Sunday, December 10, 2017

Andrew Sullivan on baking cakes

As always the following is my personal opinion and not necessarily that of my employer, friends, family or potted plants.

To follow news from the USA I regularly read the New York Magazine Daily Intelligencer. Once a week or so they have a column by Andrew Sullivan, who is the very peculiar combination of (a) Catholic, (b) homosexual, and (c) conservative. His average column follows a fairly predictable formula: first complaining about Donald Trump or the state of the Republican party, then a section break, then bashing left-wing activists over something or other. So as to maintain one's conservative reputation despite criticising conservatives, I presume?

Anyway, the most recent column takes a different approach. Titled "Let him have his cake", it takes the side of a religious baker who refused to make a wedding cake for a gay couple and now finds himself in front of the US supreme court. Then there is a section break, and then he complains about Donald Trump. It is the other way around, you see?

Anyway, his gay wedding cake argument proceeds as follows:

1. If there are alternative solutions, like finding another baker, why force the point? Why take up arms to coerce someone when you can easily let him be -- and still celebrate your wedding?

That is probably what I would do in such a situation, as I am relatively conflict-shy. But this is a legal issue, one of principles, and as always in such situations it has to be asked what would happen if everybody made use of the 'right' to refuse service.

It is my understanding that the USA had a time when a black person could find themselves in a town where every single bar served only whites. Surely given the rampant religiosity in some parts of that country it is at least not immediately absurd to think that a gay couple might find themselves traveling through a town where every single hotel would turn them away by citing religious objections to gay marriage?

2. The baker's religious convictions are not trivial or obviously in bad faith [...] those religious convictions cannot be dismissed as arbitrary (even if you find them absurd). Opposition to same-sex marriage has been an uncontested pillar of every major world religion for aeons.

This is a really interesting argument. My first response is that yes, religious convictions are all entirely arbitrary by definition. That's just the thing about religion, it is based on faith instead of logic or empirical evidence. The founders of one religion just made up some random beliefs, and the founders of another religion just made up some different random beliefs, and that is why there is not just one religion on the planet, as would be expected if there existed an actual god who communicated with people. Conversely, ideas that are not arbitrary are shared across different belief systems and accordingly not religious per se.

(Just as an aside, I don't really see where in the Bible or the Koran it actually says "Thou shalt not marry somebody of the same sex." Does it actually say so somewhere? I know that the Bible considers gay sex to be an abomination, at least between men, but funnily enough that particular "conviction" is not really insisted on very much at this time, or at least not to the degree that any significant number of religious politicians tries to outlaw gay sex. Because such convictions are indeed arbitrary.)

So yes, the conviction that gays should not marry is arbitrary. And that raises the problem that if there is a right to discriminate based on religious conviction, people can simply make up additional convictions to refuse service to other groups and in other cases. It is hard to argue that some taxi driver's newfound religious conviction that they do not want to drive around an interracial couple is 'arbitrary' if something as obviously arbitrary as not being able to use a light switch on the Sabbath is considered not arbitrary.

Interestingly, Sullivan seems to understand the problem - I worry that a decision that endorses religious freedom could effectively nullify a large swathe of antidiscrimination legislation - but ultimately this worry does not carry the day with him. Is he perhaps a bit naive about the intentions of the other side?

As a mirror image of the above we then get the following:

3. Equally, I worry that a ruling that backs the right of the state to coerce someone into doing something that violates their religious conscience will also have terrible consequences. A law that controls an individual's conscience violates a core liberal idea.

I do not understand what terrible consequences he expects. The consequences would be that people are treated equally, hardly something I would call terrible. And I think he confuses "controlling an individual's conscience" and "making them behave professionally". Those are not the same thing. An individual is allowed to believe that gays shouldn't be allowed to marry, but they should not be allowed to discriminate against gays. It is really as simple as that, even knowing that Sullivan will call me a "fanatic" for seeing it like this.

4. Much of the argument for marriage equality was that it would not force anyone outside that marriage to approve or disapprove of it. One reason we won that debate is because many straight people simply said to themselves, "How does someone else's marriage affect me?" and decided on those grounds to support or acquiesce to such a deep social change. It seems grotesquely disingenuous now for the marriage-equality movement to bait and switch on that core "live and let live" argument.

Well, I can only say that I find this argument rather disingenuous. The discussion went to the effect of, "if Bob and Jim are allowed to marry, your own heterosexual marriage does not lose any of its status, so what is it to you?" If the discussion was to the effect of "hey, we just want you to let Bob and Jim marry, but you can still treat them like second class humans and discriminate against them", then I have missed that.

5. A commenter on Rod Dreher's blog proffers a series of important questions in this respect: "If the cake shop loses, does that mean that if I'm, say, a freelance designer or an artist or a writer or a photographer, I can no longer pick and choose my clients? If the Westboro Baptist Church comes to me, I can't reject them on the grounds that they're deeply un-Christian scumbags? If I'm Jewish, do I have to design a Hitler's Birthday cake with swastikas on it? Would a Muslim cake-shop owner be forced to design a cake that shows an Islamic terrorist with crosshairs over his face, a common target design in most gun shops in America? Can a gay, atheist web designer choose not to do work for the Catholic Church, or would we have the government compel him to take on a client he loathes?"

This is perhaps the superficially most convincing argument presented by Sullivan. (Partly it may be that I find this style of argument particularly useful.) However, I feel that it mixes up a few different scenarios.

Yes, it seems to me that somebody who opens a shop or provides a service should not be able to refuse service to a church merely for being a church. That would be exactly the same kind of discrimination as refusing service to homosexuals, and it would be unacceptable to me. On the other hand, I think that a Hitler's birthday cake or a face in cross-hairs is a different kind of message to write in glazing than "Bob & Jim".

Yes, I get the idea that the latter supports gay marriage and is thus as objectionable to a certain kind of deeply religious person as mass murder is to other kinds of persons, but I believe that one would have to be quite nihilistic to not see the difference between those two points of view. One message seems objectionable because of an arbitrary, made-up religious dogma, the others are objectionable because they are demonstrably hateful and evil. Still, I understand how this is a difficult difference to see for some who hold a certain view of the first amendment of the US constitutions, for the kind of person who, for example, sees European countries outlawing Holocaust denial as engaging in a terrible restriction of free speech and taking the first step towards totalitarianism.


6. It always worries me when gays advocate taking freedom away from other people. It worries me as a matter of principle. But it also unsettles me because some gay activists do not seem to realize that the position they're taking is particularly dangerous for a tiny and historically despised minority.

Again, these are two very different types of freedom we are talking about. Historically, the freedom taken away from gays was the freedom to exist. The freedom Sullivan considers to be taken away from the baker is the freedom to discriminate against others. I find it puzzling how the latter can possibly be held to be a freedom worth defending, let alone be equated with the former.

Tuesday, December 5, 2017

Some thoughts on oral presentations

The Systematics 2017 conference in Adelaide was great, and as always I learned a great deal and enjoyed interacting with colleagues. Also this was simply the first time since I came to Australia that I saw South Australia, and it was the last state that I had not seen so far.

Looking back over the talks (oral presentations) I heard over those three days I wonder, however, about the different aspects that people decide to focus on in those talks. There are five types of talks that I find particularly odd.

The overly introduction focused talk

The average conference talk in science is structured like the average scientific paper: (1) introduction providing background information and leading into the aims of the study, (2) methods, (3) results, and (4) a discussion putting the results into context and explaining what they mean. What I call the introduction focused talk is when the speaker spends so much time telling us how cool their study group is and what had already been known about it decades ago or perhaps what they are trying to achieve that by the ten minute mark I wonder if we will ever get to hear what they have actually found out.

Now this is of course perfectly fine if the speaker is a first year graduate student who has only just started their project, but it is somewhat less understandable if a more senior researcher actually has lots of interesting data but, due to their misplaced sense of priorities, only manages to flash one tantalising results slide for twenty seconds before their talk is cut off by the session chair. In such cases something is off about the balance of the talk, just saying.

Relentless wet lab wonkery

One of the frustrations of the last few years, clearly driven by the rise in high-throughput sequencing, is the increasing amount of lab method wonkery in conference talks. People who could otherwise be great and engaging speakers go through slide after slide with little lines that are meant to be DNA fragments, explaining at length how those fragments are produced, barcoded, amplified, size selected, pooled, and sequenced, often for approaches that have been around for several years.

Maybe I am wrong, but I think most people do no want to hear, at least primarily, what somebody did on the bench, they want to hear for example how the study plants or animals evolved and what that means biologically. The lab wonk talk is like going shopping for a used car and finding that every salesman first walks you through the way a combustion engine works.

Relentless bioinformatics wonkery

This is the same as the previous, only with a focus on how the sequence reads are quality controlled, contigs are built, alignments are made, etc. Except in the context of a methods workshop it is perhaps even less helpful than lab wonkery. Most biologists in the field can at least easily visualise what happens to the DNA fragments the lab wonk is talking about (even if they don't really care and want to see the biologically meaningful results), but the bioinformatics realm is so full of impenetrable jargon that ironically only those who don't need to hear the talk will be able to understand it anyway.

Selling well known facts as great new insights

Another frustration that I have are those speakers who present as their awesome new insight something that every marginally competent audience member has been aware of for years.

High-throughput sequencing gives us more data than Sanger sequencing did? Who knew? So, museum specimens have degraded DNA? You don't say. GBIF exists, and the public can download specimen location data from it? Wow. We should be taking photos of herbarium specimens and putting them into online databases? Quick, somebody invent JSTOR Plants!

I am not saying that these are not points that can be made as part of the introduction to one's topic, to show how far we have come in a very short time. But if the entire point of the talk is something to the effect of "future directions in our field" or "where we need to be in 2028" one does expect something that did not already happen a decade or so ago.

The self-promoting and frustratingly off-topic keynote

Finally, I am starting to notice a certain type of keynote or plenary talk, where a hotshot scientist is invited to provide a broad overview of developments in their field, usually to frame the more focused and detailed talks that will follow after it in the program.

Keynotes and plenaries are always more like review articles than research articles, and I just have to admit that I do not go to conferences primarily to hear them. Nonetheless I have heard great and engaging plenaries, including at this recent conference, and can enjoy some of them even when they are largely about historical developments. It just depends on the choices made by the speaker.

What I really find frustrating are speakers who see these talks largely as opportunities for self-promotion. Their talks show at least several of the following features:
  • Nearly everything that is mentioned is the speaker's own work and that of their students, virtually ignoring contributions from others in the field.
  • Accordingly, many of the images in the slides appear to be photos of their numerous students and postdocs, usually goofing around in the field or looking awkward in front of a computer screen.
  • A good part of the remaining images are scans of the tops of the speaker's own articles, with the journal name showing prominently ("look, I have a Nature paper!").
  • The content of the talk is at best tangential to the title that it was advertised under, presumably because the speaker is re-using the same slides as for the last four such talks they gave under different titles and on different occasions.
Of course I would not expect everybody to agree with me, but my favourite type of talk is still a standard contributed presentation that is well-balanced between background and results, with methodology largely limited to a few informative bullet points.

Saturday, December 2, 2017

Is not making sense a prerequisite for being published in a newspaper?

Apparently there is a scientist who thinks that, to quote the headline of his article, "We don't need to save endangered species" because "extinction is part of evolution".

As with the people who argue that one should be allowed to discriminate against gay couples even after gay marriage is allowed but fail to make the connection with how horrified everybody would be if the same argument were made about, say, interracial couples, so in this case I am deeply puzzled how this guy can make his argument without realising that "one day you are going to die anyway, so I can brutally murder you now" follows the exact same logic. If his argument makes sense, then so does this one*.

I am somewhat less puzzled why his contribution was published. It is so idiotic as to raise an outcry, and as we know all publicity is good publicity for the newspaper, especially if they do not even claim that he represents the editor's opinion.

*) I hope it is clear that I draw the opposite conclusion, i.e. that the murder argument is the reductio ad absurdum for the extinction one.

Monday, November 27, 2017

South Australia field work, part three

The Systematics 2017 conference in Adelaide has now started, but here are a few final pictures from field work.

On our way north from Adelaide I was very happy to find the rare salt lake ephemeral Hagiela tatei (Asteraceae). It had already finished its life cycle, but I hope that I got a few seeds for my work.

The northernmost area we went to was Mt Remarkable National Park. There, however, we did not find much because it was fairly dry.

One of the few plants flowering in the area was Solanum ellipticum (Solanaceae); identification kindly provided by Tim Collins.

I have seen more millipedes last Saturday than in the first forty years of my life. What is their deal? Somewhat disappointing then to learn that they are introduced and invasive. But seriously, the situation reminded me of this comic.

Our final site was Tothill Ranges reserve which is managed by the NGO Bushland Conservation. One of the members kindly lead us around the reserve. Pictured above a slope with lots of grasstrees, but what I was after are the small white dots on the ground: paper daisies.

A nice Acacia (Fabaceae) flowering in Tothill Ranges, unfortunately I forget the name.

And finally a paper daisy. Chrysocephalum semipapposum (Asteraceae) is, of course, common and widespread, even occurring in Canberra. But it is also extremely polymorphic, and the plants in this population here are much smaller than the ones growing back home.

Thursday, November 23, 2017

South Australia field work, part two

A few more pictures from field work; not sure if I will have internet again before Sunday.

The above picture shows the lookout over Scott Cove in the north-western corner of Kangaroo Island taken yesterday.

At that very place were two species of mint bush. This one is the aptly named Prostanthera spinosa (Lamiaceae). I do not yet know the name of the other one.

The last Kangaroo Island photo is this tiny sundew (Drosera, Droseraceae), but I don't know its species name either.

Today, however, we have worked in the Fleurieu Peninsula. This is the coast as seen from the cliff-tops of the Newland Head Conservation Park.

A little birdie wondering what those weird humans are doing in its habitat. Apparently a rosella, but a different species than the ones I know from Canberra.

Also found in the heath of Newland Head: Chrysocephalum apiculatum (Asteraceae).

Finally, Hindmarsh Falls, south of Adelaide. The area here south and south-east of Adelaide is much more lush and green than I expected from South Australia and reminds me rather more of Tasmania...

Wednesday, November 22, 2017

South Australia field work, part one

Currently I am doing field work in South Australia with Tim Collins of UNE. The past three days Bev Overton very kindly guided us around Kangaroo Island, where we collected plants for Tim's research.

Kangaroo Island has a beautiful coastline, but of course so has much of Australia.

Close to this spot we ran into an angry hive of feral bees but got away relatively lucky.

Above a ball of seagrass. I read about these in one of my daughter's nature books, but this is the first time I saw them with my own eyes.

Coming to the flowering plants, this is Olearia ciliata (Asteraceae). Fairly small for a daisy bush, which is why I could not at first believe that it is indeed an Olearia.

I was very happy to find Leiocarpa supina (Asteraceae) as it was on my 'shopping list'. It is not exactly rare, I ultimately saw it in several coastal locations. I assume the orange lichen in the background would have to be the same species as the one in Tasmania, that of the Bay of Fires.

Finally a particularly rare species. We learned that Stilidium tepperianum (Stylidiaceae) is a Kangaroo Island endemic, and we were fairly lucky to see it.

Saturday, November 11, 2017

What race is a dickhead, indeed

Reading the recent news items about an Australian senator with Muslim background being abused in a pub by a bunch of racists, two thoughts occur to me. The first regards the oh so clever comeback by one of those racists after being called a racist: "what race is Muslim?"

The thing is, of course, that there are legitimate and illegitimate cases of people being called racist. If, for example, a hypothetical atheist were to say, "mainstream Islam as currently practised is problematic to me because so many of its adherents consider homophobia and sexism central to their beliefs and identity" then calling that statement racist is just wrong. Maybe that atheist is also mistaken, and maybe they are also incidentally racist, but the argument as stated would be explicitly about a belief or behaviour, regardless of what particular person holds the belief or shows the behaviour. It is not a racist statement.

This present case, however, isn't that. Somebody who says, "why don't you go back to Iran" and calls their opposite "monkey" is clearly not making an argument about theology; they are just being racist. Those statements are what is called a dead giveaway.

The second thought is the same that I always have when reading about white racism in countries like the USA or Australia: I gawk, open-mouthed in amazement, at somebody whose ancestors lived in Europe a mere two hundred years ago telling somebody else to "go back" to the country of their parents. Ye gods, one of those guys apparently called himself an "original Australian". The mind boggles. One wonders which Aboriginal tribe he identifies with, and what the other members of the tribe think about that...

Tuesday, October 24, 2017

Botany picture #254: Trifolium glomeratum

Trifolium glomeratum (Fabaceae), seen today at Mount Majura Nature Reserve. Admittedly if one asked me for the prettiest clover species this one would not even make the top fifty...

Dragonriders of Pern

Having now read the first volume of Anne McCaffrey's Dragonriders of Pern, an apparently wildly popular kind of science fiction-y series, I am somewhat puzzled why it is so popular and glad I did not buy more than two of them. Spoilers ahead, although given that I have so far only read the first of what are, according to Wikipedia, at least 23 novels, I probably still know very few of those.


My first thought is actually: this is a bodice ripper novel with dragons. The main male character, a guy with the unfortunate name F'lar, is kind of an abusive dick; the narration seems to consider it not only okay but even charming that he cannot properly express his feelings for his love interest (see next paragraph) except by violently shaking her whenever she did not do what he wanted. What is more, even in his own thoughts he describes their first sex as borderline rape. The only thing missing is a cover image of a "scantily clad woman being grabbed by the hero", to quote a relevant Wikipedia page.

The main female character, Lessa, shows nearly all key traits of a Mary Sue, at least in my eyes. She is unusually beautiful, of very noble blood, a singularly gifted telepath, and of course she bonds with the most impressive dragon ever, an unusually large and fertile golden queen dragon. She had a tragic youth but does not appear at all traumatised. The men admire her and other young women are jealous of her. (Also, other women who aren't her friends are generally depicted as sluts.) Everything she does, no matter how stupid at first sight, ultimately turns out to have been exactly the right thing to do.

Really one gets quite fed up with both F'lar and Lessa at some points.

The world

Pern is a planet that was in the distant past colonised by humans. Every 200 or 250 years a rogue planet called the Red Star comes close enough to Pern for c. fifty years to throw down spores called Thread. This Thread voraciously consumes all organic matter. The ancient Pernese reacted by genetically engineering local wildlife into fire breathing, flying dragons and bonding them to telepathically gifted humans, who form the top tier of a rigidly feudal society. Together, these teams of dragon and rider rise up in large squadrons and burn the Thread out of the sky while it is falling. Also, the dragons can teleport (!) and, under special circumstances, jump through time.

The need to bond dragons to humans is well justified in that the dragons are fairly short-sighted and impulsive without human guidance, showing for example a tendency to gorge on food. And unfortunately the early settlers soon lost their space age technology, what with having a very small starting population and a metal-poor planet, so that solving a technological challenge by leaving your descendants GMO animals seems like a good plan.

The funny thing is, and here it probably just shows that I am a biologist, that I can easily take the teleporting and fire breathing in stride but am rather bugged by the biology.

First, the Thread. How the hell does that even start to make sense? Maybe later books offer a better explanation, but Thread eats organic matter so voraciously as to be physiologically impossible; it is more like concentrated acid than like a living, growing organism. What is more, it eats and grows so quickly that it soon consumes everything and dies in turn. This is just not how life works, and the word parasite, although used explicitly by F'lar, is completely misapplied, as a parasite would be stupid to kill its host so quickly. And how does the Thread persist for thousands of years on the Red Star if it is so voracious? What does it eat there? It just does not make sense.

Next, the dragons. Again, teleporting, physically impossible but no serious hurdle for my willing suspension of disbelief. Fine. Fire breathing, ditto. The main time travel gimmick of the story, it has to be said, is actually really stupid, both because it is caused by itself and because the narrative puzzle that it solves is introduced just a few pages before. (Seriously, this should have been developed in the first quarter of the book, feeding the reader little clues here and there over the next chapters, but no... Imagine a crime mystery novel where the murderer gets introduced for the first time on page 209 and then convicted on page 211 and you get an idea of how this felt.)

But what really bugs me about the dragons is their reproductive biology. There are five colour groups:
  • the very rare golden queen dragons, which are female and fertile, and whose female riders automatically become the boss women in dragonrider society;
  • the relatively rare bronze dragons, which are male and fertile, and whose male riders have high status (the riders of the bronzes who mate with queens get to be the boss men in dragonrider society);
  • brown dragons, male and sterile, bonded to male humans;
  • blue dragons, male and sterile, bonded to male humans;
  • green dragons, female and sterile, weirdly also bonded to male humans.
Now the obvious question is, why the heck would there be any but the first two classes? Males, females, done, the rest could just as well be called "pointless dragons". And why do there have to be queens in the first place -- just because social insects are cool? Well, if that is the point then at least have golden female, bronze male, and brown sterile worker dragons, that would make marginally more sense except that top level predators do not really need a worker class.

Finally, at the time of the first novel the dragonriders have just spent 400 years reduced to a single dragon nest, with only a single queen at each given moment in time, so that she would always have had to mate with her brothers. Realistically the inbreeding would have been lethal, but instead it turns out (at the beginning of the second book) that those 400 years have made the dragons larger and more fertile than before! You fail genetics forever.

But okay, maybe others will dismiss the genetics, reproductive biology and physiology issues just as I dismiss the physical ones. The main problem is still that the book was actually not very well written. I had read Jonathan Strange and Mr Norrell just before the first Pern novel, and I am sorry to say the difference was striking.

Monday, October 16, 2017

What works and what does not work in contemporary science?

Today I participated in a workshop on the way forward for taxonomy in Australasia, so it might be a good opportunity to come back to the topic of the bioinformatician who thinks that all of science is broken and to consider what works and what does not work, at least in my view, in the field of science that I have the most direct insights into. I am not limiting myself only to taxonomy but will include all the broader field of systematics, but taxonomy is a major component.

Funding: Everybody says that funding in their field is too low, so this applies across all of science. But are scientists just whining? No, I believe that there is indeed too little competitive research funding available.

First, I have seen and heard of lots of cases where funding agencies have to reject very valuable proposals because there simply isn't enough money to fund everything that would be good to fund (sometimes apparently called 'approved but not funded'). Second, there are many funding agencies where you have success rates on the order of 2-10%. So to conclude that funding levels for competitive grants are high enough we would have to believe that 90-98% of applications are useless and that the weeks that the unsuccessful applicants have each invested into writing their many applications could not have been used in a more productive way. And that seems like a big ask.

Incentive structure: This is the big one, at least to me, and I guess here I find the most overlap with the aforementioned frustrated bioinformatician. What basically happens is that people are rewarded with jobs and promotions for (a) having publications in JCR-listed journals, in particular if those publications are cited a lot by other papers in other such journals, and for (b) getting external research grants, but of course the decision whether somebody gets a grant is also partly and sometimes mostly based on criterion (a). This is simplifying a bit, as there are also, depending on the job, teaching, textbook writing, conference participation, etc., but not by much. Publication lists are usually the key factor.

The problem is not that publications are a key factor though, because if a scientist does not publish their research it is indeed wasted. The problem is that there are lots of useful outputs that scientists can produce that are not, very specifically, research papers in JCR-listed journals.

Perhaps the most impactful thing a taxonomist can do for end users is to produce a publicly accessible online identification key or to contribute to a flora. But no matter how often this output is used to identify organisms, how many people need it for their work, it does not count the tiniest blip towards the taxonomist's number of citations or their h-index. There is no requirement for the end-user to cite a key in a paper, even if they used it during their work; and even if people cited it, it wouldn't count because an online key or flora volume is not captured by the JCR. Consequently, in terms of career advancement the taxonomist would have wasted their time and should instead have produced journal articles cited by other journal articles.

It is clear that people largely do what is rewarded, and largely cease doing what is not rewarded. So to the degree that there are useful things for scientists to do that do not result in publications in JCR-listed journals the incentive structure in science leaves something to be desired.

More generally, I feel that there is too much of a focus on flashy results and innovative methods but too little appreciation of incremental, everyday work. One of the surer ways to be cited a lot appears to be to develop a new lab method or a new piece of analysis software. This visibly leads to conferences full of rising stars each promoting their own new Bayesian analysis method or bioinformatics pipeline, but very few early career researchers contributing to specimen identifications, describing new species, or conducting taxonomic revisions.

Now to publishing itself. Apart from what I wrote in the previous section, in terms of academic papers I am actually not all that unhappy with the situation. Yes, ideally one would have all journals run as public utilities, cost-free to publish in and cost-free to read, instead of having private quasi-monopolies with massive profit rates and, pick your poison, either research locked away behind paywalls or money that could go towards research spent on publication fees.

But in a system where somebody has to pay I prefer subscription-based funding instead of author-pays open access, which is promoted by many people frustrated with the status quo, because in the latter system the incentives are perverse: journals are financially rewarded by accepting as many papers as they can instead of maximising the quality of their content.

As for peer review, again the system as currently implemented seems to work reasonably well; that is why it evolved to be like it is in the first place! I have received good feedback in many cases. I also had one or two cases where I believe the manuscript was unjustly ripped apart by an individual reviewer, but well, there are human egos involved, and one should not make the perfect the enemy of the good. I am trying to be a charitable and constructive reviewer myself but also suggest rejection papers where the conclusions do not follow from the results or where the methodology cannot address the research question.

If there is anything that I see as a current problem it is that there are rumours of journals increasingly being unable to find enough reviewers, which suggests either a lot of free-loading going on or journals being too unimaginative with reviewer invitations, or both. (Certainly I do not appear to get as many invitations from mid-level plant systematics journals as I would expect if they are struggling to find referees.)

Reproducibility: As I wrote in the previous post on this issue, I do not see any evidence whatsoever that taxonomy, phylogenetics, systematics or evolutionary biology have a reproducibility problem.

So that is how I at least perceive that part of science that I can judge best, for what it is worth. More money would be good, but an even more intractable problem is that the incentive structure currently in place does not reward some of the most useful and impactful work that systematists could be doing. Note that neither of these problems would really be solved by scrapping journals and publishing everything on preprint servers, but more on this maybe in another post.

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.

Sunday, October 15, 2017

Monga National Park

Monga National Park is c. one and a half hours east of Canberra along Kings Highway. It features wet sklerophyll / rainforest type habitats with many cryptogams.

We were there today in the hope of seeing Telopea mongaensis (Proteaceae) in flower. As can be seen in the above picture we were still a bit too early in the season, they are only just in bud. So far I have seen the Tasmanian species T. truncata, the New South Wales State Flower T. speciosissima, and, during a holiday in Victoria and southern New South Wales, T. oreades. The latter appears to be very similar and, I presume, most closely related to T. mongaensis.

What was in flower a lot in the same locality (the Waratah Walk from Mongarlowe River Picknick area) was Tasmannia lanceolata (Winteraceae), member of a 'basal' angiosperm clade, but of course it is far less spectacular.

This is the habitat; Telopea mongaensis is found particularly along the river.

The other attraction just a few hundred meters away is Penance Grove, which we had seen before. It is particularly known for its many tree ferns.

I am always fascinated by Dawsonia superba (Polytrichaceae), the largest moss in the world, which I believe is most easily accessed from Canberra by coming to Monga NP. I have written about it at least twice before, but I think this was the first time I saw it with young sporangia.

Tuesday, October 10, 2017

The world is so confusing sometimes

When will we finally reach peak gibberish in science spam?
Dear Author,
Formatting as in original - an auspicious start.
Journal of Proteomics & Bioinformatics greets you a good day!!!!
That's a new one, but at least it isn't "greetings of the day". Also, by the way, I really don't understand why my spam filter cannot finally figure out that anything that has more than one exclamation mark in a row can be binned immediately.
We are in shortfall of articles for successful release of Volume 10, Issue 10.
See this circle? That is my circle of caring. The fact that this alleged journal cannot fill its issue is about 5,000 kilometers outside of my circle of caring. So...
Is it possible for you to support us with your transcript for this issue before 30th October?
What do they mean with "transcript", which is usually a sheet showing university marks (grades)? Do they not even know the word manuscript?
If this is a short notice please do send 3-4 pages Short Commentary or Mini Review, and hope that a 5 pages article will not take much time for an eminent like you.
What does this sentence even mean? Help?
Also it will be very kind of you if you can acknowledge the receipt of this email and give your opinion to our proposal.
Better not, because if I honestly gave my opinion of their proposal there would have to be some bad language involved.
Best wishes,
Susan Williams
As usual, if this was written by somebody actually called Susan Williams... oh, excuse me, Susan Williams, then I will not only eat my hat but a whole stack of hats.


In completely unrelated news, why does GBIF suddenly use hexagons?

This looks as if somebody tries to draw in more people who enjoy strategy computer games, but it seems a bit odd given that spatial studies generally use square grid cells, either equal area or degree-based.

Saturday, October 7, 2017

No, science is not fundamentally broken just because one person had problems with their supervisor and prefers preprint servers

While on holidays I learned about an interesting case in food science, where it is suspected (at least according to some statisticians who have dived into the literature) that a very prominent researcher may have P-hacked, self-plagiarised, potentially reused the same dataset for several publications while making it appear as if they represented independent studies, and used self-citations to support statements that they don't. I find stories like those at the same time interesting, inspiring and very, very frustrating.

Interesting because, well, human nature and all that, and I am continually puzzled whether the people in question really think it won't come out in the end. Inspiring because this is how science self-corrects; not necessarily by individual scientists changing their minds (although that would be the ideal), but by open debate between scientists and careful re-examination of data. And frustrating because of exaggeration, over-generalisation, and naiveté about the solutions or alternatives to the problems that are identified. This post will mostly be about over-generalisation as found in the writings of one Jordan Anaya on Medium.

He evaluates and criticises the relevant food scientist's working practices, as do many others. But in doing so, he writes the following:
But I am interested in how academia selects for bad science, is free from any outside regulations that might prevent a crisis like the housing bubble, and how its power structure allows senior members to behave like dictators.
Science in academia is not about performing science, it is about your brand.
We are in the midst of a reproduciblity crisis in science,
all the problems science is currently facing
As it stands now, the wrong papers get published, the wrong researchers get funded. There is no incentive to share data or perform careful science. The only thing that matters is your brand, and your ability to leverage that brand into publications and grants, which circle back to feed the brand. If that means performing sloppy research, exaggerating results, and then refusing to acknowledge any errors, so be it.
Most of the literature is wrong, this is just a reminder that we need to be vigilant. It is also your daily reminder that peer review is useless and everyone should instead be preprinting their work.
I find this nothing short of astounding. Here is a bioinformatician generalising from his own bad experience in what appears to be one research group and one case in food science across all of academia and across all of scientific research. He does not write, "food science seems to have a problem", no, it is all of science, based on n=2.

When he writes that academia selects for bad science, can he really say with confidence that that is the case for, say, Australian entomologists? How would he know?

When he writes that it has no outside regulations, does he really mean to claim that it is not ultimately voters who decide through elected governments what kind of research will get funded? Is there so much money in cancer research in spite of or because of the wishes of the public? And this is before mentioning industry collaborations and industry-funded grants. (I will grant him that science isn't a democracy. The question is whether it could work as one, but that is beyond the scope of this post.)

When he writes that science as currently practiced in universities is not about science but about branding, can he know that this is the case for inorganic chemistry in southern Germany?

Do astronomy and phylogenetics really face a reproducibility crisis? I at least am not aware of that, and indeed I would be confident that if somebody were to repeat pretty much any phylogenetic study published in a serious journal with different molecular markers they would be able to reproduce all major results.

Is surface physics really facing "all the problems" that food science does? Again, how could Anaya even pretend to know?

How does he know that the wrong papers get published and the wrong researchers get funded in, say, plant ecology or archaeology? He claims that there is no incentive to share data - has he never heard of GBIF, Genbank, TreeBase or Dryad, or of all the journals that will not even accept your paper if you haven't deposited your data in a publicly available repository?

"Most of the literature is wrong." Seriously? Meaning I could pick a random article from a well-respected taxonomic, systematics or evolutionary biology journal and there would be a more than 50% chance that it is "wrong"? (And what qualifies as "wrong"? Does it mean this group of plants dispersed to Australia 16 million years ago instead of the currently accepted 15, or does it mean evolution is a lie meant to destroy Christianity?) And the alternative is to do away with all quality control whatsoever? But I am getting ahead of myself, this post is meant to be about over-generalisation, not solutions.

There is no doubt that the way science is being practiced leaves room for improvement, in particular in the areas of research funding, incentive structures, publishing, and recruitment. Okay, the same is probably true for any collaborative enterprise that humans have ever undertaken or will ever undertake, but tu quoque arguments don't change the fact that a lot can be criticised. I would have quite a few ideas for improvement myself.

Still, I hope one thing is clear: the fact that there are problems and some people acting in bad faith does not mean that an entire enterprise is broken. When we find that there are incentives for teachers to inflate grades we do not conclude that all of education is broken; when we find a certain percentage of police officers are racists we do not conclude that all criminals should go unpunished. And you may have heard that when we pour out the bathwater we usually take care not to pour the baby out with it.

Of course it is a question to be debated whether the entire system is broken. It could be. But from what I can see in plant systematics, ecology and related fields, this is so much hyperbole. In fact I am struggling to find a description of the act of dismissing all of science and the careful work of thousands of researchers with a mere "most of the literature is wrong" that is reasonably polite and does not involve phrases like "breath-taking arrogance".

It is also, of course, ridiculously irresponsible. Think of anti-vaccinationists, creationists, climate change denialists, alternative history cranks, expanding earthers, and any other set of conspiracy theorists. They already claim that science is all broken and the literature can't be trusted. Now they can say that a scientist frustrated with the review process in his field confirms it. Believe what you want, because the scientists can't be trusted!

Ye gods. Did the plain truth - science publishing and funding have serious issues that we need to tackle, and there are a few frauds just like in every other profession, but all in all we can trust most of our colleagues to be well-meaning and most of the literature to be useful - not sound sensationalist enough?

Sunday, October 1, 2017

Spring holidays 2017, final part 5

And we are back. Today we returned to Canberra passing through, among other things, the Putty Road between Wollemi and Yengo National Parks. It is a very nice, forested landscape, although it would be even better if there were one or two official lookouts in the southern part.

The above gives an impression of the road as seen from a little resting area along the way, in this case still very much towards the northern end.

About 40% or so of the way towards the south there is a locality called half-way house that was apparently once a cafe and petrol station. Now there is only a stall that sells coffee, soft drinks and snacks as well as metal and wood sculptures, thus the large statue above. I got a coffee.

Slightly before that spot we saw Conospermum taxifolium (Proteaceae) along the way. Their flowers are a bit different from the 'usual' Proteaceae that people are familiar with, such as Banksia or Grevillea. In Western Australia this genus is a striking part of the landscape in the form of the smoke-bushes, but the species here in New South Wales are less conspicuous.

Because this post does not have enough plants yet I am returning to one we saw at the beginning of the trip. It is among numerous photos that I did not upload because I was uncertain about the identification, but now I am reasonably optimistic that this is Darwinia procera (Myrtaceae), a rare and very localised species.

Thursday, September 28, 2017

Spring holidays 2017, part 4

Yesterday and today we continued to explore Myall Lakes National Park and its surroundings.

The village of Hawks Nest is very touristic, and so it is perhaps not a surprise that it has a spring flower walk that is recommended to tourists. And indeed there are masses of flannel flowers, but also other interesting plants.

At the other end of the National Park we today visited the lighthouse at Sugarloaf Point. Shown here is the view towards Seal Rocks, which unfortunately wrecked many ships even after the lighthouse was built, apparently due to prevailing wind conditions during one part of the year.

Botanically today's topic is climbers. Our first one is Kennedia rubicunda (Fabaceae), with surprisingly large red flowers.

I am reasonably certain that this would have to be Geitonoplesium cymosum (Smilaceae), a climbing monocot. The field guide calls it 'scrambling lily'.

Finally, the native passionflower Passiflora herbertiana (Passifloraceae) had been teasing us for a few days now, always there but never in flower. Today we finally found it in bloom, and that made my day!

Oops. Upon examination of the Flora of NSW key to Passiflora it turns out that this is introduced Passiflora subpeltata from Brazil, as it has large, leafy stipules. Also the Flora says that native P. herbertiana is red, which is really interesting because Fairley & Moore's Native Plants of the Sydney Region, which serves as my quick reference in the field during this trip, shows it as white.

Either way the one we saw is not native. Still, passionflowers are just something else, and they remind me of past field work in the Andes.

Tuesday, September 26, 2017

Spring holidays 2017, part 3

We spent half the day at the beach and then the rest exploring Myall Lakes National Park. We saw lots of plants, but as I haven't had the time to check many identifications I will only post two. They are nice ones though:

Actinotus helianthi (Apiaceae) is the famous flannel-flower. The petaloid bracts around the flower-heads are felt-like, thus the English name. Many people wrongly believe it to be a member of the daisy family, but it belongs to the family of parsley and fennel.

The second one makes me very happy indeed. I had heard of the flying duck orchid (Caleana major, Orchidaceae) and seen photos, but now I have seen it in the flesh, as it were. Surely one of the weirdest-looking orchids on a continent that has many weird-looking ones.

Monday, September 25, 2017

Spring holidays 2017, part 2

Well look at that, holiday parks have free Wifi now...

Today we arrived at the place where we planned to pitch our tent, Hawks Nest just at the south end of Myall Lakes National Park. On the way we spent a bit of time in Brisbane Water National Park, which of course is nowhere near Brisbane but instead just out of Sydney.

But first we had to get out of Sydney, and here it seems to me that the road engineers there might want to look into the concept of a city highway that moves travelers through the area with a minimum amount of fuss. Think a straight road with a turn-off every few kilometers instead of a winding nightmare leading right past houses and shops and interrupted by traffic lights every few meters.

Ah well, think of the flowers.

The first decent stop out of Sydney was at Moonie Moonie Creek, which I think actually deserves a promotion to "river" here.

And our last longer stop was at Girrakool, a resting area with several great walks. This photo above shows a place where one can get down to the pools and creeks, but there are also lookouts across the valley and longer loop walks.

Now for the plants. Myoporum acuminatum (Scrophulariaceae maybe? It changes), a shrub at the edge of a swamp near Moonie Moonie Creek.

There were lots of interesting plants on the shallower soils at Girrakool. Here what I take to be Kunzea capitata (Myrtaceae). It is not the plant's fault that it reminds me of Otto Kuntze, but unfortunately it does.

Right next to it we saw Grevillea speciosa (Proteaceae). There are of course lots of Proteaceae here, but there are few where I am as sure about the identification as with these characteristic leaves.

Finally, Mirbelia rubiifolia (Fabaceae), a very cute little pea-flowered legume.

Sunday, September 24, 2017

Spring holidays 2017, part 1

Family camping trip over the spring school holidays! Having previously camped in what is parochially called the "South Coast" (in New South Wales Sydney is the navel of the world, so it does not matter that the coast is on the east of the landmass) and visited the New England area further north we decided to go for the area just north of Sydney this time.

Today, however, we only made it as far as the south of Sydney, taking it slow and seeing things on the way. The main attraction here is Royal National Park, which my wife had seen fifteen years ago but my daughter and I have now seen for the first time.

The above is the view from Bald Hill lookout, as we were coming into Royal National Park from the south, via Wollongong.

We also saw some tall sklerophyll forests, but like most of south-eastern Australia this area has seen too little rain this year, and much of the vegetation was too dry. The heath looked much better. This species is Isopogon anemonifolius (Proteaceae).

Another Proteaceae, we think it is probably Grevillea oleoides given its very long and slender flowers and likewise long and slender leaves.

Again we are not entirely sure, but this may be Lasiopetalum parvifolium (Sterculiaceae); the field guide is not entirely clear but it looks as if the other species of that genus that are in the area and have similar leaves may differ in having hairs also on the inside of the sepals. It is a small shrub that I photographed in a very dark spot using the tripod.

And this is where we got out of Royal National Park, Bungoona lookout at its northern end.

As we are going camping I will presumably not be able to post anything else until Friday at the earliest, but then I hope to be able to upload a bunch more plant and landscape photographs.

Friday, September 22, 2017

Three plants near Wollongong

After a work meeting in Wollongong we made a short stop on the way back, just enough time to have a look at some plants that are flowering.

Starting with the least interesting, because invasive: Ageratina adenophora (Asteraceae), an introduced weed that was doing very well indeed all along the roadsides.

According to colleagues this is Eriostemon (Philotheca?) australasius (Rutaceae). The flowers are white; books usually show them as pink, but maybe the difference has something to do with this plant growing in shade. Very pretty, at any rate.

And finally we saw this even prettier orchid. After consulting Native Plants of the Sydney Region I presume it is Thelymitra ixioides, but orchids are not really my specialty.