Saturday, November 22, 2008
Life and thermodynamics
I still haven't read this article myself but a scan indicates it may be a good wrap up of the facsinating intersection between biology and thermodynamics from Scientific American.
Entropy and evolution
Update overdue
Nearly 2 months since last update, its almost a relief to get my traffic reports which confirm that absolutely nobody ever reads this blog. Anyway, heres my latest grab bag:
Wednesday, September 10, 2008
LHC booted up
Only one sunset so far tonight so it seems the LHC start up hasn't brought about the end of the world yet.
Another IT approach to solving biological enigmas. We're starting to untangle the deep informational structure of the global genome. I can't help thinking again that these tools will also lead to AI breakthoroughs, the potential is breathtaking.
Tuesday, July 22, 2008
Friday, July 11, 2008
OOL and evolution part 2
Here’s another blogger who is arguing that our current understanding of the mechanisms behind biological evolution encompass the origin of life. To be fair, like Myers and Natzke, Mike’s main point is not to concede the OOL ground to those expounding a religious explanation.
My view, and one of the reasons that I created this blog, is that there is nothing more to be gained by arguing scientific questions with those whose intent is to bring religious ideas into scientific discussions. The existence of God is simply not a question that can be debated scientifically. To put it bluntly, no rational argument can support the pro God viewpoint. I believe it is better to discuss areas of scientific enquiry without accommodating religious viewpoints. I do not mean that non-rational ideas shouldn’t be publicly debated, and I enjoy and am a regular poster on such admirable websites as Pharyngula and Dawkins.net. However I think that by involving religious viewpoints on scientific subjects where no strong scientific consensus exists leads to distortion of the dialogue. So, to put it simply, no religion in scientific discussion, no science in church, and anything goes in the public arena.
With regard to the OOL, there are numerous alternative scientific hypotheses in play which so far appear fairly equally plausible given the current evidence, so this is clearly not a situation where science knows the answer. That’s not a bad thing! All my personal favourite areas of scientific research are these questions at the boundary of our scientific understanding. I hasten to add I’m very confident that we will one day have a convincing and widely accepted scientific explanation of OOL.
Mike makes much of the difficulty in defining life, however this is not a good argument for claiming that the OOL is unamenable to a more definite scientific explanation; after all, perhaps a strong explanation of the OOL will lead to a better definition of life.
I think that a better approach may be to see the OOL as the origin of information. Admittedly, information itself is extremely difficult to define. However so is electricity, but we still know a lot about it.
The one single quality which seems to be unarguably a property only applicable to living systems, is information (I exclude the sense in which it is used by physicists).
It is clear that information can arise from randomness, given life – this is the basis of natural selection. The question is how did the process begin? Or, what was the first message, the garbling of which gave NS something to act on? This is the question various research groups are trying to answer, there is an answer, and we will find it.
My view, and one of the reasons that I created this blog, is that there is nothing more to be gained by arguing scientific questions with those whose intent is to bring religious ideas into scientific discussions. The existence of God is simply not a question that can be debated scientifically. To put it bluntly, no rational argument can support the pro God viewpoint. I believe it is better to discuss areas of scientific enquiry without accommodating religious viewpoints. I do not mean that non-rational ideas shouldn’t be publicly debated, and I enjoy and am a regular poster on such admirable websites as Pharyngula and Dawkins.net. However I think that by involving religious viewpoints on scientific subjects where no strong scientific consensus exists leads to distortion of the dialogue. So, to put it simply, no religion in scientific discussion, no science in church, and anything goes in the public arena.
With regard to the OOL, there are numerous alternative scientific hypotheses in play which so far appear fairly equally plausible given the current evidence, so this is clearly not a situation where science knows the answer. That’s not a bad thing! All my personal favourite areas of scientific research are these questions at the boundary of our scientific understanding. I hasten to add I’m very confident that we will one day have a convincing and widely accepted scientific explanation of OOL.
Mike makes much of the difficulty in defining life, however this is not a good argument for claiming that the OOL is unamenable to a more definite scientific explanation; after all, perhaps a strong explanation of the OOL will lead to a better definition of life.
I think that a better approach may be to see the OOL as the origin of information. Admittedly, information itself is extremely difficult to define. However so is electricity, but we still know a lot about it.
The one single quality which seems to be unarguably a property only applicable to living systems, is information (I exclude the sense in which it is used by physicists).
It is clear that information can arise from randomness, given life – this is the basis of natural selection. The question is how did the process begin? Or, what was the first message, the garbling of which gave NS something to act on? This is the question various research groups are trying to answer, there is an answer, and we will find it.
cell signalling breakthroughs in the ancient world
I favour the viewpoint that life is best thought of as a phenomenon that incorporates the flow of energy and the flow of information. I suspect that significant key breakthroughs in biological evolution are tied to the appearance of new mechanisms that markedly increase the flow of information (whether genomic or other), thanks to the bootstrapping of natural selection. One of these breakthroughs is undeniably the appearance of multicellular life forms, so it is interesting to note that genomic sequencing of choanoflagellates, the organisms suspected by many to be a link between proto and metazoans shows they have more and better cell signalling proteins than other micro-organisms.
In fact they seem to have a wider repertoire of signalling proteins than anything else, the question is: why? “we don’t have a clue” stated one of the researchers, with refreshing honesty.
Sounds like the start of some great research.
In fact they seem to have a wider repertoire of signalling proteins than anything else, the question is: why? “we don’t have a clue” stated one of the researchers, with refreshing honesty.
Sounds like the start of some great research.
Hadean life
Pinpointing when in earths history life began has been a big challenge for science. Naturally the further back you go, the scarcer the evidence becomes. At the moment the general agreement is that microfossils found in ancient rocks, together with other clues, like the banded iron formations, are proof of that life was established here on earth by around 3.5 billion years ago, but more equivocal evidence has suggested that the beginning may be yet earlier. However it is usually thought that the late heavy bombardment that tails off around 3.8 billion years ago imposes a limit on the antiquity of life’s origin. Interesting then, that recent research on to isotopic carbon ratios in ancient Australian rocks indicates that some kind of biological process may have been at work up to 4.25 billion tears ago. Living organisms concentrate the lighter isotope of carbon, and we aren’t aware of any other natural processes that do this to any significant extent, so the presence of high levels of C12 in the carbon inclusions found in these ancient zircon deposits is curious to say the least.
Monday, July 7, 2008
Origin debate on Pharyngula
Discussion currently at Pharyngula where PZ Myers complains about those who "get out of trying to answer the question of where life came from by simply saying that that isn't evolution."
His view? It is. I disagree: we have agood understanding now of how the mechanisms whereby biological evolution works. I don't think the same can be aid of abiogenesis/OOL. Thats what makes it so fun to conjecture about.
His view? It is. I disagree: we have agood understanding now of how the mechanisms whereby biological evolution works. I don't think the same can be aid of abiogenesis/OOL. Thats what makes it so fun to conjecture about.
Wednesday, July 2, 2008
Book Reviews: Margulis + Dawkins
Couple of quick book reviews. I read recently that Lyn Margulis, whose influential work on the origin of cell organelles won her the Nobel prize, currently enjoys a reputation as something of a maverick in evolutionary biology circles. Well I like mavericks so I grabbed one of her recent books, Dazzle gradually, hoping for some paradigm toppling insights. I’m sorry to say I was disappointed. In fact I’m astonished that such a well respected scientist could be associated with such tosh. I’ll be honest and say I was unable to read a single page to completion. It is undeniable that Margulis has a Nobel prize whereas I don’t even have a PhD, mind you, so does Kary Mullis and he’s bananas, although he writes more entertainingly than Margulis. That’s not saying much; Vogon poetry is probably more entertaining than the pile of tripe that is Dazzle gradually. And if you aren’t familiar with the Vogons and their poetry, I suggest you read The Hitchhikers guide to the galaxy by Douglas Adams. Now that’s a book.
On a brighter note, at the same time I picked up Unweaving the Rainbow by Richard Dawkins. I was enthralled many years ago by Dawkins first book, The Selfish Gene but found The Blind Watchmaker a bit heavy going so hadn’t read much else since. UTR however is a gem; peppered with insightful quotes, entertaining anecdotes and snatches of poetry it is an shining example of how good scientific writing can be. I recall someone saying that reading Dawkins made them feel more intelligent. UTR certainly has this effect and I think that’s a testament to the quality of the writing.
Some years ago I tried to write a book myself because no one else seemed to be writing about the things that interested me. Well Dawkins is, and it looks like there’s a whole lot of other people that are interested as well.
On a brighter note, at the same time I picked up Unweaving the Rainbow by Richard Dawkins. I was enthralled many years ago by Dawkins first book, The Selfish Gene but found The Blind Watchmaker a bit heavy going so hadn’t read much else since. UTR however is a gem; peppered with insightful quotes, entertaining anecdotes and snatches of poetry it is an shining example of how good scientific writing can be. I recall someone saying that reading Dawkins made them feel more intelligent. UTR certainly has this effect and I think that’s a testament to the quality of the writing.
Some years ago I tried to write a book myself because no one else seemed to be writing about the things that interested me. Well Dawkins is, and it looks like there’s a whole lot of other people that are interested as well.
Lunar time capsule
Its possible perfectly preserved remnants of the early earth may be waiting for us to discover on the moon. What evolutionary biologist wouldn’t give their eye teeth for such a sample, perhaps containing traces of ancestral life forms. Admittedly it seems unlikely much would remain after the solar wind, cosmic rays and meteorite bombardments but if a large enough piece was driven deep beneath the lunar surface, who knows?
Fractal universe?
I’m ambivalent about fractality; much is made of fractal patterns in nature without any suggestion as to why this might be significant. Now new evidence indicating that the universe itself may be fractal will undoubtedly lead to yet more vague speculation as to why these patterns are so ubiquitous. My own view is sometimes there isn’t a deeper reason. Fractality may be like chirality (left/right handedness), a property observed in all sorts of 3D objects from molecules and galaxies. No one suggests that chirality is a hint of some deep principle. Or perhaps they do, it wouldn’t surprise me.
Neanderthal nerds
Recently discovered artefacts show English Neanderthals were high tech for their time.
The Neanderthals generally get a pretty raw deal in the media and public discourse - Heavy browed retards that were out competed or even exterminated by our more nimble-minded ancestors. However a more nuanced picture has been emerging and the time may come when we will admit that, once again, we have allowed our innate urge to trumpet our superiority over others to cloud our judgement. Neanderthals were extremely well adapted to their environment and had developed the beginnings of material culture before the young upstart H Sapiens; it may be sheer fluke that we survived while our Neanderthal brothers and sisters did not.
The Neanderthals generally get a pretty raw deal in the media and public discourse - Heavy browed retards that were out competed or even exterminated by our more nimble-minded ancestors. However a more nuanced picture has been emerging and the time may come when we will admit that, once again, we have allowed our innate urge to trumpet our superiority over others to cloud our judgement. Neanderthals were extremely well adapted to their environment and had developed the beginnings of material culture before the young upstart H Sapiens; it may be sheer fluke that we survived while our Neanderthal brothers and sisters did not.
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.
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.
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.
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.
(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.
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.
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.
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.
Tuesday, May 27, 2008
Shrimp and holes in the net
I just noticed this great post on Pharyngula which fills in the details on the mantis shrimps with built in Polaroids.
And here's a bit more on the Internet black holes. From the article:
"Sometimes certain blocks of the Internet weren't reachable at all, Katz-Bassett reported, while other times only traffic coming from particular portions of the net fell into what's called a "routing black hole." When that happens, packets sent from one computer to another -- whether a request for a web page, or an e-mail message -- are somehow diverted to the wrong location, where they're lost forever." I love that "lost forever" - who says they won't turn up later? Anyway I guess lost forever is a common fate for information packages, just ask your average spermatozoa.
And here's a bit more on the Internet black holes. From the article:
"Sometimes certain blocks of the Internet weren't reachable at all, Katz-Bassett reported, while other times only traffic coming from particular portions of the net fell into what's called a "routing black hole." When that happens, packets sent from one computer to another -- whether a request for a web page, or an e-mail message -- are somehow diverted to the wrong location, where they're lost forever." I love that "lost forever" - who says they won't turn up later? Anyway I guess lost forever is a common fate for information packages, just ask your average spermatozoa.
Monday, May 26, 2008
Deep biosphere confirmed?
The archaebacteria show once again that when it comes to toughness and resilience, they are the undisputed champions. Already having demonstrated their capacity to thrive in saltier, more acidic, more alkaline, lower oxygen and hotter environments than more supposedly evolved organisms, they have now been shown to also cope with having 1.6 km of rock and sediment stacked on top of them.
This made Science so I expect its pretty rigorous but it’ll get a fair bit of scrutiny. I haven’t yet read the full paper but they are apparently claiming a methane based food chain so where is the methane coming from? Is it supposed to be from the sediments or what? I hope to see some good follow up on this soon. I myself favour a deep ocean network origin of life model so I wonder if this could somehow support that. And how might such bugs have evolved?
This made Science so I expect its pretty rigorous but it’ll get a fair bit of scrutiny. I haven’t yet read the full paper but they are apparently claiming a methane based food chain so where is the methane coming from? Is it supposed to be from the sediments or what? I hope to see some good follow up on this soon. I myself favour a deep ocean network origin of life model so I wonder if this could somehow support that. And how might such bugs have evolved?
Friday, May 23, 2008
More satay prawns anyone?
It comes as no surprise to find that Australians are more likely to claim non-existent food allergies. I often hear people make such claims based on exactly no medical evidence. Unfortunately such claims are rarely challenged, by me or anyone else. Still, the next time I hear “I’m allergic to…” I think I’ll respond with “did you know around 9 out of 10 people who say they have a food allergy actually don’t?”
The ensuing lull in conversation will enable me to guzzle more satay prawns with equanimity.
The ensuing lull in conversation will enable me to guzzle more satay prawns with equanimity.
Saturday, May 17, 2008
The secret, or how to extract money from foolish, ignorant people
Apparently when positive thinking fails, there is always litigation. I find it difficult to find words to describe the rage that pernicious drivel like The Secret incites in me. Its partly the wilful self delusion of the credulous nitwits who pay good money for this rubbish, partly the mindless promotion from educated, advantaged people who should know better, but go along for the ride (yes you Oprah), but mostly its the avaricious, calculating reptiles that use their no doubt considerable talents to make the world a stupider and more selfish place. I hope the fruits of their success turn to ashes in their mouths when they consider the foolish shallowness of their doctrine. Arggh.
If anyone wants me I'll be in the angry dome.
If anyone wants me I'll be in the angry dome.
Friday, May 16, 2008
Stirring the pot
When i saw this piece of fluff journalism in the Age, I thought it might be just the thing to get the unfaithful at RDnet worked up into a white hot froth, but i must say it was even more successful than I expected - a comment from the Dawk himself no less! (#100). I think the comments clearly show that when it comes to solving the energy crisis, we athiests dont have any better ideas than anyone else.
paperback autowriter + more
I was surprised to discover that books written by computers are already with us, surely its only a matter of time before Roald Dahl's Great Automatic Grammatizator becomes a reality, in fact I think Tom Clancy has already signed up.
On a similar note, its good to see Asimo taking up challenges in the arts.
New research overturns conventional scientific thought on a perennial mystery of the sea, FT brings us up to date on the freak wave phenomenon.
Still in the ocean, I never thought I’d envy mantis shrimps, but I wish I could see through their eyes. Coming on top of the recent discovery that birds may actually be able to see the earths magnetic field it raises interesting questions about the sensory data input that we call vision.
On a similar note, its good to see Asimo taking up challenges in the arts.
New research overturns conventional scientific thought on a perennial mystery of the sea, FT brings us up to date on the freak wave phenomenon.
Still in the ocean, I never thought I’d envy mantis shrimps, but I wish I could see through their eyes. Coming on top of the recent discovery that birds may actually be able to see the earths magnetic field it raises interesting questions about the sensory data input that we call vision.
Tuesday, May 13, 2008
Mapping music
I love music. To play a musical instrument and sing is one of life’s great pleasures – but what makes it so enjoyable and why has music itself come into existence? At the risk of unweaving the rainbow I like to worry at these questions like a dog at a bone (or possibly a cave bear). It is often said that music is the language of emotion, we all know it can easily bypass the higher faculties and pierce the heart. It seems paradoxical then that modern music can be mapped due to its highly mathematical structure. In terms of biological information, it seems to be complicated data generated by our brains that doesn’t map to anything in the real world at all. The structure of music was observed by Pythagoras over 2000 years ago and since then we have managed to place music in the western tradition on an increasingly sound mathematical footing such that most musicians worldwide now are all tuned to the same pitch. But, though usually a strict rationalist myself, I think music is perhaps the most outstanding example of something that cannot be explained entirely rationally. It is possible to describe in minutest detail a piece of music in terms of score development, key, timing or frequencies without giving any idea of its emotional narrative. This suspension of rationality also seems to apply to the performance – the less you think the better generally, whether listener or performer. The payoff is a feeling of transcendence as religious leaders know very well. Evolutionary theory would suggest our music is a side benefit from having evolved brains that self-reward pattern recognition – a highly adaptive trait for us humans, but I doubt well ever be able to explain exactly why major keys sound cheerful and minor keys sound sad.
Friday, May 9, 2008
Rosenhouse unmasked
I've been a regular reader of evolutionblog for some years now but I think Jason has absolutely outdone himself with this outrageous posting following his well deserved tenure approval http://scienceblogs.com/evolutionblog/2008/05/what_i_really_think.php.
If the post wasn't funny enough, the comments are hysterical.
Apparently this is an example of Poe’s law http://en.wikipedia.org/wiki/Poe
which predicts that no matter how absurd a spoof, some folks will fall for it.
Top work Jason, the comments are a reminder that we have nearly as many cranks, suckers and humourless bores within the ranks of the so called rationalists as without.
If the post wasn't funny enough, the comments are hysterical.
Apparently this is an example of Poe’s law http://en.wikipedia.org/wiki/Poe
which predicts that no matter how absurd a spoof, some folks will fall for it.
Top work Jason, the comments are a reminder that we have nearly as many cranks, suckers and humourless bores within the ranks of the so called rationalists as without.
Monday, April 28, 2008
Intelligence and complexity
Every so often scientific claims are made about the likelihood or otherwise of intelligent life evolving elsewhere in the universe, a recent example is this article:
http://www.sciencedaily.com/releases/2008/04/080416110124.htm
Leaving aside the difficulty of making predictions based on a sample of 1, I have another issue with the assumptions made in some of these discussions, inlcuding the one above. Those who have concluded intelligent life is extremely unlikely to arise in the universe point out the number of improbable steps required. For instance the linked article states:
"Prof Watson suggests the number of evolutionary steps needed to create intelligent life, in the case of humans, is four. These probably include the emergence of single-celled bacteria, complex cells, specialized cells allowing complex life forms, and intelligent life with an established language.
“Complex life is separated from the simplest life forms by several very unlikely steps and therefore will be much less common. Intelligence is one step further, so it is much less common still,” said Prof Watson"
I'm not happy with this, especially the 4th step- I think once you have evolution acting on multicellular life forms then forms of marvellous complexity seem bound to occur and human culture is not less likely than termite mounds, chameleon camoflage or even lichen. It seems as though it is because the products of human culture are so undeniably unique. But the transition from australopithecus to homo, or heidelbergensis to sapiens is not a critical and necessary step in the way that prokaryote to eukaryote is. I rather think of the human brain like the peacock's tail, a flamboyantly elaborate structure produced by the engine of evolution.
Anyhow the case still stands that it took a long time to get from bugs to people. The critical step seems to be the "bugs/protists to jellyfish" one. That life could throw up something as wonderful in its way as a cyanobacteria at the very dawn of the earth and then just sit there, soaking up the sun for a couple of billion years is terrifying and humbling. Of course that couldn't really the case, clearly the global genome would have been dynamic throughout this period, perhaps many abortive pre-precambrians and proto-ediacarian events occurred without leaving traces.
http://www.sciencedaily.com/releases/2008/04/080416110124.htm
Leaving aside the difficulty of making predictions based on a sample of 1, I have another issue with the assumptions made in some of these discussions, inlcuding the one above. Those who have concluded intelligent life is extremely unlikely to arise in the universe point out the number of improbable steps required. For instance the linked article states:
"Prof Watson suggests the number of evolutionary steps needed to create intelligent life, in the case of humans, is four. These probably include the emergence of single-celled bacteria, complex cells, specialized cells allowing complex life forms, and intelligent life with an established language.
“Complex life is separated from the simplest life forms by several very unlikely steps and therefore will be much less common. Intelligence is one step further, so it is much less common still,” said Prof Watson"
I'm not happy with this, especially the 4th step- I think once you have evolution acting on multicellular life forms then forms of marvellous complexity seem bound to occur and human culture is not less likely than termite mounds, chameleon camoflage or even lichen. It seems as though it is because the products of human culture are so undeniably unique. But the transition from australopithecus to homo, or heidelbergensis to sapiens is not a critical and necessary step in the way that prokaryote to eukaryote is. I rather think of the human brain like the peacock's tail, a flamboyantly elaborate structure produced by the engine of evolution.
Anyhow the case still stands that it took a long time to get from bugs to people. The critical step seems to be the "bugs/protists to jellyfish" one. That life could throw up something as wonderful in its way as a cyanobacteria at the very dawn of the earth and then just sit there, soaking up the sun for a couple of billion years is terrifying and humbling. Of course that couldn't really the case, clearly the global genome would have been dynamic throughout this period, perhaps many abortive pre-precambrians and proto-ediacarian events occurred without leaving traces.
Friday, April 25, 2008
Diversity in human mtDNA
Some news sites carrying stories on the following study:
http://www.ajhg.org/AJHG/abstract/S0002-9297(08)00255-3
What I find interesting is that, if their dates are correct, by the time humans had spread thorughout the world and established populations in Australia, the southern african lineages now known as the Khoi and San people (AKA Bushmen) had been isolated from other human populations for possibly tens of thousands of years.
http://www.ajhg.org/AJHG/abstract/S0002-9297(08)00255-3
What I find interesting is that, if their dates are correct, by the time humans had spread thorughout the world and established populations in Australia, the southern african lineages now known as the Khoi and San people (AKA Bushmen) had been isolated from other human populations for possibly tens of thousands of years.
Thursday, April 24, 2008
hobbit debate
A recent item on the hobbit debate http://sciencenow.sciencemag.org/cgi/content/full/2008/424/2 sent me over to John Hawks most excellent blog and I have added the link on the left. I think the current unresolved controversy over the hobbits provenance nicely contradicts the claim sometimes encountered in the global warming and creationist debates that dissenting views in the scientific community are stifled.
Incidentally I spotted the following follow-up link on scientists' beer drinking habits vs productivity: http://life.lithoguru.com/index.php?itemid=119 which settles that one IMO.
Lithoguru's site is great, he has a good essay on realism vs antirealism. I hadn't come across this distinction before and it intrigues me. To summarize: both realists and antirealists believe there is is an objective reality and that science can be used to model and make predictions regarding this. However antirealists make no claim as to whether or not the scientific model is true, but are concerned only if the model is useful. I liked the antirealist position initially, however further thought on the subject inclines me to think this may be a weak position. Surely if we agree for example that general relativity combined with classical physics gives us a more accurate representation of objective reality than classical physics alone then it is more "realistic"?
Still there is no doubt that, given the limitations of the human intellect, our scientific models will always be imperfect.
Incidentally I spotted the following follow-up link on scientists' beer drinking habits vs productivity: http://life.lithoguru.com/index.php?itemid=119 which settles that one IMO.
Lithoguru's site is great, he has a good essay on realism vs antirealism. I hadn't come across this distinction before and it intrigues me. To summarize: both realists and antirealists believe there is is an objective reality and that science can be used to model and make predictions regarding this. However antirealists make no claim as to whether or not the scientific model is true, but are concerned only if the model is useful. I liked the antirealist position initially, however further thought on the subject inclines me to think this may be a weak position. Surely if we agree for example that general relativity combined with classical physics gives us a more accurate representation of objective reality than classical physics alone then it is more "realistic"?
Still there is no doubt that, given the limitations of the human intellect, our scientific models will always be imperfect.
Wednesday, April 23, 2008
Musical brains
Kids who practice show thickening of corpus callosum
http://sciencenow.sciencemag.org/cgi/content/full/2008/416/1
The article implies the two handed nature of the instrumenet may be important although no control is mentioned, in fact its hard to think of an instrument that isn't two handed (harmonica?). It would be interesting to see if the effect is seen in young singers.
http://sciencenow.sciencemag.org/cgi/content/full/2008/416/1
The article implies the two handed nature of the instrumenet may be important although no control is mentioned, in fact its hard to think of an instrument that isn't two handed (harmonica?). It would be interesting to see if the effect is seen in young singers.
Plankton shift
Scientists estimate that one of the stars of the ocean food chain shows an unexpected predeliction for a more acidic ocean http://sciencenow.sciencemag.org/cgi/content/full/2008/416/1
They suggest total biomass of the phytoplankton has increased by 40%. I'd like to know how much this represents in actual mass - 10's or 100's of kilotonnes?
They suggest total biomass of the phytoplankton has increased by 40%. I'd like to know how much this represents in actual mass - 10's or 100's of kilotonnes?
Saturday, April 19, 2008
Science and skepticism
Although peripheral to the main themes of this blog, I think this slate article worth lining as it pre-empts many common criticisms of the science that I use to build my ideas upon: http://www.slate.com/id/2189178/entry/2189361/ (all 3 articles well worth reading).
It also reminded me of a discussion I had with a friend recently about how to make balanced judgments on political issues. For instance he asked why I thought it more likely that president Putin may have had some involvement with the death of Alexander Litvinenko than prime minister Blair having similar involvement with the death of David Kelly and suggested that my western background, rather than the evidence, made me more inclined to suspect Putin. My friend suggested that all media reports had to be interpreted sceptically to which I agreed but pointed out that if all evidence and argument is treated as suspicious then how could a person have an opinion on anything?
I have a few simple rules myself for critical assessment of received information:
For scientific claims, does the claim have widespread support in the scientific community? Although It certainly happens that new scientific ideas may be met with resistance, time eventually weeds out those that do not rest on sound evidence and good scientific practice (eg cold fusion).
For stories where opposing viewpoints are reported, who has the most to gain by lying?
Occam’s razor http://en.wikipedia.org/wiki/Occam%27s_razor works pretty well too.
Modern scientific theory is an interconnected set of models that can be used to predict and explain natural phenomena that are constantly refined and improved. The models do not need to be “true” to be useful and in fact are always a simplified reflection of reality (eg the wavefunction equations that modern molecular orbital theory in chemistry is based on can only be solved for hydrogen – the simplest of atoms). Our view of the social and political world likewise will always be a grossly simplified version of reality, however some peoples views will be more consistent with that reality than others. However its not so hard to weigh other peoples opinions and stories against their motivations and feelings, what’s really hard is to not let your own motivations and feelings interfere with your judgement. One strategy that can be helpful is to deliberately inform yourself with arguments that go against your own viewpoint. I’ve since read widely (not just on Wiki) disparate internet sources on the Litvinenko and Kelly deaths and think it unlikely that Putin or Blair were involved in these cases. There is still a shadow of suspicion in my mind with regard to Putin however, I think its because of those shifty eyes.
It also reminded me of a discussion I had with a friend recently about how to make balanced judgments on political issues. For instance he asked why I thought it more likely that president Putin may have had some involvement with the death of Alexander Litvinenko than prime minister Blair having similar involvement with the death of David Kelly and suggested that my western background, rather than the evidence, made me more inclined to suspect Putin. My friend suggested that all media reports had to be interpreted sceptically to which I agreed but pointed out that if all evidence and argument is treated as suspicious then how could a person have an opinion on anything?
I have a few simple rules myself for critical assessment of received information:
For scientific claims, does the claim have widespread support in the scientific community? Although It certainly happens that new scientific ideas may be met with resistance, time eventually weeds out those that do not rest on sound evidence and good scientific practice (eg cold fusion).
For stories where opposing viewpoints are reported, who has the most to gain by lying?
Occam’s razor http://en.wikipedia.org/wiki/Occam%27s_razor works pretty well too.
Modern scientific theory is an interconnected set of models that can be used to predict and explain natural phenomena that are constantly refined and improved. The models do not need to be “true” to be useful and in fact are always a simplified reflection of reality (eg the wavefunction equations that modern molecular orbital theory in chemistry is based on can only be solved for hydrogen – the simplest of atoms). Our view of the social and political world likewise will always be a grossly simplified version of reality, however some peoples views will be more consistent with that reality than others. However its not so hard to weigh other peoples opinions and stories against their motivations and feelings, what’s really hard is to not let your own motivations and feelings interfere with your judgement. One strategy that can be helpful is to deliberately inform yourself with arguments that go against your own viewpoint. I’ve since read widely (not just on Wiki) disparate internet sources on the Litvinenko and Kelly deaths and think it unlikely that Putin or Blair were involved in these cases. There is still a shadow of suspicion in my mind with regard to Putin however, I think its because of those shifty eyes.
Thursday, April 17, 2008
The flow
I've added a subtitle to the blog that is a first attempt at summarizing the theme. I intend to draw together news stories and my own comments to illuminate what i see as one of the big unanswered questions of our time:
How did life begin, is the apparent trend towards increasing information creation and flow here on earth an inevitable property of this type of system and, if so, what might this mean for the future?
Please note it is not my intention to introduce any religious ideas into this discussion.
How did life begin, is the apparent trend towards increasing information creation and flow here on earth an inevitable property of this type of system and, if so, what might this mean for the future?
Please note it is not my intention to introduce any religious ideas into this discussion.
Wednesday, April 16, 2008
Bugs in amber
Update on bugs in opaque amber, it appears I spoke too soon: "...they suggest their work could form the basis of an alternative means of cataloguing new species trapped in amber."
http://news.bbc.co.uk/2/hi/science/nature/7324564.stm
http://news.bbc.co.uk/2/hi/science/nature/7324564.stm
Free will in question
Man you can do some fun experiments with those MRI gaadgets:
http://www.wired.com/science/discoveries/news/2008/04/mind_decision
My interest here is that this backs up my view that intelligence and consiousness are seperate properties that give the user the illusion of being merged.
http://www.wired.com/science/discoveries/news/2008/04/mind_decision
My interest here is that this backs up my view that intelligence and consiousness are seperate properties that give the user the illusion of being merged.
Monday, April 14, 2008
Internet black holes
Just a reminder that we still only have the vaguest understanding of how information flow works:
http://www.livescience.com/technology/080411-cyber-black-holes.html
This is the kind of news byte Icreated this blog for!
when I read this I think: :"Here is a clue to the dynamics of information flow".
Now I'm sure this can be rationalized - they mention increasing efficiency to the level of the telephone system and I'd love to hear some informaticians weigh in - but nevertheless the plain fact is sometimes we lose great chunks of data "in flow" and barely have the language to describe whats going on.
http://www.livescience.com/technology/080411-cyber-black-holes.html
This is the kind of news byte Icreated this blog for!
when I read this I think: :"Here is a clue to the dynamics of information flow".
Now I'm sure this can be rationalized - they mention increasing efficiency to the level of the telephone system and I'd love to hear some informaticians weigh in - but nevertheless the plain fact is sometimes we lose great chunks of data "in flow" and barely have the language to describe whats going on.
Thursday, April 10, 2008
hidden bug treasure
http://www.livescience.com/animals/080409-opaque-amber.html
I like the comments: "We are not really studying the insects to know the insects themselves," Tafforeau said. "If you have a lot of different animals you can get a signal about the temperature and the environment 100 million years ago."
So even the most ardent entomologists quail at having to classify another whopping great bunch of beetles.
I like the comments: "We are not really studying the insects to know the insects themselves," Tafforeau said. "If you have a lot of different animals you can get a signal about the temperature and the environment 100 million years ago."
So even the most ardent entomologists quail at having to classify another whopping great bunch of beetles.
Tuesday, April 8, 2008
Science 2.0
Just saw this on SciAm and love it:
http://www.sciam.com/article.cfm?id=science-2-point-0-great-new-tool-or-great-risk
It seems to me the only risk is a certain self important types who never had an original thought in their lives may be exposed as such. This is a great example of how the internet will completely transform certain aspects of human endeavour. Although the 20th century has seen a blossoming of science, it has also created a world where most people don't feel part of this exciting and vital human activity. In victorian times for instance many gifted amateurs made significant contributions to sceintific knowledge. In the 20th century the convention arose that only those with a Phd who are actively publishing can be considered scientists and therefore qualified to opine on scientific matters. However studies have shown that this situation leads to vast amounts of virtually worthless research filling the pages of the myriad journals.
I understand the need for rigour in the peer reviewing process, but the ultimate test of science is "does it work?"
Original thinkers with a strong sense of curiosity about the natural world and a willingness to practice sound scientific technique have nothing to fear here.
http://www.sciam.com/article.cfm?id=science-2-point-0-great-new-tool-or-great-risk
It seems to me the only risk is a certain self important types who never had an original thought in their lives may be exposed as such. This is a great example of how the internet will completely transform certain aspects of human endeavour. Although the 20th century has seen a blossoming of science, it has also created a world where most people don't feel part of this exciting and vital human activity. In victorian times for instance many gifted amateurs made significant contributions to sceintific knowledge. In the 20th century the convention arose that only those with a Phd who are actively publishing can be considered scientists and therefore qualified to opine on scientific matters. However studies have shown that this situation leads to vast amounts of virtually worthless research filling the pages of the myriad journals.
I understand the need for rigour in the peer reviewing process, but the ultimate test of science is "does it work?"
Original thinkers with a strong sense of curiosity about the natural world and a willingness to practice sound scientific technique have nothing to fear here.
Monday, April 7, 2008
Chirality of amino acids due to meteorite star exposure?
I've just started checking out Science Daily again. The interface is still pretty cluttered but interesting article here:
http://www.sciencedaily.com/releases/2008/04/080406114742.htm
It suggests our amino acids are left rather than right-handed due to exposure to polarised light from neutron stars. Given that it has recently been shown that meteorites can contain up to 250ppm amino acids, this mechanism of chrality lends further support to the idea that metorites from early bombardment events are the primary source of early AAs. As Breslow points out:
"This work is related to the probability that there is life somewhere else. Everything that is going on on Earth occurred because the meteorites happened to land here. But they are obviously landing in other places. If there is another planet that has the water and all of the things that are needed for life, you should be able to get the same process rolling."
Life forms composed of proteins made in turn of chains of amino acids that is. I look forward to his work on nucleic acids.
http://www.sciencedaily.com/releases/2008/04/080406114742.htm
It suggests our amino acids are left rather than right-handed due to exposure to polarised light from neutron stars. Given that it has recently been shown that meteorites can contain up to 250ppm amino acids, this mechanism of chrality lends further support to the idea that metorites from early bombardment events are the primary source of early AAs. As Breslow points out:
"This work is related to the probability that there is life somewhere else. Everything that is going on on Earth occurred because the meteorites happened to land here. But they are obviously landing in other places. If there is another planet that has the water and all of the things that are needed for life, you should be able to get the same process rolling."
Life forms composed of proteins made in turn of chains of amino acids that is. I look forward to his work on nucleic acids.
Sunday, April 6, 2008
35,000yr old Pilbara tools
A new archaelogical find in WA will shed new light on Australian colonisation by aborigines:
http://www.theage.com.au/articles/2008/04/06/1207420202548.html
http://www.theage.com.au/articles/2008/04/06/1207420202548.html
Saturday, April 5, 2008
microGibson
Gibson at odds with Guitar hero:
http://www.reuters.com/article/entertainmentNews/idUSN2147943920080322?feedType=RSS&feedName=entertainmentNews
I assumed that this would be about Gibson litigating WRT their IP, ironnically the IP is all bought and paid for, however it appears Viacom assumed the hardware came as part of the package. As an aside, I wonder why Fender hasnt got into this obviously lucrative virtual market?
http://www.reuters.com/article/entertainmentNews/idUSN2147943920080322?feedType=RSS&feedName=entertainmentNews
I assumed that this would be about Gibson litigating WRT their IP, ironnically the IP is all bought and paid for, however it appears Viacom assumed the hardware came as part of the package. As an aside, I wonder why Fender hasnt got into this obviously lucrative virtual market?
Occasional postings and links on evolution, rock and whatever else turns up
Just started this today to collect links that interest me all in one place.
One subject of interest to myself (and apparently a lot of other people, particularly the religiously inclined) is the origin of life. Heres a link about the kind of research i just love. These guys are demonstrating that bubbles with RNA in them "outcompete" those without :
http://www.hhmi.org/news/szostak4.html
One subject of interest to myself (and apparently a lot of other people, particularly the religiously inclined) is the origin of life. Heres a link about the kind of research i just love. These guys are demonstrating that bubbles with RNA in them "outcompete" those without :
http://www.hhmi.org/news/szostak4.html
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