Hot

My weather icon said 70 F today for Boston. It’s November 30th. It hasn’t been below freezing for more than a few hours at night. Wow.

Yesterday was the usual Chorallaries rehearsal, 9-12. Tonight it’s 7:30-12 because I’m doing a focused session on my song beforehand. I am missing a party to go to rehearsal.

At least I was able to schedule rehearsals so I don’t miss tomorrow‘s party.

What’s that you say? Term paper I haven’t started due in a week, on a topic I don’t understand?

DOWN

I am trying to do my homework for my math class, but the server is acting up. Eventually it did something truly bizarre, suddenly claiming that the compiler didn’t exist when I’d used it a few second prior.

So I wrote an e-mail to the support staff asking for help, but it wouldn’t send because the mail server was down. So I went to the main page (www.fas.harvard.edu) but that wouldn’t load either. Finally I went to the Harvard personal homepage, my.harvard.edu, which was nothing but boxes saying “this data is temporarily unavailable” with a notice at the top: “Wed 11:25am: my.harvard and other FAS servers are experiencing technical difficulties.”

The best part is, I can’t e-mail my professor to tell him that the assignment is no longer possible, because the e-mail server is down.

Fact of the Day #7: Solid-Phase Protein Synthesis

Proteins are made in nature out of just 20 amino acids. Those 20, strung together like beads on an unusually sticky necklace, do essentially all the work that keeps us (and everything else on the planet) alive. It’s easy enough to hijack the machinery that makes these proteins to make any artificial protein we might dream up. But sometimes, 20 isn’t enough, and we humans decide that we’d like to make a protein that’s got something else in it, something that nature didn’t think of.

The most common application of this is probably drug development, where you want small molecules that do something extremely specific. Usually, you want a protein that’s at most 15 amino acids long. Once upon a time, the way to do this was old-fashioned chemistry. You start with a bunch of chemicals in solution. You mix them together and they react, and then you filter out the product you wanted from the soup of useless junk, and repeat. This sort of reaction and separation has to be done once for every stage of the protein synthesis, or 15 times, in this case. In the 1950s, that meant about 5 years to complete the reaction.

In 1959, a chemist at Rockefeller University in New York solved the problem. Instead of using free-floating mixtures, the first amino acid in the sequence was attached to styrofoam beads. Subsequent stages added more amino acids to the chain, but the product did not have to be filtered out after each step; it was stuck to the bead. All the junk was still in solution, and could simply be drained away. Synthesis went from PhD theses to routine lab work.

Fact of the Day #6

The protein pathway by which cells synthesize fat is fairly well-understood. A drug is under investigation that would disable this pathway, as a treatment for obesity. When tested on small worms (C. Elegans), the worms cease to store fat in their fat cells; they simply do not process it.

However, the drug also makes the worms infertile. They can be made fertile again only by supplying worm with the processed fats that it can no longer synthesize.

Return

Last night I spent time with some friends at home. We attempted to play balanced pool with 3 people by changing the number of balls and assigning each person to all non-8 balls congruent to 0, 1, or 2 mod 3. This seemed to be working right up until the end, when someone scratched on the 8-ball. In 2-player pool, the other person wins. In 3-player pool, some sort of tiebreaker is required between the remaining two, and we couldn’t figure out any good way of solving that.

Today I drove back to Boston with Paul and Erik. It was a nice chance to have a relaxed discussion with a few good friends.

Now it’s back to the grindstone.

Failure

I bought a new ethernet cable to see if I could improve upon previous results. Unfortunately, on Friday morning the iMac unexpectedly decided to refuse contact with any bluetooth device, particularly any bluetooth mouse. There were no wired mice available, and this made testing the new wireless connection essentially impossible. I gave up and went home.

Last night I hung out with a few friends from home, as per usual, and today I did a bit more Fortran for my math class. Tonight has proven difficult to schedule, but hopefully I’ll get to see some more old friends tonight, and a few of us will carpool back to Boston tomorrow (my car).

Yum

Thanksgiving was pretty much as it has been for the last few decades, which is to say excellent.

Part of our annual thanksgiving ritual is to try to figure out the password for my grandparents’ wireless network. This year, that turned into something of a fiasco. Initially, the problem was simply that we could not remember the password. We tried a million combinations, with no luck. Eventually I decided to have a look at the router’s control panel, which is accessible from the iMac upstairs (the router is an Apple Airport Extreme). The iMac is also connected wirelessly, and the network password was stored but not readable.

When I opened the control panel for the router on the iMac, I was told to install a firmware update, and I clicked “OK”. After the firmware update, the device restarted, and all connections were dropped. When I tried to reconnect the iMac, I was prompted for the unknown password. Without the password I had no internet connection, so i gave up for the night.

In the morning, I used the hotel’s wireless network to look up how to reset the Airport. I performed a hard reset and configured the router with known passwords, which I expected would fix the problem. It didn’t. I could now connect to the wireless network with both the iMac and my Thinkpad, but the Airport refused to route to external hosts. The Airport is connected to a cable modem in the basement by a custom-spliced ethernet cable that runs through the walls.

This was strange behavior. As a stopgap, I thought to try plugging this ethernet cable directly into the iMac. It reported that no cable was plugged in, as would be expected if the cable were damaged. However, when I plugged the cable into my Thinkpad, I could acquire an IP address by DHCP and browse the web unimpeded.

So that is the situation as it stands. I have thought of two scenarios consistent with the evidence, neither of which sounds likely:
1. The cable is damaged. The damage is not so bad that packets do not flow, but bad enough that, on plugging in, a card might decide that the cable’s integrity is too low to initiate a connection. My Thinkpad’s ethernet card must be less demanding of quality than the ports in both the Airport and the iMac. Since the cable was working in the Airport before, the quality must have been fine the last time it was plugged in. It must have degraded over time, undetected until the connection was reset after the firmware upgrade.

Less probably,
2. The firmware upgrade changed the router’s behavior for DHCP requests. As a result, both the iMac and the Airport have incompatible DHCP with the DHCP server on the other end of the cable modem. My Thinkpad, running Linux, must have a more compatible implementation of DHCP.

That’s where it stands. To distinguish these scenarios, I intend to buy an ethernet cable tomorrow morning and try using it to connect the Airport and the cable modem. If I can then use the wireless network on my Thinkpad, the problem will be diagnosed and essentially solved. Otherwise, I don’t have any idea what’s going on, and someone else will have to be called in to fix the mess I’ve made.

Fact #5: Introns

As some of you may have heard, genes in DNA are split into a bunch of different pieces on the chromosome (as many as 10). These segments are called “exons” and the stretches of non-gene DNA between them are called “introns”. After the DNA is transcribed to RNA, the introns are “spliced” out, before the RNA is used to make a protein.

There are two main pathways for splicing out introns: self-splicing and non-self-splicing. Self-splicing introns are themselves pretty fantastic. After the RNA copy of a gene is made, these sections of RNA spontaneously fold up into little scissor-like enzymes whose only function is to cut themselves out of the RNA and reattach the ends. They accomplish this without using any energy or requiring and proteins.

Self-splicing introns appear in bactera, but not in eukaryotes (including humans). Our introns require a tightly controlled system of proteins to get cut out, which allows greater control over the DNA copying process. So you won’t find any self-splicing introns in humans, and indeed if you look through the human genome you won’t find any such sequences.

Actually, that’s a lie. Those sequences aren’t in our genomes, but they are in us. They’re in our mitochondria. They’re also in the chloroplasts of plant cells. That’s strong evidence that our mitochondria are truly from a different branch in the evolutionary tree.