Tuesday, June 24, 2008

Google and the brain

Good article here on how the Internet is changing the way humans absorb information. I've no doubt that as a medium of communication it will in many ways surpass the other already impressive tools of this type we possess, and that we humans are so good at developing.
I am not convinced myself however that the art of absorbing the printed word is necessarily at any immediate risk. To truly understand a subject in depth a certain amount of "deep" reading is required, and perhaps always will be. It has been pointed out before that new communication technologies don't kill old ones, for instance television didn't kill radio. I admit that many people in modern society don't read frequently, however worldwide literacy rates are still rising and I must say it gives me heart to think that every day new minds are discovering the rich world of the imagination that can still be found only in books.

Kepler mission

I like Kepler, he discovered the laws of planetary motion and his name is nearly the same as Pepler. And his mother was tried as a witch (bloody Wikipedia!).
In February 2009 the Kepler spacecraft is due to be lauched into an earth trailing heliocentric orbit in order to discover other earth-like worlds in our galaxy. My hunch is they’ll find plenty.

Wasp voodoo

Individuals of one species use those of another to incubate their larvae. The larvae turn it into a zombie that protects from predators the very organisms that devour it. Yes it’s the world of parasitic wasps.

Monday, June 23, 2008

bee sting

The sterility of worker bee females was regarded as an evolutionary conundrum until sociobiologists suggested that natural selection may favour worker behaviour that assists their queenly sisters who share most of their DNA. Now it seems that some researchers have identified a region of the honeybees genome that affects fertility.
That’s great and we all look forward to the published study. But this doesnt seem to have much more to do with the selfish gene concept than any of the other hundred other genetics papers published every week and the serially reprinted press release just seems to be an attempt to cash in on Richard Dawkins' current fame/notoriety.

Tuesday, June 17, 2008

Murchison nucleobases

A great article today in SciAm on the Murchison molecule work by Zita Martins group. Some interesting comments, this from Robert Shapiro:"They're a subunit of a subunit of DNA," he says. "My opinion is that their amounts were utterly unimportant and insignificant" Strong words indeed. A bit of googling on Prof Shapiro indicates he has his own barrows to push. Heres an interesting article where he discusses various ideas including non carbon based life. He seems to have a track record of being dsimissive of more conventional origin research.
(I also think he misses the significance of information flow as a property of life in the linked article but then, I would).
The SciAm article finishes thus: Conel Alexander, a geochemist at the Carnegie Institution of Washington who specializes in meteorites, says that without more data, claims about the amounts and sources of molecules on early Earth should be taken with a grain of salt. "It really comes down to quantitative arguments about how much was made on Earth [and] how much was brought in from space," he says. "Any honest person would keep an open mind about the whole issue."
Well who could disagree with such a reasonable, if cautious, statement. Still the discovery of types of molecules associated with living organisms in samples representative of the early solar sytem is significant in my view. Carbonaceous chondrites like the Murchison meteorite give us an idea of the stuff that is around in early solar system formation, and while its true that there may have been only miniscule quantities present on the early earth, there may have been truckloads, nobody knows for sure yet. So any discovery of new and biologically useful (to carbon based life) molecules in such samples are important. In the Shapiro article linked above he is quoted as saying "But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn't be functional until it attained a certain length and could copy itself — appearing on the Earth."
I don't like this, I think its a poor comparison - but you could say it would depend on number of trials, wind direction, block shape, etc. At least we might be getting an idea of which letters were available.

Monday, June 16, 2008

Evolution in a test tube

The most interesting story of last week for my money is the latest from the Lenski files. One criticism of modern evolutionary theory is that it cant be tested in the lab. Prof Lenski, who back in 1989 started breeding escherichia coli from a single individual under artificial conditions has arguably done just that, as recently evolved populations now have the ability to consume citrate. Given that the inability to eat citrate is one of the defining characteristics of e coli, this is no ordinary mutation. What’s more, the team was able to replay the “speciation event” by thawing out earlier generations and breeding them once more. I recommend the NY times article by Carl Zimmer for the full story. Once again it has been demonstrated that new and adaptive genomic information has been generated by selective pressure acting on the random variation of replicating organisms.

Influx June links

In 1969 a hefty lump of carbonaceous solar system detritus exploded over Murchison, Victoria (Aust). The collected fragments are now known as the Murchison meteorite and the study of its rich organic content has given scientists and cosmic philosophers plenty to ponder. The meteorite was found to contain amino acids, including some very unusual types not usually found here on earth. The chirality of the amino acids has also led to discussions about the origin of the left handedness in amino acids common to life on earth. Some researchers have also claimed that structures seen under the electron microscope may be nanobacteria (similar claims have been made for the Martian meteorite ALH84001). Now uracil and xanthine, important precursor molecules to nucleic acids (DNA + RNA) have been found in the Murchison meteorite, and analysis indicates that the nucleobases contain a heavy form of carbon which could only have been formed in space.

It appears that brain synapses vary in complexity with humans presumably possessing the dual core Pentium equivalent.
Its also good to see that the most complex information processing structure in the known universe is capable of running smoothly for at least 115 years.
To another information network, the hive. Bee language is a well characterised form of communication. It appears more consistent than human language however: despite regional differences, bees from across the globe have been shown to communicate with each other.

Monday, June 2, 2008

Bo Diddley 1928 - 2008

Brilliantly original guitarist and singer/songwriter Bo Diddley died on Monday. Will always be remembered as one of the true kings of Rock and Roll.

Little creatures

Another organism justly famous for DNA repair, the bdelloid rotifer, has now been shown to be even more versatile than thought, apparently having the capability to incorporate genes from other life forms into its own genome.
And in equally astonishing news, an elegant experiment has revealed the adult form of a fairly complex larval crustacean to be a far simpler worm like creature, sort of like a butterfly changing into a caterpillar. A reminder that neither evolution or biological development always follow the path of greater complexity. Check out the video.

Ocean floor origin of life

A while back I was wondering how dynamic the Precambrian global genome might have been. I since read a discussion at Pandas Thumb (reveiwing a new Origin of Life site, link on left) where it is suggested that the global genome may have evolved fairly sluggishly until metazoans started having sex. The Precambrian bugs supposedly reproduced very slowly and concentrated their energies on DNA repair. Hmmm, that sounds a lot like those primitive archaea found living deep below the surface last week. So is a deep ocean origin of life gaining currency? Well this latest report seems to bolster the concept further. From the article: “We scratched our heads about what was supporting this high level of growth when the organic carbon content is pretty darn low," Edwards said. Perhaps, the researchers figured, chemical reactions with the rocks themselves might offer fuel for life. Lab tests confirmed the idea.”
This article doesn’t mention the nature of these reactions but we already know of bacteria that can live off the energy released by breaking down various minerals.
I suspect we will find more evidence to support the deep ocean origin of life. In the early earth the bottom of the ocean would have been the most hospitable environment available and electromagnetic radiation too intense to be used as a source of energy as it is now. The complex chemical reactions that underpin photosynthesis have their origin in the simpler chemistry utilised by the bottom dwellers.
My view is that life began as a sort of skein of rich ooze covering vast areas of the Archean sea floor where simple reactions and flow of resources slowly changed and became more complex until at some point Dawkins’ replicators appeared, not just in one spot but simultaneously at many points. Life is flow, of information, energy and resources and it has always been a network. It still is, and the ancient roots of it live on, and are only now being brought to the surface.

First contact

The world is a vast place and there are still some parts of it that modern humans have not penetrated, as the latest pictures of a group of humans who apparently are yet to have contact with modern civilization apparently show. These aren't the only guys out there who are trying to incorporate giant silver birds into their creation myths either. We are in the final stages of the collision between modern and primitive worlds, and we still have no idea how it can be handled without disastrous consequences. Here in Australia those consequences are still reverberating as the last of the wanderers are still walking up to the campfire.