Everything is about white male privilege, even writing advice it seems

I read a headline saying Why the writing advice 'show, don't tell' is inherently political and thought, well, this should be good. The links ultimately lead to an essay called Let me tell you by one Cecilia Tan.

The author discusses 'show, don't tell' (SdT) entirely in the context of world building, i.e. info dumps about the background of a story. She then argues that SdT relies on a shared cultural background, and thus this writing advice privileges writers who can rely on sharing such a background with their readers, i.e. white males.

Now, first, I would not see anything particularly wrong with this in principle, because why should it only apply to white males? If an Iranian woman wrote a novel for Iranian women, it would work the same.

But more importantly, at least to me, and while I appreciate that I am not an author of novels who has run into that criticism myself, her understanding of SdT totally misses the point. Every single time I have seen people complain about being told instead of being shown by a poor writer it was something like this (if necessary search that page for "show-don't" to find what I mean) or this.

So it is not about world building info dumps at all. It is entirely about being too poor a writer to communicate the abilities and emotions of one's characters. It is about merely stating that your protagonist is a good debater instead of introducing her by winning an argument. It is about thinking that your reader is too stupid to understand that the protagonist is sad when you simply write "Frodo cried" and instead writing something to the effect of "Frodo cried because he was sad, and he was sad because as you may not remember Gandalf had just fallen to his death, see previous page". It is quite simply about poor and lazy writing, in a way that is independent of cultural context except to the degree that some other cultures may not even have a tradition of fiction writing (e.g. if it is a culture without a written language).

But apparently everything has to be about Western privilege all the time; there is nothing in the universe that is not about Western privilege.

It's the same hubris that led the white Western establishment to assume its medicine, science, and values superior to all other cultures. We'll come back to that shortly.

Eh, no. A medicine is superior to other medicines if it heals more reliably, and a scientific methodology is superior to other scientific methodologies if it produces more reproducible and accurate descriptions of reality. There are things that demonstrably work (often including substances found in traditional healing herbs) and there are things that demonstrably don't (including the Western tradition of bloodletting). That is all there is to it, no Western or Eastern or whatever needed.

Also, apparently a story about a protagonist having an impact on the outside world is quite simply "colonialism". What? No, people interacting with each other, helping each other against a dark lord's attempt at world conquest, learning from each other isn't colonialism. Invading with an army and taking over other people's countries to exploit them, that is colonialism. Words have meanings. Or at least they should.

Book fair o'clock

It is the time of the Lifeline charity book fair again. Unfortunately I had to go alone today, but tomorrow we hope to get the whole family there. The loot so far:

Susanna Clarke, Jonathan Strange & Mr Norrell. Fantasy alternate history, as in the Napoleonic times with magic. I have read good things about this book, so I'm happy to give it a try.

Bertrand Russell's Best, edited by Rogert Egner

Terry Jones, Douglas Adam's Starship Titanic. If I understand correctly this is a book after a computer game with which I am not familiar.

Anne McCaffrey, Dragonflight. First novel of the Dragonriders of Pern series. The series has lots of volumes, and I could have bought more of them, but who knows how they are?

Anne McCaffrey, Dragonquest. Second novel in that series.

Kirk Mitchell, Cry Republic. As a teenager I read the trilogy of which this is the third novel in German translation. It is an alternate history story in which the Roman Empire never collapsed and has discovered electricity, steam and flight. Just noticed that the praise blurb on the front cover quotes Anne McCaffrey.

Great Dialogues of Plato, translated by W.H.D. Rouse. Continuing my education in classics, which perhaps should have happened in late high school but didn't.

Sean Williams, The Stone Mage and the Sea. I am afraid part of the reason I bought it is that I got confused and thought the author was Tad Williams. Ah well.

And for work:

H.T. Clifford & Gwen Ludlow, Keys to the Families and Genera of Queensland Flowering Plants. From the 1970s, but will still be useful.

Nicholas Gotelli, A Primer of Ecology. Having been trained as a systematist I am hoping to get a bit more insight into ecological modeling, and it includes a chapter on island biogeography that looks promising.

Andrew Young & Geoffrey Clarke, Genetics, Demography and Viability of Fragmented Populations. Because of a project I am currently involved with.

Two observations. First, as always I come home with loads of books but could only bring myself to donating two. Some day we will have to expand our book shelves, and I have no idea where. Second, it is astonishing how there are numerous copies of some books (e.g. McCaffrey's Nerilka's Story) but none whatsoever of other, one would think, equivalent books (e.g. the third volume of the same series).

Also, are the frequent ones frequent because they were so much more popular when they were published, or because nobody wants them now? On that note, it was interesting to see that the most frequent book in the "all faiths" section was The God Delusion. It was all the rage a decade ago, and I assume now lots of people think they don't need it anymore.

Undergraduate resumes / CVs

I don't seem to have one of those files on my current computers any more, but I know that my CV as an undergraduate looked something like this:

Name
Address

Picture taken by professional photographer while I was wearing a formal jacket and perhaps a tie

Formation

Studying biology at [university], 1996 - now
Non-military service, 1995 - 1996
[Public grammar school] (high school & college in one), 1988 - 1997
[Yet another public school], 1986 - 1988
[Public primary school], 1982 - 1986

Undergraduate scholarship of [foundation], 1997 - now

And... that was that. Black on white, Times New Roman size 11 point, 1.2 line spacing, one page, easy to see all relevant information at a glance.

Now, an Australian undergraduate's CV today appears to look something like the following:

Name
Address, e-mail

Either no picture (which is what is expected in Australia) or a selfie taken at a party

Personal details

My name is [name], I am 24 years old and live in Woolalla, New South Wales. I am currently in my third year at Ned Kelly University studying a combined degree Bachelor of Science / Bachelor of Arts majoring in biology and journalism. I hope to pursue a career in science and apply what I learned in university to better the world.

Personal attributes

Effective communicator
Reliable and trustworthy
Ability to work in team as well as independently
Hard worker
Leadership skills demonstrated by frying burgers at McDonalds
Organisation talent demonstrated during waitressing by correctly taking customer's orders

Skills

Word, Excel, PowerPoint, Internet Explorer, Google

Employment history

Sales assistant at some supermarket, 2009 - now
Waitressing at Happy Hogan's bar, 2008-2012
Frying burgers at McDonalds, 2013 - now

Volunteer work and leadership

Friends of the State Zoo, 2011 - now
Church Youth, 2007 - 2009

Education

Ned Kelly University,  Bachelor of Science / Bachelor of Arts majoring in biology and journalism, 2014 - now
Catholic College of South-eastern Western North Sydney, 2012 - 2014
Little Sisters of Perpetual Misery Private Catholic High School, 2008 - 2012

Other activities

Raising money for YUZN charity
Wildlife rescue
Greening Australia
Surfing
Blood donor for Red Cross
Debate club

Achievements

Consistently excellent marks in university*
Award for high placement
Mentor for other students
Talent Award
Award for outstanding job as house head
President of debate club
Dean's letter of recommendation

They are often carefully formatted in a fancy sans serif font with about 50% white space, perhaps a red bar at the top or a blue bar along the left margin of the page. They are often three to four pages long.

A few thoughts. First, it is not as if we didn't have extracurricular activities and hobbies back then in Germany. It just would never have occurred to most of us that a potential employer or scholarship provider would care the least bit about our participation in a badminton club. And as far as I can tell they wouldn't have, and I certainly don't. This is wasted space that merely makes it harder to find the truly relevant information.

Second, the personal attributes also seem a bit pointless. Will anybody actually truthfully write "I am lazy" or "I am a poor communicator"? Presumably not, everybody will claim the positives, honestly or not. So this is wasted space that merely makes it harder to find the truly relevant information.

Third, I assume somebody tells Australian students to put all their work experience in there to demonstrate ... well, this is where it breaks down for me. That they will show up for work if you give them a contract? That's kind of a low hurdle to clear. But beyond that, how is flipping burgers or waiting tables a relevant qualification for a job or scholarship in science? I don't get it. This is wasted space that merely makes it harder to find the truly relevant information.

Fourth, all those achievements? When I was a school or university student in Germany, we did not have even just a tenth of those awards. Here half the students seem to have lists of awards that look seriously impressive; but given how many of them have lists like that I do wonder how easy they are to get. If there is no term like award inflation (in analogy to grade inflation) then we need to create it.

Of course, given the length of the time since I left I also wonder how German undergraduate students' CVs look these days. Do they now also mention every little thing they did, no matter how irrelevant to the job or scholarship they are applying for? Do they also now try to look as if they had been written by a graphic design graduate?

Footnote

*) From what I can tell the likelihood of somebody explicitly claiming to have consistently high marks in the achievement list seems negatively correlated with the actual quality of their marks. The people who actually have near-straight high distinctions tend to have only an understated line in the CV providing their point average.

Free-association word salad is not the same as analysis

I find it remarkable what kinds of pieces are sometimes published by otherwise serious news organisations. Today during breakfast I made the mistake of trying to read something hilariously filed under "analysis" at the ABC website, Are we sleepwalking to World War III?

It starts with the claim that WW3 is coming and that Australia will be invaded:

All certainty will be lost, our economy will be devastated, our land seized, our system of government upended.

It is backed up by what a single former military commander said to the author over lunch:

This isn't mere idle speculation or the rantings of a doomsday cult, this is the warning from a man who has made it his life's work to prepare for just this scenario.

I may be missing something here, but unless there is a bit more at least circumstantial evidence I would still file this warning as mere speculation; that is kind of what the word means.

Then the author randomly quotes out of context Mark Twain ("History doesn't repeat but it does rhyme"), Alexis de Tocqueville as writing that the French Revolution was inevitable, a claim that can very conveniently be made about any historical event after the fact because it is always untestable, and then quickly moves to a historian's work on the beginning of World War I (while spelling the name of that source in two different ways).

In this latter case at least an actual argument can be discerned: Britain and Germany were trade partners and still went to war, so we should not assume that two countries today would stay at peace just because they are trade partners.

The author accelerates his already breathtaking pace to name-check a Harvard scholar and, before that person gets to say anything useful, the Ancient historian Thucydides. He seems to imply that the USA might be forced into starting WW3 to stop the rise of China, as Sparta was forced to start the Peloponnese War when Athens became too powerful. (I read Thucydides years ago, and I seem to remember it was a bit more complicated than that.)

The text descends into gibberish for a bit:

Any clash between the US and China is potentially catastrophic, but as much as we may try to wish it away, right now military strategists in Beijing and Washington are preparing for just an eventuality.

Perhaps: "just such an eventuality"?

Global think tank the Rand Corporation prepared a report in 2015 for the American military, its title could not have been more direct -- War with China: Thinking Through the Unthinkable.

Yeah, that's the job of strategists and (serious) think tanks.

It concluded that China would suffer greater casualties than the US if war was to break out now. However, it cautioned, that as China's military muscle increased so would the prospect of a prolonged destructive war.

How... what... huh? If I picked a fight with my neighbor now, I could be hurt, BUT (!) if I picked the fight an hour later, the fight could take longer. That doesn't even begin to make sense as a sentence. Even if we try to speculate about what the author may have meant here, for example that China would lose a war now but may have a better chance of winning a few decades in the future, one would have to point out that suffering greater casualties may not be incompatible with winning now either, cf. USSR in WW2. Also, why interrupt the sentence with a comma after the main verb? Did nobody proof-read this?

Having established to his satisfaction that war could happen, the author now moves to the question what precise incident could precipitate WW3 in Asia. Again a historian is cited, and again only so superficially that it is impossible for the reader to judge if what they say can be backed up. The islands of the South China Sea and other islands disputed between China and Japan are mentioned as the most likely causes of war. Okay, so I am not a military strategist, and I appreciate how useful symbolic conflicts can be to fire up nationalism when a government is in domestic trouble, but are these really the kinds of issues where a government would say, hey, let's needlessly blow up our entire economy and get hundreds of thousands killed over a practically worthless heap of rock? (Or sand, as the case may be.)

But of course we have to move on immediately. Cyber warfare! Thucydides! (Again.) Name-checking a Chinese scholar who does think that China and the USA are too economically interdependent to go to war, so at least we have an isolated counterpoint. Then the former military commander from the beginning opines that it would be helpful if politicians would also consider the risks of going to war; I am sure nobody in the history of humanity has ever had that idea before.

The piece ends with the author claiming to be more optimistic than his interview partner, only to end on a very depressing note. He takes this as an opportunity to quote Shakespeare, I presume in case the mention of Twain, de Tocqueville and Thucydides wasn't enough to signal deep erudition.

Now don't get me wrong, I am also rather pessimistic about the future. Overpopulation, resource limits and climate change may well combine to throw the world into a new dark age, with starvation, mass migrations, widespread collapse of most institutional order, and warlords duking it out with the few Byzantine Empire-like islands of stability that are left.

But that is how I would expect a serious analysis of future trends to look like: citing empirical evidence of risk factors like crop failures, water availability or shifting alliances and how they can produce unsolvable dilemmas for all involved. Merely name-checking historians in a meandering, stream-of-consciousness text without any real information or data isn't it.

In praise of Linux

I am not saying I want to proselytise or anything. I completely understand Windows users; after all, I was a happy Windows user myself until they produced Windows 8. And if somebody is into gaming, for example, then Windows is the obvious choice. But I am really, really happy using Ubuntu now.

For starters, we do not have to worry about the most common cybersecurity issues, such as the Petya attack that is currently making the rounds. Admittedly neither my wife nor I would open a suspicious attachment anyway, but still, it is nice to know that everything that attacks the most common operating system is irrelevant to us.

More to the point of what I did this evening, I program a lot in Python these days. Well, for certain values of "a lot". I am obviously not a programmer, but the language is very useful for many tasks in science, from quickly reformatting a large data file to scripting complex analyses.

And the thing is, Windows makes it unnecessarily hard to use Python (or most programming languages, really). First, I need to install the language. Okay, perhaps understandable. But then I need to figure out how to tell Windows to look for Python in the Python folder whenever I try to run a Python program. Then perhaps I need to install a specialist Python library like BioPython to run certain analyses, and that is where things really go downhill, because it usually doesn't install because some dependency is missing or whatnot.

Now compare the Linux variant Ubuntu. First, it comes with Python already installed. Second, it is clever enough to automatically access Python from any folder where you start a Python script. Third, Linux makes it really easy to install things on top of Python, because it is usually smart enough to recognise dependencies and install them also. In fact that is such an obvious advantage that it seems bizarre in retrospect that Windows won't do it.

Anyway, today I decided to spend the evening coding a simple script. I was able to just plop down in front of a computer that had Ubuntu installed two weeks ago, and I did not need to do anything in preparation. So. Nice.

Promiscuity

Recently I participated in an interesting discussion on the internet. The main topic was how some people reject scientific evidence if it contradicts their religious or ideological commitments, but the example was the nexus of evolutionary biology, male and female reproductive strategies, and differences between men and women.

It seems rather self-evident that males of nearly every species can potentially, if they are lucky and pursue the "right" strategy to achieve that end, have many more children than females. That is, after all, how female is defined in biology: it is the sex that makes the greater investment in offspring, usually at a minimum by producing a few large, immobile gametes, while the male is defined as the sex that makes the lower investment into each individual potential descendant, usually at a minimum by producing many small, mobile gametes. On top of that many species have layered additional female investment into the developing offspring, be it by giving live birth (or its botanical counterpart of producing seeds instead of spores), producing milk, or providing paternal care.

It is at this stage that the situation can, rarely, be flipped, e.g. by male sea-horses taking over the pregnancy, or male ratites raising the young; or paternal care can be shared by the sexes. But for most species, the female is the bottleneck, so to speak: How many offspring a female and a male can have is capped by the female's fertility.

It follows logically that a male can increase its number of offspring by being promiscuous, while a female cannot. The conclusion for reproductive strategies is that males in your modal species should evolve to be non-discriminating with regard to sexual encounters, and to maximise the number of partners. Females, on the other hand, do not get anything out of such behaviour. (Unless other considerations come into play, such as earning money with prostitution, or using casual sex as social glue, as it said the bonobos do.)

Whether, for example, human men are more interested in having many partners or more willing to cheat than women is a testable hypothesis. But the answer to that question is not really what I want to dwell on.

What interested me was that a lot of people who argue from reproductive strategies as discussed above write things on the lines of "men cheat more than women" or "men are more promiscuous than women". Also quite interestingly, rarely somebody will pop up who argues the opposite, claiming that "women cheat more than men". Honestly I do not understand the logic for that latter claim, as it does not even have the advantage of making sense from an evolutionary biology perspective; the idea that it is based entirely on misogyny is at least not easily dismissed.

But really for present purposes both claims can be treated as equivalent: I think both of them are, equally, mathematically impossible.

Yes, perhaps it can be shown that men are wired to seek more partners; maybe that is even biological as opposed to cultural. But that does not mean that they will be successful at having more partners, and that is unfortunately what being promiscuous means. Wishing is not doing.

Assume equal numbers of men and women, and disregard homosexual pairings, as neither of these factors are what those who claim "[gender] cheats more than [other gender]" are concerned with. Make a row of female circles on the left and a row of male circles on the right. Now draw lines between female and male circles to indicate pairings.

You can end up with very different network structures, of course. You could have three quarters of all men unpaired, while a quarter of them is paired with four women each, a harem scenario. You could first have each man paired with one woman, and very women also paired with lots of men, a prostitution / men cheat a lot scenario.

But it is simply impossible to have more average promiscuity on the left than on the right, or vice versa, because obviously all connections start on the left and end on the right, meaning that promiscuity is in all cases = number of people of that gender / connections, and we assumed equal numbers of men and women.

Arguments could perhaps be made about the median, but that is not what people intuitively mean or understand when somebody says, for example, "women cheat more than men". Claims like those just don't make any sense, and one doesn't even have to collect evidence on that. They fail right out of the gate, on basic logic.

Sturgeon's law

While on the topic of the book fair, I have to say that as much as I love browsing through the books and finding gems, it is also one of the moments that produce a certain sense of alienation from the majority of humanity in me. The only other moment that parallels it is "standing in front of the magazine rack in a supermarket".

As far as I am concerned, there are generally no more than two to three journals in the average magazine rack that one could reasonably count as a loss if somebody were to torch the lot. In fact, not only would there be no loss to the wealth and welfare of humanity if titles like "Kim Kardashian's new bikini body" or "Nicole Kidman's relationship crisis", most of them blatantly invented anyway, went up in flames, but burning the paper to generate energy would be considerably more productive than using it to print this kind of dreck. And people are actually wasting hard-earned money on all of it.

Similarly, I cannot help but observe, as I look across the dozens of tables in the book fair, that there are entire sections on astrology and "alternative medicine". These kinds of books have only one goal, and that is to make their readers more ignorant and less capable of critical thought. (You might argue that the ultimate goal is to sell, okay. But they will only sell if they first achieve the goal I mentioned. A swindler first has to swindle, only then can they extract money.) In a way it is, of course, nice to see them being sold again for a few bucks to finance a crisis hotline, but there is no way around the fact that as long they are in circulation some of these works will continue to harm gullible people by getting them to rely on snake oil and forgoing real treatment for their illnesses.

As for fantasy and science fiction novels, there are so many crappy books out there that it is extremely hard to find the few worthwhile ones between them. And I don't even have very high standards - some of the ones mentioned in my previous post are not exactly Nobel Prize in literature material either. But for an example of the 90% crud that makes browsing books so hard, I would like to present a novel that I bought on a whim at the previous fair we went to:

Stan Nicholls, Legion of Thunder. Book 2 of Orcs: First Blood.

Being part of a series is not decisive evidence of being crud, but it is a first warning sign. At a minimum I am starting to think that the better authors are the ones that write a series so that each novel can stand by itself. Think Martin Scott's Thraxas, Barry Hughart's Master Li chronicles, or Terry Pratchett's Discworld novels; each book is a self-contained story. When everything has to end on a cliff-hanger, however, it just looks cheap and like trying too hard. There is also the risk that the story will never be brought to a resolution and instead end with author existence failure.

Now as for the book itself, I was fooled into buying it because I had read other, fairly good books by different authors written from the perspective of the usual fantasy underdogs like orcs or dark elves. In the present case, however, the plot of the novel can comfortably be summarised as follows:

Protagonists search for McGuffins (yes, plural; they have to collect several).
Protagonists get into fight.
Protagonists search for McGuffins.
Protagonists get into fight.
Protagonists search for McGuffins.
Protagonists get into fight.
Novel ends on a cliff-hanger.

The fights appear to be the main attraction here, as they are written in a very voyeuristic manner. Apparently some readers really look forward to knowing which evil mook gets a knife into the eye, which one gets its arm cut off, and how far the blood sprays.

But the insults to the reader's intelligence don't stop there. In the background there is a big bad sorceress who is so comically evil and so prone to randomly killing her own followers that she should have been murdered in a palace coup years ago. During what is clearly meant to be a pivotal moment in her character development, she demands of one of her sisters, who is ruling over a people of aquatic semi-humanoids, to help her hunt for the protagonists, who are moving entirely on land. Her sister rejects the demand, and so she magics her dead.

The things is, it never really becomes clear how helping would have looked like. Why didn't her sister simply agree, on the lines of: "I will gladly help you, let me just command all my soldiers who can operate on dry land to assist you OH WAIT I DON'T HAVE ANY"?

Seriously, the world does not need this kind of book to use up paper that could be used to print decent ones.

This season's Lifeline Bookfair haul so far

Not sure if I go another time tomorrow, but so far today's visit to the Lifeline Bookfair here in Canberra has netted the following:

Tolkien JRR, The Silmarillion.
I have read that one before, although in German I think (?). But we didn't own the book ourselves, and I may want to read it again.

Orwell G, Animal Farm.
Another one that I have read once before, but as a teenager. Again I did not have the book myself, having at that time borrowed it from a friend.

Wells HG, The Invisible Man.
A classic that caught my interest.

Scott W, Ivanhoe.
Likely not the best book I have bought today. My understanding is that it is pretty cheesy. But when I was younger I played Defender of the Crown and watched Ivanhoe movies, so it might be nice to read the novel that started it all.

MacDonald G, The Wise Woman and other Fantastic Stories.
Sounds interesting because the author is billed as "the great nineteenth-century innovator of modern fantasy" who "came to influence" CS Lewis, Charles Williams and JRR Tolkien. The back cover further calls the book one of a set of four, but sadly the other three were nowhere to be seen.

Silverberg R, The Longest Way Home.
A science fiction novel from an author some of whose books I have read in Germany translation years ago (mostly Majipoor novels). Not sure how it will turn out.

Bramah E, Kai Lung Unrolls His Mat.
Finally, this is probably the weirdest of them all. My hope is it will be something in the vein of Barry Hughart's chronicles of Master Li. We shall see.

In addition, we bought several books and a puzzle for our daughter, and yesterday my wife already went for several books and CDs herself. May have to donate some books back one of these days, or the bookshelf with the novels will fold into itself and turn into a singularity.

Update 12 Feb 2017: Went back again today and spent more time in non-fiction.

James W, The Varieties of Religious Experience.
A very famous book originally published in 1902, it examines the origin of religion from a psychological perspective. The critical introduction claims that the author was actually fairly charitable ("a classic that is ... too religious to have influenced much psychological research"), but one can imagine that the whole idea behind the work wouldn't have sat too well with many of the faithful.

Baggini J, Freedom Regained.
Having participated in the never-ending online discussion on Free Will I thought it might be good to read something by a philosopher on the subject. Admittedly there might be some bias on my side, as the author clearly has the same stance as I have, at least in the broad outlines.

Machiavelli N, Il Principe.
The classic's classic of all the books I bought, this is the 16th century book that Machiavelli is famous for. I got the German translation.

Astonishing, by the way, how much has been sold since yesterday.

Just have to share my astonishment here

This morning over breakfast I read an article in the Canberra Times. When I had finished, I first scrolled up again to make sure that I had not accidentally opened The Onion or, perhaps more likely, its Australian counterpart The Shovel. But no, it was indeed the Canberra Times. Then I thought hard if I had somehow missed that it was 1 April, but again, no such luck.

The article in question?

Housing affordability in Canberra: Renting is the ACT's 'biggest issue'. It argues that rents are so high in Canberra that people cannot save up enough to buy property, which is fair enough, ... using as its only example and case study a 23 year old student to whom, and I cite, "the great Australian dream" (of owning a house) "seems just that - a dream".

Maybe I am just weird, but when I was a 23 year old undergraduate back in Germany I would not have had the money to buy a house either. I lived off a mixture of a small competitive stipend, money earned from teaching assistantships, and my parents topping up the rest. Life was nonetheless good, as the student canteen was cheap and rents reasonable. But if I had started whinging about not being able to buy a house my friends and family would have given me a lot of side-eye, to put it mildly.

I would also argue that at 23 I was not mature enough to take on this responsibility, and I think I would have said so myself, even then. It was a time of learning, of studying, of first figuring out where I want to go with my life.

Which brings up another point. After finishing my studies and doctorate in that town I moved to a different state of the same country; two years later I moved to a different country on the same continent; and nearly one and a half years after that I moved to the other side of the planet. And really something like that was to be expected, given the way the job market in science works. So even if I had been able to afford a house I would not have wanted to buy one until I was settled. Yes, I guess there are some undergrads who study economics or law and then get into a company or public service in their home town, but that cannot be assumed to be a given.

Don't get me wrong, housing is expensive in Canberra. And clearly there must be some up-bidding of prices going on, because looking at quality and size the flats and houses are objectively not worth what they are going for, so the article seems to have got that right. I am forty now, and if we were to describe our fantastic, pie in the sky dream it would be to one day be able to afford a small two bedroom flat with a little courtyard or, if that is impossible, at least a balcony. A house is totally out of the question. This just for context - and note that I am not depressed about it. Billions of people on this planet live happy, productive and fulfilled lives while renting.

But apparently somebody at the newspaper seems to think that the average 23 year old (!) student (!) is expected to be able to buy and own a house. Further, that one's main goal in life, this "great Australian dream", cannot possibly wait until the old age of, I dunno, thirty, but has to achieved before even having finished education. Somebody looked at this article and went, yes, that looks sensible, let's click "publish". I am really, really astonished.

And I am eagerly awaiting to see the next article in the series, "Marriage prospects in Canberra: how a nine year old girl despairs of ever finding Mr Right".

New Laptop, and how to get science / phylogenetics crucial software onto Ubuntu

About a week ago I finally bit and bought a new laptop, a Dell Inspiron 11 3162, as my old netbook has grown old, slow, and of short battery life.

Yes, this is not exactly high-end, but the point is, I don't want high-end. A really good, high performance, cutting edge laptop would come with two downsides. First, it would be optimised for being high performance and not for being light and small; and I really want something that travels easily. Second, it would be expensive; and I want something cheap - we are talking less than AUD400 here - so that it will not be too painful if it gets damaged or stolen during field work or a conference trip.

The new machine came with Windows 10. I think it is a psychological defect on my part, but whenever I try to use Windows 8 or 10 even just for a few minutes I get really upset. Not trying to proselytise here, just my personal problem. A real problem, however, is that this model of laptop comes with storage of only 32 G on a card, no hard-drive. I assume the idea is that many people use the cloud these days (I don't), but still this is a tad on the ridiculous side. Windows 10 took up very nearly half of that space, so install a few things and get a few security updates and you hit the wall.

Having considered these two issues, I carpet-bombed Windows and installed Ubuntu 16.04. By itself this operating system takes up about 3.3 G without and now c. 8 G with various programs and packages I installed on top of it, still only half of what Windows did by itself. So, yeah. Also, I can now click on something and the computer does not have to think for 3-4 seconds before it reacts. As a colleague sardonically commented on the performance issues of Windows, "Intel giveth, and Microsoft taketh away." I also bought a micro card to fit into the little slot on the left side of the laptop, and it works nicely as additional storage, contrary to some comments I have seen on the web. It merely had to be formatted for Ubuntu.

Mostly I use my laptop for simple things, like Skype, checking eMails, writing on a manuscript, etc., but generally not to run time-consuming analyses. That being said, I like to have some analysis software on there too in case it becomes necessary during travel. It has to be admitted that one of the disadvantages of Ubuntu is still that it is not always trivial to find and install specialised software. As I just had to do exactly that, I thought I would use this post to collect my recent experiences. Perhaps somebody will find it useful before it is too much out of date.

First, the software centre was weirdly empty. Here I found a post on the ask ubuntu forum helpful.

If you have the same problem, open terminal and run:

sudo apt update
sudo apt upgrade -y

Now for my personal must-haves and how I got them:

Inkscape
(Vector graphics program, e.g. for editing figures for a manuscript.)

No problem installing from Software Centre.

GIMP
(Pixel graphics editor, for photos.)

No problem installing from Software Centre.

R
(Statistics software.)

There are probably different ways of doing it, but I followed the instructions from digitalocean.

rstudio
(GUI for R.)

Download the relevant .deb file from the program website, right-click and select to open it with the software centre.

Java
(Required to run several of the other programs here.)

I got JDK instead of merely JRE, just to be on the safe side. Open terminal and run:

sudo apt-get update
sudo apt-get install default-jdk

Source of information: digitalocean.

Acrobat PDF Reader
(Sadly it seems to be the only PDF reader on Linux that can edit complex PDFs such as used for grant proposals by some funding agencies. Only a very old version is available as Acrobat has discontinued Linux support.)

Open terminal and run:

sudo apt-get install libatk1.0-0 libc6 libfontconfig1 libgcc1 libgdk-pixbuf2.0-0 libglib2.0-0 libgtk2.0-0 libidn11 libpango1.0-0 libstdc++6 libx11-6 libxext6 libxml2 libxt6 zlib1g lsb-release debconf

wget http://archive.canonical.com/pool/partner/a/acroread/acroread-bin_9.5.5-1raring1_i386.deb

sudo dpkg -i acroread-bin_9.5.5-1raring1_i386.deb

Source of information: ask ubuntu forum.

In my case, however, I experienced some errors. Apparently Acrobat Reader requires some outdated packages to run, and Ubuntu does not want to install them because it has got the newer versions. The system itself then kindly suggested to me to run a command to fix the problem. I hope I remember correctly, but I think it was simply:

sudo apt-get upgrade -f

The f parameter is supposed to fix broken dependencies. That command (or one very much like it) solved the problem for me, and I was able to start the reader.

AliView
(Sequence alignment editor.)

Following the instructions on the program website should have worked, in principle. However, I realised only then that Java was not yet installed, and AliView obviously wouldn't work without it. Download the aliview.install.run file, change its file preferences to make it executable, open terminal, go to relevant folder, run:

sudo ./aliview.install.run

MAFFT
(In my eyes the best sequence alignment tool, can also be called by AliView.)

After experiencing some problems trying to install from the rpm file that is available on the program homepage I found an entry on howtoinstall.co that simplified things. Open a terminal and run simply:

sudo apt-get update
sudo apt-get install mafft

That was easy.

PAUP test versions
(Phylogenetics software implementing various methods.)

This comes as an executable. Obtain Linux distribution from program website, unpack, set file preferences to allow the program being executed, done.

TNT
(Parsimony phylogenetics software.)

Obtain Linux distribution from program website, unpack, set file preferences to allow the program being executed, done. When running the program the first time you will have to accept the license agreement, as opposed to during an installation.

MrBayes
(Bayesian phylogenetics software.)

Available on github and sourceforge. I downloaded and unpacked it, opened a terminal, navigated to the relevant folder, and followed the instructions for compiling that are given in the appropriately named text file. Worked beautifully, only I had to disable Beagle, as prompted during compilation.

FigTree
(Phylogenetic tree viewer.)

Java program, so simply get it from the program website, unpack, and set the JAR file to be executable in its preferences. It should then be run by Java whenever it is opened. I find it useful to create a link on the desktop for easier access.

Tracer
(To examine the results of MrBayes runs.)

Java program, so simply get it from the program website, unpack, and set the JAR file to be executable in its preferences. It should then be run by Java whenever it is opened. I find it useful to create a link on the desktop for easier access.

jModelTest
(Model testing for Likelihood and Bayesian phylogenetics. For larger datasets I would not use the laptop, of course, as it takes forever and benefits greatly from parallel processing.)

Java program, so simply get it from the program website, unpack, and set the JAR file and the PhyML program (!) to be executable in their preferences. It should then be run by Java whenever it is opened. I find it useful to create a link on the desktop for easier access.

WINE
(Windows emulator, just in case)

No problem installing from Software Centre.

SciTE
(Text editor with many useful functions, for data files etc.)

No problem installing from Software Centre.

Skype
(Video calls.)

Download the .deb file from the program website, right-click and select to open it with the software centre.

ClamTK
(Virus scanner.)

No problem installing from Software Centre.

This season's Lifeline book fair haul

The books that I picked up at our local Lifeline book fair today are mostly SF and fantasy.

Adams D & Carwardine M, Last Chance to See. Very, very happy to have this again. I owned the book years ago, and it was one of a number that I lent to other people and did not get back. It is in my eyes quite possibly Douglas Adam's finest work.

Butcher J, White Night. I have written before about Stormfront, the first book in this long-going series, and currently I am reading the second, a birthday gift from my wife. My thoughts are still the same: I am annoyed by the constant refrain of "people don't believe in magic because they don't want to accept its existence", which is so clearly the opposite of how people function in reality that it breaks my willing suspension of disbelief. And the hero is actually rather incompetent as an investigator, again failing to pursue what appear to be obviously relevant questions. But the books are really well written, so I make a conscious decision to put the first two issues aside.

Clarke AC, Report on Planet Three and other speculations. From the back cover: "Is life possible on planet three? Martian astronomers regard the prospects as extremely poor. The atmosphere with its large quantity of gaseous oxygen is intensely poisonous. The high gravity rules out any large forms of life." Hehe. This just sounds like a cute idea.

Judson T, Fitzpatrick's War. I have read about this book, and it was described as presenting a very depressing but rather thought provoking future, so I thought I would give it a shot. It is the thickest of the novels I bought.

Nichols S, Legion of Thunder - Book 2 of Orcs First Blood. I have the greatest doubts about the wisdom of buying this one, and not just because the first part was unavailable. In this context I should also mention that the fair had volume 1 of the Flora of South-Eastern Queensland but only that volume, and I ultimately decided that there was little point in having only one of them.

Rankin R, The Japanese Devil Fish Girl. Rankin writes comedic fantasy and science fiction, and I have read some of his work with pleasure in the past. This one appears to be comedic alternate history Steampunk SF. Will see.

In addition the wife and daughter got a number of other books and puzzles.

As always I am puzzled by the classification of books used by the fair volunteers. Finding a collection of Darwin Awards under General Science presumably merely shows an individual volunteer's mistake. I am also by now used to finding the Biology section full of a distressing number of creationist propaganda items.

But why, for example, are the subsections on New Age, Alternate [sic] Medicine and Astrology under Non-Fiction? Would they not be better placed under Fiction? And why is there a separate high level Religion section, but Mythology is a sub-section of the high level Humanities section? Some of that seems a bit arbitrary.

Hollywood tactics

Sitting in an aeroplane yesterday evening I watched a bit of the original 1996 movie Independence Day. It was always cheesy, but I never before appreciated how utterly stupid the battle scenes are. This has made me think about what the three worst examples of Hollywood tactics are that I can currently remember having seen.

1. Cavalry charge at a castle wall

Snow White and the Huntsman is another movie that I watched during a flight, and I was underwhelmed on several different levels. Neither the actors nor the story nor the weird love triangle rally worked for me, with the exception of the villain, the evil queen, who I found well acted.

The two large scale battle scenes that appear in the movie are just the icing on the cake. In the first, near the beginning, Show White's father's army charges at an enemy army, and it charges, and it charges, and it charges, and by the time the horses would be so tired that they'd have to slow down the enemy army actually appears on the horizon. And that army just stands there, all infantry, with a few very very short pikes that are totally unsuitable for fighting cavalry, and let themselves be slaughtered. Okay, they were only supposed to be a pretend invasion if I remember correctly, but still, if the good guys are never in any danger where is the point?

Much worse is the final battle, depicted above. The forces of good, led into battle by that girl with the abusive vampire boyfriend, make a cavalry charge at a castle wall. Again there is an "okay, they were", in this case hoping for the seven dwarves to sneak inside and open the gates for them, but seriously, have they never heard of siege equipment? And what if the dwarves had not succeeded? Even as it was, with the plot on their side, half of the good guys were slaughtered just approaching the castle, and then they stood in front of the gate looking stupid and being showered with arrows until the dwarves finally got their act together. And let's not even mention the conspicious absence of helmets.

2. Cavalry charge at massed heavy infantry carrying 10 m pikes

The weird thing is that in the movie Lord of the Rings: The Two Towers, the Uruk Hai are actually equipped and trained in exactly the right way to neutralise Medieval cavalry. Nonetheless the Rohirrim are depicted as charging them down when they arrive to relieve the siege of Helm's Deep.

Just no. See that picture above? Anybody who cavalry charges those guys is toast, even if they have superior numbers, which the relief force clearly doesn't. There is a limit to how far my willing suspension of disbelief will go, and this is a few hundred kilometres too far. Sorry.

3. If we poke the hippo with enough pins, it will die

Okay, back to Independence Day. Warfare in that movie is really so unbelievably idiotic that it is near-incomprehensible.

The understanding appears to be this. The United States military, the best equipped in the world, has exactly two types of weapons at its disposal: fighter planes carrying four air-to-air guided missiles each, and nuclear weapons. They are concerned about using nuclear weapons because it might irradiate the planet, fair enough. So the only choice left is to attack an Alien spaceship as large as several cities stacked on top of each other with c. two dozen fighter jets optimised for dogfighting other small fighter jets.

The flaw in that plan should be immediately obvious to anybody except apparently the entire team involved in producing that movie. Let's assume that the Aliens did not have that likely physical impossibility so beloved by science fiction authors, a force field that all weapons just bounce off, and that all 4 x 24 air-to-air missiles had connected and done their worst. Judging from the explosions in the screenshot, how much of the alien ship would have been damaged? Maybe 5% of its outermost walls? Yeah, that'll make a difference.

I really have no idea whatsoever why the movie never shows a bomber fleet, the kind of weapon that one would realistically use to flatten a city sized object without causing nuclear fallout. Would that not have been cool enough or something?

I am sure there are worse offenders, but these are the ones that have offended me the most. Again, no problem with some playing along, but there are limits. And especially when the flaw would be so easily rectified.

We have a new toy

This week ALDI in our area is selling little digital microscopes, among other specials. I thought for only sixty dollars it was worth a gamble - wouldn't it be cool to have a microscope for our seven year old daughter? - and I do not regret it.

Obviously we are not talking professional quality here. The picture is a bit blurry compared to a really good microscope, and the images it takes are only 800 x 600 pixels. It also does not have an ocular but runs entirely through a connected computer. But it is still functional to show a child the beauty of nature at smaller scales, and it may even become useful for the odd, quick shot to be integrated into a lecture or presentation, e.g. if I pick something up during a walk on the weekend and don't want to go through the trouble of using our high-end microscopy facility at work for something that trivial.

But for the moment our daughter in particular loves exploring small plant parts or fibres with the microscope.

Above: A moss leaf, the first object I collected to show her. Note the individual cells are clearly visible; what more do you need to demonstrate that organisms are build from cells?

I was a bit worried at first because the microscope comes with software only for Windows and Mac. A staff member at the store told us that "the program will work on Linux, Linux uses the Mac OS anyway, trust me, I am a software engineer", but I knew even then that that was what we might euphemistically call an over-simplification.

But no matter - the software it comes with is unnecessary. It turns out that a random webcam program, in our case the pre-installed Cheese, can run the microscope camera just as well. So far I am not regretting changing over to Ubuntu either.

When do we need voucher specimens?

Yay, in the last few days this blog passed 100k views! And just when I had a whole week of not being able to find the time to add anything...

Anyway, on Friday I have been considering voucher specimens. First, in case somebody from outside the field reads this, what are they?

Imagine somebody did a study of essential oils found in the South American mint genus Minthostachys, and they published a paper reporting a pulegone-dominated oil for Minthostachys glabrescens, a menthone-rich oil for M. verticillata, and a carvone-rich oil for M. mollis. Twenty years later, a taxonomist revises the genus and finds, for example, that the name M. glabrescens had for decades been misapplied to a completely wrong species (as per the type), and that the circumscription of M. mollis needed to be changed.

A new taxonomic treatment of the genus is published, and you might now, if you were interested in its ethnobotany, biochemistry or commercial exploitation, be interested in knowing how the old oil data relates to species as currently circumscribed. What those guys who did the oil study called glabrescens definitely wasn't true glabrescens, but what was it instead? Which currently accepted name applies to the sample that had the pulegone-rich oil?

If all there was in the oil paper were names and biochemical data you're stuck. This is where voucher specimens come in. For good scientific practice, the authors of that study should have deposited a herbarium specimen of each sample they analysed in an officially recognised and accessible research herbarium (the kind of institution serious enough to be listed in the Index Herbariorum), so that we can examine them even fifty years later and figure out what exactly it was that they had in their study.

So, in short: a voucher specimen is a herbarium / museum / biodiversity collection specimen that is cited in a publication to allow later scientists to verify the taxonomic affiliation of a sample used in a scientific study. It could be a dried and pressed plant, a needled insect, a fish skeleton or a stuffed bird; it could be connected to a morphological data set, a DNA sequence, a biochemical profile or a new species name. (In the latter case it would not be a mere voucher but a type. Although types are even more valuable, the principle is the same.)

Among biodiversity researchers the importance of vouchers is well understood. It is, or should be, virtually impossible to publish a study in a good botanical journal without citing a list of voucher specimens underlying your data either in a table, in an appendix, or as part of the paper's online supplement. And we are often rather exasperated that not all colleagues in related fields have the same approach. The biochemical example from above was chosen deliberately, as I have run into many essential oil or ethnobotanical studies that neglected to cite vouchers, meaning that their results are pretty much unreproducible and scientifically near worthless.

That being said, however, I have started to wonder whether some colleagues don't go a bit overboard with this. The occasion is discussing a seed reference collection, about which several people have asked me "is it vouchered"? So the idea is, we can only use the seed samples that have a herbarium specimen as a reference somewhere.

But we are not talking here about biochemical data, a DNA sequence uploaded to GenBank, or a morphological description. The seeds themselves are biological specimens, aren't they? Can't they be their own voucher?

Granted, there may be many cases where only having the seeds is not good enough to narrow taxonomic affiliation down to species level. But is that really different in principle from a perfectly acceptable herbarium specimen of a flowering plant ... in a genus where you need fruits to identify to species?

So to me the point of a voucher is that it is a lasting, biological reference specimen for a piece of data. But a lasting biological specimen should not necessarily need another lasting biological specimen as its reference. In some cases it may be good enough to be a specimen in its own right. Or to look at it another way, there can be botanical specimens that are not dried and pressed whole plants.

Modern art or something

I am currently re-counting some photos of root tip squashes for a paper I am preparing, and I stumbled across this photo taken by the student who was working with me. Seems like the exposure was somewhat off, but I find the result actually quite interesting.

The thin area was air caught under the cover, the surrounding larger areas were liquid.

Unfortunately it seems as if the photos we haven't counted yet were largely left over for a good reason: they can't really be counted with confidence. Sigh.

Lifeline Canberra Book Fair Autumn 2016

Oh, it is dangerous to go to the Lifeline Book Fair. Within one hour, I picked up the following:

Dawkins R., Climbing Mount Improbable. Had been hoping to get that one for quite some time.

Dennett D.C., Breaking the Spell.

Jones D.L. & Clemesha S.C., Australian Ferns and Fern Allies. Intended for my office at work.

White M.E., The Greening of Gondwana. Large and lavishly illustrated palaeobotany tome, a bit out of date though.

Vonnegut K., Cat's Cradle.

McCrumb S., Bimbos of the Death Sun. This is not what it sounds like but a rather funny satire / crime mystery combo that I had heard of before.

Howard R.E., The Conan Chronicles Volumes 1 & 2. Classics! Who can say anything against classic literature, right?

Akers A.B., The Suns of Scorpio. Okay, this, however, is probably exactly as high-brow as the title sounds. The cover compares it to Burroughs' Barsoom novels. But it was only $1, so hey.

This is in addition to children’s' books and two games for the daughter and various books the wife bought yesterday and today. Where to store all this?

Have got to go through the shelf and find a few old books to donate in turn...

Lifeline Book Fair

Great haul at the LifeLine Book Fair this spring, it was a good idea to go early on Saturday this time.

Vertebratist bias in action

The 72 last silhouettes submitted to PhyloPic as of today ca. 11am Canberra time break down into (not necessarily monophyletic) groups as follows:

11 non-avian dinosaurs
1 bird
7 primates
28 other mammals
1 reptile
3 fish
8 arthropods
8 land plants (all submitted by me)
1 kelp
4 other organisms

These are known species numbers for the various groups:

>1,000 non-avian dinosaurs known from fossils
ca. 10,000 birds
ca. 450 primates
ca. 5,000 other mammals
ca. 10,000 reptiles
ca. 33,000 fish
>1,000,000 arthropods (presumably a vast under-estimate)
>300,000 land plants
ca. 1,800 brown algae kelp species?
Other groups not mentioned here would include >25,000 nematodes alone, with 1,000,000 species estimated to exist, and of course molluscs, diatoms, bacteria and so much more.

In other words, even leaving aside the 'other organisms', relative to their species number birds are over-represented by a factor of four among recent submissions, non-avian dinosaurs by a factor of 220, primates by a factor of 320. Unsurprisingly then, arthropods and plants are vastly under-represented. And of course the database was already full of monkey and dinosaur silhouettes before those last 72 submissions.

This is par for the course; the same kind of bias is why you can get a Nature paper for discovering a new species of dinosaur or sufficiently cuddly mammal but not for discovering a new species of sedges.

Still, do contributors assume that bryologists and nematologists will never need to illustrate a phylogenetic tree figure? Just wondering.

The art of PhyloPic

As discussed in the last post, the idea behind PhyloPic is to provide "silhouette images of organisms", in other words just the black outline of the organism. That works well if you want to illustrate a phylogeny of insects, dinosaurs or mammals, because these taxa have very distinctive overall body shapes. It does not work quite as well if you want to illustrate a phylogeny of flowering plants, unicellular algae, or worms, for example.

There are two distinct problems. The first is that the truly relevant differences between organisms may be in their individual organs like flowers, leaf shapes, fruits, or mouth parts, for example, as opposed to the whole body. So to be useful, a collection of silhouettes should include individual parts of the organisms in question.

Second, a silhouette of an intricate organ like, say, a flower, may miss all relevant structure. Take this one, for example. When I first saw it as a small icon, I vaguely thought it might be a marchantoid liverwort, or maybe a particularly complex plankton species. It would not have occurred to me that it is a Hibbertia flower until I looked at the taxon name it was associated with. No, in a case like this it would really be good to see stamens and style, or to have gaps between petals and sepals.

Consequently, to maximise the utility of such an image collection across diverse groups of organisms, one would hope the definition of silhouette could be relaxed to include artwork with a bit more structure.

And apparently the PhyloPic collection is already somewhat flexible. In addition to silhouettes in the stricter sense, there are at least two other types of images in the database, although admittedly they are rare: Silhouettes that employ black and grey elements as in these recently submitted insects, and black silhouettes that also allow for white elements to visualise structural complexity as here.

For purely aesthetic reasons, I would prefer the latter. Obviously they also require some thought and talent. They would have to avoid lines that are too thin so that they still look good when scaled down. But the mayor challenge is simply to capture, using only black and white areas or perhaps only black areas with white gaps between them, the characteristics of a flower or fruit so well that (a) people will recognise the organism, (b) everything is morphologically correct, and (c) the result is attractive.

Scientifically correct botanical clip art could actually be something like a very special art form - just like of course new forms of visualisation, each with unique constraints, have always inspired botanical art.

PhyloPic

A few weeks ago we discussed a paper in our journal club that used dinosaur silhouettes in its figures and referenced PhyloPic as the source. So today I finally decided to check the website out.

PhyloPic is a repository of black/white silhouettes of organisms across the tree of life. The idea is that everybody can sign up and submit their artwork under some kind of creative commons or public domain license, and everybody can use the silhouettes to do just what the authors in the aforementioned paper did: decorate phylogenetic tree figures in publications or talk slides, educate, etc.

The idea sounds great, so I played around a bit today to see how well it works. The experience was, alas, a bit mixed.