Suburban Melbourne yeast capture. The rancid smell of failure.

Wild yeast hunting doesn’t always strike gold. Sometimes you end up capturing something that faithfully recreates the odours of vomit, or sweat, or cheese, or maybe all of them at once. Even if it’s disgusting, I still find it immensely fun to be hit with a surprise nostril assault and find the words to describe it.

In the interests of publishing negative results and sharing my yeast capture method, here’s the grotesque outcome of a recent attempt to capture brewing microbes from a Eucalypt blossom.

9 April 2020
The yellow gum (Eucalyptus leucoxylon) in my Melbourne front yard is currently going bonkers. Every day its teeming with lorikeets, bees, and flies, which I assume must be moving nectar-inhabiting microbes around, spiking the very open nectaries with potentially useful fermenters.

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I clipped off several branchlets with fresh-looking flowers, and brought them inside, careful to not handle or touch the flowers I was going to use for capture. In my improvised biological safety cabinet (stove-top, gas hob on low, extraction fan on), I picked flowers off with flame-sterilized forceps and dumped them into four sterile jars of media, each jar had two flowers in about 80mL. All incubation took place in a warm spot above the heat lamp in the python’s tank. The jars probably cycle through swings from 10 – 25 degrees C.

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Wild capture media (1 litre)
86g pils DME for a target 1.030
25mL EtOH for 2.5% abv
1 drop of tetrahop
Adjust pH down from 5.5 to 4.5 with 88% lactic using narrow range pH papers

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18 April 2020
After just 9 days, there’s already a terrific pellicle growing on a couple of the jars. I removed the flowers from all of the jars with sterilized forceps, decanted some of the liquid, and topped up with fresh capture media.

My notes on appearance for the four jars below.
#1: Pellicle forming. Cloudy.
#2: Slightly cloudy, no pellicle.
#3: Robust pellicle. Cloudy.
#4: Very cloudy, no pellicle.

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01 May 2020
By now, I should have cultured up the bugs that were going to grow, and filtered out the ones that can’t survive in the presence of low pH/alcohol/alpha acids. I swirled each sample jar and decanted a small amount into a fresh and sanitized 250mL flask to inoculate fresh 1.037 LDME wort within.

05 May 2020
I think #4 has possibly caught a Saccharomyces infection. Froth and bubbles present, but were not in the initial capture.

11 June 2020
Time to smell, taste, and measure. I decanted a 100mL sample from each flask, then replaced the volume with more fresh 1.037 DME wort.

#1: Thick mat of white mould on the surface. Discarded.

#2: Gravity is 1.024. 34% apparent attenuation.
Appearance: Solution is bright. Nothing in suspension. No pellicle.
Aroma: Smells of Eucalyptus oil (most likely still hanging around in solution after coming off the flower), heavily phenolic, smokey, leather, solventy like acetone or ethyl acetate. Then there’s a faint background sick and cheesy vibe. Just faint. The whole sample is very pungent. Aroma is overpowering, and not something I want to taste.

#3: Gravity is 1.024. 34% apparent attenuation.
Appearance: Cloudy yellow. Robust white pellicle.
Aroma: Smells sharply and impressively of sour sweaty feet, with a dash of body odour, and slightly like vomit. Could be isovaleric acid. I don’t like foot smell and I am not tasting it.

#4: Gravity is 1.015, so this one has achieved a reasonable 59% attenuation, which fits with the bubbling I noted on 5th May.
Appearance: Cloudy yellow. Rocky white pellicle…. and then I tried to decant the sample and boy was it thick and ropey. It has become sticky and glutinous like Chinese takeaway sweet-corn soup.
Aroma: Smells sort of intermediate to #2 and #3. It has the light Eucalyptus and smoke presence of #2, along with the vomit and cheese of #3. Again, I’m not putting this in my mouth.

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10 July 2020
A last chance at redemption. Have any of these turned a corner and presented anything remotely appetising to warrant continuing the experiment?

#2 is dropping clear and bright. It smells phenolic, but there’s some fruitiness in there too! A white-wine like fruitiness. There’s also an enteric slightly vomity backdrop there. I dared to taste this one, just a small sip, then spit, and it does taste quite fruity too. Nothing fantastic, and the wort is still very sweet indicating no further attenuation.

#3 is hazy. Stills smells strongly of sour foot sweat. It’s going down the drain.

#4 is still grotesquely goopey and smells like it did one month ago. Kill it with fire.

Conclusion
My first attempt to capture an estate culture from my own small patch of suburban Melbourne has failed. Yet the impressive bouquet of bodily odours produced by these microbes was a fun display of nature in action.

Does Australia’s farting bird pass the sniff test?

Legend has it that skulking on Austalia’s forest floors is a bird which forages for earthworms by farting. The hapless worms are so startled by the sensory assault of a Bassian thrush’s fart that their dismayed writhing puts them in mortal danger. Following a quick toot, the gaseous bird simply plucks whichever vermiform vittles volunteer themselves from their humic harbour.

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The Bassian thrush (Zoothera lunulata) is a bird of gullies and damp forest floors. Its predominant distribution is south east Australia. Image by Leo (CC BY-NC-SA 2.0)

Today, for those who believe this marvel of natural history, the world becomes a little less magical.

Having incorrectly answered a trivia question on Bassian thrush farting, I was recently moved to fact-check this suspect nugget. My initial searches found nothing but a few webpages referring to one another, a book without citations, and nowhere could I find a reference to the primary source. A literature search also turned up nothing useful apart from a 2016 paper describing observations of Bassian thrush foraging ecology, yet there was no mention of the birds venting vapour.

Following a plea to Twitter’s sharpest bird and fart minds, the primary source was soon unearthed for all by Alex Berryman.

The original observation appeared in a 1983 paper published in South Australian Ornithologist. The reason I couldn’t find anything was that both the bird’s common name and scientific name have changed since the publication of that article.

So what is the evidence that has carried this remarkable phenomenon into Bassian thrush canon? The paper describes a behaviour of dipping the tail (“vent-dipping”), coincident with a noise “similar to a jet of air”. Probing of the soil surface for worms immediately follows. Between vent-dipping, the birds also “shiver”, and whilst shivering there is audible a “very soft sound somewhat similar to an inhalation gasp”. We aren’t told how many birds were observed doing this, and on how many occasions (the paper records 29 total observations of thrushes), so it is up to the reader to decide how common or deviant this behaviour is.

The speculative leap made from this unusual behaviour is that the fart is a strategy to induce the worms to suddenly convulse in repulsion, and reveal their location to the flatulent forager.

From Edington, JSL. 1983. White’s Thrush: Some aspects of its ecology and feeding behaviour. South Australian Ornithologist, 29, pp.57-59.

“The louder of the two noises described (that accompanied by a downward movement of the vent) may well be a ‘scare tactic’ to induce earthworms to contract reflexly (or other prey to move away) and so betray their presence to the Thrush through noise or litter movement and vibration. That these louder noises were made only during foraging, were antecedent to the probing and were more frequent with more intensive foraging, suggests that they were indeed somehow used to detect prey.”

Further, that shivering serves to reload the bird’s cloaca for another blast.

“If the source of the louder noise is assumed to be from the quick passage of air through the vent, then the softer, antecedent noises (each accompanied by a body shiver) might be explained as aerophagia – the gulping of air.”

Now this sphincter-percussion all sounds a bit bizarre, but is not without some scientific precedent. One expert to chime in on Twitter was Dr Dani Rabiotti, author of the book Does it Fart? The Definitive Guide to Animal Flatulence

Dani suggests this could be a case of ‘cloacal popping’, or simply a sick bird.

After scratching through the litter of evidence here, I feel it’s time to clear the air. There is simply no compelling evidence that the Bassian thrush uses farts to scare and catch worms. There are some curious but unquantified observations of a bird or birds at one site making some noises that could be due to aspiration and expulsion of air via the cloaca. There are no observations tying this to success in foraging. There have been no subsequent observations supporting the behaviour described in the original paper.

I’m afraid we, as lovers of truth and nature, must let the air out of this myth. Finally, we must all commit from now on, whenever we see a Bassian thrush, to carefully watch its arse, for science.

Recipe: Make your own paleo dog food

The raw food dog diet is based on the simple principle that raw meaty bones, organs, meat and vegetable scraps are what dogs have evolved to eat, and therefore what they are most likely to thrive on. In contrast to the ubiquitous mass-market dog food full of cheap carbs and offal, this is not a hard argument to accept. It’s basically the paleo diet for dogs.

As well as prey, wild dogs would typically eat vegetables and leaves from their environment, as well as the semi-digested vege-matter from the stomachs of their herbivore prey. Although she would probably survive in the wild, Pixel doesn’t have access to the stomach contents of Moose-carcasses, so we instead feed her a porridge substitute called “Vet’s All Natural” (or VAN for short). It’s a product developed by an entrepreneurial vet with good credentials in animal nutrition. When rehydrated, left to begin a natural ferment, then served with raw mince, VAN provides the nutrients and roughage required to round out the raw diet. Alternating this with raw meaty bones, and occasional organs, eggs, fruit and veg, completes Pixel’s diet.

Using the ingredients reported on the packet and website, and a series of sieves, I  reverse engineered VAN so that we could make it ourselves from scratch.

The back of the packet quotes the following ingredients:

Rolled oats, cracked barley, flax seed meal, whole cracked oats, carrots, split peas, calcium carbonate, parsley, kelp, lecithin, barley grass, vitC, dried garlic.

Assuming they are listed by conventional order of largest fraction to smallest, you can see that VAN is mostly grains (oats and barley), with some minor fractions for nutrition and taste.

The dishes photographed below show sieved fractions from 50g of VAN. I mixed the bag very well by shaking, before drawing this sample. For fractions containing multiple ingredients of similar size, I picked out the pieces with forceps (for example, all the carrot pieces). I then weighed the fractions to convert the ingredient to an overall percentage by weight. Due to the limit of measurement on my equipment, there are errors around these estimates and the totals do not add to 100%. But hey, this is nutrition, not chemistry.

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From top to bottom: 1: split peas, 2: rolled oats, 3: cracked barley and oats, 4: carrot, 5: cracked barley and oat fragments, 6: fine grain/fibre/greens/carrot, 7: powder and meal

Screenshot 2020-04-08 20.45.38

Weights for VAN fractions pictured above

So VAN is mostly cheap grain—around 50-55% oats and barley by weight, divided between rolled oats, cracked oats, and cracked barley. Dehydrated peas and carrots make up close to 10% of the mix. Judging by the substantial meal fraction and flax seed meal’s appearance as 3rd in ingredients list, it composes something like 20 – 25%. Then the remaining 10 – 20% is formed by the dried greens and supplements.

Using this guide, I concocted my own raw dog food supplement porridge recipe:

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Recipe for 1 kg dry dog porridge. To be prepared in batches by mixing with equal volumes of room temperature water, and allowed to Lacto ferment for some hours.

One could just feed raw carrot from time to time instead of dried, or sub grain fractions for other grains if necessary. The important thing with these bulk ingredients is to get fiber, carbs, and protein in there. Oats have a different protein and fat content to barley, so I wouldn’t sub them wholesale for each other, however the form they take could be flexible.

Supplements. VAN contains VitC, Lecithin, and Calcium carbonate as supplements in the mix. The calcium amount is easy to dose given the information on the package (2800mg/kg), however the others are difficult to extrapolate from my weighing. The safest policy is therefore to feed foods rich in these elements as well. e.g. fish/eggs/organs/soy for lecithin, and fruit and veges for vitamin C. VAN needs to be nutritionally complete when mixed with mince, yet my own mix does not need to be as rigorous if we are sensible in supplementing Pixel’s diet with other foods.

Puppies. This is not designed for puppies. We trusted products nutritionally designed for growing dogs when Pixel was a pup.

Some tips on sourcing ingredients

  • Homebrew shops are an excellent and cheap source for grains like torrefied oats, and cheap calcium carbonate
  • Bulk dry goods in middle eastern, medditerranean, African supermarkets are good for cracked barley
  • Cheap stockfeed kelp here
  • Many other of the ingredients are available from bulk food/health food stores

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Edit: I have updated the original recipe with less garlic after the original turned out to be rather pungent.

In case someone tells you COVID-19 was made in a lab…

Evolution, as always, is more inventive than us.

A common conspiracy these days is that COVID has been cooked up in a Chinese lab in order to bring the West to its knees. Aside from the issue that China was also very badly affected and bore the early brunt of the pandemic, the genome of the virus can be used to scan for evidence to support or refute this story. A lab has done it, I read the paper, and here’s my interpretation.

The paper finds compelling evidence for this virus having arisen via evolution, and therefore, evidence against it being an engineered virus.

It finds that COVID-19 has two unique features in it’s “spike protein”, which is the offensive appendage bit that invades our cells:

1. One part (the “receptor binding domain” or RBD) is unusually efficient at binding to our cells. But not in an optimal way you would predict from the ways all other known Corona viruses use. It’s a bit like all the other Coronaviruses you know using Samsungs, and Google Pixels, and Sonys—but wait, this new one’s using an iPhone, which seems to be as good as the other phones, but in a distinct way.

So it’s a different, but very efficient way to bind to our cells. If this were lab made, it would be easier for the engineers to use a known and simulated “optimal” binding protein (the Android phone) rather than invent a new-to-science and unpredictable solution.

2. COVID-19 has a distinct feature called a “polybasic cleavage site” (PBS from here-on). It’s distinct because its not in any of the other Coronaviruses in COVID-19’s lineage. The function of this is unknown, but there’s scanty evidence from other studies that features like this in other viruses can increase transmissability within and between hosts. We don’t know how/why.

The presence of this feature is evidence against COVID-19 being engineered, because if science simply doesn’t know what this thing does, and it’s not in all the other Coronaviruses, why would anyone cook one up with it in?

So where did COVID-19 come from?

We know the first cases were centered around one of those bloody awful “wet-markets” full of wild animals destined to be ground into Chinese placebos.

Genetically, the closest virus to COVID-19 is from a bat. But despite 96% genetic similarity, the related bat Coronaviruses don’t have the RBD-similarity and PBS features.

Also very close to COVID-19 are Coronavirus observed in Malayan Pangolins (one of the most dear little mammals you will ever set eyes on). While not quite as close as the bat ones, the pangolin viruses DO have a similar RBD bit.

The PBS thing is still lacking in both bat and pangolin viruses we know. And here it is worth pointing out that we don’t know *most* viruses in the world. There are shitloads out there making animals sick every day and we just don’t get to observe them.

So, two strong theories for the origin:

A) The virus coincidentally adapted to us while rocking around in an animal host, then jumped to humans. We know that human-adapted RBD features can evolve in nature (thanks pangolin!), so COVID-19 could have come from a reservoir of wild animals with a similar enough binding domain to humans to select for this RBD adaptation. This could have been a cat, or a ferret, or a civet, or who knows. Then through mutation, the PBS thingy arises and it jumps to humans and goes nuts.

B) The virus could have evolved just the RBD adaptation in its animal hosts, then jumped to humans. It could have remained at low levels of transmission and virulence for a while, lurking around making Chinese people mildly ill, until it struck the lucky mutation to result in the PBS feature then goes nuts.

 

The Resilient Postdoc: Keep the exit rows clear at all times.

If you are seated in an emergency exit row you may be called upon to assist crew members in the unlikely event of an emergency evacuation.

Those who contemplate disaster may enjoy the extra leg room. Thankfully, the probability of any given academic career stalling and rapidly losing altitude is orders of magnitude higher than it happening on your average flight, but my conceit is simply to make the point that preparing for emergency leads to a more comfortable ride. The same can be said for bunker-dwelling, tin-can stockpiling Doomsday Preppers, who are easy to make fun of, except that their backs must be stiffened by a dose of confidence inspired by addressing their perceived existential threat.

In this uncertain and hyper-competitive job market with falling availability of research-focused academic positions, if a postdoc is not preparing to walk away every two or three years they’re a star-performing outlier, or blissfully unaware. It is shocking therefore how often I have encountered postdoc research scientists who simply have never thought about how to get a job outside of their narrow research domain. This should start in their PhD years. In fact, in light of the harsh jobs climate in research, it is unethical for a supervisor or university department to be ignoring the pressure for postgrad students to develop career capital that can serve them and the community outside the narrow field of academic research.

At the end of my first postdoc in 2015, I was beset by anxiety blooming from the combination of scarce opportunities and academic job rejections. I needed to look beyond academia and it took me months to refine strategies to identify jobs that I might be capable of getting an interview for. Eventually I got an interview for a government department, which turned into a job offer. It sounded like an ok job, I didn’t end up taking it, but the fact that I had been offered a decently paying position after successfully marketing my unique set of skills was strong salve to my career anxiety. It gave me some confidence that I could walk away when I needed to.

The chart below shows every ongoing role I’ve applied for since completing my PhD in 2013. As you can see, I have applied for 15 ongoing university academic roles in the past six years and received exactly one interview. Contrast this to the ongoing non-academic government jobs I’ve applied for (five), where I’ve attracted two job offers—a substantially higher strike rate! My research is not easily and directly tied to government priorities, so I’d argue that my single case study supports the assertion that the world outside the ivory pressure cooker is wide and full of opportunities.

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I have applied for 24 ongoing jobs since 2013. My two job offers have come from non-academic government roles, for which I have only made five applications. (Scroll below article to see the same visualisation for fixed-term applications)

In light of my experience, this post is for academics who want some pragmatic advice on accessing the diversity of alternative careers.

– Learn to job hunt. You might not have ever used non-academic modes for job-hunting, you might be baffled as to what keywords will find you relevant positions, and one of the big uncertainties is often not knowing what’s available to you. So take the time to learn how to drive the commercial job advertisement search engines, as well as the relevant government and industry outlets. From the Australian point of view, this means Seek.com.au, federal, state, and local government job sites. Spend time using all the keywords you can think of, learn which ones are productive, then set auto-alerts for these (e.g., keyword “plant” was useful to me). Doing this, you will probably learn about interesting jobs you never knew existed.

Screenshot 2019-12-18 10.07.09

Actually there are no jobs in “speciation”. Four employers misspelled “specification”.

– Scan for jobs early and often. Start looking early. Earlier than you think is necessary. Repeat your jobs search regularly, at least once a fortnight. Make it a part of your weekly routine, or spend time doing this instead of wasting time online on a demotivated Friday afternoon. It’s really not arduous. This ongoing jobs market research will a) arm you with information about the reality of the jobs market before you need it, and b) identify opportunities that might sound attractive now, perhaps even worth leaving a postdoc for. Don’t miss out on a promising alternative career opportunity because you weren’t paying attention.

– Learn to apply for non-academic jobs.This is a big one, and something you want to practice well before your first “must-get” job. Other industries have their peculiar CV or resume formats, and virtually no industry has CV conventions like academia. Learn to craft a CV targeted to the job/industry. For example, consider adding a “skills and expertise” section highlighting your strengths and transferrable skills. While you might need to completely overhaul your academic CV, that doesn’t mean you have to avoid mentioning all your papers or teaching. Just re-phrase and perhaps contract the detail. For example, I reduced my teaching experience to eight lines on a recent CV because it offers evidence of important skills, but the detail of subjects taught and years of experience don’t matter outside tertiary teaching. Learning to apply for non-academic jobs is learning to market your skills to a non academic audience. A PhD and postdoc in science equips you with a diversity of useful skills, but you have to translate them into the keywords that employers want to hear. Examples of skills most STEM academics can speak to include:

    
Communication Analytical Management: projects & people Technical
Writing complex and technical subject matter for specialists

Communicating complex and technical concepts to non-specialists

Professional oral presentation and seminars

Grant writing

Tertiary teaching to a diverse student population
Research and synthesis of specialist and technical information

Critical thinking

Higher order logic and reasoning

Executing sound professional judgment from expert knowledge

Conducting and interpreting statistical analysis

Experimental design

Rigorous attention to detail

An ability to quickly assimilate new and often complex information

Managing complex and competing priorities

Supervision and mentorship

Communicating with influence, in writing or in person

Working effectively in teams, building and maintaining collaborations

Working independently with minimal supervision, demonstrating initiative

Careful and effective stakeholder engagement

Programming skills

Laboratory skills

Field skills

Data visualization

GIS

– Practise applying. Even if you don’t think you’ll take the job, apply anyway. If you’re offered an interview, you might find out information that changes your mind on accepting the job. If you’re offered a job, whether or not you accept, I guarantee this will make you feel better about possible future academic extinction.

– Arm yourself with skills for your desired job. See a job you like, but can’t fulfil the selection criteria? Great. Now you know what you need. Find the time during your postdoc to develop some of these skills. Craft yourself as a candidate for the job you want, ideally by building skills that you can apply to your research now. The counter to this is: Avoid sinking time into skills that are not marketable outside academia. This is a tough line to walk, because some skills that might serve you in research are a hard sell on the outside. For example, learning to master that peculiar and poorly-written R package for detecting hybrids in polyploid organisms, or the latest technique for extracting DNA from sub-fossil sea-urchins might be useful for your research program now, but long-term useless. Can you get a collaborator on that, and instead spend time learning general stats and programming skills to analyse and visualise the results?

– Network, and learn from others. Don’t just sit on the internet reading quit-lit. Tee-up coffee meetings with other scientists who have made the jump. Ask them the obvious and practical questions you think sound dumb. Meet for coffee with people you don’t know who work in the jobs markets you want to explore. Find out: where are the jobs?, how are people getting them?, what are the attractive things about the job you might be overlooking?, what are the negative things you might be overlooking? Networks pay off in unforeseen ways. A 30 minute coffee meeting with someone new is never a wasted 30 minutes.

– Share job information, help each other! Whether or not it’s an academic job, keep your close colleagues and collaborators in the loop. While an isolated job ad can be zero-sum, you operate in an environment of repeated opportunities that is certainly not zero-sum. If you’re applying for a lectureship, don’t let it pass by your postdoc colleagues, share the job ad (but only to the nice, supportive, friendly ones). If you don’t get the position, you’d prefer they got it than a stranger, right? If you see an attractive non-academic job that’s not for you, pass it on to that postdoc colleague who seems like a good fit, even if they are not looking for jobs. A small network of colleagues helping one another catch the opportunities that fall through individual nets.

Overall, the most important and productive thing is to prepare yourself for an exit before you need it, even if you never need it. Taking concrete and practical steps towards building a safety net will give you confidence working under uncertainty. Even if you stay in academia your whole life, never having to break the emergency glass, planning for the event will be invaluable experience to pass on to your future students.

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All 16 fixed-term roles and fellowships I have applied for since 2013.

 

Project update: Contrasting bird and insect pollination through use of novel camera and genetic technologies.

I recently put together some material on my work for the University of Melbourne open day. As a teaser for the papers in current preparation, here’s an abstract and some visuals on the project.

While we simply do not know what pollinates many of Australia’s plants, there is good evidence emerging showing Australia to be a global hotspot for bird-pollination. This raises questions about what ecological and evolutionary factors might encourage plant lineages to adapt to use birds as couriers for their pollen. As well, we might ask what the outcomes are when a plant species ties its reproductive fortunes to a bird, rather than an insect.

My project employs custom cameras designed for motion-capture data capture of insect visitors to flowers, in order to demonstrate contrasting bird versus insect visitation in pairs of closely related native shrubs. Fine-scale population genetic analysis in these plants is revealing evidence for systemic differences in the movement of pollen under these different pollinator regimes.

IMG1 Stomarrhena

Styphelia stomarrhena is pollinated exclusively by birds.

The video below shows bird visitation by a number of honeyeater species, as well as the way in which floral morphology excludes bee pollinators from accessing pollen or nectar in Styphelia stomarrhena.

IMG2 Xerophyllum

Styphelia xerophylla is the sister species to S. stomarrhena and has evolved a tight relationship with a single species of native bee: Leioproctus macmillanii.

 

The videos below show motion-captured footage of the native pollinator of Styphelia xerophyllum, a female native bee (Leioproctus macmillani).

However the flowers are also visited by introduced honeybees (Apis mellifera).

 

A quick note on plant names: These species recently underwent taxonomic revision, moving them from genus Astroloma to Styphelia. It is rather new, hence the confusion over these shrubs apparently having two names.

The Resilient Postdoc: How to be ok with uncertainty.

Building resilience in the face of career anxiety…
One of my favourite plants.

In arid Southern Africa there exists a most fantastic species of cucumber. Like other cucumbers, its fleshy fruits are refreshingly high in water. Unlike just about any other flowering plant, these fruits develop beneath the ground, concealed and entombed by soil and sand. This bizarre trait gives the cucumber its scientific name: Cucumis humifructus, humi- referring to soil, fructus referring to fruit. To understand this deviant fruit, you must know who or what is responsible for fulfilling the purpose of this, or indeed any fruit: to promote the spread of its seeds. The only creature capable of finding and eating the fruit of Cucumis humifructus is one of our most fanciful and enigmatic mammals: the Aardvark. And this gives the plant its common name: the “Aardvark Cucumber“. In the context of seed dispersal, Cucumis humifructus is an extreme ecological specialist, having evolved to employ just a single species to eat its fruit and distribute its seed. The Aardvark itself is also an ecological specialist, its diet is composed exclusively of ants, plus the occasional Aardvark cucumber.

One of my favourite animals.

The Queensland Lungfish (Neoceratodus forsteri) is one of only a handful of extant lobe-finned fishes, having existed largely unchanged for over 100 million years—a time when the Cretaceous Empire of the Dinosaurs was at its ferocious zenith. The fish is remarkable for having the ability to breathe air via a rudimentary lung, which when combined with its fleshy limb-lobes, gives it the power to locomote and survive for days out of water. It is also the only fish with a soul (Figure 1). The age of first breeding for a lungfish female is 22 years. Read that again. 22 years! Lungfish development and reproduction is a longer and more drawn-out affair than our own spawning. You see, the lungfish is what ecologists would class as a K-selected organism, she grows slow, reproduces slow, and invests heavily in a few offspring. A temperate and upstanding lungfish will lay a few hundred eggs over her lifetime, while for contrast, the profligate and rapacious common carp can spawn 300,000 in a single season.

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Figure 1: Cladogram for the vertebrates placing the evolutionary origin of the soul approximate to the divergence of the Actinopterygii.

The maladapted postdoc

So here I’ve described the extremities of two separate axes in ecological strategy. The generalist-specialist axis describes the narrowness with which certain organisms have adapted to specific niches in their environment. A generalist can tolerate a wide range of environmental variables, while specialists (Aardvark cucumbers) are exquisitely adapted to maximising the narrow case. The r- and K- selected life histories describe how organisms reproduce and grow, from boom-bust generations and mass dissemination of cheap offspring, to the heavy investment and delayed pay-off of fewer offspring, with better odds of survival for each one.

Academic science incentivizes production of K-selected specialists. Specialists are encouraged, and rewarded, because one has to specialise to not only reach the horizon of knowledge for a subject, but also to contribute to moving it back a meaningful amount. And academic scientists are K-selected. The gestation and development of a scientist is slow and long (4 years undergraduate and 3 years PhD at minimum), and the best outputs of academics take years to produce. It routinely takes years to get an original study from idea, to funded, to conducted, to published. It can routinely take a year to merely progress a paper from first submission to publication!

The problem with being a K-selected specialist however, is that they do very poorly in unpredictable and variable environments. The early career trajectory in research science is both highly unpredictable, and highly variable. With the scarcity of jobs, fixed term contracts lasting a maximum of three years and most frequently shorter, and low funding rates in grant schemes exacerbated for the young, those navigating this foggy career path frequently find themselves dealing with the anxiety of not knowing where or who they will be working with in the coming months. Add to that most support for ECRs drops off after five years, and its a direly unpredictable environment for a K-selected specialist to find itself in.
There are plenty of other careers that are similarly “contract-to-contract”. Freelancers, some Government roles, creatives, consultants, and so on. Compared to those careers though, academic success depends on the outcomes of projects borne of very long gestation periods (K- selected outputs). For a researcher, it can feel pointless developing new ideas, growing new collaborations, and applying for research funding if the funding outcomes are not known for nine months, and the money won’t be available for another six months—a future point for which they cannot forecast their own employment status. Therefore, many researchers must prepare to walk away every couple of years, a cycle that corrodes career momentum and mental health.

Learning to be ok with uncertainty

At the end of my first postdoc, I had a crisis. The end was steaming up and I had nothing to go to. While it’s a common feature of academic careers, no one knows how they will handle it until they get there. For many, it’s tough. The anxiety of the unknown can run riot through your life, dominating thoughts, detracting from focus at work, interrupting sleep, and sapping motivation—a cloud of noxious gas growing in saturation as the contract end date approaches.

I wasn’t totally surprised that it was hard to nail down another job straight away. What really caught me by surprise was how I responded to the uncertainty. Since I was a kid I had wanted to be a scientist, and now confronting the long-held idea that I may not be a professional biologist challenged a deeply held and largely unexamined part of my identity.

I was able to jump that chasm in 2015, and I’m on my third contract since that time. But I’m glad I went through that, because it forced me to face uncertainty, reflect, and adapt. I have learned to be ok with uncertainty, and today look at the possible future extinction of my research science career with much less emotion than I did four years ago. Not to say I don’t occasionally have bad days, but the days of amity now outweigh the days of anxiety.

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The resilient postdoc

In case the time I have invested in wrestling this might return some interest for postgrad students and postdocs with the same worries, here’s some unsolicited advice on building resilience in the face of postdoc career anxiety.

Where are the exits? The most important and productive thing to do is prepare yourself for an exit before you need it. I have a whole post on this in the works. So for now, lie down on this couch and lets talk about our feelings.

Is your job your identity? This is both an asset and a liability. Academic careers reward those who let career conform the shape of their lives. Surrender to it and your platter of opportunities broadens. But hitching your identity to a job also makes you vulnerable when things aren’t working out at work. Finding meaning outside of work is a healthy strategy for taking pressure off career as a means to fulfillment. Think of it like an investment portfolio, spreading risk and associated reward. If your relationships, family, pets, hobbies, community work etc are thriving and fulfilling, you’ll be buffered against career anxiety.

Another sensible strategy is re-framing your identity around skills, rather than a role. The talents and skills you hone are more a part of you than the job title, however society more often places prestige on the title, not the skills.

Thinking about what else you could or should be doing is totally normal. Everyone is doing it, all the time. Most postdocs I talk to, many lecturers, most people in most jobs. I don’t know if this cognitive bias has a name, but it probably should. There’s no harm in occasionally fantasizing about the vineyard/cafe/photography/alpaca business you could go and open, but you’re probably falling victim to the focusing effect (see below).

Exiting academia won’t be your last move. There’s only so much momentum a publication record gives you to exit, re-enter and remain competitive. This increases the stakes on the decision to leave or not. However your first move out of academia need not be immune to revision. Release yourself from the pressure of finding the perfect job straight out of research. Trying new things is the only way to settle on what works for you, and in many ways researchers have been conditioned to avoid swapping and changing, because singular focus and narrow expertise is rewarded in academia.

Beware the grass-is-greener. Focusing on contract impermanence might lead you to think that other jobs with ongoing status are more desirable than they really are. This is the focusing effect, where we compare complex things along only one or two axes of variation. Plenty of people with ongoing jobs are unhappy and think your job looks marvelous because…

There are perks to this job. In science and academia we have the opportunity, at times, to make work a pleasure. Take advantage of that. If you’re not going to get to do this job forever, focus on the good things, don’t make it shit for yourself. Enjoy the moment.

The abyss is exciting. The end of a contract and unemployment can be seen as a career existential oubliette, or an exciting opportunity forcing your hand into taking a risk and trying some new things. Framing is powerful. Deliberately try to look at the same event from different angles.

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Talking to colleagues can get tough. Don’t whinge, but never avoid communicating the facts. If you let your anxiety too often cloud your interactions with co-workers, you will find no one wants to get stuck in a conversation with you. When you need to talk, find the colleagues/mentors who you trust and can speak to in confidence, vent to family/friends, or speak to a counselor.

Stop looking sideways. People are going to get the jobs you want and missed out on. People are holding jobs you could probably do better than them. Dwelling on the number of people with your equivalent expertise who have found an ongoing role is demoralizing and unhelpful. It is also classic survivorship bias. It is easy to count the number of jobs that get filled by someone other than you, but much harder to count the number of failed job applications alongside yours.

If you’re feeling down, get off Twitter. Academics on Twitter are commonly whining or flexing, neither of which will make you feel better.

You won’t starve, life goes on. You’re a highly trained, intelligent individual with skills to offer. I cannot speak for all economies, but in Australia there are jobs everywhere for people like you. It’s also the case that for most of us, we return to baseline fairly quickly and adapt to what’s in front of us. The very worst outcome of a career change is highly unlikely to live up to the weight of anxiety the transition can create.

Densey Clyne 1922 – 2019

I must have been around six or seven years old, but I vividly remember being captivated by Densey’s work on late 80’s Burke’s Backyard. Her subjects were mostly invertebrates, the natural history of which she brought to life with superb macro and timelapse filmography. (For classic Densey and awesome 80’s music check out this vid about cicadas). It might not even be too far-fetched to draw a direct line from Densey’s work—  some of my earliest recollections of a natural history fascination—to my life and work now, preoccupied with the flowers and insects she revealed to me so long ago.

Clyne’s clips of flowers blooming in timelapse made a particular impression on me. In a moment of frustration with a bored and annoying child, I remember Mum sending me into the backyard to wait for a flower to bloom. Soaked in the false impressions of timelapse filmography, I stood staring at a Callistemon for what felt an age before finally conceding defeat and coming back indoors.

In the last couple of years I had the desire and embryonic plan to go and visit her, knowing she was getting on, wanting to meet her and tell her the impression she made on me, and perhaps write up an interview to share her experience and wisdom with others. But I never got around to prioritising it, and now that opportunity is gone.

From the tiniest, dankest little crevices in the bottom of my heart; thanks Densey.

(For more information about her life and achievements, the Port Macquarie news have a nice write-up)

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Photos from the field: The Great Western Woodlands.

The Great Western Woodlands (GWW) form the largest tracts of temperate woodlands left on Earth. They hold approximately 30% of Australia’s Eucalypt species, and close to 20% of Australia’s plant species overall. This is truly an overlooked gem of Australian biodiversity. Last Spring I was lucky enough to visit for my work on pollination in our native plants.

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My target there was Eremophila, a genus of approximately 250 species largely confined to arid and semi-arid Australia. The GWW represents one of the centres of diversity for the genus, and so I chose it as a likely spot to set up a new study contrasting bird and insect pollination.

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Eremophila alternifolia was one of about 15 Eremophilas I saw flowering despite the drier than average conditions.

I was joined by perhaps the best kind of field assistant: a trained and accomplished professional ecologist who also happens to be my beautiful wife. After driving 2800km from Melbourne to field sites near Norseman, Western Australia, we spent a little under two weeks observing pollinators, surveying and mapping populations of plants, and collecting samples for population genetics.

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One of the many viewpoints south of the Nullarbor Plain.

I left in awe of the scale of these woodlands, in love with the peace and isolation they offer, and a bit concerned over their insecure future. Fully 60% of the GWW is tenured “unallocated Crown land”, unmanaged and open access. With more visitors, and more appreciation of the value of these vast woodlands, I hope we can find a way to secure more of it into ongoing reserve for future generations.

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The bluebush understory contrasts dramatically with red sand in many areas. Front left is one of my study species Eremophila scoparia.

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The whole region is dotted with salt-pans.

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As predicted from the small, violet flowers, Eremophila scoparia was visited by a host of native bees.

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Eremophila decipiens has characteristic bird-adapted flowers.

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Camera traps being expertly arranged by Samantha. Footage revealed that E. decipiens was being visited by a range of honeyeater species.

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Eremophila calorhabdos

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This spectacular Grevillea hid a massive bloom of flowers underneath it

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The inflorescences are held on stems that grow along the ground underneath the shrub. The very long style with pollen-presenter is suggestive of adaptation to birds, but mammals might not be out of the question.

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Eucalyptus loxophleba with daggy botanist for scale

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Majestic Salmon gum (Eucalyptus salmonophloia) with Samantha for scale.

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The serenity of wandering amongst giant Salmon gums at dusk was magic.

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Gleaming bark on Eucalyptus salubris

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Elevating on Lake Cowan. Photo: S. Vertucci.

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For the second half of the trip I was joined by collaborator and all-round legend Dr. Renee Catullo. I made us walk 10km to collect camp gear following a single poor decision.

Stay tuned as research results emerge. The study should tell us about the way pollen moves under bee and bird pollination, and how those fine scale patterns play out on a grand landscape level.

Wild yeasts are everywhere. Some of them will even make beer for you.

I spend a lot of time thinking about flowers and beer. Thinking about flowers is part of my job, and beer—that’s my current obsession. Thoughts collide, and I recently found myself dwelling upon what they have in common: that most marvellous microbe, yeast.

Yeast is that critical fungus that converts sugar solutions into beer and wine, and while we’ve got a handful of domesticated strains harnessed for beverage production, diverse and untamed wild yeasts are everywhere. They are in the air, on plants and animals, on your skin, in your hair. Wild yeasts are particularly abundant in flowers, and that’s because flowers provide a source of freely available sugar by way of nectar.

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Brewers/baker’s yeast (Source: Wikimedia Commons)

Given this obvious overlap, a natural and totally irresistible work-hobby collaboration sprang to mind. Could I capture a wild yeast from flowers of my study species and use it to make beer?

Now I am not the first to try this. Wild yeasts and other microbes have had a long history of use in creating beer. Belgian brewers have perhaps the most celebrated and storied traditions in this area—their Lambic beers are created by leaving fresh, unfermented beer (wort) to be inoculated by whatever yeast and bacteria the atmosphere may gift them. Wild fermentation is a growing global trend now, with numerous craft breweries here in Australia (e.g. La Sirene and Wildflower), and internationally (e.g. Allagash, Trinity) establishing strong reputations for artisanal ales fermented with the help of local microbial biodiversity.

While the diversity of wild yeasts might be wide, not all are useful for producing beer however. Many yeasts die in the presence of moderate alcohol, many cannot ferment all but the simplest of sugars, many produce unpalatable by-products during fermentation.

So where are we most likely to find the best, most useful wild yeasts for beer production? This is where floral biology meets brewing.

Floral biology meets beer brewing

Nectars are produced by flowers as rewards for the service of pollinating animals. Because some flowers specialize in being pollinated by particular kinds of animals, they evolve specific traits that cater to the biology of those animals. For example, moth-pollinated flowers are white so that they are visible in low light, bee-pollinated flowers evolve UV-reflective runway markers to guide accurate landing and foraging, carrion-fly pollinated flowers smell like rotting flesh. In the same fashion, nectar is shaped by evolution to cater to the specific creatures most likely to consume it.

One way nectar becomes tailored to its consumer is by its sugar concentration, which varies wildly. At the concentrated end, exceeding 50% sugar by weight, nectar is very viscous and sticky and difficult to suck up through long or thin mouth parts. These nectars cater to insects with short tongues like bees, flies, wasps and beetles. On the other end you have dilute nectars, with 10 – 25% sugar concentrations, and these are perfect for birds to lap up. By a happy coincidence, the sugar concentrations of bird-adapted nectars are in the same range as unfermented wort. Recognizing this was what led me to try hunting for yeasts in the flowers of my study species—the bird-pollinated shrub Prostanthera walteri.

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Monkey Mint-bush (Prostanthera walteri)

Also known as the Monkey Mint-bush, this is a rare shrub growing amongst boulders on a few misty, granite peaks in remote East Gippsland, Victoria. I have been getting to know the plant for a couple of years now, using it in a study to understand how bird-pollination might differ from insect-pollination. And so on a January field trip to collect some data, I took the opportunity to collect some fresh flowers and take them back to my home lab (kitchen bench) for bioprospecting. At home, I made up a test wort: a low concentration malt-extract solution to mimic the conditions of beer, then I syringed out the nectar from several flowers and spiked the test jars with whatever might be living in the nectar.

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Kitchen-bench inoculation of test wort

And it worked. Most of the test jars began fermentation, and sniffing the results revealed various aromas of bright apple juice, white wine, earth and smoke. After months of re-culturing these initial samples I now have what I think are two different strains* of nectar yeast, one of which just produced its first beer.

So how does it taste?

Interesting, and not bad… and that’s all I’m willing to venture at this stage of the experiment! The yeast fermented very quickly, and chewed through 79% of the available sugars (which is more than some domesticated brewing strains). It has a somewhat Belgian Saison-like character, with strong pear and floral esters, some smoke and spice, and a very slight tartness.

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I was quite blown away at how well this yeast performed, fermenting much like a domesticated yeast, yet with a much bigger, bolder, dare I say “wild” flavour. It is stunning to think that it has probably existed in flowers in remote eastern Victoria for some thousands to many thousands of years, and one can just go and pick it up and persuade it to make interesting beer. And as I get to know it better, perhaps that beer will become both interesting and delicious.

 

Thanks to Ruth Barry (Boatrocker Brewery) for inspiring conversation and advice on this.

*These are technically mixed cultures, but I believe they each have come to be dominated by single strain of yeast.