I just noticed that links to my old lab server, zeus.calacademy.org, are no longer being forwarded to updated links. I really can’t go through many years of broken links and fix them all in past posts, but I will list the main page here, which is simply my staff web page at the California Academy of Sciences. Here it is
We have a new paper on paleo-food web dynamics in the Journal of Vertebrate Paleontology! The paper is one in a collection of 13 (and 27 authors), all focused on the “Vertebrate and Climatic Evolution in the Triassic Rift Basins of Tanzania and Zambia”. The collection covers work done in the Luangwa and Ruhuhu Basins of Zambia and Tanzania, surveying the vertebrates who lived there during the Middle Triassic, approximately 245 million years ago (mya). This is a very interesting period in the Earth’s history, being only a few million years after the devastating end Permian mass extinction (251 mya). They are also very interesting places, capturing some of our earliest evidence of the rise of the reptilian groups which would go on to dominate the terrestrial environment for the next 179 million years. The evidence includes Teleocrater, one of the earliest members of the evolutionary group that includes dinosaurs and modern birds.
Our paper, “Comparative Ecological Dynamics Of Permian-Triassic Communities From The Karoo, Luangwa And Ruhuhu Basins Of Southern Africa” is exactly that, a comparison of the ecological communities of southern Africa before, during and after the mass extinction. Most of our knowledge of how the terrestrial world was affected by, and recovered from the mass extinction comes for extensive work on the excellent fossil record in the Karoo Basin of South Africa, but that leaves us wondering how applicable that knowledge is to the rest of the world. We therefore set out to discover how similar or varied the ecosystems were over this large region, comparing both the functional structures (what were the ecological roles and ecosystem functions) and modeling ecological dynamics across the relevant times and spaces of southern Africa. We discovered that during the late Permian, before the extinction, the three regions (South Africa, Tanzania, Zambia) were very similar. In the years leading up to the extinction, however, communities in South Africa were changing, becoming more robust to disturbances, but the change seemed slower to happen further to the north. The record becomes silent during the mass extinction, and for millions of years afterward, but when it does pick up again in the Middle Triassic of Tanzania, the communities in South Africa and Tanzania are quite distinct in their composition. The ecosystem in South Africa was dominated by amphibians and ancient relatives of ours, whereas to the north we see the earliest evidence of the coming Age of Reptiles. Yet, and this is where modeling can become so cool, the two systems seemed to function quite similarly. We believe that this a result of how the regions recovered from the mass extinction. Evolutionarily, they took divergent paths, but the organization of new ecosystems under the conditions which prevailed after the mass extinction lead to two different sets of evolutionary players, in two different geographic regions, playing the same ecological game. As we say in the paper, “This implies that ecological recovery of the communities in both areas proceeded in a similar way, despite the different identities of the taxa involved, corroborating our hypothesis that there are taxon-independent norms of community assembly.”
“There is no royal road to science, and only those who do not dread the fatiguing climb of its steep paths have a chance of gaining its luminous summits.” Karl Marx
I have been thinking a lot lately about the state of science and its relationship to the rest of modern society. One of the most concerning issues, from my perspective, is a willingness of the part of many to use “incomplete” science to support particular viewpoints. By “incomplete”, I mean adopting and expressing a statement with either the belief or assertion that there is a substantial amount of supportive science, whereas in fact the opposite in true.There are no substitutes in science for patience, persistence, and rigour. Science is hard work, and it is fundamentally important to our society. Short cuts are not allowed.
As an example: denying that human-driven climate change is occurring, would NOT fall into this category. Denial is simple, and often willful ignorance. Arguing that the number of current deadly military conflicts has increased globally because of climate change, WOULD fall into this category. The latter is an intriguing hypothesis, but the jury is still out and we simply should not abandon other hypotheses in favour of this one. That would be dangerous.
This is something that bothered me a lot about Alexander Pyron’s recent article on the state of current species extinction. Pyron made a number of assertions about extinction which simply are not correct. He also made statements based on incomplete science, such as the manner in which the biosphere has recovered from mass extinctions in the past. His OBSERVATION that recovery has always occurred is of course accurate, but beyond that his reasoning is pure speculation. Now, here is my main point: I will level an equal criticism toward some on the opposite side of his argument, i.e. claims that we are in the midst of a Sixth Mass Extinction, and that we are now living in a new, human-characterized geological epoch, the Anthropocene. About the mass extinction, no, we are not there. Not yet anyway. Yes, humans are devastating biodiversity, but the scale of destruction has not reached levels seen in the fossil record. Furthermore, one of the features of a mass extinction is that rates of extinction greatly exceed rates of origination, i.e. the rate at which new species are evolved. That can happen either because the actual rate of extinction is accelerated, e.g. by an asteroid impact, and/or because the rate of speciation falls, perhaps because of climate change, changes of sea level, and so on. Today, what is the global rate of speciation? It has most likely plummeted in heavily urbanized and agriculturalized areas, but do we actually know? These questions are important, because their answers will hint at how much room remains for us chart a different course for both ourselves and biodiversity. We are not yet condemned to adapt to an ongoing mass extinction, but we must act to prevent one.
As for the Anthropocene; we humans will leave a mark in the geological record. But will we alter the geological future of the planet as it is currently unfolding? Will our presence be marked by a boundary or interval of mass extinction? In my opinion, the science is not yet complete.
Alexander Pyron, a professor of biology at George Washington University, recently wrote an inflammatory op-ed for the Washington Post, entitled “We don’t need to save endangered species. Extinction is part of evolution.” The post outraged many, among them an awful lot of scientists. Needless to say, the piece is a seriously misguided bit of poor reasoning and inaccurate science, particularly with regards to extinction. Myself and colleague Luiz Rocha, also at the California Academy of Sciences, wrote our own response, published several days ago in bioGraphic. Regardless of your opinion on species conservation, Pyron’s article cannot be used as the basis for sound argument, because it is a collection of fundamentally flawed arguments. You can read our own reasoning here: Betting on Conservation.
The image, by the way, shows the fossilized burrows of tiny marine snails in sediments dating to about 250 million years ago. The fossils are from a geological exposure in the mountains of Hubei, China, and is some of the earliest evidence there of the biosphere struggling back from the devastating end Permian mass extinction of 251 million years ago. There are no guarantees in the History of Life.
I’ve edited this post to add a little addendum: While I disagree strongly with Pyron’s opinions, I cannot agree with or support the personal attacks which have been leveled against him by others. The core power of rationalism and modern science is open and free discourse. I think that his science in this case is wrong, and I disagree with his moral stance, but I would not place this in the same category of, for example, charlatan climate change deniers who have alternative and exploitative agendas. So let’s keep the discussion civil.
Remember the Deepwater Horizon drilling disaster? It’s been a few years now. This video is a brief update on some of our research on how the spill might have affected, and may still be affecting oysters off the coasts of Louisiana, Alabama and Florida. This has been very slow and difficult work, mostly because we have been monitoring the oysters for several years, and have had to develop protocols for the tissue analyses. But it is now moving toward publication.
This blog might seem an odd place to find a piece related to the recent U.S. presidential election, were it not for the fact that one of the highlights of the electoral drama was the polling scene and all those wonderful data. Many of you, numbers geeks like me no doubt, probably followed one or more of the excellent polls analyses online as the whole thing unfolded. Prominent among those were the analytical poll aggregators, my favourites being Nate Silver’s FiveThirtyEight, Votamatic, and the Princeton Election Consortium. The sheer audacious accuracy of those folks was a stinging indictment of political punditry, basically handing the talking heads Algorithms, Statistics, and Science. For those of you not familiar with what I’m talking about here, the numbers guys basically took the data being gathered by the armies of pollsters out there, and algorithmically decided what they meant.
And the pundits weren’t the only ones left lying about on the battlefield. If any of you were following the polls, the swings, disagreements and discrepancies left many of us scratching our heads sometimes. What one earth was wrong with them?! I certainly do not have an answer, but apparently some of the pollsters do. Frank Newport, Editor-in-Chief of the seriously (but apparently not fatally) wounded Gallup Poll offered up an explanation, which you can read in it’s totality here. He makes three main points (as far as I can discern). First, Gallup’s poll does not try to determine the winner of the election. It’s actual objective is to assess the popular vote. Okay, but then it is rather pointless in a republic based on an electoral college. No harm done, but I’ll scratch them off my RSS feed in 2016. Second, the political campaign game really has changed, what with the invention of these things called cell phones and social networks. They promise to get caught up before the next election. Third, and this is the one that I really want to address here, Newport backhandedly slams the aggregators as parasites, but he couches it in a somewhat clever reference to the Tragedy of the Commons. Okay, my turn to get analytical.
The Tragedy of the Commons, based on Garrett Hardin’s ground breaking 1968 essay published in Science, makes a simple argument: In a situation where a resource has multiple rational users, actions that benefit an individual can bring ruin to all. For example, consider a group of herdsmen. It seems reasonable that when he is able to, a herdsman will add another goat to his flock. The benefits of the additional goat are to the herdsman only, but because all herdsmen share a common pasture, the costs are distributed to all. This is quite a favourable arrangement for all the herdsmen, except for the fact that as herd sizes increase the quality of the pasture declines until it can no longer support any goats. Ruin to all. Newport, who refers to the concept as the Law of the Commons, claims that the statisticians are operating under a reverse tragedy. His argument is that you have these polling companies out there, such as Gallup, who are doing their business as best as they can, but by releasing their results the parasitic statisticians can then aggregate multiple datasets, crunch the numbers, and come up with a better answer than any single pollster could. In other words, and here’s the reverse, each pollster incurs all its own costs while distributing the benefits to all. Good point, right? No, not so fast, and here’s why.
- Gallup is a business, not a non-profit organization. If they were the only polling company, they would still distribute their data/results in order to earn income. Their distribution of benefits therefore feeds back into the company, but the worry now is that the quality of the product is questionable.
- The collective data of the pollsters is a commons, but for the aggregators only, because they are the only ones partaking of the aggregated data. It is therefore difficult to argue that any harm is being done to Gallup if they are simply dumping grass out there for someone else’s goats.
- In fact, if Newport and friends were smart, they would take his analogy seriously and run with it. Treat the data as a commons indeed and partake of the benefits. It is clear that the analytic methods being applied to aggregated data are vastly superior to the singular reports of any particular pollster. Rather than damaging polling, I think that Silver and others have demonstrated that there actually is a good data signal in there.
Therefore, if Gallup and others are serious about providing insight, they would each take advantage of all the data, conduct proper analyses, and produce useful results. Then the reversal of the tragedy would indeed be complete: the actions of the individual bring success to all! Oh, but I forgot something: They weren’t interested in the outcome of the election. Never mind.
p.s. You can read one of our food web-related arguments on the Tragedy here:
Roopnarine, P. D. and K. D. Angielczyk. 2012. The evolutionary palaeoecology of species and the tragedy of the commons. Biology Letters 8:147-150. DOI:10.1098/rsbl.2011.0662
Therefore, please stop using phrases such as, “Extinction is the fate of all species”. True, maybe 99.99% of all species that have ever existed are now extinct, but that is a frequency, not a law. Extinction results from a failure to acclimate on a short timescale, or to adapt on a longer, evolutionary timescales. The apparent extinction of species on the long run is the result of those failures, and is neither a requirement nor a certainty.