Phosphorus

The fact that our overreliance on fossil fuels is quickly draining easily accessible resources is becoming more known in the public. Now there is talk on several scientific and environmental radio shows that warn of declining phosphorus reserves.
The concern over a possible phosphorus shortage may seem contradictory to observations of increased algal blooms and eutrophication of inner water streams – a phenomenon where increased chemical nutrients in the environment lead to algal blooms and suffocation of aquatic life with detrimental  consequences to the environment – which at least in part are caused by increased bio-available phosphorus.

All this lead me to the question: Is there really a phosphorus shortage?

Phosphorus is the 15th element on our periodic table. In nature phosphorus never exists in its elementary form due to its reactivity [1]. Phosphorus is one of the essential elements of life because it is part of many structures in living cells from simple bacteria to complex multi-cellular organisms such as plants and animals.  For instance, the cell membrane containing each cell consists of phospholipids, and the backbone of the information carrying molecules DNA and RNA consist of phosphate groups as well.  For this reason, plants require phosphorus when growing: They absorb it through the roots in the soil. Animals, too, require phosphorus. But different from plants which can derive the needed phosphorus from the environment, animals rely mostly on other animals or plants to take up phosphorus by eating them.

What is the link between fertilizers and phosphorous?

Knowing that phosphorus is an essential element of life probably makes it less surprising to find that it is part of any fertilizer.
The interesting question was to ask where the phosphorus comes from. Historically, animal or human feces were commonly used for fertilizers because they naturally contain phosphates (and other essential nutrients of course). In fact, it was through boiling, filtering and processing of about 60 buckets of urine, how Henning Schmidt discovered phosphorus back in 1669 [2].  Today, organic matter has in many parts of the world been superseded by the use of modern synthetic fertilizers which use phosphate rocks as a source for raw material, which, interestingly, are only found in a few countries such as China, Russia, Morocco and part of the United States [1].
Phosphate rock, just like coal, oil, and other forms of fossil fuels, is a non-renewable natural resource. And this is the crux of the matter: Because we rely so much on synthetic phosphate fertilizers, the rate at which we consume the phosphate rock is rapidly increasing while the natural stocks are decreasing. In this context, Hubbart’s name is frequently mentioned who first observed and predicted in 1949 that oil will at some time reach a maximal rate of production when about 50% of the resources are still in the ground, after which production rates will go down. However, if demands are going up at the same time and costs for the raw material will likely increase as well [3,4,5]. This, Hubbart called “peak oil”, but it appears that the same fate will be true for phosphate rocks as well: There will be “peak phosphorus” in form of phosphate rock deposits that are quickly declining. But there is one big difference, however: Unlike oil, where alternatives exist for sources, there is no alternative for phosphorus. It is essential for life.

“Where do eutrophication and algal blooms come from?”, you ask…

 This leaves us with the question why algal blooms and eutrophication are happening more and more often? Ironically, it is in some parts due to excessive phosphorus leaking into water streams. Overfertilization, discarded animal feces, and human feces in large cities often lead to phosphorus leakage into the natural water cycle where they stimulate excessive algal growth. The problem is partly due to the current economic model which currently promotes a very linear and inefficient use of phosphorus. Simplified, phosphorus is added to plants, which will then be eaten by food stock animals or humans. Humans and animals then use some of the phosphorus for their own body and excrete the rest again. A lot of it nowadays is flushed away, into the waste water stream where it is not always cleaned before release. This leads to the aforementioned problems.

Synthesis

There are a couple of interesting observations to make:
1.)    The poorest agricultural lands are being exploited because those who can afford it first need to import phosphorus and from one of the other countries. The farmer then applies the fertilizer to grow crops, exports these crops (and thus part of the phosphorus goes away although it is most needed in the poorer country.
2.)    So ironically, although phosphate rock deposits are rapidly declining, the concentrations of phosphates in the water is partly to blame for current problems. What then is the solution to the dilemma? Instead of the often linear processes which includes mining/manufacturing/discarding, new methods of phosphorus recovery should be searched and applied.
3.)    Declining phosphorus reserves, and the resulting price increases will also affect 1st and 2nd generation biofuel production.

Literature Cited:

1.)    http://en.wikipedia.org/wiki/Phosphorus
2.)    http://en.wikipedia.org/wiki/Hennig_Brand
3.)    Cordell, D., Drangert, J.-O., and White, S., (2009) The Story of Phosphorus: Global food security and food for thought. Global Environmental Change, 2009. 19(2009): p. 292-305
4.)    http://www.energybulletin.net/node/33164
5.)    http://phosphorusfutures.net/peak-phosphorus

Journal Club:" Correlation of cellulase gene expression and cellulolytic acticity throughout the gut of the termite Reticulitermes flavipes."

It has been a while since the last contribution to this site. Today’s blog entry shall be a summary of a journal article that a couple of friends and I started recently to educate ourselves on topics related to bio-based ideas that are of interest to us. Recently, I came across a general article in the Scientist that talked about biofuels production. The article mentioned integrated biofuel productionpipelines that could include the breakdown of agricultural waste products containing cellulose.

Cellulose is a complex sugar, meaning that it consists of long-chains of individual simple sugar units such as glucose. The glucose that is released from the breakdown of cellulose could be used for bioethanol production. But it turns out that cellulose is a very sturdy material that is difficult and energy intensive to break down. One way to reduce the cost of break-down would be to rely on enzymes that are known as biological catalysts. Catalysts can reduce the activation energy which is the energy required to get a given reaction started. Most organisms do not have the necessary enzymes to break down cellulose. However, there are some organisms that do have them. Among these organisms are the termites.

Curious to learn more about cellulases, the enzymes that break the links between each glucose unit, in termites, we picked an article with the following title:

 “Correlation of cellulase gene expression and cellulolytic acticity throughout the gut of the termite Reticulitermes flavipes.”

The authors in this paper used metagenomics approach to identify four open reading frames, predicted genes, in the sequences of the recently sequenced Reticulitermes flavipes. They then showed by PCR that these open reading frames are also expressed. The four genes are called Cell-1, Cell-2, Cell-3 and Cell-4. Cell-2 in particular was found to have at least one intron due to the fact that the genomic DNA sequence was larger than the cDNA sequence. Cell-1 was found to be highly similar to other termite cellulases. The other cellulose genes were more similar to symbiotic cellulases, meaning that these cellulases are not produced by termites themselves but by their prokaryotic symbiotic partners. Aligning Cell-2 to Cell-4, showed that only Cell-2 was lacking certain “tunnel forming loops” which are characteristic of exoglucanase. Cell-2 was then characterized as an endoglucanase.

The authors then looked at expression of the cellulose genes. They found that Cell-1 was mainly expressed in the fore-gut and salivary glands, while the remaining cellulases are expressed in the hind-gut. Characterizing endoglucanases, exoglucanases, and xylanases with respect to the location showed a strong bias of endoglucanases for foregut regions (~65% of all occurances) vs hindgut regions (~27%). For exoglucanases, the picture was reversed 61.5% occurance in hindgut and only ~14.0% in the foregut. Xylenases, on the other hand, were almost exclusively found in the hindgut. Endoglucanses break internal bonds to disrupt the crystalline structure of cellulose and expose individual cellulose polysaccharide chains. Exoglucanases cleave 2-4 units from the ends of the exposed chains produced by endocellulase, resulting tetrasaccharides or disaccharide such as cellobiose. Xylenases degrade beta-1,4-xylan into simple wood sugar. The distribution of Cell-1 through Cell-4 therefore mimics the logical breakdown of complex wood material into simple sugars.

Although most of the findings were not too surprising, I enjoyed reading this paper for the well-written introduction, and the logical approaches biologists can take to perform a relatively simple characterization of novel genes using simple bioinformatical tools. Performing these kinds of characterizations can help in the further optimization of wood degradation processes.

News Flash: 30% Efficient Solar Power Silicon and Nitrite

As reported by Greentechmedia on September 28th, Phoenix-based Rosestreet Labs Energy (RSLE) has successfully tested a new prototype of solar panels able to convert between 25-30% of sunlight into electricity. For comparison, the current maximum for conventional silicon-based solar panel is produced by SunPower can convert around 22.5% of sunlight into electricity. So the increases by RSLE represent a quantum leap in efficiency increases. The efficiency gains come at a cost of increased production costs. RSLE aims to lower production cost to below $ 1.50 per Watt by 2014 which is a goal already achieved by some solar panel manufacturers today.

RSLE claims to achieve this feat by combining silicon-based solar technology with other nitride-based alloys - in this case indium and gallium. The combination of silicon and indium and gallium nitride can make use of a broader spectrum of the visible light resulting in higher efficiencies. According to a 2005 press release, unlike conventional technology which is close to achieving the theoretical maximum, RSLE believes that their "Full Spectrum Technology" can reach efficiencies of up to 48%.

Plans for beginning of production of the HYBRID solar panels are set to start in the 4Q of 2010. In order to achieve this goal, RSLE has already received an undisclosed amount of funding from Sumitomo Chemicals and has started a Series A.

On a Broader Note

This news, and other recent news from many new start-up companies indicate that solar power generation is gaining momentum despite the current economic climate. Nanosolar or Prism Solar in particular represent technologies that potentially are disruptive in a sense that they can propel solar technologies into the main stream because their technologies can achieve such radical reductions in production costs through change in manufacturing or reduced use of resources.

On a personal note, I wonder if these technologies are compatible, and wonder what potential synergies can be achieved by combining the print-technology from Nanosolar, the nitrite alloy technology from RSLE and titanium dioxide nanostructures mentioned in my previous post for higher yields, with Prism Solar's solar concentration technology for reduced use of the raw material.

The combination of  reducing the cost of electricity generation per Watt to be competitive with conventional energy sources, innovative financing options of through solar leasing (offered by companies such as Citizenre,  SolarCity and other companies) as well as promotion of group discounts through block buying for residential applications (offered through companies such as 1bog) can sufficiently reduce the hurdles for entry into the solar market in the next few years. Bright times are ahead if political obstacles are removed and replaced with a reasonable and responsible regulatory framework that promotes the upgrade of the electrical grid.

Of Diatoms, Titanium Dioxide and A Bio-based Way to Increase Solar Power Efficiencies

Prolog:

It has been a while since last I discussed a scientific journal paper. The following post is based on a paper published in the American Chemical Society NANO Journal (Vol.2, No. 10, pp 2103-2112) with the title “Metabolic Insertion of Nanostructured TiO2 into the Patterned Biosilica of the Diatom Pinnulario sp. by a Two-Stage Bioreactor Culvtivation Process”.

What have they done?

The Rorrer lab is a nanotechnology/biotechnology engineering lab. They manipulate various microorganisms so that the microorganisms produce substances that are of use to human kind. Their latest series of publications has focused on diatoms which are single-celled algae that are able to make silica shells with very intricate patterns (see below). The Rorrer lab has a significant body of work inducing a particular diatom by the name of Pinnulario sp. to incorporate optoelectronic substances into its frustules (outer shells) that it normally would not. Optoelectronic substances can transform, transmit or sense different forms of light.

Figure 1. Microscopy Image of Pinnulario sp. Go to London Natural History Museum Website 

to read more about this organism. It's where this image is from.

In their latest work, Clayton Jeffryes et. al. have found conditions to cultivate these diatoms in such a way so that they incorporate titanium dioxide into the silica shell of the diatoms – something that these diatoms don’t do on their own. They did so by simply changing the media conditions. Initially, algal cells were starved for silicon dioxide. After starvation limited amounts of silicon dioxide mixed with titanium dioxide is fed back into the system. Under these “starved conditions” diatoms incorporate titanium dioxide into the frustules in addition to the normal silicon dioxide. When these diatoms are fixed onto glass slides and then gently washed with a detergent mixture (SDS/EDTA), the life cells are washed out of the silica shells, and the silicon/titanium dioxide skeleton is left behind.

Why is this significant?

The price per watt for solar panels is related to the cost for materials, manufacture, installation and maintenance and the amount of electricity that can be generated to payback the upfront cost. To increase distribution, the life-time cost for solar panels must come down. In different approaches, this could be achieved by reducing the use of the raw material through methods such as thin-film technology, and various light concentration technologies. Alternatively, the efficiencies of converting sunlight to electricity could be increased.

Titanium dioxide is known to be able to “trap” light particles called photons. The process of trapping these photons can dislodge additional electrons. In this way, small amounts of titanium dioxide can enhance photovoltaic properties of solar panels. The light trapping properties of titanium dioxide can be improved if titanium dioxide molecules are arranged in a certain periodic manner. However, this has been very difficult thus far. Using modified enzymes to precipitate titanium oxide out of solution has not thus far been successful in creating ordered titanium oxide structures. As an alternative, diatom frustules have been used as templates for “spraying on” titanium dioxide which requires much heat, and potentially harmful chemicals (titanium tetrachloride). This work by the Rorrer lab is significant because it describes a highly scalable, bio-based way of producing large of amounts of titanium dioxide that is arranged in a three-dimensionally ordered way.

Were this technology to be commercialized, at this time, it would still add too much cost to justify the increase. But one day, combining different technologies such as thin-film, light concentration with titanium dioxide doped bio-silica could make solar panels much more efficient than the mere ~ 20% current top-of-the line solar panel technology has to offer. The increased output could help to bring the cost of energy created per watt down sufficiently and make the dream of mostly relying on alternative energy sources come true.

Focus on Algae - Part II: Energy

In the last focus section, we discussed how algae can be used to treat waste waters and mitigate CO2 in the process. Today's post will explore how algae can be used for energy generation. As already mentioned in the last time, biofuels have become very visible as of late due to environmental, economical and geopolitcal reasons. If at the heart of traditional biofuel generation lies in the creation and decomposition of biomass, then it would be easy to substitute corn or other less controversial land-based plants with algae. Although a lot of attention is paid to the use of algae in biofuel generation, and this article also mainly focusses on this aspect, it should be noted that algae can also be used to generate electricity by direct combustion of the biomass. Plans for these kinds of schemes are already on the way in Venice and a few other European locations [1].

Algae and Biofuels

What happens to the biomass after it has been created depends on the type of biofuel that is desired.

Figure 1. Modes of Algal Biomass Conversion adapted from Bet Wang et. al. (2008).

Using biochemical techniques or microorganisms, the algal biomass can either be fermented or anaerobically digested. The first can yield ethanol, acetone and butanol while the latter would produce methane and hydrogen [2].

There are several ways of thermochemically converting the biomass into usable fuels. Pyrolysis, the process of chemical breakdown at high temperatures (~ 500°C) in the absence of oxygen, can produce some oil and coal also known as bio-oil, and biochar to better distinguish their origins from the traditional fossil fuels. Gasifiers take the biomass or biochar and convert them into a combustible gas mixture (sometimes called syngas) under even higher temperatures (~800-900°C) but limited oxygen conditions. Liquefaction on the other hand, uses uses high pressure, but rather lower temperatures (~ 200°C) to convert the biomass or biochar into bio-oil. And lastly, purely chemical processes take advantages of the abundance of lipds in the cell membrane of the algae. Additionally, many algal species are known to accumulate various amounts of oils inside the cells. These amounts can vary anywhere from ~ 30-70% of the dry biomass [1].Using transesterification reactions, biodiesels can be produced [3]. It should be noted that many of these processes have occured naturally in the environment under geological conditions. This is what produced the fossil fuels. We are just enhancing the processes in controlled and optimized conditions using current biomass instead of biomass from the past.

Advantages of Using Algae for Biofuel Production

The advantages of using algae for biomass generation are plentiful. For one, algae have the advantage of not competing with valuable arable land and water needed to cultivate food crops. Depending on the type of algae used, fresh water may not even be needed. More importantly, although there are significant differences between different algal species, the generation time, that is the time it takes for an algae cell to divide, is much faster than for any other land-based plant. This can be as little as one hour! As a result, biomass can be generated much quicker than achievable with any land-based plant.

Figure 2. Integrated uses of Algal Biomass adapted from Yusuf Chisti (2008)

The methods mentioned above are not mutually exclusive. Rather, there is great potential to combine several processes into an integrated a pipeline which is where the greatest benefits of using algae for biofuel generation lie. One possible pipeline could start with waste water streams that are used to grow algal biomass while cleaning up the water and removing carbon dioxide in the process. Some of the biomass generated could be refed to the system while the majority is used for bio-oil, or biodiesel production through various extraction methods such as transesterification. The remainder after biomass extraction can still be used further downstream. The remainder of the biomass is still rich in nitrogen, phosphorous and protein sources which is ideal for animal feed (potentially posing some public concerns that need to be addressed) or fertilizer material. Alternatively, the biomass could be pyrolysed or anaerobically digested to produce biochar or biogas usable for cogenerating electricity and heat that the surrounding communities could use [3].

Challenges to Algal Biofuels

Despite the promises of algal biofuels, the current fraction of biofuels generated from different sources of algae is rather small as costs associated with the challenges and research to overcome them are still high.

The major challenges in algal biofuels come from dealing with sources of contamination that could out-compete the algae to be cultivated, and high energy costs associated with potential circulation of the system as well as biomass recovery. To bring down the cost, test sites need to be scalable which in itself can represent difficulties with some approaches. Research on all these fronts costs money a lot of money.

All these factors contribute to current cost of biofuel generation from algae. For only biodiesel production, the estimated current cost is estimated to be about $ 33 a gallon. However, the cost significantly comes down to about $ 5.50 when integrative approaches are used such as cogeneration of electricity and heat. A further cost reduction to about $ 3.50 can be achieved from selling algal byproducts such as animal feed, fertilizer materials, or other high-value products on the near-term [4]. Although much more manageable, this is still slightly higher than the current cost of diesel. But research to enhance efficiencies are being researched to lead us to price competitiveness.

Innovations in Algal Biofuels

Despite the challenges, many companies across the world are pushing forwards with their efforts to bring algal-based biofuels to the market supported by an increased effort of academic research, government subsidies, and changes in the regulatory-framework.

Current research is focussed on finding more suitable algal species through bioprospecting. Genetic engineering can improve biomass generation, increase the oil content, or improve the sturdiness of algal species for a given condition. Up to now, the extraction process also killed the algae. But, as discussed on NPR's Science Friday show (3 July 2009), the possibility to develop technologies for "milking" the algae without killing is being researched.

On the industrial side, many companies are putting their ideas to the test by bringing their innovative approaches to the growing but challenging biofuels market. While Solazyme has adapted the approach of growing algae in completely dark vats and feeding them sugar [5], other companies such as Solix have worked on bringing improved bioreactors to large-scale [6]. Other companies, such as Sapphire Energy have focussed on directly extracting 'green crude oil' from algae [7]. There are also a couple of companies working on converting sewage water into biodiesel. A New Zealand company named, Aquaflow claims to have been the first company to successfully do so all the way back in 2006 [8].

By no means is this supposed to be an expansive list of current innovations in the field. But one thing is clear: Despite the 20 year history of research into algal biofuels, it only seems that now conditions and research have come far enough to seriously consider algae for biofuels. Which of these companies will eventually become successful is unknown at this time. Many hurdles remain. But the examples, hopefully, provide a glimps to the bright future of algal biofuels and explain why there is so much excitement in the field.

Quoted Sources:

[1] Venice Seaport Eyes Algae for Energy Needs. Visited: 2009-08-21. www.reuters.com
[2] Bet Wang et. al. (2008) CO₂ bio-mitigation using microalgae. Appl Microbiol Biotechnol 79:707–718
[3] Yusuf Chisti (2008) Biodiesel from microalgae beats bioethanol. Trends in Biotechnology Vol.26 No.3
[4] Algae Biodiesel: It's $33 a Gallon. Visited: 2009-08-22. www.greentechmedia.com.
[5] Solazyme Produces World’s First Algal-Based Jet Fuel . Visited: 2009-08-22. www.solazyme.com
[6] Solix Biofuels Begins Large-Scale Production of Algae-Based Biofuels at Coyote Gulch Demonstration Facility. Visited: 2009-08-22. www.solixbiofuels.com
[7] Sapphire Energy turns algae to 'green crude'. Visited: 2009-07-20. www.sapphireenergy.com
[8] NZ company makes bio-diesel from sewage world first. Visited: 2009-07-21. www.nzherald.co.nz

What are Biofuels?

Introduction

With prices for crude oil spiking in the recent past, and an unstable Middle East and intensifying effects of climate disruptions, the Obama administration and governments around the world have been promoting the development, and deployment of newer, more sustainable forms of energy generation, amongst which are biofuels.

What are Biofuels?

At the heart of every hydrocarbon based fuel (gasoline, diesel, kerosene, coal) are anaerobic degradation processes of organic material. For fossil fuels, the source of organic material comes from planctonic life, plants, and animals that lived and died millions of years ago. For biofuels, the source of organic material comes from planctonic life, plants or other sources of much more recent origin.

The important concepts to note are:

1.) Building up organic matter removes carbon dioxide from the atmosphere.
2.) Burning hydrocarbon based fuels releases the carbon originally tied up in the form of carbon dioxide.

So when we pump up the oil and burn it, we are releasing carbon dioxide that was removed from the atmosphere millions of years ago. The idea behind biofuels is that instead of releasing all the carbon dioxide stashed away millions of years ago, we become "carbon-neutral" by only relying on carbon sources that recently died to make gasoline.

Take corn for instance. When corn is growing, carbon dioxide is removed from the atmosphere as the plant incorporates the carbon into various cell components of the growing plant. Corn fermentation, the same process that also makes beer and fine wines, produces ethanol which can be used as a fuel to run cars. So when ethanol is burned in a car, the only carbon released into the atmosphere again in the form of carbon dioxide is the one that the plant absorbed before. Different plants can be used depending on climate and local geographical conditions. But the previous example, describe the basic idea behind the first generation biofuels. Theoretically, this describes a closed loop circuit which is close to carbon neutral because carbon dioxide released does not come from oil but from the plants we grew to make the fuel.

Disadvantages of First Generation Biofuels

In reality, however, especially corn-based ethanol has many problems. First, there are certain technical issues related to the inefficiencies of converting food crop into ethanol. Energy cost of production, and transportation of crops and fuel further reduce the theoretical yield and make these first generation biofuels less carbon neutral.

More importantly, there are concerns that high demand for energy crops could lead to increased deforestation because it may become more profitable to make more room for energy crops. Clearing of land for energy crops often happens in the form of burning forest land which releases more carbon dioxide than would be absorbed by growing just monocultures of corn. Scientist call this a "carbon debt".

Lastly, corn is also a food source for humans and other animals. Faced with limited arable land mass and water resources, increasing the demand for corn so that it can be used for fuel generation also increases the food price of these products. Because poor people can ill afford to pay more money for basic food sources, even small increases in the price can have devastating consequences on a families ability to buy basic sources of food in the third world.

Further research and careful policy making can potentially contain each of the above mentioned problems. In the next post, we shall look at the advantages one such approach and ask how algae can generally be used to solve some of the energy challenges we face today.

"Bio-based" Search Engines

I am still working on the second part of the focus on algae, and between research, and moving to a new place, I am not finding just enough time to flesh out the article just yet. It will come though!

Instead tonight, I wanted to write an informal entry on a particular aspect of "bio-based" ideas: what anyone can do for environmental protection and conservation. In most of the industrialized world and beyond, internet access is pervasive. I find that I am spending quite a bit of time on the internet be it for email, searching information, social networking or gaming. I am sure others will have their own habits on the internet.

It's easy to forget that each action on the internet actually has an environmental cost associated with it. The computers used to read this blog use electricity. Games can be demanding on the graphics card which if high-end can use even more energy than the CPU itself. Beyond the borders of your own computer, each action one takes puts a certain work-load on server machines located somewhere else. And of course these server machines also consume varying amounts of energy.

With all the talk about carbon footprint, it may not be surprising to find that surfing the internet also has a carbon footprint. Searches especially despite the apparent simplicity can consume a lot of energy - sometimes as much as a 11 Watt light bulb in an hour!

For this reason, I just wanted to introduce two green search engines:

1.) Znout
2.) Forestle

These search engines don't actually use new algorithms that are more efficient or anything. In fact, Forestle is a custom search engine using the Yahoo! search engine, while Znout uses Google. What makes these custom search engines green though is what they do with the revenue generated by searches.

According to the website, Znout stands for "zero negative output" and is a CO₂ neutral Internet search engine that turns your web searches into green web searches by keeping track of energy usage, and carbon foot-printing and off-setting these by buying renewable energy credits at the end of each month.

Forestle goes a step further. In addition to purchases of renewable energy credits, Forestle uses ALL the revenue minus 10% for administrative costs by donating the remaining profits to The Nature Conservancy's "Adopt an Acre" program.

Because the search engines are based on the two main search engines - Yahoo! and Google -, the search results should be very familiar. Switching to these search engines is easy. They even have a search plug-in feature so that you can search from the comfort of your browser.

Anyway, give these search engines a try, and help save the environment while searching/browsing the internet with them.