Man most likely evolved from a Virus

I should add that the 22 amino acids to which I was referring are proteinogenic amino acids.

There are also many more that are non-proteinogenic amino acids such as carnitine, GABA, hydroxyproline, lanthionine, 2-aminoisobutyric acid, dehydroalanine, gamma-aminobutyric acid and selenomethionine.

There are many (40 or more?) non-natural amino acids that have been genetically coded for, as well. Here's a Wikipedia article on Expanded Genetic Code which details this.

originally posted by: Noinden
a reply to: SPECULUM

Unless you want to combine evolution and creationism, when you go back far enough we evolved from the same place. The evolution of life is a very interesting study, and the best evidence is that yes we started out as something akin to a virus. The problem is by definition life really did not start until it was self-sustaining, and that is not Viruses, they need other life forms to replicate. But no this is not a new idea, just as it is thought that RNA was the possible precursor to DNA, but life moved to mostly DNA-based information storage as it is more stable.

Viruses could also be an offshoot of nature's experiment with self assembly. The formation of the DNA molecule most likely went through millions of configurations, throwing off some molecular structures which began their own self assembly process. Since some viruses have single strand DNA and cannot replicate, the question becomes when did double stranded DNA arrive on the scene? It was that final configuration that was able to replicate. The molecular structure that became a virus may have been just a "mistake" which took off on its own. So what did the virus do? It found a way to insert into a cell to harness the double stranded DNA. How did the virus know to do that?? Why didn't the structure just disintegrate and disappear? Somehow it figured out how to survive. Just speculation on my part - no evidence to back up my hypothesis.

originally posted by: Xtrozero

originally posted by: Noinden
a reply to: Xtrozero

Oy ignoring the DNA swaps. The very fact we are using DNA or RNA implies a common ancestry.

So a life form that starts on a planet 100 million light years away that uses DNA/RNA and one that starts here with the same means they are related by your logic, or...that life has a common chemical composition.

I personally think that there is other life out there, but whether it uses DNA or not would be a guess. I think it's about time we discover life elsewhere. It will answer quite a bit of questions like this. Right now we simply do not know. Maybe there is only one possible type of life that can emerge, but I'd wager that there are multiple types. Also if it turns out panspermia is a big part of it, then it is possible for life in other places to have common roots with life on earth, even if they are carbon DNA based lifeforms.

a reply to: Barcs

Something interesting in that regard.

The application of the Mid-IR radio correlation to the ˆG sample and
the search for advanced extraterrestrial civilisations

Nevertheless, I conclude
that the vast majority, if not all of the sources in the ˆG sample
do not obviously harbour Karadashev Type III civilisations, and
that therefore such civilisations are either extremely rare in the
local universe or do not exist.

arxiv.org...

As Fermi's paradox asked: "Where is everybody??"

a reply to: chr0naut

Well there we go, I am (as I've said) a Pharmaceutical Chemist, and trained in Bioinformatics as well (plus business, which has no bearing here).

For the Elements? We've discovered about 118 so far, there will be more I a sure. It has no bearing on this discussion. We are talking genetics, not nuclear chemistry.Like I said I am a chemist. I got my degrees at Otago.

Fair cop on the Pyrrolysine, I did my postgrad work in the 1990's so it was not confirmed as proteogenic, and I forget about it. That is still beyond the point. All it means is there are another set of codes in genomes for a new "letter" in the book of proteins.

You can interpret the different codes as different proteogenisis events. I don't most scientist do not. The other option is that the language changed at several points AND that some life forms speak an archaic form. It is unclear which yet.

a reply to: chr0naut

There are more amino acids than that neighbour. My PhD was in altering some of the proteogenic ones in useful ways for pharmaceuticals. On top of that I spent the 2000s in the Pharma industry. Amino acids of the natural sort simply require an amine (primary or not) and a carboxylic acid. We've found 40 odd in nature thus far, there WILL be more. This is ignoring chirality, as a number of toxins have the other enantiomer as part of their make up, and they are clearly NOT proteogenic

a reply to: Phantom423

Nature does not experiment. Nature just is (and remember I speak as a Pagan when I say this). TO experiment there needs to be a conscious effort, and there is zero evidence of that. Unless one is a creationist, then they see conscious effort every where. They can not prove it, but they see it.

originally posted by: Noinden
a reply to: Phantom423

Nature does not experiment. Nature just is (and remember I speak as a Pagan when I say this). TO experiment there needs to be a conscious effort, and there is zero evidence of that. Unless one is a creationist, then they see conscious effort every where. They can not prove it, but they see it.

I don't agree. Survival of the fittest is an example of experimentation. Nature will continue to test different combinations of DNA until the right configuration is the best fit for the organism. That's why adaptation leads to genome mutations which become permanent. If nature stood still on a single chromosomal design, nothing could evolve.

a reply to: Phantom423

You don't have to agree, you as far as I know are a free willed thinking human. You are not providing any evidence for your assertion however, which is on you to prove.

Nature is testing nothing. Experiments have a goal, set parameters. Nature is randomly doing stuff. This is evidenced by the junk in our genomes, by the flaws in designs etc.

Like I said, I'm a Pagan, I've got an affinity for nature on many levels, but its not experimenting, not in the sense you are implying. It just is.

originally posted by: Noinden
a reply to: Phantom423

You don't have to agree, you as far as I know are a free willed thinking human. You are not providing any evidence for your assertion however, which is on you to prove.

Nature is testing nothing. Experiments have a goal, set parameters. Nature is randomly doing stuff. This is evidenced by the junk in our genomes, by the flaws in designs etc.

Like I said, I'm a Pagan, I've got an affinity for nature on many levels, but its not experimenting, not in the sense you are implying. It just is.

I really don't know what Pagan has to do with it. But there are several papers that suggest that mutations are not random, at least to the extent that beneficial mutations tend to result in the same sequence regardless where the mutation took place.

Predictable evolution trumps randomness of mutations
Separate bacteria populations may respond to environmental changes in identical ways.
Lucas Laursen
19 February 2013
www.nature.com...

In the new study, published online today in Public Library of Science Biology5, Doebeli and colleague Matthew Herron, also at UBC, went back to the frozen samples from three of their test tubes and sequenced 17 gene samples from various stages of the experiment. The DNA showed that in some cases identical mutations appeared independently in all three test tubes: despite the random nature of mutations, the same changes in the environment favoured the same genetic solutions.


Evolution Is Not Random (At Least, Not Totally)
By Tanya Lewis, Staff Writer   |   October 02, 2014 07:41am ET
www.livescience.com...


Conventional wisdom states that evolution occurs by random mutations that make an individual organism better able to survive and reproduce, according to natural selection.
In the study, published Sept. 30 in the journal Royal Society Open Science, fisheries biologists Michael Garvin and his colleague Anthony Gharrett, of the University of Alaska Fairbanks, in Juneau, set out to see whether or not these mutations were truly random. [Unraveling the Human Genome: 6 Molecular Milestones]

There's a publication which discusses tests for mathematical randomness in DNA as well. I have to find it - I think it suggests that the asymmetries of substitution rates demonstrate non-randomness. When I find it, I'll post the citation. Actually, it's a book as far as I can remember.

a reply to: Phantom423

It has about as much as the belief that nature is doing experiments. It is a belief system, in this case there is usually a large sense of nature centered spirituality. So I was using it to demonstrate that I saw much of the divine in nature. However what you are talking about is essentially Deism. I do not subscribe to that however

Quoting single papers at me, does not prove a thing, and the Live Science article by a staff writer, is NOT a peer reviewed journal article. Tell me have you read and understand the Nature article? Or did you just google search and skim the abstract?

For all those comments what does this have to do with the OP prey tell? What does it illustrate? Come now, citing a single paper, and an article, which has no actual backing evidence supplied with it, that is not making an argument.

originally posted by: Noinden
a reply to: Phantom423

It has about as much as the belief that nature is doing experiments. It is a belief system, in this case there is usually a large sense of nature centered spirituality. So I was using it to demonstrate that I saw much of the divine in nature. However what you are talking about is essentially Deism. I do not subscribe to that however

Quoting single papers at me, does not prove a thing, and the Live Science article by a staff writer, is NOT a peer reviewed journal article. Tell me have you read and understand the Nature article? Or did you just google search and skim the abstract?

For all those comments what does this have to do with the OP prey tell? What does it illustrate? Come now, citing a single paper, and an article, which has no actual backing evidence supplied with it, that is not making an argument.

You're making a mountain out of a molehill. You replied to a post that I made about nature's experimentation. I never implied that my opinion was based on a religious belief. You inserted that.

If you don't like citations or disregard them because they don't reflect your comment that mutation is all random, well that's your problem. As far as I can see both articles suggest that scientists have questioned the idea of complete randomness. They've designed experiments and published their results.

You must have been stuck in a rut in the lab too long. You have an attitude of "my way or the highway". That doesn't reflect the open mind of a scientist. Just my opinion of course. Remember, I am my own human being, as you put it so well!

a reply to: Phantom423

A couple of things neighbour.

(a) You replied to me, with that post on experimentation. It implied you wished to engage.
(b) I don't disregard citations. I disregard single citations which state something out of the ordinary. You can not draw a straight line with less than three points. What this means, you need to repeat, and see if it stands up. Thus a single paper, means very little. That second "article" is the equivalent of an editorial, it was not written by an expert it was from a web based service, by a "staff writer". IT holds less water.
(c) You are misreading my comments based about religion, because I mentioned mine (obliquely, pagan is about as descriptive as "speaks english" to narrow down my spiritual frame work). IF me bringing it up causes you consternation. Then I've hit a nerve. Oh dear, what a shame, never mind.
(d) My insistence on things following scientific principals and frame work, before changing the view of science, is correct. As I said and you acknowledge, I'm a scientist. What else would you have me do? Bring out my bag of Ogam to decide what evolution was about? No.
(e) Your last point lapsed into ad homenin attack, which implies you are at a loss how to debate. Do not bring hte person into the debate, if you do not wish it brought back at you neighbour. No seriously, calling me closed inded, and having been in a rut in the lab too long. Bad choice of tactic.

So let me clue you up. You can believe anything you want, it does not influence the science. That is the mistake the lay people make. Some thought the earth was the center of the Universe, and every thing revolved around it, evidence proved otherwise. So "prevailing thought" can change. Science changes with verifiable evidence, not the belief of the masses.

originally posted by: Noinden
a reply to: Phantom423

A couple of things neighbour.

(a) You replied to me, with that post on experimentation. It implied you wished to engage.
(b) I don't disregard citations. I disregard single citations which state something out of the ordinary. You can not draw a straight line with less than three points. What this means, you need to repeat, and see if it stands up. Thus a single paper, means very little. That second "article" is the equivalent of an editorial, it was not written by an expert it was from a web based service, by a "staff writer". IT holds less water.
(c) You are misreading my comments based about religion, because I mentioned mine (obliquely, pagan is about as descriptive as "speaks english" to narrow down my spiritual frame work). IF me bringing it up causes you consternation. Then I've hit a nerve. Oh dear, what a shame, never mind.
(d) My insistence on things following scientific principals and frame work, before changing the view of science, is correct. As I said and you acknowledge, I'm a scientist. What else would you have me do? Bring out my bag of Ogam to decide what evolution was about? No.
(e) Your last point lapsed into ad homenin attack, which implies you are at a loss how to debate. Do not bring hte person into the debate, if you do not wish it brought back at you neighbour. No seriously, calling me closed inded, and having been in a rut in the lab too long. Bad choice of tactic.

So let me clue you up. You can believe anything you want, it does not influence the science. That is the mistake the lay people make. Some thought the earth was the center of the Universe, and every thing revolved around it, evidence proved otherwise. So "prevailing thought" can change. Science changes with verifiable evidence, not the belief of the masses.

Why don't you do this. Read the papers and debate the evidence. Lengthy diatribes accomplish nothing.
Yes, I am a layman. I also have more paper on the wall than you (based on your multiple comments about your expertise). But I'm always up for learning something new. So teach me. Read the papers and discuss your objection to the methodology and the results. Remember to do the math.

a reply to: Phantom423

I have read the articles, I looked closer neither is a peer reviewed paper. Both are articles. Do you understand the difference? Do you understand how peer review works? Have you read Lucas Laursen's cited works? Do the math? Sure, I'll fire R up on the server, once you provide Lucas Laursen's data for me. Guess what I can do the math, well my coding can.

As for more paper on the wall? How do you get that conclusion? No seriously. Don't be shy neighbor.

Like I said, I've read the articles. If you can not tell the difference I a not going to engage you in depth.

But I will leave you with a single point, from Laursen's article.

"Coyne adds, however, that it may not be practical to extrapolate very much from an asexually reproducing
species such as E. coli to organisms that reproduce sexually."

Do you understand that implication? No? Because if you did you would understand it is not really applicable to humans, which this thread is about!

a reply to: Noinden

Like I said, I've read the articles. If you can not tell the difference I a not going to engage you in depth.

Let's just let it stand there. I'm sure you're a lot smarter than I am. No one benefits from an adversarial conversation. The best example I can think of is Leonard Susskind's first lecture in QM at Stanford. When it came to complex numbers he asked the class if everyone knew what complex numbers were and how they're used. No one raised their hand. So Leonard said - come on - I know there's a few of you out there - raise your hand. Turned out about a half dozen people raised their hand. He stopped the whole class and taught the basics of complex numbers with a detailed explanation of how imaginary numbers came into being. Leonard never intimidated, never went through all his credentials. He didn't have to. The message is this: You never, never, ever intimate to teach. You challenge, you offer knowledge, but never insult. Just something to think about.

a reply to: Phantom423

You started off with the insults neighbour, I warned you there would be a consequence. That consequence is I am not going to play nice. Thus I am not going to teach you. That is in part, because you are unwilling to engage or learn, but it is also in aprt due to that round of insults. You set the rules for this, and as such, I will play them to the limit.

So don't cite a nice little apocryphal story to seem as if you are superior morally. I do not follow a meek and mild abrahamic based morals system.

I will also take that reply to translate to "I have not read any of the actual papers" and "no I do not know the difference between an article and a paper".

Now back to the "you have more paper on the walls. Come now don't be shy, I am pretty sure you don't, unless it is wall paper and yeah only paint here.

Ok so you've just proven a micro virus! There is still no evidence of a macro virus!!!

Just when we thought we knew everything about viruses, comes this. It's alive!!


Study adds to evidence that viruses are alive
Date:September 25, 2015 Source:University of Illinois at Urbana-Champaign

www.sciencedaily.com...

A new analysis supports the hypothesis that viruses are living entities that share a long evolutionary history with cells, researchers report. The study offers the first reliable method for tracing viral evolution back to a time when neither viruses nor cells existed in the forms recognized today, the researchers say.
The new findings appear in the journal Science Advances.

Until now, viruses have been difficult to classify, said University of Illinois crop sciences and Carl R. Woese Institute for Genomic Biology professor Gustavo Caetano-Anollés, who led the new analysis with graduate student Arshan Nasir. In its latest report, the International Committee on the Taxonomy of Viruses recognized seven orders of viruses, based on their shapes and sizes, genetic structure and means of reproducing.

"Under this classification, viral families belonging to the same order have likely diverged from a common ancestral virus," the authors wrote. "However, only 26 (of 104) viral families have been assigned to an order, and the evolutionary relationships of most of them remain unclear."

Part of the confusion stems from the abundance and diversity of viruses. Less than 4,900 viruses have been identified and sequenced so far, even though scientists estimate there are more than a million viral species. Many viruses are tiny -- significantly smaller than bacteria or other microbes -- and contain only a handful of genes. Others, like the recently discovered mimiviruses, are huge, with genomes bigger than those of some bacteria.

The new study focused on the vast repertoire of protein structures, called "folds," that are encoded in the genomes of all cells and viruses. Folds are the structural building blocks of proteins, giving them their complex, three-dimensional shapes. By comparing fold structures across different branches of the tree of life, researchers can reconstruct the evolutionary histories of the folds and of the organisms whose genomes code for them.

a reply to: Noinden

Just a bit of fun vaguely associated with the topic.