Darwin Unhinged: The Bugs in Evolution

There doesn't seem to be a fundamental problem with defining information, and defining complex at least has some criteria. For instance something highly complex is highly improbable (just one of many possibilities). For instance the sequence of cards in a well shuffled deck of cards. This is complex to a degree without having been independently specified.

But there is a fundamental problem with specification. It is a subjective measure. But it is not hard to understand and intuitively recognize. Let's say you find a 52-card deck perfectly ordered by rank and suit. If the deck was shuffled it could have any of approximately 8 x 10**67 possible arrangements. That's the complexity part. The number of possible arrangement of parts is huge, and is not determined by any physical laws.

The perfect ordering is a specification. Specification can be defined as an independently given pattern. We recognize function in a machine as a kind of specification. The problem is that although this is real, it is subjective. It is a product of mind.

http://www.talkreason.org/articles/eandsdembski.pdf

There may not be any objective formula that distinguishes specification from non-specification. But that does not negate the fact that specification is real and tangible and can be practically employed to discriminate between chance and design as we can see with the ordered deck of cards example. This pattern is specified because it is a pattern that has been identified in advance. If we claim the perfectly ordered deck came about by a random process the process had to have enough time to go through a good portion of all the possible combinations - not likely. To shorten the time the random variation process would have to have had a goal - but this is not allowed.

The ordered deck of cards is a human artifact. I don't think you can find an objective way to determine whether natural artifacts are specified. And if you could, you still wouldn't have a proof that some particular specified natural artifact must have been designed. You have no proof that specification cannot be accomplished naturally.

I wish people would stop claiming that evolution has to make a random search. There is plenty of literature about mechanisms that narrow the search to fruitful subspaces of sequence space.

Do we have any examples of complicated mechanical arrangements with function and specification where the origin can actually be determined, whose causal history is known, that are not assembled by an intelligence? The only complicated mechanical  arrangements with function and specification where the origin is causally known ("known" defined as "perceived directly, having direct cognition of"), is where the origin was via intelligent agency.

Which says nothing about natural artifacts.

First, show how an unintelligent process can create a symbolic code. DNA is a digital symbolic code composed of triplets of base 4 numerals represented by 4 nucleic acids. It even has start/stop symbols like human designed serial codes. The codes go through a lookup table to determine what action to take. This is all very familiar computer technology. Mathematical symbolism is a product of mind and a relatively advanced mind at that.

A natural process can create a code based on chemistry given enough time. The question is: has there been enough time? If you think that evolution of a code is impossible in principle, I'd love to hear why.

There is no lookup table. There are individual tRNAs that carry an amino acid and bind to a particular codon. Please don't overemphasize the computer sciencey feel of it.

Then show how the RM + NS process worked to create topoisomerase before there was the DNA replication enzyme.

https://www.ncbi.nlm.nih.gov/pubmed/17293019

https://academic.oup.com/nar/article/37/3/679/1079742

http://www.annualreviews.org/doi/abs/10....196.003223

Note that a lack of detailed description of the evolution of topoisomerases says nothing about the description of the purported intelligent design of them.

~~ Paul

PS: Fun video: https://www.youtube.com/watch?v=k4fbPUGKurI

Another interesting bit of research.

When physics gives evolution a leg up by breaking one

In a new study, physicists and evolutionary biologists at the Georgia Institute of Technology have shown how physical stress may have significantly advanced the evolutionary path from single-cell to multicellular organisms. In experiments with clusters of yeast cells called snowflake yeast, forces in the clusters' physical structures pushed the snowflakes to evolve.
"The evolution of multicellularity is as much a matter of physics as it is biology," said biologist Will Ratcliff, an assistant professor in Georgia Tech's School of Biological Sciences.
The bigger they are...
Like the first ancestors of multicellular organisms, in this study the snowflake yeast found itself in a conundrum: As it got bigger, physical stresses tore it into smaller pieces. So, how to sustain the growth needed to evolve into a complex multicellular organism?
In the lab, those shear forces played right into evolution's hands, laying down a track to direct yeast evolution toward bigger, tougher snowflakes.
"In just eight weeks, the snowflake yeast evolved larger, more robust bodies by figuring out soft matter physics that took humans hundreds of years to learn," said Peter Yunker, an assistant professor in Georgia Tech's School of Physics. He and Ratcliff collaborated on the research that documented the evolution and measured the physical properties of mutated snowflake yeast.


Read more at: https://phys.org/news/2017-11-physics-ev...g.html#jCp

[Cellular packing, mechanical stress and the evolution of multicellularity]

[Partial] Abstract:
[/url]The evolution of multicellularity set the stage for sustained increases in organismal complexity[url=https://www.nature.com/articles/s41567-017-0002-y#ref-CR1]1,2,3,4,5. However, a fundamental aspect of this transition remains largely unknown: how do simple clusters of cells evolve increased size when confronted by forces capable of breaking intracellular bonds? Here we show that multicellular snowflake yeast clusters6,7,8 fracture due to crowding-induced mechanical stress. Over seven weeks (~291 generations) of daily selection for large size, snowflake clusters evolve to increase their radius 1.7-fold by reducing the accumulation of internal stress. During this period, cells within the clusters evolve to be more elongated, concomitant with a decrease in the cellular volume fraction of the clusters. The associated increase in free space reduces the internal stress caused by cellular growth, thus delaying fracture and increasing cluster size. This work demonstrates how readily natural selection finds simple, physical solutions to spatial constraints that limit the evolution of group size—a fundamental step in the evolution of multicellularity.

https://www.nature.com/articles/s41567-017-0002-y

A natural process can create a code based on chemistry given enough time. The question is: has there been enough time? If you think that evolution of a code is impossible in principle, I'd love to hear why...

There is no lookup table. There are individual tRNAs that carry an amino acid and bind to a particular codon. Please don't overemphasize the computer sciencey feel of it.

The thing about codes is that to be codes, they necessarily have to have a lookup table or its equivalent. You claim there is no lookup table for tRNAs. I beg to differ. At one end, tRNAs contain anticodons (the name, which I didn't originate, should be a clue that they're something to do with codes)  that match codons on mRNA; and those are are specified by DNA. Hence DNA ultimately contains the lookup table for tRNAs. If you deny that tRNAs are specified by triplets in DNA, then you're denying that DNA is a code, and if so, you're challenging entirely conventional biological opinion.

As to your assertion that codes can arise through "natural process", first off you're going to have to come up with an example that is not DNA, because you've already, effectively, denied that DNA is a code. Please, snowflake me no snowflakes. Name me one code that has arisen through natural process without the help of any intelligence external to it. Explain to me how it arose, why it is a code, and what form its lookup table assumes.


For the benefit of anyone who'd like to understand the genetic code, transcription and translation, here's a useful video:

http://scienceblogs.com/dispatches/2007/...obability/

Some added depth in the comments too

From the linked article arguing against CSI (complex specified information):

  Experiment after experiment on enzyme function, including some generated by ID advocates themselves (see Axe 2000 and 2004), have shown that you can make significant substitutions in enzymes and still have the enzyme function.

This fact used to argue against Dembski's version of CSI - is at the heart of my own arguments!!!!!!!  Unintentionally this author has opened the Pandora's box of bio-evolution.  If others are really interested we can look together in the Third Way literature where it is discussed.  The question is: if DNA is a language, how is it not proof that life has used information science principles to develop from the start.  The idea that information is "special" in the hands of a human - must be lost.

A Panda with low iron in its blood is chemically in the same boat as his human counterpart.  A Panda with a hot tip on a stock, doesn't have the same range of probable activity as does a human with the same info and a couple of bucks.  Likewise, a bamboo location for the human may not be profitable.  We live in informational environments as well as physical ones.

Axe, et all -- found that the exact chemistry of enzyme function is unlike a straightforward chemical process.  There are process control operations that regulate toward a functional goal.  The function proceeds, even with some garble in the instructions.  How it appears to work - is like a language!  A message can trigger a functional process, from an array of wordings.  In chemistry. without catalysts - reactions proceed to equilibrium.  If they preform a "function" it is by accident.  There is no "god of elements" speaking to the molecules to statistically obey.  Materialism allows no organizing process coming from the natural intentions of living things.
  
Yet, organizing their environments is a fundamental function exhibited by living things.   Intentional behavior is what defines life.


The measurement system to judge environmental organization through behavior guided by feedback -- is informational.  The entropy of environments around living things decreases in direct proportion to the mutual information they store about it.  Having a natural language like the one underlying bio codes in DNA, RNA, Ribosomes, Enzymes and Proteins - appears to be a prerequisite for life as we know it.  It is an information transfer system and it is inherently purposeful.  Communication isn't measured in the terms of chemical bonding or electro-static charge.

That there is structured information that results from the minds of living things is so simple a concept. 

Life is natural.  Life involves communication of intent through activity that logically supports survival.  The first living things were converters of raw facts into strategic behavior to eat, each ions, rest and reproduce.  Life is described better and better from a chemical viewpoint.  But if you want to understand the bigger picture science offers - life's ability to process information is required as well.

The thing about codes is that to be codes, they necessarily have to have a lookup table or its equivalent.

Sure, given a broad definition of "equivalent."

You claim there is no lookup table for tRNAs. I beg to differ. At one end, tRNAs contain anticodons (the name, which I didn't originate, should be a clue that they're something to do with codes)  that match codons on MRNA; and those are are specified by DNA. Hence DNA ultimately contains the lookup table for tRNAs. If you deny that tRNAs are specified by triplets in DNA, then you're denying that DNA is a code, and if so, you're challenging entirely conventional biological opinion.

Yes, you've defined "equivalent" broadly enough to include patterns for building components that then operate nothing like a table. This is like saying that the instructions to build an old-fashioned coin sorter means that the coin sorter operates by a lookup table.

https://www.google.com/search?q=old+fash...q5bmuzUbhM:

As to your assertion that codes can arise through "natural process", first off you're going to have to come up with an example that is not DNA, because you've already, effectively, denied that DNA is a code. Please, snowflake me no snowflakes. Name me one code that has arisen through natural process without the help of any intelligence external to it. Explain to me how it arose, why it is a code, and what form its lookup table assumes.

I'm perfectly happy to say that codons constitute a code. I was arguing that the ribosome does not work by table lookup. And the genes coding tRNAs don't operate by table lookup, either. The only way to involve tables is to say that all of our DNA is a giant table, which is a rather pointless analogy.

I don't need to come up with an example, since I am not the one making the claim. If you believe that a code-like mechanism cannot arise naturalistically, then you must have some sort of proof in mind. Otherwise, what stops evolution from doing it, given enough time? What is special about a code-like mechanism, other than the observation that humans design codes?


~~ Paul

I don't need to come up with an example, since I am not the one making the claim. If you believe that a code-like mechanism cannot arise naturalistically, then you must have some sort of proof in mind. Otherwise, what stops evolution from doing it, given enough time? What is special about a code-like mechanism, other than the observation that humans design codes?


~~ Paul

So, you accept that it is a code but you want to shift the burden of proof. Could you at least describe how you think evolution did it? And how much time was required? I've read the Wikipedia page - in particular, the section on its origin - and am no wiser. What I see there is a lot of scratching around for a hypothesis that might go some way to an explanation but nothing substantive. Of course, I don't understand the science so you are welcome to point to the part I may have missed which provides the evidence of how the code evolved. A bit of further searching and reading led me to a paper by Koonin and Novozhilov and, in particular, their conclusions (I didn't read the whole paper because, for the most part, it is way over my head).

The paper is titled: Origin and Evolution of the Genetic Code: The Universal Enigma

Nevertheless, this proposal, even if quite plausible, is only one facet of a much more general and difficult problem, perhaps, the most formidable problem of all evolutionary biology. Indeed, it stands to reason that any scenario of the code origin and evolution will remain vacuous if not combined with understanding of the origin of the coding principle itself and the translation system that embodies it. At the heart of this problem is a dreary vicious circle: what would be the selective force behind the evolution of the extremely complex translation system before there were functional proteins? And, of course, there could be no proteins without a sufficiently effective translation system. A variety of hypotheses have been proposed in attempts to break the circle (see (Noller 2004; Penny 2005; Noller 2006; Wolf and Koonin 2007) and references therein) but so far none of these seems to be sufficiently coherent or enjoys sufficient support to claim the status of a real theory.

So, you accept that it is a code but you want to shift the burden of proof.

I don't have a burden of proof because I don't think a code is anything special. You must have something in mind that makes a code impossible/supremely difficult to evolve. I just want you to tell me what that reason is. It just seems like an argument from similarity to human codes. Why is this more interesting than, say, a kinesin protein?

Could you at least describe how you think evolution did it? And how much time was required? I've read the Wikipedia page - in particular, the section on its origin - and am no wiser. What I see there is a lot of scratching around for a hypothesis that might go some way to an explanation but nothing substantive. Of course, I don't understand the science so you are welcome to point to the part I may have missed which provides the evidence of how the code evolved. A bit of further searching and reading led me to a paper by Koonin and Novozhilov and, in particular, their conclusions (I didn't read the whole paper because, for the most part, it is way over my head).

You are right that we don't know how it evolved. But there are many papers on the subject. Many of them discuss the modular structure of tRNAs.

https://biologydirect.biomedcentral.com/...-6150-6-14

More papers:

https://www.bibliotecapleyades.net/cienc..._adn09.htm

https://www.nature.com/articles/6801086

I'm not sure why you would expect this problem to be solved, or why the lack of a solution is any sort of evidence against the evolutionary perspective. There must be a principle involved.

~~ Paul

I don't have a burden of proof because I don't think a code is anything special. You must have something in mind that makes a code impossible/supremely difficult to evolve. I just want you to tell me what that reason is. It just seems like an argument from similarity to human codes. Why is this more interesting than, say, a kinesin protein?

You are right that we don't know how it evolved. But there are many papers on the subject. Many of them discuss the modular structure of tRNAs.

https://biologydirect.biomedcentral.com/...-6150-6-14

More papers:

https://www.bibliotecapleyades.net/cienc..._adn09.htm

https://www.nature.com/articles/6801086

I'm not sure why you would expect this problem to be solved, or why the lack of a solution is any sort of evidence against the evolutionary perspective. There must be a principle involved.

~~ Paul

First you insist that there is no problem: that there is nothing special about the code (at least you admit it is a code) and that it should not be impossible/supremely difficult to evolve such a code. Then you go on to say that we don't know how it evolved nor should we expect this problem (suddenly, it is now a problem) to be solved.

The other (Skeptiko forum) discussions I mentioned earlier in the thread were centred around the point that there are no examples of codes appearing/evolving other than the genetic code. All other known codes have been originated by some intelligent agency. So why go over the same arguments again? You are just repeating an assertion - as Michael pointed out to you above. He challenged you to give an example yet you duck his challenge. I simply don't see the point in going further until you back up your assertion.

First you insist that there is no problem: that there is nothing special about the code (at least you admit it is a code) and that it should not be impossible/supremely difficult to evolve such a code. Then you go on to say that we don't know how it evolved nor should we expect this problem (suddenly, it is now a problem) to be solved.

I'm not saying there is no problem. I'm saying that the problem is just like the problem of evolution of every other mechanism. But people who insist that the code is something special must have a principle in mind. Why can't anyone state the principle?

The other (Skeptiko forum) discussions I mentioned earlier in the thread were centred around the point that there are no examples of codes appearing/evolving other than the genetic code. All other known codes have been originated by some intelligent agency. So why go over the same arguments again? You are just repeating an assertion - as Michael pointed out to you above. He challenged you to give an example yet you duck his challenge. I simply don't see the point in going further until you back up your assertion.

As you'll recall, we spent a lot of time discussing what makes something a code. Why is the genetic code more of a code than other selective binding molecules, or more of a code than the valence electron patterns? There must be a principle involved. Why is it interesting that there are (supposedly) no other natural codes?

You could just as well say that there is no example of a walking kinetic molecule other than kinesin molecules. Does that make it special, too?

Until someone can state the principle, why would you assume that I could explain why it's not a principle that prevents nature from evolving a code? For example, why couldn't it start as a single-base code, evolve slowly into a 2-base code, and then evolve a third degenerate base in order to improve fidelity?


~~ Paul

Sure, given a broad definition of "equivalent."

Yes, you've defined "equivalent" broadly enough to include patterns for building components that then operate nothing like a table. This is like saying that the instructions to build an old-fashioned coin sorter means that the coin sorter operates by a lookup table.

https://www.google.com/search?q=old+fash...q5bmuzUbhM:

I'm perfectly happy to say that codons constitute a code. I was arguing that the ribosome does not work by table lookup. And the genes coding tRNAs don't operate by table lookup, either. The only way to involve tables is to say that all of our DNA is a giant table, which is a rather pointless analogy.

I don't need to come up with an example, since I am not the one making the claim. If you believe that a code-like mechanism cannot arise naturalistically, then you must have some sort of proof in mind. Otherwise, what stops evolution from doing it, given enough time? What is special about a code-like mechanism, other than the observation that humans design codes?


~~ Paul

The reason I said "or equivalent" is that there isn't a literal table in the DNA or anywhere else in the cell. However, the table is unambiguously implied because triplets in DNA follow rules which biologists have elucidated and most conveniently represent as a table.

The video I posted showed this table -- from mRNA codons to tRNA anticodons, but one could just as easily construct a table from DNA triplets to tRNA anticodons. The mRNA is used because DNA is in the nucleus, whereas tRNAs, ribosomes and amino acids are found in the cytoplasm; and mRNA, unlike DNA, can conveniently pass through nuclear pores. Besides, snipping out bits of DNA is hardly a viable proposition; and so the code applies even in prokaryotes (archaea and bacteria), which don't have a membrane-bound nucleus.

It's a fact that in DNA, every one of the 64 triplet codons (except for the 3 stop codons) always ends up specifying the same amino acid. Biologists can always predict which amino acid that will be, just by looking at the table -- no exceptions*. Hence the table, although not literal, is demonstrably embodied in the DNA code. If you can't see that, then you 're either a dunderhead or engaging in sophistry as an attempted diversionary tactic.

*I should note here that apparently, the code isn't quite universal: there are some organisms that use somewhat different codes, but the principle employed is the same. This is mentioned in the paper that Kamarling linked to.

You say you don't need to come up with an example of a code produced by "natural process". Does this mean that you know of such a code but aren't prepared to name it? Or that you don't know one but in any case don't have to name it? Just because you previously asserted without evidence that it's a fact that codes can be produced "naturally"?

Go take a hike; that's about as scientific as asserting the moon is made of green cheese without showing a sample of moon rock that tastes of unripe Wensleydale. Where do you get off asserting things by fiat? And I'm meant to roll over before the force of your assertion? Think again -- grow a pair and give me your example or admit you can't.

The ID proposition uses a tenet that Charles Darwin himself ascribed to: that causes in operation in the present should be looked to first to explain the past (i.e. the uniformitarianism of Lyell -- who profoundly influenced Darwin): "He [Lyell] influenced Darwin so deeply that Darwin envisioned evolution as a sort of biological uniformitarianism." (see here).

All codes we know of outside cells originated in minds. For the code in DNA -- inside cells -- we're being asked to abandon the uniformitarian principle that  Darwin so admired and come up with some other kind of explanation than that of conscious input. But in the absence of concrete evidence that codes can in fact be generated through "natural process", any such appeal is baseless, just an assertion based on ideological faith in materialistic metaphysics coupled with promissory materialism.

Your claim is baseless, and you can't adduce any evidence for it, whereas the ID claim does at least have some basis, and the evidence comes from uniform common experience: that codes always originate in consciousness, and never through deterministic or stochastic processes. All you have to do to disprove this claim is to come up with a single code where you can fully explain how it arose without the need for consciousness. Stop trying to shift the burden of proof to others to save your own face. And do please stop asserting things without evidence.