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.

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.

Stoic Week – Running on fumes

November 30, 2013 Leave a comment

I’ve been blogging daily now for the whole of Stoic Week, some of my discussions (Marcus Aurelius joke here) I’m proud of and others… well, let’s just say I’m not expecting any blogging awards this year. I’ve come up short today. I have nothing to say about philanthropy that hasn’t been said already. Making up something important sounding to say just to fill space is not something I’m going to do. I’m not going to say anything if I don’t have anything interesting to say.

Suffice to say that I think that if everyone subscribed to stoic philanthropy, then it would be a wonderful philosophy but the fewer people who subscribe, the more difficult it will be for them. I suppose though, on the other hand, who cares how difficult it is when it’s the right thing to do. Damn, that’s almost important sounding.

Stoic Week – Sore Losers and Stoic Philosophy

November 29, 2013 Leave a comment

I am quite a sore loser. I’m not the worst sore loser I know (who shall remain nameless) but I do moan and sulk more than a grown human should. I get frustrated because I see myself as a great strategist and tactician so when the plans fail I feel as though my intelligence is being challenged, or ‘life is being unfair’.

Neither are things that actually happen when I lose a game but I still get frustrated by it. This is because we learn from our parents and my father is quick to anger, slow to apologise. I realise my mistakes and I also get frustrated by knowing when I’m acting as he does rather than acting as I should. So let’s look at my reactions from a Stoic Sage’s perspective: My feeling insulted by losing a game is the result of one of two things; either my strategy was beaten by a superior strategy, in which case my strategy wasn’t successful but I now know more about it’s weaknesses and the failure wasn’t fatal so I can always try again; or I was unlucky, in which case the random chance that resulted in my failure could easily have gone the other way and there’s no reason to be frustrated.

One reason I may feel frustration at my plans being foiled by those meddling kids might be because when I construct the plan in my mind, I assume success after success, nothing in my plan can possibly go wrong in my mind. This is of course ridiculous, so when planning I need to include contingencies for possible failures. Looking back on the computer game battle I lost on Sunday. The plan involved always hitting with mortars and that once a unit broke, that it wouldn’t regroup so when my mortars missed completely with a couple of barrages and the enemy cavalry unit regrouped, I felt frustrated and didn’t have a contingency ready. If I had included a second cavalry unit of my own, and an additional unit of infantry, I would have the additional men required to handle these failures.

This is what the Friday exercise seeks to get us to think about, sort of. Instead of having contingencies set up for when things go wrong, the exercise was about accepting the fact that things have gone wrong and not getting annoyed about things which I had no control over. So when the enemy cavalry regrouped and turned to charge into the fray, instead of being angry that this seemingly unlikely result happened, I would merely accept that it did and that it was beyond my control.

This stoicism can expand to other areas of our lives, apparently the original stoics used to contemplate their own deaths so that they could face it with stoicism. It was recommended we didn’t choose something so traumatic to begin with, but rather to build up to them beginning with small things that bother us. My sore loser attitude is, to my mind, the perfect example for this, it’s not supposed to be traumatic or a big deal in any way and so if I can work on accepting my losses in video games, I can build towards accepting my losses in day to day life, like that pile of rejection letters in my recycling bin.

Stoic Week – I think I think too much

November 28, 2013 Leave a comment

I have restarted this blog post. I was going to write it about how I was an unconscionable jerk and how I judge people as the impressions of them that I have, rather than as the person they are. I had to stop that, why? Because I found myself doing the everything-thing:

Yeah, I managed to, in my effort to realise that I shouldn’t be treating people as if they are the impressions I have of them, develop negative and unhealthy emotions regarding my decisions and desires. New start then, I think too much. This is a shorthand, if I were to type out my full meaning it would be the following:

I think a LOT and sometimes when I’m thinking, I start accepting my beliefs and impressions as truth and reality. I then ruminate on them further and decide that these facts shouldn’t be, I want to try to change things, I realise that only part of what I want to change is under my control and the parts that I do control, I think ‘I’m too lazy and stupid to do that’. I end up feeling impotent, wretched and pathetic.

There is a flipside, however, I noticed it happening and can now act against that sneaky hate spiral. Preventing these thoughts from causing further damage. I’m just going to pause here and take a moment to feel good about that.

Source: http://knowyourmeme.com/memes/a-winner-is-you

I never played this game.

It seems like there is a lot of advice for when external factors are affecting your emotions but not a lot about when your feelings get in the way of doing what is right. This sometimes is something which makes me do the everything thing because, maybe I’m just not that good person if I can’t be bothered to put in the effort to put in the extra effort required to be good. But I suppose the excuse is ‘I’m only human’ and that I can always try again tomorrow. As long as I keep trying, I suppose that is the difference between good and bad.

But then good and bad isn’t an inherent trait of a person, it’s more the evaluation of their effects over time and, as Sirius says “the world isn’t split into good people and death eaters, we all have both light and dark in us”. I think the important takeaway from today’s task for me is to stop thinking as if your thoughts are as valid as real data.

Stoic Week – On Arrogance

November 27, 2013 Leave a comment

This blog includes quite a ramble before I get to the point but…

Source: http://peachquilting.com/2012/09/27/bear-with-me/

Pun haters can take this with stoic acceptance.

I remember being called a boffin as a kid. I was labelled smart at a very young age, ha, starting school I was reading books other kids hadn’t heard of, or whose older brothers and sisters were reading. This isn’t a boast, it’s a complaint. I was labelled as intelligent and thought that this was something that I had, a trait like the colour of my hair.

Let’s skip the part where I develop the arrogance of a one-eyed man in the land of the blind and discuss the important part. My personality speaks of someone who is extremely rational. Something I hear a lot: “Hey James, you’re really rational.” Now, when something is repeated enough, whether or not it’s actually true, you start to believe it. I’m not saying I’m not clever, I think I am pretty clever, but the problem is a misunderstanding of why I’m intelligent.

This is the problem I have (re-)discovered through today’s lunch dinnertime exercise: In my arrogance I have not bothered to check my rationalism, or my ability to see the world as it truly is. The fact is that I am very arrogant and see myself as some lone genius who has a finger on the pulse of the big issues of the world. Haha no, fortunately, the rationalist inside of me, the one who got me labelled as a genius in the first place, knows that’s nonsense.

So, how the hell does this relate to accepting external things outside of my control? I’m getting there… honest. So, I grew up learning all of these wonderful things like what a mammal is, the planets in the solar system (and unlearning “Pluto is a planet”) and thought that knowing this stuff was the thing that made me intelligent. Then I found out that there are stupid people who know these supposedly ‘intelligent’ things.

Source: http://amandabauer.blogspot.co.uk/2011/03/ceres.html

P.S. James likes Ceres more too.

Then I found out that there are clever people who don’t know science (shout out to a lot of my university friends) but knew other things instead. I discovered I had been mixing two  things which we often confuse: intelligence and knowledge. Intelligence is the ability to use knowledge while knowledge is the accumulation of facts.

The world got a little more complicated for me. Now, finally, to the point when I was growing up, I had this hierarchy of people, my parents knew better than me, so did my teachers. Now I’m all grown up, I’m learning that this is really not the case and while they might have twenty years of experience on me, this makes them think that they know things beyond their experience. It also makes them likely to misunderstand a discussion.

Now here is where it relates to the Stoic Week task for today: I often get annoyed when being misunderstood, I often get annoyed when someone thinks something wrong, or doesn’t understand why something is wrong. This is my lack of stoic acceptance. I’m a very intelligent person (This is a boast) and a quite knowledgeable one too so facing the world as it is, in which there are people who don’t understand or don’t know the things that I do but this is beyond my control so there is no sense getting worked up by it.

And now, we’ve reached the conclusion of my waffle.

Stoic Week – I bought a packet of Pringles

November 26, 2013 Leave a comment

I like to think that I’m an austere person. I’m unemployed and live with my parents. I don’t have much money, I don’t have to spend much money so I don’t spend much money. I like to think this would make today’s topic of Self-Discipline and Stoic Simplicity a cake-walk. Unfortunately, being mindful of the force all of my actions means that I would have to say that the task is actually extremely difficult for me to succeed at.

To begin the day, I woke up late, as usual. I stay up late to try to make sure that I’ve done something with my day so I get up late and find that I’ve wasted half the day already. Which made the early morning afternoon reflection particularly poignant. But I didn’t get to it until after I returned from my appointment at the Job Centre. Unfortunately this trip resulted in my visiting the 99p store to buy some Pringles and sweets.

When I return home, I read about how the whole of today was supposed to be about Stoic Simplicity and letting go of external desire for health and wealth. I immediately thought of my lack of funds and how I was very good at not spending much money because I don’t have it. I concluded that I was doing well on this front.

Thinking further into it. I realised that my laziness and decision to buy tasty treats constituted  a fairly important failing of the stoic part of the simplicity. You see the difference between my austerity and the Stoic Simplicity I was meant to be striving for is that my austerity is controlled by the external pressures of economics and not by a self-discipline overcoming the desires I have.

I would suppose that the up side of this failing is that I realised it. It means that I am at least mindful of the reasoning behind my actions and how they are, or are not Stoic in nature. This is not me being stoic. This is me learning to be stoic.

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