Discovery boosts theory that life on Earth arose from RNA-DNA mix

Newly described chemical reaction could have assembled DNA building blocks before life forms and their enzymes existed.

SCRIPPS RESEARCH INSTITUTE

Research News

LA JOLLA, CA–Chemists at Scripps Research have made a discovery that supports a surprising new view of how life originated on our planet.

In a study published in the chemistry journal Angewandte Chemie, they demonstrated that a simple compound called diamidophosphate (DAP), which was plausibly present on Earth before life arose, could have chemically knitted together tiny DNA building blocks called deoxynucleosides into strands of primordial DNA.

The finding is the latest in a series of discoveries, over the past several years, pointing to the possibility that DNA and its close chemical cousin RNA arose together as products of similar chemical reactions, and that the first self-replicating molecules–the first life forms on Earth–were mixes of the two.

The discovery may also lead to new practical applications in chemistry and biology, but its main significance is that it addresses the age-old question of how life on Earth first arose. In particular, it paves the way for more extensive studies of how self-replicating DNA-RNA mixes could have evolved and spread on the primordial Earth and ultimately seeded the more mature biology of modern organisms.

“This finding is an important step toward the development of a detailed chemical model of how the first life forms originated on Earth,” says study senior author Ramanarayanan Krishnamurthy, PhD, associate professor of chemistry at Scripps Research.

The finding also nudges the field of origin-of-life chemistry away from the hypothesis that has dominated it in recent decades: The “RNA World” hypothesis posits that the first replicators were RNA-based, and that DNA arose only later as a product of RNA life forms.

Is RNA too sticky?

Krishnamurthy and others have doubted the RNA World hypothesis in part because RNA molecules may simply have been too “sticky” to serve as the first self-replicators.

A strand of RNA can attract other individual RNA building blocks, which stick to it to form a sort of mirror-image strand–each building block in the new strand binding to its complementary building block on the original, “template” strand. If the new strand can detach from the template strand, and, by the same process, start templating other new strands, then it has achieved the feat of self-replication that underlies life.

But while RNA strands may be good at templating complementary strands, they are not so good at separating from these strands. Modern organisms make enzymes that can force twinned strands of RNA–or DNA–to go their separate ways, thus enabling replication, but it is unclear how this could have been done in a world where enzymes didn’t yet exist.

A chimeric workaround

Krishnamurthy and colleagues have shown in recent studies that “chimeric” molecular strands that are part DNA and part RNA may have been able to get around this problem, because they can template complementary strands in a less-sticky way that permits them to separate relatively easily.

The chemists also have shown in widely cited papers in the past few years that the simple ribonucleoside and deoxynucleoside building blocks, of RNA and DNA respectively, could have arisen under very similar chemical conditions on the early Earth.

Moreover, in 2017 they reported that the organic compound DAP could have played the crucial role of modifying ribonucleosides and stringing them together into the first RNA strands. The new study shows that DAP under similar conditions could have done the same for DNA.

“We found, to our surprise, that using DAP to react with deoxynucleosides works better when the deoxynucleosides are not all the same but are instead mixes of different DNA ‘letters’ such as A and T, or G and C, like real DNA,” says first author Eddy Jiménez, PhD, a postdoctoral research associate in the Krishnamurthy lab.

“Now that we understand better how a primordial chemistry could have made the first RNAs and DNAs, we can start using it on mixes of ribonucleoside and deoxynucleoside building blocks to see what chimeric molecules are formed–and whether they can self-replicate and evolve,” Krishnamurthy says.

He notes that the work may also have broad practical applications. The artificial synthesis of DNA and RNA–for example in the “PCR” technique that underlies COVID-19 tests–amounts to a vast global business, but depends on enzymes that are relatively fragile and thus have many limitations. Robust, enzyme-free chemical methods for making DNA and RNA may end up being more attractive in many contexts, Krishnamurthy says.

###

“Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA” was authored by Eddy Jiménez, Clémentine Gibard and Ramanarayanan Krishnamurthy. Funding was provided by the Simons Foundation.

From EurekAlert!

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Philip
December 28, 2020 10:19 pm

In order to prosper, from the beginning life had to make a deal with the devil. Disease.

Reply to  Philip
December 29, 2020 12:16 pm

The answer? Sex

Bryan A
Reply to  Phil Salmon
December 29, 2020 1:50 pm

yes YES YES

Philip
Reply to  Phil Salmon
December 29, 2020 6:35 pm

I was thinking more in terms of viral material integration with host new cell replication at the gene level.

John Tillman
Reply to  Philip
December 30, 2020 9:55 am

About eight percent of DNA in the human genome comes from viruses, often inserted long before H. sapiens evolved.

Viruses have also probably played important roles in the evolution of all eukaryotes, and prokaryotes as well. The eukaryotic nucleus may stem from viral infection of our archaean ancestor.

Philip
Reply to  John Tillman
December 30, 2020 3:07 pm

Thank you. I remember something about it being the retrovirus (?)
IIRC NOVA had a show about that that I had watched. This was some years ago.

John Tillman
Reply to  Philip
December 31, 2020 11:09 am

Much of the viral material in our genome indeed comes from retroviruses, due to how they replicate.

John Tillman
Reply to  John Tillman
December 31, 2020 12:12 pm

Role of HERVs in, among other milestones in evolution, the placenta:

https://www.frontiersin.org/articles/10.3389/fimmu.2018.02039/full

Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses

John Tillman
Reply to  Philip
December 31, 2020 12:24 pm

Not all HERVs are of ancient mammalian and pre-mammalian origin:

https://blogs.biomedcentral.com/on-biology/2019/01/25/viral-content-human-genomes-variable-thought/

Mark - Helsinki
Reply to  Philip
December 30, 2020 5:41 am

Diseases are also life themselves. Back before diseases is the time frame here I think

Philip
Reply to  Mark - Helsinki
December 31, 2020 12:12 pm

Given what we know, I doubt the first viral RNA interactions with DNA went any better than they do today. I shouldn’t think that I’ve stretched the definition of disease here, in a single cell universe, when speaking to RNA life invading DNA life as host to replicate. Especially given the fact that the DNA host began to develop defensive measures to prohibit future invasions. DNA life evolving to adopt remnant viral RNA material in that defence seems fortuitous and, not to go down another rabbit hole but, I can see how the idea of intelligent design could come into play. The mathematics is fantastic.

Everything we don’t know for certain is such a mystery. 🙂

John Tillman
Reply to  Philip
January 2, 2021 2:29 pm

There is no evidence whatsoever for “intelligent design”. It’s merely an antiscientific attempt to sneak creationism into public school biology classes.

OTOH, evidence of idiotic design abounds on every side.

Philip
Reply to  John Tillman
January 2, 2021 7:03 pm

Where there is no evidence, people have always found a way to inject opinion, whether that be belief, or no belief. That is how a theory starts. Proving the theory is another matter.

My outlook is broader as I stand on this one tiny planet for a brief moment in time, exploring my universe among universes.I can find no more pure science than I can find pure religion, or pure anything else. There always seems to be a little something other in most everything. This article subject making the point.

My awe of the inter connectivity of systems, the problem solving, the complexity of their balancing acts, the underlying scope of the mathematics, and above all that, the raw potential of existence that will push human imagination for as long as there’s humans. That for me is an intelligence shining through this wondrous expression of outer and inner space.
There would be nothing without the beginning. I really don’t care who tries to claim it to advance their politics, their dogma, or their science. As it stands, I can’t tell the politician from the scientist from the religious from the idiots.
I don’t claim to have life’s ultimate answer. I’m just passing through.

Doc Chuck
December 28, 2020 11:28 pm

Interesting in this proposed stepwise spontaneous generation scenario that fragility is mentioned only at the end and solely regarding vital associated enzymatic proteins. What are the fragilities of these posited polynucleotide chains to the same energetic conditions (geothermal, solar, cosmic ray) that may prompt their synthesis? Will they very soon easily disassemble in those conditions instead of remaining intact for long? And so far here ‘reproduction’ is down to replication of single nucleic acid strands of whatever size and random coding, quite apart from the multiple great lengths that must survive to recurrently specify many lengthy forms of functional proteins to in turn perform ensemble the many metabolic necessities for cell survival, much less repair of ongoing mutation damage and reproduce a subsequent living generation soon enough to succeed each mortal one.

Likewise few of us were ever told that even in the original Urey-Miller spark-energized inorganic production of a couple of amino acids, these were sequestered away from recirculating in the apparatus to prevent further exposure to the same energies that would even more readily disassemble those ever so promising molecules and so only add to the life-toxic tars that constituted the vast majority of the end product.

John Tillman
Reply to  Doc Chuck
December 29, 2020 5:11 am

The Miller experiment produced dozens of amino acids and other organic compounds.

https://pdfs.semanticscholar.org/6f46/3e8a3611fa7f25c143991dfddac49c396b73.pdf?_ga=2.101443330.2063204810.1609245380-1913390977.1609245380

I don’t know to what procedure by Miller you’re referring. Please read his paper and point to whatever chemical practice you find objectionable.

https://abenteuer-universum.de/pdf/miller_1953.pdf

Similar experiments have since been conducted by Miller and many others, using reconstructed atmospheres differing from his hypothesized mix of compounds.

That amino acids arise spontaneously is a fact, observed both on Earth and in outer space, as shown by the rich troves of complex ET organics on meteorites and interstellar PAH clouds.

Nucleosides also self-assemble naturally in a variety of environments under various conditions. They also spontaneously form bonds linking nucleotides into short RNA chains (oligomers). A nucleotide is a nucleoside with phosphate groups attached, which form the links between nucleosides (the ribose sugar-nucleobase compound).

As to fragility, yes, spontaneously formed complex compounds do break down, but they also self-assemble into short chains, ie oligomers, peptides in the case of amino acids. The trick behind life is to get the monomers, eg amino acids in polypeptides (proteins), and nucleosides in DNA and RNA, to continue bonding into longer chains, ie to polymerize, without benefit of modern enzymes, mostly proteins.

However, RNA is also able to assume complex shapes, allowing it to act as an enzyme. These naturally occurring biological catalysts are called ribozymes.

bonbon
Reply to  John Tillman
December 29, 2020 8:29 am

“The trick behind life” ?
So the Biosphere is a trick?
Wow, that’s sciency even by today’s standards.

John Tillman
Reply to  bonbon
December 29, 2020 9:04 am

Would you prefer “chemical process”?

chemman
Reply to  John Tillman
December 29, 2020 12:09 pm

Directed chemical processes. They had to do a lot of controlling of variables to get those items.

John Tillman
Reply to  chemman
December 29, 2020 1:02 pm

No direction required. Just relative reproductive success of competing “designs”.

“Design” in nature is intensely idiotic, not the least bit intelligent.

bonbon
Reply to  John Tillman
December 30, 2020 3:51 am

Would that rather imperial comment also apply to the design of the speaker?

John Tillman
Reply to  bonbon
December 30, 2020 4:11 am

It applies to all “design” in nature. For instance, the human foot is idiotically designed since it’s adapted for plantigrade walking from a grasping foot. A sophomore mechanical or civil engineering student could design a better one than the Rube Goldberg apparatus with which we’re stuck.

bonbon
Reply to  John Tillman
December 30, 2020 5:15 am

I actually think the human foot was designed for the Giant Slalom –

The engineers who designed such equipment are unsung heroes….

gettyimages-1229801020-612x612.jpg
John Tillman
Reply to  bonbon
December 30, 2020 7:30 am

Ankles, maybe.

Matthew Schilling
Reply to  John Tillman
December 30, 2020 9:13 am

So, the design of ATP synthase is idiotic? That’s the adjective you’re going with? The Master’s comment about pearls before swine is as relevant today as it was the day He uttered it.

John Tillman
Reply to  Matthew Schilling
December 30, 2020 9:58 am

Yes. The ATP system is as Rube Goldberg a device as possible to imagine.

A physical or biochemist could come up with a better energy currency system in about an hour.

Have you ever studied the Krebs cycle and its evolution?

John Tillman
Reply to  John Tillman
December 30, 2020 10:13 am

Or for that matter the evolution of ATP synthase itself, which is an active field. From this year:

ATP synthase: evolution, energetics, and membrane interactions

https://arxiv.org/ftp/arxiv/papers/2006/2006.09357.pdf

Please study real science instead of buying into the blasphemous mendacities of creationist paid liars.

John Tillman
Reply to  John Tillman
December 30, 2020 11:47 am

Which is not to say that the adenosine-phosphorus combo doesn’t have advantages over alternative possible energy currencies, such as guanine and cytosine with phosphorus or pyrophosphite.

Hokey Schtick
Reply to  John Tillman
December 31, 2020 4:09 am

Let’s see you make a tree then, smartypants.

John Tillman
Reply to  Hokey Schtick
December 31, 2020 11:11 am

We’re still working on protocells. It took four billion years for the first tiny land plants to evolve, let alone trees.

John Tillman
Reply to  John Tillman
December 29, 2020 11:34 am

PAHs apparently abound in the universe.

PAH World hypothesis image, showing how a stack of polycyclic aromatic hydrocarbons could catalyze the abiotic synthesis of RNA:

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

comment image
In case you don’t want to read the whole Wiki entry, with source citations:

In the self-ordering PAH stack, the separation between adjacent rings is 0.34 nm. This is the same separation found between adjacent nucleotides of RNA and DNA. Smaller molecules will naturally attach themselves to the PAH rings. However PAH rings, while forming, tend to swivel around on one another, which will tend to dislodge attached compounds that would collide with those attached to those above and below. Therefore, it encourages preferential attachment of flat molecules such as pyrimidine and purine nucleobases, the key constituents (and information carriers) of RNA and DNA. These bases are similarly amphiphilic and so also tend to line up in similar stacks.

According to the hypothesis, once the nucleobases are attached (via hydrogen bonds) to the PAH scaffolding, the inter-base distance would select for “linker” molecules of a specific size, such as small formaldehyde (methanaloligomers, also taken from the prebiotic “soup”, which will bind (via covalent bonds) to the nucleobases as well as each other to add a flexible structural backbone.

A subsequent transient drop in the ambient pH (increase in acidity), for example as a result of a volcanic discharge of acidic gases such as sulfur dioxide or carbon dioxide, would allow the bases to break off from their PAH scaffolding, forming RNA-like molecules (with the formaldehyde backbone instead of the ribose-phosphate backbone used by “modern” RNA, but the same 0.34 nm pitch).

The hypothesis further speculates that once long RNA-like single strands are detached from the PAH stacks, and after ambient pH levels became less acidic, they would tend to fold back on themselves, with complementary sequences of nucleobases preferentially seeking out each other and forming hydrogen bonds, creating stable, at least partially double-stranded RNA-like structures, similar to ribozymes. The formaldehyde oligomers would eventually be replaced with more stable ribose-phosphate molecules for the backbone material, resulting in a starting milestone for the RNA world hypothesis, which speculates about further evolutionary developments from that point.

Louis Hunt
December 29, 2020 12:13 am

“Now that we understand better how a primordial chemistry could have made the first RNAs and DNAs, we can start using it on mixes of ribonucleoside and deoxynucleoside building blocks to see what chimeric molecules are formed–and whether they can self-replicate and evolve,” Krishnamurthy says.

How can non-living chemicals evolve? Don’t you have to have living organisms capable of dying before natural selection can act to select the fittest and trigger evolution? Can non-living chemicals overcome entropy to continually evolve to more complex forms? If so, perhaps the pyramids of Egypt were not created by intelligent design but by earthquakes piling up a bunch of rocks that were shaped into their current form by wind, sand, and water over thousands of years. Perhaps the junk in landfills will evolve into robots with AI capability that will conquer the world. That seems about as likely as chimeric molecules evolving and replicating into ever more complex forms on their own initiative.

Leo Smith
Reply to  Louis Hunt
December 29, 2020 12:58 am

I think that comparing the pyramids – 3000 years old ± with the origin of life on earth 3.5 billion years ago is worthy of the straw man of the year award.

Over aeons, the chance of a random molecular coincidence creating something self replicating is massively more than expecting it to happen in a couple of millennia involving huge lumps of inorganic material.

How can non-living chemicals evolve?

The same way everything else does, What proves stable hangs around, What is unstable disappears, what is unstable but replicates, stays around.
You didn’t think the snow at the top of Mt Everest was the same snow it had on it 10,000 years ago?
And what is unstable yet manages to self replicate, we call ‘Life’.
I can create an inorganic self replicating data pattern in a computer. Crystal structures grow and self replicate in conducive solutions.
Nothing special about DNA and RNA self replicating given enough time, and there was about a billion years of earthly existence before life did begin (according to the rational materialist narrative) .

You may argue against that narrative (and I would) , but please do so from a rational perspective.

Hum
Reply to  Leo Smith
December 29, 2020 4:22 am

The odds of a even small protein of 150 amino acids forming is 10 to the 164th power. I think a pyramid forming by chance may be much less than that as a pyramid can use all the same kind of rocks instead of a one in 20 chance the correct amino acid, and a 1 in 2 chance that is a left handed amino acid, and a 1 in 2 chance that the bond is a peptide bond.

John Tillman
Reply to  Hum
December 29, 2020 6:23 am

Proteins that long don’t form randomly in a solution of purely amino acids. But that’s not how biological polypeptides originated.

Oligomers (short chains) of amino acids, ie peptides, form naturally. Other factors in the solution enable continued bonding to achieve polymerization. In biology today, such catalysts are enzymes. In prebiotic chemistry, as shown by this research, other organic compounds, as well possibly as some minerals, facilitated polymerization.

In the case of RNA, PAHs have been shown to promote long chain formation, for instanc.

Origin of life research in this century has shown the importance of focussing not just on RNA itself, but the other chemical compounds which existed in the same concentrated solutions with nucleic acid oligomers. This applies especially to peptides. The symbiotic association of amino and nucleic acids began before life as we now know it arose.

Tom Abbott
Reply to  John Tillman
December 29, 2020 7:29 am

I love it when you talk biology, John! 🙂

John Tillman
Reply to  Tom Abbott
December 29, 2020 7:48 am

Glad you like it!

I’m glad that WUWT welcomes posts on scientific topics besides climatology and its evil usurper “climate science”, ie GIGO computer gaming.

bonbon
Reply to  John Tillman
December 29, 2020 8:34 am

The entire DNA, RNA narrative is based on information theory, i.e. GIGO computer gaming.

Trying to find life with von Neumann’s and Wieners cybernetics, is exactly the reason climate has been taken over by models. And also economics.

John Tillman
Reply to  bonbon
December 29, 2020 9:06 am

How DNA and RNA assemble proteins is not based upon information theory, but observations of nature.

JamesD
Reply to  John Tillman
December 29, 2020 8:07 am

He’s not talking about how things polymerize. Go buy an epoxy kit, mix the two components, and you’ll get a nice polymer. He’s pointing out that the odds of just one useful protein forming randomly is 10^164. That’s greater than one in a google. For one protein. It’s a valid point.

John Tillman
Reply to  JamesD
December 29, 2020 8:41 am

No, it’s not the least bit valid, since it’s a totally unbiological assertion.

As noted, long proteins don’t form randomly. They form as a result of biological and prebiotic chemical reactions.

Short peptides do form spontaneously. Further chemical reactions, catalyzed in various ways, then link them together.

Nor does a protein have to be 150 amino acids long to be useful. The shortest functional “protein” (actually oligopeptide) today is glutathione, with only three amino acids. It’s an antioxidant produced in cells, comprised largely of glutamine, glycine and cysteine.

The field of small protein research is active today. Polypeptides with fewer than 100 amino acids are generally considered short proteins, but there is no formal definition. Proteins traditionally consist of 50 to 1000 AAs. Below that the most common usage is peptide. To me, however under several AAs would be an oligopeptide.

John Tillman
Reply to  John Tillman
December 29, 2020 9:12 am

His math and assumptions are also wrong. A protein could contain 150 of the same amino acid, rather than a mix of 21.

chemman
Reply to  John Tillman
December 29, 2020 12:14 pm

That is ignoring 3D structure big time.

John Tillman
Reply to  chemman
December 29, 2020 1:04 pm

Not at all. Three-D structure arises from folding. Proteins far smaller than 150 AAs can fold. And, as shown by glutathione, peptides don’t even need to be foldable to function.

John Tillman
Reply to  JamesD
December 29, 2020 9:08 am

Assembly of proteins from amino acids is polymerization, ie stitching monomers, ie amino acids, into long chains, ie polymers.

Hum
Reply to  John Tillman
December 29, 2020 6:13 pm

OK John, I should have said useful protein for biological entities, my bad. What useful protein do you know that is at least 150 amino acids made of the same amino acid? Name it. Thought so total BS. My math is wrong? Take (2 X 2 X 2) X (22 X 2 X 2) 150 times and tell me what you get? 22 may be a little conservative since there are more than 500 amino acids found in nature, with just 22 that are translational in biology. Oh and since there are over 300 proteins in the simplest cell and the number of amino acids per protein are usually much greater than 150 10^ 164 is not even close to how impossible random chance creation is. 10^50 is the threshold for mathematically impossible.

John Tillman
Reply to  Hum
December 29, 2020 6:25 pm

Your assumption of random assembly of a protein from 21 amino acids is completely unphysical, so why not a solution containing only one amino acid?

The point is that proteins are biological entities, assembled by biology, not in random solutions.

Your GIGO math is totally meaningless. Proteins are made in cells on ribosomes via DNA, mRNA and tRNA, which process has evolved.

Hum
Reply to  John Tillman
December 29, 2020 7:38 pm

And DNA and RNA are chemical information which is coded. It is not random information. A codon codes for amino acids to make a protein. If you think have the answer for how this information was coded then why don’t you write it up and win the 10 million dollar Royal Society prize?

Information and codes and communication does not happen from chemistry. All parts of a cell are needed for biology and life. There is a huge chicken and egg problem that Abiogenisis cannot solve.

Hum
Reply to  Hum
December 29, 2020 7:48 pm

I think Dr James Tour said it best with his analogy of abiogenesis and protocells.   Go out and buy turkey meat chop it up add turkey broth, put them in a container with energy input and throw in a few feathers and then given enough time(millions of years) a proto-turkey or extant turkey will come gobbling out.

bonbon
Reply to  Hum
December 30, 2020 3:55 am

LOL!
I did that for the holiday, but feathers?

John Tillman
Reply to  Hum
December 30, 2020 7:38 am

That is a truly inept, pointless attempt at an analogy.

Turkeys result from four billion years of evolution, which started with nucleic acids and proteins, not large multicellular eukaryotic organisms.

Fatty acids, RNA and peptides self-assemble spontaneously. Start with them, not with poultry in a blender.

John Tillman
Reply to  Hum
December 30, 2020 7:33 am

Abiogenesis is being explained right before your eyes. You just don’t want to look.

John Tillman
Reply to  Hum
December 31, 2020 11:16 am

As pointed out, a three-amino acid peptide is functional.

Long proteins don’t arise randomly. They’re made on ribosomes. But shorter peptides do form spontaneously.

Why is this hard to understand?

John Tillman
Reply to  Hum
December 31, 2020 2:12 pm

Your random creation straw man is so preposterous, that a protein consisting all of the most common amino acid is just as valid/ It’s not the composition that matters, but the length, controlling the folding or action.

Hence it doesn’t matter that there isn’t a functional protein all of one amino acid. You hypothetical is ridiculous, unphysical and unbiological on its face.

As noted, a peptide of three amin acids is functional. Further, longer proteins aren’t formed randomly. Thirdly, a 150 amino acid long protein all of one AA might well be functional. It would depend upon its shape when folded.

TheLastDemocrat
Reply to  Leo Smith
December 29, 2020 2:26 pm

“And what is unstable yet manages to self replicate, we call ‘Life’.”
Unless the topic is human reproduction; in that case, you must wait until after delivery to apply the term “life,” or you are a Q-Anon racist misogynist KKK bigot.

bonbon
Reply to  Louis Hunt
December 29, 2020 3:15 am

Very good image of Pyramids spontaneously rising out of sand!
So much of “modern” science, and especially economics relies on what von Hayek of the London School of Economics put it : “the greatest psychological trick “. Economics is supposed to spontaneously emerge from the unknowable complexity of trade.
Here we are supposed to follow exactly the same line, that life emerges spontaneously from an unknowable chemical complexity.
von Hayek praised Mandeville, of the Hell Fire Clubs, for the trick. Simply magic.

We have the hilarious situation of living researchers, peering at polymers, trying to identify life, never mind the mind!

Pasteur’s and Redi’s principle that life comes only from life sure gives chemists eye-strain!

John Tillman
Reply to  bonbon
December 29, 2020 6:24 am

Pasteur wasn’t working with prebiotic chemical compounds but with modern organisms.

bonbon
Reply to  John Tillman
December 29, 2020 8:55 am

Anybody check the chirality of the Author’s “prebiotic” compounds?

John Tillman
Reply to  bonbon
December 29, 2020 9:29 am

Chirality doesn’t matter for the reaction described by the authors. DAP isn’t an amino or nucleic acid.

chemman
Reply to  bonbon
December 29, 2020 12:16 pm

They acknowledge that what they found were racemic mixtures.

John Tillman
Reply to  chemman
December 29, 2020 1:05 pm

Yes. As would be expected on the early Earth. Just because amino and nucleic acids are chiral doesn’t mean that every biologically important compound is.

bonbon
Reply to  chemman
December 30, 2020 4:24 am

Did anyone check their optical activity? Being racemic, probably none. Yet the Pasteur observation is key.

If we push life’s molecules back further, close to the solar proto phase, was there a polarized plasma with something like syncrotron radiation? Could that imprint the entire evolution?
Likely the researchers did not check that in the lab – a fusion plasma would be necessary….
Yet again we leave the domain of armchair chemistry….

John Tillman
Reply to  Louis Hunt
December 29, 2020 6:14 am

Chemical evolution occurs naturally. Selection works in chemistry as in biology. Evolution doesn’t require death, just differential success, although less successful variants can and do eventually disappear. Higher reproduction rates for more successful traits in a population is comparable to increases in chemical compounds with favorable characterixtics under varying conditions.

For example, more heat tolerant chemical species will increase in a solution being warmed. In that environment they are fitter.

Evolution doesn’t violate any entropic physical laws. Indeed, life arises precisely because of thermodynamics and evolution is driven by it.

In his 1944 “What is Life?”, Austrian physicist Schrödinger argued that free energy differentiates life from other forms of the organization of matter. The principle that entropy can only increase or remain constant applies just to a closed system, which is adiabatically isolated, ie no heat can enter or leave it. The physical and chemical processes which make life possible do not occur in adiabatic isolation. Living systems are open. Whenever a system can exchange either heat or matter with its environment, an entropy decrease of that system is entirely compatible with the Second Law of Thermodynamics. Thus life does not in any way conflict with or invalidate this law.

JamesD
Reply to  John Tillman
December 29, 2020 8:00 am

Life is immaterial. It is a system containing information.

John Tillman
Reply to  JamesD
December 29, 2020 8:43 am

Life is more than its information system. That’s why viruses and other mobile genetic elements aren’t considered to be alive.

bonbon
Reply to  John Tillman
December 29, 2020 8:53 am

Exactly. Since Shannon information is based on entropy, then life, “more than its information system”, is anti-entropic, not simply Schrödinger’s local negative entropy.
Now it gets really interesting.

John Tillman
Reply to  bonbon
December 29, 2020 9:34 am

Biologists know how DNA and RNA work to make proteins. What presumed mystery do you find really interesting?

We also are learning how the genetic code evolved.

Please study biology. It’s based upon chemistry and physics, not information theory.

There is no single agreed-upon definition of life, but in general it requires replication, metabolism and the ability to evolve.

bonbon
Reply to  John Tillman
December 30, 2020 4:01 am

Like climate is based on physics, yet off go the modellers (information theory) producing utter hell.
The same happened to biology, codons, before climate.
And to cosmology, Hawking’s information paradox, before climate.
You mentioned “mystery”, I mentioned anti-entropy.

John Tillman
Reply to  JamesD
December 29, 2020 2:36 pm

Life is completely material. There is no life outside of physical reality, as far as science is concerned.

Afterlife or life preceding physics and chemistry is the realm of religion and metaphysics, not science, which seeks natural, not supernatural, explanations for observed phenomena.

bonbon
Reply to  John Tillman
December 30, 2020 4:05 am

Life’s organizing principle is the physical reality – it cannot be kicked, yet can be known, and known better.
Gravity’s organizing principle, which even Newton said cannot be spooky action at a distance, can be known, and known better. That is the lesson of Einstein’s tensor – it “tricks” the mind out of old paradigm traps.

John Tillman
Reply to  JamesD
January 2, 2021 2:35 pm

The ever-evolving information system arose via chemical evolution, with prebiotic enzymes. The first biological information library consisted of a single gene, ie protein-coding sequence,

By various methods, new info has been constantly added, such as, to name just a few biggies, photosynthesis, the capacity to use previously poisonous oxygen, the origin of nuclei, mitochondria and chloroplasts in eukaryotes, multicellularity, requiring signaling, lignin in land plants, the ability to break down lignin in fungi, eyes and many other novel structures in animals, etc.

Louis Hunt
Reply to  John Tillman
December 29, 2020 8:25 am

It doesn’t have to take billions of years to evolve something. It should only take the right conditions to occur. So, since you know so much about it, how about you create the right conditions to evolve life from non-life and answer the question once and for all. If you can’t produce the right conditions, then your knowledge is superficial, or perhaps only mere speculation. The processes of life are much more complicated than Darwin ever imagined.

John Tillman
Reply to  Louis Hunt
December 29, 2020 9:00 am

True, evolution occurs in every generation.

But the evolution of today’s enormous genomes took time. The first genome was much simpler.

Labs around the world are researching the origin of life. Their scientists expect discovery of at least one possible pathway from nearly alive replicants to living organisms within two decades. Some are more optimistic and forecast five years, or at least in the coming decade.

The fact that there is a continuum on the scale of “aliveness” between complex organic compounds and living cells shows that finding such a path is just a chemical engineering problem. IMO, some large DNA viruses should count as alive. Smaller replicant biological entities, not so much, even though they’re capable of evolution.

The progress in this century has been remarkable. Some origin of life workers late in the last century were ready to give up. The cellular membrane problem was solved by simple experiments in Nobel Prize winner Jack Szostak’s lab at Harvard and Mass General, for instance.

Still, it’s hard in a lab to recreate or create conditions likely existing on early Earth four billion years ago, or in outer space ten billion years ago, and run reactions comparable to those among compounds at trillions per second for possibly hundreds of millions of years.

OoL research might bear fruit before nuclear fusion, although that’s looking better now, too.

chemman
Reply to  John Tillman
December 29, 2020 12:21 pm

“IMO, some large DNA viruses should count as alive.”

Why? The size of malware doesn’t change it from malware

John Tillman
Reply to  chemman
December 29, 2020 1:08 pm

Because it’s not just the size. It’s because they retain vestiges of metabolism genes, strongly suggesting that they descend from degenerate prokaryotes. Parasites tend to lose genes. Ancient parasite would have lost a great many. Hence, large DNA viruses are best explained as ancient bacterial parasites.

RNA viruses are a very different kettle of replicants.

John Tillman
Reply to  John Tillman
December 31, 2020 1:09 pm

Proposal for fourth domain of life from the discoverer of megaviruses:

https://www.the-scientist.com/features/viruses-reconsidered-37867

Megaviruses lack ribosomes, but have tricks up their membranes akin to recognized microbes.

bonbon
Reply to  John Tillman
December 30, 2020 4:15 am

Never forget, when pursuing the particle paradigm, its paradoxes were only resolved by Planck, deBroglie, Schroedinger, Einstein.
Do not discount size, never assume a continuum.
Even Quasar red-shifts are stepped.

When the researcher’s trillions of cells, with their fabulous ordered mechanisms, all work together to run an experiment on organic molecules, and not wonder how that harmony is even possible, means there is a problem between the chalk and the blackboard.

John Tillman
Reply to  John Tillman
December 31, 2020 12:49 pm

Forecast of synthetic cell from scratch within a decade, which means eight years, since prediction was in 2018:

https://www.nature.com/articles/d41586-018-07289-x

Featuring the BaSyC program from the Netherlands.

dodgy geezer
December 29, 2020 12:19 am

This lab is making self-replicating molecules.

Making self-replicating ANYTHING is a very dangerous activity. I hope that they have suitable precautions in place.

Leo Smith
Reply to  dodgy geezer
December 29, 2020 1:00 am

Yet people are still having sex…

sycomputing
Reply to  Leo Smith
December 29, 2020 7:56 am

>Yet people are still having sex…

Good grief Leo, surely you jest? Otherwise you just took your own “strawman of the year” award back from Louis.

stinkerp
December 29, 2020 12:34 am

Still waiting for someone to demonstrate, or at least plausibly explain, how organic chemicals combined in some primordial pond in exactly the right ways to form complex cellular structures that self-replicate. Even if you mix up a soup of highly evolved human DNA in a vat, nothing happens. It doesn’t replicate. It’s not “alive”. In the absence of the cellular machinery that reads the DNA, snips it, and makes copies, it can do nothing. It’s just an inert string of information, like a computer disk with billions of bits of encoded information that accomplish nothing until they’re inserted into a highly organized and complex machine that can read them and do something useful with them.

Last edited 9 months ago by stinkerp
Reply to  stinkerp
December 29, 2020 3:06 am

First, you must clear your mind of the idea that DNA evolves/ed. DNA, or rather the (chrystalic) amino acids that constitutes the chrystal called DNA, is the same chrystal since it first formed. It is the more complex macroorganism that is built up of DNA that exhibits behaviour that is best explained on some levels (only) by a THEORY of evolution.
Now add the concept of sympathetic morphology, and self-replication can be replaced by just ‘replication’, and you get the starting point for complex life. Ever come across the work of Rupert Sheldrake? Morphic resonance gets rid of many questions left by ‘evolution’.

Last edited 9 months ago by paranoid goy
John Tillman
Reply to  paranoid goy
December 29, 2020 6:33 am

Evolution is a fact and a body of theory seeking to explain it, same as the theory of gravitation, although much better understood than gravity.

Of course DNA evolves. Humans are born with an average of four mutations, and accumulate more as we age. If in our reproductive cells, these too get passed on. If the mutations are favorable or neutral, they’re more likely to accumulate in our population. Same as in any population of reproducing organisms.

Evolution is a result of reproduction.

John Tillman
Reply to  paranoid goy
December 29, 2020 6:56 am

PS: DNA is not composed of amino acids but of linked nucleotides, ie a combo of a deoxyribose sugar, one of four nucleobases and a phosphate group.

Deoxyribose, as its name suggests, is a ribose sugar lacking on oxygen atom. This allows it to form its characteristic double helical shape.

Chains of amino acids are peptides. Long chains are polypeptides, ie proteins.

Hum
Reply to  John Tillman
December 29, 2020 8:41 am

Evolution and mutation has never been shown to add information. So how do you evolve to humans with the most complicated genome without increasing information. Pretty lame to claim evolution does it all. Micro-evolution plays a part, but no-one has ever seen macro-evolution that is needed for an ape to human transition.

Not buying what you are selling John.

I see a major paper on RNA-world was just recently retracted. Abiogenesis is going nowhere.

John Tillman
Reply to  Hum
December 29, 2020 9:43 am

Evolution and mutation have been observed adding information all the time. Who told you the lie that this doesn’t happen? It can’t not happen.

A single passing cosmic ray causes a simple point mutation, turning sugar-eating bacteria into nylon-eaters.

Just a few mutations permitted the alarming ballooning of human brains:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429600/

Please cite the retraction you mention. Thanks.

Whatever may have been the cause, no retraction can invalidate the enormous body of RNA evolution research.

John Tillman
Reply to  John Tillman
December 29, 2020 3:33 pm

For “lie”, please read, “ludicrous, preposterous, shameless lie”.

Thanks.

John Tillman
Reply to  Hum
December 30, 2020 9:02 am

Is this pack of lies from the mendacious Institute of Creation Research what you had in mind?

https://www.icr.org/article/rna-world-paper-retracted

For starters, ICR lies by falsely asserting that, researchers “have found nothing but obstacles including no method of spontaneously forming RNA or its nucleotide building blocks”. In fact, researchers have discovered that not just nucleotides, but short RNA chains form spontaneously.

Nor was using peptides to catalyze polymerization “cheating”. RNA and peptide existed together in the same concentrated solutions on early Earth. The RNA World hypothesis doesn’t necessarily require only RNA, just that it preceded DNA. Peptides might well have acted as protoenzymes, since they too self-assemble from amino acids.

Indeed the recognition that RNA was always surrounded by other organic compounds, molecules and elements has been a valuable insight in OoL research in this century. This doesn’t mean that RNA ribozymes didn’t also play a role in self-replication.

However it may well be that, as in the paper above, RNA and DNA developed together.

Reply to  John Tillman
December 29, 2020 11:40 am

Cudos on correcting me viz a viz neocleotides. However, cytocine, guanine, thymine and adenine have stayed the same through the ages, and does not evolve, therefore DNA does not evolve, the organism MAY evolve (theory), rearranging those building blocks differently, but the blocks themselves remain little more that organic chrystals.Crystals?
As soon as you find one of those “missing links” we can restart the discussion on the THEORY of evolution, whereas I can demonstrate gravity by dropping a brick on your toes. Just saying, I am not married to gravity either.
I see from your other comments that you are not an idiot, just oddly …err…attached?… to what you “know” is right? Your right.

John Tillman
Reply to  paranoid goy
December 29, 2020 12:02 pm

Evolution is a fact, not “just” a theory.

Nucelobases don’t evolve. Genomes do.

The relative number of nucleobases might evolve, but probably not much. What does evolve is the size of genomes, ie the amount of DNA in an organism, and the relative abundance of alternative forms of genes (protein-coding sequences) and changes in the composition of non-coding material.

Whole genome duplication is important in evolution, since it makes possible the development of innovations, as the original function of sequences is still covered. Such duplication was important in the evolution of us vertebrates and many other lineages.

John Tillman
Reply to  John Tillman
December 29, 2020 12:32 pm

Many organisms, including amoebas, have much larger genomes than humans, with our current estimate of 19,000 genes.

But at 16,000 genes for a large organism, that’s just 14 doublings from the original one gene, ie an average of about one doubling per 300 million years. In fact, doublings occurred more frequently early on.

Louis Hunt
Reply to  John Tillman
December 30, 2020 4:23 pm

‘Evolution is a fact, not “just” a theory.’

Doesn’t proof for a theory have to be independently reproducible before it can be considered a fact? Cold fusion could be considered a fact if there’s no need to be able to reproduce the original claim.

When have scientists been able to reproduce evolution in a species that resulted in a clear improvement to the species? Mutations occur in nature and in the lab, but when have these mutations resulted in evolution rather than devolution? A mutation or defect can sometimes help an organism survive, such as sickle-cell anemia warding off malaria. But the mutation is not superior overall and can cause other problems that are worse than malaria. When the risk of malaria is not present in the environment, natural selection tends to deselect the sickle-cell anemia mutation out of the population over time.

John Tillman
Reply to  paranoid goy
December 29, 2020 4:01 pm

First, please clear your mind of the creationist lies which you have swallowed, hook, line and sinker dur to lack of biological education.

Reply to  John Tillman
December 29, 2020 10:07 pm

I retract everything I said about you earlier…

bonbon
Reply to  stinkerp
December 29, 2020 3:28 am

As Leibniz noted there is a difference between our machines, the and even now, and natural machines : at any scale and resolution they are always further machines. And all these working in harmony.
Our machines are improving beyond limit, yet to observe what nature produces is jaw dropping.
“Computers”, machines, are incomplete as shown by Gödel, so is chemical logic . Meanwhile nature bucks that incompleteness.

John Tillman
Reply to  stinkerp
December 29, 2020 6:28 am

Modern DNA and RNA are the result of billions of years of evolution. The first cellular organisms probably had just one gene. Conditions in the prebiotic environment enabled RNA, DNA and proteins to begin interacting. There was probably a precellular stage with nucleic acid-peptide combos, leading to the genetic code.

Such combos are akin to viruses and ribosomes today.

Alan Robertson
Reply to  stinkerp
December 29, 2020 8:09 am

Ah yes, the old “organic chemicals combined in some primordial pond”.
A perusal of soil chemistry texts quickly acquaints one with the view that soil provides an easier route to necessary polymerization than can be found in standing pools of diluting solvents.

John Tillman
Reply to  Alan Robertson
December 29, 2020 9:58 am

Polymerization in wet-dry cycles of volcanic ponds has been demonstrated, and is supported by geological evidence:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931461/

The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

James
December 29, 2020 2:56 am

What? Discovery said ancient aliens seed life on Earth in a different special!

Bruce Cobb
December 29, 2020 3:56 am

Ah yes, the “chemical soup” theory of life. Confirmation bias much?

John Tillman
Reply to  Bruce Cobb
December 29, 2020 6:42 am

No confirmation bias. Just an interesting result for a chemistry experiment.

DAP is not the only prebiotic catalyst of nucleic acid polymerization. Peptides, PAHs and other organic compounds work, too, as well as may do minerals, wet/dry cycles and concentration in water pockets in ice.

That solutions containing many organic compounds existed on early Earth isn’t a theory. It’s an observation, ie a scientific fact.

https://www.pnas.org/content/pnas/early/2015/10/14/1517557112.full.pdf

https://www.nationalgeographic.com/science/2018/09/news-earth-rocks-sediment-first-life-zircon/

But even without such ancient evidence, we could be sure that Earth’s waters four billion years ago contained the precursors of life, since these compounds still arrive here on meteorites. And we can form them in labs, using abiotic chemistry, given a variety of alternative compositions and conditions of Hadean atmospheres and seas.

Michael Brown
Reply to  Bruce Cobb
December 29, 2020 7:54 am

This is how Wikipedia describes how DAP is manufactured:

“Diamidophosphate compounds can be made from phenyl diamidophosphate (phenylphosphorodiamidate) reacting with sodium hydroxide in a water solution.”

The author of the article claims that this compound was:

“plausibly present on Earth before life arose”

But if you read the original article you find the following statement:

In pursuit of activated prebiotic phosphorylating compounds, trimetaphosphate has long been considered as one of the promising and potential candidate for phosphorylation in aqueous medium, even though the availability of polyphosphates in the primitive earth is believed to be scarce.”

So if it was present at all it was scarce and if you keep reading you will find that trimetaphosphate is the inorganic form and what they actually need for their little experiment is the organic form, DAP. This is easily made by organisms that have enzymes but is not reported to have occurred in the natural environment:

“Kornberg and co-workers have also shown various examples of the enzymatic synthesis of inorganic phosphates and the use of enzymatically synthesized polyphosphates for the conversion of ADP to ATP, and has hypothesized about the role of polyphosphates in prebiotic chemistry.”

Now if you read Kornberg he says that poly phosphates haven’t been studied much previously because:

“Extractions to recover poly P from cells and tissues for standard assays have generally depended on strong acids or alkali. For enzymatic assays, the extracted poly P needs to have its chain ends available (freed from any complexes), enriched relative to inhibitors, and of a chain length of 20 or more residues to be an effective substrate.” 

In other words poly P is highly reactive (as is DAP being a form of poly P) and in the absence of highly complex biological enzymes not present in the primordial soup it can’t remain unreacted for any length of time. That is why poly P is only ever found in living organisms, never in nature, and why chemists have to work very hard to extract it in a useable format.

I’m going to call BS on their hypothesis until someone can explain how the poly P was freely available to form the DAP for their hypothetical “soup” without the use of enzymes that are only found in living things to catalyze a chemical reaction that doesn’t otherwise occur in nature…

Confirmation bias indeed!

John Tillman
Reply to  Michael Brown
December 29, 2020 9:25 am

DAP compounds are produced abiotically from phenylphosphorodiamidate reacting with sodium hydroxide in a water solution. Anhydrous sodium diamidophosphate polymerizes when heated to 160 degrees C.

It would have occurred naturally on the early Earth.

Michael Brown
Reply to  John Tillman
December 29, 2020 10:38 am

The problem is that you can’t have phenylphosphorodiamidate (or any poly P) outside of biological organisms for any length of time due to its high reactivity. Once you have purified DAP it might do what these guys claim but the precursor isn’t stable so the chemical chain falls apart.

John Tillman
Reply to  Michael Brown
December 29, 2020 10:45 am

Its disassociation begins as low as 70 degrees, and accelerates past 100 degrees, but then, as noted, DAP polymerizes at 160 degrees C, which form is stable.

So under 70 degrees, its salt is stable, and its polymer above 160 degrees. Water around hydrothermal vents or in volcanic ponds on land would fall within these ranges.

Michael Brown
Reply to  John Tillman
December 29, 2020 11:37 am

So what about all the side reactions that preferentially occur between 70 degrees and 160 degrees?

Hydrothermal vents aren’t sterile lab environments so side reactions that are chemically preferred would definitely occur first before the polymer could form.

Show me that phenylphosphorodiamidate can exist at those intermediate temperatures without undergoing some other side reactions with the compounds normally found in volcanically active areas and I might concede your point.

This would be easy to test as there are plenty of geothermal ponds around the world to try it out. I’ll even let you take along some NaOH to seed the polymerization reaction…

But of course everyone playing this shell game already knows that the reaction sequence won’t work in the real world so they don’t ever try to prove that it would.

John Tillman
Reply to  Michael Brown
December 29, 2020 11:46 am

Not knowing all compounds which might have occurred around oceanic hydrothermal vents or in terrestrial volcanic ponds, I can’t comment on side reactions. However the reactions with nucleosides would happen, since they were in the mix. Maybe side reactions scarfed up all the DAP before it could so react, but again, without knowing what else was around, that’s speculative, unlike the fact of DAP-RNA-DNA reactions.

The 160-degree polymerization probably wouldn’t take place in volcanic ponds, but OTOH, they rarely if ever get over 70 degrees, so DAP in them would not disassociate..

Under high pressure at deep sea vents, temperatures can go a lot higher than 160 degrees.

Do you have some side reactions in mind which might have short-circuited this process?

John Tillman
Reply to  John Tillman
December 29, 2020 11:49 am

PS: It just occurred to me that the late Hadean atmosphere might have been a lot denser than now, so maybe volcanic ponds could reach 160 degrees. Not that it really matters much.

Michael Brown
Reply to  John Tillman
December 29, 2020 11:59 am

In terms of the sulphuric acid that is normally present in water that originates in volcanoes of all kinds, whether terrestrial or undersea, I’d say that the NaOH hypothesis is pretty much dead on arrival. In an undersea scenario it would be quite impossible for NaOH to be present in the required concentrations necessary to form DAP due to dilution with sea water. This is why the biogenesis crowd abandoned hydrothermal vents and went to the RNA world and hot ponds in the first place. Of course that doesn’t work either, as the article above eloquently points out, so we are back to square one. Which is that these reaction sequences don’t, and can’t work in the real world.

John Tillman
Reply to  Michael Brown
December 29, 2020 12:50 pm

No such abandonment happened. RNA World (1962) predates the hydrothermal vent hypothesis (1977). It predates even the discovery of deep sea vents.

chemman
Reply to  John Tillman
December 29, 2020 12:30 pm

Were the oceans deep enough in that geological era to keep H2O in its liquid form at those temperatures?

John Tillman
Reply to  chemman
December 29, 2020 12:47 pm

Yes. Earth was more of a water world four billion years ago than now. Continents were rare.

Michael Brown
Reply to  John Tillman
December 29, 2020 1:41 pm

Hi John, you haven’t addressed the point that the presence of sea water prevents the concentrations of NaOH that are necessary from forming. Actually you haven’t addressed where you get the NaOH from at all. It doesn’t hang around in nature, and certainly not near volcanoes where it would be neutralized by sulphuric acid.

In regard to the vents a good starting point as to why they don’t work is this:

https://phys.org/news/2012-02-scientist-life-began-freshwater-pond.html

While this article from 2019 canvasses the dilution effect as well as covering other reasons why the oceans are hostile environments for life to form:

https://sciencebulletin.org/earliest-life-may-have-arisen-in-ponds-not-oceans/

So oceans can’t work chemically and 4 billion years ago there were no ponds…so it is not “plausible” that these reaction sequences can occur in the real world.

John Tillman
Reply to  Michael Brown
December 29, 2020 2:08 pm

I’m agnostic as between deep sea vents or volcanic pools on land. However, as Lane points out, the chemical problems with vents can be easily solved by countervailing chemistry.

https://ui.adsabs.harvard.edu/abs/2019AGUFM.B53L2566M/abstract

But whether in outer space, the ocean depths or in ponds on land, life clearly developed via chemical evolution from complex organic compounds. The first possible pathway to be demonstrated might not be how it actually happened on our planet or in space, but it will be proof of principle.

Michael Brown
Reply to  John Tillman
December 29, 2020 2:14 pm

Actually this is what Martinez et al actually said in their abstract:

“The available bacteria used was Vibrio, which cannot survive under anoxic conditions. Further tests will need to be conducted with microbes that can live under anoxic conditions in order to replicate early earth as accurately as possible.”

I don’t believe the paper you referenced proves anything one way or another. It is simply a proof of concept for a “deep sea vent in the lab” that could be used for further study, which they haven’t done yet. They freely admit that the conditions they used don’t simulate early earth conditions.

John Tillman
Reply to  Michael Brown
December 29, 2020 3:08 pm

Yes, genus Vibrio is anaerobic, which is entirely appropriate when discussing life on Earth before the Great Oxygen Catastrophe of the Proterozoic Eon.

Sorry, but I don’t get your point.

Michael Brown
Reply to  John Tillman
December 30, 2020 1:12 am

The author clearly states that Vibrio cannot survive under anoxic (anaerobic) conditions, ergo it is not an anaerobic bacteria, as you seem to believe. My point is that the paper you quoted from doesn’t support your argument in any way as the authors didn’t study early earth conditions. I’ll include the relevant quote again in case you missed it the first time:

“The available bacteria used was Vibrio, which cannot survive under anoxic conditions. Further tests will need to be conducted with microbes that can live under anoxic conditions in order to replicate early earth as accurately as possible.”

John Tillman
Reply to  Michael Brown
December 30, 2020 4:22 am

Genus Vibrio species are facultative anaerobes, so can survive in both the presence and absence of oxygen.

Michael Brown
Reply to  John Tillman
December 30, 2020 10:56 am

John, the author clearly states that the bacteria type they used cannot survive anaerobic conditions and does not represent an accurate model of early life conditions. Ergo the paper cannot be used to support the assertion that early life could evolve in deep hydrothermal vents.

Why can’t you just admit that you made an error and site another paper that supports your thesis so we can carry on the discussion. Or is that there are none and that is why you are so staunchly digging in on this point?

If you think that the authors are wrong on this point take it up with them. You are the one who sited this specific paper as making your case for you. I am simply pointing out the facts of the matter using the words of the actual authors from their own abstract.

The way you are arguing your points simply serves to underscore the degree of confirmation bias that this field of research is riddled with, hence my support of the original posters comments. Nothing you have presented here has swayed me from that opinion in the slightest.

You have also failed to provide a single example of anywhere on earth, at any time during the history of the earth, of where an aqueous solution of concentrated NaOH at 160 degrees could have existed in order to polymerize DAP. Since this reaction does not, and has not ever occurred in nature (absent complex biological enzymes) the chemists can’t use DAP in their attempts to explain the origins of life.

It seems a simple enough point to grasp and quite relevant to the original topic of this post.

bluecat57
December 29, 2020 6:01 am

Yet still doesn’t tell us where the rna and DNA came from originally. Must have just magically came from nothing.

John Tillman
Reply to  bluecat57
December 29, 2020 7:27 am

It shows another means by which prebiotic nucleosides could have polymerized and replicated.

Of course DNA and RNA don’t come from nothing. As should be obvious they come from nucleosides, which form spontaneously from simpler constituents, ie a sugar and a nucleobase. Nucleotides also self assemble via phosphate group links into short chains of RNA.

Nucleic acids consist of atoms of hydrogen, carbon, oxygen, nitrogen and phosphorus. The oxygen is in the five-carbon sugar (a carbohydrate), the nitrogen is in the nucleobase and obviously the phosphorus is in the phospahte group bonding the nucelosides into segments of RNA or DNA.

Oro showed in 1961 that the most important nucleobase, adenine (letter A in the genetic code), forms easily from the ubiquitous compound HCN (hydrogen cyanide) simply by heating. He also found that amino acids form readily in aqueous solution from HCN and the even more common compound NH3 (ammonia).

John Tillman
Reply to  John Tillman
December 29, 2020 7:36 am

Thanks to the Sutherland Lab at Cambridge, we now know how all five nucleobases form spontaneously (three of which are shared by RNA and DNA):

https://www.nature.com/articles/d41586-019-02622-4

RNA’s uracil is a demethylated form of DNA’s thymine.

chemman
Reply to  John Tillman
December 29, 2020 12:46 pm

“This paper has demonstrated marvellously the chemistry that needs to take place so you can make all the RNA nucleosides,” says Ramanarayanan Krishnamurthy, a chemist at Scripps Research in La Jolla, California. But he and other researchers often warn that this and similar results are based on hindsight and might not offer credible guidance as to how life actually evolved.”

John Tillman
Reply to  chemman
December 29, 2020 1:00 pm

That’s how science works. Here’s an hypothesis supported by esperimental confirmation of predictions made on its basis.

If you wanted received wisdom, revelation and certainty, please turn to religion.

John Tillman
Reply to  John Tillman
December 29, 2020 8:22 am

Oxygen of course is also in the phosphate group.

Phosphate groups also combine with the nucleobase adenine to form the cellular energy currencies ATP, ADP and cyclic AMP.

bluecat57
Reply to  John Tillman
December 29, 2020 1:19 pm

Nothing comes from nothing is my point. Until you identify the original source of the universe all this is is a guess.

John Tillman
Reply to  bluecat57
December 29, 2020 2:11 pm

Holy cow!

Now abiogenesis requires indetifying the source of the universe!

How about for the purposes of OoL research, that we just stipulate that spacetime exists and that matter and energy are among its properties. The laws of our universe obviously permit the origin of life, so let’s do the scientific thing and try to find out how that happened, without recourse to supernatural, ie non-scientific explanations.

bluecat57
Reply to  John Tillman
December 29, 2020 2:37 pm

Well, how did the “laws” come about? Materialism doesn’t have the answer. This RNA/DNA theory is a guess. Sure it “works”, but how does materialism explain the thought that allows discovery of it?

John Tillman
Reply to  bluecat57
December 29, 2020 3:00 pm

The origin of our universe’s laws is beyond the purview of origin of life research.

Maybe we just happen to inhabit a universe in which these laws apply, while other universes in a multiverse infinitude obey different laws.

It’s beside the point of scientific explanations for observations in our universe.

bluecat57
Reply to  John Tillman
December 30, 2020 5:25 am

Nice cop-out. Just dismiss what you don’t know and replace it with a premise you don’t know and can’t observe.

John Tillman
Reply to  bluecat57
December 30, 2020 2:55 pm

Which is exactly what antiscientific creationism does, not I.

bluecat57
Reply to  John Tillman
December 30, 2020 3:17 pm

You are a fool to simply try an ad hominem attack. I am fine with science, just not your fantasy that materialism answers all questions. You are the unscientific one.

StevenF
Reply to  bluecat57
December 29, 2020 10:50 pm

At that point, everything is a guess.

bluecat57
Reply to  StevenF
December 30, 2020 5:27 am

Yes. And since it is a guess you can make it whatever you want so your “science” appears to work until something causes science to be rethought. Aka wrong aka not a fact.

John Tillman
Reply to  bluecat57
December 30, 2020 4:28 am

Whatever is the opposite of materialism also has no explanation for the origin of the universe.

The speculation that there is an infinitude of universes with different laws is an explanation, but presently more metaphysical than scientific, since so far without convincing evidence, although some has been adduced.

But then, what caused such a multiverse?

bluecat57
Reply to  John Tillman
December 30, 2020 5:30 am

Well, if the opposite of materialism is Christian Creationism then it has an answer and you know that.
A multiverse solves nothing including origins. And you know that too but don’t want to admit it.

John Tillman
Reply to  bluecat57
December 30, 2020 7:49 am

The God hypothesis is not an answer. It explains nothing. Saying “God did it!,” is a punt.

A scientific explanation requires testable natural hypotheses capable of being shown false. The God hypothesis fails even to come close.

And that’s the way God wants it. If His existence were demonstrable, of what value would faith be?

bluecat57
Reply to  John Tillman
December 30, 2020 8:04 am

Yep, like you can “test” the origins of the universe. How exactly do you plan to either go back 14 billion years, or start an experiment and see how it turns out in 14 billion years.
Please, provide me with your outline of that testable natural hypothesis.
You got nothing, but won’t admit it.

John Tillman
Reply to  bluecat57
December 30, 2020 2:59 pm

Apparently you’re unaware that we can see back in time billions of years.

The greatest Christian theologians, including Augustine and Calvin, knew that biblical cosmology is clearly, obviously, plainly not literally true, even before Copernicus.

Christianity isn’t antiscientific belief in blatantly obviously not literally true biblical cosmology, but the Golden Rule.

bluecat57
Reply to  John Tillman
December 30, 2020 3:24 pm

We cannot “see” back billions of years. That is your premise.
As for the rest, huh?

John Tillman
Reply to  bluecat57
December 30, 2020 3:53 pm

We most certainly can sample Earth from four billion years ago.

https://www.nationalgeographic.com/science/2018/09/news-earth-rocks-sediment-first-life-zircon/

bluecat57
Reply to  John Tillman
December 30, 2020 4:52 pm

No you can not. You are simply guessing the age based on your assumptions.

John Tillman
Reply to  bluecat57
December 31, 2020 11:19 am

The age of zircons is measured. It’s not guessed.

bluecat57
Reply to  John Tillman
December 31, 2020 12:25 pm

Nope. You start with a presupposition and then date them. Explain Carbon 14 in diamonds. Explain the millions of years of structure we see in 20 years after Mt St. Helen. Explain why it doesn’t take millions of years to form oil and coal. Explain soft tissue in dinosaur bones. Your dating methods are faulty. You fit them to your presuppositions.

Greg
December 29, 2020 6:45 am

Well we’ll soon find out now we are injecting billions of humans with synthetic mRNA. Let’s see whether we can do it again and prove this hypothesis.

Last edited 9 months ago by Greg
StevenF
Reply to  Greg
December 29, 2020 10:54 pm

That’s just plain silly. It’s not synthetic mRNA. It is mRNA that is assembled in a lab rather than through DNA translation. It uses the same nucleotides except for uracil which was modified due to allergic reactions. When it is decomposed, it decomposes to the same component parts as regular mRNA. It isn’t a synthetic product like plastic or something.

And what’s the hypothesis we are trying to prove again?

DKR
December 29, 2020 6:56 am

Right, another chemical soup theory. Let’s see if it’s falsifiable

John Tillman
Reply to  DKR
December 29, 2020 7:11 am

It’s not a theory. It’s an experiment.

Hypotheses need to be falsifiable. Experiments have only to be repeatable.

This experiment confirms the hypothesis that other chemicals in the early Earth environment could have catalyzed nucleic acid polymerization. Nothing has falsified this hypothesis. It has repeatedly been confirmed.

bonbon
Reply to  John Tillman
December 29, 2020 9:42 am

This is a replay of Newton’s “Hypothesis non fingo” – I make no hypothesis. When in fact he himself did not believe in “spooky action at a distance” in absolute space, both actually hypotheses.
This from what Keynes correctly identified, Newton the last Magi, not a scientist.

So “other chemicals in the early Earth environment could have catalyzed nucleic acid polymerization” sounds unfalsifiable, when no hypothesis about life is actually stated.

Talk about poker!

John Tillman
Reply to  bonbon
December 29, 2020 3:45 pm

Not sure what Newton has to do with origin of life, but he did argue for instantaneous action at a distance, with his theory of gravity, shown false by Einstein/

Newton most dertainly did make hypotheses, contrary to his statement.

The hypothesis about life is indeed clearly stated, ie that it arose from prebiotic chemistry. This result supports that hypothesis. Nothing falsifies it.

bonbon
Reply to  John Tillman
December 30, 2020 4:36 am

“it arose from prebiotic chemistry” sure looks like alchemy, Newton’s speciality (no kidding, see Keynes) .
Life oozed from abiotic activity? Even Newton would call that spooky.

John Tillman
Reply to  bonbon
December 30, 2020 7:55 am

Abiogenesis is a scientific hypothesis which makes testable predictions capable of being shown false. So far, they’ve been confirmed.

As predicted, fatty, amino and nucleic acids have all been made from scratch in the lab, and found in meteorites. RNA and peptides self-assemble. One by one the milestones en route to life are being passed.

bonbon
December 29, 2020 8:23 am

Life arises “because of thermodynamics”? Run that horse by us again.
Schrödinger was unable to carry the DeBroglie resolution of the atomic paradoxes over to life, proposing a disappointing “local negation of entropy” to explain the obvious upward organizing principle characterizing both evolutionary progress and cognitive human advance.
Instead if the typical modern reductionist, well equipped, look at the development of the <b>Biosphere</b> over aeons.
Instead of that limp-wristed “negative entropy”, Vernadsky’s Biosphere and Noosphere both exhibit <b>anti-entropy</b>, uniquely distinct principles from the abiotic domain.
Like the difference between simple Lobatchevsky non-Euclidean geometry and Riemannian anti-Euclidean geometry (Einstein’s choice of domain).

I fully realize this discussion of living and nooetic physical principles will put reductionists into super-helical twists of rage.

John Tillman
Reply to  bonbon
December 29, 2020 10:07 am

Under the right conditions, life is probably inevitable. England didn’t originate this hypothesis, but his equations were original.

https://www.quantamagazine.org/first-support-for-a-physics-theory-of-life-20170726/

The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. His equations suggested that under certain conditions, groups of atoms will naturally restructure themselves so as to burn more and more energy, facilitating the incessant dispersal of energy and the rise of “entropy” or disorder in the universe. England said this restructuring effect, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. The existence of life is no mystery or lucky break, he told Quanta in 2014, but rather follows from general physical principles and “should be as unsurprising as rocks rolling downhill.”

bonbon
Reply to  John Tillman
December 30, 2020 5:40 am

It is worth perusing the many links at :
https://www.quantamagazine.org/tag/origins-of-life/

John Tillman
Reply to  bonbon
December 31, 2020 8:21 am

Thanks. Hadn’t seen the Krebs Cycle study, by a Scripps researcher co-author of the DAP paper.

Shows how easily metabolism could have gotten started.

John Tillman
Reply to  bonbon
December 29, 2020 10:54 am

Mods,

Would you please say why my comment on the inevitability of life thanks to the Second Law has been awaiting approval for so long?

Thanks.

I’d like to know what posting sins to avoid in future under the new format.

John Tillman
Reply to  John Tillman
December 29, 2020 11:34 am

Too many links?

Rud Istvan
December 29, 2020 8:36 am

Color me skeptical. The old ‘primordial pond’ doesn’t cut it, DAP or not.
There are a number of other fundamental issues. The only possible solution I am aware of is A.G. Cairns-Smith’s “clay hypothesis”. This is available in his 1500 page tome, or in his delightful 131 page paperback, ‘Seven Clues to the Origin of Life’. He sets up the boundary ‘life’ problems, then offers observational solutions. His answer for the very beginning of ‘life’ is kaolinite clays that change (orientation, solubility, packing) under inorganic chemical modification, evolving for ‘permanence’, then utilizing bits of organic molecules for better ‘permanence’, eventually utilizing simple RNAs. All the while the clay crystal was the all important vesicle of evolution.

Eventually life evolved organic membrane vesicles, at which point clay was at an evolutionary dead end.

bonbon
Reply to  Rud Istvan
December 29, 2020 9:34 am

Not sure if that author focuses on the size of these vesicles.
Have a look at Chapter 8.5 of Hiley’s Undivided Universe, with lots of QM.
Quote :
“Even if such objects are suspended in liquids or gases, the possibilities of interference will be limited because their mobilities are so low. It is clear thatthere will be an interesting area of study in the mesoscopic range, between the classical and quantum domains. It is perhaps significant that in this range the simplest forms of life are to be found.”

It worries me he uses Sherlock Holmes’ method – he never found Moriarty. Perhaps Sherlock never heard of Quantum Potential….

John Tillman
Reply to  Rud Istvan
December 29, 2020 9:48 am

The short answer is that, after 54 years, there is still no evidence supporting his hypothesis. Meanwhile great strides have been made in prebiotic enzyme research.

http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old#:~:text=In%20a%20sense%2C%20physical%20flaws,%2Das%2Dgenes%20hypothesis%22.

John Tillman
Reply to  John Tillman
December 29, 2020 10:51 am

In addition to simple enzymes, ie prebioti chemical catalysts, other chemical and physical processes besides assembly on clays have also been shown to work.

John Tillman
Reply to  John Tillman
December 31, 2020 12:20 pm

I should say his baseless conjecture, or idle speculation, since to qualify as an hypothesis, the guess has to make testable predictions capable of being shown false.

Scarface
December 29, 2020 11:01 am

And how did all this end up in a cell?

John Tillman
Reply to  Scarface
December 29, 2020 11:13 am

Polymerization of nucleic acids predates cells or even protocells.

Scarface
Reply to  John Tillman
December 30, 2020 3:06 pm

That’s exactly my question: so after the polymerization of nucleic acids the cell was formed, but from what? Or because of what? Did the dna just write the instructions itself to do so?

John Tillman
Reply to  Scarface
December 30, 2020 3:58 pm

No. As Nobel Laureate Shostak’s Harvard/Mass General lab has shown, lipid vessicles encapsulated RNA and protein complexes in the first protocells, which can split simply by agitation.

Scarface
Reply to  John Tillman
December 31, 2020 2:45 am

Thank you. But I keep on wondering how all life we see and fossils we find just formed by chance, and all of this from the accidental creation of protocells with accidentally created rna. If all this is just so easy, life should be abbundant in the universe. But my guess is that we’re alone. And since we know nothing beyond what we can see, I am skeptical of life just starting from nothing.

John Tillman
Reply to  Scarface
December 31, 2020 11:25 am

Life probably is abundant, but whether it is or isn’t, there is no need to imagine supernatural intervention. Natural processes explain its origin. At present there too many from which to chose, but pathways are being narrowed down.

It’s wrong to think of abiogenesis and subsequent evolution as random. Life arose and has evolved because chemistry and physics favor it under terrestrial conditions. RNA, peptides, fatty acids and other bio molecules form spontaneously.

John Tillman
Reply to  John Tillman
December 31, 2020 11:27 am

They also form in outer space, which is why at least microbial life is liable to be common in the universe. Multicellular life might be rare.

James Donald Bailey
December 29, 2020 12:15 pm

an interesting advance in understanding, but we are still way short of understanding. too many ‘and then a miracle happened’ events yet to be explained.

put in another perspective, we have now identified the trillions(?) of monkeys, DAP, banging on typewriters, assembling random chains of molecules. but how many works of shakespeare, strands coded to instruct other molecules to perform cellular functions, does it take before a cell is actually formed? and works? and replicates itself?

serious chicken and egg dilemma. do cells form and then develop the operations to function, or do the operations for cells to function develop randomly and then somehow get gathered together to form a cell?

also, calling molecular reactions ‘life’ is a bit much. but it does imply purpose (or useful function) to random molecules randomly manipulating other random molecules.

weird thought, did viruses evolve before cells? a molecular ‘lifeform’ that hijacks other molecular ‘lifeforms’ for reproduction? then as their targets get protected in cells, a cellular attack is ‘evolved’?

kind of fun though. there are scifi stories centered around robot probes being sent out to investigate the universe. just think, the universe ‘invented’ little robot probes to struggle in the oceans out of which people evolved to imagine robot life struggling to exist in a sea of stars.

John Tillman
Reply to  James Donald Bailey
December 29, 2020 12:57 pm

There is indeed a school of thought arguing for virus-like replicants before cellular organisms. It is a school to which I belong.

But beyond the scope of comments on this topic.

StevenF
Reply to  James Donald Bailey
December 29, 2020 11:19 pm

The problem with the analogy of monkeys at a typewriter is that the combinations of keys that are hit are random or at least semi random or maybe just simian random. What instead, if rather than hitting a key that typed a letter, the key typed a standard word of circa 1500 AD English. And what if nonsensical combinations of words were excluded (not in meaning but in grammar). In that situation, it is quite likely that trillions of monkeys banging on these keyboards for a billion years (a really long time) would have come up with the works of Shakespeare. Probably quicker than you would expect.

Now is that a reasonable idea. When it comes to how organic molecules interact, yes. They way they come together is not totally random. If it were, biological processes would not occur. Nucleotides self assemble. It’s like hitting a key and you get a fully formed word. Nucleotides also just don’t connect randomly. Adenine only bonds with thymine. Cytosine only bonds with guanine. They self assemble and then only bond with certain molecules. This process is true for many organic chemicals. Much of organic chemistry relies on this self assembly. Enzymes usually just speed up the process and make it more efficient. So it is much like the monkey analogy with the modifications listed above.

December 29, 2020 12:23 pm

A German group recently did a big gene analysis of all 5 of the kingdoms of life – plants, animals, fungi, archaean bacteria and prokaryote bacteria. They looked for genes shared by all 5 indicating that those would be the most ancient species genes likely possessed by the LCA – the last common ancestor of all life.

What they found suggested that the first life arose in hydrothermal vents at the sea bed.

https://youtu.be/pk213XSSktQ

So the first energy source could have been sulphur and exotic metals rather than oxygen. The first life would have to be anaerobic in any case since an oxygen atmosphere appeared only 2.8 billion years ago.

Last edited 9 months ago by Phil Salmon
Reply to  Phil Salmon
December 29, 2020 12:27 pm

John Tillman
Its disassociation begins as low as 70 degrees, and accelerates past 100 degrees, but then, as noted, DAP polymerizes at 160 degrees C, which form is stable.

So under 70 degrees, its salt is stable, and its polymer above 160 degrees. Water around hydrothermal vents or in volcanic ponds on land would fall within these ranges.

So the DAP evidence and the genetic hydrothermal vent origin evidence mutually support each other?

John Tillman
Reply to  Phil Salmon
December 29, 2020 12:55 pm

It would appear so.

Both the terrestrial volcanic pool and deep sea alkaline vent hypotheses have points pro and con, but IMO preserved biochemistry favors deep Hell rather than milder surface Heaven.

Reply to  Phil Salmon
December 29, 2020 12:35 pm

Here’s a paper about LUCA’s physiology and implicated origin in hydrothermal vents

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007518

John Tillman
Reply to  Phil Salmon
December 29, 2020 1:13 pm

I hope people read it.

A lot of fun: four female authors before the last tag along Charlie male contributor.

The lady who first proposed hydrothermal vents as the incubators of life was an under-appreciated female Oregon State grad student who went on to a career far removed from OoL research.

John Tillman
Reply to  John Tillman
December 29, 2020 1:23 pm

Although she suggested the first found black smokers, rather than the later more likely white smoker alakaline vents.

Another female oceanographer was among the discoverers of deep sea vents:

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

Reply to  John Tillman
December 29, 2020 2:16 pm

So could we have another Lyn Margulis?

John Tillman
Reply to  Phil Salmon
December 29, 2020 2:33 pm

I hope only in her initial rebellion promoting the endosymbiotic origin of mitochondria, and not the later whackinesses.

bonbon
Reply to  John Tillman
December 30, 2020 4:59 am

The later stuff being Gaia and Lovelock?
Well, look at the wackiness of the latest Papal Encyclical Laudato Si – it is a paean to Gaia from Dr. Schellnhuber, the be-knighted de-carbonizer.
Looks like there is a wackiness pandemic…

Reply to  John Tillman
December 29, 2020 11:29 pm

Yes I was thinking of her discovery of endsymbiosis – that metabolising objects inside cells such as mitochondria and chloroplasts were derived from original bacteria that became symbionts (not the later stuff).
This made her one of the relatively few women to have made important scientific discoveries.
Along with for instance Cecilia Payne-Gaposchkin who discovered that the sun was made of hydrogen-helium, and not a ball of rock like the men were insisting.

John Tillman
Reply to  Phil Salmon
December 30, 2020 4:33 am

Margulis however didn’t originate the idea of endosymbiosis. She revived it and was savaged by the then consensus crowd. But now appears to have been right.

Reply to  John Tillman
December 30, 2020 6:01 am

“Appears to be right” is rather weak. Darwin also “appears to have been right” don’t you think? Genetic evidence makes it clear beyond all rational doubt that she was right about endosymbiosis. It was entrenched and somewhat sexist opposition to her theory that drove her to the contrarian wing of science. Opposition to her endosymbiosis proposal is in the same category as the establishment telling Cecilia Payne “no no dear girl the sun can’t be made of hydrogen, we chaps know better that it’s a ball of rock just like earth”. Not to mention Wegener’s continental drift, opposed for half a century even though a 4 year old child could see that parts of the coasts of west Africa and South America fitted like jigsaw puzzle pieces.

Sorry but the academic establishment have always been dumb a55holes and always will be dumb a55holes.

John Tillman
Reply to  Phil Salmon
December 30, 2020 8:02 am

Please see my WUWT post about recent discovery of archaean-bacterial endosymbiosis by Japanese scientists, akin to the origin of mitochondria.

Yes, I think she was right, but there are still doubters, at least as to how the endosymbiosis occurred.

Chloroplasts were apparently engulfed twice, once directly as cyanobacteria and again as algae.

John Tillman
Reply to  John Tillman
December 30, 2020 8:34 am
John Tillman
Reply to  Phil Salmon
December 29, 2020 1:18 pm

Nick Lane has long advocated this route on bioenergetic bases:

http://www.sci-news.com/biology/life-hydrothermal-vents-07772.html

December 29, 2020 7:34 pm

Very interesting from a theoretical perspective. For the circumstances for Earth’s evolution I currently prefer the theorizing by British Astronomer Sir Fred Hoyle. Among his observations is that the double helix structure of DNA is ideal for it to be pushed by sunlight.

Hoyle, F., 1981. Evolution From Space A theory of Cosmic Creationism, Harper & Row, New York

Hoyle, F., 1983. The Intelligent Universe; A New View of Creation and Evolution, Holt, Rinehart and Winston, New York.

Hoyle, F., 1984. From Grains to Bacteria, University College Cardiff Press, Great Britain.

Hoyle, F. and Wickramasinghe, C., 1987. LifeCloud; the Origin of Life In the Universe, Harper & Row, New York.

The Cambrian explosion of life then makes sense, me as a God like being would not visit each individual planet, just stand back from the Galaxy, load the shotgun with life, and fire.

John Tillman
Reply to  John MCCUTCHEON
December 30, 2020 4:42 am

The so-called Cambrian Explosion makes sense without recourse to Hoyle.

“Rapid” adaptive radiations occur after mass extinctions. There were for instance “explosions” after the end Permian, Triassic and Cretaceous mass extinction events.

The Cambrian followed the huge end Ediacaran extinction. Cambrian evolution was also driven by an arms race between sensor-equipped predators and their prey.

bonbon
Reply to  John MCCUTCHEON
December 30, 2020 4:52 am

Not sure if God is a card-carrying NRA member, concealed or otherwise….

Alex
December 30, 2020 2:32 am

When a self-replicating chemical is produced in a laboratory out of simple chemicals, that will be the result of human intelligence.

John Tillman
Reply to  Alex
December 30, 2020 4:36 am

Nope. Just chemistry.

Humans will just be setting up in a lab the conditions that existed in the Hadean. Or in outer space.

John Tillman
Reply to  Alex
December 30, 2020 4:46 am

Nor need the chemicals be all that simple. As noted, oligomers of RNA self-assemble, as do peptides from amino acids.

So the goals of OoL research are polymerization and replication, ie the separation of a duplicated nucleic acid strand. The result reported in this paper moves us closer to those goals.

bonbon
Reply to  Alex
December 30, 2020 4:50 am

Exactly, we of the nooetic principle, will surely master the biotic principle, even as now we dominate the biosphere.

Mark - Helsinki
December 30, 2020 5:40 am

“which was plausibly present on Earth before life arose”

The science media claim is based entirely on this ^

Interesting yes, actual evidence of what the headline says, not so much

Walter Sobchak
December 30, 2020 6:53 am

plausibly present on Earth before life arose,
could have chemically knitted togethe
possibility that DNA and its close chemical cousin RNA arose

Whatever you say boss.

John Tillman
Reply to  Walter Sobchak
December 30, 2020 8:44 am

It’s not speculation that DAP can mediate the joint polymerization of RNA and DNA. This team demonstrated that fact in the lab.

The previous prevailing view was that DNA evolved from RNA, by its sugar losing one O atom and replacing uracil with its methylated variant thymine, the pyrimidine nucleobase also known as 5-methyluracil. Two simple changes to produce a more stable information storage system.

But no reason why they couldn’t have polymerized at the same time. Surely five-carbon sugar deoxyribose existed simultaneously with ribose, as did uracil and 5-methyluracil.

One-ring pyrimidines (C, T, U) pair with two-ring purines (A, G) to connect DNA strands in a double helix.

John Tillman
Reply to  John Tillman
December 30, 2020 8:45 am

T in DNA; U in RNA. No U in DNA.

Matthew Schilling
December 30, 2020 9:09 am

The phrase “could have” appears in this article eight times. The article could have provided useful information if they had not been present. Those eight instances effect the value of this article the way a sprinkling of zeroes do in a set of numbers being multiplied by each other.

John Tillman
Reply to  Matthew Schilling
December 30, 2020 9:48 am

Science is always couched in such language.

The important point is that the team showed that DAP does catalyze a combo of RNA and DNA in the lab. Hence it could have done so on the early Earth as well.

That’s the take-away message.

John Tillman
Reply to  John Tillman
December 30, 2020 9:49 am

Real science, that is.

“Climate science” uses language more appropriate for religion.

December 30, 2020 1:01 pm

https://onlinelibrary.wiley.com/doi/10.1002/anie.202015910
Paywalled, but someone can probably find a preprint or other unencumbered copy.

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