Category Archives: Peer Reviewed Article Review

What are the trends in ecology and evolution for 2018?

The journal Trends in Ecology and Evolution does an annual “Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity”. I can only see the abstract so here is the one sentence describing the trends:

The issues highlighted span a wide range of fields and include thiamine deficiency in wild animals, the geographic expansion of chronic wasting disease, genetic control of invasive mammal populations and the effect of culturomics on conservation science, policy and action.

I was new to the term culturomics, and thought it might have something to do with synthesizing new compounds in giant vats of yogurt. But no, according to Wikipedia it is not that kind of culture, but relates to search and synthesis algorithms for scientific articles, which does indeed seem to be a recurring theme on this blog lately.

Culturomics is a form of computational lexicology that studies human behavior and cultural trends through the quantitative analysis of digitized texts.[1][2] Researchers data mine large digital archives to investigate cultural phenomena reflected in language and word usage.[3] The term is an American neologism first described in a 2010 Science article called Quantitative Analysis of Culture Using Millions of Digitized Books, co-authored by Harvard researchers Jean-Baptiste Michel and Erez Lieberman Aiden.[4]

At that point, I just needed to figure out what a neologism was, so I looked it up in Webster’s 1913 which some people say is the most artfully written dictionary:

Ne*ol”o*gism (?), n. [Cf. F. néologisme.]

1. The introduction of new words, or the use of old words in a new sense. Mrs. Browning.

2. A new word, phrase, or expression.

3. A new doctrine; specifically, rationalism.

Mrs. Browning? Elizabeth Barrett Browning wrote a long poem called Aurora Leigh which contains the word. And no, I wouldn’t have learned that if I had looked up neologism in the New Oxford American Dictionary.

I learnt my complement of classic French
(Kept pure of Balzac and neologism,)
And German also, since she liked a range
Of liberal education,–tongues, not books.
I learnt a little algebra, a little
Of the mathematics,–brushed with extreme flounce
The circle of the sciences, because
She misliked women who are frivolous.

It goes on like that. Forever.

Oh okay, one more, here is the definition of flounce in Webster’s 1913:

Flounce, v. t. To deck with a flounce or flounces; as, to flounce a petticoat or a frock.

Flounce, n. [Cf. G. flausflausch, a tuft of wool or hair; akin to vliess, E.fleece; or perh. corrupted fr. rounce.] An ornamental appendage to the skirt of a woman’s dress, consisting of a strip gathered and sewed on by its upper edge around the skirt, and left hanging.

Flounce (?), v. i. [imp. & p. p.Flounced (flounst); p. pr. & vb. n.Flouncing(?).] [Cf. OSw. flunsa to immerge.] To throw the limbs and body one way and the other; to spring, turn, or twist with sudden effort or violence; to struggle, as a horse in mire; to flounder; to throw one’s self with a jerk or spasm, often as in displeasure.

To flutter and flounce will do nothing but batter and bruise us.


With his broad fins and forky tail he laves
The rising sirge, and flounces in the waves.


“Sirge” I think is an old-timey spelling of “surge”. And if you look up “surge” in this dictionary, its usage is quite interesting and you want to go on. But that’s it for me.


Google Scholar, Microsoft Academic, and open science

Wired talks about how Google Scholar is changing the academic publishing industry as open science starts to take hold, and how Microsoft Academic might be an even better search engine. There are also a lot of other emerging search engines out there, which the article goes into.

I use Google Scholar quite a bit, even though Google sort of stopped advertising it and makes you go through a couple extra clicks to get to it. I didn’t know Microsoft Academic or most of these other tools existed.

should we intentionally seed life on other planets?

Some bacteria have been found surviving on the outside of the International Space Station. Tardigrades are an even hardier form of microbe that can supposedly survive even close to absolute zero. They can essentially go dormant in a state very, very near death, then bounce back if and when they find themselves in suitable conditions later on. There is even speculation that life on Earth could have arrived from space in a form like this, and/or life forms originating on Earth could be living on other planets right now.

Space dust collisions as a planetary escape mechanism (In press Astrobiology, 2017)

Hypervelocity space dust is a unique entity in planetary systems like our Solar System, which is able to go past and enter the atmosphere of planets, collect samples of those planets and deposit samples of other planets. The entire system of fast space dust in a planetary system thus contains the atoms, molecules and possibly even microbial life, from all the planets and provides a means to mix them up amongst the different planets. For collecting atoms and molecules that form atmospheres, the mechanism proposed in this paper is fairly straightforward. For collecting life and life related molecules this mechanism has interesting features, but many detailed issues would still need to be studied. The violent collisions involved in this mechanism could make it difficult for life to remain intact. There are several possible collision scenarios that would all need to be explored to get a definitive answer to this problem. But even if life itself does not remain intact, it could still permit the complex molecules associated with life to get propelled into space, and that is also interesting for the panspermia process. Since space dust is ubiquitous all over the Solar System and is believed to exist in interstellar and probably intergalactic space, the mechanism proposed in this paper for propelling small particles into space could provide a universal mechanism both for the exchange of the atomic and molecular constituents between distant planetary atmospheres and for initiating the first step of the panspermia process.

According to Wikipedia, panspermia is “the hypothesis that life exists throughout the Universe, distributed by meteoroidsasteroidscomets,[1] planetoids,[2] and also by spacecraft in the form of unintended contamination by microorganisms.”

Of course there is still the Fermi Paradox – if life is so common, why haven’t we been able to find any evidence of it, anywhere, even once? There are ethical implications of all this. We would like to perpetuate our human species and current form of civilization, of course, and that means getting into space eventually. But if we don’t manage to pull that off, and all life on Earth is wiped out for one reason or another, panspermia means that life exists elsewhere, and somewhere, sometime, intelligent life will evolve again if it hasn’t already. But if there is absolutely no life anywhere else in the universe, the loss of it on Earth would mean the end of all life forever. That would be too heavy a burden to bear, and would mean we have a strong ethical obligation to get some self-sustaining human colonies out into space as an insurance policy. But there could be a cheaper form of insurance policy – intentionally contaminate space and nearby planets with hardy germs from Earth, and in a few billion years something will survive and evolve, somewhere, into something. Do this enough and again, eventually you will have intelligent life somewhere. But finally, if it turns out there is life on other nearby planets, even very primitive life, then intentionally contaminating them with our germs would not seem like such an ethical thing to do after all.

ice apocalypse

So will it be fire or ice that gets us. Eric Holthaus, writing in Grist, says ice.

The glaciers of Pine Island Bay are two of the largest and fastest-melting in Antarctica. (A Rolling Stone feature earlier this year dubbed Thwaites “The Doomsday Glacier.”) Together, they act as a plug holding back enough ice to pour 11 feet of sea-level rise into the world’s oceans — an amount that would submerge every coastal city on the planet. For that reason, finding out how fast these glaciers will collapse is one of the most important scientific questions in the world today…

In the past few years, scientists have identified marine ice-cliff instability as a feedback loop that could kickstart the disintegration of the entire West Antarctic ice sheet this century — much more quickly than previously thought.

Minute-by-minute, huge skyscraper-sized shards of ice cliffs would crumble into the sea, as tall as the Statue of Liberty and as deep underwater as the height of the Empire State Building. The result: a global catastrophe the likes of which we’ve never seen.

I enjoy Eric’s writing. He employs some hyperbole, but always links to original sources you can drill into if you want to. Regarding the hyperbole though, here is some criticism of him in the Guardian:

I was particularly concerned about some of the implied time scales and impacts. That ‘slowly burying every shoreline…creating hundreds of millions of climate refugees…could play out in a mere 20 to 50 years’ (it could begin then, but would take far longer). That ‘the full 11 feet’ could be unlocked by 2100 (Rob and Dave predicted the middle of next century). That cities will be ‘wiped off the map’ (we will adapt, because the costs of protecting coastlines are predicted to be far less than those of flooding). We absolutely should be concerned about climate risks, and reduce them. But black-and-white thinking and over-simplification don’t help with risk management, they hinder.

Is “the entire scientific community [in] emergency mode”? We are cautious, and trying to learn more. Climate prediction is a strange game. It takes decades to test our predictions, so society must make decisions with the best evidence but always under uncertainty. I understand why a US-based climate scientist would feel particularly pessimistic. But we have to take care not to talk about the apocalypse as if it were inevitable.

Maybe, but if the cost of protecting cities is less than the cost of flooding, perhaps our U.S. politicians could get to work on that instead of continuing to bury their heads in the sand and pretend science doesn’t exist, even if the time frame is uncertain. Remember the serious scientists are arguing here over whether the most likely scenario is the one that has been presented over the past few years, or something worse. They are not arguing that it might actually be better than they thought.

buy or rent?

This academic study says that people who own houses are richer on average than people who do not. But generally, renting costs less per month than buying, so the answer must be the build-up of home equity and price appreciation, right? Well, one conclusion of this paper is that theoretically, if you rented a house for a long period of time, and invested the amount of money you saved compared to paying a mortgage diligently every month, you would come out ahead in the long term over most periods of recent U.S. history. But this doesn’t happen, so maybe the answer is that the type of people who rent homes are not the type who invest, on average, and vice versa.

I wonder if they factored in my mortgage and property tax deductions, which I am hoping do not go away. I’ve always wondered – if two friends bought equally priced houses, rented them to each other, and paid taxes as landlords rather than homeowners, would they come out ahead or behind? As a landlord you can deduct all your maintenance and repair costs, plus depreciation which is just a weird thing that only exists on paper. Would there be anything illegal about this? Could family members do it? If so, why don’t they?

I’ve owned, and rented, and been a landlord and a tenant at the same time, because I’ve moved around and been in some weird situations with a growing family and that was the easiest thing to do. The best thing about renting is how easy it is. If you want to rent a place and really put some effort into it, you can live there just a few days later. I did that once although I had to clean it myself when I got there. The best thing about owning a place is you can mess with it if you want to. Especially the yard if that is your thing. And if that is your thing, it’s a little hard to put a financial price on.

Financially speaking, the man puts money in one of your pockets and takes it out of the other, as far as I can tell, and if you play it just right you have a few pennies left to save for a rainy day. Then you eat, sleep, shit, and do it again, and that is how the financial part of the world works, so it is best to look for meaning in other parts of the world.

Sounding the alarm on biodiversity

What’s the elevator pitch to convince a skeptic that biodiversity is important? To people who value nature for its own sake and believe it is immoral to destroy it, maybe it seems as though the pitch should not be needed. But it’s needed, considering the difficulties communicating the practical/economic case against global warming when that case should be fairly obvious (reliability of the food supply; cost of food, energy, and water; cost to protect, relocate or abandon coastal cities; impacts of extreme weather, drought and fire inland).

Of course, the practical/economic case to fight biodiversity loss has to do with how much our civilization relies on free ecosystem services, and has neither the level of technology nor wealth to replace them in the near term. I believe many people will respond to the ethical case too, and more would if we emphasized ethics more in children’s education. But this paragraph is already too long for an elevator pitch now, isn’t it.

Here are a couple articles that talk about bolstering both the science and the communications.



bad news on pollution

The Lancet Commission on Pollution and Health has released a “landmark study” on health and economic effects of pollution worldwide. You can read it after going through a free but somewhat annoying registration process. There is also a pretty good summary in this Guardian article.

I find the results disturbing. Among them are that pollution causes an estimated 9 million premature deaths worldwide each year, with over 90% in low-income and middle-income countries. The Guardian article has a good Infographic showing that this is significantly more than deaths caused by other major causes like smoking, AIDS, and road deaths. (Although, you could think of smoking as a form of intentional pollution, and I believe tobacco countries are still up to their old immoral marketing tricks in developing countries. I also see a link between pollution and road deaths, with land use patterns and lifestyles centered around motor vehicles being the root cause of both, again with immoral practices by the auto, fossil fuel, and construction industries playing a role.) Other statistics are that pollution reduces GDP in low- and middle-income countries by 2% per year and global economic output by around 6% per year. (I don’t quite get how those last two statistics go together – even though the health impacts are primarily in lower-income countries, that somehow affects the economies of higher-income countries disproportionately? I guess maybe because people in higher-income countries spend money on medical care to partially offset the effects of pollution, while people in the poorer countries just die? But don’t we add medical spending to GDP, even though we should consider some of it a cost to society rather than a benefit?) One implication here is that the idea of accepting pollution for a period of time while your country develops may not be a very good strategy, even thinking in hard-nosed economic terms and neglecting the moral dimensions of allowing your people to suffer in exchange for the supposed longer-term gain.

They make a few more links I find interesting (not in a fun way). One is that we don’t really know how much of health care spending is offsetting the effects of pollution, because there is a lot we don’t know about links between pollution and health. And this is not just heart attacks, cancer, and asthma we are talking about, there are disturbing concerns about impacts on the fertility and intelligence of our species from both the small number of everyday chemicals we have good information on and the enormous and growing number we don’t. Finally, there are the somewhat obvious links between fossil fuel pollution and climate change.

Here is where I should probably draw some link to the Trump administration’s immoral policies to actually increase pollution. But it’s so obvious I’m not sure it even needs to be said. He is clearly one of the evil lizard people who eats babies and puppies and is trying to kill us all off as quickly as possible.

disappearing bugs

This surprising study from Germany raises the possibility that a catastrophic loss of insects is occurring and that it could lead to ecological collapse.

More than 75 percent decline over 27 years in total flying insect biomass in protected areas

Global declines in insects have sparked wide interest among scientists, politicians, and the general public. Loss of insect diversity and abundance is expected to provoke cascading effects on food webs and to jeopardize ecosystem services. Our understanding of the extent and underlying causes of this decline is based on the abundance of single species or taxonomic groups only, rather than changes in insect biomass which is more relevant for ecological functioning. Here, we used a standardized protocol to measure total insect biomass using Malaise traps, deployed over 27 years in 63 nature protection areas in Germany (96 unique location-year combinations) to infer on the status and trend of local entomofauna. Our analysis estimates a seasonal decline of 76%, and mid-summer decline of 82% in flying insect biomass over the 27 years of study. We show that this decline is apparent regardless of habitat type, while changes in weather, land use, and habitat characteristics cannot explain this overall decline. This yet unrecognized loss of insect biomass must be taken into account in evaluating declines in abundance of species depending on insects as a food source, and ecosystem functioning in the European landscape.

I knew about the frogs, elephants, tigers, bees, and loss of larger animal species and biomass in general, but I hadn’t really heard this idea that insects are disappearing. I can see a silver lining to this – I can’t really create elephant or tiger habitat around my house, and frog habitat is a little tough, but insects – I can actually help the little guys. On a larger scale, there is the question of green infrastructure – can we deliberately design habitats in cities, larger reserves, and corridors connecting them to support as much ecological function as we can? I think so, but I don’t think our public officials, engineers, urban planners, scientists, and others in a position to do this are tuned into the issue or even very open to hearing about it.

trees and public health

A new report from the Nature Conservancy makes the case for the value of urban trees to human health. They go through a number of economic valuation studies that are out there, and the literature on health benefits: air quality, heat stress, mental and physical health, climate change. Then they make a case that urban tree canopy in the U.S. is actually declining and that it is severely under-funded in most cities.

Also, on the tree front, here is a recent paper on the rate at which wood inside urban trees decays. I think one important concept with urban trees is to think of them as infrastructure that has to be maintained and replaced at some rate. They just don’t live as long as forest trees, because they are in stressful environments, performing functions for us, and getting worn out. And the cost of maintaining and replacing them is actually low, and their benefits high, compared to other types of infrastructure. But even though the engineering, planning and architecture professions have been talking a lot about green infrastructure for at least a decade, most of us still aren’t taking it seriously as infrastructure, and the construction industry, bureaucrats and politicians are not taking it seriously, if they have even absorbed the concepts at all. I think this is a case where wealthy private foundations or individuals could make an enormous difference if they wanted to, because the institutions to plant and maintain trees typically exist, but are just severely underfunded. So all I have to do is become a wealthy private individual and I will take care of this. Okay, a solution exists and I’ll get right on that.

The overlooked carbon loss due to decayed wood in urban trees

Decayed wood is a common issue in urban trees that deteriorates tree vitality over time, yet its effect on biomass yield therefore stored carbon has been overlooked. We mapped the occurrence and calculated the extent of decayed wood in standing Ulmus procera, Platanus × acerifolia and Corymbia maculata trees. The main stem of 43 trees was measured every metre from the ground to the top by two skilled arborists. All trees were micro-drilled in two to four axes at three points along the stem (0.3 m, 1.3 m, 2.3 m), and at the tree’s live crown. A total of 300 drilling profiles were assessed for decay. Simple linear regression analysis tested the correlation of decayed wood (cm2) against a vitality index and stem DBH. Decay was more frequent and extensive in U. procera, than P. acerifolia and least in C. maculata. Decay was found to be distributed in three different ways in the three different genera. For U. procera, decay did appear to be distributed as a column from the base to the live crown; whereas, decay was distributed as a cone-shape in P. acerifolia and was less likely to be located beyond 2.3 m. In C. maculata decay was distributed as pockets of variable shape and size. The vitality index showed a weak but not significant correlation with the proportion of decayed wood for P. acerifolia and C. maculata but not for U. procera. However, in U. procera, a strong and significant relationship was found between DBH and stem volume loss (R2 = 0.8006, P = 0.0046, n = 15). The actual volume loss ranged from 0.17-0.75 m3, equivalent to 5% to 25% of the stem volume. The carbon loss due to decayed wood for all species ranged between 69 to 110 kg per tree. Based on model’s calculation, the stem volume of U. procera trees with DBH ≥ 40 cm needs to be discounted by a factor of 13% due to decayed wood regardless of the vitality index. Decayed wood reduces significantly the tree’s standing volume and needs to be considered to better assess the carbon storage potential of urban forests.