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Author Topic:   On the Origin of Life and Falsifiability
Genomicus
Member (Idle past 12 days)
Posts: 846
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


@PaulK
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.


This message is a reply to:
 Message 61 by PaulK, posted 03-15-2016 2:26 PM PaulK has responded

Replies to this message:
 Message 79 by PaulK, posted 03-22-2016 2:15 AM Genomicus has responded

  
Genomicus
Member (Idle past 12 days)
Posts: 846
Joined: 02-15-2012


(1)
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.


This message is a reply to:
 Message 75 by Dr Adequate, posted 03-21-2016 8:48 PM Dr Adequate has responded

Replies to this message:
 Message 78 by Dr Adequate, posted 03-21-2016 11:39 PM Genomicus has responded

  
Dr Adequate
Member
Posts: 15972
Joined: 07-20-2006
Member Rating: 4.7


Message 78 of 108 (780800)
03-21-2016 11:39 PM
Reply to: Message 77 by Genomicus
03-21-2016 9:08 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.

The fact that some YECs do in fact add auxiliary hypotheses to deprive their central idea of any predictive power is a reason to criticize the people who do this. Nonetheless, the idea that (e.g.) the world and the universe are ~6,000 years old is meaningful and testable.

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.

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


This message is a reply to:
 Message 77 by Genomicus, posted 03-21-2016 9:08 PM Genomicus has responded

Replies to this message:
 Message 84 by Genomicus, posted 03-22-2016 9:18 AM Dr Adequate has responded

  
PaulK
Member
Posts: 13313
Joined: 01-10-2003
Member Rating: 2.0


Message 79 of 108 (780801)
03-22-2016 2:15 AM
Reply to: Message 76 by Genomicus
03-21-2016 8:50 PM


Re: @PaulK
quote:

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.


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.

quote:

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.

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.

i thank you for admitting that I was right, but I consider the way of doing it - presenting agreement as disagreement another sign that you are not interested in serious discussion.


This message is a reply to:
 Message 76 by Genomicus, posted 03-21-2016 8:50 PM Genomicus has responded

Replies to this message:
 Message 80 by Genomicus, posted 03-22-2016 2:26 AM PaulK has responded

    
Genomicus
Member (Idle past 12 days)
Posts: 846
Joined: 02-15-2012


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.


This message is a reply to:
 Message 79 by PaulK, posted 03-22-2016 2:15 AM PaulK has responded

Replies to this message:
 Message 81 by PaulK, posted 03-22-2016 2:46 AM Genomicus has responded

  
PaulK
Member
Posts: 13313
Joined: 01-10-2003
Member Rating: 2.0


Message 81 of 108 (780803)
03-22-2016 2:46 AM
Reply to: Message 80 by Genomicus
03-22-2016 2:26 AM


Re: @PaulK
quote:

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.

It is far from obvious that that is true. In fact your whole claim of falsifiability relies on a specific feature of lithopanspermia.

quote:

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

And yet panspermia is unfalsifiable. String theory is unfalsifiable. And you accept the first as science, and very many scientists accept the second as science. Unfalsifiability in itself is clearly not the clear bright line you are looking for.

Again, you have conceded the point that my criteria are adequate to dismiss YEC as science. Therefore any argument that I need different criteria to do so is obviously fallacious.


This message is a reply to:
 Message 80 by Genomicus, posted 03-22-2016 2:26 AM Genomicus has responded

Replies to this message:
 Message 82 by Genomicus, posted 03-22-2016 3:39 AM PaulK has responded

    
Genomicus
Member (Idle past 12 days)
Posts: 846
Joined: 02-15-2012


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.


This message is a reply to:
 Message 81 by PaulK, posted 03-22-2016 2:46 AM PaulK has responded

Replies to this message:
 Message 87 by PaulK, posted 03-24-2016 9:20 AM Genomicus has not yet responded

  
Genomicus
Member (Idle past 12 days)
Posts: 846
Joined: 02-15-2012


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.


This message is a reply to:
 Message 66 by Blue Jay, posted 03-16-2016 11:17 AM Blue Jay has responded

Replies to this message:
 Message 86 by Blue Jay, posted 03-22-2016 2:56 PM Genomicus has responded

  
Genomicus
Member (Idle past 12 days)
Posts: 846
Joined: 02-15-2012


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?


This message is a reply to:
 Message 78 by Dr Adequate, posted 03-21-2016 11:39 PM Dr Adequate has responded

Replies to this message:
 Message 85 by Dr Adequate, posted 03-22-2016 11:02 AM Genomicus has not yet responded

  
Dr Adequate
Member
Posts: 15972
Joined: 07-20-2006
Member Rating: 4.7


(1)
Message 85 of 108 (780813)
03-22-2016 11:02 AM
Reply to: Message 84 by Genomicus
03-22-2016 9:18 AM


Re: @Dr Adequate
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.

There's no way to get round the evidence that there wasn't an elephant in my house except through the invocation of increasingly unfalsifiable auxiliary hypotheses. That's 'cos it's false.

And you can in fact invoke auxiliary hypothesis to save any initial hypothesis from the evidence. (I think of this as the principle of Smacco's Rozar.)

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?

I think I would disagree somewhat with your characterization, as it has revealed itself through your posts and examples. For example, go back a few decades and we had no means to test whether other stars had planets. Was it then an unscientific hypothesis that exoplanets existed? What should we have said about someone who was in the process of building a device to test it, but hadn't finished yet? --- that he wished to conduct a scientific investigation of something that wan't even a properly constructed scientific hypothesis?

But the question of whether "There are exoplanets" is properly constructed should surely not be dependent on the state of our technology.

Now you might ask, if we admit this principle, where do we stop? Is someone allowed to say "Although we can't test this yet, we would be able to if we could construct a time machine or an omniscope"? Well, if not, where can we draw the line? If so, then the criterion of falsifiability looks more like a criterion of meaningfulness.


This message is a reply to:
 Message 84 by Genomicus, posted 03-22-2016 9:18 AM Genomicus has not yet responded

  
Blue Jay
Member (Idle past 291 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 86 of 108 (780822)
03-22-2016 2:56 PM
Reply to: Message 83 by Genomicus
03-22-2016 8:47 AM


Re: @Blue Jay
Hi, Genomicus.

Genomicus writes:

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.

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.

In fact, none of these mechanisms actually protects a microbe from ionizing radiation: rather, they repair a microbe after ionizing radiation. They would need some other means of actually surviving the radiation in order to get the chance to repair themselves afterwards (unless, again, they have some means of maintaining an active metabolism in deep space).

So, perhaps the real "trick" to panspermia isn't about being able to repair yourself: it's about having enough of yourself left to repair once you arrive. 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?

---

Genomicus writes:

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.

Genomicus writes:

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.

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."

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.

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.

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.

Edited by Blue Jay, : No reason given.

Edited by Blue Jay, : No reason given.


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 83 by Genomicus, posted 03-22-2016 8:47 AM Genomicus has responded

Replies to this message:
 Message 88 by PaulK, posted 03-24-2016 9:33 AM Blue Jay has responded
 Message 90 by Genomicus, posted 03-24-2016 1:24 PM Blue Jay has responded

  
PaulK
Member
Posts: 13313
Joined: 01-10-2003
Member Rating: 2.0


Message 87 of 108 (780843)
03-24-2016 9:20 AM
Reply to: Message 82 by Genomicus
03-22-2016 3:39 AM


Re: @PaulK
quote:

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

It seems to me that your argument assumes that such travel places very right restrictions on the organisms that could survive such travel. If that is correct, then my point is made. If it is not how can your claimed falsification possibly work ?

quote:

You haven't made a very good case that lithopanspermia is unfalsifiable,

On the other hand you are making a very good case against the hypothesis that you are engaged in honest discussion. I said "panspermia" not "lithopanspermia". And I have not been trying to make a case that lithopanspermia is unfalsifiable.

quote:

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

There is dispute over the status of String Theory as science, but that dispute has hardly been resolved against it.

quote:

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

Actually I mean that the that YEC has been effectively falsified renders further pursuit of it as non-science.


This message is a reply to:
 Message 82 by Genomicus, posted 03-22-2016 3:39 AM Genomicus has not yet responded

    
PaulK
Member
Posts: 13313
Joined: 01-10-2003
Member Rating: 2.0


Message 88 of 108 (780844)
03-24-2016 9:33 AM
Reply to: Message 86 by Blue Jay
03-22-2016 2:56 PM


Re: @Blue Jay
It seems to me that bacterial spores would be a far more promising material than live bacteria. And if the falsification relies on the assumption that living bacteria rather than spores were transferred - and it sounds to me as if that is what you're saying - then it really isn't much of a falsification. If spores can make the journey without those tricks, then the tricks aren't really necessary.
This message is a reply to:
 Message 86 by Blue Jay, posted 03-22-2016 2:56 PM Blue Jay has responded

Replies to this message:
 Message 89 by Blue Jay, posted 03-24-2016 10:22 AM PaulK has not yet responded

    
Blue Jay
Member (Idle past 291 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 89 of 108 (780845)
03-24-2016 10:22 AM
Reply to: Message 88 by PaulK
03-24-2016 9:33 AM


Re: @Blue Jay
Hi, Paul.

PaulK writes:

It seems to me that bacterial spores would be a far more promising material than live bacteria. And if the falsification relies on the assumption that living bacteria rather than spores were transferred - and it sounds to me as if that is what you're saying - then it really isn't much of a falsification. If spores can make the journey without those tricks, then the tricks aren't really necessary.

Yeah, that's what I was trying to get at.

I also think Genomicus was too dismissive of the possibility that an icy comet may in fact be sufficient protection against ionizing radiation.

I was going to hold off on the details until I saw Genomicus's rebuttal, though: give him the chance to steer the conversation, since it's his topic.


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 88 by PaulK, posted 03-24-2016 9:33 AM PaulK has not yet responded

  
Genomicus
Member (Idle past 12 days)
Posts: 846
Joined: 02-15-2012


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.


This message is a reply to:
 Message 86 by Blue Jay, posted 03-22-2016 2:56 PM Blue Jay has responded

Replies to this message:
 Message 91 by Blue Jay, posted 03-25-2016 11:52 AM Genomicus has not yet responded
 Message 96 by Percy, posted 04-03-2016 8:48 AM Genomicus has acknowledged this reply

  
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