My View

Richard Gayle

Syzygy and Synchronicity April 7, 2000

On May 5, 2000, the world as we know it will end. See, we were preparing for the Y2K catastrophe and completely missed syzygy. Even though it was foretold to all of us almost 40 years ago, in the movie 2001 by Stanley Kubrick. Syzygy is a word from astronomy. It describes the situation when the moon, Earth and sun all line up, usually creating larger than normal tides. Well, on May 5, 2000, the seven classical bodies of the solar system (moon, sun, Mercury, Venus, Mars, Jupiter and Saturn) will all align in what is known as the Grand Conjunction. From our view on Earth, they will all appear in the sky in an area covering only 25° of sky. This only happens once every 6000 years or so. We all remember what this looks like from so many of the scenes of space in 2001. Seemed like every time someone touched a monolith, those damned planets were in alignment. Obviously Arthur C. Clarke and Stanley Kubrick knew about the conjunction this May and used it as a leitmotif of their screenplay.

Now, with Y2K safely behind us, the doomsayers are starting to come out of the woods to scare us regarding the conjunction that will occur in May. The media will have a great time. Even though any knowledgeable astronomer will be able to demonstrate that the gravitational effects caused by this alignment are so minuscule as to be almost unmeasureable, we will be sure to hear from the 'other' side explaining that no scientist can tell us it WON'T happen!

Now, Jung defined synchronicity as "a meaningful coincidence of two or more events, where something other than the probability of chance is involved." Humans are driven to find patterns in things, even if there is none. This need to find meaning behind an event, such as the Grand Conjunction, is pretty typical. Synchronicity, besides being a great song by the Police, also describes my topic for this column. It really does describe a meaningful coincidence of two or more events. You will have to decide whether chance was involved or whether some higher power is at work.

Last month, Science devoted virtually an entire issue to Drosophila, the sequence of its genome and its comparison to other genomic sequences. While Drosophila is a sentimental favorite for many people, it has somewhat different memories for me

Many of us have worked with Drosophila. I did experiments with it in high school, studying gene linkage and cross-over events. At CalTech I got to work with Ed Lewis and Welcome Bender as they were dissecting the first homeotic genes in Antennepedia and Bithorax. (Both had very strong influences on my desire to be a biologist but Ed impressed me more at the time for his ability to discern the particular phenotype of a fly by looking at it with the naked eye. Not phenotypes like white eyes or four wings but ones like the lack of sex combs on the legs or the addition of a few more bristles.) My undergraduate research project looked at the expression of certain enzymes in different Drosophila tissues. So, besides learning how to maintain a fly colony, I learned how to dissect flies and remove specific organs. The sight of a stereo dissecting scope still brings back memories of separating insect brains from the head. (David Cronenberg’s movie "The Fly" gives me nightmares for reasons far different from other people.)

So, now we have the sequence of Drosophila. What do we do with it? Completely processing all of this data will take years, but there are some interesting aspects that are already apparent.

(A) Just like C. elegans, there are a large number of genes that are only found in Drosophila. Check out this excerpt from one article, comparing yeast, C. elegans, and Drosophila:

These questions are very interesting, especially considering a paper I discussed earlier. Does each organism contain a large number of rapidly evolving genes? Are these genes located at or near heterochromatin? Is this an aspect of genomic organization that we will continue to see?

Interestingly, 30% of the Drosophila genome may never be sequenced. 60 Mbases of the 180 Mbases of Drosophila are heterochromatic DNA. Highly repetitive, heterochromatic DNA can not be cloned stably into YACS or BACS. These regions contain rRNA, centromeres, telomeres, and several known genes, mixed in with a real hodgepodge of pseudogenes, repetitive DNA families and 'junk' DNA. There are at least 3 Mbases of DNA sequenced by the Celera group that does not map to euchromatin and is presumably found in heterochromatin. So it is likely that islands of genes are found in heterochromatin. Are these areas critically important for the development of novel genes? Are these locations the R&D factories of the genome?

So, if these rapidly evolving genes are found in DNA that is not clonable, how can we ever sequence it? Now, although some of these questions can not easily be tested yet (i.e. since the whole definition of heterochromatin is, well, undefined), there are some things that can be done. Because nature is a wonderful thing and, if you look hard enough, you just might find something already out there that will be helpful. Perhaps not every organism has retained the need for large amounts of heterochromatin or repetitive DNA.

It turns out that certain teleost fish have a unique genome. To wit, the pufferfish have genomes that are extremely small for a vertebrate. Fugu rubrides has a genome that is only about 400 Mbases in size. But the reason for this is not that it has fewer genes. It is because its genome is organized quite differently from humans or mice. Over 92% of the DNA is unique, only a little over 7% is repetitious. Almost the reverse of humans.

Fugu has such a small genome because it lacks many of the pseudo genes, repeats and junk DNA found in mammalian genomes. The genes are closer together on the chromosomes. Even the introns are smaller, averaging only 80 bp in length. So, it might be very possible to clone and then COMPLETELY sequence the Fugu genome. Not just the easy stuff, which is only a small fraction of the entire amount of DNA in a cell, but all of it.

In addition, since the last common ancestor of humans and pufferfish is many millions of years older than between humans and mice, comparisons of genomes should be more informative with the former than the latter. Genes that are really important will show a much larger amount of conservation than otherwise. Important non-coding regions, such as transcriptional control regions, should also show similarities. There may not have been enough time since humans and mice diverged to separate out sequences that serve identical functions and those that are orthologs serving a different function. There should be enough time between fish and humans.

Now I know Fugu as a Japanese delicacy. It has glands that contain a neurotoxin. In order to prepare fugu sashimi, the highly trained cook must remove the toxic organs in just the right order, so as to allow some neurotoxin to enter the flesh, but not enough to be deadly. You are just supposed to get a slight tinkling around the lips. You are only supposed to consume the prescribed amount of fugu. People have died by going to another restaurant and ordering a second helping. Yet, this fish could provide us with some valuable information regarding our own genome.

(B) Knowing the sequences will allow us to develop different array and chip technologies. I'll talk about some of these in the future but there is one I wanted to mention this week. It has to do with putting DNA sequences in beads rather than on glass. It was published in February in PNAS. And it is pretty nifty.

In this procedure, a library of oligonucleotides is constructed on millions of beads. A similar library of oligonucleotides is attached to a collection of cDNAs which are then amplified by PCR. The cDNAs can be loaded onto the microbeads through the complementary ends of their tags to the tags on the microbeads. So essentially every bead can be loaded up with 100,000 copies of a specific cDNA. These beads can then be probed with labeled DNA probes. In the paper, they attached a fluorophore to a DNA sequence to use as a probe, ran a lot of beads through a FACS and came up with a profile.

This has real possibilities. Using a pre- and post-PMA set of cDNAs, they examined THP-1 cells and could separate out beads that contained CDNAs that were over or under represented on beads. FACs sorting isolated the beads, they removed the DNAs and then cloned them. So you could do all the isolation and screening WITHOUT having to clone the DNA beforehand until you had the important sequences. And having a genomic sequence will permit greater discrimination in the use of probes. Very cool.

You are probably wondering how synchronicity enters the picture? Well, before the world ends on May 5, we here at Immunex will have a unique opportunity that MUST be more than just a coincidence. It ties together all the genomic work, the Fugo work, C. elegans, DNA beads into an event that gives me chills to contemplate.

For, you see, the SAME man who is identified Fugu as a model system, who published the recent paper on DNA beads, who gave C. elegans to the world, and who helped provide us with the scientific foundation that allows us to even have a job, will be speaking here on Monday, April 10, room 711, 3PM. He is Sydney Brenner and he is a unique talent in our world.

Sydney Brenner is one of the most important researchers alive today, producing seminal works that underlie everything we do in biology today. For example, take the title for this PNAS paper he wrote in 1957, shortly after he joined the labs at Cambridge: On the impossibility of all overlapping triplet codes in information transfer from nucleic acid to proteins. We know this is impossible now but no one else did until he published that paper.

He was not only present at many of the important events but was intimately involved with much of the pioneering work at the Unit for "Research on the Molecular Structure of Biological Systems" set up by the MRC in the Cavendish Laboratories. With Jacob and Crick, he elucidated the role for mRNA in translation. He helped determine what form the genetic code had to take. With Crick, he demonstrated the triplet nature of the genetic code. He is responsible for C. elegans entering the scientific world as a model system. He has started again with Fugu. He is still publishing innovative work that stimulates the mind. And he writes a column. For Current Biology. Where he pretty much writes whatever he wants and stimulates readers with his perspectives.

It is not every year that the planets align, coming so soon after the beginning of the new age (I chose to call it a new age, not a new millennium. That is next year. But people believe in portents when they will and most people believe that this year is the important one.) It is not every year that you have the opportunity to meet someone who was present at the beginning of the biological age. And he is still leading us into new frontiers, serving to find new experimental approaches to solve problems. Come hear him on Monday afternoon

The world may end in May but you will be able to say that you listened to one of the truly creative minds of the last 50 years. So get there early and get a good seat. I will. And be sure not to touch any monoliths on the way!