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Louis Pasteur
Omne vivum ex vivo William Harvey, c. 1630 (1)
Omnis cellula e cellula Rudolph Virchow, 1858 (2)
In biology all things must be proved several times Cyril Dean Darlington,
1953 (3)
The greatest biologist of the
nineteenth century was Louis
Pasteur (1822-1895). His work had
both practical use and profound
theoretical significance. On the
practical side, what discovery in
the history of mankind is more
important than the germ theory of
disease? As for theoretical
significance, Pasteur disproved the
widely held belief in the
spontaneous generation of life. In a
simple experiment using a
sterilized flask with a bent neck, he
showed that plain air cannot initiate
the growth of microorganisms. A
culture can grow in the flask only if
germs enter it. "There is no known
circumstance in which it can be
confirmed that microscopic beings
came into the world without germs,
Louis Pasteur
without parents similar to
themselves," he concluded, in 1864 (4).
Louis Pasteur demonstrated that life comes only from life. One can only
wonder what the history of biological science would be if this principle had
been taken as fundamental. Perhaps today we would still be unsure how life
on Earth began. But we would approach the question differently. We would
assume that life here had to be seeded somehow. We would investigate
possible mechanisms for this seeding. We would look for evidence that
bacteria, the simplest known form of life, can survive in space, for example.
We would look for means by which they could travel across interstellar
space and survive for the millions of years such trips might take.
For the suggestion that life can assemble itself from nonliving chemicals, we

would have the utmost scepticism. "Extraordinary claims require

extraordinary evidence," we would say (5). Such extraordinary evidence
might include:

Creation in the laboratory of any kind of life simpler than a cell.

(Nothing yet.)
Evidence in nature of any kind of life simpler than a cell. (Viruses
and prions are not alive. However, newly topical nanobacteria look
too small to contain the lowest amount of DNA previously believed
necessary for a bacterium. Yet most neo-Darwinists doubt that they
are even biological. Additional research on them will be interesting.)
Fossil evidence of a long period during which evolution of
precellular life was underway on Earth. (The fossil record indicates
that there were whole cells on Earth in a geological instant.)
Evidence that any highly organized structure specifiable only with
lengthy encoded instructions can emerge with its instructions from a
closed system containing only unorganized, simple components, over
any period of time, by any natural means whatsoever. (The
emergence of life on Earth does not demonstrate that life can
originate from nonliving chemicals; how life on Earth emerged is the
question.)

But history went a different way. People in the late nineteenth centory
believed that Earth was biologically isolated from the rest of the Universe.
Therefore, the spontaneous generation of life by natural means from
nonliving chemicals was considered the only scientific alternative for
explaining the origin of life on Earth. It is still the consensus, accepted with
little questioning, even though the process has never been observed or even
described in plausible detail. That life could have come to Earth from
elsewhere is considered to be the extraordinary claim. But the situation may
be changing.

References
1. [quoted in] Ren Dubos, Louis Pasteur: Free Lance of Science, Da Capo Press, 1950,
1960. p 159.
2. [quoted in] Franklin M. Harold, The Way of the Cell, Oxford University Press, 2001. p 99.
3. Cyril Dean Darlington, F.R.S., The Facts of Life, London: George Allen & Unwin Ltd.,
1953. p 139.
4. Ren Dubos, Louis Pasteur: Free Lance of Science, Da Capo Press, Inc. 1950, 1960. p
187.
5. Expression attributed to Carl Sagan: see Interview With..., PBS, 1996.
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Viruses and Other Gene Transfer Mechanisms What'sNEW

Viruses today spread genes among bacteria and humans and other cells, as they always have... We are
our viruses Lynn Margulis, 1998 (1)

May we not feel that in the virus, in their merging with the cellular genome and their reemerging from them, we observe processes which, in the course of evolution, have created the
succesful genetic patterns that underlie all living things?
Salvador Luria, 1959 (2)
The Darwinian paradigm holds that copying mistakes and the
shuffling of existing genes are sufficient to write the new
genes needed for evolutionary advances. Cosmic Ancestry
holds that these processes cannot write useful new genes.
Instead, for a species to make evolutionary progress, new
genes must first be installed into its genome from outside.
We will discuss well-known processes which can install new
genes into the genome of a given species. Then we will look
at viruses.

Recombination
poliovirus: Science

Mutation is the mechanism of genetic change that we hear the

most about. Every known example of a single-nucleotide
mutation, however, is either adaptive within a narrow range, neutral, or deleterious in its effect. The
rare exception is the back-mutation, which merely undoes the damage of a previous mutation and
restores the affected strand of DNA to its original condition.

Recombination is a much more powerful mutation way for DNA to change. If an organism's
genome were written out as text, single-nucleotide mutations would be single-letter mistakes,
whereas recombination takes whole words, sentences, paragraphs, pages or groups of pages and
moves them to different locations. These new locations could be elsewhere in the same
paragraph, page, bookshelf, or library. Obviously a powerful mechanism like recombination
should be incorporated into anyone's understanding of the theory of evolution. There are three
kinds of recombination:

When two strings of similar DNA line up with each other and swap sections, it's called
homologous recombination.
When shorter pieces of similar DNA line up to initiate a swap of longer, dissimilar pieces (of
which the shorter pieces can be part), that's called site-specific recombination.
Transposition enables a piece of DNA to move within the same chromosome, or to a different
chromosome, to a location with which it has no similarity.

The Transfer of DNA Across Species Boundaries

Bacteria trade genes more frantically than a pit full of traders on the floor of the Chicago Mercantile
Exchange Lynn Margulis and Dorion Sagan (3)

While recombination moves whole blocks of genetic instructions within a cell, other processes
move whole blocks of genetic information from one bacterium to another bacterium of a
different kind. In the analogy between genes and written text, this move is a transfer of
paragraphs or pages from one library to another.
One such process is transformation. Here pieces of genetic instructions are released by a
bacterium into its environment. Another bacterium, not necessarily of the same strain, picks up
the DNA and incorporates it into its own genome. For example, Streptococcus pneumoniae that
are not pathogenic can become so by transformation (4). As an illustration of transformation,
think of a passenger who jumps overboard from one ship and is later picked up by another one.
Conjugation is the bacterial version of sex. In conjugation, bacterial cells actually connect, and
the "male" donates a piece of DNA to the "female." The piece of DNA in this case was excised
earlier from the bacterial chromosome. Such excised pieces of DNA are called plasmids.
(Plasmids, being able to pass out of one cell and into another, are similar to viruses. But they
have no protein coat and no "life cycle" different from that of their host cell; in this respect they
resemble small chromosomes.) If the transferred genetic material is a passenger on a ship, in the
transfer of plasmids by conjugation, the ships come alongside each other and the passenger
walks across a gangplank to the new ship.
Transduction is yet another way for bacteria to exchange genetic material. In transduction, a
virus takes up a piece of DNA from its bacterial host and incorporates it into its own viral
genome. After the virus has multiplied, many copies of the virus erupt from the infected cell.
Depending on the kind of transduction, some or all of the daughter viruses take copies of parts of
the bacterial DNA with them. When one of them infects a new cell, it inserts the stolen DNA into
the new cell, where the stolen piece becomes integrated into the new cell's DNA. (The stolen
piece may be a whole gene with which the cell acquires a new function, as was reported in June,
1996, by two scientists at Harvard Medical School (5).) In transduction, the passenger resorts to
hiding inside some freight, hoping to get aboard a different ship that way.
Transduction by viruses works in eukaryotic organisms as well. The discovery that large
blocks of genetic instructions can be swapped and transferred among creatures is a clue that the
insertion of new genes could be the mechanism behind evolutionary advances. If viruses can
transfer eukaryotic genes across species boundaries, and can install their own genes into their
hosts, the case for the new mechanism is even stronger. As we will see, viruses do just that.

Viruses are mobile genetic elements (6)

It was an absolutely stunning surprise to us that something as strange as viruses carrying genes
from one cell to another can happen Joshua Lederberg (7)
If your computer suddenly begins to greet you with a vulgar message, you will recognize that the
computer has contracted a virus. It might have arrived via the modem, it might have come with a

new program on a disk, or someone might have stealthily keyed it in. It might even have been
there when you originally acquired the computer. However it got there, it is definitely a
computer virus, and your computer did not spontaneously generate it.
Computer viruses are called viruses because they are analogous to biological viruses that infect
living cells. Because viruses are simpler than cells, biologists used to think that maybe viruses
were the precellular life forms that Darwinism requires. Today however, even Darwinists don't
think that viruses are this link. Viruses are not independently capable of metabolism or
reproduction. Darwinists now think that viruses evolved after cells. What is a virus?
A virus is a piece of genetic instructions, usually in a protective coat. Virus particles
are tiny; a cell can manufacture and contain as many as a thousand of them before
breaking open. They were first discovered when biologists observed that some diseasecausing agents were able to pass through a filter too fine for bacteria. They can be
small because they contain almost none of the machinery of a cell, only a smallish
quantity of DNA or RNA.
Viruses are not living things. When they are outside of their host cell, they are just very complex
molecular particles that have no metabolism and no way to reproduce. In our computer
metaphor, they're like software with no hardware, floppy disks or diskettes without a computer.
Having no independent metabolism they can remain viable indefinitely, under the right
circumstances. "Some of them can even be crystallized, like minerals. In this state they can
survive for years unchanged until they are wetted and placed into contact with their particular
hosts" (8).
The viruses that infect bacteria are more specifically called bacteriophages, or simply phages.
The kind and amount of genetic instructions in phages vary from 3,600 RNA nucleotides to
166,000 DNA nucleotide pairs (9). To restate these dimensions in terms of our computer
analogy, the computer viruses that infect handheld calculators range in size from 900 bytes to
over 40 kilobytes. For comparison, the simplest handheld calculator (a bacterium) has about 200
kilobytes of stored programs.
The viruses that infect eukaryotic cells vary in size also. The
poliovirus has 7,600 RNA nucleotides; the vaccinia (cowpox) virus
has 240,000 DNA nucleotide pairs (10). To use computer terms
again, the computer viruses that infect personal computers range in
size from 1.9 kilobytes to 60 kilobytes. For comparison, a very
simple personal computer (a yeast cell) has genetic instructions
equivalent to about 8 megabytes. An advanced personal computer (a
human cell) contains about 1.5 gigabytes of stored information,
counting the backup copy and the "silent" DNA.
When a virus attaches to its host cell, the host may take the whole
virus into its cytoplasm where the virus's protective coat is removed.
However, some bacteriophages use a different invasion method.

Herpesvirus by Linda Stannard: All the

Virology on the WWW

They remain outside the cell and a chemical trigger causes them to inject their genome into the
host's cytoplasm. Either way, the virus's genome enters the cytoplasm of the host cell.
Once inside, the virus causes the machinery of the host cell to enter one of two cycles, the lytic
cycle or the lysogenic cycle. In the lytic cycle, which leads to cell degradation, the host begins to
carry out the reproductive instructions in the invading virus's genome. Those instructions are, in
summary, "make more of me." The host becomes a slave to the invader; it drops everything and
begins to manufacture copies of the virus. After many copies have been made, the cell breaks
open and dies, and many viruses are released. This is the normal way in which a virus causes
symptoms of disease in its host.
In the lysogenic cycle the host cell does not make more viruses, but simply harbors the entire
viral genome in the cell, usually by incorporating it into the cell's genome. If the virus is an RNA
virus, as many are, the RNA must first undergo "reverse transcription" into DNA. While
harboring the viral genes, the cell may grow and multiply normally, carrying the new instructions
harmlessly along with it. A virus carried in this manner is said to be latent. Recently scientists
have learned that even during latency, some of the virus's genes can be expressed (11).
Sometimes after lysogenic integration of the viral
genome into the host's DNA, an "induction event" can
cause the viral infection to revert to the lytic cycle, in
which the cell makes many copies of the virus and
dies. After this happens, the numerous new virus
particles can then infect many other cells. If the new
infections are lysogenic, the virus's genes may again
become integrated into the DNA of the new cells
without harm to them. Lytic infection of one host
Transduction
followed by lysogenic infection in another is also
called transduction. When we discussed transduction
earlier, we said viruses could tranduct a cell's genes to another cell. Here we see that the virus's
own genes can also be transducted into cells.
This method of acquiring genes is not in doubt. Among bacteria, for example, "There are some
well-documented cases of homologies between viral genes and their host counterparts. ...Some
past exchanges have occurred between distantly related phages and between phage and host"
(12). Eukaryotes are also known to acquire viral genes, and the phenomenon is not rare.
"Endogenous retroviruses and retroviral elements have been found in all vertebrates
investigated.... As a general rule, the number of groups of viral sequences found within a given
vertebrate species is proportional to the effort spent searching that species" (13).
And it has now been shown that some of the genes that viruses install have a beneficial function
for the host. In fact, doctors now use viruses to install genes in the new field of "gene therapy."
Even the virus that causes AIDS, if properly disabled, may become useful this way (14, 15).
When the genome of Bacillus subtilis was completely sequenced and published in July, 1997, the
sequencers noticed another interesting example of gene transfer. "...Some of the bacteriophages

in B. subtilis also appear to contribute genes that aid the host bacterium by helping it resist
harmful substances such as heavy metals" (16). This evidence confirms that genes installed by a
virus into the genome of the host can be beneficial, even essential, for the evolution of the host.
One example of a benefit conferred by viral genes comes from humans. A sequence installed by
a retrovirus regulates the amylase gene cluster, allowing us to produce amylase in our saliva.
This sequence that we share with a few other primates enables us to eat starchy foods we
otherwise couldn't (17).
In August, 1997, another whole-genome sequencing, of Helicobacter pylori, found that many
genes in it are more similar to those of eukaryotes or archaea than other bacteria (18). "Such
observations... are often interpreted as evidence of lateral gene transfer in the evolutionary
history of an organism," say the sequencers.
Additional evidence that genes can move across species boundaries even in eukaryotes comes in
the June 13, 1997, issue of Science. A report there by Frederico J. Gueiros-Filho and Stephen M.
Beverley of Harvard describes the "Trans-kingdom Transposition" of a gene-size piece of DNA
known as a transposable element (19). The particular transposable element they studied, called
mariner, has already been found in planaria, nematodes, centipedes, many insects, and humans
(20). Until recently, transposable elements were considered to be functionless, or "junk DNA."
But John McDonald, a professor in the department of genetics at the University of Georgia,
concludes, "It now appears that at least some transposable elements may be essential to the
organisms in which they reside. Even more interesting is the growing likelihood that
transposable elements have played an essential role in the evolution of higher organisms,
including humans" (21). Another team of biologists has demonstrated that by transformation
(discussed above in bacteria) a mariner element can become installed into the inherited genome
of zebrafish (22). So viruses are not the only mobile genetic elements.
In conclusion, viruses could easily provide a way for new genes never before encountered by a
species to become part of its genome. That viruses install new genes into their hosts is not
speculative it is a well known fact. That transferred genes are important in evolution is
becoming well established. According to Cosmic Ancestry, the horizontal transfer of genes by
viruses and other means is essential for evolutionary progress.

COSMIC ANCESTRY | Quick Guide | Site Search | Next | by Brig Klyce | All Rights Reserved

The undreamt-of breakthrough of molecular biology has made the problem of the
origin of life a greater riddle than it was before: we have acquired new and deeper
problems. Karl R. Popper, 1974 (.2)

Nobody understands the origin of life. If they say they do, they are probably
trying to fool you. Ken Nealson, 2002 (.5)
We emerge inevitably or by luck from the chipping of DNA by cosmic rays,
chemical currents in space, the bubbling of volcanic mud. Dennis
Overbye, 2004 (.6)

The RNA World And Other Origin-ofLife Theories | What'sNEW

Virtually all biologists now agree that bacterial cells cannot

form from nonliving chemicals in one step. If life arises
from nonliving chemicals, there must be intermediate
forms, "precellular life." Of the various theories of
precellular life, the most popular contender today is "the
RNA world."

RNA has the ability to act as both genes and enzymes.

This property could offer a way around the "chickenand-egg" problem. (Genes require enzymes; enzymes
require genes.) Furthermore, RNA can be transcribed
into DNA, in reverse of the normal process of
transcription. These facts are reasons to consider that
the RNA world could be the original pathway to cells.
James Watson enthusiastically praises Sir Francis
Crick for having suggested this possibility (1):
The time had come to ask how the DNA RNA protein flow of
information had ever got started. Here, Francis was again far ahead of his time. In 1968 he
argued that RNA must have been the first genetic molecule, further suggesting that RNA,
besides acting as a template, might also act as an enzyme and, in so doing, catalyze its own
self-replication.

It was prescient of Crick to guess that RNA could act as an enzyme, because
that was not known for sure until it was proven in the 1980s by Nobel Prizewinning researcher Thomas R. Cech (2) and others. The discovery of RNA
enzymes launched a round of new theorizing that is still under way. The term

"RNA world" was first used in a 1986 article by Harvard molecular biologist
Walter Gilbert (3):
The first stage of evolution proceeds, then, by RNA molecules performing the catalytic
activities necessary to assemble themselves from a nucleotide soup. The RNA molecules
evolve in self-replicating patterns, using recombination and mutation to explore new
niches. ... they then develop an entire range of enzymic activities. At the next stage, RNA
molecules began to synthesize proteins, first by developing RNA adaptor molecules that
can bind activated amino acids and then by arranging them according to an RNA template
using other RNA molecules such as the RNA core of the ribosome. This process would make
the first proteins, which would simply be better enzymes than their RNA counterparts. ...
These protein enzymes are ... built up of mini-elements of structure.
Finally, DNA appeared on the scene, the ultimate holder of information copied from the
genetic RNA molecules by reverse transcription. ... RNA is then relegated to the
intermediate role it has todayno longer the center of the stage, displaced by DNA and the
more effective protein enzymes.

Cech

Today, research in the RNA world is a medium-sized

industry. Scientists in this field are able to
demonstrate that random sequences of RNA
sometimes exhibit useful properties. For example, in
1995, a trio at the Whitehead Institute for Biomedical
Research reported "Structurally Complex and Highly
Active RNA Ligases Derived from Random RNA
Sequences" (4). (Ligases are enzymes that splice
together other molecules such as DNA or RNA.) The
results are interesting they suggest that
randomness can produce functionality. The authors
interpret the results to mean that "the number of
distinct complex functional RNA structures is very
large indeed."

There is a lot to learn about RNA, and research like this is how we learn it.
But these and other similar findings arrived at in highly orchestrated
experiments that start with biologically produced RNA are very far from
proving that the RNA world is the pathway between nonlife and life. In
nature, far from the sterilized laboratory, uncontaminated RNA strands of
any size would be unlikely to form in the first place. "... The direct synthesis
of ... nucleotides from prebiotic precursors in reasonable yield and
unaccompanied by larger amounts of unrelated molecules could not be
achieved by presently known chemical reactions" (5).

Francis Crick himself has become much less enthusiastic

about the RNA world than Watson. In 1973, he and
another eminent researcher into the origin of life, Leslie
E. Orgel, published a paper advocating the theory called
"Directed Panspermia" (6). In 1981, Crick published Life
Itself, a whole book about that theory (7). And by 1993
he says, "It may turn out that we will eventually be able
to see how this RNA world got started. At present, the
gap from the primal 'soup' to the first RNA system
capable of natural selection looks forbiddingly wide" (8).

Crick

At the Salk Institute for Biological Studies, in 1994,

Leslie Orgel observes, "Because synthesizing nucleotides and achieving
replication of RNA under plausible prebiotic conditions have proved so
challenging, chemists are increasingly considering the possibility that RNA
was not the first self replicating molecule..." (9).
Apparently NASA has lost enthusiasm for the RNA world as well. In the
Final Report issued after the "Astrobiology Workshop" held September 9-11,
1996 at Ames Research Center, California, we read (10),
It has been postulated that there was a time in protobiological evolution when RNA played
a dual role as both genetic material and a catalytic molecule ("the RNA world"). However,
this appealing concept encounters significant difficulties. RNA is chemically fragile and
difficult to synthesize abiotically. The known range of its catalytic activities is rather
narrow, and the origin of an RNA synthetic apparatus is unclear.

Other Theories
In spite of the intense level of work on the RNA world in the last decade,
there is no consensus theory for precellular life. There are many theories.
Here are some of the others

A few scientists still say that DNA could succeed in starting life on its way
(11). But even the shortest DNA strand needs proteins to help it replicate.
This is the chicken-and-egg problem.
There is a "proteins first" school. For example, Manfred Eigen of
Germany's Max Planck Institute says, "There is no doubt that proteins,
which are more easily formed, were first on the scene" (11.5). Of course,
these first proteins must be much shorter than any used in life today,
because of the sheer unlikelihood of forming useful long ones out of a
soup of amino acids.
Physicist Freeman Dyson proposes to solve the chicken-and-egg problem
with a double origin, one for metabolism (proteins) and one for replication
(strands of nucleotides) (12).
In Seven Clues to the Origin of Life (13), A. G. Cairns-Smith says that clay

crystals could have served as the scaffolding upon which the first short
DNA or RNA genome was constructed. A new elaboration of this idea
prompted one writer to wonder, "Primordial soup or crpes?" (14). Even
more recently, another tangent on this path leads to zeolite (14.5).
Biologists Harold J. Morowitz (15), David Deamer (16), and others (17),
advocate a theory that could be paraphrased as "containers first."
Jeffrey L. Bada of the Scripps Institution of Oceanography holds the
minority view that the early Earth was frozen and believes precellular life
started in "cold soup" under the ice (18, 19).
Chemists Claudia Huber and Gnter Wchtershuser say the soup where
life originated was actually quite hot, probably near undersea volcanic
vents, where iron and nickel sulfides might catalyze some of the necessary
reactions (19.5-19.7).
Cornell Astronomer Thomas Gold wonders if life might have originated in a
hot environment even deeper, in Earth's crust (19.8).
Stuart Kauffman of the Santa Fe Institute, says, "...whenever a collection of
molecules contains enough different kinds of molecules, a metabolism will
crystallize from the broth" (20).
Another idea is the "PNA world." Because starting the RNA world is so
difficult, there probably needs to be a pre-RNA world. PNA, or peptide
nucleic acid, might have some of the properties necessary to constitute
that world (21). This would be pre-precellular life.

The Time Problem

To go from a bacterium to people is less of a step than to go from a mixture
of amino acids to a bacterium. Lynn Margulis (21.5)
The only premise that all of the precellular theories share is that it would be
an extremely long time before the first bacterial cells evolved. If precellular
life somehow got going, it could then conceivably begin to crank out, by
some precellular process, random strings of nucleotides and amino acids,
trying to luck into a gene or a protein with advantages which would lead to
bacterial life. There is no evidence in life today of anything that produces
huge quantities of new, random strings of nucleotides or amino acids, some
of which are advantageous. But if precellular life did that, it would need lots
of time to create any useful genes or proteins. How long would it need?
After making some helpful assumptions we can get the ratio of actual, useful
proteins to all possible random proteins up to something like one in 10^500
(ten to the 500th power). So it would take, barring incredible luck,
something like 10^500 trials to probably find one. Imagine that every cubic
quarter-inch of ocean in the world contains ten billion precellular ribosomes.
Imagine that each ribosome produces proteins at ten trials per minute (about
the speed that a working ribosome in a bacterial cell manufactures proteins).
Even then, it would take about 10^450 years to probably make one useful
protein. But Earth was formed only about 4.6 x 10^9 years ago. The amount

of time available for this hypothetical protein creation process was maybe a
few hundred million or ~10^8 years. And now, to make a cell, we need not
just one protein, but a minimum of several hundred.
So even if we allow precellular life, there is a problem getting from there to
proteins, genes and cells. The random production of proteins does not
succeed as an explanation. Other intermediate, unspecified stages must be
imagined. We could call these stages post-precellular life. By whatever
means, life's evolution through these stages would have to be timeconsuming.
One advocate of the RNA world, Gerald Joyce, allows 400 million years for
"The Rise and Fall of the RNA World" (22):
...At some point RNA organisms began to dabble in the use of short peptides, leading
eventually to the development of protein synthesis. Other "experiments" led to the
discovery of DNA, which provided a more stable repository for genetic information. By 3.6
to 3.8 billion years ago all of these events had come to pass; the RNA world had fallen and
the DNA/protein world had risen in its place.

But other researchers see evidence for prokaryotic cells in the first 100
million years, maybe even immediately. "...Actual cells have been found in
the earth's oldest unmetamorphosed sediments...," says Gould in Wonderful
Life (23). Bada says that cyanobacteria may have emerged only ten million
years after the first precellular life (24). In November, 1996, S. J. Mojzsis of
the Scripps institution of Oceanography and others reported isotopic
evidence that cellular metabolism was under way before 3.8 billion years ago
(25). Even before the research by Mojzsis et al., Francis Crick was worried
by the time problem. "...The real fossil record suggests that our present form
of protein based life was already in existence 3.6 billion years ago.... This
leaves an astonishingly short time to get life started" (26). Another
researcher, Peter B. Moore, says this about the time problem (27):
Of one thing we can be certain: The RNA worldif it ever existedwas short-lived. The
earth came into existence about 4.5 x 10^9 years ago, and fossil evidence suggests that
cellular organisms resembling modern bacteria existed by 3.6 x 10^9 years before the
present.... There are even hints that those early organisms engaged in photosynthesis,
which is likely to have been a protein-dependent process then, as now. Thus it appears
likely that organisms with sophisticated, protein based metabolisms existed only 0.9 x 10^9
years after the planet's birth.
The "window of opportunity" for the RNA world was much shorter than 0.9 x 10^9 years.
The earth's surface was uninhabitable at the beginning due to heat generated by meteoric
bombardment and its geological differentiation. ...Thus, the interval in which the biosphere
could have been dominated by RNA-based life forms may be less than 100 million years.
Incidentally, when one starts thinking along these lines, one must consider the unthinkable,

i.e., that the length of time that RNA-based proteins actually bestrode the earth might be
zero.

The Origin of Handheld

Calculators: A spoof on
origin-of-life theories in
terms of the computer
analogy (see A Cell is Like
a Computer):

The fossil record indicates

that there were handheld
calculators with at least
240 kilobytes of stored
programs in existence
almost as soon as the
earth cooled. Possibly,
handheld calculators
originated when special
conditions allowed the
formation of silicon chips
and circuit boards
(primitive genes). Heat,
perhaps generated by
radioactivity, volcanoes
or meteor impacts, melted
some sand to form a
silicon flake. Random
splashing of molten metal
caused metal filaments to
form a circuit board on
the flake. Oily film on
ponds dried into the hard
plastic material needed
for the shell.
Lightning provided the
first source of electrical
power. Prototypes in
seawater, at just the right
distance from the strike,
received sufficient voltage
without being destroyed.
Batteries (allowing

Summary
It goes without saying that the emergence of this
RNA world and the transition to a DNA world
imply an impressive number of stages, each more
improbable than the previous one
Franois Jacob, 1997 (28)

There is no remnant or trace evidence of

precellular life anywhere today. That it
ever existed is entirely conjectural.
Although its emergence from nonliving
matter is hard to conceive, precellular
life must have appeared almost
immediately.
There was almost no time for precellular
life to evolve into the simplest bacterial
cells.
Precellular life has never been created in
a lab.
In spite of the RNA world, there is no
consensus on the model for precellular
life.

independent metabolism)
came later. The first
batteries were iron acid
batteries, formed in mud
pockets. Lithium batteries
were a very late
development.
This primitive
protocalculator somehow
acquired ten to 25 bytes of
stored programs (40 to
100 nucleotides) that
enabled it to have some
function that made it
useful. Now we find
evidence for only the fully
evolved handheld
calculators similar to the
ones used today, with
function keys and lengthy
built-in programs,
because the fossil record
is incomplete.

We said that research in the RNA world is a

medium-sized industry. This research has
demonstrated how exceedingly difficult it would be for living cells to
originate by chance from nonliving matter in the time available on Earth.
That demonstration is a valuable contribution to science. Additional research
will be valuable as well. But to keep insisting that life can spontaneously
emerge from nonliving chemicals in the face of the newly comprehended
difficulties is puzzling. It is reminiscent of the persistent efforts of medieval
alchemists to turn lead into gold.
There is another scientific explanation for the origin of life on Earth. It is
that whole cells arrived here from space.

What'sNEW
If life pops up readily in Earth-like conditions, surely it should have started many
times right here on Earth Paul Davies, 2011
Jef Akst, "RNA World 2.0" [html], The Scientist, 1 Mar 2014.
Jimmy Gollihar, Matthew Levy and Andrew D. Ellington, "Many Paths to the Origin of
Life" [summary], doi:10.1126/science.1246704, p 259-260 v 343, Science, 17 Jan 2014.

20 Dec 2013: Eugene V. Koonin's book, The Logic of Chance

Katarzyna Adamala and Jack W. Szostak, "Nonenzymatic Template-Directed RNA
Synthesis Inside Model Protocells" [abstract], doi:10.1126/science.1241888, p 1098-1100 v
342, Science, 29 Nov 2013; and commentary:
Robert F. Service, "The Life Force" [intro], doi:10.1126/science.342.6162.1032, p 10321034 v 342, Science, 29 Nov 2013. "'Laboratories will be creating a living cell within ten
years,' Colin Pittendrigh, an American biologist, predicted in 1967."
Ancient Minerals: Which Gave Rise to Life?, Carnegie Institution for Science
(+PhysOrg.com), 25 Nov 2013.

The Tree of Life What'sNEW

It has been customary since the nineteenth century to depict the progress
of evolution as a tree. A typical one, at right, was drawn by Ernst Haeckel,
in 1866, to represent the phylogeny of arthropods. Each species is
represented by a separate branch, so the diversity of species is evident
from the number of branches. The height of the tree has come to represent
the level of biological organization, so higher branches would represent
"higher" forms of life. Hence, a tree that depicted all species would have
very many low branches representing the wide variety of bacterial species,
and fewer branches at the top, where primates and ultimately mankind
emerge. Higher branches also represent later developments, as for real
trees. Thus the tree implies that biological evolution tends over time to
progress to "higher" forms of life.
Harvard biologist and writer Stephen Jay Gould believes there is
no prescribed hierarchy of life; evolution wanders aimlessly, and
is as likely to go down as up. Therefore, he has said that the tree
of life is a low bush.
The art of drawing such trees has become more scientific, it is
claimed, because now the actual sequences of genes can be
compared. It is logical to hold that the more similar genes are,
the more closely related are the organisms that carry them. Thus
the gene for the RNA in the smaller unit of the ribosome, a gene
all cells carry, has been sequenced for many species and used to
draw a mathematical tree of life like the one at left.
Work like this has been under way since at least 1977 (1). Carl
Woese of the University of Illinios at Urbana Champaign is a
pioneers of the new method. He first proposed that archaebacteria are different enough to
warrant the recognition of a new third domain called archaea. This proposal became widely
accepted by about 1996; it is corroborated by several lines of evidence, not just the sequence of
one gene (2).
But, promising as the new method is, it turns out to be flawed
from the Darwinian perspective. The problem is that when
different genes are used to draw the tree, different trees result.
This problem is explained if evolution makes extensive use of
genes that are transfered horizontally, as in Cosmic Ancestry,
instead of only vertically, as in Darwinism. Horizontal gene
transfer produces complex trees with criss-crossing branches
(3), instead of simple, fan-shaped trees.

Furthermore, Cosmic Ancestry holds that without the benefit of new genetic
programs acquired by horizontal transfer, evolution would go only sideways
or downhill, and the tree of life would be a hanging plant. In order for life to
ascend the tree for genuine improvements to evolve new genetic
programs must be supplied. These new programs could be resident already
within life somewhere, as silent DNA. Perhaps the expression of these
programs was impossible until other biological or environmental
developments were complete. Or, the genetic programs could possibly be new
arrivals, delivered in the same manner as life on Earth originally was. They
could be carried here by bacterial spores, or they could possibly arrive in
viruses. Both spores and viruses could be delivered by meteorites directly to
the Earth's surface, or descend through the atmosphere as dust. After arrival,
the new genetic programs could be installed and
transferred laterally by viruses or other methods now becoming
understood. However new programs are installed, evolution can only
climb the tree of life when new genetic programs are expressed for the
first time, according to Cosmic Ancestry.
This evolutionary process would give the the tree of life aspects of a
spruce, with branches that hang slightly downward. Darwinian
evolution can enable life to explore a given level of the canopy,
because it is not higher than its connection to the trunk. But in order
for life to climb the tree to a higher level, new genetic programs are
required which mutation and recombination alone cannot supply.
When they are supplied, a major advance may ensue. Thus, by cosmic
ancestry, the problem of punctuated equilibrium is also resolved.
A consequence of this reasoning is that life on Earth can have descended only from life
elsewhere that was at least as highly evolved as it is here.

What'sNEW
31 Oct 2013: Evolution is mediated ...also through the mixture of genomic material between individuals of
different lineages.
28 May 2013: All gene trees differ from species
phylogeny Salichos and Rokas
Pere Puigb, Yuri I Wolf and Eugene V Koonin,
"Seeing the Tree of Life behind the phylogenetic
forest" [html], doi:10.1186/1741-7007-11-46, n46
v11, BMC Biology, 15 Apr 2013 (see illustration at
left.)
Digging Down Below the Tree of Life by Michael
Schirber, Astrobiology Magazine, 28 Mar 2013.
Nigel Goldenfeld and Norman R. Pace, "Carl R.
Woese (1928-2012)" [first paragraph],
doi:10.1126/science.1235219, p661 v339, Science,

8 Feb 2013.
Harry Noller, "Carl R. Woese (1928-2012)" [html], doi:10.1038/493610a, p610 v493, Nature, 31 Jan 2013.
Elizabeth Pennisi, "New Way to Look at Life" [summary], doi:10.1126/science.338.6105.317, p317 v338, Science,
19 Oct 2012.
13 Sept 2012: ...the horizontal flow of genes is a part of the story of life.
Elie Golgin, "Rewriting Evolution" [html], doi:10.1038/486460a, p460-462 v486, Nature, 28 Jun 2012. "Tiny
molecules called microRNAs are tearing apart traditional ideas about the animal family tree."
Sophie S. Abby et al., "Lateral gene transfer as a support for the tree of life" [abstract],
doi:10.1073/pnas.1116871109, p4962-4967 v109, Proc. Natl. Acad. Sci. USA, 27 Mar 2012.
Herv Philippe and Batrice Roure, "Difficult phylogenetic questions: more data, maybe; better methods,
certainly" [abstract], doi:10.1186/1741-7007-9-91, v9 n91, BMC Biology, 29 Dec 2011.
Beyond the Tree of Life: a new thematic series from BioMedCentral, 12 Jul 2011.
17 Apr 2011: How important is lateral gene transfer? (Jerry Coyne's blog)
Graham Lawton, "Why Darwin was wrong about the tree of life" [preview],
NewScientist, 21 Jan 2009.
Discovery of jumping gene cluster tangles tree of life by David Salisbury, Vanderbilt
University, 4 Feb 2011.
Jessica E Light et al., "Evolutionary history of mammalian sucking lice (Phthiraptera:
Anoplura)" [abstract], doi:10.1186/1471-2148-10-292, v10 n292, BMC Evolutionary
Biology, 22 Sep 2010. "We find significant conflict between phylogenies constructed
using molecular and morphological data."
Ruben E Valas and Philip E Bourne, "Save the tree of life or get lost in the woods"
[abstract], doi:10.1186/1745-6150-5-44, v5 paper 44, Biology Direct, 1 Jul 2010.
Douglas L. Theobald, "A formal test of the theory of universal common ancestry"
[abstract | Editor's Summary], doi:10.1038/nature09014, p219222 v465, Nature, 13 May 2010. Also see
commentary
Mike Steel and David Penny, "Origins of life: Common ancestry put to the test" [html], doi:10.1038/465168a,
p168-169 v465, Nature, 13 May 2010. And
Katherine Harmon, "The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life" [html],
Scientific American, 13 May 2010.
W. P. Hanage, "The Trouble with Trees" (review of The New Foundations of Evolution: On the Tree of Life by Jan
Sapp), [summary], doi:10.1126/science.1185784, p 645-646 v 327, Science, 5
Feb 2010.
11 Dec 2009: ...the percentage of genes transferred ...could be close to
100% Cordero and Hogeweg.
21 Aug 2009: I find it fascinating that this prokaryotic symbiosis could so
profoundly shape the evolution of life....
20 Jun 2009: The tree of life was always a net. Nature was always a
genetic engineer.
16 Mar 2009: ...gene transfers of various types... and other forms of
acquisition of 'foreign genomes' ...are more important.... Lynn Margulis
(see tree at left | larger version)
8 Mar 2009: HGT also turns out to be the rule rather than the exception in
the third great domain of life, the eukaryotes.
11 Apr 2008: Earth's first animal... was probably significantly more complex than previously believed.
14 Jan 2008: ...Only rarely have phylogenetic studies of morphology and DNA data agreed in plant studies....

10 Dec 2007: When eukaryotes are included..., the phylogeny of life seems better represented by a network than
a tree....
Patrick J. Keeling, "Deep Questions in the Tree of Life" [summary], 10.1126/science.1149593, p 1875-1876 v 317,
Science, 28 Sep 2007.
Laura Spinney, "Evolution: hacking back the tree of life" [preview], online 13 June. Print version, "Back to their
roots," p 48-51 v 194, New Scientist, 16-22 Jun 2007. "We have vastly underestimated evolution's fondness for
pruning."
John Whitfield, "Linnaeus at 300: We are family" [link], doi:10.1038/446247a, Nature, online 14 Mar 2007.
W. Ford Doolittle and Eric Bapteste, "Pattern pluralism and the Tree of Life hypothesis" [abstract],
doi:10.1073/pnas.0610699104, p 2043-2049 v 104, Proc. Natl. Acad. Sci. USA, 13 Feb (online 29 Jan) 2007.
Ryan G. Skophammer et al., "Evidence that the Root of the Tree of Life Is Not within the Archaea" [abstract],
doi:10.1093/molbev/msl046, p 1648-1651 v 23, Molecular Biology and Evolution, Sep (online 26 Jun) 2006.
20 June 2006: Bats and horses are closely related, according to a genomic study using retroposon (L1) analysis.
15 Mar 2006: The paradigm for evolution among prokaryotes has completely shifted.
Francesca D. Ciccarelli, Tobias Doerks et al., "Toward Automatic Reconstruction of a Highly Resolved Tree of Life"
[abstract], doi:10.1126/science.1123061, p 1283-1287 v 311, Science, 3 Mar 2006. "...Detection and selective
exclusion of HGTs... turned out to be essential for obtaining a highly resolved tree."
Anne B. Simonson et al., "Decoding the genomic tree of life" [abstract], doi:10.1073/pnas.0501996102, p 66086613 v 102, Proc. Natl. Acad. Sci. USA, 3 May (online 25 Apr) 2005.
1 July 2005: A new microbial tree of life has been drawn by geneticists at EMBL.
Frdric Delsuc et al., "Phylogenomics and the Reconstruction of the Tree of Life" [abstract], p 361-375 v 6 n 5,
Nature Reviews Genetics, May 2005.
Nobuko Arisue, Masami Hasegawa and Tetsuo Hashimoto, "Root of the Eukaryota Tree as Inferred from
Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data" [abstract],
doi:10.1093/molbev/msi023, p 409-420 v 22, Molecular Biology and Evolution, Mar 2005 (online 20 Oct 2004).
Song Yang, Russell F. Doolittle and Philip E. Bourne, "Phylogeny determined by protein domain content"
[abstract], p 373-378 v 102, Proc. Natl. Acad. Sci. USA, 11 Jan 2005.
Keith A. Crandall and Jennifer E. Buhay, "Genomic Databases and the Tree of Life" [summary], p 1141-1145 v
306, Science, 12 Nov 2004.
9 Sep 2004: The ring of life! "Microbes use two mechanisms of natural variation that disobey the rules of treelike evolution."
John Whitfield, "Origins of life: Born in a watery commune" [text], p 674-676 v 427, Nature 19 Feb 2004. "We
don't understand how to create novelty from scratch that's a question for biologists of the future." Carl
Woese
T. Jonathan Davies et al., "Darwin's abominable mystery: Insights from a supertree of the angiosperms"
[abstract], Proc. Natl. Acad. Sci. USA online, 6 Feb 2004. "Diversification rates ...cannot easily be attributed to ...a
few key innovations but instead ...[reflect] the interactive effects of biological traits and the environment."
[Mathematical analysis favors Margulis over Woese], EurekAlert!, 9 Jan 2004.
"Tree of Life," a special section of six articles [first abstract with links to others], p 1691-1709 v 300 Science, 13
June 2003.
Field Museum plays key role in massive project to map Tree of Life, EurekAlert!, 30 Oct 2002.
The Tree of Life: Cold Start?, by Stephen Hart, Astrobiology Magazine, 30 Oct 2002.
Uprooting the Tree of Life, by Brendan A. Maher, v 16 n 18 p 26, The Scientist, 16 Sep
2002 (see tree at right).
2002, August 19: New evolution theory is survival by gene sharing.
Yuri I. Wolf et al., "Genome trees and the tree of life" [abstract], p 472-479 v 18 n 9

Trends in Genetics, 2002. "...Alternative approaches to tree construction that attempt to determine tree topology
on the basis of comparisons of complete gene sets."
2002, July 7: Acquiring Genomes by Margulis and Sagan (see tree at left).
New cellular evolution theory rejects single cell beginning, by Jim Barlow,
University of Illinois at Urbana-Champaign, 17 June 2002.
Sandie Baldauf, "The tree of life is a tree (more or less)" [abstract], p 450-451 v
17, Trends in Ecology and Evolution. "The Assembling the Tree of Life symposium
was held at the American Museum of Natural History, New York, USA, on 30 May
2002."
Elizabeth Pennisi, "Preparing the Ground for a Modern 'Tree of Life'" p 1979-1980
v 293 Science, 14 September 2001. Biologists to meet in New York, September 2022 to discuss a project to draw a new phylogenetic map.
Geir Hestmark, "Temptations of the tree" p 911 v 408 Nature, 21/28 December
2000. "Phylogenetic trees are common in today's scientific journals, but there it is
seldom realized how speculative they are because they look so real."
Carl R. Woese, "Interpreting the universal phylogenetic tree" [abstract] p 8392-8396 v 97 n 15 Proc. Natl. Acad.
Sci. USA, 18 July 2000. "Horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic."
2000, June 14: The genesis of life on earth... remains an unyielding problem.
Francis S. Collins and Karin G. Jegalian, "Deciphering the Code of Life" p 86-91 v 281 n 6, Scientific American,
December 1999. "A more apt analogy ...will be a net or a trellis ...rather than a tree...."
1999, July 15: A Recent Issue of Science... [4th paragraph] W. Ford Doolittle describes a new view of
phylogenetic trees that recognizes the importance of lateral gene transfer.
Common genes form new family tree for animals by Sean B. Carroll, EurekAlert, 23 June 1999.
1998, July 28: Carl R. Woese says lateral gene transfer is more important than vertical inheritance at first.

References
1. C. R. Woese and G. E. Fox: p 5088-5090 v 74, Proc. Natl. Acad. Sci. USA, 1977.
2. For discussion see Ernst Mayr: "Two empires or three?" [text], p 9720-9723 v 95, Proc. Natl. Acad. Sci. USA, 18
August 1998; and a reply by Carl R. Woese: "Default taxonomy: Ernst Mayr's view of the mocrobial world"
[abstract], p 11043-11046 v 95 Proc. Natl. Acad. Sci. USA, 15 September 1998.
3. W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree" [abstract], p 2124-2129 v 284, Science, 25
June 1999.

Why Sexual Reproduction? What'sNEW

When Maynard Smith reverse-engineered sex... he created a paradox. Sex
should not exist; natural selection will favor asexual reproduction. The
solution to the paradox is almost the Holy Grail of a large theoretical subbranch of evolutionary biology, but it still has not been satisfactorily
tracked down. Mark Ridley, 1997 (1)
In spite of the number of ways bacteria can exchange genetic instructions,
many of them haven't evolved very far not as bacteria anyway. There
mating butterflies: Greenspun
are many modern bacteria that look very similar to fossils of the earliest
bacteria of over 3 billion years ago. Eukaryotes are much better at
evolving than prokaryotes. Eukaryotes first appeared on Earth about 1.7
billion years ago. They contain complex subunits, some of which mitochondria and plastids have their own
DNA. With the appearance of eukaryotes, evolution began to accelerate. All multicelled animals and plants are
made of eukaryotic cells. Where did they come from?

Eukaryotes by Symbiosis
Research biologist Lynn Margulis has finally won acceptance for the theory that eukaryotic cells formed by
symbiosis among bacterial cells. Under the theory Margulis advocates, mitochondria and plastids did not originate
within the eukaryotic cells that now carry them. Rather, these subunits were once free-living prokaryotic cells that
infected other bacterial cells and came to reside in them with benefits for both parties. Even the bounded nucleus
that characterizes all eukaryotic cells may have evolved this way. This is a whole new kind of evolution. Not just
new genes, but new whole cells were incorporated into existing cells. This kind of evolution has already been
confirmed by experiment (2). This theory represents a significant amendment to the prevailing paradigm of
evolution. Now we know that evolution can proceed by assembling subunits. This mechanism would help evolution
to take the giant step from prokaryotes to eukaryotes relatively quickly.
This symbiotic system has an additional consequence as evolution proceeds, genes originally in the mitochondria
and plastids apparently tend to be lost. In May, 1998, molecular biologists who analyzed 210 protein-coding genes
from nine fully sequenced chloroplast genomes reported, "Some of these genes have been lost altogether,... whereas
others have been transferred to the nucleus. We have documented 44 bona fide cases of functional plant nuclear
genes among the 210 genes examined ..." (2.5). If mitochondria and plastids tend to lose genes, one can reason
backward to a time when they had genomes as large as free-living bacteria do. This evidence strengthens the case
for the symbiotic evolution Margulis advocates. And if some of those genes are transferred to the nucleus, we have
another mechanism for importing whole genes into the nuclear genomes of eukaryotes.
If you had to name one development in all of evolution that was the most important single development, it would
definitely be the evolution of eukaryotic cells. This step is apparently the prerequisite for any more highly organized
forms of life to evolve. That the mitochondria and plastids in eukaryotes probably got there by symbiosis is a
welcome insight. But we still have many other steps to explain. How did the structural system within eukaryotic
cells evolve? How did eukaryotes evolve into a multitude of species with the wide variety of features they have?
How do multicelled eukaryotes acquire new complex features? Where do the new genes for these steps come from?
How do they get installed and activated?

Viruses and The Origin of Species

Charles Darwin named his greatest work The Origin of Species. Of course, the species is only one level of biological
hierarchy. Darwin could have named his book The Origin of Phyla or The Origin of Kingdoms. A species is defined
by being reproductively isolated from every other species. Darwin was able to see that if a sexually reproducing
animal or plant were ever to take a an evolutionary step big enough to create a new species, it would be necessary

for at least a complete breeding pair one male and one female to take the step simultaneously. If only one
member of a breeding pair, say the female, acquired a speciating new feature, she would be reproductively isolated
from the male. They would be unable to reproduce.
Sometimes new species can be produced by hybridization: closely related species can produce hybrid offspring that
are able to sexually reproduce with other, similarly produced hybrids but not with members of either of the parents'
species. Hybridization alone cannot, however, produce new features; it can only add existing ones together.
The kind of speciation that interested Darwin would be that which is
accompanied by the appearance of wholly new features. If new features are
introduced by chance alone, sexual reproduction becomes a roadblock to
speciating steps. How likely is it that two members of a breeding pair
would both carry the same new, speciating feature, if it was generated by
chance? Darwin didn't propose a mechanism for the generation of new
features, but he saw that the evolution of a new, reproductively isolated
group that is, a new species was a tricky problem. This is one reason
he insisted on the tiny incremental steps; if a new feature were different by
a only a small amount, maybe the member who carried it wouldn't be
reproductively isolated from the rest of the species.
Today, with our understanding of DNA, we would state the problem
differently: new features require new genetic instructions. And small steps
are clearly possible without coordination between two members of a
breeding pair. But big, speciating steps are still problematic for neoDarwinism. If only one individual undergoes a mutation of speciating
effect, the remaining population is either unable or unlikely to follow this "hopeful monster."
sperm cells and ovum surface:
Nanoworld Image Gallery

However, if new genetic instructions are inserted by infectious viruses, then the problem of finding breeding pairs
equipped for big evolutionary steps is solved. Viruses typically infect whole populations, or substantial parts of
them, so many breeding pairs may carry the same new instructions. This is a profound new way for evolution to
advance, and in potentially larger steps than Darwin imagined. This proposed mechanism for evolution was already
understood by the farseeing genetic researcher Susumo Ohno in 1970. He wrote (3):
Uniform transformation from an old species to a new species can occur only if the heritable traits responsible for
the speciation are carried by a viral genome. Only then can widespread infection and subsequent incorporation of
the viral genome into the host genome transform a majority of the previous species members to members of a
new species.

The Germ Line

If new genetic programs are as common as viral infections, wouldn't they be more likely to wreak havoc than to
improve things especially in the larger animals and plants, for whom the genome is more complicated and
individuals are less expendable? For example, suppose the genetic programs for antlers or antennae got installed and
activated in people. That would cause a real-life horror show. The evolutionary world would be much better if each
virus infected only a narrow range of hosts. Fortunately, that is how viruses usually work. With a few exceptions,
each virus infects only one species or group of closely related species. But there are important exceptions to this
rule. For example, arboviruses have two classes of carriers, vertebrate and invertebrate. Sometimes one class of host
may not become infected, but usually both do. Over 500 arboviruses are known (4).
Some viruses infect their hosts with no harm to the host. Other viral infections can cause diseases, occasionally
lethal ones. One wishes the immune system would keep them out completely. But if evolution depends on viruses,
that capability would inhibit evolution. The situation is especially complex in sexually reproducing multicelled
animals, where the "germ line" is carefully protected. The germ line, the gametes and their ancestral cells that give

rise to the next generation, are isolated early in the life cycle from the rest of the (somatic) cells. In order for a virus
to cause evolution in sexually reproducing creatures, it must infect the germ line and become integrated into the
genome there. This process has been proven to occur already. "If, for example, the DNA is injected into the nucleus
of a mouse's fertilized egg, the genes will be found in many cells of the adult animal and sometimes even in its germ
cells" (5). And the descendants of newborn mice infected with a virus have been shown to carry the genes of the
infecting virus in their own genomes (6). Also, "When DNA from a retrovirus is inserted into fetal lambs, their
offspring inherit the retroviral DNA a clear sign that the foreign genes had entered the sheep germline" (7).
Furthermore, we now know that such insertion can happen in nature at a rate approaching one entire viral genome
per host generation (8). By the time the textbook Retroviruses was published, in 1997, this question is settled.
"...Retroviruses can become integrated into the germ line as endogenous viruses, leading to permanent genetic
consequences for the descendents of the original host, a property they share with a variety of nonviral, but related,
reverse-transcriptase-containing elements..." (9).
To accomplish this integration in nature the virus probably would have to spread by lytic infection throughout much
of the body. This process will probably have side effects that may appear as symptoms of disease. Perhaps it would
be a reasonable compromise if a new virus were able to establish a lytic infection and become widespread within the
individual host's body one time only, and never again. Guess what. That's the way our mammalian immune system
often handles viruses.
Sometimes retroviruses cause other genes in the host's genome to become "oncogenes" (10). That means they cause
cancer. If evolution involves trial and error, cancer seems to be in the error category. However, perhaps it would
make evolutionary sense, under some circumstances, for cells carrying newly acquired genes to begin to multiply
rapidly.

AIDS
Cosmic Ancestry assumes that the function of a virus is to install its genes into the germ line of its host. After this
mission has been accomplished, it serves no purpose for the host to remain susceptible to lytic infection by the virus.
It would make sense if the host's descendant inheriting the new genes were born with immunity to lytic, or diseasecausing, infection by the virus.
In fact, it has been known since 1933 that resistance to a disease caused by a virus can be inherited (11). Now there
is some reason to believe that even resistance to AIDS may be inheritable. AIDS is an incurable viral disease to
which, we once thought, no one is immune. Studies are now suggesting, however, that some children of mothers
with AIDS are born immune to the disease. This is the subject of a recent [1996] story in Science, "Can Some
Infants Beat HIV?" (12)
Among hundreds of children born to HIV-positive mothers, the studies found 21 who initially tested positive on HIV
antibody and virus tests, but later came out negative. Referring to one of the studies, Anthony Fauci, director of
the National Institute of Allergy and Infectious Diseases in Bethesda, Maryland, says: "It's pretty compelling
evidence that they were able to clear the infection, or were exposed to it, got transient infection, and then cleared
it."

Gene Conversion
Another vital advantage comes with sexual reproduction. It depends on a process of genetic recombination called
"gene conversion." Consider the following problem: as we know, in multicelled animals most DNA is silent. NeoDarwinists call it "junk DNA," assumed to be the leftovers of previous evolution. Natural selection cannot prevent
mistakes from accumulating in silent DNA there's no expressed feature to affect the struggle for survival. Nor
can having two copies of the gene offer any protection, by itself neither copy is expressed so there's no
"working" copy to be dominant. Both copies would be equally subject to the accumulation of errors. Of course, if

the silent DNA will always be silent, it won't ever matter. But if any of the silent DNA is ever to be used in the
future, it needs protection against the accumulation of errors. Cosmic Ancestry holds that at least some of the
silent DNA is for future use.
The Cosmic Ancestry paradigm proposes that the genetic instructions for big evolutionary steps are installed by
viruses or other lateral transfer mechanisms, and that some of the steps require several genes so many that they
cannot be installed all at once but only in stages. During the long installation process, the not-yet-activated DNA
would be silent. To be useful in the future, this silent DNA would definitely need protection against the
accumulation of errors.
Among the working genes of sexually reproducing creatures, gene conversion can alter one version of a gene to
match the other version. A defective gene can be edited to match the nondefective version of the gene by this
process (12.5):
Occasionally... one of the two copies of the paternal allele [version] has been changed to a copy of the maternal
allele. This phenomenon is known as gene conversion. It often occurs in association with genetic recombination
events, and it is thought to be important in the evolution of certain genes.... Gene conversion is thought to be a
straightforward consequence of the mechanisms of general recombination and DNA repair.
So if an error develops in one copy of the gene, the process of gene conversion could compare it to the undamaged
copy and fix it. In the above example, gene conversion has been demonstrated for working genes. Is there any
reason to think that gene conversion also works on silent DNA? Yes. There is indirect evidence based on an
otherwise unexplained similarity between silent DNA in humans and mice (13):
Koop and Hood have found that the DNA of the T cell receptor complex... shows 71% identity between humans
and mice. That finding is startling, since only 6% of the DNA encodes for the actual protein sequence, while the
rest consists of introns and noncoding regions.
The last common ancestor of humans and mice died at least 80 million years ago. Somehow the silent DNA has
been maintained over many millions of replications. Gene conversion could be the mechanism. Something is.
If gene conversion works for silent DNA, it becomes possible for very large genetic programs to be installed in
stages, without loss of fidelity. The parts installed first would be silent until the whole program had been installed.
With gene conversion, this silent part could get continually debugged. The process of gene conversion could clean it
up, as necessary, every time it is replicated. Thus, when the whole new genetic program is fully installed and ready
to activate, it would be far more likely to be fully functional. The process of gene conversion could make it possible
to install big genetic programs in pieces, over many generations.
Additional evidence for the longterm maintenance of silent genes comes from research on certain "retrotransposons"
by biologists at The University of Rochester. They studied two related sequences that have remained stable in
diverse lineages for over 500 million years. The sequences are always inserted at the same two precise locations in a
certain (28S rRNA) gene, inactivating it. "How then do we account for their remarkable stability?" they wonder
(14).

Summary
So it is necessary, at least intermittently..., this thing called sex. As of course you and I knew it must be. Otherwise
surely, by now, we mammals and dragonflies would have come up with something more dignified. David
Quammen (15)

Evolution can proceed by the assembly of subunits.

New genes can get installed into whole species by infectious agents, especially viruses.
Viral infections are usually specific to certain hosts only, they are not always harmful to the host, they can enter
the germline, and the host can become immune to their harmful effects.
The process of gene conversion can correct deleterious mutations even in silent genes, where natural selection and
gene dominance are useless. Gene conversion could protect large genetic programs requiring several generations to
install. Thus sex would be important because it increases the fidelity, not the mutability, of inherited genes. Indeed, a
clever recent experiment with sexual and asexual yeast cells that were otherwise identical reinforces this last point.
Clifford Zeyl of Michigan State University and Graham Bell of McGill University found that both the sexual and
asexual populations produced mutations at similar rates, but the sexual cells eliminated deleterious mutations more
efficiently (16). And yet another experiment, with viruses, affirms that sex prevents the accumulation of deleterious
mutations "because recombination lets an organism reconstruct a mutation free genome from two genomes that
contain different mutations" (17).
It seems likely that the sexual reproduction process used by multicelled animals and plants is more important than
the current paradigm imagines. It is a likely prerequisite for really big evolutionary steps.

What'sNEW
Death by asexuality: IU biologists uncover new path for mutations to arise, Indiana University (+ Newswise), 3
Sep 2013.
David Green and Chris Mason, "The maintenance of sex: Ronald Fisher meets the Red Queen" [abstract],
doi:10.1186/1471-2148-13-174, n174 v13, BMC Evolutionary Biology, 21 Aug 2013.
Christopher S Willett, "Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod
Tigriopus californicus" [abstract], doi:10.1186/1471-2148-13-148, n148 v13, BMC Evolutionary Biology, 12 Jul
2013. "The evolutionary patterns across these paralogs show how gene conversion can both constrain and
facilitate diversification of genetic sequences."
David B Carlini et al., "Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs
within cave populations of Gammarus minus (Crustacea: Amphipoda)" [abstract], doi:10.1186/1471-2148-13-89,
n89 v13, BMC Evolutionary Biology, 23 Apr 2013. "...dN/dS ratios did not indicate a relaxation of functional
constraint in the cave populations with reduced or absent eyes. Maximum likelihood analyses using codon-based
models also did not detect a relaxation of functional constraint in the cave lineages."
Slideshow: Virgin Birth Not So Miraculous in Animal Kingdom by Carrie Arnold, ScienceNow, 27 Dec 2012.
Bruce A. Curtis et al., "Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs" [html],
doi:10.1038/nature11681, p59-65 v492, Nature, 6 Dec 2012; and commentary:
Microscopic Indigestion Caught in the Act, Dalhousie University (also Newswise), 6 Dec 2012.
Sihai Yang, Yang Yuan, Long Wang et al., "Great majority of recombination events in Arabidopsis are gene
conversion events" [abstract], doi:10.1073/pnas.1211827110, Proc. Nat. Acad. Sci., USA, online 3 Dec 2012.
E. I. Hersch-Green et al., "Adaptive molecular evolution of a defence gene in sexual but not functionally asexual
evening primroses" [abstract], doi:10.1111/j.1420-9101.2012.02542.x, Journal of Evolutionary Biology, online 15
May 2012.
Lutz Becks and Aneil F. Agrawal, "The Evolution of Sex Is Favoured During Adaptation to New Environments"
[html], doi:10.1371/journal.pbio.1001317, 10(5): e1001317, PLoS Biol, 1 May 2012.
Jeremy C Gray and Matthew R Goddard, "Sex enhances adaptation by unlinking beneficial from detrimental
mutations in experimental yeast populations" [abstract], doi:10.1186/1471-2148-12-43, v12 n43, BMC
Evolutionary Biology, 30 Mar 2012.
Filip Husnik et al., "Multiple origins of endosymbiosis within the Enterobacteriaceae (gamma-Proteobacteria):
convergence of complex phylogenetic approaches" [abstract], doi:10.1186/1741-7007-9-87, v9 n87, BMC Biology,
28 Dec 2011.

Sheng Sun and Joseph Heitman, "Is sex necessary?" [html], doi:10.1186/1741-7007-9-56, n56 v9, BMC Biology,
31 Aug 2011.
Levi T. Morran et al., "Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex"
[abstract], doi:10.1126/science.1206360, p216-218 v333, Science, 8 Jul 2011. "...Coevolving pathogens can select
for biparental sex."
...researcher argues that sex reduces genetic variation, Wayne State University, 7 Jul 2011.
Shannon M. Hedtke et al., "Rare gene capture in predominantly androgenetic species" [abstract],
doi:10.1073/pnas.1106742108, Proc. Nat. Acad. Sci., USA, online 23 May 2011. "Although asexuality has shortterm evolutionary advantages, a lack of genetic recombination leads to the accumulation over time of deleterious
mutations. ...The rare capture of genetic material from other species may allow androgenetic lineages of Corbicula
to mitigate the effects of deleterious mutation accumulation and increase potentially adaptive variation."
Kids Born with HIV Growing Up Well by Arthur Nead, Tulane University, 20 Apr 2011.
18 Apr 2011 Natural selection eliminates and maybe maintains, but it doesn't create Lynn Margulis
Lutz Becks and Aneil F. Agrawal, "Higher rates of sex evolve in spatially heterogeneous environments" [abstract],
doi:10.1038/nature09449, p89-92 v468, Nature, 4 Nov 2010.
24 Sep 2010: "Seeking Signs of Life" is an upcoming symposium, 14 Oct, where Lynn Margulis is a keynote
speaker.
Audrius Menkis et al., "Gene genealogies indicates abundant gene conversions and independent evolutionary
histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma" [abstract],
doi:10.1186/1471-2148-10-234, v10 n234, BMC Evolutionary Biology, 31 Jul 2010. "We argue that gene
conversions might provide an efficient mechanism of adaptive editing of functional genes, including the removal of
deleterious mutations, within the young recombinationally suppressed region of the mat chromosomes."
Victor P Shcherbakov, "Biological species is the only possible form of existence for higher organisms: the
evolutionary meaning of sexual reproduction" [abstract], doi:10.1186/1745-6150-5-14, v5 paper 14, Biology Direct,
22 Mar 2010. "...The main advantage of sex is the opposite: the ability to counteract not only extinction but further
evolution as well."
29 Jun 2010: An online review of What Darwin Got Wrong mentions the importance of Lynn Margulis and
symbiosis.
Claudio Casola et al., "Nonallelic Gene Conversion in the Genus Drosophila" [abstract],
doi:10.1534/genetics.110.115444, p95-103 v185, Genetics, May 2010. "Nonallelic, or ectopic, gene conversion can
change the evolutionary trajectory of gene duplicates by homogenizing their sequences."
John M. Logsdon, Jr., "No Sex, Please" (review of Lost Sex: The Evolutionary Biology of Parthenogenesis, 2009)
[summary], 10.1126/science.1187970, p310 v328, Science, 16 Apr 2010.
Adi Livnat, "Sex, mixability, and modularity" [Open Access abstract], doi:10.1073/pnas.0910734106, Proc. Nat.
Acad. Sci., USA, online 8 Jan 2010.
Three New Human Genes is a related new CA webpage, posted 4 Sep 2009.
Fungus Found in Humans Shown To Be Nimble in Mating Game, Brown University, 12 Aug 2009.
Carl Zimmer, "On the Origin of Sexual Reproduction" [summary], doi:10.1126/science.324_1254, p 1254-1256 v
324, Science, 5 Jun 2009.
12 Apr 2009: Two single-celled eukaryotes have apparently used horizontal gene transfer extensively to evolve
and diverge.
Adi Livnat et al., "A mixability theory for the role of sex in evolution" [abstract], doi:10.1073/pnas.0803596105, p
19803-19808 v 105, Proc. Nat. Acad. Sci., USA, 16 Dec 2008. "The question of what role sex plays in evolution is still
open despite decades of research."
Another change to our understanding of evolution is the subject of a reply from Jonathan Sturm, 30 May 2008
Fungi can tell us about the origin of sex chromosomes, EurekAlert.org, 17 Mar 2008.

Mohammad A. Mandegar and Sarah P. Otto, "Mitotic recombination counteracts the benefits of genetic
segregation" [abstract], 10.1098/rspb.2007.0056, p 1301-1307 v 274, Proceedings of the Royal Society B: Biological
Sciences, 22 May 2007. "We conclude that asexual populations can gain most of the benefit of segregation through
[mitotic recombination] while avoiding the costs associated with sexual reproduction."
J. Arjan, G. M. de Visser and Santiago F. Elena, "The evolution of sex: empirical insights into the roles of epistasis
and drift" [abstract], 10.1038/nrg1985, p 139-149 v 8, Nature Reviews Genetics, Feb 2007. "Despite many years of
theoretical and experimental work, the explanation for why sex is so common as a reproductive strategy continues
to resist understanding."
Nick Campbell, "Evolution: The advantages of sex" [free access], doi:10.1038/nrg1851, p 240 v 7, Nature Reviews
Genetics, April 2006.
Susanne Paland and Michael Lynch, "Transitions to Asexuality Result in Excess Amino Acid Substitutions"
[abstract], doi:10.1126/science.1118152, p 990-992 v 311, Science, 17 Feb 2006. "We estimate that mitochondrial
protein-coding genes in asexual lineages accumulate deleterious amino acid substitutions at four times the rate in
sexual lineages." Also see commentary, "Why Sex?" by Rasmus Nielsen, [abstract], doi:10.1126/science.1124663, p
960-961; and
Sex, Cleaner of Genomes, Newswise.com, 16 Feb 2006.
Hengshan Zhang and Christopher W. Lawrence, "The error-free component of the RAD6/RAD18 DNA damage
tolerance pathway of budding yeast employs sister-strand recombination" [abstract],
doi:10.1073/pnas.0504586102, Proc. Nat. Acad. Sci., USA, online 24 Oct 2005. "...postreplication repair...."
Peter D. Keightley et al., "Evolutionary constraints in conserved nongenic sequences of mammals" [abstract], doi:
10.1101/gr.3942005, p 1373-1378 v 15, Genome Research, Oct 2005. "...Sex is necessary for long-term population
persistence."
Toshiyuki Hayakawa et al., "A Human-Specific Gene in Microglia" [abstract], doi:10.1126/science.1114321, p
1693 v 309, Science, 9 Sep 2005. "We suggest that this human-specific gene conversion event may be related to
the evolution of genus Homo."
Niclas Backstrm et al., "Gene Conversion Drives the Evolution of HINTW, an Ampliconic Gene on the FemaleSpecific Avian W Chromosome" [abstract], doi: 10.1093/molbev/msi198, p 1992-1999 v 22, Molecular Biology and
Evolution, Oct (online 22 Jun) 2005.
24 Mar 2005: Plants can overwrite unhealthy genes.
Obituaries: John Maynard Smith, 84 "Applied Game Theory to Evolution, Asked Why Animals Developed
Sex.... The solution remains a mystery." by Rosie Mestel, Los Angeles Times, 24 Apr 2004.
2003, August 8: Gene transfer, wholesale?
Why have sex? The answer is not as simple as we thought, EurekAlert! 29 May 2003.
2003, January 23: Wingless stick insects have re-evolved wings, perhaps many times.
Nick Colegrave, "Sex releases the speed limit on evolution," p 664-666 v 420, Nature, 12 Dec 2002.
Twin sister mechanism prevents formation of genetic mutations, EurekAlert! 24 Oct 2002.
Eukaryotic Origins: Revolution in the Classification of Life, by Stephen Hart, Astrobio.net, 31 Jul 2002.
Scientists study the inefficiency of sex, by Malcolm Ritter, CNN.com, 15 Feb 2002. "Scientists still are trying to
pin down just what the payoff is."
Richard E. Lenski, "Come Fly, and Leave the Baggage Behind" [summary], p 555-559 v 294, Science, 19 Oct 2001.
"...Sexual recombination frees beneficial mutations from the excess baggage of deleterious mutations."
Linda F. Delph, "Mutated into Oblivion" [review of The Cooperative Gene by Mark Ridley, 2001], p 2437-2438 v
292, Science, 29 June 2001. "The evolution of sexual reproduction was 'the big breakthrough that improved the
efficiency with which natural selection removes mutations'."
The Origin of Sex: Cosmic Solution to Ancient Mystery by Robert Roy Britt, Space.com, 10 July 2001. Speculative
results from a computer model.

Mysteries of Sex Remain by Menno Schilthuizen, Daily InScight, 16 October 2000.

Tim Beardsley, "Mutations Galore," p 32-36 v 280 n 4 Scientific American, April 1999. "Why aren't we extinct?
Sex... allows detrimental mutations to be eliminated."
Adam Eyre-Walker and Peter D. Keightly, "High genomic deleterious mutation rates in hominids," p 344-347 and
commentary by James F. Crow, "The odds of losing at genetic roulette," p 293-294, v 397 Nature, 28 January 1999.
"The Evolution of Sex" p 1979-2008 v 281 Science, 25 September 1998, is a special section of nine articles that
consider the evolutionary benefit of sexual reproduction. The likelihood "that sex purges the genome of harmful
mutations," is considered in several of the articles.
1998, August 25: We owe the repertoire of our immune system to one transposon insertion, which occurred 450
million years ago in the ancestor of the jawed fishes.
1998, August 12: The paradigm shifts toward lateral gene transfer as the primary driver of evolution.
Evolution: Selected Papers and Commentary (108K text + gifs and jpgs): Includes deeper analysis of reproductive
isolation, by Donald R. Forsdyke, Biochemist, Queen's University, Kingston, Ontario, Canada.

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