Category Archives: Nature

More on Plant Behavior

This week RadioLab did an episode titled “Plant Parade”, which was a set of stories about the real, if bleeping crazy, science of plant cognition and communication [1].

The reports covered plant roots that sense the sound of water, plants that apparently exhibit Pavlovian learning, and the super-mega-awesome Wood Wide Web.

[Podcast here]

The latter I had heard of, and the others are akin to other studies, not to mention The International Laboratory of Plant Neurobiology and the Society of Plant Signalling and Behavior.

The radio report tied these findings together with the general idea that plants (and fungi) exhibit these behaviors, including memory and learning, but lack both brains and nervous systems.

This isn’t quite the paradox as it might seem, at least to me.

It is clear that these organisms do not have anything that resembles a human or any animal nervous system.  But it is equally clear that they have systems that are analogous, even though we have little notion of how they might work.

For example, the tips of tree roots have tiny hairs, which very well could vibrate in response to sounds.  This could, in principle, be translated into chemical signals, which could control the growth of the root.  This hasn’t been documented, but it would amount to an auditory sense, just like human hearing.

But of all the wonders discussed, the reported ability of plants or forests (which are networks of many organisms of multiple species) can, in fact, learn and remember is the most intriguing. We have some understanding of how animals learn, which is definitely dependent on the nervous system and, in humans, our brain.  We also understand engineered memory systems we have built for our computers, which depend on physical traces encoded in various media.

But we have no clear understanding of how plants, or forest networks, might “remember” something, or related, communicate something to another plant or organism.

This question of how they might do it really rang a bell for me, of course, because I had just read about transfer of memory via RNA between two snails.

The snail study seems to indicate that the long missing “engram” may, at least in part, involve epigenetic coding of DNA via RNA.

(It is particularly satisfying to think that the answer to one of the most grievous gaps in neurobiology, “the engram”, might be another of the most grievous gaps in molecular biology, “junk (sic) DNA”.)

If snails can transfer memories via RNA, and, indeed, these memories are encoded in the DNA of certain cells, then anything with DNA could do the same.  (For that matter, any type of cell might store memories in DNA, not limited to neurons.)

Plants have DNA and RNA, as do fungi, and microbes of all types.  I can’t think of any reason, in principle, why a plant couldn’t store memories in some cells in the same way that snails apparently store it in specific types of neurons.  At least, in principle.

I would note that the forest web of multiple species of trees plus fungi and who know what else might also pass around RNA, or have some mechanism that effectively transduces RNA across a channel to create semantically equivalent RNA at the receiver.

If we understood this mechanism we could talk to the trees!  We could program the forest!

Obviously, this is all speculation.  But I think it’s reasonable enough that, were I a younger man, I’d want to investigate.  And were I a billionaire, I’d want to fund teams to investigate.

  1. Robert Krulwich, Plant Parade, in RadioLab, R. Krulwich, Editor. 2018.


Bumble-BEHAVE – The Life and Death of Bumble Bees

We’re all worried about the Bees and other pollinators.   Researchers are using every tool in the book, genetic analysis, physiological studies, field studies, naturalistic lab studies, behavioral studies, and digital sensors and networks  and more.

The overall finding from all this research is that there are a many challenges today for pollinators, which probably interact and combine in ways that are hard to predict. Not just pesticides, but multiple classes of chemicals. Diseases. Climate change and habitat loss. And who know what else.  (These insects must be pretty tough to survive as well as they are.)

It is difficult to study something this complicated, and certainly impossible to try to investigate all combinations and permutations of the pollinator’s world.

A research team in the UK report this summer on another important research tool, a detailed multi-system computational simulation of Bees.  Tagged “Bumble-BEEHAVE”, it builds on earlier work modelling honey bees to develop a detailed model of Bumble Bee colonies [1].

The model includes stressors, food sources, and bee behavior [1]. From these inputs, the model predicts “(a) individual foraging behaviour, (b) colony growth and reproduction and (c) population nest density, in realistic landscape settings.” ([1], p.2)

The agent based model (ABM) is set in a realistic landscape and populated by individual bees. Each time step (turn) is one day, and the model can run for years of simulation time.  The idea is to be able to explore the implications of different resources (e.g., habitat changes to food sources) or pathogens (disease or chemicals) for the life of both individual bees and colonies of bees.

The behavior of difference species of bees is statistically simulated to match real bees. This includes foraging for food, nesting, raising young, and so on.  This also requires realistic landscape, which includes accurate representations of the relevant food, nesting, and other areas.  (In their earlier research created tools for surveying an area to create such maps.)


The new paper also reports on some careful work to demonstrate that the computation model faithfully represents the real world [1]. They show that the model closely approximates findings from studies of real bees for both the individual bees and the colony.

The idea is to try to understand the effects of habitat and pesticides on bee populations, and possibly to mitigate harm.  Using the model might help planners and safety authorities assess policies, and might help farmers and developers minimize damage to pollinators [2].

The code is available for anyone to use.  You can make a map of your own, though that will take work. And you can experiment with different scenarios, though, again, it will take a bit of work to do something meaningful.


The program looks a bit like a game, though it’s really more of a movie or screen saver, which makes me think about how it might be used for non-scientific uses.

The graphics are, um, functional, even if you ignore complex control panel. I wonder if it would be possible revise the presentation of the map and bees to make it a more attractive decorative element. Ideally, the graphics could tell the story of how the bees are faring, in broad, visual strokes.

I’m not criticizing or denigrating the serous and important purpose of this program, I’m just suggesting an additional use, in a version that people might run just for the pleasure of watching happy bees (or the agony of struggling bee colonies).  I could imagine versions customized to locales, e.g., simulations of bee life near a science museum or in a major city park, for local interest.

I only mention this idea as a potential opportunity for a design project.

  1. Matthias A. Becher, Grace Twiston‐Davies, Tim D. Penny, Dave Goulson, Ellen L. Rotheray, and Juliet L. Osborne, Bumble‐BEEHAVE: A systems model for exploring multifactorial causes of bumblebee decline at individual, colony, population and community level. Journal of Applied Ecology, 0 (0) 2018.
  2. University of Exeter News, ‘Virtual safe space’ to help bumblebees, in University of Exeter News. ‘


New Treatment Augments Desert Soil

I’ve see quite a bit of PR about Liquid Nano Clay (LNC), which is designed to increase the productivity of desert soils.  The results are said to be impressive, huge increases in crops with huge decreases in water use.  Sounds great.

A bit of research yields the company web page, press reports, and some patents, but no refereed research papers.  Hmm.

According to the public explanations, the LNC is applied with water to sandy soils where it “bonds” to the sand.  The treated soil retains more water and is said to be favorable for Mycorrhizal fungi.  In short, this turns sandy soil into something more like prime farmland.

Wikipedia tell me there are a lot of nanoclays out there, and they are used in many industrial processes, so this is plausible if not necessarily novel technology. (The terms “nano” and “clay” are pretty generic, no?)   As far as I can tell from scanning the patents, the main technique here involves purifying the clay to get rid of impurities and isolate the good stuff that likes to snuggle up to sand grains in the desired way.

The company materials emphasize the simplicity and speed of application, and boast about the first year results. What is missing from the PR, and what I would look for in research reports, is the long term effectiveness of this treatment, as well as comparisons to other techniques.

Adding LNC plus water and fertilizer gives some very green looking fields.  Of course, adding water and fertilizer to any soil will give you quick results, so the news has to be the magnitude of the results for a given level of inputs.  The company states that this treatment uses less water (because the clay retains water), but I don’t know what the comparison is to (less than what?).  This treatment should use less fertilizer for the same reason, but I haven’t seen any report on that.

More important is the question of the long term effects. Modifying desert soils is famous for short term gains followed by long term trouble. First year results aren’t a guarantee that they can be sustained. Indeed, they ususally aren’t.

Sand + clay = brick, if you aren’t careful. And this technology surely isn’t immune to the hazards of salt poisoning and other side effects of watering the desert.  Who knows, it may have adverse side effects due to retaining the water over many years.

Another area of interest would be what kind of micro ecology develops in the treated soil. The company touts the fact that Mycorrhizal fungi like LNC treated soil, at least “when nourishment is available”.  (Fungi like anything when nourishment is available.)  But what else likes the soil?  Water in the desert will surely attract everything around, including insects, birds, and all kinds of microorganisms.  If enough “bad” ecology develops, it will more than cancel out the “good” ecology.

This technology is an interesting idea. The PR materials available suggest that it is carefully thought out. As far as I can tell, the process is fairly low input, and may reduce the inputs of water and fertilizer.  This is certainly the right idea.

But a quick spritz that produces a big jump in the first year is not necessarily the solution to food production, nor the key to the kind of “abundance” suggested by the inventors.

But the case simply isn’t made.  I’d like to see some more solid evidence, ideally, in independent, peer reviewed comparative studies.

  1. Aamir Rafiq Peerzada, The innovation turning desert sand into farmland, in BBC News – Business. 2018.


Big Expedition to Antarctic Glacier

At the same time that the bees are disappearing and dying out, the ice is melting—everywhere.

In recent years, there have been a number of careful studies using remote sensing data and computational simulations of ice in Greenland and Antarctica.  These studies show that Greenland is melting everywhere at an accelerating pace.  This trend has been confirmed by close up, in situ, studies of the ice and sea.

The studies of Antarctica show a more complex picture, with some areas experiencing rapid retreat of glaciers, and other areas apparently holding steady.  There have been relatively few in situ studies—Antarctica is a huge space, very far away, and very hard to visit.

This spring the US National Science Foundation and UK Natural Environment Research Council announced a joint expedition to intensely study the Thwaites Glacier in Antarctica.   The International Thwaites Glacier Collaboration (ITGC) will include measurements of the surface and interior of the ice, the ocean, and the local atmosphere.

Thwaites Glacier has been observed from space to be changing rapidly, shedding ice into the ocean, and apparently thinning.

This expedition will flesh out a much more detailed picture of what is really happening, and possibly better predictions of the future of this ice.

The BBC indicates that if this rapid change leads to a complete collapse, the melt water from Thwaites would raise the average sea level by 80cm—knee deep.  It would be nice to know if such a collapse is immanent, no?

The research activity will include a variety of studies including drilling (to study the history of the ice, rock, and sediments), measurements of the ocean (including deployment of the submersible Boaty McBoatface and sensors attached to marine species), and radar and other sensors.  Cool!

One of the key questions remains the interaction of the relatively warm ocean and the ice.  Studies have shown that in some cases the ocean is invading farther under the ice, changing the grounding line.  The expedition will collect close up measurements of the glacier, to determine what is happening under the ice.

I don’t know if this actually is the “Biggest ever Antarctic field campaign”, but it is certainly a major effort, and the biggest in recent decades.

It will be interesting to see the results from these studies in the coming years.

  1. Jonathan Amos, Thwaites Glacier: Biggest ever Antarctic field campaign, in BBC News – Science & Environment. 2018.
  2. National Science Foundation, US and UK join forces to understand how quickly a massive Antarctic glacier could collapse, in NSF News Release. 2018.


Pesticide Ban In EU

One of the worrying questions today is “what is happening to the bees?”  Bees and other pollinators appear to be dying out all over the world, and no one is really sure why.  Given that much of our food depends on these beneficial insects, this is not an idle question.

Research points to a role for agricultural pesticides, though the story isn’t simple or clear cut. Still, there is considerable reason to think that neocortinoids in particular may be killing pollinators, and ideally should be removed from the world of the bees.

Of course, agricultural policy is political, so limitations on these pesticides have been hotly contested.  (In the US, the debate will be largely suppressed for the duration of the current anti-science administration.)

But this month saw a significant political step, with the EU (including the UK) voting extending a permanent ban on neocortinoids.  At least, a ban on “outdoor” use—it will still be allowed in greenhouses.  (I suspect that it is no coincidence that the ban will heavily fall on sales of US products in the EU, at a time of strong tensions over international trade.)

Given the number of environmental challenges faced by pollinators, it is far from clear how much benefit will be seen from this particular policy.  The best studies have shown complex patterns of effects, which are not easy to explain,  and there are lots of other chemical hazards out there.

In addition to the direct effects there will be indirect effects. For example, the existing partial ban has already distorted agricultural practices (e.g., by shifting to imported crops from areas using neocortinoids). Also, one wonders just how much “leakage” there may be from “indoor” uses.  Studies have documented transmission of some substances out of greenhouses into wild populations.

In short, the results may not be simple or clear cut.

Nevertheless, this will be a golden opportunity to investigate the long-term effects of these chemicals and this policy.  For good reasons or bad, the EU is creating a natural (or at least a geo-political) comparative experiment.  We can hope to compare the health and populations of bees in the EU with other areas that have different policies.

  1. Matt McGrath, EU member states support near-total neonicotinoids ban, in BBC News -Science & Environment. 2018.


Megafauna Extinction Linked To Human Ancestors

One of the glaring facts of human prehistory is the correlation of the rise of humans and the decline of megafauna—big game.  This pattern continues today, with simultaneously accelerating extinctions of large animals and booming human populations.

Many of us think this pattern is no coincidence.  We know that people will hunt anything and everything to extinction.  All those nasty little apes with their pointy sticks probably did in the giant sloths and other big beats.

Cautious souls reserve judgement, because it is certainly possible that some third factor, such as changing climate, led to both more humans and fewer game animals.  Just because we are killing everything in sight today doesn’t mean that humans wiped out ancient all the ancient fauna.

Given the sparse and uncertain data about exactly when and where humans lived, and when and where species went extinct, there is only circumstantial evidence one way or the other. Correlation is not causation.

So, what role did we humans and our cousins play in the large die off at the end of the Pleistocene?

This spring, a group of researchers published a study of mammalian extinctions and human expansion from the last 125,000 years [2].  The study worked with a dataset that includes mammalian body size distributions and biodiversity over time.

“We investigated the influence of these emerging and increasingly sophisticated hominin predators on continental and global mammalian biodiversity over the late Quaternary” ([2], p.310)

Of particular interest are five broad periods of time corresponding to the expansion of hominins (humans and cousins).

The analysis showed a clear relationship between size of the animals and likelihood of extinction, especially in the earlier periods.  This means that larger animals were consistently wiped out.  Notably, a similar analysis for periods before the Pleistocene (before homonins) do not show this pattern.  (The pattern is less visible in recent times, likely because everything is being wiped out at the same time.)

“As Neandertals, Denisovans, and humans spread across the globe over the late Quaternary, a highly size-biased extinc- tion followed, a pattern distinct in the Cenozoic mammal record. The subsequent downgrading of body size was severe and differentially targeted herbivores.”

This pattern is consistent with human hunting behavior, and is seen at the precise periods when humans were expanding.

One interesting conclusion from this data is that this pattern began very early, and, indeed, before Homo sapiens evolved from earlier Hominids.  This implies that our ancestors have been big game hunters from the beginning, and have been significantly impacting big game from forever.  (Nasty little apes with pointy sticks…)

This pattern has abated in recent ages because humans have come to dominate the Earth, and domesticated animals have replaced wild animals.  The study projects into the future, assuming that threatened species die out. In the future projections, the extinctions extend into smaller animals, indeed, nearly all wild mammals.

I was inspired to make my own plots from some of their data (I drew from Table S1, Supplemental materials).  These diagrams make plain the extremely rapid decline in animals with large body mass, and the key temporal pattern:  extinctions began very early in Africa and Eurasia, spread out to Australia and then the Americas.  This is, of course, the path of human occupation.

I drew arrows suggesting when humans arrived and expanded.  Note that these marks are impressionistic, dates and scales of human occupation are not well established.

(In these diagrams the last point is the projected future extinctions in then next 200 years, which is a precipitous drop.)

From [2] Supplemental Materials, Table S1. Horizontal axis is years (1000s), vertical axis is median body mass for surviving species. Lower median body mass means fewer large animals. Arrows suggest when major human infestations may have first occurred.

  1. Christopher Joyce, New Study Says Ancient Humans Hunted Big Mammals To Extinction, in All Things Considered. 2018, National Public Radio: Washington, DC.
  2. Felisa A. Smith, Rosemary E. Elliott Smith, S. Kathleen Lyons, and Jonathan L. Payne, Body size downgrading of mammals over the late Quaternary. Science, 360 (6386):310-313, 2018.



More On Pollinator Decline

It has been pretty clear for quite a while that neonicotinoids are probably bad for bees and other pollinators. Given the importance of pollinators to food production, this risk cannot be dismissed. But the exact risk is difficult to assess, and the benefits of the chemicals assure that regulations have become a political issue.

In recent years, European regulators have banned the products, which North America has not. A recent review by the EU has confirmed that the ban will be extended in Europe, despite objections from the manufacturers and farm lobbies [3].  At least part of the justification is the findings of hundreds of studies, which show a variety of levels of risk.

The objections note that Europe is out of line with the US and Canada, and the fact that there are a lot of things that are bad for bees. I’m not especially moved by these arguments, but the second point is certainly true.

A case in point is that honey bees are also suffering from epidemics of viruses, as well as effects of chemical agents.  A recent study expands the picture to shows that three viruses that plague honey bees are also found in hoverflies [1]. These insects visit the same flowers as domestic and wild bees.

The evidence from this study is not conclusive, but it certainly raises the possibility that hoverflies and other insects may transmit these viruses from bee to bee; or they may have other roles in the transmission of the diseases.

With so many nasty things happening to our pollinators, all at the same time, it’s difficult to be optimistic about their fate.

Or our own.

  1. Emily J. Bailes, Kaitlin R. Deutsch, Judit Bagi, Lucila Rondissone, Mark J. F. Brown, and Owen T. Lewis, First detection of bee viruses in hoverfly (syrphid) pollinators. Biology Letters, 14 (2) 2018.
  2. Helen Briggs, New clues to decline of bees and other pollinators, in BBC News – Science & Environment. 2018.
  3. Helen Briggs, Pesticides put bees at risk, European watchdog confirms, in BBC News – Science & Environment. 2018.