Journal Club Schedule (Semester 2)

Date	Name
23 July	Bianca
30 July	Samantha
6 August	Sarita
13 August	Ilkser
20 August	-
27 August	Kerry
3 September	Catherine
10 September	(SAGS)
17 September	Arrie
25 September	Bianca
1 October	Paulette
8 October	Michael
15 October	Angelika
22 October	Carel
29 October	Sarita
5 November	Ilkser

MEEP Writing Workshop June 2012 - summary

Thanks to Graeme and Paulette for an excellent workshop. Below are my notes. I've made these as a pdf which I'll distribute if needed. It is very much my interpretation; give yours in comments. My apologies to Graeme for bowdlerizing his pithy quotes. I'm including a couple of comments fore and aft on where we can take it from here. Download FreeMind - it will Shake Your Tree....perhaps I will update this with a MindMap!

In preparing for the workshop I had an idea that Graeme's section would be an interesting scene setter but that we would get most out of our focal presentations. In the event it was the other way around. Our presentations and discussion were focussed on project details, not on writing papers - we needed the workshop first, before preparing presentations for another time. We need MindMaps focussing on Sense and Structure, rather than results, figures and interpretation.

Another observation on our discussions - it felt slightly prickly; defensive or critical, rather than supportive. This is counterproductive (see the WARNING below). The projects were excellent, each showing novelties in data with corresponding innovations in interpretation. These are publishable in prestige journals. The benefits of co-operation and support, however, cannot be gainsaid - everyone's confidence in writing improves. In our game there are better strategies than Tit for Tat, ones based on tolerance that give a greater overall pay-off. As JF Kennedy put it, "A rising tide lifts all boats".

___________________________________________________________________________

University of Pretoria, Genetics Dept

Molecular Ecology & Evolution Program (MEEP)

Writing Workshop

with

Graeme Addison

Otter's Haunt, Parys

Mon 4^th June 2012

ATTITUDE

Trust yourself

• Writing is an intrinsically messy & emotionally traumatic process - get used to it.
• Disorganization is inherent in the writing process, but you should not be disorganized
• Making the transition from a cloud of ideas to a railway line, of logically ordered statements on paper, is a difficult process. Trust yourself – let it come naturally. If not, relax, do something else but set a time limit, then try one of the techniques below.
• Don't get anxious, it WILL happen. The subconscious often leads. Don't try to take command, rely on your intuition...“you can not see the object if you stare at it”
• Good writing is succint and takes time...“Sorry I ran out of time, it is twice what you asked for”
• Hold off those people who demand immediate action and delivery, but keep thinking about it and discussing it.

Thinking on different levels

• The Big Picture: interpreting and analysing your position – where does this study fit in, why are we doing this, what significant outcomes are there for the field
• Be clear about your topic
• The Little Picture: attending to the details (citations, methodology, format)

You need help!

• Writing is a lonely job, you have to be able to tell people what you are doing.
• Don't withdraw, talk with supportive friends, family and colleagues.
  • BE WARNED: Avoid aggressive and overly critical audiences at this stage
• Often you don't know what you are trying to say. By telling others you will find ways to express yourself on paper. The teacher learns most from any lesson.
• Even technical readers need to be told specialist concepts in layman's terms
• The best writing is concise...bright, simple, and fun (target excess adjectives)

PROBLEMS (Brainstorming, 3 quick ideas)

Confusion & Emotional Blockage

• Uncertainty about the Big Picture; Work on conceptualization
• Fear of criticism; Fear becomes writer's block
• The pain of writing (like childbirth); Do other things but keep it in mind.
  • Do other things but keep it in mind - carry a notebook and jot down ideas
  • Communicate, talk to a friend about it – helps to concretize ideas

Procrastination & Avoidance Behaviour

• Difficulty distinguishing valid disruptions from avoidance
• Compulsive revising while writing
  • Try Snap Writing; Use the Free-Writing technique (below)

Perfectionism (the unattainable = procrastination + avoidance + emotional blockage)

• Getting stuck on details, small hurdles that obstruct overall progress
• Getting sidetracked into related topics – the reference trail
  • Synthesists versus analysts (lumpers versus splitters of concepts)
• Keats was never satisfied but realised his poems were good enough for release

Order and Disorder

• The entropy of writing: a systematic approach doesn't work
• Trying to do it all at once, in one go, usually doesn't work either
• Prioritizing what is important for the project, yourself and others is necessary but difficult
  
  

STRATEGIES

The writing process

There are five phases of writing each with its own strategies

(cf. two types of people: those who divide humanity into two types of people and those who do not)

• These steps overlap or are simultaneous: know the steps > understand the process

1. Prewriting – conceptualization, including thinking while writing
2. Drafting – just getting it down
3. Rewriting...putting the draft in order – washing line, computer cut & paste
4. Self-editing...don't lose text – paste it into a working document, getting details right
5. Presentation...go to a sympathetic friend as an initial editor

Starting

• “You can't eat the elephant at once”...You can start writing anywhere, so start with the easiest part
• Your mind will find the answer. When a good idea comes to you in the middle of the night... during a seminar, in conversation or driving home... get up, stand up, write it down.
• Brainstorming with others, in a supportive environment, is an important prewriting strategy. You need to share ideas and ways to express them. Often discussion will give you the words you need.
• Writing requires self-editing but this is done in several stages.
  • Get it all down without backtracking – bash it out, don't worry about expression
  • Edit down to what is important: sense and meaning - conceptual clarity, logical sequence

• Edit again for style: clarity and brevity, choice of words...grammar comes last.

Structuring ideas

• Remember: sense, structure, style....in that order
• Overall structure: Tell 'em what you're gonna tell 'em. Tell 'em. Tell 'em what you told 'em
• Paragraph structure is a 2^nd stage editing process (Re-writing & Self-editing)
• A good paragraph begins with a focus sentence (a thesis statement).
• Details follow in subsequent sentences. Deal with things one at a time.
• Unpack details in a logical sequence. Necessary background should be in previous paragraphs.
• Avoid stylistic fixation. Editing style is a 3^rd stage process
  • But where do you break paragraphs?
  • Should we try to write so that you can understand the content simply by reading the first and last sentence in each paragraph?
    • A paragraph should address a single concept (one point per sentence, one theme per paragraph)
    • Conceptual sections need a focus statement and a punchline but this could be within single paragraphs or might extend over several paragraphs
    • Paragraph structure alone is a 2-day workshop in the Wits writing course.

Finishing

• Let someone else read it (friends, family, colleagues, co-authors...but don't let this obstruct progress). Don't quibble on qualifications - address their comments on sense and readability.

  * Make a final check on the details (sample & specimen numbers, references) but don't get stuck crossing i's and dotting t's

  
  

  * Submit – your editor and reviewers will make you edit again before publication

  
  

  * You may not be completely satisfied, but leave that for your next paper

TECHNIQUES

1. Free writing

5 mins of constant writing without stopping or revising – open the floodgates with a priming phrase

The main issue I need to address is...

Prior organisation. I need to get my references in order, to be able to find it all when I need it all, to start constructing my figures early. I also need to stop looking at that pile of references, to stop trying to find more references, to stop looking at the minutae and openingh wormholes to much greater problems that aI wasn't previously aware of. Get the ideas down on paper, fill out the structure, stop editing and re-editing that is just another form of procrastination, let it go – even with horrendous grammatical errors. No maybe correct those ones first but just make sure that there is a story and it makes sense. This can't be all one main thing because it is several of them but I guess it is all important. What does it alll mean – what is the significance? What is the punchline of this story – that is the main thing. What distinguishes this from just another phylogeographic story – is there ever just another phylogeographic story in biology when everything is unique, when only the patterns are shadows of each other....The Mark Twain reference – history doesn't repeat but it rhymes. The conclusion is the most important part, even though in the longer term it might be superceded or made irrelevant by other perspectives, better perspectives, better analyses, new information from other fields – and the data itself might have longer term value for understanding change, what was when we was, and developing the field.

2. Random Writing

Moon

Dog-like

Pretence

Forward-looking

Revolution

Write a paragraph using these words in this order, without changing them.

Are we all just howling at the moon. Alone, at night, dog-like, staring at the distant stars, putting up the pretence of community. But maybe we should be more forward-looking, we are creating that community, listening for other howls in the night and joining the chorus before dawn. Now there's a revolution!

3. The journalist's toolbox: Who? What? When? Where? Why? How?

1. WWWWWH: Ask short questions, not necessarily these ones but these are particularly useful ones. Give simple answers. The first four questions are about data and detail (gradgrinds). The last two questions are interpretative – they are about quality
2. Rewriting: Take out the questions, pin the answers together, add linkers, add a focus sentence, remove redundancy
3. Remember: First start with making sense of the information. Secondly, come to ordering the ideas (and readability which is stylistic). Style correction comes last.

• A good technique to make a transition, to bridge thoughts, is to re-use words from the previous sentence to start the next, shifting the emphasis on that word or concept.
  
  

4. Mind mapping

• “The most important single technique you can use” (Graeme)

• Can be used to structure virtually any writing job from a shopping list to a book”
• Do it manually, on paper, or use FreeMind (Java) <http://reemind.sourceforge.net>
• Categorise things into big categories, and subcategories of these.
  
  

CONCLUSIONS (Brainstorming – participant comments)

What have you learned here that you can apply?

• 4 useful techniques: Free writing, random writing, WWWWWH, Mindmaps
• Get it down, then get it right
• sense, structure, style

• Writing is intuitive, it comes naturally
• Communicate it to others
• It is essential BUT DON'T EXPOSE YOURSELF to criticism from people you fear

• Linking sentences, bridging concepts
• Mindmaps to systematize it all on one page...don't do it with lists
  
  

  - Can also be used to prepare a presentation or speech

• The prewriting process of organizing the sense of your story
• Presenting your project to your family (good technical writing can be understood by all)
• Punchlines for paragraphs

PRESENTATIONS

• Arrie, Kerry, Paulette, Thierry and Sarita gave project / paper presentations
• Presentations from Michael, Amanda, Emilie, Bianca, Carel and Ronell were deferred
• Paulette suggested that everyone should have a manuscript or a firm structure and time-line for a manuscript by the end of June.
• GA: In these presentations you seem to be skipping the most important part – the Big Picture. The Who, What, Where, When and How, the SENSE.
• MEEP: This is because we know the projects, we are familiar with the justification and we were restricted in slides and time to shorthand of content.

___________________________________________________________________________

MJC: In hindsight, this rebuttal doesn't make sense, because Sense is the most important part of the publication, and must be the fundamental starting point for explaining any paper. In publications you must explain the WWWWH concisely in a paragraph. Surely we can do the same in a slide. The problem is that we had the wrong format. We were prepared for presentations on projects rather than on the resulting papers. With the benefit of the workshop I think that the best presentation on a paper would start with the structure – in the form of a mindmap.

Biogeographic transitions for tropical Butterflyfish around South Africa

Just to give an example of what I have in mind, I took the distribution range of the 14 species of tropical Butterflyfish (most of them from the genus Chaetodon) around South Africa. I excluded the one endemic C. marleyi as its distribution range (Maputo to Lambert's Bay) suggest that it is not tropical. Then, I recorded the presence (1) / absence (0) of each species in 20 locations along the east and south coasts. I then performed a logistic regression pooling the data from all the species. I obtained the graph below that gives the probability of occurrence of tropical Butterflyfish. The dots represents the presence/absence data in different locations and the red curve represents the regression model.

So, as a preparation for the next discussion group, we can try and interpret the graph. As guidelines, try and answer the question below:
(1) Considering the trend of the regression model, can you suggest the location I used for the "origin" (coordinate 0 on the x axis)? and the last location (x ~ 3500 km)
(2) Considering the position of T1, T2 and T3 on the graph, what do they represent in term of the occurrence of the Butterflyfish?
(3) What are the biogeographic interpretations one can make in term of species distribution using these three lines?
Try answer these questions and if you have any questions, please contact me by email or write a comment.
Enjoy!

Marine Biogeographic transitions on the east coast of South Africa

Biogeographic regions are one of the most important unit in biogeography. They are characterised by a specific history and specific environmental conditions that make their biota unique. At the boundary between two regions, there is a zone usually not well defined where species of both regions occur: the biogeographic transition zone.
I will start a small project on the marine biogeographic transition zone on the east coast of South Africa using coastal fish as model organism. The project consists first in having a discussion around biogeographic transitions in general (definition, implications and limits on questions related to biogeography) and then use the transition between subtropical and subtemperate coastal region in South Africa as a case study (with some homework for all involved).
I found a short but nice introduction to transition zone on a website that talk about the Durban transition zone, though it is on terrestrial environments (http://www.ceroi.net/reports/durban/issues/Terrestri/biogeog.htm).
If you are interested just send me an email and I'll organise the first meeting.

microsatellites for sparids

Congratulation to Kerry for her first publication!

The paper is online in the early view section of Molecular Ecology Resources.

http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1755-0998/earlyview

I am sure the paper will be useful for lots of people and highly cited !

High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

K Reid, TB Hoareau and P Bloomer

Abstract:

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed

first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units

and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandemrepeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.

Journal Club Sessions (Semester 1)

Date	Name	Venue
12 Mar	Kerry	Tea room
19 Mar	Sarita	Tea room
26 Mar	Sam	Tea room
2 Apr	Arrie	Tea room
16 Apr	Thierry	Tea room
23 Apr	Emilie	Tea room
7 May	Ilkser	Tea room
14 May	Catherine	Tea room
21 May	Amanda	Tea room
28 May	Paulette	Tea room
4 June	Bianca	Tea room
11 June	Michael	Tea room
18 June	Angelika	Tea room
25 June	Carel	Tea room

The historical Biogeography of Mammalia

Today, Sarita will present a paper on historical biogeography of mammals. The authors proposed to identify the origins of the different groups of mammals by comparing nine different methods for reconstructing ancestral areas including data on phylogenies, divergence times and ancestral areas reconstructions. This approach shows that both dispersal and vicariance triggered diversification of mammals. Thanks Sarita.

From MS Springer, RW Meredith, JE Janecka and WJ Murphy, Philosophical Transactions of the Royale Society B, (2011) 366, 2478–2502 [doi:10.1098/rstb.2011.0023]


Title: The historical biogeography of Mammalia

Abstract. Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar’s endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.