Archive for the ‘Education’ Category

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.


A Spartan Family Tree – An essay on inbreeding and cultural evolution

September 30, 2012 4 comments

Six whole weeks of bliss, a post week, like I promised myself and then… Oh dear, so two weeks ago I had my most successful post yet, most views and even before I’ve posted this one, then I go and miss a week due to being unprepared, and THEN, I go and leave it until now to finish this post from last week. I’m going to try to do a catch-up post before this week is out to make up for the lack of post last week. Any way, I’d been nursing a few thoughts for potential blog posts that I haven’t yet finished so I figured I’d put my thoughts into this one:

I thought I’d begin by prefacing the post with the statement that I was reading the Harry Potter series for the past couple of weeks, something which I started to do back in my early teens/late childhood (Note: I’ve finished them now and enjoyed them all, yes it did take me a couple of weeks, I’m bored okay?). Something I noticed is the amount of time given to the effects of cultural restrictions on breeding and the effects of inbreeding on populations and what happens when it is taken to extremes.

It is interesting to reflect on the wizarding world’s division into “purebloods”, “half-bloods” and “muggle-borns”, labelled “mudbloods” by purebloods who favour inbreeding. It is mentioned that few magical men and women aren’t halfblood or less. Why *must* this be so? Because genetics.

Well let’s begin with the assumption that the wizard population started small (I’ll cover what happens when a wizard population is large later), a reasonable assumption since populations have to begin and they don’t come into being as a fully formed population (Unless you believe certain ideas). In order for the population to be rebuilt with the genes of the surviving members, inbreeding between the wizarding families would have to happen, which inevitably creates the same problems as inbreeding does in other populations.

Small populations create problems such as the random loss of genetic information due to genetic drift. Basically, if a population is small, the chance that any particular gene does not make it through to the next generation is also small and so genetic variation in the population decreases. Think of it like this, you have a bunch of people, some blonde, some brunette and one ginger (I choose ginger because they *are* a rare allele, if you still don’t like it, I’ll change it the day that gingers outnumber any other hair colour).

If the chances of a child having their parents hair colour is 50-50, then to have a good chance of having a person in the next generation with ginger hair, then the ginger person needs to have at least two kids. But for the blondes and brunettes, it’s likely that some will have kids with their hair colour simply because of how many blondes and brunettes are in the population.

So back to the wizarding families, they’ll end up more genetically similar if they only breed within wizarding families resulting in oddities like the Weasleys (A bad example given their “Blood-traitor” status, but all that red hair, most likely they all carry only one copy of the genes which control hair colour) and Malfoys (Lucius and Draco are meant to be almost identical when compared adult with adult). But what happens if this is continued? There are numerous other problems: decreased fertility, increased risk of genetic disorders.

The continued inbreeding of the families creating greater and greater genetic similarity which would inevitably increase the sense of ‘otherness’ no doubt felt by the wizarding families. With the creation of the International Statute of Wizarding Secrecy, this isolation would be even more marked. This social and cultural separation would compound the problems caused by the genetics. We can begin to see the full scope of the problem.

But wait, there’s more: Do you think a Malfoy would marry a Weasley? What about a Black marrying a Dumbledore? Families not getting along makes the pool of potential pairings decrease still further, increasing again the problems of the social, cultural and genetic isolation. And when families are openly hostile? If we look at the Black family, it’s clear, the family is all but annihilated, the only survivors do not carry the Black name and they are few in number (Tonks and Malfoy are the only ones mentioned as being related to the Blacks). Obviously, extreme views in the wizarding world such as the “purebloods are best bloods” will generate animosity hence why there aren’t any Slytherins, Blacks or Gaunts left.

What applies to the wizarding families, applies quite well to the royal families of Europe, I am speaking of course about the haemophilia which plagued the descendants of Queen Victoria and also, the house of habsburg which shows how this sort of family ties thing works at the grandest of scales.

For the difficulties of socially imposed rules on marriage and conflict, take a look at the vast and poerful Spartan army which has dominated the world since the ancient greek city-state seized power… oh wait, yes, the Spartans were the elite forces in their day, but clearly they are no longer. The rules in Spartan society made it inflexible and the depletion of the families’ sons meant that the number of Spartan families gradually declined and inbreeding resulted in the extinction of all those family lines.

This is my loose bag of thoughts that I’ve emptied onto the blog. Hopefully something of import can be found in there by those willing to dig around.

On life’s little boxes

September 16, 2012 Leave a comment

Ever noticed how life is just things in stuff inside other stuff… It just goes on and on: We have organelles which come together in cells which group into tissues which group into organs which group into organ systems which group into organisms which group into populations which group into ecosystems which group into biomes which group into planetary ecosystems. I find it very curious that we box things like this, is it a truth of nature which we have uncovered or a construct of our pattern seeking minds. I would cede the point that up until organisms it most certainly is the way that life has developed but we also box species and populations together as if they are also some ‘thing’ which we group as a unified whole.

I think I’ll start by criticising the ideal of species first put forward as everyone will remember from their school lessons, Carl Linnaeus created it way back when we were trying to understand nature as “God’s plan” which is to say the bible was considered literally true and species were permanent things created perfect for their place by God. This ideal makes species out to be something like a box which you can put organisms into, they go in one box or another, people still use this system because it’s a useful short-hand for working with them but it’s not so much a box as a series of valleys in the landscape of life and if a trough is quite shallow and close to other troughs then cross-breeding occurs and this is were things like Ligers come from.

But is a population a thing? That is to say does such a thing as a population exist? What is a population exactly? Is 50 elephants a population? What about if they all use the the same lake as a water source? What if 10 elephants use one side and 40 use another? Is that now 2 populations? You see how slippery the definition is. So, is population equatable to the organelle in an organism idea? If not, is there something which is?

I would argue that populations are not equatable, and here’s why: Organs work together to pursue a common goal: the survival and reproduction of the organism which the organs reside in. Few populations (If any) work to the same goal. Under this view, the colonies of ants as a super-organism makes sense while standard populations (Such as the elephant one above) do not. So are there large equatable structures that make sense as far as the organ/organism structure goes? I’ve decided that while I’d like to think further on this point, I’ll leave it to any readers that might drop by to decide for themselves, I’d love to hear others’ thoughts on the matter so anyone that does read this, please feel obliged to leave a comment telling me your thoughts (Even if they are just “F1RS7!!1!!!ONE!!”).

Now, back to this whole boxes in boxes issue. Endosymbiotic theory, ever heard of it? It’s AWESOME! The idea being that some ancient prokaryotes (like bacteria, best to look up the differences between prokaryotes and eukaryotes if your unfamiliar) engulfed others but instead of destroying them, it kept them and used the things that it made, so  photosynthesising prokaryotic cell became the chloroplast. I recommend reading up on these because there is some striking things that define organelles which are explained rather wonderfully by endosymbiosis. So we have cells in cells and this makes the cells so different we put them in different domains (Bacteria, Archaea and Eukarya are like the groups above plants, animals, fungi et.c. so think ‘more different than a plant is from an animal’ and you’re getting there). Then the next level of complexity is these cells working together in multicellular organisms (Which only happens in the more complex (DO NOT READ ‘BETTER’) eukaryota) but is this the same as organelles and cells?

It’s certainly quite similar, when you get to the cell differentiation of more complex organisms such as animals which aren’t sponges (Which are the mongols of Crash Course Biology) then different cells do different things and this specialisation makes the organism more able to do different things better. Yes this time better can be applied, it’s the old tenet ‘greater than the sum of it’s parts’; the team that gives each member a specific role allows the members to be really good at one thing and do it better than a member which does it all. Just as the golgi apparatus is good at making vesicles and the mitochondrion is good at making ATP (Quick joke: ‘I’ll have some Adenosine Triphosphate please.’ “That’ll be 80p please!”) they don’t have to worry about doing the other things because they help each other out. This is exactly the same as red blood cells being good at transporting oxygen and nerve cells good at carrying information it’s just that instead of them all being inside one giant cell (Which wouldn’t physically be possible) but instead they’re surrounded by a bunch of other cells which are built to be our very uber-‘cell membrane’.

I would argue the same principle is followed up to the level of organism with tissues in organs doing different things such as the medulla and cortex of a kidney functioning to clean the blood. Then you have organs which do different things like facilitate gaseous exchange (Lungs) or digest organic matter (The whole digestive tract). So where do organisms work together to make their super-organism which has specialists which promote the survival of the structure as a whole? In the Hymenoptera (Ants, bees and wasps) and Isoptera (Termites) you have a social contract generated by chemical control, the workers cannot reproduce and are held in place by the ‘Royal’ classes (though I have simplified things a bit, it’s clear that it is vastly more complex than that). It is also useful to note that some of these groups have specialisation of labourers such as Honeybees whose task is determined by their age.

What other groups do this? I would argue that societies and social groups of any kind do further the selectivity of any organisms involved in the same way that the union of cells into multicellular organisms, though it has not had quite the same amount of time to perfect as multicellularity and I would suppose that since the individuals have different genetics it cannot perfect (Which would explain why we see such brilliant altruistic behaviour in Hymenopterans and not so much in other groups) to the same degree.

I suppose the point in what I am trying to say is that the more complex life forms seem to be just combinations of the simpler things. Much like Eukaryotes are just prokaryotes that were hungry but couldn’t finish their meals. One thing I do want to stress is that complex != better and just because something is more complex doesn’t mean it’s any more evolved or any more selective than any other modern species. But ants are the best.

On the difficulties of translation.

August 11, 2012 Leave a comment

Apologies for my absence, it’s been a rough few weeks.

This week I am going to talk about how my learning Powershell (a Text-Based User Interface or TUI rather than the Graphical User Interface or GUI that we are all familiar with today) permits me to understand better how we translate every day and what it is we translate. This is the true nature of languages and communication at it’s most basic level. Well, really it’s me trying to be scientific and philosophical so prepare for some half-baked ideas from a newly graduated idiot.

To begin with, these words are symbols that represent concepts, or rather, more literally sounds which represent concepts that anyone who knows the ‘code’ can translate and can therefore understand the meaning of this heavily convoluted sentence. To you Grammar Nazis, I know that my writing is terrible, but hey, I’m learning, be gentle, communication isn’t my strongest point.

So even when one is speaking the same language, it’s possible for confusion ‘in translation’ because the concept has to be translated a few times: From thought to vocals, to detected sounds, to thought. A thought occurs (Ahaha), a brilliant demonstration can be shown in this xkcd comic, confusion reigns through translation.

Now that we understand a little about translating intent into languages, we may look at the intent in use of Powershell, and the language used. For example, to delete a file using Powershell, you don’t say ‘delete filename’, instead you say:

‘rm filename.txt’

‘rm’ stands for remove which is the word that the programmers of Powershell decided was the way they would define deleting. Understanding the correct syntax is also important, suppose for instance that you had to state which file you wanted to remove first, it is entirely conceivable that the programmers could’ve decided that you had to state which file you wanted to do anything with before you tell Powershell what you wanted to do with it, in which case the correct syntax could entirely be:

‘filename.txt rm’

Or they could have also decided that ‘del’ was clearer as del is short for delete and so it is more intuitive to do that and so:

‘filename.txt del’

Would be the correct syntax. Understanding what language you are speaking is important to know how to say anything, this is important for different human languages too, I’m afraid the only other language I know a bit about is the dead language of Latin but it is a good example, in order to state:

‘Adam eats the apple’

You say that

‘Adam the apple eats’

So if you were to try the first one in Latin it would sound like complete gibberish. It’s interesting to reflect on the origination of syntax, who decided these laws of noun and verb order for these different but certainly related languages. Speaking of foreign languages (At least foreign to where I’m writing this blog…) there is an important point on perception which is demonstrated by a Belgian artist, René Magritte, jokingly referenced by another webcomic Calamities of Nature (Calamities, you will be missed). The original is of course:

The Treachery of Images taken from Joshua Katcher’s Blog without permission, but I cite his post so I think it’s ok. Josh if you read this: I doubt you’re petty enough to demand more since you don’t own the image but thanks, yours was the first image that showed up on GoogleImages so props to you.

This artwork makes the point that an image of something is only a representation of it. Perfectly obvious really, but important to note. The point is pertinent, in my opinion, to what I have to say on translation; that when you state something, repeating our earlier example:

‘Adam eats the apple’

When you state this simple sentence, you don’t state what is happening, rather you state an impression of what is occurring. This adds a layer of potential confusion since this impression can be misinterpreted, for example, it doesn’t say what state the apple is in, if the apple was chopped or whole (I’m sure you can picture two very different scenarios when I give this additional information to supplement the statement.

I suppose this blog post really is about being careful about what you say and how you say it because a different interpreter could translate it incorrectly, or rather in a different way to you, as with the computer example about removing (i.e. deleting) files using Powershell.


Learn Powershell or your computer’s alternative.

Joshua Katcher’s Blog post which I took the image (Heheh) of the Treachery of Images from.

On Deep Sea Grazers

This may not be a particularly interesting post for the vast majority of people but it’s one that I care about, it’s going to give the background to a dissertation I’m writing to hand in in the next two weeks (I handed it in on April the 27th). Everybody in the house interested in paleoethology, ichnology, evolution or deep sea worms that evolved around 542mya and have continued up to the present developing more and more complex grazing behaviour give me a hell yeah?! Ahem, yes well that’s what this post is all about so read on if you’re curious.

So how do we know that such behaviours actually exist? Well Ichnology, specifically paleoichnology is the study of trace fossils, fossils which record the tracks and trails of extinct animals, for instance Dinosaur footprints are on type of ichnofossil (Another name for trace fossils). Ichnology is the study of all tracks and trails and neoichnology is the branch of ichnology which focuses on extant (living today) animal tracks. There are fossils which record the movements of animals and they can be grouped by what sort of behaviours produced them. The particular group I am interested in are the group ostentatiously called Pascichnia (Pass-ik-nee-ah, I think). It literally means grazing tracks (Latin Pascos lit. Grazing Ichnos lit. Track) how inventive of them. If you want to know more about the inventive naming system, google the name Adolf Seilacher, he came up with the original categorisation system.

Pascichnia have been discovered from some of the earliest periods in history, the first fossils were simple and looked much like childrens’ scribbles, think what you did as a kid in MS paint scribbling randomly then colouring in the gaps between the lines. They look much like that but in rock and less colourful.

The next stage along was a couple of hundred million years later when the animals had learned to loop back and forth (This is but one example) but the loops were quite loose and there were often large gaps before the animal moved back to follow alongside it’s path. The final part of this example I will describe is those trace fossils which have been found from the Cretaceous, again, a few hundred million years after the previous ones. These showed a very tight strafing pattern back and forth minimising the area left unused by the animal.

So the patterns have gotten more complex, but why? There has to have been some sort of pressure to force the worms to develop more complex behaviours. It is possible that the behaviours developed by chance, that is, genetic drift in the development of their neurons would develop such behaviours, however there are a couple of reasons why this is unlikely.

First, neurons are expensive, unless the worms had another reason for the development of the neuronal capacity to develop these complex patterns then they wouldn’t have the neuronal capacity in the first place and no amount of genetic drift could generate these behaviours.

Second, the behaviours are temporally distinct, that is, each level of complexity is isolated from the others in time, only simple behaviours at the start, semi-complex behaviours in the middle and complex behaviours at the end (Or at least at the present, who knows what will happen in the future of such animals). This would suggest a directionality to the behaviour, if it were mere chance that developed these patterns then it would be a reasonable assumption that all behaviours would be represented at almost the entire length of their history. The fact that this is not the case would suggest that the complex behaviours are more selective.

So to conclude, these behaviours have gotten more complex over time, and it is highly likely that this is not the result of genetic drift, rather an evolutionary response to an environmental or ecological pressure which forced the development of such behaviours.

Comments and criticisms welcome.