John Tierney, pseudo-intellectual

This is in the New York Times science section:

Until I talked to Nick Bostrom, a philosopher at Oxford University, it never occurred to me that our universe might be somebody else’s hobby. I hadn’t imagined that the omniscient, omnipotent creator of the heavens and earth could be an advanced version of a guy who spends his weekends building model railroads or overseeing video-game worlds like the Sims.

But now it seems quite possible. In fact, if you accept a pretty reasonable assumption of Dr. Bostrom’s, it is almost a mathematical certainty that we are living in someone else’s computer simulation.

How is this novel? Is it different from being a brain in a vat? Or Descartes' Meditations on First Philosophy (circa 1641)? Or Zhuangzi's Butterfly (circa 4th century BCE)? And since when is philosophy a science? But we continue...

Dr. Bostrom doesn’t pretend to know which of these hypotheses is more likely, but he thinks none of them can be ruled out. “My gut feeling, and it’s nothing more than that,” he says, “is that there’s a 20 percent chance we’re living in a computer simulation.”

My gut feeling is that the odds are better than 20 percent, maybe better than even. I think it’s highly likely that civilization could endure to produce those supercomputers. And if owners of the computers were anything like the millions of people immersed in virtual worlds like Second Life, SimCity and World of Warcraft, they’d be running simulations just to get a chance to control history — or maybe give themselves virtual roles as Cleopatra or Napoleon.

Ahh... gut feelings. The basis of no science. Can we move this garbage to the fashion section?

If simulations stop once the simulated inhabitants understand what’s going on, then I really shouldn’t be spreading Dr. Bostrom’s ideas. But if you’re still around to read this, I guess the Prime Designer is reasonably tolerant, or maybe curious to see how we react once we start figuring out the situation.

Ahhh, the experimental test. God let me say it, therefore he's caring and understanding.

Then again, maybe the Prime Designer wouldn’t allow any of his or her creations to start simulating their own worlds. Once they got smart enough to do so, they’d presumably realize, by Dr. Bostrom’s logic, that they themselves were probably simulations. Would that ruin the fun for the Prime Designer?

Please, please, please. Just because something *can* happen, doesn't mean it *is* happening.

Make the stupid stop! It's hurting my brain!

Mark this day in 2007, the day that gene networks were discovered

There are at least two major ways that science articles in newspapers can fail.

The first is the "No, duh." coverage. That is, the article is presenting things that scientists have known for years if not decades, but presenting it like it's a major new discovery that will require major rethinking of how that area is studied. The second is the "the goblins will get you!" coverage, that is that if it weren't for the genius working at PETA, we wouldn't know that we're all going to die, when in fact the data say nothing of the sort.

Denise Caruso managed to hit a double this weekend in the New York Times entitled (stupidly): A Challenge to Gene Theory, a Tougher Look at Biotech. Let's start with her grandiose opening statement:

The $73.5 billion global biotech business may soon have to grapple with a discovery that calls into question the scientific principles on which it was founded.

Gee whiz! That sounds exciting! If only it were true...

Last month, a consortium of scientists published findings that challenge the traditional view of how genes function... (snip) ...To their surprise, researchers found that the human genome might not be a “tidy collection of independent genes” after all... (snip) ...Instead, genes appear to operate in a complex network, and interact and overlap with one another and with other components in ways not yet fully understood.

*gasp!* Really? They operate in networks? Sort of like this paper by Jacob and Monod suggested in 1961? The statement that "genes appear to operate in a complex network" is like saying that "the liver operates in a complex environment". Of course the liver works with other organ systems. This is not news. We've known about networks for a really long time, and with each year we're understanding more and more of these networks, and finding more and more spokes to them. In the last ten years, the study of networks has even become a discipline of its own, called systems biology. This is not new.

Biologists have recorded these network effects for many years in other organisms. But in the world of science, discoveries often do not become part of mainstream thought until they are linked to humans.

Or at least, in the world of newspapers. This has been mainstream for years.

Unfortunately, Francis Collins (director of the National Human Genome Research Institute) gave a misleading quote on their website, which is quoted in the New York Times article:

Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved.

While Ms. Caruso seems to think this means that he's discovered that gene networks exist, it seems more likely that he means that they have discovered particular networks that will make it easier to understand particular diseases. I admit, he's not being clear, and she bases the first half of her article off of this quote. (And I find it hard to believe that Francis Collins is stupid enough to think this study marks the discovery of gene networks).

So where does she take this credulous party off to next? Why not fearmongering?! (I've covered her scaremongering here in the past). Enter fearmonger Jack Heinemann, (director of the Center for Integrated Research in Biosafety):

“Because gene patents and the genetic engineering process itself are both defined in terms of genes acting independently,” he said, “regulators may be unaware of the potential impacts arising from these network effects.”

They're also unaware of the possible interactions between cheese and tomato sauce, and yet we don't test these in combination (and cheese is a living food product, after all!). This is yet another case of someone demanding that testing be done of every possible interaction between different genes and the food that they are placed in. Why? Knowing that your food has a complex network of genes that may be changed by the introduction of a foreign gene doesn't change the fact that the constituents of that food don't change.

Here's an analogy. If you remove someone's kidneys, you will find that they now require dialysis because they can no longer process out the urea from their blood. Without dialysis, they will eventually poison themselves and have multiple organ failure. However, you can say for sure that they will not grow wings and breathe fire, just because you messed up their organ homeostasis.

In the same way, adding foreign genes to plants, you can only get what you put in. You may increase the amount of protein, or decrease the amount of carbohydrate, or make the plant grow slower, but you won't get a corn plant with wings that is poisonous to humans merely by inserting the BT-gene. You can only get what you put in.

From Denise Caruso:

Now that the consortium’s findings (that there are gene networks) have cast the validity of (the gene) theory into question, it may be time for the biotech industry to re-examine the more subtle effects of its products, and to share what it knows about them with regulators and other scientists.

Oy. This just makes me cringe. Please, Ms. Caruso. Please. The stupid. It burns...

Friday beautiful science

Today's Friday beautiful science focuses on the work of Felice Frankel. She's a photographer at MIT who works with scientists to take cool photos of their work. The photo above was taken of a ferromagnetic fluid on a glass slide with seven magnets underneath. There are several other of her photos displayed in a recent New York Times profile of her. She has one book of photos (On the Surface of Things) that's out of print, and another (Envisioning Science: The Design and Craft of the Science Image) that is intended for photographers.

If anyone can point me towards a source for her prints, I would appreciate it.

Cost benefit analysis of a vaccine (Gardasil)

Kudos to the New York Times (again). They publish a simple, fantastic piece about the risks and benefits of the new Gardasil vaccine against HPV. The risks?

They may include pain, swelling, itching and redness at the injection site, as well as fever, nausea and dizziness.

Well, this sounds like what you might expect from any vaccine. The pain, swelling at the injection site are basically signs that your immune system is working. And the fever as well. Nausea and dizziness are pretty common side effects of any injection. And:

Another concern involves long-term safety. How do we know this vaccine will not eventually cause other problems like autoimmune or neurological disorders or lose its protective powers or foster the dominance of other HPV variants?

Actually, we don’t. But we do have at least five years of safety data that include no hints of long-term risks or waning effectiveness. But if the vaccine should begin to lose potency over time, that could easily be remedied by a booster shot.

Honest, informative. Some people may not feel comfortable with the idea that we don't know the effects of the vaccine in the long term. But any new vaccine, you won't know what the long term effects are for 20 years (until you've been using it for a long term). And so far, there are very few vaccines that have had any serious long term effects.

Hmmm... So should you have give your daughter the vaccine? What can she get from it? Well, it prevents infection with the subtypes of HPV that cause up to 70% of cervical cancer. And, in a 3 year followup, it prevents pre-cancerous lesions in nearly 100% of vaccinees who got the vaccine prior to exposure to HPV. It even provides some protection to women who have previously been exposed to the virus. Up to 17% protection from pre-cancerous lesions for women who had already been exposed.

This is why it's so important to give this vaccine to children, before they are exposed to HPV through sex. Once they're old enough to choose the vaccine for themselves, it's likely already too late to get much benefit from it.

Granted, we can't say whether or not it prevents cancer. It takes twenty to thirty years for cancer to show up in women who have been exposed to HPV, and this vaccine has only been in production for a few years. But it prevents HPV infection of the most prominent subtypes, it prevents precancerous lesions... it's not a stretch to suggest it will almost certainly prevent cancer. And that sounds pretty good to me.

There are no known risks of Gardasil (though to be fair, there is a small chance that longer term studies will find some). There are some very clear benefits to getting the vaccine. So when you're making up your mind for your child - make the calculation - prevent HPV vs. no known risks. It seems pretty clear to me.

Bees in the New York Times - an addendum

I'm really pretty excited about the story that appeared in the New York Times today about Colony Collapse Disorder (CCD). I already posted about it once today, but I thought I'd post again about what a good job of presenting science this article does. First off, they could have said that "scientists have decided that CCD is caused by a microbe", but instead, they demonstrated the experiment that shows us that, which is much more powerful:

Mr. Hackenberg, the beekeeper, agreed to take his empty bee boxes and other equipment to Food Technology Service, a company in Mulberry, Fla., that uses gamma rays to kill bacteria on medical equipment and some fruits. In early results, the irradiated bee boxes seem to have shown a return to health for colonies repopulated with Australian bees.

“This supports the idea that there is a pathogen there,” Dr. Cox-Foster said. “It would be hard to explain the irradiation getting rid of a chemical.”

Nice experiment. Thanks for showing us. Secondly, they actually give us reasonable data, instead of sensational data. Compare for example how Spiegel showed us how many bees have been affected:

In isolated cases, says Hederer, declines of up to 80 percent have been reported. He speculates that "a particular toxin, some agent with which we are not familiar," is killing the bees.

Well, sensational, but not quite useful. How many bees have actually been affected? Could be 80% of bees in the U.S., or could be one farmer lost 80% and most lost none. This is sensational, not useful. Now notice how the New York Times presents the same data:

More than a quarter of the country’s 2.4 million bee colonies have been lost — tens of billions of bees, according to an estimate from the Apiary Inspectors of America, a national group that tracks beekeeping.

Thank you. That means something, and we've actually been told how many bees are affected, rather than taking the highest number presented, it's showing what is occurring (and showing that the numbers are quite large) without sensationalizing it. We need more reasonable reporting on science. I look forward to finding more articles by Alexei Barrionuevo. I hope they're all this good.

Colony Collapse Disorder - bees on the run

I've written several posts about Colony Collapse Disorder. This is a die-off affecting commercial bees. Bees seem to be dieing and outside their hives and not being repopulated. The unique feature of this is the failure to repopulate the hive (often when bees die, the hive will get hijacked by a nearby colony). In this case, the hives are generally left empty.

This is a major problem for farmers of various fruit crops, who rely on these commercial bees for pollination. Indeed, owners of bee hives will truck their hives all around the country to rent them out to farmers. However, over a quarter of the commercial bees in America have died over the last year, and large numbers of bees have died in other countries as well. If you've been reading about this in the news, then you've heard a few of the crazier ideas.

Finally, a voice of reason has spoken. The New York Times published a credible story today:

As with any great mystery, a number of theories have been posed, and many seem to researchers to be more science fiction than science. People have blamed genetically modified crops, cellular phone towers and high-voltage transmission lines for the disappearances. Or was it a secret plot by Russia or Osama bin Laden to bring down American agriculture? Or, as some blogs have asserted, the rapture of the bees, in which God recalled them to heaven? Researchers have heard it all.

Rapture. I hadn't heard that one. But unlike Spiegel the New York Times actually asks some entomologists who are studying Colony Collapse Disorder what they think (what a crazy idea!). And what do they find?

Mr. Hackenberg, the beekeeper, agreed to take his empty bee boxes and other equipment to Food Technology Service, a company in Mulberry, Fla., that uses gamma rays to kill bacteria on medical equipment and some fruits. In early results, the irradiated bee boxes seem to have shown a return to health for colonies repopulated with Australian bees.

“This supports the idea that there is a pathogen there,” Dr. Cox-Foster said. “It would be hard to explain the irradiation getting rid of a chemical.”

Indeed. So it looks like we need to find what pathogen is causing this bee die-off.

Genetic testing at Columbia University has revealed the presence of multiple micro-organisms in bees from hives or colonies that are in decline, suggesting that something is weakening their immune system. The researchers have found some fungi in the affected bees that are found in humans whose immune systems have been suppressed by the Acquired Immune Deficiency Syndrome or cancer.

“That is extremely unusual,” Dr. Cox-Foster said.

Great. So there's also an immune system component, and may be a chemical (or chemicals) that are altering the immune system:

Among the pesticides being tested in the American bee investigation, the neonicotinoids group “is the number-one suspect,” Dr. Mullin said. He hoped results of the toxicology screening will be ready within a month.

Stay tuned.

Insulin in your vegetable oil?

Hot on the heels of the splendidly stupid Spiegel article on BT-corn and bees, comes this new article from the New York Times about genetically modified plants. The author manages to inject a few fairly sensible points before descending into anti-intellectual fear mongering.

The article raises issues that I have commented about elsewhere: that there are real concerns to be debated in the use of genetically modified food (though largely, these issues have been ignored in the popular press - major news organizations prefer the tidier, if uninformed Monsanto vs. Greenpeace debate). I've written a bit of a primer here, for anyone who wants to brush up on what genetically modified food is (in more descriptive terms than "Frankenfoods" that groups like Greenpeace employ).

One of my concerns in the use of genetically modified foods is in the production of pharmaceuticals. Many companies have decided that putting genes into plants is cheaper and easier than growing vats of bacteria under sterile conditions. You may not realize this, but since the 1980s most human insulin that is produced in the pharmaceutical industry is produced in genetically engineered Escherichia coli that contains the human insulin gene. It's cheaper to produce (and more humane) than chopping up pigs, and it's actual human insulin instead of pig insulin (pig insulin is similar, but has slightly different properties).

Now, various companies have decided that it's even easier to produce insulin (and other similar pharmaceuticals) in plants. That way, rather than having to employ microbiologists, and maintain expensive sterile manufacturing plants, they can merely sell seed to farmers, and buy back the genetically modified plants (and purify the insulin from the plant). Sound great? Well, yes. Mostly. It should make many drugs a lot cheaper and safer than they currently are. Who doesn't want cheaper, safer drugs? Farmers will work for less than microbiologists, which cuts costs. And plants have none of the nasty things that you have to worry about in bacteria (for example, the fever inducing LPS molecule). So purification is simpler. Wonderful. But what about contamination of neighbouring crops? What happens when your biopharmaceutical gets mixed in with the regular food supply. This is (and should be) a major concern. Granted, insulin is probably not one to worry too much about, but what about blood thinners and painkillers? Clearly, we need to ensure that these plants don't find their way into the food supply. How to do this? From the New York Times article:

“I don’t think that engineering plants for pharma is a bad idea, with two caveats,” Professor Ellstrand said. One, he says he thinks that planting should be done in greenhouses rather than in open fields. “The other issue is food,” he said. “Why do we have to do this in food crops? It doesn’t matter what you’re squeezing the compound out of. It could be a carnation, a corn plant or a castor bean.”

I concur. In the case of pharmaceuticals where we know that the active molecule will be bioavailable, let's keep this stuff out of general circulation, because accidents do happen. No one would worry about genetically engineered poplar trees getting into the food supply.

The article continues:

Once the rogue seeds are replanted, could the plants thrive in their new home and possibly overtake native varieties or wild relatives? Could the pharma trait increase in frequency and concentration, until it reaches a “dose” that causes health effects in those who consume it unwittingly? The probability for any one of these situations may be low, Professor Ellstrand said, but the scientific answer to each question is yes.

Well, the probability that umbrellas cause cancer is low, but is it possible? Scientifically, yes. But let's make our decisions based on rational cost/benefit analysis, not merely on what is "possible".

Now the article-writer starts to get a little ridiculous:

But there is some scientific evidence not acknowledged in biopharma risk assessments that casts a dark cloud over this silver lining. For starters, the “system” under discussion is nature, and despite our best efforts it always manages to elude our puny attempts at controlling it.

What does that mean? This evokes a "Jurassic Park"-like scenario, of hybrid canola-Tyrannosaurus rex terrorizing the countryside. We have actually done a lot to manage nature. Have you ever seen anything that looks like a cow in nature? How about a wheat plant? These have been highly managed, and yet very few have escaped and "contaminated" the wild. Reason being, our modifications don't make positive fitness changes to the plant. They make them more commercially valuable, but much less viable in the wild.

And:

Scientists often dismiss the idea that people without technical knowledge can help them make risk assessments. As a result, biotech scientists and regulators have long made safety determinations from within an opaque system of their own design, using only the evidence they accept as valid.

Should we be having plumbers determining health risk of heart drugs? And using data about global-warming that science fiction authors think are valid? What about genetically-modified foods? I think what we want as a society is a well-educated, independent regulatory organization, like the FDA, not a group of parents at a PTA meeting.

But scientific evidence is not a constant, like the speed of light or pi. Especially in biology, where we still know so little, “evidence” is often just a small circle of light surrounded by the darkness of the unknown. Decisions about risk cannot safely be made in a private club that accepts only its members’ notions of scientific evidence.

Oy. What an anti-intellectual load of crap. Yes, decisions about risk can be made by people who accept scientific evidence as valid. The author is basically saying that everyone's opinion on safety matters. This is simply not true. I have no idea how airplanes are built. I should clearly get a voice in saying that I would like the airplanes I travel on to be safe, but I shouldn't be the person deciding which particular rivets should be used in an aircraft (or deciding that any particular airplane is safe - I'm simply not qualified). A safety determination is going to be best made by someone with the education to make it. We just need to ensure that the folks making said decisions are sufficiently independent from the businesses applying for permits to grow this stuff.

(edited for clarity - I wrote this rather late last night)