Biorefinery Design

This part of our feasibility study deals with the engineering design and economics of a biorefinery plant implementing the synergistic breakdown of cellulose. To produce a comprehensive feasibility study it is necessary to examine technically, how it would work and how our project would be integrated into a biorefinery. By doing so we are better able to assess its implications on society, from understand the ethical concerns behind procuring raw materials to the biosafety from possible release of microorganisms.


What is a biorefinery?

A biorefinery is a processing plant that converts biological raw materials into a variety of products that can be used as industrial intermediates or sold directly to consumers. Biorefineries offer flexibility in both the types of products that can be made and the raw materials that can be used; flexibility that conventional chemical/food plants aren’t able to offer. However, for this technology to be successful it has to be integrated within a bio-based economy where its raw materials can be sourced both sustainably and cheaply.

Using synthetic biology, by creating BioBricks and incorporating them into genetically designed microorganisms, it should be possible to make products from biological feedstocks that range from food additives to chemicals.

This page develops a design for a biorefinery based on our iGEM project of synergistic cellulose breakdown. We examine one engineering design for this biorefinery with a detailed process flow diagram. An analysis of the economics of this plant is also made, investigating its required capital and projected profits. This detailed economic and technical investigation is part of our bigger feasibility study, and it is related in important ways to questions about what role synthetic biology might have in the future, and whether biorefineries are a realistic short-term application area for this technology.

Raw Materials

Building a biorefinery, and the investment required to do so, can only be justified if the procurement of its raw materials is done both economically and sustainably. There are very important questions about where these biological feedstocks should come from. Nicholas Peyret, from Scottish Enterprise, a public body which encourages economic development, asks,

“Can we take advantage of Scottish feedstock?” (Interview with Nicholas Peyret, 25/08/2011)

He says that more research is needed to analyse the potential of different Scottish feedstocks. But in principle it makes more sense than shipping biomass across the world — for example, growing sugarcane in Brazil to export for industrial use in the United States or Europe. Eric Hoffman, Biotechnology Policy Officer for Friends of the Earth asks,

“What happens if we start switching more and more land which is currently used in agriculture production and start shifting that for feedstock for synthetic bugs?” (Interview with Eric Hoffman, 11/08/2011)

His concerns shouldn’t be ignored in a bid to make synthetic biology commercially successful in the short term, but should be addressed with a careful rationale and with humility.

The raw material to be used in our proposed biorefinery is open for debate as the biorefinery is not constrained in the exact material but only in its source. Lignocellulose is the primary structural material in plants and is made up of hemicellulose, cellulose and lignin. The biorefinery will separate lignocellulose into its three constituents, and from cellulose will come glucose and the desired product.

Traditionally those sourcing lignocellulosic biomass would look to softwoods, hardwoods and grasses. Biomass such as switchgrass, corn stover and sugar cane are popular options. But what if the biomass sourced is mere waste that can be recycled? We suggest that old newspapers, furniture, straw and other lignocellulose- based waste could be possible input feedstocks. Commercially, this method could be significantly cheaper, but a challenge nonetheless to the contractors to find reliable sources at the necessary volumes. The biorefinery proposed by the Edinburgh iGEM team aims to use up to 700 kg/h of biomass, to make it commercially worthwhile. Current biorefineries operate at around 500 kg/h, with company Elsam Essential energy (European commission, 2004) looking do develop pilot lignocellulose plants of up to 1000 kg/h of biomass. 700 kg/h was assessed to be both realistic in the short to medium term and ensure good returns to any potential investor.

Science and Engineering


One of the biggest challenges for any biorefinery is cost-effective pre-treatment of raw materials. Vom Stein et al (2011) have proposed a ‘one step fractionation of lignocellulose components by the selective organic acid and catalysed deploymerisation of hemicellulose in a biphasic system’. Our proposed biorefinery process incorporates this method using oxalic acid at 140 degrees Celsius at a pressure of 20 bar, which is moderate compared to other methods. Steam is fed into reactor 1 (R-1) along with oxalic acid, controlled by a series of proportional, integral, derivative (PID) control mechanisms used to regulate flow, level and temperature. Here the depolymerisation of hemicellulose to soluble sugar in aqueous phase occurs, while the cellulose-pulp (which is more crystalline) remains solid and unreachable to the acid catalysis. Crystallisation is used to separate the oxalic acid from the aqueous stream and then after further processing, it is recycled back into reactor 1.

In a second organic phase involving bio-based compound 2-methyltetrahydrofuran (2-MTHF), ‘lignin is directly separated from the pulp and the soluble carbohydrates by in situ extraction’ (Vom Stein et al, 2011). 2-MTHF allows for relatively easy separation and recycling using distillation due to its low boiling point, 80 degrees Celsius.

Synthetic biology is currently not incorporated within the pre-treatment phase of the proposed biorefinery. Assuming the efficiency of the Vom Stein et al (2011) process is high and cost effective, is there any reason for it to be? One of the lessons that can be learnt from previous research, and even previous iGEM projects, is that synthetic biology is not always the best solution for a problem. For pre-treatment, finding the optimum chemical solution will be far easier than developing one that involves microorganisms, as survival of the microorganisms is problematic with the high temperatures and pressures needed to convert biomass into cellulose. Having said that, if synthetic biology can find a better solution based on enzymes, and requiring lower operating temperature and pressure, then it would significantly change the design of future biorefineries and even future chemical plants. Therefore, biorefineries built today should be flexible enough to incorporate tomorrow’s synthetic biological advances.

Lignin treatment

Lignin makes up approximately 30% of lignocellulose, and the potential to convert it into chemical feedstock is significant. The proposed biorefinery utilises this potential and aims to convert lignin into phenols using hydrous pyrolysis. Hydrous pyrolysis refers to the thermal decomposition of organic compounds when heated in the presence of water. However, pure lignin has a low melting point (ranging from 80-200 degrees Celsius) and the process is very energy-intensive. Furthermore, lignin is a complex bio-polymer, which makes it difficult to convert it into valuable monomeric chemicals. Aston Inventions (an enterprise subsidiary of Aston University) cite the process’s potential if a sufficiently large-scale and efficient method for lignin conversion is developed, but warn of lignin’s ‘resistance to chemical, thermal and biological degradation’ (Aston University, 2010).

However what if a technology can be developed that operates at ambient temperatures and bypasses the need for energy intensive work? Lead researcher Dr. Michael E. Scharf from the University of Florida suggests creating synthetic recombinant enzymes produced out of genes from host termite tissues. ‘These enzymes include two cellulases that act on cellulose and hemicellulose, and laccase that acts on lignin’ (Redahan, 2011). He recognises that efficient and inexpensive cellulases are already used in industry, but inexpensive and efficient processes for the treatment of lignin and hemicellulose are yet not available. Therefore, ‘In this respect termite digestomics has already offered significant insights.’ (Scharf and Tartar, 2008). It is possible that genetic engineering and synthetic biology will impact every stage of the biorefinery process; which is more than we have foreseen. This should be treated as both exciting for the field in years to come and with great caution. Those designing the biorefineries of the future will have to think harder on how ‘synthetic biology-based biorefineries’ will impact society. They will be biorefineries in the truest sense: every stage will have an element influenced by the field of synthetic biology.

Cellulose degradation and potential products

The cellulose pulp which leaves the pre-treatment phase of the plant is pumped to a reactor containing our designed E. coli enzyme display solution. Using the Edinburgh iGEM team’s cell-surface and phage display scaffolds, enzymes that degrade cellulose will be displayed on an extracellular surface in close proximity to one another, in order to increase the efficiency of cellulose conversion to glucose. By using BioBricks already in the Registry of Standard Biological Parts, and by designing new ones, our biorefinery plant could produce a range of products from the initial feedstock. Which products are eventually chosen will depend on potential yield and selling price. As an example, the biorefinery produces high-fructose corn syrup and sorbitol, which are chosen because they are both widely used in the food industry. However, given the flexibility of biorefineries, a much wider range of products can be achieved. For example, isoprenes can be used as a chemical feedstock in the production of all sorts of other products.

Combined heat and power (CHP)

It is essential that any biorefinery operates under the European Union emission trading scheme which covers 10,000 installations with a net heat excess of 20MW in energy. Our biorefinery therefore includes a combined heat and power (CHP) system to minimize the amount of energy released. CHP captures heat from reactors that would otherwise be released into the natural environment, and uses it for heating purposes. Our biorefinery would emulate what is already being done in Scandinavia, supplying this heat to local communities.

Process flow diagram (PFD)

A PFD is an engineering design tool, used to show in detail what a plant will look like. Going through the PFD design process takes the synthetic biology-based biorefinery from a conceptual idea and gives it a degree of reality. The PFD itself asks more questions than it answers, and this design process has reiterated for us the complexity of designing a biorefinery. As it is based on a series of assumptions, the PFD is not a definitive answer to what a biorefinery should look like but an articulation of what it could look like. Perhaps the most profound questions this process raised in our minds were: is synthetic biology the best approach to tackling the challenge of cellulose degradation, and does this biorefinery model improve on current systems? Research would have to be carried out through a small-scale model, to give detailed answers. Only if it can be shown that synthetic biology provides a significant improvement to the status quo, can the level of investment be justified.

You view the Process flow diagram here. Click twice to see in greater detail:

To view an equipment list which details equipment type, name and number visit biorefiney appendices, Appendix 2


If the model of using synthetic biology in biorefineries is to be at all successful, biosafety has to be at the centre of all discussion, design and economics. There must be no compromise on safety for plant workers, nearby communities and the surrounding environment. Armin Grunwald, Director of the Office for Technological assessment in Germany, as well as a philosopher and ethicist, said of Edinburgh’s iGEM project,

“My immediate concerns would affect possible release of modified E.Coli with new properties to the Environment not knowing about possible impacts and side-effects (a typical bio-safety issue)” (Written interview with Armin Grunwald, 01/09/2011)

Therefore complacency is not an option, and work has to be carried out with honesty and a degree of humility. The consequences of not doing so will lead to a rejection of synthetic biology similar to the rejection of genetically modified (GM) foods in many European countries. Armin Grunwald adds,

“..assuming that synthetic biology will even stronger intervene into organisms used for food production compared to classical genetics I guess that it will take a long time until SB products could be used for food production. A lot of research on possible side effects will be necessary to create trust and acceptance (at least in Europe)” (Written interview with Armin Grunwald, 01/09/2011)

Economics of biorefineries

If the biorefinery shown on the PFD is ever to be constructed it has to make commercial sense. The level of necessary investment calculated in our study is significant. Using the book, ‘Chemical engineering design’ by R.K Sinnot we have made a detailed analysis of costings. These costs are based on the factorial estimating method, and detailed calculations can be found in Appendix 1.

We have calculated that an investment of $2.3 million dollars is needed on top of the cost of buying land. This includes all major equipment, piping, instrumentation, contingency, etc. To run the plant, $4.5 million of capital is needed per annum. This includes raw materials, labour, and overheads. Based on a series of assumptions about how much cellulose can be degraded in our system, we estimate a product yield. The assumptions were made on the basis of what we thought the most realistic amount of glucose we could expect to be produced. Using information about the selling price of sorbitol and high-fructose corn syrup, we suggest our biorefinery could make $820,000 gross profit. However, considering the level of investment needed in year 1, as well as the cost of production and taxes, an investment of over $10 million dollars in capital will be required for start-up.

So does it make commercial sense? A large initial investment with any large-scale project is expected, but the level of profit we project is too low to make it justifiable in the short term. Approximately 15 years would be needed for our biorefinery to break even and in that time the capacity of synthetic biology might significantly change becoming cheaper and easier. However, as we stated earlier, this biorefinery has the potential to provide a flexible range of products. Therefore, further research is needed to create BioBricks for products that are higher in value, to maximise profit. But for a biorefinery to really make commercial sense, it would have to be integrated within a bio-based economy, where costs could be reduced in every stage of production: from the sourcing of raw materials to transport and research. For this to happen, significant investment is needed from both government and private enterprise.

Here is an infographic giving essential information about the economics of the biorefinery:



So why did we develop a design for the biorefinery in such detail and what has it got to do with human practices? We thought it wasn't enough to simply state our intentions for the future of our project. By doing a detailed design we were able to fundamentally see how a biorefinery would impact society. Therefore questions were asked that wouldn't have been before. For example, we changed the impact of the biorefinery on the environment by incorporating the installation of a combined heat and power system and by using enzymes from termites in the treatment of lignin which would bypass high pressures and temperatures. Both aspects are key in addressing the environmental impact of the biorefinery but wouldn't be understood if we hadn't gone through the process. Human practices is largely concerned with the impact of science on the society around us, but also has concerns in how our practice is developed and how society impacts on science.


  • Sinnot RK (2005) Coulson & Richardson's chemical engineering. Vol. 6, Chemical engineering design. Oxford: Elsevier Butterworth-Heinemann.