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New study sheds light on origins of life on Earth


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12 minutes ago, Arthur Smith said:

You won't get a definitive, consensus, universally accepted explanation from anyone, because there isn't one yet. Current life on Earth is all commonly descended from one remote ancestor, the last, universal common ancestor. I can't tell you much about those early organisms except there is no reason to think they were not preceded by simpler, different organisms and systems of which there is no trace. First life may have exploited other sources of energy, anaerobic chemosynthesis rather than needing light or oxygen, life may have got going in deep sea vents where chemicals emerge from the crust at high concentration in very hot water which rapidly cools on mixing. There are surfaces, holes and crevices that are potentially almost infinite in their micro-niche properties. 

There's always the possibility of a second data point. Something on Mars or further afield. Till then, speculation (based on what we know and what we can show) is available. Nick Lane is someone to google.

I'm an inveterate speed-reader. Apologies if I missed or misunderstood a point you were making. Please feel free to ask again or link to what I missed.

I didn't ask for a consensus, I asked for Mathematics. Chemical kinetics is maths, not unsupported waffle.

 

12 minutes ago, Arthur Smith said:

Current life on Earth is all commonly descended from one remote ancestor, the last, universal common ancestor.

How do you know ?

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4 minutes ago, studiot said:

I didn't ask for a consensus, I asked for Mathematics. Chemical kinetics is maths, not unsupported waffle.

 

How do you know ?

Well, the strongest evidence is the almost universal triplet code DNA =>RNA=>protein etc used by almost all organisms we know of. The few exceptions are illuminating and reinforce rather than undermine the concept.

Just now, Arthur Smith said:

Chemical kinetics is maths

Mathematics is a branch of philosophy useful in science for modelling.

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1 minute ago, Arthur Smith said:

Well, the strongest evidence is the almost universal triplet code DNA =>RNA=>protein etc used by almost all organisms we know of. The few exceptions are illuminating and reinforce rather than undermine the concept.

That's only evidence.

You made a much strionger statement.

In particular you precluded the possibility that the same or similar sequence of events occured more than once on Earth.

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2 minutes ago, studiot said:

In particular you precluded the possibility that the same or similar sequence of events occured more than once on Earth.

That's a misunderstanding. I absolutely intended to make the point that LUCA is not necessarily the first life  that got going on Earth. There may have been many early false starts and failures. No-one knows.

5 minutes ago, studiot said:

You made a much strionger statement.

That was one piece of evidence. Universal Common Descent is the best fit. You may like to look at Theobald if you are not already familiar. No need for me to reinvent the wheel, I hope.

10 minutes ago, studiot said:

In particular you precluded the possibility that the same or similar sequence of events occured more than once on Earth.

Though if you mean some life around on Earth today has a separate origin, then, I'd like to see an evidenced claim to the contrary.

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15 minutes ago, Arthur Smith said:

Though if you mean some life around on Earth today has a separate origin, then, I'd like to see an evidenced claim to the contrary.

I made no such claim.

If you want claims about biology, ask a biologist.

I merely pointed out that your statement

31 minutes ago, studiot said:
43 minutes ago, Arthur Smith said:

Current life on Earth is all commonly descended from one remote ancestor, the last, universal common ancestor.

How do you know ?

Rejects all other possibilities.

 

However I would observe that in the geological record at one time there was (almost) no free oxygen on Earth.

All early life must therefore have been anaerobic.

The presence of Life did indeed change the planet geologically.

 

I would also observe that following each of the 5 great extinctions known, many, if not the mojority, of lifeforms were quite different before and after the horizon in the fossil record.

A good study of this is given by Professor Benton of Bristol University in his book "When Life Nearly Died."
Another study, unfortunately only stretching back to the Cambrian, is by Professor Beerling of Sheffield University  "The Emerald Planet".
This one is the only detailed paleohistory of the atmousphere that I know of.

 

Finally, in case you think that I support the clarion call you here to often in these forums, "Science must be Mathematic", here is my favourite passage showing how rational thinking can be at least as strong as an equation.

Quote

Professor Swinnerton, Nottingham University

From what is seen in the crystals of granite, it is evident that the felspar crystallized out before the quartz. Quite often you will find small crystals of mica, inside the large crystals of felspar, so they must therefore have been formed first.

 

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23 minutes ago, studiot said:

However I would observe that in the geological record at one time there was (almost) no free oxygen on Earth.

All early life must therefore have been anaerobic.

The presence of Life did indeed change the planet geologically.

I broadly agree on all those points. Here. Doesn't affect the point that all surviving life is descended from a common ancestor. Whilst I'm happy to defend that claim with more evidence, finding a black swan might be quicker.

35 minutes ago, studiot said:

Finally, in case you think that I support the clarion call you here to often in these forums,

I'm new here. I have no idea what that means.

37 minutes ago, studiot said:

Professor Benton of Bristol University

 

41 minutes ago, studiot said:

I would also observe that following each of the 5 great extinctions known, many, if not the mojority, of lifeforms were quite different before and after the horizon in the fossil record.

Well, sure. Different is not synonymous with unrelated. Michael Benton is an excellent scientist, deserving his OBE, and I can't imagine you have gained any impression from him that the Permian extinction killed any species that arose from a separate origin. 

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13 minutes ago, Arthur Smith said:

the point that all surviving life is descended from a common ancestor

AFAIK all surviving life descended from three ancestors: Archaea, Bacteria, and Eukarya. There is evidence that both Eukarya and Bacteria split from Archaea. All is needed then is to strengthen this evidence.

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38 minutes ago, Genady said:

AFAIK all surviving life descended from three ancestors: Archaea, Bacteria, and Eukarya. There is evidence that both Eukarya and Bacteria split from Archaea. All is needed then is to strengthen this evidence.

Don't worry about Eukaryotes, they're just the result of a get-together of an ancient bacterium and an engulfing Archeon. There's no question bacteria and Archeans share a common ancestor. Again, they share the universal genetic code (with interesting exceptions that hint at the evolutionary pathway).

ETA, for spelling pedants, Archaeon, Archeon, Archæon, Archaean, Archean, Archæan are all accepted alternatives

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1 hour ago, Arthur Smith said:

I'm new here.

Exactly.

That is why I am asking, as clearly as I can, for the required level of support for an absolute claim such as

1 hour ago, Arthur Smith said:

Doesn't affect the point that all surviving life is descended from a common ancestor.

You, sir, have stated this absolutely at least three times now, without consideration for alternatives.

Or do you deny that alternatives exist ?

 

The very title and question of this thread would suggest that the OP (and I ) acknowledge that we (and Science) do not know if there is a definite answer, let alone what such an answer might be.

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4 minutes ago, studiot said:

Or do you deny that alternatives exist ?

I know of no alternative organisms than those related by descent from a common ancestor. I'd be surprised to learn of any that you can present. You have not argued the point that the genetic code is practically universal across all the three main branches of the tree of life. I think it is reasonable to deal with one point before requiring others to produce more evidence. Not that there isn't plenty but, carry on. Unrelated life-forms?

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5 minutes ago, Arthur Smith said:

I know of no alternative organisms than those related by descent from a common ancestor. I'd be surprised to learn of any that you can present. You have not argued the point that the genetic code is practically universal across all the three main branches of the tree of life. I think it is reasonable to deal with one point before requiring others to produce more evidence. Not that there isn't plenty but, carry on. Unrelated life-forms?

The simple fact remains that you made the absolute claim in the first place and repeated it twice (rather like someone in the Bible ?)

Since you introduced it as a 'scientific fact', and since it would be a very fundamental fact if substantiated, I am asking you to substantiate it properly.

Please note I am also responding to your general posting which seems to show a proper scientific nature rather than something different.

 

Is that too much to ask ?

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6 minutes ago, studiot said:

The simple fact remains that you made the absolute claim in the first place and repeated it twice (rather like someone in the Bible ?)

Since you introduced it as a 'scientific fact', and since it would be a very fundamental fact if substantiated, I am asking you to substantiate it properly.

Please note I am also responding to your general posting which seems to show a proper scientific nature rather than something different.

I don't think you realize what the significance of a shared genetic code is? It's hugely significant. What is the alternative explanation to a code structure that is virtually identical throughout life on Earth. Just one simpler point. The stereochemistry of DNA (B-DNA type found in most cells) is referred to as "right handed". There is no reason that a perfectly viable organism could not operate with the left-hand isomer. There are no such. Again, it would be easier for you to find a black swan than me keep pointing out there aren't any.

Here is Wikipedia's list of alternatives to the standard code.

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

Scroll down to the table.

 

26 minutes ago, studiot said:

Please note I am also responding to your general posting which seems to show a proper scientific nature rather than something different.

That looks dangerously near to a personal opinion. ;)

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Shall we just stick to the facts? I've mentioned DNA stereochemistry (though that extends to other biomolecules) and the almost-universal genetic code. I linked you to a table showing the similarities and differences in the genetic code to support my contention, which is not the least controversial among biologists. You don't seem to have addressed that yet. As I said, an example of an organism unrelated in some way to the mainstream could be an avenue for consideration but I don't know of one to suggest.

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20 minutes ago, Arthur Smith said:

The stereochemistry of DNA (B-DNA type found in most cells) is referred to as "right handed".

Wouldn't it be very interesting to have two independent trees of life with opposite chirality with independent evolution and ecology on one planet. Any sci-fi writers around? :) 

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1 minute ago, Genady said:

Wouldn't it be very interesting to have two independent trees of life with opposite chirality with independent evolution and ecology on one planet. Any sci-fi writers around? :) 

Indeed! But what if there were competing chiralities? All metabolisms that I know of depend on one or other set of chiralities. Who could eat who? There's an advantage in using ready-made chemicals rather than having to deconstruct/reconstruct.

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6 minutes ago, Arthur Smith said:

Indeed! But what if there were competing chiralities? All metabolisms that I know of depend on one or other set of chiralities. Who could eat who? There's an advantage in using ready-made chemicals rather than having to deconstruct/reconstruct.

I guess they wouldn't generally eat each other. Rather for each kind the other kind would be just like other non-living natural phenomena -- wind, rain, waves, ... 

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23 hours ago, studiot said:

Primordial chemical processes will not have had the benefit of these catalysts, as we would have to believe that not only did the right components come togther for the protein etc to form but also the right components for the catalyst as well. (Most such catalysts are complicated biomolecules in their own right).

 

Indeed it begs the question, which came first the catalyst or the product protein ?

You mean this question? I.e. what molecules would likely be the first? As mentioned (I think) this is an open question. I mostly only remember that there is still an ongoing dispute regarding whether there really was a an RNA world predating a DNA world. There is even more uncertainty regarding molecules that may have dominated before that. As you have noted, it is unlikely that RNA itself is a prebiotic molecule. There is a good report here, but it is a oldish and I am not really up to date on the latest findings. https://doi.org/10.1016/S0092-8674(00)81263-5

 I think some work have been focused on thermodynamic models for early molecules and alternative pathways for formation of early carbon bodies.

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18 minutes ago, Genady said:

I guess they wouldn't generally eat each other. Rather for each kind the other kind would be just like other non-living natural phenomena -- wind, rain, waves, ... 

Which is the serious point I was making about right-handed DNA. Right-handed DNA is explained by common descent but perhaps there were left-hand variants. As you say, those variants would neither benefit from consuming right-handers nor be useful for right-handers to consume. But if we did have another indisputably alien life-form to examine, what are the limits of possibilities? Prior to CGI, imagination seemed to run out with "man in a suit". But are we limited to carbon-based, even? Limited to molecules?

I live in hope of the second data point; evidence of life elsewhere.

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3 minutes ago, Arthur Smith said:

Which is the serious point I was making about right-handed DNA. Right-handed DNA is explained by common descent but perhaps there were left-hand variants. As you say, those variants would neither benefit from consuming right-handers nor be useful for right-handers to consume. But if we did have another indisputably alien life-form to examine, what are the limits of possibilities? Prior to CGI, imagination seemed to run out with "man in a suit". But are we limited to carbon-based, even? Limited to molecules?

I live in hope of the second data point; evidence of life elsewhere.

Have you come across Japp's theory in relation to chirality ?

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

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5 minutes ago, CharonY said:

I mostly only remember that there is still an ongoing dispute regarding whether there really was a an RNA world predating a DNA world.

There was a lively debate at one time. Robert Shapiro was picked as the RNA world skeptic by ID proponents back in the day and much was made of the chicken or egg argument, DNA first (replication) or protein first (metabolism). RNA world, where RNA is both replicator and catalyst, neatly sidesteps the argument. I still have Shapiro's last book, Planetary Dreams, so I'll refresh my memory of what his issue was with RNA world. (Had some dealings with Shapiro back in 2005 - most charming and self-effacing man). 

Anyway, looking for an article, I came across something else:

https://www.sciencedaily.com/releases/2021/03/210302094102.htm

 

12 minutes ago, studiot said:

Have you come across Japp's theory in relation to chirality ?

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

No. I see Kékulé was a mentor of his. Kékulé is a god among biochemists. What precisely is Japp's theory?

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9 minutes ago, Arthur Smith said:

There was a lively debate at one time. Robert Shapiro was picked as the RNA world skeptic by ID proponents back in the day and much was made of the chicken or egg argument, DNA first (replication) or protein first (metabolism). RNA world, where RNA is both replicator and catalyst, neatly sidesteps the argument. I still have Shapiro's last book, Planetary Dreams, so I'll refresh my memory of what his issue was with RNA world. (Had some dealings with Shapiro back in 2005 - most charming and self-effacing man). 

Anyway, looking for an article, I came across something else:

https://www.sciencedaily.com/releases/2021/03/210302094102.htm

 

No. I see Kékulé was a mentor of his. Kékulé is a god among biochemists. What precisely is Japp's theory?

japp1.thumb.jpg.9f2a896d42db1b679b305758646c4b75.jpg

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10 minutes ago, studiot said:

japp1.thumb.jpg.9f2a896d42db1b679b305758646c4b75.jpg

Does that paper contain Japp's theory. Unfortunately I can only read the abstract:

IT appears to me that Prof. Kipping and Mr. Pope unintentionally attribute to me opinions which I have never expressed, and which I do not hold. I never for a moment imagined that in each separate crystallisation—either of molecularly symmetric substances which, like sodium chlorate, may form either right-handed or left-handed crystals, or of the externally compensated mixture of dextro- and laevo-rotatory sodium ammonium tartrates, in which the asymmetry is molecular—equal amounts of the two kinds of crystals would necessarily be deposited. I never thought of this equality as holding good, except as the mean of a great number of experiments. In my address, when referring to Messrs. Kipping and Pope's results obtained with sodium chlorate, I therefore used the expression “on the average.” Besides, I was acquainted with Landolt's experiments on the subject, which prove the same thing. In the case of the dextro- and laevo-rotatory sodium ammonium tartrates, the Pasteur-Gernez method of separating these by starting the crystallisation with a crystal of one of the two kinds, and Jungfleisch's experiments, to which I will refer more fully later on, were sufficient to make me aware of the influence of initial bias on crystallisation, and to prevent me from expecting equality, except as a mean result.

I've tried searching but not pulling up anything. Any chance of a brief outline of his theory of chirality?

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6 minutes ago, Arthur Smith said:

Does that paper contain Japp's theory. Unfortunately I can only read the abstract:

 

I've tried searching but not pulling up anything. Any chance of a brief outline of his theory of chirality?

Here is a summary from a 2004 view  (John Buckingham  "Chasing the Molecule")   - the original reference also came from this book.

japp2.thumb.jpg.d4adecbeb05f049029b01c4c775dd570.jpg

japp3.thumb.jpg.d140ea49120a2b19423297f15c300bc5.jpg

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Pasteur first noticed sodium aluminium tartrate formed crystals of two sorts which, when sorted by eye and redissolved, the solutions were either dextrotatory or levorotatory, leading to the idea that molecules could form enantiomers, spacially opposite mirror reflections.

But hang on, here's an article about Japp:

http://www.scielo.org.za/pdf/sajs/v103n1-2/06.pdf

 

 

OK, vitalism. Chirality arises from some fundamental law or is just an accident? 

That's a great story,  the Dorothy L Sayers plot an all

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