Authors’ Responses to Reviewers Due to the addition of figures, the page, line, reference, and figure numbers are no longer the same as before. Therefore, all changes listed below are based on the updated page, line, reference, and figure numbers. Comments by reviewers are shown below in red, followed by the respective response in black. Referee: 1 Reviewer General Comment 1 It should perhaps be mentioned that in addition to the 10 companies/projects described here, numerous other technology developers are also working in this area. While their initial project scale may be less than 25 MGY, or their timing may be later than 2014, many other companies are actively working towards commercial development. These include Aemetis, Amyris, Cobalt, Coskata, Enerkem, Fulcrum, Gevo, LanzaTech, LS9, Mascoma, UOP, Virent, and others. Author Response to General Comment 1 The following sentence has been added starting at page 22, line 9: “DuPont, KiOR, POET, and Sundrop have publicly discussed building additional commercial-scale cellulosic biofuel facilities in the U.S. beyond 2014 should their initial projects prove successful, while companies including Genahol, Lanzatech, Rentech, and Virent have proposed building their first such facilities during the same time frame.” Reviewer General Comment 2 Biofuel terminology is always confusing. In part, this derives from the EPA definitions under the RFS2 standard for renewable fuel, advanced biofuel, cellulosic biofuel, and biomass-based diesel. In this paper, it would be especially helpful to explain the differences between “advanced biofuel” and “cellulosic biofuel.” The term “cellulosic biofuel” seems to imply fuels produced only from cellulose, which may limit them to biochemical processes involving hydrolysis of cellulose, such as those technologies being developed by POET, DuPont, BP, and others. Are thermochemical processes that treat lignocellulosic biomass even considered to be “cellulosic biofuels,” or are these “advanced biofuels”? Author Response to General Comment 2 The EPA’s biofuel category definitions have unfortunately led to significant confusion in the field, as its definition of “advanced biofuels” includes 1st generation pathways such as sugarcane ethanol that most observers don’t consider to meet the general definition of “advanced”. Unfortunately, the addition of an overview of the RFS2 biofuel category definitions and their differences with commonly accepted definitions would greatly increase the word count and risk confusing readers as to the scope of the analysis. The ambiguity of the phrase “cellulosic biofuel” is noted, however, and the EPA’s formal definition of the category has been referenced by adding the following sentence beginning at page 3, line 7: “This category is limited to renewable fuels derived from cellulose, hemicellulose, or lignin feedstock that originates from renewable biomass.” Reviewer General Comment 3 It would also be helpful to add a few comments about algal feedstocks. As algae contain no cellulose, fuels produced from them can’t be classified as cellulosic biofuels. However, they could be classified as “advanced biofuels” and/or “biomass-based diesel.” Some of the products from pyrolysis and/or gasification of lignocellulosic feedstocks (including the KiOR and ClearFuels cases described in this paper) will also produce “biomass-based diesel.” It might be helpful to add a column in Table 1 to indicate the expected biofuel(s) produced in each case. Author Response to General Comment 3 Microalgae lipids were excluded from this analysis because, as a non-lignocellulosic feedstock, they do not meet the EPA’s definition of a cellulosic biofuel (see Author Response to General Comment 2). Algal fuels do qualify for the biomass-based diesel biofuel category, however, which has been enormously successful. The inclusion of algal fuels would therefore greatly increase the scope of the analysis, which is limited to the cellulosic biofuel category, which has yet to achieve successful commercialization. Regarding Table 1, all of the facilities listed will produce cellulosic biofuel. (Due to the nested nature of the RFS2 biofuel categories the biofuels produced at these facilities will also qualify for the other categories as well, although they will almost certainly pursue the cellulosic biofuel category due to its higher expected RIN values.) The EPA’s formal definition of “cellulosic biofuel” has been added beginning at page 3, line 7 so as to make the scope of the analysis clear. Reviewer General Comment 4 There is currently considerable interest in bio-based butanol fuels, although this is not mentioned in the paper. It would be useful to add something about bio-butanol, and explain how it could contribute to the “advanced biofuel” and/or “cellulosic biofuel” categories under RFS2. Author Response to General Comment 4 Biobutanol will only qualify as a cellulosic biofuel if it is derived from lignocellulosic biomass. At present there are no official plans for the commercial-scale production of cellulosic biobutanol, apart from vague statements from officials at Gevo and Butamax about aiming to achieve such production by the end of the decade. We decline to include biobutanol because it does not meet the scope of this paper. Reviewer General Comment 5 Can something be said about the matching of feedstocks with conversion technologies? For example, are herbaceous feedstocks more suitable for enzymatic hydrolysis processes, while woody feedstocks are more suitable for thermochemical conversion processes? Where does municipal solid waste (MSW) fit into the feedstock picture? Author Response to General Comment 5 While it is possible that feedstock composition influences product yields and can be optimized for specific pathways as a result, there is currently insufficient experimental data to demonstrate such a relationship with statistical significance. With regard to the cellulosic biofuel facilities, there doesn’t appear to be a pattern with regard to pathway and feedstock: two of the thermochemical facilities use woody biomass, one of the thermochemical and one of the biochemical facilities employ mixed biomass, one of the biochemical facilities employs woody biomass, and three of the biochemical facilities employ herbaceous biomass. MSW (other than separated yard and food waste) does not qualify as “renewable biomass” according to the EPA’s Final Rule on the regulation of fuels under the RFS2, and therefore does not qualify as a cellulosic biofuel feedstock. Reviewer Specific Comment 1 On page 4, the authors describe upgrading of bio-oil as involving either fluid catalytic cracking (FCC) or hydroprocessing. I would expect that FCC-produced bio-oil would also require some degree of hydroprocessing before a satisfactory fuel blendstock is produced. Also, it is stated that “Bio-oil can be fractionated into carbohydrate-derived and lignin-derived components for separate upgrading to optimize the process.” How is such fractionation achieved? Author Response to Specific Comment 1 While hydrotreating prior to FCC improves yields of hydrocarbon monomers, recent work has shown that it is not necessary to produce hydrocarbons from bio-oil (Vispute et al. 2010). The following citation has been included as Reference 9 to further support this statement: Vispute TP, Zhang H, Sanna A, Xiao R, Huber GW. Renewable Chemical Commodity Feedstocks from Integrated Catalytic Processing of Pyrolysis Oils. Science. 2010;330(6008):1222-7. Bio-oil fractionation can be achieved via a series of condensers and electrostatic precipitators. This sentence has been revised and now reads: “Bio-oil can be fractionated into carbohydrate-derived and lignin-derived components via a series of condensers and electrostatic precipitators for separate upgrading to optimize the process.” Additionally, the following citation has been added as Reference 10 to the end of the sentence to support this statement: Pollard AS, Rover MR, Brown RC. Characterization of bio-oil recovered as stage fractions with unique chemical and physical properties. Journal of Analytical and Applied Pyrolysis. 2012; 93:129-38. Reviewer Specific Comment 2 In describing biomass gasification and Fischer-Tropsch synthesis on page 5, the authors point out that such processes can convert “both carbohydrate and lignin into biofuels.” The same could be said about pyrolysis processes. Author Response to Specific Comment 2 The sentence prior to the quoted sentence has been revised and now reads: “Like fast pyrolysis and upgrading, this approach to biofuels has the advantage of converting all the components of the biomass into fuel.” Reviewer Specific Comment 3 In the methanol-to-gasoline (MTG) process described on page 7, dimethylether (DME) is produced as an intermediate. In certain applications, DME is an excellent fuel in its own right. Is DME considered an “advanced biofuel”? Author Response to Specific Comment 3 DME has been proposed as an alternative transportation fuel and, providing the pathway meets a 50% reduction in GHG emissions relative to gasoline, could qualify as an advanced biofuel. We are not aware of any plans to produce fuel DME (as opposed to DME as an intermediate product) in the U.S. on a commercial scale, however, and it falls outside the scope of this analysis. Reviewer Specific Comment 4 On page 12 (authors’ line 8) the term “MTPD” is used without definition. Presumably, this means metric tonnes per day. The capacity value of 1637 MTPD looks odd, likely because it was derived by translation of a plant capacity defined in terms of U.S. tons/day. It might be clearer to show the plant capacity in both terms. Author Response to Specific Comment 4 This sentence (page 12, line 16) has been revised and now reads: “Facility capacity is based on 1637 metric ton (MT) per day (1800 tons per day) feedstock consumption with expected initial fuel yield of 75 gal/MT feedstock.” Reviewer Specific Comment 5 The BP Biofuels Highlands project described on page 15 has recently been cancelled by BP. This news update should be confirmed, and the text modified accordingly. Author Response to Specific Comment 5 All references to the BP Biofuels Highlands project have been removed from the manuscript to reflect its recent cancellation, and the rest of the manuscript has been updated accordingly. Reviewer Specific Comment 6 Figures 7 and 8 should be combined into a single figure – perhaps a pie chart showing red for hydrocarbon-based fuels and green for cellulosic ethanol, with individual slices for the subcategories of each. To provide greater context, this information about cellulosic biofuel output could be shown as an “exploded pie chart,” with an unexploded pie also containing slices for corn ethanol and biomass-based diesel. Author Response to Specific Comment 6 Figures 7 and 8 have been combined into a single stacked column figure. Each column is divided according to pathway for each fuel type. The caption for Figure 8 has been deleted, as have both of the original figures. Reviewer Specific Comment 7 Page 3, author line 2: The sentence should be re-worded to avoid use of both “mandates” and “mandatory.” Author Response to Specific Comment 7 The word “mandatory” has been removed from the sentence (page 3, line 2), which now reads: “The revised Renewable Fuel Standard (RFS2) mandates the utilization of minimum volumes of biofuel in the U.S. transportation fuel supply.” Reviewer Specific Comment 8 Page 8: The last sentence on the page is confusing, and should be re-written. Author Response to Specific Comment 8 The sentence beginning on page 8, line 24 has been rewritten and now reads: “Pretreatment readily hydrolyzes hemicellulose, enabling this separation.” Reviewer Specific Comment 9 Page 9, author line 2: “While fermentation to ethanol is a possible route, one dilute acid hydrolysis pathway …” Author Response to Specific Comment 9 The sentence beginning on page 9, line 4 has been revised and now reads: “While fermentation to ethanol is a possible route, one dilute acid hydrolysis pathway currently being considered for commercialization…” Reviewer Specific Comment 10 Page 13, author line 4: “Rentech also stated that the decision on whether or not to proceed ...” Author Response to Specific Comment 10 The sentence beginning on page 13, line 12 has been revised and now reads: “Rentech also stated that the decision on whether or not to proceed…” Reviewer Specific Comment 11 Page 16, author line 15: The term “MGY” should be used rather than “BGY.” Author Response to Specific Comment 11 The sentence beginning on page 16, line 22 has been revised to read: “Project Liberty is the first step in the joint venture’s plan to produce 3500 MGY of cellulosic ethanol by 2022, 1000 MGY of which will come from adding cellulosic ethanol capacity to POET’s 27 existing corn ethanol facilities.” Referee: 2 Reviewer General Comment 1 However, I found the technology section to be unbalanced in the description of the technologies. Author Response to General Comment 1 One challenge in drafting an overview of several different pathways, as this analysis does, is that the volume of literature available for each varies widely. Whereas processes such as FT synthesis and cellulosic ethanol via enzymatic hydrolysis have been investigated (and, in the case of the former, operated on a commercial scale) quite literally for several decades, other pathways such as consolidated bioprocessing have been the subject of research for only a fraction of that time. Furthermore, the varying complexity of the different pathways directly influences the amount of space needed to describe each. With these limitations in mind, we believe that the technology section is balanced as it currently stands. Reviewer General Comment 2 The perspective part was underwhelming and obvious. Some insights on how the US will meet its liquid fuel demand without cellulosic biofuels would be additive vs. it will be harder for cellulosic biofuels if these commercial facilities fail. Author Response to General Comment 2 The following paragraph has been added beginning at page 22, line 9: “DuPont, KiOR, POET, and Sundrop have publicly discussed building additional commercial-scale cellulosic biofuel facilities in the U.S. beyond 2014 should their initial projects prove successful, while companies including Genahol, Lanzatech, Rentech, and Virent have proposed building their first such facilities during the same time frame (61). The success of these early projects would likely lead to a significant increase in capital investment within the cellulosic biofuels sector in the near-to-intermediate term. Their failure, on the other hand, could lead to a substantial shift in the direction of U.S. alternative fuels policy. The recent adoption of new processes enabling the widespread extraction of shale gas has caused the domestic price of natural gas to fall sharply, and the U.S. Energy Information Administration (EIA) forecasts it to remain low on a historical basis due to large domestic shale gas reserves. A continued lack of success by cellulosic biofuel producers could lead policymakers to instead pursue natural gas-based alternative fuels, whether in the form of compressed natural gas (CNG) vehicles or gas-to-liquid (GTL) pathways. In 2011 a bipartisan group of U.S. representatives introduced legislation that would subsidize the use of natural gas-powered vehicles (62). While the bill has been in subcommittee for more than a year, support for similar proposals is likely to grow if the cellulosic biofuels industry fails to prove its commercial-scale technical and economic feasibility in the next few years.”