Day 1: Thursday
My trip started quite poorly. I wrote a whole post on the first day so if you want more detail go here: A squatter's journey to the Marine Biological Lab (MBL). I posted (of course) to twitter along the way. Here are some of my posts:
- Heading to Woods Hole/MBL-giving talk for symposium for the Microbial Diversity Class http://t.co/o2hx0tf #fb
- Anyone out there recommend best way to get from Logon to Woods Hole after 10:30 PM (no Peter Pan bus) w/o renting car?
- Got lots of responses to this including from @ctitusbrown and @PhoebeFossil and @larry_parnell
- Best suggestion was from Julie Huber
- Thank you Delta for out early arrival in MSP- not so many thanks for sitting on runway for 20 minutes ad more waiting for gate
- Yhgtbfkm - we finally got to a gate at MSP and the gate agents keep missing our door with jetway
- @nwheat maybe I'll see you as I head to my connection
- Had a long twitter conversation with her about the fact that both of our flights were becoming disasters
- Plane was very late bit now in a nice Prius from Green Shuttles on way to Woods Hole #gomicrobes http://t.co/zwAHWy
- UGGGH - arrived Woods Hole/MBL; got dorm room key at 1am; woman in room not very happy; finally got other hot crummy dorm room; Ahh MBL
Woke up at the Swope Dorms and, thanks to the lovely reception I got from the Housing Staff (see A squatter's journey to the Marine Biological Lab (MBL) again for more detail) I was not very happy. I went in to town to get a latte and something to eat and then made it over to the Microbial Diversity Course to hear a few talks and see some of the folks there. Then I went back to my dorm room, packed up my stuff and abandoned Swope and went to the Sleepy Hollow Motor Inn just up the road, a bit out of town. I had already called and they held a room for me (I tried the one place actually in town but they were full). So I checked in, dumped my stuff and then walked back in to town. I eventually ended up going to dinner with some of the course TAs and other personnel.
Here are some tweets from the day
- Fun- MBL housing team can give me wrong keys for 1 AM checkin but rushes in to new room in early AM b/c I'm a squatter - Ahh MBL
- At least the view is nice #MBL #WoodsHole http://t.co/MPEBmHk
- The Tree of Life: A squatter's journal to the Marine Biological Lab (#MBL) http://goo.gl/fb/yFfXe #travel #teaching
|View from my second room at Swope|
|View from my room of Eel Pond|
|View from my room - nice view - but room was unbearably |
hot even on a cool day.
|Microbial Diversity course lab|
|Eel Pond again|
|Eel Pond again|
|Art around MBL|
|Fun chairs in the Candle House|
|Squid on a fence|
|Squid on a fence|
|More eel pond|
Saturday was the day for the genomics symposium I had come for. The symposium was hosted by the Microbial Diversity Course and was focused on microbial genomics. There were four speakers - me, Howard Ochman, Nancy Moran and Eugene Koonin. I thought the symposium went quite well --- each speaker did a good job of not both complimenting and complementing the other speakers. I hope the students liked it.
I spent many hours the night before and in the AM working on my talk, trying to fine tune it for the audience. I grabbed a latte in the morning at a nice Woods Hole place, and eventually walked on over towards the lab.
- Good morning Woods Hole http://t.co/yyoKrC2 http://t.co/oxGL0aOhttp://t.co/18j6qTh http://t.co/jbUFTaJ
I headed over to Swope and fortunately found a person from the course who told me where the talks were. I gabbed some breakfast in the dining hall and then went to the room next door where the Symposium was going to be held. I set up my laptop and alas noticed I had forgotten my Apple remote. So I did a App store search to see if my iPhone could serve as a remote for Keynote and it can (for 99 cents). So I downloaded the App and got it working and was ready to go.
I got a nice introduction from Dan Buckley, one of the Course organizers and then gave my talk. I think I went a bit fast in parts but people seemed to like it. I got some good questions and then it was time for a break. Anyway - here are my slides, which I posted on Slideshare: Eisen Talk for MBL Microbial Diversity Course
View more presentations from Jonathan Eisen Then Howard Ochman gave a talk. Here are some tweets from his talk:
- Done with my talk at MBL for the Microbial Diversity course Symposium on Microbial Genomics - now listening to Howard Ochman
- Howard Ochman discussing how genes in a bacterial genome w/ atypical composition are considered likely to have entered by lateral transfer
- Ochman referencing classic paper by Sueoka "ON THE GENETIC BASIS OF VARIATION & HETEROGENEITY OF DNA BASE COMPOSITION" http://t.co/zBCPHnb
- Ochman showing time course of the plot of genome size vs. # of genes for bacteria - all looked good 1kb=1 gene until M. leprae genome
- Ochman quotes "Less than half of the genome contains functional genes but pseudogenes .... abound" http://t.co/B1SsFd2
- Ochman: Why aren't there lots of pseudogenes in most bacterial genomes? B/c there is a mutation bias towards deletionshttp://t.co/MPZWVHl
- Ochman referencing "Bacterial genome size reduction by experimental evolution" http://t.co/I8jjKLl re: deletion bias
- Ochman making genetic drift personal: sometimes you pull out just the blue M&Ms, which of course you really don't like #funny
- Ochman referencing "The consequences of genetic drift for bacterial genome complexity" http://t.co/hTTatjV
- Ochman: an increase in genetic drift from reduced effective population size can lead to increase in Ka/Ks
- Ochman discussing how effect of drift on bacterial genome size is opposite trend predicted in Lynch and Conery 2003
Nancy Moran. Here are my tweets:
- Listening to talk by Nancy Moran about tiny bacterial genomes - she is discussing her work w/ now retired #UCDavis prof. Paul Baumann #fb
- Moran - discussing work of Allison Hansen in her lab on bacterial gene expression in bacteria containing cells in aphid gut
- Moran discussing incredible diversity of insect symbionts that help hosts obtain nutrients from nutrient poor diets #microbesrule
- Moran discussing the Tremblaya genome which has recently shown up in Genbank http://t.co/Cy9ydrz
- GavinHThomas: @phylogenomics Tremblaya is awesome. John McCutchoen is the man - hope this is published soon.
- GavinHThomas: @phylogenomics 58% GC in an insect symbiont - simply weird. McCutcheon talked about this at SGM Insect Symbiosis in Harrogate, UK in April.
- @GavinHThomas yes, high GC but it is related to organisms with even higher GC
- Now listening to the one and only Eugene Koonin discussing evolution of archaea/bacteria at MBL Microbial Diversity course #fb
- I note my start in genome evolution really came from reading papers by Koonin on helicases
- Koonin showing figures from one of my favorite papers of his: ... the emerging dynamic view of the prokaryotic world http://t.co/sHxjYjg
- Koonin: Archaeal genomes are even more gene dense than bacterial genomes
- Koonin: the majority of genes in bacterial and Archaeal genomes are part of conserved families
- Koonin: most gene families show patchy phyletic patterns across bacterial and Archaeal genomes
- Note - Koonin has more than 500 papers listed in Pubmedhttp://t.co/KuU7Oaz
- Koonin : most of the universal genes in bacteria and archaea are involved in translation
- Koonin describes "bureaucratic ceiling" to genome size b/c of exponential incr. in regulators vs. genome size - can't get too big
- TRyanGregory @phylogenomics Limit on "genome size". He means gene number (which does correlate in bact/arch but not euk)
- @TRyanGregory Sorry .. He is only discussing bacteria and archaea ... So here it does correlated w/ genome size
- @TRyanGregory indeed .. He was using gene number as his key feature
- Koonin describing 1998 Aravind et al paper on Aquifex which was 1st report of massive gene transfer between bacteria / archaea
- Side story: when Thermotoga genome paper came out (I was buried as middle author) Koonin called me, POd that we had not refd Aquifex paper
- @leonidkruglyak yes but this was a bit of a big deal ... Press coverage ... Nature paper, etc etc ...
- @leonidkruglyak The funny part was . He was POd at me even though I was buried in the middle b/c he said I should know better ...
- I must say Koonin is giving a damn excellent talk on bacteria and Archaeal evolution
- Koonin discussions how there is a central tree-like structure in the "forest of life" of trees of conserved genes
- Koonin discussions this: Comparison of phylogenetic trees and search for a ... http://t.co/9n9t27Q
- Koonin: there is a strong signal of vertical evolution even among much lateral gene transfer, b/c transfer is mostly random
- ATGC: a DB of orthologous genes from closely related prokaryotic genomes & a research platform for microevolutionhttp://t.co/uAUy5zl
- Koonin: "There is such a thing as a prokaryote" (gives many reasons)
- Koonin discussing my favorite topic these days: CRISPR-CAS system
- Koonin discussing his paper on early finding of crispr elementshttp://t.co/ksp1ZGA
- Prediction: A Nobel in the near future will go for work on CRISPR/CAS system of adaptive immunity in bacteria / archaea
- Koonin discussing the journal he helped start called Biology Directhttp://t.co/2sY75BX which is both #openaccess and has open review
- Koonin has a new Book: The Logic of Chance: The Nature and Origin of Biological Evolution: ProQuest Tech Bookshttp://t.co/94cvGr5
|Sloan Urinal (inside joke about http://microbe.net|
|Deck for party|
|Deck for party|
|Photosynth stiched together pic|
I then headed in to town where my friend Nipam Patel was having a party for the Embryology Course he was teaching. And I hung out as his house for a bit and then went back to my room.
Day 4: Home
Got up late. Checked out. Wandered into town with my suitcase. Took some pics.
And after some internal debate, decided to switch my flight to return that day rather than go visit relatives in Boston (sorry Diana, Hal --- just wanted to get home). So I took the Bonanza Bus to Logan - discovered that Karl Stetter was also going on the bus to Logan. I tried to watch the US-Brasil women's soccer game on my iPad using the wireless they have on the bus but it was choppy. So I just followed updates on the game - and even that was exciting.
Here are my tweets from the day:
- I'm at Pie in the Sky (10 Water St, Woods Hole)http://4sq.com/r0HOFh
- MBL -> BOS -> JFK -> SMF - sorry to leave microbial diversity course; wonder if @lancearmstrong will still be in #Davisca tonight
- Eel pond - Woods Hole, MA - last night #fb twitpic.com/5ob3ka twitpic.com/5ob3iy #fb
- Can't get away from the deepsea - even at Logan Airporthttp://t.co/3k8gX3t
- #Scienceart at MBL in Woods Hole twitpic.com/5oc5f0twitpic.com/5oc5bj twitpic.com/5oc5vd twitpic.com/5oc5fbtwitpic.com/5oc625