Mutation (split from The Selfish Gene Theory)

[Arthur Smith]

5 hours ago, Evomumbojumbo said:

if apes have 98% our DNA then why wouldn’t retroviruses be in the same place, or maybe 2% out

Inow

We share some retrovirus remnants with chimps. That strongly confirms ancestry and common descent. 

ETA had to edit predictive typing error from wrongly to strongly 🥴

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137791/ for instance.

Edited January 21, 2022 by Arthur Smith

[exchemist]

8 hours ago, Evomumbojumbo said:

 

Exchemist

natural selection selects from an existing gene pool. Evolution needs new genes.

i won’t be going anywhere until I break a site rule which I’m sure is inevitable

 

 

Well that's good. (As you can tell, I am pretty jaded when it comes to internet creationists🙄. But if you are prepared for a serious discussion I'll try not to let it show.) 

To your point, then, yes natural selection operates on the gene pool in the population. But that gene pool is not static, because of mutations.

The current waves of variants of the SARS-CoV-2 virus are a testament to that.  

Edited January 21, 2022 by exchemist

[Evomumbojumbo]

They will be when they evolve into something other than viruses. Do you have an example of that level of change?

[exchemist]

11 minutes ago, Evomumbojumbo said:

They will be when they evolve into something other than viruses. Do you have an example of that level of change?

No, let's deal with my point before you raise a new one.

There have been many new variants of this virus. What do you think accounts for them, if not mutations in their genetic material? 

[Evomumbojumbo]

Either low frequency alleles  already present or mutations. I’d have to research which 

[Arthur Smith]

19 minutes ago, Evomumbojumbo said:

Either low frequency alleles  already present or mutations. I’d have to research which 

In that case they'd be there when sequence analysis is run on virus samples and we would see "already present" sequences. This frontloading idea can be dismissed for other reasons. Virus RNA does not have anything as sophisticated as regulatory sequences, viruses are stripped down to the absolute minimum. RNA, I'm broad-brush-painting, is less stable than DNA, so is more prone to copying errors. Other corona-viruses exhibit the same propensity for relatively rapid mutations. No vaccine yet for the cold virus. Flu vaccines reasonably effective against last year's variant.

[Evomumbojumbo]

Thanks Arthur that saves a lot of time 

[exchemist]

39 minutes ago, Evomumbojumbo said:

Either low frequency alleles  already present or mutations. I’d have to research which 

In the light of  @Arthur Smith's contribution, it is mutations.

So the new variants of SARS-CoV-2 arise via variation by mutation and then natural selection of those variations best able to reproduce. Agreed? 

Edited January 21, 2022 by exchemist

[Evomumbojumbo]

Agreed

[bangstrom]

 New viruses tend to become more contagious but less lethal with time and flu viruses are thought to evolve into cold viruses. Cold virus strains number in the several hundreds which stymies vaccine development.

[Evomumbojumbo]

Thanks Arthur and Bangstrom

Im marking you down as our resident virus experts 

[bangstrom]

I have always thought, if evolution worked by adding new structures, men should have three arms. That would be handy. Evolution works by adding or subtracting from existing structures which is why snakes and whales have vestigial limbs. Pictures below.

https://search.yahoo.com/yhs/search;_ylt=AwrUiZ2ToOphKiMAMkwPxQt.;_ylc=X1MDMjExNDcwMDU1OQRfcgMyBGZyA3locy1kb21haW5kZXYtMTkxMTEEZnIyA3NhLWdwLXNlYXJjaARncHJpZAN3Snd2NnNyM1NYS1FwUENOWXNCRTlBBG5fcnNsdAMwBG5fc3VnZwM0BG9yaWdpbgNzZWFyY2gueWFob28uY29tBHBvcwMxBHBxc3RyA3NuYWtlcyBhbmQgd2hhbGVzIHZlc3RpZ3VhbCBsaW1icwRwcXN0cmwDMzMEcXN0cmwDNDIEcXVlcnkDc25ha2VzJTIwYW5kJTIwd2hhbGVzJTIwdmVzdGlnaWFsJTIwbGltYnMlMjBwaWN0dXJlcwR0X3N0bXADMTY0Mjc2OTE4MgR1c2VfY2FzZQM-?p=snakes+and+whales+vestigial+limbs+pictures&fr2=sa-gp-search&hspart=domaindev&hsimp=yhs-19111&type=__alt__ddc_intl_linuxmint_com

[exchemist]

1 hour ago, Evomumbojumbo said:

Agreed

OK, so that means that nature can create new genetic code, does it not? 

[Evomumbojumbo]

So to follow your example, taking it one step at a time, you agree that DNA is a code? What is it a code for? 

[dimreepr]

17 minutes ago, Evomumbojumbo said:

So to follow your example, taking it one step at a time, you agree that DNA is a code? What is it a code for? 

It's not a code it's an instruction, that's how the enigma was de-coded...

“This is rather as if you imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in — an interesting hole I find myself in — fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!' This is such a powerful idea that as the sun rises in the sky and the air heats up and as, gradually, the puddle gets smaller and smaller, frantically hanging on to the notion that everything's going to be alright, because this world was meant to have him in it, was built to have him in it; so the moment he disappears catches him rather by surprise. I think this may be something we need to be on the watch out for.”

― Douglas Adams, The Salmon of Doubtma was de-coded...

Edited January 21, 2022 by dimreepr

[Arthur Smith]

7 minutes ago, Evomumbojumbo said:

So to follow your example, taking it one step at a time, you agree that DNA is a code? What is it a code for? 

There can be confusion that follows the use of the word "code". There is no code in the sense of cipher or computer programs. DNA stores information in the form of a sequence of four nucleotides that, so long as the reading "machinery" (anthropomorphism creeps in everywhere) begins at the right point, results in a sequence of amino acids, a protein. (This is done via the intermediate of messenger RNA and not all sequences are translated into proteins but we can come back to that). The essential point is that there are 64 possible triplet codes, all output to one of twenty amino acids, "start replicating with a methionine" or "stop replicating". The process is purely biomechanical. The trick is in the genotype/phenotype feedback (I jumped a few steps there).

[Evomumbojumbo]

Thanks Arthur 

brilliant as always, I am reading that viruses are a very special case in that they are RNA based and prone to copying errors. I’m also thinking that any definition of positive, neutral of negative mutations do not apply to viruses, mainly because I don’t really know how they become immune to vaccines and other than that whether the mutation would be considered negative.

Exchemist

also, and I realise you are using shorthand, but I am wary of agreeing to nature as a creative force, it sounds a bit Druid 

[exchemist]

4 hours ago, Evomumbojumbo said:

So to follow your example, taking it one step at a time, you agree that DNA is a code? What is it a code for? 

Proteins. @Arthur Smith has explained this in more detail. Also that when we say a code we do not imply there is an intention in it, merely that it is a biochemical template, in the form of sequences of a small number of base pairs, from which proteins are constructed.  

But to continue my point, now that we agree nature can create new code by variation and natural selection, and that this new code affects the structure and function of the resulting organism, as the virus case shows, you have accepted that this mechanism of evolution has real explanatory and predictive power, i.e. it is a sound scientific theory. Not mumbo jumbo. And clearly "garbage in garbage out"is inapplicable, or it would not work the way that we can see it does. 

What, then, is your objection to applying it to other cases?  

 

 

Edited January 21, 2022 by exchemist

[Arete]

3 hours ago, Evomumbojumbo said:

brilliant as always, I am reading that viruses are a very special case in that they are RNA based and prone to copying errors.

1) Virus genomes can be dsDNA, ssDNA, dsRNA or ssRNA. They can also be linear, circular, segmented or continuous. 

2) Directional selection of mutations in viruses can be measured by directly rate of replication. If a mutation increases replication rate, its effect on fitness is positive, if the effect is reduced replication, the effect is deleterious. No change to replication, neutral. 

3) Of course selection is environmentally dependent. Mutations can result in life history trade offs where they are beneficial in one environment, but detrimental in another. E.g. increased host range at the expense of thermotolerance in Vesicular Stomatitis Virus. 

4) The main mechanism, at least for SARS-COV-2 for the evolution vaccine escape mutants is mutations to the S protein which reduce the binding efficiency of vaccine derived antibodies. If the S protein changes shape, the antibodies selected for by the vaccine don't adhere as well to the novel variant, and the immune response of the host not as effective. Commonly referred to as antigenic variation. 

5) The evolutionary origin of viruses is not well elucidated and likely resultant from several independent sources. Standard evolutionary theory would not predict a virus to evolve into a different kingdom of organism, nor necessarily infer common ancestry with prokaryotes/eukaryotes/archaea. We do regularly observe the evolution of novel viruses, especially via interviral recombination (e.g. the recombination of John Cunningham Virus and Epstein-Barr Virus to produce novel variants).  

 

Edited January 21, 2022 by Arete

[Evomumbojumbo]

4 minutes ago, exchemist said:

Proteins. 

Do viruses make proteins?

[CharonY]

3 minutes ago, Evomumbojumbo said:

Do viruses make proteins?

Viruses do not have an active metabolism- they use the host to make their proteins but provide the genetic material (RNA or DNA) to do so

[Arete]

X-Post with CharonY

Edited January 21, 2022 by Arete

[Arthur Smith]

4 hours ago, Evomumbojumbo said:

I am reading that viruses are a very special case in that they are RNA based and prone to copying errors. I’m also thinking that any definition of positive, neutral of negative mutations do not apply to viruses, mainly because I don’t really know how they become immune to vaccines and other than that whether the mutation would be considered negative.

 

Well, see above, Arete's comment. Not all viruses use RNA to store information, many use DNA. Viruses are indeed special in that they are perfect (not in the philosophical sense, don't get me started) parasites. They don't bother to retain their own metabolism. The interesting thing is that viruses could only have evolved from more complex precursors that were free-living, but that's another story.

Regarding mutations being beneficial, neutral, or deleterious, context matters. Apart from lethal mutations, the niche matters. If there is one thing you should take home from my comment, it is the niche - the micro-environment that an organism occupies, interacts with and influences. Among the many things viruses lack is intent. Opportunity (niche) arises and viruses flourish.

[CharonY]

13 minutes ago, Arthur Smith said:

They don't bother to retain their own metabolism. The interesting thing is that viruses could only have evolved from more complex precursors that were free-living, but that's another story.

One line of thought assumes that they developed from mobile genetic elements (think transposons, plasmids, integrons and so on), which incidentally fits the original thread (Selfish gne) quite well.

[Arthur Smith]

43 minutes ago, CharonY said:

One line of thought assumes that they developed from mobile genetic elements (think transposons, plasmids, integrons and so on), which incidentally fits the original thread (Selfish gne) quite well.

I keep making the excuse that I'm new here. Haven't read that thread. A link to  the relevant comment(s) would be greatly appreciated if not too much trouble.

Never mind, I found it. I see it dates from 2004 and Dawkins' Selfish Gene crops up in the early comments. I'll wade backwards.

-----------------------------------------------------------------------------------------------------------------------------------------------------------

Hmm. wading through a lot of oyster guts but no pearls so far.

3 hours ago, Arete said:

Virus genomes can be dsDNA, ssDNA, dsRNA or ssRNA. They can also be linear, circular, segmented or continuous. 

TIL

Archaea have their own double-strand DNA viruses.

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008574

Edited January 21, 2022 by Arthur Smith