Saturday, August 31, 2013

Having fun at the public fun bath

Today, and for the first time since I came to Australia three years ago, I went to a public indoor swimming pool, or perhaps one should rather say an aquatic family fun centre if that is a valid term. This was one of those occasions where I cannot help reflecting on cultural differences between Germany and Australia.

Here, one gets a strong feeling of being on Ferenginar because one has to pay for everything extra on top of paying an entrance fee. Want to use the water slide? Pay extra. Want to have a box to lock away your clothes and valuables? Pay extra. In Germany, these things are included. On the downside, in Germany one has to pay for use of the facility per hour while here it is the same entrance fee regardless of how long you stay.

Strangely, it is considered normal for people to walk around the entire pool area in their street clothes and, crucially, their dirty street shoes. This would be completely unacceptable in Germany.

In what is surely a complete coincidence and without any connection to the previous item, the pool area as well as the changing rooms here are significantly dirtier than any swimming hall I have seen in my home country. You can actually feel sand and sometimes even small pebbles under your feet in parts of the pools, and the floors of some of the male showers were beyond description.

Interestingly, there is only one common changing area for each gender, no one-person changing rooms, which might be difficult for more bashful people.

There are signs at the entrance indicating that taking photographs is forbidden but a at any given moment a good number of people is walking around the pool area with clearly photograph-capable smartphones or even tablets. Why anybody would want to take their tablets with them when they go swimming is another good question.

Well, at any rate we enjoyed ourselves. Should do that more often.

Thursday, August 29, 2013

Botany picture(s) #100: Riccia

Hooray! The 100th botany picture post on this blog. To celebrate, there are actually two species although I don't know the name of either.

In two weeks I want to start field work, and a bryologist colleague has asked me to keep my eyes open for Riccia. So that I recognize the genus, she has shown me two species in the lawn in front of my workplace. Having graduated from a department of systematic botany whose research focused on liverworts and ferns, I knew a few basic facts about Riccia, but before I came to Australia I never actually saw it alive.

So, what is that genus? You may know that the bryophytes, the paraphyletic "group" of non-vascular land plants, consist of three clades: liverworts, mosses, and hornworts. Within the liverworts, there are again three rough groups although as far as I know only one of them is monophyletic: simple thallose liverworts, complex thallose liverworts, and leafy liverworts.

The research in my former institute focused on the leafy liverworts. Simple thallose liverworts are, as the name indicates, really quite simple in their structure, with the thallus consisting mostly of an undifferentiated bunch of photosynthetizing cells. Riccia, however, is a complex thallose liverwort, a small group that builds thicker, more drought resistant thalli with several highly specialized types of cells, although admittedly in that group Riccia itself has one of the least complex morphologies.

Although I had never seen Riccia in Europe or during my field work in Latin America, the genus is actually quite easy to recognize. The thalli have a very typical dichotomous branching pattern, clearly visible in the picture of the larger species above, and they do not build stalks to raise their sexual organs above the ground. Instead, the sporangia remain embedded in the thallus of the mother plant, and the spores only get released when the mother dies and rots away. One would think that this is not conductive to wide dispersal, but I assume that they are happy being dispersed with mud sticking to animal feet or with dust being blown around by the wind when the ground is dry.

Wednesday, August 28, 2013

Lab equipment

Recently I bought a shiny new piece of lab equipment. It is essentially a strong neodymium magnet with 96 holes, so that you can place a 96 well reaction plate in it.

It is used in DNA purification: You bind the DNA in the wells of the reaction plate to tiny metal beads, place the reaction plate on the magnet plate and presto! within seconds the beads are drawn to the walls of the wells. Now you can remove the liquid that contains everything but the DNA and the beads, wash the well, and then put pure water or elution butter in each well. You remove the reaction plate from the magnet, let the DNA go back into solution, and then you use the magnet once more to separate the metal beads from the water which now contains your cleaned DNA.

Two things are remarkable about this magnet plate. The first is how heavy it is compared to its small size (and considering the fact that a lot of it is holes). If you pick it up, you really have something in your hand.

The second is the product description slip that came with it. Because this magnet is really super strong, it contains a lot of colourful warnings:
Individuals with pacemakers or implantable cardioverter-defibrillators should avoid contact with this product.
Not surprising. I remember that the university where I studied had entire corridors with warning signs telling people with pacemakers to keep out because strong magnets were being used.
Do not allow the unit to come in contact with metal objects or other magnets. Damage will occur to magnetized media, such as diskettes or credit cards, near the plate. Damage will also occur to computers and CRT-based monitors near the magnets.
Unsurprising again, and clearly I will not use it on a bench where we have cyclers or other expensive equipment.
Under no circumstances should two magnet plates be allowed to "snap" together; the magnets are strong enough to cause injury and separating them is almost impossible.
In other words, anybody having fingers between two of those plates would find reason to regret it. However, I would assume that most average labs do not need more than one of these plates anyway.

Obviously this item needs some thoughtful handling. But at the moment I am mostly impressed by the strength of its magnetic field - and by the fact that we measly humans are able to manufacture something like it.

Sunday, August 25, 2013

Mulligan's Flat, and botany picture #99: Acacia dealbata

After lunch today we had a very nice walk through Mulligan's Flat Woodland Reserve, part of the Canberra Nature Park system of protected areas.

As mentioned a few days ago, spring is in the air. The weather was beautiful and there are wattles (Acacia) flowering everywhere. The reserve was in fact full of the scent of wattle flowers.

That being said, unfortunately the part we went through is not that terribly diverse, and the only species in bloom were a heath (Melichrus urceolatus), the aforementioned species of wattle (Acacia dealbata in this case, picture directly above), and a lilac pea flowered Fabaceae whose name we did not remember (and no, it is not Hardenbergia). This means that I once more amused myself photographing lichens, such as these:

Odd sights like these feeding traces on dead wood:

And these weird looking fungal fruiting bodies, also on dead wood:

They really remind me of mollusc shells. Unfortunately I don't have names either for them or for the lichens above. Not my area, I'm afraid.

Friday, August 23, 2013

Botany picture #98: Erica arborea

Erica arborea (Ericaceae), France, 2010. This heath is, as the name implies, quite impressive in size, growing up to be a small tree. This picture was taken in south-western France but the species has a very wide distribution including parts of eastern Africa.

Wednesday, August 21, 2013

Australian voting system explained

Not that I can vote or anything, not being a citizen, but here can be found a nice little comic explaining how the voting system works in Australia.

Personally, I consider it regrettable that nearly all Anglo-Saxon countries are still saddled with some form of single winner system and thus with some form of two-party system, but at least the Australian one has preferential voting. In place like the United Kingdom you could theoretically win all the seats in parliament with only 10% of the national vote as long as there are so many other parties that nobody ever gets more than 9% in any district. And in case you think that these distortions are only a theoretical concern, I give you the parliament of Papua New Guinea from 1975 to 2001!

Hat tip to Jim Croft.

Botany picture #97: Phlomis viscosa

Phlomis viscosa (Lamiaceae), Botanic Garden of Zürich, 2010. As mentioned before, the mint family Lamiaceae is one of my favorite plant groups, and in the case of Phlomis I am not alone. There are several ornamentals in the genus, and apparently some people collect the species, although it is of course nowhere near as popular as cacti or orchids.

Tuesday, August 20, 2013

Optical pollution in Canberra

Clearly there things that are better in Germany and things that are better here in Australia. For example, the German three-tiered school system is very embarrassing to explain, and I much prefer the simple Australian Medicare to the convoluted health insurance system we have in Germany.

One thing I really dislike here are, however, these stupid posters that are perennially lining the streets:

They are set up by real estate agents to advertise flats or houses for sale or rent. Here are seven of them in one place because there is a complex with many individual flats nearby, and a few of them are always vacant. What is more, the agents have a tendency to let them stay in place even weeks after the deal has been done, often with a "sold" sticker prominently added to them, to maximize the time their company name can adorn the sidewalk.

Believe it or not, in Germany we have these things called "classified ads" and "the internet" (shocking, I know), which mean that nobody has to set up posters to advertise the same information in a much less efficient but much more obnoxious way. And somehow people coming to see the vacant flat appear to be able to find it by writing down the address instead of expecting a poster in front of the property in question. Posters like those above do not appear to exist in Germany.

All of that means that outside of election times German streets are generally not plastered with garish posters, while Australian streets are, constantly.

Monday, August 19, 2013

Botany picture #96: Acacia boormanii

Acacia boormanii (Fabaceae), ACT, 2013. Here in south-eastern Australia, the 'wattles' (genus Acacia) herald spring. The landscape is turning yellow, and bees are getting busy on them. This species is native further south in the mountains of New South Wales and Victoria but has been widely planted as an ornamental.

Sunday, August 18, 2013

We do not have "faith" in science, and we don't need to justify science a priori

Another piece of text quoted from Jerry Coyne's WEIT website, this time written by himself, because it so clearly and concisely expresses a point that so many are confused about (or perhaps only pretend to be):
Science, however, doesn’t operate on that kind of faith, but rather on belief or confidence based on evidence (and evidence that is sufficient to command assent from every reasonable person).  Scientists and laypeople who trust science don’t get their “faith” from revelation or scripture, but from evidence that has passed critical scrutiny by other scientists.  And you don’t trust your doctor, or your next plane flight, based on revelation: you trust them because your doctor prescribes antibiotics based on data showing that they work, and you trust your plane because it’s designed on principles of aerodynamics.
Exactly right. Science is not another faith, it works, and everybody who is sane agrees on that already, no matter how religious they otherwise are, as demonstrated by the fact that they accept it in all areas that don't conflict with their particular superstitions.
Wax’s incursion into philosophy, which smacks of the odious Alvin Plantinga, leads him to claim that “there is no scientific evidence to prove that science is the only reliable way to discover truth.”  So bloody what? Experience, not a priori reasoning, has taught us that science is the only reliable way to discover truth, and so we rely on science and its attendant naturalism, rather than the lucubrations of religion, to discover how our cosmos works.  There are plenty of spiritualists and faith healers who derive their methodology from “revelation” (often the revelation that quackery makes you rich), but who trusts them? If you had an infection, would you take a drug that has been tested in double-blind studies to kill the bacteria, or would you go to a shaman or faith healer? Your chances of surviving are much higher if you go to the doctor. That is what the data show. We don’t need to justify this through a priori philosophical rumination.  The difference between a shaman and a doctor is the difference between scientific “belief” and religious faith. It is by the fruits that you distinguish them.
Again, it could not have been said better. A great many armchair philosophers, postmodernists and believers are very proud of having grasped the problem of induction, i.e. that there is no way to show the validity of the inductive reasoning used by science through deductive reasoning. Others think they have arrived at a very important conclusion when they realize that the validity of science cannot be demonstrated through a scientific experiment.

Newsflash: Nobody cares. Quite apart form the fact that an insistence of deductive reasoning is exactly as self-defeating as pure positivism because you could not even formulate your argument without first having used inductive reasoning to learn your own language, I have yet to understand why science would have to be justified through deductive reasoning to be acceptable. Who went and said that deduction is the gold standard? A philosopher who very much likes deductive reasoning, I presume?

And as nice as deduction is, really science has to work as long as the universe you find yourself in shows some kind of regularity, and if it didn't it could most likely not contain an intelligence capable of asking these kinds of questions in the first place.

As I have argued before, even if we were to lean over backwards and accept the ludicrous idea that empiricism, science, and reason in general are faiths on equal footing with religion, there still remains the fact that every human being is agreed on the acceptance of those first few "faiths" except in a few cases where they conflict with the wishful thinking or religious dogma particular to that human being. In other words, the difference between the skeptical scientist and somebody who rejects a piece of science for religious reasons is not that of one faith versus another faith, but that of intellectual consistency versus special pleading.

Friday, August 16, 2013

Botany picture #95: Globba winitii

Globba winitii (Zingiberaceae), Botanic Garden of Zürich, 2009. Not much I can tell you about it except that it is a member of the ginger family, but doesn't it have a great genus name?

Wednesday, August 14, 2013

Bush Blitz Symposium, one final time

All the talks from the Bush Blitz Symposium that I blogged about last month have been made available online, including my own. In case you are interested, find them via this finely crafted link.

Perhaps more conferences should think about doing this, although admittedly it would strongly discourage scientists from presenting unpublished results.

Botany picture #94: Agrostemma githago

Agrostemma githago (Caryophyllaceae), Germany, 2005. This wild carnation used to be a common weed of crop fields in Germany. I have heard of the saying "Rade, Rade rot, morgen frisches Brot", meaning that if this species is in flower the harvest would be close. These days, however, it has become very rare due to modern agricultural practices.

This plant is also a good example for the different classification of plant species between countries. Here in Australia, people differentiate between native and introduced species. In Germany, there are three categories: (1) native, (2) archaeophytes, that is plants introduced thousands of years ago with the advent of neolithic agriculture, and (3) neophytes, plants introduced after 1492.

Monday, August 12, 2013

What I learned today

So I had to take a first aid course today because I did not take any refreshers during the last two years. A few thoughts.

I wonder how much I learned today that does not neatly fall into either the category of things nobody needs to be taught because they are bloody obvious (don't put fat onto a burn wound, don't move people with spinal injury, etc.) or the category of things that I will have forgotten by the time I need them, if ever (e.g. where does the apex of the triangular bandage go when making a St John sling?).

It is interesting that legally one does not have to help a casualty if there is no relationship. Admittedly, that relationship is easily established, say by you asking them if they need help or by you having a partial responsibility for their state, for example because you hit them, so from that moment on you have to help. But is still odd that you don't have to if you don't establish that relationship. At least here in Australia one can apparently walk past a dying person and face no repercussions as long as one does not personally know them. I may be mistaken, but I think in Germany that would be unterlassene Hilfeleistung and carries a sentence of up to one year in prison.

We also learned about adrenaline auto-injectors for the treatment of anaphylactic reactions. There are two brands on the market, both very expensive plastic pens that shoot out a needle with synthetic adrenaline when activated. The fun thing is that one of them has an orange release button at the upper end and the other has an orange lower end that activates when being pressed against the patient's leg. In other words, they appear to be deliberately designed to make it maximally likely that a confused or panicked first aider shoots the adrenaline into their own finger. Yay, the power of the free market at work!

Finally, because the venue of the course was south of the lake I had to take the car today. Going through that experience has once more made me wonder why the heck anybody in their right mind would take the car if they live less than 30 min by bicycle away from their workplace or have a bus connection. The traffic jams at around 8:30 and 17:30 are truly nightmarish, and this is not even Sydney or something, it is only much smaller Canberra. People are just weird. When I cycle, I can just roll past them, and I get exercise without having to pay for a fitness club.

Sunday, August 11, 2013

Historical "versus" experimental science - a nice analogy

One of the favorite arguments of creationists is, at its root, "have you seen evolution happen"? Because nobody has seen the transformation from microbe to worm, from worm to fish, from fish to tetrapod, etc., happen in real time, there is supposedly no reason to believe it happened, despite the wealth of fossil, phylogenetic and other data supporting the conclusion.

More sophisticated creationists try to wrap this idea into slightly more reasonable sounding language. They make a distinction between experimental science and historical science, arguing that only the first is real science because its experiments can be reproduced at any time. Evolutionary biology, they say, is a historical undertaking and thus much more open to interpretation.

Now obviously this argumentation is completely idiotic anyway. We can infer things about the past, we can infer to the best explanation, and we can reproducibly test hypotheses. For what is perhaps the simplest example, every time a palaeontologist fails to find fossils of mammals before the first fossils of marine fish, they provide a little more support for evolution and against special creation because under the latter "theory" one would expect fossils of all lineages to co-occur together right from the earliest strata.

However, it is always best to have a pithy analogy in these situations. At least I strongly believe that a good mental picture is worth a thousand carefully weighted words (which is why I crafted this recent post, for example). And for this historical versus experimental silliness, for this "have you seen evolution happen" idiocy, a commenter at Jerry Coyne's WEIT website has just given the perfect analogy:
Becca Stareyes: I’ve also never seen an acorn grow into a giant oak tree, or a baby boy grow into an old man, but I would look pretty darn silly if I implied such things should be treated with skepticism. Because between my personal observations of human and tree growth and aging, and less-direct evidence, it becomes pretty damn obvious what’s going on.
This is definitely worth making a mental note of; the acorn example is beautiful in its simplicity, much easier to visualize and much better at showing the absurdity than an analogy using archaeology, for example. As a bonus, there is a reply poking fun at the infamous question "if humans evolved from monkeys, why are there still monkeys".
Rob: If acorns are trees why are there still acorns? Checkmate atheists!
That one could, of course, also be addressed by asking back "if you are descended from your mother, why does your mother still live?"

Friday, August 9, 2013

Tokogenetic relationships

During a discussion about species, a visiting colleague has argued that I am misusing the word "tokogenetic" (see here, here and basically everywhere I discuss phylogenetic systematics). Apparently the way Hennig originally intended the concept of a tokogenetic relationship to be used was not as a synonym for "net-like" but instead to describe the ancestor-descendant relationship, as from mother to daughter across generations.

If that is so, I will from now on try to avoid making that mistake. That being said, my previous misuse, both on this blog and in research papers, does not appear all too problematic because nearly everybody else seems to use the term in the same way, as a Google search easily demonstrates.

The important point, however, is that this insight does not change anything that matters: Regardless of whether they can or cannot be called tokogenetic in the original sense of the word, networks, or net-like structures, definitely do not contain monophyly or paraphyly. Only tree-like, phylogenetic structures can contain monophyly or paraphyly.

This is why anybody arguing that reticulation makes it necessary to accept paraphyletic taxa only demonstrates their own conceptual confusion. As do those arguing that the members of the same sexually reproducing species form a monophyletic group or clade, of course.

Thursday, August 8, 2013

Botany picture #93: Mandragora officinarum

Mandragora officinarum (Solanaceae), Botanic Garden of Zürich, 2009. The mandrake is of course well known from legend and, lately, Harry Potter. The root was believed to possess magical properties but the plant would utter a deadly scream when harvested. Supposedly some people would bind dogs to the plant and then walk off, hoping that only the dog would die when the plant screamed and one could afterwards pick up the root.

Tuesday, August 6, 2013

Consciousness raiser: Trade-offs

Some recent discussions I was involved in appeared to suffer from two circumstances: First, that many participants were talking past each other because they were not quite agreed on what the controversy was actually about, and, two, a lack of appreciation of certain aspects of reality on one side of the discussion. Aspects of reality, admittedly, that we humans are very likely to get wrong. So this post is once more mostly exploring the issue for my own benefit and perhaps for later reference if ever needed.

Today, let us consider the concept of trade-offs. When discussing the potential for future technological innovations with the kind of people one might classify as singularitarians, transhumanists, cornucopians or simply technology-optimists, one cannot help but become puzzled at their often very simplistic view of technological feasibility and progress. Many of them seem to believe that the history of engineering can be summarized as undertakings that had previously been impossible gradually becoming possible once the awesome power of the human mind is properly applied to them, and that this trend will merrily continue into the future.

That is, of course, a very one-sided perception. Yes, there have been many cases where doubters were proved spectacularly wrong, for example when it was stated that trains could not go faster than a couple tens of kilometers per hour without killing the passengers. However, Jules Verne's cannon shooting astronauts into orbit really has to remain fiction for just that reason: there is no way of accelerating a projectile (as opposed to a rocket) fast enough to reach escape velocity without killing the astronauts. There simply isn't, and that is how it will remain regardless of how much science and engineering progress.

The same is true of perpetua mobiles, for example. Some things are ruled out by the physical realities of our universe, and the same is very likely to be true for many other pipe dreams futurists are coming up with. It may well be that there is no way of traveling to another star system and surviving the journey, of running a stable fusion reaction at a scale smaller than a star, or of uploading a mind into a computer. (Then again, I am only certain about the last of these.)

But beyond plain "this violates the laws of physics" level of impossibility, one of the really under-appreciated reasons that something might turn out to be impossible are trade-offs. What does that mean? It is simply the observation that to achieve some benefit A you often have to accept some correlated downside B.

Monday, August 5, 2013

Botany picture #92: Cladia retipora

We have a lichenologist visiting our institute this week, and so I thought I could upload a picture of the only Australian lichen whose name I know at the moment. And isn't it stunning? Cladia retipora (Cladoniaceae), Tasmania, 2012. Its common name is 'coral lichen'.

Friday, August 2, 2013

Botany picture #91: Scrophularia nodosa

Scrophularia nodosa (Scrophulariaceae), Botanic Garden of Halle, Germany, 2008. These plants are mostly wasp-pollinated, a rather rare pollination syndrome with often small, easily accessible, dull coloured flowers.

Thursday, August 1, 2013

Botany picture #90: Ornamental cherry tree

Winter, if you can call it that, is odd here in Canberra. The locals like to complain how cold it is but for a German it is really only like three or four months of late autumn; there is no snow and ice, and unless there is severe fog it always warms up nicely during the day. (Perhaps it would help if Australians would dress for the weather, but no! They seem to insist that one should be able to walk around in flip flops and shorts even at 5°C because this is Australia goddammit.)

The flora at least perceives the non-winter precisely as I do. The last leaves of introduced trees in the city parks have hardly fallen and you can already see spring flowering coming into full swing. It is now end of July/beginning of August, translating into end of January/beginning of February in a northern hemisphere winter, which would in Germany generally be followed by a full month of more deep frosty winter, with spring flowers then usually only really starting to come out in March. Yet here the cherries are already blooming and, as you can see in today's botany picture taken last Saturday, even quite close to finishing (note the brown colour of most stamens). As for native plants, the wattles (Acacia) are also beginning to bloom.

Admittedly, this July is also exceptionally warm after a summer that was so ridiculously hot that new colours had to be added to weather maps.