Biofuels: biotechnology, chemistry, and Sustainable development

BIOFUELS

Biotechnology, Chemistry,

and Sustainable Development

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BIOFUELS

Biotechnology, Chemistry,

and Sustainable Development

DAVID M. MOUSDALE

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Library of Congress Cataloging-in-Publication Data

Mousdale, David M.

Biofuels : biotechnology, chemistry, and sustainable development / David M.

Mousdale.

p. ; cm.

CRC title.

Includes bibliographical references and index.

ISBN-13: 978-1-4200-5124-7 (hardcover : alk. paper)

ISBN-10: 1-4200-5124-5 (hardcover : alk. paper)

1. Alcohol as fuel. 2. Biomass energy. 3. Lignocellulose--Biotechnology. I. Title.

[DNLM: 1. Biochemistry--methods. 2. Ethanol--chemistry. 3. Biotechnology.

4. Conservation of Natural Resources. 5. Energy-Generating Resources. 6.

Lignin--chemistry. QD 305.A4 M932b 2008]

TP358.M68 2008

662’.6692--dc22 2007049887

Visit the Taylor & Francis Web site at

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v

Contents

Preface ......................................................................................................................xi

Author ....................................................................................................................xix

Chapter 1

Historical Development of Bioethanol as a Fuel .......................................................1

1.1 Ethanol from Neolithic Times ...........................................................................1

1.2 Ethanol and Automobiles, from Henry Ford to Brazil .....................................4

1.3 Ethanol as a Transportation Fuel and Additive: Economics and

Achievements .................................................................................................. 11

1.4 Starch as a Carbon Substrate for Bioethanol Production ................................ 17

1.5 The Promise of Lignocellulosic Biomass .......................................................26

1.6 Thermodynamic and Environmental Aspects of Ethanol as a Biofuel .......... 33

1.6.1 Net energy balance .............................................................................. 33

1.6.2 Effects on emissions of greenhouse gases and other pollutants .........40

1.7 Ethanol as a First-Generation Biofuel: Present Status and

Future Prospects .............................................................................................. 42

References ................................................................................................................44

Chapter 2

Chemistry, Biochemistry, and Microbiology of Lignocellulosic Biomass ..............49

2.1 Biomass as an Energy Source: Traditional and Modern Views ......................49

2.2 “Slow Combustion” — Microbial Bioenergetics ............................................ 52

2.3 Structural and Industrial Chemistry of Lignocellulosic Biomass ..................56

2.3.1 Lignocellulose as a chemical resource ................................................56

2.3.2 Physical and chemical pretreatment of

lignocellulosic biomass ....................................................................... 57

2.3.3 Biological pretreatments .....................................................................63

2.3.4 Acid hydrolysis to saccharify pretreated

lignocellulosic biomass .......................................................................64

2.4 Cellulases: Biochemistry, Molecular Biology, and Biotechnology ................66

2.4.1 Enzymology of cellulose degradation by cellulases ...........................66

2.4.2 Cellulases in lignocellulosic feedstock processing .............................70

2.4.3 Molecular biology and biotechnology of cellulase production ........... 71

2.5 Hemicellulases: New Horizons in Energy Biotechnology ............................. 78

2.5.1 A multiplicity of hemicellulases.......................................................... 78

2.5.2 Hemicellulases in the processing of lignocellulosic biomass .............80

2.6 Lignin-Degrading Enzymes as Aids in Saccharifi cation ............................... 81

2.7 Commercial Choices of Lignocellulosic Feedstocks

for Bioethanol Production ............................................................................... 81

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vi Contents

2.8 Biotechnology and Platform Technologies for

Lignocellulosic Ethanol ..................................................................................86

References ................................................................................................................86

Chapter 3

Biotechnology of Bioethanol Production from Lignocellulosic Feedstocks ...........95

3.1 Traditional Ethanologenic Microbes ...............................................................95

3.1.1 Yeasts ...................................................................................................96

3.1.2 Bacteria .............................................................................................. 102

3.2 Metabolic Engineering of Novel Ethanologens ............................................ 104

3.2.1 Increased pentose utilization by ethanologenic yeasts by

genetic manipulation with yeast genes for xylose

metabolism via xylitol ....................................................................... 104

3.2.2 Increased pentose utilization by ethanologenic yeasts by

genetic manipulation with genes for xylose isomerization ............... 111

3.2.3 Engineering arabinose utilization by ethanologenic yeasts .............. 112

3.2.4 Comparison of industrial and laboratory yeast strains for

ethanol production ............................................................................. 114

3.2.5 Improved ethanol production by naturally

pentose-utilizing yeasts ..................................................................... 118

3.3 Assembling Gene Arrays in Bacteria for Ethanol Production ......................120

3.3.1 Metabolic routes in bacteria for sugar metabolism and

ethanol formation ..............................................................................120

3.3.2 Genetic and metabolic engineering of bacteria for

bioethanol production ........................................................................ 121

3.3.3 Candidate bacterial strains for commercial

ethanol production in 2007 ............................................................... 133

3.4 Extrapolating Trends for Research with Yeasts and Bacteria for

Bioethanol Production .................................................................................. 135

3.4.1 “Traditional” microbial ethanologens ............................................... 135

3.4.2 “Designer” cells and synthetic organisms......................................... 141

References .............................................................................................................. 142

Chapter 4

Biochemical Engineering and Bioprocess Management for Fuel Ethanol ............ 157

4.1 The Iogen Corporation Process as a Template and Paradigm ...................... 157

4.2 Biomass Substrate Provision and Pretreatment ............................................ 160

4.2.1 Wheat straw — new approaches to

complete saccharifi cation .................................................................. 161

4.2.2 Switchgrass ....................................................................................... 162

4.2.3 Corn stover ........................................................................................ 164

4.2.4 Softwoods .......................................................................................... 167

4.2.5 Sugarcane bagasse............................................................................. 170

4.2.6 Other large-scale agricultural and forestry

biomass feedstocks ............................................................................ 171

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Contents vii

4.3 Fermentation Media and the “Very High Gravity” Concept ........................ 172

4.3.1 Fermentation media for bioethanol production ................................. 173

4.3.2 Highly concentrated media developed for

alcohol fermentations ........................................................................ 174

4.4 Fermentor Design and Novel Fermentor Technologies ................................ 179

4.4.1 Continuous fermentations for ethanol production ............................. 179

4.4.2 Fed-batch fermentations .................................................................... 184

4.4.3 Immobilized yeast and bacterial cell production designs ................. 185

4.4.4 Contamination events and buildup in fuel ethanol plants ................. 187

4.5 Simultaneous Saccharifi cation and Fermentation and

Direct Microbial Conversion ........................................................................ 189

4.6 Downstream Processing and By-Products .................................................... 194

4.6.1 Ethanol recovery from fermented broths .......................................... 194

4.6.2 Continuous ethanol recovery from fermentors ................................. 195

4.6.3 Solid by-products from ethanol fermentations .................................. 196

4.7 Genetic Manipulation of Plants for Bioethanol Production .......................... 199

4.7.1 Engineering resistance traits for biotic and abiotic stresses .............. 199

4.7.2 Bioengineering increased crop yield .................................................200

4.7.3 Optimizing traits for energy crops intended for biofuel

production ..........................................................................................203

4.7.4 Genetic engineering of dual-use food plants and dedicated

energy crops ......................................................................................205

4.8 A Decade of Lignocellulosic Bioprocess Development:

Stagnation or Consolidation? ........................................................................206

References .............................................................................................................. 211

Chapter 5

The Economics of Bioethanol ................................................................................227

5.1 Bioethanol Market Forces in 2007 ................................................................227

5.1.1 The impact of oil prices on the “future” of

biofuels after 1980 .............................................................................227

5.1.2 Production price, taxation, and incentives in the

market economy ................................................................................228

5.2 Cost Models for Bioethanol Production ........................................................230

5.2.1 Early benchmarking studies of corn and lignocellulosic

ethanol in the United States .............................................................. 231

5.2.2 Corn ethanol in the 1980s: rising industrial ethanol prices

and the development of the “incentive” culture ................................238

5.2.3 Western Europe in the mid-1980s: assessments of biofuels

programs made at a time of falling real oil prices ............................ 239

5.2.4 Brazilian sugarcane ethanol in 1985: after the fi rst decade

of the Proálcool Program to substitute for imported oil ...................242

5.2.5 Economics of U.S. corn and biomass ethanol economics

in the mid-1990s ................................................................................243

5.2.6 Lignocellulosic ethanol in the mid-1990s:

the view from Sweden .......................................................................244

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viii Contents

5.2.7 Subsequent assessments of lignocellulosic

ethanol in Europe and the United States ...........................................246

5.3 Pilot Plant and Industrial Extrapolations for Lignocellulosic Ethanol ......... 251

5.3.1 Near-future projections for bioethanol production costs ................... 251

5.3.2 Short- to medium-term technical process improvements with

their anticipated economic impacts ................................................... 253

5.3.3 Bioprocess economics: a Chinese perspective .................................. 257

5.4 Delivering Biomass Substrates for Bioethanol Production:

The Economics of a New Industry................................................................258

5.4.1 Upstream factors: biomass collection and delivery ...........................258

5.4.2 Modeling ethanol distribution from

production to the end user .................................................................259

5.5 Sustainable Development and Bioethanol Production ..................................260

5.5.1 Defi nitions and semantics ..................................................................260

5.5.2 Global and local sustainable biomass

sources and production ...................................................................... 261

5.5.3 Sustainability of sugar-derived ethanol in Brazil ..............................264

5.5.4 Impact of fuel economy on ethanol demand

for gasoline blends .............................................................................269

5.6 Scraping the Barrel: an Emerging Reliance on

Biofuels and Biobased Products? .................................................................. 271

References .............................................................................................................. 279

Chapter 6

Diversifying the Biofuels Portfolio .......................................................................285

6.1 Biodiesel: Chemistry and Production Processes...........................................285

6.1.1 Vegetable oils and chemically processed biofuels .............................285

6.1.2 Biodiesel composition and production processes ..............................287

6.1.3 Biodiesel economics ..........................................................................293

6.1.4 Energetics of biodiesel production and effects on

greenhouse gas emissions .................................................................295

6.1.5 Issues of ecotoxicity and sustainability with expanding

biodiesel production ..........................................................................299

6.2 Fischer-Tropsch Diesel: Chemical Biomass–to–Liquid Fuel

Transformations ............................................................................................ 301

6.2.1 The renascence of an old chemistry for

biomass-based fuels? ......................................................................... 301

6.2.2 Economics and environmental impacts of FT diesel ........................303

6.3 Methanol, Glycerol, Butanol, and Mixed-Product “Solvents”......................305

6.3.1 Methanol: thermochemical and biological routes .............................305

6.3.2 Glycerol: fermentation and chemical synthesis routes ......................307

6.3.3 ABE (acetone, butanol, and ethanol) and “biobutanol” ....................309

6.4 Advanced Biofuels: A 30-Year Technology Train ........................................ 311

References .............................................................................................................. 314

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Contents ix

Chapter 7

Radical Options for the Development of Biofuels ................................................. 321

7.1 Biodiesel from Microalgae and Microbes ..................................................... 321

7.1.1 Marine and aquatic biotechnology..................................................... 321

7.1.2 “Microdiesel” .....................................................................................324

7.2 Chemical Routes for the Production of Monooxygenated

C6 Liquid Fuels from Biomass Carbohydrates .............................................324

7.3 Biohydrogen .................................................................................................. 325

7.3.1 The hydrogen economy and fuel cell technologies ........................... 325

7.3.2 Bioproduction of gases: methane and H2 as products of

anaerobic digestion ............................................................................ 328

7.3.3 Production of H2 by photosynthetic organisms ................................. 334

7.3.4 Emergence of the hydrogen economy................................................ 341

7.4 Microbial Fuel Cells: Eliminating the Middlemen of

Energy Carriers ............................................................................................. 343

7.5 Biofuels or a Biobased Commodity Chemical Industry?..............................346

References .............................................................................................................. 347

Chapter 8

Biofuels as Products of Integrated Bioprocesses ................................................... 353

8.1 The Biorefi nery Concept ............................................................................... 353

8.2 Biomass Gasifi cation as a Biorefi nery Entry Point ....................................... 356

8.3 Fermentation Biofuels as Biorefi nery Pivotal Products ................................ 357

8.3.1 Succinic acid ...................................................................................... 361

8.3.2 Xylitol and “rare” sugars as fi ne chemicals ......................................364

8.3.3 Glycerol — A biorefi nery model based on biodiesel ........................ 367

8.4 The Strategic Integration of Biorefi neries with the Twenty-First Century

Fermentation Industry ...................................................................................369

8.5 Postscript: What Biotechnology Could Bring About by 2030 ...................... 372

8.5.1 Chicago, Illinois, October 16–18, 2007 ............................................ 373

8.5.2 Biotechnology and strategic energy targets beyond 2020 ................. 375

8.5.3 Do biofuels need — rather than biotechnology — the

petrochemical industry? .................................................................... 377

References .............................................................................................................. 379

Index ...................................................................................................................... 385

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xi

Preface

When will the oil run out? Various estimates put this anywhere from 20 years from

now to more than a century in the future. The shortfall in energy might eventually

be made up by developments in nuclear fusion, fuel cells, and solar technologies,

but what can substitute for gasoline and diesel in all the internal combustion engine￾powered vehicles that will continue to be built worldwide until then? And what will

stand in for petrochemicals as sources of building blocks for the extensive range of

“synthetics” that became indispensable during the twentieth century?

Cellulose — in particular, cellulose in “lignocellulosic biomass” — embodies

a great dream of the bioorganic chemist, that of harnessing the enormous power of

nature as the renewable source for all the chemicals needed in a modern, bioscience￾based economy.1 From that perspective, the future is not one of petroleum crackers

and industrial landscapes fi lled with the hardware of synthetic organic chemistry, but

a more ecofriendly one of microbes and plant and animal cells purpose-dedicated

to the large-scale production of antibiotics and blockbuster drugs, of monomers for

new biodegradable plastics, for aromas, fragrances, and taste stimulators, and of

some (if not all) of the novel compounds required for the arrival of nanotechnologies

based on biological systems. Glucose is the key starting point that, once liberated

from cellulosic and related plant polymers, can — with the multiplicity of known

and hypothesized biochemical pathways in easily cultivatable organisms — yield

a far greater multiplicity of both simple and complex chiral and macromolecular

chemical entities than can feasibly be manufactured in the traditional test tube or

reactor vessel.

A particular subset of the microbes used for fermentations and biotransforma￾tions is those capable of producing ethyl alcohol — ethanol, “alcohol,” the alcohol

whose use has both aided and devastated human social and economic life at various

times in the past nine millennia. Any major brewer with an international “footprint”

and each microbrewery set up to diversify beer or wine production in contention

with those far-reaching corporations use biotechnologies derived from ancient times,

but that expertise is also implicit in the use of ethanol as a serious competitor to

gasoline in automobile engines. Hence, the second vision of bioorganic chemists

has begun to crystallize; unlocking the vast chemical larder and workshop of natu￾ral microbes and plants has required the contributions of microbiologists, microbial

physiologists, biochemists, molecular biologists, and chemical, biochemical, and

metabolic engineers to invent the technologies required for industrial-scale produc￾tion of “bioethanol.”

The fi rst modern social and economic “experiment” with biofuels — that in

Brazil — used the glucose present (as sucrose) in cane sugar to provide a readily

available and renewable source of readily fermentable material. The dramatic rise

in oil prices in 1973 prompted the Brazilian government to offer tax advantages to

those who would power their cars with ethanol as a fuel component; by 1988, 90%

of the cars on Brazilian roads could use (to varying extents) ethanol, but the collapse

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xii Preface

in oil prices then posed serious problems for the use of sugar-derived ethanol. Since

then, cars have evolved to incorporate “dual-fuel” engines that can react to fl uctua￾tions in the market price of oil, Brazilian ethanol production has risen to more than

16 million liters/year, and by 2006, fi lling up with ethanol fuel mixes in Brazil cost

up to 40% less than gasoline.

Sugarcane thrives in the equatorial climate of Brazil. Further north, in the mid￾western United States, corn (maize, Zea mays) is a major monoculture crop; corn

accumulates starch that can, after hydrolysis to glucose, serve as the substrate for eth￾anol fermentation. Unlike Brazil, where environmentalists now question the destruc￾tion of the Amazonian rain forest to make way for large plantations of sugarcane and

soya beans, the Midwest is a mature and established ecosystem with high yields of

corn. Cornstarch is a more expensive carbon substrate for bioethanol production, but

with tax incentives and oil prices rising dramatically again, the production of ethanol

for fuel has become a signifi cant industry. Individual corn-based ethanol production

plants have been constructed in North America to produce up to 1 million liters/day,

and in China 120,000 liters/day, whereas sugarcane molasses-based facilities have

been sited in Africa and elsewhere.2

In July 2006, the authoritative journal Nature Biotechnology published a cluster

of commentaries and articles, as well as a two-page editorial that, perhaps uniquely,

directed its scientifi c readership to consult a highly relevant article (“Ethanol Frenzy”)

in Bloomberg Markets. Much of the discussion centered on the economic viability of

fuel ethanol production in the face of fl uctuating oil prices, which have inhibited the

development of biofuels more than once in the last half century.3 But does bioethanol

production consume more energy than it yields?4 This argument has raged for years;

the contributors to Nature Biotechnology were evidently aware of the controversy

but drew no fi rm conclusions. Earlier in 2006, a detailed model-based survey of the

economics of corn-derived ethanol production processes concluded that they were

viable but that the large-scale use of cellulosic inputs would better meet both energy

and environmental goals.5 Letters to the journal that appeared later in the year reiter￾ated claims that the energy returns on corn ethanol production were so low that its

production could only survive if heavily subsidized and, in that scenario, ecological

devastation would be inevitable.6

Some energy must be expended to produce bioethanol from any source — in

much the same way that the pumping of oil from the ground, its shipping around

the world, and its refi ning to produce gasoline involves a relentless chain of energy

expenditure. Nevertheless, critics still seek to be persuaded of the overall benefi ts of

fuel ethanol (preferring wind, wave, and hydroelectric sources, as well as hydrogen

fuel cells). Meanwhile its advocates cite reduced pollution of the atmosphere, greater

use of renewable resources, and erosion of national dependence on oil imports as key

factors in the complex overall cost-benefi t equation.

To return to the “dream” of cellulose-based chemistry, there is insuffi cient arable

land to sustain crop-based bioethanol production to more than fuel-additive levels

worldwide, but cellulosic biomass grows on a massive scale — more than 7 × 1010

tons/year — and much of this is available as agricultural waste (“stalks and stems”),

forestry by-products, wastes from the paper industry, and as municipal waste (card￾board, newspapers, etc.).7 Like starch, cellulose is a polymeric form of glucose; unlike

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Preface xiii

starch, cellulose cannot easily be prepared in a highly purifi ed form from many plant

sources. In addition, being a major structural component of plants, cellulose is com￾bined with other polymers of quite different sugar composition (hemicelluloses) and,

more importantly, with the more chemically refractive lignin. Sources of lignocel￾lulosic biomass may only contain 55% by weight as fermentable sugars and usually

require extensive pretreatment to render them suitable as substrates for any microbial

fermentation, but that same mixture of sugars is eminently suitable for the produc￾tion of structures as complex as aromatic intermediates for the chemical industry.8

How practical, therefore, is sourcing lignocellulose for bioethanol production

and has biotechnology delivered feasible production platforms, or are major develop￾ments still awaited? How competitive is bioethanol without the “special pleading” of

tax incentives, state legislation, and (multi)national directives? Ultimately, because

the editor of Nature Biotechnology noted that, for a few months in 2006, a collection

of “A-list” entrepreneurs, venture capitalists, and investment bankers had promised

$700 million to ethanol-producing projects, the results of these developments in the

real economy may soon refute or confi rm the predictions from mathematical mod￾els.9 Fiscal returns, balance sheets, and eco audits will all help to settle the major

issues, thus providing an answer to a point made by one of the contributors to the

fl urry of interest in bioethanol in mid-2006: “biofuels boosters must pursue and pro￾mote this conversion to biofuels on its own merits rather than by overhyping the rela￾tive political, economic and environmental advantages of biofuels over oil.”10

Although the production of bioethanol has proved capable of extensive scale up,

it may be only the fi rst — and, by no means, the best — of the options offered by the

biological sciences. Microbes and plants have far more ingenuity than that deduced

from the study of ethanol fermentations. Linking bioethanol production to the syn￾thesis of the bioorganic chemist’s palette of chemical feedstocks in “biorefi neries”

that cascade different types of fermentations, possibly recycling unused inputs and

further biotransforming fermentation outputs, may address both fi nancial and envi￾ronmental problems. Biodiesel (simple alkyl esters of long-chain fatty acids in veg￾etable oils) is already being perceived as a major fuel source, but further down the

technological line, production of hydrogen (“biohydrogen”) by light-driven or dark

fermentations with a variety of microbes would, as an industrial strategy, be akin to

another industrial revolution.11

A radically new mind-set and a heightened sense of urgency were introduced in

September 2006 when the state of California moved to sue automobile manufactur￾ers over tailpipe emissions adding to atmospheric pollution and global warming.

Of the four major arguments adduced in favor of biofuels — long-term availability

when fossil fuels become depleted, reduced dependence on oil imports, develop￾ment of sustainable economies for fuel and transportation needs, and the reduction

in greenhouse gas emissions — it is the last of these that has occupied most media

attention in the last three years.12 In October 2006, the fi rst quantitative model of

the economic costs of not preventing continued increases in atmospheric CO2 pro￾duced the stark prediction that the costs of simply adapting to the problems posed by

global warming (5–20% of annual global GDP by 2050) were markedly higher than

those (1% of annual global GDP) required to stabilize atmospheric CO2.

13 Although

developing nations will be particularly hard hit by climate changes, industrialized

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xiv Preface

nations will also suffer economically as, for example, rising sea levels require vastly

increased fl ood defense costs and agricultural systems (in Australia and elsewhere)

become marginally productive or collapse entirely.

On a more positive note, the potential market offered to technologies capable

of reducing carbon emissions could be worth $500 billion/year by 2050. In other

words, while unrestrained increase in greenhouse gas emissions will have severe

consequences and risk global economic recession, developing the means to enable

a more sustainable global ecosystem would accelerate technological progress and

establish major new industrial sectors.

In late 2007, biofueled cars along with electric and hybrid electric–gasoline and

(in South America and India) compressed natural gas vehicles represented the only

immediately available alternatives to the traditional gasoline/internal combustion

engine paradigm. Eventually, electric cars may evolve from a niche market if renew￾able energy sources expand greatly and, in the longer term, hydrogen fuel cells and

solar power (via photovoltaic cells) offer “green” vehicles presently only known as

test or concept vehicles. The International Energy Agency estimates that increasing

energy demand will require more than $20 trillion of investment before 2030; of that

sum, $200 billion will be required for biofuel development and manufacture even if

(in the IEA’s assessments) the biofuels industry remains a minor contributor to trans￾portation fuels globally.14 Over the years, the IEA has slowly and grudgingly paid

more attention to biofuels, but other international bodies view biofuels (especially

the second-generation biofuels derived from biomass sources) as part of the growing

family of technically feasible renewable energy sources: together with higher-effi -

ciency aircraft and advanced electric and hybrid vehicles, biomass-derived biofuels

are seen as key technologies and practices projected to be in widespread use by 2030

as part of the global effort to mitigate CO2-associated climate change.15

In this highly mobile historical and technological framework, this book aims to

analyze in detail the present status and future prospects for biofuels, from ethanol

and biodiesel to biotechnological routes to hydrogen (“biohydrogen”). It emphasizes

ways biotechnology can improve process economics as well as facilitate sustainable

agroindustries and crucial elements of the future bio-based economy, with further

innovations required in microbial and plant biotechnology, metabolic engineering,

bioreactor design, and the genetic manipulation of new “biomass” species of plants

(from softwoods to algae) that may rapidly move up the priority lists of funded

research and of white (industrial biotech), blue (marine biotech), and green (environ￾mental biotech) companies.

A landmark publication for alternative fuels was the 1996 publication Hand￾book on Bioethanol: Production and Utilization, edited by Charles E. Wyman of

the National Renewable Energy Laboratory (Golden, Colorado). That single- volume,

encyclopedic compilation summarized scientifi c, technological, and economic data

and information on biomass-derived ethanol (“bioethanol”). While highlighting

both the challenges and opportunities for such a potentially massive production

base, the restricted use of the “bio” epithet was unnecessary and one that is now

(10 years later) not widely followed.16 Rather, all biological production routes for

ethanol — whether from sugarcane, cornstarch, cellulose (“recycled” materials),

lignocellulose (“biomass”), or any other nationally or internationally available plant

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