Songbird
Sometime around 7:00 am I felt the ship begin moving. The rocking motion seems to change when the ship moves forward. The ship is now enroute to station 3. It will take us 24 hours to arrive at our next destination. People are using this time to get caught up on work, repair equipment, and for attending lectures. I spent most of the day reading. I did get a chance to play cards this evening with some of the crew. We played Spades. The Chief Marine Engineer and I got schooled by two of the ships officers. Starting tomorrow some of the scientists will start putting on seminars.
I would compare traveling by ship to a long airplane ride or a train trip. There is always a constant rocking and loud noise in the background. The ship is quite noisy and there is a constant beep/blip about every 20 seconds. I am going to time it to see if it varies in timing. In addition to the motor noise there are continual loud bangs on the hull of the ship that echo through the structure. The NOAA personnel tell me it is waves, but I am not convinced. I have always been leery of government explanations for events. My conspiracy hypothesis is that we are colliding with whales surfacing for air. This is all kept secret because many whale species are threatened.
Sitting at lunch was interesting. People from Norway, Spain, and Turkey were all conversing in English with strong accents. No, this is not the start of a joke. I asked them how they could understand each other's English when they each had such strong accents. It turns out, they told me, that it is easier for them to understand one another than many native English speakers. It is also hard for them to hear accents that are very apparent to Americans, such as southern twang or Jersey pride. I enjoy the diversity aboard the ship. This is a real treat coming from Montana, which has far less racial and cultural diversity than the makeup of the ship's occupants. I encourage all of my students to visit other places and to experience the diversity of people and cultures whenever life provides these opportunities.
A small blue and brown bird landed on the ship today. It was probably migrating for the breeding season and stopped to rest. The bird seemed exhausted. I was told that they can get seasick after landing on ships and then die because they are unable to continue flying. I will have to Google this claim to see what the ornithologists think. We also saw a few flying fish propelling out the water and out of the way of the ship. I was told that when we stop at night the flying fish will be attracted to the light and sometimes they leap out of the air and onto the deck. Since these fish can swim up to 20 knots they are like little missiles and can slam into you with considerable force.
I have been spending some time in the DNA bar-coding lab learning more specifically what they are doing. Samples of identified species are brought to the bar-coding lab and the DNA is extracted. Once the DNA is extracted from the species they are run through a PCR (Polymerase Chain Reaction) machine. This machine amplifies the COI (cytochrome oxidase subunit 1) gene into millions of copies. It works in the following way. First it heats the sample of DNA to 95o C. At this temperature the DNA unzips itself. Then the temperature is quickly lowered to 60o C. At this temperature the COI gene anneals (attaches) a primer to the DNA strand. A primer is a short complementary strand of DNA that matches the starting point of the COI gene. These primers were specially made to match the beginning portion of the COI gene. Then the temperature is quickly changed to 72o C. At this temperature a special enzyme called Taq attaches to the primer end of the gene and then replicates the DNA. In other words it makes an exact copy of the gene. Taq is a special enzyme found in an extremophile. The PCR machine runs this process over and over until there are millions of COI genes. PCR machines are also called thermocyclers and are used in forensics to amplify small quantities of DNA from crime scenes. Once the gene has millions of copies it is fed into a DNA sequencer. This machine reads each nucleotide in the gene in sequence and provides the sequence in the form of a graph. This graph is interpreted and from it a gene sequence is determined. Around 700 base pairs for each COI gene from each species will be collected. The sequencer can process around 96 samples every 24 hours. We may collect well over a 1,000 different species on this trip. The DNA sequencing of organisms identified to species is the primary focus of this project.
Daily question: What does Taq stand for? Where was it discovered? and What is the significance of the place it was found for its role in PCR (aka thermocylers)?
Picture 1: Sunset over the Atlantic today.
Picture 2: Rob Jennings, post-doctoral investigator from Avery Point(UConn), running PCR.
Picture 3: Barbara Costas, a Ph.D. student from Avery Point, running gel-electrophoresis.
Picture 4: Mr. Catron standing next to a beautiful DNA sequencer.
Picture 5: Recording species richness as scientists pick through the catch.
Picture 6: Another goodnight from the Ron H. Brown.