Darwin Unhinged: The Bugs in Evolution

[Laird]

Just as a minor addendum to Michael's excellent rejoinder:

what stops evolution from doing it [i.e. producing the code which is DNA --Laird]

Oh, I don't know, perhaps the fact that evolution (in the neo-Darwinist terms which you seem to accept i.e. random mutations plus natural selection) is predicated on the existence of that code in the first place?

Just as a minor addendum to Michael's excellent rejoinder:


Oh, I don't know, perhaps the fact that evolution (in the neo-Darwinist terms which you seem to accept i.e. random mutations plus natural selection) is predicated on the existence of that code in the first place?

I'm missing something and maybe you can explain. What is it about neoDarwinism that ruffles feathers?

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.

But we represent lots of things with tables. The periodic table comes to mind. My objection is to use the fact that we can represent things as tables to imply that those things are designed like humans design.

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.

Hang on. There is nothing in the DNA that we could snip out to interact with the anticodons. What's in the DNA are genes that code for RNAs and proteins that make up the ribosome, tRNA, tRNA synthetases, and so forth. There is nothing like a codon table in the DNA.

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.

Of course there are exceptions.

http://medicine.jrank.org/pages/2292/Gen...-Code.html

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.

There you go.

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"?

My assertion is there is nothing stopping a code-like mechanism from being produced naturally, given enough time. To refute my assertion, you can specify the principle that prevents such a thing. But before you do that, you need to carefully define "code." Is the periodic table a code? Are other kinds of selective binding a code?

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.

I'm not asking anyone to roll over. I'm asking for the principle that you must have in mind. Because if you don't have a principle in mind, then surely you are not going to accuse me of making unwarranted assertions without doing a double-take.

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.

Really, you're not doing a double-take here?

You apparently have no principle that prevents nature from inventing a code via evolution. You just assume it can't because humans can. And in the process, you ignore all the research on the evolution of the genetic code.

~~ Paul

Just as a minor addendum to Michael's excellent rejoinder:


Oh, I don't know, perhaps the fact that evolution (in the neo-Darwinist terms which you seem to accept i.e. random mutations plus natural selection) is predicated on the existence of that code in the first place?

So you don't think it could have started as, say, a single base code? Then slowly evolved to use two bases? Then evolved to use three in a degenerate manner (the third codon in highly degenerate).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

Why do people keep imagining the evolution of life on Earth as an "all of it, all at once" sort of process?

Here's a particularly interesting paper:

https://www.sciencedirect.com/science/ar...9314000113

~~ Paul

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?

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

I have followed only bits and pieces of these previous discussions. Was there ever a time, when you gave examples of what it was that was asked for (e.g. natural codes), that those examples were accepted? For example, is there a reason that pheromones or polymorphic crystals aren't codes?

Linda

I have followed only bits and pieces of these previous discussions. Was there ever a time, when you gave examples of what it was that was asked for (e.g. natural codes), that those examples were accepted? For example, is there a reason that pheromones or polymorphic crystals aren't codes?

Linda

We talked about those two things, along with the periodic table. None were accepted. I don't think we ever converged on a definition of "code" that includes the genetic code but excludes those things.

As I'm about to post, there seems to be some serious question begging going on.

~~ Paul

Please correct me if I'm wrong here. The logic appears to be:

1. I do not accept that there are any codes in nature that developed naturalistically.

2. There are codes designed by humans.

3. Therefore, all codes require intelligent design.

This is obvious question begging, so I must be incorrect. 

~~ Paul

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

 
For a point-by-point rejoinder to Elsberry and Shallit, see http://www.ideacenter.org/contentmgr/sho...hp/id/1488. 

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.

Which says nothing about natural artifacts.

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.

This is basically an argument by assertion. You want us to take your word for this. If you want to talk about proof, you have no proof that codes can evolve from chemicals, no proof that specification can evolve. Only some ingenious sketchy just-so stories. Only faith in an almost omnipotent capacity of nature to evolve anything small step by small step given enough time.  It just has to be accepted on faith, and the fact ignored that codes and specifications have only been observed to originate from intelligent agents. As I have mentioned, this concept is fundamentally in principle unfalsifiable and unscientific, because theoretically there could be an infinite number of logically possible (though vanishingly improbable) just-so stories, and falsifying them all would be impossible.

 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.

Concerning the evolution of enzymes, see my response in the following post #505. As I have mentioned, the design inference is just that - it does not attempt to identify the nature and methods of the designer.

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

Some added depth in the comments too

For a research paper on problems with the neo-Darwinian evolution of new enzyme functions, see "The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway", at http://bio-complexity.org/ojs/index.php/...O-C.2011.1:

Abstract

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

Article on problems with the neo-Darwinian evolution of new enzyme functions: See http://www.worldscientific.com/doi/pdf/1...08728_0022:

"First obstacle: Because gene expression is costly, it cannot be assumed that weakly converted enzyme functions isolated by laboratory selection would provide net selective benefit in wild populations.
...Second obstacle: Beneficial mutations appearing less than about once per generation in a global bacterial population may remain unfixed for a billion years or more.
...Third obstacle: Adaptations requiring duplication and modification of an existing gene should not be presumed feasible if they require more than two specific base substitutions, which seems to exclude most functional conversions. Enzymatic innovations requiring more than two specific mutations in a spare gene (provided by a duplication event) are implausible in neo-Darwinian terms." 

Here is a 2010 review paper by Michael Behe in Quarterly Review of Biology which found that when bacteria and viruses undergo adaptations at the molecular level, they tend to lose or diminish molecular functions: Michael Behe, “Experimental Evolution, Loss-of-Function Mutations, and the “First Rule of Adaptive Evolution,” The Quarterly Review of Biology 85(4) (December, 2010).

An empirical study by Ann Gauger and Ralph Seelke found that when only two mutations along a stepwise pathway were required to restore function to a bacterial gene, even then the Darwinian mechanism failed (Ann Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” BIO-Complexity 2010 (2): 1-9).


I notice you haven't responded to the three challenges at the end of my post.

I have followed only bits and pieces of these previous discussions. Was there ever a time, when you gave examples of what it was that was asked for (e.g. natural codes), that those examples were accepted? For example, is there a reason that pheromones or polymorphic crystals aren't codes?

Linda

 We talked about those two things, along with the periodic table. None were accepted. I don't think we ever converged on a definition of "code" that includes the genetic code but excludes those things.

As I'm about to post, there seems to be some serious question begging going on.

~~ Paul

http://cosmicfingerprints.com/dna-atheis...ring-code/