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Author Topic:   On the Origin of Life and Falsifiability
caffeine
Member (Idle past 42 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 27 of 108 (780056)
03-10-2016 2:43 PM
Reply to: Message 8 by Genomicus
03-09-2016 8:31 AM


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

I don't see this to be the case from looking at the evidence you've presented for panspermia. Of the four studies you cited in support of panspermia; Rampelotto's you described as overcoming objections, which sounds very much like establishing plausibilty (I haven't read the article) and Mautner's and Melosh's are both explicitly establishing the plausibility of micro-organism's being transported through space.

The fourth, Wallis (2003), I'm a bit surprised that no one else has picked up on yet, as this is a wildly speculative article about the dinosaurs being wiped out by poisonous fungi from space. It's short, and I would highly encourage everyone to read it; including yourself, as I get you impression you may not have based on your relatively complimentary description.


This message is a reply to:
 Message 8 by Genomicus, posted 03-09-2016 8:31 AM Genomicus has responded

Replies to this message:
 Message 62 by Genomicus, posted 03-15-2016 11:10 PM caffeine has responded

  
caffeine
Member (Idle past 42 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 69 of 108 (780557)
03-16-2016 2:56 PM
Reply to: Message 62 by Genomicus
03-15-2016 11:10 PM


Re: caffeine -- Some Genomic Evidence for Panspermia
Molecular clocks of prokaryotes based on 32 well-conserved proteins present in both bacteria and Archaea suggest that bacteria diverged ~4.1 Gyr ago and Archaea diverged at ~4 Gyr (Battistuzzi et al. 2004). Yet the most ancient, definitively microbial fossils are found in Archaean rocks about 3.5 Gyr in age.

The problem with this sort of reasoning is that there do not really exist many meaningful calibration points when we're discussing this sort of age. It's very complex to establish whether ancient bacterial fossils are in fact fossils rather than abiotic artefacts - assigning them to a clade is essentially impossible. We can only assume the emergence of bacterial clades by geochemical arguments - we can tie the rise in atmospheric oxgyen c. 2.4 Gya to cyanobacteria, for example. The problem with this is that geochemistry in complicated and there is still much we don't understand, so there is little agreement on when oxygenic photosynthesis actually arose. While we can agree it's there by 2.4 Gya, some researchers push it up to a billion years earlier; as their geochemical models include sinks for oxygen that explain it's late rise. The origins of methanotrophy are argued to be anywhere between 4 billion and 700 million years ago, as the same chemical data can often be explained by different biotic and abiotic processes.

From a phylogenetic point of view, of course, we have the further issue of assuming that a particular chemical pathway was done by the same organisms 3 billion years ago as it was now, so these aren't necessarily that useful as calibration points. You were talking earlier about Cavalier-Smith's arguments about polarity in evolution - worth noting is that his argument on this subject has Archaea diverging only about 850 million years ago.

On the subject of the oldest definitively prokaryotic fossils, I think more caution is needed. You can read here Brasier et al. (2006) on the difficulties of ruling out abiotic processes to form Archaean 'fossils' (but look relatively quick if you want to, as this goes behind a paywall at the end of the year). The science on early life is too difficult for us to proclaim any dates with confidence yet.

However, even if we did choose to accept that life is this old, there seems to be a huge unjustified leap in the next step in your reasoning. Without any clear model of the actual process by which life arose, how can we possibly be justified in saying something is a long or short time? We're not talking about life arising in an hour. Is 16 million years a short time? Why? That's an incredibly long time from our perspective - maybe that's an ample sufficiency of time for life to arise.

It is premature to seek an explanation of how x could happen so quickly without a model of how long x should be expected to take.

--------------------

I will try to come back to Wallis' article later. Been a while since I actually tried to put some work into a post - takes time! Don't know how you can bang all these out.


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 Message 71 by Genomicus, posted 03-21-2016 5:16 AM caffeine has responded
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caffeine
Member (Idle past 42 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 70 of 108 (780772)
03-20-2016 3:33 PM
Reply to: Message 62 by Genomicus
03-15-2016 11:10 PM


Fungi from spaaaaaaace!
I did, in fact, read Wallis' 2003 paper prior to writing up the OP. It is indeed speculative, but it's not "wildly" speculative IMHO -- unless you would also grant that label to the RNA world model. The distribution of Aib-polypeptides in the paleontological record are tentatively suggestive of a biogenic origin; further work would have to be done in order to shed more light on this.

'Wildly speculative' was the polite way of puttiing it. 'Steaming pile of horseshit' would be the franker and more accurate way of describing it. I had intended to get around to writing a more detailed critique, but learning about the evolution of polypeptides via Google is more complicated than expected.

Such knowledge is unnessecary to dismiss this article, however. Before you discussed the use of phylogenetic arguments to dismiss panspermia scenarios. Phylogenetically, we know that fungi are deeply embedded in the terrestrial tree of life. They are opisthokont eukaryotes closely related to animals. And yet Wallis is seriously proposing as a plausible hypothesis that peptaibol-producing fungi like Trichoderma arrived from space just over 65 million years ago. This is not a suggestion we should be taking seriously.


This message is a reply to:
 Message 62 by Genomicus, posted 03-15-2016 11:10 PM Genomicus has responded

Replies to this message:
 Message 73 by Genomicus, posted 03-21-2016 9:11 AM caffeine has responded

  
caffeine
Member (Idle past 42 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 92 of 108 (781054)
03-30-2016 1:55 PM
Reply to: Message 71 by Genomicus
03-21-2016 5:16 AM


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

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.

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.

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?

Since Cavalier-Smith's (arguably weak) transition analyses can't be used to establish absolute dates of origin, his figure in the paper (from which I believe you got the 850 million years) cannot be taken to be any sort of evidence for absolute ages.

I got the date of 850 million years by reading the words that he wrote, here and elsewhere, rather than looking at a figure. The idea comes from his belief that eukaryotes and archaea are nested deeply with bacteria due to the plausibility of different evolutionary steps.

Now, I don't think that his argument is very convincing, and is even less so now than ten years ago, as it requires dismissing an enormous number of putative eukaryotic fossils from far too early. My point was simply that an argument which relies on divergence dates between archaea and bacteria may be premature when the estimates for this in the literature span an order of magnitude.

More importantly though, I don't see how it helps. You note that:

(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.


This message is a reply to:
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Replies to this message:
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caffeine
Member (Idle past 42 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 93 of 108 (781055)
03-30-2016 2:07 PM
Reply to: Message 73 by Genomicus
03-21-2016 9:11 AM


Re: Fungi from spaaaaaaace!
And not one Wallis is making per se. He proposes the following two scenarios as possible explanations for the geologic distribution of Aib peptides: (1) that fungi from space landed on Earth, and that the genomes of these fungi encoded genes for Aib polypeptides, or (2) an unknown kind of microbial organism landed on Earth, equipped with genes for Aib polypeptides; these genes were subsequently transferred to fungal genomes.

Your attempt to refute (1) by pointing to the long branches of fungi in eukaryote phylogenies fails to consider that it's hypothetically possible for fungi-like organisms to land on Earth with that lineage going extinct -- but not before some of their genes were laterally transferred to other fungi clades and certain prokaryotes.

So you mean that he's using fungi as description of a type of organism, rather than as a clade? That's slightly more plausible, but it does mean that we're talking about a constant stream of DNA-based life flying through the cosmos, rather than a one-off event four billion years. What I don't see is any evidence that this is the case.

Anyways, what's your explanation for the particular distribution of Aib in the K/T transition?

What particular distribution? All he mentions in the article is two sites associated with the Chicxulub impact which contain the amino acid Aib. He also points out that that same amino acid was found in a meteorite that fell in historical times. If I had to make an explanation it would be that it's a compound sometimes found in meteorites. I don't know why, but I don't see any reason to invoke space organisms.


This message is a reply to:
 Message 73 by Genomicus, posted 03-21-2016 9:11 AM Genomicus has not yet responded

  
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