Chapter eleven
Reverse transcriptase writes human memories

The idea has been lofted, and is lofted again here, that reverse transcriptase literally writes memories: not just genetic memory, but also immune memory and memory in the brain. It goes very much against the grain of course but if you can suspend disbelief for a moment, you may discover the idea has a certain fascination.

The background news that makes this idea worth bringing up, again, is the sudden new importance of Alternative Splicing — and the still rather obscure discovery that we humans contain the genetic fossils of 30-odd ancient retroviral infections.

The engine of each of these old viruses was, of course, reverse transcriptase. In some of the viral sequences the engine is now missing but in others, it is still in there.

When the draft of the human genome was published in June, 2000, it revealed at least two unexpected results. One is famous. Not enough genes. The other unexpected outcome was less remarked. Maybe it was less of a surprise, but it certainly surprised me. It shows that not quite half of our DNA was “written back” from RNA. All this retro DNA was written into the genome by the remarkable enzyme reverse transcriptase.

Reverse transcriptase has almost doubled the genome. It did most of this work a very long time ago. It was mainly an internal process of retrotransposons reproducing themselves — but some of that retro DNA, to be exact 4.7 percent of the human genome — was written into our chromosomes by reverse transcriptases inherent in retroviruses.

We are infected.
We know of only 4 modern, active human retroviruses: Two are HTLVs (human T-cell leukemia Virus) and two are HIVs. These four familiar viruses are exogenous, not endogenous – they initially arrive from outside the body.

Scans of the human genome have shown that our DNA contains the residues of about 30 ancient, now endogenous retroviruses – 30, that is, thus far identified. There are probably more. Anyway, there you have 4.7% of your own personal DNA: Retroviruses. Say yikes.

A virus exists to write and rewrite itself. Retroviruses can infect many different types of cells, but when they infect germ line cells, in the testes or ovaries, they can write themselves into the genome – to be passed from generation to generation. In this sense they have the power to violate Darwin’s dictum, ‘No inheritance of acquired characteristics.”If the “characteristic” you acquired happened to be a retrovirus you could indeed pass its DNA sequence along to your offspring and theirs. In this way, a virus becomes endogenous. By infecting the germ line, it takes up permanent residence in the genome.

They are called HERVs, for Human Endogenous RetroViruses. Some are ancient indeed, on the order of 30 or 100 million years old. They infected us before we were human.But some HERVs are of relatively recent origin – which is to say, recent infection. One entered the human germ line just 200,000 years ago. This particular virus is lodged uniquely in the human genome – it is not to be found in the genomes of our cousins, the chimps and gorillas. Potentially it is dangerous because it is still, apparently, in good enough shape to be or become infectious.

Are we sick with prehistoric viruses? Could they kill us?
Logic and scrutiny of the sequences suggest that the older retroviruses have been pretty much detoxified, tamed. In some cases their most dangerous sequences have been pruned out altogether. In others, the sequence is too drifted and degenerate to work.

The systematic transcription of any really lethal retroviruses seems unlikely. (If these retroviruses were killers, that is to say, quick-killers, they themselves would not have survived in our genomes, since by killing their hosts they would have themselves committed suicide long ago.)

Probably some of the ancient retroviruses are in fact involved in disease processes. Its not clear how. It is not even clear in every case who’s side they are on, that of the host or that of the disease.

The younger the retrovirus, the more likely it is to be dangerous in the conventional way, since its infective machinery may be intact or restorable.

There is evidence that ancient retroviral genes are able to promote or enhance or alter the splicing of other genes. Considerable research is now focused on the effect, on normal gene transcription and splicing, of nearby or intrinsic viral sequences (promoters, enhancers, etc). In these models, the HERVs are involved in, maybe, launching disease processes that are not well understood: MS, diabetes, cancers, and autoimmune diseases are candidates.

There exists the possibility of another level of control, here. And another possible way to make trouble. Since we all contain retroviruses, and since they seem to be passive for the most part – it seems reasonable some biochemical machinery evolved to put them out of business and keep them out of business. A disease could start when the machinery who’s job it is to inhibit or inactivate the endogenous retroviruses – glitches.

Captured weapons
One fascinating idea is that our endogenous retroviruses have not merely been domesticated — but actually turned into weapons against disease. For example, the expression of an endogenous viral protein (a coat protein) has been found associated with Multiple Sclerosis.

The first thing you might think of is that maybe MS follows from a revival of an ancient retroviral infection. A different explanation, however, is that the body is borrowing the old virus’s capacity to manufacture coat proteins – then using them to fight the disease by blocking cellular receptor sites.

The fundamental idea is that we have probably turned our endogenous retroviral code to advantage in defending ourselves against disease. This is a very good idea but it perhaps understates the possibilities for cooperative arrangements — deals that may have been cut, over the eons, with our inborn HERVs.

Retroviruses have the power to break all the rules — to both store and spread biological information within an organism. What couldn’t we do with that?

What else could you make from these rusty retroviral parts?
Reverse transcriptase is one characteristic enzyme all active retroviruses encode. They use it to write themselves into the genome. It was discovered independently by Temin and by Baltimore in 1970. Reverse transcriptase is the only enzyme of which one could say: “It writes memory.” Although this verbal construct makes some people deeply uneasy, it is unarguable.

In theory the retroviral mechanisms have the power to both write and broadcast memory, through the process of infection, from cell to cell. If our ancient endogenous retroviruses have indeed been tamed, de-toxed and put to work doing something useful in the cause of human physiology — this would be an attractive and natural job for them: Writing memory.

Memory as an infective process
Reverse transcriptase has quite a history of high performance and remarkable feats. It was responsible for nearly doubling the genome. And it is still in us, however suppressed or motheaten or domesticated — this strange and dangerous writing enzyme. Constrained to do strictly boring work, it is the engine of the enzyme telomerase. A waste of talent. Couldn’t reverse trascriptase be made to do something much more interesting?

Perhaps we could revisit (knowing what we know now) Lineas Pauling’s long shelved notion of an “instructive” immune system; the discovery of “immune RNA”; and the swirl of ideas in the 1960s surrounding the notions of DNA and RNA as memory media for the brain.

There is a parallel stream of ideas to the effect that memory might be an infective process. It takes several days to consolidate memory in the brain, and it was once imagined that this long period of time was needed for a process of distribution, perhaps an “infection” of the brain tissue with new information.

In neurons, synaptic vesicles are formed, fuse with the cell wall at a specific pore site — evert and release their contents into the synaptic cleft. A message is thus delivered to the neighboring nerve cell. The machinery of the synaptic vesicles is suggestive of the viral budding and viral invasion processes. Pockets of RNA have been found at the nerve endings. What’s RNA doing out there, so far from the nucleus? It is thought to support local protein synthesis, but is that the whole story?

Maybe the clonal response isn’t one. Maybe it is instead a massive infection – or counter infection – that transfers and broadcasts the code for an appropriate antibody.

If you were going to invent memory…
In the mid 1960s, when the notion of biochemical memory enjoyed a brief vogue, they knew DNA was a stabile long term storage medium, and they had the most basic form of the Central Dogma to describe gene expression:

DNA => RNA => Protein

To turn a machine for expressing genes into a recording machine for sequences, it seemed reasonable, as a place to start, to visualize a reversal of the central dogma, so that somehow:

Protein => RNA => DNA

This was before reverse transcriptase had been discovered, so both of the arrowheads seemed hopeless — there was no known way for the process to proceed. Most biochemical memory enthusiasts focused, therefore, on RNA, some on protein. In 1965, the whole pursuit ended in a failure-to-replicate paper, and scandal, and that ended all that.

To follow in the footsteps of the original line of reasoning, today, suppose we were to begin as they did, with an innocent eye and a reversal of the central dogma.

As a first step, re-sketch the central dogma to reflect the reality given us by the published genome. Instead of one gene => one protein, we must now make an adjustment to show that one gene => 2 or 3 proteins. Or, in the extreme case, one gene => tens of thousands of different proteins. So let’s just write:

DNA => mRNA => Protein 1 or Protein 2 or Protein 3

To show that one gene codes for a cluster of possible proteins, depending upon how you splice it. To make a biological recording machine you could reverse the central dogma, as follows:

Protein 1 or Protein 2 or Protein 3 => RNA => DNA

That second step, RNA => DNA, is what reverse transcriptase does. The first step, from protein back to RNA, still does not seem possible.

But what do you really want to record as a memory? Probably not the protein, per se, but its identity — and its identity reflects a choice that has just been made between or among various alternative protein domains.

Notebook RNA
A useful immune memory, for example, could consist of a code that simply identifies or points to the protein sequence of an antibody — an assembly of domains that works perfectly against a specific antigen. You don’t have to remember and reiterate the whole sequence. You just need to be able to call its name, loudly, in an emergency.

It is possible to imagine ways to keep an RNA record of what proteins are being made – as they are being made. That record, essentially an RNA notebook on protein production, could be written back into DNA by reverse transcriptase. The notebook would tell you which proteins had been made, how (i.e., how their mRNA was spliced), and in what order they came off the line.

How might such a notebook be kept?
The gene splicing process leaves specific introns behind, like a dressmakers cuttings on the floor. If you collect the cuttings, you can readily reproduce the shape of the dress.

From a sequential collection of introns, you can re-construct the program used to make a specific protein. And it would not be necessary to actually gather in all those introns. Tags, consisting of just enough sequence to uniquely identify each intron, would suffice. A notebook in shorthand RNA becomes the protein factory record — the thing to be memorized.

As a final step, reverse transcriptase writes the RNA notebook into DNA, that is, into the stabile long term memory storage medium.

Cut and Try
If you integrate this reversed-dogma recording machine with Pauling’s old, outlawed idea of an instructive immune system, you can begin to imagine how a process of protein cut-and-try against the template of an invading antigen could lead to the construction of an appropriate, perfectly fitting antibody.

The missing element in the story thus far is a signal of success. Somehow the winning antibody has to be associated with the specific RNA notebook of splicing instructions that produced it. If you then reverse transcribe the RNA notebook on how to construct a successful antibody into DNA, which is to say, memorize it — and broadcast it through the immune system using a process analogous to infection, voila: Immune response, immune memory.

Meanwhile, the considerable body of notebook RNA describing all the antibodies which did not work can be digested and, well, forgotten.

The story treads much the same path as the “Generation of Diversity” narrative familiar from immunology. Scrambling of sequences, cutting and trying. But it discards the Darwinian notion that one cell produces one antibody pre-destined to greet one antigen. All the cells in confrontation with a fresh antigen are scrambling their sequences all the time. And it replaces the clonal response with cell-to-cell communication — a massive infection with the right answer, the ideal sequence.

We are just surfing along on new facts, here — the wildly interesting possibilities inherent in the HERV machinery and in alternative splicing. But here is an old fact that pertains.

Immune RNA
An RNA that seemed to instruct the immune system was actually reported, in 1957, and became something of a cause célèbre. It was called immune RNA. It is largely a forgotten finding, now, but it was never successfully controverted. Only scoffed down.

The most telling criticism of immune RNA was that the molecule was too short, too small, to describe an antibody. Even though it apparently did exactly that. This criticism now resonates as a promising observation — it is exactly what one would wish to hear about a notebook RNA, which only encodes a splicing program. It is also pertinent that it was discovered wandering from cell to cell, and could be used experimentally to coax appropriate antibodies from still other cells.

If one sifted through new found knowledge about spliceosomes and HERVs, perhaps all parts and pieces for a memory machine are actually in there. If it is RNA that must be memorized, then the final common path to memory has to be reverse transcriptase.

Reverse transcriptase makes a lot of mistakes. In some applications, perhaps in the immune system, this error prone work could be useful, a way to manufacture variety. In others inaccurate transcription would have to be policed, corrected.

Secrets of successful viruses?
Suppose that, by whatever means, the immune system were instructive, that is, creative. Viruses confronting such a system will have evolved ways to beat it. One way would be for the virus to change its identity (cell surface antigens) faster than a creative immune system can retool its antibody production. Not a new tactic, but a new way to explain it. The virus could monkey-wrench some step in the creative process.

Not incidentally, an attack on the immune system’s “creativity” would automatically and completely elude detection in the lab, since immunology does not recognize the possibility that a creative immune system might exist. Straight under the radar.

There is an excellent long article on HERVs by Michael Specter in The New Yorker of December 3, 2007. Specter interviewed an eclectic selection of HERV researchers and interested commentators, including Thierry Heidman, John Coffin, Robin Weiss, Paul Bieniasz, Harmit Malik, Michael Emerman, Aris Katzourakis, Robert Belshaw, and Luis P. Villarreal. If you are interested in learning more about this field, or thinking about getting into it, there are a number of additional labs whose work should be searched, including the Eugene Sverdlov lab in Moscow and the Jack Lenz lab at Einstein. Sverdlov’s recent book, Retroviruses and Primate Genome Evolution, is a helpful resource.

RNA is a far a more capable system than we once imagined. For new thinking on this broader subject, a number of starting places can be found in this overview piece in the March 28, 2008 Science: The Eukaryotic Genome as an RNA Machine by Paulo P. Amaral, Marcel E. Dinger, Tim R. Mercer, John S. Mattick

What about memory in the brain?
Biological information is typically stored as sequences and shapes. There is no reason to imagine that information in the brain should be stored in some entirely different way. But in the immune system, the thing to be memorized, which is the shape and sequence of a specific antibody, is clear.

To make some guesses about how reverse transcriptase could write memory in the brain, where the thing to be memorized remains a complete mystery — it will first be necessary to think through the consequences of the multichannel neuron.

One should probably start with the photoreceptors of the retina, which are specialized neurons.

The eye is the last place in the brain where anything can happen at the speed of light. What happens is image formation and everything that image formation entails, including Fourier transformation. It will be suggested that the “thing to be memorized” is a transformed image, or perhaps a geometric and a transformed image simultaneously.

Ghosts in the machine
Some old, toothless and discredited ideas from the biochemistry of four, five and six decades ago, like the old, supposedly de-fanged retroviruses we still carry with us, may be – after all — stirring restlessly in the museum by night.

Many of the potential talents and implications of HERVs are upsetting, in the sense of upsetting the applecart. The power to self-infect, to write and broadcast memory from cell to cell within a mature organism, even from generation to generation — threatens bedrock notions of the clonal response or the synaptic memory or “no inheritance of acquired characteristics”. The very idea of memory as an infective process is probably a little dangerous to toy around with. In this sense, if you like revolutions or comeback stories, HERVs could turn out to be quite delightful.