Category Archives: Nature

Where are the bees?

In the past decade, scientists have raised alarms about the decline in pollinators, including the semi-domestic honey bee.

There seems little doubt that honey bees are dying off at alarming rates. It would be surprising if similar trends were not occurring across many species of bee, wasp, beetle, and butterfly.

Data point: in my pollinator friendly yard, we get lots of insects. Up to two years ago, we had honey bees and at least three other species of bees, as well as butterflies, and numerous identified insects. Every day, all summer.

Last year, there were no honey bees. None this year, either. From hundreds to zero in one year. I assure you that the flowers are the same, so where are the bees?

Suspicions fall on agricultural chemicals, insecticides intended to protect crops from being eaten by insects. But with a bazillion dollar industry and possibly huge crop losses at stake, trivial ideas like, “just stop using pesticides” are neither reasonable nor feasible. We need to know exactly what is happening to bees, and we need to know as soon as possible.

For one thing, there are a number of stressors for bees, including the familiar refrains of habitat loss and climate shift. For that matter, there are a lot of human introduced chemicals that might be involved. And, in the end, the bees must contend with the combination of all these.

But out of all the troubles plaguing our bees, fingers have pointed to neonicotinoid chemicals which are applied as a coating on crop seeds. Bees don’t have much to do with seeds, but the worry is that these chemicals persist for months, and small quantities are on the flowers that bees and other insects visit. Visiting hundreds of flowers, a bee may be exposed to tiny amounts of chemical many times. Furthermore, insects may carry the chemicals to other flowers and back to nests, spreading small amounts of the toxins.

An assessment of the problem requires examining how tiny amounts of chemicals persist and spread, as well as how much pollinators pick up from these sources. Investigating this in real settings is a non-trivial challenge, because the amounts of chemicals are small and must be measured over long periods of time. There are many possible variables, including how the chemicals are used, weather and soil conditions, and who know what else.

This month a European team reports a large scale study of these effects, comparing the effects over two years of neonicotinoid with control [3]. The careful study found a rather complicated set of results, different for different countries in the study. In some cases, there was clear losses of the bees, in others there were no differences between conditions. In the case of the UK, so many bees died in all conditions that there could be no statistical comparison of the effects. The study also found traces of the chemicals in the nests of wild bees, which appears to be related to reduced populations.

Overall, their results seem to show that there definitely are losses of bees, and these chemicals may contribute to the losses, at least in some cases. Most likely, neonicotinoids weaken some of the bees, making them more vulnerable to other challenges.

This study also confirms that the chemicals persist for months, and seem to accumulate in the nests of wild bees, far from the location of the deployment, and far from the intended target. This is consistent with other studies [2].

There is certainly cause for concern here. The EU and Canada are moving to stop using these chemicals, with a calculus that even with uncertainty, the benefits don’t outweigh the risks [1].

With the current administration, the US EPA will almost certainly not act to restrict these chemicals, study or no study. Sigh.

If you still have bees, be sure to say goodbye to them this summer. There won’t be very many left in a few years.

  1. Rebecca Morelle, Large-scale study ‘shows neonic pesticides harm bees’, in BBC News – Science & Environment. 2017.
  2. Erik Stokstad, Controversial pesticides can decimate honey bees, large study finds, in Science – News. 2017.
  3. B. A. Woodcock J. M. Bullock, R. F. Shore, M. S. Heard, M. G. Pereira, J. Redhead, L. Ridding, H. Dean, D. Sleep, P. Henrys, J. Peyton, S. Hulmes, L. Hulmes, M. Sárospataki, C. Saure, M. Edwards, E. Genersch, S. Knäbe, and R. F. Pywell, Country-specific effects of neonicotinoid pesticides on honey bees and wild bees. Science, 356 (6345):1393, 2017.


Celibrate World Giraffe Day: June 21

June 21 is World Giraffe Day!

Visit a Zoo or explore information on the web.

I think the closest giraffes to me are in Peoria:

This celebration is organized by The Giraffe Conservation Foundation, which seeks funding to help preserve this iconic and beloved species. Their website has lots of images of giraffes, and invites people to “stick their necks out” to save the giraffes.

I have to say that I would not want to live on an Earth without giraffes.


Remote Sensing Penguin Guano

There is so much we don’t know about the Earth and the biosphere. Even for relatively big and easy to see species such as birds, it is hard to know how and where they live, or even how many individuals exist. There are only so many biologists, and humans can only go and see so much.

Remote sensing of the planet from space has gives important insights about large scale processes that can’t be seen easily form a human perspective. For instance, a few images from space make absolutely clear how important dust storms in Africa are for the Amazon forests in South America.

In the past, it has been difficult to learn much about animal populations, because individuals are small and elusive. Biologists are getting better at detecting and tracking animals, especially mass movements of them.

This month NASA calls attention to a successful long term project that uses satellite imagery to locate colonies of Penguins [3]. Penguins are, of course, far too small to be reliably detected from most satellite imagery. However, Penguins live in colonies, and produce immense amounts of guano, which can be seen from space.

In fact, Penguin colonies could be seen from space 30 years ago [2], and space imagery and analysis have gotten a lot better since then.

The basic technique is to detect the color of guano covered rocks, and to infer how many Penguins live there from the area covered. Cross checking on the ground has confirmed that this indirect and remote measure is a pretty good estimate of and many Penguins there are and where they nest.

As the researchers note, Penguins live on sea ice, which means that they are a sensitive indicator of how ice conditions change. As sea ice is melting in parts of Antarctica, we can document how Penguins relocate in response. Penguins are also eat krill and fish, so they are a visible indicator of the health of these foods in an area.

Mathew Schwaller, Heather Lynch and colleagues have completed a global census of Adelie Penguins using imagery from several satellites [1]. They use machine learning techniques to identify the visual signature of nesting areas. Based on the very characteristic nesting habits of Adelies, it is possible to estimate the number of Penguins based on the area. Naturally, the satellite data is combined with on-site investigations and other reports, in order to validate the remote sensing and the estimation.

From [1] FIGURE 1. Map of extant Adélie Penguin colonies, as well as penguin colonies not found in imagery and presumed extinct. Solid bars represent sections of coastline in which populations are generally increasing in abundance, and dashed lines those in which populations are generally decreasing. Areas with no bar are either a mix of increasing and decreasing populations, are not changing in abundance, or do not have sufficient data to assess population change (see Supplemental Material Appendix A). Right: example of high-resolution imagery from Devil Island (−63.797°, −57.290°; location indicated by black arrow). Areas identified in the analysis as guano are shaded in light green. Imagery © 2014 by DigitalGlobe, Inc.
One huge advantage of the satellite data is that there is continued coverage of the whole world, so it is possible to track the changes in Penguin populations. For instance, the 2014 report indicates that over the last twenty some years, nesting sites in West Antarctica have dwindled. This is where sea ice is shrinking. In the same period, new nesting sites have appeared in East Antarctica, where sea ice has increased. Overall, the total population of Adelies seems to have increased in recent years, even as the birds have migrated to more favorable ice.

Ideally, the census can be maintained for a number of years to accumulate a much more detailed baseline, to improve the technique, and refine the understanding of the Penguin population. This census is only one species, so it remains to be seen how similar techniques might track other species.

  1. Heather J. Lynch and M. A. LaRue, First global census of the Adélie Penguin. The Auk, 131 (4):457-466, 2014/10/01 2014.
  2. Heather J.  Lynch,  and Mathew R. Schwaller, Mapping the Abundance and Distribution of Adélie Penguins Using Landsat-7: First Steps towards an Integrated Multi-Sensor Pipeline for Tracking Populations at the Continental Scale. PLOS ONE, 9 (11):e113301, 2014.
  3. Adam Voiland, Penguin Droppings Are Fertile Ground for Science : Image of the Day. NASA Earth Observatory.2017,

PS.  Wouldn’t “Penguin Guano” be a good name for a band? How about ‘Adelie Census’?



Space Saturday

Baby Bison Born!

I’m a long time Bisonophile and enthusiastic supporter of restoring wild Buffalo herds to North America. I’m particularly happy with the strong role of various Native America tribes, working through the political and technical barriers, and finding land to host the new herds. It almost goes without saying that this restoration has immense symbolic and cultural significance for the peoples who once lived with the Buffalo.

There has been a steady stream of reintroductions, notably to Banff earlier this year and  Blackfeet Reservation and Ft. Peck Reservation in earlier years This month was marked by another milestone, the birth of a calf on the Eastern Shoshone Wind River Reservation.

The birth of the bison calf catalyzes important conversations to be had about tribal protection of this spiritually important ungulate on tribal lands. CREDIT COURTESY OF JASON BALDES

You go little guy!

As part of a twenty year project to restore buffalo to tribal lands, the Eastern Shoshone received ten buffalo last fall. The new baby is a welcome sign that the Bison are settling in, and a promise of a permanent presence in the future.

Jason Baldes considers this to be more than wildlife management, for him it is a form of restorative justice. He commented on Yellowstone Public Radio,

What happened to Native people similarly happened to buffalo and we’re now isolated on former pockets of our once vast territories, you know, Indians on reservations and buffalo on national parks and refuges. And we’re kinda in a time now where we can handle that different.

At a time when knuckle draggers and latter day Medicis in Washington are plunging down a deeply destructive path, we can only hope that this little guy and his small tribe of buffalos can survive and thrive.

I’ll end with a culturally mixed welcome to the young one in Lakota, Taŋyáŋ yahí.

(I know very well that Lakota is not the same as Shoshone. But I have an online translator for Lakota, and this was an opportunity to learn a new word. I’m sure Lakota people are happy at the birth as well.)

  1. Brie Ripley, Eastern Shoshone Tribe Celebrate First Baby Buffalo Born On Reservation In Over A Century Yellowstone Public Radio.May 8 2017,


Weidensaul on “The New Migration Science”

Of all the cool things about birds (they fly! they sing! they have feathers! they are living dinosaurs!) one of the most profound is their astonishing seasonal migrations.

Scott Weidensaul writes for the Cornell Lab of Ornithology about technologies that are coming on line that enable scientists to gain unprecedented information about bird migrations.

[T]oday really is a truly exceptional time for migration science, with so many new avenues for documenting the journeys of birds.

First on the list are twenty first century leg bands, one gram geolocation recorders. Some larger birds can carry a satellite tag that tracks their travel and reports by radio. A cheaper and lighter option is a recording tag that logs the data, to be recovered when the bird is recaptured.

A third option are tiny radio transmitters that can be picked up by a network of collaborating receivers. With standardized signals and networked databases, a receiver can pick up and report any pings in its area, no matter who tagged the animal. The bird does not have to be recaptured, so there is much higher probability of encountering the tagged inividuals.

Weidensaul reports that both DNA and chemical isotope analyses can be made from a single feather or scrap of tissue. DNA can help sort out subpopulations, and isotope analysis can identify geographical history, e.g., of what the bird has eaten or drunk recently.

Recent improvements in data processing have enabled the routine use of NEXRAD weather radar to detect migrating flocks of birds each night. High resolution weather radar can also detect individual birds and reveal details of behavior. These studies, combined with remote sensing of vegetation and water, are enabling a detailed understanding of critical way stations where migratory birds rest for the day, and then continue.

With decades of archived NEXRAD, scientists are also studying trends over time. (The main trend is “down”, as we all might expect.)

Digital networks enable the combination of data from all these soruces, The internet also has automated the centuries-old traditions of collaboration among birders, creating massive crowdsourced datasets of observations.

Weidensaul reports current efforts to deploy cameras to automatically identify birds in cities. With today’s powerful visual analytics, it seems likely that inexpensive digital cameras will soon routinely identify and report individual birds.

Finally, inexpensive microphones on mobile devices or not can record high quality digital sound, which soon will enable a detailed picture of all the unseen birds in the area.

All of these digital technologies were developed for purposes other than ornithology. Almost no one develops complex and expensive technology just for observing birds. But birders will not be denied! These are some excellent examples of repurposing technology, and using powerful general purpose tools such as image and signal processing algorithms and machine learning.

And, of course, birders have been collaborating and crowd sourcing for centuries, long before computer scientists got into the game. Birders are some of the original citizen scientists, and, just as our feathered friends have persisted from dinosaur days, the global collaborative community of bird enthusiasts has survived centuries.  Now we have picked up digital technology and put it to good use.

  1. Bird Studies Canada. Motus Wildlife Tracking. 2017,
  2. Cornell Lab of Ornithology. eBird – Birding in the 21st Century. 2017,
  3. Scott Weidensaul, The New Migration Science, in All About Birds. 2017, Cornel Lab of Ornithology: Ithaca.

The Biological Computation in a Lizard’s Skin

Many plants and animals display fascinating multicolor geometric patterns, spots, stripes, swirls, and so on. How do these patterns develop? How does one bit of skin know it is supposed to be one color, and the bit next door another color?

At the dawn of the computer age, this question was recognized as a form of “computation”, in which the molecules, cells, and other structures of the organism somehow “calculate” a geometric equation.

Sensei Alan Turing himself explored the mathematics of reaction-diffusion (RD) equations, which describe some chemical reactions. He proved that some RD systems can produce patterns such as spots or swirls that resemble patterns seen in nature.

Around the same time, the other founding Olympian of computing, Johnny Von Neuman, explored cellular automata. These discrete systems are closely related to digital technology, and have become familiar through John Conway’s Game of Life. These systems can also produce geometric patterns that resemble natural biological systems.

Intuitively, these two systems seem similar (at least to me), but the math is not in any way similar. Like many interesting computer science problems, we have a continuous and a discrete “solution”, with a conceptual abyss between. They may both be correct, but it isn’t easy to get from one to the other.

This month Liana Manukyan, Sophie A. Montandon and a multidisciplinary team from University of Geneva and other institutions published a very beautiful study in Nature [1]. They examined the skin color of the ocellated lizard (Timon lepidus). The young lizard is brown with white spots, and as it matures, the skin becomes black with green spots. More interesting, the spots are a pattern of colored scales, not a continuous patterns of cells.  I.e.,  “clumps” in a nearly hexagonal grid. This looks like a cellular automaton, at the level of these scales. How does this develop?

Credit: Michel C. Milinkovitch

The team observed maturing lizards for several years, and discovered an additional wrinkle: the pattern changes continuously, with scales becoming green, and then switching to black over time, maintaining the spotted pattern. (I.e., when a scale turns gree, the surrounding scales turn black.  Clearly, there is some sort of dynamic process that is calculating “rules” analogous to a cellular automaton.

scale colour change in ocellated lizards follows a probabilistic CA process” ([1], p. 176)

Attacking this problem with computer simulations, the team found that the pattern could indeed be described as a cellular automaton (CA).  But what short of physical or chemical process could produce these “rules”?

Calling in the heavy cavalry from the Math department (or maybe they are the Pros from Dover), the team discovered that a RD system could produce this CA when the continuous functions are constrained by “interactions (cell–cell contacts) are substantially reduced between scales compared to within scales” (p. 177).

In other words, the 3D nubbiness of the skin moderates the continuous physical diffusion processes to create a discrete “computation”.  The scales are thicker in the middle, forming small islands with troughs between. This geography forms natural boundaries, and turns out to be a critical feature.

I love this study for many reasons.

The result is a deep and brilliant description of this biological process. As put it,

The highly multidisciplinary team of researchers had closed the loop in this amazing journey, from biology to physics to mathematics … and back to biology.” [2]

It is also a beautiful example of both computational thinking (conceiving the lizard’s spots as a biological computation) and computational methods (simulations of several types were essential).

Achieving this kind of beautiful result was only possible with a multidisciplinary collaboration, which is the great strength of major research universities. (And, by the way, this is much maligned “curiosity driven research”, with no commercial spin off in sight.)

Finally, the entire enterprise depended on a careful and long term observation of the natural system in question. All the theory and computation could not even begin without the solid empirical observations of the biologists.

Starting from the new- born stage (about 2 weeks after hatching), animals were scanned for a period of 3–4 years and with a frequency of two weeks to four months” ([1])

Google might have the math and computing resources, but they are unlikely to observe live lizards for four years as a run up.

  1. Liana Manukyan, Sophie A. Montandon, Anamarija Fofonjka, Stanislav Smirnov, and Michel C. Milinkovitch, A living mesoscopic cellular automaton made of skin scales. Nature, 544 (7649):173-179, 04/13/print 2017.
  2. How to color a lizard: From biology to mathematics. 2017,

UK Dawn Chorus Research

Our planet is awash in birdsong, and probably has been for hundreds of millions of yearsBirds are singing mostly to each other, and we humans can pick out individual songs and exchanges, if we work at it. But it’s a giant cocktail party problem, and it’s not easy for computers to separate out what’s going on.

In recent years there has been significant progress using machine learning techniques to recognizes and separate individual bird sounds from the natural chaos [2]. This is an interesting research tool, because it makes possible further studies of what birds are saying, and who is talking to whom [1].

This year this technology is being applied in a UK research project to study and decode the “dawn chorus”, the glorious time when all the songbirds wake and chatter at once [3].  This work seeks to extend earlier investigations on individual and small groups to this much more complex natural setting.

In addition to the boldness of the goal (and who doesn’t love the phrase “dawn chorus”), what caught my eye is that this project has a citizen science component, which has been building a large dataset of samples collected by a mobile phone app.

An earlier version of this concept was called Warbler, which records bird sounds and uses machine classification to identify the species.

Unfortunately, I’m not sure what this app does because I can’t get it.

The press release and the web site talk about “citizen science” and the general public, it turns out that they really mean “The Great British public”.  No foreigners allowed.

While I suspect that the project is most interested in recordings from their target areas in the UK, I’m pretty sure that the reason the app is restricted is political. These days, all UK research software is “free for Britons, not available for anyone else”. Sigh.

[Rambling complaints about the stupidity of this policy deleted.]

For the record, this project is based on research that depends on analysis of datasets openly available from around the world, and data from earlier studies is freely available.  It is software that the seems to be blockaded, no doubt under the mistaken impression that it is somehow commercially valuable.  Double sigh.

Anyway, I look forward to the study of the Dawn Chorus, and hope that we’ll be allowed to see the results beyond the press release.

  1. Dan Stowell, Lisa Gill, and David Clayton, Detailed temporal structure of communication networks in groups of songbirds. Journal of The Royal Society Interface, 13 (119) 2016.
  2. Dan Stowell and Mark D. Plumbley, Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning. PeerJ.2014, 2488
  3. The Engineering and Physical Sciences Research Council. Research teaches machines to decipher the dawn chorus. 2017,
  4. Warblr. Warblr: the birdsong recognition app. 2016,