It has been three months since I last posted. During that interval, I wrote two proposals, one to the Marine Biological Laboratory and the other to the NSF. I finished the latter in mid-January. At that point, rather than diving headlong into experiments, I continued on with academicky things, and only managed the briefest forays into bench world, the most recent of which I will describe here in a moment.
First, wondering “out loud”, I should blog about writing itself? I want this blog to give insight into what a scientist does and if that scientist is doing writing, well should not that be fair game to describe? To my surprise, blogging about experiments has helped me think about them, would not the same be useful for writing? Perhaps. But writing, as an action, is abstract. To some extent, writing could be a definition of abstraction. I don’t mean the movement of my fingers hitting the keys, or the kind of software I use to convert keystrokes to words-on-the-page; those actions are concrete enough. I mean what goes on in my head. When I wrote above that the idea motiving this blog was to show what a scientist does, I was thinking about concrete doings. I put a slide under the microscope; I mixed these chemicals together. Of course, those doings are swaddled in a sea of ideas, and in writing about manipulating hardware, I have to include all that abstraction. So perhaps my worry about the pure abstraction of writing about writing is overblown?
Happily, I do have a little bit of lab-work to describe today. Last week, I looked at two (!) slides through the microscope. The microscope in question uses polarized light, and the signal I needed to see is weak, I took the trouble to clean the slides and coverslips first with some glass cleaner. I haved looked through the polarized-light microscope at coverslips right out of the box and they look like a starry night in the woods far from town. Most of those ‘stars’ are washed away by glass cleaner. I spotted 20 µL of a solution on each of the two cleaned slides, eased a cleaned coverslip on top, wicked away excess solution so the coverslip would be bang up against the slide, and ran a fillet of nail polish around the coverslip, affixing it to the slide and preventing the water from evaporating.
In the solution were cell walls. I was looking at what happens to the cell wall of the BY2 cell cultures when they are ground up for cellulose assay. The postdoc in the my, Eri Kamon, is helping me here. She has been measuring the amount of cellulose in the BY2 cell wall. In the protocol she developed, the cell culture is frozen, ground up, cytoplasm removed, and eventually the more-or-less purified cell wall is boiled in acid, which removes everything from the cell wall except for cellulose. Last summer, Eri gave me some of these ‘cellulose ghosts’ for my work at MBL. You can see a picture here (Fig. 2, factlets July 22.). A few weeks ago, Eri told me that for the material she gave me, she omitted the grinding step. Indeed, even after soaking in boiling acid, the cells stay whole and even in filaments, although they collapse with one side wall flattened down upon the other. You can see that in the figure referred to above.
But, I would like to break the cells open so that a single cell wall would lie flat on the glass, rather than a pair of walls (one from each side of the cell). To see if the grinding protocol we use opens up the cells, I asked Eri to make some cell wall samples for me, one with grinding, one with out. These are the two things I examined.
The results were clear: grinding failed to open the cells. Well, perhaps one in a million. But basically they looked the same as not-grinded. That’s too bad, opening the cells up would be useful for polarized light work because having a single layer of cell wall removes artifacts from two walls superimposed. But we are not quite ready to give up. Eri is going to try a different way to grind, one that is suggested to be more … hostile. Maybe that will work? With any luck, I’ll have something to write about next week too!