Archive for October, 2012

On spirals, stripes and zigzagging.

October 28, 2012 Leave a comment

So this week I thought I’d take the time to go into a bit of depth about what I was looking at for the dissertation I completed for my degree. If you’re not interested, I’m sorry to hear that, go be boring somewhere else. It’s all about moving, particularly, moving in ways listed in the title, spirals, stripes and zigzags. In order to understand this however, you need to understand the details of my dissertation.

Nah, just kidding, but it would be good for you to understand the background of my project because my work is based on the hypotheses of a few good men. It is based on the fact that in the fossil record there are remains of what was originally thought to be seaweed but which were later reinterpreted as the tracks, trails and burrows of ancient sea creatures. Think about the last time you were on a beach, you know that worm cast? Well that’s because of a ‘U’ shaped burrow of a worm which it uses to collect nutrients by passing water over it’s gills through the burrow.

Worm Cast: This stuff is the sand pushed out of the back (On the right) of the burrow (The front is the hole on the left) to make room for the worm. Source.

Okay, now imagine that worm lived millions of years ago and the sand it burrowed through was turned to rock and the burrow remains as an imprint in the rock. This is one type of fossil which has been studied, the types that I studied where probably made by a species which crawled across the ocean floor, grazing. These patterns changed of the course of history, the first recorded paths are quite ancient, I believe the earliest ones I found in the literature were from the Silurian period (in the region of 450mya, for contrast, humans diverged from chimps around 4mya).

The Silurian Period: This is the geologic time scale, Earth was fully formed by At the very bottom on the left. Animals evolved around the start of the Paleozoic (In blue) and all the time since then has been expanded on the right. The Silurian is the 3rd period from the bottom on the left, the dinosaurs fit into the pink section on the right; all of human existence fits into the Quaternary at the very top of the right. Source.

So these things have been around a while, but they’ve not been idle, oh no, there are several different groups of fossils, some with spirals, some with zigzags, but they didn’t start out that way: The first records are simple stripes which overlapped a lot. Then millions of years later, we find record of some with loose zigzags and some with loose spirals. Millions of years after that there is record of tighter zigzags and very tight, double spirals. Millions of years after that and we’re around the time when mammals are about to take centre stage as the largest animals on the planet, and we find tight corkscrews drilling into the ocean floor.

Trace Fossils: So called because they are the traces and tracks of animals rather than their bodies. This is from Raup and Seilacher’s original paper, the left side shows the fossils they based their model on and the right shows what the computer model did. Source.

My work was based off of this and the Prescott and Ibbottson paper I got the picture above from. Along with a paper with the wonderful title ‘In Search of the Optimum Scumsucking Bottomfeeder’. The question is: Why bother to make yourself able to develop such complex patterns as that double spiral? What is pressuring these creatures to develop the complex neural pathways required to make such patterns? Well Hayes in the paper named above suggested that the ocean floor is a uniform resource and the best tactic is to just munch on the resources as you move along it and the more efficiently you use up the space, the better off you’ll be.

Well I think that’s a good idea except I was convinced of the patchiness of the resources, the ocean floor isn’t uniform, far from it. In the end, I decided that a strong contender as one of the reasons for the behaviours would be competition from others. In other words, the population density within an area would mean that the organisms would be all crowded together to a certain extent. This crowding would mean they should watch out for where they move because if they move over an already grazed patch, that’s a waste of the energy used to move over that patch.

I tested the idea by looking at the various behaviours and how Raup and Seilacher suggested the decision tree would work. I built a whole bunch of different behaviour sets based on how they would move in a free environment without depleted areas getting in the way; I also behaviour sets based on how they would react to the path they were moving along being obstructed by depleted patch. The pictures below should illustrate what I mean:

Movement behaviours: The three different ways that the organisms would move, there was (a) the straight path (with a little wobbling because nothing in nature is perfect); (b) the curve, the organism would gently turn as it walked; (c) the zigzag, similar to the straight path but after a set number of steps, the creature would reverse it’s path. Source: Self.

Reaction behaviours: These three are how the organisms would react when they came across a depleted patch (Which if all the world is filled with food, would only occur if another organism has already grazed the area and represented by the horizontal arrow. (a) the simplest option is to do nothing about it and keep going with your movement behaviour; (b) a more complex choice is to look out for it and when you see a patch ahead, turn a fixed amount and then carry on with your movement behaviour; (c) this is the most complex choice, in it, the organism attempts to follow along the edge of the already depleted patch and graze alongside it. Source: Self.

The next step for me was to simulate what different populations would do given these behaviours, so if there where 10 in an area, how much food could each gather under each behaviour set (Each model organism is given one movement behaviour and one reaction behaviour to use and I chose to make each population run just one of each of the nine combinations) then compare that with 20 in the same size area, and 30, and 40 all the way up to 900 (Just looked that up in the file I used to record all of this and it turns out that the file was created 29/10/2011 what a coincidence). So because the size of the area was the same for each one, I was looking at population density and what happened to the benefits of each behavioural set.

The short story is that after I collected something in the region of 3.5 million data points, I used some basic statistics and discovered that the reaction behaviours that tried to avoid the paths did VASTLY better than the one which didn’t avoid the paths at all at high population density. So if there’s lots of competition about, it pays to be smart about where you’re going. But at low population density, the reaction behaviour of ‘keep doing your movement behaviour’ did at least as well and often better (Depending on the movement behaviour) than the more complex reaction behaviours.

The reason for this, I think is that when there’s not many organisms around, it doesn’t matter if you go over a track every now and then, if you try to ‘take evasive maneuvers’ you’ll end up staying nearby to an area which has already been grazed on whereas not reacting to the grazed areas, you end up heading out to ‘greener pastures’ and not running into the paths again. It also seems that population density did have a significant effect on these ancient animals’ behavioural effectiveness. As for why all this matters, well, that I think I’ll save to waste your time with on another post.


What is science? Part II: How do you know?

October 21, 2012 Leave a comment

This week I finally return to a task I set myself on my second blog post, to try to give a set of posts which cover the possible answers to the question “What is Science?”. This week I will attempt to blunder through my understanding of the differences between a scientific viewpoint, a religious viewpoint and philosophical viewpoints (plural because philosophy isn’t a single thing).

So, how do you know? How do you know anything? That is a complex question. How do we know some things? Some things such as our names and categories are simply identifiers we use, this blog is UrsusCetacea, but that isn’t necessarily *what* this blog is, it’s really an amorphous cloud of my thoughts ranted out of my fingertips onto the internet but it could just as easily be called “THE GREATEST BLOG EVER” but that would neither make the statement “The greatest blog ever is the greatest blog ever” true, nor would it make this blog any different besides the name at the top.

Bear whale (Ursus cetacea): The story of a bear swimming along capturing insects in it’s mouth inspired Charles Darwin to suggest (incorrectly) the origin of whales as a bear taking this strange behaviour to extremes. Source.

But there are things which we assume to be universally true, that are true regardless of what happens. I subtly and totally on purpose described one earlier, that my blog is an amorphous cloud et.c. et.c., it doesn’t really matter what I called this blog, it would still be what it is. Other things are also universally true, if I drop an apple it will fall towards the centre of the Earth (Unless I’m REALLY far away or going fast enough).

Still other things aren’t easily set into True and False categories, they may be simple explanations of True/False events, such as the answer to the question “Why does the apple fall towards the Earth’s centre?” we say the answer is because gravity pulls Earth and the apple together but the apple has a lot less inertia so it goes further towards the Earth than the Earth does towards the apple. How do we distinguish the difference between the gravitational explanation and, say, “The Flying Spaghetti Monster pushes objects back down onto the Earth“?

Intelligent Falling: The idea here is that the FSM pushes down on people keeping them attached to the Earth instead of floating away. Source.

What is the difference between such hypotheses (Quick note: A hypothesis is an expectation of what will happen in an experiment, a theory is a set of explanations, hypotheses and facts which fit together to provide a comprehensive understanding of the process described, such as Germ Theory, Atomic Theory, Theory of Evolution, Genetic Theory, Big Bang Theory, Theory of Gravity, Theory of Electromagnetism, et.c., et.c, all of these have the same level of strength, doubt one and you doubt them all.)? The difference is what makes science and what doesn’t. The scientific explanations quite simply may be tested by the scientific method and are abandoned if the method disproves the hypothesis.

Theories, hypotheses and facts: all neatly joined together, if only life was this easy. Source: me.

An important thing to consider here is that I have not mentioned when a hypothesis is accepted, nor when a theory is. This is because it’s unique for each hypothesis and theory. It’s also different for different sciences, for instance, in biomedical science it’s much more strict than any other biology, because human lives are at stake. As a general rule of thumb, when there’s a large body of testing and none of it has yet disproved the theory and/or hypothesis, then it is accepted to be true.


The scientific method according to UrsusCetacea: I had to draw this myself but it shows essentially how scientists fact check and develop our growing scientific knowledge.

Now, let us return to our example with the FSM vs gravity and take a look at what the scientific method can tell us about the two hypotheses. So, gravity predicts with great precision (through it’s use of mathematics) exactly what forces will act and the results will be under almost any circumstance. FSM intelligent falling makes no predictions (it’s not meant to, it’s not a scientific explanation). Ergo, gravity is a scientific hypothesis, FSM intelligent falling is a religious idea.

The fact remains that some things are beyond science, how should you behave in society? Is it morally acceptable to hurt another human? Another animal? Why does the universe exist? Why is the universe the way that it is? As yet, science has no way of answering these questions. Some may never be answered. I doubt there would ever be a way that we could determine morals from scientific truth, the old saying “You can’t deduce an ought from an is.”

These areas are were philosophy and religion develop their ‘ways of knowing’ as separate from the scientific ‘way of knowing’. Pre-emptive note to philosophers: Sorry I don’t do your subject proper justice, please comment with corrections/criticisms. So how do philosophers determine what truth is? Fundamentally, philosophical truth is based on reason. Does the internal logic of the statement work? Do the premises hold true under all cases? Do the premises actually support the conclusions? The reasoning is the path to truth and is how statements of truth are assessed.

How do religious leaders find truth? I would say that the religious truth is easier to describe, as religion gives it a word: Revelation. The divine gift of knowledge. The idea being that a supernatural being, a god say, implants the knowledge directly into a person’s mind. This sort of truth is difficult for a sceptical person, one who doesn’t believe in the supernatural being, to accept. Likewise, should a sceptic question the revelation, it would be impossible for the religious person to understand how the sceptic could doubt the revelation.

The difficulty of verifying the source combined with the fact that it isn’t based on reason but rather divine mandate dictating truth makes it difficult to trust without you being the individual who receives the revelation or it being revealed to someone who you would trust the authority of but the truth will not be a universal one that works for everyone.

To conclude, science is but one way of knowing and it is dependent on your own reasoning and beliefs to determine the truth of other ways of knowing. The fact that scientific knowledge is based on evidence however makes it unequivocal, it does no good to argue against what happens, nor does it make sense to argue against a reasonable explanation that has been shown to work. I don’t believe in any god, but I understand that people look for meaning where they will, if someone would choose to seek morals through a religion, that’s their choice. I myself would rather determine the moral action through my own thought and conversation with others. All I can hope is that I don’t come off too preachy in this post.

On shades of grey, be they fifty or infinite.

October 7, 2012 Leave a comment

There was a time when I believed in absolutes, the world was black and white, it was good vs evil, order vs chaos, school started here and ended there. Well, things have changed. The world is not so sharply defined today. This is not because the world has changed, but rather I have. I have learnt more about the world and I have explored more of it (admittedly still only a tiny portion of the whole, but come on, it’s early days yet).

The trouble with this is the difficulty it throws in making decisions. It’s easy to make a choice between one thing and another when it’s good against bad, but what about when the options are a mix? I’ve always had trouble making choices. I remember being paralysed by indecision when my parents gave me a 50p piece and I was allowed to buy a chocolate bar (Remember the days when 50p would but more than one chocolate bar?). Later I worked out the best method, Freddos, and lots of them (At least until they become 15p each, god dammed inflation). Anyway, decisions that were completely arbitrary such as choosing a chocolate to eat (I would be happy with just about any chocolate I was given, I was a child) but I couldn’t just pick one, it had to be the BEST ONE.

Freddo: The best damn solid chocolate bar in existence. Don’t know if America has these so thought it’d be a good excue to take some useful advice. Source

This determination to not make a decision unless it was the best one often left me with little or no time to make decisions. The trouble with life is there are a hell of a lot of paths to walk and a hell of a lot of decisions to make so if you worry about every little choice and which one is the best to make then you’ll go nowhere fast. Of course it’s all very well and good to state my philosophy, it’s quite another to put it into practice.

The trouble I found is that when it is black and white, the option is obvious, if you like black, pick black, if you like white, pick white and if you like arguments, troll away on the benefits of white over black, even without any evidence for such contentions. When it’s a grey-scale it’s a big mess and it isn’t clear which side to pick. It’s even less clear if there are sides. Having a grey-scale multiplies the choices to make but the grey-scale also makes it possible to pick more than one option there’s no us and them, so it’s not damming to pick both. No this little paragraph is not me subtly having a go at the pricks who think one race is superior to others, not at all. Excuse my preachiness, the rest of the post is 50% less preachy, I can’t remove more preachiness, otherwise you might not know it was me writing.

I’m not sure but it seems there’s a lot of resistance to the idea that the world isn’t black and white. Law for instance you’re either guilty or you’re not, there’s little gradation (Any experts feel free to explain to the ignorant exactly why I’m wrong, I’d genuinely be interested in examples of where this does not apply). I think this ideology fits nicely into the simplification of the world that comes with humans trying to understand it, as a computer modeller of biological systems, I can sympathise but we mustn’t then try to peddle our wares as if they are the real world, they are only reflections of it and ones in a rippled and dirty pond at that.

We draw arbitrary lines across the grey-scale and this makes the distinction between one and another. You are a child until you are eighteen, then you are an adult, despite being moral or ‘adult’ about things not being connected at any point (You know, besides brain growth during childhood) but even the point at which we become fully grown is not on the morning of our eighteenth birthday, but well before that we stop being a child. Mental growth however is even more arbitrary, I plan on continuing to learn for the rest of my life; I don’t want to stop learning, even if I went on to teach.

Mortarboard: Three Guesses what I’m going to talk about next. Source

These temporal gradations (GREY-dations, geddit? I’m all about the grey today) are the reason I’ve decided to write on this today. My graduation is this week, late for a graduation in my mind, I finished my course back in June. It seems I’m sort of in limbo at the moment, not fully graduated, nor a student. This originally disturbed me, it bothered me that there wasn’t a clear demarcation for when I was one and then the other. What I have to remember though, is that I’m never fully one thing, I’m reminded of Stephen Fry speaking in a debate on whether the Catholic church is a force for good:

Although they like to accuse people like me, who believe in Empiricism, and the Enlightenment of somehow, what they call ‘moral relativism’ as if it’s some appalling sin when what it actually means is Thought. They, for example, thought that slavery was perfectly fine […] and then with a wave of a hand and a stamp of a seal, it was no longer true, something which had been eternally, or at least true for 2000 years, suddenly wasn’t, because the truth is complicated, it’s hard.

We don’t have absolutes in our world of ethics, choices and societies. We define the limits of our own worlds but this does not mean we have to squash all human experience into a narrow spectrum. We are not photons, experience doesn’t vary like light on the spectrum. We are in a landscape of choice and making the decisions we do day in day out changes that landscape. It’s important, in my mind at least, to understand that; if we imagined the world as our simple version then we may make bad decisions for the future.

Norway’s Fjords: If you don’t get the joke, that’s ok, read on and then Google will solve your problems. Source

I have decided, in Slartibartfast’s word’s to “Hang the sense of it and keep myself busy.” I’ve decided this fuzziness is okay, how boring would the world be if we had just two options to choose from? It’s clear as black and white.

This rambling and preachy post brought to you (NOW WITH PICTURES) by UrsusCetacea, who knows all the answers, except to his own questions.