Handheld Mass Spectrometry

Mass-Spectrometry is pretty much magic. A tiny sample of matter can be analyzed to get a chemical fingerprint which reveals exactly what it is.

Today, mass-spectrometry requires a large and expensive machine, and generally requires a fairly large sample which is destroyed by the process, which takes 30 minutes or more to complete. This is fine for laboratory studies, but impractical for many medical applications.

This fall a group from University of Texas report on a new device intended for use in course of cancer surgery [3]. The device is a pen-sized sampler that is touched to the tissue around a removed tumor. It samples the chemistry of the tissue without damaging it, feeds the sample to a mass-spectrogram machine, and quickly screens the results to determine if the tissue is cancerous (and so should be removed). The algorithm is highly accurate, enabling a surgeon to find the edges of what must be removed.

The quick turn around and spatially precise sample are essential for use during surgery. The technique picks up metabolites from the tissue without destroying it, which is a great improvement over previous methods.

As Emily Waltz points out, this technique still requires a mass-spectrogram machind, which is impractical for most operating rooms. However, there are new developments that will make smaller and cheaper mass-spectrogrametry possible [1].  And, of course, machine learning can be used to create many different fast classifier algorithms.

Combining these developments, as well as other non-invasive sensing will lead to some pretty amazing medical tech.


Aside:  Please note the careful experiments and detailed open report of their validation studies in [3].  Compare to the usual Silicon Valley hype-intensive, data-light technology.

  1. Dexter Johnson, Mass Spectrometry Gets a New Power Source and a New Life, in IEEE Specturm – Nanoclast. 2017. https://spectrum.ieee.org/nanoclast/semiconductors/materials/mass-spectrometry-gets-a-new-power-souce-and-a-new-life
  2. Emily Waltz, Handheld Mass-Spectrometry Pen Identifies Cancer in Seconds During Surgery, in IEEE Spectrum – The Human OS. 2017. https://spectrum.ieee.org/the-human-os/biomedical/devices/handheld-mass-spectrometry-pen-identifies-cancer-in-seconds-during-surgery
  3. Jialing Zhang, John Rector, John Q. Lin, Jonathan H. Young, Marta Sans, Nitesh Katta, Noah Giese, Wendong Yu, Chandandeep Nagi, James Suliburk, Jinsong Liu, Alena Bensussan, Rachel J. DeHoog, Kyana Y. Garza, Benjamin Ludolph, Anna G. Sorace, Anum Syed, Aydin Zahedivash, Thomas E. Milner, and Livia S. Eberlin, Nondestructive tissue analysis for ex vivo and in vivo cancer diagnosis using a handheld mass spectrometry system. Science Translational Medicine, 9 (406) 2017. http://stm.sciencemag.org/content/9/406/eaan3968.abstract


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. http://birdcast.info/forecast/eclipse/


Book Review: “Discovering the Mammoth” by John J. McKay

Discovering the Mammoth by John J. McKay

Speaking of paleontology….

Before there were dinosaurs and other prehistoric wonders, there were petrified remains of animals, plants, sea shells. From earliest days, humans have found them, and recognized that they appear to be life that no one has seen alive.

But to understand fossil remains, you have to be able to imagine that what we know now is not all there is to know. You have to be able to accept that the Earth is old, that it has changed a lot through time, and, above all, species of animals and plants emerge, change, and may even die out.

These concepts are hard to grasp, even when there aren’t dogmatic religious or folks stories contending.

McKay recounts how European thinkers “discovered” the Mammoth, a prehistoric elephant that died out at the end of the last ice age. As he notes, the tusks and other bones of Mammoths were known for many centuries, as well as other related species. But the notion of extinction was alien to the Western philosophy (Pagan, Christian, Jewish, and Muslim, alike), and almost no one thought of the world as being millions of years old.

Most of the book is a history of Renaissance and Enlightenment times, during which Europeans became aware of the wider world, including the remains of unknown animals. He tracks down nearly every written mention of Mammoths and related fossils. This is a tangled mess of speculation and blinkered assumptions that only slowly recognized the actual evidence.

This story meanders through central Europe, Colonial New Spain, Colonial America, and, above all Siberia. In Siberia, there are not only massive numbers of Mammoth tusks and bones, but there are whole frozen Mammoths! It’s difficult to mistake or deny that these remains are a real and once living animal when you can smell the rotting carcass from miles away.

I learned lots about the early exploration of Siberia, and more than I really care about the politics of eighteenth and nineteenth century Russia.

McKay says that understanding the Mammoth is basically the beginning of paleontology, and he has a good point. Working out that Mammoths are related to but not the same as modern elephants, that they lived a long time ago, and that they are extinct took huge leaps of imagination. Furthermore, establishing the case required moving from travellers’ tales and biblical analogy to careful excavation, comparative anatomy, geological stratigraphy, and knowledge of similar finds all around the world. These are the very definition of modern paleontology, and the problem of the Mammoth was one of the first real successes.

Ironically, the Mammoth is also one of the most intriguing of all the extinct species because it overlapped with Homo Sapiens, even if there is no living memory of that fact. We know this because we have paintings and etching of Mammoths and other extinct fauna, made by our ancestors, who knew them and likely hunted them.

Thus, figuring out the story of the  Mammoth also helped push the history of humans far into the past, and far beyond most folk stories and Biblical narratives. This is one of the crucial intellectual turning points where a thinking person is forced choose between science and received revelations.  Do I believe the traditional story, or the evidence of my own eyes?

The beginning of paleontology is also one of the great beginnings of natural science in general. Mammoths are not only old and extinct, but they were normal (if extraordinary) animals who lived by the same natural laws that we live by today. This notion that scientific theory extends to all times and places is the essence of the scientific enterprise.

McKay appears to be really, really into Mammoths. The book jacket says he is “the Mammoth Guy”, and that seems to be accurate. He is also a historian, and it shows. This book has some interesting history in it, possibly too much history. (Honestly, I completely lost track of who was who in Russia circa 1800.)

Personally, I wouldn’t have minded a lot more about Mammoths, and less about eighteenth century opinions about Mammoths. I suspect that McKay could write such a book, and maybe he will.

  1. John J. McKay, Discovering the Mammoth: A Tale of Giants, Unicorns, Ivory, and the Birth of a New Science, New York, Pegasus Books, 2107.

Sunday Book Reviews

Cassini End of Mission

After twenty years in space (launched 10 years Bi, Before iPhone), traveling over a billion KM, and returning data for 13 years from more than a light-hour from Earth, the Cassini Spacecraft ended its mission this week.

The project has accomplished lots of amazing science, represented by 3,948 papers so far. There will surely be a few more—lets go for 5K papers!

The end was a planned dive into the atmosphere of Saturn, collecting a few more bits of data on the way down, and assuring the complete destruction of the spacecraft.

As has been explained before, the spacecraft needed to be vaporized to prevent even the slighted chance that it might contaminate the area with Earth microbes. Aside from not wanting to harm any life that might exist on the moons or dust, we also don’t want to accidentally leave something that a later spacecraft might find and not realize was inadvertently sent from Earth.

(Which, if you think about it is way, way cool. How many human endeavors have to worry about the possibility of contaminating alien ecosystems, even in principle?)

Hence, the final dive.

This montage of images, made from data obtained by Cassini’s visual and infrared mapping spectrometer, shows the location on Saturn where the NASA spacecraft entered Saturn’s atmosphere on Sept. 15, 2017. Credit NASA/JPL-Caltech/Space Science Institute

Cassini signed off permanently on September 15. Loss of Signal. End of Mission. Lots of accomplishments.


Space Saturday

Inaudible Speech Commands Hack Your Home

I’m not a huge fan of speech interfaces, or of Internet connected home assistants a la Alexa in general.

I have already complained that these devices are potentially nasty invaders of privacy and likely to have complicated failure modes not least due to a plethora of security issues. (Possibly a plethora of plethoras.) I’ve also complained about the psychology of surveillance and instant gratification inherent in the design of these things. Especially for childred.

Pretty much exactly what you don’t want in your home.

This fall a group at Zhejiang University report on yet another potential issue: Inaudible Voice Commands [1].

Contemporary mobile devices have pretty good speakers and microphones, good enough to be dangerous. Advertising agencies and other attackers have begun using inaudible sound beacons to detect the location of otherwise cloaked devices. It is also possible to monkey with the motion sensors on a mobile device, via inaudible sounds.

Basically, these devices are sensitive to sound frequencies that the human user can’t hear, which can be sued to secretly communicate with and subvert the device.

Zhang, Guoming and colleagues turn this idea onto speech activated assistants, such as Alexa, or Siri  [1]. They describe a method to encode voice commands into innocent sounds. The humans can’t hear the words, but the computer decones it and takes it as a voice command.

These devices are capable of almost any operation on the Internet. Sending messages, transferring money, downloading software. The works.

In other words, if this attack succeeds, the hacker can secretly load malware or steal information, unbeknownst to the user.


Combine this with ultrasound beacons, and the world becomes a dangerous place for speech commanded devices.

The researchers argue that

The root cause of inaudible voice commands is that microphones can sense acoustic sounds with a frequency higher than 20 kHz while an ideal microphone should not.

This could be dealt with by deploying better microphones or by software that filters out ultrasound, or detects the difference between voiced commands and the injected commands.

I would add that a second root cause is the number of functions of these devices, and the essentially unimodular design of the system. Recent voice activated assistants are installed as programs on general purpose computers with a complete operating system, and multiple input and output channels, including connections to the Internet. In general, any program may access any channel and perform any computation.

This is a cheap and convenient architecture, but is arguably overpowered for most individual applications. The general purpose monolithic device requires that the software implement complicated security checks, in an attempt to limit privileges. Worse, it requires ordinary users to manage complex configurations, usually without adequate understanding or even awareness.

One approach would be to create smaller, specialized hardware modules, and require explicit communication between modules. I’m thinking of little hardware modules, essentially one to one with apps. Shared resources such as I/O channels will have monitors to mediate access. (This is kind of “the IoT inside every device”.)

This kind of architecture is difficult to build, and painful in the extreme to program. (I’m describing what is generally called a secure operating system.) It might well reduce the number of apps in the world (which is probably a good thing) and increase the cost of devices and apps (which isn’t so good). But it would make personal devices much harder to hack, and a whole lot easier to trust.

  1. Guoming Zhang, Chen Yan, Xiaoyu Ji, Taimin Zhang, Tianchen Zhang, and Wenyuan Xu, DolphinAtack: Inaudible Voice Commands. arxive, 2017. https://arxiv.org/abs/1708.09537


IOTA’s Cart Is Way, Way Before the Horse

Earlier I commented on SatoshiPay microcrasactions switching from Bitcoin to IOTA. Contrary to early hopes, Bitcoin has not been successful as a medium for microtrasactions because transaction fees are too high and latency may be too long.

IOTA is designed for Internet of Things, so it uses a different design than Nakamoto, that is said to be capable of much lower latency and fees. SatoshiPay and other companies are looking at adopting IOTA for payment systems.

The big story is that IOTA is reinventing Bitcoin from the ground up, with its own home grown software and protocols. I described it (IOTA) as “funky” in my earlier post.

It is now clear that this funkiness extended to the implementation, including the cryptographic hashes used [1,2]. This is not a good idea, because you generally want to use really well tested crypto algorithms.

So when we noticed that the IOTA developers had written their own hash function, it was a huge red flag.

Unsurprisingly, Neh Haruda reports that their home grown hash function is vulnerable to a very basic attack, with potentially very serious consequences.

The specific problems have been patched, but the fact remains that IOTA seems to be a home made mess of a system.

Narula also notes other funkiness.  For some reason they use super-funky trinary code which, last time I checked, isn’t used by very many computers. Everything has to be interpreted by their custom software which is slow and bulky. More important, this means that their code is completely incompatible with any other system, precluding the use of standard libraries and tools. Such as well tried crypto libraries and software analysis tools.

I have no idea why you would do this, especially in a system that you want to be secure and trusted.

The amazing thing is not the funkiness of the software. There is plenty of funky software out there. The amazing thing is that lots of supposedly competent companies have invested money and adopted the software. As Narula says, “It should probably have been a huge red flag for anyone involved with IOTA.

How could they get so much funding, yet only now people are noticing these really basic questions?

It is possible that these critiques are finally having some effect. Daniel Palmer reports that the exchange rate of IOTA’s tokens (naturally, they have their on cryptocurrency, too) has been dropping like a woozy pigeon [3].  Perhaps some of their partners have finally noticed the red flags.

The part I find really hard to understand is how people could toss millions of dollars at this technology without noticing that it has so many problems. Aren’t there any grown ups supervising this playground?

I assume IOTA have a heck of a sales pitch.

Judging from what I’ve seen, they are selling IOTA as “the same thing as Bitcoin, only better”. IOTA certainly isn’t the same design as Bitcoin, and it also does not use the same well-tested code.  I note that a key selling point is “free” transactions, which sounds suspiciously like a free lunch. Which there ain’t no.

IOTA’s claims are so amazingly good, I fear that they are too good to be true.

Which is the biggest red flag of all.

  1. Neha Narula, Cryptographic vulnerabilities in IOTA, in Medium. 2017. https://medium.com/@neha/cryptographic-vulnerabilities-in-iota-9a6a9ddc4367
  2. Neha Narula, IOTA Vulnerability Report: Cryptanalysis of the Curl Hash Function Enabling Practical Signature Forgery Attacks on the IOTA Cryptocurrency. 2017. https://github.com/mit-dci/tangled-curl/blob/master/vuln-iota.md
  3. Daniel Palmer, Broken Hash Crash? IOTA’s Price Keeps Dropping on Tech Critique Coindesk.September 8 2017, https://www.coindesk.com/broken-hash-function-iota-price-drops-on-tech-critique/
  4. Dominik Schiener, A Primer on IOTA (with Presentation), in IOTA Blog. 2017. https://blog.iota.org/a-primer-on-iota-with-presentation-e0a6eb2cc621


Cryptocurrency Thursday

Agility Robotics’ Terrifying “Cassie” Robots

OK, this is a cool (and scary looking) robot! Actually, they seem to run in packs, which makes them even scarier.

Cassie from Agilty Robots is an amazingly capable bipedal robot, with better balance and coordination than I have.

The company is trying to build robots to “Go where humans go”, which probably accounts for the uncanny bipedalism.

However, these Cassies remind me mostly of dinosaurs; agile, bipedal carnivores to be specific.

In fact, Cassie isn’t exactly naturalist or bio inspired. I’ve never seen anything that does this kind of side-stepping, and I’ve definitely never seen anything except human dance companies that move in such coordination.

It’s really terrifying.

And the things don’t even have a head or eyes, which only makes them more inhumanly scary.

Forget the uncanny valley, these guys inhabit the archetypal pit of species memory. My hind brain is screaming, “they are coming to eat me!”

This psychological effect might not be a big advantage for the home delivery market they are shooting for.

Robot Wednesday

A personal blog.

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