Research parasites

…research synthesists in medicine have recently been described as “research parasites” of primary studies and the researchers who conduct them… ‘Research parasites’ can… serve to increase scientific diversity by adding another ‘trophic level’, thus improving the functioning of the scientific ‘ecosystem’.

Gurevitch et al. (2018)
Nature 555: 175


Tree identification

What are the leaves of the mango tree like? It’s enough to pick up one leaf and look at it to know. Even if you look at ten thousand leaves, you won’t see much more than you do looking at one. Essentially they are all the same. By looking at one leaf, you can know all mango leaves. If you look at the trunk of the mango tree, you only have to look at the trunk of one tree to know them all. All the other mango tree trunks are the same. Even if there were a hundred thousand of them, I would just have to look at one to really see them all. The Buddha taught to practise Dhamma in this way.

– Ajahn Chah
The Key to Liberation and the Path to Peace
p. 14

Pascal vs. the Buddha

Pascal’s Wager is sometimes said to be the first formal use of decision theory. Blaise Pascal of the 17th century reasoned thus: if one believes in the Christian God

  • and the belief turns out correct, one is rewarded with an eternity of gain (or, conversely, avoids an eternity in hell);
  • if the belief is wrong, one loses almost nothing.

The thought struck me that the lesser known second part of the Kalama Sutta is also a similar application of decision theory. This is about 2,200 years earlier than Pascal. But it was not as formally laid out, and is also a far more complicated (but therefore more realistic) case.

The Buddha applied it to moral decisions in the context of the extent to which one believes in the cause and effect of one’s actions, or simply put, Kamma/Karma, the full extent of which is necessarily linked to rebirth.

Although how causes, moderated by conditions, lead to their effects is a highly complex matter, they are generally still apparent to us (think physics) and therefore believable… except for the catch that there might not be enough time for all effects to come to fruition within one lifetime. Therefore rebirth completes the idea of Karma by providing opportunity in the future for fruition of effects.

Ordinary people, however, do not have knowledge of their past lives or that of others’, so the idea of rebirth is not as apparent and believable.

According to the Buddha’s reasoning as re-told by the Kalama Sutta, if one acted accordingly to avoid unwholesome deeds and carry out wholesome ones throughout this life:

  • if rebirth were true, one benefits in this life as well as after the end of this life by having a better rebirth;
  • if rebirth were not true, one most probably still benefits by having lived blamelessly and avoided substantial suffering in this life.

I did a quick Google and found out that other people have linked this to Pascal’s Wager before. In fact, some folks online called this the Buddha’s Wager. There is also another scripture that is in the same spirit: the Apannaka Sutta.

The Buddha’s Wager is a far more complex application of decision theory, however, because:

  1. Pay-offs is positive (according to the formulation above; just like Pascal’s Wager, it can be formulated in the negative sense, i.e., living an unwholesome life) in both options, just that one (with afterlife) is on top of the other (this life only). In Pascal’s case, pay-off is usually taken as neutral (=zero) in the worse of the options (but see below).
  2. The degree of uncertainty is different between the two pay-offs. It seems to me that this is a critical part of the Buddha’s version. Cause and effect within this life is more believable (=lower uncertainty) because it is usually observable; rebirth (i.e., continuation of cause and effect after death) on the other hand is usually not observable and therefore highly uncertain. (In Pascal’s case, there is only one non-zero pay-off option so uncertainty is only relevant for that pay-off.)
  3. There is a cost involved, because this case, in contrast to Pascal’s in the context of Christian doctrine, is not just about belief but about taking action. Acting incurs opportunity cost in the process, e.g., effort invested, or “opportunities” missed from not taking advantage of others or not indulging oneself.

The Buddha’s case is therefore pitting a additional pay-out (P1) that has higher uncertainty (U1) together with a basic pay-out (P2) that has lower uncertainty (U2) against the cost of action (C). So one should only take action and incur the cost if one can be sure that the combined expected benefits are high enough:

P1* (1-U1)+ P2* (1-U2) – C > 0

The Buddha’s Wager is not so much of a wager as it is a statement of inequality: that P2* (1-U2) > C so that the value of U1 is irrelevant, i.e., the benefits of a wholesome life are sufficient in itself to justify us taking the trouble, whether or not there is an afterlife. In such a formulation, the Buddha portrays moral behaviour as cost-beneficial regardless of afterlife belief.

If we go strictly by the Kalama Sutta, U2 seems to be taken to be zero, which reduces the inequality condition to an even simpler one: P2 C. Herein lies the link back to the rest of the Kalama Sutta, and the difference between Pascal’s Wager and the Buddha’s version.

In Pascal’s Wager, the pay-off in choosing to believe is positive infinite. In such a system, nothing finite can be greater than positive infinite, so the pay-off for disbelief, even if positive and not zero, will never outweigh the pay-off for belief. This means that Pascal’s Wager, while logical, is still a non-falsifiable statement of theistic belief.

On the other hand, the Buddha’s inequality statement is possible to be false, and therefore can be subjected to testing; one just needs to estimate P2 and C. This is why it fits in with the first half of the Kalama Sutta: the Buddha’s exhortation to the Kalamas not to base their actions on the sole basis of belief, but to test it out for themselves and weigh the benefits and costs of their actions for themselves and others.

Australia: 10 months

Time flies.

I just passed my 10-month mark two days ago.

I think I can tell that we’re starting to move on from late winter now towards early spring. Although Brisbane winters are mild, I had to learn how to cope. Nonetheless, give me winter over an Australian summer any time, especially in a house without air-conditioning (nor with a heater for that matter).

When I first arrived, I was sort of counting down to my next trip back to Singapore (which has been rather frequent, I must say). Six months in, however, I felt more-or-less adapted. Now, I enjoy every day I spend here.

There’s plenty of time to ruminate and reflect here, and the mindset change happened when I decided that I can’t spend all my life counting down to the next life stage.

When I was in primary school, I couldn’t wait to be taking the nine subjects in secondary school, including the cool stuff like history and geography, instead of the boring old four.

When I was in secondary school, I couldn’t wait to be sitting in junior college lectures, as a refreshing change from the usual classes in classrooms.

When serving National Service, everyone counts down to the last day.

For the first couple of my undergraduate years, I was counting down the semesters to graduating. In fact, I mentally divided them into half-semesters so that they would seem to pass by more quickly. I wanted to get out of school to start working.

In grad school, who doesn’t count down to the day when you hand in your thesis?

And I was counting down to the wedding mostly because I had forcibly stuffed my anxiety of organising such huge events into a corner of my mind, and keeping anxiety stuffed is mentally draining.

Imagine it going on: counting down to the day your child gets born; counting down to them growing out of their terrible twos and threes and angsty teens, to them graduating and getting a job; counting down to retiring… So I’ve told myself: this counting down has to stop.

If nothing fatally unfortunate happens, I can expect to live to 70 at minimum. The Economist recently ran an article saying that many of us would probably live to 120. Nonetheless, it’s a finite number of years. I’m already 33; to wish away the days of my life, just so I can escape the things I don’t like about today, would be foolish.

Whenever I’m in Brisbane, I have ample time and leisure to reflect about life… Something that in recent years I haven’t been able to do properly.

What is important to me? What are my priorities? What do I want to be when I am lying on my deathbed?

This overseas fellowship was supposed to get me to network with other researchers, come up with new ideas, learn new skills, etc. I’m actually surprised that in 10 months I really managed to do some of all of that.

But I think far more consequentially is that I have learnt to truly live on my own (e.g., cook real meals), and also had the space and time to contemplate, not just about science but also other things. I’ve regularized my life: meditation practice, work patterns, etc. These are not the things that my fellowship programme cared about, but I know they will be the things that really matter.

I had been reluctant to leave my secondary school and junior college. I found my National Service to be a fulfilling time, when I was serving others instead of serving myself (as a student). Towards the later half of my undergraduate life, I was no longer counting down; if I did, I wouldn’t have signed up for postgraduate studies.

These days, I am no longer so jubilant before my short trips back that I find it hard to concentrate at work, and also don’t feel quite so reluctant to leave Singapore because there’s the upside of getting back to quiet times in Brisbane.

When some folks heard I was going to Australia for two years, they made the jokes about not wanting to come back. I pooh-poohed them.

I still look forward to going back to Singapore, come October 2017. Just that I also know that I would miss this phase of life when it’s over, as I did with the others.

Journal article titles on Pokemon ecology and evolution

Pokemon Go is out in Singapore and is all the craze now. There can be two common reactions by biodiversity science workers to this. One is to ask: What’s that? After all, we’re too busy doing real work… The other is to roll our eyes, and wonder why so few people appreciate the real plants and animals around us.

Some call this passive-aggression. To be honest, I did go on a rant to the wife about how I would absolutely give a student zero if I caught him/her playing Pokemon Go on a field trip.

But the world of Pokemon should be really intriguing to us who search for patterns in the (real) natural world. It led me to think: what research hypotheses would I test using Pokemon Go? Which in turn leads me to fantasize: what would the titles of the papers look like?


1. Excessive use of lures homogenizes Pokemon beta diversity

2. Fourth-corner analysis reveals habitat preferences of Pokemon functional groups

3. A test of temporal niche-partitioning in nocturnal- vs. diurnal-spawning Pokemon

4. Invasive species, or urban commensals? Population control of Rattatas and Pidgeys does not increase Pokemon diversity nor abundance

(On evolution:)

5. A phylogenomic approach to estimating speciation rates in the Eevee clade

(Typical review bullshit:)

6. The role of Pokestops in sustainable harvesting: prospects and challenges

7. Ontogenetic shifts in life history strategies for Pokemon displaying multi-stage metamorphosis

(‘Cos you gotta have one for the taxonomists:)

8. Lectotypification of Nidoran

9. Dynamic occupancy modelling of the amphidromous Magicarp

There are only nine because I could only think of nine. After all, I don’t play the game, so I don’t know enough about their natural history. For those who do, why not grab your nearest/favourite journal article, and think about how you might change it to one on Pokemon! It might help others understand the kind of work we actually do.

Singapore’s MFA on the environment

I was browsing the Ministry for Foreign Affairs website because my flight home from Edinburgh is on Turkish Airlines and transits through Istanbul. Given the coup attempt just less than 48 hours ago, I was wondering if I should (spend an obscene amount of money to) change my flight.

I chanced across a page “Sustainable Development and Climate Change” and professional curiosity caused a momentary digression.

The opening line for the page was:

As a land-scarce and highly-urbanised city-state, Singapore is aware that economic development should not come at the expense of harming the environment or reducing the quality of one’s living conditions.

Gotta hold ’em to it.

Australia: 5 months

The wife came over to spend the past five weeks with me in Brisbane.

We visited the Glass House Mountains up north:

20160317_102302 labelled

Members of the Glass House Mountains as seen from a look-out. Names and heights taken from the information panels at the look-out.

And we visited Lamington National Park down south, as urged by Alvin Lok.


Epiphyte-laden tree limb, seen from climbing up a ladder to a deck, along a tree-top walk near the Lamington National Park visitors’ centre and resort.

The in-laws came over for the fifth week, and we went to Tasmania. We started with Launceston (which I think is pronounced “lawn-sass-tehn”), the second-largest city in the state.


The Cataract Gorge at Launceston.

Then we went to Cradle Mountain National Park (which apparently in Chinese would be called 摇篮山). In fact, we went up to it twice, because it was drizzling rather badly the first time. A cold place, with delightful wombats lumbering around in the scrub.


Dove Lake up the Cradle Mountain, seen from the Glacier Rock, on the second visit when the weather was better.

Next we headed to Bicheno, a small seaside town.


Rocky shore at Bicheno at sunset. The red algae on the rocks is probably the same one that covers the rocks at the Bay-of-Fires up north, which we skipped.

We didn’t see any penguins making landing that night. But it was really more of a rest stop for visiting Freycinet National Park next. So Freycinet is pronounced “fray-sin-nay”. So I guess the genus Freycinetia should be pronounced “fray-sin-nay-sure”.


Wineglass Bay. Tip: this look-out is not a good spot for morning selfies without a flash. The sun is behind the peak, casting a shadow over this side of the slope. My guess is that in the afternoons, the sun will be glaring right into the camera lens.

Finally, Hobart, the state capital. Can’t get away without paying a visit to a nature spot too.


Evening view of Hobart from the peak of the towering Mount Wellington. Very very high up, but you can drive all the way; felt like I was driving into the sky, and the legs were turning to jelly on the accelerator. Very strong winds and very cold.

The wife has just gone back and I’m all alone again. 😦

“Luckily, I’m a botanist…”

I’m late, I know.

I just caught it via streaming online two days ago. They were telling me to see it before I left Singapore in October, and I had wanted to catch it with the wife, but there wasn’t time.

In November I was just re-watching the Bourne movies with Matt Damon in them.


“Luckily, I’m a Botanist. Mars will come to fear my botany powers.” (Image from

More mock arrogance:

I don’t want to come off as arrogant here, but I’m the greatest botanist on this planet.

And what must be the favourite quote of all for science nerds in general:

…I’m gonna have to science the shit out of this.

I want that on a T-shirt.

Leaving The Lab

Finally, it my turn to “Leave The Lab”.

While packing up, there was no sadness, but a certain amused satisfaction going through all the mementos accumulated over the years.

Perhaps this is a lesser version of what we need to strive for by the time we reach our deathbeds: that I have done my best and I have no regrets at all (see William Hung).

Perhaps it is also because I know I’m coming back.

Is that what a tulku feels on the brink of passing away, satisfied with his life’s work, and knowing that where he’s going is simply an intermediate stage, a “bardo”, between lives?

This (part of the) world will not wait for me. But I’m coming back.

An invasion ecology paper in Chinese

I had some fun trying to read a scientific paper (Lee and Shieh, 2005; 特有生物研究 7:1) in Chinese today. It’s really refreshing to see some of the standard ecology phrases and concepts in such a different form!

The defintion of invasive species:


“When non-native bird species endanger native biodiversity, they are termed as invasive species. Types of impacts of invasive species include predation, competition, exclusion, genetic pollution, and the transmission of diseases and parasites.”

The invasion “stages”:


“There are four stages involved in exotic bird species invasions: transport, introduction, the establishment of [wild] populations, and spread.”

On propagule pressure:


“The probability of successful establishment of wild populations by non-native species is correlated with the number and frequency of release events as well as the the number of individuals released in each event.”

On resource-use overlap and competitive exclusion:


“The use of the same resources by organisms will result in competitive exclusion, usually leading the species that is the weaker competitor to be in danger of extinction.”

And just for fun, something about statistics:


“Two-tailed chi-squared tests of non-independence and non-parametric tests of comparisons were conducted, with the level of significance at 0.05.”

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