Thursday, July 19, 2007

Kofi Annan's missed opportunity

Here is one of the many articles this week in overseas papers covering the announcement that the new organization, Alliance for a Green Revolution in Africa or AGRA led by the former UN chief Kofi Annan will attempt to engineer a green revolution in Africa without the aid of genetically modified (GM) crops. This decision is very short sighted.

From the article:
Conventional methods of farming have not yet been applied to the fullest extent in Africa. Simply working with conventional breeding, we can do a lot,' said Joseph De Vries, programme director with AGRA.
Yes, but, with GM crops, even more could be done. I understand that GM crops are controversial and many people find their use disturbing. However, on a continent where so many go hungry, closing the door completely on a technology that has the potential to improve the drought and pest resistance of important crops makes no sense. One of AGRA's primary goals is to improve "crop varieties for larger, more diverse, and more reliable harvests". How can anyone suggest that in this day and age, GM crops have no role to play in this endeavor?

The genie is out of the bottle. GM crops are here to stay. They should stay. On a planet with 6 billion people and counting, the potential they offer to increase yields, reduce chemical usage and expand arable land is too great to ignore.

The big challenge with the development of GM crops (and the aspect that I am most uncomfortable with) is that too many decisions about which traits to manipulate and what risks are worth taking are made by big agribusiness. This is where Annan's new organization could have played a constructive role. AGRA is headed by a former Secretary-General of the UN and bankrolled by the Gates and Rockefeller foundations to the tune of $150 million. Such an organization has the potential to be a powerful voice in the debate over the best use of GM crops for improving the quality of life and sustainability of agriculture in Africa.

By this decision, AGRA has removed itself a discussion that will occur whether they chose to participate or not.

Wednesday, July 18, 2007

Gecko/mussel hybrid velcro

This looks cool:

A reversible wet/dry adhesive inspired by mussels and geckos

Lee, Lee & Messersmith
Nature 448, 338-341 (19 July 2007)

From the abstract:

Researchers have attempted to capture these properties of gecko adhesive in synthetic mimics with nanoscale surface features reminiscent of setae; however, maintenance of adhesive performance over many cycles has been elusive and gecko adhesion is greatly diminished upon full immersion in water. Here we report a hybrid biologically inspired adhesive consisting of an array of nanofabricated polymer pillars coated with a thin layer of a synthetic polymer that mimics the wet adhesive proteins found in mussel holdfasts. Wet adhesion of the nanostructured polymer pillar arrays increased nearly 15-fold when coated with mussel-mimetic polymer. The system maintains its adhesive performance for over a thousand contact cycles in both dry and wet environments. This hybrid adhesive, which combines the salient design elements of both gecko and mussel adhesives, should be useful for reversible attachment to a variety of surfaces in any environment.
Check out the gecko images here:

Stability - Diversity relationships

I mentioned in this post, my concerns about speculations by Xu et al on the role of the human host in the maintenance of a diverse gut microbial community. The proposed benefit to us is that the high diversity encouraged stability and assured that our guts continued to provide the desired services, but the mechanism by which we control diversity was not clear.

An article by Ives and Carpenter in a recent issue of the journal Science makes it clear that Xu et al. are in good company. Ives and Carpenter state that we lack of a good understanding of the relationship between diversity and stability in part because term stability is actually used in several related (but distinct) ways in the ecology literature.

Understanding the dynamics of complex systems such as the human gut is challenging. Here is the background knowledge Ives and Carpenter suggest is necessary for beginning to develop an understanding of the diversity/stability relationship:

Before designing an empirical study, it is necessary to know enough about the dynamics of an ecosystem and the environmental perturbations that impinge upon it to select appropriate definitions of stability; there will often be several appropriate definitions. These concepts also identify key features—we will refer to them as mechanisms—that together dictate stability. These mechanisms involve the strength of interactions among species, the mode in which species interact (whether they are competitors, predators, mutualists, etc.) that gives the food-web topology, and the ways in which species experience different types of environmental perturbations. Because both species interactions and environmental perturbations can drive fluctuations in species densities, these must be sorted out and quantified to understand their mechanistic roles in diversity-stability relationships.

And, here is a excerpt from the recommendations they make at the end of the paper:

The relationship between diversity and stability has interested ecologists since the inception of the discipline (35), and the absence of a resolution reflects the complexity of the problem. Much of the complexity derives from the multiplicity of diversity-stability relationships, depending on the definitions of diversity and stability and on the context in which an ecosystem is perturbed. We cannot expect a general conclusion about the diversity-stability relationship, and simply increasing the number of studies on different ecosystems will not generate one.

Rather than search for generalities in patterns of diversity-stability relationships, we recommend investigating mechanisms. A given diversity-stability relationship may be driven by multiple mechanisms, and the same mechanisms may evoke different diversity-stability relationships depending on the definitions of diversity and stability. We need more studies revealing exactly what these mechanisms are. This requires models joined to empirical studies that can reproduce, in a statistically robust way, not only a diversity-stability relationship but also the dynamics exhibited by a system.
The human gut community does exhibit characteristics of a stable system such as the ability to resist perturbations. So, what are the mechanisms that maintain the diversity, what is the diversity stability relationship and how do we go about studying it.

Monday, July 09, 2007

More on human guts

Yet another interesting open access gut microbe paper in PLoS Biology came out in June. This one describes patterns in the colonization of the intenstines of human infants. As mentioned in a previous post, we are born with a sterile intestinal tract and depend upon the ingestion of compatible microbes for the establishment of our gut community. This study used 16S rhibosomal DNA sequences to document changes in the structure and diversity of infant guts over the first year of life. As with the previous paper, Liza Gross wrote a nice summary article.

Some key points:

  • 14 babies were followed (including one set of twins) for one year. Early the communities were quite different but by the end of the first year they had acquired a composition similar to that of the adult human.
  • At one week of age, two babies delivered by cesarian had fewer total gut bacteria indicating that during natural child birth, the colonization begins during the birthing process.
  • While broadly similar to each other and to the adult community, each infant had a distinct profile that persisted over time.

This paragraph from the end of the Gross summary provides a good overview of the most interesting findings:
The idiosyncratic nature of the early stages of colonization suggests that a baby’s initial bacterial profile largely results from incidental microbial encounters. The fact that some of the early stool samples matched their mother’s breast milk or vaginal sample supports this interpretation. Shared environment may also explain the coincidental appearance of microbes in the twins. The researchers explain the tendency of these communities to eventually converge by hypothesizing that the human–microbe symbiosis has likely evolved under strong selection and that certain well-adapted microbes repeatedly “win” the battle over the opportunistic early colonizers.
Selections from the final paragraph describes some of the future directions the work will take:
By comparing the surprising range of microbial profiles found in these healthy babies to the microbiota of infants born prematurely or with health problems, future studies can explore how diet, delivery method, or other factors might spell the difference between health and disease.
and that the approach used in the study will allow us to explore questions about
the environmental and genetic factors that shape and personalize the amazing “alien” ecosystem that lives within us.

Saturday, July 07, 2007

Bacteriorhodopsin phototrophy

Classification of the metabolic capabilities of microbes can be challenging. With few exceptions, macroorganisms are either photosynthesizing primary producers (photo-autotrophs) or consumers (organotrophs or more commonly, heterotrophs).

For microbes, the story is more complicated. In addition to phototrophy, microbes can be chemo- or litho-trophs meaning they are able to derive energy from the oxidation of inorganic compounds such as reduced sulfur. If they can use light or chemical energy to fix carbon, then they are considered autotrophs. If the energy they acquire can be used to synthesize ATP but not to fix carbon, they are dependent on external sources of organic carbon making them mixotrophs.

An example of a phototrophic mixotroph is pictured above. These are salt loving haloarchaea in salt production ponds near (in?) San Francisco. The red color is due to the transmembrane protein bacteriorhodopsin. Using this protein some haloarchaea can harness sunlight to pump protons across their cell membrane. This establishes a proton gradient across the membrane. This gradient can be used to generate ATP.

There is a large number of scientific papers on bacteriorhodopsin because of its relative simplicity, it has become a model system for the study of membrane associated ion pumps.

Image from here

These salt ponds are near San Francisco. If you want another view of the bay area ponds follow this link, select the satellite map and zoom way in. I tried this for a few of the other places I know these salt production ponds exist but the satellite images did not provide good enough resolution. An example is Bon Aire in the Netherlands Antillies

Friday, July 06, 2007

Friday dog post?

This one is for ERV

This photo won us a years supply of dog food at a local fundraiser a few years ago. The muzzle has gotten whiter since then. It may be due to the fact that he now shares the house with two young kids.

Thursday, July 05, 2007

In The Bay 3 July 2007 II

Another diatom this time. Striatella unipunctata in girdle view. These cells form chains with adjacent cells often attached by the corner as seen at the top if this image.

400x phase contrast image.

This week at the CSA

Just back from the local CSA. Here is some of what we picked up:

Find one near you

Sustainable education

The most recent issue of the journal Nature has a review (behind a subscription barrier) of a new book: Degrees that Matter: Climate Change and the University by Ann Rappaport & Sarah Hammond Creighton. I have not read the book but some of the information is interesting.

The book documents a 15 year effort by Tufts University that began in 1991 to reduce its energy consumption. From the review:
The central observation from Degrees that Matter is that universities are in a unique position to offer leadership on climate change and carbon emissions through their educational, research and wider roles in society.
The conclusion is a bit disheartening:
The bad news is that despite the intense programme, carbon emissions at Tufts — both net and normalized — seem to have increased over time. The university as a whole has become more energy intensive, with the consequence that it will not meet its Kyoto target. This should, however, be set against other higher-education institutions, where the rate of increase over similar time periods is much greater and the reversal of trends, if at all, much slower. A large part of the increase is due to growing demands from personal equipment.

I assume the "personal equipment" are computers which consume an enormous amount of energy.

Wednesday, July 04, 2007

In the Bay 3 July 2007

Since I wrote about marine cilliates in my previous post, I thought I'd try to find some for this edition of In The Bay.

This is a group of Vorticella or Vorticella-like stalked cillates. As you watch the movie you can see the feeding current they are creating with their cillia. About 21 seconds into the movie (6 seconds from the end) the whole colony retracts. This is a defensive mechanism and occurs extremely fast.