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Author Topic:   On the Origin of Life and Falsifiability
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Posts: 852
Joined: 02-15-2012

Message 76 of 108 (780797)
03-21-2016 8:50 PM
Reply to: Message 61 by PaulK
03-15-2016 2:26 PM

Sure, and falsifying the RNA world model does not in itself falsify abiogenesis. If you have a falsification scenario for the RNA world model, by all means present it. I will then immediately concede that the RNA world model is falsifiable.

By now you certainly ought to realise that I am not claiming that the RNA world is falsifiable. I am claiming that panspermia is not.

You are correct if by "panspermia" you mean the broad idea that life on Earth has a non-terrestrial origin. This idea is as general as abiogenesis (the notion that life arose on Earth through non-directed chemical processes), and so both are not falsifiable. But then again, they are not supposed to be falsifiable as they aren't hypotheses.

Admittedly, I use a different definition of panspermia in the OP -- one that is more appropriately called "lithopanspermia" -- and this is a falsifiable hypothesis, as I have argued in several other posts.

If Young Earth Creationism requires loads of ad hoc auxiliary hypotheses to protect it from falsification then it is already not science by my criteria. Why then, do I need to appeal to,any other ?

Because "loads of ad hod auxiliary hypotheses" isn't exactly a good line of demarcation between science and pseudoscience. If, for instance, a scientific hypothesis required a large number of auxiliary hypotheses -- but these all increased the degree of falsifiability of that hypothesis -- then it is quite a stretch to say that that hypothesis is pseudoscience or in some way non-scientific.

What matters when it comes to auxiliary hypotheses is that the degree of falsifiability of the original hypothesis is increased. If the auxiliary hypotheses do not do that -- they instead function as an excuse for some difficulty with the hypothesis -- then that hypothesis may be rightly condemned as non-scientific. It all leads back to the criterion of falsifiability.

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Message 77 of 108 (780799)
03-21-2016 9:08 PM
Reply to: Message 75 by Dr Adequate
03-21-2016 8:48 PM

Re: @Dr Adequate
The point is that creationism is falsifiable, unless you allow the creationists the sort of auxiliary hypotheses that we don't allow anyone.

Well, here's why I disagree with the notion that creationism of the YEC variety is falsifiable: the auxiliary hypotheses which are proposed as a way around rather extraordinary problems do not increase the degree of falsifiability of the creationism scenario. So YEC isn't falsifiable because the further back you chase these auxiliary hypotheses, the less falsifiable the whole model is.

Basically, invoking gods to wash over problems with a hypothesis is a horrible strategy because gods do not increase the degree of falsifiability -- so the hypothesis becomes pseudoscience.

As you can see, it all leads back to the criterion of falsifiability.

Well, no. Falsifiability is a very low bar, it just identifies the sort of thing that could be science.

It identifies whether a hypothesis qualifies as a scientific construct or not. The caloric theory, then, is a properly constructed scientific hypothesis. That it has been falsified does not mean it is not properly constructed in the philosophy of science sense.

It doesn't mark off science from pseudoscience: there are any number of things which are eminently falsifiable and would be science if they were true, but are pseudoscience because they are false --- or, strictly speaking, because the weight of the evidence is against them.

You're right in the sense that falsifiability isn't the only criterion that delineates science from pseudoscience. However, the caloric theory isn't pseudoscience. It's a dead scientific theory. Just because it's false doesn't make it pseudoscience. Pseudoscience exists in a rather particular social and political fabric.

Homeopathy, for example, is practically the paradigmatic pseudoscience, and is readily falsifiable: we can test whether homeopathic medicine works better than placebo. It's a pseudoscience because it doesn't.

No, it's a pseudoscience because its adherents ideologically refuse to adapt their beliefs to conform to the evidence. The caloric theory isn't pseudoscience because it doesn't exist in the kind of socio-political-ideologic fabric that homeopathy, creationism, or UFOlogy does.

Edited by Genomicus, : No reason given.

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Message 80 of 108 (780802)
03-22-2016 2:26 AM
Reply to: Message 79 by PaulK
03-22-2016 2:15 AM

Re: @PaulK
In other words the OP tried to pass off a particular panspermia hypothesis off as panspermia and wrongly compared it to more general ideas which are not expected to be falsifiable, That pretty much accepts my initial criticism.

Not quite, because comparing lithopanspermia to specific scenarios like the RNA world and metabolism first models is quite reasonable. The RNA world scheme is as highly specific as lithopanspermia, so it really should be falsifiable if we are to accept it as a properly constructed scientific hypothesis.

You know if you want to agree with me it is rather easier to do so explicitly rather than writing two paragraphs which effectively say the same thing without explicit agreement,

I did not say that "many auxiliary hypotheses" were a sufficient condition for the pseudo-science label. I sad that a hypothesis that "requires loads of ad hoc auxiliary hypotheses to protect it from falsification" is pseudoscience.

Right. And why does that make it pseudoscience? That, I believe, is where our different positions will become most apparent. I would say that the above scenario -- creationism requiring many auxiliary hypotheses to protect it from reasonable falsification -- makes creationism pseudoscience because of the falsifiability criterion. In other words, these ad hoc auxiliary hypotheses make creationism unfalsifiable, and therefore non-science in the Popperian sense.

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Message 82 of 108 (780804)
03-22-2016 3:39 AM
Reply to: Message 81 by PaulK
03-22-2016 2:46 AM

Re: @PaulK
It is far from obvious that that is true.

From Message 49:

The RNA world hypothesis:

Free-floating nucleotides stochastically assembled into short sequences with catalytic properties --> Primitive catalysis propelled the generation of ever-longer nucleotide sequences --> Base-pairing coupled with thermal and catalytic activity allowed for polynucleotide replication --> Replication lead to molecular evolution and increased efficiency of RNA catalysts --> Catalytic RNAs allowed for extensive peptide bond formation among amino acids --> Primitive protein molecules thereby emerged, which eventually evolved into the sophisticated protein machinery of modern cellular life. The RNA-to-protein system was also upgraded to a DNA --> RNA --> protein system.

The Lithopanspermia hypothesis:

Biological life emerged on another planet, rich with organic chemical resources around the time of the origin of the Earth --> Much of this microbial life evolved sophisticated machinery for resistance against ionizing radiation --> Ejecta from this planet following an impact contained members of these microbes --> This ejecta traveled through space and eventually struck Earth at approximately 3.6 Ga.

How again is the RNA world model more general than lithopanspermia?

Your response:

Strictly speaking lithopanspermia doesn't include abiogenesis so much of what you said is irrelevant. And I would say that the whole "travel to earth on a meteorite" - which is the only part you offer as falsifiable - is quite specific.

Your response basically amounted to providing your own personal opinion that "traveling to Earth on a meteorite" is somehow more specific than "Base-pairing coupled with thermal and catalytic activity allowed for polynucleotide replication." Unless you can explicitly show that the former is significantly more specific than the latter, you don't really have much of a case that lithopanspermia is considerably more specific than the RNA world.

In fact your whole claim of falsifiability relies on a specific feature of lithopanspermia.

Well, obviously. Falsifiability of any hypothesis will rely on the specific features of that hypothesis. That's not really under contention AFAIK.

And yet panspermia is unfalsifiable.

You haven't made a very good case that lithopanspermia is unfalsifiable, I'm afraid. Dr Adequate and Blue Jay have made generous attempts to demonstrate that my approach to falsifying lithopanspermia is flawed -- and that's largely the point of this discussion thread -- but you, PaulK, haven't done anything particularly compelling that refutes my scenario for falsifying lithopanspermia.

String theory is unfalsifiable. And you accept the first as science, and very many scientists accept the second as science.

String "theory" is not a scientific hypothesis. Why is that? The answer lies in falsifiability and testability.

Again, you have conceded the point that my criteria are adequate to dismiss YEC as science.

If by "your criteria" you mean the requirement that a scientific hypothesis be increasingly falsifiable as more auxiliary hypotheses are added to it, then yes. But then again, I never disputed that.

Edited by Genomicus, : No reason given.

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Message 83 of 108 (780810)
03-22-2016 8:47 AM
Reply to: Message 66 by Blue Jay
03-16-2016 11:17 AM

@Blue Jay
Hey Blue Jay,

Wait. So in your effort to demonstrate that lithopanspermia is not falsifiable, you're divining the possible existence of analogs of proteases, ABC transporters, and nucleases, which would have then been lost under mysterious selective pressure that somehow allowed such a loss to not affect the reproductive fitness of the population in a negative way, and wherein no homologs were preserved; and then cells evolved proteases, ABC transporters, and nucleases.

I have three objections to your comment here:

1. I don't really understand why this evokes such incredulity from you. The validity of this data as a falsification hinges on the premise that there is no other means of tolerating cosmic radiation aside from certain patterns in the abundance/diversity of proteases, ABC transporters and nucelases. Accepting that premise requires a fair helping of hubris, doesn't it?

Let me try to explain my argument with a bit more depth. In order for microbial cells to survive space transport in a lithopanspermia scenario, they must necessarily be capable of surviving the ionizing radiation of galactic cosmic rays. Now, the following details concerning radiation resistance in prokaryotes have been elucidated:

  • Radiation resistant microbes contain significantly higher manganese ion concentrations than other microbes. This high concentration of Mn(II) allows the rapid breakdown of destructive reactive oxygen species into smaller molecules that can quickly exit the cell membrane (Gross, 2007: Paradox Resolved? The Strange Case of the Radiation-Resistant Bacteria).
  • This, in turn, requires a robust manganese ion transport apparatus.

  • Breakdown of activated oxygen species that have particularly long half-lives. This is accomplished by enzymes like superoxide dismutases and catalases; it helps reduce damage to cellular components and molecular structures.
  • Construction of DNA synthesis precursor molecules.. Executed efficiently through ribonucleoside diphosphate reductases, which help accelerate the process of DNA synthesis after the cell has been exposed to a dangerous dose of radiation.
  • Pronounced synthesis of proteins involved in DNA repair and maintenance. Proteins like RecA and various elongation factors -- involved in DNA repair and maintenance -- are synthesized at a pronounced level.
  • Expression of mRNAs which encode other repair proteins. These proteins include glycosylases, deoxyribophosphodiesterases, nucleotide excision repair enzymes, polymerases, helicases, ABC transporters, phosphatases, and hydrolases.

So there is a preponderance of biochemical, genetic, and molecular biological evidence that radiation resistance in the context of biological organisms bounded by lipid membranes and peptidoglycan and possessing DNA genomes which encode amino acid polypeptides requires a core set of protein functions. This set of protein functions include specific ion transporters (manganese, because of its chemistry, is what's needed -- instead of ions like iron), diphosphate reductases because of the nature of DNA chemistry, enzymes which can break down activated oxygen species, elongation factors, and various other catalysts.

There is, then, a consilience of observations which reveal a very particular interplay between the chemistry of DNA, the cytosol and other cellular compartments, protein molecules, and reactive oxygen species. So I would argue that it is not hubris at all -- but rather sound molecular biology -- to assert that a population of prokaryotes traveling through space on a rock would require a fairly specific repertoire of protein parts.

I don't really understand why you think LUCA and FUCA should be similar. After all, in the panspermia model, FUCA is supposed to have come from an alien planet, so it seems quite reasonable to anticipate a whole suite of very novel selection pressures immediately after arrival on Earth. So, there seems plenty of reason to anticipate massive genomic changes occurring between FUCA and LUCA; and it seems a bit hasty to dismiss any possibilities the way you have.

1. FUCA is indeed supposed to have come from an alien planet, but not one so starkly different than Earth that FUCA could not have survived the early environ of Earth. This means that there is a not inconsiderable degree of overlap with respect to selection pressures.

2. There would indeed be fairly massive genomic changes during the transition from the FUCA to the LUCA; however, as many of the above protein parts carry out very important functions in prokaryotic cell biology, one would have to find a way around the following argument (Message 32):

"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."

And besides, isn't this the exact form of the argument you used to demonstrate the unfalsifiability of the RNA World hypothesis? That is, what if someone published a phylogenetic tree claiming to provide evidence about the existence of self-catalytic RNA's coded in the genome of LUCA? Wouldn't that beg a couple of big questions about whether or not those RNA's were the actual prebiotic RNA catalysts, and about why/how those prebiotic catalysts became encoded into LUCA's DNA? How is that substantively different from the questions Dr A is asking now about Panspermia?

This is substantively different because under the lithopanspermia model the FUCA must possess a particular repertoire of protein parts -- protein parts which would, by their function in the context of prokaryotic cell biology and in light of molecular evolutionary processes, be retained and passed onto LUCA. They should therefore be found in the LUCA.

The RNA world is considerably different. In principle, at any point during the transition from RNA replicators to RNA-based genomes to DNA-based genomes, the LUCA could have emerged. Further, the functions of enzymatic RNAs were -- in the RNA world model -- gradually replaced by protein enzymes. This would loosen up the constraints on RNA sequence identity, so there's not much of a reason why the absence of catalytic RNAs at the base of the tree of life would falsify the RNA world.

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Posts: 852
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Message 84 of 108 (780811)
03-22-2016 9:18 AM
Reply to: Message 78 by Dr Adequate
03-21-2016 11:39 PM

Re: @Dr Adequate
Well, here's why I disagree with the notion that creationism of the YEC variety is falsifiable: the auxiliary hypotheses which are proposed as a way around rather extraordinary problems do not increase the degree of falsifiability of the creationism scenario. So YEC isn't falsifiable because the further back you chase these auxiliary hypotheses, the less falsifiable the whole model is.

But as you can do that with anything, this is not a criticism of YEC as such.

Yes, you can do that with anything, but YEC requires this array of auxiliary hypotheses which do not increase its falsifiability. In other words, there's no way for YEC to get around isotope data concerning the age of the Earth except through the invocation of increasingly unfalsifiable auxiliary hypotheses. Contrast with the rather scientific hypothesis that type III secretion systems evolved from a bacterial flagellar system.

This hypothesis could be falsified in a single stroke by molecular phylogenies which revealed a monophyletic relationship between the two main protein systems. Auxiliary hypotheses to account for this apparent monophyly by postulating an increased rate of evolution for TTSS systems could be falsified by demonstrating that TTSS genes have evolved at a rate similar to flagellar genes (using, e.g., relative rate tests).

This is just a single example, of course, but IMHO it nicely illustrates the difference between an actual scientific hypothesis that does not require auxiliary hypotheses that decrease the degree of falsification and a model that relies on its auxiliary hypotheses to survive -- auxiliary hypotheses that do decrease the degree of falsifiability. And into the latter camp falls the YEC ideology.

Nonetheless, the idea that (e.g.) the world and the universe are ~6,000 years old is meaningful and testable.

Sure, that idea in a vacuum free of rampant ideology is testable; but then again, creationism as formulated by YEC "scientists" doesn't exist in such a vacuum, does it?

Yeah, sure, in order for something to be pseudoscience someone has to promote it as science.

Right. So what's the minimum threshold form an idea must take in order to be considered a properly constructed scientific hypothesis? I argue that the minimum threshold requirement is that it must be falsifiable and testable. Of course, these are not the only requirements, but they are the bare minimum. Do you disagree?

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Message 90 of 108 (780850)
03-24-2016 1:24 PM
Reply to: Message 86 by Blue Jay
03-22-2016 2:56 PM

Re: @Blue Jay
Hey Blue Jay,

This is well outside my area of particular expertise, but one pattern really jumps out to me. See all the words above that I highlighted in yellow? Those words all describe active processes; as in, they only work when the cell is actively metabolizing. And every one of those mechanisms you describe includes these yellow-highlighted words. So, unless a microbe is actively metabolizing during its long space voyage, these are not mechanisms that would enhance an organism's survival during panspermia.

See Mautner 2002 and Mautner et al. 1997, and other work along these lines, for observations that meteorite material can sustain growth and metabolism of prokaryotic organisms. Most published papers on lithopanspermia AFAIK are based on the premise that prokaryotes will continue to metabolize during the voyage through space.

Otherwise, you're right: these mechanisms would do little good for bacteria which are unable to metabolize. But most lithopanspermia researchers aren't proposing that the bacteria wouldn't be able to metabolize and grow.

And, if it's possible to survive a panspermia voyage without activating any genomic mechanisms, wouldn't it be hypothetically possible to find a panspermia scenario that doesn't actually require any particular genomic characteristics at all?

Well, when it comes to non-directed panspermia, we're pretty much limited to lithopanspermia and space transport via comets. Panspermia hypotheses like transport via small "micro-meteorite" grains have been mostly falsified.

My discussion so far has been mainly focused on lithopanspermia because I don't find the cometary model as convincing; nonetheless, survival of prokaryotes in the icy interior of a comet would require its own set of proteins for (1) protection from cold temperatures, and (2) mechanisms allowing for activating a dormant state among these prokaryotes, as they would not exposed to the kind of organic molecules (for metabolism) found in meteorites. Which means that the cometary panspermia model is also falsifiable through comparative genomic approaches.

1. FUCA is indeed supposed to have come from an alien planet, but not one so starkly different than Earth that FUCA could not have survived the early environ of Earth. This means that there is a not inconsiderable degree of overlap with respect to selection pressures.

There are a lot of weasel words in there. How different is "starkly different"? What degree of overlap is "not inconsiderable"? And, what does that imply for the mutability of a planet-jumping genome? You can't falsify a hypothesis by applying assumptions that are not strictly essential to the hypothesis. Any putative falsification must work equally well for any range of possible tolerances, or it isn't a true falsification.

Well, a planet with a surface temperature of several thousand degrees Celsius isn't exactly going to be friendly to prokaryotic life. So the planet(s) from which life on Earth would purportedly come from would have a relatively constrained surface temperature. The planet would also need to be more-or-less solid, so that the prokaryotes can actually travel through space via solid planetary ejecta. Liquid water would need to be present, given life's dependence on water molecules. So, compared to most planets out there, the planet on which life would have come from would be quite similar to Earth. And that means similar selection pressures.

I agree with this. But you've slipped into an argument about the plausibility of what I'm going to call the "LUCA~FUCA Hypothesis." As you said in Message 1, "...no amount of evidence for the plausibility of {a hypothesis} will be able to establish the historical accuracy of that hypothesis."

Plausibility certainly plays a role when it comes to falsification scenarios. I don't believe I've ever denied that in this discussion; my concern is when abiogenesis models are patently shown to face chemical difficulties -- but these can always be cavalierly tossed aside with the riposte, "Well, we don't really know how early Earth was like, so maybe the conditions were just right to make this particular chemical scenario plausible." So, in a way, an appeal to ignorance is made in an effort to keep the hypothesis alive -- but at the expense of falsifiability IMHO.

It is entirely possible that the genome of FUCA was radically different from the genome of LUCA, with different types of proteins serving the functions of ATP transport, breakdown of oxidizing agents, etc.; and that entire suites of FUCA's molecular machinery, optimized for function in an alien environment of unknown character, had been completely replaced in LUCA by entirely new machinery that operates more efficiently in Earth's environment.

Yes, it's possible in the sense that the probability of this happening is above 0. But is it biologically realistic? Or is this merely the conjuring of a molecular evolutionary fantasia in an effort to demonstrate that lithopanspermia is not falsifiable?

Is that possibility plausible? I don't know, but your own conditions were that we don't incorporate evidence about plausibility, so I raised my objections and proposed alternative hypotheses.

There are several reasons why I would argue that the scenario you outlined above is not biologically realistic:

(1) Such a scenario has never occurred on Earth. Despite a truly enormous variety of environments and ecological niches on Earth, no prokaryotic population has ever been discovered that has completely re-invented entire suites of core molecular machines (ATP synthases, transcription machinery, ABC transporters, etc.). That this has not occurred suggests that the core molecular machinery of biological life is not so easily replaced by evolutionary processes, regardless of the environment.

(2) The scenario would not be believable from a molecular evolutionary perspective. If the hypothetical FUCA -- containing a wide range of radically different core protein sets -- could survive on Earth upon landing, then these protein sets would most likely be tinkered with and gradually co-opted and improved upon, instead of massive deletions taking place along with massive molecular innovations.

(3) A large number of these core proteins function in an information processing context and so are not immediately affected by the external environment. E.g., polymerases are involved with nucleic acid polymers and do not interact with the external environment, so postulating a radically different external environment for the "source planet" would not require a radically different set of information processing proteins. These proteins would arguably retain their basic tertiary and quaternary structure regardless of the external environment.

There are several other reasons why your theoretical scenario isn't biologically realistic, but I'll let you respond to the above points first.

Further, even if your speculative scenario was biologically realistic, we could still determine if it was a historically accurate scenario. For starters:

(1) Molecular clock analyses. If the core protein machinery of prokaryotic life was the product of radical evolutionary innovation, then molecular clock analyses should place the time of origin of core protein machines at around 3.5 Ga, in concordance with paleontological evidence for when membrane-bound prokaryotes emerged on Earth. This is not the case, however, so this conjecture is not consistent with molecular phylogenetic evidence.

(2) Such rapid evolutionary innovation would require an extraordinarily rapid rate of evolution. So where's the evidence for this in the form of Ka/Ks ratios considerably above 1 in the conserved sequences of core protein parts?

Moreover, assuming your scenario was plausible, my falsification model for lithopanspermia would still hold: the FUCA --> LUCA scenario you propose involves the elimination of functional analogs of ABC transporters + the innovation of ABC transporters. Yet since the function of ABC transporters is so important to prokaryotic life, it is exceedingly difficult to imagine an evolutionary scenario wherein prokaryotic life would ever exist without the functional equivalent of ABC transporters from the FUCA --> LUCA transition. So, once again, we'd still expect to see certain protein functions in the LUCA; in short, at no point in life's history on Earth would it have been a progenote. It would always be a fully-fledged prokaryotic organism, even under your scenario.

It seems to me that any falsification attempt will inevitably require components addressing both the plausibility and the historicity of the proposed hypothesis. Much of the historicity is only available to us via extrapolation, no matter which route we take, and we will ultimately rely on arguments about plausibility to fill in those gaps.

Yes, but that plausibility should be interpreted in the light of biological and chemical knowledge. Otherwise, the hypothesis under consideration cannot really be falsified since we can always make vague appeals to unknown prebiotic conditions.

Edited by Genomicus, : No reason given.

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Message 95 of 108 (781199)
04-01-2016 10:27 PM

Will Be Replying Shortly
Just FYI, I haven't abandoned this thread and will be responding shortly.

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Posts: 852
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Message 97 of 108 (781964)
04-12-2016 7:34 PM
Reply to: Message 92 by caffeine
03-30-2016 1:55 PM

Re: caffeine -- Some Genomic Evidence for Panspermia
Sorry for the big delay.

Back at you!

This sort of comment might get a layperson thinking that the dozens and dozens of scientific papers published on molecular clock analyses of prokaryotic phylogeny is little more than evolutionary biologists dreaming stuff up. I find this argument suspect as it seems to imply that the aforementioned problem has not been tackled by those in the field, when in fact the paper I cited -- and many others -- understood the nature of the problem and properly addressed it with the appropriate methodology.

There are much smarter and more educated people than me working on this. Of course they've thought of the problem and tried to deal with it. And some have concluded that the variation in subsitition rates between different bacterial groups and lack of clear calibration means that estimates of deep divergences are still highly problematic.

From the paper you linked to:

"By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes."

The variation in substitution rates between different bacterial groups is a well-known phenomenon in molecular evolution research, and tools have been created to ameliorate the problems that may arise for a given gene or protein sequence set. E.g., see relative rate test and likelihood ratio test for tests to determine if a sequence set resolves to a constant molecular clock. For sequence sets that do not adhere to a constant clock, local clock approaches can be used.

I lack the expertise to talk about your different points, but I did want to ask if you could expand on:
(2) The use of node age constraints as calibration points, thereby providing information as to the minimum absolute ages of the nodes in the tree (which can be pretty easily done with Bayesian software like MrBayes).

as I don't really understand what you mean.

Node age constraints are constraints on the molecular clock nodes based on external paleontological or geological information. See here for a discussion on this technique. Here's a quote from that paper discussing node age constraints based on paleontology and geology:

"(1) Fossil. The earliest known fossil assigned to a lineage provides a minimum age constraint on the divergence event (i.e., internal node) at the base of its clade (Donoghue and Benton, 2007). Depending on the quality of the fossil record, the probability that the actual divergence falls around the fossil date may be expressed as a parametric distribution between minimum and maximum bounds (i.e., soft bounds; Yang and Rannala, 2006). (2) Geological event. Geological calibrations are assigned to internal nodes based on the assumption that phylogenetic divergence was caused by vicariance. Examples include the appearance of land bridges generating barriers to gene flow in aquatic organisms (minimum age constraint), or the emergence of an island on which a clade is inferred to have diversified (maximum age constraint) (Ho et al., 2011). As with fossils, the degree of uncertainty surrounding correspondence between the geological event and date of divergence may be expressed probabilistically."

Hope that helps!

A further problem which occured to me as I was thinking about what you wrote is that calibration points are only of limited value given that we do not actually possess a consensus phylogeny of bacteria. If chlorobactane is a clear biomarker for Chlorobi that's all well and good, but what does that actually mean if we don't know where they fit in a bacterial phylogeny?

We do not possess a consensus phylogeny of bacteria phyla. The internal branching order of many bacteria is well-established. Chlorobactane is a good biomarker for Chlorobi, and we can establish an approximate age of origin for Chlorobi through this biomarker's presence in the geologic record. This, in turn, allows us to calibrate a molecular clock of protein sequences. So if we have a given protein phylogeny, we can determine the divergence dates of the various sequences of those proteins. That protein phylogeny may not be reflective of actual bacterial phylogeny, but they do tell us information regarding the particular phylogeny and divergence dates of that kind of protein. Just because it might not wholly reflect bacterial phylogeny doesn't somehow skew the molecular clock estimates mapped onto that phylogeny.

(2) Molecular clock analyses based on (a) multiple protein sequences from multiple prokaryotic taxa, and (b) different molecular clock approaches with a variety of calibration points in each study all converge on a more-or-less unanimous conclusion: that prokaryotes are more than 4 billion years old, and less than 4.5 billion years old.
(3) This is complete accordance with lithopanspermia(..)

But it is also in complete accordance with life evolving here, on earth. Panspermia adds an additional step while explaining nothing more.

Well, it's not all that in agreement with life arising on Earth, because there's very little convincing biomarkers for full-fledged prokaryotic organisms existing on Earth 4 billion years ago, but the molecular clocks suggest otherwise. This observation is explained by lithopanspermia, in a single stroke, by positing that life is older than the time at which Earth became habitable -- and this ancient age of fully-fledged prokarya is reflected in protein molecular clocks. In other words, if life arose elsewhere and evolved for several hundreds of millions of years before being transported to Earth, these molecular clock observations would be immediately explained.

Edited by Genomicus, : No reason given.

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Message 98 of 108 (782583)
04-26-2016 9:59 AM

I've been letting this simmer in the back of my mind. A number of criticisms were levied against my OP, the most challenging of which have come from Blue Jay and Dr Adequate.

While I will be writing up responses in the near future, at the moment I will continue to think and re-think what has been said here. In particular, my OP suffers from the flaw that it equates panspermia with lithopanspermia -- when, in fact panspermia is a general idea and lithopanspermia is more specific model that I have argued is properly falsifiable in the Popperian sense.

I thought I owed this update to those who have invested time and energy in this thread, as I don't want to be one who suddenly vanishes when serious critiques are raised.

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Message 100 of 108 (784167)
05-13-2016 10:15 AM
Reply to: Message 99 by bluegenes
05-13-2016 5:00 AM

Hey bluegenes, and welcome back. Some of the stuff you've said has indeed been overviewed, but I'll respond to your post nonetheless.

It was considered perfectly reasonable to hypothesise the existence of planets outside our solar system before their existence was verified, but as we could never conceivably positively establish their absence from all stars in all galaxies, the hypothesis wasn't falsifiable.

In this thread, I've contrasted exploratory science from properly constructed scientific hypotheses. So the notion of extrasolar planets does/did fit under the umbrella of exploratory science, but as this idea wasn't falsifiable, it could not be considered a properly constructed scientific hypothesis in the Popperian sense.

Panspermia relies on the hypothesis that there is (or has been) life elsewhere in the universe. That's hypothetically verifiable, but not falsifiable. For me, that's absolutely no reason to exclude Panspermia from science. Of course it's a scientific hypothesis, although it's not actually an OOL one, of course.

The broad idea of panspermia is not falsifiable precisely because it is a general idea and not a specific model; however, lithopanspermia is falsifiable (as I've argued here) and thus qualifies as a scientific hypothesis.

The strange thing about your post is that the hypotheses you're suggesting aren't falsifiable actually are. For a start, the general hypothesis of the origin of life being on earth would have been falsified by the discovery that the planet was too young or that it was frozen for the first 4 billion years, or that it had been subject to a massive recent impact that would have sterilized it etc. etc.

Sure, but that would falsify virtually all non-teleological models for the origin of life on Earth, including panspermia -- for the simple reason that if the Earth was, say, frozen for the first 4 billion years, then there would be only 500 million years to get from prokaryotes to fully-fledged mammalian organisms.

So this falsification scenario falsifies the general premise of a non-teleological origin of life; however, it does not allow us to falsify specific abiogenesis models in a way that would be relevant only to those models.

Beyond that, some of the objections you list for "RNA" world and "Metabolism first" could conceivably be confirmed, which would be falsification. It's always hypothetical. I'd give them a better chance than observing planets moving in squares to falsify Kepler, wouldn't you?!

Some of the objections have been confirmed, but I don't see any OoL researchers abandoning the RNA world in droves. The reason is simple: the RNA world model functions as a good framework for exploratory science; but this does not make it a properly constructed scientific hypothesis.

Usually, wrongly. Although a general hypothesis of intelligent design isn't falsifiable, neither are the planets or life elsewhere hypotheses I mentioned above. It could conceivably be verified. But many specific intelligent design hypotheses could be regarded as falsifiable, as you know. The standard YEC model is an obvious example that can and has been reasonably falsified.

Well, I'd hesitate to say that the standard YEC model is falsifiable, precisely because "Goddidit" can always be invoked when there's a seemingly insurmountable problem. That creationism has this magic card -- Goddidit -- means it's really not falsifiable and so never qualified as a properly constructed scientific hypothesis.

I've not been around for a while, and haven't read the thread, so what I'm saying may well have already been said. Firstly, Popper's falsifiability notion can easily be questioned as in the examples I've given.

Popperian falsification is IMHO a very good criterion to determine whether something is to be considered a scientific hypothesis; that exploratory science still goes on does not mean that Popperian falsificationism is a flawed concept.

Secondly, the OOL hypotheses you've discussed would be regarded as falsifiable anyway.

So how would one specifically falsify the RNA world model?

Thirdly, I'm sure there are specific Panspermia hypotheses that are falsifiable, although it's difficult to think of a falsification of the general proposition.

I've cited lithopanspermia in this thread as a panspermia hypothesis that is falsifiable; there has been discussion over that, so you may want to read the previous pages.

That, however, doesn't make it unscientific, just possibly un-Popperific, and who cares?

Well, not only would it make a model under consideration "un-Popperific," it would also mean it's not a scientific hypothesis (as accepted by most of the scientific community and many philosophy of science scholars). As to who cares, I would say it's very important to stress where in science there are properly constructed scientific hypotheses (e.g., the notion of common descent can be falsified in multiple ways, and so is a good example of a properly constructed scientific theory) and where there is only exploratory (and even conjectural science).

The abiogenesis models for the origin of life are exploratory, and not hypotheses of the Popperian kind.

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Message 103 of 108 (784239)
05-15-2016 1:23 AM
Reply to: Message 102 by bluegenes
05-14-2016 8:40 AM

Re: Popperific hypotheses
That it wasn't Popperian was my point. But it was, demonstrably, a damned good scientific induction.


Hypotheses don't become any less Popperian if possible falsifications also falsify other hypotheses. Think of your own chosen example from Ruse of "planets moving in squares". I don't know how many hypotheses that would falsify, but we could probably give the whole set an umbrella description like "cosmology"!

That would seem to eliminate the utility or purpose of Popperian falsificationism though, wouldn't it? Indeed, I suspect that if extrasolar planets were to be observed orbiting in squares throughout much of the cosmos, then the RNA World model would be falsified, as would lithopanspermia (as such an observation would have profound implications on physics and thus chemistry).

Nor does it seem to be a notion that Popper ever espoused, as all his examples of the application of falsification -- e.g., Einstein's theory of relativity -- dealt with predictions made specifically and exclusively by Einstein's theory.

It's certainly Popperian. To add to the things I've already mentioned that would falsify it, future experimentation could establish that RNA is definitely too unstable to support even the simplest life forms on its own.

As I have argued above, I do not consider your previous examples of "falsification" of the RNA World correct applications of Popper's falsificationism.

As to this next example you raise, it is far too vague in its present formulation to be of much use IMHO. It is already well known among chemists and OoL researchers that ribose is quite unstable, making this a serious challenge for the RNA World model. This problem is usually "patched up" with the addition of stabilizing chemicals, such as borate and various silicates.

In short, the RNA World doesn't exactly postulate that ribonucleic acid would ever have to support primitive cells "on its own," as the RNA World incorporates a variety of other chemicals (e.g., metal ions).

Not really, because their standard model is meant to be testable. The earth should appear 6,500 yrs. old and that should fit the data. That differs from other YEC models, particularly my favourite, the Omphalist version.

Well, I will grant that some YEC models are falsifiable. But my experience from this forum with YECers is that YEC is generally not falsifiable.

The problem arises if someone implies that the hypothesis that the moon is made of cheese (Popperian) is inherently more scientific than the hypothesis that there are planets outside this solar system. The thing about the planets hypothesis is that the only reason it could be described as unfalsifiable is practical, unlike the Omphalist idea, which is untestable by its nature.

I agree that is problematic, but that is not what I am contending here. First, I am arguing that the lithopanspermia hypothesis should be considered as a "properly constructed" -- that is, Popperian -- scientific hypothesis, by virtue of its falsifiability through phylogenomics.

Second, while the "moon is made of cheese" notion may be falsifiable, it certainly does not have the kind of gravitas that would be accorded to the idea of extrasolar planets.

This is because there simply is no reason to suspect the moon is made of cheese; and there are numerous reasons to postulate that extrasolar planets exist (and we now know they do).

Scientific hypotheses must, of course, be more than just falsifiable. It's not like falsifiability is the one thing that determines if something is science or not. But the point is this: lithopanspermia may be considered to be on basically equal footing with the RNA World model (and other abiogenesis scenarios). The RNA World model has several lines of circumstantial evidence, as well as many serious difficulties. On the other hand, lithopanpsermia also has circumstantial evidence -- as well as some other pieces of evidence, such as the molecular phylogenetics argument I presented in previous posts -- and arguably not as many difficulties as the RNA World model.

They're definitely falsifiable.

You may very well be right; however, I have yet to see a compelling, detailed falsification scenario for the RNA World model, so consider this your opportunity to present just such a scenario.

Edited by Genomicus, : No reason given.

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 Message 102 by bluegenes, posted 05-14-2016 8:40 AM bluegenes has responded

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Message 104 of 108 (784240)
05-15-2016 1:27 AM
Reply to: Message 101 by Dr Adequate
05-13-2016 12:28 PM

But I'm not sure that this is Popper's sense. I understood him to be talking about hypotheses which are so constructed that no acquisition of data would cause one to abandon them; not merely hypotheses where we are presently unable to acquire the data.

You are correct, yes.

So the challenge here is to present the kind of data that would need to be acquired in order to falsify the RNA World model or the metabolism-first scenario.

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Message 107 of 108 (784818)
05-23-2016 9:33 PM
Reply to: Message 106 by bluegenes
05-15-2016 9:17 PM

Re: Popperific hypotheses
Based on the arguments you and Dr. Adequate, and others, have presented here, I concede that the RNA World model for the origin of life is falsifiable. I suspect that the metabolism-first model is perhaps more difficult to falsify, but I can imagine scenarios where it could be considered refuted.

This means the core argument in my OP has been knocked down. However, I would like to see exactly how you view the whole issue of Popperian falsification. Simply put, given that you don't seem to be particularly enthralled by Popperian falsificationism, what -- in your view -- is the proper place of Popperian falsificationism in the broader fabric of science?

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 Message 106 by bluegenes, posted 05-15-2016 9:17 PM bluegenes has responded

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