This Saturday I finally inoculated my flasks for my big experiment. Saturday was a long day, but I was excited to finally start. Today I spent the entire day sampling my flasks and sampling my cultures. I'm getting my samples prepped and ready to send them off to U of Hawaii where a lab there will give me the elemental ratio of what's in my cells. I've also been taking samples for some intracellular allocation (RNA, DNA, and protein). I'm presenting the first draft of my presentation tomorrow in front of the post-docs in my lab who have been mentoring me throughout the internship. Things are finally starting to come full circle.

I've spent this week finishing up the things I need to physically do at MBARI since I will be away next week on the ship. I cleaned up all my data and double checked some things against the video archives, made some photos and clips for my presentation, planned out what I'll do with any squid I catch on the cruise, and started analyzing my data. I'm going to do the bulk of my data analysis and writing on the ship so it's going to be a busy week next week. Can't wait to be at sea!

Mixed week in terms of progress. I decided to do some error analysis for my program at the end of last week. Most of Tuesday comprised editing test images and adding masks on MATLAB, a program in which I have little experience using. I realized, Wednesday, that the files I edited were tiff files and not b16 ones (the necessary format to run them through the program I've developed). Paul and I are working on a way to create the same masks on a b16 format file. Despite everything, I had so much fun messing around with MATLAB that I'm signing up for a MATLAB-based class this fall (registration opens tomorrow at 5!).

This week has been pretty eventful! I've finally decided which squid species to focus on. The winner is... Pterygioteuthis! The sequencing results I got after cloning were quite good, but I'm STILL having trouble getting the extreme 5' and 3' ends. We've decided to do RACE (rapid amplification of cDNA ends) to get those last bits of sequence. The reason I need the whole chunk of gene is because if I want to express the gene in E. coli and get some things to glow, I need to have the correct start and stop codons. We've found several viable candidates, but there is a definite chance that the real start and stop are in regions of sequence we don't have yet. The good news is that I was able to design new primers using a very promising hit. Today we're going to make cDNA and tomorrow we're going to do RACE. Fingers crossed!

I started my write up. I also reminded myself how much I prefer research to the write up stage. I've been writing and making sweet graphs all week. As a side note, I also found housing in Berkeley so I am no longer homeless, seemingly unlike most of my neighbors.

How to quantify bits of information has been the question on my mind this week.  For exisitng numerical information I am growling at Excel, because the graphs it produces are horrible and next to useless.  I guess this means taking it all to R and tackling the matter there.  I'm missing my Grapher software!

In terms of progress, I'm chasing up odds and ends.  Interaction between different faults and what this tells me about the relative timing of lava emplacment.  Why are there so few hydrothermal vents on Alarcon Rise?  Why do faults and fissures act in the way they do as they approach transform faults?

Draft title of presentation (but will be amended because it's terribly dull).  The significance of faults and fissures of Alarcon Rise.

Progress this week has certainly been slowed by the ear infections. I am glad to be guzzling antibiotics, and even more glad that my sea legs might actually be sturdier than demonstrated...

I am just finishing the last image annotations for my spatial analysis of traces on the seabed at Station M. I have processed most of the time-lapse data and am ready to match it to the spatial data once I get it done. I am going to try binning my spatial data (density, diversity and seabed coverage of traces) by 10-day interval to match my environmental data, but I will have to see if that gives enough measured seabed area in each bin.

I discussed the outline of the write up/paper and my presentation with my mentors yesterday, and will go over the figures on Monday. I also have a list of non-project-related tasks to take care of before leaving MBARI, which I am whittling down.

This week I outlined what I wanted to get out of the remainder of my time here. What I decided was to drill down into the nitty-gritty of the math and theory behind all the control, filtering, and dynamics of this system.

Its nothing short of luxurious to be curious about something and be able to pursue some idea/thought either to a compact fundamental relationship, or some arbitrary point at which I say, "that's an acceptable solution."

 As a concrete example of this, I've been investigating and studying signal filters. Our float has a pressure sensor that gives us depth of the float. If/when the float is coming to the surface, the pressure sensor will most likely have some sinusoidal signal due to wave action. It would be energetically wasteful to try and correct for this, so one way to mitigate this is to filter the pressure sensor signal. Creating a low-pass filter capable of of filtering out a 0.1Hz wave signal is easy, but it comes at a cost: real (non-noise/disturbance) signals are delayed. In the case of of a second order filter with the design constraints I've chosen, a 0.1Hz LPF will have a delay of approximately 10s. That's significant, and potentially problematic if I want to the float to ascend at, say, 20 cm/s and hit a target depth of 50m, with 5% overshoot. With a 10 s delay, the float is at 48 m by the time the control algorithm gets a signal saying it's at 50m.

So I asked myself the question, "At what point does the vertical motion of a particle due to wave action in the ocean (effectively) stop?" So I spent the morning learning about waves, how their actions differ in shallow vs. deep water etc. Those who've taken Phys. Oc. probably learned this stuff on Day 1, but I find it fascinating! The short of it, is that I'm pretty confidant I can create an adaptive filter that knocks out big wave signal disturbances near the surface, but then is de-tuned in an informed way, so signal delay is minimized at depth.

Kind of a nifty idea, but unlikely to be a new one. Many people smarter than myself have been playing in the ocean for a long time.

Spent this week tying up loose ends here on shore before I head out to sea and pump out the bulk of my paper and presentation. I have all the necessary materials now and progress is occurring at the expected rate I think. It has been nice to finally start analyzing the data I have been working so hard to collect and organize. I am a very visual person so it is good to look at the trends and compare them to my hypotheses. I am very excited to go out to sea. Ill have to ask the 8 ball if we will see any Dosidicus, but I am optimistic. See ye landlubbers the week of the presentation! (Unless I have to do confluence while I'm out to sea... my guess is yes?)

I am still busy in the lab and analyzing sequence data, though I plan to finish these steps at the beginning of next week. I will then apply specific programs for population genetic and phylogenetic analyses on the data to define the level of gene flow and the taxonomic status of my mussel populations. The title of my talk will be: "Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus brevior complex".

This week I finally started my main experiment, which is really exciting! I have been taking samples daily and flash freezing them in liquid nitrogen wahaha (evil scientist laughter)!! Starting tomorrow I am also going to have to take my exponential growth phase samples which includes filtering and sending off samples to Hawaii for particulate organic phosphorus, carbon and nitrogen.

I have been recently working on my presentation and paper which have also been coming along nicely. Hopefully next week wont be so busy that I won't have time to finish it.

This week's been kind of a drag. I got sick on Tuesday, the day after our amazing whale kayaking tour (I have a theory that I caught it from inhaling "whale breath"). It doesn't seem like it was a bug that was going around since I'm the only intern who seemed to have caught it. As a result, this has been a relatively slow week for me. I'm trying to rest up so that I will be 100% for the Flyer cruise on Saturday.

Cross your fingers!

So all of the logging I have been doing for the last eight weeks now needs to be digitised. It's just a case of tracing the scanned images in Illustrator but it does take an absolute age. Luckily though, for the purposes of this report and presentation only every other one needs to be digitised. As of now (Friday lunchtime) I have one transect (6 logs) left to digitise. I'm hoping to get it done before next week. I have also made another five figures for the report, but will need to be amended for the presentation. The main figure is an overview of the canyon and transect locations. The bathymetry was easily accessible in Arc but the cross sections had to be done manually which was a pain. The other figures are the result of my grain size analysis, each transect plotted in a separate figure. Next week will be mainly writing a think but I may get a few more cores out to inspect, just to add something else to the report as I think it will strengthen my discussion.

Just got back from a SIMZ cruise. We had a really good run this week. I mostly assisted Julio in water processing, but also got some practice operating the CTD. Next week, I plan to start working through wednesday's AUV gulps for direct comparison with the LISST-HOLO. Hans made some adjustments to the intake of LISST-HOLO prior to this cruise and we look forward to seeing the results.

This week I have continued designing and modeling components for the exhibit. The designs for the drive shaft and other load bearing components connected to the drive shaft have been completed and the shop has started machining them. Recently I have been doing many iterations of force and stress calculations to design plastic pieces that will snap on and hold tight without breaking. These should hopefully be in the machine shop by the end of the day. By early next week the entire assembly for the exhibit should be designed and finalized. The tentative name for my paper is "Engineering Mechanics and Design of the Monterey Bay Aquarium AMP Exhibit". I smell a Nobel Prize...

Done with my analysis! Finally have 2 working classifiers that are trained, tested and compared. Had an interesting conference call meeting with my collaborators from Oregon State University and got to present some results over the phone. Past couple of days were all about producing figures and animations for my presentation. Next week writing.

After depurating the databases, analyzed the trends, integrated the climatic indices and performed basic statistical analysis. This week I had classified the information, so that I began to edit the graphics and also to select the most relevant information so I was able to work on 50% of my presentation.

I'm late again with this one - I tried! Last week was a mix of productive and frustrating as I had to sandwich writing a cover letter for a lab assistant position at University of Georgia in between the beginning of my data analysis. I've been making large spreadsheets with many pages each in order to convert raw voltages from my pH sensors into actual pH values. It's coming along nicely and I'm almost finished. The next step will be to average each half-hour segment in the 24-hour day together for the 14 day period. I can't wait to see the data represented on a graph!