The Stupiding

There is a case being prepared in the US to prevent the shiny new Large Hadron Collider (LHC) from being turned on. Built over the last 14 years at a cost of 8 billion dollars it is the world’s largest particle accelerator, with a circumference of 14 kilometers. Particle accelerators are used to study things that just don’t exist to be studied in nature. Everyone knows about “atoms” as the unit of matter. Atoms contain protons, neutrons and electrons and protons, the properties of which are well studied in chemistry. When one starts looking at the bits that make up these sub-atomic particles then things start getting weird. For a good primer into quantum weirdness and string theory, check out the Three part NOVA documentary The Elegant Universe which PBS has made available for free on their website.

My own understanding of particle physics is pretty limited. In fact, I don’t think particle physists actually understand particle physics, which I guess is the gist of this post. To study the building blocks of protons and neutrons etc, one has to smash them and see whats inside. Thats basically what these particle accelerators do. Stick atoms of something into an incredibly powerful electro-magnet and accelerate them to ridiculous speeds, fire them at a target and watch the (very small) fireworks. There is a pretty bewildering amount of stuff inside an atom. But the LHC was built to get even down to even more fundamental levels like the nature of gravity itself.

So what is this court case all about? Well, the larger the collider the more energy can be generated for the collisions. The LHC is so incredibly powerful, that there are some who are worried about what will happen when it is turned on this summer. The plaintiffs claim that there is a chance that the collider will generate a small black hole which could consume the earth.

Yup, you read that right.

No one thinks that a catastrophe like this is “likely” or “probable” but it is not a chance that the plaintiffs are willing to take. As scientists, we go off screwing with things that we don’t really understand and unfortunately there is just no certainty about the outcome. If you sat down with the people at CERN for a few drinks I’ll bet that you wouldn’t find many people over there who think that this could never never never never happen. In so far as any scientific theory must at least have the possibility to be proven wrong, the theory that “The LHC will not destroy the earth” must also be falsifiable. But, I wouldn’t be too worried about it.

The article points out another story that had people wondering if they were going to end the human race in a similarly spectacular fashion. During the building of the first atomic bomb it was Emil Konopinski’s job to determine the likelihood of the earth’s atmosphere being set on fire by a nuclear explosion (I guess the risk was acceptable). These kinds of dooms day scenarios aren’t limited to physics either. If you’ve seen I am Legend you’ll be entertained to know that people are actually studying the use of viruses to kill cancer cells. Hopefully, the human race will survive.

This is one of the oddest stories I’ve come across in a while.

I’ve heard of the term “Research Whaling” applied to the what the Japanese whaling fleet is doing, but never really though too much about it. The whales are eaten and “Research Whaling” is obviously just a pretense. I never thought that they’d actually go through with the research part on any level to keep up the charade.

But wait! Research is actually being done! Sort of… All sorts of strange things are afoot at the Institute of Cetacean Research Trying to fertilize cow eggs with whale sperm, attempting to make “Testube Whales.” This story reads like a Victorian monster novel. Think The Island of Dr. Moreau or Frankenstein.

I’m a meat eater, so I don’t have any particular moral problem with the eating of whales. However, I’m not overly fond of the misuse of “science” as a thin justification for distasteful things. But this is so delightfully odd, that I have a hard time staying mad a Japan…

I missed a wordpress update and ended up getting spammed up all to hell. Hopefully that has been solved. If you’re in the market for Cialis, Viagra, or MILF porn you’ll have to look elsewhere… (Sorry)

The somewhat cryptically named 23andMe.com has been launched today. This company, for a fee of $1000.00, will decode your genome for you.

This is actually quite an important event in human history, even though it might be over the heads of many of us. It opens the door to a kind of self-awareness that has never before existed. But, like any great advance, it can (and will) be abused. If you haven’t seen the movie Gattaca yet, now might be a good time to do so.

The technical bits of 23andMe’s science are quite interesting, if maybe a little bit dense. The site itself has nice little slide shows about basic genetics for those that need a refresher.

The basic concept here is the “single nuclotide polymorphism” or SNP (pronounced “snip”). The difference between your DNA and the DNA of the person beside you is very small (less than 0.5% sequence difference). Most of those differences are in the regions between genes and thus do not contribute to traits. The reason your eyes are brown and your neighbor’s eyes are green is due single changes in the sequence of some eye color gene. Likewise, whether your earlobes are attached and whether you can roll your tongue. These are all caused by differences in single genes. Those are all fairly trivial things, but the same variation between people is being studied to predict much more important things, such as predispositions to cancer.

Copies of a gene that differ in sequence are called alleles. For each gene there are normally only a handfull of different alleles that are common in the population. However with 25,000 genes or so, there is an awful lot of possible variation.

If we know all the SNPs that result in the different alleles of a gene then its really easy to figure out what allele a person has. If you scale this up to each allele of each of 25,000 genes then you would be able to find the particular allele a person has for every gene. This is the theoretical basis for what 23andMe is doing.

The Human Genome has now been decoded for quite some time and the genomes of more and more individuals have been added to sequence databases. If you find the sequence of the “tongue rolling” gene possessed by 10 people and line up the letters there will only be a few SNPs that represent all the variation in those people. If you scale this up look at the SNPs in all 25,000 genes for these 10 people you’ll have a catalog of variation which accounts for the vast majority of the differences in this group. If you increase the scale again and include the sequences of 1,000 or 10,000 people which are a representative cross section of the human population then you come close to a list that accounts for all human genetic variation. All this variation can probably be distilled down to a few million SNPs. This cataloging has been underway for quite sometime. The HapMap project website contains up to date info on the status so far. On October 17th 2007 HapMap published a paper summarizing the results of the second phase of their project and reported 3.1 million SNPs found.

Having this SNP data set has simplified things significantly. We don’t have to sequence a person’s entire 3 billion base pair genome or even all 25,000 genes. All we have to do is find out what SNPs they have. Thanks to advances in Microarray technology we can test for the presence of these SNPs a few hundred thousand at a time (ultimately all in one shot) and construct someone’s entire genotype. All for the low low price of $999.99 US. ($950.00 Cnd)

What will having this kind of information do for you? What kind of things can be done to you with this information? I’ll talk about this in a future post.

Pursuant to some comments below I started looking around for information on exactly how people are thinking of using algae as a source for bio-fuels.

Evidently there are some species that accumulate lipids up to 50% of their biomass under laboratory conditions, which got some people excited. The current state of things is that we’re a long way off from harnessing Algae to do anything useful.

Here is a very long review of the research that has been done in this area. Basically, there are a few people fiddling with algae without a lot of success.

It takes specific conditions to get the algae to accumulate lipids. They demand constant temperature, meaning that unless you are in an equatorial country you are going to be heating in the winter. Maintaining a mono-culture (single species) in fermenters of a size needed to make bio-diesel on an industrial scale would require enormous energy for sterilizing the growth media and equipment. If you use a broth rich enough to allow algae to grow at their maximal rate you can bet that any other micro-organism around will grow in it too, and faster. Algae has a theoretically higher yield per biodiesel per acre, than say soybean, but its not like you can just throw algae seeds into a pool of water and come back in a few months to harvest it.

Found another alternative algae application: using it to produce Hydrogen Gas which could then be collected and used for fuel. Apparently some species produce a small amount of H2 just through normal photosynthesis. If one could get these algae to divert 100% of their photosynthetic potential to making hydrogen gas one could apparently “80 kilograms of hydrogen could be produced commercially per acre.” Problem number one is that the algae needs this photosynthesis to make sugar for its own energy requirements and for division, so you’ve basically crippled them. Grow them in a non-sterile environment and the will be trounced handily anything that lands in their media. Second, expressing this hydrogen production in terms of “acres” suggesting that this is going to occur outdoors in huge pools. Even if this is done in an equatorial region with relatively constant temperature, and you could keep these pools from being taken over by the billions of fungus and bacteria in the environment, how are you going to collect the hydrogen? It is a gas… It will bubble into the atmosphere.

I wonder how much biodiesel I could extract from the algae in my aquarium…

Had a spammer hit the blog so I’ve changed it so you must register to post.  Login is under the heading of “Meta” in the right hand column.

Cheers

Corey

This article is a pretty long read, but its a good, sober assessment of the whole “Bio-Fuels” concept. Agricultural groups are pushing ethanol and bio-diesel hard as they see it as a great way to increase crop and make farming profitable again. Auto-makers are happy because it takes very little modification to make your Hummer run on ethanol.

Making alcohol from corn or other agricultural crop as a gasoline substitute amounts to burning food! I have no idea why people are so enamoured with bio-fuels. It has the whiff of innovation, and new technology, even though we’re basically talking about brewing and distilling here. It also fosters hope of breaking our dependence on fossil fuels in a pain free way (ie not having to give up our SUVs). However the reality is that making fuel from agricultural crops cannot be the solution. From the article:

Corn requires large doses of herbicide and nitrogen fertilizer and can cause more soil erosion than any other crop. And producing corn ethanol consumes just about as much fossil fuel as the ethanol itself replaces. Bio-diesel from soybeans fares only slightly better… …if we turned our entire corn and soybean crops into bio-fuels, they would replace just 12 percent of our gasoline and a paltry 6 percent of our diesel.

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Lisa, in this house we obey the laws of thermodynamics! -Homer Simpson

There is an “alternative energy” story floating around that the media is jumping all over. From the CBC:

A cancer researcher in Erie, Pa., has stumbled on a technique that could turn salt water into fuel, a novel invention that is being touted by one chemist as the “most remarkable” water science discovery in a century

Sounds pretty amazing right? The video demonstration looks pretty impressive too!

Its like the continents of the earth are all surrounded by an “ocean” of a gasoline substitute! Right?!? Alas, no…

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Its that time of year again, where we send our kids back to the filth encrusted cess-pools that are our public schools. Good Morning America has decided to show you just how scary it is out there with the old “swab things and grow nasty stuff on agar plates”

So, “Good Morning America” investigated playground cleanliness across the nation by collecting 60 samples at public playgrounds. The samples were tested to determine which playground was the cleanest and which had the most germs.

Of those samples, 59 had evidence of bacteria or mold that could make children sick tests showed

So what did they find? A whole collection of potentially nasty bugs. Things like Escherichia coli, Staphylococcus aureus, beta-hemolytic Streptococcus, Shigella, Salmonella. Ok, that sounds really nasty. But is it dangerous? Probably not. Children have been filthy little mongrels for pretty much all of human history Before the advent of alcohol hand sanitizers, hyper-vigilant parents, and fear mongering media outlets on slow news days, they were probably more so. Somehow, we as a species have survived, some would say even thrived.

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