Category Archives: Philosophy

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

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

the battle of the sexes: taking a look back at dating, roles and culture

I read an article the other day over at The Last Ditch. It concerns the notion that the sexes have different roles to play in the world. A lot of people would find it offensive, but not me: I’m not easy to offend. I think there are some nuggets of wisdom in there, and at the very least I can identify a talented rhetorician when I read one. In any case, the point he makes is this: the sexes are not identical and, to a degree, they are equipped for different tasks; that different equipment affects their economic roles. In these vague terms, it seems obvious. I hope it’s hard to argue with that framing.

The problem (and the place that people get offended) is that the people who ‘agree’ with the sentiment are agreeing for the wrong reasons, and the people who are offended are offended for the wrong reasons. Men who feel like victims of women will see this article as saying that women should have a role in society determined by their biology. Those who disagree will see another opresive man trying to determine womens’ future through control of the culture.

There are tendencies given to us by biology and culture, but neither determine us. There is plenty of evidence that Nature and Nurture both play important roles in the development of an adult human. Twins can have the same genes and very different personalities, even to the point of one having a terrible debilitating mental illness and another being spared. At the same time, identical twins separated at birth have been shown to lead remarkably similar lives in many cases.

What’s the answer? Are women determined by their two x-chromosomes to be homemakers? Of course not. Should they be required to be homemakers? Of course not. Is it shameful to consider the possibility that many women might be happier being homemakers than doing other things? I don’t see why. The big upshot is that one bias is as bad as the other. Being offended by a proposition that maybe families would be better off with a mother around is as foolish as asserting that women are irrational. Taking the position that the culture is wholly responsible for peoples’ lives is as foolish as assigning that responsibility to genes. All of these foolishnesses ignore personal choice. More on that next time.

-Peter

economic value in terms of pie: an analogy for communism, capitalism, prosperity and social justice

The best kind of science science serves to advance some aspect of human endeavor (e.g. health, understanding, wonder). It is a contribution. The same can be said for art, engineering, or commercial enterprise. Work done in this manner will create a world far better than one where there is a perfect cornucopia of material prosperity. In fact, a culture of service is more idealistic than a utopic vision of material prosperity. And I believe that it’s achievable, while state-sponsored universal material prosperity isn’t.

Why do I say this? It comes down to pie. Would you rather have a disproportionately small piece of a very large pie (and get more pie), or a equal share of a small pie (and get less pie)? I think, ultimately, a lot of people would rather take the lesser quantity of pie as long as it was ‘fair’.

That doesn’t make rational sense, but we are not rational creatures. We are spiteful, semi-domesticated primates. Monkeys will do the same thing: they will give up their own small treat to see a rival denied a large one.

The maximal economic condition would be capital highly concentrated in the hands of those who continually invest it in labor-saving technology. This is the ‘trickle down’ notion. The workers are paid the minimum viable amount, since they will fail to invest wisely any excess. This produces a huge surplus of economic goods, but the world is divided into two groups: those who can afford to have any/all of the goods that they want, and those who can afford just enough that they are motivated to work very hard for just a little bit more. This assumes, of course, that there is a good way to catch cheaters: people who end up with a large slice without making any pie at all.

Here’s the crux: under these idealized conditions, the most people get the most pie possible (that’s good) but the distribution is not fair (and that’s bad). Even the people who are working really hard for a disproportionately small piece get a lot more than they would if the pie were smaller, but they feel disenfranchised because they have relatively little. So what do you want: a fair slice, or a large pie?

That has been the central economic question of the 20th century: communism (fair slice) or capitalism (large pie)? Could there be a third alternative? I think there is. I think that it’s possible to see past the total numerical economic value and see more fundamental needs. I think we can work on those. And that can co-exist with either system. The big upshot is this: I see the world arguing over the big pie versus the fair slice but what I want to see is people wondering if maybe they would like a different sort of pie altogether.

-Peter

green politics, chemistry, utopia and simplistic economics: greenwashing

Green is fashionable now, and that is great. “Green chemistry” is becoming a buzz word, and that is great, too: “green is the new nano!” Nanotechnology, as we all know, is derived from the Greek root meaning “successful grant application.”

If you asked me 10 years ago, I would have told you all about the Future when we would do away with material scarcity and people would have “enough“. I was young and naive. There is enough right now. And I’m not a communist: I don’t think the solution is taking it away from those who have in order to give to those who have not. The solution is not try to make more stuff, but to try to live a happy life. The solution is not to satisfy more wants, but to want good things. The solution is not for the rich to have less, but for people to see each others’ needs instead of their own desires. A happy culture is one that values service over material prosperity.

Where does Green fit into this? It’s hubris to think that we can grab the world by the carbon and shake the prosperity out of it. “Better living through chemistry,” is only half of the issue. We can make more stuff (e.g. chemicals, beef, plastic, homes, anything), but it has to be directed by a culture of service or it is just that: stuff. For it to be wealth, it has to represent substantive connections between people. Green can be just more stuff, or it can start to recognize the interdependent nature of the scientific game we are all playing. Our research means better living not through chemistry, but through the contribution we make to a safer, cleaner world – a goal that is only definable in terms of our connectedness to it and to each other.

The big upshot is that green is good, but look out for “greenwashing.” Greenwashing is where an organization cashes in on the Public Relations benefits of going green without making changes that reflect the rhetoric. It’s the same with the term ‘organic.’ It’s fine, but be careful that it represents what you think it represents. As Mark Bittman tells us in his TED talk while chilean farmed salmon fed organic chicken bones flown on ice in a huge freight plane from south america to your doorstep may be technically organic, it doesn’t represent the ideals. It’s elitist and unsustainable and the green sticker doesn’t change that.

-Peter