Written The publication process



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  • The publication process
  • Write paper (more on this in a minute)
  • Submit paper (usually electronically)
  • Make sure format of the paper agrees with journal style
  • Editor acknowledges receipt
  • Paper is sent to 2 or 3 reviewers
  • Reviewers recommend acceptance or rejection
  • Reviews are mixed
  • Sent to a 3rd or 4th reviewer
  • Editor decides to accept or reject
  • Accept as is
  • Accept with revisions
  • Reject
  • Rewrite and submit
  • elsewhere
  • Revised for comments you think are reasonable: rebut those you think are unreasonable
  • Re-submit paper with changes
  • Editor gives final acceptance
  • Paper is reviewed again
  • PUBLISHED!!
  • About a year
  • Generally- two types of work
  • Essay
  • -less structured
  • Scientific Paper
  • Title
  • Abstract
  • Keywords Introduction
  • Materials and Methods
  • Results
  • Discussion
  • Conclusions
  • Literature Cited
  • Types of Writing
  • Scientific writing is more structured and economical than non-scientific (e.g. writing for Arts/Humanities courses)
  • e.g. this is from an essay in a Biology course at Mt. A.
  • When most people think of algae, they either think of the “slimy” green stuff in a lake, or the masses of seaweed that float aimlessly in the sea. Chlorine companies make millions a year producing products that would prevent the build up of algae in a swimming pool. However algae, although it might seem as a nuisance to some, undoubtedly is very important to the ecosystem. It is also of substantial economic use to human society. We have learned to exploit algae’s natural properties and use it for our own beneficial needs., Throughout this paper, several areas of algae will be covered, which will include: physical characteristics, reproduction, types of algae, and their economics uses in society.
  • Types of Writing
  • Scientific writing is more structured and economical than non-scientific (e.g. writing for Arts/Humanities courses)
  • e.g. this is from an essay in a Biology course at Mt. A.
  • When most people think of algae, they either think of the “slimy” green stuff in a lake, or the masses of seaweed that float aimlessly in the sea. Chlorine companies make millions a year producing products that would prevent the build up of algae in a swimming pool. However algae, although it might seem as a nuisance to some, undoubtedly is very important to the ecosystem. It is also of substantial economic use to human society. We have learned to exploit algae’s natural properties and use it for our own beneficial needs., Throughout this paper, several areas of algae will be covered, which will include: physical characteristics, reproduction, types of algae, and their economics uses in society.
  • A gentle critique
  • Too diverse for one essay
  • Scientific Paper
  • Title: Titles should be informative but
  • not overly long OR overly cute.
  • Good title:
  • The effects of three levels of cadmium on the production of thyroid stimulating hormone in Richardson’s ground squirrel, Spermophilus richardsoni,
  • Too long a title:
  • The effects of levels 13, 27 and 40 nmol of cadmium on the pre- and post-lactation production of thyroid stimulating hormone in small fuzzy mammals as exemplified by studies on captive populations of Richardson’s ground squirrel, Spermophilus richardsoni.
  • Too cute a title:
  • Mate choice in hermaphrodites: you won’t score with a spermatophore
  • Scientific Paper
  • Abstract:
  • An abstract is a précis of the entire paper and should be about 5% of its length.
  • This means that for a 3000 word paper the abstract is about 150 words (or 10-15 typed lines)
  • Every section of the paper (Introduction, Materials and Methods, Results, Discussion, Conclusions) should be represented by at least one sentence in the Abstract.
  • Scientific Paper
  • Keywords:
  • Keywords are words that describe a paper. They serve as locators for topics when researchers are search for papers in a particular area.
  • For example, a recent paper with the title:
  • Mechanisms of reproductive isolation among sympatric broadcast spawning
  • corals of the Monastrea annularis species complex
  • Has the keywords:
  • Coral reef, fertilization, hybridization, mass-spawning, speciation
  • Scientific Paper
  • Introduction:
  • one of the hardest sections to write
  • should present historical and/or theoretical precedents to the problem or subject
  • should outline the main areas of the argument in the field
  • should end with a statement of the objectives or hypothesis of the work to follow
  • Literature review
  • INTRODUCTION
  • The Earth is divided into two different planes. Longitude refers to the globe on an ëeast to westí axis, whereas latitude refers to the Earthís division in a north to south orientation. The effects of different latitude have long been of interest to biologists, as different geographic position along a north to south axis is hypothesized to change abiotic factors, such as food availability (Linse et.al., 2006), temperature and salinity (Bertness and Ewanchuk, 2002). These abiotic factors, in turn, play a large role in determining specific biological interations, as well as species responses to changing environmental conditions.
  • It is widely recognized in the biological sciences that differences in latitude result in changes in environmental condition. Several studies regarding the influence of latitudinal differences on biological systems have been completed. Bergmanís and Allenís rules, which states that animals living closer to the North Pole have shorter appendages and larger body sizes than their conspecifics at lower latitudes is an example of one of the many effects different latitudes may have on development (Darlington, 1966). Bertness and Ewanchuck (2002) investigated the role that latitudinal variation plays in the biological interactions of New England salt marshes. They found that at higher latitudes, competition between neighbouring plants increased, and at lower latitudes the relationship between neighbouring marsh plants became more facilitative (Bertness and Ewanchuck, 2002). Leonard (2000) concluded that interactions between the common intertidal algae, Ascophylum nodosum, and the Northern rock barnacle (Semibalanus balanoides) vary according to geographic location. He reported that the reproductive fitness potential of barnacles at southern sites was facilitated by the algal canopy, whereas at northern sites the reproductive fitness potential of individuals was reduced by the algal canopy (Leonard, 2000).
  • Molecular analysis has also revealed that genetic differences in the Northern rock barnacle (Semibalanus balanoides) exist between different sites along the Maine Coast (Rand et.al., 2002). Differences in allozyme genotypes between barnacles sampled at sites along the Maine Coast have been attributed to differences in microhabitat between the different sampling sites (Rand et.al., 2002). Caldwell (2004), found that S. balanoides found at different regions within the rocky intertidal are subject to differing abiotic environments. Due to the high energetic costs required to survive high on the intertidal, such as dessication, low nutrient availability and oxygen stress, barnacles found in this area show a slower rate of development (Caldwell, 2004). Barnacles were sampled from low, middle and high tide levels at Cape Enrage, New Brunswick. Differences in rates of development were found in individuals sampled from the high intertidal area, with these individuals showing almost a monthís developmental delay when compared to their conspecifics found within the mid to low intertidal areas (Caldwell, 2004). In addition to this delay in development, almost half of the barnacles sampled at high tide were found to be lacking any development ovary and oocyte development (Caldwell, 2004).
  • The northern rock barnacle (Semibalanus balanoides) is a common inhabitant of the north Atlantic rocky intertidal (Bertness, 1999). As a dominant organism within the intertidal area, it presents an ideal organism for the study of the effects of latitudinal variation within the Bay of Fundy. S. balanoides are sessile, filter feeding invertebrates, and are commonly found along the mid to high intertidal region of the rocky intertidal (Bertness, 1999). Described as shrimp-like organisms encased in calcium carbonate shell (Bertness, 1999), they feed by extending appendage-like cirri through an open operculum, and ìbeatingî their cirri in order to allow for water current formation and nutrient uptake (Anderson, 1994).
  • S. balanoides are simultaneous hermaphrodites, meaning that they are capable of acting as male and female at the same time (Charnov, 1982). As such, the northern rock barnacle has both functional male and female gonads encased within its body cavity. This makes S. balanoides an interesting organism for the study of the effects of geographic variation on the rate of gonad development. In S. balanoides, the ovaries lie in basal mantle tissue, near the attachment point of the barnacle to the substrate (Anderson, 1994) (Figure 1). The testes are subdivided into several follicles, located within the body cavity in the prosoma, thorax and limb bases (Anderson, 1994)
  • (Figure 1).
  • S. balanoides exhibit internal fertilization (Bertness, 1999). Upon fertilization of the eggs, brooding embryos are incubated within the mantle cavity, after which they are released as naupliar larvae (Bertness, 1999). At this stage, the larvae act as passive particles in the water column, and pass through four naupliar larvae stages (Bertness, 1999). After the fourth naupliar larvae stage, the larvae metamorphoses to a cyprid larvae (Bertness, 1999). It is at this stage that the developing barnacle will attach to the substrate via the use of adhesive antennal glands, and will begin to secrete its calcerous external plates, leading to its adult form (Bertness, 1999) (Figure 2).
  • Figure 1: Lateral section through body cavity of Semibalanus balanoides, showing the location of the ovaries and testes.
  • Figure 2: Diagram of life cycle of Semibalanus balanoides.
  • Living organisms have a given amount of energy available for the purposes of growth, maintenance and reproduction (Heath, 1977). Simultaneous hermaphrodites face the added cost of having to invest in the production and maintenance of both male and female reproductive structures (Heath, 1977). Thus, when compared to a similar gonochoristic species, the simultaneous hermaphrodite is at an energetic disadvantage due its higher investment in reproductive structures (Heath, 1977). Charnov (1982), notes that the production of male and female gametes is directly proportional to the barnacleís access to resources. Thus, if resources are low, this condition is expected to be identifiable by the amount of energy allocated to reproduction.
  • The purpose of this study is to determine how changing latitude affects the timing of the development of sperm, eggs and embryos. Furthermore, I will determine whether or not the size of S. balanoides varies significantly with latitude.
  • I hypothesize that as latitude increases, a delay in development of Semibalanus balanoides will be detected. I further hypothesize that the size of sampled barnacles will decrease as latitude increases
  • Bouchard, 2007
  • Original thesis introduction
  • INTRODUCTION
  • Studies on the correlation of latitudinal gradients with various aspects of any species ecology are well known. Early studies resulted in the generation of several ecophysiological rules (e.g. Allen’s, Bergmann’s, Gloger’s and Rapoport’s) (Hall and Hallgrimson, 2008). These very general rules hide the fact that the response of several species to ecological and climatic changes associated with different latitudes are not always consistent. Some studies show predictable changes with latitude (e.g. Barnes and Barnes 1965, Crisp 1959, Hummel et al 1985, Jonsson and L’Abbé- Lund 1993, Nebel 2005). Others show discontinuous latitudinal clines that can be ascribed to variation in local conditions such as temperature (Barnes 1958, Rand et al 2002, Schmidt and Rand, 1999), primary productivity (Bertness et al, 1991), restriction of gene flow (Brown et al, 2001, Dufresne et al, 2002, Holm and Bourget, 1994), hydrodynamic conditions (Connoly et al 2001, Haase 2003, Hayden and Dolan 1976) shoreline exposure (Kirby et al 1997) and behaviour (McClain 1985, Nebel 2005). Still other studies point to the interactions between biotic and abiotic factors on a species (Leonard, 2000).
  • The acorn (or northern rock) barnacle (Semibalanus balanoides L.) is a common inhabitant of rocky intertidal shorelines of the western Atlantic. Its distribution on the shore is confined to the ‘barnacle band’ (Stephenson and Stephenson, 1972) whose lower limit within the tide range is thought to be determined by biological interactions and the upper limit by abiotic factors (Bertness, 1999).
  • Studies on clinal variation in S. balanoides have pointed to temperature as a controlling factor. While temperature may be involved, its influence is not simple. Barnes (1958) and Crisp (1959) showed that temperature was a factor in egg development only above an 8 or 9C winter isotherm and the effects of temperature lessened as development proceeded. Davenport et al (2005) concluded that temperature had no effect on breeding phenology in S. balanoides . Responses to temperature and thermal stress can depend on the genetic composition of local populations (Rand et al 2001, Schmidt and Rand 1999) and restriction of gene flow (Brown et al, 2001). Finally, some authors (Barnes and Barnes 1958, Bertness et al 1991) have shown that primary production and food availability is a more important factor than temperature in growth and reproduction.
  • We examined changes in the reproductive phenology and size of S. balanoides across a latitudinal gradient in the Bay of Fundy. At one location we have studied (Cape Enrage, N.B), S. balanoides typically mates in October and November, broods embryos in January and February and releases nauplii in February and March (Aiken, unpublished). In this study, we hypothesize that this cycle would start earlier in the lower (southern) Bay of Fundy and become progressively later at higher latitudes.
  • Scientific Paper
  • Materials and Methods:
  • should allow exact duplication of the experiment or field study
  • can be tricky to decide this - how much detail is too much??
  • Scientific Paper
  • Results:
  • Should be very well organized
  • Should present data so that the relevance of the results to the hypothesis is clear
  • Present data once - either in a table or in some figure but NOT both
  • Use the text to highlight important trends or results but not as a written restatement of the results
  • Scientific Paper
  • Results: Some presentation hints
  • 1. Use an appropriate graph
  • For continuous data
  • For discrete data
  • And generally - use a graph instead of a table
  • (more important in a talk)
  • Proportion of infected birds
  • Locality
  • Vancouver
  • Toronto
  • Halifax
  • New York
  • Dallas
  • ??
  • Proportion of infected birds
  • Locality
  • Vancouver
  • Toronto
  • Halifax
  • New York
  • Dallas
  • ??
  • For a publication – don’t use colour
  • This is a ‘bar graph’
  • Proportion of infected birds
  • Locality
  • Vancouver
  • Toronto
  • Halifax
  • New York
  • Dallas
  • This is a ‘grouped bar graph’
  • 2003
  • 2005
  • 2007
  • Histograms
  • -x-axis is continuous
  • Line graphs
  • Heart rate
  • Exercise time
  • Interpolated (“join-the dots”)
  • Heart rate
  • Exercise time
  • Fitted (regression)
  • Avoid too much information
  • Avoid too much information
  • Scientific Paper
  • Results: Some presentation hints
  • 2. Write the results from a biological point of view not a statistical one
  • Bad:
  • An unpaired t-test with a t value of 4.56, 23 degrees of freedom and a p of .001 of the number of days that nestlings spent in the nest showed that offspring of older birds left their nest later than offspring of younger birds
  • Better:
  • The number of days that nestling spent in the nest was significantly lower for young parents (unpaired t-test, t = .456, df =24, p=.001)
  • Scientific Paper
  • Discussion:
  • should analyse in words what you think your data mean
  • should show the relevance of your findings to other literature in the field
  • should show how your findings contribute to any controversies or ambiguities in the field
  • should BRIEFLY suggest avenues for further research
  • Scientific Paper
  • Literature cited:
  • Few people appreciate that there is a difference between a “Bibliography” and “Literature (or References) Cited”
  • Bibliography is all the reference material you looked up on a subject whether you cited it in the text of your paper or not
  • Literature (or References) Cited are ONLY those references that appear in the text of your paper
  • Scientific Paper
  • Literature cited:
  • There are a great number of stylistic differences in how references are cited but there are a few general rules that apply to most papers:
  • All cited literature goes in alphabetical order of first author at the end of the paper.
  • All references used in the paper must be cited at the end.
  • References from the non-professional literature (e.g. National Geographic, newspapers, popular magazines) are generally frowned upon
  • Websites are terrible reference material. Never use them!
  • The only exception to (4) is electronic peer-reviewed journals
  • For a summary of ways to cite various kinds of articles:
  • http://www.mta.ca/~raiken/Courses/4401/citation.html
  • A final sneaky little trick:
  • My own preference when writing a scientific paper is to write the sections in the following order:
  • Working title
  • Materials and Methods
  • Results
  • Discussion
  • Conclusions
  • Introduction
  • Literature Cited
  • Title
  • Abstract
  • Keywords
  • Essays
  • Essays are more difficult to assign rules (beyond style and grammar) but a few things to keep in mind
  • An essay should have a well-defined theme to it. Its not just an arbitrary collection of facts on a topic.
  • 2. An essay should have a fairly narrow theme to it. If you wanted to do an essay on “The behaviour of beavers”, you’re already in trouble. An essay on “Maternal behaviour in beavers and its consequences for offspring survival” would be much better because you have already focussed the topic.
  • 3. Avoid extraneous, “off-the-topic” material. You would not put information on how beavers build dams or the effect of beaver dams on farmland in the essay above.
  • 4. Generally, follow the rules for writing introductions and discussions of scientific papers. The only thing to keep in mind is that the “data” you use in support of whatever arguments you are making comes from the literature and not from your own experiments
  • Essays
  • Essays are more difficult to assign rules (beyond style and grammar) but a few things to keep in mind
  • Avoid dramatic, cute or flowery writing
  • e.g. In our maternal behaviour in beavers example:
  • A really bad introduction is:
  • Beaver mothers, like all other mothers in the animal kingdom, give their babies a great deal of care and affection
  • A really bad conclusion is:
  • So we have seen how beaver mothers work hard to make sure their babies will have a successful life. Perhaps we, as humans, can learn from their example and build a better societies for all of us to live in.
  • Aiken’s
  • Use-These-Words-Incorrectly-And-You’ll-Die
  • List
  • Effect and affect - effect is a noun, affect is a verb
  • Impact - it’s a noun - don’t use it as a verb (better still, don’t use it at all)
  • Amount and number - amount refers to continuous quantities, number refers to discrete quantities (i.e. “number of people” not an “amount of people”)
  • Varying - it means changing or fluctuating - it does not mean “different”
  • Basically - overused and drifting to being meaningless
  • Data - it’s plural - “data are” not “data is”
  • Compare to - the proper expression is “Compare between”
  • Between/among - between refers to two objects, among to more than two
  • Which/that - this is tricky but “that” is restrictive, which means it tells you a necessary piece of information about its antecedent. “Which” is non-restrictive: it does not limit the word to which it refers.
  • http://andromeda.rutgers.edu/~jlynch/Writing/index.html
  • Aiken’s
  • Use-These-Words-Incorrectly-And-You’ll-Die
  • List
  • AND JUST FOR BIOLOGY
  • Genus - the plural is genera not genuses
  • Species -singular and plural are the same word
  • Italics - either underline or put in italics the genus and species name (= the binomial) for any organism - e.g. Homo sapiens or H. sapiens
  • Methodology -”-ology” on the end of a word means “study of”. For example, Biology is the Morphology study of life. Methodology is the study of methods and morphology is the study of
  • Etc. structure. Use “methods” and “structure”.
  • Aiken’s
  • Use-These-Words-At-All-And-You’ll-Die
  • List
  • quite,
  • very,
  • extremely,
  • as it were,
  • moreover,
  • it can be seen that,
  • it has been indicated that,
  • basically,
  • essentially,
  • totally,
  • completely,
  • therefore,
  • it should be remembered that,
  • it should be noted that,
  • thus,
  • it is imperative that,
  • at the present moment in time.


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