Category Archives: Nature

How Zebra Finches Learn A Song

The second coolest things about birds (the coolest thing is that they can fly, fer goodness sake!) is that they sing. Furthermore, song birds learn their songs from the examples of their local group, just like humans learn to speak.

Learning a new song, just like learning to speak a new language, is hard, especially with only examples to work from. In fact, it would seem to be logically impossible—but everybody does it!

This month Dina Lipkind and colleagues in New York and Zurich report a neat study of how Zebra Finches learn a new song [1].

Their basic observation is that learning a song (or utterance) requires learning to make the sounds and learning to make them in the right order and timing. In any but the shortest song, the number of possibilities is far too large for trial an error, or even for progressive approximation of the model. It’s computationally infeasible, AKA, impossible. (The imperfection of the model, and the presence of multiple exemplars only makes things more complicated.)

Lipkind and colleagues explore a possible simple, if non-optimal, strategy: decompose the learning into pieces. Specifically, the student might learn to make all the sounds individually, and then fix up the sequence later.

The experiments use Zebra Finches, a favorite and well studied species. The investigators presented recorded and synthetic songs, and recorded the partially learned songs. Specifically, they analyzed the errors in detail. (See the paper for details.)

Their conclusion is that these birds have neural machinery for learning the pitch of tones (i.e., the pieces of the song), which learns the tone relative to neighboring tones, not the whole song. Essentially, this learns each piece, without trying to keep things in order.

A second phase learns the correct sequence, which involves learning the transitions between the pieces. The researchers conclude that this is a separate neural mechanism.

“Thus, zebra finches break down the computationally difficult task of exploring the entire space of possible motor permutations, into two simpler tasks, yielding a search for solutions that is non-optimal, but manageable.” (p. 8)

This is an interesting finding, because it parallels aspects of human learning. Furthermore, it is analogous to the most successful strategy for computing document similarity. This isn’t so much bioinspired design as bio-confirmed convergent design. Cool!

This study was non-invasive and didn’t directly measure the brain activity. So it is not known how these processes are realized in the finch brains. The study does constrain the types of neural structures that might perform as observed, though. Future research may be able to document the internal processes.

The study leaves a number of questions open. For one thing, how are the individual segments (“gestures”) learned or, for that matter, identified as units. E.g., for human babies, learning to utter phonemes is relatively simple, but only if you know how to find the beginning and end of a phoneme—which isn’t obvious.

I would note from experience that this problem is endemic in learning algorithms. I have struggled with machine learning attempts to recognize gestures from movements. It’s very hard, if not impossible, to induce where gestures begin and end, at least without supervision.

Further studies of songbirds may offer bioinspired tricks for learning gestures from examples. (E.g., hints about what is a gesture to be learned.)

The researchers speculate that this decomposition might be an evolutionary compromise between that offers efficient learning with relatively little neural resources. The intuition is that the two simpler learning processes require significant neural tissue and energy, but much less than more complicated optimization strategies. Proving this case will require a lot more information about how zebra finch brains actually work, and also what conceivable alternative architectures might be.

  1. Dina Lipkind, Anja T. Zai, Alexander Hanuschkin, Gary F. Marcus, Ofer Tchernichovski, and Richard H. R. Hahnloser, Songbirds work around computational complexity by learning song vocabulary independently of sequence. Nature Communications, 8 (1):1247, 2017/11/01 2017.


Bison Restoration: Wind River Herd Is Growing

I’m a huge fan of Bison restoration, and I’ve been pleased to see the careful reintroduction of wild bison to Banff, Montana, and Wind River, among other places. It is particularly gratifying that Native Americans are stewards of this process, which bolsters and renew ancient cultures and guarantees thoughtful human protectors for the Bison.

Last year we celebrated the introduction of 10 Bison to a free range on the Wind River Reservation in Wyoming, and a calf was born in May, to great acclamation. The project is led by the Eastern Shoshone Tribe’s Boy-zshan Bi-den (Buffalo Return) program.

This fall, an additional ten animals will be added to the herd.  The latest batch is another group of “genetically pure” animals, unmixed with domestic cattle, which will further broaden the gene pool of the Wind River herd.

At 21 animals (I assume), the tiny herd can’t be considered self sustaining (the program aims for 1000 head), but it’s a start. Presumably, happy Buffalo will make more Buffalo themselves, so things should take off.

I probably will never see these Bison in person, but it makes me happy to know they are there, living as they should.

  1. Melodie Edwards, Eastern Shoshone Tribe To Add Ten More Wild Bison To Herd in Wyoming Pubic Media. 2017.
  2. Garrit Voggesser, Buffalo Break New Trails on Wind River, in National Wildlife Federation – Blog. 2017.


More Evidence of Pesticide Harm to Pollinators

Bees and other pollinators seem to be dying off or disappearing in many parts of the Earth. This is a bad thing—if only because humans depend on these species to help plants grow.

In the past decade, evidence has accumulated, confirming the grim picture of world wide decline. It isn’t clear why this is happening, but one leading factor seems to be pesticides, specifically, neonics. These chemicals are applied to seeds to protect them which is much less dangerous than broad spraying or soaking the soil. However, it appears that residues persist and are picked up and accumulate in the bodies of pollinators. Neonics are potent neurotoxins for bees, and they certainly could be dangerous.

This month a group from University of Neuchâtel published a study of 198 samples of honey from around the world [2]. Traces of neocortinoids were found in 75% of the samples, representing every continent except Antarctica. These traces suggest that the bees that made the honey have indeed been exposed to these chemicals.

The levels of the chemicals in the honey are not dangerous, per se. It also isn’t clear what the reported contamination implies about exposure of the bees. I.e., how much exposure do these samples represent? Do these residues indicated harmful effects on the pollinators?

The findings certainly raise concern because of the broad geographic range, and the presence of multiple chemicals in the samples. Whatever is going on, it seems to be happening everywhere.

This issue is becoming mired in controversy. Manufacturers of the pesticides seem to be in a “denial” stage, rejecting early evidence of the harm to pollinators, and demanding higher standards of proof (e.g., [1]). Obviously, they have reason to want solid evidence that their lucrative products need to be withdrawn. (There is also a geopolitical dimension, as some countries have found it easy to ban US made products, regardless of the reason.)

I have to wonder a bit at the criticism of this study. The press and industry organizations were emphatic that the reported contamination level isn’t dangerous to people <<link BBC>>. That, of course, is nearly irrelevant. The important point is how healthy the bees are, which we don’t know.

There was also criticism that the sample is “too small” to draw conclusions. This is a bit hard to understand. The conclusion is that traces were found in many samples all over the world. Who cares if it is 75% or 50% or 10% of the samples, when the same contaminants are found everywhere. If these tiny traces show up in a small sample, they aren’t likely to disappear in any larger sample, too.

I would hope that these trade associations that reject this research as inconclusive are conducting their own, larger studies to determine what the actual facts are. If not, then they are just playing PR games to protect their profits, and I will have no trust in anything they say on the topic.

  1. Matt McGrath, Pesticides linked to bee deaths found in most honey samples, in BBC News -Science & Environmen. 2017.
  2. E. A. D. Mitchell, B. Mulhauser, M. Mulot, A. Mutabazi, G. Glauser, and A. Aebi, A worldwide survey of neonicotinoids in honey. Science, 358 (6359):109, 2017.


What do birds do in an eclipse?

The August solar eclipse had a noticeable impact on solar power generation and other human activities (such as tourism).

Birds are quite aware of the sun and weather conditions. Many birds are active at particular times of day, hunting in sunlight or in darkness. So what do birds make of a sudden, unexpected nightfall and then another dawn

Benjamin Van Doren, Andrew Farnsworth, and Ian Davies write in BirdCast about “What Do Birds Do During a Total Eclipse?” The article is a collection of field observations during the solar eclipse.

Overall, birds seem to have responded to the darkness the same way that they behave at night. Daytime species seem to have gone to roost, and nighttime species came out to hunt. The eclipse doesn’t last very long, though, so nobody had time to completely go to sleep or wake up.

One interesting image shows radar data that detects birds in the air. As the total eclipse passed the area, the air cleared in the shadow. Daytime birds dropped down toward their roosts, and nighttime birds did not take off yet. The result is a circular trace of “empty sky”. Cool!

The reports also note that insects woke up, and flowers started to close.  Many of the reports indicate that the birds seemed confused, which is certainly reasonable under the circumstances.

BirdCast also reminds us that It will take a long time for the Southern coast of the US to recover from the Hurricanes of September 2017. We will no doubt learn that wildlife was affected by the huge storms. For instance, it is likely that birds (and other animals) were pushed North by the powerful winds. As they find there way back to the usual homes, like the people the birds will find trees (their homes) destroyed, and flood waters everywhere. As everyone returns and rebuilds, birders will no doubt report how birds cope with the storms.

  1. Benjamin Van Doren, Andrew Farnsworth, and Ian Davies, What Do Birds Do During a Total Eclipse? Observations from eBird and Radar on August 21, , in BirdCast. 2017.


Armadillos On The March!

It’s a good thing the climate isn’t changing, because if things were getting warmer, then all those crazy animals from Florida and Texas would be moving North.

Such as Armadillos.

In recent years, these weird Paleolithic beasts have been sighted more and more frequently farther North than in past centuries. They have been found in Illinois, and this month one was sighted within blocks of my house.


Overall, the data indicates that Armadillos are definitely spreading North.

Pictured here is the range of armadillos.


Naturalists say that these guys really can’t stand really cold winter days, so they used to not live here. But the last decades have seen warmer winters, and we are now habitable territory for armadillos.

I guess this could be yet another clever hoax by those sneaky scientists. Everyone knows that Big Armadillo hates America and is waging war on coal and oil. “They” will stop at nothing, including fake Armadillo sightings. Could this be opossums dressed up in foam armor?


  1. Prairie Rivers Network, Armadillos, Illinois’ Armored Invader, in Prairie Rivers Network Home. 2017.
  2. Mark Schultz, First Armadillo Confirmed In Champaign County, in WILL Radio News. 2017: Urbana.



Science makes you think, man. It makes you think big. And it makes you see yourself as tiny.

The Universe seems to be 98% Dark Matter and Energy—which we know nothing about.  Earth is teeming with life, 99% of it microscopic, and much of it unknown to humans [2]. The Earth is certainly several billion years old, and humans have been around only the last tick of that clock. Life has almost died out at least five times in those billions of years.

This month, Jochen Brocks and colleagues have published a rather fiddly study of biochemical traces in very old rocks [1]. The chemicals are left by squishy aquatic microlife that leaves little other fossil record.

Detecting these compounds is difficult because rocks are usually contaminated with younger chemicals (prominently including “anthropogenic petroleum products”) which swamp the faint older deposits. The researchers carefully screened out known contaminants, in order to measure the proportions of steranes and hopanes in the rocks. These are markers for eukaryotic cells, so the data indirectly indicate the predominance of bacteria in the environment.

They link these studies to current understanding of paleoclimate. They find evidence for a remarkable story. Roughly 700 million years ago was “Sturtian snowball glaciation”, an extreme ice age that froze the oceans all the way to the bottom. Before this period, eukarytes predominated, and they died back dramatically during the 100 million year ice age.

At the end of the Sturian, the abundance of bacteria increased, reaching modern abundance within a few tens of million years. Then something happened that enabled Algae to overcome the cyanobacteria, and eventually flood the world with oxygen and animals like us.

The researchers suggest that the glaciation and subsequent melting flooded the oceans with nutrients ground up by the ice cover, which eventually tipped the balance in favor of algae. They offer a possible scenario for this transition. At some point, algae evolved as a hybrid eukaryte engulfing a cyanobacteria, and thrived. This led to rapid evolution of animals that feed on algae.

If this scenario is correct then algae emerged and survived, but only came to dominate the oceans after a billion years. If so, then an episode of extreme global climate change probably led the rise of the biochemistry and ecology that we need to exist.

This study is very interesting, but far from conclusive. Even assuming the data is correct, it still isn’t clear whether the emergence of algae really triggered the evolution of animals, or how other factors were involved.[2].

Still, this is a reminder that the world we see is scarcely the only possible way things could work. It is also makes us realize just how much deep history is floating around in our own cells—we are descended from life that thrived on a radically alien Earth.

  1. Jochen J. Brocks, Amber J. M. Jarrett, Eva Sirantoine, Christian Hallmann, Yosuke Hoshino, and Tharika Liyanage, The rise of algae in Cryogenian oceans and the emergence of animals. Nature, advance online publication 08/16/online 2017.
  2. Friend, Tim, The Third Domain: The Untold Story of Archaea and the Future of Biotechnology, Washington, DC, Joseph Henry Press, 2007.
  3. Roland Pease, The algae that terraformed Earth, in BBC News – Science & Environment. 2017.


Penguin Feathers Tell All

One of the important questions for filed biology is to document and understand the movements of animals, which reveals many aspects of behavior, including nesting, mating, what they eat, and what eats them. But it isn’t at all easy to track animals in the wild.

For centuries, this difficult problem was tackled through personal observations and with tags. The former is possible only in some fortunate circumstances, and the latter requires capture, release, and recapture, which is difficult, expensive, and lossy. But 21st century technology is now available (and cheap enough) for filed biologiists to use.

In recent years, electronic location tags have become small and cheap, opening a new age of animal tracking. With a small radio tag attached, almost any animal can be tracked, on land, sea, or air. This still requires capture and release or at least touching the animal to tag it. And tags are cheap but not free.

Another cool advance is the use of chemical analysis of tissue to infer the travels and history of an animal. These techniques have advanced to the point that one discarded feather can speak volumes—without harming the animal.

This month Michael J. Polito and colleagues report on some successful experiments tracking Penguins through this method [2]. The study tagged Penguins with location tracking tags and when recaptured, took one tail feather.

The chemical analysis of the feathers detected the isotopes of Carbon in the feathers, which are different in different regions of the ocean, which have different plankton and fish to eat. The study showed that this method was as accurate as the location tag in identifying which waters were visited by each bird that winter.


This means that catching a sample of Penguins once (rather than twice) and plucking one feather (rather than attaching a tracker) can reveal where they fed during the dark winter.

  1. Sarah Gabbott, Penguin feathers record migration route, in BBC News -Science & Environment. 2017.
  2. Michael J. Polito,, Jefferson T. Hinke, Tom Hart, Mercedes Santos, Leah A. Houghton, and Simon R. Thorrold, Stable isotope analyses of feather amino acids identify penguin migration strategies at ocean basin scales. Biology Letters, 13 (8) 2017.