Wednesday, July 30, 2014

Botany picture #167: Anthyllis vulneraria subsp. praepropera

Anthyllis vulneraria subspecies praepropera (Fabaceae), France, 2014. This picture was taken in the grounds of the Chateau de Peyrepertuse. Not only is it an amazingly beautiful castle ruin, not only does it have an awesome view over the landscape of the Corbieres mountains, but it also has a diverse and colourful rock-garden like flora. Definitely worth a visit but due to the steep climb it takes a bit of stamina.

Tuesday, July 29, 2014

Bracketed and indented keys

As mentioned before, the identification keys published by taxonomists and used by all manner of end-users of taxonomic literature to identify organisms to species are traditionally analytic, single entry and dichotomous. That means they consist of series of nested questions that have to be answered one after the other in a fixed order to arrive at the correct species name.

In technical terminology, the individual questions are called couplets, and the two alternative answers of each are called leads. A good key should have leads describing a limited number (perhaps ca. three) of clear, distinctive, and easily understood characters.

However, even for the exact same content there are two different ways of formatting these keys. The first option is a bracketed key. It looks as follows:

1     Leaves 0.5-2.0 cm long ... 2
      Leaves 3.0-10.0 cm long ... 3
2(1)  Corolla red ... Planta australis
      Corolla white or yellow ... Planta latifolia
3(1)  Fruit a capsule ... 4
      Fruit a berry ... Planta vulgaris
4(3)  Flowers solitary ... Planta palustris
      Flowers in axillary clusters ... Planta debilis

Here the two leads of the same couplet are always directly below each other. This has the advantage that it is very easy to compare the two alternatives, but on the other side the couplets need to be numbered in some way so that we know where we have to go next. In larger keys, it may also be harder to find the next or, if back-tracking, the previous couplet because one has to jump around so much.

In the above case, each couplet except the first also has a number in brackets directly after its own. This indicates where the user had to be coming from to arrive at this place, making back-tracking in large keys easier. But of course not all large keys have them.

The second option is called an indented key. Here is exactly the same key as above in an indented form:

Leaves 0.5-2.0 cm long
   Corolla red ... Planta australis
   Corolla white or yellow ... Planta latifolia
Leaves 3.0-10.0 cm long
   Fruit a capsule
      Flowers solitary ... Planta palustris
      Flowers in axillary clusters ... Planta debilis

   Fruit a berry ... Planta vulgaris

In this case, the follow-up, nested couplets are directly after the lead that, well, leads to them. On the one hand, this makes navigation easier, and couplet numbers are not strictly necessary. On the other hand, it is harder to compare the two leads of each couplet. Worse, indentation does not work very well to indicate what couplets belong together if the key is long enough to spread over several pages. Imagine reading trying to find the second lead two or three pages down the book and then deciding that the first one was right after all! Unfortunately, some authors do not seem to see a problem with that.

Reading between the lines, it may have come across that I prefer bracketed keys, and that is indeed the case. It seems that bracketed keys are more popular in continental Europe while indented ones are traditionally more popular in Anglo-Saxon countries. Be that as it may, with the increased availability of digital keys the bracketed variant appears to be on the rise.

Of course internet and other computer based keys allow designs that go far beyond the limitations of analytic single entry keys. But the latter are still widely used, and they do have their advantages. At a conference two years ago some colleagues pointed out that working through a single entry key makes it much easier to learn about the whole diversity of and character distribution in the group, whereas using a table-based key is much more of a 'black box' experience.

The thing is, when single entry keys are used on a digital medium, there is pretty much no point in separating the two leads, especially if the key is supposed to work on small displays. In effect digital keys therefore tend to be increasingly bracketed.

Monday, July 28, 2014

Botany picture #166: tiny Western Australian sundew

Today (or to-die, as the Australians pronounce it) I lectured about leaves and indumentum, that is the hairs, scales or glands that can be found on plant leaves and stems. One of the pictures I showed in the presentation was the above, a really really tiny Drosera or sundew from Western Australia.

It nicely demonstrates not only two of the very many functions that leaves have evolved to fulfil - in this case, photosynthesis and capturing and digesting insects to improve nutrition - but also, obviously, glandular hairs.

Thursday, July 24, 2014

The Doomsday Argument

There exists something called the Doomsday Argument, and it is considered to be one of the most controversial probabilistic arguments that have been advanced.

Randall Munroe has given a very good summary of the argumentation:
Humans will go extinct someday. Suppose that, after this happens, aliens somehow revive all humans who have ever lived. They line us up in order of birth and number us from 1 to N. Then they divide us divide them into three groups--the first 5%, the middle 90%, and the last 5%:
Now imagine the aliens ask each human (who doesn't know how many people lived after their time), "Which group do you think you're in?"
Most of them probably wouldn't speak English, and those who did would probably have an awful lot of questions of their own. But if for some reason every human answered "I'm in the middle group", 90% of them will (obviously) be right. This is true no matter how big N is.
Therefore, the argument goes, we should assume we're in the middle 90% of humans. Given that there have been a little over 100 billion humans so far, we should be able to assume with 95% probability that N is less than 2.2 trillion humans. If it's not, it means we're assuming we're in 5% of humans--and if all humans made that assumption, most of them would be wrong.
To put it more simply: Out of all people who will ever live, we should probably assume we're somewhere in the middle; after all, most people are.
If our population levels out around 9 billion, this suggests humans will probably go extinct in about 800 years, and not more than 16,000.
He goes on to state that most people immediately conclude that the idea is obviously wrong, but "the problem is, everyone thinks it's wrong for a different reason. And the more they study it, the more they tend to change their minds about what that reason is."

Well, there are two reasons why that could be so. One is that the argument is really quite clever but most people don't realise it. The other is that there is so much wrong with it that people discover new layers of wrongness every time they look at it.

I guess I would have to be counted among those who think that the Doomsday Argument is, indeed, idiotic. Admittedly I cannot come up with a super-deep Bayesian counter-argument such as are referenced in the linked Wikipedia article. But I don't think that is necessary because this does not look like a job for probabilistic reasoning anyway.

Wednesday, July 23, 2014

Another brilliant piece of science spam

Lately I get the feeling that, on average, scientific spam trolling for paper submissions to poor quality, for-profit journals gets somewhat sleeker and more professional looking. And perhaps I have now blocked so many of these spammers that I get less of the really obvious ones.

But sometimes a real howler still gets through. Look at this beauty:

Tuesday, July 22, 2014

Botany picture #165: Blackstonia perfoliata

Blackstonia perfoliata (Gentianaceae), south-western France, 2014. This little yellow Mediterranean gentian was all over the place when we visited family in June. Strangely we never noticed it during previous visits to the area.

Monday, July 21, 2014

How to make a bad identification key

Today was my first lecture of the year, and after an introduction to the course as a whole I started with identification tools.

For the non-biologists, I have blogged before about identification keys; the most common type consists of a series of nested questions asking about characters of the organism you are trying to identify. In the style of a choose your own adventure book, answering the questions correctly will ultimately lead to your happy end, in this case the name of the species you are interested in.

Looking over my lecture brought to mind some of my own painful experiences trying to identify plants in the past. (The willow key in the Flora Europaea, argh argh argh...) I may write something more positive soon, for example explain different ways of designing a key or point towards really good examples, but for the moment let's brainstorm a list of what a taxonomist should do if they want to produce a really atrocious key.

To make them as difficult to use as possible, one should:
  1. Use arcane terminology. Anybody can confound an untrained lay user of the key by writing "adaxial leaf side" instead of "upper leaf side". The real prize is to find expressions that are so specialised to your group of organisms or so local to your geographic area that only three other taxonomists on the planet will be able to understand what you mean. Prime example in Australian daisies: the "claw", which is the petiole of an involucral bract. (And non-botanists will of course not know either expression.)
  2. Instead of writing questions that divide the number of remaining species neatly into two approximately equal halves, have a string of questions that divide between one single species and all others. Bonus points if the first answer to each question is a long list of characters and the alternative is always a laconic "characters not found in this combination".
  3. Divide the species so that the 'distinguishing' characters are strongly overlapping, for example "glomerule diameter 1.5-2.7 mm versus glomerule diameter 2.2-3.5 mm". When faced with categorical characters, the ideal solution is something like "hairy versus naked or hairy", although a similar effect can be achieved through liberal use of "usually", "sometimes", or "except in [species that really shouldn't be in that part of the key]".
  4. In a similar vein, distinguishing characters can be made less useful through the simple expedient of adding the prefix "sub-", which means kind of but not really. Examples: subglabrous = not quite entirely without hairs, subacute = a bit pointy but not really pointy, subspicate = somehow like a spike-like inflorescence but, I dunno, also a bit different? No idea really.
  5. Make liberal use of characters that cannot be observed in the field, for example because you'd need a microscope. This will particularly endear you to all the park rangers and bushwalkers trying to use your key.
  6. Another option is to design the key so that the first few questions are all about characters that most users will not have available. The classic example are keys to some subgroups of the daisy family (Asteraceae) or to the parsley family (Apiaceae) that focus obsessively on fruit characters. Collected a Calotis in full bloom but before fruits start to develop? Well, you are out of luck - even if in that particular genus half the species have yellow flowers and the other half have purple ones, that character is never mentioned in the key.
  7. If all else fails, write a long and convoluted key that contains the same question twice, such as the key to European willows mentioned above. So you want to identify a dwarf willow from the alpine zone of the Pyrennees, and the very first question in the entire key is whether you are (a) dealing with a dwarf willow from an Arctic or alpine area or (b) a large shrub usually at least 2 m tall when mature from a lowland temperate area. You chose (a)? Silly you, of course you should have gone down the path (b) because ten or so questions in you will again be asked if you have an alpine dwarf willow, and that will then lead you to Salix pyrenaica.
The sad thing is, I am fairly sure that the colleagues in these cases I am thinking of actually thought they were writing simple and useful keys. Nobody would do these things on purpose, right?

Thursday, July 17, 2014

So what is so great about Hans Christian Andersen anyway?

I should really write something about plant systematics again, but at the moment something else is going through my head.

My daughter brought a children's book version of The Snow Queen from the library, probably inspired by Frozen. She likes to have it read, but neither I nor my wife can really appreciate the story. If you can call it a story.

So there is this troll who builds a magical mirror that reflects everything in an evil, distorted way, and when he tries to have it reflect the angels of heaven in a negative way, it shatters into thousands of tiny shards. These shards blow around the world and turn people evil who get them into their eyes and hearts. Okay, a mythical explanation for why people can be bad, so far so good. Apart from the fact that the whole story is nauseatingly in-your-face Christian I could live with it.

Next there is this boy called Kai who is infected with two of the shards and turns bad, starting to ignore his close friend Gerda. Again, so far so good. Then in a complete non sequitur the Snow Queen comes and abducts Kai, making him forget all about his previous life. Why? No idea, at least in our version it just happens. And despite the title of the book that is also the last we ever see of that character.

Tuesday, July 15, 2014

Botany picture #164: Teucrium polium

Teucrium polium (Lamiaceae), France, 2014. Interestingly, this widespread Mediterranean species comes in white, yellow and pink varieties. In the south-western part of France where my in-laws are living I have only ever seen the yellow morph.

Monday, July 14, 2014

A few quick things

Currently reviewing a manuscript, and it is so full of hyperbole that I can only stand it in homoeopathic doses, like two paragraphs per day.

If I read "paradigm shift" another time I am going to scream.


Whoever compiled this slide show of photographs from the World Cup Final must be really fond of (1) Bastian Schweinsteiger's girlfriend, (2) Lukas Podolski's son, and (3) sad Argentinean fans. Not sure what that says about their state of mind.


Jason Rosenhouse demolishes the weird idea that until about 150 years ago all Christians saw the bible as merely symbolic and allegoric. Part 1, part 2.

The general problem with holy books is this: They all contain wrong, stupid and hateful things, be it that the world is flat, that the world is a few thousand years old, that insects have four legs, that women should have less rights than men, that adulterers should be stoned, that heretics should be killed, or that holy war is the duty of every believer.

There is no doubt that, believers mostly being decent people, you can have four generations or so of everybody saying, "this is our holy book, it was inspired by the benevolent creator of the universe, you must accept it as a moral compass but please ignore this stuff about a recent creation, about stoning and holy wars".

But, believers being human beings, it is unavoidable that at some point, perhaps in the fifth generation, there will be somebody who reads the book and says, "wait a second, you told me this is our holy book, it was inspired by the benevolent creator of the universe, and I must accept it as a moral compass. But here it says that the world was recently created in pretty much the state it is now." And if you are a bit less lucky, they will say, "but here it says that I should kill the unbelievers, the homosexuals and the adulterers. To prove that I am a more pious person than you, and to gain favour in the eyes of the LORD, I will now do some killing."

As long as texts containing stupid and nasty parts are seen as sacred, peaceful and tolerant religion is not necessarily a stable state of affairs.


This is awesome.

Saturday, July 12, 2014

Botany picture #163: Aceras anthropophorum

It is winter here, and I am currently not interested in digging out older pictures, so I will continue with plants we saw on our trip to Europe. This well-known orchid is Aceras anthropophorum (Orchidaceae), again from south-western France. The specific epithet means "man-carrying" because the lower lip of the flowers could be interpreted to show a little man with two arms and two legs.

Descriptive names like that are fairly common in the older taxa. Indeed the entire orchid family is named, strangely enough, after the supposed resemblance of the tubers of some European species to testicles (Greek όρχις). Nice to know, I guess.

Thursday, July 10, 2014

So, how would we get a murderous super-AI, anyway?

Dwelling a bit on the obsessions of MIRI and other singularitarians from the LessWrong spectrum, I have idly wondered how exactly they imagine the kind of superhuman artificial intelligence (AI) they are so afraid of would come about. Even hand-waving the question of whether certain kinds of technology are even possible outside of fever dreams and Science Fiction novels, I see a rather limited number of options for the generation of AI.

Tuesday, July 8, 2014

Singularitarians are really really really strange

Only a few days ago I shook my head about people who breezily assume that, fast forward a few decades of technological progress, interstellar flight will be achievable. (And affordable!)

Now, made curious by a post on a blog that I read from time to time, I checked out the website of the Machine Intelligence Research Institute (MIRI), a kind of Singularitarian think tank. Remember, Singularitarians are futurists who are convinced that progress is accelerating and will soon - that is, within the next few decades - produce a "technological singularity" beyond which everything will be unbelievably different.

The particular MIRI brand of singularitarian appears to be a computer nerd who further believes the way to achieve singularity is to build a self-improving artificial intelligence (AI), because it will then get even more intelligent in a fraction of the time it took to develop it, and the next iteration will improve itself even more, and one day later it has turned into Robot Jesus and there will be immortality, space flight and ponies for all. Because obviously a very intelligent computer must only do some super-quick armchair thinking and it will have solved all social, technological and scientific issues ever. Without having to do painstaking empirical testing of its ideas because it will just be that intelligent. And resource limits won't matter either because, hey, it will just be that intelligent.

(Yes, one does get the feeling that a certain kind of futurist computer nerd considers intelligence, which is sometimes even equated with computing speed, to be magic pixie dust.)

Conversely, they believe that the single greatest danger humanity faces is not resource depletion, antibiotics becoming useless, soil erosion, water shortages, biodiversity loss, or global change induced mass starvation, but instead that Robot Jesus may decide he'd be better off without us useless humans. So the mission of MIRI is to "ensure that the creation of smarter-than-human intelligence has a positive impact" as opposed to Terminator style genocide against humans. Which is obviously a very important goal, much more important than avoiding those other things I mentioned two sentences ago, and so we must all give them lots of donations to finance their, ahem, "research".

Before I looked at their website, I had unavoidably developed some preconceptions about what they might be like. Now that I have seen it, I find it depressing how accurate my preconceptions turned out to be.

Judging from their website, they seem to spend their time approximately as follows:
5% designing websites that look superficially sleek and professional but weird me out once I look closer. (Seriously, "apply to research this math"? "As featured in The New York Times"? Yes, that totally sounds like a legitimate research institute. Please go on.)

10% taking super pretentious staff portraits that they will later find embarrassing when if they grow up.

25% standing in front of white boards trying to look intelligent. Whether they succeed is in the eye of the beholder I guess.

30% writing "papers" that use a lot of big words in their titles to distract from the fact that no actual empirical research or AI development appears to be happening at MIRI (at least as far as I can tell). It is basically as if a biologist claimed that we are going to figure out how to repair telomers and thus achieve eternal youth and then spent their entire career merely writing letters to the editor and review articles summarising other people's work instead of, well, developing an enzyme that repairs our telomers.

20% calling for donations.

10% being unable to believe what a sweet gig they managed to land.

As far as their staff goes, this is what the page "our team" shows as of 7 July 2014. There are seven guys who look so young that unless told otherwise I would assume they'd be university students doing an internship but no, apparently one of them is the director; one guy who has made himself look a bit more senior by growing a beard; and one young woman - that's a full 11%! Yay for diversity and inclusiveness!

Their "research associates" are broadly similar in profile, only this time there is actually an emeritus professor among them. On the downside, there are zero women among them, which kind of reduces the percentage of women playing any role at MIRI to near 0%.

Looking at the titles of their publications:
  • Problems of Self-Reference in Self-Improving Space-Time Embedded Intelligence
  • Definability of Truth in Probabilistic Logic
  • Robust Cooperation on the Prisoner's Dilemma: Program Equilibrium via Provability Logic
  • A Comparison of Decision Algorithms on Newcomblike Problems
  • Ontological Crises in Artificial Agents' Value Systems
  • Intelligence Explosion and Machine Ethics
  • Intelligence Explosion Microeconomics
  • How We're Predicting AI--or Failing To
  • Intelligence Explosion: Evidence and Import
Although that is the title of the relevant web page, I hesitate to call it "research" because, again, most of these are review articles, opinion pieces and meta-stuff looking at how we look at the singularity. The only interesting papers are what we might broadly call philosophical treatises (especially logic and ethics), but I'd rather ask a MIRI-independent philosopher for their opinion before taking them seriously.

Ye gods but this must be awesome. Imagine spending your days fantasising about the potential implications of inventions that will never be made and actually being paid for it. And the sweet thing is, if they play their cards right they can ride that gravy train forever because despite the fact that all we have programmed to date is pretty stupid and that the only self-aware intelligences we have any experience with are biological, nobody has proof positive that a self-aware, highly intelligent and self-improving AI cannot be built. Prove me a negative, won't you?

As long as they don't set a date and perennially keep the moment Robot Jesus will come and make us immortal vaguely in the future (kind of like Christian Jesus has been said to come back any time now for the last two thousand years) MIRI can still ask for our donations in 80 or 200 years. And this being humans we are talking about, they will find takers.

Wishful thinking is a powerful force.

Monday, July 7, 2014

Botany picture #162: Rhamnus alaternus

Rhamnus alaternus (Rhamnaceae), France, 2014. Not much I can tell you about this plant except that I saw it on a rocky roadside slope when we were stopping to admire a waterfall. I then thought to myself, I have not the foggiest idea what this is but with such distinctively coloured fruits it cannot be hard to figure it out. And so it proved.

Friday, July 4, 2014

Techno-optimists are strange

Recently a post by PZ Myers at his blog Pharyngula, originally about how frequent intelligent life can be assumed to be in the galaxy, got derailed into an argument about whether the colonisation of space is possible and if yes, how. And I got drawn into it for some time, because I find the airy-fairy, dewy-eyed assumption that it is rather bizarre.

It is, of course, not just in that thread that I have run into the same line of thinking, and everywhere we look we can observe other types of techno-optimists. They fall into several categories, although those are partly overlapping and partly nested. Perhaps a small taxonomy as I grasp it:

Transhumanists are those who believe that we will become able to improve ourselves, perhaps through genetic engineering or cyborg implants, to the point where we will transcend the human condition. Immortality of some kind and freedom from disease are obvious items on their wish-list.

Singularitarians believe that humanity will achieve a stage of technological progress after which everything will be so different that we just cannot imagine how seriously different everything will be. Why and how varies; there are those who see technological progress as accelerating exponentially and simply anticipate the singularity as some moment when that acceleration becomes unprecedentedly fast. Many others believe in the coming of the Messiah the development of self-improving artificial intelligence which will conveniently solve all our problems for us.

Finally, Cornucopians are quite simply those who believe that the combination of human ingenuity and, usually, the incentives provided by the free market (praise be upon it) can magically overcome any limitation or shortage that we will ever be faced with. They include people who promote that ideology quite explicitly but in a wider sense also all those who reply, when for example the unsustainable use of resources is brought up, with the naive mantra that "they" will think of something once those resources really run out. (The irony being of course that if what is meant with "they" are scientists then the scientists have long thought of something: we should stop wasting so many resources. Sadly nobody wanted to hear that answer.)

Anyway, no matter how precisely the individual techno-optimist imagines our glorious future to be brought about, the colonisation of space is perhaps the most ludicrous idea of all.

Wednesday, July 2, 2014

Botany picture #161: Ornithogalum cf narbonense

Today's botany picture is a liliaceous monocot from south-western France which I would tentatively call Ornithogalum narbonense (Asparagaceae). While the plant itself is not all that spectacular, the picture gains a lot from that cute little guy hanging onto one of the tepals. Didn't even notice him while taking it.

By the way, the leaf-like floral organs are sepals and petals, respectively, if there is an outer green whorl and an inner colourful whorl. If, as in this case, there is no differentiation into two different types then they are all called tepals. Strangely my computer knows the first two terms but not the third.

Tuesday, July 1, 2014

In biological classification, rank is arbitrary

Today one of my alerts for scientific literature, well, alerted me to a newly published paper in the journal Paleobiology: Hendricks et al., The Genericifiation of the Fossil Record.

The starting point of the article is something that I had also noticed before: Studies of changes in diversity across geological time scales often use supraspecific taxa as their operational taxonomic units (OTU). Hendricks et al. stress the use of genera but there are cases of even higher level groups being counted, for example when the number of animal phyla before or after an extinction event is compared.

The problem is that while we can have a productive discussion about whether species are comparable with each other under this or that species concept, everybody but the most blinkered systematist will agree that higher ranks in the classification aren't - if you compare their numbers, apples and oranges don't have anything on it.

There are several reasons why that is the case.