There is a meme going round Facebook called "15 Authors" in which you list (you guessed it) 15 authors who have "influenced you and that will always stick with you". This is mine...
1. Joseph Heller -- Catch-22 is funniest book ever written - also: it's profound. Pity the fools who don't get it. [You know who you are].
2. Sophocles -- his plays are masterpieces. I've read Oedipus Rex five times, and it still gives me goose-bumps.
3. Dan Dennett -- too many brilliant books to count. Darwin's Dangerous Idea is arguably one of the best non-fiction books of the 90s. His "Postmodernism and Truth" shaped my thinking significantly.
4. Jorge Louis Borges -- author of innumerable mind-bending and beautiful short-stories. If you've not done so yet, listen to "The Library of Babel" (the mp3 is here).
5. John Stuart Mill -- On Liberty is his most important book, but his autobiography and A System of Logic are also very good.
6. Mancur Olson -- An economist actually worth reading. The Logic of Collective Action and Power and Prosperity are both must-reads. (The speculation about the origins of states in P&P is fantastic).
7. Vladimir Nabokov -- I've not read enough of his work, but Lolita is a disturbing, incisive study of obsession. His prose is sublime.
8. Simon Blackburn -- I actually like only one of his books - Think. The latter is the best single-volume introduction to philosophy. I read it at a pivotal time in my intellectual development.
9. Steven Pinker -- possibly the best popularizer of science around. Like Think, I read How the Mind Works at a pivotal time: it was really the start of my interest in science as a whole, and psychology and evolution in particular. The Blank Slate is also excellent.
10. Jared Diamond -- Guns, Germs and Steel is in my opinion THE best non-fiction book of the 90s. Must. Read. The Third Chimpanzee is also worth a read. (But avoid Why is Sex Fun?)
11. Cormac McCarthy -- The Road and Blood Meridian are wonderful both. I've decided to read his entire oeuvre over the next couple of years.
12. Paul Theroux -- his travel writing is something to behold. I'm not a huge fan of his fiction, other than The Mosquito Coast.
13. Richard Dawkins -- He's had a tremendous influence on me. The Selfish Gene first introduced modern theoretical biology to me, and it's had a lasting impact. The God Delusion inspired me to "come out" to my family as an atheist. His best book since The Blind Watchmaker is The Ancestor's Tale, if you haven't read it yet, do so.
14. Malcolm Gladwell -- my favorite science journalist. I've read all three of his books (Outliers is the best, followed by Blink, then The Tipping Point). He's actually on the list for his long-from New Yorker essays. Have a look at his archive.
15. John Rawls -- A Theory of Justice is the locus classicus of 20th century political philosophy. Reading it had an absolutely profound effect on me.
Showing posts with label Biology. Show all posts
Showing posts with label Biology. Show all posts
Tuesday, November 23, 2010
Tuesday, June 22, 2010
3 Quarks Daily science blogging award
- "Gut bacteria in Japanese people borrowed digesting genes from ocean bacteria" by Ed Yong of Not Exactly Rocket Science.
- "Skullcaps and Genomes" by Carl Zimmer of The Loom.
- "The Evolution of Chloroplasts" by Margaret Morgan of My Growing Passion.
A slight criticism... As I pointed out in the comments at 3 Quarks Daily, the winning entries this year are rather similar - too similar. Not only are all three on biology,
Wednesday, April 7, 2010
Guest post: Neuroscience through Optogenetics
A guest post from Hugh Pastoll, my good friend and long-time intellectual sparring partner. Hugh's introduction follows, and then his article.
Michael and I met while studying PPE at the University of Cape Town. Like him, I’ve completely changed direction since then and am now doing a PhD in Computational Neuroscience at the University of Edinburgh.
As part of my postgraduate studies I’ve been fortunate enough to use an exciting new and truly revolutionary technology known as optogenetics. Optogenetics permits fine-grained control of brain activity with light, dramatically increasing the range of interesting experiments we can do. Since it is likely that it will soon become the technology of choice for investigating brain function, Michael has invited me to give a short primer on optogenetics in general and channelrhodopsins in particular.
----------------------------------------------------------------------------
As a computational neuroscientist I am ultimately motivated by understanding how neural activity determines behavior. Frustratingly, for a long time even attempting to answer this sort of question has been pretty much impossible. This has been a major barrier to understanding how brains work… until recently.
To see why we have been stuck, imagine that I want to test the hypothesis that some pattern of neural activity causes a particular behavior. In order to test this hypothesis I’d need to conduct an experiment where I manipulated the animal’s neural activity and observed its behavior (simply noticing that the pattern and behavior both occur when I give the animal a stimulus only establishes correlation, not causality). Now, we’ve been able to control neural activity for quite a while - the sticking point was that we weren’t able to do it with the millisecond fidelity, neuron type specificity and sub-cubic-millimeter spatial precision we need to test most of our important hypotheses.
To illustrate, say I hypothesize that synchronized firing of excitatory neurons in the subthalamic nucleus at 20 Hz is responsible for akinesia (deficit in movement initiation). Testing this typical hypothesis would require me to synchronize only sub-thalamic excitatory neurons without changing their overall firing rate or affecting activity in nearby brain areas while the animal is behaving. I can’t think of any way we would have to able to accomplish this with drugs, electrical stimulation or any other standard technique for controlling neural activity.
Thanks to the recent development of optogenetics, though, such control is not only possible, but relatively easy. I can’t really exaggerate how completely cool this is - it is going to allow the field of computational neuroscience to hit its stride and start delivering the kinds of insights we need to understand what’s really going on in the brain.
So how does optogenetics work? To understand this, you need to know how ion channels control action potentials in neurons. Very briefly, ion channels are specialized protein channels that, when open, conduct ions (charged molecules) across cell membranes. The brief rise in membrane potential during an action potential is due to positive ions rapidly moving from the outside to the inside of a cell. Channelrhodopsins are ion channels that open when you shine blue light on them! This means we can force the membrane potential of a neuron to become more positive and generate an action potential. This is the ‘opto’ part of optogenetics.
Channelrhodopsin-2 (ChR2 - the most useful original kind) was first described in a species of green algae called Chlamydomonas reinhardtii in 2002 and found to work in mammalian neurons. Since then, genetic engineers have found that strategically mutating different amino acids changes the kinetics of the channel (how quickly it opens and closes). So, now there are different versions that allow different types of control. The fastest type (named ChETA ) opens in about 2 milliseconds and closes after about 5ms; fast enough to pulse blue light at 200 Hz and have the neuron fire at virtually every pulse. Another type (ChR2-C128S) usually takes minutes to close but shuts off very quickly if you shine green light on it. This means it can act as a kind of bi-stable on-off neuron switch. With such fine-grained control we can manipulate neuron spiking in pretty much any way we like.
Now for the ‘genetic’ part of optogenetics: Different kinds of neurons make different kinds of proteins. Since channelrhodopsin is a protein, we can use the cellular machinery that determines whether a protein is expressed in a neuron to restrict channelrhodopsin expression to a specific type of neuron.
This allows us to make one type of neuron in an area fire, without directly disrupting the normal activity of other types in the same area, giving us the neuron sub-type specificity we need for our experiments.
Furthermore, we can restrict channelrhodopsin expression to a very small area of the brain. Since we know that genes code for proteins, if only cells in one area have the channelrhodopsin gene only those cells in that area will respond to light. We can accomplish this by infecting a group of neurons with a non-replicating retrovirus that carries the channelrhodopsin gene. This gene will then be integrated into the genome of the infected neurons and expressed, introducing channelrhodopsins with spatial specificity.
However, although this combination of temporal, neuron sub-type and spatial specificity will enable a wide range of experiments, even more is possible. Another class of membrane proteins, known as halorhodopsins, have the opposite effect to channelrhodopsins. Halorhodopsins are not passive channels - they actively pump negative ions into a cell when illuminated with yellow light, making it more negative and stopping it from firing. Additionally, proteins that pump positive hydrogen ions out of cells to make their interior more negative have been described recently. These proteins are more effective than some types of halorhodopsins at preventing neurons from firing and different types respond to a different light colors – allowing researchers to pick colors that don't interfere with other rhodopsins the animal may also be expressing.
With such powerful optogenetic tools at our disposal we can imagine performing complex experiments, orchestrating neural activity with an array of different color intra-cranial LEDs. Although such experiments will be technically challenging, at the moment it feels like we are only limited by our imagination.
Selected references:
Nagel, G. et al. (2002) "Channelrhodopsin-2, a directly light-gated cation-selective membrane channel," PNAS, doi:10.1073/pnas.193619210.
Boyden, E. et al. (2005) "Millisecond-timescale genetically targeted optical control of neural activity," Nature Neuroscience, doi:10.1038/nn1525
Berndt, A. et al. (2008) "Bi-stable neural state switches," Nature Neuroscience, doi:10.1038/nn.2247
Gradinaru, V. et al. (2009) "Optical deconstruction of Parkinsonian neural circuitry," Science, doi:10.1126/science.1167093
Chow, B. et al. (2010) "High-performance genetically targetable optical neural silencing by light-driven proton pumps," Nature, doi:10.1038/nature08652
Gunaydin, L. et al. (2010) "Ultrafast optogenetic control," Nature Neuroscience, doi:10.1038/nn.2495
Michael and I met while studying PPE at the University of Cape Town. Like him, I’ve completely changed direction since then and am now doing a PhD in Computational Neuroscience at the University of Edinburgh.
As part of my postgraduate studies I’ve been fortunate enough to use an exciting new and truly revolutionary technology known as optogenetics. Optogenetics permits fine-grained control of brain activity with light, dramatically increasing the range of interesting experiments we can do. Since it is likely that it will soon become the technology of choice for investigating brain function, Michael has invited me to give a short primer on optogenetics in general and channelrhodopsins in particular.
----------------------------------------------------------------------------
As a computational neuroscientist I am ultimately motivated by understanding how neural activity determines behavior. Frustratingly, for a long time even attempting to answer this sort of question has been pretty much impossible. This has been a major barrier to understanding how brains work… until recently.
To see why we have been stuck, imagine that I want to test the hypothesis that some pattern of neural activity causes a particular behavior. In order to test this hypothesis I’d need to conduct an experiment where I manipulated the animal’s neural activity and observed its behavior (simply noticing that the pattern and behavior both occur when I give the animal a stimulus only establishes correlation, not causality). Now, we’ve been able to control neural activity for quite a while - the sticking point was that we weren’t able to do it with the millisecond fidelity, neuron type specificity and sub-cubic-millimeter spatial precision we need to test most of our important hypotheses.
To illustrate, say I hypothesize that synchronized firing of excitatory neurons in the subthalamic nucleus at 20 Hz is responsible for akinesia (deficit in movement initiation). Testing this typical hypothesis would require me to synchronize only sub-thalamic excitatory neurons without changing their overall firing rate or affecting activity in nearby brain areas while the animal is behaving. I can’t think of any way we would have to able to accomplish this with drugs, electrical stimulation or any other standard technique for controlling neural activity.
Thanks to the recent development of optogenetics, though, such control is not only possible, but relatively easy. I can’t really exaggerate how completely cool this is - it is going to allow the field of computational neuroscience to hit its stride and start delivering the kinds of insights we need to understand what’s really going on in the brain.
So how does optogenetics work? To understand this, you need to know how ion channels control action potentials in neurons. Very briefly, ion channels are specialized protein channels that, when open, conduct ions (charged molecules) across cell membranes. The brief rise in membrane potential during an action potential is due to positive ions rapidly moving from the outside to the inside of a cell. Channelrhodopsins are ion channels that open when you shine blue light on them! This means we can force the membrane potential of a neuron to become more positive and generate an action potential. This is the ‘opto’ part of optogenetics.
Channelrhodopsin-2 (ChR2 - the most useful original kind) was first described in a species of green algae called Chlamydomonas reinhardtii in 2002 and found to work in mammalian neurons. Since then, genetic engineers have found that strategically mutating different amino acids changes the kinetics of the channel (how quickly it opens and closes). So, now there are different versions that allow different types of control. The fastest type (named ChETA ) opens in about 2 milliseconds and closes after about 5ms; fast enough to pulse blue light at 200 Hz and have the neuron fire at virtually every pulse. Another type (ChR2-C128S) usually takes minutes to close but shuts off very quickly if you shine green light on it. This means it can act as a kind of bi-stable on-off neuron switch. With such fine-grained control we can manipulate neuron spiking in pretty much any way we like.
Now for the ‘genetic’ part of optogenetics: Different kinds of neurons make different kinds of proteins. Since channelrhodopsin is a protein, we can use the cellular machinery that determines whether a protein is expressed in a neuron to restrict channelrhodopsin expression to a specific type of neuron.
This allows us to make one type of neuron in an area fire, without directly disrupting the normal activity of other types in the same area, giving us the neuron sub-type specificity we need for our experiments.
Furthermore, we can restrict channelrhodopsin expression to a very small area of the brain. Since we know that genes code for proteins, if only cells in one area have the channelrhodopsin gene only those cells in that area will respond to light. We can accomplish this by infecting a group of neurons with a non-replicating retrovirus that carries the channelrhodopsin gene. This gene will then be integrated into the genome of the infected neurons and expressed, introducing channelrhodopsins with spatial specificity.
However, although this combination of temporal, neuron sub-type and spatial specificity will enable a wide range of experiments, even more is possible. Another class of membrane proteins, known as halorhodopsins, have the opposite effect to channelrhodopsins. Halorhodopsins are not passive channels - they actively pump negative ions into a cell when illuminated with yellow light, making it more negative and stopping it from firing. Additionally, proteins that pump positive hydrogen ions out of cells to make their interior more negative have been described recently. These proteins are more effective than some types of halorhodopsins at preventing neurons from firing and different types respond to a different light colors – allowing researchers to pick colors that don't interfere with other rhodopsins the animal may also be expressing.
With such powerful optogenetic tools at our disposal we can imagine performing complex experiments, orchestrating neural activity with an array of different color intra-cranial LEDs. Although such experiments will be technically challenging, at the moment it feels like we are only limited by our imagination.
Selected references:
Nagel, G. et al. (2002) "Channelrhodopsin-2, a directly light-gated cation-selective membrane channel," PNAS, doi:10.1073/pnas.193619210.
Boyden, E. et al. (2005) "Millisecond-timescale genetically targeted optical control of neural activity," Nature Neuroscience, doi:10.1038/nn1525
Berndt, A. et al. (2008) "Bi-stable neural state switches," Nature Neuroscience, doi:10.1038/nn.2247
Gradinaru, V. et al. (2009) "Optical deconstruction of Parkinsonian neural circuitry," Science, doi:10.1126/science.1167093
Chow, B. et al. (2010) "High-performance genetically targetable optical neural silencing by light-driven proton pumps," Nature, doi:10.1038/nature08652
Gunaydin, L. et al. (2010) "Ultrafast optogenetic control," Nature Neuroscience, doi:10.1038/nn.2495
Monday, January 4, 2010
Fun with fossils
So the fiancée, her family and I had a lovely holiday in Clarens (Google Maps) over the December holidays. While there, we took a day trip to the Golden Gate National Park (go if you have a chance, it's gorgeous) and to everyone's delight, I discovered some fossils! Well, I think they're fossils - they certainly look like fossils to me. But, obviously, I'm no paleontologist so I might be entirely wrong. (Angela, the aforementioned fiancée, already blogged about the incident by the way). Anyway, some of the best pictures are below the fold.
Thursday, October 22, 2009
Ida: Damp squib...
So remember Ida? The fossil that was going to "change everything"? That was a "missing link"? That was supposed to be a human ancestor? Well it seems all that media hype was for nothing because, according to a new paper in Nature, Ida was the ancestor of... nothing. (Or at least nothing extant).I don't have the necessary expertise to have an opinion about the controversy itself, but lots of people who do were skeptical right from the start and the naysayers now hove more ammunition that ever. Note to all: doing science by media is a really, really Bad Idea.
Further reading:
- "When It Comes To Being The "Missing Link", Ida -- You Are NOT The Candidate" at Prancing Papio.
- "Breaking the Link - Darwinius revealed as ancestor of nothing" at Not Exactly Rocket Science.
- "Bone Crunching Debunks ‘First Monkey’ Ida Fossil Hype" at Wired Science.
- "Ida Redux" at NeuroLogica.
Friday, October 16, 2009
Lazy Linking
"The Durban Boredom Festival"
"Dear Penn and Teller: Bullshit!"
- So a friend, my fiancée and I went to a local psychic fair recently. I was planning to write about it... but it was a horrid experience, so I never got round it it. Luckily, Angela (the aforementioned fiancée) has written a great account of what went down at the fair and trust me, short as it is, her post contains everything you'll possibly want to know about it. Overall conclusion: way too much incense, rampant woo, boring as hell, complete ripoff.
- BPS Research Digest reports on using fMRI et. al. to spot lying. Short version: it doesn't work. (At least not yet).
- Malcolm Gladwell's latest New Yorker piece in which he compares the morality of dogfighting - almost universally reviled - with that of American football. It turns out that, like with boxing, a football career often results in an Alzheimers-like condition called chronic traumatic encephalopathy. Amazingly, new resarch using accelerometers has revealed players regularly suffer hits to the head of up to 90gs. Not surprisingly this is a Bad Thing that does severe damage to the brain over the long run. Gladwell suggests this may make football morally comparable to dogfighting: the injuries and suffering of the players are an inherent and ineradicable feature of the game.
- As a big rugby fan I couldn't help wondering what the situation is like for my favorite Saturday diversion. Do rugby players also suffer as much damage? Obviously, only research could settle the issue (and some may already exist, I don't know). From the armchair, it's difficult to tell: on the one hand, there are many fewer hits to the head in rugby but, on the other, the players don't wear helmets or much protective gear. My (rather bland) guess, for the little that's worth, is that brain trauma is not as common in rugby as it is in football or boxing, but significantly more prevalent than in the general populace. I'm not going to stop watching though, that's for sure.
- A great Nature editorial calling for evidence-based clinical psychology in the United States. I'd say it's also much needed elsewhere, the training of psychologists is often criminally devoid of science or even critical thinking.
- "Clinical psychology at least has its roots in experimentation, but it is drifting away from science. Concerns about cost–benefit issues are growing, especially in the United States. According to a damning report [pdf] published last week an alarmingly high proportion of practitioners consider scientific evidence to be less important than their personal — that is, subjective — clinical experience."
- "The irony is that, during the past 20 years, science has made great strides in directions that could support clinical psychology — in neuroimaging, for example, as well as molecular and behavioural genetics, and cognitive neuroscience. Numerous psychological interventions have been proved to be both effective and relatively cheap. Yet many psychologists continue to use unproven therapies that have no clear outcome measures — including, in extreme cases, such highly suspect regimens as 'dolphin-assisted therapy'."
- Interesting piece by the excellent Ann Gibbons about new research on the causes of human genetic homogeneity (relative to other primates).
- "Modern humans are a lot alike - at least at the genetic level - compared with other primates. If you compare any two people from far-flung corners of the globe, their genomes will be much more similar than those of any pair of chimpanzees, gorillas, or other apes from different populations. Now, evolutionary geneticists have shown that our ancestors lost much of their genetic diversity in two dramatic bottlenecks that sharply squeezed down the population of modern humans as they moved out of Africa between 60,000 and 50,000 years ago."
- See also: John Hawks' fairly critical analysis of the same study.
- Razib Khan over at Gene Expression on how Ardi drives home the message that drawing analogies between humans and the other extant apes can be misleading. Six million years is a long time, and there's no reason to think our common ancestor with the chimps and bonobos was particularly chimp-like. Somewhat counterintuitively, the opposite might even be true.
- I've only recently remembered that I have Season 6 of Penn & Teller's Bullshit so I'm only watching it now. And like Massimo Pigliucci in the above post, I just hated their episode (6-06) on environmentalism. Libertarians so obviously have blinkers on when it comes to global warming that it positively amazes me that they're not more self-critical. It also reminds us all, of course, that being vigilant about our own biases is important.
- One of the most widespread misconceptions about Islam is that most of its faithful are Arabs. In actual fact, Asian Muslims vastly outnumber Muslims from other parts of the world, making up 61.9% of the global number of 1.57 billion believers.
- "A new survey of the world’s Muslim population, by the Pew Research Center based in Washington, DC, will help those who are keen to break that link [i.e. the perception that most Muslims are Arabs]. It estimates the total number of Muslims in the world at 1.57 billion, or about 23% of a global population of 6.8 billion. Almost two-thirds of Muslims live in Asia, with Indonesia providing the biggest contingent (203m), followed by Pakistan (174m) and India (160m)."
- "Perhaps more surprising will be the finding that the European country with the highest Muslim population is not France or Germany, but Russia, where 16.5m adherents of Islam make up nearly 12% of the total national population. Compared with other surveys, the report gives a lowish estimate for the number of Muslims in France (3.6m), as it does for the United States (2.5m); in both those countries, secular principles make it impossible to ask religious questions on a census."
- A superb edition of the Carnival of Evolution - there are many worthwhile posts to check out. My pieces on foxes and on chameleons were featured.
Tuesday, September 8, 2009
Chameleons DO change their color to blend in with their environment
For reasons that are not to hard to fathom, myths about chameleons abound. The Victorians thought they lived entirely on air; a common Zulu superstition is that they're evil (as I confirmed for myself a while back when I tried to show a chameleon I had caught to our gardener); and, more recently, I've been hearing a lot of people say chameleon color changing has nothing to do with camouflage. Even Cracked has got in on the act with an article on "bullshit animals facts", which argues a chameleon's color is determined largely by its mood. I call bullshit on their bullshit.
Thanks to frequent childhood visits to a family farm, I've had lots of encounters with these amazing critters and I've seen them change color to blend in with their environment with my own eyes. Not particularly good evidence, I hear you say. Agreed, so I spent 2 minutes on Wikipedia, followed a link, and found this New Scientist piece, about this study in Biology Letters. And guess what? At least one species of chameleon, Smith's dwarf chameleon (which, incidentally, is South African), does change color to camouflage itself from predators. The paper, "Predator-specific camouflage in chameleons" by Stuart-Fox et. al., demonstrated in several behavioral trials that these chameleons engage in background matching when presented with model predators. In other words, these guys do their best to blend in with their environment when they encounter things that want to eat them. (You can see a clear example of a chameleon matching its background in this YouTube clip [Note: James informs me in the comments that this might be fake]).
So why do people think chameleon camouflage is a myth? It seems other research (also by Stuart-Fox) that concluded color changing evolved for social signalling has been misinterpreted. The conclusion of this second paper was: "our results suggest that selection for conspicuous social signals drives the evolution of colour change in this system, supporting the view that transitory display traits should be under strong selection for signal detectability." In other words, the primary evolutionary 'function' of color changing in chameleons seems to be social signalling. But it does not follow from this that chameleons cannot also use color changing for crypsis -- the ability may have evolved for social signalling, but nothing stops it from being exapted for camouflage. It is such an obvious evolutionary trick that I'm surprised anyone interpreted Stuart-Fox et. al. second paper in this way. If you already have a visual system (to detect background color), you can already change color, you suffer predation and camouflage thus increases fitness, we should positively expect exaptation for crypsis.
As I also pointed out on my fox domistication piece, I'm not a biologist so you should be especially skeptical of my opinions on this (though, I managed to convince biologist Richard Glor over at Dechronization that my interpretation is right). But still... At least some chameleons change their color to blend in with their environment. Obviously.
UPDATE: I emailed Stuart-Fox and asked whether my take is correct. Here is the reply in part (my emphasis):
Stuart-Fox D, Moussalli A, & Whiting MJ (2008). Predator-specific camouflage in chameleons. Biology letters, 4 (4), 326-9 PMID: 18492645
Stuart-Fox D, & Moussalli A (2008). Selection for social signalling drives the evolution of chameleon colour change. PLoS biology, 6 (1) PMID: 18232740
Thanks to frequent childhood visits to a family farm, I've had lots of encounters with these amazing critters and I've seen them change color to blend in with their environment with my own eyes. Not particularly good evidence, I hear you say. Agreed, so I spent 2 minutes on Wikipedia, followed a link, and found this New Scientist piece, about this study in Biology Letters. And guess what? At least one species of chameleon, Smith's dwarf chameleon (which, incidentally, is South African), does change color to camouflage itself from predators. The paper, "Predator-specific camouflage in chameleons" by Stuart-Fox et. al., demonstrated in several behavioral trials that these chameleons engage in background matching when presented with model predators. In other words, these guys do their best to blend in with their environment when they encounter things that want to eat them. (You can see a clear example of a chameleon matching its background in this YouTube clip [Note: James informs me in the comments that this might be fake]).
So why do people think chameleon camouflage is a myth? It seems other research (also by Stuart-Fox) that concluded color changing evolved for social signalling has been misinterpreted. The conclusion of this second paper was: "our results suggest that selection for conspicuous social signals drives the evolution of colour change in this system, supporting the view that transitory display traits should be under strong selection for signal detectability." In other words, the primary evolutionary 'function' of color changing in chameleons seems to be social signalling. But it does not follow from this that chameleons cannot also use color changing for crypsis -- the ability may have evolved for social signalling, but nothing stops it from being exapted for camouflage. It is such an obvious evolutionary trick that I'm surprised anyone interpreted Stuart-Fox et. al. second paper in this way. If you already have a visual system (to detect background color), you can already change color, you suffer predation and camouflage thus increases fitness, we should positively expect exaptation for crypsis.
As I also pointed out on my fox domistication piece, I'm not a biologist so you should be especially skeptical of my opinions on this (though, I managed to convince biologist Richard Glor over at Dechronization that my interpretation is right). But still... At least some chameleons change their color to blend in with their environment. Obviously.
UPDATE: I emailed Stuart-Fox and asked whether my take is correct. Here is the reply in part (my emphasis):
Yes, your interpretation is correct. Colour change in chameleons serves multiple current functions including camouflage (background matching), thermoregulation and communication (courtship and male-male contests). But we need to distinguish current functions from the selective pressures driving the evolution of the abiltiy to change colours. Some species can change colours much more than others - the question I was trying to answer is why such variation? And it seems that sexual selection for communication (signalling) is the most important selective pressure because the species that change colour the most have the most conspicuous colour patterns that they use to communicate.---------------------
Stuart-Fox D, Moussalli A, & Whiting MJ (2008). Predator-specific camouflage in chameleons. Biology letters, 4 (4), 326-9 PMID: 18492645
Stuart-Fox D, & Moussalli A (2008). Selection for social signalling drives the evolution of chameleon colour change. PLoS biology, 6 (1) PMID: 18232740
Wednesday, September 2, 2009
Silver fox domestication
Behavioral responses, [Belyaev] reasoned, are regulated by a fine balance between neurotransmitters and hormones at the level of the whole organism. The genes that control that balance occupy a high level in the hierarchical system of the genome. Even slight alterations in those regulatory genes can give rise to a wide network of changes in the developmental processes they govern. Thus, selecting animals for behavior may lead to other, far-reaching changes in the animals’ development. Because mammals from widely different taxonomic groups share similar regulatory mechanisms for hormones and neurochemistry, it is reasonable to believe that selecting them for similar behavior—tameness—should alter those mechanisms, and the developmental pathways they govern, in similar ways.Now, this may be entirely correct but I can think of a fairly obvious alternative explanation: subtle biases in the researchers that meant the foxes were not really selected based purely on tameness. (A bit like Clever Hans in reverse). There is an Olympus Mons-sized literature on how human decision-making is influenced, entirely subconsciously, by a dizzying array of crazy things. To take one random example (also previously linked to), holding a heavier clipboard affects judgments of value and importance. Given the ubiquity of such latent biases, are we really to believe that some mutation (unconnected behavior) that merely made the affected fox look tame – made it look a bit more like a dog, say – didn't influenced judgments of tameness? To flesh this thought out a bit more, consider how the foxes were classified. Trut again:
At seven or eight months, when the foxes reach sexual maturity, they are scored for tameness and assigned to one of three classes. The least domesticated foxes, those that flee from experimenters or bite when stroked or handled, are assigned to Class III… Foxes in Class II let themselves be petted and handled but show no emotionally friendly response to experimenters. Foxes in Class I are friendly toward experimenters, wagging their tails and whining. In the sixth generation bred for tameness we had to add an even higher-scoring category. Members of Class IE, the “domesticated elite,” are eager to establish human contact, whimpering to attract attention and sniffing and licking experimenters like dogs.
Class III seems unambiguously defined and it’s likely pretty straightforward to spot animals that belong to this category. The differences between the other classes, though, are significantly more subjective, and thus liable to all sorts of subtle biases. What, exactly, is an ‘emotional or friendly response to an experimenter’? What, exactly, is ‘eagerness to establish human contact’? It seems entirely possible – indeed likely – that animals that just looked tamer, had stereotypically domesticated features, were more likely to be assigned to Class I than to class II. If so, the foxes were not really selectively bred for “tameness and tameness alone”. No matter how scrupulous and honest the experimenters tried to be, I find it very hard to believe that they succeeded, continuously and without fail, to assign animals objectively to categories. Indeed, the researchers working on the foxes (including Trut) outlined a new scoring method in a 2007 paper, in which they admitted that a cross-breeding experiment “clearly demonstrates that the traditional scoring systems established for selection of foxes for behavior has limited resolution for measuring behavior as a continuous variable”. Assuming, as seems likely, that tameness-aggressiveness forms a continuous behavioral axis, we cannot be confident that Belyaev and his colleagues invariably selected for tameness alone. If this is correct, the pleiotropy story is somewhat undermined, though by no means refuted, of course. It seems significant, however, that the alternative explanation is more parsimonious: it need not posit nearly infallible experimenters, nor a priori unlikely pleiotropic linkages.Of course, I’m no expert on this topic, so maybe I’ve misunderstood the protocols, or perhaps the alternative I sketch was been refuted somewhere in the literature. I would, however, be very interested to find out how the researchers ruled out this alternative hypothesis...
-------------
Trut, L. (1999). Early Canid Domestication: The Farm-Fox Experiment American Scientist, 87 (2) DOI: 10.1511/1999.2.160
Kukekova, A., Trut, L., Chase, K., Shepeleva, D., Vladimirova, A., Kharlamova, A., Oskina, I., Stepika, A., Klebanov, S., Erb, H., & Acland, G. (2007). Measurement of Segregating Behaviors in Experimental Silver Fox Pedigrees Behavior Genetics, 38 (2), 185-194 DOI: 10.1007/s10519-007-9180-1
Monday, March 16, 2009
Books III
I do book reviews once in a while, but I've been naughty and haven't done one in months... To make up for it, here are no less that 8 mini-reviews.
Somewhat strangely, I was introduced to the theory of evolution by natural selection (while I was in high school) through evolutionary psychology, specifically, through Steven Pinker’s How the Mind Works. And, following Pinker’s references, I read Dawkins, Dennett, Cosmides, Tooby and that crowd. To put it mildly, Stephen Jay Gould was never popular with these writers so I found myself being suspicious of and vaguely hostile to Gould, despite having read only bits of his work. When I came across a collection of Gould’s writings, The Richness of Life, in a bookshop last year it struck me how unreasonable this attitude was: partisans never paint a flattering picture of their opponents. I would have to read Gould himself to come to a fair assessment. So I bought the book and read all 600+ pages and I am extremely glad I did. Gould was without doubt a masterful essayist, a stupendously gifted writer, enormously erudite and capable of making charming connections between seemingly disparate topics. In fact, I would go as far as to say that Gould was one of the greatest 20th century essayists, up there with Medawar and Berlin.
That is not to say that I agree with Gould about everything or that I think his work was uniformly excellent. On the contrary, I think “The Spandrels of San Marco” was a travesty (and unoriginal to boot), and “More Things in Heaven and Earth” (his infamous New York Review of Books piece) was just horrendous. Gould's views about evolutionary psychology (“ultra-Darwinism” he called it) and the evolution of the human mind generally were silly. And, the actions of Science For the People – with which Gould was centrally involved – were inexcusable. Moreover, Gould misled the public because he failed to be clear about when he was explaining or illustrating settled science and when he was engaging in partisan debate.
All that said, I don’t think we should condemn him too much: it’s human (‘all too human’) to be led astray by one’s passionate political and moral convictions. Besides, there is no doubt that nearly anyone has much to learn from Gould and that his essays are, on the whole, delightful, cogent and enlightening. Read Gould (but with eyes open and pinches of salt at the ready).
Unfortunately, South Africa does not have very many science journalists who know their stuff (see George Claassen on this point), so we better support and treasure the ones we do have. Leonie Joubert (who blogs and has a Mail & Guardian column) is certainly on the side of science and reason and, yes, she knows her stuff. Scorched, her first book, is a riveting and beautiful account of the science of climate change and the projected effect this will have on South Africa. While not perfect (there are a few stylistic solecisms, there are missing references and Joubert sometimes bombards her readers with facts) Scorched ought to be widely read. The South African reality-based community, at a minimum, should all go out and buy this book and policy-makers would do well to pay attention.
The Tipping Point, published in 2000, is Malcolm Gladwell’s first book and though it is considerably less serious than his subsequent offerings, it is still worth a read. (It helps that it is short and very easy to read – I finished it in a couple of hours). The book, says Gladwell, is a biography of an idea: that products, messages and behaviors spread like epidemics. Broadly speaking, then, Gladwell is popularizing a kind of memetics, with the addition that ‘little causes can have big effects’ and that there can thus be dramatic and rapid changes when the Tipping Point is crossed. Gladwell illustrates these ideas with his trademark case studies and anecdotes, in this case, the sudden popularity of Hush Puppies in the 1990s, the dramatic fall in crime in New York, the success of Sesame Street, suicide in Micronesia, and others. Along the way, he outlines three ‘rules’ of the Tipping Point: the Law of the Few (“a tiny percentage of people do the majority of the work” [p. 19] and these people can be divided into Connectors, Mavens, and Salesmen), the Stickiness Factor (“there are specific ways of making a contagious message memorable” [p. 25], often by tinkering at the margins [p. 131]), and the Power of Context (“human beings are a lot more sensitive to their environment than they might seem” [p. 29]).
Gladwell has often been criticized for being unoriginal and not particularly rigorous and, frankly, I mostly agree. Indeed, Gladwell has admitted to the former (he’s a popularizer of science, not a scientist). The latter charge is more damning and is in evidence throughout the book. The ‘rules’ of the Tipping Point, for instance, are extremely vague, even when fleshed out considerably more than above, and there are no doubt many exceptions. Moreover, several of Gladwell’s examples are rather pat – he seems to simplify complicated phenomena for the sake of narrative clarity. For example, the story Gladwell tells about how HIV spread in North America – through so-called Patient Zero, Gaetan Dugas – crudely simplifies the real situation, and has been disputed.
Nevertheless, Gladwell remains my favorite science journalist, despite his flaws. I read his articles and his books because they introduce me to interesting research, which I can (and do) then follow up for myself. This may be condescending, but I don’t really expect scholarly rigor from Gladwell: he writes popular science for a wide-audience, not academic tomes for specialists. Just like you don’t watch the latest shoot-‘em-up for intellectual stimulation, or read trashy romance novels for their literary merit, or, indeed, read Science for its humor, so you shouldn’t read journalists for unimpeachable rigor or entirely justified true beliefs. In short, read journals, not journalists, for rigor. A well-written and entertaining but simplified account of solid research, worked into an interesting narrative, certainly has its place. And that is exactly what Gladwell provides.
Dark Continent My Black Arse by Sihle Khumalo is an engrossing, entertaining, funny and wonderfully politically-incorrect account of the author’s trip, entirely overland and by public transport, from Cape to Cairo. While not quite up there with Paul Theroux or Bill Bryson’s travel writing, the book is nevertheless very good indeed and worth the price of admission. A single complaint (the skeptic in me couldn’t let this go…): Khumalo on a number of occasions endorses bollocks, most notably, saying that rhino horn is ‘the best medicine for sexual vigour’. Six words: magical thinking + placebo effect + lamentable superstition.
Philip Roth’s The Plot Against America is an absolute tour de force, a modern masterpiece. [Mild spoilers follow]. The central character is the eight-year-old American Jew Philip Roth, who inhabits an alternative history where Charles A. Lindbergh, the notoriously anti-Semitic aviator who was the first person to fly solo across the Atlantic, wins the 1940 presidential election. True to form, Lindbergh then tacitly supports the Axis powers in World War II (under the guise of isolationism) and enacts successively more repressive anti-Jewish laws (under the guise of assimilation). The rest of the novel follows Philip and the rest of the Roth clan as they come to terms with, and accommodate to, the new dispensation. [Spoilers end].
I don’t pretend to be a competent literati, so I won’t do much of a review except to note that the prose is sublime and that Roth has a preternatural ability to render the psychology of people buffeted by events beyond their control and understanding. I said the same about McCarthy, but I think it’s equally true of Roth: he deserves the Nobel Prize for Literature.
The Ancestor’s Tale: A Pilgrimage to the Dawn of Life is, in my view, Richard Dawkins’s best book since the excellent Blind Watchmaker. The device around which the book is built, modeled on Chaucer’s Canterbury Tales, is a pilgrimage starting at the present with Homo sapiens, and working backwards in time to meet our common ancestors with the rest of life. The first rendezvous, for example, is with chimpanzees and bonobos (our common ancestor lived 5-7 million years ago), the 6th with the New World Monkeys (40 million years ago), the 17th with amphibians (about 340 million years ago), the 23rd with lancelets (very approximately 560 million years ago), and so on. Along the way, various creatures tell tales, among other things, about the history of life, the principles and quirks of evolution, and the methods and techniques biologists use to figure all this out. The book, then, is simultaneously a history of life, a primer on evolution, an account of human ancestry, and a survey of the diversity of life.
While it’s quite an investment of time – 629 pages in paperback – The Ancestor’s Tale richly repays that investment: I haven’t learned so much from a single book in a very long time. Not only that, but it’s as beautifully written as we’ve come to expect from Dawkins, and, perhaps more importantly, it illustrates the wonders of life, and sparks one’s curiosity and enthusiasm for such under appreciated critters as sponges, lungfish and fungi.
The dust jacket quotes the Financial Times thusly: “One of the richest accounts of evolution ever written”. It’s not hyperbole.
John Allen Paulos is a rare specimen indeed: an effective popularizer of and unflinching advocate for mathematics who is himself an academic mathematician. Not only are his mathematical credentials excellent, more importantly for his role as popularizer, Paulos writes exceedingly well. In his third book, Innumeracy, Paulos argues mathematical and, more particularly, statistical ‘illiteracy’ (the eponymous innumeracy) leads to the misunderstanding and misinterpretation of reality. He shows persuasively that the innumerate are vulnerable to personalizing the random, and thence to charlatanism, magical thinking and pseudoscience. The book is not, however, an abstract treatise on the importance of mathematics, it’s a vade mecum for the educated but innumerate. As such a guide, the book succeeds admirably: it gently introduces the basics of number and probability with a series of well-chosen examples. Overall, it is a superb little book which, I daresay, might benefit the numerate as well.
I can’t resist quoting Paulos at length:
Somewhat strangely, I was introduced to the theory of evolution by natural selection (while I was in high school) through evolutionary psychology, specifically, through Steven Pinker’s How the Mind Works. And, following Pinker’s references, I read Dawkins, Dennett, Cosmides, Tooby and that crowd. To put it mildly, Stephen Jay Gould was never popular with these writers so I found myself being suspicious of and vaguely hostile to Gould, despite having read only bits of his work. When I came across a collection of Gould’s writings, The Richness of Life, in a bookshop last year it struck me how unreasonable this attitude was: partisans never paint a flattering picture of their opponents. I would have to read Gould himself to come to a fair assessment. So I bought the book and read all 600+ pages and I am extremely glad I did. Gould was without doubt a masterful essayist, a stupendously gifted writer, enormously erudite and capable of making charming connections between seemingly disparate topics. In fact, I would go as far as to say that Gould was one of the greatest 20th century essayists, up there with Medawar and Berlin.That is not to say that I agree with Gould about everything or that I think his work was uniformly excellent. On the contrary, I think “The Spandrels of San Marco” was a travesty (and unoriginal to boot), and “More Things in Heaven and Earth” (his infamous New York Review of Books piece) was just horrendous. Gould's views about evolutionary psychology (“ultra-Darwinism” he called it) and the evolution of the human mind generally were silly. And, the actions of Science For the People – with which Gould was centrally involved – were inexcusable. Moreover, Gould misled the public because he failed to be clear about when he was explaining or illustrating settled science and when he was engaging in partisan debate.
All that said, I don’t think we should condemn him too much: it’s human (‘all too human’) to be led astray by one’s passionate political and moral convictions. Besides, there is no doubt that nearly anyone has much to learn from Gould and that his essays are, on the whole, delightful, cogent and enlightening. Read Gould (but with eyes open and pinches of salt at the ready).
Unfortunately, South Africa does not have very many science journalists who know their stuff (see George Claassen on this point), so we better support and treasure the ones we do have. Leonie Joubert (who blogs and has a Mail & Guardian column) is certainly on the side of science and reason and, yes, she knows her stuff. Scorched, her first book, is a riveting and beautiful account of the science of climate change and the projected effect this will have on South Africa. While not perfect (there are a few stylistic solecisms, there are missing references and Joubert sometimes bombards her readers with facts) Scorched ought to be widely read. The South African reality-based community, at a minimum, should all go out and buy this book and policy-makers would do well to pay attention.
The Tipping Point, published in 2000, is Malcolm Gladwell’s first book and though it is considerably less serious than his subsequent offerings, it is still worth a read. (It helps that it is short and very easy to read – I finished it in a couple of hours). The book, says Gladwell, is a biography of an idea: that products, messages and behaviors spread like epidemics. Broadly speaking, then, Gladwell is popularizing a kind of memetics, with the addition that ‘little causes can have big effects’ and that there can thus be dramatic and rapid changes when the Tipping Point is crossed. Gladwell illustrates these ideas with his trademark case studies and anecdotes, in this case, the sudden popularity of Hush Puppies in the 1990s, the dramatic fall in crime in New York, the success of Sesame Street, suicide in Micronesia, and others. Along the way, he outlines three ‘rules’ of the Tipping Point: the Law of the Few (“a tiny percentage of people do the majority of the work” [p. 19] and these people can be divided into Connectors, Mavens, and Salesmen), the Stickiness Factor (“there are specific ways of making a contagious message memorable” [p. 25], often by tinkering at the margins [p. 131]), and the Power of Context (“human beings are a lot more sensitive to their environment than they might seem” [p. 29]).Gladwell has often been criticized for being unoriginal and not particularly rigorous and, frankly, I mostly agree. Indeed, Gladwell has admitted to the former (he’s a popularizer of science, not a scientist). The latter charge is more damning and is in evidence throughout the book. The ‘rules’ of the Tipping Point, for instance, are extremely vague, even when fleshed out considerably more than above, and there are no doubt many exceptions. Moreover, several of Gladwell’s examples are rather pat – he seems to simplify complicated phenomena for the sake of narrative clarity. For example, the story Gladwell tells about how HIV spread in North America – through so-called Patient Zero, Gaetan Dugas – crudely simplifies the real situation, and has been disputed.
Nevertheless, Gladwell remains my favorite science journalist, despite his flaws. I read his articles and his books because they introduce me to interesting research, which I can (and do) then follow up for myself. This may be condescending, but I don’t really expect scholarly rigor from Gladwell: he writes popular science for a wide-audience, not academic tomes for specialists. Just like you don’t watch the latest shoot-‘em-up for intellectual stimulation, or read trashy romance novels for their literary merit, or, indeed, read Science for its humor, so you shouldn’t read journalists for unimpeachable rigor or entirely justified true beliefs. In short, read journals, not journalists, for rigor. A well-written and entertaining but simplified account of solid research, worked into an interesting narrative, certainly has its place. And that is exactly what Gladwell provides.
Dark Continent My Black Arse by Sihle Khumalo is an engrossing, entertaining, funny and wonderfully politically-incorrect account of the author’s trip, entirely overland and by public transport, from Cape to Cairo. While not quite up there with Paul Theroux or Bill Bryson’s travel writing, the book is nevertheless very good indeed and worth the price of admission. A single complaint (the skeptic in me couldn’t let this go…): Khumalo on a number of occasions endorses bollocks, most notably, saying that rhino horn is ‘the best medicine for sexual vigour’. Six words: magical thinking + placebo effect + lamentable superstition.
Philip Roth’s The Plot Against America is an absolute tour de force, a modern masterpiece. [Mild spoilers follow]. The central character is the eight-year-old American Jew Philip Roth, who inhabits an alternative history where Charles A. Lindbergh, the notoriously anti-Semitic aviator who was the first person to fly solo across the Atlantic, wins the 1940 presidential election. True to form, Lindbergh then tacitly supports the Axis powers in World War II (under the guise of isolationism) and enacts successively more repressive anti-Jewish laws (under the guise of assimilation). The rest of the novel follows Philip and the rest of the Roth clan as they come to terms with, and accommodate to, the new dispensation. [Spoilers end].I don’t pretend to be a competent literati, so I won’t do much of a review except to note that the prose is sublime and that Roth has a preternatural ability to render the psychology of people buffeted by events beyond their control and understanding. I said the same about McCarthy, but I think it’s equally true of Roth: he deserves the Nobel Prize for Literature.
The Ancestor’s Tale: A Pilgrimage to the Dawn of Life is, in my view, Richard Dawkins’s best book since the excellent Blind Watchmaker. The device around which the book is built, modeled on Chaucer’s Canterbury Tales, is a pilgrimage starting at the present with Homo sapiens, and working backwards in time to meet our common ancestors with the rest of life. The first rendezvous, for example, is with chimpanzees and bonobos (our common ancestor lived 5-7 million years ago), the 6th with the New World Monkeys (40 million years ago), the 17th with amphibians (about 340 million years ago), the 23rd with lancelets (very approximately 560 million years ago), and so on. Along the way, various creatures tell tales, among other things, about the history of life, the principles and quirks of evolution, and the methods and techniques biologists use to figure all this out. The book, then, is simultaneously a history of life, a primer on evolution, an account of human ancestry, and a survey of the diversity of life.While it’s quite an investment of time – 629 pages in paperback – The Ancestor’s Tale richly repays that investment: I haven’t learned so much from a single book in a very long time. Not only that, but it’s as beautifully written as we’ve come to expect from Dawkins, and, perhaps more importantly, it illustrates the wonders of life, and sparks one’s curiosity and enthusiasm for such under appreciated critters as sponges, lungfish and fungi.
The dust jacket quotes the Financial Times thusly: “One of the richest accounts of evolution ever written”. It’s not hyperbole.
John Allen Paulos is a rare specimen indeed: an effective popularizer of and unflinching advocate for mathematics who is himself an academic mathematician. Not only are his mathematical credentials excellent, more importantly for his role as popularizer, Paulos writes exceedingly well. In his third book, Innumeracy, Paulos argues mathematical and, more particularly, statistical ‘illiteracy’ (the eponymous innumeracy) leads to the misunderstanding and misinterpretation of reality. He shows persuasively that the innumerate are vulnerable to personalizing the random, and thence to charlatanism, magical thinking and pseudoscience. The book is not, however, an abstract treatise on the importance of mathematics, it’s a vade mecum for the educated but innumerate. As such a guide, the book succeeds admirably: it gently introduces the basics of number and probability with a series of well-chosen examples. Overall, it is a superb little book which, I daresay, might benefit the numerate as well.I can’t resist quoting Paulos at length:
The discrepancies between our pretensions and reality are usually quite extensive, and since number and chance are among our ultimate reality principles, those who possess a keen grasp of these notions may see these discrepancies and incongruities with greater clarity and thus more easily become subjects to feelings of absurdity. I think there’s something of the divine in these feelings of our absurdity, and they should be cherished, not avoided. They provide perspective on our puny yet exalted position in the world, and are what distinguish us from rats. Anything which permanently dulls us to them is to be opposed, innumeracy included. The desire to arouse a sense of numerical proportion and an appreciation for the irreducibly probabilistic nature of life – this, rather than anger, was the primary motivation for the book.
Monday, February 2, 2009
The Mouse Man
Image by Laura-Elizabeth via Flickr
It's an interesting little vignette in the history of science and biology -- have a look.
Tuesday, October 21, 2008
Video: Amazing Ocean Depths
David Gallo is a pioneering oceanographer and in the TEDTalk embedded below (or click here) he surveys some of the astonishing life forms that live in the ocean's depths around hydrothermal vents.
(I've posted another of Gallo's TEDTalks before, which is most certainly also worth watching if you haven't previously seen it).
(I've posted another of Gallo's TEDTalks before, which is most certainly also worth watching if you haven't previously seen it).
Wednesday, July 9, 2008
Books I
Since starting this blog I have labored under the delusion that I would write a proper review for each and every book I read. Clearly, that was never going to happen (I like reading far more than writing), so I’ve now decided to follow Cosma Shalizi’s example and write regular mini-reviews.
Einstein: His Life and Universe by Walter Isaacson is a superb biography that incorporates all the materials that were embargoed until 2006. Isaacson does his level best to explain the science in a cogent manner and, while I remain as mystified by relativity and quantum mechanics as ever, that illustrates the near impossibility of explaining modern physics to a popular audience rather than Isaacson’s limitations as an author. A particularly noteworthy aspect of the book is the astounding amount of fact checking that went into its creation as revealed by the Acknowledgements: I don’t think I’ve come across another book as carefully peer-reviewed as this one. (I spotted just one small error that got past the reviewers).
Einstein’s life, it should be said, was full and extremely interesting and thus certainly worthy of a long biography. Isaacson lives up to his subject: he writes well (if not brilliantly), adroitly weaves together the different threads of Einstein’s personality and career, and manages to convey Einstein’s greatness without becoming obsequious. Apart from a couple of inevitable differences in interpretation, the only negative thing I have to say is that Isaacson is unnecessarily repetitive in places. Overall, though, it’s a fascinating life, brilliantly portrayed. (See also: Isaacon’s interview about the book on The Skeptics Guide to the Universe starting at 34:30).
Why Is Sex Fun: The Evolution of Human Sexuality by Jared Diamond is utter junk. I can’t believe the author of Guns, Germs and Steel could produce something this bad. The less said about it the better – don’t read it, ever.
No Country for Old Men by Cormac Mccarthy (fiction). Atmospheric, absorbing, sublime prose, and totally believable. I’m not a huge fan of the ending (or the movie adaptation, for that matter), but it’s still one of the best novels I’ve read in ages.
The Classical World: An Epic History of Greece and Rome by Robin Lane Fox is an enormously ambitious book: it is a survey of almost a thousand years of complicated and interesting history in only 600 pages. Frankly, I’m generally skeptical about epic surveys – telescoped history is often watered-down history. Not so with The Classical World, it is a magnificent, full-blooded, exciting and sympathetic account of Greece and Rome. Few scholars, I suspect, could pull-off anything similar: Lane Fox’s classical knowledge is veritably encyclopedic. A particularly congenial aspect of the book is how Lane Fox’s love for his subject matter shines through; he makes no apologies for his passion. Negatives: a sometimes-ponderous writing style and a surfeit of French words, the themes of ‘luxury’, ‘freedom’ and ‘justice’ seem occasionally procrustean, the book has a slow and somewhat confusing start and Lane Fox can be a bit pompous at times. All that said, the book is a recommended introduction to the classical world.
Contact Wounds: A War Surgeon’s Education is Jonathan Kaplan’s sequel to The Dressing Station (which I read – and loved – a couple of years ago). The book is a memoir of Kaplan’s early life (including a trip to Israel just after the Six Day War) and his medical education both as a student at the University of Cape Town (my alma mater) and his residencies in various parts of the world. The book ends off with events in Kaplan’s life subsequent to the publication of The Dressing Station, most notably, his stints in Angola and Iraq. Kaplan writes exceedingly well and Contact Wounds radiates humanity, remains interesting throughout and documents an amazing life. My only worry about the book is that it reads like a novel, which isn’t bad in itself, but I’m somewhat dubious Kaplan remembers as many details as he pretends to about when he was, say, 14. Nevertheless, Contact Wounds is a riveting, eye-opening read.
I hate to say this, but I was thoroughly unimpressed with Christopher Hitchens’ God Is Not Great: How Religion Poisons Everything. Hitchens writes beautifully, is widely educated and is a highly skilled polemicist, but, honestly, I found his arguments unconvincing. Given that I already agree with many of his conclusions and given the purpose of the book, this criticism is very harsh: Hitchens has failed to contribute to the ‘new atheist’ debate in a meaningful way. A relatively small failing I think speaks volumes: like a bad undergraduate essay, God Is Not Great is based almost exclusively on secondary-sources, it seems without Jennifer Hecht’s Doubt: A History Hitchens would not have been able to write his book. Bottom-line: watch Hitchens speaking (where he is second to none), but don’t read his book. (See also: Hitchens' interview about the book on Point of Inquiry).
A Guinea Pig’s History of Biology: The Plants and Animals Who Taught Us the Facts of Life by Jim Endersby is a new kind of intellectual history of biology that doesn’t focus on personalities (‘great men’) but on specific model organisms. Each of the 12 chapters focuses on one particular organism (Drosophila, humans, Equus quagga, guinea pigs etc.) and discusses at length how the organism came to be used and what questions biologists used it to answer. A theme running through the book is how difficult it is to transform a wild-type into a model organism: often it took years of patient work that bore no fruit in the short term. George Streisinger, for example, is the unsung hero of evo-devo; it took him nearly a decade to breed zebrafish suitable for scientific work. Another interesting theme of the book is that it took a whole community of researchers, collaborating openly and trusting one another, to produce scientific breakthroughs using a specific organism. Thomas Hunt Morgan and his ‘fly-boys’ (champions of Drosophila) set the precedent: they gave away whole colonies of newly standardized flies to any interested researcher and eventually even produced a newsletter, Drosophila Information Service, to spread useful fly information.
Negatives: Endersby’s last chapter reveals little about its purported subject, OncoMouse, and degenerates into an entirely uninteresting essay about what Endersby thinks about genetic engineering, the philosophy of science and so on. His editor should have spared him. A final, much less serious, criticism: the book sometimes gets bogged down in historical minutia (like what effect Great Britain’s 1845 abolition of the tax on glass had on the cultivation of flowers) but Endersby rarely strays too far from biology.
Overall, A Guinea Pig’s History of Biology is an original, interesting, well-researched and informative history. It comes highly recommended.
Einstein: His Life and Universe by Walter Isaacson is a superb biography that incorporates all the materials that were embargoed until 2006. Isaacson does his level best to explain the science in a cogent manner and, while I remain as mystified by relativity and quantum mechanics as ever, that illustrates the near impossibility of explaining modern physics to a popular audience rather than Isaacson’s limitations as an author. A particularly noteworthy aspect of the book is the astounding amount of fact checking that went into its creation as revealed by the Acknowledgements: I don’t think I’ve come across another book as carefully peer-reviewed as this one. (I spotted just one small error that got past the reviewers).Einstein’s life, it should be said, was full and extremely interesting and thus certainly worthy of a long biography. Isaacson lives up to his subject: he writes well (if not brilliantly), adroitly weaves together the different threads of Einstein’s personality and career, and manages to convey Einstein’s greatness without becoming obsequious. Apart from a couple of inevitable differences in interpretation, the only negative thing I have to say is that Isaacson is unnecessarily repetitive in places. Overall, though, it’s a fascinating life, brilliantly portrayed. (See also: Isaacon’s interview about the book on The Skeptics Guide to the Universe starting at 34:30).
Why Is Sex Fun: The Evolution of Human Sexuality by Jared Diamond is utter junk. I can’t believe the author of Guns, Germs and Steel could produce something this bad. The less said about it the better – don’t read it, ever.
No Country for Old Men by Cormac Mccarthy (fiction). Atmospheric, absorbing, sublime prose, and totally believable. I’m not a huge fan of the ending (or the movie adaptation, for that matter), but it’s still one of the best novels I’ve read in ages.
The Classical World: An Epic History of Greece and Rome by Robin Lane Fox is an enormously ambitious book: it is a survey of almost a thousand years of complicated and interesting history in only 600 pages. Frankly, I’m generally skeptical about epic surveys – telescoped history is often watered-down history. Not so with The Classical World, it is a magnificent, full-blooded, exciting and sympathetic account of Greece and Rome. Few scholars, I suspect, could pull-off anything similar: Lane Fox’s classical knowledge is veritably encyclopedic. A particularly congenial aspect of the book is how Lane Fox’s love for his subject matter shines through; he makes no apologies for his passion. Negatives: a sometimes-ponderous writing style and a surfeit of French words, the themes of ‘luxury’, ‘freedom’ and ‘justice’ seem occasionally procrustean, the book has a slow and somewhat confusing start and Lane Fox can be a bit pompous at times. All that said, the book is a recommended introduction to the classical world.
Contact Wounds: A War Surgeon’s Education is Jonathan Kaplan’s sequel to The Dressing Station (which I read – and loved – a couple of years ago). The book is a memoir of Kaplan’s early life (including a trip to Israel just after the Six Day War) and his medical education both as a student at the University of Cape Town (my alma mater) and his residencies in various parts of the world. The book ends off with events in Kaplan’s life subsequent to the publication of The Dressing Station, most notably, his stints in Angola and Iraq. Kaplan writes exceedingly well and Contact Wounds radiates humanity, remains interesting throughout and documents an amazing life. My only worry about the book is that it reads like a novel, which isn’t bad in itself, but I’m somewhat dubious Kaplan remembers as many details as he pretends to about when he was, say, 14. Nevertheless, Contact Wounds is a riveting, eye-opening read.
I hate to say this, but I was thoroughly unimpressed with Christopher Hitchens’ God Is Not Great: How Religion Poisons Everything. Hitchens writes beautifully, is widely educated and is a highly skilled polemicist, but, honestly, I found his arguments unconvincing. Given that I already agree with many of his conclusions and given the purpose of the book, this criticism is very harsh: Hitchens has failed to contribute to the ‘new atheist’ debate in a meaningful way. A relatively small failing I think speaks volumes: like a bad undergraduate essay, God Is Not Great is based almost exclusively on secondary-sources, it seems without Jennifer Hecht’s Doubt: A History Hitchens would not have been able to write his book. Bottom-line: watch Hitchens speaking (where he is second to none), but don’t read his book. (See also: Hitchens' interview about the book on Point of Inquiry).
A Guinea Pig’s History of Biology: The Plants and Animals Who Taught Us the Facts of Life by Jim Endersby is a new kind of intellectual history of biology that doesn’t focus on personalities (‘great men’) but on specific model organisms. Each of the 12 chapters focuses on one particular organism (Drosophila, humans, Equus quagga, guinea pigs etc.) and discusses at length how the organism came to be used and what questions biologists used it to answer. A theme running through the book is how difficult it is to transform a wild-type into a model organism: often it took years of patient work that bore no fruit in the short term. George Streisinger, for example, is the unsung hero of evo-devo; it took him nearly a decade to breed zebrafish suitable for scientific work. Another interesting theme of the book is that it took a whole community of researchers, collaborating openly and trusting one another, to produce scientific breakthroughs using a specific organism. Thomas Hunt Morgan and his ‘fly-boys’ (champions of Drosophila) set the precedent: they gave away whole colonies of newly standardized flies to any interested researcher and eventually even produced a newsletter, Drosophila Information Service, to spread useful fly information.Negatives: Endersby’s last chapter reveals little about its purported subject, OncoMouse, and degenerates into an entirely uninteresting essay about what Endersby thinks about genetic engineering, the philosophy of science and so on. His editor should have spared him. A final, much less serious, criticism: the book sometimes gets bogged down in historical minutia (like what effect Great Britain’s 1845 abolition of the tax on glass had on the cultivation of flowers) but Endersby rarely strays too far from biology.
Overall, A Guinea Pig’s History of Biology is an original, interesting, well-researched and informative history. It comes highly recommended.
Sunday, June 22, 2008
Plants, it turns out, are not nearly as boring as we thought
I have to admit: I'm not a huge fan of botany. My high school biology teacher was a botanist, and I have horrible memories of trying to memorize the names and functions of organelles in various plant cells. A new article in the New York Times, however, summarizes the growing evidence that plants are in fact much more animal-like (and in my parochial view, at least) therefore much more interesting that we ever thought.
There is evidence, for one thing, that the Great Lakes sea rocket practises kin altruism, that is, it can detect related plants and treat them favorably. The study the NYT piece refers to in this regard is Susan Dudley and Amanda File's "Kin recognition in an annual plant" (pdf). Their conclusion is that
Even more remarkable is the finding (also summarized in the NYT article) that the parasitic plant Cuscuta pentagona (aka dodder) uses chemical cues to detect the most desirable hosts, which it then grows towards. This finding comes from a paper ("Volatile Chemical Cues Guide Host Location and Host Selection by Parasitic Plants" [pdf]) published in Science in 2006. Watching the time-lapsed video (.mov file) of this behavior (and it is most definitely behavior) really gives one a new perspective on plants.
There is even a Society for Plant Neurobiology! (Yes, that's neurobiology). The locus classicus of this emerging field seems to be Bremmer et. al.'s "Plant neurobiology: an integrated view of plant signaling" (pdf) that appeared in Trends in Plant Science in 2006. They defined the field as follows:
(See also: an NPR podcast on the dodder's abilities)
There is evidence, for one thing, that the Great Lakes sea rocket practises kin altruism, that is, it can detect related plants and treat them favorably. The study the NYT piece refers to in this regard is Susan Dudley and Amanda File's "Kin recognition in an annual plant" (pdf). Their conclusion is that
in the annual plant Cakile edentula, allocation to roots increased when groups of strangers shared a common pot, but not when groups of siblings shared a pot. Our results demonstrate that plants can discriminate kin in competitive interactions and indicate that the root interactions may provide the cue for kin recognition. Because greater root allocation is argued to increase below-ground competitive ability, the results are consistent with kin selection.In other words, these lowly seeming plants, remarkably, can somehow directly detect kin (something that has not been demonstrated in many animals) and thus they have a family-life.
Even more remarkable is the finding (also summarized in the NYT article) that the parasitic plant Cuscuta pentagona (aka dodder) uses chemical cues to detect the most desirable hosts, which it then grows towards. This finding comes from a paper ("Volatile Chemical Cues Guide Host Location and Host Selection by Parasitic Plants" [pdf]) published in Science in 2006. Watching the time-lapsed video (.mov file) of this behavior (and it is most definitely behavior) really gives one a new perspective on plants.
There is even a Society for Plant Neurobiology! (Yes, that's neurobiology). The locus classicus of this emerging field seems to be Bremmer et. al.'s "Plant neurobiology: an integrated view of plant signaling" (pdf) that appeared in Trends in Plant Science in 2006. They defined the field as follows:
Plant neurobiology is a newly focused field of plant biology research that aims to understand how plants process the information they obtain from their environment to develop, prosper and reproduce optimally. The behavior plants exhibit is coordinated across the whole organism by some form of integrated signaling, communication and response system. This system includesWhile I suspect some of this is a tad overexcited rhetoric and while these ideas are controversial (pdf), they're certainly stimulating and exciting. If the research holds up, plant neurobiology promises to transform our view of a large segment of the natural world and, as has happened repeatedly in Western intellectual history, we will have to abandon a view dominant since Aristotle.
long-distance electrical signals, vesicle-mediated transport of auxin in specialized vascular tissues, and production of chemicals known to be neuronal in animals. Here we review how plant neurobiology is being directed toward discovering the mechanisms of signaling in whole plants, as well as among plants and their neighbors.
(See also: an NPR podcast on the dodder's abilities)
Wednesday, March 12, 2008
Video: Craig Venter and Artificial Life
Craig Venter is a scientific maven and maverick who leads a team that is on the verge of creating artificial life that, among other things, might produce artificial organisms capable of replacing the entire petro-chemical industry. This is Important Stuff.
Venter's 2008 TEDTalk is embedded below, or here is the direct link.
Venter's 2008 TEDTalk is embedded below, or here is the direct link.
Wednesday, February 27, 2008
The Encyclopedia of Life
The always wonderful Carl Zimmer has a terrific NYT article about the launch of the Encyclopedia of Life, a free online collaborative encyclopedia that aims to document every species on earth. (Visit it at www.eol.org). As anyone who regularly follows the links in this blog will know, I am a big fan of collaborative online encyclopedias (Wikipedia!): I think the model has proven itself beyond all reasonable doubt. As a result, I am extremely excited about this project, it will prove to be an invaluable resource to scientists and laypeople alike.
The project, by the way, is being spearheaded by the seemingly ubiquitous E. O. Wilson: check out his TEDTalk on the encyclopedia.
The project, by the way, is being spearheaded by the seemingly ubiquitous E. O. Wilson: check out his TEDTalk on the encyclopedia.
Tuesday, December 4, 2007
Video: Evo-Devo in 60 seconds
Scientific American recently launched an interesting new vodcast, Instant Egghead, to accompany their 60 Second Science stable of podcasts. As you might have guessed, Instant Egghead explains various scientific concepts, theories or ideas in 60 seconds (tagline: "Explain Big Ideas. Fast.") . The two previous episodes covered Dark Matter and Moore's law, respectively; Episode 3 (embedded below, or click here to go to the SciAm site) is on Evo-Devo:
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