Progress in origin of life research - RNA world

[Paprika]

So why didn't you say so as opposed to writing

This explanation you have, but which you are very coy about - do you have anything to match, either theoretical or experimental?

I was curious how far you would try to push the red herring. Curiosity has since been satisfied: you show all signs all pushing as far as it can go to try to distract from what I've said. Admirable faith, but your debating tactics are questionable at best.

Not really.

Right. Continue ignoring what I've said and banging on the 'what alternative do you think happened' drum.

Do you think this kind of understanding was possible back in the 1950s:-

http://www.sciencedirect.com/science...67593114001264?

No, but I didn't say anything to the contrary.

Tell us all: what is so notable about the findings collated in this review paper? Or did you just pull out a random paper based on the abstract?

[rwatts]

I was curious how far you would try to push the red herring. Curiosity has since been satisfied: you show all signs all pushing as far as it can go to try to distract from what I've said. Admirable faith, but your debating tactics are questionable at best.

What I wrote and asked was this:-

So why didn't you say so as opposed to writing:-

"I may, or I may not. It is hardly relevant to the discussion, but I suppose you need the red herring to distract from the points I've made."?

So clearly you have nothing.

But we do have something - first the "impossible" synthesis of urea, followed a few hundred years later by Urey-Miller in the 1950s, and progress since then ...

No, but I didn't say anything to the contrary.

So, a bit of progress beyond U-M, do you think?

In the 1950s do you think the U-M experiment was capable of this:-

http://msb.embopress.org/content/10/4/725

And this scenario you are very coy about, is it capable of this level of sophistication as well? Can it match U-M even?

Or did you just pull out a random paper based on the abstract?

I just pulled it out randomly, based on the abstract.

Now tell me why you think that the 1950s U-M experiment was at this level of understanding such that the paper doesn't represent much beyond or in addition to U-M.

[shunyadragon]

I may, or I may not. It is hardly relevant to the discussion, but I suppose you need the red herring to distract from the points I've made.

It is more likely that you 'may not' since you have cited no 'scientific' sources to support your assertions. The points you claim to have made are not supported by anything of substance.

[shunyadragon]

I have not heard of that. But since then? It's been more than six decades since Miller-Urey. What has happened since then?

A great deal in the genetics research. What you describe as 'intensive research' is problematic. The ongoing research involving the genetics of abiogenesis is less then forty years old, and not even near as intensive is you exaggerate. They could really use more funding. Your demands the they should have more by now, lacks scientific understanding, as your cynicism indicates this negative view of science without support of citations.

The amount of different types of scenarios that OOL research throws up (these three papers alone cover cyanide catalysis in a specific environment, meteorite catalysis, DNA ligation) show that the scientists still have little if any definite idea about what actually happened, which is why they are exploring in many many different directions. The pathways suggested here require highly constrained conditions and only cover a small part of the large reaction cycle which would be needed for life to begin.

First, the required amount of the amino acids for pre-evolution to take place is 'miniscule.' Second the appropriate ideal environment for abiogenesis to take place is well known and widespread throughout most of the history of the earth, the vast mid-ocean spreading zones that circle the earth.

[Truthseeker]

If natural abiogenesis is highly unlikely but nevertheless much more likely than supernatural abiogenesis then it becomes much more plausible in comparison.

If "supernatural" includes the property of being simply unpredictable (like flipping a coin or throwing a pair of dice), the notion of likelihood does not apply to supernatural phenomena ("miracles") at all. Now, possibly human action is also supernatural, in that it is not predictable either--of course, up to a point, human action can be predicted, sometimes, but--well, consider how wrong people are, trying to predict closely the prices in the financial markets.

[rwatts]

If "supernatural" includes the property of being simply unpredictable (like flipping a coin or throwing a pair of dice), the notion of likelihood does not apply to supernatural phenomena ("miracles") at all.

Well flipping a coin does have a degree of predictability about it. I'd be much more prepared to gamble on the flip of a coin than a throw of a dice.

Besides, if certain posters are happy to provide me with guesses about the supernatural, then I'm happy to offer my own guesses in return.

[Paprika]

But we do have something - first the "impossible" synthesis of urea

Quite disingenuous since the synthesis of urea predated Darwin's Origin of Species and the widespread scientific consideration of the problem of abiogenesis. The synthesis of urea was an advance in chemistry in general and not OOL science which only was launched by Oparin decades later.

In the 1950s do you think the U-M experiment was capable of this:

What part of 'I didn't say no progress was made' is so hard to understand?

And this scenario you are very coy about, is it capable of this level of sophistication as well? Can it match U-M even?

That's hardly relevant to the appraisal of the various scenarios proposed.

I just pulled it out randomly, based on the abstract.

As I thought: you want to squabble over significance but you don't take the actual time to read the paper, merely elephant-hurling an entire review paper.

Now tell me why you think that the 1950s U-M experiment was at this level of understanding such that the paper doesn't represent much beyond or in addition to U-M.

You summarise it for me and tell me what is so significant about it that my judgment that not much significant progress has been made is wrong.

By forum rules I don't need to deal with your argument by weblinks; I have no reason to continue this silly conversation where you can keep hurling papers you haven't read - one after the other - to make some point you are unlikely to understand.

[Paprika]

It is more likely that you 'may not' since you have cited no 'scientific' sources to support your assertions.

I've actually quoted scientists and pointed to papers, which is much more than you have done. See below:

A great deal in the genetics research. What you describe as 'intensive research' is problematic. The ongoing research involving the genetics of abiogenesis is less then forty years old,

How is ‘genetics’ relevant since the topic is the chemistry research? Which, by the way, is more than 6 decades old.

First, the required amount of the amino acids for pre-evolution to take place is 'miniscule.'

Assertion without reference.

Second the appropriate ideal environment for abiogenesis to take place is well known and widespread throughout most of the history of the earth, the vast mid-ocean spreading zones that circle the earth.

Which is why scientists are still looking at other scenarios such as meteorites (rwatts paper 3) and streams and pools with high cyanide content (paper 1).

Also, another assertion without reference.

[rwatts]

Quite disingenuous ...

Not really. It was one of the discoveries which brought an end to vitalism.

What part of 'I didn't say no progress was made' is so hard to understand?

So there has been progress in OOL research since Urey-Miller.

Do you think U-M was able to demonstrate this:-

http://www.nature.com/nchem/journal/...chem.2155.html

?

Or is it progress?

If it's progress, then that makes it 3 or 4 papers (including one from you) which appear to constitute progress.


These naturalists, whether they are Christian or not, seem to be more prepared to put their ideas to the test that your side is.

[Paprika]

Not really. It was one of the discoveries which brought an end to vitalism.

As I said, an advance in chemistry in general and not OOL science which postdated it.

So there has been progress in OOL research since Urey-Miller.

DING-DING-DING.

He finally gets it. Someone give him a medal.

If it's progress, then that makes it 3 or 4 papers (including one from you) which appear to constitute progress.

Or maybe not. For the last time, what part of 'I didn't say no progress was made' is so hard to understand?

Or do you need a distraction so badly that you resort to burning so much straw?

These naturalists, whether they are Christian or not, seem to be more prepared to put their ideas to the test

Not at all. Rather, the naturalists are desperate to find support for what they think happened because the scientific understanding up to the present date still contradicts a crucial aspect of the naturalistic myth. So faith drives them on.

that your side is.

You don't even know what I believe, let alone what my 'side' is.

[rwatts]

As I said, an advance in chemistry in general and not OOL science which postdated it.

With the downfall of vitalism, chemistry moved squarely into the realm of the natural from which modern OOL takes its framework.

Of course, any remaining vitalists could behave as you and proffer that not much has happened since Urey-Miller, with the faint suggestion that there are alternatives, but its just that what these will not be revealed.

Or maybe not. For the last time, what part of 'I didn't say no progress was made' is so hard to understand?

Well the title of my thread is "Progress in origin of life research - RNA world"

You don't even know what I believe, let alone what my 'side' is.

Correct. After a faint hint that you might reveal your alternative, you then refused to do so. So I was left playing with my own guesses as opposed to yours. After refusing to tell me what you thought the chances of a non natural origin of life were, I guessed and told you that the chances of a natural origin were much, much greater than a non natural one. Given this, a natural origin is more plausible. Besides, the Christians and non Christians who explore a possible natural origin are at least game to reveal their cards and show you their experiments.


Anyway, do you think Urey-Miller explored this:-

http://www.ncbi.nlm.nih.gov/pubmed/21838407

?

Or do you think, like the other papers I've been presenting you, it represents progress?

[shunyadragon]

I've actually quoted scientists and pointed to papers, which is much more than you have done. See below:

NO, your references have not supported your unwarranted cynicism based on a religious agenda.

How is ‘genetics’ relevant since the topic is the chemistry research? Which, by the way, is more than 6 decades old.

The Chemistry of life is the genetic origins of RNA and DNA. Not more then 6 decades. DNA and RNA were not well defined and described until the 1950's. Don't confuse DNA/RNA research with the abiogenesis research based specifically on the origins of DNA/RNA that followed later.

The first research on the origins of DNA/RNA directly related to abiogenesis was in the 1970's.

Source: http://en.wikipedia.org/wiki/Abiogenesis#The_origin_of_the_terms_biogenesis_and_abiogenesis

In the early 1970s, Manfred Eigen and Peter Schuster examined the transient stages between the molecular chaos and a self-replicating hypercycle in a prebiotic soup.[113] In a hypercycle, the information storing system (possibly RNA) produces an enzyme, which catalyzes the formation of another information system, in sequence until the product of the last aids in the formation of the first information system. Mathematically treated, hypercycles could create quasispecies, which through natural selection entered into a form of Darwinian evolution. A boost to hypercycle theory was the discovery of ribozymes capable of catalyzing their own chemical reactions.

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Which is why scientists are still looking at other scenarios such as meteorites (rwatts paper 3) and streams and pools with high cyanide content (paper 1).

Also, another assertion without reference.

Scientists will always be looking for different environments, mechanisms and processes of origins of DNA/RNA. So what?

The issue of your assertion was the problem (scarcity? which is a bogus unsubstantiated claim) of the environment where these processes and mechanisms of origins can take place. The ocean ridge spreading regions have existed for most of the history of the earth, and considered a suitable environment for abiogenesis. Cyanide is present in the mid-ocean ridge environments suitable for abiogenesis.

Source: http://www.geochemicaltransactions.com/content/10/1/9

Hydrogen cyanide is an excellent organic reagent and is central to most of the reaction pathways leading to abiotic formation of simple organic compounds containing nitrogen, such as amino acids, purines and pyrimidines. Reduced carbon and nitrogen precursor compounds for the synthesis of HCN may be formed under off-axis hydrothermal conditions in oceanic lithosphere in the presence of native Fe and Ni and are adsorbed on authigenic layer silicates and zeolites. The native metals as well as the molecular hydrogen reducing CO2 to CO/CH4 and NO3-/NO2- to NH3/NH4+ are a result of serpentinization of mafic rocks. Oceanic plates are conveyor belts of reduced carbon and nitrogen compounds from the off-axis hydrothermal environments to the subduction zones, where compaction, dehydration, desiccation and diagenetic reactions affect the organic precursors. CO/CH4 and NH3/NH4+ in fluids distilled out of layer silicates and zeolites in the subducting plate at an early stage of subduction will react upon heating and form HCN, which is then available for further organic reactions to, for instance, carbohydrates, nucleosides or even nucleotides, under alkaline conditions in hydrated mantle rocks of the overriding plate. Convergent margins in the initial phase of subduction must, therefore, be considered the most potent sites for prebiotic reactions on Earth. This means that origin of life processes are, perhaps, only possible on planets where some kind of plate tectonics occur.

© Copyright Original Source

your references are selective and incomplete, and reflect a cynicism of science based on a religious agenda. Your Jorge smiley faces only reinforce the hyperbole ridiculousness of your argument.

[shunyadragon]

Source: http://www.geochemicaltransactions.com/content/10/1/9

Reduction of nitrogen compounds in oceanic basement and its implications for HCN formation and abiotic organic synthesis
Nils G Holm* and Anna Neubeck



The chemical reactions behind the formation of common metabolites in modern organisms could have formed spontaneously in the earth's early oceans, questioning the events thought to have led to the origin of life.

In new research funded by the Wellcome Trust, researchers at the University of Cambridge reconstructed the chemical make-up of the earth's earliest ocean in the laboratory. The team found the spontaneous occurrence of reaction sequences which in modern organisms enable the formation of molecules essential for the synthesis of metabolites such as amino acids, nucleic acids and lipids. These organic molecules are critical for the cellular metabolism seen in all living organisms.

The detection of one of the metabolites, ribose 5-phosphate, in the reaction mixtures is particularly noteworthy, as RNA precursors like this could in theory give rise to RNA molecules that encode information, catalyze chemical reactions and replicate.

It was previously assumed that the complex metabolic reaction sequences, known as metabolic pathways, occurring in modern cells were only possible due to the presence of enzymes. Enzymes are highly complex molecular machines that are thought to have come into existence during the evolution of modern organisms. However, the team's reconstruction reveals that metabolism-like reactions could have occurred naturally in our early oceans, before the first organisms evolved.

Almost 4 billion years ago life on Earth began in iron-rich oceans that dominated the surface of the planet. This was an oxygen-free world, pre-dating photosynthesis, when the redox state of iron was different and much more soluble to act as potential catalysts. In the Archean sea, iron, other metals and phosphate, facilitated a series of reactions which resemble the core of cellular metabolism occurring in the absence of enzymes.

© Copyright Original Source

More to follow . . .

[shunyadragon]

rwatts only cited the tip of the ice berg of the current research supporting abiogenesis.

Source: http://astrobiology.com/2014/04/reconstructed-ancient-ocean-reveals-secrets-about-the-origin-of-life.html

Reconstructed Ancient Ocean Reveals Secrets About the Origin of Life

Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
Markus A Keller, Alexandra V Turchyn, Markus Ralser

Researchers from the University of Cambridge have published details about how the first organisms on Earth could have become metabolically active.

The results, which are reported in the journal Molecular Systems Biology, permit scientists to speculate how primitive cells learned to synthesize their organic components - the molecules that form RNA, lipids and amino acids. The findings also suggest an order for the sequence of events that led to the origin of life.

A reconstruction of Earth's earliest ocean in the laboratory revealed the spontaneous occurrence of the chemical reactions used by modern cells to synthesize many of the crucial organic molecules of metabolism. Previously, it was assumed that these reactions were carried out in modern cells by metabolic enzymes, highly complex molecular machines that came into existence during the evolution of modern organisms.

Almost 4 billion years ago life on Earth began in iron-rich oceans that dominated the surface of the planet. An open question for scientists is when and how cellular metabolism, the network of chemical reactions necessary to produce nucleic acids, amino acids and lipids, the building blocks of life, appeared on the scene.

The observed chemical reactions occurred in the absence of enzymes but were made possible by the chemical molecules found in the Archean sea. Finding a series of reactions that resembles the "core of cellular metabolism" suggests that metabolism predates the origin of life. This implies that, at least initially, metabolism may not have been shaped by evolution but by molecules like RNA formed through the chemical conditions that prevailed in the earliest oceans.

"Our results demonstrate that the conditions and molecules found in the Earth's ancient oceans assisted and accelerated the interconversion of metabolites that in modern organisms make up glycolysis and the pentose-phosphate pathways, two of the essential and most centrally placed reaction cascades of metabolism," says Dr. Markus Ralser, Group Leader at the Department of Biochemistry at the University of Cambridge and the National Institute for Medical Research.

"In our reconstructed version of the ancient Archean ocean, these metabolic reactions were particularly sensitive to the presence of ferrous iron that helped catalyze many of the chemical reactions that we observed." From the analysis of early oceanic sediments, geoscientists such as Alexandra V. Turchyn from the Department of Earth Sciences at the University of Cambridge, one of the co-authors of the study, concluded that soluble forms of iron were one of the most frequently found molecules in the prebiotic oceans.

The scientists reconstructed the conditions of this prebiotic sea based on the composition of various early sediments described in the scientific literature. The different metabolites were incubated at high temperatures (50-90oC) similar to what might be expected close to a hydrothermal vent of an oceanic volcano, a temperature that would not support the activity of conventional protein enzymes. The chemical products were separated and analyzed by liquid chromatography tandem mass spectrometry.

© Copyright Original Source

[Paprika]

With the downfall of vitalism, chemistry moved squarely into the realm of the natural from which modern OOL takes its framework.

Your point being? Advance in chemistry in general does not necessarily translate into advance in OOL, though one would think otherwise from how you were trumpeting the synthesis of urea.

Of course, any remaining vitalists could behave as you and proffer that not much has happened since Urey-Miller, with the faint suggestion that there are alternatives, but its just that what these will not be revealed.

The synthesis of urea predated Miller-Urey.

Well the title of my thread is "Progress in origin of life research - RNA world"

Correct. After a faint hint that you might reveal your alternative, you then refused to do so. So I was left playing with my own guesses as opposed to yours. After refusing to tell me what you thought the chances of a non natural origin of life were, I guessed and told you that the chances of a natural origin were much, much greater than a non natural one. Given this, a natural origin is more plausible. Besides, the Christians and non Christians who explore a possible natural origin are at least game to reveal their cards and show you their experiments.

As you mention above, the topic is advance in research of the RNA world hypothesis - my own beliefs about how life first started are not pertinent to the topic.

Anyway, do you think Urey-Miller explored this:-

http://www.ncbi.nlm.nih.gov/pubmed/21838407

?

Or do you think, like the other papers I've been presenting you, it represents progress?

I have no desire to entertain any of your elephant-hurling, especially when I have not denied that progress has been made.

Read the paper yourself, and make your own summary here, and I might humour you.