If you follow Pleiotropy via RSS, then you may not have noticed that the blog has moved. By invitation I've joined the science blog network Field of Science, and am indeed very pleased with the move. The URL has changed, but no worries - the old URL redirects here. Otherwise it's business as usual.
Check out the other blogs in the network. Lots of good blogs there, several of which I already subscribe to myself, and several who are contributors to Carnival of Evolution.
And for the bloggers in this network, you are hereby cordially invited to submit posts about evolution to CoE. Next edition is going up on Sandwalk in just ten days.
Hocus-pocus conference
Someone really wants me to go to this conference in India on holistic medicine. I have just received the third email inviting me to register. Not sure why, except of course the more the merrier. However, I am an evolutionary biologist, and don't really have anything to say about holistic medicine. Except bad stuff:
Here is the list of topics covered, with Wikipedia links to those that I judge to be hocus-pocus:
Modern Medicine (Allopathy), Ayurveda, Homeopathy, Naturopathy, Alternative Medicine, Complementary Medicine, Reiki, Touch Therapies [no Wikipedia page], Siddha, Colour Therapy, Aroma Therapy, Geriatric Health, Chiropractic Therapy, Acupuncture, Unani, Yoga, Massage, Radiation Therapy, Traditional Chinese Medicine, Traditional Medicines of all the Countries and Medicinal Plants.
Note that Allopathy is a derogatory term for conventional medicine, aka evidence-based medicine. In start contrast with other kinds of medicine.
Now, I am not saying that none of the linked practices are without effect at all. For example, I do believe that chiropractic can do good things for the spine (but am skeptical of the claim that chiropractic can cure other diseases and of "innate intelligence"). I also think that it might be that aroma therapy can affects a person's mood (dare I say of course?). But some practitioners of all of those alternatives to evidence-based medicine claim that it can do more than what the evidence suggests.
On more than one occasion have I been called arrogant because I am rather quick to dismiss practices that I most often call hocus-pocus. Astrology, tarot, and religion belong in that category. The idea here is that it is arrogant to claim to know something doesn't work without having intricate first-hand knowledge of the subject. "Maybe homeopathy works - how can you be sure it doesn't? How can you claim to know there is nothing supernatural? It is arrogant to dismiss it like that."
But this is completely backwards. I consider it arrogant to claim that something works when that is based on no evidence. And there is no evidence for those things. No evidence that isn't just personal anecdote and that hasn't been verified in proper experimental settings. I consider it amazingly arrogant that people claim to know the mind of God, based exclusively on the Bible.
I won't be going to India in September. I have better things to do and no money to spare. However, I think it could be fun nonetheless, meeting these people, and especially asking questions about the missing evidence.
Here is the list of topics covered, with Wikipedia links to those that I judge to be hocus-pocus:
Modern Medicine (Allopathy), Ayurveda, Homeopathy, Naturopathy, Alternative Medicine, Complementary Medicine, Reiki, Touch Therapies [no Wikipedia page], Siddha, Colour Therapy, Aroma Therapy, Geriatric Health, Chiropractic Therapy, Acupuncture, Unani, Yoga, Massage, Radiation Therapy, Traditional Chinese Medicine, Traditional Medicines of all the Countries and Medicinal Plants.
Note that Allopathy is a derogatory term for conventional medicine, aka evidence-based medicine. In start contrast with other kinds of medicine.
Now, I am not saying that none of the linked practices are without effect at all. For example, I do believe that chiropractic can do good things for the spine (but am skeptical of the claim that chiropractic can cure other diseases and of "innate intelligence"). I also think that it might be that aroma therapy can affects a person's mood (dare I say of course?). But some practitioners of all of those alternatives to evidence-based medicine claim that it can do more than what the evidence suggests.
On more than one occasion have I been called arrogant because I am rather quick to dismiss practices that I most often call hocus-pocus. Astrology, tarot, and religion belong in that category. The idea here is that it is arrogant to claim to know something doesn't work without having intricate first-hand knowledge of the subject. "Maybe homeopathy works - how can you be sure it doesn't? How can you claim to know there is nothing supernatural? It is arrogant to dismiss it like that."
But this is completely backwards. I consider it arrogant to claim that something works when that is based on no evidence. And there is no evidence for those things. No evidence that isn't just personal anecdote and that hasn't been verified in proper experimental settings. I consider it amazingly arrogant that people claim to know the mind of God, based exclusively on the Bible.
I won't be going to India in September. I have better things to do and no money to spare. However, I think it could be fun nonetheless, meeting these people, and especially asking questions about the missing evidence.
Twittering evolution
As the keeper of Carnival of Evolution, I also inherited a Twitter account, @CarnyEvolution. I use this irregularly to highlight blog posts about evolution. And there is a lot, and only a fraction of them are submitted to Carnival of Evolution.
"I want to save the whales throughmodeling evolution."
on 
"I want to save the whales through
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More on high-dimensional fitness landscapes
In a post from a few days ago about a paper I just got published, John Wilkins asked how my work ties in with Gavrilets' stuff on high dimensional landscapes. Here's my answer:
In terms of the discussion about the strength of the metaphor of the fitness landscape, my view is that the people who argue that it's not useful or even misleading are wrong. Yes, some people may take the analogy with a geographic landscape too far. However, a fitness landscape is simply a fitness function, and mathematically functions can of course be of as many variables as one likes. Thus, the high-dimensionality of real fitness landscapes does nothing to diminish the value of thinking in terms of fitness landscapes. Also, while high-dimensional fitness landscapes cannot be nicely visualized, there are other ways to get information about its structure (which is crucial for evolutionary dynamics). Here's is a paper from last year I wrote on that: Critical properties of complex fitness landscapes.
You can read Gavrilet's contribution to the Altenberg conference here: High-dimensional fitness landscapes and the origins of biodiversity.
I agree with Gavrilets' conclusion that much of empirical fitness landscapes will contain neutral networks, akin to his 'holey landscapes'. He cites papers showing this is the case in RNA, proteins, bacteria, viruses, and artificial life. However, there is ample evidence from those as well that fitness landscapes are rugged, i.e., contains multiple peaks and valleys. The paper by Chou and Khan cited in the OP are direct evidence that there is at least one peak, for example. The particular implementation of NK that I am using here does not result in neutral networks, but even if it was set up to contain many neighboring genotypes of effectively equal fitness, it wouldn't change the results much, provided there are still peaks and valleys.
Also in the comments to the OP, Nofutur876 mentions Kryazhimskiya et al. (2009). That paper makes one assumption that is very unrealistic in bacterial species, such as E. coli (which they compare with): "We assume that the mutation rate is sufficiently small that, at most, one mutant segregates in the population at any time". But the mutation-supply rate can be as much as 20,000, which results in multiple mutations segregating at the same time, so I am not comfortable accepting their results. They look at three different types of landscapes, two of which are highly unrealistic (an uncorrelated fitness landscape in which there is no correlation in fitness between neighboring genotypes, and the "stairway to heaven", in which all mutations have the same effect), and then one where there is no epistasis, which is only somewhat unrealistic, in that there could be parts of biological fitness landscapes that are non-epistatic. However, evolutionary dynamics in these single-peak landscapes bears little resemblance to that in rugged - and more realistic - landscapes.
Nofutur876 also asks how I measure landscape ruggedness. Ruggedness is simply a measure of how many peaks a fitness landscape contains. The more peaks the more rugged it is. One may also describe a landscape with the same density of peaks but with a greater range in fitness (global peak minus deepest dip) as more rugged. However, there aren't any formal definitions, as far as I know. Since knowing the structure of real fitness landscape is very difficult, it is not a measure that has much utility. In the NK model ruggedness increase both as a function of N and K. That is, the more loci the model contains (N), the more peaks is has, and the more loci interact to produce the fitness of each trait (K+1), the more peaks there are and the greater the fitness range will be.
In terms of the discussion about the strength of the metaphor of the fitness landscape, my view is that the people who argue that it's not useful or even misleading are wrong. Yes, some people may take the analogy with a geographic landscape too far. However, a fitness landscape is simply a fitness function, and mathematically functions can of course be of as many variables as one likes. Thus, the high-dimensionality of real fitness landscapes does nothing to diminish the value of thinking in terms of fitness landscapes. Also, while high-dimensional fitness landscapes cannot be nicely visualized, there are other ways to get information about its structure (which is crucial for evolutionary dynamics). Here's is a paper from last year I wrote on that: Critical properties of complex fitness landscapes.
You can read Gavrilet's contribution to the Altenberg conference here: High-dimensional fitness landscapes and the origins of biodiversity.
I agree with Gavrilets' conclusion that much of empirical fitness landscapes will contain neutral networks, akin to his 'holey landscapes'. He cites papers showing this is the case in RNA, proteins, bacteria, viruses, and artificial life. However, there is ample evidence from those as well that fitness landscapes are rugged, i.e., contains multiple peaks and valleys. The paper by Chou and Khan cited in the OP are direct evidence that there is at least one peak, for example. The particular implementation of NK that I am using here does not result in neutral networks, but even if it was set up to contain many neighboring genotypes of effectively equal fitness, it wouldn't change the results much, provided there are still peaks and valleys.
Also in the comments to the OP, Nofutur876 mentions Kryazhimskiya et al. (2009). That paper makes one assumption that is very unrealistic in bacterial species, such as E. coli (which they compare with): "We assume that the mutation rate is sufficiently small that, at most, one mutant segregates in the population at any time". But the mutation-supply rate can be as much as 20,000, which results in multiple mutations segregating at the same time, so I am not comfortable accepting their results. They look at three different types of landscapes, two of which are highly unrealistic (an uncorrelated fitness landscape in which there is no correlation in fitness between neighboring genotypes, and the "stairway to heaven", in which all mutations have the same effect), and then one where there is no epistasis, which is only somewhat unrealistic, in that there could be parts of biological fitness landscapes that are non-epistatic. However, evolutionary dynamics in these single-peak landscapes bears little resemblance to that in rugged - and more realistic - landscapes.
Nofutur876 also asks how I measure landscape ruggedness. Ruggedness is simply a measure of how many peaks a fitness landscape contains. The more peaks the more rugged it is. One may also describe a landscape with the same density of peaks but with a greater range in fitness (global peak minus deepest dip) as more rugged. However, there aren't any formal definitions, as far as I know. Since knowing the structure of real fitness landscape is very difficult, it is not a measure that has much utility. In the NK model ruggedness increase both as a function of N and K. That is, the more loci the model contains (N), the more peaks is has, and the more loci interact to produce the fitness of each trait (K+1), the more peaks there are and the greater the fitness range will be.
My real time-machine
I have a mental time-machine that I like to use to reflect on my own life. I am 90 years old, and I am thinking about the things I wish I had done differently. Like, if only I had hugged my kids more when they were young, or if only I had read more books, etc. And then I travel back in time to now, and I am able to make those changes. It's brilliant.
So, on your deathbed (why would anyone buy a deathbed?), how would you wish you had lived your life differently?
According to someone who have worked a lot with dying people (get the details on Rationally Speaking), here are the top five regrets:
1. I wish I’d had the courage to live a life true to myself, not the life others expected of me.
2. I wish I didn’t work so hard.
3. I wish I’d had the courage to express my feelings.
4. I wish I had stayed in touch with my friends.
5. I wish that I had let myself be happier.
Personally, I'm mostly good with the first three, but not so much on the fourth. I do wish I had stayed more in touch with old friends, but then moving abroad makes that hard. Somehow there is the expectation that those who move away are the ones who must work to keep in touch, and not the other way around. Good thing I'm in Denmark now, so I can call of old friends and go see how they are.
As for the fifth one, I don't know what that means, really. Seems to me the first four are what people wished to do in order to have lived a happier life. Just saying I wish I could have been happier really doesn't make much sense. Do people really ever "let" themselves be happy? How does one do that, if not by trying to be true to oneself, work less, express one's feelings more, and keep in touch with friends? [After writing that, I read the to the end of Massimo's post, and realized he thinks the same thing about point 5.]
Anyhow, I highly recommend using the mental time-machine once in a while. It's effective for thinking about what we are doing right now. Is that really what we want to tell out grandchildren that we were spending our time doing? If we cheat and lie and hurt other people, are we comfortable telling that story to the grandchildren? Is anger and fighting what we want to write about in our memoirs? When you're on your deathbed (personally, I'm not getting one), are you going to be regretful or not? Now is the time to do something about it. As I said once to a dear friend who I am seeing very soon, I don't know what you should do, but I know when: Now.
So, on your deathbed (why would anyone buy a deathbed?), how would you wish you had lived your life differently?
According to someone who have worked a lot with dying people (get the details on Rationally Speaking), here are the top five regrets:
1. I wish I’d had the courage to live a life true to myself, not the life others expected of me.
2. I wish I didn’t work so hard.
3. I wish I’d had the courage to express my feelings.
4. I wish I had stayed in touch with my friends.
5. I wish that I had let myself be happier.
Personally, I'm mostly good with the first three, but not so much on the fourth. I do wish I had stayed more in touch with old friends, but then moving abroad makes that hard. Somehow there is the expectation that those who move away are the ones who must work to keep in touch, and not the other way around. Good thing I'm in Denmark now, so I can call of old friends and go see how they are.
As for the fifth one, I don't know what that means, really. Seems to me the first four are what people wished to do in order to have lived a happier life. Just saying I wish I could have been happier really doesn't make much sense. Do people really ever "let" themselves be happy? How does one do that, if not by trying to be true to oneself, work less, express one's feelings more, and keep in touch with friends? [After writing that, I read the to the end of Massimo's post, and realized he thinks the same thing about point 5.]
Anyhow, I highly recommend using the mental time-machine once in a while. It's effective for thinking about what we are doing right now. Is that really what we want to tell out grandchildren that we were spending our time doing? If we cheat and lie and hurt other people, are we comfortable telling that story to the grandchildren? Is anger and fighting what we want to write about in our memoirs? When you're on your deathbed (personally, I'm not getting one), are you going to be regretful or not? Now is the time to do something about it. As I said once to a dear friend who I am seeing very soon, I don't know what you should do, but I know when: Now.