Gel of the Day: What the Heck Happened Here?

Sometimes, a perfectly good gel gets funkified in the process of handling. I think that's what happened with this gel, which was otherwise indicative of a near-perfect PCR:
The specimens in this case were three adult and one larval Bolitotherus cornutus which I collected at the MSA foray in Pennsylvania on August 10. The last eight lanes, 25-32, are from the larva. I haven't successfully sequenced a larva before; maybe my dissection technique is improving. The cox1 bands (31) look a bit weak, but the product should do for sequencing.

If you're familiar with electrophoresis gels or have at least been peeking at previous gels of the day, you're probably asking about now, "Mike, what the heck happened to lanes 21, 22 and 27?"

Well, I'll tell you. In order to take this photo using a UV light, I have to remove the gel from the casting tray, put it in a weigh boat and take it to a dark room upstairs from my lab. In the process of transferring the gel from tray to boat to camera, it gets a little scrape over an edge or two. This time, for whatever reason, that caused the bands in three lanes to get smeared. Nonetheless, there are bands there and since they are duplicates from two different dilutions (as far as specimen and gene go, 21=17, 22=18 and 27=31), it's not a problem.

Also, every fourth well is a control; there shouldn't be anything there. There seems to be a very faint band in lane 4, but it's nothing to worry about. I may just try and sequence it to see what the contamination is, since the position of that band is unlike that of any of the legitimate bands on this gel. I suspect that the culprit is a dirty microtube; if my primers, buffers, etc. had been contaminated, I would expect to see that phantom band in all of the control lanes.

The reason I'm running another batch of B. cornutus is that these are the first specimens I've collected from a site outside of Massachusetts. It's worth looking at them just to see if there are any polymorphisms present in introns in the sequences I'm analyzing.

I also read a very interesting paper today:

Leschen RAB and TR Buckley. 2007. Multistate characters and diet shifts: evolution of Erotylidae (Coleoptera). Systematic Biology 56(1):97-112. DOI: 10.1080/10635150701211844.

It's very much relevant to my own research. In this paper, Leschen and Buckley analyze the evolution of Erotylidae, a family of beetles only distantly related to the family I'm studying, and link their hyperdiversity to a shift to a diet of macrofungi. It sounds rather familiar, no? It's a very interesting read if you're into this sort of thing. It's based on morphology, not molecular biology, and finds a good link between diet and the external reproductive structure (gonocoxa and ovipositor) of Coleopteran females. Mycologists (at least those with an interest in basidiomycetes) and coleopterists alike will undoubtedly find something of interest in the paper. Enjoy.

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Albert Hoffman, Father of LSD, Takes the Big Trip

Albert Hoffman, the Swiss scientist who discovered LSD, has passed away in Basel at the age of 102.

Hoffman's discovery of the potent psychotropic drug came while investigating the biochemistry of the ascomycetous fungus Claviceps purpurea, a pathogen of grasses. It was one of history's classic accidents, really. Hoffman knew that C. purpurea synthesized a number of alkaloids and those compounds were already known to be useful in medicine when Hoffman isolated one of them, D-lysergic acid, and from that produced the first ever batch of lysergic acid diethylamide, in 1938. In a moment of fateful laboratory sloppiness, some of his product got on his fingers and thereafter into his bloodstream purely by accident. While it's not the most glamorous of hypotheses about how this happened, one urban legend suggests that this might have occurred because he was picking his nose.

However it happened, Hoffman was floored by the experience and duly noted the effects. The potent mind-altering effects later targeted the drug as a potential treatment for some mental disorders and experiments were carried out for several years before the US counterculture of the 1960's got wind of the stuff, largely through the efforts of a wacky little Harvard psychologist named Timothy Leary (who was also a Massachusetts native, by the way, and started his university education at Worcester's own College of the Holy Cross). For better or for worse, Hoffman's discovery changed American and arguably all of Western culture thereafter. The recreational use and abuse of LSD led to it being made illegal in the US in 1966.

Unlike Leary, Hoffman wasn't a flamboyant character. He eventually became head of the research department of Sandoz pharmaceuticals and wrote a book about LSD, LSD, My Problem Child. He believed all his life that the drug could be used as a treatment for mental and emotional diseases — and he was probably right, although its doubtful that it will ever be accepted for such applications. Hoffman's "oops" of 1938 spawned events that were far beyond anything that Hoffman himself would have advocated for his "problem child."

If nothing else, Hoffman's claim to fame stands as testament to the accidents that happen in the course of scientific research that have the power to radically transform the world.

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Short Notes: Nom d'Blog and Taxes

I've finished off doing my taxes. Perhaps the only good thing about being a dirt-poor student is that it makes doing my taxes very, very easy. Between state and federal refunds, I'll be getting back just over $1300, all of which will go to paying down debts. The "economic stimulus" payment I anticipate in May will go for the same thing.

On an entirely unrelated point, I've been noticing that I get a lot of Google-generated hits here based on searches for the word "risal" by people from Arabic-speaking countries. I've just asked LL about that, and she told me that the word risal means something like "a newsletter" in that language. I had no idea of this; the name "Mike O'Risal" is a pun on the mutualist relationship between certain trees and fungi (mycorrhizal). That part of that name has resulted in Middle Easterners and North Africans finding my blog while searching for a newspaper to read is kinda sorta funny.

But, as the old saying goes, Pantalon daya k'tir!

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Wasting My Time on a Slushy, Wet Night

I'd been planning all day to attend the meeting of the Greater Worcester Humanists this evening. LL teaches tonight and had an appointment this afternoon, so we had to do some serious car-juggling. Still, I gave her a ride to the university, came back home to eat and then set out for the meeting despite the snow-sleet-slush-rain that was everywhere.

At the end of the five mile drive, I arrived at the Unitarian Universalist church about 15 minutes early. There were only two other cars in the parking lot. Uh-oh. I'd come this far, though, so I went in.

I wandered through the hallway looking for something that seemed like a meeting until I heard a voice call out from an office. A very pleasant woman asked me if she could help, so I told her I was there for the Humanist meeting. She told me she thought it had been canceled. Hadn't there been a sign on the door? Of course, there wasn't one or I wouldn't have been wandering the hall in the first place. She called someone who told her that the meeting, which had already been postponed once, had now been canceled because the scheduled speaker had laryngitis. Apparently the cancellation had happened a couple of days ago.

Nothing to do about it but to drive back home through what had now become just rain.

I just checked the GWH website and, sure enough, the event is now marked "canceled." I don't know when that change was made, but it surely wasn't there this morning.

The group's next event is scheduled for March 11; it's a workshop on secular student activism. I doubt I'll bother with it; organizing secular students at my university would be as worthwhile a project as trying to convert people to Mormonism in Utah.

So now there's nothing to do except wait until LL calls to tell me she's done with her class and I can pick her up — from her Jesuit-run college. Maybe she ought to go to that meeting on March 11.

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Thanksgiving 2007

LL and I spent Thanksgiving with my family. We started out with Thanksgiving dinner in upstate New York and then moved on to another Thanksgiving in central Pennsylvania at the Nittany Mountain KOA camp, which is owned by my sister-in-law and her partner. Yes, two Thanksgiving dinners. I don't remember the last time I ate so much. My family is rather non-traditional; aside from my sister and brother-in-law, nobody is married to one another, so we're all partners, but still family. I'm not sure what that means, if anything, but I think we've all sort of come to the same conclusions about the institution of marriage in general. It's an unusually diverse group of people, too, in terms of ethnicity and education and everything else. We're certainly not the typical 2.2-kids middle class model. We can certainly eat, though.

LL and I stayed in the cabin shown above. One of the first people we met at the camp was a nearby camper who goes by the name of Snooky. Snooky is obsessed with blowing leaves. He spends whole days, from sunrise to sunset, with his leaf blower. Things could be worse, I suppose... he could be obsessed with an axe. To say the guy is eccentric is probably an understatement. Meeting him made me wonder if Stephen King has ever written a story about a leaf blowing maniac.

Of course, there were other things to do beside blowing leaves. My niece, for instance, prefers playing miniature golf to just about anything else. She has her own rules for the game, the first of which is "I win!" When she got tired, she had the good fortune of free and unlimited access to the camp store, so she could always "sugar up" on candy and hot cocoa when she started getting tired. I've sat through hurricanes that packed less energy than that kid. For her, the long weekend consisted of miniature golf, Spongebob and sugar. Oh, and telling all the adults how to play whatever game she made up at the moment. It's too bad none of us had nearly the same energy she does.

There's a petting zoo at the camp. LL made friends with a couple of goats. My niece, for whatever reasons, wasn't generally too interested in the animals. Not all of the animals present were from the petting zoo; my brother-in-law's mother (my aunt-in-law? I still don't know the proper kinship term) brought along her pug, Zeus. Also present was a ridiculously friendly three-legged cat; he lost the fourth leg in a jaw trap some years ago and makes do with the remaining limbs as best he can. There was also a very hyperactive Maltese named CD and a few other critters lurking about.

What family gathering would be complete without at least one faux pas? Ours took the form of a social misstep by my sister-in-law's partner's daughter's boyfriend (I dare anyone to give me the kinship term for that relationship!) delivering a line about how mean Arabs are while LL was sitting at the table. This was made a bit funnier by the fact that the guy is half Italian and half Jamaican himself and was meeting the family for the first time. It was all taken in stride with good humor and a quick comeback from LL resulting in a blush and an embarrassed "Oh, are you Arab?" from Alfredo, the boyfriend in question. I don't think anyone will be letting him live that one down anytime soon.

We stayed at the camp and ate ridiculously well through Saturday night, then left early on Sunday morning to begin the trip home. I decided to take a detour through Binghamton on the way to check out a few places that were part of my life about 20 years ago when I lived up there. The first stop was at 160 Conklin Avenue, a house that I lived in during my first stint at university. I lived there with five other students, including one girlfriend, in a sort of commune that resulted in the place being called Helter Shelter. There were a lot of drugs and craziness. The place is essentially the spot where my life absolutely went to pieces and I felt a need to revisit the site of the most traumatic time in my existence. It hasn't changed at all. In fact, it looks as if it hasn't seen so much as a coat of paint since I left in 1988. To me, it seems a dark, brooding, decaying place, perhaps a bit Lovecraftian in its presence. It's like a combination of fossil and historic landmark in my life. Standing there at the corner of Conklin and John was surreal; I felt as if I were dreaming, especially because LL was there with me. My room in the house was the one with the windows just above the door in this photo. The door itself was the spot where, in 1987, a guy named Jimmy Puccio drank a votive candle full of hot wax thinking it was a shot of tequila and then passed out. He's probably long forgotten about the incident, wherever he is now. If there were such a thing as ghosts, this house would certainly be haunted by the spirits of many acid trips, not to mention some devastating heartbreaks. I wouldn't want to be the poor slobs living in it now in that case. In my mind, at least, this is a place with much mojo.

After my pilgrimage to Helter Shelter, I headed to the SUNY Binghamton campus. Everything was closed and parking was no problem. We visited College-in-the-Woods, dorms I'd been tossed out of years ago after my roommate and I accidentally set a fire in Oneida Hall that got the place evacuated at 4 AM in the middle of a winter night. You see, we wanted to find out whether Bacardi 151 was really flammable, so we filled the cap of a peanut butter jar with the stuff and lit it. It ignited, of course... and then my roommate jerked his hand away and knocked over the entire bottle onto my desk. That set off the alarms and destroyed a couple of my textbooks and all of my notebooks, too. The next day, we were told that we could no longer live on campus. We wound up finding a place in Johnson City, right on Main Street. That's what's shown in the image to the right; our apartment was the top floor of the building to the right of the one with the "1892" decoration on the top. I lived there for about a year with my roommate, Duncan, as well as the son of the Fijian ambassador to the United States. After that year, I took some time off from school. By the time I got back, Duncan had graduated and I wound up living at Helter Shelter. The store with the blue awning, now a clothing store, used to be a sub shop called The Pig Out. It had the best spiedies in all of Broome County, and I'd been hoping to take LL there, but it's gone. Actually, most of the storefronts on Main Street are empty these days. Downtown Johnson City is a very sad, desolate place. Even Fat Cat Books, an institution for Triple Cities comic book and RPG fans, moved out of downtown. The building it once occupied, just across the street from my old apartment, now sits empty.

We spent some time poking around the area and then got back on the road home. Along the way, we got hungry and stopped for lunch in Cobleskill. Not wanting to hit the usual fast food places, LL chose our lunch spot, a diner on route 9 attached to the Colonial Motel — the Diner Motel. Not the Motel Diner, mind you, but the Diner Motel. Seeing that they'd gotten the name wrong on the sign, we probably should have known better than to eat there... but we went ahead and did it anyhow. I ordered grilled chicken on a pita, expecting something like a gyro. What I got was a piece of grilled chicken on a pita and nothing else. This was easily the most literal lunch I've ever eaten. It was exactly one piece of chicken breast on half of a pita with no lettuce, no tomato, no onions, no nothing. LL ordered a proper gyro, but that was bland and useless, too. After lunch, we agreed that the best thing about the food we'd just had was that it probably wouldn't make us sick.

Because our own GPS unit is in the shop for repairs, we were traveling with a loaner. Quick qord of advice here; avoid the Mio GPS like the plague. We told the thing to avoid toll roads and, as if to punish us, it took us on the most backwards, time-wasting route home possible. At one point we even wound up on a dirt road (Tory Hill Road) somewhere near Central Brunswick, NY. We were trying to avoid taking the Mass Pike, but we finally gave in and took it and paid for that mistake by getting stuck in a traffic jam that easily added close to hours to our trip. We finally got off 90 and picked up 20... but that was backed up, too. The final insult came when we got off 20 and onto Stafford Road, just a couple of miles from home. I was pulled over by a cop because I had a license plate frame. No kidding; license plate frames are technically illegal in Massachusetts, and this particular cop decided to stop me because of it. Luckily, he gave me a warning instead of a ticket. By that time, though, we'd been on the road for more than twelve hours. Ugh. We left New Columbia, PA at 6:00 AM. By the time we got back to Worcester, it was 8:30 PM. It was an awful trip. Next year, we'll do things differently. I don't know how, but I'm not doing that haul on a holiday weekend ever again.

The weekend was great, the road trip sucked, and I'm now functioning on 3.5 hours of sleep, having awakened at 1:30 this morning for no good reason I can fathom. I have to teach lab until 9:00 tonight, too. It's going to be a looooooooooooong day.

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One of Those Days

Today started out well enough. The fungus popping up outide of the lab turned out to be Phallus ravenelii; I shot pictures and took a specimen which I put on the dehydrator with predictably amusing results for the first floor of our building. "Oh god, what is that smell? Did something die in here?" Somebody also went through the dehydrator looking for something and my specimen got hidden from view, so I got to ask one of the post-docs, "Hey, have you seen my Phallus? I left it on the dryer and now I can't find it." I mean, it just started out to be a great day.

Ah, but then I attempted to load my plate and somehow lost track of what I was loading into which wells, so there's a good chance that when I get my results back they'll be meaningless and I'll have to start over again, which means I essentially know what I may be doing this weekend.

Embarrassed and angry with myself for making such a careless, stupid mistake, I came home for lunch. I immediately poured borscht (beet soup, which stains everything it touches purple) on the table because I dumped it into my bowl too hard. Then I noticed that I'd left my MP3 player on all day in my pocket and the battery was dead, so I took off the skin and put in a new battery... backwards. So I took off the skin and fixed the battery, then put the skin on upside-down.

I have a theory about all of this; for some reason, I have started producing an over-abundance of natural antisense transcripts. The stuff has completely overwhelmed my normal RNA, and so I am left producing nothing but the notorious BMBLFQ-OS product. I no longer am making sense.

I still have to manage to drive to the train station, pick up LL and then go food shopping. I'm hoping to survive the trip at this point.

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Perils of the Field: What Do You Do When Bees Want Your GPS Unit?

Collecting yesterday was good but not great. It wasn't a great day for gilled mushrooms, but it wasn't a bad one for polyporoids. I found a couple of of Fomitopsis and one wood-decomposer on cut hemlock that I couldn't even begin to identify. I'll have spores from the bizarre thing today and should be able to at least get a genus on it.

The day didn't get off to a very good start, though. I found an absolutely pristine specimen of Amanita fulva growing in the debris that had fallen from a very decomposed tree. I set out my GPS to record its position, took my backpack off and got my specimen case ready, took some notes, and set up to take a photo. There was a little fern frond in the way, so I pulled it out... and bees began swarming out of a little hole in the ground right next to my GPS. I did what any hominid would do in the situation. I yelped and ran away, leaving everything but my camera on the ground outside the bees' lair.

I got stung only once, just behind my right ear. The bees didn't follow me after I'd run away, so I backed off about twenty yards. The last time I was swarmed was about a year ago in Florida; those bees were Africanized and chased me a great distance but New England bees are a good deal more polite, it seems. Nonetheless, I could only watch in dismay as the angry insects swarmed over my backpack and camera bag, no doubt stinging them to death. I couldn't get back to the trail I needed, either, without going right past the hive. With my GPS unit so near the entrance, I spent a good deal of time wondering whether my meager budget could include the cost of a new unit and what, exactly, bees would do with the thing. I suppose that if bees had GPS technology, they wouldn't need to do the old waggle-dance anymore. Clearly I had stumbled upon a hive of bees in the vanguard of cultural revolution!

All I could do was wait, so wait I did. I waited for about 40 minutes for the bees to calm down, having convinced themselves that my gear no longer posed a threat to their hive. I found a very long branch and managed to hook it into the shoulder strap of the camera bag and retrieved that safely, and then I managed to fish my backpack out of the danger zone as well. My poor little GPS unit was quite another story, though. The only thing I could do with that was to use my long stick to push it a couple of feet away from the hive entrance. The bees didn't seem to be responding to that stimulus, so I strapped on my bags and made a run through the area, snagging my specimen case and GPS off the ground as I went. Thankfully, no further stinging occurred. I probably could have just walked by and picked them up casually, but I wasn't about to take any chances.

This morning, the area behind my ear is a bit red and swollen and itches a good deal, but other than that I'm fine. This is just part of fieldwork, albeit an amusing (at my expense) one. Sometimes, Mother Nature is a bitch!

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O Crappy Day

This morning started off with Tycho waking me up at 5:00 because he wanted to go out. Scratch scratch, tap tap, wake up human and let me outside so that I may insure no other lizards are encroaching on MY territory! I've been in a crabby mood all day as a result.

Then I spent hours trying to figure out CSS to tweak a few things with my blog. Big, steaming heap of FAIL right there. I surrender. It's good enough.

We went to lunch at what we thought was a Jewish deli; it's called Maury's, after all. Ah, but it's under new management, and my hopes of finally getting a good tongue sandwich (no wiseass remarks, please) were dashed. It's now an Italian deli with a Jewish name. Their sign advertises some rather curious delicacies, such as "pastromi" and "capicollo." I call false advertising. Change the name to "Maurizio's" if you're going to serve Italian sausage and genoa salami and NO TONGUE.

LL bought us an air conditioner; we've been living with uncomfortable temperatures and she finally caved in. But it didn't fit the window correctly, so she had to go back to the hardware store to get some wood. She got home with the wood and promptly dropped a glass of water which shattered and skittered throughout the foyer. Then she realized that she'd left the manual for the air conditioner at the hardware store, so she's gone back to get it.

Today can't be over soon enough. LL is still trying to get the air conditioner installed. I'm going to leave the room now, before it catches fire...

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