Looks like we are on the same page

[Tom Hendricks]

Looks like this author's idea of stability is a lot like mine.

http://aeon.co/magazine/science/stability-how-life-began-and-why-it-cant-rest/

My blog post.

http://musea.wordpress.com/2014/03/10/the-origin-of-life-a-different-perspective/

[n***@bellsouth.net]

Post by Tom Hendricks
Looks like this author's idea of stability is a lot like mine.
http://aeon.co/magazine/science/stability-how-life-began-and-why-it-cant-rest/

However, the author, Addy Pross, also goes into a few concrete facts
of the sort that are missing from your blog post,

Post by Tom Hendricks
http://musea.wordpress.com/2014/03/10/the-origin-of-life-a-different-perspective/

However, these few bits of data are overwhelmed by philosophizing on a very
low level. The closest we get to something one can sink one's teeth into
is this:

"Gerald Joyce, professor of chemistry at the Scripps Research Institute
in La Jolla, California, recently demonstrated how a single replicating
RNA molecule, on its own, is a relatively inefficient replicator.
In contrast, a two-molecule RNA replicating network, in which each
RNA molecule catalyses the formation of the other, is far more effective."

If they are both RNA polymerases of the ribozyme sort, of course each will
replicate the other in two steps: first making a "mirror image" of the
other and then turning the mirror image into a copy of the original.

OTOH neither is able to replicate itself because it cannot twist around
to act upon itself in the right way. It must wait for the right
nucleotides to attach themselves to it in the right places.
Granted, once a "mirror image" of itself is formed in this way, it
can act on the mirror image to make a copy of itself.

Two random RNA molecules can't be expected to act on each other
in this way, so I wonder what the La Jolla experiment was all about.
Unfortunately, no reference was given. I suspect it is this one
that I found by looking up Gerald Joyce's home page:

Science 27 February 2009: Vol. 323 no. 5918 pp. 1229-1232
DOI: 10.1126/science.1167856
Self-Sustained Replication of an RNA Enzyme
Tracey A. Lincoln,
Gerald F. Joyce*
http://www.sciencemag.org/content/323/5918/1229.abstract

The full page is paywalled, but already the abstract leads me to
believe that these are very special sorts of RNA molecules that are
like RNA polymerases:

"An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted
to a format whereby two enzymes catalyze each other's synthesis from a total
of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo
self-sustained exponential amplification in the absence of proteins or other
biological materials."

Unfortunately, Addy Pross shows no awareness of this kind of mechanism
and speculates cluelessly:

"The two-molecule system is more effective for the same reason that
picking up an object with two fingers is a lot easier than with just one,"

No, it isn't. A much closer analogy is that two people can take turns
lifting each other up into the air while one person cannot lift himself
up into the air.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/
nyikos @ math.sc.edu

[Tom Hendricks]

My point is this - what specifically is any living thing coding for? What is the RNA or DNA coding for? What is it's message over and over again.

It is stability - a very special two part stability
1. keep what is working
2. change the rest or improve.

When we look at all life we see two directions; hold what works, fix or improve what doesn't.
That two part stability is what I think, I and the author have in common.

That is a major shift in what we are looking for in first life or OOL
It is not coding for things that scientists want to get to - specifically some type of replication, or metabolism, or cell or ....etc.
That is secondary to the stability that keeps this going long enough to do what ever it needs
to continue that stability. Then replication, metabolism, a cell membrain, all help that stability.

[n***@bellsouth.net]

I've been very busy elsewhere, and my posts in talk.origins took priority
where Usenet is concerned, but I hope to become more active in s.b.e.
before long. It has several features that talk.origins is short on.

Post by Tom Hendricks
My point is this - what specifically is any living thing coding for?
What is the RNA or DNA coding for? What is it's message over and over again.
It is stability - a very special two part stability
1. keep what is working
2. change the rest or improve.

That presupposes evolution is governed by natural selection, and
that natural selection follows our ideas of "working" and "improve."

When we get to specifics, there are some puzzles. Why did birds get
rid of their clawed fingers? Flightless birds suffer in comparison
with their upright reptilian forbears, some of which seemed to be
heading towards our level of intelligence when the K-T disaster struck.
Descendants of dinosaurs like Troodon might have developed opposable
thumbs and achieved human-level intelligence by now. Mammals of the
time do not seem to have had quite as advanced a brain as Troodon had.

Post by Tom Hendricks
When we look at all life we see two directions; hold what works,
fix or improve what doesn't.

If I think about this for a few days, I might come up with more exceptions
like the one I've described just now.

Post by Tom Hendricks
That two part stability is what I think, I and the author have in common.
That is a major shift in what we are looking for in first life or OOL
It is not coding for things that scientists want to get to -
specifically some type of replication, or metabolism, or cell or ....etc.

Sorry, IMO these are still the gold standard and you will have to
work hard to convince me otherwise.

Post by Tom Hendricks
That is secondary to the stability that keeps this going long
enough to do what ever it needs to continue that stability.

Stability is impossible without faithful replication. But replication
has many more aspects than just stability. Too much stability produces
stasis. And indeed, there were long periods in our earth's history
where stasis seemed to dominate. There was probably a long stretch
between the first prokaryote and the first eukaryote, then a long
stretch (at least 1000 million years) before the first eumetazoan.

The difficulty of programming an entire trilobite
(for example) into one germ cell is probably far greater than
programming an alga of perhaps 1000 million years earlier.

It gets worse where *Homo sapiens* [or indeed any
large mammal] is concerned. The concept of "cancer",
where one word encompasses a multitude of developmental things
gone wrong, testifies to that, as well as an entire discipline
of teratology. A tree can easily survive a Witches' broom;
a human being can't survive most tumors that keep growing,
even if they don't metastasize.

Plants are far more stable, in other words, than animals. But
how much poorer our world would be, if animals did not exist!

Post by Tom Hendricks
Then replication, metabolism, a cell membrain, all help that stability.

What kind of stability do you envision where these things are lacking?

Cell membranes [note the spelling] are almost indispensible for faithful
replication and evolution.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/
nyikos @ math.sc.edu
.

[Tom Hendricks]

Post by n***@bellsouth.net

Post by Tom Hendricks
What is the RNA or DNA coding for? What is it's message over and over again.
It is stability - a very special two part stability
1. keep what is working
2. change the rest or improve.

That presupposes evolution is governed by natural selection, and
that natural selection follows our ideas of "working" and "improve."

Yes - specifically every selection is for better anabolic processes (nurture in) or catabolic processes (waste out)

Post by n***@bellsouth.net
When we get to specifics, there are some puzzles. Why did birds get
rid of their clawed fingers? Flightless birds suffer in comparison
with their upright reptilian forbears, some of which seemed to be
heading towards our level of intelligence when the K-T disaster struck.
Descendants of dinosaurs like Troodon might have developed opposable
thumbs and achieved human-level intelligence by now. Mammals of the
time do not seem to have had quite as advanced a brain as Troodon had.

Natural selection seems to be more for tinkering to fit the present circumstances, than achieving some future perfection.
......

Post by n***@bellsouth.net

Post by Tom Hendricks
That two part stability is what I think, I and the author have in common.
That is a major shift in what we are looking for in first life or OOL
It is not coding for things that scientists want to get to -
specifically some type of replication, or metabolism, or cell or ....etc.

Sorry, IMO these are still the gold standard and you will have to
work hard to convince me otherwise.

What if bacteria divide, just to get rid of waste - then replication is no more than another
way to get rid of waste so the cell can grow again?
Replication or metabolism are just words for ways to achieve this stability.
Thinking outside the usual we could say
Replication is just a way of getting rid of waste, so the parent cell can grow again
Metabolism is just a way of dealing with forced UV light in the most stable way.

Post by n***@bellsouth.net

Post by Tom Hendricks
That is secondary to the stability that keeps this going long
enough to do what ever it needs to continue that stability.

Stability is impossible without faithful replication. But replication
has many more aspects than just stability. Too much stability produces
stasis. And indeed, there were long periods in our earth's history
where stasis seemed to dominate. There was probably a long stretch
between the first prokaryote and the first eukaryote, then a long
stretch (at least 1000 million years) before the first eumetazoan.

Can't stress this enough, We need a new word for my "Stability"
Which again is two p;art
Stable in what works
Changeable in what doesn't work or needs improvement.

Remember both sides of my definition. Perhaps "Tom's Two Part Stability definition" LOL

Post by n***@bellsouth.net
The difficulty of programming an entire trilobite
(for example) into one germ cell is probably far greater than
programming an alga of perhaps 1000 million years earlier.
It gets worse where *Homo sapiens* [or indeed any
large mammal] is concerned. The concept of "cancer",
where one word encompasses a multitude of developmental things
gone wrong, testifies to that, as well as an entire discipline
of teratology. A tree can easily survive a Witches' broom;
a human being can't survive most tumors that keep growing,
even if they don't metastasize.
Plants are far more stable, in other words, than animals. But
how much poorer our world would be, if animals did not exist!

Post by Tom Hendricks
Then replication, metabolism, a cell membrain, all help that stability.

What kind of stability do you envision where these things are lacking?

Well they are integral to that stability - so it's like saying what color is red without red?
Remember my two part stability.
Zircon are probably the closest to being as stable as life.
Both are about as old. But though zircon has one part of my stability definition,
it doesn't have the 2nd part.
Tom's Stability Definition, that's different from the stability definition from the dictionary in having two parts.

Stable in what works
Changeable in what doesn't work or needs improvement.

Post by n***@bellsouth.net
Cell membranes [note the spelling] are almost indispensible for faithful
replication and evolution.

They are - and are stable in two ways
Stable in what works
Changeable in what doesn't work or needs improvement.


Perhaps a main reason why the OOL research is not moving forward very much is that
instead of looking at what life is, we are trying to get chemicals to get to metabolism and replication.
There is a difference.

Post by n***@bellsouth.net
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/
.