Matt Reusswig's Weblog

Month: September, 2007

Multifunctionality and Interviews

Just found this short interview Hector gave where he discusses the paper I wrote about in the last post.

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Multifunctionality and Biodiversity

Here’s a relatively new paper (Hector & Bagchi; 2007; Biodiversity and Ecosystem Multfunctionality; Nature 448, 188-190) that looks at the effects of species richness on multiple ecosystem functions/services. It takes a very novel approach (such that I doubt I can comment all that intelligently on it) in that Hector & Bagchi eschew the typical statistical models used in these types of studies and adopt an information theory mode of analysis.

Here’s the abstract:

Biodiversity loss can affect ecosystem functions and services. Individual ecosystem functions generally show a positive asymptotic relationship with increasing biodiversity, suggesting that some species are redundant. However, ecosystems are managed and conserved for multiple functions, which may require greater biodiversity. Here we present an analysis of published data from grassland biodiversity experiments and show that ecosystem multifunctionality does require greater numbers of species. We analysed each ecosystem function alone to identify species with desirable effects. We then calculated the number of species with positive effects for all possible combinations of functions. Our results show appreciable differences in the sets of species influencing different ecosystem functions, with average proportional overlap of about 0.2 to 0.5. Consequently, as more ecosystem processes were included in our analysis, more species were found to affect overall functioning. Specifically, for all of the analysed experiments, there was a positive saturating relationship between the number of ecosystem processes considered and the number of species influencing overall functioning. We conclude that because different species often influence different functions, studies focusing on individual processes in isolation will underestimate levels of biodiversity required to maintain multifunctional ecosystems.

Emphasis added.

The results seem pretty intuitive. I can’t recall any papers off the top of my head that support this assertion, but it seems like between species low overlap in realized niche should require differing between species contributions to a given function. And as you add species/competition, the dominance overlap between functions should shrink as (generally) competition will shrink the realized niches of all species (ie more functional dominants due to differing comparative advantage).

A very nice paper. It would be interesting to see someone do something similar with activated sludge reactors as microbial non-culture methods continue to improve.

Update: Or a constructed wetland may be better since there is less direct selection against microbial metabolic diversity. One could look at functions that are important from an engineering perspective like nitrogen transformations and removal (where there would be necessarily low overlap) species membership and map it with other less obligately metabolic functions like CBOD removal, total phosphorous removal and NPP.

Metagenomics and Colony Collapse Disorder

For those of you still interested in bees and the CCD issue, Jonathan Eisen has a brief comment up on the methods used in the paper I pointed to before.   To wit:

Now – I am not sure if this method is quantitative or exactly how robust it is, but it does provide an alternative to rRNA PCR (which has all the biases of PCR) and also provides an alternative to separately sequencing RNA and DNA from a sample. Certainly many have used RNA to cDNA and then sequencing to survey RNA viruses before. But usually they do this in material in which the cellular organisms have been first removed so that one does not get overwhelmed by the RNA from those organisms. But here, they used the power of massively high throughput sequencing and turned this “problem” of getting RNA from cellular organisms on its head and used it to sample RNA viruses and cellular organisms at the same time.

Drawing Lines

Now, this is a a mission statement. Here’s Yudowsky’s money quote:

Orwell was clear on the goal of his clarity:

If you simplify your English, you are freed from the worst follies of orthodoxy. You cannot speak any of the necessary dialects, and when you make a stupid remark its stupidity will be obvious, even to yourself.

To make our stupidity obvious, even to ourselves – this is the heart of Overcoming Bias.

Evil sneaks, hidden, through the unlit shadows of the mind. We look back with the clarity of history, and weep to remember the planned famines of Stalin and Mao, which killed tens of millions. We call this evil, because it was done by deliberate human intent to inflict pain and death upon innocent human beings. We call this evil, because of the revulsion that we feel against it, looking back with the clarity of history. For perpetrators of evil to avoid its natural opposition, the revulsion must remain latent. Clarity must be avoided at any cost. Even as humans of clear sight tend to oppose the evil that they see; so too does human evil, wherever it exists, set out to muddle thinking.

Svelte Information

Superfund 365 is a cool site.

I recommend checking it out even if your not into environmental remediation–if nothing else, S-365 communicates a great deal of complex information in an incredibly elegant manner. Some of symbols can be difficult to parse at first, but if you poke around a little bit you can find keys and explications for the more occult hazardous rankings, ratings, etc.

But even more, what S-365 does really well is illustrate the complexity of these places and the administrative, legal, and financial wastelands in which they can persist for decades.

Here’s a pair of sites that set this out well:

First, take a look at the page for Old Roosevelt Field. The first things I notice are:

  1. There are only four chemicals to remediate (although the contaminated area is big–1.3 square miles). All four are volatile organic contaminants in the groundwater which means they’ll be relatively easy to clean up, say, with an air stripping system.
  2. There are no listed responsible entities, which makes it an orphan site. All the clean-up costs will come from the Superfund (there is an actual pool of money-hence the name) that congress set-up in 1980, which is significant because it means that the money isn’t coming from the organizational entity that caused the problem–its listed as a pre-WWI US Army site which is presumably how it was contaminated.
  3. The administrative examination/approval as a Superfund site and clean-up assessment went fast. Two years for this sort of thing is nothing.

Now look at the page for the Universal Oil Products Scientific Chemical Processing site.

  1. Notice the large, diverse set of contaminants and that they can be found in several media. Compared to the other site, these will require a comprehensive (and probably much more expensive) remediation plan.
  2. Roll your mouse around that solid looking ring around the contaminant arrows. Those are all responsible entities associated with the site. The shear number of companies and organizations involved here are likely to turn the project into a morass of legal and public wrangling which will last for decades (and clearly it has been going on since the early 1980’s).
  3. It took this project 10 years to accomplish what was accomplished at the Old Roosevelt Field site in two. You (and, honestly, I) can’t imagine the amount of legal maneuvering and public lobbying that goes into organizing this sort of clean-up; and, as I mentioned above, it takes many years to get the EPA, the public, the NGO’s, and the companies themselves to agree on, follow through with, and pay for a framework for cleaning up a Superfund site. This can be further complicated as the companies who did the original polluting go out of business (which does happen pretty frequently in the States) over the span of the administrative and engineering technology assessment phases at the “beginning” of the project (which, again, can last anywhere from a couple years to decades).

The upshot of all this complicatedness is that the clean-up gets more expensive both for the companies and the public. In fact, when the companies dissapear, the sites become orphaned and taxpayers foot the entire bill.

I haven’t looked into it, but it would be interesting to find out whether (from a cost-benefit point of view) its cheaper for the taxpayers to pick up the tab from the get-go in terms of lowering health-risks due to public exposure reduction to the sites and elimination/defraying of legal costs. On the other hand, it would remove a huge incentive that companies have to keep sites clean and to remediate them when there not.

Don’t forget that, though these sites are a big headache for the public and the EPA, the companies want to avoid these situations as well. Its no mistake that most of the existing Superfund sites were contaminated prior to the revolution in environmental regulation that has occured in the last thirty to forty years.

UPDATE For some reason half of this post didn’t show up when I put it up last night. This has been fixed.

Synthetic Biology

Check out this gallery of origami insects & animals!   They’re the work of Japanese artist Taketori.

Hat Tip:  Aptly named Neatorama

BEES

It looks like the famously cryptic source of the bee problem (AKA Colony Collapse Disorder) that has been in the news off and on the past six months may have been identified in a new paper in Nature.

Heres the abstract:

In colony collapse disorder (CCD), honey bee colonies inexplicably lose their workers. CCD has resulted in a loss of 50 to 90% of colonies in beekeeping operations across the United States. The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD. We used an unbiased metagenomic approach to survey microflora in CCD hives, normal hives, and imported royal jelly. Candidate pathogens were screened for significance of association with CCD by examination of samples collected from several sites over a period of 3 years. One organism, Israeli acute paralysis virus of bees (IAPV), was strongly correlated with CCD.

Whole paper here. Slightly less technical bee related material can be found here.

Science Skin Deep

Carl Zimmer‘s been collecting images of science related tattoos and the one pictured below is my favorite so far (although this one is pretty great too).

Homonculus Tattoo

This is what Scott Pitnick (the individual pictured) had to say about his tattoo:

“I’m an evolutionary biologist who investigates the evolution of sperm form, sperm-female interactions and sperm competition. So…yeah, it’s pretty much about sperm. Wanted to bring the concept of the homunculus to life, as all illustrations of it have always been rather cartoonish. Found a guy (Anil Gupta at Inkline Studio) with the skill and creativity to do it justice.”

Zimmer has posted his collection to a flickr group which you can see here. Anil Gupta is worth checking out as well.

Sewers, Spelunking, and Photography

                     Vanishing Drain; Micheal Cook

The BLDBLG has an amazing interview up with Micheal Cook, a photographer who explores urban subterranean spaces.    His photos are pretty spectacular in and of themselves, but his work also provides those of us who are into sewers (figuratively/occasionally literally) with a document of the knotty geography that exists below our feet.  The interview is a nice complement to an older post on BLDBLG about the London sewer system.

Theres a lot of sewer down there.  For example, the City of Chicago currently manages 4,300 miles of sewer (not counting however much pipe has been abandoned in situ).  And the EPA estimates that it will cost $390 billion to replace all the pipe that will need to be replaced over the next 20 years.