OOL I - Manifesto and metatheory

From: Perplexed in Peoria (jimmenegay_at_sbcglobal.net)
Date: 02/27/05 

Date: Sun, 27 Feb 2005 01:04:41 -0500 (EST)

This is the first of a planned series of postings in which I will present
my viewpoint and some of my ideas regarding the origin of life. The word
"viewpoint" was chosen carefully - in no sense will I be presenting a
"theory" of life's origin.

Feedback, both positive and negative, is, of course, welcome as the series
of postings proceeds. I particularly welcome answers by knowlegeable
persons to the queries that I pose [in brackets like this!]. However,
negative reviewers should be aware that my purpose here is more
explicatory than hortatory. I want to explain my viewpoints and ideas, as
well as the reasons I have adopted them, rather than necessarily to
convince anyone else to join me in my position.

Along the way, I will present various "slogans" that summarize my
thinking. In a forum such as this, presentation and explanation of
slogans is about all that can be accomplished.

This first posting is mostly introduction. My approach to OOL is notable
in three main ways:
1. In the way I define the problem.
2. In the methodology which I think has the best chance of leading to
success in attacking the problem.
3. In key assumptions of fact which I believe will ultimately be
incorporated as a keystone in any ultimate successful theory of the
origin.

-------------------------
Definition of the Problem:
-------------------------

The problem is to explain how life as we know it came to be. This is a
larger and broader problem than most OOL theorists address.

Many of them see the origin as a event - something that happened once.
They focus on some key feature of life (at least it seems to them to be
the key feature) and try to explain ITS origin. A typical example of a
key feature for this kind of theorist would be genetics, and a typical
example of such a theorist would be Cairns-Smith.

Others see the origin as a process - something that took place over time.
They look for some kind of organizing principle for life's origin that
is perhaps as profound as Darwin's NS. They hope that such a principle
can be found in the unexplored wilderness of non-equilibrium
thermodynamics or of complex systems theory. (Their hopefulness reminds
me of the American congressman who supports the space program because he
thinks it will find the cure for cancer. "We haven't found it down here,
so it must be up there.") A typical example of such a theorist might be
Stuart Kauffman.

So, which is it? Event or process? It is time for our first slogan:

   Slogan: Neither an event nor a process. It is a series of events.

In my mind, the "Origin of Life" comprises at least everything that
happened leading up to the MRCA (most recent common ancestor). In fact, I
don't think that it goes too far to include the origin of eukariotes and
sex in the package as well. (Including the origin of metazoa probably
goes too far.)

There may well have been a "creative" process involved. In fact, for the
later stages we KNOW there was a process - natural selection. At earlier
stages, there may have been a different process, or more likely, a
sequence of different processes. But, according to my slogan, they are
not so important as the actual sequence of events.

Most importantly, we want to know what happened. In what order did the
features that are now universal in life arise. Which came first, DNA or
proteins? Which came first, cells or RNA? What was the first
"biochemical reaction"? The first use of phosphate? In what order were
the twenty canonical amino acids added to the genetic code?

Once we know WHAT happened, then we can address the question of WHY it
happened. Understanding the process(es) is important, but first we need
to understand the sequence of events. What we need is not a "just-so
story". We need a multi-volume "just-so saga", with the narrative thread
progressing from one generation of protagonists to the next generation.
The problems, plot devices, and leading characters of the next stage of
our saga derive from the plot resolution of the the previous stage. There
will be a narrative unity in our saga, but not necessarily a unity of
theme. As in a family saga, one stage may be a love story, the next a
tragedy, the next a story of triumph over adversity.

But how can we construct such a saga?

-----------
Methodology:
-----------

   Slogan: Work backward from the present.

Although we intend for our "saga" to be read front-to-back, we will have
to construct it back-to-front. The first step is to learn all that we can
about the MRCA. The MRCA had all of the modern universal features of life
- cellular structure, DNA, RNA, proteins, genome replication, coenzymes,
high energy phosphates, the F0F1 complex, etc. But at an earlier stage of
our saga, one or more of these features was missing. Which one(s)? Can
we construct a credible model of what life was like at that earlier stage?

The generally accepted notion of an RNA world came about by a "reverse
engineering" methodology such as this. The RNA world did not have DNA, or
the F0F1 complex. It did have RNA, genome replication, coenzymes, and high
energy phosphates. This leaves cellular structure and proteins
unresolved. We need to resolve them.

Textbooks nowadays tend to focus on the experimental results of Cech and
Altman, or the exposition by Gilbert. However, earlier speculative
theorists such as Crick, and most importantly Visser, had the basic concept
much earlier. It is important to study the logic of these theorists,
because we will be using the same logic repeatedly. Visser focused on the
coenzymes, many of which have a structure that is clearly related to RNA.
But in a protein world, we would expect any new coenzyme to be a peptide
molecule (like glutathione). There is no particular reason why a new co-
enzyme produced by evolution would look like a nucleic acid fragment. But
there is every reason to believe that evolution will not significantly
tinker with the structure of a coenzyme, once it becomes established.
Hence, it is natural to speculate that coenzymes originated in a "world"
without proteins. Coenzymes are older than enzymes. They are "frozen
accidents".

   Slogan: Frozen Siberean mammoth - accident or fossil?

Answer: it is both. In fact, every "frozen accident" is a fossil, a
window into the past. And, it is a fossil precisely because it is
frozen. This principle has been explained most cogently by Steven Benner
in multiple papers and most amusingly in an exchange of Letters to Nature
[or was it Science?] against Alan Weiner.

As a hint of things to come in future postings, we will try to decipher
the ultimate frozen accident/fossil - the genetic code - to see what it
can tell us about the origin of translation.

   Slogan: Clues regarding OOL may be found in modern biochemistry.

Molecular fossils can potentially take us back to the beginnings of the
RNA world, but they probably cannot take us much farther. However, there
are other kinds of frozen fossils besides molecules and we will discuss
some of them in future postings. However, the "fossil record" definitely
becomes more sparse and more cryptic the farther back in time we go. To
get all the way back to the ultimate origins, we are going to have to make
some assumptions to limit the range of possibilities.

-------------------
Assumptions of fact:
-------------------

There are two dichotomies sometimes used to classify theories of the
ultimate origin. One is the distinction of "autotrophy" vs.
"heterotrophy". The other is the distinction of "genetics first" vs.
"metabolism first". My assumption regarding this second dichotomy may be
summarized in another slogan:

   Slogan: Morphology and Metabolism First!

Explaining this slogan will take several postings, so I will just leave it
at that.

The dichotomy of autotrophy vs heterotrophy may seem odd to someone who is
new to the OOL literature. The meaning of these words is slightly
different in an OOL context than it is in modern ecology. In this
context, a heterotrophic organism is one which extracts nutrition from ANY
kind of organic molecule, whether of biological or geochemical origin. An
autotroph does not. I suppose that one can define degrees of autotrophy
depending on how one defines "nutrition" and "organic". I will define an
"organic" molecule as any molecule that contains a carbon-carbon bond.

[Query: how does this compare to the standard definition?]

CO, HCN, and CO2 are inorganic. Acetate is organic. "Nutrition" is any
essential use - whether incorporated into structure or used in some kind
of metabolism. And of course, autotrophic theories permit the FIRST life
to be constructed using organics of geochemical origin. That "spontaneous
generation" is a permitted exception. However, a strictly autotrophic
origin theory will insist that, once it comes into existence, that first
lifeform must grow and reproduce without any further necessary organic
nutrition.

   Slogan: Life has been autotrophic since day one.

But what about the Miller experiment? Throw it out! What about the
prebiotic soup? Throw it out! If it even existed, it would have been
indigestible. In fact, as one autotrophic OOL theorist (Gunter
Wachtershauser) opined, the ocean should be seen as a sewer, rather than a
soup. It's prime function is to carry away organic wastes, rather than to
supply organic nutrients.

[Query: Does anyone know who coined the "soup" metaphor? Was it Haldane?]

Explaining and justifying this assumption will also take several postings,
beginning with the next posting. I will examine the most misleading
metaphor in all OOL theory - the "building blocks" of life.

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