Category Archives: Science

Dinosaur blubber!

As I have remarked many times, back when I was a young dinosaur enthusiast, we learned that we could never know much about the soft parts of ancient animals. Only bones and occasional imprints would be preserved in fossils, we were told.

Well, these days we are recovering many, many traces of flesh, skin, and feathers, and learning all kinds of things such as what color these ancient animals actually were.  Whoa!

This winter there is yet another wonderful find, this time the skin and tissue of a Jurassic ichthyosaur.  These animals visibly resemble porpoises and other whales, suggesting the results of convergent evolution toward highly optimized ocean swimmers.

The newly examined fossil contained traces of the skin and flesh of the animal, which strongly resemble the scaleless skin and blubber found in contemporary whales.  As the researchers say, the resemblance to whales “resemblance is more than skin deep “ ([1], p. 1)

In contemporary animals, insulating blubber is a “a hallmark of warm-blooded marine amniotes”, so this study provides the first direct evidence that these animals were warm blooded like whales.

The study also detected pigments indicating dark skin on the back (toward the surface).  This might have been camouflage and or might have contributed to thermoregulation.  The camouflage might protect against “flying pterosaurs, attacking from above, and pliosaurs (even bigger marine reptiles), which would have attacked from below”. It’s not easy being  an ichthyosaur!

The fossil belongs to a type of ichthyosaur called Stenopterygius . Credit: Science Photo Library Image

Overall, the fossil remains are quite similar to contemporary whales and sea turtles. These species are only distantly related, so this is a pretty clear case of convergent evolution.

Cool!


  1. Johan Lindgren, Peter Sjövall, Volker Thiel, Wenxia Zheng, Shosuke Ito, Kazumasa Wakamatsu, Rolf Hauff, Benjamin P. Kear, Anders Engdahl, Carl Alwmark, Mats E. Eriksson, Martin Jarenmark, Sven Sachs, Per E. Ahlberg, Federica Marone, Takeo Kuriyama, Ola Gustafsson, Per Malmberg, Aurélien Thomen, Irene Rodríguez-Meizoso, Per Uvdal, Makoto Ojika, and Mary H. Schweitzer, Soft-tissue evidence for homeothermy and crypsis in a Jurassic ichthyosaur. Nature, 2018/12/05 2018. https://doi.org/10.1038/s41586-018-0775-x
  2. Paul Rincon, Fossil preserves ‘sea monster’ blubber and skin, in BBC News- Science & Environment. 2018. https://www.bbc.com/news/science-environment-46457674

Good names for a band:

Fossil blubber
Jurassic ichthyosaur

 

 

More on Bird of Paradise Evolution

One of the coolest things about birds is their amazing color schemes.  They are the prettiest animals, and they are so diverse!

This, of course, poses a challenge for biological theory. Just how could such astonishing diversity develop, and what possible function can it serve.  (Being admired by me is not really much of an advantage for a bird.)

Sensei Charles Darwin, and many later theorists hypothesize that plumage, along with bird song, and other behaviors, have evolved by sexual selection. The idea is that certain features that have no other obvious survival advantage may simply be attractive to mates, and result in more breeding opportunity and success for the individual.

This theory has always been awfully hand wavy, even more than many ex post facto hypotheses about evolution.  Without access to the perception and cognition of individual animals, it’s really hard to know what features are even salient, let alone preferred.

A new study this winter suggests an alternative perspective on this question [1].  The team used data about the family of Birds of Paradise from the Cornell and other collections, which have an extremely diverse, and, indeed stunning array of visual features.  (At least they seem stunning and diverse to humans. Do we know what BoPs think?)

The researchers note that studying the features across this family is challenging, because they are so diverse. For example, species that are closely related should have similar features—but how do we assess “similarity”?  Just as an example, should we rate the displays by color (e.g., distance in a color wheel)?  Or in length and shape of feathers?  Or patterns?  Or all of the above?

The research approach is to broaden the “space”, to include everything that is involved in courtship displays: plumage, sounds, and behavior (dancing, nest building, etc.)  And viewing the broader data, they find that many of these features form correlated complexes of features.  And these complexes reduce the data, and suggest the dimensions that may be biologically relevant.

The data was broken down into (taxonomically unbounded) classes, i.e., descriptive features. In the case of ornaments, this described elements of the display.  Courtship behavior was classified in specific temporal actions (e.g., “upright posture”).  And sounds were statistically clustered into classes.

Together, these form a (large) feature space.  Individual species were then rated on the number and diversity of features in this whole space.

“Specifically, we evaluated richness (the number of unique elements) and diversity (using an index dependent on the number and relative contribution of each element type) “ p. 3

Fig 1. Birds-of-paradise exhibit extreme diversity in colors, sounds, and behaviors used during courtship displays, necessitating novel methods to quantitatively evaluate the evolution of their complexity. (A) Sixteen exemplar species (purple tips) are shown with their phylogenetic relationships to highlight variation in plumage color, acoustic signals, and courtship display behavior. (B) Behavioral subunits were scored from field-captured videos of displaying males (S3 and S4 Tables). Behavioral subunits were combined to create composite behaviors describing any behavior across species and facilitating sliding-window analysis of behaviors and behavioral sequences. (C) UV and visual spectrum images were taken of museum specimens (S7 Table) and used to generate avian visual model-informed image stacks. Color values were clustered with respect to modeled avian discriminability, enabling whole-specimen quantification of color richness and diversity. (D) All bird-of-paradise sounds were placed into a multidimensional acoustic space defined by principal components analysis. Sounds were then given identities based on locations within acoustic space, facilitating a sliding-window analysis of sounds and acoustic sequences (S8 and S9 Tables). lws, long-wavelength sensitive; mws, medium-wavelength sensitive; sws, short-wavelength sensitive; UV, ultraviolet; uvs, ultraviolet sensitive. https://doi.org/10.1371/journal.pbio.2006962.g001

Analysis revealed correlations between color diversity and acoustic diversity and behavior diversity and acoustic diversity (though not between color diversity and acoustic diversity).

The researchers argue that these findings show “functional integration of ornamental traits into a composite unit—the “courtship phenotype.” “ (p.1)  In short, BoP’s have a similar ancestral composite “courtship stuff”, which varies due to specific adaptations, such as ground versus understory courtship.  Looking at “signal extremes” in plumage, for instance, is misleading, if the behavior and sounds are not taken account.

The researchers also argue that this conservation of this composite courtship stuff is evidence of strong sexual selection. Essentially, the “robust” feature space allows individual features to evolve rapidly and significantly, while conserving the overall composite signal.

Hmm.  I can see that this integral composite feature space opens the way for evolutionary divergence under some kinds of selection.  I’m not sure that the case for sexual selection is any stronger than others.  It’s still hand waving—we don’t know what selected for diversification of these features, so let’s fall back on the explanation that “girls like that stuff”.

To be fair, the paper is careful to say that this study suggests the kinds of questions to investigate “the perceptual abilities … and psychology of signal receivers … as well as the environments through which signals are transmitted.” (p. 10)  That is, the overall set of features is a composite “signal” to the females, and any sexual selection would be due to how those signals are received, perceived, and preferred.

So even if this isn’t direct evidence about purported sexual selection, it is a really useful guide to what to look for in the “signal receivers” (i.e., the “girls”).

Neat.

I’ll note that this is an excellent example of the uses of digital media archives (combined with physical specimens).  It isn’t really “big data”, but it is “getting to be enough data to do something useful”.


  1. Russell A. Ligon, Christopher D. Diaz, Janelle L. Morano, Jolyon Troscianko, Martin Stevens, Annalyse Moskeland, Timothy G. Laman, and Edwin Scholes, III, Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise. PLOS Biology, 16 (11):e2006962, 2018. https://doi.org/10.1371/journal.pbio.2006962

Evidence that Shark skin patterns grow a la Turing

Toward the end of his life, Sensei Alan Turing turned his thoughts to biological systems [2], in particular, to possible natural algorithm-like developmental processes [3].  This pioneering work is a fascinating preview of the profound effect that computational thinking would come to have on biology.  Grand Master Turing  glimpsed the possibilities, without knowing anywhere as much as we do about the molecular mechanisms that might implement them.  (We ar not worthy!)

In his early deep vision of mechanical computing, his morphogenesis concept was crude and limited by the technology of the time. But it still seems to be valid.

This month researchers from Britain report that a Turing reaction-diffusion model describes the development of the pattern of bumps on shark’s skin. The skin of a shark has distinctive denticles,  variations of which play a role in “protective armor, hydrodynamic drag reduction, feeding, and communication” ([1], p. 5)

First, the study indicates that the patterns are not random, but correspond to a reaction-diffusion process.  The research followed the development of baby sharks, recording the development of their skin.  They find that the denticles develop as expected from a RD model. Furthermore, the study identified an array of genes that appear to express during development in just this way.

Besides offering a possible example of a Turing RD development process, these findings are interesting in two other ways.

The key point of  the Turing RD concept is that a relatively simple process can yield many different results by “tuning” parameters to the RD process.  The computational simulation in this study showed exactly this feature. Retuning the simulation yielded patterns found in different species and areas of the skin.  Thus, it is very possible that a single set of genes could generate a variety of different shark skins, “tuned” by other genes.

“The plasticity of this system may underlie broad variations covering the vast spectrum of vertebrate epithelial appendage patterns.” [1],  p.5)

At an even deeper level, the genetic mechanisms identified in this study are present in birds, and appear to have a similar role in the development of feathers.  In other words, this is a very old mechanism, shared by many vertebrates. Superficially different features such as denticles, feathers, and hair, are built on this fundamental process inherited from some long ago vertebrate.  The skin of sharks, birds, and mammals are deeply similar, which makes sense because we share an ancient ancestor.

“We suggest that diverse vertebrate groups share this common, conserved patterning mechanism, before deviation in later morphogenesis gives rise to clade-specific integumentary appendages, such as denticles, feathers, and hair.” ([1],  Pp6)

It is pleasing to see that Sensei Alan not only got it right, he was seeing right down into the deep core of life.

Cool.


  1. Rory L. Cooper, Alexandre P. Thiery, Alexander G. Fletcher, Daniel J. Delbarre, Liam J. Rasch, and Gareth J. Fraser, An ancient Turing-like patterning mechanism regulates skin denticle development in sharks. Science Advances, 4 (11):eaau5484, 2018. http://advances.sciencemag.org/content/4/11/eaau5484.abstract
  2. Andrew Hodges, Alan Turing :the enigma, New York, Simon & Schuster, 1983.
  3. Alan M. Turing, The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 237 (641):37, 1952. http://rstb.royalsocietypublishing.org/content/237/641/37.abstract

Asteroid Visit – OSIRIS-REX on station at Bennu

The Japanese/ESA Hayabusa2 A asteroid probe is on station and mapping Ryugu, and has already dropped three surface probes, in preparaton for a touch down to collect a sample, a cool “penetration” probe, and then return to Earth starting in 2020.

Meanwhile, the NASA OSIRIS-Rex probe has caught up with and taken station at it’s target asteroid, Bennu [2].  The spacecraft will map and measure Bennu close up, and will observe the Yarkovsky effect there.

Up close, the initial images show the peculiarly rectilinear shape, and a really rough surface.  (The latter is probably a result of aforesaid Yarkovsky effect. I dunno about the former.)

This series of images taken by the OSIRIS-REx spacecraft shows Bennu in one full rotation from a distance of around 50 miles (80 km). The spacecraft’s PolyCam camera obtained the 36 2.2-millisecond frames over a period of four hours and 18 minutes. Credit: NASA/Goddard/University of Arizona. (From [2])
Out there, things move at a stately celestial pace, so it will be a while before OSIRIS-Rex drops in to scoop and sample, and they ultimately returns in 2021, to arrive in 2023.

If these efforts succeed, we should get not one but two asteroid samples circa 2022.

Not one, but two asteroid return missions! Cool!


  1. Jonathan Amos, Osiris-Rex: Nasa probe arrives at Asteroid Bennu, in BBC News – Science & Environment. 2018. https://www.bbc.com/news/science-environment-46428018
  2. OSIRIS-REx Asteroid Sample Return Mission, NASA’S OSIRIS-REx Spacecraft Arrives at Asteroid Bennu, in OSIRIS-Rex – News. 2018. https://www.asteroidmission.org/?latest-news=nasas-osiris-rex-spacecraft-arrives-asteroid-bennu

Space Saturday

What’s happening with all those whales?

We’ve all been worried by recent mass strandings of whales, including several in a few days in New Zealand.  Is this just bad luck, or is there something seriously wrong?

Whales have foundered for as long as there have been whales, and people tend to notice—it’s a big mess and often very sad to watch.

No one really knows what happened to these animals.  Whales are generally exceptional swimmers (obviously), and live their entire lives without swimming onto a beach. I mean, c’mon, shamu!

Over the years, I have heard various theories from mundane (sick, struggling animals), through speculative (navigation errors, communication errors, suicide, predator attacks), to the mystical (psychically reverting to an earlier life when that whale lived on land).

Naturally, in recent years other hypotheses have sought to implicate humans (secret military sonar, pollution) and climate change.

With a sudden local up tick in strandings, we have to wonder if there is something causing them.

Gareth Evans reports on these questions with respect to the recent groundings in New Zealand [1]. It’s a pretty good summary of the main (non-mystical) hypotheses.

First of all, in the case of mass strandings of tens of whales, it generally isn’t because they are all sick or dying.  That may be true in some cases of individual beached whales, but the rarer group deaths are surely different.

One probable cause is navigation errors in places where a bit of dangerously shallow water has unfavorable conditions for whale sonar.  In these cases, whales may be confused and come too close, and perhaps become trapped by receding tides.  (Human activity such as military sonar conceivably might play a role in this, but generally probably not.)

Another likely cause is herd behavior.  Many whales swim together in groups, and follow the pack. If a lead whale makes a mistake or is ill, or for whatever reason goes into shallow water, many whales might follow the lead right into danger.  Pilot whales seem particularly apt to such herd behavior, and there is at least one documented case of mass beaching that seems to have been due to many pilot whales following a distressed and distracted mother onto the beach.

It wouldn’t seem that these cases would be any more frequent now than any other time.

Of course, it is possible that pollution, sonar, or other human disturbance is debilitating (or deranging) whales.  In fact, we know human activity definitely is endangering and killing whales.  But what would specifically cause beaching?

One possibility could be climate change. Specifically ,warming water at the surface changes where food sources are found.  Chasing food into unfamiliar waters might be risky, especially because the whales would not have learned the local hazards. However, this hypothesized link to climate change is a bit hand wavy, at least in cases where we don’t know how food sources have actually changed (which basically we know nothing much about).

However, if changing environments and unfamiliar waters are an important role in mass beachings, then we may see these incidents decrease in the coming decades. Whales are pretty smart and social, so they should figure these things out and pass along what they have learned.  (Assuming that whales survive long into the Athropocene, which is very much in doubt.)

We’ll see.


  1. Gareth Evans, New Zealand beached whales: Why are so many getting stranded?, in BBC News – Science & Environment. 2018. https://www.bbc.com/news/world-asia-46400957

 

Why so many fires in California?

A young friend asked me, what’s going on with all those fires in California?   I think he wanted me to refute or agree with recent comments by the President.

I was pretty sure I knew the basic answer:  California is a fire ecology, it always has fires.  And with millions of people now living in fire prone areas, at least part of the “news” is simply due to fires and people being in the same places.  (And, in this battle, my money is on “fire”.)

I also know that we have known for many decades that putting out wild fires is neither good for the forest, nor ultimately for people.  No fire this year only means that there will be a bigger fire next year or the year after. And bear in mind that even non-forest areas of California are fire ecologies of one kind or another—practically all of California is a fire-prone area.  (Again–this is a game that “fire” is going to win.)

My young friend and I also thought about the fact that it only takes one stupid or crazy person to start a fire, even if 10 million other people are very careful.  Millions of people living in fire prone areas is pretty much guaranteed to mean something happens.

These are all things I learned in high school, but they are pretty general.  What is really going on in California?  And does the Tweeter-in-Chief (TOTUS?) have a point that better management could prevent or lessen these fires?

Ash Ngu and Sahil Chinoy report in the NYT this week on the historical substance of these questions [1].   They have some great graphics, along with solid background.

Before European settlement, something like 1.5 million acres of forest burned per year in what is now California, and a given patch burned every 5-20 years or so.  These fires clear out dead material and the forest regrows with new, healthy trees in the sunny, open areas.

In my lifetime, and since 1950, people have worked hard to suppress these small fires, so that less than a few per cent as many acres burned, and consequently, many areas go many decades without a fire.  With no fires, the forest floor piles up with fuel.

In addition, some areas have see logging, which removes the largest, older trees, making way for dense growths of young trees.  These are much more fire prone than the fewer, older trees.

Finally, people have indeed been moving into the forests, building millions of houses and buildings in fire prone areas.  The article cites estimates that 11 million people currently live in “wildland-urban interface” areas. If nothing else, this makes it nearly impossible to do controlled burns to reduce the fire risk.  It also, of course, increases the likelihood of human error igniting a fire.

It is also true that recent decades have been very dry, and forests have been dying, at least in part due to human activities such as pollution and habitat change.  Given the long history of droughts and related die-offs, it’s hard to parse out human contributions from natural cycles, but massive human activities can’t be helping the forests very much, and probably are accelerating trends.

So is there any kind of sensible management that could actually control this situation, as implied by DJT?  To date, the main approach has been controlled burns, which, in principle, mimic the natural biology of the area.  Of course, these are expensive and tricky to get right, and deeply unpopular (not least with billionaire property developers who want the some to only blow over poor people.)

The “interface” can, of course, be done better, keeping areas near buildings clear of fuel, and making buildings fire resistant.  That takes money, planning, and cooperation, all of which are hard to make happen (not least because billionaire property developers resist “big government” and the “nanny state” interfering with profits).

It probably would be a good idea to reduce logging and housing developments in wild areas, but that’s certainly not the policy of the current administration in Washington.

So, sure, there is room for improvement in a lot of ways. But a lot of the challenge isn’t that we don’t know what the problem is, it’s that we simply don’t have the political ability to implement it.

Think about it:  the best solution would be to pull back from the forests, and burn a lot of small areas every year.  Basically, continuous small fires all the time, instead of sudden gigantic fires.

No one really wants that, especially said billionaire property developers.

On the other hand, Mother Nature will ultimately “fix” the problem.  Fire will happen.  If humans put off the fire for years or decades, eventually, the fire will overcome human defenses.

So there is a more complete and up to data answer.  It’s nice to know that what I was taught was basically correct.


  1. Ash Ngu and Sahil Chinoy (2018) To Help Prevent the Next Big Wildfire, Let the Forest Burn The New York Times, https://www.nytimes.com/interactive/2018/11/29/opinion/sunday/california-wildfires-forest-management.html

 

Space Intefereometry to Measure Earth’s Gravity

Earth observation from space has always been full of cool technologies, using simple ideas to make incredibly sensitive measurements.  (If you ever get a chance, have a scientist explain, say, how they interpret each photon captured by an orbital instrument—it’s an awesome feat of applied physics!)

It is now cheap enough to send many satellites up at the same time, and, in fact, to create swarms of satellites working together.  This opens yet more cool modes for measuring things.

This year NASA and the German Space Program are booting up a new mission, GRACE-FO (the ‘FO’ stands for ‘follow on’ from the first GRACE mission).  This instrument is actually two satellites, identical twins, that orbit one after another in the same 500km orbit.  The satellites have microwave range detectors and other instruments to keep track of the position and distance between the two spacecraft.

As the spacecraft orbit, small local variations in Earth’s gravity cause each satellite to speed up and slow down in turn, which is detected in tiny changes in the distance between the instruments.  These changes are due to small differences in the mass and density of the Earth, e.g., the presence of mountains or accumulations of water

There is an excellent illustration of how this works at the NASA Earth Observatory [1].  The tiny jiggles can be interpreted to detect the Himalayas versus the Indian Ocean.

From [1]
The new spacecraft have a new laser ranging system which should make the measurements ten times as sensitive.

With this instrument continuously orbiting and extending the fifteen years of the first satellite, it will be possible to track subtle changes, such as seasonal melting snow cover, and the rise and drop of groundwater.

It probably can detect other things, such as earth movements before a volcanic eruption or earthquake.  It may also measure changes in icecaps, and I think it can detect major ocean currents such as El Nino.

Cool!


  1. Michael Carlowicz, The Himalaya Plot, in NASA Earth Observatory – Image of the Day. 2018. https://earthobservatory.nasa.gov/images/144205/the-himalaya-plot