Comments on: Probabilities and the Genesis of Life

By: Nakashima

Nakashima — Sun, 20 Dec 2009 10:28:13 +0000

Mr Frank,

The Wiki (English) entry for “Oxygen catastrophe” has a clearer and more detailed image.

While I can imagine a link between oxygen levels and a motile, carnivorous lifestyle, just being multicellular could apply to plants as well.

On a related note, I wonder if anyone has studied the timing of the endosymbionic events for chloroplasts and mitochondria.

By: Clive Hayden

Clive Hayden — Thu, 17 Dec 2009 18:31:52 +0000

lastyear,

That is correct. There’s all manner of things that we cannot rule out. But just because something cannot be ruled out doesn’t mean it has any merit or even makes sense.

Nor does it mean that it doesn’t make sense. We cannot make sense of nature, therefore we have no real basis for comparison when comparing nature to super or non natural things. If we don’t understand the rule, we cannot rule out the exception.

By: Mark Frank

Mark Frank — Thu, 17 Dec 2009 15:14:11 +0000

#141

Yes – but this diagram on Wikipedia suggested to me that the oxygen content was low until just before the Cambrian – mind you it is in German so maybe I don’t understand it!

By: Nakashima

Nakashima — Thu, 17 Dec 2009 13:54:00 +0000

Mr Frank,

If the atmosphere became oxygenated 2.4 billion years ago, and metazoa appeared 600 million years ago, there is still a vast gulf of time not explained by that hypothesis.

Somewhere in that gap, life invented and refined the idea of sexual reproduction. Judging by memories of my own teenage years, I am not at all surprised if this took a billion years to figure out!

By: Dave Wisker

Dave Wisker — Thu, 17 Dec 2009 10:56:20 +0000

Mr Nakashima & vjtorley, you both might enjoy this article as well: Costanzo G, S Pino, F Ciciriello, & E Di Mauro (2009). The generation of long RNA chains in water. The Journal of Biological Chemistry 284: 33206-33216.

The synthesis of RNA chains from 3?,5?-cAMP and 3?,5?-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40–90 °C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3?,5?-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3?, 5?-cGMP to ?25-nucleotide-long RNA molecules, and of 3?,5?-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3?,5?-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.

By: lastyear

lastyear — Thu, 17 Dec 2009 10:41:28 +0000

Clive Hayden

We don’t know what nature is, and cannot rule out super or non natural things.

That is correct. There’s all manner of things that we cannot rule out. But just because something cannot be ruled out doesn’t mean it has any merit or even makes sense.

By: Dave Wisker

Dave Wisker — Thu, 17 Dec 2009 10:24:21 +0000

vjtorley,

I would like to echo Mr Nakashima’s comments and say this discussion has been a pleasure.

By: Dave Wisker

Dave Wisker — Thu, 17 Dec 2009 10:21:44 +0000

Mr Nakashima,

That was a good reference. Tied in with the following article, we can begin to see how tRNAs (which are actually very small)could form from random RNA sequences. This then ties in well with the stereochemical hypothesis for the origin of the genetic code.

Nagaswamy U & GE Fox (2003). RNA ligation and the origin of tRNA. Origins of Life and Evolution of the Biosphere 33: 199-209

A straightforward origin of transfer RNA, (tRNA), is difficult to envision because of the apparently complex idiosyncratic interaction between the D-loop and T-loop. Recently, multiple examples of the T-loop structural motif have been identified in ribosomal RNA. These examples show that the long-range interactions between the T-loop and D-loops seen in tRNA are not an essential part of the motif but rather are facilitated by it. Thus, the core T-loop structure could already have existed in a small RNA prior to the emergence of the tRNA. The tRNA might then have arisen by expansion of an RNA that carried the motif. With this idea in mind, Di Giulio’s earlier hypothesis
that tRNA evolved by a simple duplication or ligation of a minihelix RNA was re-examined. It is shown that an essentially modern tRNA structure can in fact be generated by the ligation of two 38-nucleotide RNA minihelices of appropriate sequence. Although rare, such sequences occur with sufficient frequency, (1 in 3 × 107), that they could be found in a standard in vitro RNA selection experiment. The results demonstrate that a series of RNA duplications, as previously proposed, can in principal account for the origin of tRNA. More generally, the results point out that RNA ligation can be a powerful driving force for increased complexity in the RNA World.

By: Mark Frank

Mark Frank — Thu, 17 Dec 2009 10:08:37 +0000

Oramus 115, Joseph 116, vjtorley 133

You are right! I had not thought about the requirement to create an oxygen rich atmosphere to sustain multicellular life.

I do disagree with Joseph’s line in #116

One doesn’t have to know the motivations to critique the design

If you don’t know what the design is intended to do – how can you know if it does it well?

By: Clive Hayden

Clive Hayden — Thu, 17 Dec 2009 06:44:50 +0000

lastyear,

There is no utility in trying to compare the natural and the non natural. Simply chalk the concept of the later up to the generous ‘nature’ of language and the creative abilities of the human mind.

Then call it super instead of non natural. It doesn’t much matter. We don’t know what nature is, and cannot rule out super or non natural things.