Evolution as a Learning Process

8/3/2019 Evolution as a Learning Process

1/32

Evolution as a Learning Process:

An Alternative Perspective.

A Short Version of the Thesis Presented at the Poster Session in the Cellular and Molecular

Biology Section of the American Association for the Advancement of Science 2003 Annual

Meetings Held in Denver CO in February.

A SPECULATION ON EVOLUTION

AS A LEARNING PROCESS

Dolores Landy Bentham

February 6, 2003


2/32

Evolution as a Learning Process

D. Landy Bentham

2

Until RNA showed that its role was more than ancillary, meaning and innovation had

been attributed solely to DNA. Changes in DNA were said to be random with respect to the

needs of the organism. But since both DNA and RNA are abstraction removes from protein,

where the action is, it seems reasonable to propose protein as a non-random source of novelty.

However, for novel proteins to be heritable there needs to be feedback to DNA. The one-

way only process of protein synthesis, from genetic DNA to RNA to protein

(DNA>RNA>protein), proposed by Crick (1970) was replaced by DNARNA>protein when

Baltimore (1970) and Temin (1970) discovered reverse transcription of RNA to DNA.

In an even more radical departure from Crick's "central dogma", Mekler (1967)

hypothesized reverse translation from protein to RNA. (look (1979) and Craig (1981) followed

him in this idea. Reverse translation has since been supported by the findings of Nashimoto

(2001) and Gold (1998).

Sakai (2001) has proposed a calmodulin-mediated reversible non-chromosomal gene

expression route in which DNA, RNA or protein can be converted to any one of the other. They

have found that a "new gene expression route differing from a conventionally known gene

expression route (irreversible chromosomal gene expression route) is present in vivo. . .and that

these reactions are all promoted by calmodulin."

Sources of novelty in proteins:

Resistance (R) to antibiotics may have arisen in proteins rather than DNA. The accepted

view is that mutations, which encode resistance, arise spontaneously without reference to the

antibiotic. The bacteria in the laboratory setting are said to be naive in this respect. However,

bacteria have long lineages and may have met the antibiotic in the wild. Bacteria, fungi, plants


3/32


D. Landy Bentham

3

all are equipped with arsenals of antibiotics and R factors to the antibiotics, which they produce

for self-defense. The appearance of what seem to be random mutations" may have been the

regularly turned on gene for the disarming of the antibiotic. It could also have been the

acquisition of a plasmid encoding the R factor (Hardy 1986). But the origin of the R factor

remains in question. Some antibiotics may not have correlates in the wild; in this case resistance

must arise de novo.

Burnet (1964) proposed the neo-Darwinian model for the generation of antibody diversity.

In the instructionist model, which it replaced, the antigen is the template on which the antibody

forms itself. That is, antibodies arise in proteins rather than randomly in DNA.

Current theories, which invoke combinatorial events of germ-line variable genes (Nezlin

2001), don't necessarily rule out that the origin of these genes was in protein templates. The

newly formed protein fed back to RNA and DNA would be given access to the genes by a means

suggested later in this paper.

Long-term memory storage requires protein synthesis (Ungar 1971) (Kandel 2002).

Ungar's view that peptides encode long-term memory has been discarded in favor of Kandel's

work that shows that it is the strengthening of synapses and the multiplying of connections which

requires protein synthesis. Reductionism has served Kandel well (2002). However it has not

answered the question of how the memory itself is encoded. Kandel calls the molecular biology

of memory storage "a dialogue between genes and synapses", but grants that there is much work

to be done to understand the encoding of memory.

Moreover, peptides may have been the first molecules of life (Hazen 2001). Since

peptides/proteins are the workhorses of life this seems reasonable. DNA had been ruled out,

because of its dependence on protein enzymes for replication. Then RNA, with the discovery of


4/32


D. Landy Bentham

4

its enzymatic capability, became a leading candidate for first molecule. Lipids have been

proposed too (Segre 2001), as well as co-evolution of some of the contenders. However, Orgel

(1998) makes a case for peptides as first molecules because they polymerize on minerals

especially calcite, which was abundant on the early earth (Hazen, Filley and Goodfriend). With

the finding that peptides can self-replicate, their candidacy is bolstered (Lee 1996).

Novel proteins, which reverse translate to RNA, and in turn reverse transcribe to DNA

complete a circuit of protein synthesis; however, there needs to be access of the DNA to the

germ line cells in order for the novelty to be heritable. Lo (2001) discusses circulating DNA.

Lavitrano et al. (1997) have shown that pig "sperm cells bind and internalize exogenous DNA".

Sin (1998) found in a series of experiments, that foreign DNA, injected into the proximal region

of the vas deferens of mouse and rat, was recovered six hours after the injection, in 60% of the

sperm. Shamila (1998) found that a foreign gene injected into the testis of fifth instar silkworm

larvae, which existed extrachromosomally in the founder larvae," was transmitted to the progeny,

indicating that the sperm cells picked up the injected DNA (Sin 1998).

Integration of the foreign DNA would be accomplished by "natural genetic engineering"

(Shapiro 1998, 2001), just as plasmids become part of the genomes of the prokaryotes, which

receive them (Hardy 1986), and endosymbionts become part of the host's genome (Buchner

1953) (Margulis 1989).

In summary:

As one of the ways of evolution, I propose a learning process in which novelty arises in

protein, reverse translates to RNA, reverse transcribes to DNA, and is heritable by gaining access

to the germ line cells.


5/32


D. Landy Bentham

5

Literature Cited:

Baltimore, David. 1970. RNA-dependent DNA polymerases in virions of RNA tumor viruses.

Nature 226:1209-2l1.

Buchner, Paul. 1953.Endosymbiosis. New York: John Wiley and Sons, Inc.

Burnet, F. Macfarlane. 1964. A Darwinian approach to immunity.Nature 203:451.

E Cook, Norman D. 1977. The case for reverse translation.J. Theor. Biol. 64: 113-135.

Craig, Robin. 1981. The theoretical possibility of reverse translation of proteins into genes. J.

Theor. Biol.88:757-760.

Crick, F. H. C. 1970. The central dogma.Nature 227: 561-563.

Gold, Larry, Craig Tuerk, David Pribnow, Jonathan Drew Smith. 1998. CODEN:USXXAM

5843701 A 1998 1201 Patent written in English.

Hardy, K.G. 1986.Bacterial Plasmids 2nd Edition. Wockinham, U.K. Van Nostrand F Reinhold.

Hazen, Robert M. 2001. Life's rocky start. Scientific American April:77-85. Hazen, Robert M.,

Timothy R. Elley, and Glenn A. Goodfriend. 2001. Selective adsorption of L-and D-

amino acids on calcite: Implications for biochemical homochirality. PNAS 98 10:5487-

5490.

Kandel, Eric R. 2002. The molecular biology of memory storage: A dialogue between genes and

synapses. Science 294 (5544): 1030.

Lavitrano, M., B. Malone, E. Forte, M. Francolini, and C. Spadafora. 1997. Sperm mediated

gene transfer in pig: Selection of donor boars and optimization of DNA uptake. Exp. Cell

Res. 233: 56.

Lee, David H., Juan R. Granja, Jose A. Martinez, Kay Severin and M. Reza Ghadiri. 1996. A

self-replicating peptide.Nature 382:525.


6/32


D. Landy Bentham

6

Evolution as a Learning Process: An Alternative Perspective and Personal Inquiry

"Why would you want to study evo1ution?" Jerome Wolken asked. "Nobody knows how

evolution works." Jerome Wolken studied the effect of light on organisms at Carnegie Mellon,

Pittsburgh PA, and at the Marine Biological Laboratories (MBL) Woods Hole, MA. In another

conversation in the summer of1997, Mary Eubanks said she saw evolution as working in many

different ways. She had discovered that corn had originated by hybridization. She was from

Duke University in North Carolina and was at the MBL for a workshop on molecular evolution.

Despite the views of Wolken and Eubanks, mainstream evolutionary thinking remains decidedly

neo-Darwinist; that is, mutations, random with respect to the needs of the organism, are acted on

and given orientation by natural selection. By natural selection we mean that those organisms,

best adapted to the environment, out-reproduce the competition(Kendrew 1994). Nevertheless,

among the ways of evolution cited below, random mutations are not players as sources of

novelty.

Some of the ways of evolution: Citations refer to those who have either originated

or furthered the theory,

Hybridization, cross-mating to form new species (Eubanks 1997). Endosymbiosis, merger to form a new species (Buchner 1953) (Margulis 1989). Adaptive mutations (Caims et al. 1988) (Rosenberg et al 1994). The continuum of development and evolution (Gerhart and Kirschner 1997). Morphogenesis (Sheldrake 1995). Regulatory RNA's role in evolution (Eddy 2001) (Mattick 2001). Transposable and retro-transposable elements (McClintock 1957) (Shapiro 1999) Intracellular information processing (Shapiro 2002)


7/32


D. Landy Bentham

7

Inheritance of Acquired Characteristics (Lamarck 1809) (Landman 1993). Reverse translation in evolution (Mekler 1967) (Cook 1977), now known as The

RNA/protein symmetry theory (Nashimoto 2001) or SPERT (Systematic Polypeptide

Evolution by Reverse Translation) (Gold et al.1998).

These ways of evolution are not mutually exclusive and certainly overlap, representing

various aspects of the same phenomenon. The last on the list has engaged my interest for the

past 25 years. I was struck by the possibility of reverse translation when first reading about

molecular encoding of memory (Milner, Peter M. 1970). If molecules encode memory why

would there be no feedback to the genome? Norman D. Cook also takes off from molecular

encoding of memory when he makes "The case for reverse translation". Although molecular

encoding of memory had been dropped as a line of inquiry in thel970's, it has recently

reappeared in the literature. In Science, of 2 August, 2002, Nobelist Eric Kandel and Kausik Si

speculate "that a common protein called CREB can self-perpetuate in mammalian

brainsalthough cautioning that the evidence is extremely preliminary, they speculate that it

might play a role in storing information- in other words, in memory".

"Evolution as a learning process" would have been as apt as a title for Cook's article.

Peptides change in response to experience to encode the memory of that experience. The

peptides are then fed back to the genome by reverse translation to nucleic acids, probably RNA.

RNA then reverse transcribes to DNA. In other words, what is learned may become part of

DNA.

In his article, published in the Journal of Theoretical Biology 1977, Cook cited, among

others, the work of Hyden and Egyhazi (1963) for peptide encoding of memory; Mekler (1967)

on the hypothesis of reverse translation; and Baltimore (1970) and Temin (1970) on reverse


8/32


D. Landy Bentham

8

transcription. In a paper for an independent I study at Queens College, I cited some of the same

sources and came to the same conclusions as Cook. That paper is dated May 1977. I hadn't

heard of Mekler, and his speculation on the possibility of reverse translation, but had counted on

its possibility. I knew the work of Baltimore and Temin on reverse transcription and of Hyden

and Egyhazi and others on peptide encoding of memory. There are gaps in this hypothesis of

evolution as a learning process. Neither Cook nor I addressed the question of how the new or

altered DNA enters the germ line cells. And if entry were possible, what then? Twenty-five

years later there are some answers to these questions and I address them later in this paper.

As much as Cook's (and my) hypothesis may have a logical appeal, trends in theoretical

biology don't always run a straight course. The following describes the fate of some of the work

cited by Cook:

Despite the central dogma, which states that protein synthesis proceeds in one direction

only, DNA>RNA>Protein (Crick and Orgel), reverse-transcription from RNA to DNA is now

part of mainstream biology. This was discovered independently by David Baltimore (1970) and

Howard Temin (1972). Reverse transcription was first observed in the RNA Raus sarcoma virus

and now infamously in HIV. Reverse transcription is not limited to RNA viruses. The

retrotransposon, one of the mobile genetic elements first discovered by McClintock (1948),

encodes reverse transcriptase, the enzyme involved in reverse transcription. But the rule against

reverse translation from protein to DNA or RNA remained in place until now. In fact it still

remains in the minds of most biologists given the results of my searches.

Reverse translation of protein to RNA seems to have been lost in the scientific literature.

No one I asked knew of it and no searches I tried came up with anything on it When I asked

James Shapiro about reverse translation, he suggested that although it was theoretically possible


9/32


D. Landy Bentham

9

to translate backward from protein to RNA- he even spelled out how it could be done- he didn't

know of anyone who had tried it (appendix A). He added that I should check with a

knowledgeable biochemist before I went too far with it. A biochemist, Lars Backman who

responded to my e-mail query, hadn't heard of anyone doing it either and wondered why anyone

would want to. He didn't "believe in this idea", but went on to cite the difficulties that could be

encountered in trying to reverse translate protein to RNA (appendix B). Of the two other

respondents, one found the question "very interesting" with three exclamation points (appendix

C) and another referred me back to the central dogma.

A search on Sci Finder Scholar at the New York University Library turned up more on

"reverse translation". The hypotheses of Mekler, Cook and Craig were raised to the level of

theory with the experimental work of Nashimoto (2001) and a method for reverse translating in

vitro patented by Gold et al. (1998)Inherent in neo-Darwinist theory, is the genome as a

blueprint for life. Sometimes the blueprint is mis-transcribed or damaged, introducing novelty.

However, an organism with mistakes in its genome is actually at a disadvantage. Errors mean a

loss of information and are therefore deleterious to the organism There is elaborate molecular

machinery in place to correct these mistakes (Lowenstein 1999).Some mistakes are neutral,

having no effect on the protein product, due to the redundancy of the genetic code- some amino

acids are coded for by more than one RNA codon triplet. The rare mistake, which is not neutral,

lethally deleterious, nor corrected, is said to be the source of the novelty upon which natural

selection works. Should the uncorrected novel gene, when expressed, be advantageous to the

organism, in that its bearers out-reproduce the competition, the novelty would be retained and

would be spread throughout the population (Kendrew 1994).


10/32


D. Landy Bentham

10

But rather than viewing the genome as a blueprint for life, we see it as a file- the

repository of information that a living thing uses to form itself and to function- we may come

close to what the evidence reveals (Shapiro 1999, A third way). Although all organisms are

made up of cells, cells differ from each other depending on the tissue and organ in which they

exist. Each cell accesses the parts of the genome necessary to make it the kind of cell that it

needs to be to do the job that it needs to do. The cell must necessarily "know" what parts of the

genome to access (Shapiro 2002). Although the cell has some autonomy- it is separated from its

environment by a membrane- it is not isolated from that environment. It is inconstant

communication with the milieu in which it finds itself. It may receive messages directly from

adjacent cells or from a distance by way of the nervous, endocrine, immune, and circulatory

systems. The cell therefore looks both outward and inward for the role it plays in the organism

and for the means to fulfill that role. The process, which unfolds, is called cellular

differentiation.

Looking inward the cell calls on the parts of the genome, which spell out how to fulfill its

role. Primitive, undifferentiated cells seem not yet to have "decided" on their roles and are

hardly distinguishable one from another. But the differentiating cell moves from one stage of its

development to the next until its mature appearance is characteristic of its type, and its function

appropriate to its kind (Kendrew 1994). The cell must necessarily process thousands of bits of

information both from without and within to achieve this end (Shapiro 2002).

The genome, far from being the start of a one way street to the production of an organism,

is part of a dynamic hierarchical system. Arthur Koestler (1967) invoked the two-headed god,

Janus, as a metaphor for this system. The heads of Janus face in opposite directions. One looks

down the hierarchy, the other, up. At the cellular level, Janus looks both outward (up) and


11/32


D. Landy Bentham

11

inward (down). Both views inform its mode of existence. At each level of organization the

Janus heads look up and down the hierarchy. Stanley Salthe an evolutionary biologist who

invokes a similar metaphor wonders where the hierarchy ends. Candace Pert (1997) prefers the

metaphor, "network", to "hierarchy, because all systems affect tall others in a more egalitarian

way than the word hierarchy implies.

Support for the idea of the genome as part of an interactive system rather than a blueprint

for life comes from comparisons of DNA from members of different species. Genetic sequences

of chimps and humans turn out to be 98.5% identical. Human and mouse sequences are about

60% the same. What has been compared is the protein encoding genes which make up only 3%

of the entire human genome. The remaining 97% of the genome is non-protein coding, formerly

called junk DNA". These stretches of DNA are described as made up of repetitive sequences

(Enard 2002).

Obviously we are not so close phenotypically to chimps as we are genotypically (Travis

2000) (Enard 2002). Since these comparisons of genomes were made before the first draft of the

human genome project was completed or even well underway, the question arises: Which genes

were compared? Were they simply marker genes such as those for hemoglobin of mitochondria?

That there is only a small percentage of genes which encode proteins further supports the idea

that these genes are more akin to a file, or repository of information, than to a blueprint for life

(Shapiro 1999). Therefore, we must look to the whole genome for the answer to the question of

the origin of complexity and diversity (Enard 2002).

However, non-protein coding DNA has certain characteristics which elevate its status to a

role of more importance than that of junk. Some of it instructs DNA transcription to start here

and end there or farther along- there, to form two different peptides or proteins (Kendrew 1994).


12/32


D. Landy Bentham

12

Also, when subjected to linguistic analysis, repetitive sequences show characteristics of language

(Pennisi 1994).DNA has computational capacity as well and has been used as a test tube

computer to solve a complex "shortest distance" problem (Kolata 1994). The relevance of some

of these characteristics is unclear. What may be of significance is the finding that it is the non-

protein coding DNA which separates one individual of our species from another. This is the

basis for the use of DNA in forensics. Each of us has what we call a "DNA fingerprint" since,

like actual fingerprints, no two are exactly alike (Kendrew 1994).

Do these differences in our non-protein coding DNA have a meaning larger than that of

its usefulness as a forensic tool? Some have thought that it is residual- the DNA chucked out

when no longer needed, its origins part of our evolutionary history. Others have thought that the

non-protein coding DNA is a repository for new DNA - a warehouse of nucleotide sequences at

the ready for use- to signal protein encoding DNA to start or stop at yet other places along its

sequence creating novel proteins. Or that it may be used to code for new proteins from scratch.

Further, it has been recently discovered that some DNA codes for short non-protein

encoding RNA. Like non-protein encoding DNA, the RNA has a regulatory function (Lee and

Ambros 2001). These RNAs were the subjects of a review article (Travis 2002) on "biological

dark matter" named for the large numbers of these previously undetected genes. These short

regulatory RNA's were first discovered in mutants of C. elegans. Mutant worms did not move

beyond the first of four larval stages. Instead they repeated the first- getting larger, but not

proceeding to the next stage. Victor Ambros (Travis 2002 Darkmatter) of Dartmouth Medical

School discovered in the early 90's that a missing bit of DNA, which codes for RNA as its end

product was the cause. These bits of regulatory RNA have also been found in bacteria, flies, and


13/32


D. Landy Bentham

13

mammals, including humans. There are also the bits of RNA called introns, which are edited out

of RNA before translation. These too may have a regulatory role to play in development.

John Mattick (2001) of Queensland University, Brisbane Australia goes further. He

believes that these short RNAs may be the answer to the question of the sources of complexity

and diversity in evolution. That short RNA s may regulate both development and evolution

underlies the notion that development and evolution form a continuum. How does diversity

originate? Mattick's answer is that it is certainly not from the increase in the number of genes

coding for proteins. He points out that V flies and worms have roughly twice the number of

these genes as bacteria. Fish and humans have about the same number, which is twice the

number of those of flies and worms. So, they reason, diversity has another source. Ninety

eight % of the genome, by their count, is non-protein encoding. (They're factored in the introns.)

What this 98% is doing is a matter under study by several labs besides those mentioned above.

They include Gary Ruvkun's at Massachusetts General Hospital, Boston; Sean Eddy's at

Washington University School of Medicine, St. Louis MO; Gisela Storz and Susan Gottesmarfs

at the National Institutes of Health, Bethesda, MD (Travis 2002, Dark matter).

More than one evolutionary biologist has noted that a mouse or an elephant can be built

from similar proteins (Gerhart and Kirschner 1997). The difference lies inform. Development

and evolution, which were historically treated as separate disciplines, have recently merged- each

informing the other. The merger has been marked by the publication of a new journal, which

includes both "development" and "evolution" in its title and by a nickname, "Evo-Devo".

Regulatory genes, those which control development, can have far reaching effects. Note that

should the infant chimp retain its head to body ratio and its orthogonal human like face, he would

no longer be considered chimp. (Milner, R. 1990).


14/32


D. Landy Bentham

14

However the body plan plays out in development, there have to be raw materials

available from which the body makes itself. Important among these materials are amino acids.

At some point there had to have been the invention of proteins.RNA has been suggested as the

first molecule of life because it can act as an enzyme that edits parts of itself out and splices

disparate parts together (Cech 1986). With the help of enzymes it can also replicate itself and

code for proteins. Until this discovery of the ribozyme, peptides and proteins were considered to

be the sole molecules capable of enzymatic activity. But as discussed above, by current neo-

Darwinist theory, DNA, not RNA, is the sole molecule of protein invention, and novelty is

random with respect to needs. According to this theory there is no feed back to DNA. However,

with the discovery of reverse transcription from RNA to DNA there are at least some cases

where what is encoded in RNA is fed back to DNA. This discovery places RNA in a pivotal

position in the process of protein synthesis. It can not only translate to protein; it can transcribe

back to DNA. For this reason it has been put forward as the first molecule of life (Orgel 1998).

Even though RNA as enzyme supports the case for RNA as the first molecule of life,

there have been other arguments against it because of the lack of cytosine in the early

environment (Shapiro, R.1999). As important as RNA is as an enzyme, most of the enzymatic

jobs of the cell fall to peptides or proteins. Since this is the case, it seems reasonable to suggest

that the origins of novelty lie not only in DNA and RNA, but in protein itself. Segre et al.

(2001) suggest that even lipids in the early earth had some enzymatic capability. DNA has a few

non-random tricks up its sleeve, as well, under the rubric "directed mutations". These mutations

are, in fact, in response to need. And far from being the inevitable end product of a synthesis

which is, for the most part, one-way, protein too edits itself, paralleling, as it does, RNA editing.

Inteins are edited out and exions remain to fold into useful proteins, sometimes with the help of


15/32


D. Landy Bentham

15

chaperones" or chaperonins (Kendrew 1994). And even end products are subject to change.

Proteins may substitute one amino acid for another. (Sahl and Bierbaum.1998) In short, proteins

are not just products; they are part of the process of creating themselves.

Relevant to the idea of proteins' creating themselves is the "Instructionist" model for the

generation of antibody diversity. In this model it is the antigen which instructs antibody

formation. Although this model was discarded in favor of the "clonal selection model (Bumet

1964), in its time it was championed by among others, Linus Pauling. Lending new support to

the old instructionist model is the work of Mosbach (1998) and others (Ansell 1996). Mosbach

has actually synthesized antibodies from templates. Although they do not themselves extrapolate

their in-vitro findings to explain the generation of antibody diversity, these findings suggest that

a new look at the instructionist model may be in order. The contrasting clonal selection model is

a neo-Darwinian application to the study of the immune system. Antibodies are generated in

random diversity and selected for by their specific antigens. Clones, of the immuno-competent

cell producing the relevant antibodies, are produced. This theory gained wide acceptance, but

the recent "imprinting" of antibody mimics from templates suggests that the instructionist model

may have something to say for itself after all.

Steele (1998) for one, has invoked the workings of the immune system to support his

theory of somatic mutations fed back to the genome. He invokes RNA with its capacity to

reverse transcribe to DNA as the principle player in this scenario. His theory is much like neo-

Darwinism with one exception: Random mutations, which occur in somatic cells, among them

immuno-competent cells, are acted on by natural selection. Because these acquired

characteristics (the random mutations in the somatic cell genome) are inherited, his theory has

been characterized as Lamarckian. However, because it is nevertheless based on random


16/32


D. Landy Bentham

16

variation acted on by selection, it has more in common with neo-Darwinism than with

Lamarckism. I am invoking the generation of antibody diversity to a non-Darwinian end. If the

immune system works according to the instructionist model, there needs to be feedback, not

only from RNA to DNA(reverse transcription), but also from the template formed protein to

RNA or to DNA (reverse translation). This latter was not supposed to happen, but hypothesis

has gained support with the work of Larry Gold, Craig Tuerk et al. (1998) among others. Their

acronym for the process- SPERT (Systematic Polypeptide Evolution by Reverse Translation) is

given along with patent application information. This I work was carried out at Nexstar

Pharmaceuticals, Inc, USA.

Bacterial resistance to antibiotics is another example of seemingly non-Darwinian forces

at work. No sooner is a new antibiotic devised then bacteria find a way to disarm it. According

to neo-Darwinism, bacteria, before dividing, occasionally make a mistake in transcription,

substituting one nucleotide for another. Over time an accumulation of mistakes, add up to

something useful to the bacterium. A sugar that was previously indigestible becomes useful or

anantibiotic is disarmed by the creation of a new enzyme. These changes are said to be random

with respect to the need to digest the sugar or to disarm the antibiotic. They occur in the absence

of the sugar or the antibiotic. Sometimes these changes take place at regular intervals (Lederberg

1952).

However, bacteria have long lives. Their life histories stretch back eons. Bacteria split in

two to reproduce. The mother cell duplicates the genome before dividing so that each daughter

cell receives a full complement of genes. Even though the mutation occurs in the absence of the

sugar or the antibiotic in the experimental set-up, bacteria as well as other organisms in the wild

produce antibiotics. There is no guarantee that the bacterium in question has not encountered


17/32


D. Landy Bentham

17

that antibiotic or that sugar in its long past. Given that only a small fraction of the bacteria of the

world have been described and an even smaller fraction have been cultured in the laboratory, it

seems that the assumption that there has been no previous contact is insupportable.

Rather than a mutation, random with respect to a need, a gene may be turned on or off at

regular intervals or, in the case of the conversion to lactase producing E coli, by a shift in frame

(Cairns, Overbaugh and Miller 1988) (Foster and Thaler 1994). The frame-shift itself could be

thought of as a turning on of a gene, which in fact already exists.

Bacteria also exchange genes promiscuously, even crossing over species lines. Plasmids,

small rings of DNA, are passed from bacterium to bacterium by a process known as

"conjuga1ion". The plasmid is a duplicate, so that the donor retains a copy of the gene. The

recipient may incorporate the DNA of the plasmid into its own genome by natural genetic

engineering (Shapiro 1999 Transposable elements) and may now become a donor.

Even this exchange of genes is far from random. A bacterium lacking a bit of DNA

sends a signal, which another responds to by supplying the appropriate plasmid. Even though

the occurrence of new genes in bacteria can be explained by turning on an existing gene, or

shifting frame or exchanging plasmids, the question that still remains is how the enzyme was

invented in the first place.

Of course the immune system and bacterial resistance make up only part of the picture.

The resolution of the problem of the encoding of instinct could be instructive to evolutionary

theory. No one can deny that there is such a thing as instinct; that is, inherited knowledge. Birds

build nests according to an inborn plan; birds sing song, which has an inherited, as well as a

learned part. Border collies herd other dogs as well as children when there are no sheep to herd.

German Shepherds, on the loose, herd cars.


18/32


D. Landy Bentham

18

How are these characteristics, this knowledge, these ways of being encoded? They must

necessarily be encoded in the genome of the germ line cells. That is what is passed on from one

generation to the next. Because neo-Darwinism holds that information encoded in the genome is

generated by random events, the question of how learned information gets into DNA of the germ

line cells is rendered moot. Germ line cells are theoretically inviolate, uninfluenced by their

environments according to August Weismann (1891-1892). If this were indeed the case, we

should not expect to find molecular receptors on the membranes of germ line cells. But in fact

they are there by the thousands. Receptors are invitations to molecules to enter. If Weismann

were right and they have no purpose, why are they there? Frank Y. T, Sin (1998) reviews

"Interactions between exogenous DNA and sperm of vertebrates and invertebrates", but plays

down their relevance to evolution even though in the cases of injection of foreign DNA into the

proximal region of the vas deferens of mouse and rat "over 60% of the spermatozoa were found

to have the exogenous DNA". Also testicular injection of fifth instar silkworm larvae with a

foreign gene resulted in transmission of it to their progeny.

If genes can gain access to germ line cells, one wonders how the genes get there. An

article, which appeared in Science News October 7, 1989, was entitled "DNA's Extended

Domain, Sightings of cell-surface DNA turn scientific orthodoxy inside out". The reporter,

Ingrid Wickelgren , states that "Although most scientists still think of this vital nucleic acid as

residing only within cellular confines, accumulating evidence- some nearly 20 years old-

indicates some DNA exists outside that domain, securely anchored to cell membranes". Then

the question arises- how do the nucleic acids get to the cell membrane? Recent published Annals

of the New York Academy of Sciences, has as its subject circulating nucleic acids. Putting it all


19/32


D. Landy Bentham

19

together: Nucleic acids circulate, attach to cell membranes, and gain access to cells, even germ

line cells, by molecular receptors.

Going back to proteins and their capacity for self creation, Leslie E. Orgel (1998), in an

about face on his early championing of an RNA world, has lately declared that in the twenty

years or so since its conception there has not been a shred of evidence to support it. Meanwhile

his interests have centered on the self-assembly of peptides on minerals common in the early

earth. There has been experimental support for this theory (Hazen (2001). These findings

bolster the notion that proteins rather than RNA were the first molecules of life. We have

already touched on the formation of proteins on templates (Mosbach).

Let's consider that these new proteins may reverse translate to RNA and then reverse

transcribe to DNA, which have entry to germ line cells. If this were the case, the back-flow of

information from protein to germ line cell would be complete. This, followed by the insertion by

recombination of the new DNA to the genome, is all that is required for the inheritance of a

novel protein. Recombination of DNA occurs naturally (Shapiro, 2002). The finding that genes

of plasmids are inserted into the genomes of bacteria is now part of mainstream biology (Travis

2000), as is the insertion of genes of endosymbionts into the genomes of organisms. In turn,

excess or redundant DNA of the endodsymbiontis discarded (Margulis 1989).

Although the neo-Darwinian theory of evolution is still considered incontestable by many

mainstream biologists there are still unknowns which may relate to evolution. In Nature

Reviews Genetics of December 2001, Sean Eddy of the Howard Hughes Medical Institute and

Department of Genetics, Washington University School of Medicine defines Cajal bodies (coiled

bodies) as "Nuclear organelles of unknown function". Also unknown is the function of proteins

which surround the RNA mass of the large sub-unit of the ribosome, the organelle where RNA is


20/32


D. Landy Bentham

20

translated to protein. This was reported in the August 11, 2000issue of Science. The appearance

of the RNA was as had been expected, but the proteins were a surprise:

"In many places, the proteins give the impression of a man-of-war Jelly fish," says Peter

B. Moore, Yale University. "Instead of being the compact globular structures that mostproteins are, these things will often have a globular part and then there will be a little

strand that extends deep into the structure of the ribosome."These novel protein structures

appear to stabilize the ribosome, while the RNA assembles amino acids into peptidechains. (Science News, Vol. 158.)

The phrase "they appear to stabilize the ribosome" suggests that the function of the

protein structure is not in fact known and is assumed to be a structural component rather than

functional. What may be more important than what is not known, is what IS known. James A.

Shapiro in a debate in the Boston Review: Is Darwin in the details? (1999) points to four

categories of molecular discoveries which were unknown when the neo-Darwinian theory of

evolution was formulated:

The Organization of the Genome.Repair capabilities of the cell.

Mobile genetic elements and natural genetic engineering.

Cellular information processing.Given both what is not yet known in biology and what has become known since the

formulation of neo-Darwinism it seems ostrich-like to continue "believing in" an explanation

which falls short of even being a theory, according to Poppers definition(Soka1 1999). A theory

must be falsifiable; that is, it must be testable in such a way that either a positive or a

NEGATIVE result is possible. Neo-Darwinism is not testable by this criterion. It is time to look

to other models or theories to begin to explain the complexity and diversity of living things.

Frequently we hear of brains being compared to computers in which synapses are

switches and that memory is only a matter of strengthening those, which are used, or losing those,

which are not used-, a matter of selection. Again this follows the model of neo-Darwinism.

Matt Ridley has this to say:


21/32


D. Landy Bentham

21

It is misleading to think of a brain as a computer for many reasons, but one of the obvious

is that an electrical switch in a computer is just an electrical switch. A synapse in a brainis an electrical switch embedded in a chemical reactor of great sensitivity. (Genome p.

162)

James Shapiro, however, uses the computer analogy to advantage in discussing

information processing in the cell. Given that there is such a thing as artificial intelligence, he

considers how reasonable it is to see that the cell in all of its complexity has at least this capacity

for intelligence. If intelligence consists of taking in information, remembering it, making

connections among the things learned, making decisions based on what is learned, and giving out

information as needed, the cell does indeed have this capacity for intelligence (Shapiro 2002). In

more complex organisms such as mammals, the brain is the organ specializing in all of the above,

but intelligence resides elsewhere in the body as well. In humans, the enteric nervous system has

as much nervous tissue as the spinal cord (Gershon 1998). The heart has something akin to

intelligence (Pearsall 1998) as do all systems, organs, tissues, and cells.

Analogously all parts of the cell participate in its intelligence not just the cell brain" or

nucleus. It is the interaction of all the molecules of the cell which make up this intelligence.

Very important among these molecules are the peptides and proteins. Even DNA cannot

replicate without protein enzymes. Enzymes are the organic catalysts which speed up reactions

between and among molecules to make life possible. RNA can also act as a catalyst as described

above. But the primary catalysts are proteins and peptides.

Proteins are also the molecular motors within cells, which move other proteins along

actin, fibrils also made up of proteins. The protein molecules decorated with sugar recognition

sites let in information. Protein molecules may be the information itself. Proteins, sugars, lipids,

nucleic acids are all essential to the life and function of the cell. But none is independent of


22/32


D. Landy Bentham

22

proteins which as catalysts are involved in the construction of all the others including protein

molecules themselves.

To sum up: Maybe Jerome Wolken was right in saying that no one knows how evolution

works and maybe Mary Eubanks was right too in saying that it works in many ways. As a start

to understanding one of the ways in which evolution may work I have discussed some of the

non-random events which can be sources of innovation, with emphasis on evolution as a learning

process. This is in contrast to current neo-Darwinist theory, which states that novelty arises

randomly with respect to the needs of the organism and that orientation of evolution is the result

of natural selection (differential reproduction rates). I offer an alternative hypothesis:

The centerpiece of evolution as a learning process is a homeodynamic genome, within a dynamic

cell, in which all factors in the process of protein synthesis and heredity influence each other.

Dolores Bentham,

August 31, 2002

Literature Cited:

Ansell R. J., O Ramstrom, K. Mosbach. 1996. Towards artificial antibodies prepared by

molecular imprinting. Clin. Chem. 42,9: 1506-1512.

Baltimore, David. 1970. RNA-dependent DNA polymerases in virions of RNA tumor viruses.

Nature 226:1209-1211.

Bentham, Dolores Landy. 1977. Evolution as a learning process. Unpublished Paper.

Berg, Rolf H., Soren Hvilsted and P. S. Ramanujam. 1996. Peptide oligomers for holographic

data storage.Nature 383:505-507.

Buchner, Paul. 1953.Endosymbiosis. New York: John Wiley and Sons, Inc.


23/32


D. Landy Bentham

23

Bumet, F. Macfarlane. 1964. A Darwinian approach to immunity. Nature _203:451

___1969. The evolution of adaptive immunity in vertebrates. Acts. Pathol. Microbiol. Scand.

76:1 1-11.

Cairns, John, Julie Overbaugh, and Stephan Miller. 1988. The origin of mutants. Nature. 335:

142-145.

Caporale, Lynn Helena, ed. 1999.Molecular strategies in biological evolution . New York: New

York Academy of Sciences.

Cech, Thomas R. 1986. RNA as an enzyme. Scientific American. November: 64-74.

Cook, Norman D. 1977. The case for reverse translation. J. theor. Biol. 64: 113-135.

Craig, Robin. 1981. The theoretical possibility of reverse translation of proteins into genes. J.

theor. Biol. 88:757-760.

Crick, F. H. C. 1970Nature 227,561-563.

Eddy, Sean R. 2001. Non-coding RNA genes and the modern RNA world. Nature Reviews

Genetics 2:9l9-929.

Enard, Wolfgang, Philipp Khaitovich, Joachim Klose et el. 2002 Intra- and interspecific variation

in primate gene expression patterns. Science. 296,5566:340-343.

Eubanks, Mary. W. 1997. Molecular analysis of crosses between Tripsacum dactyloides and Zea

diploperennis (Poaceae). Theor. Appl. Genet. 94(6-7):707-712.

Federoff, Nina V. 1999. Transposable elements as a molecular evolutionary force.Ann. N. K

Acad. Sci. Molecular Strategies in Biological Evolution 870: 251-264.

Fletcher, Liz. 1999.New Scientist:38-40.


24/32


D. Landy Bentham

24

Gerhart, John and Marc Kirschner. 1997. Cells, embryos, and evolution: Toward a cellular and

developmental understanding of phenotypic variation. Malden, Massachusetts: Blackwell

Science.

Gershon, Michael D.- 1998. The second brain. New York: Harper Collins.

Gold, Larry, Craig Tuerk, David Pribnow, Jonathan Drew Smith. CODEN:USXXAM 5843701

A 1998 1201 Patent written in English.

Grindl, Wolfgang, Wolfgang, Wende, Vera Pingoud and Alfred Pingoud. 1998.Nucleic Acids

Research. 26,8: 1857-1862.

Hardy, K. G. 1986Bacterial Plasmids 2ndEdition. Wockinham, U.K. Van Nostrand Reinhold.

Haupt K, K. Mosbach. 1998. Plastic antibodies: developments and applications. Trends

Biotechnol. 16,11:468-475.

Hazen, Robert M. 2001. Life's rocky start Scientific American April:77-85.

Hazen, Robert M., Timothy R. Filley, and Glenn A. Goodfriend. 2001. Selective adsorption of L-

and D-amino acids on calcite: Implications for biochemical homochirality. PNAS 98

10:5487-5490.

Hyden H. and E. Egyhasi. 1963. Glial RNA changes during a learning experiment in rats. Proc.

N. A. B. 49:618-624.

Kauffman, Stuart 1996. Even peptides do it.Nature 382.

Kendrew, John ed. 1994 The encyclopedia of molecular biology. Oxford:Blackwell Science.

Koestler, Arthur. 1967. The ghost in the machine. New York. The Macmillan Company.

Kolate, Gina. 1994. Novel kind of computing: Calculation with DNA. The New York Times

Tuesday, November 24.


25/32


D. Landy Bentham

25

Lamarck, Jean Baptiste. 1809.Zoological Philosophy. 1984. Reprint Chicago:University of

Chicago Press.

Landman, Otto E. 1993. Inheritance of acquired characteristics revisited. Bio Science 44,10:696-

705.

Lee, David H., Kay Severin, Yohai Yokobayashi. 1997. Emergence of symbiosisin peptide self-

replication through a hypercyclic network.Nature 390,11:590-594.

Lee Rosalind C. and Victor Ambros. 2001. An extensive class of small RNAs in Caenorhabdidis

elegans. Science 294:862-864.

Lederberg, Joshua and Esther M. Lederberg. 1952. Replica Plating and indirect selection of

bacterial mutants.J. Bact. 63: 399-406.

Lo, Y.M. Dennis. 2001. Circulating nucleic acids in plasma and serum: An overview.Ann NY

Acad. Sci. 945: 1-7.

Lohse, Peter A. and Jack W. Szostak. 1996. Ribozyme-catalysed amino-acid transfer reactions.

Nature. 381.

Loewen, James W. 1995.Lies my teacher told me: Everything your American history textbook

got wrong. New York: The New Press.

Loewenstein, Wemer R. 1999. The touchstone of life: Molecular information, cell

communication, and the foundations of life. New York: Oxford University Press.

Margulis, Lynn. 1989. Symbiogenesis and symbionticism. Margulis, Lynn and Kenneth H.

Nealson, eds. Symbiosis as a Source of Evolutionary Innovation. Conference Center in

Bellagio, Italy, June 25-30.

______1996. Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic classification

of life.1996. Proc. Natl. Acad. Sci. USA. 93:1071-1076


26/32


D. Landy Bentham

26

______1998. Symbiotic planet (A new look at evolution). New York: Basic Books.

Mattick, John. 2001. Non-coding RNAs: the architects of eukaryotic complexity.EMBO Rep.2,1

1:986-991.

Mayor, Ugo, Chirstopher M. Johnson, Valerie Daggett, and Alan R. Fersht. 2000.Protein folding

and unfolding in microseconds to nanoseconds by experiment and simulation. PNAS. 97,

25:3518-3522.

McClintock, Barbara. 1948. Mutable loci in maize. Carnegie Inst. Wash. Ybk47: 155-169.

Mekler, L. B. 1967. Mechanism of biological memory. Nature 215:481-484.

Milner, Peter M. 1970. Physiological psychology. New York: Holt, Rinehart and Winston, Inc.

Milner, Richard. 1990. The Encyclopedia of Evolution, Humanity's Search for its Origins. New

York: Facts on File.

Nashimoto, Masayuki. 2001. The RNA/protein symmetry hypothesis: Experimental support for

reverse translation of primitive proteins.J. theor. Biol. 209: 181- 187.

Nohturfft, Axel and Richard Losick. 2002. Fats, flies and palmitate. Science 296:857-858.

______l999. Transposable elements as the key to a 21st century view of evolution. Genetica

107:171-179.

______2002. A 21* century view of evolution.J. Biol. Phys. In press (in the PROCEEDINGS of

the 4th International Conference on Biological Physics, Kyoto, Japan, July 30- August 3,

2001.

______Patricia Foster and David Thaler. 1994. Adaptive mutation. Science 2665:1994-1996.

Shapiro, Robert. 1999. Prebiotic cytosine synthesis: A critical analysis and implications for the

origin of life. Proc. Natl. Acad. Sci. USA, Biochemistry. 96:4396-4401

Sheldrake, Rupert. 1995.A new science of life. Rochester, Vermont: Park Street Press.


27/32


D. Landy Bentham

27

Simpson, George Gaylord. 1964 This view of life, the world of an evolutionist. New York: A

Harbinger Book, Harcourt, Brace & World, Inc.

Simpson, M.L., G.S Saler, J.T. Fleming and B. Applegate. 2001. Trends in Biotechnology

19,8:317-323.

Sin, Frank Y. T. 1998. Sperm-DNA interaction. Trends in Comparative Biochem. & Physiol. Vol.

5.

Sokal, Alan and Jean Bricmont. 1999. Fashionable nonsense: postmodern intellectuals' abuse of

science. New York: Picador USA.

Spetner, Lee. 1998.Not by chance! Shattering the modern theory of evolution . New York: The

Judaica Press, Inc.

Steele, Edward J., Robyn A . Lindley and Robert V. Blanden. 1998. Lamarck's Signature.

Reading, Massachusetts: Perseus Books.

Temin, Howard M. and S. Mizutani.l970. RNA-directed DNA polymerases in virions of Rous

sarcoma virus.Nature 226: 121 I-1213.

Normile, Dennis. 2002. Molecular computing: DNA-based computer takes aim at genes. Science

295, 5557:951.

Orgel, Leslie E. 1998. Polymerization on the rocks: Theoretical introduction: Origins of life and

evolution of the biosphere. Netherlands: Kluwer Academic Publishers 28:227-234.

Pearsall, Paul. 1998. The heart's code: tapping the wisdom and power of our heart energy . New

York: Broadway Books.

Pennisi, Elizabeth. 2002. Evo-devo devotees eye ocular origins and more. Science 296: 1010-

1011.

______1994. Does nonsense DNA speak its own dialect? Science News. December 10.


28/32


D. Landy Bentham

28

Pert, Candace B. l997.Molecules of emotion. New York: Scribner.

Popper, Karl R. 1959. The logic of scientific discovery. London: Hutchinson.

Ridley, Matt 2000. Genome: the autobiography of a species in 23 chapters . NewYork: Harper

Collins.

Rosenberg, Susan M., Simonne Longerich, Pauline Gee, Reuben S. Harris. 1994. Adaptive

mutation by deletions in small mononucleotide repeats. Science. 265:405-407.

Sahl, Hans-Georg and Gabriele Bierbaum. 1998. Lantibiotics: Biosynthesis and biological

activities of uniquely modified peptides from gram-positive bacteria.Annu. Rev.

Microbiol. 52:41-79.

Segre, Daniel, Dafna Ben-Eli, David W. Deamer and Doron Lancet. 2001. Origins of life and

evolution of the biosphere 31: 119-145. Netherlands Kluwer Academic Publishers.

Shapiro, James A. 1999. More articles on evolution. A third way.Boston Review University of

Illinois Press. September 7.

Travis, John. 2000. Human, mouse, rat...What's next? Scientists lobby for a chimpanzee genome

project. Science News 158:236-238.

_____Biological dark matter 2002. Newfound RNA suggests a hidden complexity inside cells.

Science News 16:24-25.

Varmus, Harold. 1987. Reverse transcription: Years ago a group of viruses was found to convert

RNA into DNA, reversing the usual sequence of molecular events. Now it appears this

process is native to other viruses and many higher organisms. Scientific American

September:56-65.

Weismann, August. 1891-1892.Essays upon heredity and kindred biological subjects 2 vols. Ed.

E. B. Poulton et al. Oxford: Oxford University Press.


29/32


D. Landy Bentham

29

Wickelgren, Ingrid. 1989. DNA's extended domain: Sightings of cell-surface DNA turn scientific

orthodoxy inside out. Science News 136:234-237.

Wu, Shao, lndraneel Ghosh, Reena Zutshi and Jean Chmielewski. 1998. Selective amplification

by auto-and cross-catalysis in a replicating peptide system.Nature 396:446-450.


30/32


D. Landy Bentham

30

Bacterial Resistance

There are few that can resist giving bacteria credit for ingenuity, guile, even brilliance,

when describing how these otherwise lowly creatures can get around antibiotics. No sooner is an

antibiotic extracted, synthesized or invented, when up pop bacteria that knowhow to disarm it. If

there is an enzyme, which destroys bacteria's ability to produce cell wall, there are bacteria

which "know how" to render that bit of biochemistry useless. The swiftness with which that

news travels from cell to cell, bridging not only individuals, but even species is remarkable.

It used to be said- and still is- that what happens is this: Bacteria, before dividing

occasionally make a mistake in transcription, substituting one nucleotide for another in a gene.

Over time these changes build up and eventually an accumulation of mistakes add up to

something useful to the bacterium. That could mean that it is now able to use a sugar that it

couldn't use before by synthesizing an enzyme previously absent or it could mean, more

significantly for us, that the bacterium has created and enzyme capable of dismantling an

antibiotic. These changes are random with respect to the need to digest a sugar or to disarm an

antibiotic. They occur in the absence of the sugar or the antibiotic. Sometimes these changes

take place at predictable time intervals. There was an ingenious test of this devised by the

Nobelist Joshua Lederberg, (Replica Plating and Indirect Selection of Bacterial Mutants, March

1952) in which he showed that in the laboratory, bacteria, which have not previously been

exposed to an antibiotic, convert to forms resistant to that antibiotic. These tests were done to

show that mutations take place without reference to need.

The problem with that line of thought is that bacteria have long lives. Their life histories

stretch back eons. A bacterium simply splits in two to reproduce, so that each daughter cell is


31/32


D. Landy Bentham

31

half the mother. The mother has duplicated the genetic material before dividing, so that each

daughter receives a full complement of her genes. Even though the mother has given up her own

existence, she has become her daughters, and so it goes through the millennia. For just as many

eons other organisms have been around. Bacteria as well as other organisms produce what we

now call antibiotics. In the life histories of these organisms there has been a myriad of

opportunities for contact. Some have been for the good- mergers with blue-green algae which

became plastids that yielded the plants as we know them, and mergers with other bacteria which

became mitochondria, the energy producing machines of the cell. But some of the contact

resulted in all-out war; antibiotics are the artillery in that war. So, the ingeniously devised test to

ensure that bacteria have never been in contact with a particular antibiotic is flawed. It works

only for the present laboratory situation. It doesn't take into account all the other opportunities

for contact over the organism's long history. What seems a regular appearance of mutants, with

or without contact with whatever may have influenced the change, could be seen as something

else.

Instead of a random mutation, the change in an organism's adapting to a situation to a

sugar, an antibiotic- could simply be the turning on of a gene at regular intervals. This may be

what happens. Genes are not after all static entities which change willy nilly, but dynamic

systems parts of which may be turned on or off. They can be rearranged and parts of them can

be passed around. A small piece of genetic material in a ring may be passed from bacterium to

bacterium in "conjugation". There is exchange of genetic material in bacterial after all. In a

phenomenon, which resembles mating, rings of genetic material, called plasmids, are injected by

one bacterium into another. These plasmids may contain the genes for disarming antibiotics, for

digesting a sugar or even for adding a bit of toxic punch to the bacterium's existing arsenal. The


32/32


D. Landy Bentham

donor has copied these plasmids first, so there is one to give away and one to keep to be copied

again as needed. Some bacteria have thus acquired the means to render all known antibiotics

ineffectual. There is no need to invoke chance mutations to explain an organism's seemingly

sudden genetic change. Whatever was needed may have been simply provided by turning on a

gene or acquired from another in conjugation. These too could happen at regular intervals as the

"mutations" were.

All of the proceeding deals with the question of what laboratory results may or may not

mean, but there still remains the question of how the bacteria developed the enzymes to digest a

sugar or to breakdown an antibiotic in the first place. Somewhere in its long history it has

encountered the substance for the first time, This must still go on. Some antibiotics that have

been engineered by people are novel. No organism, so far as we know, has developed them until

now. What now? Are we still to believe that enzymes to disarm them are randomly produced by

point mutations in the genome? Mutations are nearly always, if expressed, lethal to the organism,

which carries it. Rare are those which are beneficial.

Some work, now discounted for reasons discussed elsewhere in this paper, but which

may still have merit; showed that RNA itself could be changed by learning. Whether or not it is

the RNA that changed itself or was influenced to change by other factors, that it can change and

be reverse transcribed to DNA, provides an alternate way to introduce novelty into a genome.

There are even hints that it may be possible to translate protein back to RNA. These are only

hints, but in any case they are paths to explore. The possibility of reverse translation of protein

to RNA is discussed elsewhere in this paper.

Evolution as a Learning Process

Documents

Transcript of Evolution as a Learning Process