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Updated: 2014-10-28T08:36:44.196-04:00


Who's watching your dishwasher


I followed a link in this Seth Godin blog post to a video of a presentation given by Tim O'Reilly at a recent conference. The theme of the talk was the importance of data and data accessibility to future web based applications. I did not watch the whole thing, but a point he made about 10 minutes into the talk really struck me. He was talking about smart metering of electricity consumption.

Smart metering has been around for a while and is touted as a way to promote energy conservation by allowing consumers to observe their energy consumption habits. More sophisticated versions would also provide utility companies the information and control needed to allow them to balance loads and control levels of peak demand. In order for utility companies to gain information about consumption of individual appliances it was believed that each appliance was going to need to have some connectivity to the Internet, possibly in the form of unique IP addresses.

The cool thing that O'Reilly said was that people studying data from smart meters have discovered that each type of appliance and even appliances of the same type from different manufacturers have distinct energy consumption profiles. This fact along, with the appropriate reference dataset would allow data miners to identify the type of equipment being used from raw energy consumption data without any connectivity to the Internet or unique identifiers for each piece of equipment.

As O'Reilly himself states in his talk, there are clearly privacy implications for this use of the energy consumption data. However, the more interesting aspect is that it is yet another example of the unanticipated consequences of our ever increasing ability to collect, store and share vast quantities of information.

14 inch teeth!!


Fossil remains of a predatory whale related to the modern sperm whale were recently found in Peru. Their teeth were up to 36 cm (more than 14 inches) long.

The full report is behind a subscription barrier but a summary can be read here.

Eating oil


The productivity of modern industrial agriculture is a phenomenal technological achievement. The amount of food produced per unit of arable land has increased dramatically over the past 40 years. But, this productivity comes at a cost. Current high yield methods are resource intensive and are completely dependent on substantial inputs of fossil fuel. in a 2008 article in the New York Time Magazine author and journalist Michael Pollan puts it bluntly
"When we eat from the industrial-food system, we are eating oil and spewing greenhouse gasses."

Carbon is released into the atmosphere during multiple steps of the modern industrial food production process. CO2 sources include:

  • Release of carbon during the clearing and tilling of land
  • Production of synthetic fertilizers
  • Use of petroleum based pesticides
  • Energy consumed during the transformation of farm products into the highly processed products that makes up a large fraction of the modern american diet
  • Long distance transportation of food from farmer to consumer
  • and the fuel used by heavy farm equipment at multiple stages of the process

In fact, food production is second only to transportation for its relative impact on our carbon footprint. As a result, chainging our food consumption habits will help mitigate the impacts of climate change.



The discovery of antibiotics is one of the most significant medical accomplishments of the last century. Their impact has been profound. Along with improvements in sanitation and vaccinations, the use of antibiotics remains at the forefront of our largely successful efforts to control infectious diseases. As with PCR, we owe the availability of antibiotics to evolution. They are not invented, they are produced naturally by a variety of different organisms.

The modern era of control of bacterial infections began in 1927 with the discovery by Alexander Fleming that extracts from the mold Penicillium notatum lysed bacterial cells. He was not able to isolate the active compound but gave it the name Penicillin after the mold’s genus. The active compound was eventually isolated and developed into a therapy in the early 1940’s by a groups led by Chan and Florey. For their efforts, they shared the 1945 nobel prize for physiology and medicine with Fleming. The receipt of the Nobel Prize just a few short years after the introduction of penicillin as a drug speaks to the impact this medication had.

Many new antibiotics have been introduced since the 1940's but Penicillin and penicillin like antibiotics remain in wide use, comprising almost 20% of all antibiotics manufactured.

Image source



From the CDC website on Obesity
American society has become 'obesogenic,' characterized by environments that promote increased food intake, nonhealthful foods, and physical inactivity.
In 2007-2008 almost 70% of representative sample of 5,555 adults from the US population were found to be overweight or obese. 33% were found to be obese (defined as a BMI of 30 or greater)1.

1 Flegal et al 2010. Prevalence and Trends in Obesity Among US Adults, 1999-2008. JAMA 303:235-241

Flavobacterium columnare


I study the bacteria Flavobacterium columnare. It is a fresh water bacteria found all over the world. It is an opportunistic fish pathogen and is the cause of Columnaris Disease (CD). It infects many commercially important fish species. Outbreaks in aquaculture facilities are common. Costs associated with CD are high and represent a major barrier to the development of commercially viable aquaculture enterprises.

Outbreaks are brought on by stress and can occur suddenly. Mortality rates can reach 100%. The most virulent strains F. columnare kill susceptible fish within 24 to 48 hours, leaving little time for treatment.

CD is common in tropical aquaria where it is called by various names including, fin rot, tail rot and cotton mouth. These are frequently discussed on websites for aquaria hobbyist. The bacteria responsible is often identified as Flexibacter columnaris, an obsolete genus and species name replaced in the mid 1990. The characteristic fuzzy white growth the bacteria cause, often results in hobbyists mistaking it for a fungal infection.

CD also effects wild fish stocks. Outbreaks usually occur in the spring as the water warms. These outbreaks can be quite dramatic with hundreds or even thousands of moribund fish washing ashore covered with lesions. In less populous areas, these outbreaks go unnoticed. When they occur in lakes in populated areas, the fish die-offs make the news.

No one likes to see (or smell) tons of dead fish washing up on their shore.

China in Africa


Howard French has an article in the Atlantic describing the significant investments China is making to build infrastructure across Africa. Chinese investment in Africa currently exceeds $100 billion annually. China’s approach to development differs from the west. The west provides support primarily in the form of grants and heavily subsidized loans. China’s focus is on trade and investment in commercially viable enterprises.

In this model, China provides infrastructure development to Africa. In return, China gets access to the continents vast natural resources including iron, cobalt, copper and other minerals needed to feed its enormous manufacturing based economy.

The key question is if this openly capitalistic, investment based approach can offer sustainable development for Africa. Or, is China gaining access to the continents mineral resource for short term unsustained infrastructure improvements.

History shows that this concern is well founded. French illustrates this by describing a trip on the poorly maintained Tazara train line in Tanzania. The Tazara train line was built by the Chinese in the early 1970’s. It is as an example how mismanagement and corruption led to this big past investment failing to realize its potential.

Simply building infrastructure is not enough. In order to take full advantage of physical infrastructure improvements, investments to train the human capital needed to maintain the infrastructure is also needed. It is not necessarily the obligation of foreign investors such as China to do this, but if the goal is to help the continent develop, it is essential.

It all boils down to educating to empower the local population.

Nature's contribution to modern science


The polymerase chain reaction or PCR is central to much of the molecular biology research performed today. The technique was used for the human genome project, is used as the definitive test to identify many pathogens including H1N1 and is the basis for our understanding of the tree of life. Hundreds of thousands, if not millions of PCR’s are performed every day in labs all over the world. The enzyme used for PCR is called Taq Polymerase1. It is at the heart of the PCR reaction and it was not engineered by man. Rather, it evolved billions of years ago. It is a beautiful example of natures power to innovate.

Polymerases are a class of enzyme that catalyze the synthesis of a chain, or polymer, from component parts. Taq polymerase is a DNA polymerase, catalyzing the syntheses of DNA from nucleic acids. All living things have to have at least one DNA polymerase in order to synthesize the DNA required for growth and reproduction.

The exponential amplification characteristic of PCR stems from ability to repeat the reaction steps over an over again by cycling the reaction through a series of temperatures. These temperature steps include one at near boiling. This high temperature separates the double strands of DNA allowing each strand to be used as a template to synthesis more DNA.

Most enzymes (including most DNA polymerases) are not heat stable. They denature when heated and lose their activity, even after they are cooled back down. Taq polymerase isolated from the thermophilic bacteria Thermus aquaticus retains it activity after being heated to near boiling (95 °C). It is not active at 95 °C, but renatures and regains its activity upon being cooled. The ability of Taq polymerase it to remain active after repeatedly being heated allows the cycling of the PCR to create billions of copies of a target sequence from a single template using reagents added at the begining of the reaction.

1This was the first theromostable polymerase to be widely used. In the more than 25 years since its introduction, other heat stable polymerases have been introduced.

*last edited 11 May 2010 - minor edits and links added

clearly stated target outcomes are needed to form good policy


In my current job, I have participated in the planning and writing of several multi-million dollar grants. On more than one occasion I have been struck by how meager the planning process was. Programs are developed with little in the way of clear objectives, evaluation metrics or paths to sustainability. Of course, this problem is not unusual as Jeffery D. Sachs explains in the May issue of Scientific American:

During 14 months of debate over health care, the administration did not put forward a clear, analytical policy white paper on the aims, methods and expected results of the proposed reforms. Only the Congressional Budget Office’s budget scoring of legislative proposals was even partly systematic; no comparable independent analysis exists on other substantive issues. The actual health consequences of the legislation were never reviewed or debated coherently.

Happy Earth Day!



Green glowing frogs detect pollution


Just came across this article from last December about engineering tadpoles to express green fluorescent protein when exposed to pollutants. A strength this approach has over more traditional techniques is that the tadpoles only respond to bioavailable forms of target toxins.

Since this is fluorescence not luminescence, the detection would require at minimum a special light source and a filter. My first thought when seeing this was to wonder how they detect the fluorescence. According to the researchers this turned out to be “nontrivial.”

"Tadpoles aren't just going to sit still while you measure them. They're usually off and running."

Product literature available at the website of the company the researchers founded, WatchFrog, says that the method can be used to detect hormonal disruptors and heavy metals.

It is a microbial world!


Researchers scouring the world's oceans have been forced to drastically revise estimates for the number of microbial species residing there after a census indicated up to one hundred times the expected diversity may be present.
Qiu 2010. Nature Online

Open access mandated by law


This is excellent news! The big funding bill Bush just signed into law includes the provision that all NIH funded research be made open access within 12 months of publication.

Read more here.



It is an exciting time to be following progress in the field of microbial ecology. While the awareness of the abundance of microscopic organisms is not new, the development of new methods to observe the microscopic world continue to deepen our understanding. Some of these methods have been described briefly on this blog. See the entry on 454 sequencing for example.One of the most important techniques for modern microbial ecology and biology as a whole is the polymerase chain reaction or PCR. I suspect most of my modest readership is familiar with the technique, if any of you are not, it is something that you ought to take the time to learn about. A google search of the term PCR reveals a large number of pages devoted to explaining the technique. Many people have also developed diagrams and animations to aid in the understanding. The problem is, most of the good animations do not stand on their own. To make use of them, some background knowledge is needed.The best animation I have seen on the web is this one. Go ahead and look at both the amplification animation and the interactive graph showing the number of copies of the target molecule present after each cycle.Here are some things to keep in mind:DNA is a double stranded molecule and the two strands are held together by hydrogen bonds. Each individual bond is weak, the strength of the bonding between the two strands arises from the sheer number of individual bonds present. Key point for PCR: The bonding that holds the double strand together is easily disrupted by heat. Thus the 95 deg C stepsDNA is made up of 4 nucleotides: adenine, thymine, cytosine and guanine attached to each other along a sugar-phosphate backbone. The hydrogen bonding between the two strands of the double stranded molecule are between these nucleotides. The pairing of the nucleotides is specific. Adenine always binds with thymine and guanine with cytosine. Key point for PCR: knowing the sequence of one of the strands of the double stranded DNA makes it possible to deduce the sequence of the opposite strand.DNA polymerase is the enzyme required for PCR. The enzyme is capable of synthesizing double stranded DNA from single stranded DNA using the single strand as a template. The activity of this enzyme is specific in several ways. Most importantly for PCR:The nucleotide bases strung along the sugar-phosphate backbone of each DNA strand has directionality.a and each of the two strands in the double stranded molecule are oriented in the opposite direction. DNA polymerase can elongate in only one direction. Key point for PCR: the DNA polymerase must elongate each of the two strands from opposite ends.bDNA polymerase can not elongate single stranded DNA. A short fragment of double stranded DNA is needed. Key point for PCR: Small lengths of double stranded DNA need to be created flanking the region targeted for amplification (these are the primers).The exponential nature of PCR amplification depends on multiple cycles of amplification involving both strands of the double stranded molecule. Key point for PCR: Two primers are needed.The ingredients needed for a PCR reaction are:DNA polymerase - the enzyme.2 primers - Small fragments of single stranded DNA. These are used to produce short regions of double stranded DNA flanking the sequence targeted for amplification.Free nucleotides - These must be in the form of nucleotide triphosphates. In this form, they provide the source of the bases needed to build new strands of DNA and the energy required to drive the reaction.Template - some DNA containing the region that is to be targeted.When I teach people the basics of PCR, a question I use to assess comprehension is: How many cycles of amplification[...]

Bacteria and the cost of oil


(image) Oil is considered sour if it contains reduced sulfur compounds (sulfides) at concentrations of 1% or greater. High concentrations of sulfides in oil are problematic for a variety of reasons including:

  • Hydrogen sulfide is extremely corrosive and can cause damage to the pipes used to transport oil.
  • When complexed with other metals such as iron, the sulfides can form precipitates that restrict the flow of oil in the pipes.
  • Sulfides are toxic and cause environmental and health problems in areas where sour oil is produced, processed or burned.
Removal of sulfides is costly and so refining costs for sour oil is significantly greater than for sweet oil.

Souring of oil is exacerbated by the common practice of pumping water into older oil fields to increase the pressure in the fields as a way to increase oil recovery. Depending on the source of the water used, this practice can introduce large quantities of sulfate (SO4) into the oil/water mixture. Any oxygen present in the water when it is first pumped underground is rapidly consumed by microbial activity. Once the oxygen is gone, anaerobic microbes can contiune to extract energy from the organic mater present by using compounds other than oxygen as terminal electron acceptors. Sulfate reducing bacteria or SRBs are anaerobes that are able to use sulfate as an electron acceptor. The process results in the production of oxidized carbon compounds and reduced sulfur (sulfides). Biocides are often added to the water to inhibit microbial activity but this process is not efficient requiring enormous amounts of toxic compounds to be added to the water to have a lasting impact.

Thus, microbial activity in oil fields contributes the the cost of oil production. Microbial sulfide production is not limited to oil reservoirs. SRBs are also responsible for the 'rotten egg' smell associated with other anaerobic environments such as swamps and septic systems.

Kofi Annan's missed opportunity


(image) 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.

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.[...]

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.

Bacteriorhodopsin phototrophy


(image) 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 dog post?


This one is for ERV

(image) 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.

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.

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.

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