An Update! Wow!
Today has been an exceptional day. Actually, it has been the conclusion of an exceptional two weeks, which started off with the return of our collaborator. At that point, I was essentially on loan to her, and we did a lot of transmission electron microscopy.
Things started off slowly, actually. Our collaborator got a bit sullen about halfway through (a week ago now), fearing that she would not get enough work done to justify the grant that she was hoping to get renewed. Then our specimens started getting dark spots all over them, making them unusable, and which took us half of a week to troubleshoot.
That was fun. It is not very often that scientists actually use the "scientific method". The observation/hypothesis/prediction/test thing that we are taught in elementary school is not in fact very helpful for a lot of science work, which is often exploratory and usually requires refinement. However, last Monday was a very clear case of the scientific method being used to great effect. We could not figure out why the latest batch of specimens was so awful, and initially assumed that it was the stain. This made sense, inasmuch as the lead stain is rather awkward to make, and can easily not work out right. I made a couple of batches of it, as did our post-doc, but the effects on the specimens did not vary much. So, on Monday, we decided to get methodical. I prepared five specimens. Four were from an earlier series that I had cut: one using each of the two stains that we usually use (lead and uranium), one using both, and one using neither. I also obtained an unstained specimen from our collaborator's latest series.
Late on Monday (I think that it was about six in the evening -- science only rarely works according to a "normal" schedule!) we all went down to the TEM, and I popped in the specimen with both stains. It looked moderately spotty, though not unusably so. Next was the uranium-only specimen, which looked great (although without the lead stain, some cell features were of course not highly visible). Right, we thought, the lead stain was at fault. But in the interest of consistency, we put the lead-only specimen in, expecting to see the spottiness that made the previous series unusual. Amazingly, it looked great! There was a hint of the spottiness that we saw in the specimen with both stains, but that was less noticeable than the lack of features stained with uranium. Likewise, the unstained specimen was pretty good, although of course unstained and therefore low in contrast. The definitive answer on the problem came when we put in the unstained specimen from our collaborator's latest series, which had nasty spotty things all over it. Aha! Her diamond knife was the problem.
So our collaborator cleaned her knife (a harrowing undertaking, given that diamond knives cost several thousand dollars each and are extremely fragile) and cut another series, which turned out to be wrinkly and uneven and did not hold together. My advisor suggested, noting concern for our collaborator's ego but more interested (as was she) in getting results than anything else, that I cut a series, and that was when things got really fun.
This was on Tuesday. The suggestion came in the afternoon. Specifically, the suggestion was that I would cut a few specimens and go home, and that we would stain and examine them on Wednesday. However, I was feeling ambitious. To begin with, I started cutting 50-nanometre-thick sections rather than the usual 70-nanometre-thick variety, which is generally much more difficult. That part was my advisor's idea. In fact, our collaborator likes to cut thicker sections than normal, usually 90 nanometres, which are easier to handle, but the work that we are doing is made much easier with thinner sections. To my surprise, I had pretty good luck with my sectioning, and I got curious about the results. So I stained them that evening, and, my curiosity if anything amplified, fired up the TEM at around one in the morning and had a look.
The sections were beautiful. I was absolutely captivated, and kept working on them for another four hours. Finally, at five in the morning, I decided that I was starting to tire, and shut things down. I made some notes about the specimens, copied the images onto a flash drive, and sent an e-mail to my advisor and our collaborator instructing them to look at it.
I got home just before eight in the morning. I got three hours' sleep, and woke feeling absolutely great. I arrived on campus half an hour before our next scheduled session on the TEM, and was greeted with enthusiasm and amazement by my advisor. The all-nighter turned out to have been very helpful, giving us a much better idea of what to do next with the specimens. We plugged away at them until early evening, at which point the lack of sleep was starting to catch up with me.
That brings us to today. Getting going this morning was incredibly hard, but angharad was very helpful in keeping me on task. I arrived on campus early, and did a little work on the TEM with our collaborator until we determined that we needed more sections. Our collaborator suggested that I give it another try, and to let her know as soon as I found myself too tired to work (I was forgetting random things from lack of sleep). To my bewilderment, though, after a couple of false starts, I found myself cutting a near-perfect ribbon of 50-nanometre sections. I was starting to get a bit shaky by the time I had finished collecting them all, and our collaborator helped at that point with the fine-motor-skills part of the staining while I got lunch. Then we went down again to the TEM -- and once again, I had done a superb job. (I am feeling a bit self-conscious typing this all, but it is the truth. I have to say that it feels spectacularly good to be competent! Honestly, though, there is a generous portion of good luck in all of this as well.)
Of course, now that our collaborator has left, things change, and in more ways than I was expecting. The specimens that we had been working on are of an organism of complicated provenance, and for political reasons we all agreed that it was best that I not work on it by myself. So the intense productivity that I have been enjoying for the past few days cannot be continued in its present direction. My advisor and our collaborator both insist that I deserve a break, and I certainly need the sleep, but I do not want to slack off too much. I have other work to do, of a similar nature to that of what I had been doing with our collaborator, and I can start on that now that she is gone. It should continue to be good.
Now, though, I am going to take a little break and relax. That should be good as well.
Things started off slowly, actually. Our collaborator got a bit sullen about halfway through (a week ago now), fearing that she would not get enough work done to justify the grant that she was hoping to get renewed. Then our specimens started getting dark spots all over them, making them unusable, and which took us half of a week to troubleshoot.
That was fun. It is not very often that scientists actually use the "scientific method". The observation/hypothesis/prediction/test thing that we are taught in elementary school is not in fact very helpful for a lot of science work, which is often exploratory and usually requires refinement. However, last Monday was a very clear case of the scientific method being used to great effect. We could not figure out why the latest batch of specimens was so awful, and initially assumed that it was the stain. This made sense, inasmuch as the lead stain is rather awkward to make, and can easily not work out right. I made a couple of batches of it, as did our post-doc, but the effects on the specimens did not vary much. So, on Monday, we decided to get methodical. I prepared five specimens. Four were from an earlier series that I had cut: one using each of the two stains that we usually use (lead and uranium), one using both, and one using neither. I also obtained an unstained specimen from our collaborator's latest series.
Late on Monday (I think that it was about six in the evening -- science only rarely works according to a "normal" schedule!) we all went down to the TEM, and I popped in the specimen with both stains. It looked moderately spotty, though not unusably so. Next was the uranium-only specimen, which looked great (although without the lead stain, some cell features were of course not highly visible). Right, we thought, the lead stain was at fault. But in the interest of consistency, we put the lead-only specimen in, expecting to see the spottiness that made the previous series unusual. Amazingly, it looked great! There was a hint of the spottiness that we saw in the specimen with both stains, but that was less noticeable than the lack of features stained with uranium. Likewise, the unstained specimen was pretty good, although of course unstained and therefore low in contrast. The definitive answer on the problem came when we put in the unstained specimen from our collaborator's latest series, which had nasty spotty things all over it. Aha! Her diamond knife was the problem.
So our collaborator cleaned her knife (a harrowing undertaking, given that diamond knives cost several thousand dollars each and are extremely fragile) and cut another series, which turned out to be wrinkly and uneven and did not hold together. My advisor suggested, noting concern for our collaborator's ego but more interested (as was she) in getting results than anything else, that I cut a series, and that was when things got really fun.
This was on Tuesday. The suggestion came in the afternoon. Specifically, the suggestion was that I would cut a few specimens and go home, and that we would stain and examine them on Wednesday. However, I was feeling ambitious. To begin with, I started cutting 50-nanometre-thick sections rather than the usual 70-nanometre-thick variety, which is generally much more difficult. That part was my advisor's idea. In fact, our collaborator likes to cut thicker sections than normal, usually 90 nanometres, which are easier to handle, but the work that we are doing is made much easier with thinner sections. To my surprise, I had pretty good luck with my sectioning, and I got curious about the results. So I stained them that evening, and, my curiosity if anything amplified, fired up the TEM at around one in the morning and had a look.
The sections were beautiful. I was absolutely captivated, and kept working on them for another four hours. Finally, at five in the morning, I decided that I was starting to tire, and shut things down. I made some notes about the specimens, copied the images onto a flash drive, and sent an e-mail to my advisor and our collaborator instructing them to look at it.
I got home just before eight in the morning. I got three hours' sleep, and woke feeling absolutely great. I arrived on campus half an hour before our next scheduled session on the TEM, and was greeted with enthusiasm and amazement by my advisor. The all-nighter turned out to have been very helpful, giving us a much better idea of what to do next with the specimens. We plugged away at them until early evening, at which point the lack of sleep was starting to catch up with me.
That brings us to today. Getting going this morning was incredibly hard, but angharad was very helpful in keeping me on task. I arrived on campus early, and did a little work on the TEM with our collaborator until we determined that we needed more sections. Our collaborator suggested that I give it another try, and to let her know as soon as I found myself too tired to work (I was forgetting random things from lack of sleep). To my bewilderment, though, after a couple of false starts, I found myself cutting a near-perfect ribbon of 50-nanometre sections. I was starting to get a bit shaky by the time I had finished collecting them all, and our collaborator helped at that point with the fine-motor-skills part of the staining while I got lunch. Then we went down again to the TEM -- and once again, I had done a superb job. (I am feeling a bit self-conscious typing this all, but it is the truth. I have to say that it feels spectacularly good to be competent! Honestly, though, there is a generous portion of good luck in all of this as well.)
Of course, now that our collaborator has left, things change, and in more ways than I was expecting. The specimens that we had been working on are of an organism of complicated provenance, and for political reasons we all agreed that it was best that I not work on it by myself. So the intense productivity that I have been enjoying for the past few days cannot be continued in its present direction. My advisor and our collaborator both insist that I deserve a break, and I certainly need the sleep, but I do not want to slack off too much. I have other work to do, of a similar nature to that of what I had been doing with our collaborator, and I can start on that now that she is gone. It should continue to be good.
Now, though, I am going to take a little break and relax. That should be good as well.