Wednesday, August 30, 2006
Latest reviews
I reviewed two books on human paleontology and evolution for the July issue of Discover. They were: The First Human, by Ann Gibbons, and Before the Dawn, by Nicholas Wade.
Diversity's hidden iceberg
Many of us keep a list of the bird species that show up in our back gardens, or the types of fungi in our local wood. The species is perhaps our most simple, fundamental, and useful tool for describing the living world. But it's a more slippery concept than it might first appear — and the harder one looks, the more slippery it becomes.
Take, for example, the hoverfly Microdon mutabilis. The flies' larva infiltrates an ant's nest — probably by chemically mimicking its host — and spends two years eating ant eggs and larva before pupating. In 2002, entomologist Karsten Schönrogge of the Centre for Ecology and Hydrology in Dorset (soon to be closed by the UK government) and his colleagues showed that M. mutabilis was in fact two species, each specialized to parasitize a different species of ant.
Now, Schönrogge's team have found that the fly's diversity is still finer-grained. Working on the Scottish island of Mull, they moved eggs of M. mutabilis from the ant nests in which they were laid to different nests of the same species.
Almost no eggs survived a move of more than three kilometres. Ants from a different neighbourhood were able to recognize and destroy hoverfly eggs before the larvae could gain entry.
So the species that we have called Microdon mutabilis seems, in fact, to be many populations closely adapted to their local ant hosts, and unable to survive elsewhere. As the fly is found from Ireland to Japan, the one name may conceal a mind-boggling number of cryptic fly species.
This kind of extreme specialisation, and the diversity that comes with it, is especially likely to evolve in parasites, which must trick their hosts into accepting their malign embrace. Faced with overcoming the host's powers of detection, natural selection will hone the parasite's powers of deception, until it may become so expert at exploiting one host that it closes off all its other options, and paints itself into an evolutionary corner.
Microdon, however, might have a trick up its sleeve. It prefers to eat small larvae or eggs. This causes the ant's brood to become biased towards large larvae. These are more likely to be potential queens and males — the sexual forms that found new colonies. And so the hoverfly might be able to promote the reproduction of the colonies that it infests, and ensure a new supply of susceptible hosts.
In general, the smaller you get, the vaguer our notions of biodiversity become. We have a pretty good idea of how many species of bird and mammal there are, and what a species of bird is. But we have almost no idea how many different types of insect, fungi or microbe there are, or how we should classify them. DNA sequencing is revealing yet another world of diversity, that biologists are unsure how to reconcile with their more traditional categories.
Our understanding of what diversity is, and how much of it there is, also has practical implications. Microdon is listed in the Red Data Book as being of conservation concern. But what should we be trying to conserve? The species as a whole? Individual populations? And how should we conserve it? It certainly doesn't look as if one could move hoverflies from one place to another.
The hoverfly is a small example of how important it is to keep the fabric of life intact. It's not even that we won't know what we've lost until it's gone. Even then, we still won't know.
Take, for example, the hoverfly Microdon mutabilis. The flies' larva infiltrates an ant's nest — probably by chemically mimicking its host — and spends two years eating ant eggs and larva before pupating. In 2002, entomologist Karsten Schönrogge of the Centre for Ecology and Hydrology in Dorset (soon to be closed by the UK government) and his colleagues showed that M. mutabilis was in fact two species, each specialized to parasitize a different species of ant.
Now, Schönrogge's team have found that the fly's diversity is still finer-grained. Working on the Scottish island of Mull, they moved eggs of M. mutabilis from the ant nests in which they were laid to different nests of the same species.
Almost no eggs survived a move of more than three kilometres. Ants from a different neighbourhood were able to recognize and destroy hoverfly eggs before the larvae could gain entry.
So the species that we have called Microdon mutabilis seems, in fact, to be many populations closely adapted to their local ant hosts, and unable to survive elsewhere. As the fly is found from Ireland to Japan, the one name may conceal a mind-boggling number of cryptic fly species.
This kind of extreme specialisation, and the diversity that comes with it, is especially likely to evolve in parasites, which must trick their hosts into accepting their malign embrace. Faced with overcoming the host's powers of detection, natural selection will hone the parasite's powers of deception, until it may become so expert at exploiting one host that it closes off all its other options, and paints itself into an evolutionary corner.
Microdon, however, might have a trick up its sleeve. It prefers to eat small larvae or eggs. This causes the ant's brood to become biased towards large larvae. These are more likely to be potential queens and males — the sexual forms that found new colonies. And so the hoverfly might be able to promote the reproduction of the colonies that it infests, and ensure a new supply of susceptible hosts.
In general, the smaller you get, the vaguer our notions of biodiversity become. We have a pretty good idea of how many species of bird and mammal there are, and what a species of bird is. But we have almost no idea how many different types of insect, fungi or microbe there are, or how we should classify them. DNA sequencing is revealing yet another world of diversity, that biologists are unsure how to reconcile with their more traditional categories.
Our understanding of what diversity is, and how much of it there is, also has practical implications. Microdon is listed in the Red Data Book as being of conservation concern. But what should we be trying to conserve? The species as a whole? Individual populations? And how should we conserve it? It certainly doesn't look as if one could move hoverflies from one place to another.
The hoverfly is a small example of how important it is to keep the fabric of life intact. It's not even that we won't know what we've lost until it's gone. Even then, we still won't know.
Tuesday, June 27, 2006
An MRI scanner darkly
I've got a feature in the 22 June issue of Nature about some neuroscientists useing Richard Linklater's films to probe how the brain responds differently to realistic and meaningful, but obviously unreal stimuli.
Raymond Mar and his colleagues used Linklater's 2001 film 'Waking Life', an movie made using a technique called rotoscoping, which involves turning video footage into animation. The researchers sat their subjects in a brain scanner and showed them clips of the original video footage, and then the animated version of the same shot.
They were particularly interested in the brain areas involved in attributing motives to others, and trying to work out what they are thinking and planning on doing. We will attribute intentionality to almost anything - characters in books, cartoons, a malfunctioning computer. But it seems, Mar's team found, that the brain areas involved fire more strongly when the stimuli are more realistic. But no one is quite sure why, or what this means.
The piece also looks at how our brains cope with the reality/fiction divide more generally, and the psychology of narrative. It seems the the suspension of disbelief is a myth, and that, as long as information comes in the form of a story, we are ready to believe almost anything.
One of the reasons I wrote this now is that Linklater has another rotoscoped film out next month, A Scanner Darkly, based on the Philip K. Dick novel. Dick, of course, was well into the untrustworthiness of our brain's picture of reality.
Raymond Mar and his colleagues used Linklater's 2001 film 'Waking Life', an movie made using a technique called rotoscoping, which involves turning video footage into animation. The researchers sat their subjects in a brain scanner and showed them clips of the original video footage, and then the animated version of the same shot.
They were particularly interested in the brain areas involved in attributing motives to others, and trying to work out what they are thinking and planning on doing. We will attribute intentionality to almost anything - characters in books, cartoons, a malfunctioning computer. But it seems, Mar's team found, that the brain areas involved fire more strongly when the stimuli are more realistic. But no one is quite sure why, or what this means.
The piece also looks at how our brains cope with the reality/fiction divide more generally, and the psychology of narrative. It seems the the suspension of disbelief is a myth, and that, as long as information comes in the form of a story, we are ready to believe almost anything.
One of the reasons I wrote this now is that Linklater has another rotoscoped film out next month, A Scanner Darkly, based on the Philip K. Dick novel. Dick, of course, was well into the untrustworthiness of our brain's picture of reality.
Wednesday, June 14, 2006
100 conservation questions
Everyone loves a list, including ecologists. And some of the bigwigs of British conservation have now released one with the snappy title of " 100 ecological questions of high policy relevance in the UK".
The list is grouped by topic rather than importance, which will make the five-hour special on Channel 4 less interesting. There are 14 categories, such as forestry, urban development, and invasive species. Questions include: 21. Why have many woodland birds declined? 32. What are the impacts of recreational activities on biodiversity?, 67. How can soil carbon be retained and further carbon be sequestered in the soil?
The authors acknowledge that these are rather vague. This, they say, is the product of input from policymakers, because policy is typically focussed on quite general questions. The challenge for researchers is to derive meaningful specific research projects to address these (I wonder if framing grant applications in terms of this list will help people get funding) and, conversely, to stress what can be generalized from their own tightly focussed projects.
One hundred questions seems to me rather a lot — a shorter list would have been easier to get one's head around, and so perhaps more galvanizing. But these 100 were boiled down from a longlist of 1,003 (!), so perhaps we should be grateful.
The lead author is Bill Sutherland, of the University of East Anglia, who is working hard to promote what (with reference to medicine) he calls ' evidence-based conservation': i.e., making sure that conservation practices are tested, and that they work, rather than doing things just because they're traditional, or seem like a good idea.
You'd be surprised how little we know about whether conservation strategies work or not. I touched upon this earlier this year in a Nature piece on farmland biodiversity called "How green was my subsidy?" [subscription required].
Billions of euros of EU money are spent each year on agri-environment schemes, but many have no clear goals and are not monitored. When people look at whether they do enhance biodiversity, about half seem to have no effect. It would be a mistake to be down on these subsidies as a whole, though — they take many approaches, and have many goals, and some undoubtedly do work. An international project called AE footprint is currently trying to work out how to evaluate them.
How about a global version of the same list (perhaps there already is)? My guess would be that understanding hotspots and carbon sinks and sources would feature large.
The list is grouped by topic rather than importance, which will make the five-hour special on Channel 4 less interesting. There are 14 categories, such as forestry, urban development, and invasive species. Questions include: 21. Why have many woodland birds declined? 32. What are the impacts of recreational activities on biodiversity?, 67. How can soil carbon be retained and further carbon be sequestered in the soil?
The authors acknowledge that these are rather vague. This, they say, is the product of input from policymakers, because policy is typically focussed on quite general questions. The challenge for researchers is to derive meaningful specific research projects to address these (I wonder if framing grant applications in terms of this list will help people get funding) and, conversely, to stress what can be generalized from their own tightly focussed projects.
One hundred questions seems to me rather a lot — a shorter list would have been easier to get one's head around, and so perhaps more galvanizing. But these 100 were boiled down from a longlist of 1,003 (!), so perhaps we should be grateful.
The lead author is Bill Sutherland, of the University of East Anglia, who is working hard to promote what (with reference to medicine) he calls ' evidence-based conservation': i.e., making sure that conservation practices are tested, and that they work, rather than doing things just because they're traditional, or seem like a good idea.
You'd be surprised how little we know about whether conservation strategies work or not. I touched upon this earlier this year in a Nature piece on farmland biodiversity called "How green was my subsidy?" [subscription required].
Billions of euros of EU money are spent each year on agri-environment schemes, but many have no clear goals and are not monitored. When people look at whether they do enhance biodiversity, about half seem to have no effect. It would be a mistake to be down on these subsidies as a whole, though — they take many approaches, and have many goals, and some undoubtedly do work. An international project called AE footprint is currently trying to work out how to evaluate them.
How about a global version of the same list (perhaps there already is)? My guess would be that understanding hotspots and carbon sinks and sources would feature large.
Tuesday, June 06, 2006
Sensible sheep, and cheeky monkeys
A couple of things in the most recent Animal Behaviour caught my eye.
One, Sheep self-medicate when challenged with illness-inducing foods, by Juan Villalba and colleagues, found that lambs can learn which compounds will relieve a stomach ache brought on by, say, tannins. Then, if given the same tannins in the future will choose the appropriate remedy.
I’d put this down in the cute, but not earth-shattering category. Villalba and co write that:
“From prehistoric times, people have looked to the presumed self-medicative behaviour of animals for remedies of ailments but it is still not clear whether animals seek medicinal compounds to recuperate from illness. Evidence of self-medication is based almost exclusively on observations rather than experimental analyses.”
On the other hand, there’re already whole books on animal self-medication.
The other is called Rhesus monkeys, Macaca mulatta, know what others can and cannot hear, by Laurie Santos and colleagues. The researchers set up an experiment where the monkeys competed for grapes with a human experimenter. The monkeys had a choice between picking grapes from a noisy container, and from a silent one.
If the human was looking in the other direction, the monkey preferred the silent container, presumably showing it was out to sneakily get the grape. If the human was paying attention, the monkey didn’t care which container it took — showing that the monkeys understand the connection between hearing and knowing. This also hints that they have theory-of-mind type notions of what others are thinking.
One, Sheep self-medicate when challenged with illness-inducing foods, by Juan Villalba and colleagues, found that lambs can learn which compounds will relieve a stomach ache brought on by, say, tannins. Then, if given the same tannins in the future will choose the appropriate remedy.
I’d put this down in the cute, but not earth-shattering category. Villalba and co write that:
“From prehistoric times, people have looked to the presumed self-medicative behaviour of animals for remedies of ailments but it is still not clear whether animals seek medicinal compounds to recuperate from illness. Evidence of self-medication is based almost exclusively on observations rather than experimental analyses.”
On the other hand, there’re already whole books on animal self-medication.
The other is called Rhesus monkeys, Macaca mulatta, know what others can and cannot hear, by Laurie Santos and colleagues. The researchers set up an experiment where the monkeys competed for grapes with a human experimenter. The monkeys had a choice between picking grapes from a noisy container, and from a silent one.
If the human was looking in the other direction, the monkey preferred the silent container, presumably showing it was out to sneakily get the grape. If the human was paying attention, the monkey didn’t care which container it took — showing that the monkeys understand the connection between hearing and knowing. This also hints that they have theory-of-mind type notions of what others are thinking.
Friday, May 12, 2006
Seals go from the arctic to Siberia. But how?
Lake Baikal in Siberia and the Caspian Sea each has its own species of seal that evolved from marine species a few million years ago. But which species they evolved from, and how they got there, has remained controversial. A new study by Jukka Palo and Risto Vainola at the University of Helsinki challenges existing ideas, and adds new mysteries.
It was previously thought that the Baikal seal Phoca sibirica and the Caspian seal P. caspica were most closely related to the Arctic ring seal P. hispida. But analysing mitochondrial DNA sequences, the two Finns find that the Caspian seal is in fact more closely related to the grey seal Halichoerus grypus, and that several other seals, including the boreal harbour seal, are just as, if not more closely related to the landlocked seals than the Arctic ring seal. It looks as if a bunch of species evolved in a bit of a burst, and that the old triad of Caspian, Baikal and Arctic ring seals — the three species were lumped together in their own sub-genus — does not reflect evolutionary history.
The DNA suggests that the two landlocked seals evolved in the Arctic Ocean about 2-3 million years ago (although DNA dates are controversial), in the Late Pliocene. This raises another problem, of how the seals could have made their journey from the Arctic to their current homes. Previous hypotheses suggested that the seals got to the Caspian first, and then spread out, or hopped across the continent in glacial lakes during an ice age. But the DNA doesn't fit with the paleoclimate data. We have no idea what water features may have existed at this time that let the seals' ancestors make the journey south.
It was previously thought that the Baikal seal Phoca sibirica and the Caspian seal P. caspica were most closely related to the Arctic ring seal P. hispida. But analysing mitochondrial DNA sequences, the two Finns find that the Caspian seal is in fact more closely related to the grey seal Halichoerus grypus, and that several other seals, including the boreal harbour seal, are just as, if not more closely related to the landlocked seals than the Arctic ring seal. It looks as if a bunch of species evolved in a bit of a burst, and that the old triad of Caspian, Baikal and Arctic ring seals — the three species were lumped together in their own sub-genus — does not reflect evolutionary history.
The DNA suggests that the two landlocked seals evolved in the Arctic Ocean about 2-3 million years ago (although DNA dates are controversial), in the Late Pliocene. This raises another problem, of how the seals could have made their journey from the Arctic to their current homes. Previous hypotheses suggested that the seals got to the Caspian first, and then spread out, or hopped across the continent in glacial lakes during an ice age. But the DNA doesn't fit with the paleoclimate data. We have no idea what water features may have existed at this time that let the seals' ancestors make the journey south.
Quick update
Since I last posted I've had a short piece on turtle conservation in Science Now (Green turtles make a comeback) and a longer piece on conservation, agriculture and subsidies in Nature (How green was my subsidy?). I'm going to be regular now, I promise.
Wednesday, February 08, 2006
A rotten theory
Why don't we like mouldy food? It seems like a no-brainer, but why, in fact, should most foods become unpalatable when colonized by microbes? The existence of Roquefort, after all, shows that mould does not always equal bad food.
1977, Dan Janzen suggested that microbes spoil food so that they can keep it for themselves — it's a trick that helps them compete for resources with animals, and avoid being eaten themselves. It's not just humans that prefer fresh food to rotten — birds do to, given the choice.
The idea has attracted a lot of favourable comment from researchers, but, say Tom Sherratt and his colleagues in Ecological Modelling, it has never been properly analysed. They have done this — and it's not good news for Janzen's idea.
Sherratt's team present a mathematical model that shows that if producing chemicals that spoil food is costly, then the microbes that do it will be displaced by free-loaders, that take the benefit of living on spoiled food, but don't pay the cost.
The 1970s (around the time the Selfish Gene came out) were a bit of a golden age for ideas like Janzen's, that propose for ingenious adaptive explanations for biological phenomena. It's surprising that no one got around to putting the idea through the theoretical wringer before now, but not so surprising that the idea hasn’t stood up to close analysis, because freeloaders are probably a powerful force against group behaviour of this sort.
If all the microbes in a group belong to a genetically identical clone, then spoiling might work, but Sherratt and co suggest that microbes move around too much for clones to maintain their integrity. (Entirely tangentially, for my PhD I worked on a similar problem regarding the evolution of altruism, in the form of soldier behaviour, in aphids.)
The researchers suggest, more prosaically, that spoiling chemicals might be used in competition between microbes sharing a food source, or they might just be a by-product of the process of decomposition.
1977, Dan Janzen suggested that microbes spoil food so that they can keep it for themselves — it's a trick that helps them compete for resources with animals, and avoid being eaten themselves. It's not just humans that prefer fresh food to rotten — birds do to, given the choice.
The idea has attracted a lot of favourable comment from researchers, but, say Tom Sherratt and his colleagues in Ecological Modelling, it has never been properly analysed. They have done this — and it's not good news for Janzen's idea.
Sherratt's team present a mathematical model that shows that if producing chemicals that spoil food is costly, then the microbes that do it will be displaced by free-loaders, that take the benefit of living on spoiled food, but don't pay the cost.
The 1970s (around the time the Selfish Gene came out) were a bit of a golden age for ideas like Janzen's, that propose for ingenious adaptive explanations for biological phenomena. It's surprising that no one got around to putting the idea through the theoretical wringer before now, but not so surprising that the idea hasn’t stood up to close analysis, because freeloaders are probably a powerful force against group behaviour of this sort.
If all the microbes in a group belong to a genetically identical clone, then spoiling might work, but Sherratt and co suggest that microbes move around too much for clones to maintain their integrity. (Entirely tangentially, for my PhD I worked on a similar problem regarding the evolution of altruism, in the form of soldier behaviour, in aphids.)
The researchers suggest, more prosaically, that spoiling chemicals might be used in competition between microbes sharing a food source, or they might just be a by-product of the process of decomposition.
Friday, January 27, 2006
Big botany
Two papers on plants caught my eye this week. The first is from Nature on the scaling of plant metabolic rate. Peter Reich and his colleagues say that plant respiration increases linearly with plant size — that is, a plant has a metabolic rate twice that of one half its size.
This seems to contradict the West, Brown and Enquist (WBE) model of metabolic rate, which says that metabolic rate in all organisms is proportional to the 3/4 power of body mass — so a plant would have a metabolic rate only about 1.7 times that of one half its size.
Whether this is true, and whether the WBE model is the right way to explain metabolic rate, is controversial. I think that there is good evidence for what's known as quarter-power scaling over a wide range of plants and animals, and I also think that the WBE model makes a lot of sense (but then I've written a book about all this, so I would say that). But these things take decades to sort out, so there will be a lot of to-ing and fro-ing between both sides before any hard consensus emerges. Don't expect the quarter-power people to give up their ideas in the face of this new evidence.
The other paper deals with another big issue in ecology — what maintains the high diversity in tropical forests? Writing in Science, a massive team of ecologists led by Christopher Wills present evidence from forest plots in Panama and Malaysia showing that rare species are more likely to survive than common ones — an advantage that buffers against extinction.
The team don't seem to plump for a reason as to why this should be. One possibility is the Janzen-Connell hypothesis, which says that mature trees attract pathogens, herbivores and so on that make it harder for seeds of the same species to germinate in the vicinity. Another possibility stems from the fact that all species compete most strongly with other members of their own kind — because their needs are so similar — than with other species, and that this competition is weaker for rare species.
I am reading Jonathon Silvertown's new book on plant ecology, Demons in Eden at the mo. He has an excellent discussion of these issues that comes down in favour of the J-C view of things. I don't think things are as clear cut as all that, but there does seem to be good evidence that the process is important in forests.
This seems to contradict the West, Brown and Enquist (WBE) model of metabolic rate, which says that metabolic rate in all organisms is proportional to the 3/4 power of body mass — so a plant would have a metabolic rate only about 1.7 times that of one half its size.
Whether this is true, and whether the WBE model is the right way to explain metabolic rate, is controversial. I think that there is good evidence for what's known as quarter-power scaling over a wide range of plants and animals, and I also think that the WBE model makes a lot of sense (but then I've written a book about all this, so I would say that). But these things take decades to sort out, so there will be a lot of to-ing and fro-ing between both sides before any hard consensus emerges. Don't expect the quarter-power people to give up their ideas in the face of this new evidence.
The other paper deals with another big issue in ecology — what maintains the high diversity in tropical forests? Writing in Science, a massive team of ecologists led by Christopher Wills present evidence from forest plots in Panama and Malaysia showing that rare species are more likely to survive than common ones — an advantage that buffers against extinction.
The team don't seem to plump for a reason as to why this should be. One possibility is the Janzen-Connell hypothesis, which says that mature trees attract pathogens, herbivores and so on that make it harder for seeds of the same species to germinate in the vicinity. Another possibility stems from the fact that all species compete most strongly with other members of their own kind — because their needs are so similar — than with other species, and that this competition is weaker for rare species.
I am reading Jonathon Silvertown's new book on plant ecology, Demons in Eden at the mo. He has an excellent discussion of these issues that comes down in favour of the J-C view of things. I don't think things are as clear cut as all that, but there does seem to be good evidence that the process is important in forests.
Darwin, Homer and Austen
I've got a piece in this week's Nature called "Textual selection" that looks at the newish field of Darwinian literary theory (registration required — see here for a summary). These guys (mostly) want to chuck out Freud, Marx et al, and interpret texts from a Darwinian perspective — mate choice, kin selection and all that. It was interesting speaking to non-scientists (including the author Ian McEwan), and try to get my head around someone else's issues and arguments for a change.
These folk think like scientists — they want to make testable hypotheses, collect data, get robust answers, move on. This is very different to a lot of literary criticism, which is also about kicking ideas around, as kicking them out. Many literary critics seem to read Freud, or Marx or Derrida, as if it was a novel, rather than anything with a claim to objective truth — whether an idea is stimulating is as important as whether it is true.
This has got a bit of coverage recently. For more, try here, and here to read Mark Lawson slagging whole idea off in the Guardian. The NY times also had a big piece, but it seems to be subscriber-only now.
These folk think like scientists — they want to make testable hypotheses, collect data, get robust answers, move on. This is very different to a lot of literary criticism, which is also about kicking ideas around, as kicking them out. Many literary critics seem to read Freud, or Marx or Derrida, as if it was a novel, rather than anything with a claim to objective truth — whether an idea is stimulating is as important as whether it is true.
This has got a bit of coverage recently. For more, try here, and here to read Mark Lawson slagging whole idea off in the Guardian. The NY times also had a big piece, but it seems to be subscriber-only now.
Thursday, January 12, 2006
Did viruses invent DNA?
What with the threat of bird flu, the reality of HIV, and the general unseemliness of having one's cells pressed into labour on behalf of something alien and microscopic, it is small wonder that people don't much like viruses. But it's possible that we may actually have something to thank the little parasites for. They may have been the first creatures to find a use for DNA, a discovery that set life on the road to its current rich complexity...
This feature in Nature (by me; registration required) looks at Patrick Forterre's idea that viruses invented DNA as a way of invading cells in the RNA world — just as many viruses today use similar genetic tricks to evade cellular defences. It's a neat idea, and raises the useful question of what the original advantage of DNA might have been. It is more chemically stable than RNA (which biologists think came first) and can be used for longer genomes.
But, Forterre points out, no cell could know that it wanted a longer, more complex genome and evolve DNA accordingly, because evolution has no foresight. Not everyone agrees, but there is a lot of excitement about viral diversity and evolution at the moment - there's some crazy stuff out there, virus-wise, much of it currently being discovered by David Prangishvili.
This feature in Nature (by me; registration required) looks at Patrick Forterre's idea that viruses invented DNA as a way of invading cells in the RNA world — just as many viruses today use similar genetic tricks to evade cellular defences. It's a neat idea, and raises the useful question of what the original advantage of DNA might have been. It is more chemically stable than RNA (which biologists think came first) and can be used for longer genomes.
But, Forterre points out, no cell could know that it wanted a longer, more complex genome and evolve DNA accordingly, because evolution has no foresight. Not everyone agrees, but there is a lot of excitement about viral diversity and evolution at the moment - there's some crazy stuff out there, virus-wise, much of it currently being discovered by David Prangishvili.
Tuesday, November 29, 2005
Big in the tropics
How big can a cold-blooded animal get? It depends how hot it is (perhaps).
Larry Li's team argues that animals have a minimum metabolic rate, below which they become too sluggish to function. This limits their size, because as animals get bigger, their relative metabolic rate declines — which is why a shrew needs to eat its own body weight each day, and you or I get by on about 2% of our weight. But body temperature also has an exponential effect on metabolic rate: a 5 °C rise leads to a 150% increase in metabolic rate. In tropical climates, then, the effects of increased temperature compensate for those of increased size, so animals can get bigger. Li and his colleagues back their idea up with evidence that in a variety of beasts — earthworms, millipedes, cockroaches, frogs and so on — the biggest tropical species is much larger than the biggest temperate species.
I suspect that this idea will be quite controversial. One can think of other reasons why tropical species might be bigger — there could be more food around, for example. It's also often argued that animals get bigger towards the poles, because it helps them keep warm (because they lose heat less quickly). This idea is known as Bergmann's rule.
Also, if I understand their earlier papers correctly (see here and here, these researchers have taken the highly unusual step of arguing that mass-specific metabolic rate does not change with size — i.e. that a big animal's cells do not burn energy more slowly than a small one's, which goes against more than 150 years of thinking about metabolic rate. This also seems to contradict their ideas on body size.
It's another entry into the strange history of metabolic rate, which everyone agrees is a fundamental biological property, but which has also generated more than its share of confusion and disagreement. My book looks at scientists' efforts to understand metabolic rate — which have been going on for about 200 years — as well as some recent powerful theories that seek to explain it (with which Li and co disagree), and the other things in nature that metabolic rate can explain. Check out the metabolic ecology link on the right to know a bit more. Check out my book next year to know more than you'll ever need.
Generality in ecology
The same issue of Oikos contains an interesting paper by Norman Owen-Smith of the University of Witwatersrand, South Africa, promoting what he calls a 'metaphysiological' approach to ecological theory. He argues (I think I have this right) that scientists studying the biology of populations — the rate at which they grow and the reasons they go extinct — have focussed too much on numbers of individuals, and not enough on flows of energy and matter, and that this approach has given their science shaky foundations, liable to fall foul of the basic laws of physics and biology. 'I believe that population ecology … has tended to seek mathematical rigour at the expense of biophysical rigour,' Owen-Smith writes. Getting it right matters, he adds, because our models will play a large part in how we try to conserve endangered populations.
Larry Li's team argues that animals have a minimum metabolic rate, below which they become too sluggish to function. This limits their size, because as animals get bigger, their relative metabolic rate declines — which is why a shrew needs to eat its own body weight each day, and you or I get by on about 2% of our weight. But body temperature also has an exponential effect on metabolic rate: a 5 °C rise leads to a 150% increase in metabolic rate. In tropical climates, then, the effects of increased temperature compensate for those of increased size, so animals can get bigger. Li and his colleagues back their idea up with evidence that in a variety of beasts — earthworms, millipedes, cockroaches, frogs and so on — the biggest tropical species is much larger than the biggest temperate species.
I suspect that this idea will be quite controversial. One can think of other reasons why tropical species might be bigger — there could be more food around, for example. It's also often argued that animals get bigger towards the poles, because it helps them keep warm (because they lose heat less quickly). This idea is known as Bergmann's rule.
Also, if I understand their earlier papers correctly (see here and here, these researchers have taken the highly unusual step of arguing that mass-specific metabolic rate does not change with size — i.e. that a big animal's cells do not burn energy more slowly than a small one's, which goes against more than 150 years of thinking about metabolic rate. This also seems to contradict their ideas on body size.
It's another entry into the strange history of metabolic rate, which everyone agrees is a fundamental biological property, but which has also generated more than its share of confusion and disagreement. My book looks at scientists' efforts to understand metabolic rate — which have been going on for about 200 years — as well as some recent powerful theories that seek to explain it (with which Li and co disagree), and the other things in nature that metabolic rate can explain. Check out the metabolic ecology link on the right to know a bit more. Check out my book next year to know more than you'll ever need.
Generality in ecology
The same issue of Oikos contains an interesting paper by Norman Owen-Smith of the University of Witwatersrand, South Africa, promoting what he calls a 'metaphysiological' approach to ecological theory. He argues (I think I have this right) that scientists studying the biology of populations — the rate at which they grow and the reasons they go extinct — have focussed too much on numbers of individuals, and not enough on flows of energy and matter, and that this approach has given their science shaky foundations, liable to fall foul of the basic laws of physics and biology. 'I believe that population ecology … has tended to seek mathematical rigour at the expense of biophysical rigour,' Owen-Smith writes. Getting it right matters, he adds, because our models will play a large part in how we try to conserve endangered populations.
Thursday, November 17, 2005
Is everything everywhere?
"...For about a century, microbiologists have believed that the organisms they study are unhindered by geographic boundaries, traveling the world and thriving wherever they find their preferred environment--be it hot springs, freshwater ponds, or rotting fir trees. That view gives researchers who study microbes a rather different perspective on the world. As the Dutch biologist Lourens Bass-Becking put it in 1934: "Everything is everywhere; the environment selects."
Or maybe not. In the past few years, many microbial ecologists have come to believe that microbes are not infinitely mobile. Bass-Becking's dictum is really only "an assumption,"says Jessica Green of the University of California, Merced. "It's based on a confusion of hypotheses for facts."..."
I've got a new feature in Science (registration required) looking at microbial giogeography, and whether the patterns seen for plants and animals - such as the fact that bigger islands contain more species than small, or that the life in two blocks of forest becomes more different as the distance between them increases - hold for microbes. Many have thought that they don't, but the recent boom in studies of DNA fished out of the environment suggests that perhaps they do, in some form or other.
The scientists I spoke to: Jessica Green,Bland Finlay, Claire Horner-Devine, Jennifer Hughes, Tom Fenchel.
Or maybe not. In the past few years, many microbial ecologists have come to believe that microbes are not infinitely mobile. Bass-Becking's dictum is really only "an assumption,"says Jessica Green of the University of California, Merced. "It's based on a confusion of hypotheses for facts."..."
I've got a new feature in Science (registration required) looking at microbial giogeography, and whether the patterns seen for plants and animals - such as the fact that bigger islands contain more species than small, or that the life in two blocks of forest becomes more different as the distance between them increases - hold for microbes. Many have thought that they don't, but the recent boom in studies of DNA fished out of the environment suggests that perhaps they do, in some form or other.
The scientists I spoke to: Jessica Green,Bland Finlay, Claire Horner-Devine, Jennifer Hughes, Tom Fenchel.
Wednesday, November 09, 2005
Junk food makes gulls dumb
The old wives are right — fish is good brain food. But only if it's the right fish. Kittiwake chicks fed on a diet of smelt, which is low in lipids, are stupider than those that get lots of oily fish.
This, coupled with climatic changes, could help explain why the gull species has been "in precipitous decline" in Alaska over the past few decades, say Alexander Kitaysky of the University of Alaska, Faribanks and his colleagues.
Kitaysky's team fed some captive red-legged kittiwake chicks as much fish as they could eat, but gave others more meagre rations. They also fed some chicks on oily silverside, and others or lipid-poor smelt.
At the end of the test, the birds on a restricted diet showed, not surprisingly, higher levels of nutritional stress, as revealed by their high levels of the hormone cortisone. Oily fish has more calories per-gram than other types, so the smelt-eaters had a harder time getting enough calories.
Hungry birds also showed cognitive impairments. Birds learnt how to open a plastic pot with food in, and then had to learn that black pots had food in, and white ones were empty. Those on the restricted diet did worse in these tests, and the birds on the poorest diets never learned to associate black pots with food.
A diet of smelt exacerbated the effects of nutritional stress alone, showing that both calories and lipid content seem to affect the chicks' learning ability.
Once they fledge, kittiwake chicks must fend for themselves, so slow learners might struggle to survive. Why kittiwakes have declined has been a puzzle — adults have been have having as many chicks as ever, but fewer birds survive to adulthood.
The change in diet is probably linked to a climatic change in the mid 1970s — a switch in a cycle called the Pacific decadal oscillation from cool to warm waters —that caused populations of oily fish— such as herring and mackerel — to decline, and favoured other fish such as pollock.
This finding also lines up alongside a theory to explain the similar decline of Steller's sea lions over the same period. The 'junk food' hypothesis advocated by Andrew Trites at the University of British Columbia and his colleagues argues that sea lions and seals have declined because they do worse on a diet of non-oily fish — experiments show that they have to eat more to get the same calories, and gain weight more quickly, for example. The whole issue of sea lion declines is controversial (registration required); some see this as an attempt to get the fishing industry off the hook, and view Trites' links with the industry with suspicion. (Although for what it's worth, the junk-food idea seems reasonable to me.)
Weirdly, Robert Winston, the avuncular face of British science communication, has recently got into trouble for advertising milk with added omega-3s (i.e. fish oil), and hinting that drinking it might make kids smarter. Perhaps he should market the magic milk to kittiwakes.
This, coupled with climatic changes, could help explain why the gull species has been "in precipitous decline" in Alaska over the past few decades, say Alexander Kitaysky of the University of Alaska, Faribanks and his colleagues.
Kitaysky's team fed some captive red-legged kittiwake chicks as much fish as they could eat, but gave others more meagre rations. They also fed some chicks on oily silverside, and others or lipid-poor smelt.
At the end of the test, the birds on a restricted diet showed, not surprisingly, higher levels of nutritional stress, as revealed by their high levels of the hormone cortisone. Oily fish has more calories per-gram than other types, so the smelt-eaters had a harder time getting enough calories.
Hungry birds also showed cognitive impairments. Birds learnt how to open a plastic pot with food in, and then had to learn that black pots had food in, and white ones were empty. Those on the restricted diet did worse in these tests, and the birds on the poorest diets never learned to associate black pots with food.
A diet of smelt exacerbated the effects of nutritional stress alone, showing that both calories and lipid content seem to affect the chicks' learning ability.
Once they fledge, kittiwake chicks must fend for themselves, so slow learners might struggle to survive. Why kittiwakes have declined has been a puzzle — adults have been have having as many chicks as ever, but fewer birds survive to adulthood.
The change in diet is probably linked to a climatic change in the mid 1970s — a switch in a cycle called the Pacific decadal oscillation from cool to warm waters —that caused populations of oily fish— such as herring and mackerel — to decline, and favoured other fish such as pollock.
This finding also lines up alongside a theory to explain the similar decline of Steller's sea lions over the same period. The 'junk food' hypothesis advocated by Andrew Trites at the University of British Columbia and his colleagues argues that sea lions and seals have declined because they do worse on a diet of non-oily fish — experiments show that they have to eat more to get the same calories, and gain weight more quickly, for example. The whole issue of sea lion declines is controversial (registration required); some see this as an attempt to get the fishing industry off the hook, and view Trites' links with the industry with suspicion. (Although for what it's worth, the junk-food idea seems reasonable to me.)
Weirdly, Robert Winston, the avuncular face of British science communication, has recently got into trouble for advertising milk with added omega-3s (i.e. fish oil), and hinting that drinking it might make kids smarter. Perhaps he should market the magic milk to kittiwakes.
Tuesday, November 01, 2005
Homeric wildlife
The Homeric epics and the founding texts of European civilization, one of the wellsprings of our culture — and, it turns out, a handy field guide to prehistoric Greek wildlife.
Two Greek biologists, Eleni Voultsiadou and Apostolos Tatolas at the Aristotle University of Thessaloniki have gone through the works of Homer and Hesiod, which were written down around 600-800 BC, and recorded what animals are mentioned in the texts. The results tell us both what the ancient Greeks knew about the animals around them, and also how things have changed.
In total, the epics refer to animals 2442 times, and give them 71 different names. The ancient Greeks were, naturally enough, most concerned about useful animals — the majority of references are to domestic or food species such as goat, sheep, pig, dog and honeybee. They also took notice of pests, such as ticks, flies, and the woodworm that ate Odysseus' bow.
But the Greeks also knew their wildlife: lions, wolves and bears appear, as do tortoises, peregrine falcons, swan, geese and the night heron. Sea life is not as well represented as land animals, but dolphins and monk seal appear, and even octopus, sponge and an edible sea squirt. Apart from the eel, all fish were lumped together.
Some animals appear metaphorically. The owl — Athena's bird — appears as a word meaning 'having shining eyes'. People are described as chatting like cicadas.
The epics show which animals have disappeared from Greece in the past three millennia, such as the lion. They also show what hadn't arrived at the time of writing — there are no mentions of the domestic cat or chicken, for example.
Ancient Greeks also had a reasonable knowledge of animals' habits and behaviour. They knew which animals where predators, which their prey, and which parasites, for example. Voultsiadou and Tatolas do not mention if animals were attribute with magical powers, although the myth of the Cyclops, a one-eyed giant, might have their origin in Greeks finding the skulls of the elephants that once roamed their land. These would have seemed freakishly huge, and also have a large hole in the middle, for the trunk, that looks very much like a huge eye socket.
This study, published in the Journal of Biogeography, is reminiscent of a much earlier study by the Scottish scientist D'Arcy Wentworth Thompson. Thompson, who as well as being a professor of biology was expert in ancient Greek, published two works cataloguing the animals in classical literature: A Glossary of Greek Birds (1895), and A Glossary of Greek Fishes (1947). I know this because my forthcoming book, due next year, contains a chapter on his life and work.
Two Greek biologists, Eleni Voultsiadou and Apostolos Tatolas at the Aristotle University of Thessaloniki have gone through the works of Homer and Hesiod, which were written down around 600-800 BC, and recorded what animals are mentioned in the texts. The results tell us both what the ancient Greeks knew about the animals around them, and also how things have changed.
In total, the epics refer to animals 2442 times, and give them 71 different names. The ancient Greeks were, naturally enough, most concerned about useful animals — the majority of references are to domestic or food species such as goat, sheep, pig, dog and honeybee. They also took notice of pests, such as ticks, flies, and the woodworm that ate Odysseus' bow.
But the Greeks also knew their wildlife: lions, wolves and bears appear, as do tortoises, peregrine falcons, swan, geese and the night heron. Sea life is not as well represented as land animals, but dolphins and monk seal appear, and even octopus, sponge and an edible sea squirt. Apart from the eel, all fish were lumped together.
Some animals appear metaphorically. The owl — Athena's bird — appears as a word meaning 'having shining eyes'. People are described as chatting like cicadas.
The epics show which animals have disappeared from Greece in the past three millennia, such as the lion. They also show what hadn't arrived at the time of writing — there are no mentions of the domestic cat or chicken, for example.
Ancient Greeks also had a reasonable knowledge of animals' habits and behaviour. They knew which animals where predators, which their prey, and which parasites, for example. Voultsiadou and Tatolas do not mention if animals were attribute with magical powers, although the myth of the Cyclops, a one-eyed giant, might have their origin in Greeks finding the skulls of the elephants that once roamed their land. These would have seemed freakishly huge, and also have a large hole in the middle, for the trunk, that looks very much like a huge eye socket.
This study, published in the Journal of Biogeography, is reminiscent of a much earlier study by the Scottish scientist D'Arcy Wentworth Thompson. Thompson, who as well as being a professor of biology was expert in ancient Greek, published two works cataloguing the animals in classical literature: A Glossary of Greek Birds (1895), and A Glossary of Greek Fishes (1947). I know this because my forthcoming book, due next year, contains a chapter on his life and work.
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