason to believe that the initial, presumably simple, chemical system had to involve nucleic acid and amino acid polymers.

A number of plausible systems have been proposed (with RNA based life high on my personal list as at least a likely stage in the route from chemical soup to the present biosphere), and some have had some analytic or experimental support as possibly practical. None, however, has really been demonstrated to be clearly likely. Without time travel, we are unlikely to ever be able to say with certainty how it did occur here (if it did, I'm not averse to panspermia) even if we are someday able to observe the transition from prebiotic to biotic systems on other planets or in the test-tube.

Again, prebiotic evolution is a fruitful but perhaps incorrect hypothesis, not the established theory that biological evolution is. You could completely demolish prebiotic evolution without it having any bearing on the likelihood of neo-Darwinism.

No such process is known, so insisting that there must be one is simply promissory materialism.

I like that phrase, I don't remember seeing it before.

In any case, you are the one claiming that no such process does nor can exist. I'm just saying that it is possible that it may. Your claim; your requirement to back it up; your promissory non-materialism ("promissory teleological idealism"?, "promissory dualism"?, "promissory designerism"? None of them have the ring of the original, I'm afraid).

[confused]

God, this is complicated. I can't understand half of it.

[Topher Cooper]

Topher's use of the word "deterministic" in my view is deliberately obscurantist.

I certainly was not attempting to obscure anything -- the precise opposite. "Deterministic" is simply the antonym of "random" it means that someone could, in principle, given enough information, determine in advance what the outcome of a process will be. There are several mathematical definitions of what it means to be unable to determine an outcome, the historically most important being the Von Mises/Church definition, though the Kolomogorov definition has risen in prominence over the last few decades. These definitions can be inverted to define what "deterministic" means.

I may have left some issues unaddressed (I'm prolix enough without attempting to address all possible issues) but I do not believe that I obscured anything, and know that I did not intend to.

The question remains: determined by who?

Technically, I answered that above -- anyone or anything with sufficient information and computational resources to do so. It is "to determine" like "he determined that John was elsewhere when the crime occurred" not "determine" like "he was determined that they would obtain the Crown Jewels" or like "the Gang determined the Olaf would pick the locks."

Setting that aside, it is an interesting question that is well worth considering -- as long as its kept in mind that asking it assumes that action requires teleological agency rather than demonstrating that such agency exists. Its a question like (though less deliberately unfair) as the famous "Have you stopped beating your wife?" -- any answer requires an arbitrary assumption, and the only accurate answer may (or may not be) no answer at all.

[Topher Cooper]

I did not bring up the historical, political and ideological connection between Creationism and Intelligent Design for purposes of guilt by association. It is no sin to believe in either Creationism nor Intelligent design. The only sin is to deliberately deceive and mislead in order to further a hidden agenda. Most of the proponents, and almost certainly those taking part in this discussion, are the deceived rather than the deceivers.

No, the point was that if you want to analyze and dispute the Theory of Biological Evolution by Selection then you need to address what that theory actually is, and the literature of the Creationists cum Intelligent Designers is a poor source of information about that. It is largely the product of a group whose agenda is not particularly concerned about scientific truth and which has, in fact, been openly opposed to it in the past. Again they have been shown in the past to have engaged in deliberate and egregious misrepresentation (or to be less polite about it, lying and cheating) and there is no reason to suppose that the core of the movement has changed in the least. However much it supports your own philosophical or religious beliefs they are not reliable sources of information.

If you can find someone with any qualifications clearly unaffiliated with this group by all means give them the benefit of the doubt (though I have yet to find any who, if not outright affiliated, at least depend on those who are for most of their facts).

If you think an argument is solid, by all means accept it -- the source of an argument is irrelevant to its soundness. But do confirm the supposed facts on which it is based, do confirm that their aren't critical things being left out (e.g., the context in which some well known biologist said something, or that it isn't something that was rejected by the scientific community and that therefore is not part of the theory at all), and do confirm that it does not contain subtle fallacies that have been thoroughly demonstrated elsewhere.

[Topher Cooper]

The trajectory of any single particle is random, but masses of particles have a predictable trajectory, as determined by classical physics. Therefore the issue of "not enough time" doesn't come up, since a large mass like the Earth would never deviate significantly from its averaged-out orbit; it would exhibit that orbit the very first time, and every time.

Actually, one of the fundamental results of QM (and important step in establishing its viability) was that the multiple paths that an individual moving particle can/does take undergo strong destructive interference everywhere but very, very close to the classical trajectory, so that the probability of the particle being anywhere but on that trajectory (with a small amount of fuzz, consistent with the uncertainty principle) is zero. QM provides the constraints that result in this very, very close to deterministic behavior.

Aggregation does nothing to change this -- each and every particle within, say Jupiter, follows this same principle and each has precisely the same fuzziness as it would have in isolation. It's just that the same fuzziness in trajectory (say and Angstrom's worth) is a lot less noticeable for Jupiter than for the individual particle.

The point is that Jupiter's trajectory is the result of raw randomness "channeled" by constraining laws. Underlying it all is randomness and if we ignore the processes channeling that randomness -- performing selection in a very real sense -- from moment to moment Jupiter could be found anywhere in the universe and the very idea of a trajectory would be meaningless.

That also means that under those circumstances the probability of the Earth being at any point along its classic trajectory would be infinitesimal -- almost certainly not only a smaller probability than that a fully formed paramecium would arise purely by chance out of a primordial soup, but almost certainly with a much smaller probability than that an MIT grad, complete with lab coat, pocket protector and memories of a hot date the night before would arise from it. Finding it at the appropriate point along that trajectory a millisecond later is of immensely lower probability (the square of the first probability). Finding it on the trajectory at frequent observation over years or centuries would result in the probability shrinking exponentially -- the probability of the first observation raised to the power of the number of observations made.

These immensely small probabilities are irrelevant because there are constraints that eliminate the alternatives. Both dynamics and evolution are the result of alternatives being pruned by constraints -- destructive interference in one case and failure to reproduce in the other -- into a more highly organized form.

My argument about the impossibility of the Earth revolving around the Sun has exactly the same form as your argument about the impossibility of the formation and/or diversification of life by evolutionary processes. They only look at the random component and ignore the organizing principles. The only differences are that a) the spurious "impossible" probabilities on the basis of which you reject evolution are immensely more probable than those on which I rejected celestial mechanics, and b) In the celestial mechanics argument there is only one possible trajectory for the Earth according to celestial mechanics, while there are many, many, many, possible paths that could be followed by evolution to create a diverse, structured biosphere.

So, if my argument about the impossibility of a heliocentric solar system is flawed how is your argument about evolution different? It certainly is not because I neglected selective processes and you did not. Your whole argument is about how improbable it is that fully formed DNA/RNA/Protein reproduction systems, fully formed complex, functional proteins and functional, fully formed modern organs like eyes could from at random -- simply declaring the possibility of incremental development of these thing as not on the table (a classic example of "begging the question" -- you "prove" that evolution is impossible by assuming that it could not occur).

If you ignore the constraints,

[Barbara]

I understand, Topher. The world ends in mid-sentence because there is no "point" in going on (no purpose = no point).

[Topher Cooper]

:-)

Oops, part of an earlier draft.

Evolution may not have a purpose, but life is its own purpose.

[Dave]

Topher - the problem here is that if this evolutionary process actually is totally driven by natural selection operating on random mutations and other random genetic variations, all the notions regarding spirituality and survival held dear to many in this blog are thrown in the ashcan. The modern synthesis of Darwinism holds that the process that created all of life up to and including mankind is completely purposeless and meaningless in the largest sense. It is just a random walk accumulating complexity because natural selection of random variations favors reproductive fitness. This is not just the human body but also human emotions and ethical and value systems - these all supposedly originated also by this process (evolutionary psychology).

So, the essence of the human being is then the result of a purposeless, semi-random, ultimately mechanical process, according to some very strongly evidenced scientific disciplines, especially evolutionary biology. The Darwinistic process can't in principle produce anything like a soul or spirit, or even psi abilities, since the process is a mechanical one operating solely on the genetic structure utilizing mostly small random changes. Inherent in Darwinism is the assumption that human consciousness is an epiphenomenon or an emergent property of the physical brain, since variation and selection can affect only genes which in turn code for proteins and physical biological developmental patterns. Darwinism is materialism down to the bone and denies anything paranormal.

Yet there is also a mountain of evidence for the existence of the paranormal, psi, esp, and even survival. As a parapsychologist, how do you deal with the resultant cognitive dissonance?

[XXII]

Ok, good thing most of my post went by unawnsered.

In any case, there's a further issue that one can purse in these matters: wether Evolution is generating qualitative and categorical novelties in life systems or wether it is a process whereby these systems as individuals partake, along larger processes, in unveiling faculties that are embedded or lie already in the principle of existence, if one admits to that conceptual formulation. Is Evolution permissive or generative?

I think that F. W. H. Myers made a good case for it and an interesting introduction can be found in Kelly & Kelly's Irreducible Mind. I think that we could do good dealing with these issues on their own right and stop alluding to 'hidden agendas' and 'political deception'.

[jshgfcre98ijyds]

I think the important question is not about whether evolution occurred but about the mechanism. Was it natural selection?

Also, I don't think natural selection contradicts spiritual beliefs.

When scientists want a new strain of bacteria that can grow under some new type of conditions, they put bacteria in a flask of growth medium and subject it to those new conditions. They let the flask sit for a few hours or a few days and only those bacteria with mutations that allow them to grow will survive and fill the flask with their descendants.

If spiritual entities wanted to create a new type of container for souls to incarnate into, maybe they would crate a physical universe in which biological life self-assembles from chance interactions of atoms, and leave it sit for a short time, a few billion years, and then have a look at the new containers that developed in it.

Or, maybe, occasionally, some mutations would be put in deliberately to direct evolution of life. Who would notice?

Who can say if there is a faster more efficient way to terraform a planet and develop a biosphere suitable for the incarnation of intelligent souls.

I don't think of "creation" as the work of an omnipotent god, but possibly it is the work of entities subject to natural law and scarcity of natural resources like energy.

Based on what is said by NDErs, mediums, UFO abductees etc. I think it is very possible that there is some combination of natural selection and intelligent design going on.

You also have to consider that what we call natural, including the spirit planes, might actually be technology. Why is telepathy not the spirit's equivalent of the cell phone and clairvoyance their equivalent of the internet?

Given the age of the universe and the possibility of previous universes I think the likelihood of intelligence existing previous to humankind is almost certain. Given the rapid development of human technology who can deny that a civilization a million or a billion years old would not look like spirits to us? Or that they would refrain from intervening in the development of the physical universe and life within it.

[Topher Cooper]

There is only so much I have time to respond to.

Technical point: Both Darwinian and neo-Darwinian evolution involve both natural and sexual selection, not just the former.

[Topher Cooper]

Keep in mind neo-Darwinian evolution (NDE) does not actually say that all biological diversity is a result of selection acting on mutation and recombination. It says that that process is sufficient to explain that diversity, both present and fossil. If NDE is sufficient to explain the evidence then there is no evidence that anything else is responsible.

NDE also predicts patterns within the diversity which are found, over and over again. These patterns are totally arbitrary according to all the alternatives (unless you consider "and they are trying to deceive us by making things look exactly like NDE is happening" as not arbitrary). These patterns are therefore extraordinarily unlikely unless NDE has been operating.

While that means that there is overwhelming evidence that NDE is responsible for biological diversity, it does mean that other processes could occasionally tweak things a bit. There just hasn't been any evidence for it.

If you are philosophically wedded to a "2001, A Space Odyssey" scenario, for example, and don't insist that the old, thoroughly discredited Creationist anti-Evolution arguments (however, prettied up) prove that your preferences must be so, then I have absolutely no problem with this at all. We all have beliefs about things where the evidence says nothing either way. Sometimes, evidence eventually comes along that confirms or denies those beliefs, but mostly, it never does.

[Topher Cooper]

wether Evolution is generating qualitative and categorical novelties in life systems or wether it is a process whereby these systems as individuals partake, along larger processes, in unveiling faculties that are embedded or lie already in the principle of existence, if one admits to that conceptual formulation. Is Evolution permissive or generative?

Interesting question.

Neo-Darwinian Evolution (NDE) is quite clear on the question. NDE combines a generative component (mutation and genetic combination) and a permissive component (or more accurately a non-permissive or restrictive one) which is selection.

As to whether it "[unveils] faculties that are embedded or lie already in the principle of existence" statistical physics and QM supply the answer to that: the answer is an unquestionable "yes." Information (in the mathematical sense) cannot be created, only transformed or transferred. There is a vaguely defined (though there have been some interesting attempts to make those definitions less vague) mathematical concept of the "quality" of information -- something that can be increased.

Evolutionary processes manifests the underlying information ("negentropy") into the macroscopic level of living systems, boosting, not the amount of information/structure in the universe but the quality of it.

To give another, quite different example of increasing the quality but not the quantity of information, purely within familiar mathematics:

There are some things called the Peano Postulates, a few short, simple mathematical postulates. They contain, at most, an amount of information in the low hundreds of bits. There are several extensions to these -- extra postulates -- that all together are probably roughly the same number of bits. Altogether then we are talking about somewhere in the range of perhaps 64 bytes of information (that's probably generous).

All of the "Queen of Mathematics", number theory, the mathematics of integers, are derived from these few bits. Hundreds of thousands (more likely millions) of pages of mathematics, thousands of lifetimes of effort, about the implication of these bits. There is not one additional bit of information in all of this, its all implicit in the augmented Peano Postulates.

There is no new information (in the information theoretic sense) in all this -- everything correct in the entire literature of number theory, and a great deal more, would be known and understood by a sufficiently intelligent receiver once they have received the augmented Peano Postulates. The Peano Postulates is a losslessly compressed representation for all of Number Theory (and not just the known parts).

Obviously, although information has not be added, a very great deal has been. Pretty much the entire foundation of our current information processing civilization can be found in Number Theory. In fact, using Goedel Encoding, all modern mathematics can be represented as Number Theoretic statements -- its just a matter of choosing subsets of Number Theory theorems to pay attention to.

What has been added to the Augmented Peano Postulates is immense amounts of information quality.

Similarly, all the information, all the novel structure, produced by NDE is already contained in the universe -- primarily in the form of the different entropy levels in different chemical combinations of elements, the gigantic amount of information contained in the temperature differential between the Earth and the Sun (primarily itself a result of the difference in entropy between four hydrogen nuclei and one helium nucleus, with a dollop of the entropic difference for objects at different distances from the center of the Earth). NDE only changes the level of manifestation of this information and adds to its quality.

Thanks for the question.

[Topher Cooper]

The path that a drop of water on a piece of earth takes is goal-less, purposeless and somewhat random. The drop reacts only to the physical things that it is in contact with, moving in the direction of the steepest gradient at the point it finds itself. It has no goal in mind, no place where it wishes to be, no preference as to whether it moves north, south, east or west. When the gradient is shallow, or complexly structured relative to the area of the drop's surface in contact with the ground, its direction may be, to some extent, indeterminate.

A landscaper, however, might contour the land in such a way, so that there are basins that some drops will inevitably reach -- though exactly which drops, and exactly what paths they take, and which ones end up in unplanned puddles, absorbed by the Earth or evaporated instead are of no interest to the landscaper. And so, a pleasant, marshy stream, a small waterfall and a restful pond are created.

Certain science commentators, wishing to make a point, have made a great deal about the randomness (by which they actually mean arbitrariness, thereby sowing unnecessary confusion) of evolution. They have unfortunately, overstated the case, substituting one level of misunderstanding for another. There are unquestionably certain nexii, channels and pools and ponds, which are almost inevitably going to be reached. If not on this particular slime covered ball, then on one somewhere in the universe.

Flight developed independently at least four times (insects, pterosaurs, birds and bats) so it is probably nearly inevitable given land and air -- perhaps the land is not strictly necessary. There are at least eight distinct, independent, kinds of imaging eyes so the development of an imaging eye is probably nearly inevitable given light and a transparent medium.

So evolution can be an arbitrary and purposeless process, and yet have a purpose if the universe and its laws and even, perhaps its logic, was created with a purpose. For example, the universe may be so structured so that biological evolution will inevitably produce perfect homes, or rest-stops (or prisons if you are a classical Gnostic) for wandering sparks emitted by the ultimate soul. The precise form of those homes -- one head or none, four limbs or thirteen -- may be irrelevant and arbitrary but that is not important -- variety might even be desirable. (That, of course, leaves unanswered, assuming the truth of this speculation, as to whether we, or perhaps cockroaches are those cottages for the soul arranged for by The Great Real Estate Developer).

So no, despite the baseless, ultimately harmful, and vehement assertions by Fundamentalist Atheists, while evolution may contradict some beliefs associated with spirituality (e.g., all the Earth and all the life it contains was created in six 24 hour days), it is not in the least contradictory to spirituality, a belief in a purposeful creator, the existence of an extra-physical soul, or many other spiritual beliefs.

[Topher Cooper]

Psi phenomena clearly are beyond the explanatory range of our physical laws. It does not follow that they lie beyond the explanatory range of any set of physical laws. At one point, the observed constancy of the speed of light, the form of the blackbody radiation curve, the photoelectric effect, the changes in the perihelion of mercury and the spectrum of hydrogen where all beyond the explanatory range of the then current set of physical laws. It was precisely to clarify the distinction between phenomena beyond current physical law and all possible physical law that the term "paranormal" was coined to contrast with "supernatural".

Although we have only observed psi in connection with living, cognitively capable things it does not follow that it can only appear as part of a non-physical consciousness. The first person to artificially synthesize urea from inorganic chemicals was derided as a fraud since it was "well known" that the products of life (even the waste products of life) could only be produced from life.

Many of my most respected colleagues in parapsychology (most prominently Dean Radin) are of the opinion that psi is fundamentally and unquestionably about consciousness. There is, however, absolutely no evidence (unless you take our ignorance about mechanisms or specific organs as evidence) that it is any more closely (or less, for that matter) linked to consciousness than is vision, odor, or manual manipulation.

So if psi is a subtle manifestation of the physical, then its use could most certainly have evolved. It might also have simply emerged as a side effect of the evolution of something else. For example, the evolution of the immensely complex, highly "critical" (in the complexity theory sense) neural system that supports intelligence (to avoid issues, I'm speaking only of intelligence, not consciousness) might have lead automatically to a small but natural linkage to these otherwise incoherent physical mechanisms.

Even if psi is in some sense the result of processes beyond physical law, it is coupled, in some coherent fashion with strictly physical system -- the brain (again setting aside, for the moment whether or not there is another extra-physical system or another aspect of the same extra-physical system that we call consciousness that is also coupled). Either that coupling is lawful and coherent -- in which case the coupling itself represents a regularity that could be expressed as additional physical laws -- or it is incoherent, random, undetectable noise. In the latter case we could never have detected it. In the former case, that coupling to the physical would be subject to evolutionary processes -- the physical composition and structure of the brain to make use of its beneficial characteristics and to ameliorate its harmful ones.

(This kind of a lawful, essentially physical and knowable interface between the rest of the physical universe and an entirely physically unobservable and unknowable "otherness" was the basic structure of the original formulation of the Copenhagen Interpretation by Bohr. In that case they physical universe was described by classical physics, the interface was QM and the "other" was unknowable so to ask anything about it was to be derided by him as a mystic).

Bottom line, to the extent that anything extraphysical -- e.g., psi, consciousness, the soul -- has a meaningful influence on an organism (or on a living non-organism like a bacterium) that influence might be modulated by evolutionary processes.

[Michael Prescott]

I guess Topher's strategy is to post so many lengthy comments that no one will be able to read, much less respond to, all of them, and he'll win by default!

He made two points that I'll address (briefly, I hope). First, he says he doesn't know why the formation of a protein is a statistical issue. But this problem has been well known for decades. The likelihood of even a single protein being assembled by chance is infinitesimally small, and a cell requires more than one protein. One statistician, Coppedge, calculates that 239 proteins are needed at a minimum, and the odds that all these would be assembled by chance are one in 10 to the power of 119,879. Because of calculations like these, it has long been accepted that chance alone cannot account for the origin of proteins. See Robert Shapiro's book Origins for a good overview. (Shapiro is a mainstream biologist specializing in abiogenesis.) Or see the last chapter of The Way of the Cell, by molecular biologist Franklin M. Harold, for a brief but thorough review of problems in abiogenesis.

Second, the QM analogy is misconceived, because there are no known laws of chemistry that would direct the assembly of amino acids into proteins. Amino acids will chain together spontaneously, but have never been observed to spontaneously form proteins. In the absence of any natural law that would direct (say) only left-handed amino acids to bond with each other, the proteins necessary for life would not develop by chance. This also is well known, which is why some biologists are looking for evidence of self-organizing systems. Maybe such evidence will turn up. It hasn't yet. That's why the assertion that such a mechanism must exist and will someday be found is promissory materialism (a term coined by John Polkinghorne).

[Topher Cooper]

A protein is a polymer of amino acids. Put some amino acids in a test tube and wait a while (or include a catalyst and wait for less time) and you will find that you have a bunch of dimers and trimers of amino acids -- simple proteins but proteins never-the-less. I think that there are a few peptides (small, biologically active proteins) that are Amino Acid trimers. This will occur in reasonable time with probability 1.

A statistician might be useful in telling you how long you would have to wait to get a particular percentage of dimers, trimers etc., but, given the physical characteristics of the system the probability we are talking about but we talking about high school probability theory is sufficient.

So I really do not see, as I said, why we need a statistician.

There are commonly simple, natural systems that act as templates, containing niches in which monomers are held in place for a while near other such niches, that will act, completely physically, as catalysts for various kinds of polymerization -- most prominently zeolites which are important tools for chemists. I can't say for certain that there isn't some odd reason why out of the millions of possible substrates none exist that would help polymerize amino acids (of course, we do know of one such substrate, in fact, a rather selective one -- its called RNA but that just puts the problem back a step), but if some natural mineral form has a regular structure roughly the size of an amino acid in a polymer then much larger proteins will easily form.

Now it is a different question if we are asking about whether a particular large protein would form. Again, it doesn't need a statistician to say that it would take a very, very long time.

Of course, there is no one in the debate who claims that life developed from the spontaneous assemblage of amino acids, hydrocarbons, lipids, nucleic acids, etc into a fully formed, operating cellular structure. What is being discussed is the possibility that this mechanism referred to as "evolution" (heard of it?) which does not require any such unlikelihood to occur.

Prebiotic evolution does not require a starting point involving DNA, RNA, lipid membranes forming cell walls, proteins, etc.
All that is required, is a chemical system 1) that is self-replicating within a physical/chemical environment consistent with conditions on the early Earth, and 2) robust enough to allow self-replication to continue in the presence of damage (what would be called mutations in a living system). Any competent statistician will tell you that the probability is high that such a system will bootstrap itself into more and more complex and robust systems, involving components that were not any part of the original system.

That some such system would have developed in the complex organic (but non-biological) mix that it seems existed on the early Earth we do not have a specific candidate that would clearly be able to evolve into the specific system we call life. Its an unproven hypothesis.

Anyone who wants to claim that this could not have occurred needs to either admit that their claim is equally unproven or to produce some evidence that it could not. Calculations proving that implausible scenarios, never considered by anyone, are indeed implausible do not constitute evidence for the claim. This -- not arguments of exactly the same form and similar content intended to show the inadequacy of an argument -- is what is meant by a "straw man" argument.

A defense attorney who basis the defendants plea of innocence on demonstrating that it would have been impossible for her client to gain access to the crime scene by bringing up enough heavy machinery to lift the building up when the door was wide open is, shall we say, incompetent.

(Sorry my postings contain so much content. If you have trouble with the technical details, perhaps you should wonder about whether or not you are well enough informed about the subject to make a judgement? Very little of what I have said is not available in introductory undergraduate biology and physics texts.)

[invet]

"If you have trouble with the technical details, perhaps you should wonder about whether or not you are well enough informed about the subject to make a judgement?"

Topher Cooper really has nothing unique to offer in his argumnets. Instead he tries to come off as of superior intellect by bringinp up other areas of science to show us how much he knows. He also does this because his arguments for his neo-Darwinism belief system really aren't that good.

He shows further arrogance by trying to steal the acronym "NDE" for his own purpose, as if the near death experience is nothing.

He even tries to posture himself as if he is a lawyer to boot - so do not ty to think we can take him on as he his so sound in argument.

Topher Cooper, what are we supposed to do: bow to your pseudo-intellect?

[Dave]

So evolution can be an arbitrary and purposeless process, and yet have a purpose if the universe and its laws and even, perhaps its logic, was created with a purpose. .... So no, despite the baseless, ultimately harmful, and vehement assertions by Fundamentalist Atheists, while evolution may contradict some beliefs associated with spirituality (e.g., all the Earth and all the life it contains was created in six 24 hour days), it is not in the least contradictory to spirituality, a belief in a purposeful creator, the existence of an extra-physical soul, or many other spiritual beliefs.

This is a distinctly minority interpretation of modern evolutionary theory, that seems to relate to the approach of many modern Christian thinkers who try to somehow embrace Darwinism and retain some respectability in scientific circles, and at the same time remain Christian believers. The issue seems to involve the definition of what is "random". The Oxford English Dictionary defines 'random' as: "Having no definite aim or purpose; not sent or guided in a particular direction; made, done, occurring, etc., without method or conscious choice; haphazard." Applied usage in science, mathematics and statistics recognizes a lack of predictability when referring to randomness. Random with respect to fitness is the basic nature of all genetic variation, according to NDE. Random means unpredictable (except statistically) and purposeless. Would Mind or a Creator leave it purely up to an endlessly long and unlikely series of accidents along with selection to just happen to result in a being such as Homo Sapiens that can fully manifest Mind in the physical world? Just one of the accidents: the Cretacious-Tertiary asteroid impact that wiped out the dinosaurs and allowed mammals to take over. The suggestion is that in order for mankind to evolve, this meaningless and purposeless conjuction of the celestial mechanics of orbiting bodies left over from the formation of the Solar system was somehow prearranged at the creation of the Universe. This event is just one of uncountable millions of other accidents that had to be prearranged despite their inherent unpredictability.

[Topher Cooper]

Topher Cooper really has nothing unique to offer in his argumnets.

I agree. These arguments are pretty standard.

Instead he tries to come off as of superior intellect by bringinp up other areas of science to show us how much he knows.

Glad to know that you somehow can read my mind in order to know my hidden motives. And here I thought I did it because I hoped that by drawing comparisons to other areas of knowledge things might be clearer, and just maybe it might be interesting.

He also does this because his arguments for his neo-Darwinism belief system really aren't that good.

And yet no on seems to have any refutation except to keep repeating over and over, that contrary to what is believed by those who work with and believe in it that neo-Darwinian evolution is a theory that assumes that features appear instantaneously, spontaneously, and fully formed in their final state (because, apparently, evolution is a goal directed process so that it makes sense to talk about their final form).

He shows further arrogance by trying to steal the acronym "NDE" for his own purpose, as if the near death experience is nothing.

Huh. Do you believe that acronyms are only allowed to be used to refer to a single thing, even in different fields? That every time someone refers to a political statement as being "PC" that they are thereby declaring that Mac's are the only kind of computer? That a parapsychologist has no awareness or interest in near death experiences? What would you suggest as a convenient abbreviation for "neo-Darwinian evolution"?

OK, from now on I'll use the abreviation QZYYAZ for "neo-Darwinian evoltuion" so as to make sure no one thinks that I'm referring to a near death experience when I say things like "all the information, all the novel structure, produced by NDE is already contained in the universe" even though I take care to define what I mean by the acronym in each message before I use it.

Or maybe I'll just continue to be clear.

"He even tries to posture himself as if he is a lawyer to boot - so do not ty to think we can take him on as he his so sound in argument."

Anyone who uses a courtroom metaphor is is posturing as if they are a lawyer? Do you disagree with my -- purely lay, I assure you -- assessment that a lawyer is incompetent who who defended their client by claiming that the prosecution case is based on the defendent lifting a building to gain access rather than using the open door?

For the record, I make no claim to being a lawyer, a physicist or a biologist. Just someone with an ordinary education in these subjects. My relevant formal qualifications is a BS in math with a computer science option, professional experience in statistical computing and evolutionary computation. For those who feel that it is relevant, I have been active in parapsychology research and have been a member of the Parapsychological Association (which requires a finding of significant contributions to the field) for several decades

Topher Cooper, what are we supposed to do: bow to your pseudo-intellect?

No, you are supposed to either respond to my refutations of the standard arguments, go get some new ones that actually deal with what QZYYAZ (the new, transparent abbreviation for neo-Darwinian Evolution) says, or concede the argument.

If you wish to bow to my pseudo-intellect, I can't stop you, but you'll have to find it first.

[Topher Cooper]

This is a distinctly minority interpretation of modern evolutionary theory,

The compatibility between evolution and spirituality is a minority on those who are moved to denounce spiritual matters. Those who believe otherwise, do not, by that very belief, feel that they are professionally competent unless they are also a professional in spiritual matters. My own, perhaps unrepresentative, experience most biologists I've spoken to agree with what I said -- that when people make claims about the physical state of the universe or its history on the basis of religious beliefs and without regard to physical evidence, then there is a conflict between science and religion, but otherwise they are dealing in discrete domains and there is no conflict.

In any case, I was presenting my own conclusion, not the result of a vote. Since the issue is not within the discipline of evolutionary biology, my opinion is as good here as theirs, and in fact, it is a pretty simple and straightforward conclusion.

[Topher Cooper]

The Oxford English Dictionary defines 'random' as: "Having no definite aim or purpose; not sent or guided in a particular direction; made, done, occurring, etc., without method or conscious choice; haphazard."

That is the popular meaning, which as you go on to explain is somewhat divergent from the technical one, leading to confusion. Mutation and recombination are random (in both the technical and common meanings), but selection is not, and thus it is incorrect to say that evolution is purely random, the basis of these arguments. I could give you the Von Mises/Church definition of randomness (the established definition) but I think that that's a bit much. Rest assured that it is precisely about unpredictability. Neither it nor the Kolomogorov definition say anything about purpose. Purposelessness can be deduced from unpredictability, however, since if the a specific result can't be predicted it can't be depended on to further a purpose.

Would Mind or a Creator leave it purely up to an endlessly long and unlikely series of accidents along with selection to just happen to result in a being such as Homo Sapiens that can fully manifest Mind in the physical world?

They might, particularly if they are not depending on the Earth as the sole place that this might take place. Furthermore, although a precise sequence of events were required to produce the precise species we call human, there may be many, many alternative outcomes that would meet this hypothetical creator's purposes. If the insects had not developed flight, the pterosaurs came along, if they had not, the birds did, if they had not the bats did, if they had not, wait a few million years, something will come along to fill that niche.

Remember the probability of any specific result from sampling a continuous distribution is zero, but the probability that some value (with prior probability of zero) will be sampled is one.

The development of birds, specifically, is unpredictable. That a large, practical niche like the sky would be eventually filled is quite predictable.

The Cretaceous Extinction event certainly had a major influence on the specific evolutionary path that lead to us, and certainly was an important factor in the timing of our development. But that does not mean that some form of intelligence would not have developed at some time without it. One thing is clear, change is inevitable, and evolution will continue to create novel life-forms, filling all accessible niches, whatever the circumstances. Specific massive extinction events may be random, but the fossil record says that they will occur. We are in the middle of the most rapid such event we know of.

Mind you, I am not claiming that these speculations represent my belief about The Purpose of Life and the Mind of the Creator. I do not know or have strong beliefs that intelligence is a wide open, multiply approachable niche like flight (I rather suspect it is, but I would not be shocked to be proven wrong -- it is certainly a survival strategy that depends as a prerequisite of an evolution having operated for a long period of time to produce very complex systems).

My point is that since we cannot rule out the possibility out that our species serves the purpose of some greater other (it is not really a scientific question), then there is no conflict between spirituality based on such a belief and science. You can choose to believe it, disbelieve it, or be undecided on the issue without being in any conflict with science at all. All three are equally compatible with the science (claiming that science supports your specific belief over the others, however, is in conflict with science).

Furthermore, not all spirituality depends on an external purpose to our existence. As I said previously -- life is its own purpose.

[Sbu]

Well, it's a relief that for once the discussion is about something else than the holographic universe and mark hortons nde.

Topher, your usage of "mathematical Sound" and "any statistican can show" kind of arguments is a chicken and egg argument. It doesn't matter what you can show mathematically if the underlying assumptions are incorrect. Evolution is at the end of the day nothing but a theory.

[XXII]

I (generally) agree with you, Topher, specially on your comment about life being inherently purposeful, regardless of the teoleology, or lack thereof, in which is is embedded.

If anything, Evolution does seem to bring about a greater degree of consciousness and 'understanding', which seems to me to lead to a greater degree of harmony between individuals and within the Individual itself. This in turn leads to a greater degree of average 'enjoyment'.

I do want to make a couple of remarks: First, although you are correct in asserting that the complexity that arises from Evolutionary processes is indeed contained within the principle of existence, this deals mostly with the formation of compounds as a result of certain patterns of the fudamental characteristics of the physical nature of the universe. While consciousness itself is shaped by these compounds (i.e. the brain and the nerual system), I dont think that it is reducible to the interplay between physical forces and thus we're left with the problem of explaining the place and role of consciousness in Evolution.

This leads me to the second remark: There is no reason to think of matter and mind as ontologically distinct substances, although such a separation is convenient for practical purposes. This means that the same problems that arise in the exploration of consciousness and intelligence may arise, although subdued, in realms that we usually consider to contain only inorganic and dead matter.

Finally, on purposefulness: Purpose can be used to describe an action wether or not the outcome meets the purpose that caused it or wether one can predict faithfully the outcome of the action, naturally. I disagree that purposelessness can be deduced from unpredictability, on the grounds which you're arguing for it, but I'm not wed to that disagreement and would very much welcome further explanation from your part on that issue to sway me into agreement.

[Art]

"Well, it's a relief that for once the discussion is about something else than the holographic universe and mark hortons nde." - sbu
--------------------------------------------

That was mean, nasty, and totally uncalled for. Why is it that atheist/materialist/skeptics always have to resort to being mean and small?

[Topher Cooper]

Topher, your usage of "mathematical Sound" and "any statistican can show" kind of arguments is a chicken and egg argument.

Nope. Statements have been made that are mathematical in content, statements about probability. If someone says, "two apples were put in the box, and then two more, so there has to be five apples." The reasonable response is "two plus two doesn't equal five, it equals four." Whether in fact, two apples were placed in the box on two occasions, whether they were in fact apples, whether any were removed, whether apples turn spontaneously into apple sauce are all reasonable topics of discussion -- but they are different discussions.

Evolution is at the end of the day nothing but a theory

Yup, as is the Theory of Gravity, the Theory of Electrodynamics, the Atomic Theory, The Theory of Relativity. "Theory" means an organized system of scientific or mathematical knowledge. Of course, we do not need to worry about you reading this -- the engineers who built the Internet were just using theories.

[Topher Cooper]

the complexity that arises from Evolutionary processes is indeed contained within the principle of existence, this deals mostly with the formation of compounds as a result of certain patterns of the fudamental characteristics of the physical nature of the universe.

There is some ambiguity here, so I may just be saying the same thing as you, but the evolutionary selection is equally a part of this. Selection is a fundamental part of statistical mechanics (another theory I didn't list in my previous posting). Remember "Maxwell's Daemon"? Modern resolution of this conundrum are about how selection itself is a thermodynamic operation, requiring specific expenditures of energy and resulting in specific compensatory changes in entropy.

[Topher Cooper]

There is no reason to think of matter and mind as ontologically distinct substances, although such a separation is convenient for practical purposes

That is, of course, the fundamental assumption of both forms of monism -- materialism and idealism. There is also no reason to think that they are distinct, which is dualism.

Finally, on purposefulness: Purpose can be used to describe an action wether or not the outcome meets the purpose that caused it or wether one can predict faithfully the outcome of the action, naturally. I disagree that purposelessness can be deduced from unpredictability, on the grounds which you're arguing for it, but I'm not wed to that disagreement and would very much welcome further explanation from your part on that issue to sway me into agreement.

Actually, you are right. Pure randomness could be associated with purpose -- as long as we are talking about a completely impotent purpose -- a purpose without consequence. One can have as a purpose to make unlimited money by betting even money on the flip of a fair coin, but that purpose is guaranteed to be thwarted and the purpose cannot be deduced on the basis of the outcome of those bets.

Now the use of randomness I am talking about here is direct -- a purpose that depends directly on the outcome of each event. If one selects or samples, one introduces structure that can be used. That there can be purpose when the randomness is not total was the point I was making. We are communicating over the Internet which depends on the Dining Philosopher's Theorem -- which demonstrates that computational processes that include randomness are more powerful than those that do not.

A Mind whose purpose depends on a specific genetic sequence appearing at a particular time and place is a pretty impotent one (not totally, since the probability is incredibly small but not zero), but one whose purpose depends on a broad niche being eventually filled sometime, somewhere is not.

[XXII]

Yeah, but I was suggesting that something like neutral monism may do a better job at describing reality.

[W Vogt]

Myself when young did eagerly frequent

Doctor and Saint, and heard great Argument

About it and about: but evermore

Came out by the same Door as in I went.

[chrisb]

I once wrote a small computer program to evolve the phrase "to be or not to be that is the question" from a string of random characters. It's a well known technique: you make a random change to the string (a "mutation") and compare the new string to the target, Shakespearian string. If it's a closer match than the old string, you mutate the new string. If it's less close, you mutate the old string. You continue this process until you reach the target string.

It took about 1000 iterations to get from random gibberish to "to be or not to be that is the question."

Remarkably, the second-to-last interation was "to be or not to be t*at is the question." (The asterisk stands for "w".) With apologies for the off-colour language, this is undoubtedly the funniest of all 1053 possible second-to-last iterations. As a proposition about the centrality of s*x in human existence, it actually makes sense.

[Topher Cooper]

This isn't criticism, just confusion:

What is "neutral monism".

Nihilism says that nothing exists.

Dualism says that there are two distinct kinds of existence: the physical and consciousness.

Materialism (one form of monism) says that there is only one kind of existence: the physical, and that consciousness is a physical epiphenomenon.

Idealism (in this sense of the word, another form of monism) says that there is only one kind of existence: consciousness and that the physical is a mental epiphenomenon.

What would neutral monism be? That there is only one kind of existence and that it is neither consciousness nor physical but that both of these emerge as distinct epiphenomena from this "urr-stuff"? Unless we can describe specific characteristics of it, we are left with two different, derived domains, the physical and the mental. But with the only characteristic of the urr-stuff being that it is neither physical nor mental, and that it is the source of both -- that it involves neither intent nor law in itself -- it is not apparently relevant except to provide justification for the monism label. It is otherwise indistinguishable, with no real philosophical distinctions from, dualism.

I'm not disagreeing -- I'm exressing puzzlement. A jumping off point for you to understand my confusion so that you can address it directly.

[Michael Prescott]

"A protein is a polymer of amino acids. Put some amino acids in a test tube and wait a while (or include a catalyst and wait for less time) and you will find that you have a bunch of dimers and trimers of amino acids -- simple proteins but proteins never-the-less."

What you'd have in that case are peptides, not proteins. No protein consists of only two or three amino acids. The smallest known protein has, I think, twenty amino acids, but nearly all proteins have fifty or more, and some have tens of thousands. Titin, the largest, consists of more than 34,000 amino acids. The dimers and trimers would equate to the single words produced by the Shakespeare-monkey program; true proteins would equate to whole sonnets or even whole plays.

I understand the argument that the process is not truly random because there is a selection mechanism at work. But I don't know what that selection mechanism would be. We are talking about a mechanism that would favor the assembly of proteins exclusively from left-handed amino acids (all righties excluded - how?), in long chains - a mechanism that either would assemble the protein quickly (how?) or, if time-consuming, would ensure that the developing protein retains its structural integrity despite being buffeted by currents, zapped by electricity, and subjected to all the natural shocks that amino acids are heir to. The forces at work to tear down or misdirect this fragile, growing chain of molecules would be considerable. Again, I recommend "Origins" by abiogenesis expert Robert Shapiro, a molecular biologist.

I also understand that it's not necessary to have a fully functional modern cell emerge spontaneously, but at a minimum the first cell would need to metabolize and replicate. That's a pretty sophisticated level of development already. As I said, one expert calculates that even the simplest cell would require 239 proteins. And these are not peptides, but actual proteins. The whole panoply presumably would develop over a long time, but that in itself poses further problems. Even if a few of the necessary proteins developed early, would they remain stable over time, or would the first ones fall apart before the latecomers arrived? Would they all develop in close proximity? What process would drive the assembly of ever more elaborate proteins, when there would be no survival advantage to such proteins until there were enough of them to form a living cell? Would there be enough time for any of this to happen, especially considering that the first cells appear to have emerged much earlier in Earth's history than previously thought?

Perhaps there are answers to these questions that obviate any role for a directing, creative intelligence. I don't rule it out. But I do think the hurdles for a purely materialist explanation of the origin of life, which includes the origin of the genetic code, are dauntingly high.

Anyway, it's been an interesting and lively discussion, and a refreshing change of pace for this blog. I'm sorry if I came across as overly combative. Sometimes the sharpest reply isn't the best.

[Topher Cooper]

What you'd have in that case are peptides, not proteins. No protein consists of only two or three amino acids. The smallest known protein has, I think, twenty amino acids, but nearly all proteins have fifty or more, and some have tens of thousands.

In biology it is convenient to not have to constantly talk about "proteins that act functionally in the incredibly large number of ways that large amino acid polymers act rather in those more specialized ways that require small polymers." They are created the same way within the cell, subject to the same evolutionary pressures, etc. In most contexts, when a biologist refers to a protein (e.g., protein synthesis) they take it as a given that protein includes peptides.

In biochemistry (and we since we are talking about prebiotic evolution so we are talking biochemistry) a protein is any polymer of amino acids (in fact, you will find some places where the definition of protein includes amino acid monomers -- i.e., amino acids) and peptides are only a matter of interfacing with biology.

Linguistically, a generic term sometimes refers to all exemplars and sometimes to typical members. That ornithologists say (to use the paradigmatic example) that "birds fly" does not mean that ostriches are not birds, that birds stop being birds when they break their birds, that birds are not birds when they are perched, that the dead birds in museum collections are not birds, etc.

Any particular category of protein, such as structural proteins or peptides, are atypical by dint of being part that category. Typical proteins are large but that does not mean that peptides aren't small.

Only Creationists and Intelligent Designers consider peptides as being distinct from proteins. It makes their argument appear stronger if they can make it seem as if there is a huge gulf between the two.

You do realize that you are arguing about arbitrary distinctions of language, here rather than anything with any physical reality?

[Topher Cooper]

The dimers and trimers would equate to the single words produced by the Shakespeare-monkey program; true proteins would equate to whole sonnets or even whole plays.

I essentially agree with you, though I will point out again that the program in question is based on arbitrary fixed-length sequences, not words. The program demonstrates how applying selection to such small units results in complex structures.

The distinction between "natural selection" and "intelligent selection" is totally external to the process. Replace the short sequences of letters with "short sequences of proteins", replace the "fitness function" of comparison to the works of Shakespeare with a more free-form one of survivability and exactly the same thing will occur -- slowly increasing complexity and longer and longer sequences.

There is no magic fluid that flows down the programmers fingers, through the keyboard, and along the wires and into the computer to coat the bits with some property called "teleology" so that they are now incapable of modeling natural processes that similarly lack the same kind of film.

[Michael Prescott]

"You do realize that you are arguing about arbitrary distinctions of language, here rather than anything with any physical reality?"

Right, but the important distinction is that peptides of two or three amino acids are significantly less complex than proteins that consist of hundreds ot thousands of amino acids. The difference in complexity, and therefore functionality, is why there's a distinction in language, though the exact dividing line between peptides and proteins is arbitrary. It's like the difference between a high-rise and a skyscraper - the exact number of floors distinguishing the two is arbitrary, but a five-story apartment building is not a skyscraper.

"replace the 'fitness function' of comparison to the works of Shakespeare with a more free-form one of survivability"

Except, in a prebiotic context, there's no reason to think that a long protein has more survivability than a short one. Nor is there any reason why chains of exclusively left-handed amino acids would offer more survivability than chains of left- and right-handed amino acids mixed together. Yet, since chance alone cannot account for the development of long, left-handed proteins, the materialist view is that there is, or must be, some selection mechanism that channeled the assembly of proteins in this way. Maybe there is. But no one has found it yet.

Survivability won't serve as a mechanism in the prebiotic world, unless it can be shown that long, exclusively left-handed proteins were more likely to survive (i.e., persist) than other types. This is the big problem to me (in addition to the huge problem of assembling the genetic code, or even a simplified version of it, without any intelligent input).

However, we seem to be going over the same ground here, so I will bow out and let Topher (or others) have the last word. One last thing: for anyone who found this discussion interesting, I again recommend Origins, by biologist Robert Shapiro - sadly out of print but worth tracking down. It presents what we know about the origin of life, and what we don't know, in clear and entertaining terms.

[Topher Cooper]

But I don't know [...]

Ah yes, proof by personal ignorance.

[...] what that selection mechanism would be. We are talking about a mechanism that would favor the assembly of proteins exclusively from left-handed amino acids

A number of the current hypotheses has that characteristic, but it really isn't actually necessary. This is one of those inevitables of evolution. Any complex that is made of incompatible components will fail to survive. Only complexes whose reproduction mechanism passes along that bias will successfully reproduce. This will produce a prebiosphere with two incompatible forms of chemical systems but "founder effect" will eliminate that in relatively short order.

in long chains - a mechanism that either would assemble the protein quickly (how?) or, if time-consuming, would ensure that the developing protein retains its structural integrity despite being buffeted by currents, zapped by electricity, and subjected to all the natural shocks that amino acids are heir to.

Not initially in long chains -- just in slightly longer chains.

Nor is the rate of assembly necessary for the functions of modern life a requirement.

The harsh conditions that you are referring to are localized. Some scenarios assume very high heat everywhere, but I haven't actually seen any justification for that assumption.

Proteins are pretty stable -- when I go to the fridge for a steak I do not expect it to have melted down to a puddle of amino acids (I guess you do). Even after I've tossed it on the grill many of the proteins survive. In fact, most of the breakdown that we do find in that steak are due to biological processes -- something that our simple replicating pre-biotic chemical system does not have to contend with.

Of course, even if harsh conditions are widespread this doesn't preclude the existence of protected environments that sum to very, very large volume (or perhaps area is the meaningful measure). One proposal is fine interstitial cracks in rocks. Another is the interior of spontaneously self assembling, spheres of any kind of simple molecule with a certain property. Any molecule with a hydrophobic and a hydrophilic end will spontaneously from such spheres with a bit of turbulence. These, initially produced independently of the chemical systems inside them, would be the distant ancestors of cell walls (which have, however, precisely this composition).

I also understand that it's not necessary to have a fully functional modern cell emerge spontaneously, but at a minimum the first cell would need to metabolize and replicate.

Who is talking about the first cell? We are millions if not billions of generations before this. How did metabolism enter the discussion? We are talking about pre-biology: chemistry not biology. As I said before, there is no requirement that proteins are involved at all. Since they are not self replicating they would probably only be part in a later stage of the process, although I suppose we might be talking about some simple complex of amino acids and something else that cannot exist under present conditions (the existence of life) that later split into separate RNA like substances and protein or the other part of the complex may have been replaced by the RNA-oid.

I also find that 239 protein assumption extraordinarily unlikely. Haven't read the argument so I obviously cannot debunk it, but it rather sounds like it is similar to the many that assumes modern conditions, forms and solutions as given. Viruses certainly require very much less than that.

A virus is certainly not an example of historic pre-life. Viruses depend on the machinery of developed life to reproduce. The problems they face in reproduction though are rather more difficult than those faced by our self-replicating, prebiological chemical systems. A virus must avoid detection by the immune systems (of the individual cells or of the organisms). It must breach the cell wall. It must avoid destruction being "eaten" by living systems hungry for biochemicals. Our hypothetical pre-biote floats in a soup of organic (but non biologenic) chemicals, not too different from a cell interior except without the structure and protective mechanisms found in the cell. The cell does provide complex mechanisms that the virus uses to rapidly reproduce itself, but the prebiome isn't in the race that the virus is in. A typical (not an exceptionally small one) virus consists of RNA coding for two proteins. I think that demonstrates pretty conclusively that the upper limit for our prebiome is two or less.

The number of proteins needed to form something identifiable as a functional living cell is totally irrelevant. This is just another example of arguing against evolution by starting with the assumption that neo-Darwinian evolution doesn't occur, and that evolution is about the formation of radically new forms in one go -- of fish eggs hatching frogs.

[Topher Cooper]

I again recommend Origins, by biologist Robert Shapiro

For what it is worth, Shapiro was a vehement and active proponent of pre-biotic evolution as the origin of life. In an article in Scientific American a few years ago (I don't remember exactly when -- you can look it up yourself) he argued part of what I keep bringing up. That there is no need to start particularly far up the line of complexity in looking for plausible routes of prebiotic evolution. He argued that even simple biochemical systems are unnecessarily complex.

He was certainly not arguing against starting points so far up the chain of complexity as the fully functional living cells that Michael has been arguing. He could have made such arguments, but didn't need to since no one was making such a claim. He was not given to arguing against straw men.

Shapiro may have been right. The issue is certainly not open and shut (disagreements about what environment actually existed, protected environments, what rate of destruction would actually interfere -- everyone agrees that a relatively high rate of destruction of the "offspring" would be acceptable, especially in the very early stages, since selection would rapidly select for the more resistant variants), and I do not have the expertise to come down on one side or the other. The majority, though not all, of the people qualified to have an opinion, disagree with Shapiro, but that does not mean that this will always be the case.

Citing arguments within the field about the details as evidence for disagreements about the viability of evolution itself is one of the standard techniques of the Creationists. If Michael came to this reference and mis-interpretation of Shapiro through the Intelligent Design literature, this would be a further demonstration of the continuity between the Creationist and Intelligent Design core communities.

[Michael Prescott]

Oddly, my comment keeps disappearing. TypePad is really getting glitchy!

Anyway, I just wanted to say for the record that I've read Shapiro's book, so I wasn't relying on secondhand info about it.

I have little confidence that this comment will stick around, so enjoy it while you can!

[Topher Cooper]

Michael, I have too much respect for you to have ever considered the possibility that you were recommending a book without having read it yourself. I apologize if it seemed I was implying otherwise.

I was suggesting that you might have come to it with preconceptions about the implications -- that a researcher who was suggesting a need for adjustment in the theory was arguing against the theory itself.

Of course, I have not read the book, I only know his thinking from an article written two decades later (I looked up the copyright). Its possible, that he was more negative about the concept back when it was so undeveloped. The pre-biotic hypothesis is not the established theory of neo-Darwinian evolution, then or now.

[sbu]

Topher, What is your own position on psi and spirituality in general? Is it all wishfull thinking or could it be real?

[Michael Prescott]

No problem, Topher. Thanks for your kind words.

[Topher Cooper]

Psi is physically real -- there is overwhelming evidence for it. When I first became involved in parapsychology somewhere about 40 years ago, the evidence was already overwhelming.

Spirituality is distinct, in general, from psi though some peoples ideas about spirituality includes psi phenomena -- as others' ideas include morality, kindness, or food as part of spirituality.

Something is "true" scientifically (in my personal philosophy) if it is not precluded by evidence and if it simplifies the description some meaningful subset of reality ("level") better than alternatives.

Is "joy" scientifically real? On the level of human psychology, there is absolutely no question that it is -- any description of human behavior that attempts to leave it out will be more complex than those that include it. On the level of neurology -- there are things that correlate to "joy" that are also clearly real, though whether you wish to put the label "joy" to this pattern of neuro-chemical behavior is a matter of choice. On the level of atoms -- nothing that could be referred to as "joy" (except perhaps metaphorically) does anything to simplify things -- it simply does not exist on this level of description/reality.

Spirituality is not as simple as a more or less "atomic" emotion like joy, but I am quite sure that it also is scientifically real at this level -- and that is just as real as "electrons" or "stars" or as any other thing at any other level.

As to various beliefs that individuals tie to their sense of spirituality. If they are about objective reality then whether they are "real" in the scientific sense depends on the evidence -- the world was not literally created in six days, people's interaction with the world is not limited by the known physical modalities, but community does strengthen its members.

There are other kinds of "truth", other meanings of "real", then the scientific. Some aspects of spiritual beliefs are real in these other sense -- even where someone else, or the same person in another context, has a different, contradictory, equally valid truth. The six day creation of the world in six days is true, as is the creation of the world from the corpse of a giant or the creation of the world from the ejaculate of one of a pantheon of gods. Just recognize that this subjective reality is distinct from scientific reality and does not, nor need to, describe the physical world, its history nor its future.

Sorry you asked?

[sbu]

Thanks for a lengthy response, Topher. With spirituality I was refering to what I think is at the core of most peoples interest in this subject namely "evidence for survival". Do you believe based on the available evidence that life after death is more than wishfull thinking?

[Topher Cooper]

Do you believe based on the available evidence that life after death is more than wishfull thinking?

Yes, I believe that it is more than wishful thinking. My personal judgement, though, does not rise to a level of scientific conviction without a prior predilection towards that belief.

Given how little we know about psi, we cannot reasonably rule out that the survival evidence is not due to its action -- what some opponents of this idea have dubbed "super-psi" in an effort to make it seem less likely.

Psi seems manifest quite powerfully, sporadically. We don't know what conditions result in this, or whether they might not sometimes (and all the extant, veridical evidence comes down to "sometimes") include the conditions surrounding the survival evidence. What part might clairvoyance, forward-acting PK, perhaps guided by precognition, and the psi ability of living witnesses play in the production of the events that appear to support survival? Could psi imprint a location or object with information that is no more essential survival than a diary entry?

The pattern of some cases seem very arbitrary relative to an explanation in terms of familiar psi phenomena, which is why I feel that there really is meaningful, though insufficient, evidence for survival. But we don't know what part the beliefs, hopes and fears of the living and the forward-acting once living might have in producing these survival consistent events.

If survival is real then I may find out some day (or will if survival is universal).

Your mileage may vary, of course.

[Paul]

Hi Topher - in terms of survival evidence - what about full form materialisations in decent light such as by Alec Harris amongst others and voice phenomena?

[Topher Cooper]

Although some of the EVP (Electronic Voice Phenomena) are quite stunning, the degree to which it is dependent on subjective judgements and subject to possible contamination by stray radio signals make it difficult to evaluate as evidence.

I've heard stories of Alec Harris, but do not know (and I do mean "do not know" -- classic mediumship phenomena is not my area of expertise) of any thorough, positive, independent investigations of him. Remember that a report of independent investigations, of spectacular observations by neutral observers etc. are worthless if they source of those reports of those observations and investigations is from those close to the medium.

And for the record, red light, however bright, is better than no light at all, but it is not "decent light". Its quite hard to see anything too clearly, and (like any monochromatic light) objects of the same color are essentially invisible.

In any case, both are subject to the possibility of psi acting. EVP especially represents a system almost ideally set up for PK -- a system with lots of randomness in which very slight influences can add some structure. The difference between equipment used in EVP and the random event generators (REGs) that are now the standard in psi research is that the EVP results are evaluated subjectively and even the best equipment is virtually uncontrolled from external, conventional influences.

Remember that all spirit communication evidence presumes a form of psi. The issue is whether the source of the psi is the disincarnate or the incarnate. If a spirit can create a roomful of temporarily materialized visitors (though only in the presence of a particular individual) through some kind of PK (influence on the physical world through mechanisms outside those known by mainstream science) or active agent telepathy (influence on the thoughts and perceptions of human beings through mechanisms ...) then how can we be confident that this is not being done by the living?

[Paul]

Hi Topher

I didn't mean EVP, I meant what is referred to as the Independent Direct Voice. I won't go into the details but you might find the work of Leslie Flint interesting.  I ought to have been clearer in my question really. It was to do with your observation about alternative explanations for apparent psi phenomena.

I was more interested in how you thought such alternative explanations might apply to materialisation mediums (making the assumption that they are not fraudulent).

As an aside, whether the red light used is 'decent' or not seems a subjective judgement. Unless one is there, I would think it might be difficult to form a view either way. As you say, you don't know the phenomena so I don't want to get into a debate about the pros and cons, but assuming it is a genuine phenomenon, how would concepts such as super-psi etc explain it and what do you think of such explanations?

I don't see how all spirit communications rely on psi - independent direct voice purports to be real voices via a materialised voice box, and materialised spirits purport to communicate verbally both having  allegedly been tape recorded many times.

[Topher Cooper]

My statement about red light is general -- monochromatic light of any kind limits vision, and red is worse than most shades. My father was a scenic designer so I spent many hours as a child playing with colored gels -- holding them up to my eyes and putting them in front of lights. If you want a headache (and who doesn't?!) trying to read a book under pure red light is a good way to accomplish it.

And as I said, monochromatic light of any color makes it easy to hide things.

I don't know much about independent direct voice, I've rarely heard it mentioned under that name. As far as evidence is concerned I'll have to place it in the same category as speaking trumpets and floating violins.

We really can't simply set aside the possibility of fraud, if an apparent phenomena is produced by fraud, or as is frequently the case, by later exaggeration and memory distortion then we do not need to judge whether it is an example of an unexplained produced by the incarnate or the disincarnate -- its neither.

In any case, while materialization is not a phenomena much studied in the parapsychology lab that does not mean that it is not psi. It is an instance of intention (the spirits', the medium's, the onlooker's or that of someone remote in time or space) being translated into a physical or shared subjective effect without the operation of known physical mechanism. Presuming the materialization is that, and not a paranormally produced mental phenomena, the movement of the lips, vocal chords, air etc is more conventionally PK.

Is this the "same kind" of PK studied in the laboratory? We don't know. We don't know that PK studied on Tuesdays is the same underlying phenomena as the PK on Thursdays. PK is not label for what is necessarily a single phenomenon with a single cause. It is a label for a particular class of observations. It might be like a rash -- something that looks roughly the same but might be caused by many quite different things.

[Dave]

My point is that since we cannot rule out the possibility out that our species serves the purpose of some greater other (it is not really a scientific question), then there is no conflict between spirituality based on such a belief and science. You can choose to believe it, disbelieve it, or be undecided on the issue without being in any conflict with science at all. All three are equally compatible with the science (claiming that science supports your specific belief over the others, however, is in conflict with science).

Furthermore, not all spirituality depends on an external purpose to our existence. As I said previously -- life is its own purpose.

Regardless of such contortions of logic, there is a fundamental disconnect and incompatibility between modern evolutionary science and spiritual beliefs (including belief in a soul and survival). This requires believers in both to entertain a deep cognitive dissonance, whether it is admitted or not.

The best area to demonstrate this is in the field of evolutionary psychology. This is generally accepted and taught as truth in academia and applies the rules of evolutionary biology to the origins of human psychology. It is accepted as part and parcel of modern Darwinism. Most of human behavior is believed to be the output of psychological adaptations that evolved to solve recurrent problems in human ancestral environments. Along with memory, perception and language, all morality, altruism, love and compassionate acts are explained as evolved behavior of social animals which had tended to enhance reproductive fitness within groups. For example, two general ways are theorized that altruism offers reproductive advantages: (1) even though it may require sacrificing oneself, it may allow blood relatives to survive and therefore
promoting one's genes; (2) reciprocal exchange - "you scratch my back, I'll scratch yours."

This view is inherent in modern Darwinism, that morality comes from the natural world, not from some supervening spiritual system associated with souls and survival in a spiritual realm. The gradual construction, genetic and behavioral, of beneficial codes of behavior in social species is where human ethics and morality supposedly originated. There is a lot of evidence derived from study of non-human animals to support this.

It used to be argued that only human beings exhibit what is taken to be ‘compassionate’ behavior towards others. That position is thoroughly debunked by scientists in the field. Empathic and compassionate behaviors are claimed to have been observed across all social species. Very pointedly, they have not been observed among non-social species, such as snakes and other reptiles, or (in general) spiders. These species do not have elaborate “social contracts” and so they have not evolved ethical behaviors, such behaviors existing to allow coherent and productive activity in larger than family groups.

So for modern Darwinism it is wilfully ignorant nonsense to believe that morality, including love, compassion and altruism, came into being with humans, or with human religion. Evolutionary psychology is accepted as part of modern evolutionary theory and of course assumes the prevailing reductionist materialist model of brain/mind held by mainstream neuroscience, which rejects notions of spirit, soul or survival. For this belief system Mother Teresa and countless more common examples of genuine human goodness are explained away as some form of twisted self interest or just a malfunction of the genetic program.

So it must be realized what the consequences are of modern Darwinist evolutionary theory. Those that believe in modern Darwinism, and at the same time for instance, in the transcendental significance and validity of Near Death Experiences, are entertaining two vastly conflicting belief systems at one time. That is what is called cognitive dissonance.

[Topher Cooper]

It never fails to amuse me how self proclaimed atheists (I don't know whether Dave considers himself an atheist) always seem to know precisely the nature of the god they don't believe in.

The belief that scientific truth is the only truth is not a scientific belief. It is a belief about the world that is beyond the possibility of scientific proof.

Until a few years ago, it was part of the standard beliefs of neo-Darwinism that "true altruism" was exclusively a human characteristic. In fact, you will see that still being argued -- that the examples of altruism found in non-human animals is "proto-altruism" and that only humans show a willingness for self-sacrifice towards unrelated others whom they will never meet again or even will never meet at all.

Furthermore, most religions throughout the world and throughout history have not insisted on morality, or the soul, being restricted to humans. Nor do all insist on the existence of an immortal soul at all (in fact, survival of death is not part of the Jewish religion, though such a belief has been part of common non-religious Jewish culture for millennia).

In any case, there is no essential conflict between spirituality and a belief that human psychology evolved. Some people's specific view of spirituality is in conflict with evolution and they may resolve this by denying science, by trying to prove that evolution is non-scientific, by denying that view of spirituality (which perhaps sometimes creates a conflict that they must therefore also deny) or by changing their view of spirituality.

The belief that the human physical form and brain evolved is not in conflict with the idea that the first species apparently capable of more than rudimentary abstract thinking might have also thereby connected, in some sense or way, to something beyond the physical is something that science and more specifically evolution is neutral about. It is external to scientific theory. The assumptions that a) such a connection is true, b) that no such connection exists or c) that it is unknowable whether a or b holds; are all equally consistent and equally inconsistent with science (I include "c" because it requires the unscientific assumption that only what is scientific is "true" and therefore knowable).

Evolution is full of examples of one adaptation opening up novel functions that had nothing to do with the selective pressures that brought the organism to that point. One will be hard put to find, for example, direct evolutionary selection for science, advanced mathematics, abstract art and The Three Stooges. These are side effects, facilities and capabilities that emerged as side effects of capabilities that were selected for (such as, perhaps, the requirements of dealing with the complexities of collecting and harvesting highly varied food sources, or keeping track of reciprocities and predicting the behavior individuals of a large ever more complex social group).

Perhaps some connection to something beyond the spiritual came about in this way. Or perhaps not -- but all that is required to disprove an essential conflict is a "perhaps".

And there is, however insistent some are to deny it by all sorts of special pleadings, physical evidence that there does exist human capabilities that are outside of those that are currently scientifically explainable -- and in fact are beyond current assumptions about what physical reality is (which does not mean that a better understanding of physical reality won't include them).

And once again -- spirituality does not require any of that. Spirituality does not depend on the existence of spirit outside of the physical. Ask most Buddhists.

[Roger Knights]

MP: "I again recommend Origins, by biologist Robert Shapiro - sadly out of print but worth tracking down. It presents what we know about the origin of life, and what we don't know, in clear and entertaining terms. "

There's a new book out, Evolution: A View from the 21st Century, by James Shapiro. (I got it on a special deal day for my Kindle.) Here are excerpts from Amazon about it at http://www.amazon.com/Evolution-View-Century-Press-Science/dp/0132780933/ref=sr_1_1?s=books&ie=UTF8&qid=1317890745&sr=1-1

Product Description

James A. Shapiro's Evolution: A View from the 21st Century proposes an important new paradigm for understanding biological evolution. Shapiro demonstrates why traditional views of evolution are inadequate to explain the latest evidence, and presents a compelling alternative. His information- and systems-based approach integrates advances in symbiogenesis, epigenetics, and mobile genetic elements, and points toward an emerging synthesis of physical, information, and biological sciences.

From the Author

Most debates about evolution sound like the last fifty years of research in molecular biology had never occurred. Evolution: A View from the 21st Century aims to acquaint the reader with previously "inconceivable" but currently well-documented aspects of cell biology and genomics. This knowledge will prepare the reader for the inevitable surprises in evolutionary science as this new century runs its course.

The capacity of living organisms to alter their own heredity is undeniable, and our current ideas about evolution have to incorporate this basic fact of life. The genome is no longer the read-only memory (ROM) system subject to accidental changes envisaged by conventional theory. We now understand genomes to be read-write (RW) information storage organelles at all time scales, from the single cell cycle to evolutionary eons.

The contemporary concept of living organisms as self-modifying beings coincides with the shift in biology from a mechanistic to an information- and systems-based view of vital functions. The life sciences have converged with other disciplines to focus on questions of acquiring, processing and transmitting information to ensure the correct operation of complex adaptive systems.

Today, we endeavor to understand how new vital capacities arose in the course of evolution during at least 3.5 billion tumultuous years of earth history. Two broad lines of research have made it possible to formulate a new vision of the evolutionary process. One examines how cells regulate the expression, reproduction, transmission and restructuring of their DNA molecules. The other comprises advances in studying interspecific hybridization, symbiogenesis, epigenetics, horizontal DNA transfer and mobile genetic elements. 21st Century evolution science explains abrupt events in the DNA and fossil records. Moreover, this contemporary mode of thinking makes it possible to envisage realistic paths to complex evolutionary innovations.

Additional online material for this book can be found at
FTPress.com/shapiro and
shapiro.bsd.uchicago.edu/evolution21.shtml

[Topher Cooper]

Yes, evolutionary theory is an active, developing field. Peripheral assumptions of that past have been set aside greatly expanding the understanding of the different kinds of variation that can appear, demonstrating the subtlety of the mechanisms that selection can create (e.g., alternate sets of features with genetic switches that whose position can be passed down until conditions change enough to flip the switch to the other state, or the selection of powerful, variable controls on the rate of mutation, so that in times of stress the rate of adaptation can increase).

In addition to an expansion in our understanding of the way genetics and genetic variation can occur, there has been an increase, prompted largely by the ability to use simulation to investigate mathematical models, in the ways that selection can occur. For example, there has been a still controversial reappearance of a more subtle form of group selection being argued about (mostly the argument seems to be about whether it should be called group selection).

All this strengthens the core concept of random variation ratcheted by selection.

We should perhaps be talking about neo-neo-Darwinian evolutionary theory. Neo-Darwinian evolution was born from the synthesis of Darwinian evolution with Mendelian genetics, but modern genetics sets aside many of the black and white absolutes of Mendel's simple concept of dominant and recessive genes.

[Paul]

Hi Topher - thanks for your reply. I was suggesting we set aside the idea of fraud in materialisation mediumship for arguments sake since you suggested all spirit communications rely on psi, and I was interested to explore whether this is necessarily so. Fraud is a possible explanation in almost any scenario.

I still cannot see how psi is necessary to explain materialisation in 'sufficient light to see what was going on' let's say (some allegedly occurred in white light of varying descriptions). I cannot see what such phenomena has to do with PK.

If we were to assume for arguments sake there was no fraud, I would have been interested to hear your view as to how it might be explained by some form of super-psi or how it might require some form of psi.

Your observation that Independent Direct Voice is merely related to floating violins and speaking trumpets is probably because, as you say, you don't know anything about it (tho trumpets have been used).

I don't propose continuing the conversation as it is off topic for this thread but your original general statement: "Remember that all spirit communication evidence presumes a form of psi" didn't seem to account for all the reported phenomena.

I am sure you would agree that it is important to make sure that statements about things we are not sure of are better phrased less assertively. I enjoy reading your comments but it could somewhat undermine mine confidence in other things you assert as fact.

Thanks anyway.

[Michael Prescott]

"Perhaps some connection to something beyond the spiritual came about in this way."

This is a recurrent theme of Ian Lawton's books - that spirit entities waited until hominid evolution had progressed to the point where the CNS was advanced enough to interface with spirit. Nanci Danison's viewpoint (very controversial for some people) is similar. I'm not saying it's true - who knows? - but it's one way of reconciling evolution and spiritualism.

[Topher Cooper]

Paul, I take your point about this being off topic, so I placed my response on my own blog. I invite you and anyone else interested to read that posting at Metaskepticism: Mediumship Necessarily Requiring Psi, and if you wish to comment on it.

[Paul]

Cheers.

[Dave]

In any case, there is no essential conflict between spirituality and a belief that human psychology evolved. Some people's specific view of spirituality is in conflict with evolution and they may resolve this by denying science, by trying to prove that evolution is non-scientific, by denying that view of spirituality (which perhaps sometimes creates a conflict that they must therefore also deny) or by changing their view of spirituality.

I wonder what form of spirituality can be compatible with evolutionary psychology, which sees the origin of all human moral codes as being divided roughly into several categories:
(1) Justice or punishment of misdeeds. This social contract supposedly evolved to prevent disintegration of social groups into destructive anarchy, a condition in which they cannot survive. This is often authority driven with a hierarchy. In gorillas, the ultimate authority in a group is the silverback, who has the top level say on the disciplining of others in the group.
2) (Limited) protection of the vulnerable and weak. But only up to the point where it does not compromise the rest of society too much. This social contract evolved first as an extension of protection for young, which to a varying degree and for a varying length of time depending on what particular social species we are talking about, obviously pass through an extended phase of being vulnerable and weak.
3) Defense against incursion. “All is fair in love and war” and this applies pretty much in the animal kingdom too. Specifically, there is a whole “ethic” of defending one’s group or troupe against dangerous invaders or threats. To take the silverback example again, he will (as the most powerful member) come to the rescue of individuals in the group, or the entire group, and may sometimes end up dead as a result.
4) Sex and family ties. The family is the core unit of most social species. Protecting one’s own bloodline above all others is one of the most commone features of the natural world. Again, this ensures not only that the species genes continue, but that your particular genes continue, as they are represented in your offspring. Hence all the familial level social contracts among the social species, which we see elaborated today in the human species.

There are high stakes here. If all moral codes, love, compassion and other qualities considered the essence of what is considered to be human are ultimately derived from the natural world through ages of a slow, contingent process of survival of the fittest (applied mostly to groups), then any notions that these qualities have transcendent or absolute existence in a spiritual existence are seen to be irrational. Huxley's Perennial Wisdom is seen as ridiculous fantasy, as are all of the various spiritual insights claimed by NDEers. This isn't my view, but I am just pointing out the inevitable cognitive dissonance between two bodies of evidence that are at our present level of understanding completely contradictory.

Of course it can be conjectured that Mind has influenced evolution in the desired direction even though random mutation plus natural selection is the primary process. This would be some sort of dualistic Darwinism, but it doesn't seem very viable. This would presume that what brains have evolved to do (at least in part) is access independently existing consciousness, rather than generate it. Perhaps Mind has physically influenced the evolutionary process by for instance injecting certain "random" genetic changes, in the direction of an intentionality to manifest in physical bodies. Unfortunately there are many problems with this concept.

Especially, why would some being or power of Mind, or spiritual entities in another realm having such power in the physical world, choose a process that has been so incredibly wasteful, time consuming, cruel and dependent on contingent accidents? Certainly such a possibility can't totally be ruled out as a logical possibility, but it appears unreasonable for such hypothetical beings to behave in such a way. Anyway, such a dualistic Darwinism would be a heretical version that would be totally rejected by most biologists and other scientists, who ascribe to philosophical materialism and strictly materialistic theories of mind. It would be claimed that there is not a bit of evidence for it.

There is an immense body of evidence for psychical phenomena in general, survival and for interactive dualist theories of mind, in the form of the data of parapsychology. Unfortunately there is also a huge body of evidence for evolution and for Darwinism (random genetic variation + selection) as the main mechanism of evolution. I reiterate that it is unfortunately necessary to maintain a certain cognitive dissonance and simply not deal with the problem until a viable theory is available that reconciles the two.

[Topher Cooper]

As is common in claims of an essential conflict between science and spirituality, Dave, you assume rather strict limits on the forms that spirituality can take, excluding not only possibilities for personal spirituality but also excluding many formal spiritual systems found throughout the world.

For example, you assume that a moral code is an essential, fundamental part of the core of spirituality, rather than simply informing it, or philosophically (not causally) derived from it, or even irrelevant to it.

You assume that any kind of spirituality requires a belief that moral codes are absolute, timeless and descend from a source outside the natural world. Taoism and Buddhism provide two obvious religious systems that explicitly deny this, but to my knowledge there are few religions, outside the Abrahamic and those influenced by them, that hold this as particularly important.

More fundamentally, you assume that spirituality is about belief/faith at all. As near as I have been able to tell, that was a fundamental innovation of Christianity (probably as a variant of the quite different Gnostic emphasis on the importance of knowledge). Islam seems to have also taken this up, and it has colored (but only colored) other modern religions. That isn't to say that religions are not generally associated with explicit sets of beliefs, but only that those beliefs are not considered fundamental to the religion. As long as the gods get their proper due, no one, least of all the gods themselves cares about whether the rituals and behavior comes out of belief in them.

At its core, spirituality is about a sense of connection with something much greater than oneself that is beyond the comprehension of the self (the extreme connection of "oneness" is what is technically meant by "mysticism"). There is no real requirement that that thing connected to must be super-physical nor that it must be understood in terms of having more than simply metaphorical teleological characteristics.

Personally, I'm quite happy associating my personal spirituality with a purely physical connectedness to the universe, and finding in science reinforcement for that connection rather than a conflict with it. To take a now trite example (if it can be articulated, its a weak example, anyway) we can use Sagan's "We are star stuff" which seems to me to be as spiritual a statement as can be found in any of the great works of religion.

And besides, you waaay overstate the case for Evolutionary Psychology. First of all it is a quite new and far from central part of evolutionary theory -- proposed extension of evolutionary theory into a new area. It is essentially a rebranding (with improved care and rigor) of the discredited field of sociobiology. At this point, it is primarily a collection of hypotheses -- basically plausible just-so stories justified by retrodiction rather than prediction, though with some successes in demonstrating that human behavior seems to be somewhat influenced by a few of their hypothesized evolutionary scenarios. Few believe that the current set of hypotheses (for example, your list of sources of morality) are anywhere near complete. None of these hypotheses do a very good job (though there have been some attempts at handwaving) to explain why, for example, a man would leave his child unattended in a place unsafe for a unattended child, to leap in front of a train in order to attempt to save a fallen stranger -- without any particular reason to expect reward or even to meet the person again.

Finally, I realize that I am in a minority, but I do not feel the need to assume that psi phenomena are in any real sense extra-physical. They clearly violate some of the limiting principles of contemporary physics, but then, so did relativity and QM for 19th century physics. Although the consequences of the release of the limiting principle is so much closer to our everyday life (which makes it pretty scary for many) it may require much less of a fundamental change to physics to develop a physical theory that includes it.

And if psi is ultimately physical, or even if just interacts lawfully with the physical, than it is subject to acquisition through evolutionary processes.

I can't say that I didn't feel some cognitive dissonance while I was working this out for myself (which includes the recognition that my personal take is only one of a very large number of possible resolutions), but I do not feel any fundamental cognitive dissonance now.

I am not saying -- far from it -- that science, or ones personal take on the philosophy of science (e.g., radical objectivism) may not be in conflict with the sets of beliefs that some people associate with their spirituality. And I can no more deny the validity of the resulting cognitive dissonance than I can deny other people's taste in ice cream flavors (which is not intended to trivialize it). But the claim that there must be a conflict between all philosophies of science and all possible kinds of spirituality is simply objectively untrue.

[Michael Prescott]

For an entertaining takedown of evolutionary psychology, see the book "Darwinian Fairy-Tales" by David Stove.

[Topher Cooper]

A random factoid of relevance to this discussion, though no great significance, just came to mind.

The discoverer of evolution by variation was raised as, and continued to believe in, spiritualism.

No, not Darwin, his co-author on the original publication, Alfred Russel Wallace.

At least some historians (all those who I have read their opinion on the matter) believe that is contribution has mostly been side-lined specifically because of his class and his not being "Church of England".

Darwin had dabbled privately with the theory for years, when Wallace sent him his version of the theory for possible publication (back then, peer review had not yet been invented -- senior scientists published whenever they wanted to, and junior researchers would send them papers for review and publication). Darwin, proposed that they co-author a paper instead.

This was only one of Wallace's many accomplishments. Among other things he was an active explorer, and not just someone who accompanied a ship and taking day trips from it to collect specimens. He was the first European, for example, to see a living bird of paradise.

[Dave]

Personally, I'm quite happy associating my personal spirituality with a purely physical connectedness to the universe, and finding in science reinforcement for that connection rather than a conflict with it. To take a now trite example (if it can be articulated, its a weak example, anyway) we can use Sagan's "We are star stuff" which seems to me to be as spiritual a statement as can be found in any of the great works of religion.

This would be a rather arid and unfulfilling version of "spirituality", at least to many. Maybe adopting this belief system would avoid the conflict. In such a diluted "spiritual system" all ethics,moral values, love, empathy, altruism and compassion do not come direct from a higher source as Soul directives, but are at base derived animal survival drives complexified by culture (the current scientific model). This would not be much different than no spirituality at all, and it would of course reject survival.

If such essential parts of people as ethics, morals, love, compassion and altruism are basically evolved animal characteristics, whatever there may be left over that is "spiritual" and transcendental can't be very significant. A personal view.

And besides, you waaay overstate the case for Evolutionary Psychology....... None of these hypotheses do a very good job (though there have been some attempts at handwaving) to explain why, for example, a man would leave his child unattended in a place unsafe for a unattended child, to leap in front of a train in order to attempt to save a fallen stranger -- without any particular reason to expect reward or even to meet the person again.

Such examples are indeed hard for evolutionary psychology to explain. In particular the Holocaust rescuers. These people, at great personal risk, helped members of persecuted groups, primarily Jews, during the Holocaust in defiance of Third Reich policy. Thousands survived the Holocaust because of the daring of these rescuers. Prominent examples are Oskar Schindler and Chiune Sugihara. Rescuers had an inner core of unshakable values and beliefs that enabled them to take a stand against the horrific injustices Hitler perpetrated during his twelve years in power. They had their own moral compass. To contend that these people were merely carrying out an evolutionary program is ultimately insulting to their heroism and incredibly cynical.

However, evolutionary psychologists just point out that a number of species show instinctual behaviors to aid others of their own (or even other) species in distress, saying it is natural that these generalized instincts should exist, as some simpler animals cannot "think things through". Like the publicized case where a crow risks its life to help a kitten, a video on youtube. The explanation is that in the case of human beings, the whole upper storey of the brain, the frontal lobes, comes into play on top of these instinctual feelings, with cultural/religious learned behaviors and emotions. But the biological basis of them is still in play. From this point of view there is no reason to assume that altruism comes from "somewhere else", any more than aggression or sex come from "somewhere else".

[Topher Cooper]

And a view of spirituality that insists that morality is something essentially external to the world and in some sense imposed from without rather than inextricably a part of ot, an addenda to life rather than being something that grew, you will pardon the expression, organically as a part of it, might seem to be a "rather arid and unfulfilling version of 'spirituality'" to others.

Again, you are presenting a primarily Christian and post-Christian view of spirituality as if it were universal except for a few of us impoverished souls.

Different strokes for different folks...

As for the "they got confused" explanation for acts of true altruism, I don't really disagree with it, but scientifically it is just a patch that can cover almost any hole in the theory. Until it is made more concrete it is compatible with but non-evolutionary in character.

But what you miss is that even if we accept this (and I myself use it as a working hypothesis) then what we have is true compassion and altruism as naturally emergent from evolutionary processes rather than being a "functional" product of them. That we went from "members of our tribe" to "all humans everywhere" and even beyond that to animals and sometimes plants means that a true morality transcended its origin as indirect self interest.