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Author Topic:   On the Origin of Life and Falsifiability
kbertsche
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Message 31 of 108 (780240)
03-12-2016 7:52 PM
Reply to: Message 29 by ringo
03-12-2016 11:28 AM


Ringo writes:

Science is the process of going from data to conclusions.


All that you are decribing here is "data analysis". Science involves data analysis, of course, but so do many endeavors outside the world of science. Science is much more than just data analysis!

The opposite would be to start with the conclusion and try to find data to confirm it.

Science is actually somewhere between the two extremes that you have described. Science proceeds by abduction; it starts with one or more theories (which could be viewed as "potential conclusions") and collects data in an attempt to prove one or more of these theories false. Hopefully one theory will be verified and will be tentatively concluded to be correct.

That's exactly what creationism and its bastard child ID do, the opposite of science.

I agree that creationism and ID are not science, but not for the reasons that you have given.

"Science without religion is lame, religion without science is blind." – Albert Einstein

“I am very astonished that the scientific picture of the real world around me is very deficient. It gives us a lot of factual information, puts all of our experience in a magnificently consistent order, but it is ghastly silent about all and sundry that is really near to our heart, that really matters to us. It cannot tell us a word about red and blue, bitter and sweet, physical pain and physical delight; it knows nothing of beautiful and ugly, good or bad, God and eternity. Science sometimes pretends to answer questions in these domains, but the answers are very often so silly that we are not inclined to take them seriously.” – Erwin Schroedinger


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Genomicus
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Message 32 of 108 (780257)
03-13-2016 7:14 AM
Reply to: Message 11 by Dr Adequate
03-09-2016 10:04 AM


Well, not exactly, unless you can provide strong reasons to suspect that the initial "seed" population of microbes would be under strong selective pressure to lose these genes necessary for radiation protection.

On the contrary. Someone who wished to falsify the proposition that FUCA traveled through space, only by referring to evidence that LUCA would not have been able to, must show for certain that the requisite genes could not have lost between FUCA and LUCA --- over a period of time, and under conditions, of which we know nothing. He would have to demonstrate the existence of a strong, indeed inexorable, selective pressure to retain these genes under these unknown circumstances. Which hardly seems likely, since most bacteria don't have them.

You are somewhat mistaken when you say that "most bacteria don't have them." Here are a few proteins known to confer radiation resistance in microbes (Krisko and Radman, 2013, "Biology of Extreme Radiation Resistance: The Way of Deinococcus radiodurans"):

- Proteases
- Nucleases
- Phosphatases
- ATP-binding cassette transporters

You will note that most of these (or their homologs) are quite widespread among bacteria, as well as Archaea. You can confirm this with a BLAST search of the protein sequences under consideration or a look at the genomic literature on the subject.

This, then, significantly strengthens my argument that it is biologically unreasonable and unrealistic to argue that a FUCA -- equipped with a repertoire of efficient proteases, nucleases, phosphatases, and ABC transporters -- would lose these genes as a consequence of some as-of-yet undiscovered selective pressure.

Consider, for instance, ABC transporters -- which are present in all prokaryotic phyla. Under a lithopanspermia hypothesis, the initial microbial population would need ABC transporters in order to survive space transport. They would then arrive on Earth and diversify upon occupying various niches.

We can now muster a transition analysis argument of our own. It is inconceivable, and indeed improbable if we use the equations of population genetics, that a microbial population would (1) suffer a deletion of its ABC transporter parts without harming the reproductive fitness of the microbes under consideration, (2) have this phenotype spread not only throughout this microbial population, but throughout enough prokaryotes such that this phenotype would be present in the LUCA. I don't think T. Cavalier-Smith could come up with a more compelling transition analysis than this. So falsifying panspermia on the basis of the genetic repertoire of the LUCA makes a great deal of biological sense when you consider the above argument.


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Genomicus
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Joined: 02-15-2012
Member Rating: 4.7


Message 33 of 108 (780258)
03-13-2016 7:18 AM
Reply to: Message 12 by Dr Adequate
03-09-2016 10:06 AM


Well panspermia does admittedly remove a lot of steps. But only by leaving them behind on Planet X, where abiogenesis took place ...

...and where there is more time and more chemical resources for abiogenesis to take place, thus making it a questionable line of reasoning to argue that panspermia adds an unnecessary step, and that is the crux of the matter of whether panspermia is less parsimonious than the RNA world or metabolism first scenarios.


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Genomicus
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Message 34 of 108 (780259)
03-13-2016 7:21 AM
Reply to: Message 15 by Pressie
03-10-2016 7:16 AM


Pressie: Wut?
Umm, the theory of universal common descent is a fairly broad model, and it's perfectly falsifiable (Karl Popper argued otherwise, but I don't find his argument particularly compelling). Is it your position, then, that the broader a model is, the less falsifiable it needs to be?

The first forms of life, as we know it, all were forms of prokaryotes. You're most welcome to start digging, instead of writing stuff on the net.

Wut? How is your response here relevant to my quote above?


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Genomicus
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Member Rating: 4.7


Message 35 of 108 (780260)
03-13-2016 7:27 AM
Reply to: Message 20 by Pressie
03-10-2016 7:57 AM


Yes, it was. It doesn't matter how many words you use; how many sentences you put in, how many paragraphs you write down; how many essays you publish somewhere; how many books you write; ID still is the opposite of science.

That's largely contingent on how you're defining "ID," as that is a rather broad term with a variety of definitions. If, by "ID," you're referring to an ideologically inspired political-religious movement of the American right-wing, then you are correct. If by "ID," one is referring to a biological hypothesis like front-loaded evolution -- a modest extension of Francis Crick's direct panspermia hypothesis -- then it's science in the sense that it's testable and falsifiable. That doesn't mean it even approaches the kind of rigorous and pragmatic science that the Neo-Darwinian synthesis is.


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Genomicus
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Message 36 of 108 (780261)
03-13-2016 7:36 AM
Reply to: Message 18 by PaulK
03-10-2016 7:46 AM


The more possibilities encompassed by a model the less falsifiable it will be - in general.

I concur.

And yes, I argue that falsifiability is desirable but not a necessity. When we get down to detailed hypotheses it becomes far more necessary.

Okay. And do you think that, say, the RNA world model is sufficiently detailed to necessitate the possibility of falsification? If not, why?

If you're invoking extra-solar planets then I have to ask how you plausibly get life from there to Earth without making assumptions.

What kind of assumptions would be made?

Since panspermia doesn't address abiogenesis I'd suggest that steps in abiogenesis are off the table. You can't say that they are "extra" while just taking abiogenesis somewhere else for granted.

Well, panspermia does mean that biological life from which we descended did not originate on Earth. Abiogenesis -- that is current models like the RNA world scenario -- argues precisely the opposite. So panspermia implies that life necessarily evolved outside of Earth; this, then, increases the likelihood of life ever appearing on Earth, since evolution of biological life beyond Earth could be more chemically realistic.

And you concede that my original point was correct, since you can't say anything against it.

I'll address your original point (regarding falsification of abiogenesis models) in a response to Dr Adequate's "Second Problem" post.

So why is the panspermia hypothesis better at generating evidence of a historical nature in contrast to the RNA world and metabolism first models?

Hypotheses don't generate evidence.

You're right: hypotheses don't generate evidence. I didn't word that correctly. So let me re-phrase: why is the evidence for the panspermia hypothesis generally of a historical nature, in contrast to the RNA world and metabolism first models?

To return to the point, proposals that are never offered can't be rejected due to bias or any other reason. There's no use saying "spend more" with nothing to spend it on.

So am I correct in stating that you believe that pursuing panspermia research is a dead-end for pragmatic purposes?


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Genomicus
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Message 37 of 108 (780262)
03-13-2016 8:18 AM
Reply to: Message 22 by Dr Adequate
03-10-2016 10:46 AM


Re: Second Problem
I said your post had a number of problems. Here's another.
You say that the lithopanspermia model is falsifiable because if the work of Cavalier-Smith could be shored up and made more rigorous, then lithopanspermia would in fact have been falsified.

But why is that not also true of the RNA world hypothesis and the criticisms of Bernhardt, Kurland, and Harish & Caetano-Anollés? The two cases would seem to be on a par.

After all, if you really think that the RNA world is unfalsifiable, why are you citing these people at all? For the RNA world to be unfalsifiable, these criticisms would not merely have to be wrong, rather they'd have to be either (a) in principle and by their nature undemonstrable or (b) irrelevant even if they were right --- neither of which you have argued for.

This is an argument that has been levied several times, so I will address it here. "The two cases would seem to be on par," writes Dr Adequate, yet this glosses over this fundamental insight: that attempts to refute abiogenesis scenarios are based on arguments regarding the implausibility of these scenarios, whereas potential falsifications of panspermia are mainly arguments resting on historical reality. Let me break this down on a finer level.

Take, for instance, Kurland's "The RNA dreamtime," 2010. Here Charles Kurland's central argument is that:

"RNA coding is not a sine qua non for the accumulation of catalytic polypeptides. Thus, cellular proteins spontaneously fold into active structures that are resistant to proteolysis. The law of mass action suggests that binding domains are stabilized by specific interactions with their substrates. Random polypeptide synthesis in a prebiotic world has the potential to initially produce only a very small fraction of polypeptides that can fold spontaneously into catalytic domains. However, that fraction can be enriched by proteolytic activities that destroy the unfolded polypeptides and regenerate amino acids that can be recycled into polypeptides. In this open system scenario the stable domains that accumulate and the chemical environment in which they are accumulated are linked through self coding of polypeptide structure."

In other words, he argues that the origin of biologically functional polypeptides does not require RNA coding; therefore the RNA world is an unnecessary hypothesis, and an implausible one at that. There are several relevant points worth considering here:

1. Arguing against the necessity of a given model is not a viable approach to falsification of that model. Many criticisms of various abiogenesis scenarios are arguments about whether a particular model is necessary in light of another, purportedly superior model.

2. When it comes to abiogenesis, chemical arguments regarding the implausibility of certain steps isn't a particularly forceful means of potential falsification. This is because implausibility cannot be quantified in a realistic way. For example, authors may argue that the chemical synthesis of ribose is "difficult," but this only makes the model "difficult." It is not a falsification, because implausibility -- in itself -- is not falsification. You cannot say that "the conditions of primordial Earth were such that the probability of the chemical generation of ribose is 10^100" (as some creationists have done in scabrous fashion).

On the other hand, potential falsifications of panspermia can easily be historical in nature because they are molecular phylogenetic in nature. For example, Cavalier-Smith's transition analyses suggested a relatively primitive LUCA lacking HslV proteases. This is a historical argument; it is the argument that the LUCA in actual biological history lacked a certain category of proteases. And this argument can be assessed from the perspective of biological history with phylogenetic approaches. Potential falsification based on arguments rooted in history is much more powerful in this case than potential falsifications steeped in vague appeals to physico-chemical implausibility -- these aren't exactly compelling falsifications. The former are more powerful because they address historical questions with observations rooted in history.

Edited by Genomicus, : No reason given.


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Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 38 of 108 (780264)
03-13-2016 9:38 AM
Reply to: Message 23 by Blue Jay
03-10-2016 12:17 PM


Hey Blue Jay,

To me, this analogy holds perfectly true with these values inserted. The two evidences (x and a) address very similar questions about their respective proposed protobionts, don't they?

They both rely on a reasonable modern surrogate to examine the chemical/physiological shortcomings of their putative biotic progenitors.

Where they differ is in where their explanatory power comes from. I would argue that the phylogenetic falsification of the Panspermia hypothesis has more power from a historical perspective, but less power from a mechanistic perspective, than the biochemical falsification of the RNA World hypothesis.

I argue that where they differ is in the nature of a potential falsification. "Prokaryotes are vulnerable to cosmic rays, therefore for lithopanspermia to occur, any microbes arriving to Earth must have been resistant to radiation" is a statement that can be assessed through the lens of biological history using phylogenetic/bioinformatic approaches. On the other hand, it's much harder -- and I daresay impossible with present technology -- to falsify the RNA world model with the historical approach. One must then look to mechanistically falsifying the RNA world model, but this leads us to vague arguments that the RNA world is "implausible" or "difficult." Yes, a particular step in the RNA world model might be difficult, but does that mean it didn't happen?

And thus the supposed biochemical falsification of the RNA world is not a falsification in any meaningful sense.


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Dr Adequate
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Message 39 of 108 (780266)
03-13-2016 11:01 AM
Reply to: Message 37 by Genomicus
03-13-2016 8:18 AM


Re: Second Problem
This is an argument that has been levied several times, so I will address it here. "The two cases would seem to be on par," writes Dr Adequate, yet this glosses over this fundamental insight: that attempts to refute abiogenesis scenarios are based on arguments regarding the implausibility of these scenarios, whereas potential falsifications of panspermia are mainly arguments resting on historical reality.

But this distinction in how a proposition has been falsified makes no difference to whether a proposition has been falsified. I can, for example, perfectly well falsify the proposition "This elephant was in my house while I was out shopping" by observing that it's too big to fit through any of the doors. An argument that it's physically impossible is a splendid argument that it didn't happen.

Moreover, the argument against lithopanspermia requires its own implausibility argument --- besides requiring that LUCA (actually FUCA, as I have pointed out) should have certain genes, it also requires the proposition that FUCA couldn't have survived travelling through space without such genes. It requires one to say "X couldn't have happened, because chemistry". Take that away, and where's your argument against lithopanspermia? So why shouldn't "X couldn't have happened, because chemistry" be acceptable as a form of argument against the RNA world?


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PaulK
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Member Rating: 2.7


Message 40 of 108 (780267)
03-13-2016 11:04 AM
Reply to: Message 36 by Genomicus
03-13-2016 7:36 AM


quote:

Okay. And do you think that, say, the RNA world model is sufficiently detailed to necessitate the possibility of falsification? If not, why?

By my understanding the RNA World simply postulates that RNA-based replicators preceded DNA-based life. That is certainly general, and I would not expect it to be falsifiable (excepting effective falsification through the weight of problems) given the limitations of the evidence available (other than evidence that lead to it's formation. If, for instance, RNA replicators turned out to be impossible, as seems to have been widely assumed at one time the RNA World would have been clearly falsified.

quote:

What kind of assumptions would be made?

Why would you even ask? If you can show that life could get from any or all of the planets in your count to Earth without making additional assumptions please make the case. If you can't then you may as well concede the point. Asking me to concoct scenarios whereby it could happen seems to be an obvious diversion of no worth.

quote:

Well, panspermia does mean that biological life from which we descended did not originate on Earth. Abiogenesis -- that is current models like the RNA world scenario -- argues precisely the opposite. So panspermia implies that life necessarily evolved outside of Earth; this, then, increases the likelihood of life ever appearing on Earth, since evolution of biological life beyond Earth could be more chemically realistic.

And if you produce a scenario including abiogenesis that can be evaluated as a who,e we could do that. But until you do, the process of abiogenesis itself can't be compared, and therefore should remain off the table.

quote:

You're right: hypotheses don't generate evidence. I didn't word that correctly. So let me re-phrase: why is the evidence for the panspermia hypothesis generally of a historical nature, in contrast to the RNA world and metabolism first models?

That seems obvious. Panspermia leaves out the difficult problem of abiogenesis altogether. If you tried to include it you would find a mu he greater need for possibility-based work. For instance, trying to identify plausible settings where abiogenesis would be easier.

quote:

So am I correct in stating that you believe that pursuing panspermia research is a dead-end for pragmatic purposes?

Giving people money just because they favour a particular idea certainly seems to be a poor way of generating useful research. Do you disagree with that ?


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Dr Adequate
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Posts: 15921
Joined: 07-20-2006
Member Rating: 3.8


Message 41 of 108 (780270)
03-13-2016 11:14 AM
Reply to: Message 32 by Genomicus
03-13-2016 7:14 AM


You are somewhat mistaken when you say that "most bacteria don't have them."

You seemed, stop me if I'm wrong, to be suggesting that the bacteria in lithopanspermia would have required special extraordinary resistance to radiation to survive their space voyage; the sort of high radiation resistance found in (e.g.) Deinococcus radiodurans and B. subtilis. If you just meant that they need the genes for radiation resistance that bacteria usually have, then sure, I was wrong to say "most bacteria don't have them" but then on the other hand having such genes is not particularly indicative of survival in space.

So which way do you want to go with this?


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PaulK
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Posts: 12680
Joined: 01-10-2003
Member Rating: 2.7


Message 42 of 108 (780271)
03-13-2016 11:15 AM
Reply to: Message 37 by Genomicus
03-13-2016 8:18 AM


Re: Second Problem
Supposedly this post was going o address my points, but it doesn't seem to do so.

First, we have the obvious double standard of demanding that the RNA world and metabolism-first ideas be generally falsifiable while panspermia need only provide falsifiable scenarios. No general falsification for panspermia has been proposed.

Second my point that falsification of such general models effectively occurs when the problems become overwhelming has not really been answered. Following the Duhem-Quine thesis it is usually impossible to falsify general theories, since auxiliary hypotheses can be generated to protect them from falsification (e.g. The epicycles of Ptolmaic cosmology). Given that the falsification I propose is exactly what we'd expect to be required (and both the complexity of the problem and the paucity of evidence add to that) I can't say that there is truly a problem which would lead us to prefer investigations of another model on purely philosophical grounds - the more so since naive falsificationism is hardly considered to be good philosophy in the first place.


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Genomicus
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Member Rating: 4.7


Message 43 of 108 (780300)
03-13-2016 8:48 PM
Reply to: Message 39 by Dr Adequate
03-13-2016 11:01 AM


Re: Second Problem
But this distinction in how a proposition has been falsified makes no difference to whether a proposition has been falsified. I can, for example, perfectly well falsify the proposition "This elephant was in my house while I was out shopping" by observing that it's too big to fit through any of the doors. An argument that it's physically impossible is a splendid argument that it didn't happen.

It is a splendid argument, because if something is impossible, then the probability of it happening is 0 -- or, at least, extraordinarily close to 0. So, for example, you can argue that your door has x*y dimensions, and the elephant would be too large to fit through this doorway. You can then point to the structural integrity of the walls surrounding the doorway, citing its Young's modulus and so on. Then you can say that the elephant's musculature and biomechanics would not have allowed for this Proboscidean creature to generate sufficient force to squeeze through the doorway. All of these would be very rigorous arguments that would rule out the possibility that the elephant was in your house while you shopped.

If you can propose or cite equally rigorous experiment or series of experiments that could potentially falsify the RNA world or metabolism first scenarios, then I will gladly concur that these models are falsifiable.

Moreover, the argument against lithopanspermia requires its own implausibility argument --- besides requiring that LUCA (actually FUCA, as I have pointed out) should have certain genes, it also requires the proposition that FUCA couldn't have survived travelling through space without such genes. It requires one to say "X couldn't have happened, because chemistry". Take that away, and where's your argument against lithopanspermia? So why shouldn't "X couldn't have happened, because chemistry" be acceptable as a form of argument against the RNA world?

Because in the case of lithopanspermia our reasoning is very well-grounded in the radiobiology of microbes. A dose of 5,000 Gy will kill a whole population of E. coli -- and this can be experimentally verified -- while it will not kill a population of D. radiodurans. So now we can determine what kind of radiation resistance would be required for a population of microbes to make it through space and land on Earth. We can ascertain this down to the level of what specific protein parts would be needed.

On the other hand, what experiments would establish that the RNA world model couldn't happen because chemistry?


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Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 44 of 108 (780301)
03-13-2016 8:58 PM
Reply to: Message 41 by Dr Adequate
03-13-2016 11:14 AM


You seemed, stop me if I'm wrong, to be suggesting that the bacteria in lithopanspermia would have required special extraordinary resistance to radiation to survive their space voyage; the sort of high radiation resistance found in (e.g.) Deinococcus radiodurans and B. subtilis. If you just meant that they need the genes for radiation resistance that bacteria usually have, then sure, I was wrong to say "most bacteria don't have them" but then on the other hand having such genes is not particularly indicative of survival in space.

First, extraordinary radiation resistance a la D. radiodurans and B. subtilis is largely conferred by extra gene copies of particular genes (which are found among many bacteria), or increased expression of such genes, or redundant metabolic pathways.

Second, my argument isn't that core genes like ABC transporters is indicative of survival in space That isn't the point; I'm not presently attempting to muster evidence for panspermia. Instead, I am proposing a route to potential falsification. A progenote population lacking proteases, ABC transporters, nucleases, and a variety of catabolic enzymes would be rather quickly exterminated by galactic cosmic rays. So for panspermia to be correct the initial population of microbes must necessarily have the above protein parts.


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Dr Adequate
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Posts: 15921
Joined: 07-20-2006
Member Rating: 3.8


Message 45 of 108 (780306)
03-14-2016 12:02 AM
Reply to: Message 43 by Genomicus
03-13-2016 8:48 PM


Re: Second Problem
It is a splendid argument, because if something is impossible, then the probability of it happening is 0 -- or, at least, extraordinarily close to 0. So, for example, you can argue that your door has x*y dimensions, and the elephant would be too large to fit through this doorway. You can then point to the structural integrity of the walls surrounding the doorway, citing its Young's modulus and so on. Then you can say that the elephant's musculature and biomechanics would not have allowed for this Proboscidean creature to generate sufficient force to squeeze through the doorway. All of these would be very rigorous arguments that would rule out the possibility that the elephant was in your house while you shopped.

So this sort of argument is a perfectly valid method of falsification.

If you can propose or cite equally rigorous experiment or series of experiments that could potentially falsify the RNA world or metabolism first scenarios, then I will gladly concur that these models are falsifiable.

If you can show that in principle no such discoveries could ever be made, even if the RNA world did not exist and could not have existed, then I will gladly concede that it is unfalsifiable.

Because in the case of lithopanspermia our reasoning is very well-grounded in the radiobiology of microbes.

Now all you have to do is learn an equal amount about the biochemistry of RNA, and you're all set.

If all your argument boils down to is that we should prefer lithospermia to the RNA world because in our present state of knowledge we'd be better able to falsify one than the other, then from the point of view of epistemology that's hardly significant.

Before the invention of the microscope, was the hypothesis that Jews caused epidemic diseases preferable in principle to the idea that tiny little organisms caused epidemic diseases? The former was potentially much easier to falsify in practice, given the state of science in that era, because it was much easier to observe the activities of Jews than of these tiny organisms ... but did that make it somehow more scientific?


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