Here is the second of my in-depth replies; it deals with Steve's comments
concerning the characteristics of protocells.
>
> KO>These microspheres look and act like modern cells in every
> >important detail, except that they do not contain genetic material.
>
> This is self-evidently false, because if it were true, it would mean that
> "genetic material" was not really necessary for *any* "important detail"
of
> "modern cells", which is absurd.
>
Apparently Steve has no formal training or experience in biochemistry,
otherwise he would know that it is not absurd, but a known biochemical fact.
Genetic material serves only only one function: it carries instructional
material for the making of proteins. That's all. It is the proteins that
perform virtually all of the important functions in the cell. They run and
control metabolism, muscle contraction and nerve induction, ion and molecular
transport across membranes, as well as communication between cells and
immunology. They create and maintain the cytoskeletal structures that
determine and control a cell's shape. They run and control replication,
transcription and translation. They even run and control mitosis and
meiosis. Proteins do not form the plasma membrane, but they make the lipids
that compose it and they construct it. By itself, in the absence of
proteins, genetic material can do nothing; that's why viruses need to take
over a cell in order to reproduce themselves. They need proteins to
replicate, but they do not have the protein-based apparatus to make make
proteins on their own, so they have to co-opt one that already exists: that
of a living cell. Cells that have been deprived of their genetic material do
not die immediately, but continue to live until their protein-based apparatus
wears out and stops functioning; such cells can live for days, even weeks.
But cells that are deprived of their proteins die within hours, if not
sooner, even if their genetic material is intact.
In other words, cells do not need genetic material to live; they need
proteins to live. Genetic material simply acts as a source for more protein,
but if cells could get their proteins from some nongenetic source, they would
not need genetic material at all. Prebiotic cells got their proteins from
thermal copolymerization; that is why proteinoid microsphere protocells can
be alive without genetic material.
"What chemical feature most clearly enables the living cell to function, grow
and reproduce? Not DNA, the genetic material. Despite its glamor, DNA is
simply the construction manual that directs the assembly of the cell's
proteins. The DNA itself is lifeless. What gives the cell its life and
personality are enzymes. Nothing in nature is so tangible and vital to our
lives as enzymes, and yet so poorly understood and appreciated by all but a
few scientists." A. Kornberg (1989) For the Love of Enzymes, Harvard
University Press.
"The nucleic acids contain and process the genetic information that specifies
the structures of all cellular macromolecules. The proteins carry out many
of the most-important functions required for maintaining and replicating
cells." R.H. Abeles, P.A. Frey and W.P. Jencks (1992) Biochemistry, Jones
and Bartlett Publishers, pg. 3.
"The nucleic acids serve universally to store and transmit genetic material.
In all cells the proteins are the direct products and **effectors** of gene
action [emphasis mine]." A. Lehninger (1975) Biochemistry, Second Edition,
Worth Publishers, pg. 20. In other words, even granting that genetic
material can directly run and control cellular activities, it still needs
proteins to do it, even to replicate.
"Proteins ... are fundamental in all aspects of cell structure and function."
A. Lehninger (1975) Biochemistry, Second Edition, Worth Publishers, pg. 57.
"All biochemical reactions are carried out by the protein catalysts of cells
known as enzymes." J.D. Rawn(1983) Biochemistry, Harper & Row Publishers,
pg. 13. Even though genetic material codes for enzymes, the enzymes are
ultimately responsible for keeping cells alive.
"Protein -- A word coined by Jons J. Berzelius in 1838 to emphasize the
importance of this class of molecules. Derived from the Greek word proteios,
which means 'of the first rank.'" L. Stryer (1981) Biochemistry, Second
Edition, W.H. Freeman and Company, pg. 21. Even the very name "protein"
indicates their primary importance as the molecules of life.
"While nucleic acids carry the genetic information of the cell, the primary
responsibility of proteins is to execute the tasks directed by that
information....Thus, proteins direct virtually all activities of the cell.
The central importance of proteins in biological chemistry is indicated by
their name, which is derived from the Greek word proteios, meaning "of the
first rank." G.M. Cooper (1997) The Cell: A Molecular Approach, Sinauer
Associates, pg. 48. Again, genetic material makes proteins, but proteins
keep cells alive. If proteins can be made non-genetically, genetic material
would not be necessary.
"The predominant organic molecules in cells are proteins, a fitting term
adopted from the Greek word proteios, meaning first or prime. To a large
extent, the structure, behavior, and unique qualities of each living thing
are a consequence of the proteins they contain." K.P. Talaro and A. Talaro
(1999) Foundations in Microbiology, Third Edition, McGraw-Hill, pg. 43.
"Proteins are called the 'shapers of life' because of the many biological
roles they play in cell structure and cell metabolism." K.P. Talaro and A.
Talaro (1999) Foundations in Microbiology, Third Edition, McGraw-Hill, pg. 50.
"In all areas of biological and medical research today there is increasing
need for knowledge about proteins. These complex macromolecules, with
particle weights ranging from the thousands to the millions, comprise in
essence the **working machinery of life**. They cannot claim the central
position held by the nucleic acids as the carriers of heredity, yet certain
proteins are responsible for the control of expression of hereditary
information from its first transcription from the gene to its final
translation into new polypeptide chains. Hundreds of proteins have been
identified in the category of enzymes, catalyzing a myriad of complex
biochemical reactions. Others are responsible for the basic structural
framework of living organisms; in higher animals these structural proteins
include collagen of bones, cartilage, and tendons; keratin of hair and nails;
elastin of blood vessels and ligaments; and myosin of muscle [emphasis
mine]." R.H. Haschemeyer and A.E.V. Haschemeyer (1973) Proteins: A Guide to
Study by Physical and Chemical Methods, John Wiley & Sons, pg. 3. So while
proteins are not the carriers of heredity, they control heredity, such that
if proteins did not exist, neither would heredity. Yet proteins can exist
without heredity, as is evidenced by thermal copolymerization. And since
proteins constitute "the working machinery of life", life can exist without
heredity, but it cannot exist without proteins. As Fox states it, "life
arose before the mechanism to inherit it arose."
S.W. Fox, et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
While most of these quotations are not as strong as the first or the last,
they establish that the consensus among biochemists is that genetic material
is limited to being the carrier of biological information, while proteins are
the molecules of life and living systems. If proteins can be made without
genetic material, as in prebiotic circumstances, then genetic material is
unnecessary for life.
>
> Thaxton, et. al., conclude that proteinoid "microspheres possess only
> outward likenesses and nothing of the inward structure and function of a
> true cell":
>
> "In the present-day cell, there are thousands of different chemical
> reactions taking place.
>
True, but Oparin recognized in the Twenties that primitive cells would not
need to be as complex as modern cells to be alive. As Lehninger explains,
"the first structure possessing 'life' was not necessarily a modern cell,
complete with a membrane, a chromosome, ribosomes, enzymes, a metabolism, and
the property of self-replication. The minimum requirement is that it could
potentially evolve into a complete cell." Morowitz defines the minimum
protocell as being a structure with a semi-permiable membrane capable of
self-replication and the conversion of sunlight into chemical energy. And
basic experimental results from Herrera, Oparin and Fox to current molecular
modeling work demonstrate that living cells can be quite simple.
A. Lehninger (1970) Biochemistry, Worth Publishers.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox (1988) The Emergence of Life, Basic Books.
H.J. Morowitz (1992) Beginnings of Cellular Life, Yale University Press.
C. Ponnamperuma (1995) "The Origion of the Cell from Oparin to the Present
Day" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Negron-Mendoza (1995) "Alphonso L. Herrera: A Mexican Pioneer in the
Study of Chemical Evolution" in C. Ponnamperuma and J. Chela-Flores, eds.,
Chemical Evolution: Structure and Model of the First Cell, Kluwer Academic
Publishers.
A. Pohorille, C. Chipote, M.H. New, and M.A. Wilson (1996) "Molecular
Modelling of Protocellular Functions" in Pacific Symposium on Biocomputing,
World Scientific Publication Co.
>
> Not even one chemical reaction takes place in microspheres....
>
This is incorrect. Each of the following types of chemical reactions have
been detected in microspheres:
esterolysis (the ability to break ester bonds)
phosphatation (the ability to remove phosphate groups from biomolecules)
decarboxylation (the ability to remove CO2 groups from biomolecules)
peroxidation (the ability to use hydrogen peroxide to perfom
oxidation-reduction reactions)
photodecarboxylation (the ability to remove CO2 groups from biomolecules
using light energy)
synthesis (the ability to create biomolecules -- specifically peptides and
polynucleotides using phosphate groups or ATP)
The last is especially important because a specific type of protocell, called
the metaprotocell, has been observed to convert sunlight into ATP, to use ATP
to synthesize polynucleotides from proteinoids, and then to synthesize
polypeptides from the polynucleotides.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
"When microspheres are formed from solutions of proteinoids that exhibit
catalytic activity, the resulting vesicles can carry out a primitive type of
metabolism." L.J. Kleinsmith and V.M. Kish (1995) Principles of Cell and
Molecular Biology, Second Edition, HarperCollins, pg. 637.
>
> ...only mechanical and physical processes due to simple,
> attractive forces.
>
Here is a list of the "mechanical and physical processes" exhibited by
protocells:
electrotactism (the ability to sense an electrical field)
aggregation (the ability to collect into colonies)
mobility (the ability to move more or less at will)
osmosis (the ability to absorb material from the environment)
permselectivity (the ability to selectively pass materials across a
semi-permiable barrier)
fission (the ability to break about into smaller functional units)
reproduction (the ability to create functional copies)
conjugation (the ability to join directly to another)
communication (the ability to pass information directly to another)
excitability (the ability to generate and utilize energy, especially
electrical fields)
Of these, only aggregation is due to "simple, attractive forces", and it is
interesting to note that when modern cells aggregate they use the same
"simple, attractive forces". Proteinoid microspheres form bilayer
semipermiable membranes (also by "simple, attractive forces" in exactly the
same way modern cells form lipid membranes) that can detect and generate
electrical fields. These membranes possess osmotic characteristics identical
to those of modern lipid membranes. Microspheres are able to undergo fission
to produce fully functional daughter cells, which is a form of reproduction
performed by modern cells. Aggregated microspheres are able to form gap
junctions between them, allowing them to pass material between themselves in
a nonrandom fashion. (Microparticles have been observed to move in specific
directions through chains of conjugated microspheres, rather than simply
drift by diffusion.)
In summary, the physical and mechanical characteristics of proteinoid
microsphere protocells are not due to "simple, attractive forces" in most
cases, and even when they are they are the same "simple, attractive forces"
that organize modern cells as well.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox (1988) The Emergence of Life, Basic Books.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
>
> We question listing these purely physical forces as
> resemblances to true cell processes. In truth, they have scant relation
> to actual processes in living cells.
>
Living cells possess electrotactism and some are excitable; living cells are
able to aggregate, form conjuctions and communicate by passing genetic
material or proteins between themselves in nonrandom fashions; modern cells
are mobile; modern cells have semipermeable membranes that exhibit osmosis
and permselectivity; modern cells are able to reproduce by fission. Modern
cells use more complex mechanisms ro accomplish these processes, but that is
because they are more complex than protocells. In effect, the mechanism is
irrelevant; both protocells and modern cells are able to accomplish many of
the same activities.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox (1988) The Emergence of Life, Basic Books.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
"Hence several properties we associate with living cells [semipermeability,
metabolism, fission and budding] are exhibited by these unique vesicles which
can be formed under simulated primitive earth conditions." L.J. Kleinsmith
and V.M. Kish (1995) Principles of Cell and Molecular Biology, Second
Edition, HarperCollins, pg. 637.
>
> Actually, microspheres possess only
> outward likenesses and nothing of the inward structure and function of
> a true cell.
>
In fact proteinoid microsphere protocells can compartmentalize and the
different compartments can exhibit different catalytic functions. However,
protocells do not need the internal structure of the modern cell to be
functionally alive.
S. Brooke and S.W. Fox (1977) "Compartmentalization in proteinoid
microspheres," BioSystems, 9 (1), 1-22.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
>
> They contain no information content....
>
The proteinoids themselves serve as informational molecules.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
>
> ...no energy utilizing system....
>
The proteinoids themselves, associated with porphyrins (which are made under
prebiotic conditions and can be incorporated into proteinoids during thermal
copolymerization or into microspheres), flavins and pteridines (which are
formed during thermal copolymerization and are incorporated into proteinoids
as a result), can capture sunlight and convert it into ATP, and the
proteinoids themselves can then use this ATP in metabolic reactions or to
make polynucleotides.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
>
> ...no enzymes....
>
It's amazing they have the hubris to make such a bald-faced false claim. It
has been known since the Sixties that nearly all proteinoids have catalytic
activity, some exhibiting Michaelis-Menton kinetics. Fox and others have
also demonstrated that specific activities unique to modern proteins -- such
as hormonal activity -- can be reproduced in proteinoids by using mixtures of
amino acids that include those found in the active sites of these modern
proteins.
Usdin VR, Mitz MA, Killos PJ. "Inhibition and reactivation of the catalytic
activity of a thermal-amino acid copolymer." _Archives of Biochemistry and
Biophysiology_ 1967; 122:258-61.
Fox SW, Wang C-T. "Melanocyte-stimulating hormone activity on thermal
properties of amino acids." _Science_ 1968; 160:547-8.
Rohlfing DL, Fox SW. "Catalytic activities of thermal polyanhydro-amino
acids." _Advances in Catalysis_ 1969; 20:373-418.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
>
> ...no nucleic acid, no genetic code....
>
This is true, but proteinoid microsphere protocells can make polynucleotides
using proteinoids as templates and they can incorporate polynucleotides into
themselves. Besides, they don't need it to be alive.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
>
> ...and no replication system.
>
This is false, because proteinoid microsphere protocells have been observed
to incorporate polynucleotides with proteinoids to form protoribosomes, that
can then synthesize polypeptides using the polynucleotides as templates.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
>
> They contain only a mixture of polymers of amino acids, the
> so-called proteinoids.
>
While this is true on the face of it, it is not strictly true, because in
fact proteinoid microspheres have been made from aggregations of proteinoids
and lipids, proteinoids and polysaccharides, proteinoids and polynucleotides,
even proteinoids and nucleic acids. Each type have different properties, but
properties can be combined by combining ingredients. However, these
structures do not have the same degree of evolutionary continuity that simple
proteinoid microspheres have, because the lipids, saccharides and nucleic
acids used are of biotic origin rather than prebiotic origin. Nonetheless,
they establish that if, on the prebiotic earth, lipids and polysaccharides
and nucleic acids had been present in the same enviroment as the proteinoids,
they could have been incorporated into the resulting microspheres.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C. Ponnamperuma and J.
Chela-Flores, eds., Chemical Evolution: Structure and Model of the First
Cell, Kluwer Academic Publishers.
>
> Microspheres cannot be said to be living in any
> sense of the word....
>
This is self-evidently false, because there are so many different senses of
the word life that purely by chance at least one could fit proteinoid
microsphere protocells.
There are two general ways of defining life. One way is philosophically, the
other way is biologically. Though some biological definitions of life
include information and entropy, the majority define life practically, in
terms of the properties that all living things share. For example, Kornberg
defines it in terms of biofunctionality, growth, and reproduction, while
Berra defines it in terms of metabolism, growth, reproduction, and
responsiveness to stimuli. Eirich lists these and adds the quality of
rhythmicity. Even critics of proteinoid microspheres as living structures
tend to define life in terms of metabolism, growth and reproduction; they
would simply include a genetic coding system. Morowitz prefers to define
life in global and ecological terms, but he also recognizes that life can be
defined in terms of characteristics including metabolism, reproduction and
response to external stimuli. Other suggested characteristics include
mutability, information and intelligence. Fox would add cellularity and
membranicity, which is echoed by Morowitz and Lehninger.
In any event, it should be quite obvious that one sense of the word life
means that any cellular structure that has a membrane and exhibits properties
such as metabolism, growth, reproduction, rhythmicity, response to stimuli
and evolution is a living structure. As such, since all of these features
can be seen in proteinoid microsphere protocells, in at least one sense of
the word life, they are alive.
A. Lehninger (1975) Biochemistry, Second Edition, Worth Publishers.
S.W. Fox (1991) "Synthesis of Life in the Lab? Defining a Protoliving
System," Quarterly Review of Biology, 66 (2), 181-185.
F.R. Eirich (1995) "Thoughts on the Origin of Life and Intelligence on Earth"
in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution: Structure
and Model of the First Cell, Kluwer Academic Publishers.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
>
> ...and it is questionable whether they should even be
> given the name "protocell."
>
The best way to answer this is with the following quote. Kleinsmith and Kish
are critics of proteinoid microsphere protocells, but they understand the
proper use of terminology:
"Microspheres are no more than small vesicles containing mediocre catalysts
and therefore capable of a primitive type of metabolism, growth and division.
Microspheres ... have no genetic system for encoding and accurately
transmitting hereditary information. Of course there is no reason for
believing that the first cells arising on earth had to resemble those
occurring today, so the term protocell has been introduced to refer to a
primitive cell-like structure that might have been the evolutionary precursor
of contemporary cells. Microspheres are certainly a plausible model for such
protocells." Kleinsmith, L. J., and V. M. Kish (1988) Principles of Cell
Biology, Harper and Row, pg. 28.
>
> They are merely an aggregation of polymers,
> and do not help to bridge the gap between life and non-life." (Thaxton
C.B.,
> Bradley W.L. & Olsen R.L., "The Mystery of Life's Origin", 1992, p175)
>
As has been shown, this conclusion is based on assumptions that are
simplistic and false; in other words, a strawman view.
>
> KO>Thus
> >they are called protocells, and those that are capable of transforming
> >sunlight into chemical energy and which use that chemical energy to
> >synthesize polynucleotides, from which they synthesize polypeptides, are
> >called metaprotocells.
>
> Thanks to Kevin for this, but it is not clear if this is a quote or Kevin's
> own words. If the former, I request Kevin to provide the reference.
>
It is a summary in my own words of the conclusions reported in a paper. The
paper is: A. Pappelis and S.W. Fox (1995) "Domain Protolife" in C.
Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution: Structure and
Model of the First Cell, Kluwer Academic Publishers. I posted it to the
group earlier this month; it can be found at
<http://www.calvin.edu/archive/evolution/199907/0062.html>.
Kevin L. O'Brien