The evidence for strong emergence in chemistry

Good summary description. I would just add that this is just the protein coding portion of DNA. There is still all the non-coding DNA, which has progressively been found to embody more and more also essential functions such as information determining organismal form for instance. This was simply called "junk DNA" by Darwinists for years.

Thanks, as I wrote that piece I felt just how daft the conventional position has become. I mean the resemblance between DNA and computer programming really is uncanny! There was a conference in 1966, the Wistar conference, in which biologists, mathematicians and physicists came together to discuss the viability of Darwin's theory in the aftermath of the discovery of the function of DNA. I think it was only the Biologists that supported Darwin (roughly speaking). The problem is that scientists in one discipline are extremely reluctant to criticise some other discipline.

When people try to argue against other areas of parapsychology, which are inevitably empirical, I like the fact that this area provides some solid facts. Some entities were busy designing our DNA and the rest of our biochemistry before life had even started - fact!

I do know DNA has other non-coding functions but I don't know much about them, and Sbu was specifically objecting to the fact that he is not a biochemist (nor am I). Behe's work makes the idea that this was not designed even less plausible, and I'll move on to that area if he takes the bait!

David

Well strangely you don't really need to understand biochemistry or biology to explore this subject. Genes are basically digital - C, G, A, T. The chemistry of those four ingredients of DNA barely matters, they are simply labels. They act as a code (but I guess you must know that) so their chemistry is no more relevant than the voltage levels used within your computer to represent 0 and 1.

Although this DNA code is probably used in other ways, its primary use is to represent the linear string of amino acid bases that make up each different type of protein in a living system. The amino acids have names, but again these can usually be thought of simply as labels.

Think of a string of bytes in C, there has to be one byte which just represents the end of the string. In C that is a zero byte, in the genetic code the corresponding string terminator is TGA.

A strand of DNA contains thousands of genes (strings) and there can be gaps between the genes, therefore ATG acts as a start of gene marker if it is at the start of a gene, but otherwise encodes the amino acid methionine.

This scheme could code for 64-2 possible amino acids, but only 22 amino acids are used in life, so some amino acids can be encoded in more than one way. I guess an alternative would generate an "invalid codon" error in such a situation - but living things don't have a suitable output device attached.

Even a cursory reading of that must make you wonder if it could really have 'emerged' or arrived by chance. Remember that until you get to the stage of a single cell, there is no such thing as natural selection to devise such a scheme.

Of course, a computer is made in a special factory, and similarly there is a substantial collection of proteins needed to use the code I have just described. The strange thing is that al the proteins for this mechanism are simply encoded in the same scheme.

I have not got into the work of the DI, but without all the baggage of the debate as to where life came from, would you really say "Aha - that is obviously something that could have happened by chance!?"

If I have whet your appetite I'll continue.

David

I understand your point and acknowledge the strength of your argument, particularly regarding the numerous possible combinations of amino acids. I advocate for scientific methodology, which for me centers on observation and replication. I firmly believe in relying on objective evidence to draw conclusions. However, I question how we can replicate or observe phenomena like the 'Big Bang' or study chemical and biochemical processes that occurred billions of years ago. It's impossible without making numerous prior assumptions. For this reason, I have never placed much stock in the theory of evolution or the Big Bang theory. The idea that humans share a common ancestor with apes has never captivated my interest. These remote events can probably never be investigated to any higher level of satisfaction (at least for me).

I believe I can succinctly summarize your message as follows: 'Since human DNA couldn’t have evolved by chance, there must be a greater meaning.' It’s a compelling argument, and I have no substantial counterarguments to offer.

I believe I can succinctly summarize your message as follows: 'Since human DNA couldn’t have evolved by chance, there must be a greater meaning.' It’s a compelling argument, and I have no substantial counterarguments to offer.

Well it isn't exactly "there must be a greater meaning", which sounds a bit New Age, it is that some entity must have designed the whole thing in order to get it off the ground. It isn't an argument for God, but it is, I think a powerful argument for discarnate entities.

SETI searches for intelligent life in outer space require similar reasoning - i.e. they look for signals that must have come from an intelligent source. A mere sequence of binary encoded prime numbers would probably be accepted as evidence of alien intelligence, so the design of the mechanism I outlined above should certainly pass the test!

Behe's argument takes this a bit further, by showing that RM+NS progressively damages the genome of an entire species. This seems to mean that life requires the injection of fresh design work from discarnate entities to keep it going!

Behe's book is not full of heavy biochemistry, so I think you would feel perfectly comfortable reading it, though you might find its logical conclusion a bit indigestible

Don't you feel a bit ashamed that science has obfuscated this particular piece of information just because it is inconvenient? My wider view is that modern science has totally betrayed the founders of modern science, who achieved so much with so little equipment.

Also, doesn't this change the a priori probabilities in any Bayesian estimate of the probability of discarnate life after death?

David

Well it isn't exactly "there must be a greater meaning", which sounds a bit New Age, it is that some entity must have designed the whole thing in order to get it off the ground. It isn't an argument for God, but it is, I think a powerful argument for discarnate entities.

For me, the improbability of RM+NS producing complex systems like human biology doesn't necessarily imply direct evidence for discarnate entities. A plausible naturalistic alternative is the existence of an infinite number of causally distinct universes (this is a distinct idea to the QM many-worlds interpretation), each with slightly different initial conditions, possibly due to a true randomness factor. With an infinite number of RM+NS experiments, the emergence of humans (or other forms of biological life) is no longer an unlikely outcome.

Furthermore, a significant portion of mathematics deals with infinities. For example, the exponential function, e, which students learn about in school, is defined as the limit of an infinite series. Calculus, arguably the most important branch of mathematics in engineering, fundamentally involves infinite sums in integrals and limits approaching infinitely small intervals in derivatives. Therefore, the concept of an infinite number of universes does not seem far-fetched to me.

Behe's argument takes this a bit further, by showing that RM+NS progressively damages the genome of an entire species. This seems to mean that life requires the injection of fresh design work from discarnate entities to keep it going!

What's the evidence for fresh design work being introduced into biological life?

Don't you feel a bit ashamed that science has obfuscated this particular piece of information just because it is inconvenient? My wider view is that modern science has totally betrayed the founders of modern science, who achieved so much with so little equipment.

I don't view science as a political party with which I might disagree. Instead, I see it as a methodology for evaluating evidence supporting various hypotheses—all of which aim to find natural causes. Sometimes the evidence is weak, and sometimes it's strong. Science is inherently self-correcting; over time, outdated hypotheses are discarded and new ones are proposed.

Also, doesn't this change the a priori probabilities in any Bayesian estimate of the probability of discarnate life after death?

I'm not sure statistical terminology can be used to settle this question as we don't have ways to estimate the posterior probability distribution. But I hope very much for life after death myself. I agree that there's definitely a hope for life after death for a whole range of reasons, the topic of this discussion just being one of them. I assign most weight to the (obvious) existence of consciousness. In a pure naturalistic explanation for the universe there's no known need for consciousness. And yet our own consciousness is the only thing we can ever be sure that exists.

For me, the improbability of RM+NS producing complex systems like human biology doesn't necessarily imply direct evidence for discarnate entities. A plausible naturalistic alternative is the existence of an infinite number of causally distinct universes (distinct from the many-worlds interpretation), each with slightly different initial conditions, possibly due to a true randomness factor. With an infinite number of RM+NS experiments, the emergence of humans (or other forms of biological life) is no longer an unlikely outcome.

Furthermore, a significant portion of mathematics deals with infinities. For example, the exponential function, e, which students learn about in school, is defined as the limit of an infinite series. Calculus, arguably the most important branch of mathematics in engineering, fundamentally involves infinite sums in integrals and limits approaching infinitely small intervals in derivatives. Therefore, the concept of an infinite number of universes does not seem far-fetched to me.


What's the evidence for fresh design work being introduced into biological life?


I don't view science as a political party with which I might disagree. Instead, I see it as a methodology for evaluating evidence supporting various hypotheses—all of which aim to find natural causes. Sometimes the evidence is weak, and sometimes it's strong. Science is inherently self-correcting; over time, outdated hypotheses are discarded and new ones are proposed.


I'm not sure statistical terminology can be used to settle this question as we don't have ways to estimate the posterior probability distribution. But I hope very much for life after death myself. I agree that there's definitely a hope for life after death for a whole range of reasons, the topic of this discussion just being one of them. I assign most weight to the (obvious) existence of consciousness. In a pure naturalistic explanation for the universe there's no known need for consciousness. And yet our own consciousness is the only thing we can ever be sure that exists.

Plausible?

Derived from https://evolutionnews.org/2022/01/spider...nt-design/:

These are some problems with even your suggested kind of Multiverse, and it's just the beginning:

(1) The Multiverse Destroys Science

It would effectively destroy the ability of scientists to study nature. A short hypothetical example shows why.

Imagine that a team of researchers discovers that 100 percent of an entire town of 10,000 people got cancer within one year — a “cancer cluster.” For the sake of argument, say they determine that the odds of this occurring just by chance are 1 in 10**10,000. Normally, scientists would reason that such low odds establish that chance cannot be the explanation, and that there must be some physical agent causing cancer in the town.

Under multiverse thinking, however, one might as well say, “Imagine there are 10**10,000 universes, and our universe just happened to be the one where this unlikely cancer cluster arose — purely by chance!” Should scientists seek a scientific explanation for the cancer cluster, or should they just invent 10**10,000 universes where this kind of event becomes probable? The multiverse advocate might reply, “Well, you can’t say there aren’t 10**10,000 universes out there, right?” Right — but that’s the point. There’s no way to test the multiverse, and science should not seriously consider untestable theories. Multiverse thinking makes it impossible to rule out chance, which essentially eliminates the basis for drawing scientific conclusions.

(2) Since we cannot observe anything outside our universe, multiverse theories are 100 percent philosophical speculation, not science.
That last point leads to a deeper reason to reject the multiverse hypothesis. Scientific analyses include a requirement that is violated by the multiverse concept: they should be testable. The inability of science to observe anything outside our universe does not seem likely to change anytime soon, or ever.

Uncountable billions of universes — and of galaxies and copies of each of us — accumulate with no possibility of communication between them or of testing their reality.

(3) What is the mechanism that keeps cranking out all of these hypothetical universes, and how did it originate? There is no explanation for the cause of the multiverse.
The theory relies on the assumption that the universes would be different from each other. If there are multiple universes, why wouldn’t many or all of them have the same characteristics?

(4) This is an absolutely massive and ultimate violation of the Occam's Razor principle of parsimony of explanations.

For me, the improbability of RM+NS producing complex systems like human biology doesn't necessarily imply direct evidence for discarnate entities. A plausible naturalistic alternative is the existence of an infinite number of causally distinct universes (this is a distinct idea to the QM many-worlds interpretation), each with slightly different initial conditions, possibly due to a true randomness factor. With an infinite number of RM+NS experiments, the emergence of humans (or other forms of biological life) is no longer an unlikely outcome.

Furthermore, a significant portion of mathematics deals with infinities. For example, the exponential function, e, which students learn about in school, is defined as the limit of an infinite series. Calculus, arguably the most important branch of mathematics in engineering, fundamentally involves infinite sums in integrals and limits approaching infinitely small intervals in derivatives. Therefore, the concept of an infinite number of universes does not seem far-fetched to me.

So is the very idea of a discarnate being so obnoxious to you that you would rather introduce the concept of an infinite number of universes? My mental version of Occam's Razor would definitely favour the former. I have never been a fan of the Many Worlds interpretation of QM.

What's the evidence for fresh design work being introduced into biological life?

You really need to read Behe's book, but here is an outline of his argument:

It is possible to classify mutations into four types

0: Mutations which are harmless. For example, since the genetic code is redundant, mutations can occur to a codon (3 bases) that don't change the corresponding amino acid.

1: Mutations that severely impair the ability of the organism to reproduce, or which kill it.

2: Mutations that destroy or damage a gene but happen to benefit the organism in particular circumstances.

3: Mutations that actually improve the organism as a whole.

Type 2 mutations may sound rather odd, but a common example of this is the mutation to the haemoglobin gene that causes sickle cell anaemia. This change makes people more resistant to malaria at the expense of the health complications caused by sickle cell anaemia.

Now it is necessary to consider the viability of the whole species.

If humans were exposed to a lot of malaria it is conceivable the wild form of haemoglobin would be lost - everyone would have sickle cell anaemia. In that case that gene would be gone forever from our collective genome. Fortunately there are plenty of people with the original haemoglobin gene, and if at some point everyone lives in places without malaria the mutated gene might die out.

Another example of type 2 mutations is to be found in bacteria that mutate so that they can evade a particular antibiotic. Often this results in a bacteria that outcompete normal bacteria because the antibiotic kills the normal bacteria. However, in the wild the antibiotic resistant bacteria is less efficient than the original.

Thus type 2 mutations gradually damage an entire species. Over geological time species should become extinct because of this (admittedly rather obscure) process.

Note that type 2 mutations are going to be a lot more common than type 3 because it is much more likely that a mutation will destroy or damage a gene than that it will actually improve it.

This means that for a species to survive over geological periods of time, they need to be 'serviced' by a thinking entity!

David

So is the very idea of a discarnate being so obnoxious to you that you would rather introduce the concept of an infinite number of universes? My mental version of Occam's Razor would definitely favour the former. I have never been a fan of the Many Worlds interpretation of QM.

The idea presented is not the Many Worlds of QM. In Many Worlds, every time a QM superposition is measured, the current universe branches into new universes for each possible measurement outcome of the superposition. I don’t like that idea either.

What I suggest is the existence of an infinity of causally disconnected universes not sharing a common origin as in MWI. My mental version of Occam’s Razor makes this the simpler explanation—we already know one universe exists, so why shouldn’t there be more? However, we don’t have any empirical evidence for any discarnate beings with the power to design an entire universe.

I think we can probably agree that the Occam’s Razor argument is pretty worthless in these discussions!

You really need to read Behe's book, but here is an outline of his argument:

It is possible to classify mutations into four types

0: Mutations which are harmless. For example, since the genetic code is redundant, mutations can occur to a codon (3 bases) that don't change the corresponding amino acid.

1: Mutations that severely impair the ability of the organism to reproduce, or which kill it.

2: Mutations that destroy or damage a gene but happen to benefit the organism in particular circumstances.

3: Mutations that actually improve the organism as a whole.

Type 2 mutations may sound rather odd, but a common example of this is the mutation to the haemoglobin gene that causes sickle cell anaemia. This change makes people more resistant to malaria at the expense of the health complications caused by sickle cell anaemia.

Now it is necessary to consider the viability of the whole species.

If humans were exposed to a lot of malaria it is conceivable the wild form of haemoglobin would be lost - everyone would have sickle cell anaemia. In that case that gene would be gone forever from our collective genome. Fortunately there are plenty of people with the original haemoglobin gene, and if at some point everyone lives in places without malaria the mutated gene might die out.

Another example of type 2 mutations is to be found in bacteria that mutate so that they can evade a particular antibiotic. Often this results in a bacteria that outcompete normal bacteria because the antibiotic kills the normal bacteria. However, in the wild the antibiotic resistant bacteria is less efficient than the original.

Thus type 2 mutations gradually damage an entire species. Over geological time species should become extinct because of this (admittedly rather obscure) process.

Note that type 2 mutations are going to be a lot more common than type 3 because it is much more likely that a mutation will destroy or damage a gene than that it will actually improve it.

This means that for a species to survive over geological periods of time, they need to be 'serviced' by a thinking entity!

David

It's a good theory. One that can neither be proven or falsified. For that reason it's not science (and neither is the multiverse idea of course). There's only so much we can derive from processes spanning "geological time".

These god of the gaps arguments are great for hypothesis generation, but for me at least, they don’t constitute evidence.

Without more insight into the rate of mutation and so forth I can’t offer more specific commentary on the work ny Michael Behe.

The idea presented is not the Many Worlds of QM. In Many Worlds, every time a QM superposition is measured, the current universe branches into new universes for each possible measurement outcome of the superposition. I don’t like that idea either.

What I suggest is the existence of an infinity of causally disconnected universes not sharing a common origin as in MWI. My mental version of Occam’s Razor makes this the simpler explanation—we already know one universe exists, so why shouldn’t there be more? However, we don’t have any empirical evidence for any discarnate beings with the power to design an entire universe.

I think we can probably agree that the Occam’s Razor argument is pretty worthless in these discussions!


It's a good theory. One that can neither be proven or falsified. For that reason it's not science (and neither is the multiverse idea of course). There's only so much we can derive from processes spanning "geological time".

These god of the gaps arguments are great for hypothesis generation, but for me at least, they don’t constitute evidence.

Without more insight into the rate of mutation and so forth I can’t offer more specific commentary on the work ny Michael Behe.

Can neither be proven or falsified, and the argument doesn't generate evidence when experimentally tested?

You seem to be unaware of or totally ignore the well-known long-term (50,000 generations) bacterial evolution experiment of Richard Lenski, in which he sought to generate many examples of complex evolution of new biological functions and mechanisms by culturing large populations of e-coli bacteria in his lab for very many generations, trying to simulate the assumed very much longer term evolution of more complex and longer lived organisms.

In short, the experiment failed and completely verified Dr. Michael Behe's premise in Darwin Devolves, that Darwinian RM+NS does essentially nothing but generate cell lines of progressively more and more broken genes. The E. coli of the long term evolution experiment were accumulating degradative mutations much faster than any mutations that might with charity be called constructive. And the one apparently constructive mutation turned out to really also involve more broken genes. It should be emphasized that there was no overall increase in functional complex specified genetic information, but instead a large decrease, as predicted by Dr. Behe.

Derived from an excellent article by Dr. Michael Behe at https://www.discovery.org/a/citrate-death-spiral/ :

The resulting E. coli was one sick puppy. Inside the paper on the experiment they report that “The spectrum of mutations identified in evolved clones was dominated by structural variation, including insertions, deletions, and mobile element transpositions.” All of those are exceedingly likely to break or degrade genes. Dozens more genes were lost.

There was one highly touted "advancement" - the occurence of one new function - a citrate metabolism mutation. But in reality in the experiment the citrate mutant achieved this not by generating new functional genes (as would be expected from classic undirected RM+NS Darwinistric processes), but by breaking even more genes, tossing genetic information with mindless abandon for short term advantage.

In a particularly telling result, the authors “serendipitously discovered evidence of substantial cell death in cultures of a Cit+ clone sampled from … the LTEE at 50,000 generations.” In other words, those initial random “beneficial” citrate mutations that had been seized on by natural selection tens of thousands of generations earlier had led to a death spiral. The death rate of the ancestor of the LTEE was ~10 percent; after 33,000 generations it was ~30 percent; after 50,000, ~40 percent. For the newer set of experiments, the death rate varied for different strains of cells in different media, but exceeded 50 percent for some cell lines in a citrate-only environment. Indeed, the authors identified a number of mutations — again, almost certainly degradative ones — in genes for fatty acid metabolism that, they write with admirable detachment, “suggest adaptation to scavenging on dead and dying cells.”

In other words, the bacteria adapted in part by learning how to eat their dead.

Since the overwhelming majority of mutations were damaging and degradative, genes were being degraded left and right, both when they directly benefited the bacteria and when they did so indirectly in support of another mutation. The occasional, particularly noticeable modification-of-function or gain-of-function mutation couldn't turn back the overall tide of damaging and loss-of-function ones, which greatly degraded the overall fitness of the "evolved" bacterial line.