Date	Name
17-Feb-14	Connor
24-Feb-14	Kerry
03-Mar-14	Anton
10-Mar-14	Tessa
17-Mar-14	Carel
24-Mar-14	Michael
31-Mar-14	Samantha
07-Apr-14	Ilkser
14-Apr-14	Public holiday
21-Apr-14	Public holiday
28-Apr-14	Paulette
05-May-14	Arrie
12-May-14	Catherine
19-May-14	Masethabela
26-May-14	Sarita
02-Jun-14	Stephen
09-Jun-14	Carel
16-Jun-14	Public holiday
23-Jun-14	Connor
30-Jun-14	Anton
07-Jul-14	Amanda
14-Jul-14	Tessa
21-Jul-14	Masethabela
28-Jul-14	Ilkser

Date	Name
22-Jul-2013	Thierry
29-Jul-2013	Michael
5-Aug-2013	Sarita
12-Aug-2013	Carel
19-Aug-2013	Kerry
26-Aug-2013	Angelika
2-Sep-2013	Stephen
9-Sep-2013	Arrie
16-Sep-2013	Samantha
23-Sep-2013	Ilkser
30-Sep-2013	Bianca
7-Oct-2013	Paulette
14-Oct-2013	Catherine
21-Oct-2013	Thierry
28-Oct-2013	Michael
4-Nov-2013	Sarita
11-Nov-2013	Carel
18-Nov-2013	Kerry
25-Nov-2013	Angelika
2-Dec-2013	Stephen
9-Dec-2013	Arrie

Discovery of a new phylum: from barcoding to taxonomy

One of the new way to discover cryptic diversity is to sequence environmental clone libraries. In 2007, researcher discovered a new and very deep lineage of picoeurcaryote from plankton samples using 18S. After years of survey, they could finally isolate this unicellular organism and describe it. The cell is 3.0 x 2.2 micrometers, it is biflagellate, it has a single mitochondrion and has a unique stereotypic motility. Based on these features, they decided to establish a new phylum: Picozoa. It is a nice example on how genetics helps in biodiversity survey and taxonomy. The paper was published the 26 March in Plos One (see reference below).

Figure 2. A Picomonas cell. 2A. Differential interference contrast of a chemically fixed cell. Inset shows phase contrast image of a live cell from tissue culture flask photographed with an inverted microscope (Scale bar 5 µm). 2B. Fluorescence and phase contrast overlay, nucleus (blue), mitochondrion (red). 2C. SEM image. 2D. A longitudinal section through a cell in the plane of the flagella, viewed from the cell’s left. 2E. A 3 D serial section reconstruction of the cell depicted in 2D. AF/PF (anterior−/posterior flagellum); AP/PP (anterior/posterior part of the cell); G (Golgi body); M (mitochondrion); MB (‘microbody’); N (nucleus); tr1,tr2 (distal [tr2] and proximal [tr1] flagellar transitional regions); P (posterior digestive body); Cl (cleft separating the anterior from the posterior part of the cell); vc (vacuolar cisterna). doi:10.1371/journal.pone.0059565.g002

Source: Seenivasan R, Sausen N, Medlin LK, Melkonian M (2013) Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as ‘Picobiliphytes’. PLoS ONE 8(3): e59565. doi:10.1371/journal.pone.0059565

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059565

From the jungle to The Dell

Wallace Anniversary - Commemorating a great Evolutionary Biologist

2013 is the 100th year since the death of Alfred Russell Wallace (8th Jan 1823 - 7th Nov 1913), in the words of David Quammen "the best field naturalist of the nineteenth century." See Quammen's retrospective review of Wallace's seminal book, "The Malay Archipelago".

Wallace tends to get short shrift in evolutionary compendiums, especially those from the mid-20th century. This is probably because he held to some unconventional ideas that, with more information, were largely rejected as unnecessary, wrong or irrational. This is unfortunate because, as Darwin himself recognised, Wallace was an impressively original independent thinker. His 1855 Sarawak paper, which he also discussed with Darwin, raised the concept of regional allopatric speciation leading to sister species in adjacent areas. In his Ternate paper, he independently arrived at the concept of evolution by natural selection, leading to the joint presentation with Darwin to the Linnaean Society. A later paper on the biogeography of Malesia first described his eponymic disjunction between Bali and Lombok in Indonesia, although the term "Wallace's Line" came later (I'm not quite sure who coined it, probably Huxley in 1868. I want to note too that Wallace was not the first, nor the only great biogeographer working in Malesia around that time, both Müller and the Sclater brothers also drew lines in the same area, viz Simpson "Too many lines").

Among diverse interests Wallace was a socialist, who campaigned for nationalisation of land and protectionism in the first era of global trade. He was also interested in mysticism - communing with spirits through séances - in fact he did not believe that evolution applied to the human mind or soul (greatly to the dismay of Darwin and peers such as Huxley, Hooker and Lyell). But, he was also a very modern thinker in other senses, being an environmentalist concerned with extinction far ahead of his time. Even more so, in his last decade he wrote two books on exobiology and the unlikelihood of life on Mars (perhaps responding to HG Wells's 1989 War of the Worlds).

Wallace and Darwin maintained good relations and a lively correspondence throughout Darwin's life - much of it in strident, though amicable disagreement.

Should anyone care to purchase a lovely portion of evolutionary history's history, The Dell, a house built by Wallace in Grays on the lower Thames, England, is up for sale (although perhaps you may first need a lottery ticket).

Journal club schedule - 1st semester 2013

Date	Name
28-Jan-2013	Kerry
4-Feb-2013	Angelika
11-Feb-2013	Stephen
18-Feb-2013	Michael
25-Feb-2013	Arrie
4-Mar-2013	Thierry
11-Mar-2013	Samantha
18-Mar-2013	Sarita
25-Mar-2013	Carel
1-Apr-2013	Public holiday - Family Day
8-Apr-2013	Paulette
15-Apr-2013	Bianca
22-Apr-2013	Ilkser
29-Apr-2013	Catherine
6-May-2013	Kerry
13-May-2013	Angelika
20-May-2013	Stephen
27-May-2013	Michael
3-Jun-2013	Arrie
10-Jun-2013	Thierry
17-Jun-2013	Public holiday
24-Jun-2013	Samantha
1-Jul-2013	Sarita
8-Jul-2013	Carel

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.