Down in the dumps…

So here’s a story…

Yesterday while walking on a path in Wolwekraal Nature Reserve, Stefan (previous SAEON Arid Lands Node intern) and I heard a puppy crying. An electric fence separates Wolwekraal from the rubbish dump site, and she was on the other side. We turned right around and went straight to go find her. After driving to the dump site, we had to climb down a mountain of people’s domestic garbage to get to her. She had a head wound (looked like someone had hit her with something sharp), her face covered in blood and flies, and had been tossed in the furthest corner of the dump.

I called the animal welfare service – Prince Albert Dieresorg (“animal care” in Afrikaans) or ‘PADS’ – and someone came to fetch her. I didn’t get a chance to inspect her properly, because I didn’t know how injured she was and didn’t want to aggravate any existing injuries. I’d never been so angry in my life. Shaking, silent and so tense… I even needed some time to cool down and debrief before I could go back to work.

The woman from PADS called me multiple times asking for more info about how and where we found her, because they want to press charges. I asked her to keep me updated with the puppy’s status – by the afternoon, they’d put her on penicillin and electrolytes, and wanted to feed her a little bit once she’d woken up.

Early this morning I received an SMS from her which read:

“Morning Hana

Thank you very much for all your care and effort in trying to save the puppy. I am sorry to tell you that she passed away last night. We are going to do everything we can to try to attain justice. Many thanks

Karen

PADS”

I am feeling a little disheartened by the whole experience, but I’m also very glad we found her and managed to retrieve her. No animal deserves to die in pain in a rubbish dump… So I guess this is a post of gratitude to PADS for their dedication to helping the helpless animals here in Prince Albert. It is also a post of hope, encouraging people to do what feels right. I was scared when we heard her the first time… but my heart and my gut and all my other vital organs told me that it was my moral obligation to do something about it. So I’m grateful that I had the courage to help her, and I’m grateful for the lesson she taught me. This place has me growing a lot faster and in more ways than I’d ever imagined. After a walk up the Robert Gordon koppie this morning, I am feeling much more positive and at peace with it. Rest In Peace, little girl.

About Prince Albert Dieresorg:

Prince Albert Dieresorg / Animal Welfare (PADS) is a registered not-for-profit organisation (NPO) run by unpaid volunteers and is wholly dependent on public donations of money and materials.

Contact details:

Phone – 071 571 8600

Email – animalwelfarepa@gmail.com

Facebook – PADS Prince Albert Dieresorg

PADS is a registered not-for-profit organisation with NPO nr 043-813-NPO

Banking details for donations:

PADS Animal Welfare

ABSA account nr 930 700 5754

(Use your name and surname as reference)

Advertisements

Women in Science (a thank-you letter)

Today (11 February) is the International Day of Women and Girls in Science. I’d like to take this opportunity to highlight a few women (in science) in my life. This is by no means a comprehensive list, and any women in my life who are not mentioned here are no less inspirational to me. I admire you all.

As a young grasshopper, I used to watch wildlife shows on TV with my dad and grandmother quite often. One of my most vivid childhood memories is of my grandmother laughing at my efforts to mimic the way Jeff Corwin said the word “habitat”. Growing up, my family never went away on safari or to nature reserves, but we were blessed to live at the foot of Devil’s Peak (part of Table Mountain in Cape Town, SA). At the time, our lawn graded from alien grass on our doorstep, up into montane fynbos vegetation with no clear separation between where our property ended and where the Table Mountain National Park began. We had little tortoises and guinea fowl as regular visitors – even a little deer (or so I was told). Long story short, I grew up with a natural curiosity and appreciation for nature and its diversity. And that curiosity drew me inevitably into the realm of natural sciences, with the wholehearted support of my educators, my peers, my colleagues, and my mother. This is a thank you letter to all of you.

Mrs Jackie Wibberley

Mrs Wibberley was my high school Life Sciences (biology) teacher. She went far out of her way to keep us (my classmates and I) curious about not only the natural sciences, but science in general. She encouraged us to read popular articles (she even brought them to class and read them to us), she gave anecdotes to help us remember the difficult, boring parts of the curriculum, she paid attention to those who asked questions and if she couldn’t answer, she would do the research and find out. She noticed a burning curiosity in me, and she helped cultivate it. She encouraged me all the way through my Matric year (12th grade) and was thrilled to hear my plans to study biological sciences. I owe a lot of my motivation to her, and I wish I had spent more time getting to know her background before losing touch. I hope to reconnect with her once I submit my thesis and obtain my MSc… I think that would make her very happy. Thank you, Mrs Wibberley.

Gabriella Leighton

Gabi, apart from being the person I am most likely to be seen having tea with, is a pretty cool person to know. She has been involved in the development of a web application which allows researchers to cache images using a Google Image search and use them to test hypotheses involving phenotypic polymorphisms. She’s published an article about it in a renowned international scientific journal, and was awarded a prize by the British Ecological Society for her efforts. She’s currently pursuing a PhD… Oh, and she hasn’t even hit a quarter-century yet. I’m probably her biggest fan and she doesn’t even know it. I have so much faith in you, Gabi. Thanks for always being there for Academic Hana, and for being a layabout with me.

Nikita Finger

Nikita was a co-supervisor on one of my Honours projects in 2015. Last year, Nikita and I spent many, many weekends calling each other and using TeamViewer to co-author a paper on our combined findings using behavioural and acoustic data she collected for her MSc in 2013/2014. It has been one hell of a ride, but it is very nearly complete. Her dedication to the task and her insights into the field of animal behavioural ecology have made her a researcher that I look up to in many respects. I struggle to imagine working that many hours on the same manuscript with anyone else. And throughout the whole ordeal, she’s been nothing but supportive and motivational – someone who listened and sympathised when I complained about the things that frustrated me about research and academic writing. Another incredible woman in science. Thanks, Nikita. I can’t wait to get this paper published and give you a big hug and a high five, because words will not adequately encapsulate the relief we’ll both be feeling at that point…

Morea Petersen

My mother. What a woman. Life filled her basket with lemons during the years she spent pursuing her Master’s degree in Medicine (specialising in medical cell biology) part-time, but she kept going. I cannot imagine the amount of dedication and courage it took to complete that thesis, but she did it, and she finally received her degree last year. She’s inspired me, encouraged me, guided me, supported me, and uplifted me in more ways than I can even begin to describe. She has been my biggest fan since day one, and always will be. If I can model myself by her example, I have no doubt that a successful career as a woman in science is what lies ahead for me. Thank you, mom. For everything, as always.

And thank you to all the amazing, inspirational women out there doing their bit in the name of science. Diversity in STEM will always be something to strive for.

Creating a site/plot by species matrix of Whittaker plot data for use in statistical software (R & PC-ORD 6)

Apparently, formatting data into site by species matrices is a common issue encountered by ecologists. This is because our field data sheets are not in the same format as what is required for community composition analysis (ordination). More often than not, we use the first column for species names, with multiple columns thereafter for various plots or sites, and other information. This is true when collecting data using the modified Whittaker plot method (see figure below). The modified Whittaker plot design involves ten peripheral 0.5m x 2m plots from which cover data are collected, and four larger plots from which presence data are collected. My sampling method involves paired Whittaker plots, one on a slope and one on the adjacent plain, at each of my sample sites.

Modified Whittaker plot design

Modified Whittaker plot design

For ordination, the data are required to have species as columns, and plots/sites/samples as rows. This is true for R and PC-ORD (I used version 6). Ecological data can be collected in a variety of forms, so the actual cell values can be presence/absence (binary data), cover/abundance values (proportion data), or counts (count data). I had per cent cover values for each observed species at each site, for plains and slopes. This formed my primary matrix.

For ordination to be interesting (because let’s be honest, it doesn’t give very much information just as is), you need a secondary matrix with covariates or other associated data. My secondary matrix was comprised of various climatic and biophysical variables, both quantitative and categorical. As an example, habitat type (slope vs plain), vegetation type, and bioregion were important categorical variables to include in my secondary matrix, so that I could colour code my ordinations later on.

R software

The data are handled differently with different software, depending on the user interface. In R, I used the following code to load, subset and create vectors to use in my stats:

setwd("C:/Users/Hana/R/working_dir")

# load primary matrix
allspp <- read.csv("matrix1_final.csv", header=T)
# subset the data into plains and slopes
# the first 30 rows are for plains, the last 30 are for slopes
# I removed the first 3 columns because they do not contain species data
spp.plains <- allspp[1:30,-c(1:3)]
spp.slopes <- allspp[31:60,-c(1:3)]

# load secondary matrix
allcov <- read.csv("data_env_all.csv")

# subset the data into plains and slopes
# select which variables to include (I didn't use all the variables)
# rename the variable to a shorter name that looks nicer in the plots
cov.p <- allcov[1:30,-c(1:4, 6, 7, 13, 14, 29:31, 32:65)]
colnames(cov.p) <- c("Alt", "MAP", "MAT", "MPAN", "FR", "WS", "SF", "MaxHot", "MinCold", "pH", "EC",
                     "[Ca]", "[Mg]", "[Na]", "[K]", "[P]", "NH4", "Sand", "Silt", "Clay")
cov.s <- allcov[31:60,-c(1:4, 6, 7, 13, 14, 29:31, 32:65)]
colnames(cov.s) <- c("Alt", "MAP", "MAT", "MPAN", "FR", "WS", "SF", "MaxHot", "MinCold", "pH", "EC",
                     "[Ca]", "[Mg]", "[Na]", "[K]", "[P]", "NH4", "Sand", "Silt", "Clay")

My code is still a bit messy and there are easier ways to do it, but doing it this way made it easy for me to change variable names if I wanted to represent them differently in my plots later on. This is what my data set looks like before subsetting:

All species data, before subsetting in R

All species data, before subsetting in R

And after subsetting:

Plains species data, after subsetting in R

Plains species data, after subsetting in R

And lastly, my secondary matrix, after subsetting:

Plains covariate data, after subsetting in R

Plains covariate data, after subsetting in R

Data in this format are easy to manipulate. More on that in another post…

PC-ORD 6

If you’re using PC-ORD, you will need to specify “Q” or “C” for quantitative/categorical data in both matrices, otherwise the program will read your data incorrectly. Furthermore, if you are importing data using an Excel spreadsheet or a CSV spreadsheet, you need to specify the number of rows and number of columns, and give them names. This needs to be done before importing the data, and should be typed into the first two rows, in the first column — PC-ORD won’t know how to read your data if this is missing.

I called my rows “Plots” and my columns “Species”. I subset my data in PC-ORD 6 by simply deleting the rows I didn’t want to use yet i.e. if I wanted to work with my plains data, I deleted the slopes rows and saved it as a new matrix. PC-ORD has a neat way of doing this, allowing you to delete data by filtering it using a variable in the secondary matrix. To subset my plains and slope data, I simply deleted row by filtering by “HABTYPE”. The result is what you see below:

Primary and secondary matrix (for plains) in PC-ORD 6

Primary and secondary matrix (for plains) in PC-ORD 6

 

If you’re looking for a simple program to suit your basic ordination needs for quick analysis and unimpressive graphics, I’d say that PC-ORD 6 is a pretty nifty first option. Further than that, it is outdated and slightly limited in its capabilities. Some of the data manipulation is also a little bit unintuitive and takes some getting used to. So if you’re going to spend time doing ordinations and are willing to experience a bit of a learning curve, I would recommend using R for more control. Jari Oksanen’s vegan package is pretty much your go-to for ordination of ecological data.

 

SIDE NOTE: when transcribing your data from field data sheets to spreadsheets, it’s important to keep in mind what your blank spaces or zeroes mean in your data set. A zero could mean “absence” (as in presence/absence), or “not observed/counted”, or “no cover”. It is also important to note that R treats “N/A” and “zero” differently. The zeroes need to make sense in your data, otherwise your statistical analyses may draw out patterns that do not exist in reality. 

(inspired by a blogpost called “R for Ecologists: Creating a Site x Species Matrix”, which is unfortunately no longer available as the authors have deleted it)

雨 • Ame • Rain

This morning I woke up to the sound of soft rain on my window. I went from feeling comfortable, to nostalgic, to sad. Comfortable because, like most other people, I really enjoy the sound of rain falling against the windowpanes. There’s something considerably more romantic about it than the constant drone of passing cars (my house is right on one of the main highways in Cape Town). Then I felt nostalgic because I hadn’t heard that sound for so long… and that’s what made me sad.

The drought situation in the Western Cape has become so terribly dire, that our dam levels, last I checked, are at around 10.7% total capacity. We’re scheduled in the next few days to move on to Level 4 water restrictions. We’ve been asked time and time again to reduce water consumption, and to some degree that’s been achieved. But like most issues, once the initial emphasis is lifted, people sort of forget that there was a problem to begin with because it isn’t affecting them directly.

I work in a hardware store on weekends. People have over the past few rainless weeks of winter (when most of our rain is due in this Mediterranean climate) come into the store to buy new fixtures for their taps and hose pipes and pools. Being the idealist I am, I assumed that they were addressing problems that resulted in water wastage: leaking taps, worn pool pipes, and so on. But when I asked some of them, the responses were a little more than disappointing.

“Well I can’t just let my grass die, now can I?”

“We don’t have a grey water system, I can’t just dump my dishwater in buckets on the grass…”

“What’s the point of having a pool if I can’t use it?”

It’s a classic case of ‘that’s not my problem, I pay for this service.’ You know what, Cape Town? It is your dam(n) problem. Having water is not a service, it’s a privilege.

“No, it’s my right.”

Sure. Humans have the right to clean water… but what if there’s no more water available? Whose problem is it then?

I get myself worked up about issues of sustainability and longevity of resources when people have this ‘it’s not my problem‘ attitude towards them. It’s the most frustrating thing. Get with it, people.

/endrant

First field work of 2017: Eastern Karoo

My co-supervisor Sam Jack and I spent another week sampling sites in the Eastern Karoo last week. Last time we were out was in September last year, sampling the icy cold slopes in Sutherland. The situation this time round was quite the opposite.

The eastern-most extent of the Eastern Karoo that we sampled ranged from Colesberg to Middelburg to Cradock (north to south), and comprises the most mesic (wettest) part of the environmental gradient that my MSc research investigates.

Study area - Eastern Karoo. Points labelled "A" are dolerite koppies that have been sampled.

Study area – Eastern Karoo. Points labelled “A” are dolerite koppies that have been sampled. The blue demarcated area shows the central Karoo (encloses sites 2 – 8) and eastern Karoo area (encloses sites 1, and 13 – 18) designated for shale gas exploration.

On day one, we drove all the way up to Colesberg in the Northern Cape (my first time visiting), a 9-hour drive from Cape Town. We stayed in a quaint little caravan park in a tiny bungalow, and were eaten alive by mosquitoes, despite how well-armed I was with my citronella oil burner. I feel like they almost enjoyed the smell of citronella… Alas.

Itchy bites notwithstanding, we sampled near Colesberg and then went in search of accommodation further east. We ended up in Oviston, a small town on the edge of the Gariep Dam (also my first time). What was interesting to see was how lush the vegetation in the grasslands looked compared to the western reaches of my study area, and of the country in general. The landscape was carpeted in green, with some impressive annuals showing their vibrant faces. After a stay at a farmer’s house between Steynsberg and Venterstad, and a day devoid of sampling due to rain, sampling was fairly easy sailing from then on. We missioned between Venterstad and Cradock, sampling four sites along the way, before heading towards Graaff-Reinet for another site, then to Beaufort West and eventually back home to Cape Town.

We were met with thundershowers more than once and, consequently, very muddy district roads. At this point I will mention that we were driving a bakkie with no 4WD – mud was our nemesis. I had many tiny panic attacks along the way because of this (which I suspect Sam enjoyed just a little bit). We had to postpone an entire day of sampling due to weather conditions (it is not advisable to carry aluminium rods up a koppie during a thunderstorm), which we spent catching up on species IDs, digitizing datasheets, and other work (and also a few sneaky episodes of Planet Earth).

Overall it was a very successful trip. Just one more two-week long trip and I’ll be done with my data collection. At this point I’d like to say thanks again to Sam Jack – I literally would not be able to do any of this without him. He is my mentor, my friend, my driver, my field assistant, my photographer, and my Afrikaans translator and diplomat. This degree belongs as much to you as it does to me. Thank you so, so much.

Read the official article for this blog post on the Plant Conservation Unit website here.

Keystone

In an attempt to distract ourselves from scientific writing for a while, I challenged a friend of mine to a short story writing challenge near the end of 2016. The challenge involved providing each other with a single word, which then had to be translated into a short story of no more than 2 pages. It was harder than I thought it would be to get back into the swing of writing fiction. Being primarily a descriptive writer, I spent a lot of time just sitting quietly and letting my brain run on its own – not thinking, but imagining. The word given to me was “keystone“, and this is how it played out.

 

Keystone, by Hana Petersen

I felt her before I saw her.

She had followed me. Her amber eyes stared intently at me, though I avoided looking her way altogether. I didn’t want her to know that I was aware of her presence. I kept my posture confident yet vigilant. I walked through the grass, allowing my fingertips to brush against their awns and collect fine white pollen from the exerted stamens hanging limp in the absence of wind. The pollen clung to me. Her eyes clung to me. I wandered closer to the edge of the grassy plain, eager to be nearer to a more heterogeneous landscape. My heart pounded in my chest. Large, hot beads of sweat poured from my temples down my neck, between my breasts, and down my legs. I suddenly felt the weight of my solitude. Where were the others? The scouting should have ended at second noon, and they should have returned by third. The fourth star now shone brightly at its red zenith, leaving the plains awash with golden hues, and setting her unfaltering amber gaze on fire.

I had to run. My only salvation was that if I knew anything in this world, I knew these plains. I knew the exact spot where I was born, just above the first terrace. Minutes after I was jolted to life, I instinctively knew my way from that terrace to the place where my people gathered water. I could smell it. From the minute I was born, my instincts had guided me across every inch of these plains. I had seen the same instincts in my children. I knew the exact path they followed as they grew accustomed to using their legs, strong like their mother’s, to chase their father as he cantered into the distance to scout. My people had thrived here for aeons, blending in to the tawny grasses that nourished us. When the tawny grasses grew thin at the turn of the season, we would migrate northward to the mountains and allow our land to recover, and then return here to bear our children so that they too would know these plains. These were our plains, and we thrived here, until They came. And when They came, They brought Man with Them.

We had heard about Them and Their Men before. News had travelled from the grasslands in the far East that people were being slaughtered and eaten, and the grasslands cleared for construction of Their dens. Wherever They moved with Their packs of bloodthirsty Men, destruction had followed. Our people, we heard, were shepherded into enclosures and guarded by Men through all four cycles of stars. The Men had even gone so far as to bind and bridle our people, enslaving them for hard labour and transportation until they collapsed of exhaustion. The grasslands far East of here, and our people who resided in them, were laid to waste. Where grasslands once stretched for as far as the eye could perceive, the landscape was now scarred with garish brown mounds of earth and fenced enclosures. Our people were now all but extinct in those parts, and the system was mourning them.

We had been forewarned of Their movements, and had been scouting more and more frequently. We were to evacuate as soon as They showed an intention to invade. The scouts that had gone out at first dawn had yet to return, and now here was this intruder with the amber eyes, eerily alone, as was I. I had no choice. I had to run. I knew she would be after me the moment I tensed my muscles, so I began at a walk. Then a trot. I fixed my eyes on the line of trees beyond the terraces and broke into a gallop. I galloped as fast as my legs would carry me, feeling the sweat fly with centrifugal force from my face and away from the centre of my chest. I could not see her, but I could hear her brushing through the tall grass with remarkable agility. Her legs carried her at a speed that was engineered to challenge us. She was designed a predator, and I the prey. My legs, though strong, could only gallop for so long before they needed rest. My body was heavy. I felt the sweat pour from me in burning hot streams. The air felt thick and viscous in my airways. My hooves pounded the earth with so much force that I felt throbbing all the way up my abdomen and in my shoulders and neck. My veins stood thick and dilated at the surface of my skin. The trees in the distances were still only in the distance. How long had I been running for? When had it become so dark? What were these blotchy figures moving in the grass beside me?

All I remember as I took my last step was the excruciating pain in my left flank. Hit with such tremendous force, and my flesh pierced with something so sharp and unrelenting, I could no longer move. My legs seized. I crumbled to the ground on my haunches, as my torso was thrust forward with yet another blow. As the light faded ever more rapidly, I could still see bright amber eyes – several pairs of them now – peering at me, coupled with menacing growls. I closed my eyes and wished never to reopen them, realizing what must have happened to the others. My people had been stalked and ambushed by Them and Their Men, never to return home. That day, I was hunted and killed by Them, skinned and spit-fired by Their Men, and my carcass tossed comfortingly near to the place just above the first terrace where I was born. Perhaps my death was a better release from this life than to be enslaved to Them and Their Men. Where They went, Man followed. These plains were ours, we thrived here. We held it all together; as we took from it, so we fed back into it. These Men only took, and never gave back. And where Man went, and where They took and did not give back, destruction and collapse was sure to follow.

 

I had a cold-blooded baby

On 7 December 2016 I came across a clutch of small white eggs, about 1 cm in length, hidden comfortably in a crack in a face-brick wall at my home in Cape Town. I knew they were gecko eggs, from having seen a pregnant gecko just once in the previous year:

Found a preggo gecko last night! Hey mama 👀

A post shared by ハナ ピータセン (@hana.petersen) on

It always intrigued me, and I’d wanted to watch one lay its eggs, and then watch the eggs hatch. So I decided I could at last satisfy the latter – I stole an egg from the clutch and took it with me to UCT to incubate it.

Once I got over my general excitement at having found an egg to incubate (with much excitement in the car on the way to campus, thinking it was about to hatch in my hand), I did some research. I found out that house geckos (Family Gekkonidae, Genus Hemidactylus) took typically between 2 – 6 months (months!) to hatch. This drained my excitement a little bit more. I also found out that the temperature at which the eggs incubate is instrumental in determining the sex: hotter temperatures usually yield males. So here I was, at the end of the academic year, with a baby to incubate. At this point I was being a bit irresponsible… I had come to the conclusion that me holding the egg and moving around so much must probably have made it so that the yolk was now suffocating the embryo. I gave up and placed the egg in my friend’s office in a little box that used to hold a pocket-sized 10x magnifying eyepiece. And there I left it, until we returned to campus in the second week of January 2017.

I picked up the box assuming the egg would still be in tact and the gecko would never hatch. But the box felt different – lighter – when I picked it up. I shook it a bit, and then passed it to my friend, not wanting to see a broken gecko egg with a tiny unhatched embryo. She then opened it and announced that the gecko was staring at her and that we were parents.

image of Gary the gecko

Gary the Gekkonidae

The little guy (we assumed it was male on account of the hot weather conditions over Christmas), christened ‘Gary’ by my supervisor (“You have to call him Gary. Gary the gecko.”), was a resident of my office in the Plant Conservation Unit for two days, fed on ants and a housefly, for two days before we released him into the wild of UCT Upper Campus.

 I hope the little guy is still alive and growing. Cheers, Gary.