A Ducklike Dinosaur?

Dinosaurs occupied all of Earth, including the skies and waters.  Just as contemporary avian dinosaurs, ancient dinos evolved a plethora of bodies, specialized for different environments and ways of life.

This month, a team from Europe and Mongolia report on a new analysis of what appears to be a unique and weird looking aquatic dinosaur [1].  The particular specimen has an uncertain provenance, having been sold on the black market, and only recently examined by scientists [2].  Such a history screams “fake”, and the features of fossil are so unexpected that any reasonable person would assume it is phony.

However, careful examination with X-rays revealed that Halszkaraptor escuilliei is real, if unusual and, indeed mysterious. About the size of a Turkey, the specimen is clearly adapted for swimming – sort of.  Flipper like wings? Check.  Webbed feet? Nope?  Crocodile like snout? Check.

This is a reconstruction of Halszkaraptor escuilliei. The small dinosaur was a close relative of Velociraptor, but in both body shape and inferred lifestyle, it more closely recalls some water birds like modern swans. (Lukas Panzarin, with scientific supervision from Andrea Cau)

The paper offers an interesting diagram comparing the anatomy of Halszkaraptor to other animals. It seems to be partway between specialized swimmers and land animals. With only one specimen, and working only from the skeleton, it is difficult to know how to interpret this finding.

Morphometric analyses of aquatic adaptations in the Halszkaraptor forelimb. a, Binary plot of length ratios among manual digits I–III in aquatic and terrestrial sauropsids (n = 84): Halszkaraptor clusters with long-necked aquatic reptiles. b, Binary plot of principal components 2 and 3 from a morphometric analysis of ten skeletal characters of the forelimb and sternum in birds (n = 246; principal component 1 describes body size variation and is therefore not considered; see Supplementary Information): Halszkaraptor clusters with wing- propelled swimming birds. Silhouettes in a provided by D. Bonadonna and L. Panzarin.


This specimen is in the raptor family, which is the first aquatic raptor known. Indeed it is a rare swimming dinosaur.  Most of the dinosaur age sea life are not actually in the dinosaur family (they are related to turtles, et al.)

This study is a great example of how imaging technology is increasing the ability to understand fossil remains. Intensive but non-destructive examination made it possible to determine that this is not a fake, and to pull out details within the rock. Almost every paleontological report these days includes some form of “see through” imagery. This is a tremendous advance, and we can hope that methods will continue to improve.

(Many reports also include statistically constructed taxonomic trees, which I consider less of a boon. These family trees are as much art as science, and the visual appearance suggests far more certainty than is generally justified.)

Anyway, the dinosaur of the week is Halszkaraptor escuilliei!  (the designation “esculliel” honors the person who returned the fossil to Mongolia.)

  1. Andrea Cau, Vincent Beyrand, Dennis F. A. E. Voeten, Vincent Fernandez, Paul Tafforeau, Koen Stein, Rinchen Barsbold, Khishigjav Tsogtbaatar, Philip J. Currie, and Pascal Godefroit, Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs. Nature, 12/06/online 2017. http://dx.doi.org/10.1038/nature24679
  2. Nicholas St. Fleur, This Duck-Like Dinosaur Could Swim. That Isn’t the Strangest Thing About it., in New York Times – Trilobites. 2017: New York. https://www.nytimes.com/2017/12/06/science/duck-dinosaur-swim.html


Book Review: “The Adventurist” by J. Bradford Hipps

The Adventurist by J. Bradford Hipps

Hipps has worked as a software engineer, and this novel is set in a contemporary corporate software division.  Work life is described fairly realistically.  The protagonist is unhappy, though apparently not about work, per se.

I thought this story might be another of the growing “Revenge of the English Majors” genre, ferocious fictional accounts of the horrors of contemporary high tech capitalism (such as Touch, Startup, The Assistants, or even Sourdough).

But Hipps seems to be sympathetic to corporate life, however gawdawful it seems in his portrait.  Mostly he’s worried about lonely, lost people, who don’t seem to know what they want, let alone how to get it.  If anything, work offers a stage for lost people to act and interact.

Also unlike the emerging “revenge of the English majors” genre, the protagonist does not drop out to start a new, more humane life.  At the end, his troubles are unresolved (though his career does seem to be over).

Overall, this is a depressing and unsatisfying story. Everybody is unhappy, and there is no solution.

  1. J. Bradford Hipps, The Adventurist, New York, St. Martin’s Press, 2016.


Sunday Book Reviews

VR for Bacteria?

A group of researchers in Austria report an interesting immersive computer environment – for individual bacteria [1].

The key problem is to connect between the computer and the ‘sensory’ and ‘motor’ apparatus of the user-bacteria.  Touch screen and ear buds?  Not so much.

In the case of the E. coli, the I/O channels are chemical and light.  In particular, the subject bacteria have “a light-regulated gene transcription module.” (p.3 ) As this gene is switched on and off, the bacteria fluorescence changes (output detected by a microscope). Inputs are various nutrient chemicals.

The overall apparatus pins the individual bacteria in a channel with chemical input and outflows to sustain it for days under the microscope.  Immobilized this way, the bacteria’s environment is controlled by a computer, and its responses picked up by the computer.  I.e., this is a fully immersive computer interface for the E. coli!


This apparatus was designed to aid experimentation, but their paper shows various demonstrations that manipulate the bacteria into human recognizable patterns.  Interestingly, thee look a lot like the patterns generated by Conway’s Game of Life, which is a completely artificial digital “organism”.

Ironic demo of the year:  implement Game of Life with a grid of real E. coli!

The Institute for Science and Technology press release described this work as “Virtual Reality for Bacteria [2]. <lnk>> That’s an interesting claim.  It is true that the device creates an environment where the computer controls the perceptual input of the “user” bacteria, and the “user” interacts through natural behaviors in the environment, which are detected.  These are the essential features of and “immersive” computer interface.

Is it “virtual reality”?  It hard to say, because the essential feature of VR is that it “fools” the user, and is accepted as “real”.  These concepts are iffy for humans, and beyond dubious for E. coli.  My own view is that this is a questionable use of the term “virtual reality”.

Anywy, this is a great case to think about, because it really pushes the concepts to the very logical limits.

  1. Remy Chait, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Călin C. Guet, Shaping bacterial population behavior through computer-interfaced control of individual cells. Nature Communications, 8 (1):1535, 2017/11/16 2017. https://doi.org/10.1038/s41467-017-01683-1
  2. IST Austria, Virtual Reality for Bacteria, in IST Austria – News. 2017. http://ist.ac.at/nc/news-media/news/news-detail/article/virtual-reality-for-bacteria/6/

Birds Caching Food – Make That “To Go”, Please.

In 2016, Shailee Shah discussed why and how birds cache food for later [1].

As most everyone has observed, birds often grab food from a feeder and flit away without eating it. Sometimes, the same bird will come and go to a feeder many times, which seems like a lot of work compared to just sitting down and eating.

Why are they doing it?

In season, the birds may be taking food to nestlings.  But many birds choose take-out all year round.  Shah notes several reasons why birds might do this.

Some birds are worried about predators, so they seek safe cover.  Others may need to manipulate the food in specific says, e.g., to crack open nuts and seeds.

But, “arguably the most fascinating reason”, Shah says, is caching food for later.

The potential benefit of caching is obvious. When food is plentiful, store some of it away to eat later when there is less available.

But caching is hardly trivial.  Strategically, you need to hide the goodies well enough that others won’t find it, yet remember where you put it many months later. Birds are remarkably good at this memory game, keeping track of dozens or thousands of caches.  They are better at it than humans, I’m sure.

Shah lists eight different strategies and adaptations seen in different species of birds.

  • Caching for the short term or long-term
  • Specialized adaptations (e.g., cheek pouches)
  • Spatially precise, the ability to find the fold months later
  • Caches in niches and cracks in bark
  • Various patterns of scattering among multiple locations, up to thousands of locations per individual bird
  • Deception and camouflage to disguise the location of caches
  • Deceptive behavior to cache inconspicuously (e.g., out of sight of rivals)

This is a remarkable set of behaviors, and evidence (if we needed more) of how remarkable these feathered dinosaurs truly are.

Obviously, saving for future consumption implies a sense of time, natural cycles, object permanence, and goal.  It is difficult to say what, if anything, birds “understand” about this behavior.  But when humans do it, we praise it as “delayed gratification”, call it both wise and moral, and even base political economic policies on the supposed virtues of such savings.

Just remembering or rediscovering stored food months later is a difficult task. For many birds, this is aided by astonishingly effective visual memory, which is reflected by specialized brain structures.  In some cases, the brain structures may even grow larger during peak caching season.  (Note that these structures are unlike anything found in human or primate brains.  Humans can do it, but we aren’t doing it the way birds do.)

In addition, some of the strategies require sophisticated concepts about the world and other birds. In particular, deception and camouflage imply implicit knowledge that there are other foragers, and what their perceptual capabilities are. I.e., there are thieves out there, and they might be fooled in certain ways.

Even more interesting, some birds exhibit sophisticated social knowledge of their own species. They working to mislead or hide food from other individuals of their own species or, conversely, spying and stealing from others’ caches. In some cases, mates or comrades work together to mislead observers.

  1. Shailee Shah, Where Is That Bird Going With That Seed? It’s Caching Food for Later, in All About Birds. 2016, Cornell Lab of Ornithologyå. https://www.allaboutbirds.org/where-is-that-bird-going-with-that-seed-its-caching-food-for-later/


As I Said, Ethereum is Winning the CryptoTulip Award

I already tapped Ethereum as the favorite for CryptoTulip of the Year, but the goofiness goes on.  Not content with complete breakdowns and hundred million dollar oopsies, Ethereum is now plagued by a successful fad – CryptoKitties.

I learned about CryptoKitties from the BBC, which goes to show you that the mania is so manic it’s visible in the wider culture.

The idea of the game is slightly clever, though nothing that wasn’t done on a PDP 8 circa 1977. You can buy digital kitties, and, more interestingly, you can breed them.  I’m assuming you could trade or sell them.

The news is that this very simple artificial life game is implemented on the Ethereum blockchain, and financed via Ether.  Of course, you could have implemented this game in any number of ways.  It’s hard to say that the blockchain per se adds anything other than novelty.

There have been efforts to implement games using a blockchain before, but CryptoKitties has really caught on.  And that’s a problem.

Ethereum executable contracts are Turing Complete, which means that you can implement any computer program on the Ethereum blockchain. However, these scripts are going to be really, really slow, and there isn’t much storage available.  So most programs are going to suck badly on the blockchain.

In this case, the storage used by CryptoKitties has become a significant fraction of all the records in the entire Ethereum universe.  Recapitulating the history of campus mainframes, game playing is pushing out all other uses of the shared blockchain.

Of course, unlike University computing facilities, there is no authority to shut down the game on Ethererum.  So who knows what will happen?

Philosophically, we see that this episode illustrates that the classis Nakamotoan blockchain is vulnerable to a tragedy of the commons. In fact, it seems designed to be a demonstration of this phenomenon. And, by the way, there will certainly be attempts to clone the success of CryptoKitties.  So there could be multiple games, all sucking down the common resources.

This game shines an interesting light on the “value” of digital currency. CryptoKitties are fundamentally no different than any other tokens traded on a blockchain.  But these are dressed up with a concrete, human-visible representation, and a bit of human-oriented gameplay.  So these cryptographically secured digital tokens are selling like hotcakes, unlike most Ehtereum based apps.  Value depends on people.

It is also interesting to observe the cognitive dissonance produced by this challenge to the system. A lot of users are surely feeling that playing this pointless game a waste of blockchain resources, and taking away from the important, serious things they want to do. On the other hand, CryptoKitties is becoming one of the most successful businesses ever to use Ethereum. And if playing a game isn’t “serious”, it’s at least as reasonable a use as the endless variations on EBay or PayPal.  So, CryptoKitties is dumb, but people want it enough to actually pay for it.

Now, criticizing all the other users of the shared blockchain is just not done.  I mean, the whole Nakamotoan design requires a libertarian tolerance for what all those transactions you help with are really about. Did I just help implement an extortion payment?  Tax evasion?  Human trafficking?  Don’t ask.

It will be interesting to see if CryptoKitties continues to grow, and if so, what will happen to the whole system. Aside from the performance issues (at some point, CryptoKitties and clones could exceed the total capacity of the network protocols), crowding out other uses threatens the underlying logic of the consensus mechanism. I don’t think I’ve seen a design where a blockchain is dominated by a single massive application, while maintained by many independent nodes voluntarily participating in the verification and consensus protocols.

If one game is using all the resources and sucking much of the revenue, will that drive away everyone else?  If so, will there be a feedback effect, as fewer nodes lead others to drop out?  Will developers walk away?  Or just be hired by the game company?


  1. BBC News, CryptoKitties craze slows down transactions on Ethereum, in BBC News – Technology. 2017. http://www.bbc.com/news/technology-42237162


Cryptocurrency Thursday

Bitcoin Will Crash – Soon

Even the grown up news is filled this week with stories about Bitcoin’s soaring exchange rate against the USD and other currencies.  We also see the watershed moment when the CME gets in the game.

Who knows what may develop next, even in the instant between key strokes of a blogger?

So I’m not going to chase the skyrocket here. Instead, I will go on record and we’ll see how my predictions go.

For the record, I am saying:

Bitcoin is bubbling irrationally and will crash very soon. Probably by the end of the year.

There will be a lot of ups and downs, of course. Unregulated electronic trading is a recipe for chaos, and that will happen.  The details of chaos mean nothing other than, well, chaos.

There will be fall out from all the movements.  Systems will fail, will be hacked, and in some cases will cheat their customers.  Naïve speculators will discover that “at your own risk” means “too bad for you”. People will discover that unregulated, offshore, “autonomous” systems are, well, not protected by law or anything at all.

Ultimately, Bitcoin will be tarnished and with good reason. Whatever Bitcoin might be useful for, the world never needed this kind of virtual Tulip Mania.

I also predict that regulators will step in to close the barn door.  There will also be schemes floated to create various self-regulatory and self-insurance schemes that reproduce the conventional financial system.  These will have little impact on the giddy Bitcoinistas.

And finally, remember that Bitcoin still hasn’t figured out how to solve its scaling problem.  Sooner or later, technological obsolescence will take its toll, and the masses will boot up new cryptocurrencies, to recapitulate history.


(Note: this was originally drafted on Monday December 5, 2017.   Who knows what may happen in the interim while the post is queued.)



Cryptocurency Thursday

Semantic Web and The Internet of Things

I’m not a gigantic fan of the contemporary Internet of Things (AKA The Internet of Way To Many Things), but this is not because I don’t understand the concept. Quite the reverse actually – I was doing this stuff back at the fin de vingt-et-unième siècle.

I must say that I thought most of that early work was out of date, surpassed by big data, machine learning, and billions of dollars.

This month I was shocked to see not one but two articles about using the Semantic Web for the Internet of Things—exactly what I was talking about back in ought-five [4].

Problem:  the world is filled with more and more autonomous devices which need to connect, configure, and cooperate with each other.

In the IoT, there are no system admins, let alone configuration files, and so on.

So how do nodes know who is who, what is what, and how to talk to anything?

This was the motivating problem at the beginning of my own thesis work (circa 1998-9).

Configuring these devices requires something like scripts, rules, and triggers, but simple scripts

can only apply to known places, users, and IoT devices personal needs.

This lack of discovery and adaptation severely restricts the rules’ expressive power.” ([1], p. 18)

Way back in the last century, I started exploring the use of Semantic Web technology to address this challenge (“Semantic Infrastructure for a Ubiquitous Computing Environment” [4])  I thought it was the right idea, but I haven’t seen much development in the ensuing ages.

Fulvio Corno and colleagues at Politecnico di Torino describe a system that follows this very approach.  Key elements are [1]:

  • An abstract desctiption of devices, fucntions, etc.
  • Logical rules for composing and reusing about these descriptions
  • Standard, cross-vender representation

The purpose is to have a way for computers to know when a rule applies to some ‘node’, and how to apply it, even when the node is a complete stranger.

Corno and colleagues are particularly interested in “programming by functionality”, i.e., making the right thing happen without knowing all the details in advance.

Their system includes a “Semantic Reasoning block” which “maps user-defined trigger-action rules to devices and services in the IoT Ecosystem in order to reproduce the desired behaviors.” (p. 21 )  In other words, it takes an abstract description of what is supposed to happen, and figures out a set of concrete devices and actions that will accomplish the intended goal. (This is “semantic” because the computer is deducing what is “meant” to do.)

The project uses semantic web standards because they (a) are universal and portable and (b) they define a formal logical model for the reasoning that is needed.  The former means that the rules can be vendor independent and will work anywhere, and the latter means that you can do the mapping they need to do.

A second article discusses the more general problem of “Machine to Machine” (M2M) interoperability [2]. Even absent the swarm of IoT things, there is a plethora of computers, systems, and data on the network. Getting systems to work together can be a painful process, and in principle, semantic web technology is designed to ease this process.

However, Hodges and colleagues point out that most semantic models are poorly written and unlikely to be useful for interoperability.

many of these ad hoc ontologies are information silos

This group is working to develop better semantic models based on accepted industry standards.  I.e., the semantic models describe the concepts of existing standards, as well as mapping between multiple standards.

These models have obvious advantages.  Based on accepted standards, they represent existing models, with existing audiences, and known domain applicability. In short, given the effort invested in creating, promulgating, and implementing a standard, it is worth the trouble to create a good semantic model for it.

I would also say that a good standard has a rigorous definition of conformity, so it is possible to check that a node actually implements the standard correctly. That means that it is possible to know that the semantic model can map to one or more concrete implementations.

The big news, though, is that the formal logic of the semantic web makes it possible to formally map between multiple standards, making it possible for a computer to translate.

The general idea here is to use these standards as the basis for the abstract description of the decentralized system.  The semantic web makes it possible to automatically combine and translate between descriptions from many sources.

(Another blast from the past: Hodges et al. suggest using PROV-O ontology to model the behavior of a sensor.  PROV-O is a representation of the Provenance Data Model, which I contributed to at its birth.)

It was nice to see these articles confirming that the technology I called out as important might actually be important.  The motives and general approach are pretty much exactly as I was thinking way back when.  It is great to feel like a vindicated pioneer.

On the other hand, these articles were a pleasant surprise because these technologies are not actually in use yet.  Ten years and more, and it’s still a future wonder.  “They hold the promise of interoperability in name only.” ( p. 27)

I still think this is a good approach, not least because of the principle that:

Any problem in computer science can be solved by an extra level of indirection.”  (The original source of this quote is not precisely known. Lampson et al. [3] attribute this phrase to David Wheeler, citing the authority of Roger Needham.)

I also think that the burgeoning Internet of Too Many Things will make this problem more and more pressing.  However, the IoT is currently dominated by centralized architectures managed by large vendors.  These companies are selling silos, and have little reason to provide open solutions.

  1. Fulvio Corno, Luigi De. Russis, and Alberto Monge Roffarello, A Semantic Web Approach to Simplifying Trigger-Action Programming in the IoT. Computer, 50 (11):18-24, 2017. https://www.computer.org/csdl/mags/co/2017/11/mco2017110018-abs.html
  2. Jack Hodges, Kimberly. García, and Steven Ray, Semantic Development and Integration of Standards for Adoption and Interoperability. Computer, 50 (11):26-36, 2017. https://www.computer.org/csdl/mags/co/2017/11/mco2017110026-abs.html
  3. Butler Lampson, Martin Abadi, Michael Burrows, and Edward Wobber, Authentication in Distributed Systems: Theory and Practice. ACM Transactions of Computer Systems, 10 (4):265-310, 1992. https://www.cs.utexas.edu/~shmat/courses/cs380s/lampson92.pdf
  4. Robert E. McGrath, Semantic Infrastructure for a Ubiquitous Computing Environment, in Computer Science. 2005, University of Illinois, Urbana-Champaign: Urbana. http://hdl.handle.net/2142/11057


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