Arthur Smith

Well, not sure about the connection to thalidomide (there is a Kékulé ring in there). The thalidomide tragedy certainly highlighted the lack of drug regulation. The molecule exists in two enantiomers and I presume the drug was administered as a racemic mixture. Are you suggesting all the therapeutic worth was in one enantiomer and all the disastrous side effects in the other? When I consider origin of life, I consider opportunity and emergence. Given scenario A, what emerges? There is no "bringing about" force. --------------------------------------------------------------------------------------------- Found it. [Planetary Dreams: The Quest to Discover Life Beyond Earth] Shapiro's take on RNA world is understandable from his viewpoint as a chemist. But that is a sideshow to the main theme which is advocating a search for the second data point, life elsewhere. The Second Data Point. Maybe a topic for another thread. https://en.wikipedia.org/wiki/Robert_Shapiro_(chemist) A discussion elsewhere on origin of life. Mikkel Rasmussen has assembled a plethora of articles and there is ensuing discussion. https://discourse.peacefulscience.org/t/raw-materials-for-life/13951 https://discourse.peacefulscience.org/t/landmark-achievement-in-rna-world-experiments/13956

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.

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

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?

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?

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.

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.

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.

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. That looks dangerously near to a personal opinion.

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?

You have to admit the scrabble/poop insult was funny! So evolution is wrong? OK, do you have an alternative explanation? I mean, we see what we see and you may not need one, just reject ones that you don't like. Or is it six days, six thousand years and an ark? Because there are evidenced rebuttals to that story.

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).

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

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

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. 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. 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.

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

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.

Does have. The sharp end of our (human) ribosomes is RNA.

Science is not static. https://bme.gatech.edu/bme/node/3152 Though I concede, origin-of-life research has more ideas than definitive evidence.

We'll see!

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.

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.

Ribozymes are RNA catalysts. And the ribosome is an example that has not been superseded by a protein complex. Proteins are ubiquitous in living organisms today but proteins do not self-replicate, unlike RNA. That proteins have assumed the rôle of catalyst in most metabolic processes doesn't rule out that RNA could have done both replication and catalysis in the earliest self-sustaining self-replicators. It only needed to work, the first living entities would have no competition.

He's still around. He is still being paid by the Discovery Institute. https://www.discovery.org/about/fellows/

No maybe. COVID is an RNA virus, storing it's genetic information in RNA. When it infects a cell the replication system it hijacks is the ribosome, the functional catalytic element is RNA. RNA World is a good hypothesis of "why not both".