Life in the Lab -- Basic Concepts
Tue, 11 May 1999 00:07:13 EDT

Greetings to One and All:

In this essay I will try to explain how the concensus that life has been
created in the lab was arrived at by biologists. I will present it in three
parts; this is the first part.

I would like to begin by trying to dispell some misconceptions. Anyone
expecting news items -- even from journals such as _Science_, _Nature_ or
_Scientific American_ -- is going to be disappointed. Contrary to popular
belief, or even recent experience, scientific breakthroughs are not revealed
at press conferences with a role of drums and a fanfare of trumpets. Most
researchers prefer to announce their results in published reports and at
conferences (which is how the press finds out about them), and most
researchers prefer to be circumspect in their claims. For example, even
people announcing the discovery of a new solar system prefer to say, "we have
found indications of what appear to be planets in orbit around the star
such-and-such." It is the press that announces in screaming headlines "NEW
SOLAR SYSTEM DISCOVERED." Scientists are by nature cautious, even more so
with momentous discoveries, because reputation means alot in science, and a
scientist who makes grandious claims -- even if he is proved right! -- very
soon looses the respect of his colleagues, especially if he turns out to be
wrong. So people who will not believe that life has been created in the lab
until they read about it in a newspaper or a popular magazine, or even as a
news item in a science journal, will obviously not be convinced by my actual

The vast majority of times these breakthroughs come more as after-thoughts,
from reading the accumulated scientific literature. My graduate advisor was
a postdoc member of the lab that is credited with establishing the validity
of the fluid mosaic model of phospholipid bilayer biological membranes, and
he told me that they had arrived at their conclusion based more or less
solely by reviewing the literature. The same is largely true for the basic
concepts of enzymology (including the recognition of enzymes as biological
catalysts) and the kinetic molecular theory of gases.

Even in those cases where it is possible to claim that a breakthrough is
based on a specific series of classical experiments, these experiments form
only the tip of an immense iceberg of research that had to be done first in
order to lay the foundation for the definitive work. The researchers who do
the classical experiments knew what experiments to do only because they knew
all that foundational research and used it guide them. An example of this is
the establishment that polypeptide chains must fold into proteins to become
functional. The definitive work was done by Christian Anfinsen and his
colleagues in the late 1950s and early 1960s, but it was based on research
that began in the last century.

Anfinsen's report of his results [Sela M, White FH Jr., Anfinsen CB.
"Reductive cleavage of disulfide bridges in ribonuclease." _Science_ 1957;
125:691-2] is also an excellent example of scientific circumspection. He and
his colleagues knew quite well the implications of their work and the impact
it would have, but they did not announce that they had solved the riddle of
the source of protein functionality. Instead they simply reported their
results, which clearly showed that the activity of ribonuclease was directly
related to its three-dimensional structure, which was itself determined by
its primary amino acid sequence. After a series of further experiments they
then proposed what they called the thermodynamic hypothesis, which states in
essence that the native three-dimensional structure of a protein corresponds
to the thermodynamically most stable state under physiological conditions, as
determined by interactions between its constituent amino acids. At no time
did they or anyone else claim that they had solved one of the most
fundamental mysteries of modern biochemistry, yet this is exactly the
concensus arrived at by modern biologists [e.g., Geoffrey M. Cooper. _The
Cell_. Sunderland, MA:Sinauer Associates (1997) pg. 50-1]. So people
expecting citations that will describe any series of experiments as the
definitive and classical creation of life in the lab will also not be
convinced by my actual citations.

Even when a breakthrough seems to be ingenious, it is nearly always based on
the work of more than just those who get the credit. Everyone knows that it
was James Watson and Francis Crick who figured out the three-dimensional
structure of DNA, but they would never have done it if they had not been
inspired by Linus Pauling's description of hydrogen bonding and the
three-dimensional structure of the alpha-helix, and if they had not had
access to (some say stole) the x-ray crystallography data of Rosalind
Franklin and Maurice Wilkins. Nor would they have gotten the base pairing
right if it were not for the earlier work of Edwin Chargaff. Most people do
not realize that Watson and Crick had to share their Nobel Prize with Wilkins
(Franklin was dead by then and the prizes are not awarded posthumously,
otherwise she would have shared it as well), but by rights Pauling and
Chargaff should have been included, along with all the research techs who did
the actual work for the principle investigators.

In summation, I believe Newton said it best: "If I have seen farther than
others, it is because I stood upon the shoulders of giants." In other words,
no breakthrough can be made in a vacuum, but only as the result of often a
great deal of research done by many people over a period of many years. So
people expecting me to provide a citation for a single critical experiment
will also not be convinced by my citations.

Speaking of Nobel Prizes, to my knowledge Anfinsen was never awarded a prize
for the thermodynamic hypothesis, or received any other public recognition
for that matter, despite the fact that biochemistry would be nowhere near as
comprehensive as it is today without it. So people (like Moorad Alexanian)
who will not believe that life has been created in the lab if no one has won
a Nobel Prize for the achievement will also not be convinced by my citations.

Another misconception, shared interestingly enough by both Brian Harper and
David Tyler, is that the creation of life in the lab must be significantly
important for abiogenesis. Brian wrote: "Another reason [for asking for
references of consensus] is that the individual that I'll quote is Sydney Fox
with the candidate for lab-life being his proteinoid microspheres. I know
from my own reading that a number of prominent scientists...raise serious
doubts as to whether Fox's protocells had anything to do with the origin of
life." David wrote: "All the [abiogenesis] research that I read about is
still seeking to solve fundamental problems, and it seems to me that this is
exactly how people like Thomas Gold and Paul the literature.
If these fundamental problems have been solved, why are the researchers
keeping it so quiet!" In other words, they seem to be suggesting that if we
can create life in the lab then we must also know how abiogenesis occurred.

I will discuss the significance that life in the lab has for abiogenesis
later (it serves in essence as proof of concept), but (as Brian also pointed
out in the same post) the validity of life in the lab is not dependent upon
the validity of abiogenesis in general or of any particular abiotic
mechanism. To better illustrate this, let me return to protein folding for a
moment. Even though Anfinsen demonstrated that proteins must fold into a
specific three-dimensional structure to be functional and that this specific
structure is determined by the primary amino acid sequence, we still have no
clear idea of exactly how proteins fold and we still cannot deduce the
three-dimensional structure of a protein directly from its amino acid
sequence. Yet it would be foolish to claim that because we cannot explain
how a protein folds that Anfinsen is mistaken about protein function being
based on a thermodynamically stable three-dimensional structure established
by the amino acid sequence. Similarly, it would be foolish to claim that our
inability to explain exactly how abiogenesis occurred means that life has not
been created in the lab. Even if the origin of life on Earth was itself a
unique -- even inexplicable -- event, this would not invalidate the abiotic
creation of life in the lab.

Another misconception is that the life created in the lab must be essentially
the same as a contemporary unicellular organism, including a lipid bilayer
membrane, compartmentalization and a full-fledged genetic system; i.e., a
modern cell. In point of fact, however, no has ever claimed that modern-type
cells have been created in the lab. What has been claimed is that what was
created would be the equivolent of the simplest, most basic ancestor of
modern cells. Even those few abiotic researchers who demand that true
protocells must have a lipid bilayer membrane or a genetic system agree that
any synthetic organism will be simple. As such, people expecting citations
that describe the creation of a modern cell in the lab will also not be
convinced by my actual citations.

A final misconception is that consensus means unanimity, but this is not the
case. It simply means a general agreement. As such, there are biologists
and abiotic researchers who do not accept that life has been created in the
lab. But such is the nature of science. This does not automatically
invalidate the consensus that life in fact has been made in the lab any more
than the fact that a few biochemists do not accept the fluid mosaic model
automatically invalidates the consensus that the model in fact is the best
description of the structure of a biological membrane.

I would also like to clarify the definitions of "protocell" and "protolife".
As Fox himself states (as quoted by Brian) the most basic unit of life is the
cell. As Fox also points out there are those few abiotic researchers who
disagree with this assertion, but it is nonetheless a generally held
consensus among biologists. For example, in his book _Beginnings of Cellular
Life_ [New Haven, CT:Yale University Press (1992)] Harold J. Morowitz states
that cell theory is central to all biology, and adds, "it is so much a part
of an overview that rarely is it necessary to make explicit the following
elementary statements...." He then goes on to list the postulates of cell
theory: all life is cellular; the nonaqueous portion of a functional
biological system consists of proteins, lipids, carbohydrates and nucleic
acids; the flow of energy is accompanied by the formation and hydrolysis of
phosphate bonds; metabolic systems are composed of a "universal" network of
intermediate reactions; biological information is structural; biological
membrane structure is universal; genetic information is universal; all
replicating biological systems give rise to altered phenotypes resulting from
mutated genotypes; ribosomes are the site of protein synthesis; and
metabolism is catalyzed by enzymes (pg. 38-58). Cooper largely confirms this
in his textbook on cell biology, as do John Gerhart and Marc Kirschner in
their textbook on ontogeny and phylogeny [_Cells, Embryos, and Evolution_
Malden, MA:Blackwell Science (1997)]. It is the standard paradigm, the
"central dogma," taught to all biologists.

The dictionary definition of "proto-" is "first in time; earliest; first
formed; primitive; original." As such, a protocell would be the the "first"
cell, the "primitive" cell, the "original" cell. In the 1970 edition of his
textbook _Biochemistry_ (New York:Worth Publishers), Albert L. Lehninger
states that "the first structure possessing 'life' was not necessarily a
modern cell, complete with membranes, nucleus, a metabolism and the property
of self-replication. Rather, the minimum requirement is that it could
potentially lead to a complete cell" (pg. 782). One version of this view is
stated by Morowitz in his book (pg. 88): "First, we conclude that although
we do not know how many independent origins of cellular life may have
occurred, all present life is descended from a single clone. This follows
from the universiality of the basic biochemical networks and programs of
macromolecular synthesis. However, we envision the Ur-cells [protocells] as
being very simple, whereas the universal ancestor must--by comparison to
these--have been quite complex." Later (pg. 105) he states: "The simplest
protocell that fulfills the principle of continuity is a bilayer vesicle made
from a single type or mixture of small amphiphiles." Nothing else, not even
peptides; the vesicles themselves would be able to capture light energy to
create more amphiphiles and replicate themselves. Of course, some of these
new vesicles would be expected to trap primitive enzymes and genetic
molecules, which could then use the captured energy to develop and evolve a
polymer synthesis system [Morowitz HJ, Heinz B, Deamer DW. "The chemical
logic of a minimum protocell." _Orig Life Evol Bios_ 1988; 18(3):281-7].

Morowitz presents a somewhat extreme version. Sydney W. Fox presents a
somewhat more reasonable version, but even he admits that the proteinoid
microsphere is not a modern living system. As such, I believe that if "cell"
refers to a modern cell complete with biological membrane,
compartmentalization and genetic system, a "protocell" would be a simpler
structure that would have the potential of evolving into a modern cell.
Similarly, if "life" refers to the complex, integrated metabolic system of a
modern cell, then "protolife" would refer to the most basic aspects of what
constitutes life. I'll have more to say about that shortly.

Finally, I would like to explain that any discussion of whether life has been
created in the lab must also deal simultaneously with three other topics:
the definition of life, the possible mechanisms by which life arose on earth
(abiogenesis) and whether the life created in the lab as any significance to
abiogenesis. The definition of life is important, because if you don't know
what it is, you can't say whether to was created in a lab or not. However,
in a case like this, it is insufficient to merely define life; you must use
the definition to assemble a list of characteristics which can be used as a
test to see if the created structures are in fact alive.

The generally accepted biological working definition for life, which I
express as a dynamic, integrated, molecular metabolic system that uses
polymeric catalysts to break down certain simple structures to obtain the
energy and raw materials needed to build macromolecular structures, makes it
clear that any candidate must have at least some form of metabolic system.
However, this alone is insufficient, because an assumption of abiogenesis is
that before the existence of the first living organism there were probably
nonliving structures that could mimic metabolic reactions. That's where the
postulates for cell theory come in. The first and foremost postulate is that
any candidate for life should be cellular. It could be (and has been) argued
that the first living system need not be cellular, but in fact most abiotic
researchers -- including Morowitz and Fox -- agree that since all modern life
is cellular, cellularity is a necessary characteristic for a structure to be
alive. (They simply disagree over what constitutes a proper cell; more about
that in the second part of my essay.) It may not be absolutely necessary,
but it is easier to demonstrate that a cell-like structure is alive than to
try to prove that some other non-cellular structure (like a virus) is alive.

Virtually all of the rest of the postulates describe metabolism, which we
already accept as a necessary characteristic. A few, such as the
universalness of lipid bilayer biological membranes, genetic systems and
ribosomes for protein synthesis, are generally believed to be modern features
acquired as protocells evolved into modern cells. However, assumed by the
postulates are two other characterists of living cells: the ability to
reproduce and the ability to evolve. Additionally, virtually all cellular
life demonstrates some ability to react to environmental stimuli. While
there might be other characteristics that we could include, I would agree
with Timothy M. Berra that the core characteristics we should expect to see
in any protoliving system are cellularity, metabolism, reproduction and
response to environmental stimuli (_Evolution and the Myth of Creationism_
Stanford, CA:Stanford University Press (1990) pg. 75). Fox specifically
agrees with this claim, and I believe that Morowitz would as well, based on
his requirements for a minimum protocell.

The last two considerations -- the possible mechanisms by which life arose on
earth and whether the life created in the lab as any significance to this --
can be handled together. No one has ever claimed that the abiotic mechanisms
discovered through laboratory research **must** be the mechanism by which
life arose on earth. These laboratory mechansims count as abiotic events,
since the strict definition of abiogenesis is the non-biological origin of
metabolism and the biomolecules that support it, and so have significance to
abiogenesis as a specific scientific discipline. But whether these were the
mechanisms by which life arose on earth we may never know. David Tyler is
fond of questioning whether the fundamental questions of the origin of life
have been answered, usually by quoting examples of dissent in the abiogenetic
community or examples of unique new ideas, but in doing so he misses the
point. No biologist who is not a creationist, vitalist or intelligent design
advocate questions that life arose on earth by naturalistic mechanisms (to my
knowledge not even Yockey), because they accept the laboratory research which
demonstrates that biomolecules, polymeric catalysts, simple metabolic systems
and even primitive cellular structures can be synthesized abiotically. They
also accept that this research has not only answered the fundamental
questions of strict abiogenesis, but those of the historical origin of life
on earth as well. What they argue over is specifically which mechanisms
applied specifically when under what specific conditions; in other words, the
precise historical chain of events. In that respect, abiogenesis is alot
like evolution, where there are known specific mechanisms for various macro-
and microevolutionary phenomena, but the precise protocol for any specific
event is difficult if not occasionally impossible to determine. So when
biologists argue about how life originated on the earth, they are not
disputing the fact of abiogenesis, the validity of the laboratory research or
even generally accepted answers to the fundamental questions; they are
disputing what was the most most likely way in which life appeared.

Similarly, when biologists deny that any specific living structure created in
the lab has any significance for abiogenesis or the historical origin of
life, they are not necessarily denying that the structures are alive or that
they were abiotically synthesized. They just question whether the structures
could evolve into modern cells, or assuming that they accept that they
question whether those structures actually appeared in nature. Fox obviously
believes that his proteinoid microspheres are significant for both
abiogenesis and the origin of life on earth, but even he accepts the
possibility that he might be wrong.

However, the purpose of this essay is not to discuss what were the first
living structures to appear on the earth, but whether life has been created
in the lab. Even if Fox's proteinoid microspheres were an evolutionary dead
end or historically nonexistent, if in fact they are alive then life has been
abiotically synthesized in the lab. I will, however, also discuss evidence
that I believe demonstrates that proteinoid microspheres are not at all
irrelevant to strict abiogenesis (at least).

I will post the second part of this essay when I see that this part has been

Kevin L. O'Brien