Posts Tagged ‘Evolution’

Resurrection Biology Part 2: On Mammoth Steak and Coral Reefs.

January 26, 2014 Leave a comment

It seems there is a larger conversation to be had about the notion of resurrection biology. A friend of mine and I had that conversation after I posted up my last blog post. I thought it was that fun that I would do a follow up post on my thoughts regarding two issues he raised in that conversation: resurrection biology for food production and ecological services.

Food Production

The whole reason for this section is this comment:

Another potential use of resurrection biology which I think most people would object to is farming; imagine mammoth farms, admittedly their natural behaviour wouldn’t be as great, their habitats altered, but considering how many farm animals have been altered and placed into habitats we have designed it does seem a viable option for extinct edible megafauna. – Washington Irving

I don’t think I need to tell you that the human population is growing, I hope it’s also self-evident that the population increase has sped up over time. To demonstrate, the time it took to go from 1 billion to 2 billion was 123 years (according to United States Census Bureau (USCB) data) while the time from 6 to 7 billion was 12 years (again, USCB data) and it’s estimated we’ll pass 8 billion by another 16 years (you guessed it, USCB data). This last one actually surprised me but it seems that we’re living in an age in which, due to an ageing population and an increased life expectancy for children and infants, the rate of growth is finally sloping off. All these extra people need a place to live and food to eat so, maybe if we resurrected extinct species they’ll provide the food we’ll need?

I would be inclined to think not and here’s why: First off, you have to actually make a population of organisms from scratch, which is no small task, take a look at conservation and reintroduction efforts across the globe and how much effort has been put into these programmes to see why this is difficult. Secondly, we would be producing food from an organism that, potentially, no human has eaten before so there would necessarily be testing required to see if this food is a healthy alternative to currently farmed species. This is closely related to another point, the fact that these foods would fall under the domain of Genetically Modified Food and here we open a hornet’s nest of political debate on the nature and safety of GM food which I’m not going to wade into here, except to say that it would make some people hesitant to buy into the new food source.

The example species Wash gave for the possibility of farming extinct species was farming Mammoth for steaks. Unfortunately, this is a terrible example for the potential of resurrected farm animals. Mammoth are close relatives of Elephants and as such we can say with a level of certainty that they would be long lived, slow to grow and, what is called k selected which essentially just means that they have relatively small numbers of children, perhaps one at a time which are then cared for by parents or members of a group; the opposite is r selection which is where many offspring are born all at once and are typically abandoned to fend for themselves.


Unfortunately, this might not be feasible.

What this means is that it might take a decade to grow the initial population of mammoth to adulthood and then you’d need to leave many of them alive to produce the next population. Mammoths would also require huge tracks of land to maintain their population with tonnes and tonnes of grass every day. So there are quite a few problems I can see, my final problem is that the economic costs are really quite high given the genetic meddling needed, the set up of the population et c. but are there any cases which would be suitable for resurrection farming.

Now to raise a point I didn’t realise until I started typing up this post which is the fact that we don’t even need to resurrect extinct megafauna to farm, we could equally easily resurrect extinct plants, or fungi, or yeast or any living thing which we have records of their genetic material (Mesozoic organisms are apparently too old for this, sorry Jurassic Park). It’s possible we could develop an extinct species with higher yields than current farmed species, or with different nutritional benefits. It seems to me that the possibilities here are basically the same as with the genetically modified crops which we are already developing and that extinct species won’t really add anything to their potential.

There is one example that I’d mention for it’s possibilities, which is the Gros Michel, this is a banana variety which was used until the 1950’s when it was devastated by a fungal infection which spread extremely rapidly due to the low genetic diversity of the variety. Everyone switched to the Cavendish cultivar and now the only legacy left is the banana flavouring which is still the same as when it was developed to taste like the Gros Michel. The possibility of bringing back species or cultivars devastated by diseases gives hope to the extremely homogenous cultivars used today, because were they wiped out, it might be possible to resurrect them based on this technology.


Spot the difference.

Ecological services

The other half of our conversation was on the potential to help with problems caused by extinctions, such as the destruction of species which provide what are called ecological services. Ecological services are basically things which species naturally do, which benefit human society, the canonical example being bees pollinating flowers of crops but there are other, more subtle ecological benefits such as the protection forests provide against flooding.

So what if there are species which used to exist which was better at providing some ecological services than current ones, perhaps there is an extinct species of tree with roots particularly adept at drawing up the water during floods but does not dry out the soil too much when water isn’t quite so abundant. Conditions on this planet has varied so much that it’s entirely possible such species have existed.

The difficulty I see with this plan is that you first need to resurrect the species and then see how it would interact with an ecosystem before introducing it. This would mirror the process already used to determine if biological control agents introduced into new environments would potentially become invasive and harm the ecosystem more than it would help. So given the added cost of trying to create a viable population, nearly, from scratch you then have to make sure you’ve not resurrected a species which is going to oust other members of the ecosystem you intended to fix.


Imagine the Harlequin Ladybird was extinct and we thought we’d reintroduce it to control aphid populations.

The final point I think which would probably be raised first by others, again it is quite Jurassic Park: The species went extinct for a reason, maybe it should have stayed that way. While I don’t personally believe in a grand plan for evolution, I could modify this argument to the notion that the environmental changes which caused the species’ extinction in the first place could still be in effect and so the species would be doomed to extinction all over again. This would be my response to my friends comment:

I think it depends also how you would re-introduce extinct species, as some are able to readjust to natural settings after human interaction. I’m thinking more along the lines of coral reef communities where some species will go extinct and if these can be resurrected it’d be extremely useful, even if it is in potential new habitats due to warmer oceans… – Washington Irving

It’s possible we could reintroduce species such as those coral reefs which Washington mentions but the result could be another extinction all over again. Even if we got everything right, we cannot be sure that the species would provide the ecological services we want and that they would not be destroyed by some process, whether artificial or natural.

In the end, the only use I can see for resurrection biology is for the purpose of maintaining species which already exist as Washington says:

I’ve wondered at times how species could be integrated into existing areas, and the only result I see is that the competition negatively effects the previous community. […] I still think that resurrection biology would have a potential use primarily for helping current species with low populations and natural behaviours which are known be able to recover or even to try and mitigate losses from global warming and ocean acidification events. – Washington Irving

If we can maintain the species which are at risk today, that is the best outcome for resurrection biology. We aren’t here to fix the world, the world isn’t broken, the problem is that it may become just a little less interesting if we allow processes currently shaping our world to continue along their path.

Resurrection Biology and Behavioural Ecology

January 26, 2014 8 comments

To begin with, I think it would be best to ensure that you know what the hell resurrection biology and behavioural ecology mean before we move onto why this is interesting and important. So, resurrection biology is the notion that we can create a real-life Jurassic Park of extinct animals, or reintroduce extinct animals to an ecosystem by reconstructing their genetic code and then incubating the resulting egg in a related organism. Behavioural ecology is the study of what animals do and why they do it, instead of asking ‘does an animal have horns?’ it asks ‘what do the horns do?’ and this question may have different answers for different organisms, for some it might be defence against predators while for others it might purely be to display the health and vitality of the animal.

Now, why are these two fields important to each other? Well, it has been suggested that we might be able to reintroduce, for example, dodos, woolly mammoths or thylacines (Tasmanian Wolves) to their old ranges. It comes up in the news every now and then and every time it is, they rarely discuss the ecological implications of such a reintroduction could cause, at least that is my faint impression from the back of my hermit’s cave.


Imagine these guys roaming across Russia, Northern Europe and Canada.

First off, let’s talk reintroductions of endangered species. Endangered species are notorious for causing problems for people trying to help them survive. The image of giant pandas stubbornly refusing to mate comes to mind. A study by Jule, Leaver and Lea entitled “The Effects of Captive Experience on Reintroduction Survival in Carnivores: A Review and Analysis” found

the results of the ANOVA show that wild-caught carnivores survived significantly more (53%) than captive-born carnivores (32%), F(1,4.66) = 17.697, p = 0.01.

For the uninitiated, this means that animals caught from the wild and introduced to an area where they had been wiped out were nearly twice as likely to survive as those born in the zoo. Now, this is a very good example study to illustrate my point, which is raised probably more eloquently in the paper, that the behavioural ecological differences such as confidence near humans, feeding behaviours et c. (Though it is very important to point out that the paper did not look into these differences, doubtless due to the lack of data available on this matter) can potentially have a major impact on the survivability of an animal being reintroduced into habitat. And these are animals which are still alive and so have parental guides to how they should act!

Imagine a dodo, now imagine all the things it does in a lifetime, are you sure your imagination is entirely accurate? This is the behavioural ecological problem for resurrection biology: we don’t know how to create the environment which a dodo would develop in so would we actually make a dodo? This point is pretty Jurassic Park, I cannot find the quote online but I believe Dr Alan Grant, in Jurassic Park 3, says something to the effect of “the genetic creations of InGen are not dinosaurs, the last dinosaurs died out 65 million years ago” and while this is not entirely accurate, many dinosaurs continue to thrive today, it’s just that they are covered in feathers and restricted to the dinosaurian group Aves, the birds.


Ok, so maybe they didn’t smoke pipes and wear waistcoats and wigs, but we cannot be sure of other, less stupid, behaviours that the dodo may have performed.

Getting back on the point, behavioural plasticity within a species is quite high, especially in birds and mammals. I would provide definitive evidence for this point but I don’t know that a study exists which has looked at the plasticity of development in large groups of animals and found this. It’s more of a theoretical argument which, while not as good as a study, is a starting point. Feel free to complain to me that my hypothesis is inaccurate because X, Y, Z. So my reasoning for increased behavioural plasticity in mammals and birds is the fact that there are many and varied studies on many different species of bird and mammal which showed their ability to learn and adapt their behaviours according to the requirements of their environment. The reasoning for the behavioural plasticity of all animals is that it seems far more likely that every species will have at least one epigenetic process involved in their development and thus plasticity in final form. I hope this reasoning is strong enough to stand on its own until some concrete evidence is found to swing the facts one way or the other*.

To move on, the ecosystem which an extinct animal used to be a part of may not exist any more, many species that have been pushed to extinction by humans, went extinct because of habitat loss. Here I would say that the link is difficult to establish so once again, this is me armchair ecologising (Totally a word). But it is reasonable given what Brooks et al. point out about biodiviersity hotspots in their abstract:

Nearly half the world’s vascular plants and one-third of terrestrial vertebrates are endemic to 25 “hotspots” of biodiversity, each of which has at least 1500 endemic plant species. None of these hotspots have more than one-third of their pristine habitat remaining. Historically, they covered 12% of the land’s surface, but today their intact habitat covers only 1.4% of the land.

To understand this, endemic means ‘only found there’ so, for example, kangaroos are endemic to Australia. Biodiversity is a measure of how many different types of organism are in a particular place, so a rainforest is more diverse than an ice floe. Look at it this way, hotspots of biodiversity are like cities full of different people and if we destroy a city, we kill many more unique individuals than if we destroyed a farming community. Even before we made the mass migration into cities during the Industrial Revolution, even though most people would live in a farming community, because they are so diffuse, less people would die if the same area of farmland were destroyed compared to a city.

So the lack of good habitat would make reviving a species a mute point, not to mention that the lack of habitat might mean that symbioses, predator-prey relations, parasite-host interactions and so on that were present in the animals’ original ecosystem that the animal would not survive in an equivalent ecosystem, such as moving an Orangutan into the Amazon.

To conclude, I would point out that my career in behavioural ecology is probably not even in its infancy, it’s gestating still, and these are the problems I could rattle off. Perhaps given a more skilled or experienced mind, a brighter mind, there are even more issues which could arise for the field of resurrection biology from behavioural ecology.

I hope this hasn’t been too boring for my first post of 2014 and that it gives someone, somewhere a few fun and interesting things to think about, if it has, let me know, if it hasn’t, let me know, feedback is how I can make this blog something worth reading.

*Just a note to say that my suggestion in this paragraph is exactly that, it is a suggestion, it is not a theory, theories require evidence and testing and a whole bunch people doing their utmost to tear it down, and then failing. Theoretical does not mean theory, it means that based on my understanding of how the system works, this may be true; theoretical work is based on theories and experimental work is based on theoretical work.

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 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.


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).


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.