I had an amazing discussion with a devoutly Christian friend this week. We have discussed religion before, and one of the things that we agreed was not at issue was a question of morality: we agreed that it was inherent, that living a moral life requires no external dictum (such as the Ten Commandments). Our trains of thought departed on the origin of this moral sense (the product of evolution acting on social animals versus a gift of God), but it was refreshing not to have to defend my ability to make moral decisions without God.
This week we returned to the topic, and expanded it to include other things that are (at least commonly considered to be) uniquely human, which he and others have thought evidence of a divine hand. Among those things was ethics, the ability of humans to act in a fair and just manner even to our detriment. But, I contended, we are social animals; experiments with other social animals have shown at the very least a rudimentary sense of justice or of fair play. Our consciences are a safety mechanism that allows us to live together, to rely on one another. I contend that the conscience has its root in the ability to empathise, to imagine ourselves in the place of others. "How would I feel if someone treated me the way that I am thinking of treating this other person?" is perhaps one of the most fundamental questions that we can ask ourselves on a day-to-day basis, and it guides our behaviour in ways too varied and subtle to describe.
Our conversation moved on, and my friend appealed as well to a sense of the spiritual that most people have, the ability to be awed by nature, as well as by great works of humankind. This is something that neither of us had thought much about: where does that sense of awe come from? What would its predecessor be in our pre-human forebears? Again, he thought this to hint at the divine: God gave it to us, a gift with which to appreciate our world. At one point my friend described the feeling that he got admiring a beautiful sunset as "hollow".
Another friend, who was sitting in on the whole conversation, did not quite get what he meant, but think that I did. This is not the bad sort of hollow that we equate with guilt or loss or failure. It is a feeling of inadequacy, of humility, that we can appreciate something so much vaster and more beautiful than ourselves. But, I said, we also feel a sense of gratefulness: we know how much talent and hard work goes into making something beautiful, and we appreciate the sacrifice of those who invest such skill and energy in making beautiful things. It is our ability to empathise with others that gives us this ability -- we put ourselves in the place of the artist, and see how poorly we would do in creating work of such power, and we thank them for having done that for us.
To give an example, there has been and will forever remain, for instance, only one Johann Sebastian Bach, and nobody will ever be able to write what he did. The level of brilliance in his music is so far beyond that of anyone most of us will ever meet that to contemplate it being played -- to contemplate it being written -- for us is to imagine ourselves indebted beyond any hope of repayment. It was not written for us, and unless we are very priveleged we will not ever even experience it being played for us, but we can still appreciate it, and we are grateful beyond words for it. (Of course, one can replace Bach with any icon of artistic brilliance if this example does not stir one's own emotions. I could argue that this would be evidence of a deficiency in taste or exposure, but I will leave that for another argument.)
But what of our ability to appreciate nature? Scientists have possibly the highest proportion of atheists amongst the professions, and yet what drives one to be a successful scientist is exactly this sense of wonder. How can one feel indebted to the Universe? And yet, how can one not? We exist, we experience things. As scientists we appreciate (I cannot honestly say "understand") just how complicated and contingent everything is: how fragile is that existence, how precious is that experience. We empathise with the Universe, knowing at the same time just how impossible it would be for one of us to create the thing being appreciated, and we feel indebted to the Universe for having made it for us. There is a sense of guilt at not being able to repay it -- ever -- and a sense of duty to appreciate it. But more than that, there is a sense of gratefulness, that it is there to be appreciated, and that we are here to appreciate it.
All of this springs from our conscience. It is not the primary function of our conscience, but it is hardly a bad side-effect. It is also not something that I would have connected before this conversation: ethics and aesthetics are not things that I would guess were intertwined, but I am drawn to the simplicity and elegence of this idea. I have no clue how original it is, but I think that I rather like it.
Saturday, 27 December 2008
Monday, 2 June 2008
Rejected!
This morning I received one of the least-welcome messages it is possible for a scientist to receive: my manuscript was rejected for publication. I was assured by the professor for whom I had originally written the paper that it would sail through peer review, but apparently it did not: both reviewers were negative.
This was my first real introduction to the receiving end of peer review. I have always been in favour of the process: it is a sort of quality control for science. It has its flaws, to be sure, but they are far less significant than some of the other problems with science.* I always figured that I could take a rejection gracefully, that I would grow from it and make my work into something better when I resubmitted it. It took this experience to show that I was really not prepared for dealing with it. I managed to pull myself together, though, and thought about it on my way into campus.
For one thing, my paper is not on a topic in which I am actually doing research. It is a review of work done in a distantly related field, written for a class and coached into publication by the class's professor. I suppose that I had started to feel somewhat overconfident of my talents in the latter stages of submission. Getting a paper published outside of my field would be something of a coup, proof of my versatility. But at the same time, there is nothing halfway about this. Publishing a paper is not playing in a sandbox: submitting something for publication is tantamount to saying that one is ready to play with the big kids. One is asking for the roughest treatment that one's work could possibly merit. Like the saying goes, "what doesn't kill you makes you stronger," and that is certainly true here. If a paper survives the peer-review process, it was either exemplary to begin with, or (more likely) was considerably improved through its criticism. I was asking to be taken seriously as an expert in a field in which I have in fact had little formal training (none at all, in the case of palaeontology, of which I had much to say in this paper), and I should have expected a thorough smacking in any way that could be delivered.
However, things are not as negative as that implies. One of the reviewers provided about four pages of commentary, which I take to mean that s/he thought my work of sufficient merit to indicate at the very least that I was thinking along the right lines. If nothing else, s/he has helped me learn more about the field, pointing out where I was making false assumptions or missing critical papers. Although there was nothing explicit by way of encouragement in what s/he wrote, it is not reading between the lines too much to see that, at the very least, the reviewer respected my effort.
The other review was quite different. For one thing, it was well under half a page. It began with explicit praise for my writing, and regards the paper's principal flaw as a lack of novel ideas (which, being a review paper, is not a particularly hurtful observation). However, the second paragraph reads almost as if it were describing a different paper entirely. It deplores my lack of expertise and experience, and concludes by calling my work "poor". I am not sure what to make of the conflicting messages in this review, but I will continue to ruminate on the matter, and both the professor for whom I originally wrote the paper and my supervisor have promised advice and encouragement. I may take the first reviewer's suggestions to heart, rework the manuscript, and resubmit it. I may get my coup after all. But overall, this is a side project, and not a critical one to my career, and if it fails to produce anything that can go on my CV, so be it.
In any event, I have made it through the day with my dignity largely intact -- challenged, to be sure, but not broken. This is part of the process. I would expect nothing less: I have asked for my work to be taken seriously, and it was, even if that amounted to being told that it was not an effort worthy of being taken seriously. This is a sign that science is working. If I am to make anything of my effort, it will be all the better for having weathered such a challenge. In short, things are not so bad.
* This is worthy of another post in and of itself. The principal problems with science that concern me are research priorities, funding, job availability, and regard for educational talent -- but those are all problems within science. More significant still is the general public ignorance of what science is, how it works, and what scientists do, running from general lack of exposure all the way to the mistruths spread by Creationists. But I will restrain myself: I will post about that another time.
This was my first real introduction to the receiving end of peer review. I have always been in favour of the process: it is a sort of quality control for science. It has its flaws, to be sure, but they are far less significant than some of the other problems with science.* I always figured that I could take a rejection gracefully, that I would grow from it and make my work into something better when I resubmitted it. It took this experience to show that I was really not prepared for dealing with it. I managed to pull myself together, though, and thought about it on my way into campus.
For one thing, my paper is not on a topic in which I am actually doing research. It is a review of work done in a distantly related field, written for a class and coached into publication by the class's professor. I suppose that I had started to feel somewhat overconfident of my talents in the latter stages of submission. Getting a paper published outside of my field would be something of a coup, proof of my versatility. But at the same time, there is nothing halfway about this. Publishing a paper is not playing in a sandbox: submitting something for publication is tantamount to saying that one is ready to play with the big kids. One is asking for the roughest treatment that one's work could possibly merit. Like the saying goes, "what doesn't kill you makes you stronger," and that is certainly true here. If a paper survives the peer-review process, it was either exemplary to begin with, or (more likely) was considerably improved through its criticism. I was asking to be taken seriously as an expert in a field in which I have in fact had little formal training (none at all, in the case of palaeontology, of which I had much to say in this paper), and I should have expected a thorough smacking in any way that could be delivered.
However, things are not as negative as that implies. One of the reviewers provided about four pages of commentary, which I take to mean that s/he thought my work of sufficient merit to indicate at the very least that I was thinking along the right lines. If nothing else, s/he has helped me learn more about the field, pointing out where I was making false assumptions or missing critical papers. Although there was nothing explicit by way of encouragement in what s/he wrote, it is not reading between the lines too much to see that, at the very least, the reviewer respected my effort.
The other review was quite different. For one thing, it was well under half a page. It began with explicit praise for my writing, and regards the paper's principal flaw as a lack of novel ideas (which, being a review paper, is not a particularly hurtful observation). However, the second paragraph reads almost as if it were describing a different paper entirely. It deplores my lack of expertise and experience, and concludes by calling my work "poor". I am not sure what to make of the conflicting messages in this review, but I will continue to ruminate on the matter, and both the professor for whom I originally wrote the paper and my supervisor have promised advice and encouragement. I may take the first reviewer's suggestions to heart, rework the manuscript, and resubmit it. I may get my coup after all. But overall, this is a side project, and not a critical one to my career, and if it fails to produce anything that can go on my CV, so be it.
In any event, I have made it through the day with my dignity largely intact -- challenged, to be sure, but not broken. This is part of the process. I would expect nothing less: I have asked for my work to be taken seriously, and it was, even if that amounted to being told that it was not an effort worthy of being taken seriously. This is a sign that science is working. If I am to make anything of my effort, it will be all the better for having weathered such a challenge. In short, things are not so bad.
* This is worthy of another post in and of itself. The principal problems with science that concern me are research priorities, funding, job availability, and regard for educational talent -- but those are all problems within science. More significant still is the general public ignorance of what science is, how it works, and what scientists do, running from general lack of exposure all the way to the mistruths spread by Creationists. But I will restrain myself: I will post about that another time.
Monday, 25 February 2008
Perils of Electron Microscopy
I do a lot of work with electron microscopes. This is amazingly neat stuff, every bit as fun as I imagined it would be, and perhaps the closest thing that biologists have to being astronauts. I get to play with exotic, highly expensive equipment, and I get to see alien things that nobody has ever seen (or, in some cases, dreamed of) before. Twice in the last six months my lab has had a visiting scientist come to do work that is right up my alley, and since I am checked out on the microscope and she is not, I got to "drive" (the term that we seem to use for operating the 'scope) with her giving me instructions. It was very illuminating, seeing what is pertinent to our study and what can be skipped over, and at the same time there were several moments of both of us sitting and gaping and asking each other, "What on earth is that?!" It is fantastic stuff.
There are several kinds of electron microscope. The one that my lab uses most is the transmission electron microscope (or TEM), which operates in a very intuitive way: it works just like a regular light microscope, except that instead of shining a beam of light through the specimen, it shines a beam of electrons. The electrons are focussed using lenses, and (just as with the more expensive light microscopes) the images are captured by a camera. Of course, there are other significant differences as well: the lenses are in fact magnetic fields, and because electrons do not travel very far through air, the inside of the microscope is pumped down to a high vacuum.
Specimens for a light microscope are generally mounted on slides. This means that the specimen, usually aqueous in nature, is dropped onto a glass slide, over which is placed a coverslip. If the specimen is important enough, and stable enough not to degrade on its own, the slide may be sealed using Vaseline or fingernail polish, which can preserve the specimen indefinitely, but otherwise, that tends to be it. Of course, there are often also specific ways of preparing specimens, but I will not get into that right now.
Specimens for a TEM are analagous. The specimens are mounted not on slides but "grids", which are little (3 mm diameter) copper circles with a slot-shaped hole in the middle. (Yes, they are not actually gridlike: this is a historical term, used because other grids actually do have mesh gridwork in the holes. Many labs use those kinds as well, but my lab has so far used only the other kind, called slot grids.) The specimen is actually mounted on a very thin plastic film, on the order of 40-100 nm thick, which is suspended in the middle of the grid. Like a well-preserved slide, the specimen will last indefinitely.
There are of course other differences, many of which are obvious upon contemplation, and some of which require further explanation (which I may get to in other posts). However, one difference that is significant here is that electron microscopes (all of them, but particularly TEMs) are not just sending a beam of light through the specimen: they are shooting charged particles, which can and often do interact with the specimens. Electrons can be really harsh! In the case of my recent work, for which I was using very thin films (40 nm or so), the electrons can rip right through the specimen. This means that -- often right after discovering the perfect example of a cell amongst dozens of unusable contenders -- one can watch one's precious work tear apart, wrinkle, and wither away before one's eyes. No amount of preparation can prevent this: it just happens. Thicker films are less prone to this sort of damage, but they also impede the electron beam more, and so lose resolution. Resolution is the reason why we use electron microscopes in the first place, so we tend to use the thinnest films that we can. Obviously, I need to experiment more with this, to find a better film thickness that will not break apart in the electron beam, without losing too much resolution.
There are numerous other ways in which TEM specimens can be irreparably lost. One of the most frustrating is tweezering -- putting a hole in the film with clumsily handled forceps while moving the grid around. I have had much hapless experience with that. Another is that some of the stages (the devices that hold the specimens inside the microscope) hold the specimens in place with spring clips, which can and often do tear through the films when removed (or, on occasion, when put in). There are ways of minimising this, which I have only recently become competent at.
Unfortunately, "recently" means that I had lost several specimens while learning how to handle, mount, and dismount them. Up until last Friday, I had only one pristine specimen left, undamaged by my apprentice clumsiness. That specimen, last Friday, self-destructed in the 'scope, as the film gave way spontaneously. This is a setback, of course, but I can always make more specimens. This is of course how science works. Only now, I will try thicker films!
There are several kinds of electron microscope. The one that my lab uses most is the transmission electron microscope (or TEM), which operates in a very intuitive way: it works just like a regular light microscope, except that instead of shining a beam of light through the specimen, it shines a beam of electrons. The electrons are focussed using lenses, and (just as with the more expensive light microscopes) the images are captured by a camera. Of course, there are other significant differences as well: the lenses are in fact magnetic fields, and because electrons do not travel very far through air, the inside of the microscope is pumped down to a high vacuum.
Specimens for a light microscope are generally mounted on slides. This means that the specimen, usually aqueous in nature, is dropped onto a glass slide, over which is placed a coverslip. If the specimen is important enough, and stable enough not to degrade on its own, the slide may be sealed using Vaseline or fingernail polish, which can preserve the specimen indefinitely, but otherwise, that tends to be it. Of course, there are often also specific ways of preparing specimens, but I will not get into that right now.
Specimens for a TEM are analagous. The specimens are mounted not on slides but "grids", which are little (3 mm diameter) copper circles with a slot-shaped hole in the middle. (Yes, they are not actually gridlike: this is a historical term, used because other grids actually do have mesh gridwork in the holes. Many labs use those kinds as well, but my lab has so far used only the other kind, called slot grids.) The specimen is actually mounted on a very thin plastic film, on the order of 40-100 nm thick, which is suspended in the middle of the grid. Like a well-preserved slide, the specimen will last indefinitely.
There are of course other differences, many of which are obvious upon contemplation, and some of which require further explanation (which I may get to in other posts). However, one difference that is significant here is that electron microscopes (all of them, but particularly TEMs) are not just sending a beam of light through the specimen: they are shooting charged particles, which can and often do interact with the specimens. Electrons can be really harsh! In the case of my recent work, for which I was using very thin films (40 nm or so), the electrons can rip right through the specimen. This means that -- often right after discovering the perfect example of a cell amongst dozens of unusable contenders -- one can watch one's precious work tear apart, wrinkle, and wither away before one's eyes. No amount of preparation can prevent this: it just happens. Thicker films are less prone to this sort of damage, but they also impede the electron beam more, and so lose resolution. Resolution is the reason why we use electron microscopes in the first place, so we tend to use the thinnest films that we can. Obviously, I need to experiment more with this, to find a better film thickness that will not break apart in the electron beam, without losing too much resolution.
There are numerous other ways in which TEM specimens can be irreparably lost. One of the most frustrating is tweezering -- putting a hole in the film with clumsily handled forceps while moving the grid around. I have had much hapless experience with that. Another is that some of the stages (the devices that hold the specimens inside the microscope) hold the specimens in place with spring clips, which can and often do tear through the films when removed (or, on occasion, when put in). There are ways of minimising this, which I have only recently become competent at.
Unfortunately, "recently" means that I had lost several specimens while learning how to handle, mount, and dismount them. Up until last Friday, I had only one pristine specimen left, undamaged by my apprentice clumsiness. That specimen, last Friday, self-destructed in the 'scope, as the film gave way spontaneously. This is a setback, of course, but I can always make more specimens. This is of course how science works. Only now, I will try thicker films!
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