Eisen Lab Blog

“How many species exist?” Seminar, Mark Costello. Dec 7,Fri. 3:10 2342 Storer”

Just got this in email:

Mark Costello will be giving a seminar on Friday, December 7th, at 3:10pm in Storer Hall room 2342. His talk will focus on several of his recent papers on “Can we discover Earth’s species before they go extinct?” If you have any questions, please contact Eliot Crafton (recrafton).

Mark is an Associate Professor as the University of Auckland Leigh Marine Laboratory. His work focuses on biodiversity, ecology, biogeography, and ectoparasites with an interest in conservation. He has done extensive work looking at biogeography of marine species, including invasive species, and examining the biodiversity of the world’s oceans. This work has relied on both taxonomic records and statistical modeling of these systems. In addition, Mark has been an active participant in developing and proliferating access to biodiversity data, including positions as the founding chair of the World Register of Marine Species (www.marinespecies.org), President of the International Association for Biological Oceanography (www.iabo.org), and Vice-Chair of the Global Biodiversity Information Facility Science Committee (www.gbif.org), among several other positions. More information regarding Mark’s activities can be found on his university webpage, http://www.marine.auckland.ac.nz/uoa/home/about/our-people/dr-mark-costello/

Seminar Topic: ‘Can we discover Earth’s species before they go extinct?’

Mark will be presenting findings from several of his 2012 papers. Poor estimates of how many species exist on Earth and extinction rates, coupled with a perception of declining taxonomic expertise, have led to concerns that many or most species may be extinct before they are discovered. In contrast to widespread beliefs, we find that hyper-estimates of species richness cannot be supported, that there have never been so many taxonomists, and that extinction rates are not yet out of control. Thus most species are likely to be described within this century, especially if taxonomic productivity increases.

Predicting Total Global Species Richness Using Rates of Species Description and Estimates of Taxonomic Effort

Mark J Costello, Simon Wilson, and Brett Houlding

http://sysbio.oxfordjournals.org/content/61/5/871.short

The Magnitude of Global Marine Species Diversity

Appeltans et al.

http://www.cell.com/current-biology/retrieve/pii/S0960982212011384

Seminar “DNA repair in bacteria: from genomes to single cells”

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. Meriem El Karoui
(Lactic Acid Bacteria and Opportunistic Pathogens Unit, INRA)

"DNA repair in bacteria: from genomes to single cells"

Wednesday November 28, 2012

4:10 pm

1022 Life Sciences

El Karoui 11-28-12.doc

Returning to Walt Whitman High School, home of supposed overachievers

And now for something completely different … But I thought this might have some connection to the theme of this blog here since this was a bit about education …

Yesterday I was a member of panel of alumni from my high school Walt Whitman High School in Bethesda, MD discussing the book “The Overachievers”.

Why on Earth was there a panel of alumni from my high school discussing a book?  Well, there is a course at UC Davis “Integrated Studies Honors Seminar” which was for this quarter discussing the book The Overachievers. The book is by a WWHS alum (Alexandra Robbins) about WWHS students.  Anyway, Sharon Knox, a WWHS alum heard about this course and suggested to the instructor Jim Shackleford the idea of a panel of WWHS alumni to discuss WWHS with the students.  And thus the WWHS panel was born.

I got an email from Sharon a month or so ago inviting me to participate and found out there would be three other WWHS alums who are in the area involved.  Sue Greenwald (ex mayor of Davis and husband of one of my faculty colleagues Michael Syvannen.  Max Chertok – a UC Davis physics professor.  And Kim Addonizio a poet/artist living in Oakland.

Anyway .. the panel discussion was at 4 PM yesterday on campus at UCD.  I showed up a few minutes early, and eventually went into the room where I was the first of the WWHS alumni to arrive.  Eventually the others showed up as did the ~ 100 students and we had a somewhat interesting discussion of Whitman (we covered the 60s, 70s and 80s pretty well with the different people on the panel).  Most of what we discussed was whether we thought WWHS was somehow different in producing overachievers in some way.  Most of the panel felt that it was not really about the school – that it was really more about the demographic (in general this apparently agrees with the message of the book which also said WWHS was no unique in any special way).

Anyway – I don’t want to bore people with discussions of WWHS.  But one thing came up in the discussion with the students that was quite interesting and disturbing.  This relates to the excessive march towards having everything in K-12 be about preparing for college and about getting in to college.  Students are clearly more stressed these days about their futures.  They (on average — not everyone obviously) get tested and prodded and tested some more.  They have coaches and counselors and parents and others all telling them what they need to do.  And it seems they are less and less doing things they are passionate about and more and more doing things they think they should do.  This sounds bad.  Amazingly and sadly I even see this in my kids school.  And my kids are five and seven years old.  In Davis, there is, for example a “GATE” program for the supposedly gifted and talented students.  And kids get tested for this and if they score highly they can move into a completely separate “GATE” program – segregated from the other kids.  This program is very controversially right now in our town (e.g., see here)  and I personally think it should be dumped.  I must say I am pretty shocked by all of this.  Don’t we want kids to be able to just be kids.  To have fun?  To play a little bit?  Do they really have to have second graders getting stressed out about how they will do on a test to determine if they are gifted?  Uggh.  I mean – I am all for doing well in school and for education for educations sake.  But to plot out your kids lives when they are seven seems wacky beyond recognition.

Anyway – going to probably expand more into K-12 education issues here on the blog as my kids get more into the school system …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Water Chemistry

So I meant to post this yesterday, but I couldn’t figure out why it wouldn’t let me blog. Apparently my computer signs me off wordpress every so often so I have to sign back in.. So this information is from my time in the lab yesterday.

Dissolved oxygen, nitrate, and ammonia tests came with no reagents… really? It’s almost as if they expect us to have an abundance of reagents for nitrate test before we have the tools to run the test. Oops, our bad! So that’s a bit frustrating, but we ordered more reagents for everything which should come by tomorrow hopefully.

 

The Phosphorous and Nitrite kits came with a couple reagents (still annoying), but this allowed us to run a couple trial runs with them on salt water from one of the tanks. Alex did a few tests in the morning (check out her blog entry) and I did a few in the afternoon.
I’m glad I familiarized myself with the tests because I had to make a few modifications to the procedure, because it was just… not good. For example in these tests, you have to blank the meter (makes sense, right?) but then you have to add the reagents from a small packet into a small cuvette (harder than it sounds) and mix for at least two minutes according to the instructions. However, the meter turns off after two minutes. I solved this by having two cuvettes: one to blank the meter and one with the reagent in it.

 

Phosphorous gave a reading of 200 ppb, which leads me into our next problem. The meter maxes out at 200, so we can assume phosphorous is at a level higher than 200. We need to get another kit with a meter that measures a higher concentration of phosphorous. I measured Nitrite at 70 ppb, which was similar to what Alex measured.

 

I also measured pH at 7.46 and salinity at 48.3 mS

 

David and I hoped that the hardness and alkalinity tests would give similar results since they both test for CaCO3. If we had gotten the same result, we could eliminate one of the tests and save time. I measured alkalinity at 114ppm CaCO3. When I ran the hardness test, it didn’t work. I attempted twice and had the same result: failure. We’re thinking the test just doesn’t work with salt water? We’re going to look into it.

 

It was really good to familiarize myself with all the equipment because now when we begin our intensive sampling and testing of the succession of the coral ponds, I’ll be ready to go with those water chemistry tests!

 

And now we wait! We wait for an email telling us they’re going to load the water into the containers for the coral ponds. At this point we have a lot of sampling to do! I’ve decided to call it Occupy Bio Labs since we’ll be spending quite a bit of time in there 🙂

Water Chemistry!

Most of our new gadgets and gizmos for water chemistry have finally come in, so we have started testing them out. Some of the kits we ordered include tests for nitrate, nitrite, phosphorus, chlorine, hardness, sulfate, and iron. At first, we were testing the kits out on tap water to get comfortable with all the tests, and then Matt collected sea water samples from one of the tanks so we started using those.

Today I tried the nitrate kit, which has never been used before. It was a surprisingly simple and quick test, and I found 79.5 ppm (mg/L) nitrate in the sea water. Unfortunately, I do not know the significance of this value, so David suggested that I try the test on tap water for comparison. The amount of nitrate in the tap water sample was 23.2 ppm (mg/L). According to Wikipedia, marine aquariums are only supposed to have trace amounts of nitrate in order to be healthy, so I do not know what our values mean.

A few of the kits we ordered do not have the range to collect values from sea water, so we are thinking of diluting our sea water samples with DI water. We will then use that mixture to conduct the tests that did not work (i.e. the phosphorus and hardness tests). In order for this plan to work, however, there must be small amounts of chemicals in the DI water or our data will be skewed. I checked the level of phosphorus in the DI water and the value came out to be 34 ppb. I am not sure if this means that our dilutions will work, but I am sure we will be able to figure out how to analyze our data after doing some more research.

Water Chemistry Testing Acclimation

The water chemistry kits seem to be pretty straightforward, with a few nuances here and there. I conducted the titration-based tests as well as the tests to detect phosphorous and hardness. For the tests I used DI water to compare values, and so far the values I have been getting are comparable to values other people are getting, as well as make sense, which is good. 

So a few tips. The phosphorous meter turns off after a few minutes, and it will forget the blank sample. So it is a good idea to make the reagent+sample tube before you begin. 

Also, it is good to choose the low range of testings, because the high range is too much for our samples. 

Sample testing using new equipment

We finally got all our equipment for gathering metadata on the water, and decided to do some sample testing using tap water and saltwater from the tank. We ended up with the following:

 

Tap water –

NO2-N levels: 65 ppm

NO2 levels: 154.63 ppm

Phosphorus: 105 ppb

 

Saltwater –

NO2-N levels: [TRIAL ONE] 65 ppm, [TRIAL TWO] 57 ppm

NO2 levels: [TRIAL ONE] 213.85 ppm, [TRIAL TWO] 187.53 ppm

Phosphorus: [TRIAL ONE] 48 ppb, [TRIAL TWO] 200 ppb

 

Some problems we encountered: When I did the trial one on the saltwater phosphorus test, I used the wrong reagent (phosphate reagent is used for the nitrite scanner, while phosphorus reagent is used for the phosphorus scanner). In addition, the phosphorus scanner maxes out at 200 (Andrew later confirmed this by doing additional scans on the saltwater), which means we’ll need a broader range scanner.

Lab meeting Nov 27th 2012

We will be having a journal club for lab meeting.
Please bring a paper of your choice and be prepared to talk about it for 5 minutes or so.
We will be meeting in room 4202 of the genome center. We have the room reserved from 2 to 4pm.

CPB Tuesday Seminar: James Mallet – November 27, 2012 – 1022 Life Science

CPB Seminar Series: Fall 2012

When: Tuesdays, 4:10 – 5:30PM

Where: 1022 Life Sciences Building

November 27: James Mallet, Distinguished Lecturer

Department of Organismic and Evolutionary Biology, Harvard University


Title: “Hybridization and speciation in Amazonian butterflies: rainforest genomics”


Host: Rick Grosberg

Abstract:
It is a seductive idea that species are independent evolutionary units. Natural hybridization is rare in nature on a per-individual basis, but it may affect many species. Brightly-coloured Heliconius butterflies engage in Müllerian mimicry of other species. Although most of this mimicry is due to adaptive reconstruction of similar patterns, we’ve long suspected that colour patterns are exchanged among some closely related species that hybridize occasionally in nature. We have recently shown that genomic regions that determine mimicry have been exchanged repeatedly among species to form new, adaptive combinations. Through their joint effects on mating behaviour and signalling to predators, these novel colour patterns are also involved in triggering evolution of new species.

Trial and Error

First off I hope everyone had a great Thanksgiving break!
If you read Andrew’s previous posts regarding the project, you would know that we have decided to scrap all of the samples we have extracted DNA from and start from the beginning. This is so we will have water chemistry data collected at the same time as DNA is collected thus providing the most consistent and accurate data.

On Tuesday, we received a portion of our water chemistry kit, which tests Hardness, Sulfites, Alkalinity, Iron, pH, and Chloride. We decided to do a practice run on a couple of the tanks so we can familiarize ourselves with the reagents as well as fine tune our sampling procedure. The results are listed below:

Freshwater Tank A
Hardness Test: 93 ppm CaCO3
Sulfite Test: 2 ppm Na2SO3
Alkalinity Test: 90 ppm CaCO3
Iron Test: No detectable amount
pH: 7.3
Chloride Test: 20 ppm Cl-

Saltwater 1088
Iron Test: No detectable amount

We learned a couple of important points through this test run that will speed up our water chemistry sampling process in the future. For every single test we did, we started using the high concentration detection procedure, but found all of the concentrations in the tanks were extremely low, and had to redo it using the low concentration detection procedure. For our real samples that we will hopefully will be taking in the next week, we can save reagents and time and just jump right to the low detection procedures. We also noticed that the Hardness and Alkalinity tests detected the same molecule (CaCO3) and also had similar concentrations and have thus decided to use only one of the tests. (I will get back to you with the chemistry behind this reasoning, which I didn’t really understand). For both the Freshwater and Saltwater Test, we were not able to get a detectable amount of Iron and will likely scrap that water chemistry test. Lastly our pH meter results were a little different from Russell’s highly sensitive pH meter (pH=8.3) that takes continuous measurements and Tweets them. (Eisen is probably going to like the idea of that!) We will either scrap our pH meter and just use his or will have to verify if our pH meter is giving is accurate readings, by putting it in solutions of known low acidity. This is just an idea of mine, not sure if it’s a good way to check for its accuracy.

That’s where we are in the project as of Tuesday. I will get back to you about the differences between Hardness and Alkalinity and also update when we start taking samples again!