"I woke today and found the frost perched on the town
it hovered in a frozen sky, and gobbled summer down."
-Joni Mitchell
Rostock has its first real frost this morning. In anticipation of this event, the first bad cold of the year has been going around. I think about half the Institute has gotten it so far. I have been sick to varying degrees for a week now. Without having actually looked at the relevant research, my understanding is that we get so many more colds when it gets colder because the airborne viruses break down much more slowly when the areas cold and dry and sunlight is weak. I've also heard somewhere that the cold air makes mucous membranes more susceptible to viruses. This all makes sense, and helps explain why that other common airborne virus that spreads every year, the flu, also concentrates in winter, but it leaves me wondering this: is the pattern the same in species that are adapted to highly seasonal climates? Humans are basically a tropical species that construct tropic-like microclimates for ourselves wherever we go. Our ancestors a few thousand generations ago would not have experienced the yearly cold season as we do today. Moose on the other hand have been living in cold climates forever. Their bodies should expect high virus conditions every winter and prepare accordingly. I speculate that the immune systems of such animals are seasonal, being better at fighting airborne viruses in the winter, and perhaps skin fungus is in the summer. I wouldn't personally want to do the experiments to find out, but I would read the paper if somebody else wrote it.
Monday, October 18, 2010
Saturday, October 16, 2010
Not buying a PC
The paper I recently submitted was written almost entirely by dictating to my computer at work. I've been finding it hard to do any work, or other writing at home. I am dependent on dictation software, and the best available dictation software for Macs was okay but not nearly as good as the PC version. I had started to toy with idea of buying a PC for home use, despite already having a couple of good Macs, just so I could dictate easily and quickly. But now they updated the Mac software, and it is in theory the same as the latest PC dictation software. I'll wait for the reviews to come out, but I'll probably buy the $40 upgrade instead of a whole new computer.
Friday, October 15, 2010
The LPU
This big grant on applying for, to lead my own group, requires me to do all sorts of things beyond just completing the grant application. I need my CV to look as good as possible when I submit, and that doesn't just mean checking for typos. A lot of the work that I've done recently is not yet in the form that goes on a CV, so I need to get it in that form. A paper that is written but just sitting on my computer is not a publication. So last week I submitted a draft to a high-profile journal is very rapid turnaround time, hoping to have accepted before my application deadline. I am now working on what is called an LPU.
The Least Publishable Unit has a long and proud history in science. It is often the case that one can either toil for months over a very long paper, or chop that up into several smaller papers which will come out faster, often in lower profile journals. The quality of the work is not necessarily any lower, but the step is more incremental and the CV filled out faster. This particular LPU is a simple reanalysis of some data from my doctoral work. I started writing it today, and expects to have completed draft by sometime next week. I will submitted to a low-profile journal with rapid turnaround and hope to have an answer from them before I send in my CV.
I do not feel at all bad about this, my first LPU, for several reasons. First, looking through the CVs of most of the very successful scientists I know, there are quite a few little papers among their giant publications. Second, I can think of several papers which seem to me to have started out as LPUs but which turned out to be tremendously important and widely cited. Third, experience and mentors have told me people are more likely to read a short paper. Fourth and finally, writing short papers is a hell of a lot easier when one has to dictate everything.
There is one way in which this paper does not really meet the classical definition of an LPU: there are lots of data behind it. The true LPU should have just enough data to make a publishable paper. In this case, the sample being analyzed is fairly enormous, although not much bigger than is needed to answer the question.
All in all, writing a little paper seems a good change from the massive review article I've just submitted. I hope it turns out to be as easy as I think it will.
The Least Publishable Unit has a long and proud history in science. It is often the case that one can either toil for months over a very long paper, or chop that up into several smaller papers which will come out faster, often in lower profile journals. The quality of the work is not necessarily any lower, but the step is more incremental and the CV filled out faster. This particular LPU is a simple reanalysis of some data from my doctoral work. I started writing it today, and expects to have completed draft by sometime next week. I will submitted to a low-profile journal with rapid turnaround and hope to have an answer from them before I send in my CV.
I do not feel at all bad about this, my first LPU, for several reasons. First, looking through the CVs of most of the very successful scientists I know, there are quite a few little papers among their giant publications. Second, I can think of several papers which seem to me to have started out as LPUs but which turned out to be tremendously important and widely cited. Third, experience and mentors have told me people are more likely to read a short paper. Fourth and finally, writing short papers is a hell of a lot easier when one has to dictate everything.
There is one way in which this paper does not really meet the classical definition of an LPU: there are lots of data behind it. The true LPU should have just enough data to make a publishable paper. In this case, the sample being analyzed is fairly enormous, although not much bigger than is needed to answer the question.
All in all, writing a little paper seems a good change from the massive review article I've just submitted. I hope it turns out to be as easy as I think it will.
Key Words
Grant applications,
publishing,
science as process
Friday, October 08, 2010
Big grant, small grant application
Applying for a grant is nothing new, but this one is big, at least by the standards of the grants have applied for previously. The Max Planck Society sponsors Independent Research Groups, headed by a promising young scientist to explore some innovative and important niche. My task is to convince them I am promising and young, and that my work is innovative and important. They don't actually say young, they say "early career," for which I qualify, as I just got my PhD last year. I'm also fairly confident that my work is innovative, as everyone I tell about my work tells me that nobody else has thought about the question. The problem is, "nobody else has thought about the question," can be taken to mean, "who could possibly be interested in that?" So I am young and innovative, and my challenge is to seem promising and important.
Assuming I can convince them of these things, more so than the many other applicants, it will be a pretty sweet deal. They will not only give me a significantly increased salary for five years and enough funding to get my experiments going, they will pay for me to hire a couple of graduate students and a postdoc or two. Frankly, this is more of a career advance than I think I am likely to receive at this point.
The nice part, other than the generosity of the award should I get it, is how little work they ask of me for the application. They want only a one-page statement of my Scientific Accomplishments (I'm not sure what these are yet) plus 2 pages of Research Plans. I could give them 20 pages of research plans with little difficulty if my hands worked well, but under the circumstances I'm much happier to give them 2.
How my health issues will work into this whole application is an interesting question. There is no doubt that I would have been more productive this year and in grad school had been healthy, but I doubt that they can or should take this into consideration. The best I can hope for is that one of my letter writers will mention something about dedication to science or gumption or the fact that I just keep coming back, like a bad case of poison ivy.
On a more philosophical level, I can ask this question: if someone has a disability which interferes with their productivity, and is likely to continue interfering with their productivity, should an employer consider how productive the worker would be without the disability, or should they simply asked of each candidate, "how productive is he/she likely to be?" I would like to say the former, but from the employer's point of view, it's hard to make the case against the latter.
On the other hand, my joint problems potentially make me better qualified to think of the questions and tell other people to gather the necessary data to answer them than I am for actual data gathering and analysis. The higher they promote me, the more qualified I may be.
Assuming I can convince them of these things, more so than the many other applicants, it will be a pretty sweet deal. They will not only give me a significantly increased salary for five years and enough funding to get my experiments going, they will pay for me to hire a couple of graduate students and a postdoc or two. Frankly, this is more of a career advance than I think I am likely to receive at this point.
The nice part, other than the generosity of the award should I get it, is how little work they ask of me for the application. They want only a one-page statement of my Scientific Accomplishments (I'm not sure what these are yet) plus 2 pages of Research Plans. I could give them 20 pages of research plans with little difficulty if my hands worked well, but under the circumstances I'm much happier to give them 2.
How my health issues will work into this whole application is an interesting question. There is no doubt that I would have been more productive this year and in grad school had been healthy, but I doubt that they can or should take this into consideration. The best I can hope for is that one of my letter writers will mention something about dedication to science or gumption or the fact that I just keep coming back, like a bad case of poison ivy.
On a more philosophical level, I can ask this question: if someone has a disability which interferes with their productivity, and is likely to continue interfering with their productivity, should an employer consider how productive the worker would be without the disability, or should they simply asked of each candidate, "how productive is he/she likely to be?" I would like to say the former, but from the employer's point of view, it's hard to make the case against the latter.
On the other hand, my joint problems potentially make me better qualified to think of the questions and tell other people to gather the necessary data to answer them than I am for actual data gathering and analysis. The higher they promote me, the more qualified I may be.
Friday, October 01, 2010
The news from me
I've just started using Dragon 11, the latest version of the dictation software I've gotten used to over the last few months. I was on version 8, and over some months of using it fairly intensively it had gotten pretty good at recognizing my voice and words. This new version does about as good a job as the old one did, maybe a bit better, but without the months of training. I haven't yet tried out how it works with other applications, in Excel, PowerPoint, Firefox, etc. but at least word it seems to work surprisingly well for never having heard my voice before.
I had carpal tunnel surgery on my left hand about a month ago and am pleased to report that had very little numbness or tingling since then in that hand. I still have pain around where the incision was and some of the internal cuts but they assure me that will fade with time. I'm having the same surgery on my right hand on Monday. I'm supposed to be on sick leave for all of next week, but I suspect I'll end up coming in to use the dictation software, as I don't have it at home (I have a Mac it works on PC.) I hope that by the end of the year I'll be able to use my hands fairly normally again.
I also just found out today that a large grant application I need to submit is due on November 17. This may interfere somewhat with my plans to post here more regularly.
I had carpal tunnel surgery on my left hand about a month ago and am pleased to report that had very little numbness or tingling since then in that hand. I still have pain around where the incision was and some of the internal cuts but they assure me that will fade with time. I'm having the same surgery on my right hand on Monday. I'm supposed to be on sick leave for all of next week, but I suspect I'll end up coming in to use the dictation software, as I don't have it at home (I have a Mac it works on PC.) I hope that by the end of the year I'll be able to use my hands fairly normally again.
I also just found out today that a large grant application I need to submit is due on November 17. This may interfere somewhat with my plans to post here more regularly.
Fall
Sunrise splashes across autumn-spangled tree tips. A hooded crow, black and gray and flapping methodically, meanders between the swaying, glowing, multicolored peaks. Wingtip sweep up, flashing into horizontal sunlight, and down, into shadow and raucous foliage.
Wednesday, June 16, 2010
experimentation
I have discovered that it is actually less effort to unlock the door to my apartment with my pocket knife than with the key. Perhaps it is time to change the lock.
Thursday, May 27, 2010
Look Ma, ...
I find myself unable to use my hands for very much of anything, and wondering how to be a productive scientists given this peculiar handicap. The problem is not that I lack hands, I have them and they looked perfectly complete, if slightly blue. The problem is not even I can operate them, I have full control and enough strength to do most simple tasks. Rather my problem is that I mustn't use my hands, for a fight to the swell up become quite painful and remain so for some time. It's not yet entirely clear why this is, so for the time being the blame Levitis Syndrome.
There are many jobs for which not using one's hands would be a greater problem than they are for me as a scientist. A carpenter, a cellist, or a cashier would be much less able to work around this problem and I am. Furthermore, there is extremely little short-term pressure for me to get anything done. In the long term, I have to publish papers to keep my job and move to better jobs in the future. In the short term I want to get things done simply because it is too frustrating to not do so.
I'm using dictation software which, now that I've used for some time, is quite quick and accurate for creating text. Not quite as fast as typing, but a hell of a lot faster than I thought dictation software was before I started using it. I have students to do my lab work for me, I'm not doing any field work, and I have access digitally most of the literature I need. Given all this, why should a small matter like hands make much of a difference?
In practice, there are all sorts of things that I find myself unable to do. The dictation software supposed to make it possible to use many different programs, for surfing the web, analyzing data, sending e-mails and so on; in fact many of these thing are quite difficult to do without moving the mouse or touching the keys. Writing code is extraordinarily difficult. Reading heavy paper books is quite hard. Many software tools are simply inaccessible.
My latest stratagem is to order a mouse controlled by foot. The ability to point and click should solve many of my problems, in combination with this dictation software.
The other challenge of being productive despite my hands, is one of concentration. Doing things so differently requires a lot of thought about how I do them, which distracts me from the ideas and tasks to concentrate on. In addition to that, my hands hurt, tingle, throb and otherwise distract me. I am frankly not so good at ignoring it to the point that I can think deeply.
Ultimately, my hands will probably get better with time and coddling. When that happens, I can add dictation software and foot-controlling a mouse to my long list of random and not particularly useful skills. Until then, I'll be studying the list of available voice commands and wearing slip ons.
There are many jobs for which not using one's hands would be a greater problem than they are for me as a scientist. A carpenter, a cellist, or a cashier would be much less able to work around this problem and I am. Furthermore, there is extremely little short-term pressure for me to get anything done. In the long term, I have to publish papers to keep my job and move to better jobs in the future. In the short term I want to get things done simply because it is too frustrating to not do so.
I'm using dictation software which, now that I've used for some time, is quite quick and accurate for creating text. Not quite as fast as typing, but a hell of a lot faster than I thought dictation software was before I started using it. I have students to do my lab work for me, I'm not doing any field work, and I have access digitally most of the literature I need. Given all this, why should a small matter like hands make much of a difference?
In practice, there are all sorts of things that I find myself unable to do. The dictation software supposed to make it possible to use many different programs, for surfing the web, analyzing data, sending e-mails and so on; in fact many of these thing are quite difficult to do without moving the mouse or touching the keys. Writing code is extraordinarily difficult. Reading heavy paper books is quite hard. Many software tools are simply inaccessible.
My latest stratagem is to order a mouse controlled by foot. The ability to point and click should solve many of my problems, in combination with this dictation software.
The other challenge of being productive despite my hands, is one of concentration. Doing things so differently requires a lot of thought about how I do them, which distracts me from the ideas and tasks to concentrate on. In addition to that, my hands hurt, tingle, throb and otherwise distract me. I am frankly not so good at ignoring it to the point that I can think deeply.
Ultimately, my hands will probably get better with time and coddling. When that happens, I can add dictation software and foot-controlling a mouse to my long list of random and not particularly useful skills. Until then, I'll be studying the list of available voice commands and wearing slip ons.
Sunday, April 18, 2010
Planeless sky
The unpronounceable Icelandic volcano has left my place of work quite empty. This last week was the largest demography conference of the year, and a large portion of my colleagues flew to Dallas for it. They have not been able to return.

This map (from the NYTimes) shows which European airports are currently closed. Rostock is right in the middle of the gray area, half way between Berlin and Copenhagen. The closest operating airports right now are Madrid (2500km), Rome (1700 km including crossing the Alps) or St. Petersburg (2 days by ferry), and they are all booked up. So I may not have many coworkers around until this dust blows over.
The sunsets have been colorful the last couple of days, and the horizon looks hazier than usual, but other than that and the lack of airplanes flying over, I can see no smoke. Also, the grocery stores are out of bananas.
The airlines are starting to question the science behind the flight ban. I am doubtful myself. The concentration of particles (which hasn't actually been measured in most places) must be pretty minute, as the emissions from a small eruption are dispersed over perhaps 100,000,000 cubic kilometers.
I come to that rough estimate because the effected area is about 5000km east to west, 5000km north to south and the cloud is about 4 km top to bottom. I've not seen an estimate for how many tons of ash are up there, or what concentration is dangerous, but I'm guessing the concentration of particulate matter up there is no higher than that over LA or Houston in the summer.

This map (from the NYTimes) shows which European airports are currently closed. Rostock is right in the middle of the gray area, half way between Berlin and Copenhagen. The closest operating airports right now are Madrid (2500km), Rome (1700 km including crossing the Alps) or St. Petersburg (2 days by ferry), and they are all booked up. So I may not have many coworkers around until this dust blows over.
The sunsets have been colorful the last couple of days, and the horizon looks hazier than usual, but other than that and the lack of airplanes flying over, I can see no smoke. Also, the grocery stores are out of bananas.
The airlines are starting to question the science behind the flight ban. I am doubtful myself. The concentration of particles (which hasn't actually been measured in most places) must be pretty minute, as the emissions from a small eruption are dispersed over perhaps 100,000,000 cubic kilometers.
I come to that rough estimate because the effected area is about 5000km east to west, 5000km north to south and the cloud is about 4 km top to bottom. I've not seen an estimate for how many tons of ash are up there, or what concentration is dangerous, but I'm guessing the concentration of particulate matter up there is no higher than that over LA or Houston in the summer.
Wednesday, April 14, 2010
Die Fledermaus
It was only the second warm evening of the year and a Friday no less, so I came home at 5. Iris, having also noticed the weather, was up at Warnemunde, strolling the beach line of the still frigid Baltic with a couple friends, so I decided to go for a walk myself. The riverfront in town, which as been transformed from port to shops and restaurants, had been surrendered all winter to the ice and wind. The brick walkways and cement steps along the riverfront were still strewn with New Year's Eve firecrackers and beer bottles. The ice that had covered the Unterwarnow was gone, and the only remaining snow was nubbins of the huge piles the city had dumped in a parking lot. I strolled along the waterfront, enjoying the presence of other people in a place that for six months had been abandoned, and watching the grebes bring up small wriggling bits of silver from the river. The Institute is on the waterfront and I came to it as the sun went down. I thought about going inside to see if any colleagues wanted to stroll with me, but decided instead to wander through the unoccupied lot next door. That whole section had been a major port and while much of it has been built over, much, including the peace next to the Institute has gone to grass and the occasional tree. A two-story heap of dirt and rocks, dug up to make space for some building's foundation, is all that distinguishes the lot from a small unmaintained park. As I gazed up at this heap in the fading light, something fluttered over and around it. The silhouette of a tiny bat flitted and floated, gliding and diving after nothing I could see. I tried and failed to detect any insects it could be after. yet it repeatedly visited the same spots, just under those exposed tree roots, just over the top of the dirt pile, just past that lighted window of the Institute. closing my eyes and concentrating, I could just barely hear its wings and a rapid ticking at the upper end of audibility, the lowest notes in its echolocation. I could hear no insects flying, calling or crawling. Watching the lightest part of the sky, I spotted a single midge flying a few feet from my head. Moments later it had disappeared into the hunting bat. This qualified me to be added to its circuit; on each subsequent round of the lot, it would make a small circle around me, perhaps a meter way, checking what other insects I may have attracted. I watched it past when I could see anything, and will return on subsequent dusks.
little posting
I"ve been posting not at all for a while; I have carpal tunnel syndrome, and can't easily type. However, over the next several days I will be posting several thing either dictated using dictation software, or copied and pasted.
The following is from the
"PLoS Medicine, PLoS Biology and PLoS ONE do not consider for publication papers where any of the research costs or authors' salaries have been funded, in whole or in part, by a tobacco company. "
Discuss
The following is from the
PLoS Biology Editorial and Publishing Policies
"PLoS Medicine, PLoS Biology and PLoS ONE do not consider for publication papers where any of the research costs or authors' salaries have been funded, in whole or in part, by a tobacco company. "
Discuss
Sunday, March 14, 2010
Evolutionary models of evolution
I've been asked to attend an upcoming workshop on modeling the evolution of aging. Modeling in this sense means building a computer model that provides insight into a process. Most of the people who will be there have some experience in modeling, which I don't. So I decided my roll, as the participant most focused on evolutionary theory, should be to make sure that they are doing evolution right. We were asked to each produce a seed, or opening idea, to get the conversation going. Following is a draft of mine. Note that while you can figure out what most of this means, it was written for other scientists and so includes a smattering of jargon and techniquese.
As an evolutionary biologist, I would like to encourage those modeling the evolution of aging to include in their models actual evolution. Optimization models and even Markov Chain models, while very useful, are not evolutionary. By this I mean that they do not include populations changing through descent with modification. To meet a biologist's definition of evolution, a process must include individuals who are reproducing and the offspring must be modified copies of the parents. This requires a population of individuals with heritable traits and mutation rates which modify the parents' traits in the offspring. In order for adaptive evolution to occur, these heritable traits must also influence how many copies of its genome each individual passes on to the next generation.
Markov-chain models, while somewhat closer to evolutionary, still lack the aspect of a population, which is essential for evolution. In many cases the outcome of evolution will depend on having competing or interacting sets of genes within the same population. This cannot be meaningfully understood if the whole population is assumed to have only one set of genes at any one time.
A truly evolutionary model of aging must therefore be fairly complex. It must simulate individuals, who have age-specific mortality and fertility probabilities. These age-specific schedules must be determined by a set of genes. These genes in turn must be determined by a process of inheritance and a process of mutation.
Using such a method, we can address questions that are difficult to get at through optimization. For example, suppose we would like to know why closely related populations have similar patterns of aging, even when they live in different habitats, or occupy different niches. This pattern has been observed in comparative data and comes under the heading of phylogenetic inertia. With an evolutionary simulation, we can impose environments which mediate the relationship between the genes and the demography. We can then ask what characteristics of the environment or what characteristics of the relationship between environment and demography would allow the starting point (that is the initial genes and demography of the population), to influence the ending point (that is the genes and demography the population ends up with).
To take another example, optimization models generally lack any information on the structure of the genome or the process by which that genome changes. However, genomic structure and mutation process are not irrelevant to what demography the population evolves. An evolutionary simulation will allow for modification of the genomic structure or the mutations process. Compare for example, two populations, each of which has a genetically controlled pattern of investment in various tasks such as reproduction, repair, growth or immune function. In population A, as many genes control this at the beginning of life as at the end. In population B, many genes control the pattern of investment early in life, while relatively few are still influencing late life investment. In both populations the genes affecting these investments are subject to mutational pressure and to selection. In each a mutation-selection balance will emerge, but these mutation selection balances will differ between the two populations. The two populations living in the same environment will arrive at different demographies, each nonoptimal.
These are but two of the many complicating factors which can be explored using an evolutionary simulation and are difficult to get at in a model that does not include explicit evolution. Of course models should be simple enough that one can figure out what factor is influencing what outcome. A model cannot include every complicating factor biologists might like to throw in. As such, I propose a modular evolutionary simulation. By this I mean we start with as simple a model as we can which still has real evolution going on and we write it in such a way that one can add more complicated processes. For example, the basic model could have an extremely simple process of mutation, but could be written such that that this process is easy to remove and replace with a more complicated mutational process. Reproduction could be clonal, but again that process of inheritance could be coded such that it could be pulled out and replaced with sexual reproduction by someone who is interested in what effect the mode of reproduction would have on the evolved demography. The environment could be extremely simple and replaceable with a more complicated environment. I am a slow and inexpert programmer but I imagine that it would not be impossible to write such a simulation in a way that genome, inheritance, mutation, environments, and demography are interacting pieces which can be replaced as one replaces the batteries, bulb, wire, switch and casing of a flashlight. One need not modify the casing to replace acid batteries with rechargeables, or replace rechargeables batteries with lithium rechargeables. One can swap a white bulb for a yellow one without modifying the wires or switch. A properly designed base simulation would allow each of us to experiment and still be able to compare our results without any one model becoming unnecessarily complex.
As an evolutionary biologist, I would like to encourage those modeling the evolution of aging to include in their models actual evolution. Optimization models and even Markov Chain models, while very useful, are not evolutionary. By this I mean that they do not include populations changing through descent with modification. To meet a biologist's definition of evolution, a process must include individuals who are reproducing and the offspring must be modified copies of the parents. This requires a population of individuals with heritable traits and mutation rates which modify the parents' traits in the offspring. In order for adaptive evolution to occur, these heritable traits must also influence how many copies of its genome each individual passes on to the next generation.
Markov-chain models, while somewhat closer to evolutionary, still lack the aspect of a population, which is essential for evolution. In many cases the outcome of evolution will depend on having competing or interacting sets of genes within the same population. This cannot be meaningfully understood if the whole population is assumed to have only one set of genes at any one time.
A truly evolutionary model of aging must therefore be fairly complex. It must simulate individuals, who have age-specific mortality and fertility probabilities. These age-specific schedules must be determined by a set of genes. These genes in turn must be determined by a process of inheritance and a process of mutation.
Using such a method, we can address questions that are difficult to get at through optimization. For example, suppose we would like to know why closely related populations have similar patterns of aging, even when they live in different habitats, or occupy different niches. This pattern has been observed in comparative data and comes under the heading of phylogenetic inertia. With an evolutionary simulation, we can impose environments which mediate the relationship between the genes and the demography. We can then ask what characteristics of the environment or what characteristics of the relationship between environment and demography would allow the starting point (that is the initial genes and demography of the population), to influence the ending point (that is the genes and demography the population ends up with).
To take another example, optimization models generally lack any information on the structure of the genome or the process by which that genome changes. However, genomic structure and mutation process are not irrelevant to what demography the population evolves. An evolutionary simulation will allow for modification of the genomic structure or the mutations process. Compare for example, two populations, each of which has a genetically controlled pattern of investment in various tasks such as reproduction, repair, growth or immune function. In population A, as many genes control this at the beginning of life as at the end. In population B, many genes control the pattern of investment early in life, while relatively few are still influencing late life investment. In both populations the genes affecting these investments are subject to mutational pressure and to selection. In each a mutation-selection balance will emerge, but these mutation selection balances will differ between the two populations. The two populations living in the same environment will arrive at different demographies, each nonoptimal.
These are but two of the many complicating factors which can be explored using an evolutionary simulation and are difficult to get at in a model that does not include explicit evolution. Of course models should be simple enough that one can figure out what factor is influencing what outcome. A model cannot include every complicating factor biologists might like to throw in. As such, I propose a modular evolutionary simulation. By this I mean we start with as simple a model as we can which still has real evolution going on and we write it in such a way that one can add more complicated processes. For example, the basic model could have an extremely simple process of mutation, but could be written such that that this process is easy to remove and replace with a more complicated mutational process. Reproduction could be clonal, but again that process of inheritance could be coded such that it could be pulled out and replaced with sexual reproduction by someone who is interested in what effect the mode of reproduction would have on the evolved demography. The environment could be extremely simple and replaceable with a more complicated environment. I am a slow and inexpert programmer but I imagine that it would not be impossible to write such a simulation in a way that genome, inheritance, mutation, environments, and demography are interacting pieces which can be replaced as one replaces the batteries, bulb, wire, switch and casing of a flashlight. One need not modify the casing to replace acid batteries with rechargeables, or replace rechargeables batteries with lithium rechargeables. One can swap a white bulb for a yellow one without modifying the wires or switch. A properly designed base simulation would allow each of us to experiment and still be able to compare our results without any one model becoming unnecessarily complex.
Key Words
conferences,
evolution,
modeling,
science as process
Saturday, March 06, 2010
Kudzu Power
For several years I've mused that if only we could find some efficient way to make ethanol from Kudzu (the incredibly fast growing invasive weed that has taken over much of the southeastern US), we could stop importing petroleum, vastly improve many ecosystems and tremendously improve the US economy, all in one swell foop. I didn't take this idea very seriously. It appears that somebody else has. Consider the following abstract from a recent volume of the journal Biomass and Bioenergy:
This will, of course, take longer and be more complicated than anyone currently expects, but I'd be surprised if we don't eventually have industrial scale application of this technology, using many sources, including kudzu.
We determined the amount of standing biomass of kudzu (Pueraria montana var lobata) in naturally infested fields in Maryland and Alabama, USA. At each site, we evaluated the carbohydrate content of roots, stems, and leaves. For a third site from Georgia, we evaluated the carbohydrate content of kudzu roots of varying diameters. Belowground biomass in Alabama exceeded 13 t ha−1, and contained an average of 37% fermentable carbohydrates (sucrose, glucose, and starch). Roots from Georgia of all size classes contained over 60% fermentable carbohydrates. Biomass and carbohydrate levels in roots from Maryland were low compared to plants growing in Alabama and Georgia, producing 5 t ha−1 of roots with 20% non-structural carbohydrate. Stems from Alabama and Maryland contained 1–3% carbohydrates. Based on the yield and carbohydrate content, we estimate wild kudzu stands in Alabama and Georgia could produce 5–10 t ha−1 of carbohydrate, which would rival carbohydrate production from maize and sugar cane fields. If economical harvesting and processing techniques could be developed, the kudzu infesting North America has the potential to supplement existing bioethanol feedstocks, which could be of significance to the rural economy of the southeastern USA.
Further consider this economical processing technique, from next month's PNAS:
Abundant plant biomass has the potential to become a sustainable source of fuels and chemicals. Realizing this potential requires the economical conversion of recalcitrant lignocellulose into useful intermediates, such as sugars. We report a high-yielding chemical process for the hydrolysis of biomass into monosaccharides. Adding water gradually to a chloride ionic liquid-containing catalytic acid leads to a nearly 90% yield of glucose from cellulose and 70–80% yield of sugars from untreated corn stover. Ion-exclusion chromatography allows recovery of the ionic liquid and delivers sugar feedstocks that support the vigorous growth of ethanologenic microbes. This simple chemical process, which requires neither an edible plant nor a cellulase, could enable crude biomass to be the sole source of carbon for a scalable biorefinery.
Key Words
energy,
global destruction,
invasive species,
plants,
technology
Friday, March 05, 2010
neologistic challenge
In demography, we spend a lot of time thinking about how the risk of dying increases with age. Economics calls itself the dismal science, demography is the morbid science. Anyway, we call the increase in mortality risk with age in adults "senescence", from the Latin root senex (old). I prefer to think and write about the fact that mortality rate decreases with age in those who are not yet adults. My problem is that there is no word equivalent to senescence that mean this, so I have to invent one.
So I want a word that can be defined as "the decline in mortality risk with age from conception to maturity." A root that means improvement, growth, blossoming, development, growing up, or something along those lines would be best. Twelve points for whoever comes up with the best term.
So I want a word that can be defined as "the decline in mortality risk with age from conception to maturity." A root that means improvement, growth, blossoming, development, growing up, or something along those lines would be best. Twelve points for whoever comes up with the best term.
Saturday, February 06, 2010
Cold and Fat
Cold places tend to have fatty cuisines. The usual explanation for this, although I know of no rigorous test, is that cold weather requires us to burn lots of energy to stay warm, and our bodies respond to this greater demand by causing us to eat more rich foods.
This simple idea has several profound implications that I will now proceed to invent.
The first implication is that " burn lots of energy to stay warm" means something very similar to "increase metabolic rate." So people in colder environments should have higher metabolisms. This matches with the current experience of myself and my wife. For the past months the temperature outside our apartment has rarely gotten above freezing, the wind is always blowing and it is generally damp. Our apartment is somewhat difficult to heat, so it is generally cool and sometimes downright cold inside. We have been eating a very rich diet, and rather than gaining weight, I think we are both loosing a bit. And although the short days cause a degree of lethargy, I have been generally quite productive, with fewer problems of concentration than usual.
There is good reason to think, in fact, that colder climates lead to greater productivity. Colder countries are systematically more economically productive than hotter countries, air conditioning raises productivity considerably, and hot countries experience more economic growth in cool years than in warm ones. My preferred speculation is that this is because the experience of coolth induces greater physiological throughput, allowing for greater activity. If one needs to expend energy to keep oneself warm, why not put that energy to some good use, such as thinking, building, or working. Why shiver when I can use the same energy sharpening the knives or generating a hypothesis?
Allow me one further observation and conjecture. Germans, who eat very heavy diets but on the average are less heavy than Americans, are in the habit of opening all the windows whenever it gets warm inside, even if it is below freezing out. Two apparently unrelated stereo-types of modern Americans, both of which have some basis in fact, may in fact be causally related. These are, we are very fat, and we keep our houses very warm in the winter. Perhaps the miracle diet so many have been searching for should include turning down the thermostat. If we burn more calories when we experience cold, and we want to burn more calories, perhaps we should experience more cold.
This simple idea has several profound implications that I will now proceed to invent.
The first implication is that " burn lots of energy to stay warm" means something very similar to "increase metabolic rate." So people in colder environments should have higher metabolisms. This matches with the current experience of myself and my wife. For the past months the temperature outside our apartment has rarely gotten above freezing, the wind is always blowing and it is generally damp. Our apartment is somewhat difficult to heat, so it is generally cool and sometimes downright cold inside. We have been eating a very rich diet, and rather than gaining weight, I think we are both loosing a bit. And although the short days cause a degree of lethargy, I have been generally quite productive, with fewer problems of concentration than usual.
There is good reason to think, in fact, that colder climates lead to greater productivity. Colder countries are systematically more economically productive than hotter countries, air conditioning raises productivity considerably, and hot countries experience more economic growth in cool years than in warm ones. My preferred speculation is that this is because the experience of coolth induces greater physiological throughput, allowing for greater activity. If one needs to expend energy to keep oneself warm, why not put that energy to some good use, such as thinking, building, or working. Why shiver when I can use the same energy sharpening the knives or generating a hypothesis?
Allow me one further observation and conjecture. Germans, who eat very heavy diets but on the average are less heavy than Americans, are in the habit of opening all the windows whenever it gets warm inside, even if it is below freezing out. Two apparently unrelated stereo-types of modern Americans, both of which have some basis in fact, may in fact be causally related. These are, we are very fat, and we keep our houses very warm in the winter. Perhaps the miracle diet so many have been searching for should include turning down the thermostat. If we burn more calories when we experience cold, and we want to burn more calories, perhaps we should experience more cold.
Wednesday, February 03, 2010
A month of snow
A cubic meter of fluffy freshly fallen snow weighs about 80kg, while a cubic meter of water weighs a metric ton, 1000kg. This implies that a meter of fresh snow will melt into a paltry 8cm deep layer of water. Enough to make the ground very soggy, but not nearly as impressive as a meter of snow. As ice is slightly less dense than water (about 92% as dense) a meter of snow will squish down into a slightly thicker layer of ice, almost 9cm. A third possibility is to catch a plane to someplace warmer, where the snow never fell at all.
Friday, January 29, 2010
Sprouting collaborations
In the last week I have agreed on two major collaborations (with a Harvard professor and the Director of a Max Planck Institute) ordered some tens of thousands of Euros worth of equipment for my own experiments, hired two lab assistants for those experiments and promised my boss that I would perform a significant reanalysis of a set of data I already have in collaboration with another member of the lab. My wife and I also made some very tasty Brussels sprouts with garlic, soy sauce and lemon juice.
Here's the recipe:
Wash the sprouts, peel off any out leaves that don't look good, and cut each sprout in half.
Cut up a head of garlic.
Juice 2 lemons.
Heat a large cast-iron skillet or other frying surface, large enough to fit all the halved sprouts in a single layer. Put on a fair bit of oil and bring to very hot. Pour in the sprouts and use a spatula or fork to flip them over so that the flat side of each is down. Slide them around some so they all cook evenly. Cook them like that until they are somewhat charred on the bottom. Then flip them over and roll them around so that the other surfaces get cooked. They will still be somewhat too hard inside, so pour in a scant cup of water and cover while the water rapidly boils off, steaming the insides. Once the water cooks off, taste a couple of sprouts and if they are still too hard inside, pour on a little bit more water. Once they are done, remove them to a large bowl and put the garlic on to fry. After a minute, pour some splashes of soy sauce over the garlic, and let it cook down a little bit. Mix this with the lemon juice, salt and pepper, and pour it over the sprouts. Serve hot.
Here's the recipe:
Wash the sprouts, peel off any out leaves that don't look good, and cut each sprout in half.
Cut up a head of garlic.
Juice 2 lemons.
Heat a large cast-iron skillet or other frying surface, large enough to fit all the halved sprouts in a single layer. Put on a fair bit of oil and bring to very hot. Pour in the sprouts and use a spatula or fork to flip them over so that the flat side of each is down. Slide them around some so they all cook evenly. Cook them like that until they are somewhat charred on the bottom. Then flip them over and roll them around so that the other surfaces get cooked. They will still be somewhat too hard inside, so pour in a scant cup of water and cover while the water rapidly boils off, steaming the insides. Once the water cooks off, taste a couple of sprouts and if they are still too hard inside, pour on a little bit more water. Once they are done, remove them to a large bowl and put the garlic on to fry. After a minute, pour some splashes of soy sauce over the garlic, and let it cook down a little bit. Mix this with the lemon juice, salt and pepper, and pour it over the sprouts. Serve hot.
Wednesday, January 27, 2010
The flapper in winter
It was -10C this morning, and fresh snow on ice made an unbroken expanse of flat whiteness where the harbor usually is. The small ferry constantly crossing back and forth kept one thin line open, and the water birds congregated around that oasis; compared to sub-freezing air, freezing water is relatively warm. A few birds seemed not to have gotten the memo and instead made lumps in the snow at random points on the ice. One large lump the color of dirty ice seemed bird shaped, and I looked at it on and off seeing if it moved. It was the right size and about the right shape and color to be a juvenile swan, but it could also be a pit of trash or a chunk of refrozen slush someone slid out onto the ice.
My colleague, who also watches birds came into my office to ask if I had noticed it, and if so what I thought it was. He said there were footsteps in the fresh snow near it. He was right. Through my binoculars I could see swan prints leading to where it sat. And that lump on top might be a bit of neck leading to a head tucked entirely under a wing. But it must be dead I thought, why else would it sit so still for so long in such a windy spot on the ice?
I glanced at it occasionally though the morning, and it didn't move. Then some people walking their dog passed by, and the dog made like it was going to run out onto the ice to get the swan. A long gray neck snaked out from under the wing and looked straight back at the dog. The dog must have realized the ice was too thin to hold it. As soon as the dog was gone, the head disappeared under the wing again, and there it stayed.
In the early afternoon a fire department rescue truck pulled down the road to the harbor near the swan. Two guys, one holding binoculars, got out and looked at the swan for a while. I wondered if they thought it was a child. They drove away and came back with a third guy, who threw snowballs near the swan and yelled at it until it got up and walked a few steps. They left again, and the swan sat back in its usual spot, head under wing. The snow got heavier and started to pile up on the windward side of the swan, but it stuck to its spot, and still was there when the sun went down.
My colleague, who also watches birds came into my office to ask if I had noticed it, and if so what I thought it was. He said there were footsteps in the fresh snow near it. He was right. Through my binoculars I could see swan prints leading to where it sat. And that lump on top might be a bit of neck leading to a head tucked entirely under a wing. But it must be dead I thought, why else would it sit so still for so long in such a windy spot on the ice?
I glanced at it occasionally though the morning, and it didn't move. Then some people walking their dog passed by, and the dog made like it was going to run out onto the ice to get the swan. A long gray neck snaked out from under the wing and looked straight back at the dog. The dog must have realized the ice was too thin to hold it. As soon as the dog was gone, the head disappeared under the wing again, and there it stayed.
In the early afternoon a fire department rescue truck pulled down the road to the harbor near the swan. Two guys, one holding binoculars, got out and looked at the swan for a while. I wondered if they thought it was a child. They drove away and came back with a third guy, who threw snowballs near the swan and yelled at it until it got up and walked a few steps. They left again, and the swan sat back in its usual spot, head under wing. The snow got heavier and started to pile up on the windward side of the swan, but it stuck to its spot, and still was there when the sun went down.
Monday, January 25, 2010
Almost finished
I'm about ready to submit this paper, and I have very mixed feelings as to its chances of acceptance. I've shown it to two people who told me they thought it was quite good and that I should send it to the high end journal I'm sending it to, and to a third who said he didn't think it would make it past any reviewer without major rewriting including changing which variables I was analyzing and the whole point of the paper. I've worked the paper over so many times I no longer have any idea if is it brilliant and revolutionary or a pile of misconceived hackary. What I do know for certain is that I am not going to start rewriting it at this point, and I'm going to hope that my friend who suggested I needed to do so just missed the point that the other two saw. The paper is methodologically sound, whatever its other flaws, and if the first journal rejects it I'll send it to lower profile journals until someone thinks it is important enough to print.
Friday, January 22, 2010
I really didn't want to get into discussing testis size.
I'm writing a paper on the choice male primates face between caring for the young they already have, and fighting other males for access to mates so they can have more young. There are, of course, other reproductive strategies they could also be investing in, like trying to impress the ladies without fighting, or impressing the ladies by being such good carers. I didn't want to get into all of these, because it just gets to big and complicated, and the relationship between the variables I have is already complicated and interested enough. But my colleague who read the paper for me thinks it is important to include something on investment in sperm competition. Sperm competition occurs when a female mates with more than one male, but only one of them will end up being the father of each baby she produces. The male with the strongest, fastest, healthiest, most numerous sperm will tend to be the father, and as such will tend to pass on his genes for big healthy sperm to the most sons. And to make lots of big healthy sperm, a male needs big testicles. Testicle size turns out to be closely correlated with how much multiple mating the females do, and in highly promiscuous species, males may dedicate a significant portion of their body mass to testes. And this is how I came to be typing search terms like "bush baby testis mass" and "monkey sperm competition" into Google Scholar. You would be amazed what Google is willing to label as a scholarly article.
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