The Genetic Code

[AV1611VET]

You could look into it if you actually were interested. Several links to pages and videos have been posted in recent threads on this topic.

If you don't know, it's okay to say so.

I've been known to say that from time to time.

 

[Hans Blaster]

If you don't know, it's okay to say so.

I've been known to say that from time to time.

It is complicated and I don't have the facts fully integrated in a way that I can easily write out a coherent summary for a lay audience. That's why I suggest you go find a summary if you really care.

 

[Kylie]

So because some chemicals exists they must have randomly created life?

I said it's evidence, not proof.

But of course we can't even do it now in a controlled environment.

You know evolution takes a very long time, right? At least compared to Human life times.

 

[Kylie]

You mean my "completely irrelevant belief" that evolution will wax stronger and stronger, culminating in a time where it will be explained so simply a child can understand it?

My daughter could understand the basics of it before she was ten.

 

[SelfSim]

You could look into it if you actually were interested. Several links to pages and videos have been posted in recent threads on this topic.

Can't help but think these ridiculously trivial, unthinking, junk posts of @AV1611VET's are just some kind of tactic to bury the useful ones(?) .. Or am I being too generous in even suggesting that(?)

 

[AV1611VET]

It is complicated and I don't have the facts fully integrated in a way that I can easily write out a coherent summary for a lay audience. That's why I suggest you go find a summary if you really care.

10-4

Couldn't have said that better, myself!

 

[SelfSim]

10-4
Couldn't have said that better, myself!

(Namely because you don't care and so you won't make the attempt ..)

?

 

[SelfSim]

For reference purposes: here's a list of the links including relevant extracts (in quotes) and contextualisations I've provided thus far in this thread .. (ie: before @AV1611VET hijacked the thread and buried them with unrelated, irrelevant, OT chatter):

1) Abiogenesis Model:
See this one (from Wiki):


2) Non Terrestrial Nucleobases found in Meteorites:
Just as an fyi and for reference purposes, strong evidence has recently been published, (April 2022), which shows the detection of nucleobases in three carbonaceous meteorites. This is yet another empirically evidenced 'precursor' building block 'rung' up the ladder leading to self-replication, and thus also supports the abiogenesis hypothesis.

Feasible pathways for generation of these via photochemical reactions prevailing in the interstellar medium and later incorporated into asteroids during solar system formation, have now thus been established.

This study demonstrates that a diversity of meteoritic nucleobases can serve as building blocks of DNA and RNA on the early Earth.

PS: For readers: nucleobases are one of the structural components of nucleic acids forming the basis of all known life.

3) Earth Biology Preference for Triplet Code:
Could Life Use a Longer Genetic Code? Maybe, but It’s Unlikely:

Triplet codons work well on Earth, but it’s not clear if that would be true elsewhere—life in the cosmos might differ significantly in its chemistry or in its coding. The genetic code is "presumably derivative and subservient to the biochemistry of peptides" that are required for life to work, said Drew Endy, an associate professor of bioengineering at Stanford University and president of the BioBricks Foundation, who was not involved in the study. In environments more complex than Earth, life might need to be encoded by quadruplet codons, but in much simpler settings, life might get by with mere doublet codons—that is, of course, if it uses codons at all.

So, in those contexts, would it still be called 'life'?

Its speculative .. but they're setting about modifying the genetic code to quadruplet codons, to see if it still functions. Yes .. we have a human designer in this case because they're leaving behind a trail of objective evidence showing how they're going about it (and it'll be repeatable). And, they may still not be able to achieve their goals because life as we know it, is adapted towards preferring a triplet code.

No-one is saying anything about life's origins being known, or that the currently known encoding scheme is 'the only one'.

Further:

Not everyone agrees that creating a full quad-coded life form will be simple. “I don’t think anything they show suggests that it’s going to be easy—but they do show it’s not impossible, and that’s interesting,” said Floyd Romesberg, a synthetic biologist who cofounded the biotech company Synthorx. Getting something that works poorly to work better is a “very, very different game” than trying to do the impossible.

4. The Role of Autocatalytic Sets:
The autocataytic set hypothesis, is based on lab experiments, which show that small protein peptide molecules, in a increasingly complex 'soup', undergo a spontaneous phase transition, which creates self catalysing, auto-catalytic sets. This phase transition is dependent on the ratio of uncatalysed reactions in the soup, to polymers of a given length. At the moment, (2018), this has been demonstrated in a set of 16 ribosymes.

The autocatalytic hypothesis, (emboldenment for @Mountainmike only), then arises by applying this demonstrated phenomenon to the question of the origins of template based replication (ie: life's genetic code).

Evolution then takes over, once some random event changes any given peptide in a peptide autocatytic set (or cluster). Stuart Kauffman (its proposer) tries to simplify this, with his nursery rhyme-style explanation about peptides he names 'Patrick, Gus', (etc) co-existing in a calm lagoon, billions of years ago, on the coast of Western Australia. Those peptide characters then become the first sessile feeder and the first predator.
See his 30 minute, highly condensed (and therefore, not so easy to follow), Youtube: The Emergence and Evolution of Life: Stuart Kauffman .. all the published references, supporting his hypothesis, are shown in his projected slides (and in his words).

One might not believe his hypothesis .. (that's optional and quite irrelevant). It is however, deeply rooted in empirical lab testing results and well established information theory, and is actively being pursued as part of research into the field of molecular reproduction. Like it or not: they have shown that its possible.

5) Peptides found in Space:
A pathway to peptides in space through the condensation of atomic carbon, (Nature Astronomy, Feb 2022):

Organic molecules are widely present in the dense interstellar medium, and many have been synthesized in the laboratory on Earth under the conditions typical for an interstellar environment. Until now, however, only relatively small molecules of biological interest have been demonstrated to form experimentally under typical space conditions. Here we prove experimentally that the condensation of carbon atoms on the surface of cold solid particles (cosmic dust) leads to the formation of isomeric polyglycine monomers (aminoketene molecules). Following encounters between aminoketene molecules, they polymerize to produce peptides of different lengths. The chemistry involves three of the most abundant species (CO, C and NH3) present in star-forming molecular clouds, and proceeds via a novel pathway that skips the stage of amino acid formation in protein synthesis. The process is efficient, even at low temperatures, without irradiation or the presence of water. The delivery of biopolymers formed by this chemistry to rocky planets in the habitable zone might be an important element in the origins of life.

 

[SelfSim]

An up-to-date hypothesis, (published May 2022), proposes the coexistence of prebiotic RNA and peptides, and then links this to protein synthesis:

6) A prebiotically plausible scenario of an RNA–peptide world:

The RNA world concept is one of the most fundamental pillars of the origin of life theory. It predicts that life evolved from increasingly complex self-replicating RNA molecules. The question of how this RNA world then advanced to the next stage, in which proteins became the catalysts of life and RNA reduced its function predominantly to information storage, is one of the most mysterious chicken-and-egg conundrums in evolution.

Here we show that non-canonical RNA bases, which are found today in transfer and ribosomal RNAs, and which are considered to be relics of the RNA world, are able to establish peptide synthesis directly on RNA.

The discovered chemistry creates complex peptide-decorated RNA chimeric molecules, which suggests the early existence of an RNA–peptide world from which ribosomal peptide synthesis may have emerged. The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth.

 

[renniks]

It's being worked on, may even succeed. As I asked before, what's your hurry?

You are literally asking us to believe a miracle happened.

 

[renniks]

Peptides and nucleotides aren't just any old random chemicals.
On Earth, they are specifically, directly associated with biology.

May you missed the fact that in the 1960s experiments the forms of energy suggested to have initiated abiogenesis actually destroy the amino acids formed in the process.

 

[ottawak]

You are literally asking us to believe a miracle happened.

No, we are asking you to believe that scientists are doing their best to form a coherent theory of abiognesis. You want to characterize abiogenesis as a miracle for some reason and it may be a miracle--as theists believe--but if it was you will still have to wait for the science to learn how it happened. What's the hurry? It all happened a long time ago and knowing the technical details is going to be intersting but it's not going to change our lives very much. Be patient. Or enter that field of research yourself.

 

[renniks]

No, we are asking you to believe that scientists are doing their best to form a coherent theory of abiognesis. You want to characterize abiogenesis as a miracle for some reason and it may be a miracle--as theists believe--but if it was you will still have to wait for the science to learn how it happened. What's the hurry? It all happened a long time ago and knowing the technical details is going to be intersting but it's not going to change our lives very much. Be patient. Or enter that field of research yourself.

No, you don't get it. You believe it happened with no solid evidence that it's even possible. That's a miracle by definition.
It's even more fantastic to believe it happened without any guidance. It would actually be more consistent to claim that life always existed because all we can observe is life coming from other life.

 

[Hans Blaster]

May you missed the fact that in the 1960s experiments the forms of energy suggested to have initiated abiogenesis actually destroy the amino acids formed in the process.

What "1960s experiments"?

Do you mean "Miller-Urey"? First that was in 1952. Second it *made* 20 amino acids, not destroyed them.

 

[Bungle_Bear]

No, you don't get it. You believe it happened with no solid evidence that it's even possible.

You've been given plenty of evidence that it is possible, but you don't want to accept it.

That's a miracle by definition.

Incorrect. A miracle is a supposed event where the evidence says it is not possible. There's a difference between "we don't know if it's possible or not" and "it is not possible".

It would actually be more consistent to claim that life always existed because all we can observe is life coming from other life.

That's certainly an option, but it is not consistent with the evidence we have.

 

[Mountainmike]

Was this supposed to have some sort of meaning? It rambles and says nothing.

(And "Origin of Life" is the name used for the research in that field as used by the people who do it.)

It means what it said. You have given a reasonable summary of what is status of conjecture, with little evidence to support it. Not least if all these steps were likely there would be some evidence of intermediate parts of that process continuing so discoverable. But there is nothing in evidence except a highly developed minimum cell.

There is still the philosophical problem that one step defines the change to the point at which the first cell could evolve, or the change from no life to life, but the problem is before that step there was no evolution so no change is possible. Yet that minimum cell is hideously complex.

So I remain fascinated but as yet far from convinced, and I await the first hypothesis for the critical step ( which is the abiogenesis step)

 

[ottawak]

No, you don't get it. You believe it happened with no solid evidence that it's even possible. That's a miracle by definition.
It's even more fantastic to believe it happened without any guidance. It would actually be more consistent to claim that life always existed because all we can observe is life coming from other life.

Believe what happened? That life began at some point? Don't you?
I don't know how it happened. I'll have to wait while scientists struggle with the question. But as a Christian I already know who brought it about and why, so I am content to wait for the how of it.

 

[ottawak]

It means what it said. You have given a reasonable summary of what is status of conjecture, with little evidence to support it. Not least if all these steps were likely there would be some evidence of intermediate parts of that process continuing so discoverable. But there is nothing in evidence except a highly developed minimum cell.

There is still the philosophical problem that one step defines the change to the point at which the first cell could evolve, or the change from no life to life, but the problem is before that step there was no evolution so no change is possible. Yet that minimum cell is hideously complex.

So I remain fascinated but as yet far from convinced, and I await the first hypothesis for the critical step ( which is the abiogenesis step)

Assuming there is a single point at which life can be said to have begun. In a continuum of development, assigning such a point is merely arbitrary and has no effect on the course of development itself.

 

[Hans Blaster]

1. I would not say there is little evidence. What we have is a lot of experiments carried out under conditions that seem appropriate (a lot of OOL researchers seem to prefer shallow tidal pools these days) and these experiments keep reproducing parts of the apparently needed sequence of development to a primitive cell. I'm pretty sure everyone in OOL research understands that they will never likely demonstrate "what actually happened", but that doesn't mean they can't learn a great deal about what could have and couldn't have happened.

(Let's try a similar hypothesis: The Nebular Hypothesis for star and planetary system formation. Proto-planetary disks were hypothesized in such a model with proto-planets in them. And then, with IR and sub-mm observatories, the proto-planetary disks were seen, then the actual proto-planets orbiting their proto-stars. OOL will probably never get quite this good, but science works all of the time in such regimes.)

2. At first I thought you were looking for some sort of fossil evidence, which would be extremely unlikely. (Even if modern looking cells appeared suddenly, they would be unlikely to be fossilized as soft organisms don't fossilize well to begin with.) Then I realized that you probably meant that some intermediate form (either a pool of self-replicating proteins or a simple proto-cell population or something else) should still exist. But I don't see why they should. Those proto-organisms (or chemistries) just look like food to modern micro-organisms. I would expect that in the course of developing to the proto-cell and then beyond toward something like a simple bacterium there were many breakthroughs that made the new organisms vastly more competitive than their neighbors and there was rapidly a near replacement with the old kind on the long-term way out. (They beat them out for resources, grew faster, ate them all, whatever.)

It means what it said. You have given a reasonable summary of what is status of conjecture, with little evidence to support it. Not least if all these steps were likely there would be some evidence of intermediate parts of that process continuing so discoverable. But there is nothing in evidence except a highly developed minimum cell.

 

[renniks]

Believe what happened? That life began at some point? Don't you?
I don't know how it happened. I'll have to wait while scientists struggle with the question. But as a Christian I already know who brought it about and why, so I am content to wait for the how of it.

Then you know life didn't begin on earth but always was. We only observe life from life which is consistent with what the Bible says about creation. Abiogenesis is a theory that life happens by accident. Christians don't believe that story.