Archive

Posts Tagged ‘complexity’

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.

Source: http://sprudge.com/saturday-sept-th-san-francisco-huge-block-party-with-coffee-bar-sf-and-scout-mob-plus-ribs.html

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.

Source: http://tangerinetravels.blogspot.co.uk/2011/02/am-reading-banana-fate-of-fruit-that.html

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.

Source: http://www.bioimages.org.uk/html/p7/p71469.php

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.

Advertisements

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.

Source: http://forum.phish.net/thread.php?thread=1375181970

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.

Source: http://aliceinwonderland.wikia.com/wiki/The_Dodo

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 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.

The Façade of Progress: A Personal Perspective

August 20, 2012 Leave a comment

Okay, so it’s ~13hrs late, sue me.

Bacteria –> Fish –> Amphibian –> Lizard –> Rat –> Monkey –> Human

As common a motif as any for evolution, this ladder (not the exact ordering or the creatures named but the concept at least) dates back to Ancient Greece (or at least so Wikipedia tells me :p *slaps wrist*). The idea basically being that animals are organised in a scale (The name for this ladder of life in latin was: Scala Naturae) from the least complex (bacteria) to the most and of course humans sit atop all because most complex life is best life.

But this view of life is terribly stunted in it’s vision, take for example these things, just take a look at the pictures and tell me, what is it? It’s actually a chordate, just like you and I, just like snakes, frogs, sharks, goldfish et.c., it’s a highly specialised version of one though and it’s like a barnacle in that it gives up the pelagic (Open sea) life to live attached to a rock and filtering out their food from the water around them.

These animals are perfectly suited to their environment, you are suited to yours, despite your supposedly ‘more’ evolved complex form, you could not possibly hope to survive doing what the barnacle or sea squirt does; neither, importantly, could their ancestors, the ancestor of the barnacle is also the ancestor of shrimp, crabs and lobsters so it’s best to think of a generic (pun intended (nested brackets for those who don’t get it, look up taxonomy and think about specific and general as words)) sort of crustacean. Despite the barnacle and sea squirt each losing features and simplifying down to a seemingly more basal form, they are in fact more evolved than their ancestors and far better adapted to their environments than their more complex cousins.

This concept is a general fallacy built into our minds or at least ingrained at a young age, I know of a time when I saw progress as the way things must be. When I was a child I was always told to ‘cheer up’ and to ‘smile more’ that ‘things will get better’. Despite there being nothing wrong really, I got bullied a little, but I think it’s just how things are at school. Most people are bullied. I should say that doesn’t mean that bullying is justifiable, what I mean is that my bullying was slight and no more than I would expect of being smarter than literally everyone at your school; I was before I moved to a different area where I was much closer to the mean and when I was bullied there, well I was the new kid and everyone had known each other since they could remember, I was an outsider and a weird one at that.

I took this general theme and applied it to evolution myself in my GCSE Graphics project where I re-designed monopoly into a game of evolution, though, really it was a Scala Naturae game and it didn’t really make evolution work how it was supposed to, a bit like another game I know about.

ANYWAY, putting my past where it belongs, the point I’m trying to make is that I was told that things would get better and that matched up with a general trend where we think that things are improving and getting better, I think this is a trend which began back in the ’60s with world wars and depression receding into the distance, science improving and young and exciting new culture being developed, everyone breathed a collective sigh of relief and it seemed things were going to be getting better, follow this up with the ’90s and ’00s of my own life and we’ve seen the internet take off, we’ve seen the fall of the Berlin Wall, and the end of the Soviet Union, these events have given us a sort of ‘things can only get better’ view, one popularised by Brian Cox no less.

This view seems to make the assumption that what must be true of science must be true for the history of things science has discovered, that since science has increased knowledge, improved technology, therefore, stuff should be getting better throughout the world. But just because we have managed to improve our human lives does not mean that on the geologic time scale, things must conform to the same rule.

Combine this with the radiation of groups of organisms as they diversified through time and it gives you a sense that most things around today showed up a long time ago and that was it, they never changed. Hence the old anti-evolutionist cry of “Well if we evolved from monkeys, why are there still monkeys?!” of course there’s more to it than that but putting on a sense of progress from when we evolved through to today gives credence to that old battlecry, if they were to understand that monkeys didn’t STOP evolving when the ape branch split off from them they’d be able to understand why monkeys are a far more successful branch than apes are (Compare number of species between Cercopithecoidea and the Hominidae, it’s clear which is the healthier bush*.

Finally, I’d like to say HEY look at me, I managed to get another post done in a consecutive week (sort of), let’s hope I manage to get a third one, and a fourth and so on until my posts number as many as the intermediate fossils between me and my most distant ancestor.

* Note: The Cercopithecoidea only include the Old World Monkeys of Asia, Africa and Europe, not the New World Monkeys so by that measure, Hominidae are even worse. (Taxonomists read on: I know, the New World Monkeys and Old World Monkeys as a group excluding the Great Apes is a paraphyletic group but shush, baby steps for people who don’t know as much as you, that is, people like me)

References

This essay was inspired by my recent reading of Stephen J. Gould’s book Eight Little Piggies along with some other books of his that I’ve read, I’m probably just repeating what he’s said in a less eloquent voice but hey, I think I’m getting better? No, okay then.