Tag Archives: Science

Bacteria ‘invent’ new enzyme in the lab under scientific supervision

The importance of this cannot be overstated. There are levels of understanding of evolutionary theory. In Chemistry, my chosen field, you learn the “basics” of chemistry about 5 times before you’re done with an undergraduate degree. Every time you re-learn it, you learn all of the problems with the old way you learned it and all of the ways the new way of understanding is better. It’s unrealistic to teach graduate chemistry to elementary school students – they need the context of a few benign simplifications in order to approach the deeper understanding. It’s the same way with evolution. I’m not an evolutionary biologist, but I understand that there are levels of subtlety and that the simple explanations are not the whole story.

One of the most hard-to-believe concepts is that biologcal ‘designs’ come from the vast sea of probability. How could randomness produce an invention? Doesn’t invention require intelligence? It all comes down to amplification. Looking for a fully formed functional enzyme in the sea of randomness would take forever (almost literally). But if you had a way to amplify every useful step along the way from any random junk all the way to something useful, then the whole thing can happen pretty fast.

How fast? About 30,000 generations. Scientists have put bacteria in an environment where it would be advantageous to invent an enzyme. The bacteria did it in 30,000 generations. That’s ‘macro-evolution’ on a pertri-dish. It’s a terrible blow to those who have touted the idea of ‘irreducible complexity,’ and people who consider evolution to be an unproven hypothesis.

Of course, they hold themselves to a different standard of truth, so there’s really no basis for rational argument. I’m not sure about it being a ‘miracle,’ but I will concede this: the wow factor is really high for the feat of making critters invent an enzyme on cue.

-Peter

myths, pseudoscience and the water powered car

I am perpetually amused by conspiracy theories and pseudoscience for several reasons. Most of it is good for a laugh. A tiny minority of it highlights some legitimate gap in scientific understanding. Also, I think it’s good mental exercise to try to understand a strange world view. Most institutions (scientific, religious) see a lot of danger in allowing yourself to sink into a false mode of thinking. But I take the view of Thomas Jefferson:

“We are not afraid to follow truth wherever it may lead, nor to tolerate any error so long as reason is left free to combat it.”

There was an interesting narrative in the popular understanding of science: “the myth of the oppressed underdog.”
The notion is that scientists are dogmatic and refuse to tolerate new ideas. The article above does a great job of discussing this narrative and why it is false in most cases, but I would like to highlight one argument: most of the alternative, new ideas postulated by “oppressed underdog” scientists contradict each other. The implication is that ‘establishment’ science is justified in ignoring at least the vast majority of alternative scientists. But just because a theory is disprovable on evidence doesn’t mean it is worthless. It can be an interesting exercise. It can be a teaching tool. But I suppose it may be dangerous for the gullible.

Here’s my favorite example. Take water and electricity. Split it into hydrogen and oxygen. Burn the hydrogen and oxygen. Make water and generate electricity! It’s like an infinite circle. But like Escher’s infinite waterfall, it only works in the imagination. Philip Ball did a great explanation of why this myth keeps popping up.

-Peter

myths, conspiracies and a little about the scary side of science

From the Berkeley Language Center – Speech Archive SA 0269: Huxley, Aldous. The Ultimate Revolution, March 20, 1962:

“We are in process of developing a whole series of techniques which will enable the controlling oligarchy… to get people actually to love their servitude… There seems to be a general movement in the direction of this kind of ultimate revolution, this method of control by which people can be made to enjoy a state of affairs which by any decent standard they ought not to enjoy.”

Aldous Huxley wrote Brave New World in 1932. Here are a few things in fairly recent news:

FDA Panel Backs Implant To Counter Depression – washingtonpost.com

CDC: Antidepressants most prescribed drugs in U.S. – CNN.com

Understanding individual human mobility patterns – Nature

I’m not a conspiracy theorist. I don’t think that people need to ‘conspire’. The memes of consumerism, quick fix, and the drive to power are going to have their effects irrespective of the existence of some shadowy cabal. But it’s hard not to see the parallels between Huxley’s Brave New World and the world we are all creating.

-Peter

a bad day for mice makes the future a little brighter for humans

I read an article in Nature news about about a cure for palsied mice. It brought to mind a little quote a while back that made me chuckle. A researcher was asked how she felt about how close science was to a cancer cure. She replied “If you’re a mouse with cancer… I have good news.”

Joking aside, it is a lot harder to do medical research on humans. I read the original paper that inspired the news bit and I was struck by this graph. There are 3 lines: mutant palsied mice, identical mice injected with a placebo and identical mice injected with human brain cells. The mutant mice lack a functional kind of cell that surrounds and protects the other brain cells. These glial progenitor cells become cells that produce myelin. Brains without proper myelin produce symptoms like Multiple Sclerosis. If a mouse accepts the new, human cells, the mouse recovers. So why not just skip the mice and cure people? I imagine there are a hundred good reasons, but take this graph as one example.

The fact is that that if you are a mouse with Multiple Sclerosis, I don’t have very good news. The red line is your best bet, and even there you don’t have a great chance of ending up ‘cured.’ This will take a bit of work before it’s time to try this out on people.

But it’s a good step, and that’s what it’s all about. I am really impressed with this kind of work. Look at the scale of the X axis on that graph: that’s a year of someone’s life devoted to taking care of a population of sick mice. I think this understated fact is the really amazing thing about science. It is not about a smart loner spending a few weeks in a laboratory and then fighting the ‘establishment’ for recognition. It’s about year-long endeavors that, in the end, produce one graph. That graph represents a small, hard-won step toward a loftier goal. I find it more noble to work so hard for a small, steady step than to blaze brilliantly onto the scene with claims of a scientific revolution. The fact is that most ‘scientific revolutions’ aren’t.

-Peter

Are our fates determined by our genes? I doubt it. It’s not that simple even for worms.

I have done some work with the C. Elegans model organism. They are fun little bugs, and the PETA doesn’t get all up-in-arms when you shoot their brain with a laser. Here are some fun C. Elegans Facts:

They are about 1 mm long at maturity
They are transparent
They have about 300 nerves
Their genome was sequenced in 1998
They can hunt down food on a plate
They have forms of memory and learning

Here are some things I have noticed: When illuminated with a blue laser, they panic and squirm all over the place. When you use a UV laser to blow up a portion of their outer cuitcle, they practically turn inside-out due to internal pressure. Some of the strains available through the WormBank have single nerve cells that express fluorescent protein, so that not only do their brains glow, but only the part you might be interested in glows.

Why are these critters cool? Well, despite being really small, they share a lot of biochemistry with humans. Their neurons function in the same way and the cellular processes that allow the worm to grow from an egg into a larva and from a larva into an adult are all analogous on a cellular level to changes in human development. But if you do an experiment on a worm, you can see what happens in a few days instead of months (rats) years (monkeys) or decades (humans). Also, there are some ethical constraints with humans that don’t apply to worms.

Here’s a new fact just released in Nature: they seem to have a sleep-like state. “Lethargus is a Caenorhabditis elegans sleep-like state” by Raizen et. al. “Conserved effects on sleep-like behaviour of homologous genes in C. elegans and Drosophila suggest a common genetic regulation of sleep-like states in arthropods and nematodes. Our results indicate that C. elegans is a suitable model system for the study of sleep regulation.”

They sleep, they eat, they learn (sort-of), they have lots of sex with themselves (they are hermaphrodites) and they make eggs. And they do it all in 3 days. And despite the fact that we know the fate of every cell in its body from birth to death – where it comes from, what it becomes and where it goes – we still don’t know how it manages most of its behavior.

I’d like to point out that this leaves very little hope for a reductionist perspective on psychology. We know every connection of every nerve in this worm’s body and the thing is still a mystery. I wrote a post recently about how foolish it is to make sweeping assertions about genetic differences. Just to reiterate the big upshot: even in the simplest case, our understanding of the causes-and-effects that make up psychology is limited. To think that a human being is perfectly predictable is… well… just plain dumb.

-Peter