Calilasseia: 78 Papers on Abiogenesis

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Re: Calilasseia: 78 Papers on Abiogenesis

#61  Postby hackenslash » Apr 12, 2010 3:33 pm

That's not necessarily true, actually. It may be that there is only one set of circumstances under which it could occur. Indeed, the range of initial conditions is probably quite narrow, given the fact that we haven't found them yet.
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Re: Calilasseia: 78 Papers on Abiogenesis

#62  Postby dinkum » Apr 12, 2010 3:37 pm

Rumraket wrote:Those 78 papers themselves constitute evidence. They don't present the whole picture, but they are evidence nonetheless. To say that you have no evidence is simply bullshit.

But when one hasn't actually read the said papers, one can technically say that one has no evidence. One need simply skim the titles, glean a common thread (the same sciency word in two titles), hit Wikipedia for ten minutes and quibble on vapid bullshit.
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Re: Calilasseia: 78 Papers on Abiogenesis

#63  Postby Rumraket » Apr 12, 2010 3:50 pm

hackenslash wrote:That's not necessarily true, actually. It may be that there is only one set of circumstances under which it could occur. Indeed, the range of initial conditions is probably quite narrow, given the fact that we haven't found them yet.


That's technically correct, but it would be extremely difficult to "prove" that abiogenesis could only occur in a certain way.
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Re: Calilasseia: 78 Papers on Abiogenesis

#64  Postby hackenslash » Apr 12, 2010 3:55 pm

Absolutely, and even given a set of circumstances under which abiogenesis could naturally occur, we could never be certain that that's how it did occur.
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Re: Calilasseia: 78 Papers on Abiogenesis

#65  Postby byofrcs » Apr 12, 2010 6:05 pm

I suspect that we'll find out at least one, if not more, probable and reproducible paths for abiogenesis before we get any sensible answers from any intelligent design advocates as to what the heck was God thinking when it designed the Sputnik virophage.
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Re: Calilasseia: 78 Papers on Abiogenesis

#66  Postby rainbow » Apr 13, 2010 7:33 am

Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.
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Re: Calilasseia: 78 Papers on Abiogenesis

#67  Postby byofrcs » Apr 13, 2010 7:43 am

rainbow wrote:
Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.


No, the same evidence that supports evolution supports abiogenesis too. If we did not find evidence for evolution then I think worrying about evidence for abiogenesis would be the least of our problems.
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Re: Calilasseia: 78 Papers on Abiogenesis

#68  Postby rainbow » Apr 13, 2010 7:46 am

byofrcs wrote:
rainbow wrote:
Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.


No, the same evidence that supports evolution supports abiogenesis too. If we did not find evidence for evolution then I think worrying about evidence for abiogenesis would be the least of our problems.

Wrong, you're making a common mistake of confusing the two.
Abiogenesis and Evolution are not the same, and would not be a result of the same mechamisms.

Please present some fossil evidence of Abiogenesis.
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Re: Calilasseia: 78 Papers on Abiogenesis

#69  Postby Darwinsbulldog » Apr 13, 2010 7:50 am

rainbow wrote:
Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.



Well, not quite. While it is true that there are no mineralized old bones or teeth to support abiogenesis, there is some molecular evidence that is suggestive. Not strong, I would agree, but not totally absent either. Abiogenesis has not been proven to be wrong. There seems nothing "irreducibly complex" about abiogensis in principle, even though we can't say exactly how it happened, at least not yet, and perhaps for ever.

Several researchers have suggested possible ways in which life got started, and have successfully eliminated others that seem very unlikely in any credible early-Earth scenario.

For example, there is no need to assume that photosynthesis was needed right at the start, as production of "foods" such as sugars, amino acids and the like can be produced abiotically. So photosynthesis right at the beginning is something we can discount as unnecessary. Likewise, oxygen is an electron acceptor now, but sulfur could have played that role in the beginning. Two of the 20 biologically active amino acids contain sulfur. And so we go on.......
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Re: Calilasseia: 78 Papers on Abiogenesis

#70  Postby Darwinsbulldog » Apr 13, 2010 8:10 am

Wrong, you're making a common mistake of confusing the two.
Abiogenesis and Evolution are not the same, and would not be a result of the same mechamisms.

Please present some fossil evidence of Abiogenesis.


Also wrong. Although the mechanisms for evolution and abiogenesis are not the same [as you correctly point out], there are somewhat similar.

Evolution is about mutations being selected or deselected by natural selection to change gene frequencies in a population due to the differential success of genes and gene combinations [and recombinations] in bodies where there is phenotypic expression.

Abiogenesis is thought to work by massively parallel chemical "experimentation" [subject to chemical laws] that give rise to a replicator. This replicator must have the ability to copy itself, and was probably auto-catalytic. In other words, some natural selective process [Not Natural Selection in the exact sense of evolution, as there were no genes in the beginning] ] was acting on variation in the chemical soup to produce that replicator. As I have already stated above, the chemical soup already possesses some of the nutrients and building blocks, so catabolism for example, would not have been necessary. One only needs some mistakes to happen when that replicator is copying itself to produce variation, and then we can have differential reproduction of the different forms or replicator to make improvements. Other stuff could be added later, and rudimentary cell membranes spontaneously form from lipids.

Certain metals, such as iron, zinc, copper, etc can catalyse certain reactions, and later some of these became chelated into proteins like hemoglobin and myoglobin.

Nope, at the very least abiogenesis is plausible, and although we have not dotted all the "I's" and crossed all the "T's", it is valid scientific investigation which may bear lots more intellectual fruit. Just because we may not get a total and complete answer to the "origin of life" riddle does not make the quest futile. Nor is the evidence totally lacking, as you would imagine. The point you may be trying to make is that if we can't prove abiogenesis by natural means, then we will have to default to a god-creator? If so, then that has it's own problems of evidentiary support, and I would suggest, that the lack of support for a creator-god is much more of a problem than a natural explanation for the origins of life.
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Re: Calilasseia: 78 Papers on Abiogenesis

#71  Postby byofrcs » Apr 13, 2010 8:16 am

rainbow wrote:
byofrcs wrote:
rainbow wrote:
Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.


No, the same evidence that supports evolution supports abiogenesis too. If we did not find evidence for evolution then I think worrying about evidence for abiogenesis would be the least of our problems.

Wrong, you're making a common mistake of confusing the two.
Abiogenesis and Evolution are not the same, and would not be a result of the same mechamisms.

Please present some fossil evidence of Abiogenesis.


...if you can tell me if viroids are "alive" or not. We assume to know what is alive and we assume to know what is not alive. It's deciding the bit in the middle that needs some cleaning up first.

I didn't say evolution was the same as abiogenesis. I said that the evidence of one supports the other. We *should* find the same mechanisms that we find with evolution all the way down to the first chemical reactions. At some arbitrary point we will stop calling it "Biology" and at some point we start to call this "Organic Chemistry". That gap is where abiogenesis resides. We are unlikely to find a god-of-gaps hiding in that transition area thus we should expect,

Organic Chemistry -> Biology

and not,

Organic Chemistry -> Theology -> Biology

or,

Organic Chemistry -> Aliens -> Biology
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Re: Calilasseia: 78 Papers on Abiogenesis

#72  Postby rainbow » Apr 13, 2010 8:35 am

Darwinsbulldog wrote:
The point you may be trying to make is that if we can't prove abiogenesis by natural means, then we will have to default to a god-creator? If so, then that has it's own problems of evidentiary support, and I would suggest, that the lack of support for a creator-god is much more of a problem than a natural explanation for the origins of life.

Strawman.
Let me remind you that this topic resides in the Science Section, under 'Chemistry'. If you wish to introduce 'creator-gods', please do so in the appropriate subforum.
Please produce the appropriate molecular evidence for Abiogenesis.
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Re: Calilasseia: 78 Papers on Abiogenesis

#73  Postby rainbow » Apr 13, 2010 8:38 am

dinkum wrote:
Rumraket wrote:Those 78 papers themselves constitute evidence. They don't present the whole picture, but they are evidence nonetheless. To say that you have no evidence is simply bullshit.

But when one hasn't actually read the said papers, one can technically say that one has no evidence. One need simply skim the titles, glean a common thread (the same sciency word in two titles), hit Wikipedia for ten minutes and quibble on vapid bullshit.

I suggest then that you read the papers.
When you've done so, please show us the particular piece of evidence for Abiogenesis that YOU consider to be particularly compelling.
Thanks.
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Re: Calilasseia: 78 Papers on Abiogenesis

#74  Postby rainbow » Apr 13, 2010 8:44 am

Darwinsbulldog wrote:
Wrong, you're making a common mistake of confusing the two.
Abiogenesis and Evolution are not the same, and would not be a result of the same mechamisms.

Please present some fossil evidence of Abiogenesis.


Also wrong. Although the mechanisms for evolution and abiogenesis are not the same [as you correctly point out], there are somewhat similar.

Evolution is about mutations being selected or deselected by natural selection to change gene frequencies in a population due to the differential success of genes and gene combinations [and recombinations] in bodies where there is phenotypic expression.

Abiogenesis is thought to work by massively parallel chemical "experimentation" [subject to chemical laws] that give rise to a replicator. This replicator must have the ability to copy itself, and was probably auto-catalytic. In other words, some natural selective process [Not Natural Selection in the exact sense of evolution, as there were no genes in the beginning] ] was acting on variation in the chemical soup to produce that replicator.

OK, lets stop here for a moment.
Up to the point where the Replicator was formed, there could not have been any selection. Please describe this Replicator.
What was it made of?
RNA?
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Re: Calilasseia: 78 Papers on Abiogenesis

#75  Postby Darwinsbulldog » Apr 13, 2010 9:08 am

rainbow wrote:

OK, lets stop here for a moment.
Up to the point where the Replicator was formed, there could not have been any selection. Please describe this Replicator.
What was it made of?
RNA?

To be honest, I am not sure. Some precursor of RNA perhaps. :ask: Chemicals self-select themselves all the time. Some abiotic reactions are auto-catalytic. In titration, suddenly the buffer solution can no longer hold back the change, and a tipping point is arrived at. The colour changes. My point is that there are all sorts of selectors and filters in nature that do not need life to happen.

How can pure water happen naturally? Evaporation! So light/heat from the sun makes water evaporate. When it evaporates from the salty sea, the salt is left behind, and it falls as pure [well almost] rain. The are natural catalysts that overcome the activation energy to make reactions occur at lower temperatures than they would normally. Nature is FULL of naturally selective filters. Why does a snowflake grow?

A human can make a solar still, and so can nature, as I explained with the rain. Nature abounds with information and filters. Nature has variations. Gradients of temperature, pressure, concentrations.

Of course, some natural algorithms are useless for life, but others are not.

So my point is all you need is variation and some natural selector. And time. Time for all the massively parallel, complex natural computations to occur.

It is the same in physics. Cosmologists say that the universe is uniform on the large scale. That is true. What matters is the natural "clumpyness" locally. A little higher local density in a gas cloud, and contraction. More contraction. And if there is enough gas eventually, a star.

If you have a star then you have a local energy/mass gradient. Some bits of gas and dust in the proto-star gas cloud formed planets. Ah an energy/mass gradiant! What is that? A local variation. Now you have a system which can "defy" the Second Law of Thermodynamics! [Of course it doesn't, as the input of sunlight on Earth is external to the earth System, while the star and the universe in general is running down].

So at every level, there is good cause to think that local variations can be acted upon by natural selectors of some sort. In fact, in the absence of a creator-god, then all these processes I have suggested, would have to arise naturally.
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Re: Calilasseia: 78 Papers on Abiogenesis

#76  Postby Rumraket » Apr 13, 2010 9:11 am

rainbow wrote:
Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.


You are setting an almost impossible standard. Whatever direct evidence of abiogenesis there was is surely lost now. I can't even begin to imagine the circumstances required to fossilize and preserve protocellular material for >3500 million years in the earth's ever changing crust.

Even if some kind of fossilised protocellular material exists in some obscure rocks somewhere, we might not even be able to identify them as that. How do you even get direct evidence for a chain of chemical events that old? It's not like there's going to be a fossilised schematic of the formose reaction laying around with a detailed summary of the circumstances wherein it happened.

Microoganisms don't fossilise that well(http://www.ucmp.berkeley.edu/bacteria/bacteriafr.html), they mostly leave behind some metal and mineral deposits in the shape of their "bodies", and may sometimes contain clues to membrane material.
http://www.biomedcentral.com/content/pdf/1741-7007-7-9.pdf
Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber
Background
A major problem for understanding the origin of life, microbial evolution and phylogeny is the lack of microbial fossils. It is especially evident when we consider the available well-preserved record of pluricellular organisms, animals and plants [1]. Microfossils are not only useful for elucidating biological macro- and microevolution but also the biogeochemical history of our planet. Amber is a fossilized resin originating from the trunk and roots of certain trees, particularly of the genera Agathis and Hymenaea. It acts as a natural embedding agent and it has properties similar to amorphous polymeric glass [2]. Amber consists of a complex mixture of terpenoid and/or phenolic compounds. The organisms that are embedded in it
are maintained in their three-dimensional form and their morphological features are preserved, making it possible
to compare them with their present-day descendants [3].
Trapping in amber is not the most frequent mechanism of preservation of biological systems, especially of the socalled
soft-bodied fossils (for example, nematodes and insects); mineralization as a result of both microbial and abiotic processes is the most common mechanism. Two main mechanisms of fossilization by mineralization are recognized: permineralization, which is the result of early infiltration and permeation of cells and/or tissues by mineral-charged water; and replication of morphology in authigenic minerals which are mainly a product of bacterial activity [4]. Mineralization in pyrite is called pyritization.
Pyrite is the most common sulphide mineral found in marine argillaceous sedimentary rocks, where it can occur in a variety of crystallographic and textural forms [5]. Pyritization is considered an important mode of preservation and/or fossilization in animals and plants, with or without a skeleton or cuticle [6-8]. Although little detailed work has been published on pyrite in fossils, three grades of biological preservation by pyritization have been recognized [5,9]: 1) permineralization, involving
pyrite precipitation in cellular cavities or cell walls made of poorly biodegradable components such as cellulose and chitin; 2) formation of mineral coats, which is usually involved in the preservation of very degradable biological components. These pyrite coats have a limited and clearly defined thickness; and 3) formation of mineral casts or moulds. This style of preservation causes the greatest degree of biological information loss, since only the fossil outline is preserved. The main difference between these three modes of preservation by pyritization is the extent of mineral precipitation.


The oldest clues we have are the stromatolites at abot 3,5 billion years and these themselves don't contain any direct clues to the constituents of whatever life it may have been, since all there is left are conical shaped microstructures.

http://www.fossilmuseum.net/Tree_of_Life/Stromatolites.htm#Warrawoona
Warrawoona Group in Western Australia - a scientific dispute
The putative stromatolites with microstructures resembling bacteria from the extensive stromatolitic formations of the 3,430-million-year-old Strelley Pool Chert within the Warrawoona Group in Western Australia have been hotly debated ever since their discovery by Lowe (1980, 1983). Lowe (1994) later ascribed conical form genera to abiotic evaporative precipitation, as did Grotzinger (1999), and Brasier (2002) also found no support for the microfossils as biomarkers. Whether microstructures within the Warrawoona Group stromatolites are the imprints of ancient filamentous and possibly photosynthetic microbes as argued by Schopf (1987, 1993) and Awramik (1992) became a heated debate that remains unresolved. A recent and extensive study of seven distinct stromatolitic form genera by Allwood (2006) certainly lends support to proponents of biogenetic origins of the chert, since the simultaneous set of forms is more difficult to explain with known abiogenic processes. However, whether the microstructures are fossil microbes remains unresolved. If they are microbe fossils, there would still remain the critical question of what type they are, archaea, cyanobacteria, another type of photosynthetic bacteria, chemosynthetic bacteria, or some combination of these.


The most recent paper I could find on the subject actually found *some* organic material leftover, but it was more or less unidentifiable:
Controls on development and diversity of Early Archean stromatolites (2009)
http://www.pnas.org/content/106/24/9548.full.pdf+html
The 3,450-million-year-old Strelley Pool Formation in Western
Australia contains a reef-like assembly of laminated sedimentary
accretion structures (stromatolites) that have macroscale characteristics
suggestive of biological influence. However, direct microscale
evidence of biology—namely, organic microbial remains
or biosedimentary fabrics—has to date eluded discovery in the
extensively-recrystallized rocks. Recently-identified outcrops with
relatively good textural preservation record microscale evidence of
primary sedimentary processes, including some that indicate probable
microbial mat formation. Furthermore, we find relict fabrics
and organic layers that covary with stromatolite morphology,
linking morphologic diversity to changes in sedimentation, seafloor
mineral precipitation, and inferred microbial mat development.
Thus, the most direct and compelling signatures of life in the
Strelley Pool Formation are those observed at the microscopic
scale. By examining spatiotemporal changes in microscale characteristics
it is possible not only to recognize the presence of
probable microbial mats during stromatolite development, but
also to infer aspects of the biological inputs to stromatolite
morphogenesis. The persistence of an inferred biological signal
through changing environmental circumstances and stromatolite
types indicates that benthic microbial populations adapted to
shifting environmental conditions in early oceans.

...

Genesis and Variability of Stromatolites
The existence of microbial mats during formation of stromatolites in the Strelley Pool Formation can be deduced from different sets of evidence in multiple stromatolite types. In domical stromatolites, evidence of microbial mat formation lies in the observation that cohesive layers of organic material formed at discrete, regular intervals at the surface of stromatolites, coupled with the fact that those laminae adhered to the steep stromatolite margins and did not preferentially thicken into topographic lows. In the coniform stromatolites,microbial activity is inferred from the juxtaposition of
contemporaneous but contrasting sedimentary fabrics and their arrangement within the context of stromatolite morphology. In both instances the interpretation benefits from comparisons with microbially-influenced microstructure in well-preserved Proterozoic stromatolites (25). Unfortunately, microfossils are not preserved because of redistribution of the organic material by neomorphic crystal growth during recrystallization. Biomarker preservation is possible but perhaps unlikely because of the thermal maturity of the organic matter (28).
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Re: Calilasseia: 78 Papers on Abiogenesis

#77  Postby rainbow » Apr 13, 2010 12:01 pm

byofrcs wrote:
rainbow wrote:
byofrcs wrote:
rainbow wrote:
Rumraket wrote:If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.

There is a great deal of fossil evidence to support Evolution.
There is EXACTLY ZERO fossil evidence to support Abiogenesis.
Therefore you are wrong.


No, the same evidence that supports evolution supports abiogenesis too. If we did not find evidence for evolution then I think worrying about evidence for abiogenesis would be the least of our problems.

Wrong, you're making a common mistake of confusing the two.
Abiogenesis and Evolution are not the same, and would not be a result of the same mechamisms.

Please present some fossil evidence of Abiogenesis.


...if you can tell me if viroids are "alive" or not. We assume to know what is alive and we assume to know what is not alive. It's deciding the bit in the middle that needs some cleaning up first.


If you wish to open a thread on the definition of life, then perhaps we can discuss it.
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Re: Calilasseia: 78 Papers on Abiogenesis

#78  Postby rainbow » Apr 13, 2010 12:07 pm

Darwinsbulldog wrote:rainbow wrote:

OK, lets stop here for a moment.
Up to the point where the Replicator was formed, there could not have been any selection. Please describe this Replicator.
What was it made of?
RNA?

To be honest, I am not sure. Some precursor of RNA perhaps. :ask: Chemicals self-select themselves all the time. Some abiotic reactions are auto-catalytic. In titration, suddenly the buffer solution can no longer hold back the change, and a tipping point is arrived at. The colour changes. My point is that there are all sorts of selectors and filters in nature that do not need life to happen.


Perhaps not.
However, such Replicators aren't found anywhere in nature - outside of living systems.
We don't come across molecules which copy themselves, and evolve to more complex molecules - unless they were originally based on the chemistry of life.
Chemistry and Time alone don't seem to do it.
...or do you have evidence that they do?
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Re: Calilasseia: 78 Papers on Abiogenesis

#79  Postby rainbow » Apr 13, 2010 12:15 pm

Rumraket wrote:
You are setting an almost impossible standard. Whatever direct evidence of abiogenesis there was is surely lost now. I can't even begin to imagine the circumstances required to fossilize and preserve protocellular material for >3500 million years in the earth's ever changing crust.


Not 'almost'. It is impossible to find evidence that isn't there.
All the evidence that we have is for a Biotic Period, abeit a very early Biotic Period.
According to the Postulate, there was a period of 100-500 million years wherein life arose from the 'Prebiotic Soup' - but there is no evidence of the broth, not a noodle.
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Re: Calilasseia: 78 Papers on Abiogenesis

#80  Postby byofrcs » Apr 13, 2010 12:37 pm

rainbow wrote:
byofrcs wrote:
rainbow wrote:
byofrcs wrote:....

No, the same evidence that supports evolution supports abiogenesis too. If we did not find evidence for evolution then I think worrying about evidence for abiogenesis would be the least of our problems.

Wrong, you're making a common mistake of confusing the two.
Abiogenesis and Evolution are not the same, and would not be a result of the same mechamisms.

Please present some fossil evidence of Abiogenesis.


...if you can tell me if viroids are "alive" or not. We assume to know what is alive and we assume to know what is not alive. It's deciding the bit in the middle that needs some cleaning up first.


If you wish to open a thread on the definition of life, then perhaps we can discuss it.


I don't need to as I have my answer. I didn't know if you saw it as on the inanimate, or animate, side of matter. Unless you have a clear definition of what is inanimate then I fail to see how you can ask for fossil evidence of something that you do not know what it looks like to start with.

I do not see a need to differentiate between living and non-living other than as useful pigeon-holes to stick differently structured matter using as many arbitrary properties as we decide. Obviously creationists see a need to differentiate between the two as that is essential to their dogma.

When you are asking for "fossils" then you are asking for something from an undefined grey area of organic chemistry dating somewhere about 3.5 Billion years ago. The onus is on you to first identify which pigeon-hole that you want evidence for.
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