Storm Over-reactions and Italian Earthquakes

I have read a lot of facebook and twitter posts concerning over cautious storm forecasts.  One post made fun of a weather forecaster talking about a “cone of uncertainty” in the storm track. Lets contrast the doom and gloom we get in the US with what some say happened with the Italian seismologist. According to the prosecutor (see link to Science) they failed to assess and communicate the risks. My question is: do we want to know that there is a real non-zero risk when we live on the edge of the cone of uncertainty? I think we want forecasters to tell us when there is a risk, and when we might want to prepare for a natural disaster. However, we want them to be certain, and that is just not possible. I don’t think any one would prosecute weather forecasters for minimizing the threat for folks on the edge of the cone of uncertainty, but we would be very angry when they were wrong. As it is, we are just annoyed (and not dead or homeless) when forecasters seem to overstate the risk and we over prepare.


My Bad Writing

I started this blog in part to practice writing, but I have not touched it in almost a year. This is not good. It is not like I have not been writing. However, this is one of the causes of crappy writing, not rereading and rewriting your work. I have told people writing is rewriting, but I don’t seem to believe it! When I visited the blog today I thought I would post something about Strombidium purpureum (look it up). I ended up reading by last post and cringing. I have edited out some of the sentence splices and some sentences that added nothing to the post. I think that this might be bad blogging etiquette, but this is why I started the blog in the first place… I see some subject verb stuff that needs fixing and I am going to do it! I will probably have to fix this post too.

Picojonah Meets Microwhale

Colpoda is a common freshwater ciliate genus.  It is usually associated with moist soils and grasses.  First et al (2011) show the bacteria Campylobacter jejuni resists digestion by Copoda; to point that live bacterial cells are egested (not quite pooped, not quite puked).  Campylobactor jejuni is the leading cause of gastroenteritis.  I am sure that there is a micro-to-meso scale Leviathan out there for Colpoda, but that is different issue. The authors suggest the ciliate might act as a reservoir for the bacteria.

I have to wonder how common this is; could there be other advantages to surviving a digestive adventure.  First et al site papers that describe amoeba that pass live bacteria that actively resist their own digestion.  However, a couple of other examples come to mind.  Many fruit seeds pass through the digestive tracts of birds and other organisms.  This is the whole point of fruit; in exchange for a nice snack the plant gets its offspring dispersed farther than it would be possible otherwise.  Parasites like guinea worms must be ingested to survive and reproduce, and only leave the host for dispersal.  A percentage (about 15%) of Japanese land snails that are eaten by birds are still alive when “released.”  Dispersal is offered as an advantage for the snails but is seems like that might be a side effect of just making it out.  Of course, Luke, Jonah and Geppetto were spit up by their consumers through some action (their own or others).  Is Campylobacter: finding a refuge, using the ciliate as a dispersal agent, just riding out digestion like a snail, or are they Jedi?

Bob! what is that in your pants!? or We need a new sponge, this one is full of cyanobacteria!

There is a multitude of microbes to be found in non-square, non-pants-wearing, non-kitchen sponges. Many of these microbes are symbiotic, photosyntheticly active cynaobacteria (used to be blue-green algae). Cyanobacteria can provide the sponge with organic carbon (think sugar). This relationship is similar to dinoflagellates and corals. In “Complex interactions between marine sponges and their symbiotic microbial communities” Christopher J. Freeman and Robert W. Thacker inform us that the amount of organic carbon provided to the sponge from the symbionts varies from species to species. They also mention a previous observation by Thacker that not all sponge species have the same symbionts. They leave use with the question of whether the variation in symbiont organic carbon contribution is due to differences in sponge species (ie. the sponges’ ability to take up dissolved organic carbon) or the photosynthetic activity of the symbionts.

The link:

The abstract:

To investigate the importance of symbiont-derived nutrition to host sponges, we coupled manipulative shading experiments with stable isotope analyses of isolated symbiont and host cell fractions. Experiments were conducted with four common reef sponges: Aplysina cauliformis, A. fulva, Neopetrosia subtriangularis, and Niphates erecta. The sponge N. erecta lacks photosymbionts, had a higher growth rate under shaded conditions, and displayed no difference in chlorophyll a (Chl a) concentrations across treatments. Isotope values suggested that this sponge obtains nutrition from particulate organic matter in the water column. In contrast, sponges hosting cyanobacterial symbionts (Aplysina spp. and Neopetrosia) had lower growth rates and lower Chl a concentrations under shaded conditions, suggesting that these hosts rely on photosymbiont nutrition. d15N and d13C values of sponge and microbial cell fractions demonstrated that, while both carbon and nitrogen are transferred from symbionts to host cells in A. cauliformis, only carbon is transferred in N. subtriangularis, and only nitrogen is transferred in A. fulva. Under shaded conditions, shifts in symbiont d13C values were coupled to shifts in host d13C values in some, but not all, host species, suggesting that the stability of these interactions varies across host species. Symbiont-derived nutrients are transferred to the cells of host sponges, and the variability observed among host species indicates that these interactions are more complex than originally hypothesized.

I know there are no protists, but I liked the paper.

Blog CPR needed

Ok I have let this thing slide… but I hope to resuscitate it, today even!

Bill Nye is my master now

Automated microbiology

I am not a molecular biologist… I see it all the time, it lives on the other side of the lab where DNA is extracted, amplified, and sequenced; often so that a particular microbe can be identified or detected. So my perception of it is that it is something that is generally done very carefully in a very clean environment. “I think this is contaminated” is something I have heard from that side of the lab. When trying to ID a cultured critter contamination from another coulter could give you a false ID. When trying to detect a critter from say, a water sample contamination from another water sample or a culture can give you a false positive.

These apparently persnickety techniques are extremely useful for doing things like detecting the presence of toxin producing algae. There are a bunch of algae species that produce a range of toxins that in turn have a range of effects on other organisms. Because these algae can have a significant economic and human health impact you really want to keep track of them; you want to know when and where they are most abundant, where they are going and how they got there.

Monitoring is a pain, it is long term and expensive. It often seems more rewarding to do (relatively) cheap experiments that yield lots of data quickly (I definitely take this way out). Using a persnickety technique to monitor toxin producing algae could be a double pain in the ass… if you are doing it all by hand. Bring on the automation.

Here is a project that used automated molecular biology labs to monitor coastal waters for toxic algae in Monterey Bay (Ryan et al 2011). On the same buoy that the molecular “lab” were also instruments for measuring a range of other chemical and physical parameters. They also deployed underwater autonomous vehicles, while the buoys are stationary these roam and gather data (mostly physical, some time chemical) on the water bweteen buoys. So, lots of instruments in the water collecting a ton of data. Oh, and don’t forget the satellites (I am not kidding).

What did they learn from all those measurements? They put it this way:

The molecular analytical and environmental observingnetwork revealed clear relationships between environmentalconditions and HAB species composition in MontereyBay.

So which harmful algal bloom (HAB) forming species was present relied heavily on environmental conditions. Some might of guessed that was the case but the interesting thing is the correlation between toxic diatoms and strong upwelling (surface water is pushed off shore and colder more nutrient rich deep water comes up to replace it) and dinoflagellates and weaker upwelling.

If you can correlate things like wind driven upwelling with toxin producing algal species then you can predict when a bloom might occur and plan appropriately.

The abstract

Using autonomous molecular analytical devices embedded within an ocean observatory, we studied harmful algal bloom (HAB) ecology in the dynamic coastal waters of Monterey Bay, California. During studies in 2007 and 2008, HAB species abundance and toxin concentrations were quantified periodically at two locations by Environmental Sample Processor (ESP) robotic biochemistry systems. Concurrently, environmental variability and processes were characterized by sensors co-located with ESP network nodes, regional ocean moorings, autonomous underwater vehicle surveys, and satellite remote sensing. The two locations differed in their longterm average physical and biological conditions and in their degree of exposure to episodic wind-forced variability. While anomalously weak upwelling and strong stratification during the 2007 study favored toxigenic dinoflagellates (Alexandrium catenella), anomalously strong upwelling during the 2008 study favored toxigenic diatoms (Pseudo-nitzschia spp.). During both studies, raphidophytes (Heterosigma akashiwo) were detected within a similar range of concentrations, and they reached higher abundances at the relatively sheltered, stratified site. During 2008, cellular domoic acid reached higher concentrations and was far more variable at the shallower ESP node, where phytoplankton populations were influenced by resuspended sediments. Episodic variability caused by wind forcing, lateral mixing, internal waves, and subsurface phytoplankton layers influenced ESP detection patterns. The results illustrate the importance of mobilizing HAB detection on autonomous platforms that can intelligently target sample acquisition as a function of environmental conditions and biological patch encounter.

The L&O link (I think this is free access)

The Ref

Ryan, J., D. Greenfield, R. Marin III, C. Preston, B. Roman, S. Jensen, D. Pargett, J. Birch, C. Mikulski, G. Doucette, and others. 2011. Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnol. Oceanogr 56: 1255–1272.