Archive

Archive for September, 2012

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 Technobabble in Evolutionary Theory Part Two

September 9, 2012 2 comments

Last week I discussed some of the most controversial words in the public view of science today. Chief-most: Evolution and natural selection. I hope that I cleared up a little confusion and hopefully educated a few people. Some seemed to enjoy the blog post enough to think it deserved a like so following that and the fact that it’s 3 o’clock in the afternoon on the day I’m supposed to publish this, I’ve decided to rush through and write part 2 for this week. I don’t know if I’ll need to do a part 3 or if I will think of adding anything so for now I’ll assume this will be a conclusion of the previous blog.

I’m going to focus on some of the other mechanisms for evolution and use them to explain evolution in a more accessible manner that also gives people an idea as to why it is both random (In the sense of being directionless) and purposeful (That it can create complexity and apparent ‘design’). So to begin this, we must cover the ‘basic’ concepts of randomness and design.

Randomness is a part of probability statistics. Probability statistics being two long words that includes the word statistics can terrify people but it can be quite easy to understand. Fear not, I’ll leave out the numbers for today (Numerophiles, fear not, I’ll do a post for you at some point) The basic idea of randomness in evolution is that mistakes can occur in the copying of genetic code and these mistakes are undirected and random. The idea being that one mistake is roughly equal in occurrence as any other.

This random variation is required to start off the engine of evolutionary change, this is the spark plug of evolution. It ignites the fuel which is variation and the engine of natural selection uses this to generate forward momentum. The thing is, while natural selection generates this forward momentum, there is some steering in our ‘car of life’ and that determines where on the ‘map of possibility’ we will end up. Allow me to explain, The engine of natural selection attempts to ensure that whatever our organisms are supposed to do, they do it as well as possible (This is the forward pushing of the engine), however the direction they travel is dependent on what is steering and it’s not always purely one single trait that is being developed by natural selection to it’s extreme and all other traits are secondary.

For example, a bird which wishes to fly would remove as much weight as possible, brains are heavy, so a bird optimised for flight wouldn’t have a brain (Please, no bird-brain jokes). However, a bird without a brain wouldn’t be able to do much without it’s central control for it’s nerves and endocrine system, so a bird has to ‘steer’ for optimum flight capability AND ability to think.

There are other things which can also steer and can even appear to make things go in reverse. These are the sorts of things I’m going to discuss in the rest of this blog: To begin, with, the fun one, or rather, the one with the name that makes it seem fun but actually is all about limiting fun to some special ones with special characters. Yes, I’m talking about sexual selection. This is your peacock, your birds of paradise, your deer antlers et.c., et.c. The idea being that a trait in a particular sex (such as a peacock’s tail) is selected for by preference of the other sex, that is, the peahen loves a man with a big bushy tail and so mates with the peacock with the largest most impressive tail. This is taken to extremes with some species such as the peacock where it appears to be a severe handicap, but the woman gets what the woman wants. Even though a large tail can mean a shorter lifespan than a short tail, it means more snu snu so the big tailed peacocks produce more offspring.

The next one I’ll cover is what happens when you don’t steer at all, it’s called genetic drift and it happens when there isn’t much pressure to direct evolution down a particular path. A good example of genetic drift is the lobed vs unlobed ears of humans, some humans have flappy lobes on the bottom of their ears (Where the earring attached) some people have attached lobes (Have a look at this for pictures if you’re unfamiliar) The idea being that some traits are neutral and give no benefit or disadvantage and so the genes mutate and increase and decrease with frequency independently of survival rates and by chance some versions may increase in frequency. (Note: this is not the main force of evolution, it is likely genetic drift only occurs rarely on very few genes so to say that this in any way explains evolution as an entirely random process at best shows a severe misunderstanding of the point and at worst a deliberate and malicious attempt to misinform)

Another mechanism I’ll attempt to explain this week will be phylogenetic inertia, this is where the evolutionary history of a species maintains a stable mechanism. For example, horses have fused their fingers and wrists and toes and ankles respectively into a line of bones shown here in figure 1. This is very good at what it does and is maintained but what if the horse needed to do something different? It would be difficult for a horse to evolve the fingers and toes required to construct a hand like a human’s with a thumb for grasping because the phylogenetic inertia keeps the horses hoof as it is. Indeed, even with 5 digits, there is more than one solution to the grasping problem, as shown by the panda’s thumb. Which is often cited as a wonderful example of our next word:

Exaptation is where something which evolved for one thing is co-opted for use as something else. The sesamoid bone of the panda evolved for the support of a tendon within the foot, it was used by the ancestor of the giant panda to pin bamboo shoots against with it’s fingers, allowing it to grasp them. This in time selected the bone for use in this new function. Another example is the ear bones of mammals which were originally jawbones, as evidenced by the study of embryological development where the bones form as part of the jaw before moving up into the skull. Or Jawbones themselves which form as gill arches which would have originally supported the gills of our fishy ancestors before being used to support the mouth and in time hinging so that the mouth could open and close.

Now, I’ve sort of just thrown out all of these mechanisms which have been observed in nature to select particular traits in some, suppress traits in others, but why? What use is saying that ‘natural selection isn’t the only mechanism’, what use is saying ‘Darwin didn’t know everything’, why say ‘evolution is not just natural selection’? Because it’s not. If we want to understand the world we live in then we need to understand all of it and as I believe I said last time, Darwin wasn’t a prophet, he didn’t know everything and it’s important to show that we’ve got somewhere in our understanding of life since him.

All of these mechanisms show how it’s not just about who lives or dies in evolution, it isn’t just ‘every man for himself’ sexual selection is just one form of selection that demonstrates a species can select itself towards particular traits. Humanity has selected towards traits that involve cooperation within a group (Intergroup competition still exists and has always existed of course) and this is something which defines humanity. Removing religion won’t remove humanity from humans (I would personally argue it would give us a bit more humanity but that’s an argument for another time). Evolution doesn’t mean that we are in a dog-eat-dog world, it means that those that die without leaving as many descendants as others will eventually be wiped from a population.

I will conclude with the point that humans are more in control of their environment than ever before and we can effectively decide to remove a lot of the natural selection from our populations should we wish, we can make sure that people don’t die off from other things. I, for one, would be very interested to see what would happen if humans decided to select for traits which reduced world suck and increased awesome. I mean, we could totally select for people who were good with genetics and get dinosaurs in space even sooner. I hope I didn’t ramble too far from the point, see you next week.

References

Potholer54: The car metaphor is a more in depth version of his metaphor from a video on evolution from his youtube channel (If I remember correctly at least).

On Technobabble in Evolutionary Theory Part 1

September 2, 2012 Leave a comment

There is a lot of confusion amongst a lot of people about what these terms actually mean so I’m going to present my interpretations of each term and why I’ve chosen those terms, I’m also going to use this as an opportunity to explain the various principles in evolutionary theory. Experts, remember, this is the basics, so if you see something you disagree with, first think “Is what I’ve said a good enough simplification for someone who doesn’t know so much as you?” then comment based on what you’ve thought, because, hey, I’m human, it’s possible (Probable or even likely, I would say) that I will make some errors.

So, without further ado, I will start with possibly the most contentious: Darwinism. Darwinism is often used as a synonym for the “theory of evolution by means of natural selection” which while being quite a mouthful, is often what is meant by “evolutionary theory” today which I would argue is much more accurate than Darwinism. Why do I think “Darwinism” is a bad synonym for “evolutionary theory”? Because Darwin wasn’t our prophet, he wasn’t infallible nor omniscient. He didn’t discover everything through revelation, he discovered it through ‘plain old boring’ thinking about it.

As evidence for this, I present “Things Darwin Didn’t Know About”:

  • Genetics: Gregor Mendel was a contemporary of Darwin, that is, he lived at the same time as Darwin and published his work in 1866 a full 16 years before Darwin finally kicked the bucket, however, Darwin never read his work. No-one even discovered the connection between Mendel and Darwin until the early 20th century.
  • The Age of the Earth: Dating the Earth to millions of years was typical for theorists in Darwin’s time, however, with the discovery of radiometric dating in 1905 by Ernest Rutherford expanded the age into billions of years before eventually giving us the current age of 4.54 ± 0.05 billion years.
  • The structure of the ‘tree of life’: Darwin didn’t know much about the relationships between species and groups of species. Indeed, in one of his earlier editions of “On the Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life” (Wonderful title) he hypothesised that a bear which swam through the water catching insects would be through natural selection transformed into a whale.

These principles, central to modern evolutionary theory, were at least in their infancy, and at worst, were completely misunderstood in Darwin’s time. Darwinism should effectively mean the original ideas theorised by Darwin and so does not represent current understanding in evolutionary theory.

Why is this important? Because it shows we’ve advanced since Darwin, that Darwin’s ideas weren’t accepted as dogma and then any dissenters were quickly ostracised by the scientific community. Evolutionary theory has been debated ever since the first ideas were put forward (There were several ideas concurrent to and even proceeding Darwin that suggested a mechanism for how diversity was generated in life, see Alfred Russel Wallace for an epic beard and a forgotten hero, also Lamarck who’s greatest contributions to science were not his blunders, see references below).

The problem for science in these debates was never about whether evolution occurred (See below for definition of evolution) but rather how it occurred. What effect does natural selection have? How much does genetic drift effect genetics of species? How fast does speciation occur? How important is extinction for the creation of new niches? Notice how none of these questions target the age of the earth, the permanence of species nor the fossil record? Creationists take note.

So, Darwin wasn’t perfect and therefore it’s important to separate out his ideas, the ones which began our modern evolutionary study from those that make up our current view. This also helps us to discuss controversy within science and the difference between debating an issue (Such as the effect of natural selection in evolution) and debating the fact of an issue (Whether evolution occurs).

Now, what is evolution then? If evolution isn’t Darwinism then what is evolution? Well what it isn’t is the theory of evolution nor evolutionary theory. Evolution on it’s own is the fact of evolution which is evidenced in the existence of fossils which are dated using radio-metric methods of all different sorts which are used depending on the condition of the rock. The fact of evolution is also evidenced by the studies of Grant and Grant on the Galapagos Finches, or the enormous amounts of studies done on fruit flies. Evolution, put simply, is the observed change in life as time has passed. The oldest rocks contain different animals and plants than younger rocks which are different again to modern flora and fauna.

But of course, if evolution is that, then what is the theory of evolution? Well to begin, you’d need to know the differences between theories, hypotheses, ideas, laws of nature, facts, et.c. but suffice to say that a theory is a body of tested ideas which explain facts. The theory of evolution explains how life has changed since it first emerged. It does not seek to explain the origin of life, the origin of the solar system, it is not the big bang theory, nor does it seek to disprove any god (Uncapitalised to point out all the gods that people think that word means.).

The theory of evolution is really the collection of tools we use to explain and demonstrate the way that life changes and has changed. The main tool that everyone knows about is of course, natural selection. To demonstrate natural selection, think about this:

A female weevil lays 300 eggs which mature in a month, roughly half of those weevils will be female, so 150 females in the next generation, each lays 300 eggs, that’s then 450000 weevils in two months, multiply that out after one year and there are nearly 260 septillion (260 followed by 24 zeros) weevils. If the weevils weigh 1g each, then the total mass of all the weevils would be equal to nearly half the mass of the earth (Earth mass = 5.97e24kg). Clearly, since we aren’t swimming in a sea of weevils, something is limiting them, preventing them from reaching this enormous mass.

Now, evolutionary theory, isn’t about what is limiting the weevils, but rather how the weevils are limited. The idea being that the limits on the weevils are selective, that is, weevils the best at being weevil-y will be better at resisting the factors which limit them. So, for example, the weevils I’m talking about are rice weevils (Sitophilus oryzae) and they live in enormous grain stores where there is a bit of an issue about how much oxygen they acquire, so, if a weevil is pretty good at living without much oxygen, they’ll do better in that environment.

However, this problem happens across the generations, it’s not just a problem for the current weevils, but also their descendants. So any benefit will only help the weevils as a whole survive if any resistance to low oxygen levels is heritable. If a weevil passes on it’s ability to use less oxygen then it’s descendants will be better equipped to survive than others.

This is just one mode for variation in a population to facilitate change (read: evolution). Hopefully you can see why this is such a big deal, to limit organisms in their way of life is the ground state for nature, things aren’t limitless and so animals will not all survive. This means that organisms will compete with each other for their ‘place’ in the population and their opportunity to reproduce. Then if the differences between the organisms can be passed on, then the populations will change over time.

This is all the basics of evolutionary change. This is what we use to understand biology today. Shocking it could be so simple. This post is getting pretty long now so I’ll cover other things in another post at some point. Things like sexual selection, the role of genes etc will be covered next time (If I ever do get around to carrying on this mini-series).

References

Lamarck: See Eight Little Piggies by Stephen J. Gould. In one essay (I forget which and don’t have my copy to hand) he discusses the misrepresentation of Lamarck. Though I know in the book he also discusses Goethe, Haley and Ussher as representatives of people who have been misrepresented by history.

Ideas: This essay is based heavily on my thoughts prompted by reading Scientists Confront Creationism: Intelligent Design and Beyond. Defining terms used in evolution is a topic discussed in a section of the book and it helped me to realise the issues surrounding lay readership of technical work. The use of differing terms confuses even experts (Not me, rather my lecturers when I ask them about issues in the literature) so the various terms will undoubtedly confuse anyone unacquainted with the literature.

A note on Wikipedia: I don’t know if I’ve mentioned my heavy use of Wikipedia references before but I think that in this blog a lay reference is fine and accessible for the interested reader who doesn’t want a long technical paper detailing the various arguments and counter-arguments presented by the expert.