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Author Topic:   On the Origin of Life and Falsifiability
Genomicus
Member (Idle past 134 days)
Posts: 852
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Message 1 of 108 (779851)
03-08-2016 3:23 AM


“In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality,” wrote Karl Popper in The Logic of Scientific Discovery. Although Popper's notion of falsifiability as the linchpin of a scientific enterprise has been critiqued from inductivist schools of thought (see, for example, Grünbaum, 1976), it has been widely lauded as one of the most significant criteria required of scientific hypotheses (see, e.g., Ruse, 1982). Writes Michael Ruse:

“...a theory must be open to possible refutation. If the facts speak against a theory, then it must go. A body of science must be falsifiable. For example, Kepler's laws could have been false: if a planet were discovered going in squares, then the laws would have been shown to be incorrect.”

So we can see that falsifiability as a criterion for truly scientific hypotheses has become well-established within the scientific community, the objections from certain philosophical schools of thought notwithstanding. Indeed, this criterion has been used extensively in the debate over whether intelligent design qualifies as a scientific concept. Though the fires of that debate have now been reduced to barely visible embers – the Intelligent Design Movement has very starkly failed in its attempt to refute the Neo-Darwinian evolutionary synthesis and gain significant traction within the scientific community - the origin of the biochemical complexity which characterizes biological life remains a deeply difficult puzzle to put together.

In the essay that follows, I argue that present abiogenesis models for the origin of biological life on Earth are largely – if not wholly – unfalsifiable, and therefore should not be given the kind of gravitas accorded to legitimate scientific hypotheses. Furthermore, I propose that panspermia – a necessary model for any engineering-based scenarios for the origin of life – is in fact falsifiable and should thus be researched in greater depth than it has been.

However, before I elaborate on the above topic, I will present a brief overview of present origin of life models, providing the necessary backdrop to assess whether models of abiogenesis are properly falsifiable.

The RNA World

The RNA world hypothesis postulates that self-replicating RNA molecules preceded DNA- and protein-based cellular life (Orgel, 2003). Under this model, RNA was the carrier of biological information before the origin of DNA genomes, as well as the catalyst of chemical reactions in the first rudimentary life forms. Thus, in the RNA world, neither DNA nor proteins were necessary for the initiation of Darwinian evolutionary processes.

The ability of polynucleotides to base pair means that replication is relatively straightforward. One polynucleotide string acts as a template from which another is constructed. However, in the absence of a catalyst, such a mechanism of replication is inefficient (Alberts et al., 2002). Thus, in modern cells, the synthesis of nucleic acid polymers is driven by protein enzymes known as polymerases. Efficient self-replication in the RNA world is thought to have resulted from RNA functioning as a catalyst (Pace and Marsh, 1985). The discovery of enzymatic RNA molecules (see, e.g., Kruger et al., 1982), termed ribozymes, added plausibility to the RNA world hypothesis. Many naturally occurring ribozymes have been described, including the peptidyl transferase of the ribosome (Polacek and Mankin, 2005), ribonuclease P (Guerrier-Takada et al., 1983), and the hammerhead (Forster, 1987) and hairpin ribozymes (Fedor, 2000). Artificial ribozymes have also been created through in vitro selection methods. Significantly, Lincoln and Joyce (2009) have been able to construct ribozymes capable of self-sustained replication, despite the lack of proteins. Other studies have reinforced the plausibility of the RNA world. Although RNA is a very complex molecule, Powner and colleagues synthesized pyrimidine ribonucleotides using hypothesized prebiotic molecules (Powner et al., 2009).

Nonetheless, the RNA world hypothesis has been critiqued in numerous scientific papers, and has been described as "a prebiotic chemist's nightmare" (Benner et al., 2012) and “the worst theory of the early evolution of life (except for all the others)” (Bernhardt, 2012). Bernhardt (2012) succinctly outlined many of the problems with the RNA world hypothesis, while offering some possible responses. One of the difficulties with the RNA world hypothesis is the inherent instability of the RNA molecule, which could have prevented the accumulation of RNA molecules in the prebiotic environment (Bernhardt, 2012). Furthermore, the plausibility of prebiotic RNA synthesis has been questioned, and Benner et al. (2012) criticized aspects of the work of Powner et al., 2009. Other dilemmas remain. It is thought by some researchers that only long RNA sequences are capable of catalytic activity (Bernhardt, 2012); one of the most efficient ribozymes created to date is approximately 190 bases long (Bernhardt, 2012). It is difficult to envision how a ribozyme of that length could arise by stochastic assembly. Shorter catalytic RNAs are not unknown, however. Small self-cleaving RNAs can be 50 nucleotides in length, and a study by Vlassov et al. (2005) explored ribozymes with even shorter lengths. A ribozyme that is just 5 nucleotides long has also been isolated in vitro (Turk, 2010).

Further objections to the RNA world hypothesis will be briefly summarized. The metabolic needs of the RNA world may have been greater than the catalytic repertoire of RNA (Bernhardt, 2012); it has been argued that the RNA world makes no reference to a possible energy source (Kurland, 2010); and there is phylogenetic evidence that ribosomal proteins and rRNA co-evolved (Harish and Caetano-Anollés, 2012), with neither component originating first.

On Falsifying the RNA World

Finally, we come to the issue of falsifiability or refutability. In the words of Eugene Koonin (in a review of Bernhardt, 2012), “[t]he RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts.”

Indeed, one will find it a rather perplexing task to imagine an experiment that would falsify the RNA world scenario. It should be noted that the RNA world hypothesis attempts to provide an answer to a historical question; namely, how life on Earth arose. As such, no amount of evidence for the plausibility of the RNA world hypothesis will be able to establish the historical accuracy of that hypothesis. Yet much (if not most) of the evidence for the RNA world hypothesis merely strengthens its plausibility. For example, observations which demonstrate that RNA can catalyze its own replication say nothing about whether self-replicating RNA was indeed historically the precursor to modern cellular life.

I will finish this section with the following question for the reader to ponder: what experiment, if any, would falsify the RNA world scenario? If no experiment – or series of experiments – could reasonably falsify the RNA world model, then any notions as to its validity as a scientific hypothesis must be heavily scrutinized.

Metabolism First

Metabolism first models propose that autocatalytic metabolism arose prior to self-replicating nucleic acids. The metabolism of virtually all modern life forms is based around the tricarboxylic (TCA) cycle, and it has been asserted that a reverse TCA cycle could result in an overall autocatalytic reaction (Morowitz et al., 2010). Under such a scenario, autocatalytic reactions form the basis of self-replicating systems from which Darwinian evolution could proceed. The reaction system could be improved by the addition of a protein enzyme.

In a landmark publication, Günter Wächtershäuser (1988) suggested that the first life forms – named “pioneer organisms” – evolved in hydrothermal vents under high temperatures. These primal organisms possessed catalytic transition metal centers which were involved in the catalysis of carbon fixation pathways. This allowed the production of small organic molecules. Under this model, a primitive metabolism was thereby manifested early in the evolution of life.

Compartmentalization of the metabolic systems would result in the first cells. Gradual evolution of these cells (e.g., the evolution of nucleic acid replication) would then follow, ultimately producing the last universal common ancestor from which modern life diversified.

The crucial difference between metabolism first and the RNA world hypothesis is that in the former model protein enzymes arise before the appearance of nucleic acid replicators. Several observations have been cited as support for the metabolism first hypothesis. The core metabolic reactions of prokaryotic autotrophs are quite similar to the chemistry of H(2)-CO(2) redox couples that is harbored by hydrothermal vents, suggestive of Wächtershäuser’s (1988) model. Further, the possibility of a reverse TCA cycle has been established by Buchanan and Arnon (1990).

Yet there is a large body of data that casts doubt on the validity of the metabolism first models. Pross (2004) argues that “there is no substantive evidence for a 'metabolism first' mechanism for life's emergence.” Moreover, there is a lack of evolvability in autocatalytic metabolic networks (Vasas et al., 2010), and Orgel (2008) pointed out that the occurrence of metabolic cycles on the prebiotic earth is implausible.

On Falsifying Metabolism First

Like the RNA world scenario, it becomes a challenging ordeal to imagine what kind of experiment would refute the metabolism first model. And if no amount of experiments can falsify such a model, should it really be treated as a strictly scientific hypothesis? While exhaustive work has been conducted on assessing the plausibility of metabolism first, little has been done to root this model in the reality of biological history.

The Panspermia Model

Terrestrial life may not have originated on Earth, but could have instead originated elsewhere in the universe before being transported to Earth from outer space. Although this concept, known as “panspermia,” does not enjoy widespread support from the scientific community, a number of publications have viewed it favorably. The panspermia hypothesis is attractive because life would have more time to originate than if life evolved on Earth. Over the years, most of the major difficulties with panspermia have been refuted (Rampelotto, 2010), and tentative evidence in favor of panspermia has grown. For instance, there is some geologic evidence that genes encoding Aib-polypeptides were one of the driving forces behind species extinctions during the K/T transition, and that these genes were from cosmic pathogens that infected the earth’s biosphere (Wallis, 2003).

Mechanisms for the interstellar transport of microbial organisms have been extensively discussed. For instance, microcosms consisting of meteorite interiors provide an effective medium for panspermia (Mautner, 2002). A variety of material is now known to move naturally throughout the solar system and it is accepted that rock fragments can be ejected from and exchanged among planetary surfaces (Melosh, 2003), so there is no fatal difficulty with the transport of microbial cells from one planet to another.

Unlike the RNA world and metabolism first hypotheses, panspermia does not address the initial origin of biological life; instead, it merely explains where terrestrial life may have come from. While panspermia does give more time and chemical resources for life to evolve, it fails to furnish a mechanism for the origin of the biochemical complexity that is at the heart of life.

However, I argue that although panspermia only addresses how life emerged on Earth, it is in fact a properly falsifiable scientific hypothesis.

On Falsifiability and Panspermia

Natural – that is non-directed – panspermia is inherently falsifiable. Most plausible panspermia scenarios involve lithopanspermia, wherein highly resilient biological cells are housed in meteorites which splash down on planetary surfaces. These meteorites provide protection from the enormous amount of heat generated during ejection from a planet and subsequent landing on another planet. They also protect against the vacuum of space, which would otherwise desiccate any microbes wafting through the vastness of space. They do not, however, offer complete protection against radiation (which largely consists of high-energy protons). Thus, any microbes transported through space to another planet via meteorites must have molecular machinery which protect them from radiation.

Both hyperthermophile Archaea and bacteria like Deinococcus radiodurans and B. subtilis have high radiation resistance. There are several molecular mechanisms behind the extraordinary radiation resistance of microbes like D. radiodurans (see Krisko and Radman, 2013):

(1) Redundant antioxidant pathways and an abundance of metabolites leads to low production of reactive oxygen species, resulting in a radio-protective effect.

(2) A high degree of proteolytic efficiency means that microbes can quickly rebuild their proteins during recovery from exposure to ionizing radiation.

(3) With as many as 90 ABC transporters utilized for peptide and amino acid uptake, D. radiodurans can – again – quickly rebuild protein components after exposure to radiation.

In short, D. radiodurans (as well as other radiation-resistant microbes) house a relatively large number of genes which code for catabolic enzymes and unique molecular pathways; these enzymes are responsible for protection against radiation by virtue of their production of small antioxidant molecules.

What does all this mean? It means that for panspermia to take place, microbes must be more than mere cell membranes with a sprinkling of protein parts. No – they must be relatively complex organisms with sufficient molecular machinery (and therefore genes) to protect against radiation. When this is taken into consideration, it is plain to see that panspermia becomes remarkably easy to falsify:

If it could be demonstrated that the last universal common ancestor (LUCA) was a population of very simple cells that did not have the necessary protein parts to survive extensive radiation, then non-directed panspermia will have been effectively falsified.

That this is a viable approach to falsifying panspermia has been borne out in the scientific literature; for example, the panspermia scheme has been criticized by Di Giulio (2010), who argued that life has passed through progenotic stages (that is, stages where life was not able to survive transport through space) and that this was evidence against panspermia. Di Giulio (2010) noted that the existence of split tRNA genes in Nanoarchaeum equitans suggests that tRNA molecules evolved through the assembly of two hairpin structures and that these split genes are ancient, indicative of a progenotic LUCA. An initial phylogenetic study of N. equitans concluded that N. equitans is a basal archaeal lineage – representing a novel archaeal kingdom, termed Nanoarchaeota (Waters et al., 2003). The tRNA split genes in N. equitans could therefore have been ancestral and ancient. If this were the case, it would be strong molecular evidence against the panspermia hypothesis. However, a subsequent and more thorough phylogenetic analysis found that N. equitans nests within the archaeal phylum Euryarchaeota, and is probably related to Thermococcales (Brochier et al., 2005). Thus, the current phylogenetic evidence indicates that N. equitans is not a basal archaeal lineage, and consequently the thesis that the tRNA split genes in N. equitans are ancient is of dubious merit. Based on the phylogenetic positioning of N. equitans in the archaeal tree of life, it is logical to conclude that the tRNA split genes in N. equitans are a relatively recent innovation (and evidence from tRNA gene introns support this), and not the relics of a progenote world.

Another possibility for the refutation of the panspermia hypothesis emerged with T. Cavalier-Smith's 2006 paper, “Rooting the tree of life by transition analyses” (Cavalier-Smith, 2006). In this paper, Cavalier-Smith used the classical transition analysis approach employed in paleontology and applied it to molecular systems in an attempt to root the tree of life. Transition analyses, in principle, are able to root phylogenies in this way: by finding characters that could only have evolved in one direction (for instance, reptile legs evolving into wings is far more plausible than the reverse for mechanistic reasons), these characters polarize the phylogeny under consideration.

Based on a number of such character polarizations among prokaryotes, Cavalier-Smith concluded that the LUCA “was more primitive than other eubacteria in probably lacking lipopolysaccharide, hopanoids, cytochrome b, catalase, the HslV ring protease homologue of proteasomes, spores, the machinery based on outer membrane (OM) protein Omp85 used by more advanced negibacteria to insert outer membrane proteins, type I, type II, and type III secretion mechanisms, and TonB-energized OM import systems.”

In other words, if these transition analyses are correct, then the LUCA would have lacked a good deal of molecular machinery. Of particular importance it would have lacked efficient proteases like the HslV ring, and efficient proteases are needed by radiation-resistance microbes. Although Cavalier-Smith did not set out to refute the notion of panspermia, this study had the potential to do so.

However, his tree polarizations based on molecular transition analyses are refuted by rigorous molecular phylogenies. For example, he argued – based on transition analyses – that the TonB system first emerged in gram-negative bacteria, when later phylogenetic work by Marmon (2013), using maximum-likelihood methods combined with statistical analysis of GC-content of various bacteria phyla, indicated that the TonB system first arose in a gram-positive phylum – upending Cavalier-Smith's transition analysis.

Summary

After a brief survey of current origin of life models, I have argued the following:

(1) Both the RNA world and metabolism first scenarios for the origin of life are largely unfalsifiable, arguably moving them beyond the purview of proper scientific hypotheses. Most work on these models consists of establishing their plausibility, rather than their historical actuality.

(2) The panspermia hypothesis is falsifiable based on the fundamental requirement that microbes traveling through space be resistant to galactic cosmic rays. This requirement, in turn, necessitates the presence of particular protein parts that the LUCA would not have required had it emerged on Earth.

(3) At present, the panspermia hypothesis has yet to be effectively falsified – and attempts to do so do not have merit when seen under the light of more recent advances in molecular phylogenetics.

A word of caution: the reader may be inclined to believe that I am dismissing the value of abiogenesis models outright. Far from it! I am, instead, adding a critical voice to the current methodological bent of most origin of life studies with the hopes that future research will ground such studies in historical reality rather than mere plausibility. Furthermore, if panspermia is a more proper scientific hypothesis than the RNA world or metabolism first scenario, as I have argued here, then it makes sense that the panspermia model should be investigated with more depth.

Addendum: See Message 107.

References

Popper, K., 1959. The Logic of Scientific Discovery, p. 316.

Grünbaum, A. 1976. Is Falsifiability the Touchstone of Scientific Rationality? Karl Popper Versus Inductivism. Volume 39 of the series Boston Studies in the Philosophy of Science, pp 213-252.

Ruse, M., 1982. Creation Science Is Not Science. Science, Technology, & Human Values. Vol. 7, No. 40, pp. 72-78.

Orgel, L.E., 2003. Some Consequences of the RNA World Hypothesis. Origins of Life and Evolution of the Biosphere.

Alberts, B., et al., 2002. Molecular Biology of the Cell. 4th edition, The RNA World and the Origins of Life.

Pace, N., Marsh, T., 1985. RNA catalysis and the origin of life. Orig Life Evol Biosph.

Kruger, K., et al., 1982. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell.

Polacek, N., Mankin, A., 2005. The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit Rev Biochem Mol Biol.

Guerrier-Takada, C., et al., 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell.

Forster, A., 1987. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell.

Fedor, M., 2000. Structure and function of the hairpin ribozyme. Journal of Molecular Biology.

Lincoln, T., Joyce, G., 2009. Self-sustained Replication of an RNA Enzyme. Science.

Powner, M., et al., 2009. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature.

Benner, et al. Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA.

Bernhardt, 2012. The RNA World: the worst theory of the early evolution of life (except for all the others).

Vlassov, et al., 2005. The RNA world on ice: a new scenario for the emergence of RNA information.

Turk, R., 2010. Multiple translational products from a five-nucleotide ribozyme. PNAS.

Kurland, C., 2010. The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was.

Harish, A., Caetano-Anollés, G., 2012. Ribosomal history reveals origins of modern protein synthesis. PloS One.

Morowitz, H., et al., 2010. Ligand field theory and the origin of life as an emergent feature of the periodic table of elements. Biol. Bull.

Wächtershäuser, G., 1988. Before enzymes and templates: theory of surface metabolism. Microbiol Rev.

Buchanan, B., Arnon, D., 1990. A reverse KREBS cycle in photosynthesis: consensus at last. Photosynth Res.

Pross, A., 2004. Causation and the origin of life. Metabolism or replication first? Orig Life Evol Biosph.

Vasas, V., et al., 2010. Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life. PNAS.

Orgel, L.E., 2008. The implausibility of metabolic cycles on the prebiotic Earth. PLoS Biol.

Rampelotto, P. H., (2010). Panspermia: A promising field of research. In: Astrobiology Science Conference. Abs 5224.

Wallis, M., 2003. Cosmic Genes in the Cretaceous-Tertiary transition. Astrophysics and Space Science.

Mautner, M., 2002. Planetary resources and astroecology. Planetary microcosm models of asteroid and meteorite interiors: electrolyte solutions and microbial growth--implications for space populations and panspermia. Astrobiology.

Melosh, H., 2003. Exchange of meteorites (and life?) between stellar systems. Astrobiology.

Krisko, A., Radman, M., 2013. Biology of Extreme Radiation Resistance: The Way of Deinococcus radiodurans. Cold Spring Harb Perspect Biol.

Di Giulio, M., 2010. Biological evidence against the panspermia theory. Journal of Theoretical Biology.

Waters, E., et al., 2003. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci.

Brochier, C., et al., 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol.

Cavalier-Smith, T., 2006. Rooting the tree of life through transition analyses. Biology Direct.

Marmon, L., 2013. Elucidating the origin of the ExbBD components of the TonB system through Bayesian inference and maximum-likelihood phylogenies. Molecular Phylogenetics and Evolution.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 7 of 108 (779888)
03-09-2016 8:25 AM
Reply to: Message 4 by Dr Adequate
03-08-2016 11:00 PM


No, you'd need to demonstrate that of FUCA, not LUCA.

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. Some of these genes are very basic to cell survival once incorporated in a cell's genome and overall architecture. I see little reason to suspect that such an initial population -- occupying a wide range of niches and diversifying -- would begin losing these rather useful genes (proteases, ABC transporters, etc.). The argument to the contrary starts looking awfully ad hoc, as there are sound biological reasons for subscribing to the notion that such genes would be conserved from the FUCA to the LUCA.


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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 8 of 108 (779890)
03-09-2016 8:31 AM
Reply to: Message 5 by nwr
03-08-2016 11:59 PM


I agree that assertions about origin of life (OOL) are usually not scientific conclusions. Mostly, they are speculative hypotheses. However, that's not a criticism. A lot of science starts with speculative hypotheses.

Yes, speculative models are of considerable value in driving exploratory science further. This is not -- in itself -- a criticism. However, there is much focus in current OOL research on establishing the biochemical plausibility of abiogenesis models, instead of hunting for clues that these models are grounded in historical reality. Contrast this with panspermia, where much of the evidence is of a historical nature rather than a focus on mere plausibility.

Finding other planets with life would be interesting and might give insight.

Certainly. If such life consisted of DNA or RNA genomes, then this would shed a great deal of light on the origin of life on Earth. For starters, we'd actually have a tangible outgroup with which to root the terrestrial tree of life.


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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 9 of 108 (779893)
03-09-2016 8:43 AM
Reply to: Message 6 by PaulK
03-09-2016 1:03 AM


I'll agree with nwr that falsifiability is not of overriding importance in this case - a minor advantage in falsifiability is not really that big a deal.

And why is it not of significant importance in this case? How do we determine which cases falsifiability should be of importance, and which cases it should not be?

Both abiogenesis models potentially offer more explanatory power...

How so?

and are more parsimonious

Maybe, but only if we operate under the notion that the relative rapid emergence of biological life on Earth is reasonable. A model is more parsimonious because it includes as few unnecessary steps as possible, but a case can be made that the extra time and chemical resources afforded by the panspermia model means that it doesn't add a purely unnecessary step.

Further I find the difference in falsifiability overstated. First the comparison is between general models and a feature of some panspermia models - albeit ones which are arguably more plausible.

And that's the key insight: that the falsifiability of panspermia is based on a model that's been demonstrated to be physically possible. Sure, we can conjure all sorts of rather implausible panspermia models (or for any other scientific notion), but that's not exactly a valid argument against the falsifiability of panspermia, is it?

Second, the objections raised against the models do suggest that there are potential paths to effectively falsify them - the weight of problems can be sufficient to reject a broad hypothesis even if there is no clear proof against it.

So which experimental lines in particular do you believe have been carried out that could potentially falsify the RNA world scenario or metabolism first model for the origin of life?

Finally, the call for a more historical approach is not really justified, nor the call to put more effort into panspermia. Both are more dependent on other factors that are not addressed.

In the first, the availability of evidence...

At what point do you conclude that a model's incapacity to generate historical evidence is reflective of the fact that it is not, in fact, historically accurate?

... and in the second concrete and promising research proposals

Well, it could be argued that this is a symptom of the fact that a relatively small amount of effort has been put into investigating the notion of panspermia. Why do you think there has been a lack of promising research proposals for panspermia?

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 14 of 108 (779975)
03-10-2016 7:06 AM
Reply to: Message 10 by PaulK
03-09-2016 9:13 AM


Because we are talking about broad models - and because panspermia doesn't seem a lot more falsifiable.

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?

A working model of abiogenesis seems to be at least potentially more general than a model which only deals with the question of how life arrived on Earth.

This was in regard to explanatory power. Which, in pragmatic terms, means the capability to (1) generate useful, testable predictions, and (2) connect a broad range of seemingly unrelated observations under one explanatory umbrella. So why do you think that models of abiogenesis would outperform panspermia with regards to the above two points?

That seems a weak argument. Panspermia may offer more time - although that in itself requires assumptions - but it certainly adds in the extra step of getting life from it's putative source to Earth.

1. It would not require assumptions; the thesis that panspermia offers more time is tied to the available evidence we have that indicates that there was a relatively large number of already habitable planets at the time of Earth's origin about 4.5 Ga.

2. You are correct in stating that panserpmia adds in the extra step of getting biological life from a putative source to Earth. But then again, many subsets of abiogenesis models invoke an extraterrestrial source for life's putative organic precursor molecules. Further, if the origin of life outside of Earth is much more realistic instead of an origin of life within Earth, then this additional step the panspermia model adds is not unnecessary -- and therefore does not make the panspermia model particularly less parsimonious than the RNA world or metabolism first scenarios.

I think you mean that it is the fatal error in your argument. Panspermia is a whole family of models - even directed panspermia is - just as the RNA world and metabolism-first are. Falsifying one of the models doesn't falsify all of them.

So, following your "key insight" lead you to fail to show that panspermia or even directed panspermia were falsifiable.

This doesn't address my argument that conjuring all sorts of speculative panspermia models isn't exactly a fair way to test the falsifiability of actually plausible panspermia hypotheses.

I never claimed to know of any. Rather I refer you to the list of objections in your own post and point out that if they prove too intractable or sufficient additions objections arise the RNA World, for instance, would be effectively falsified (or in Lakatos' terms it would become a degenerate research program and eventually abandoned)

Okay. So you don't know how the RNA world model could be definitively falsified.

(Note: you may wish to add a citation for the specific piece by Lakatos you're referring to)

And another misreading. In fact I hold that the ability to make historical enquiries is dependent on the availability of evidence.

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


Well, it could be argued that this is a symptom of the fact that a relatively small amount of effort has been put into investigating the notion of panspermia. Why do you think there has been a lack of promising research proposals for panspermia?

The first objection does not work, If there are ways the effort could usefully be spent there wouldn't be a problem.

That's not necessarily true, though. There can be a priori biases against investigating panspermia based on conformity to scientific orthodoxy.

And I am not making any claims about the existence of research proposals, merely pointing out that the availability of such proposals is a far more important issue than anything you have raised with regard to actually doing research.

So what, in your view, is the reason for a lack of panspermia research proposals relative to abiogenesis models?


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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 16 of 108 (779977)
03-10-2016 7:17 AM
Reply to: Message 13 by Pressie
03-10-2016 4:43 AM


Indeed, this criterion has been used extensively in the debate over whether intelligent design qualifies as a scientific concept.

Nope. There's no debate at all. Intelligent design is not science. ID is the opposite of science. No debate about that in scientific circles.

Really, Pressie? Semantic nitpicking is the only thing you have to add to this discussion?

If you will look up the definition of the word "debate," you will find that what I said was wholly correct.

If you carefully read what I wrote, you will also see that I said nothing about there being an ongoing debate over ID in scientific circles. What I said was that the criterion of falsifiability was used in the debate over ID's scientific legitimacy or lack thereof. Both scientific and pseudoscientific discourse doesn't happen in a vacuum; they occur within a social, political, and philosophical context, and debate can very well be found in the fibers of this social-political-philosophical fabric, even if it is not found within the scientific community or in the halls of academia.

Generally speaking, I endeavor to structure my sentences in ways that reveal very particular nuances, so knee-jerk semantic nitpickings might gloss over that. Read carefully and don't assume.


This message is a reply to:
 Message 13 by Pressie, posted 03-10-2016 4:43 AM Pressie has responded

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 Message 17 by Pressie, posted 03-10-2016 7:33 AM Genomicus has responded

  
Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 19 of 108 (779982)
03-10-2016 7:47 AM
Reply to: Message 17 by Pressie
03-10-2016 7:33 AM


Yes. Really. ID is not science. ID is the opposite of science.

With respect, you might want to improve your verbal comprehension skills. My sentence "Really, Pressie?" was linked to my following sentence regarding your semantic nitpicking, not to your claim regarding ID and its non-scientific status.

Doesn't matter how long your word salads are.

Yeah, you're not actually going to address the argument I made dissecting your semantic nitpickings, are you?


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 Message 17 by Pressie, posted 03-10-2016 7:33 AM Pressie has responded

Replies to this message:
 Message 20 by Pressie, posted 03-10-2016 7:57 AM Genomicus has responded

  
Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


Message 30 of 108 (780233)
03-12-2016 4:28 PM


FYI
Thanks for all of your responses. I appreciate the critical interest this has generated. I've had a busy, caffeine-fueled past couple of days so wasn't able to reply. I'll be getting to this over this weekend though.
  
Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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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 Message 41 by Dr Adequate, posted 03-13-2016 11:14 AM Genomicus has responded

  
Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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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 Message 18 by PaulK, posted 03-10-2016 7:46 AM PaulK has responded

Replies to this message:
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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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.


This message is a reply to:
 Message 22 by Dr Adequate, posted 03-10-2016 10:46 AM Dr Adequate has responded

Replies to this message:
 Message 39 by Dr Adequate, posted 03-13-2016 11:01 AM Genomicus has responded
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Genomicus
Member (Idle past 134 days)
Posts: 852
Joined: 02-15-2012


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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