Goodbye for now

Hello everyone - it's been a good ride. I intend to pick up this blog again in future when I have more time on my hands, but thank you for all your time and comments. I have thoroughly enjoyed writing here and I've learnt a lot, and I hope you all have as well (Or else I haven't done a very good job!). I'd like to leave you with one closing thought, or ramble as it may turn out to be.

Should we be optimistic? In writing this blog, I think I've definitely made more negative conclusions than I have positive. Whilst some of the facts and figures I, and many of my colleagues, have come across and written about are pretty sobering, I feel that it is important to maintain some kind of positive outlook, as hard as it may be. Yes, probably some things are set in stone from the emissions, chemicals and otherwise that are already in the earth systems but unless we try to fight to stop anything else being written off, the black list of species is going to be a lot longer. That fight is a hell of a lot easier if we don't give up, and that attitude needs to grow and extend beyond the reaches of academia.

As I've emphasised in many of my posts there is a relationship between society and the media and the sciences that we are wise not to ignore. Personally, I feel that there should be a dialogue between the public and academics and that those of us who have been privileged enough to learn have a responsibility to communicate some of these ideas to everyone else. In fact, I think this is an essential part of how we should approach global environmental issues such as climate change, mass extinctions and the rest of it. The interface between science and society is now more important than ever and I hope through this blog I have done (some of) my part in bridging that gap.

Thank you!

Thank you everyone!; Source.

Estimating Extinction

The extinction of a species can be a difficult thing to precisely pinpoint in the fossil record. Beyond recent history, extinction is not something we can directly observe. Some species may survive after our last known record of them, and we have no way of knowing how long. There might be instances where, for whatever reason, no remains of that species were preserved or simply instances where the remains have been lost through tectonic movements. Some remains might still be waiting for us to stumble upon them, given that there is a considerable geographic bias in palaeontological research. 

Extinction is actually something we have gotten wrong in the past. For years, it was thought that coelacanths went extinct in the End-Cretaceous mass extinction 65 million years ago. In 1938, a living coelacanth was found in the western Indian Ocean and although it was a distinct species from the fossil variants, it was anatomically very similar and what is called a "living fossil". "Living fossils" are species that are, mostly superficially, morphologically similar to their extinct ancestors and are thought (wrongly) to have undergone little to no evolutionary change. Whilst these species may retain the plesiomorphic phenotypical states, it does not mean they are not still evolving and palaeontologists dislike the misleading using of the term in pop-sci press. Another species of coelacanth was discovered in South East Asia in 1997, cementing the idea that we were wrong, both about its apparent extinction and also its static evolution. Whilst this doesn't happen very often, it begs the question, what if we're wrong about other organisms?

The Coelacanth, a "living fossil"; Source.

Two mockumentaries (fake documentaries) aired by the Discovery Channel over the last year or so attempt to answer exactly that question. The focus of the two programmes was the Megalodon, a gigantic shark which patrolled the seas between 15.9 - 2.6 million years ago. These are interesting programmes, but do have a tendency to spread misinformation, with 73% of viewers thinking that the Megalodon is still roaming our oceans. Many actual scientists, as oppose to the actors posing as scientists in the programme, were unhappy about the misrepresentation of palaeontological research, calling Discovery Channel "the rotting carcass of science on TV". Others, however, created a positive outcomes from the documentaries and worked on more robust mechanisms of estimating the extinction of the Megalodon, if only to put the rumours to bed once and for all. The authors, novelly, utilised a method that had previously been used to estimate the extinction of more modern species, such as the dodo. The method, a model called Optimal Linear Estimation (OLE), infers time to extinction from the temporal distribution of species sightings, or in the case, fossil instances. This method may not be applicable to all fossil taxa, but is an excellent step in out-of-the-box thinking towards a better extinction estimations.

I wasn't joking about them being big; Source.

Extinction is something we should be aware of and it can be a great tool to provoke changes in peoples outlook on human activity. Whilst "lazarus taxa", "living fossils" and the rest of it make for great sci-fi, their place in actual science should be profoundly separate from this.

De-Extinction: Return of the Endlings?

This blog has looked at the extinction and extirpation of many species and admittedly, has been fairly pessimistic. However, it has yet to consider the growing phenomenon of 'de-extinction', perhaps there is room for a little optimism? Is this a realistic approach to conservation or is it a load of Jurassic Park wannabe nonsense? The idea based on using preserved or "ancient" DNA from several individuals of an extinct species and creating clones of each of them, we would be able to create a new and viable population of that species. There are cryo-zoos, such as the one in San Diego, which store frozen DNA of extinct species with the potential to form these clones. Much of the attention given to, and work within, de-extinction focuses on this cloning aspect, but other researchers have attempted to work through selectively back breeding a species from its genetically similar living descendants.

De-extinction efforts have already been made for many species that we have seen recent endlings of, such as the passenger pigeon, the Pyrenean ibex and the Tasmanian tiger, whereas some scientists are working on much older animals such as the woolly mammoth. However, 60,000 years is effectively the age limit for use of DNA, so dinosaurs won't be happening any time soon. The first de-extinction in history was the Pyrenean ibex, which was done in 2009 by creating a clone egg using the DNA of Celia, the (formerly) last ibex, which was taken shortly before she died in 2000. Unfortunately, the ibex was short lived and died within 10 minutes but scientists are planning to reattempt when cloning techniques have improved. This attempt, in itself, was an improvement on previous attempts in 2003 which had failed to produce an egg capable of surviving the full gestation period. Significant progress has also been made for the passenger pigeon, where DNA has been preserved in museum specimens. Unfortunately the DNA of these specimens is contaminated and fragmented due to the way they have been preserved and kept, as oppose to the ibex DNA which was stored in liquid nitrogen. However, it is still possible to reconstruct the genome by synthetic hybridisation of the DNA fragments with the genome of its closest living relative, the band tailed pigeon, which scientists are currently working on. This would then be used to create cells which contain passenger pigeon genes, which would then be injected into band-pigeon embryo with the goal to create a band pigeon which lays passenger pigeon eggs and acts a surrogate parent for it.

National Geographic cover of de-extinction issue; Source.

Since 2013, a team of scientists from South Korea and Russia have been working on the de-extinction of woolly mammoths.  There have been difficulties as although mammoths have been found well preserved, their DNA has not been intact enough to produce viable embryos for a clone based de-extinction. Alternatively, a second method has been investigated which involves the artificial insemination of elephant eggs with preserved woolly mammoth sperm. The elephant-mammoth hybrid offspring would be able to be cross-bred over several generations to produce near pure mammoths. Again, this has been unsuccessfully due to mammal sperm cells lose their potency after over 15 years in freezing. The major problem has been finding usable DNA, blood recovered from the 2013 carcass provides an apparently good chance of successful cloning - we will have to wait and see. Others are pursuing different routes to restoring the mammoth, Harvard geneticists are working on migrating components of the mammoth genome into the Asian elephant genome in order to create viable hybrids. Adrian Lister, a renowned mammoth expert, highlighted that there is a lack of suitable habitat remaining for any resurrected mammoths and that, as highly social animals, they would suffer from existing in very small numbers. However, a Pleistocene rewilding experiment known as 'Pleistocene Park' (not joking), could provide refuge for the mammoths and would also benefit from the grazing herd behaviours in recreation of steppe. Interestingly, Pleistocene Park also aims to prove that it was not climate change but over-hunting and other human interferences that lead to the disappearances of these grasslands and associated species during the Pleistocene. This could be a exciting new evidence in the debate surrounding the Pleistocene megafaunal extinctions.

Pleistocene Park in Siberia; Source.

As mentioned earlier, selective back-breeding from the closest living relatives of animals is another option for potential de-extinctions. This is being done for aurochs in Europe, based on genetic material taken from bone and teeth fragements. The last European aurochs were lost in 1627 after a long history of over-hunting and exploitation, but their descendants (most modern cattle breeds) are abundant throughout Europe. The genetic material provides a goal, so that cattle can be bred to try and reach as close to the original aurochs as possible, both phenotypically and genotypically. Early attempts resulted in the created of a new breed, Heck cattle, which are at best vague-lookalikes. Currently there are two projects, the TaurOs Project and the Uruz Project, which are competing to resurrect a true, or atleast very close to, aurochs within the next 20 years. Earlier this year, it was proposed that there could be the potential to bring back Lonesome George, or at least a genetically very similar species, by a breeding programme rather than cloning. Even if the animals themselves are clones, captive breeding, which has proved successful in many conservation efforts, will be a major part of de-extinction.

So, whilst it seems that de-extinction is scientifically possible, the bigger question is rather, should we actually be doing this? Proponents of de-extinction such as Stewart Brand would argue that we have the ability and the moral obligation to repair the damage we have done, so there is no excuse not to. Others such as Adrian Lister would say that efforts and resources should be focused on conserving currently endangered extant species. The lack of suitable habitat is also a concern for many species. I feel that whilst there is certainly value and appeal in resurrecting species and "righting our wrongs", it must be done carefully and must not detract the need for conservation efforts to currently endangered species. This is not an alternative to conservation. This is an unfortunate second best to not having lost the species in the first place.

Worrying Predictions for the Amazon

Earlier in the week, a massive review paper was published by 170 authors from 102 affiliated institutions. The paper estimates and assesses the extinction risk of over 15,000 Amazonian tree species and produced the fairly alarming figure that 57% of them qualify as globally threatened under IUCN Red List criteria. Furthermore, they predict that the trends observed in Amazonia apply to tree throughout all tropical biomes and that likely over 40,000 tropical tree species worldwide would  qualify as globally threatened on the same criteria. The study has gained quite a bit of media attention for its 'shocking' claims that over half of Amazon tree species are going extinct, including coverage in mainstream news outlets such as the BBC and The Guardian. As we discussed in Part 3 of the 6th Mass Extinction, this can be an important way of communicating the severity of anthropogenic extinctions to the public.

Closer examination of the paper, however, reveals that some of its claims are not quite as dramatic or eye-catching as the media would make out. The 57% figure comes from Business as Usual (BAU) scenario which estimates that by 2050 40% of the original Amazon forest will be destroyed. BAU is commonly considered "worst-case-scenario" in environmental models, so we cannot take this as what will happen. An improved governance scenario (IGS), which estimates forest loss by 2050 at 21%, suggests that only 36% of species will be threatened. This is perhaps a more realistic (hopefully) estimation, as we know that governments and international bodies are working towards improving management and conservation of tropical ecosystems.

Results of the new study, showing the severity of a BAU scenario; Source.

Importantly, the paper highlights the urgency with which we need to address these projected losses in order for them to be prevented. It shows that protected areas in the Amazon are likely to be a successful way to protect populations if these areas to do not suffer further degradation. Clearly, improved governance has the potential to reduce species loss dramatically within the next 35 years, and this paper and the message it carries has come just in time to help highlight this at the COP21 later this week.

Are We Mass Murderers? Earth's 6th Mass Extinction - Part 3: Implications

The third and final entry in my discussion on whether or not we are entering a 6th mass extinction event. In this post, having got all the complicated stuff out the way, I will be discussing the societal implications of the 6th Mass Extinction as a concept and also the message we need to be taking away from this research, regardless of a definitive 'yes' or 'no' answer to the question. I hope you've enjoyed the journey and I would be really interested to know if your opinion on the 6th MEE has changed throughout it, let me know in the comments :)

If you missed them, check out Part 1 and Part 2!

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The results of the poll that you, my lovely readers, have been partaking in over the last few weeks show that really, we're all a bit confused about what's going on but we know it's something significant. To be fair, I think that quite adequately sums up how the academic community feel as well. There are a lot of big unknowns and uncertainties in the data, as discussed in the previous post, which have led to a lack of definite answers about extinction rates and extinction magnitude. Some of this can be improved by collecting more data on currently understudied groups, especially invertebrates - reminder that only 1% of bivalves have been assessed by the IUCN! However, there are many, many unsolvable issues with fossil data as every good palaeontologist knows, we can extrapolate and model and adjust for bias to our hearts content, but there are some species we will never know about and we will never know exactly what happened to them and their relatives. There are inherent problems with comparing data gathered in completely different ways and from animals in different states of existence, so perhaps the question is simply one we cannot easily answer. I pose a new question to you - does this actually matter? Does it matter that current extinction rates don't quite fit with the technical definitions of a mass extinction? We are well aware from the data of the abnormality of current extinction rates in comparison to natural variability through time, and well aware that we hold the majority of the blame for this. Do we need a dramatic title for it?

Your votes! Homegrown data.

In some ways, the answer is yes. It's a kind of depressing yes. If you Google "6th Mass Extinction", you will be greeted by a plethora of sensationalist news articles claiming that the 6th MEE has begun , and more importantly, will humans survive it?! Humans tend to care more about things when humans are involved, as we have demonstrated time and time again throughout history. If we look in the comments on some of these articles, readers actually don't seem to be getting the message that we need to change our collective behaviours. See the enlightened comment below from a Daily Mail reader, sporting the 2nd highest amount of up votes on the article:

"Whatever changes the climate may experience, the consequences will pale into insignificance compared to the catastrophe resulting from massive unrestrained population growth in the developing world. Open borders will make this our problem too"

Bringing it back to humans, with a hint of UKIP. Daily Mail readers aside, if you ask anyone in the street, they would probably say that of course they are aware of humans causing extinctions, but do they understand the extent of the problem? Probably not. Education, if you can call it that, through sensationalism is one way to get the message to the wider public. However, as the above shows, we need to be doing this in a more effective way. If scientists did agree on a technically defined or supported 6th MEE, then perhaps it could be something that got more serious journalistic attention and much needed political attention. Social scientists have suggested that "inadvertant envrionmentalism" is the way forward, as often there is a gap between our values, however sincere, and our actions. They advocate that government policies, such as limiting deforestation in this instance, as they have the power to change behaviours without the need for values. This is one way in which mainstream attention to a dramatically definite 6th MEE has the power to help. If we want to be more optimistic and think about changing values via awareness, Racing Extinction and the #StartWith1Thing campaign is great example that again relies on the sensationalism associated with the 6th MME (The working title of the film was 6!).

Sensationalist and melodramatic representation of the 6th MEE, could it be useful?; Source.

In others, the answer is no. In light of the sheer numbers of species lost, and the potential there is for that to increase in coming years, what we need to be thinking about are urgent conservation measures. As multiple papers have highlighted, the extinction rates and magnitude is likely to increase as years, and harmful anthropogenic practices, continue. In particular, Barnosky et al. highlight the destructive potential  for synergy between co-occurring environmental factors such as atmospheric composition and unusual climate dynamics, similar to how co-occurrences of bolide impacts and flood basalt volcanism have interacted dangerously in the past. Without mitigation of these unnatural factors, particuarly pollution and CO2 levels, extreme ecological stresses will be placed upon most living species, especially given the feedback of individual stressors. Ceballos et al. point out that, in human timescales, the loss of these species and the ecosystems services they provide would be effectively permanent. They argue, as do Barnosky et al, that avoiding a biodiversity crisis (regardless of what it may be called) requires rapid and greatly intensified efforts to alleviate pressures on endangered species and protect them from exploitation. Many of the pressures are intrinsicly related to population growth and economic inequalities, and have the potential to threaten humans alongside other species.

Are we going to run ourselves into the ground? Let me know your thoughts in the comments!; Source.

In summary, it is debatable whether or not the 6th Mass Extinction being confirmed matters, but there is one thing that isn't debatable, and I will leave this as a closing thought for you:

The window of opportunity to act is rapidly closing and with the COP21 talks starting in under a week, it is imperative that we are mindful of the extent to which we have affected global biodiversity and will continue do whilst CO2 levels continue to rise and corporate greed is placed above moral concerns.