Writing a review paper is tedious but well worth it

1. NRES 720How I Write a Review Paper(Not the only way, but a way that has been very rewarding for me.) Dale W. JohnsonSpring 2013 Chapter 8 in the book gives great guidelines for the mechanics and ethics (plagarism, source attribution) of writing review papers. This lecture will complement that by attempting to encourage you to write your own review papers, starting now. Nothing but good can come from this effort. (How many things in life can you say that about?)

2. Writing a review paper is tedious but well worth it • You are not too young to do it. Old guys are often too lazy to do it and want to write books citing their own work instead. • Reading 50-100 papers is in fact very tedious and time consuming. Face this fact. Bulldoze through it. • If you take the time to do it, you will find that you are the world expert – or at least one of them - on the subject. • And it is my experience, at least, that review papers get accepted much more often than regular science study papers. • This in turn will likely lead to: • Speaking invitations • Grant money • Reputation building

3. Techniques for reviewing the literature • Google and Google Scholar • Other search engines and library resources (Amy Shannon) • Sequential “skimming” • Note taking • Meta Analysis (?) • Synthesis

4. Google and Google Scholar • Wonderful tools for recent and classic literature • Not so great for older, more obscure but potentially very relevant literature – you still need to look at literature cited sections for this! • Worthless for data sets that were collected for another purpose but might be useful to you

5. The volume of literature on your review subject can be daunting. You should view yourself as a bulldozer: relentless, unstoppable, mowing down all obstacles in its path. And there are shortcuts. References relevant to a review on biofuels

6. Sequential “skimming” – my technique Skim abstract for key words/phrases Find any? Yes No Read abstract, skim tables and figures Put in reserve pile Items of even remote interest? Yes No Make notes (bullets on paper, 3 x 5 cards) Make a small note and put in possibles pile Items considerable interest? No Yes Read the entire paper in depth, make extensive notes, put in definites pile Put in probables pile

7. I am doing a review on the effects of atmospheric N deposition on soil exchangeable calcium and acidification. Skim this in 10 seconds and tell me where it goes in the decision tree. Carbon and Nutrient Contents in Soils from the King’s River Experimental Watersheds, Sierra Nevada Mountains, California D. W. Johnsona*, C. T. Hunsakerb, D. W. Glassa, B. M. Raua, B.A. Roathc ABSTRACT Soil C and nutrient contents were estimated for eight watersheds in two sites (one high elevation, Bull, and one low elevation, Providence) in the King’s River Experimental Watersheds in the western Sierra Nevada Mountains of California. Eighty seven quantitative pits were dug to measure soil bulk density and total rock content, while three replicate surface samples were taken nearby with a bucket auger (satellite samples) to the same depth as surface pit samples. Results showed that the higher elevation Bull watersheds had significantly greater C, N, and B contents and significantly lower extractable P, exchangeable Ca2+ Mg2+, and Na+ contents (kg ha-1) and lower pH than the lower elevation Providence watersheds. Soil NH4+ and mineral N contents were high in both the Bull and Providence watersheds and could not be related to any measured soil property or attributed to known rates of atmospheric deposition. Nutrient analyses on satellite samples were comparable to those taken from pits when averaged on a watershed or site (Bull and Providence) scale, but quite variable on an individual grid point basis. Elevated Zn values from the quantitative pit samples suggested contamination by field sieving through a galvanized screen. Had the amount of large rocks within the soil sample not been accounted for with quantitative pit analyses, estimates of fine earth and associated C and nutrient contents (kg ha-1) would have been overestimated by 16 to 43%. Keywords: Quantitative soil pit, carbon, nutrients, coarse fragments, Sierra Nevada Mountains

8. I would give it a remote interest and skim on. Where does reading the full abstract get you to in the decision tree? Carbon and Nutrient Contents in Soils from the King’s River Experimental Watersheds, Sierra Nevada Mountains, California D. W. Johnsona*, C. T. Hunsakerb, D. W. Glassa, B. M. Raua, B.A. Roathc ABSTRACT Soil C and nutrient contents were estimated for eight watersheds in two sites (one high elevation, Bull, and one low elevation, Providence) in the King’s River Experimental Watersheds in the western Sierra Nevada Mountains of California. Eighty seven quantitative pits were dug to measure soil bulk density and total rock content, while three replicate surface samples were taken nearby with a bucket auger (satellite samples) to the same depth as surface pit samples. Results showed that the higher elevation Bull watersheds had significantly greater C, N, and B contents and significantly lower extractable P, exchangeable Ca2+ Mg2+, and Na+contents (kg ha-1) and lower pH than the lower elevation Providence watersheds. Soil NH4+ and mineral N contents were high in both the Bull and Providence watersheds and could not be related to any measured soil property or attributed to known rates of atmospheric deposition. Nutrient analyses on satellite samples were comparable to those taken from pits when averaged on a watershed or site (Bull and Providence) scale, but quite variable on an individual grid point basis. Elevated Zn values from the quantitative pit samples suggested contamination by field sieving through a galvanized screen. Had the amount of large rocks within the soil sample not been accounted for with quantitative pit analyses, estimates of fine earth and associated C and nutrient contents (kg ha-1) would have been overestimated by 16 to 43%. Keywords: Quantitative soil pit, carbon, nutrients, coarse fragments, Sierra Nevada Mountains

9. Note: This is basically a report on soil characteristics and only mentions atmospheric N deposition in passing. Maybe useful background, but not right on the target. It would go into the possibles file. Carbon and Nutrient Contents in Soils from the King’s River Experimental Watersheds, Sierra Nevada Mountains, California D. W. Johnsona*, C. T. Hunsakerb, D. W. Glassa, B. M. Raua, B.A. Roathc ABSTRACT Soil C and nutrient contents were estimated for eight watersheds in two sites (one high elevation, Bull, and one low elevation, Providence) in the King’s River Experimental Watersheds in the western Sierra Nevada Mountains of California. Eighty seven quantitative pits were dug to measure soil bulk density and total rock content, while three replicate surface samples were taken nearby with a bucket auger (satellite samples) to the same depth as surface pit samples. Results showed that the higher elevation Bull watersheds had significantly greater C, N, and B contents and significantly lower extractable P, exchangeable Ca2+ Mg2+, and Na+contents (kg ha-1) and lower pH than the lower elevation Providence watersheds. Soil NH4+ and mineral N contents were high in both the Bull and Providence watersheds and could not be related to any measured soil property or attributed to known rates of atmospheric deposition. Nutrient analyses on satellite samples were comparable to those taken from pits when averaged on a watershed or site (Bull and Providence) scale, but quite variable on an individual grid point basis. Elevated Zn values from the quantitative pit samples suggested contamination by field sieving through a galvanized screen. Had the amount of large rocks within the soil sample not been accounted for with quantitative pit analyses, estimates of fine earth and associated C and nutrient contents (kg ha-1) would have been overestimated by 16 to 43%. Keywords: Quantitative soil pit, carbon, nutrients, coarse fragments, Sierra Nevada Mountains

10. Note taking • Paper notes – flexibility for where to review (outside, on the bus, plane….) • I like notebook paper with Author, date as if a citation then some very brief notes • Spreadsheets have the advantage of being sortable by subject, but inconvenient on bus, plane, etc. • After you are all finished, make some meta-notes and try to see where things coalesce and where the gaps are • Start writing at this point and do not try to get the first draft right; plan on many drafts.

12. Synthesis • After you are all finished with notes, make some meta-notes and try to see where things coalesce and where the gaps are • Start writing at this point and do not try to get the first draft right; plan on many drafts. Be objective!! • As you write, go back to 1) key papers and 2) possibles and probables for data sets that may be of use even if they were not intended for what you want.

13. Meta Analysis • A response to criticisms of thetraditional, ‘narrative’ review: • Influenced by unstated reviewer biases. • Conflicting conclusions possible from reviews of the same literature. • Inefficient, often biased, literature sampling. • Lack of statistical rigor. • Simple vote counting with no account of the rigor (sample size or other factors) of any individual study

14. A review paper based on simple vote counting

15. Simple histograms tell us nothing about quality of each study (for example, the number of replicates can range from 1 to 20

19. Meta Analysis

21. Meta Win http://www.metawinsoft.com/

23. Now we can assign some error bars on the overall patterns, weighting each study by the number of replicates or whatever other factor is relevant.

27. Meta Analysis • Meta Analysis disadvantages • Has to be based on data common to many studies • Not conducive to really new insights based on accumulated knowledge • No substitute for the “traditional literature review” where ideas rather than data are reviewed

29. Pay attention to older papers • There is much reinventing of the wheel out there • Good ideas and sound results are not limited to the age of the computer and internet • Example: the concept of “Progressive Nitrogen Limitation” for forest growth response to elevated CO2

30. Progressive Nitrogen Limitation of Ecosystem Responses to Rising Atmospheric Carbon Dioxide YIQI LUO, BO SU, WILLIAM S. CURRIE, JEFFREY S. DUKES, ADRIEN FINZI, UELI HARTWIG, BRUCE HUNGATE, ROSS E. MCMURTRIE, RAM OREN, WILLIAM J. PARTON, DIANE E. PATAKI, M. REBECCA SHAW, DONALD R. ZAK, AND CHRISTOPHER B. FIELD A highly controversial issue in global biogeochemistry is the regulation of terrestrial carbon (C) sequestration by soil nitrogen (N) availability. This controversy translates into great uncertainty in predicting future global terrestrial C sequestration. We propose a new framework that centerson the concept of progressive N limitation (PNL) for studying the interactions between C and N in terrestrial ecosystems. In PNL, available soil N becomes increasingly limiting as C and N are sequestered in long-lived plant biomass and soil organic matter. Our analysis focuses on the role of PNL in regulating ecosystem responses to rising atmospheric carbon dioxide concentration, but the concept applies to any perturbation that initially causes C and N to accumulate in organic forms. This article examines conditions under which PNL may or may not constrain net primary production and C sequestration in terrestrial ecosystems. While the PNL-centered framework has the potential to explain diverse experimental results and to help researchers integrate models and data, direct tests of the PNL hypothesis remain a great challenge to the research community. Bioscience 54: 731-739 (2004)

32. Turner, J. 1981. Nutrient cycling in an age sequence of western Washington Douglas-fir stands. Ann. of Bot. 48: 159-169 .

33. Turner, J. 1981. Nutrient cycling in an age sequence of western Washington Douglas-fir stands. Ann. of Bot. 48: 159-169 .

34. Stages of forest stand development: • Increasing foliage mass, high increment, great demand for N from soil • Foliage and litterfall reach steady-state; increment decreases dramatically because only woody biomass increases; forest floor continues to increase and tie up nitrogen (progessive N limitation, PNL) • Senescence and decline, PNL continues Cool Ecosystem III I II Forest Floor Mass or N (kg ha-1) Woody Biomass Understory Foliage Time (years)

35. My own reviews Johnson, D.W., and D.W. Cole. 1977. Anion mobility in soils: Relevance to nutrient transport from terrestrial to aquatic ecosystems. Ecological Research Series, U.S. Environmental Protection Agency, Corvallis, OR. EPA-600/3-77-068. 27 p. Johnson, D.W., and D.W. Cole. 1980. Anion mobility in soils: Relevance to nutrient transport from terrestrial ecosystems. Environ. Int. 3: 79-90. Johnson, D.W., J. Turner, and J.M. Kelly. 1982. The effects of acid rain on forest nutrient status. Water Resour. Res. 18: 449-461. Johnson, D.W., H. Van Miegroet, D.W. Cole, and D.D. Richter. 1983. Contributions of acid deposition and natural processes to cation leaching from forest soils: A review. J. Air Pollut. Cont. Assoc. 33: 1036-1041. Johnson, D.W. Sulfur Cycling in forests. 1984. Biogeochemistry 1: 29-44. Johnson, D.W., and D.D. Richter. 1984. Effects of atmospheric deposition on forest nutrient cycles. Tappi J. 67: 81-85. Johnson, D.W., M.S. Cresser, S.I. Nilsson, J. Turner, B. Ulrich, D. Binkley, and D.W. Cole. 1991. Soil changes in forest ecosystems: Evidence for and probable causes. Proceedings, Royal Society of Edinburgh 97B: 81-116. Johnson, D.W. 1992. Effects of forest management on soil carbon storage. Water Air, and Soil Poll. 64: 83-120.

36. My own reviews Johnson, D.W. 1992. Nitrogen retention in forest soils. J. Environ. Qual. 21: 1-12. Johnson, D.W., R.B. Susfalk, R.A. Dahlgren, and J.M. Klopatek. 1998. Fire is more important than water for nitrogen fluxes in semi-arid forests. Environ. Sci. Pol. 1: 79-86. Johnson, D.W., and P.S. Curtis. 2001. Effects of forest management on soil carbon and nitrogen storage: Meta Analysis. For. Ecol. Managem. 140: 227-238. Johnson, D.W., R.B. Susfalk, T.G. Caldwell, J.R. Murphy, W.W. Miller, and R.F. Walker. 2004. Fire Effects on Carbon and Nitrogen Budgets in Forests. Water, Air, and Soil Pollut. Focus 4: 263-275. Johnson, D.W. 2006. Progressive Nitrogen Limitation in Forests: A Review of the Literature and Implications for Long-term Responses to Elevated CO2. Ecology 87:64-75

37. Johnson and Cole, 1977 Invited Review for EPA (based on dissertation) Johnson and Cole, 1980 Invited Review Basic Research NSF Proposal funded Solicited Review (paid for) Johnson et al 1982 1st EPRI Proposal funded The Acid Rain Bonanza Days 2nd EPRI/EPA/SCS Proposal funded ($12.5 M, 5 yrs) More funding by EPA Multiple publications, reviews, book

38. Johnson 1992 (Nitrogen) Found old (1940’s era) Swedish papers dealing with abiotic N retention Wrote proposal (nearly got scooped) NSF Proposal funded (via Indy Burke) Several publications

39. Johnson 1992 (Soil C) Review funded by NCASI Widely cited, many invited talks, projects on harvesting effects on soil C and nutrients Funded again for update, used meta analysis Johnson and Curtis, 2001 Even more widely cited, many invited international talks, projects on harvesting effects on soil C and nutrients Multiple additional publications

40. Johnson 2006 (N and CO2) Invited post-script for CO2 work Review for symposium and new journal (Biogeochemistry) Johnson 1985 (Sulfur) Well cited, projects sulfur associated with acid rain research Nice compliments, no followup as yet And so on. My experience is that it is well worth the effort