A recent paper out of Richard Lenski’s lab at MSU details the evolution of a Cit+ strain of E. coli among the 12 replicate lines that are part of the Long Term Experiment in Evolution running in his lab

I haven’t read the paper yet, but from the abstract, it seems the evolution of a relatively radical new trait (for E. coli) which is the utilisation of citrate as a carbon source has been demonstrated and also it is shown that this trait was contingent on the “history” of that particular line that developed the trait. Essentially, the other 11 lines did not gain the ability to use citrate even on subsequent experiments with earlier generations, but the line that did evolve could do so again and again from earlier generations that didn’t have the ability.

Understandably, this is an important study in evolution for the role of historical contingency (read “chance”) but also in demonstrating that an ability (or lack of) that partially defined the species in question had evolved in the lab.

But more on that in another blogpost.

What has struck me about the news surrounding this paper on the net has been the vigour with which the results, the science (and sometimes even the scientists) are been questioned and attacked by what I can only charitably call the “god” brigade.

Part of the reason could possibly be because of the way the New Scientist article about the paper ends:

Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.”

That one short paragraph seems to have got their collective goat and has led to a flood of comments on the New Scientist site. The giant leap backwards is that a lot of the people commenting seem rational, coherent and somewhat aware of the biology but somehow perversely blind to the idea of evolution.

The old chestnuts about micro-evolution and macro-evolution are trotted out numerous times as well as variants of “But it’s still a bacterium” not to mention “It’s all random therefore we are random.”

A quick sampling of some of the inane comments:

Back on topic, i’m a more logical guy so I think things through. There’s no black and white, noobs.

…

Anyway, personally, it seems to me the mutation at generation 20,000 could be evolution (however, evolution refers to advantage, and until this scientist figures out what REALLY happened, we don’t know if that change was technically advantageous or disadvantageous. I think we can assume advantages since they survived. Survival of the fittest, right?)

However, I see this article fails to mention epigenetics!! Epigenetics very well could be the CAUSE of the WHOLE series of changes, OR, there was a random mutation first (evolution), which made it easier for epigenetics to take over, causing the Cit+ trait.

Sigh. Where do you begin with comments like that?

On the other hand if the basis of evolution is randomness, then that destroys the entire foundation that science is built upon. The evolution to human beings is also random. What we see and think are also therefore random. All our theories are therefore random. We cannot really be sure whether we have really evolved or not, if we base evolution on randomness, since everything is random. We cannot even be sure that we are thinking, after all it might be just some random hallucination. We cannot be sure of anything. One cannot build a rational world on disorder.

Oh wow.

This article doesn’t explain why this is a a major innovation.

A flagellum would be major.

I suppose if someone WERE to demonstrate the evolution of a flagellum it would be dismissed as not major. Like clockwork, the next comment states:

Even a flagellum would not be major. If evolution is responsible for all biological structures — and that is a BIG IF — then the human brain, which is capable of advanced mathematics, language, and philosophy, is evolution’s greatest triumph.

And to end:

What Bothers Me Most Is that the evolutionary biologist at UC has already formed a conclusion before the initial research has been completed and published. This doesn’t seem very scientific of him, or the article for quoting him. I kind of get the impression that New Scientist has a chip on it’s shoulder when it comes to creationist. There are loads of “theories” out there on a milieu of topics, which aren’t accepted by the scientific community at large (creationism obviously falls into this category), yet NS seems to single creationism out for needing repeated condescension…

I guess 20 years of experiments and published papers don’t count for squat?

Their research was published this week in the British Medical Journal, and the Guardian has a story about them here.

What can I say? I told you so, Ma!

The physicist: “The measurement was not accurate.”

The biologist: “They have reproduced.”

The mathematician: “If one person enters the house, then it will be empty again.”

From: Eric’s favourite Math jokes

David Bolinsky, former lead medical illustrator at Yale, lead animator John Leibler, and Mike Astrachan are some of the creators at XIVIO who made the movie. They created the animation for Harvard’s Department of Molecular and Cellular Biology. Most of the processes animated were the result of Alain Viel’s Ph.D. work describing the processes to the team.

14 months to create for 8.5 minutes of animation! Well worth it, don’t you think?

For more on how it was made, read Studio Daily’s report here. And an interview with Wired here.

From the cartoons of R J Matson

I guess a science blog will fit right in at a site called Absolute Geeky! What’s the story behind that name? Well, I’d long wanted my own domain and when I finally decided to go ahead and book it, I decided my geekiness is what sets me apart from most people. So I didn’t have to spend too much time figuring out what should be called (and thanks to A for the suggestion.)

Expect to see some new posts here real soon now since I’ve berated Madgenius and Samudrika for not posting, they’ve both assured me that they have new posts up their sleeve.

Who wouldn’t be interested? Harish and I watched the short clip on ZDnet and we were both a bit taken aback by what Page was saying. (You can get a video of the complete speech on this page.)

If you look at your DNA its just about 600 MB compressed, which is smaller than any operating system. Your Linux, windows, any operating system. That includes booting up your brain, right … by definition. So your algorithms are probably not that complicated, its probably about the overall computation.

I spotted the obvious flaw there that genome size is directly related to complexity of the system. Now any biologist worth her salt will tell you that this is simply not true. Gone are the days when we believed that knowing the complete genetic code of an organism will tell us everything we need to know about that organism. Far from it, the questions raised by sequencing genomes are far more than ones it answers!

But what does this all have to do with artificial intelligence or AI? Well apparently, a lot of people are buying Larry Page’s argument! Now believe what you will about the complexity or simplicity of AI. I’m no expert in the field. But to use the supposed “simplicity” of the DNA “program” to prove your point about AI is plain wrong.

I spent some time explaining to Harish the biology behind my thinking and he converted his understanding into a blog post with a clever title. He also went around posting comments in the blogosphere talking about why Page’s logic was flawed and pointed back to his post. Except for a couple of people, most didn’t understand the point Harish was trying to make with all the biology in his post, so let me try it this one time.

Page’s argument as I understand it is:

1. Human DNA is simple to understand.
2. Human DNA programs for the human brain.
3. The human brain makes human beings intelligent.
4. Therefore, AI is simple

All cut and dried. What’s wrong? Well, a couple of things. I could debate about how simple or not simple human DNA is, but lets assume it is simple. We’d still be stuck at step 2. DNA does NOT “program” in any sense the human body or brain. Using the metaphor of a “program” is quite wrong and it is this precisely that which leads most people to make mistakes in assuming what DNA can or can’t do.

My point is that the sequence of DNA in a genome is an incomplete description of a living system. Therefore it is not a good way to estimate how easy or hard it would be to build an AI system.

I do not know enough about AIs, nor the current state of research in that field to be able to debate how close or far away we are from building one. But I do know enough biology to tell you that using DNA to argue that AI is around the corner is wrong.

Now if only science experiments in schools and colleges were like this!

What a great way to learn about the contents of carbonated beverages, a common candy, materials science (the surface of the Mentos), theories about boiling, phase transitions, nucleation sites… and more!

(If you’re too lazy to wait for the video to download and watch it, it’s these two guys from eepybird.com who have made very elaborate fountains using Diet Coke and Mentos. Put a Mentos into a two litre bottle of Diet Coke and voila, instant fountain. Of course, it’s more complicated than that, but still relatively simple. Watch the video, it’s a lot of fun! And well choreographed!)

Like this innovative way to settle an age old controversy – that of whether brain cells can form anew after birth it is a well known fact that brain cells once formed are not made again. unlike say for example the skin cells which are shed and then replaced. (Actually we go through a new skin every 1-3 months.)

But research in the early 70’s showed that we actually make new brain cells even after we have grown up. (the technical term is adult neurogenesis).

How is this done? In animals you give them stuff called BRDU which gets in the DNA of the cells. Now a cell only makes new DNA once ie when it is forming. Therefore only those cells take up DNA which are being born. If you look for which cells have taken up BRDU you know these are the cells which have been born after you gave the BRDU to them.

Does adult neurogenesis happen in humans at all? Can’t you give humans BRDU and see? Well no because BRDU is a mutagen. (causes mutations and therefore cancer). What would you do?

Well, here comes the innovation that works around this problem. In the period from 1955-63 there were a lot of nuclear bombs being detonated above ground for “tests”. This lead to the C14 levels in the atmosphere going up. In fact it follows a pattern with the levels coming down exponentially after 1963 when the test ban treaty was signed. This is shown in this graph.

(ignore the line and dot for now)

These ratios of C14 to the normal level would be reflected in the DNA of the cell as well because the C14 is all over the atmosphere which would get into plants and therefore into human food as well. When a cell is born this C14 would go into the nucleus as well. If you could measure C14 levels in the cell DNA you could tell when it is born.

You could do this for all the cells in body and determine the age of each groups of cells – like brain versus intestine. neat.

Next big question – Did it work? Did they show that new neurons are born in the brain after birth? did they? did they?

Well – short answer yes!

The vetical line in the year of birth of the indivudual(~1973). The red dots represent the date of birth of the cells of the different organs. The intestine cells (also have high turnover rates like the skin cells) are the youngest having C14 levels corresponding to being born in ~1995 while the cerebellar cells are the oldest – being born in ~1975.

The clincher here are the cortex cells being clearly born in 1982 or thereabouts, indicating clearly that new neuronal cells can be formed after birth.

Who would ever have thought that nuclear bomb testing would have such a scientifically useful fallout (pardon the pun). And yes truth is stranger than fiction.

For the ones who revel in the details here is the original paper.