Category Archives: Science

The Long awaited paper on observing evolution in E. Coli

Some sixteen months ago, we here at The Big Upshot took note of an amazing 21 year study in which bacteria were grown in a high citrate environment to which they were poorly adapted. After some 40,000 generations, the bacteria actually invented a new phenotype, true evolution in action.

This was not mere adaptation, but real bona-fide generation of novel “designed” attributes. This is like an animal with a beak turning into an animal with teeth given sufficient time and incentive. It turns out that what might seem “irreducibly complex” is not actually all that irreducible. Richard Lenski’s lab carefully saved samples of the little creatures all along the way, like an artificial fossil record. So not only is the proof eating citrate in a petri dish, something its ancestors couldn’t do, but the precise genetic changes that got it there are all “on file,” so to speak.

I’ve been waiting with bated breath for the follow up study where they go through the lineage of the Strain that Evolved. And lo, it has arrived. I’m going to level with you all, this is really, really cool. Kudos to all of the authors. If anybody ever tries to sell some intelligent design (deity-sign?) to you, slap this on the table like it’s your enormous stick of science.

-Peter

Happy birthday to the iron lung – forgotten legacy of polio

Credit Wikimedia Commons Wired magazine has a piece this morning on the iron lung, the amazing machine that let polio stricken children breathe (instead of suffocating when their nerve-damage became severe enough to cause respiratory failure). What is hard for us to understand in this modern age is that this hellish contraption was an amazing success – being trapped in a metal cylinder was better than dying for lots of little kids. This is the real picture of polio: life in a tube. That’s why it irritates me when people go disparaging vaccines in general.

-Peter

Addendum: There’s a nice article over at the Huffington Post that covers some more details on the “debate” over vaccines that’s going on in the news. My favorite part:

There is a lot of fear-mongering about the dangers or effectiveness of vaccines, particularly swine flu vaccine. But if you look at the sources of this information, they come from less than credible sources.

That “less than credible source” is David Icke. Less than credible, indeed.

Vaccines post – ‘moral statistics’ case-in-point

 

Let’s say that you’re a doctor some day. Or a professor, for that matter. And someone (e.g. your patient, a party guest, or friend on facebook) starts talking about the Dangers of Immunization. You could respond with “The anti-vaccination people are misled, crazy or amoral…” but that will be highly counterproductive. I think I’ve got a better one. I must preface, however: this argument applies to life-threatening childhood endemic diseases like polio, not so much to optional flu shots and such, whose risks and efficacy are less well known.

Why a person might not want a vaccine: All medical treatments carry a certain measure of risk. Like crossing the street or taking a bus, everything is a risk at some level. The problem is causation. If you get hit by a bus, it’s not your fault. If you choose to get vaccinated and there are some side effects, then you feel like you’ve screwed yourself. And that is a terrible feeling.
But, look, we need to evaluate risk in a sane and rational way. Let’s say that the choice is between:
1. Doing nothing and taking a 1 in 100 risk of contracting a life-threatening disease

or

2. Take a concrete action which carries a complication risk of 1:1000.

Clearly, your odds are better with option 2. But a 1:100 chance of being screwed by external random events may feel preferable to a 1:1000 chance of screwing yourself. So why not just say “screw statistics, I’m going with my gut”? Because there’s more at work than a choice between possible regret and ‘leaving the matter to fate’. There’s a moral imperative at work.

Why we are morally obligated to get vaccinated: Now, if everyone but one selfish guy gets vaccinated, then he will still be safe (because there’s nobody from whom he can catch the disease) and he has no risk of side-effects. So he gets all the reward without any of the sacrifice. That makes him a freeloader. It’s profiting from others’ misfortune. It’s cheating.

How good people avoid seeing this moral issue: If we can avoid the statistics and just say “vaccines are poison” then the vaccine looks worse than the disease it was meant to prevent. The moral/statistics problem is solved. Some people have heard that there is mercury in vaccines. That happens to be partially true for some vaccines. Mercury is not healthy. Thus the logic progresses.

But is mercury really so toxic? There is potassium in lethal injections and there is chlorine in bleach. Is potassium bad? Chlorine? No. Very different chemistry, scenario, concentration, etc. can give rise to wholly different levels of toxicity. Some mercury compounds are pretty nasty. Others are pretty benign. But gram for gram, there was more mercury in one salmon than was in the whole first-year vaccine course for an infant. And that was prior to it being removed completely in the last few years from infant vaccines.

In some other vaccines, there is a small amount of a mercury compound called thiomersal (not metallic mercury or methyl-mercury which are relatively nasty kinds). No mercury compound is good for you, but a little mercury-based preservative turns out to be statistically better than the risk of a bad batch of vaccine. Vaccines are made of protein – they are like broth. They will rot. Rotten vaccine is useless. Useless vaccine leaves you vulnerable to the disease that is supposed to be prevented.

A slight risk of low level toxicity is better than risking polio. The odds are still in your favor if you get vaccinated. But since there is a known risk (mercury!) versus an unknown risk (nobody gets polio any more, right?) people will be misled into false beliefs about relative risks.

The point is: this all comes down to statistics. We have to weigh the relative risks of a terrible disease becoming endemic again versus the risks of mass-scale injections. We have to weigh the risks of a trace quantity of mercury versus the risks of inactive or contaminated medicine. There’s math involved. And to someone who sees the world in terms of “us” and “them” – who sees Nefarious Motivations in the hearts of his fellow men – this can all look like obfuscation. I wish it were as simple as “it either works or it doesn’t” but in actual real life, things work with some probability, and weighing those probabilities is never an easy job.

Strangely enough, sound moral reasoning requires statistical analysis. And that puts us all at a disadvantage when trying to Do the Right Thing. Try telling someone that on Facebook. Or, for that matter, good luck getting your patient’s HMO to cover your time explaining all of that to your patient.

-Peter

Correlation and causation: meditations on violence

XKCD looks at causation and correlation

XKCD looks at causation and correlation

With XKCD’s comic firmly in mind, I considered the news today. Constance Holden with the ScienceNOW Daily News over at Science Magazine drew my attention to an article linking violence to childhood sugar consumption. The telling quote is this:

Although lower education levels correlated with daily sweet-eating, the connection with violence remained significant even when the researchers controlled for factors such as family circumstances, parental attitudes, and IQ. “Try as I did, I couldn’t get rid of the sweets-violence connection,” says Morris.

So… it may be that highly sugared children (sugartots?) are made more violent by sugar… or it could be that violent people are drawn to sugar as children… the candy manufacturers may be drugging children to reduce their impulse control… or kids whose without parents failed to help them learn impulse control lack impulse control in adulthood… it’s all very complicated.

-Peter

Risk, statistics and ethics: the AIDS Vaccine

This idea of risk that we have been discussing on TBU for a while now has come up again. The results of a new HIV/AIDS vaccine study were released this week. The Thai trial has shown some promise. The incidence of HIV was 30% lower in the group vaccinated with RV 144 than the control group.

First: the basic bioethics question. Was it OK to give a lot of people a placebo which might let them think they were protected from HIV when they were not at all protected? (Answer: Yes) First-off, they were not told that they were getting an effective drug. They were told they were getting either a placebo or a probably ineffective, experimental vaccine. So the subjects knew beforehand that this shouldn’t be considered a real vaccine.

Second question: why not just give the vaccine to everyone in the study (16,000 people) and compare the effectiveness to the general population? The problem is that you would have a change in HIV incidence that was due to lots of factors. Behavior, knowledge, unknown risk factors (maybe people at higher risk had a greater desire to be in the study than the general population) all could affect the measured efficacy. How would you know which produced your result?

If the vaccine were 100% effective, then there would be no need for a placebo controlled trial. But nothing is 100% effective and – besides – how would you know before you tried?

Now, here’s the more difficult bioethics question: if you have a 30% effective vaccine, who should get it?

This is more tricky. You don’t want to encourage risky behavior (the ‘conservatives’ are always concerned about this). So there is a question to be answered by a careful psychology study: do people modify their behavior after receiving a drug that may or may not prevent a transmissible disease? It seems like they might, but scientists don’t make decisions on “might” if they can avoid it. We make decisions based on what is demonstrably consistent with experiment.

But then it becomes a quantitative statistics problem (more statistics!). It’s only worth vaccinating people if their behavior changes don’t outweigh the efficacy. And then it’s only worth vaccinating people who are at risk… but what if the higher risk people are more prone to behavior modifications? Is is possible to isolate a medium-risk category?

And in all of this, there are massive political problems, not the least of which are form the anti-vaccination people, which I will talk about next week. The vaccine is a real achievement, in any case. Lots of people thought it wouldn’t work. And it reminds us how complicated it gets when trying to do the right thing with imperfect tools.

-Peter