Darwin Unhinged: The Bugs in Evolution

The evolution of a code is not a physical thing.  It is an informational thingy.   You would measure the transformation in terms of changes to the symbolic structures, to the sequence of activity, to the logic of the functionality being encoded and in changes to new potential molecules that would attach or be repulsed.

The evolution of the genetic code is most certainly a physical thing. If you believe it is not, could you point to the "information mechanism" that drove its evolution?

The periodic table is an add-on.  DNA/RNA/Ribosome communication tables are inclusive in the organism.  Other than that the are similar.  Paul you are still looking for the magic, when mind and sense of self - (human or any other living thing) are natural things.  Living things are intelligent and have designed themselves.

The periodic table is no more an add-on to valence electron chemistry than the code table is an add-on to biology.

~~ Paul

As I said earlier, in this country I cotton no talk of design because those that squeak most loudly asserting there is design are too willing to insert their Christian God into all areas of public life undermining the liberties our Constitution grants us citizens. To think they are simply questioning the science of evolution is absurdly naive.

That's a pretty lofty function you've given yourself.

Its also comical (in a sad sort of way), naïve, arrogant, and I would argue for this community: misplaced.

Yes, there are those here who likely hope there is 'something' beyond materialism behind the proverbial scenes.  Call it God if you wish.  I am certainly one of those and realize that it creates some bias in how I choose to interpret what I see and read.

However, you aren't fighting religious dogma on these boards.  Seems you could save posts like what I highlighted above for the fundamentalist sites you must frequent to fulfill your crusading responsibilities.  Why not grant a bit of leeway since as Dante aptly pointed out: you yourself are sounding awfully dogmatic about things you can not prove.

I will leave this up to the many biologists, some of whose papers I have linked. The project is ongoing and will be for some time.

To me this is vital, because you are evoking ideas such as evolution at a point where you don't have any genes - I don't care if those are carried on RNA or DNA, but if the code is in the process of being established, it can't also provide the mechanism of evolution!

I think you're comparing apples and oranges. Many architectures have fixed-size opcodes. The IBM 1130 and DEC VAX come to mind. Also, in the case of the genetic code, there are exceptions, so that the same codon results in different amino acids.

~~ Paul

Well fixed size opcodes simply fill up all the possibilities as time goes on - they can't evolve much. Variable sized opcodes offer much more scope for expansion (the PC is the obvious example), but we are really discussing DNA here, and DNA has fixed size codons.

Did you mean one codon giving rise to two amino acids, or the other way round - there are certainly some amino acids that are coded in more than one way, but I can't quite see how the other way would work at all!. All of which is irrelevant to the question of how the genetic code came into being!!!!!

David

I'll check it out, though I am not hopeful.

https://www.openlettersmonthly.com/book-...se-desire/

https://smile.amazon.com/Purpose-Desire-...0062651560

I'd recommend his book strongly, and I suggest anyone interested read it for themselves - bearing in mind that he is a professor of biology.

David

As I said earlier, in this country I cotton no talk of design because those that squeak most loudly asserting there is design are too willing to insert their Christian God into all areas of public life undermining the liberties our Constitution grants us citizens. To think they are simply questioning the science of evolution is absurdly naive.

You seem to be awfully keen to talk about (your?) Christian God, when nobody else here is doing so - are you sure you don't have a dog collar on?


David

To me this is vital, because you are evoking ideas such as evolution at a point where you don't have any genes - I don't care if those are carried on RNA or DNA, but if the code is in the process of being established, it can't also provide the mechanism of evolution!

Why not? There could be a series of proto-codes. You appear to believe that it's the final genetic code or it's nothing at all. Surely you'll agree there could be a simpler code based on RNA. In fact, we can start with no code at all and just have random amino acid polymerization. You should be okay with this idea, just as you are okay with the IBM S/360 architecture suddenly having 2-byte opcodes when the S/370 came along.

There is no point in posting the relevant papers again, since no one wants to read them.

Well fixed size opcodes simply fill up all the possibilities as time goes on - they can't evolve much. Variable sized opcodes offer much more scope for expansion (the PC is the obvious example), but we are really discussing DNA here, and DNA has fixed size codons.

Note that the 3-base codon allows for 64 amino acids but there are only 21 or 22. So the opcode is plenty large enough as it is.

Did you mean one codon giving rise to two amino acids, or the other way round - there are certainly some amino acids that are coded in more than one way, but I can't quite see how the other way would work at all!. All of which is irrelevant to the question of how the genetic code came into being!!!!!

A 1-base codon would allow 4 amino acids, while a 2-base codon would allow 16. There is no reason the code couldn't have started this way and eventually evolved to 3 bases to allow 21 or 22 amino acids. There is plenty of literature on this.

~~ Paul

That's a pretty lofty function you've given yourself.

Its also comical (in a sad sort of way), naïve, arrogant, and I would argue for this community: misplaced.

Yes, there are those here who likely hope there is 'something' beyond materialism behind the proverbial scenes.  Call it God if you wish.  I am certainly one of those and realize that it creates some bias in how I choose to interpret what I see and read.

However, you aren't fighting religious dogma on these boards.  Seems you could save posts like what I highlighted above for the fundamentalist sites you must frequent to fulfill your crusading responsibilities.  Why not grant a bit of leeway since as Dante aptly pointed out: you yourself are sounding awfully dogmatic about things you can not prove.

You can no doubt see why I lost patience with Steve001 and put him on ignore (although, obviously, his comments appear in the replies from others). He is like those Jehovah's Witnesses who knock on your door - no point in arguing with them because there is no argument which will scratch that shell of blind faith and indoctrination.

Here's a post from way back in this discussion (before I put him on ignore) saying much the same as you are saying here. Clearly everyone but Steve himself can see what's going on.

http://psiencequest.net/forums/thread-da...9#pid10379

Life apparently didn't have much time (in the evolutionary sense) to come about spontaneously and chemically. The vast informational distance between chemicals and the first living organisms was bridged in the relative blink of an eye. You would think it would have taken the longest time of all, longer than from the first organisms to eukaryotes (about 2 billion years), longer than multicellular animals. These findings make things even harder for the OOL theorists. Food for thought. From https://phys.org/news/2015-10-life-earth...h.html#jCp: 

"

UCLA geochemists have found evidence that life likely existed on Earth at least 4.1 billion years ago—300 million years earlier than previous research suggested. The discovery indicates that life may have begun shortly after the planet formed 4.54 billion years ago.

The research is published today in the online early edition of the journal Proceedings of the National Academy of Sciences.
"Twenty years ago, this would have been heretical; finding evidence of life 3.8 billion years ago was shocking," said Mark Harrison, co-author of the research and a professor of geochemistry at UCLA.
"Life on Earth may have started almost instantaneously," added Harrison, a member of the National Academy of Sciences. "With the right ingredients, life seems to form very quickly."
The new research suggests that life existed prior to the massive bombardment of the inner solar system that formed the moon's large craters 3.9 billion years ago."

The RNA world hypothesis is popular with some OOL researchers, but it has massive problems and probably should be abandoned. From https://evolutionnews.org/2017/02/putting_the_rna/":

In Susan Mazur’s book The Origin of Life Circus, leading origin-of-life researchers describe the utter disaster of the RNA world scenario in one-on-one interviews she recorded in person.

Lawrence Krauss tells her (p. 35): “The question is, can RNA result naturally? That’s been a big stumbling block.”
David Deamer tells her (p. 43) that the RNA and DNA monomers don’t link up naturally: “the laws of thermodynamics do not allow them to polymerize because there is a tremendous energy barrier to getting them to form bonds.” That’s especially true in water, he says, which breaks down (hydrolyzes) RNA.
Sara Walker tells Mazur that researchers need to move away from the RNA World, “because most of the origin-of-life community don’t think that’s the definitive answer.” Walker herself says, “I don’t see how an RNA world with only RNA can work” (p. 68).
Loren Williams tells her the original RNA World (“all RNA, all the time, and nothing else”) is unreasonable and dead. RNA can’t have done everything originally claimed. “Another problem is related to the origin of RNA itself. Where did RNA come from? Where did RNA precursors come from?” (p. 96).
Steven Benner tells Mazur (p. 81), “we don’t know how useful function is distributed among sequence spaces. You have 4 raised to the power of 100 different sequences of RNA 100 nucleotides long. We don’t know how productive function is distributed there compared to destructive function.” Chances are destructive processes are increased as much as productive processes, he adds. On page 151-152, Benner lists four major “paradoxes” of the RNA world: the tar problem, the water problem, the entropy problem and the destruction problem.
RNA-world champion Nick Hud has abandoned the idea that RNA would form on its own. He’s looking for candidates of not only proto-RNA, but “pre-proto-RNA” because, as Mazur reminds him, “RNA itself falls apart” (p.87).
Stuart Kauffman tells Mazur that they “tried for 40 years to get single-stranded RNA molecules to replicate, perhaps hundreds of chemists, and they all failed. It should work. But it hasn’t. And after 40 years or 50 years, you think – maybe it’s the wrong idea. People really tried hard” (p. 111).
Jack Szostak ups the time estimate to 60 years that researchers have worked on this problem of non-enzymatic replication. “The problem is RNA falls apart,” he says (p. 218).
Norm Packard tells Mazur, “There are issues with the RNA world approach. The main one is how do you get RNA starting to get produced in the first place” (p. 297). He envisions an enzyme doing it. This speculation, of course, leads to an obvious problem: “But how do you get that enzyme?”
Pier Luigi Luisi is merciless in his attack, calling the RNA world a “baseless fantasy.” Mazur puts his criticisms in bold print on pages 362-363, where he finds it “full of conceptual flaws,” including its origin, the thermodynamics, the sequencing problem, the concentration problem, and more. The story of RNA turning into ribozymes he calls “chemical non-sense” (p. 363).
Luisi then makes a confession so bold, Mazur says, “It’s remarkable to hear you say that.” Luisi: "The real problem is to make ordered sequences of amino acids - and on that the prebiotic RNA world is absolutely silent. But this view of the prebiotic RNA world is still the most popular. I think it is a case of social science psychology more than science itself."

That's a pretty lofty function you've given yourself.

Its also comical (in a sad sort of way), naïve, arrogant, and I would argue for this community: misplaced.

Yes, there are those here who likely hope there is 'something' beyond materialism behind the proverbial scenes.  Call it God if you wish.  I am certainly one of those and realize that it creates some bias in how I choose to interpret what I see and read.

However, you aren't fighting religious dogma on these boards. Seems you could save posts like what I highlighted above for the fundamentalist sites you must frequent to fulfill your crusading responsibilities.  Why not grant a bit of leeway since as Dante aptly pointed out: you yourself are sounding awfully dogmatic about things you can not prove.

Do you really think it would remain just a bit of leeway?  Surely you have strong unwavering sentiments about something. Notice most of my comments were directed towards nbtruthman who really played the design angle with their continuing reference to the Design Institute and some of its members. If this thread had never mentioned ID I likely would have not said a word. Notice I've not participated in anything Paul and David are sparing over. That's because they are actually debating a bug in evolutionary theory. Ah, but I am counter pointing dogma. It's just a different dogma.

You seem to be awfully keen to talk about (your?) Christian God, when nobody else here is doing so - are you sure you don't have a dog collar on?


David

I was addressing no one but Dante.

David you must understand America's religious culture first in order to understand what I'm saying.  Do you know the history of religious conservatism, the politics. Do you know what the "Moral Majority" was? Do you know any of this?

Notice or not I've not said a word since the topic has turned to coding... 
Notice David it was none of the"atheists" brought up ID. Within the first and third posts Karmarling mentions ID and Stephen Myers. And what's the insinuation of the title "Darwin Unhinged"? That Darwin was of such feeble mindedness his theory should be regarded as utterly absurd?

"Dog collar on"? Is that a British idiom?