Lord, can I has thinking skills?

D. Scarlatti (of Illusory Tenant) at the Freethought Forum, commenting on the anti-evolution arguments put forward by cdesign proponentsist "Dr" Geoffrey Simmonds (of the cdesignist Discovery Institute), in a radio debate with real biologist PZ Myers:

Simmons' publisher: "Committed to providing high-quality books that affirm Biblical values and proclaim Jesus Christ as the answer to every human need." If Simmons ever needed Jesus, it was from 3-4 p.m. today.

Snicker.

Among Simmons' gems:

"[the fossil record] is even more incomplete than it was 200 years ago"

"Perhaps they [neurons, during the development of an infant brain] are pruned by design"

Apparently Simmons (who from the sound of it has written an entire book detailing his misconceptions about and ignorance of evolutionary biology) has a problem with neuroscience, too.

In outlining the ideas he objects to, Simmons' repeatedly says "the scientists say...", apparently acknowledging that

1. he is not one and

2. there is a near-universal scientific consensus that evolutionary theory is the only game in town

...then asks why we are not exposing our children to other [unscientific] views in educational environments.

Perhaps he feels they should be exposed to Gene Ray's Time Cube Theory in science classes?

Snort.

The entire cringe-inducing debate can be heard here.

Its alive! Alive! Well, almost.

Warning: a longish, unfocused post about the linked news because I was excited by this and just felt like brain dumping.

Craig Venter, who led the team that published the first complete genome of an individual human, is in the news again. A team led by Venter has constructed a complete genome from scratch (more at The Guardian) .

The genome is based on the bacterium Mycoplasma genitalium but has been built entirely from scratch rather than simply being a modified genome from an existing organism. The artificial genome has a third less genetic material than that of Mycoplasma genitalium, copying only the bare essentials required for it to function in a living cell.

Its not quite artificial life yet. For that, Venter and his team must replace the DNA of an existing cell with the artificial DNA, at which point, if all goes well, the artificial DNA will take control of the cell. They plan to do this over the next few months.

The team has named the anticipated organism Mycoplasma laboratorium.

Positive Applications

The reason I'm blogging about this is that there are obviously an enormous number of potential applications. Living organisms are self-manufacturing and have the kind of intricate machinery that takes enormous effort to emulate using non-organic materials and methods. The buzz around nanotechnology has always been predicated on the obvious benefits of having millions of tiny machines working in concert that we see in organisms.

The manufacturing applications of piggybacking custom functionality on a self-replicating molecule like DNA are numerous. In terms of the opportunities the technology affords its akin to the harnessing of electricity, which we use to power so many processes.

Among the uses being suggested by Venter is the production of biofuels. Current techniques for extracting biofuels from crops are costly in terms of the arable land required to produce useful amounts of fuel and threaten our food security. But pared-down, dedicated biofuel-producing bacteria could conceivably increase the efficiency of production to the point where we can meet the world's renewable energy requirements without threatening food security.

Not Entirely Novel

It obviously has to be acknowledged that genetically modified organisms are old news. But reconstructing the genome in its entirety the way Venter's team have done allows a significant increase in the efficiency of the final organism in doing whatever the designer wants it to do.

Concerns

Obviously its a Pandora's Box. The techniques used by Venter's team could be used to engineer sophisticated bioweapons. Also, I predict a great deal of criticism based on widely held views about the sanctity of life, especially the life that is represented by complex metazoans like humans.

According to the Guardian article, Mycoplasma laboratorium has 580,000 base pairs. The human genome has roughly 3 billion, more than 5,000 times more. So assuming the construction of Mycoplasma laboratorium took a fair amount of time, I doubt the same techinques could be used to build completely customised humanoids in the near future.

However, most useful manufacturing processes have a way of rapidly advancing when they enjoy significant commercial success - and even the problem of designing such a complex creature, which appears at first glance to require a lot of conscious human-powered analysis, could be significantly enhanced by sophisticated computer programs. So I don't think its too outlandish to say its a short leap from a designer bacterium to Frankenstein's monster, absent likely restrictions.

For those who revere life as sacred - in the original, religious sense - I foresee the possibility of artificial biological humanoids, or even artificial biological cats and dogs, being a major bogeyman, but it doesn't concern me too much, since I don't. Not to say I don't feel compassion for all complex metazoans and passionately support kindness and respect for said, just that the respect I feel is premised on an instinctive sense of compassion and empathy rather than a belief in any natural or God-given ethic that prohibits meddling. And I don't think someone is going to do mass experimentation on large organisms or produce a clone army, a la Star Wars, without a lot of people noticing and intervening.

What is more concerning is the potential for sophisticated bioweapons. Already there are no small number of conspiracy theorists who believe that AIDS is an artificial disease designed to wipe out this ethnic group or that unpopular lifestyle. The ability to customize living molecules at this level obviously brings with it the potential to make weapons that are at the same time devastatingly effective and precisely targeted. The nightmare scenarios are those already in wide circulation among conspiracy theorists and in popular fiction: Deadly diseases that target specific genders (read Frank Herbert's White Plague), ethnic groups, people with particular lifestyles - or specific combinations of all three.

I have no idea how we will limit these possible negative applications in the future and have little doubt there will be calls in some quarters to put a stop to this kind of research (actually I'm surprised at how little debate about this there is on the Web right now). But the genie is out of the bottle. A lot of people know it can be done. And if they want to do it, they eventually will. If/when that happens, we will need the scientific expertise to be up to the challenge of responding appropriately

Blackouts and racism

Professor Steven Friedman, my current favourite South African blogger, has a great post over at Thought Leader about how the recent rolling blackouts have brought an undercurrent of white racism in South Africa to the surface.

[Post truncated because I realised it was mostly redundant. Friedman says it all more eloquently]

Evolving watches

Via Ensign Steve, Dean of Star Trek Studies at Freethought Forum, some cool YouTube videos of computer simulations, from a scientist, that demonstrate how evolution works and address creationist misconceptions about evolution. Links to the Mathlab code used are supplied on the Youtube page:

How evolution really works



Evolution is a blind watchmaker


More here

In the linked forum thread about the videos, it seemed clear to me that some people misunderstood what the author was demonstrating in the latter video.

The creationist analogy of a watch, clearly designed, for a living organism (also, in creationist thought, clearly designed) is nonsensical because a real watch lacks many aspects of organisms that evolutionary theory is premised on.

So the video's author first gives the elements of the watch analogy the qualities necessary to make it a working analogy, then shows how, given these qualities, watches would evolve over time

Fostering autodidacticism

The discussion following this post over at Crooked Timber helped me clarify some thoughts on encouraging self-directed learning in children. I've lifted my comment posted there in its entirety:

This discussion brings to mind a vivid memory of being 8 years old and cutting an apple in the kitchen while my father was cooking.

Having cut the apple in half, then half of that in half, I turned to my dad and asked him something to the effect of “Dad, if I keep cutting a half away from what I have left, then half of that and so on, forever, will I cut down to nothing, without having disposed of anything?”

My dad, who worked in a lab and had a amateur interest in science, replied “Well, son, as far as I know you will eventually reach a limit, like atoms, which as far as I know means ‘uncuttable’ in ancient Greek – you can split atoms, but somewhere in the region of that scale you’ll reach a limit”

We chatted about it for a while and he reached what was clearly the limit of his knowledge and that would have been the end of it but my dad was unsatisfied with his incomplete answer, so the next day he came home with a book from the library about physics at an atomic level for me to read.

Since it was fresh in my curious mind I eagerly read the book, cover to cover, in the space of the next two days. By the end of the week I was boring my close friends with lengthy descriptions of the construction of atom bombs.

Years later, while working from home as a developer, a friend hooked me up with someone who ran a Montessori Method pre-primary school that was looking for a part-time computer-skills teacher.

I got a brief run-through of their self-directed learning technique which places a heavy emphasis on supplying information and tools for learning about a particular subject when a child’s attention is focused on that subject, rather than trying to herd their attention towards the adult’s focus.

I was immediately reminded of the incident described above, from my own childhood, and many other incidents like it, and realised then that an attentive parent that reacts quickly and appropriately to a curious child can greatly enrich that child’s education.

Lessons learned eagerly by a self-focused child are far more effective even that lessons simply learned willingly by a disciplined child. And parents are generally in a better position to leverage that insight than school teachers.

But it doesn’t mean educational authorities can’t extract value from that insight. I don’t know what American educational budgets look like but here in South Africa the thinking seems to be that education budgets are set at the amounts required to barely achieve an assembly-line style education, while enormous amounts have been spent elsewhere on military facilities we don’t need – and misguided attempts at getting private enterprise to do more adult education.

It strikes me that methods like the Montessori method, which in my limited experience is enormously beneficial to young students, actually do bring some of the enriching effects of intelligent parental involvement to the classroom. So there is a case to be made for much bigger budgets enriching the learning environment rather than ineffectively bloating the education system – properly spent, the extra money could be very effective.