02/07/2007
A Relative Sequenced
Greetings from sunny, warm Marco Island in Florida. Actually, everything is relative, isn’t it? When I started this column at around noon on Monday, the day after Super Bowl Sunday, the temperature outside was 59 degrees Fahrenheit and it was “breezy”. When the local TV weather people say “breezy”, the wind is howling outside and the wind chill factor definitely comes into play. As for the sun, there were three days during which sunshine was virtually nonexistent and in the week we’ve been here I’ve only managed three of my early morning walks on the beach.
However, one reason we like Marco Island is that it’s generally warmer and often escapes stormy weather north of here in Florida. This certainly was the case last week and we are especially grateful to have missed those deadly tornadoes up in Central Florida. On the day of the tornadoes our weather was indeed sunny and warm. It’s ironic that one of the places hit hard by the tornadoes was The Villages, a retirement community that advertises heavily on the New York TV stations we watch back in New Jersey.
Longtime readers know that I look forward to my early morning walks on Marco’s impressive beach. My first walk here this year was illuminated by a full moon but a cloudbank precluded my ideal of a moonset combined with a sunrise. This morning, after a 3-day weather-induced hiatus, I resumed my walking and was happy to see that three walkers I’ve traded greetings with over many years are back. Another fellow, a tall gaunt runner, has also returned but this fellow has never waved or said a word of greeting in at least ten years that we’ve passed each other.
So far, I’ve been surprised at the lack of any but the smallest shells on the beach. While I haven’t seen any interesting shells on the beach, as in most Marco condos, there are containers of shells collected by the owners. As I write this I’m looking at one such collection topped by the shells of two sea urchins, a segue into the subject I had planned since last November to write about when I came to Marco - the purple sea urchin.
I decided that the purple sea urchin would be a suitable subject here on Marco when I found a special section on it in the November 10, 2006 issue of Science. The section contained several papers on the urchin, a perspective, a news report and a colorful poster suitable for wall hanging. Why all the fuss about the sea urchin? It dates back to a day in December of 1997, when a male purple sea urchin gave up some of its sperm to an international group of over 200 researchers from 78 institutions in the U.S., Canada and Europe. The group, known as the Sea Urchin Genome Sequencing Consortium, took that sperm and sequenced the genome of the purple sea urchin. Thus the sea urchin joins the human, chimpanzee and other animals whose genomes have now been decoded or are being decoded.
What’s so interesting about the sea urchin? It was back in the 1870s that H. Fol and G. Hertwig took advantage of the fact that the sea urchin’s eggs are transparent. It was in a sea urchin egg that these researchers for the first time observed the fusion of the nucleus of a sperm with the nucleus of the egg. In 1902, Theodor Boveri showed that only if each cell in a sea urchin embryo had a full set of chromosomes would the embryo develop normally into a normal adult. Ever since those early days, scientists have used the transparent and easily manipulated sea urchin egg to study embryonic development and the effects of introducing different types of DNA into the egg.
Aside from the relatively easy access to the egg and its contents, the sea urchin has another important feature. It’s a deuterostome. I admit that, before reading the Science articles, I didn’t have the foggiest idea what a deuterostome is and was shocked to learn that you and I are deuterostomes! (I regret that I never took biology in college and my only significant memory of biology in high school is dissecting a frog.) To more or less complete the classification scheme, you and I are vertebrates, a subset of chordates, which in turn are a subset of deuterostomes. Another class of deuterostomes includes the echinoderms, which includes such critters as the starfish and the sea urchin. If you have trouble following this, the bottom line is that the sea urchin is related to us humans more closely than you might think.
If a sea urchin doesn’t get eaten or otherwise done in, its lifespan can be similar to our own. The purple sea urchin that donated its sperm may live about 30 years while another type of sea urchin can live a hundred years! Surprisingly, to me at least, the sea urchin is more closely related to you and me than it is to sea dwellers such as clams or crabs. The fruit fly, the subject of vast numbers of studies that have helped shed light on human maladies or characteristics, is not even a deuterostome. It’s a protostome, another major class of animal life that also includes the mollusks.
It was roughly 540 million years ago that we and the sea urchin last shared a common ancestor and the deuterostome group began to branch out into different forms of life. One of the fascinating things about the achievement of the sequencing of the sea urchin genome is that we can now compare the genes in the sea urchin with the genes in our human genome. This means we can see which genes have been preserved by both us and the sea urchin over these millions of years and we can see which genes are new or have been dropped by either human or urchin. One thing already is clear – we both have a similar numbers of genes. The purple sea urchin has roughly 23,300 genes while the last I heard the human gene count was also in the low 20 thousands.
One of the surprising things to emerge from the sea urchin genome studies concerns the fact that the sea urchin has no eyes, no nose, no antennae and doesn’t even have a centralized brain to handle visual or odor cues. Yet it has nearly a thousand genes that code for proteins that we vertebrates use to sense odors or light. You may recall that some time ago I wrote about a possible evolutionary route for forming an eye and I mentioned a protein called “opsin”. Opsin is a key molecule in sensing light. The researchers have found genes for opsin in the tips of the sea urchin’s tube feet and in tiny pincers below the spines. Urchins do respond to light. Are they “seeing” with their feet?
Perhaps equally surprising is the immune system of the sea urchin. Its immune system is amazingly wealthy in genes that are associated with various diseases in humans. Some of the genes found in the sea urchin are involved in humans in the production of antibodies to combat various pathogens. The sea urchin has these genes even though it doesn’t produce antibodies. The sea urchin genome also contains genes that help cells stick together. One such gene in humans helps in our mammalian brain development. Yet the sea urchin doesn’t have the brain! The implications are that we vertebrates have taken genes that existed long before we came along and have taken those genes and adapted them to our own uses. Evolution is real!
A report on the work by Elizabeth Pennisi in Science quotes immunologist Chris Amemiya as calling it “mind-boggling to think of all the many inferences one can make with the genome sequence [of the sea urchin] in hand.” If I find any urchins on the beach I’ll treat them with greater respect!
Allen F. Bortrum
|