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Ubuntu and my computer’s brain transplant

I have a Sharp MP30, which I love. It’s a dual boot system, Fedora Core 3 (a Linux operating system) and WinXP. The OS I use 99% of the time is (or I should say, was) Fedora.

The Sharp is getting old now, over two, which is about 80 in computer years. It also has ATI graphics which does not play at all well with Linux. Meanwhile Fedora Core 3 was new-ish when I got the laptop, and so old by now that it is officially not supported. A three year old OS, and it’s considered such a fossil by the open sourcerers that it’s consigned to museum status.

(I can’t resist pointing out that Microsoft worked on Vista for five damn years. And even with that long a gestation, most reviewers are saying it was released before it was ready and with way too many bugs. Bunch of volunteers: 1. Monopoly: 0.)

Okay, so I’ve been casting around for an updated OS for about a year now. But every LiveCD I tried refused to boot right when it had to start interacting with the graphics. I tried CentOS, every variety of Ubuntu, every variety of Fedora (they’re up to 7 by now), and so on. I have enough CDs to decorate a large Christmas tree.

I heard about something called an installfest. Linux users groups get together to help ordinary schmoes install the OS. You bring the computer, they help you over the rough spots.
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Biofuels: good, bad, and ugly

We’re hearing more and more about biofuels because they’re an alternative fuel (i.e. “good”), because they don’t increase carbon dioxide in the air (“good”), because they can be produced any time any where (“good”), they can be used in current cars (best of all), and are generally the solution to a zillion looming problems.

If it sounds too good to be true, that’s because it is.

The first problem with biofuels is figuring out what people are talking about. Ethanol from corn? Crop waste used in power plant cogeneration? Methane gas from landfills? Or composting toilets? Alcohol from cellulose? Fryer oil biodiesel?

The second problem is that “bio” doesn’t equal “good,” no matter how green it sounds. Some of these technologies are shaping up to be worse than our current oil-based one. The worst problems are at the production end, not during consumption, which makes it much easier to bamboozle rich-country consumers into thinking they’re helping the planet. We need to be aware of what different biofuels really mean before rushing into alternative energy “solutions” that are anything but.
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Meet the relatives: Sea Squirts

These are astonishingly beautiful animals sometimes confused with jellyfish. They’re not. They are actually our cousins. (Admittedly, jellyfish are also beautiful, and if you go far enough back, they’re also our cousins, but work with me here, okay?)

Since sea squirts are related to us, that means they’re useful as well as beautiful. Useful in medical research, that is. Pictures and fun facts below the fold.

    tunicate, with resident goby

    tunicate, with resident goby
    photo: Chika

    tunicate, didemnium molle

    Tunicate
    Didemnium molle,
    beautiful, but not quite the same movie star quality.
    photo: Boogies with Fish

To be exact, only the immature stages have the famous rudimentary “backbone,” the notochord, that makes these things so interesting to us vertebrates. The adults, as happens so often, just sit on their duffs and eat crap.

What this means is that vertebrates evolved after a mutation in tunicates allowed the mutants to stay juvenile their whole lives. In other words, they could reproduce even though in other ways they were still “kids.” That’s a fascinating and recurring theme in evolution. Humans are another example, since we’re basically baby apes.

< tangent>
I’m rather taken with the philosophical implications of all this. I mean, compare the following:

trilobite

trilobite         photo: Kevin Brett
armored

tunicate larva, ciona, showing notochord
squishy,
barely visible to the naked eye
western lowland gorilla

photo: Wikipedia

chimp baby

photo: Tim Ellis

To me it suggests that “the meek shall inherit the Earth” is not wishful thinking. It’s just a statement of fact. Maybe we don’t have a very good understanding of what strength really is.
< end tangent>

Anyway. Onward and upward. Medicine. I wasn’t joking when I said the adults sit there and eat crap. They’re filter feeders, like oysters, and are often found in muddy, bacteria-laden waters.

About 80% of their genes are also found in humans and other vertebrates, but the total amount of DNA they have per cell is only about half that of vertebrates. They’re missing a lot of genes that we have, and some of them are the more advanced immune system genes. So you have a mystery. Somehow, a creature with very few immune system tools is staying healthy under conditions that would kill us, even though we’re quite similar (all appearances to the contrary notwithstanding).

Scientists started looking and found all sorts of interesting things. As you might expect from something that eats dirt, tunicates produce weird antibiotics. They’re not only new, but they have a different mode of action, which means that currently resistant bacteria are not resistant to the tunicate antibiotics at all. Unfortunately, some of these compounds are just as good at blowing up red blood cells as bacteria, so they need more work. But because of the way they’re formed (see pdf if you want a bit more of the science), genetic engineering is likely to be able to modify them to keep the good and toss the bad.

Anti-virals, immune suppressants, and anti-cancer compounds have also been found (e.g. Wikipedia, but, like the antibiotics, they’re too effective. They need work to make them less toxic to normal cells. (This isn’t unusual with cancer drugs. The Vinca alkaloids, which ultimately stopped childhood leukemia from being a death sentence, started out the same way.)

And then there’s the fascinating field of regenerative medicine, something which didn’t exist ten years ago. This includes things like re-growing spinal cords or limbs, and growing replacement organs like livers, hearts, skin, or eyes. Because tunicates are rather simplified versions of us, it’s easier to study processes of cell growth and regulation. The result is that a team of Stanford scientists published a paper (abstract just this past May describing how they made an abnormally growing colonial tunicate grow normally again over a period of time. A tumor is nothing but an abnormally growing set of cells, so people are agog about this work. Now that they’ve found this pathway, they can study it in detail and find out exactly how the cells regulate themselves back to normality. Then they can try to modify that so it works in humans. It’ll take a few years….

So next time you happen to be snorkelling or scuba diving in a mangrove swamp, peer through the muddy water until you see bright geometric jewels loom up in front of your face and think about the cloud of invisible possibilities they represent.

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There is hope for the human race

Any species that is capable of this there’s hope for.

From the report (update: link invalid, but Seattle Times has the same report) (via Cartalk):

Last weekend, Kent Couch settled down in his lawn chair with some snacks — and a parachute. Attached to his lawn chair were 105 large helium balloons.

Destination: Idaho.

With instruments to measure his altitude and speed, a global positioning system device in his pocket, and about four plastic bags holding five gallons of water each to act as ballast — he could turn a spigot, release water and rise — Couch headed into the Oregon sky.

Nearly nine hours later, the 47-year-old gas station owner came back to earth in a farmer’s field near Union, short of Idaho but about 193 miles from home.

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Female Genital Mutilation

It’s gone by other names, primarily female circumscision, as if it was nothing more than the male equivalent of removing the foreskin. It’s supposedly another one of those awful things that “can’t happen here.” Read the CNN report about the British, who may finally get serious about stopping the practice, and you’d never guess that tens of thousands of children suffer through the mutilation and its lifelong consequences right here in the good old U. S. of A.

Why the bizarre silence? Because it’s a “cultural issue,” you know. The approved term is now female genital cutting. Some people felt that the term “mutilation” was culturally insensitive.

For those occasions when somebody starts suggesting that this is a “cultural” matter, consider the facts.

First, an anatomy lesson, developmental anatomy, to be precise. The tissues in males and females come from the same embryonic structures. They just follow a different path of development. The biologists’ term for that is homologous structures. The types of nerves and arousal present in the different male and female structures are much the same, with some differences I’ll note below.
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Gene Scans and Single Payer Health Insurance

At first glance, an avantgarde diagnostic technique might seem to have little in common with a beancounter topic like insurance. The first glance couldn’t be more wrong.

Gene scanning means you’ll soon be able to find out just how susceptible you are to a whole series of diseases. And so will other people.
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Global warming: links to rebut deniers

With the Live Earth concerts rolling and the wingnuts whining in the woodwork, I thought it might be useful to give the Shakers one of the best links I’ve seen for the facts about global warming. Just in case you find yourself contending with wingnut talking points. (The acronym being WTP, interestingly enough.) The New Scientist (May, 2007) had an excellent and complete rebuttal of WTPs: Climate Change: A Guide for the Perplexed. They cover everything.

From what I’ve seen without looking for it, the wingnuts seem to have moved away from the “hockey stick graph is false” bullshit. I guess because the new facts, with that nasty liberal bias they have, insisted on landing higher and higher up the curve until they got into the handle and then blew right off the top of the graph. (I’m exaggerating, but not by much.)

Now one favorite line is, “The glaciers are too NOT melting. Or if they are, only a bit. Or if it’s a lot, then it has nothing to do with global warming.” … Read more »

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They Get No Medals

The fighters who do most of the dying in war don’t get special graves. Those most wounded don’t get special hospitals. They don’t get invited to the White House, or to any other Big House. They don’t get armor. They don’t get guns. They get to walk through the soldiers who have all that without anything except courage so huge, we can’t even see it.

Look at this graph from the BBC, and see if anything strikes you about it.

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Tuberculosis: the problem we could have avoided

People went on red alert about SARS, where the fatality rate was approximately 10%. Bird flu doesn’t even spread between people (yet), but we’re on red alert about bird flu. Don’t get me wrong. Prevention is way better than cure. But it would make sense to deal with actual current threats before panicking about possible ones.

Tuberculosis is a much bigger problem than SARS, and it’s here, now, and killing millions. Untreated TB has a fatality rate of around 55%. TB treatment in the days before drugs reduced that rate to around 30%. In developed countries, with anti-TB drugs, the fatality rate was around 7%. (TB stats from the CDC.) Most of the current fatalities worldwide are people who had ordinary TB and couldn’t afford the cure. From a callous perspective, that’s not a problem in developed countries. But the drug-resistant strains that evolve in people who can’t or don’t take the full course of treatment is everybody’s problem.

As if that wasn’t bad enough, drug-resistant TB just took a turn for the worse.

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It’s not about Muslims

I am not an admirer of Gordon Brown, the new UK Prime Minister, but I’m starting to think better of him. He’s banned ministers in his Cabinet from using the word “Muslim” in connection with the terrorism crisis. (report)

And the new Home Secretary, Jacqui Smith, has said, “[T]errorists are criminals, whose victims come from all walks of life, communities and religions. Terrorists attack the values shared by all law-abiding citizens.”

The cry immediately went up that this was political correctness run amok, that mollycoddling the sensitivities of any given community was pathetic, that “I don’t think we need pussyfoot around when talking about terrorism.”

I swear, some of these people manage to win a seat in government, but couldn’t fight their way out of a paper bag.

You dignify terrorists by calling them Muslims. It gives them a cloak of cosmic truth that they could never get on their own.

The fact that there are violent elements in the tenets of Islam doesn’t make that any less true. There are violent tenets in the Old Testament. That doesn’t mean every Planned Parenthood clinic bombing should be called a Christian act.

It dignifies the criminals to associate them with religions. Religion is something good in the minds of millions. By letting the terrorists wrap themselves in it, millions of people start thinking the terrorists mean well.

That is why you stop parroting the criminals’ excuses for their crimes.

Sure, it’s more respectful of the religion, and of the community, and of the real human beings in that community. It’s also a whole lot less respectful of the criminals.

Technorati tags: terrorism, Muslim, Gordon Brown, politics, current events

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