[My apologies for the tardiness of this response. New contributions to this
discussion are indicated by KLOB.]
BH: Apparently you are unaware that the same word is often defined
differently in different fields.
KO: Which is irrelevant, since abiogenesis is a biological/biochemical
phenomenon, so therefore the biochemical definition is the only one that
matters.
BH: My main interest is in clarity.
KLOB: Clarity means "clearness of thought or style"; should that not
include accuracy as well? In other words, we may all agree on a definition
of abiogenesis simply for the sake of argument, but if that definition is
inaccurate, even misleading, are we not in fact working against clarity
rather than for it?
BH: I will concede your point to a certain extent in that greater clarity
would be achieved by using the biochemical definition for abiogenesis and
then simply referring to the origin of life as the origin of life. I will
try to do this in the future.
KLOB: Though you deny it later in this post, here you are definitely
treating the "origin of life" as something separate from abiogenesis.
Philosophically there may be a difference (though Haldane at least didn't
think so), but that is only because the philosophical definition of life
usually includes some sort of vitalistic assumption. Biochemically
speaking, there is no difference between "life" and the
biomolecules/metabolic systems that make life possible. Arguing otherwise
is simply an attempt to avoid this simple truth.
BH: BTW, do you have some technical references that establish this
definition. If you presented them in the past I'm afraid I missed them.
BH: May I inquire again as to technical references?
KLOB: If by "technical references" you mean journal articles, there
probably aren't any. Abiogenesis is too basic a term for biochemists to
routinely define in research reports. You might as well ask for a technical
reference that defines enzyme. The only time abiogenesis might be defined
is in a review article (though rarely), in an article written for lay people
or when the author chooses to define it differently from the accepted
definition.
If, on the other hand, you mean a textbook, most modern textbooks do not
even deal with this subject, so they would have no need to define the term.
The only textbook I found that does deal with abiogenesis (and my search was
not exhaustive) was the 1970 version of _Biochemistry_ by Lehninger. What
is interesting is that Lehninger doesn't use the term abiogenesis; at that
time the field was still new enough that specific terms had not yet been
agreed upon, so different terms were used by different people to express the
same meaning. (I'll have more to say about this later.) For example,
Lehninger used "abiotic synthesis," but it is clear from his definition that
this term means the same as abiogenesis. What is also interesting is that
he did not define his term using a specific phrase, but instead he defined
it by discussing the theoretical concept behind the term and then by giving
examples. (In fact his basic discussion goes on for 2.5 pages, but he also
devotes an entire chapter to it as well.) If, however, you distill out the
essential meaning from all that discussion you would get something like:
abiotic synthesis is the creation of biomolecules and the metabolic systems
they support by non-biological methods. (Sound familiar?)
What is doubly interesting is that one example he gives of abiotic synthesis
is the Miller-Urey experiment. This thread began when I suggested to Burgy
that the Miller-Urey experiment was an example of an abiogenetic event and
others objected to this claim since the experiment had not created "life",
only certain biomolecules. Apparently Lehninger also believes that
Miller-Urey is an abiogenetic event (despite the fact that no "life" was
created) since he uses it as an example of what he calls abiotic synthesis.
The final chapter of his textbook is entitled "The Origin of Life", but the
entire chapter is devoted to a detailed discussion of what (at that time)
were considered to be the most likely scenarios for how biomolecules and an
organized integrated metabolic system originated. Though he used the term
"life" frequently, it is clear from his discussion that he is using it as a
simpler way to refer to an organized integrated set of metabolic systems and
not to some philosophical concept that transcends molecular organization and
activity. The only apparent exception comes at the point where he discusses
how this set of organized metabolic systems first became integrated; he
places "life" in quotations marks and suggests that "life" cannot be defined
accurately enough to pinpoint when it first appeared. However, as in all
other cases, it is clear from the context of that section that Lehninger is
referring to the specific set of organized metabolic systems that
biochemists now recognize are necessary for "life".
BH: But, if one is interested in clear communication then one should take
into account what meaning someone else might be attaching to a word.
KLOB: Again, however, "clear communication" also requires accuracy. If the
meaning someone else wants to attach to a word is an inaccurate meaning,
then communication will not be "clear" even if both participants understand
the false meaning.
BH: This is not a biochem e-mail list after all.
KO: No, but that would be like trying to have a scientific discussion using
a definition of work as "the sweat of one's brow".
BH: This is a poor analogy.
KLOB: Actually it's a pretty good analogy, if you think about it for
moment. I am trying to define abiogenesis precisely, so that the meaning is
clearly understood by all involved in this discussion; you on the other hand
have been trying to define it vaguely (using "the origin of life on earth")
and have refused at least twice now to explain precisely what you mean by
the terms you use in your definition. It is as if we were trying to have a
discussion about work and you were defining it precisely as W = Fs, whereas
I insisted upon defining it as "the sweat of one's brow". Until you define
what you mean by "the origin of life" your definition explains nothing about
abiogenesis, just as "the sweat of one's brow" explains nothing about work.
All either phrase does is introduce vague subjective philosophical ideas
into a discussion that should be more rigorous in order to make any sense
out of what is being debated.
BH: In the present instance the meaning being attached to the word
abiogenesis is the origin of life on Earth.
KLOB: Which is an inaccurate meaning, since you have not defined "life".
BH: The origin of life on Earth is a concept suitable for scientific
discussion.
KLOB: Of course it is, but before you can discuss it, you have to define if
first. The vast majority of biologists/biochemists "define" life as an
organized, integrated metabolic system that uses certain polymeric catalysts
to break down certain biomolecules to obtain the raw energy and materials
needed for other polymeric catalysts to build up biomolecules needed by the
organism. Notice that this working definition (as opposed to some set
"official" definition that can cover all cases) takes us right back to
abiogenesis as the origin of biomolecules/metabolic systems; as such
abiogenesis is the "origin of life" as long as one recognizes that "life"
refers to biomolecules/metabolic systems. It is generally
non-biologists/non-biochemists who insist on an "origin of life" separate
from biomolecules/metabolic systems, largely because they tend to apply
philosophical considerations of life rather than stick to strict scientific
usage.
BH: If you know that this is the meaning that someone is attaching to a
word I have a hard time understanding what the fuss is about.
KLOB: The "fuss" has to do with someone applying to a scientific term being
used in a scientific discussion a non-scientific meaning. It would be as if
we were using the physical term "work" in a scientific discussion, but I
insisted upon defining work as "the sweat of one's brow" since that was the
more general meaning used by non-physicists.
BH: Further, within the context of a discussion of the origin of life (as
opposed to a technical biochem discussion) abiogenesis is taken to mean the
origin of life. For example, in the abstract of their paper "Impact
Frustration and the Origin of Life" [_Nature_ 331:612-614, 1988], Maher and
Stevenson provide the following definition of abiogenesis: "the development
of life through chemical evolution from inorganic materials".
KLOB: Without realizing it you have raised an interesting point. In
physics, especially mechanics, the vast majority of technical terms are
defined by mathematically. We may define "work" as "force applied over a
distance," but that is simply the verbalization of the mathematical formula
W = Fs, where W is work, F is force and s is distance. In biochemistry,
however, very few if any technical terms are defined mathematically; instead
they are defined conceptually, using description and example. Terms like
amino acid, protein, enzyme and metabolism have no precise mathematical
definition, so they have no precise set official definition. Instead
biochemists have come to agree through consensus on what the terms mean;
then each biochemist expresses that meaning differently. Some terms are so
basic and so commonly used that there are certain commonly used phrasings,
but even in these cases there can be a variety of expressions. For example,
the most commonly used expression of the meaning of the term "enzyme" is "a
protein that acts as a catalyst," but I have also heard the expression "a
polypeptide that speeds up chemical reactions". Since biochemists know that
protein and polypeptide refer to the same kind of biomolecule, and since
they accept as a definition of catalyst the expression "a substance that
speeds up chemical reactions," both "definitions" are automatically accepted
because both reflect the accepted meaning of the term enzyme. However, if
you did not know that a protein was a polypeptide or what catalysis was, you
might think these were two different definitions.
The biochemical meaning of abiogenesis, accepted by consensus, is the
non-biological origin of metabolic systems and the biomolecules that support
those systems (and this is my own way of phrasing that meaning). Since the
biochemical meaning of life, also accepted by consensus, is an organized
integrated set of metabolic systems, we can see that Maher and Stevenson can
indeed define abiogenesis as the origin of life without violating the
accepted biochemical meanings of those terms.
Where the problem comes in is if the terms being used to express the
meaning of a biochemical term are not themselves properly defined. As you
yourself pointed out, your example is not a technical discussion, but a more
general one. In it, Maher and Stevenson did not define what they meant by
life, and because they did not people who did not know what they meant by
life could confuse the "origin of life" as being something separate from the
origin of biomolecules/metabolic systems.
Here is another example of the confusion that can occur if biochemists use
alternate terms without properly defining them. In general discussions of
enzyme kinetics, biochemists often define catalysts as substances that speed
up chemical reactions. I know of people -- scientists and non-scientists
alike -- who have mistakenly thought that this meant that catalysts reduce
the time needed for reactants to form products; that is, they increased the
speed of the process in which the transitional state formed by the reactants
decays into product. As any good physical chemist would tell you, however,
this is flat wrong. Catalysts have no affect on how fast reactants are
converted into products. Rather, catalysts increase the **probability**
that reactants will combine with the right amount of energy in the right
orientation to form products. This probability is called the reaction rate
and it is directly proportional to the collisional frequency and inversely
proportional to the activation energy. Biochemists of course know this, but
because they don't **say** it it can lead to confusion among people who
don't understand the basic theory. Sometimes a biochemist will use
"reaction rates" instead of "chemical reactions", but unless they explain
what they mean by "reaction rate" the same kind of confusion can result.
So there is nothing wrong with defining abiogenesis as the "origin of life",
as long as you then in turn define life. And biochemically speaking life is
defined as an organized integrated metabolic system that balances break-down
with build-up.
[...]
KO: You didn't answer my question, though. If "life" is not metabolism
based on biomolecules, then please define "life".
BH: I didn't answer because I failed to see the relevance of your question.
KO: If we are discussing the origin of life, we need to know what "life"
means to have a reasonable discussion. I simply wanted to hear yours since
you seemed to insistent upon separating the origin of "life" from the origin
of biomolecules.
BH: Once again jumping to conclusions, in this case a truly phenomenal
leap.
KLOB: Then explain to me how "I will concede your point to a certain extent
in that greater clarity would be achieved by using the **biochemical
definition for abiogenesis and then simply referring to the origin of life
as the origin of life**" should be interpreted in any way other than "the
origin of life is different from the origin of biomolecules".
BH: First of all, I previously stated that: "...it seems clear enough to
me that 'the origin of life on earth' will have involved several abiogenetic
processes and events. Burgy's point is that not all abiogenetic processes
and events necessarily have anything to do with "the origin of life on
earth". This can hardly be taken as the separation of the "origin of 'life'
from the origin of biomolecules." Further, I have already expressed my
preference for the hydrothermal vent scenario which, I assure you, involves
the origin of biomolecules.
KLOB: You may acknowledge that the "origin of life" involves the origin of
biomolecules/metabolic systems, but you continue to use the term "life" as
if it were separate from biomolecules/metabolic systems, as you do earlier
in this post. All I want from you is a definition of "life" so that
whenever you use it I will know exactly what you mean by it and will not
have to "jump to conclusions" because I am trying to interpret what you
mean. I do not see how that is too much to ask.
[...]
BH: Yes, very good. I like this idea a lot and would not be surprised at
all if this is the way it turns out. But my point has to do with necessity.
It isn't necessarily so. For example, there may be many laboratory
abiogenesis experiments involving conditions never present on early earth.
All of these examples of abiogenesis would therefore have nothing to do with
the origin of life.
KLOB: Here again you use "life" as something separate from abiogenesis,
which you have conceded as being the origin of biomolecules (I would now
add "metabolic systems" to that as well.)
KO: And those that have already been done have been proved wrong fairly
quickly, at least so my literature searches tell me.
BH: Since you agree that it is possible to perform a laboratory experiment
qualifying as abiogenesis (technical meaning) under conditions never present
on early Earth then you agree with the point Burgy and I were trying to
make, which I will repeat again for sake of clarity: "...it seems clear
enough to me that 'the origin of life on earth' will have involved several
abiogenetic processes and events. Burgy's point is that not all abiogenetic
processes and events necessarily have anything to do with 'the origin of
life on earth'."
KLOB: Not only do I not agree with that assessment, I will again point out
that you are using "life" as something separate from abiogenesis. My
overall point is that abiogenesis and life are NOT separate. Life is
biomolecules/metabolic systems; abiogenesis is the origin of
biomolecules/metabolic systems; therefore, abiogenesis is the origin of
life. As such, all abiogenetic processes -- whether they were active on the
early earth or not -- necessarily will have something to do with the "origin
of life". Only if the "origin of life" and the origin of
biomolecules/metabolic systems were two separate phenomena would you and
Burgy be correct.
Kevin L. O'Brien