Anyone for Pufferfish Rights?

One of the commonly heard refrains about non-human primates is that since they are close to humans genetically, they should be granted rights. If that’s the case, then what about the poor pufferfish?

The pufferfish is largely known for its potential to kill those who eat it. The pufferfish contains a neurotoxin and, if not prepared properly, can quickly kill a human being who eats it (which, of course, makes it all that much more interesting for thrill seekers).

The pufferfish is also of great interest to medical researchers, however, who are busy trying to sequence its genome. What might surprise a lot of people is that the odd-looking pufferfish is genetically very similar to human beings, which is what makes it of such potential use in research.

“In terms of gene complement, we are least 90% similar — probably higher,” said Greg Elgar, who heads up the effort to sequence the pufferfish genome. “There are big differences in gene expression levels and alternate transcripts, but if you’re talking about diversity, number and types of proteins, then it’s pretty difficult to tell us apart.”

Last October, Elgar announced that one species of pufferfish, Fugu rubripes had been sequenced, and sequencing of another species, Tetraodon nigroviridis, is under way.

Aside from the similarity with the human genome, the other advantage of sequencing the pufferfish genome is that it is relatively small — only about one-tenth the size of the human genome. This is because it lacks the so-called “junk DNA” present in many species, including human beings. This makes it easier for researchers to determine the function of the DNA. According to Elgar,

We’re pretty good at spotting coding sequences, mostly through cDNAs and EST [expressed sequence tags] work, but we’re very poor at finding regulatory sequences, basically because no one knows what we’re looking for. These control sequences are often shared between Fugu and mammals, and because the rest of the ‘junk’ is not well conserved, as it often is when you compare mouse and man, they stand out and slap you if you know how to look.

Already, the pufferfish effort has led to important findings about the human genome. For example, one of the things of interest to researchers are evolutionarily conserved regions (ecores) — these are parts of the genetic makeup of animals that exist across species and are the result of a shared evolutionary past.

Because the pufferfish genome lacks much of the junk DNA that makes it difficult to spot ecores, researchers were able to use the pufferfish to identify 207 new ecores between humans and other species.

Source:

Pufferfish genomes probe human genes. Ricki Lewis, The Scientist, 16[6]:22, March 18, 2002.

Are Weblogs Just a Fad?

Glenn Reynolds points to this Boston Globe article that suggests weblogging might be just a fad. Maybe, but that might not be the tragedy the Globe writer Hiawatha Bray thinks it is. Here’s Bray has to say,

How long can that last? There are a number of rival blog companies to contend with. More troubling is the fact that three quarters of [Pyra’s Evan] Williams’ subscribers got bored and gave up. Blogs are far easier to maintain than traditional Web sites, but they still need more effort than most bloggers are willing to supply.

This suggests that blogging is an ephemeral fad, destined to burn itself out in a year or two.

This does not surprise me at all, but is it really any reason to consider the activity a fad? I’ve been an information and writing junkie since I was very young, and, for whatever reason, most people do not share in my particular obsession. Very few people are going to have the time or interest to post with the frequency that someone like Reynolds does.

But that’s not really necessary. According to Bray, 473,000 people have used Blogger alone to start weblogs (and that does not include, obviously, people using Manila, Conversant, SlashCode or any of other available tools). Bray thinks it is a problem that only 25 percent of those people still update their weblogs on a regular basis.

But lets do some number crunching. Suppose between all of the weblog tools available, there have been 600,000 weblogs started in the past few years. Now lets assume that by 2005 only 5 percent of those will still be updated regularly. That would leave 30,000 regularly updated weblogs.

In contrast, the U.S. Census Bureau reports that in 1999 there were barely over 10,000 newspapers in the United States. Of those only about 1,700 newspapers daily newspapers — the rest were either weekly or semiweekly.

In addition, there were almost 10,000 periodicals. Of those, only 648 were published weekly or semimonthly.

So even if only 5 percent of those people keep updating their weblogs regularly, there would still be a third more weblogs as there are newspapers and periodicals, and there would be far more frequently updated weblogs than newspaper and periodicals.

And, of course, that does not even take into account ongoing growth and creation of weblogs. The bottom line is that there are regularly updated weblogs on almost every topic imaginable and, moreover, for most topics there are far more weblogs than there is time to read them in a day.

Certainly many people will start and then abandon weblogs, just as many individuals and companies started and then abandoned various topical weblogs. But the tools are so cheap and the weblog idea so obvious, that weblogs are almost certainly here to stay.

Sources:

Pyra Labs at the forefront of Weblogging phenomenon. Hiawatha Bray, Boston Globe, March 25, 2002.

Communications and Information Technology (PDF) Statistical Abstract of the United States, U.S. Census Bureau, Table No. 931.

Is There A Longevity Gene? Sort Of

Back in February researchers with DeCode Genetics announced the discovery of what the media called a “Methuselah gene” — a gene that seems to confer on those born with it a relatively longer life span than the rest of us.

Those researchers compared a group of 1,200 long-lived people in Iceland with a group that lived the average age, and found that the 1,200 long-lived people had more family connections with each other than did the control group of average-lived people.

They hen began looking at those long-lived people and claim to have found “a simple, single gene” that predisposes those folks to living a very long time. “Somehow this gene is making a protein in the body that is helping people live to ripe old ages,” said DeCode CEO Karl Stefansson.

Well, that all depends on what they were looking for and what this gene, assuming their discovery holds up, actually does. There are, after all, two separate but closely related issues with aging. First, there are diseases and other problems that occur more frequently as we grow older (such as the risk of a heart attack), and, second, there are those age-related problems that occur even when we remain relatively healthy, such as the changes that occur in our skin, the decline in the quality of muscle tissue, etc.

Most likely, this gene governs the former sort of problems. There are a number of known genes and variants where people who end up with a gene variant end up having a much lower risk of certain diseases. Science is already aware of genes that cause people to have increased risk of developing diseases such as breast cancer, heart disease, etc. Finding and compensating for these genes will, of course, extend our lifespan. If I have a gene that makes it likely I will die of a heart attack before I am 50, and somebody figures out a way to neutralize that — either with a fancy cure or just an optimal diet — then they are extending my life span.

But figuring out how to reduce those other age-related problems is a much bigger problem. The bottom line there is that there was simply no evolutionary pressure for humans to live past 80 or 90 and so our bodies lack systems to preserve the integrity of our biological systems into advanced ages. Not that that cannot be overcome, but it is a lot harder than simply lowering the risk of heart attacks or cancer that our genes have conferred on us. After all, even if we avoid major diseases well into our 80s or 90s, the other aging problems eventually will catch up to us and cause our bodies to fail.

It is very unlikely that phenomenon is controlled by a single gene. Rather it is the complete absence of types of genes (i.e. those that would be responsible for long-term maintenance) across all of our body’s systems that guarantees we will succumb to death.

Source:

Discovery of ‘Methuselah gene’ unlocks secret of long life. Robin McKie, Observer, February 23, 2002.

Researchers Closing in on the Malaria Genome

Researchers are making good headway in a project began in 1996 to sequence Plasmodium falciparum, the deadliest strain of malaria.

Malcolm Gardner of The Institute of Genomic Research in Rockville, Maryland, told The Scientist, “I would say we have over 99% of the genome in the database.”

That last one percent may prove to be somewhat tricky, however. Five of malaria’s 14 chromosomes have been completely mapped, but there are some parts of the malaria genome which have proven extremely difficult to map. Part of the problem is that many of this strain’s genes do not have any similarity to genes in other organisms, and many of those genes are downright strange.

On the other hand, researcher Michael Ferdig told The Scientist that these oddities about malaria may help researchers better understand how the disease operates and, hopefully, give new ideas on how to counteract the disease. According to Ferdig,

The tantalizing bit is that we’ll discover the malarial parasite has a distinct way of operating, a distinct way of evolving. Common sense tells you that’s usually not the case, but these are the kinds of questions you can’t start to answer until you have the whole genome.

Excellent news for those parts of the world still afflicted by malaria.

Source:

Closing in on the malaria genome. Brendan A. Maher, The Scientist 16[6]:28, March 18, 2002.

Neil Bartlett Sentenced to Four Years in Jail

British animal rights activist Neil Bartlett was sentenced last Friday to four years in jail after he had earlier plead guilty to six counts of phoning in fake bomb hoaxes to Huntingdon Life Sciences, GlaxoSmithKline, Novartis, and other firms with connections to animal research.

In sentencing Bartlett, Judge Anthony Thorpe said,

Offences of this nature cause great concern to the public, particularly in the light of terrorist attacks all too common all over the world. The courts have a duty to protect the public particularly from acts tending to induce fear and panic.

Thorpe apparently did not buy the argument from Bartlett’s lawyer, Michelle Strange, that, “He did not realize how much disruption he caused. He had no idea of the number of people’s lives would be interrupted. He thought it was a matter between himself and the companies.”

Strange need not worry — her client will now have four years to contemplate just this matter.

Source:

Man jailed for London bomb hoaxes. Ananova, March 22, 2002.

Ingrid Newkirk Is a Liar and Bill Press Is an Idiot

Ingrid Newkirk appeared on CNN’s Crossfire last week, and she was in a neck-and-neck competition with cohost Bill Press to see who could make the most outlandish statement.

Newkirk outright lied about People for the Ethical Treatment of Animals’ tactics. Here’s a partial transcript of an exchange between Newkirk and cohost Tucker Carlson,

CARLSON: Actually, I don’t. I’ll save that for later. You call meat-eaters bullies. The rest of us are bullies. You say you’re pro- animal. It strikes me that you are anti-human. Let me give you an example and I want an explanation and I want an apology for this.

Last spring, I took my children to the circus here in Washington. I had my four-year-old son, very nice boy, in my arms walking up to go into the circus. And some monster from PETA leans forward and shoves in his face a photograph of a wounded elephant, and says, “This is what the circus is,” to my four-year-old son.

NEWKIRK: I doubt it very much.

CARLSON: I watched it. He was in my arms. And I want you to apologize for that.

NEWKIRK: If anyone did that, I absolutely apologize.

CARLSON: Well, good.

NEWKIRK: Because everything we do is based at adults. We’re asking adults be responsible. You were telling me about giving your children meat and milk. They’re going to be to grow up to be tubs of lard. They’re getting heart attacks.

This is an outright lie. PETA has had an open practice of targeting children with their message, including numerous demonstrations outside of schools. In fact, PETA has in the past sued schools that tried to limit their ability to protest.

Newkirk is apparently so used to habitually lying, she cannot even tell the truth about PETA’s own practices.

But Press managed to make a statement about animal rights so idiotic that it almost upstaged Newkirk’s lie. Explaining to Newkirk that he sympathizes with her cause, Press said,

Let me get to the American Meat-out. Okay? And what bothers me about it is that you connect animal rights to the American Meat-out.

I am an animal lover. I’ve received awards from animal rights groups for my commentaries on animal rights. I really believe in it. I wouldn’t go duck hunting. I wouldn’t go deer hunting. I’m against animal testing unless somebody tells me it’s absolutely necessary to save a life. I think I qualify as an animal rights person, but I eat steak and I’ll eat chicken.

He wouldn’t go duck hunting or deer hunting but he eats steak and chicken. Does Press think that chickens and cows just show up outside of supermarkets and volunteer for the opportunity to become sandwich meat and steak? What a maroon!

Source:

Is It Time to Investigate Investigator?; PETA Celebrates American Meat-Out Day. Crossfire, Transcript, March 21, 2002.