Darwin Unhinged: The Bugs in Evolution

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/":

It is probably true that life did not start with a pure RNA world.

Work continues on RNA that can replicate other RNA and itself:

https://arstechnica.com/science/2013/10/...n-of-life/

https://www.sciencedaily.com/releases/20...173205.htm

http://www.cell.com/cell-chemical-biolog...13)00426-2

Edited to add: Hang on a mo! That's the same Susan Mazur who made a huge crapfest out of the Altenberg conference.

~~ Paul

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.

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.

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

Actually you have to allow for a stop codon at the very least, so that cuts those figures by 1.

I don't see how a 2-base code 'evolves' to a 3-base code. That change invalidates all the genetic information in the proto-cell, or whatever you want to call the thing. 2-base coded information is gibberish in a 3-base system!

Also what exactly is the point in random polymers of amino acids?

David

I don't see how a 2-base code 'evolves' to a 3-base code. That change invalidates all the genetic information in the proto-cell, or whatever you want to call the thing. 2-base coded information is gibberish in a 3-base system!

Why? Remember that the third base is highly degenerate. Perhaps when it was added on it didn't do anything. Then as time went by it allowed additional amino acids to be incorporated.

This is like saying that all the opcodes of the S/360 would no longer function when 2-byte opcodes appeared in the S/370. And yet you have no trouble with that development.

Also what exactly is the point in random polymers of amino acids?

Many small peptides have useful properties. There are peptides made by the ribosome, just like other proteins. There are also peptides made without the ribosome. Some are short enough to have been created at random.

https://en.wikipedia.org/wiki/Nonribosomal_peptide

Here is a database of them:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238963/

~~ Paul

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/":

I suspect those quotes are taken out of context. I started looking up the names (excluding the physicist) and found that they weren't denying the role of RNA, but rather RNA-only. Deamer is keen on the role of membranes and lipid layers to isolate RNA and aid in polymerization. Williams talks about the co-evolution of ribosomes and proteins. Etc. 

It doesn't look like anything coming from "Evolution News" can be taken at face value, so far. 

Linda

In case you thought it couldn't get any weirder, check this out.

Here is an article about the fact that methionine amino acid residues in proteins act as an antioxidant:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630790/

So guess what? Sometimes it's useful to toss extra methionines into proteins where there are normally some other amino acids. This is accomplished by incorrectly charging non-methionine transfer RNAs with methionine:

https://academic.oup.com/nar/article/40/...94/2414817

Because complexity.

~~ Paul

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 don't have the scientific background to contribute much to this discussion but for the very first time I find myself in agreement with steve001
The discovery site is embedded with a right wing American Christian political agenda. Maybe you would need to be from around here to get the smell but for me it reeks- which is to bad because I am on board with most of the science they present.

If you read further in he document you will find he makes a distinction between mind and "organic" as agents. What he means by organic and how it differs from mind I have not been able to fathom.


So, if I read him correctly, he seems to be saying that, as some might say that mind or consciousness is a fundamental, so too is organic information or meaning. I'd prefer to class them together as a single phenomenon.

Maybe the term "organic information" refers to MAL, the source of all? He doesn't use the word consciousness, but the "or meaning" bit sort of hints at a consciousness that isn't self-aware except in restricted ways through its alters. Are alters a means of its experiencing what we think of as the world in a self-aware manner?

I've been trying to find the post that mentioned instinct but have failed because this thread is so long -- was it posted by Kamarling? I can't remember -- apologies for that.

It's an interesting question, which I have been turning over. Are instincts coded for in DNA? Does a gene cause a newly-born lamb to quickly stand on its legs and seek out its mother's teat? What about DNA sequences in non-coding (so-called "junk") regions of chromosomes? Do they have something to do with behaviour?

I've been trying to find something useful on the web but so far haven't had much success. There's a tidbit here (under the heading "Instinctive Behaviour") where it's simply asserted that since instinctive behaviours are inherited, they must in some way be coded for in DNA, but doesn't seem to offer any evidence for that.

For example, are there any experiments where genes have been knocked out that result in the disappearance of instinctual behaviours? That resulted in, say, lambs that didn't stand up and seek out the teat as soon as they were born?

Trouble is, it's difficult to formulate that question in a pithy way that can be searched for on the Web. A search for "genes that specify instinct" led me to a video by Richard Dawkins:



-- It's another just-so story, with no real evidence for the Baldwin effect. Notice also how he rubbishes Lamarkism: maybe he's not aware of epigenetic discoveries or simply in denial about them? I don't know.

I wonder whether instinctive behaviours are actually inherited: they could be a property of the whole organism which every member of the species displays once it's been born. The whole idea of "inheritance" is predicated on extending the known principle of genes passing on the ability to execute molecule-level instructions in cells. That doesn't necessarily mean that they govern instinctive behaviours, though.

If anyone can find an experiment that knocks out genes and results in the disappearance of an instinctive behaviour, please link to it and I'll check it out.

It is probably true that life did not start with a pure RNA world.

Work continues on RNA that can replicate other RNA and itself:

https://arstechnica.com/science/2013/10/...n-of-life/

https://www.sciencedaily.com/releases/20...173205.htm

http://www.cell.com/cell-chemical-biolog...13)00426-2

Edited to add: Hang on a mo! That's the same Susan Mazur who made a huge crapfest out of the Altenberg conference.

~~ Paul

I'll stick with the expert comments on RNA world theories already posted. Mazur's book was published a while after the first two links that you posted were published, and long after the starting enzyme in the third linked paper was produced. The interviewees' opinions, unless you claim Mazur fabricated them, would have taken that research into account. The research needs to produce RNA molecules that can form spontaneously, store information and perform useful reactions, and reproduce themselves, all in a plausible prebiotic environment. It hasn't done it. 

The third paper involves a starting RNA enzyme that was originally produced in a laboratory using very artificial conditions and many artificial procedural steps including special screening (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579227/). A little presumptuous to cite research that started with an enzyme produced with artificial carefully controlled laboratory conditions and procedures, hardly what would have applied on the early Earth.

I suspect those quotes are taken out of context. I started looking up the names (excluding the physicist) and found that they weren't denying the role of RNA, but rather RNA-only. Deamer is keen on the role of membranes and lipid layers to isolate RNA and aid in polymerization. Williams talks about the co-evolution of ribosomes and proteins. Etc. 

It doesn't look like anything coming from "Evolution News" can be taken at face value, so far. 

Linda

The "RNA world" is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins (Wiki). The RNA world hypothesis apparently speculates that RNA carried out the great majority of biochemical reactions before the evolution of complex protein enzymes, through the evolution of ribozymes - noncoding RNA that carry out various activities, especially self-replication and catalysis. This was the RNA world I referred to. Please cite how the quoted interview comments didn't refer to this definition of the "RNA World". The interview excerpts are clear, to the point, and valid expressions of the interviewees' opinions. Unless you claim Mazur fabricated them. 

As far as your opinion of Evolution News is concerned, this is a fine example of the hasty generalization fallacy (reaching an inductive generalization based on insufficient evidence),
the jumping to conclusions fallacy (the making of a determination without all of the information required to do so), all combined with the genetic fallacy. Please cite specific errors in the science.