The NSA is leading us to a dark place

The United States has a long history of maintaining covert intelligence agencies, and that can make sense in the realpolitik, game theory world of geopolitics. During the Cold War, knowing the behind-the-scenes position of the U.S.S.R likely helped avoid mis-steps that could have resulted in nuclear catastrophe. Likewise, on issues such as US-China relations, Iranian nuclear negotiations, and trade talks, there is a place for covertly acquiring information about the intentions of other players to avoid serious blunders. Spying is often called the "world's second-oldest profession," and it's not going anywhere soon.

That said, the growth of the military-intelligence-industrial complex since 9/11 is unprecedented in its scope, brazen unconstitutionality, and lack of accountability or oversight. Collecting data (or metadata) about the communications of millions of citizens and non-citizens alike, without a warrant or an even a stated suspicion, is clearly a violation of the fourth amendment of the Constitution, no matter how much garbled legal justification the intelligence community condescends to toss us. Instead of allowing the NSA to collect the whole haystack in hopes of finding the needle, we need to return to traditional police work of following leads. As the fourth amendment declares: "no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized." If we choose as citizens to accept the NSA's assertion of authority to collect "things" (metadata is a thing) without warrant, we are agreeing to retreat on the fundamental ideals of our nation.

"Verily, we shall remove SSL certificates betwixt the public internet and Google Cloud" 

Furthermore, this spying program has failed to provide us with workable intelligence. The NSA has recently admitted that their surveillance program has foiled at most one or two terrorist plots in the US. The increased scope of our spying has also backfired dramatically on several fronts. The NSA's programs have weakened the structure of internet security for everyone, and raised doubts about products offered by US tech companies, risking about $35 billion in sales. Our major alliances, which have a much more real and substantive effect on security than one or two terrorist plots, are being greatly strained by revelations that we're tapping their communications to an unprecedented extent. In the meantime, the image of the USA around the world is becoming one of an enormous, ominous, secretive empire, dealing illegal assassinations from airborne robots and collecting every communication. It is hard to imagine that this does not effect our ability to partner with state and non-state actors around the world. With all this considered, a reasonable argument could be made that the power grabs made by the intelligence community in recent years have done more to weaken U.S. security than to enhance it.

After the abject tragedy of 9/11, Americans shifted priorities in the (dubious but workable concept of a) balance between security and freedom by enacting the patriot act and funneling hundreds of billions of dollars to spy agencies. This recalculation was understandable at a time of great trepidation, but it is now time to seriously reassess the choices we made. I do not deny the need for good intelligence, nor do I doubt the motives of the people working for these agencies. The military-intelligence-industrial complex, like all bureacracies, has a tendency to perpetuate itself, and to grab power - their evil is banal. Our spooks have a certain threat-centered perspective, and that perspective is blind to important priorities that we have as citizens, such as maintaining open relations with our allies and a secure internet. We have to accept that no amount of spying or drone striking can ever guarantee that there will never be a terrorist attack again. A reduction in the risk of a terrorist attack from 1% to 0.1% is not worth throwing our principles out the window and becoming the death-robot in the sky. 

Truth and Beauty: Sea Slugs

Check out this National Geographic photo gallery of gorgeous sea slugs by photographer David Doubilet! These sea slugs, called nudibranchs, have evolved zany colors for your personal enjoyment, and also to warn predators about the toxic compounds they contain. Some nudibranchs make these compounds themselves, but many extract and concentrate toxins from the sponges they eat.

Photo: Alexander Jenner

But retaining toxic compounds is far from the only trick that sea slugs pull. Fellow

Soaking up the rays
Photo: EOL

Euthyneurans (the group that contains nudibranchs) like Elysia chlorotica have evolved "kleptoplasty," whereby they extract the photosynthetic structures (chloroplasts) out of algae they eat, and retain them within special cells in their guts. This allows the slug to get energy from the sun like a plant, for up to 9 months after they eat the algae - Elysia is a temporarily photosynthetic animal!


Let's all take a second to think about how cool it would be to photosynthesize.

Nobel Prize if you figure out how this works!
Photo: Genny Anderson

Another Euthyneuran, Aplysia californica, has been extensively studied for decades as a model of learning and memory. Eric Kandel won the Nobel Prize in Physiology in 2000 for this research. Aplysia has a relatively simple nervous system, making it easier to study what's going when the slug learns. Kandel and others mapped out changes in individual synapses (the connections between neurons, where the action happens) as they conditioned the slugs the way Pavlov conditioned his dogs. This research regime showed in detail the mechanics of Hebbian plasticity, the theory that "cells that fire together, wire together*." That is to say, neurons form stronger connections with other neurons that they communicate with frequently. It's like the way foot paths form after a fresh snow - as more people follow the tracks laid by the first person, the path becomes more defined. This is a fundamental principle in neuroscience, and explains a good deal about how our brains change according to the ways we think.

Photo: Chika Watanabe

Each strange branch on the tree of life has its own marvels, and I find that taking time (not easy, I know) to take a good look at something as "lowly" as a sea slug can really bring a fresh perspective and appreciation to life. I hate to film a shopping bag here, but beauty and truth are often hiding in the weirdest corners, as these sea slugs show. It's a big part of why I study biology, although there are many ways to reach the sublime outside of living things. We are surrounded by beauty, even if that beauty is a way of saying "I'll kill you if you eat me."

*Dr. Carla Shatz probably said this first

Phylogenetics

Note: this was originally in my post about the application of phylogenetics in language, but several people pointed out that it should really be its own post.

Photo: UC Museum of Paleontology

Evolutionary biology has been revolutionized over the last ~40 years by phylogenetics, a way of using information about the traits of organisms to figure out how they are related to each other (explanation here). This tool has yielded an immense amount of knowledge about how different groups of species are related to each other, when they diverged from each other, and which traits are likely important in the evolution of a given group. Basically, the idea is that species that are more similar to each other are likely more closely related, based on the assumption that species descend from other species, and gain modifications along the way (that is, that evolution is real).

Phylogeneticists (in their earlier form called cladists) would measure and score traits like producing milk, having fur, and producing body heat, and show quantitatively that there is a group (mammals) that all come from a common ancestor that had these traits. This is based on the assumption that the simplest explanation for the distribution of these traits is the one that involves the fewest changes across the tree, and that the simplest explanation is the best. So the simpler explanation for the distribution of the traits of milk, fur and body heat across animals is that the ancestor of all mammals had all these traits and passed them on to its descendants, instead of these traits evolving independently many times. Phylogeneticists had to deal with difficulties like the fact that birds also produce body heat (convergence), but by carefully scoring information about traits, they could tell us that whales are not fish and bats aren't bugs.

Things got substantially more intense
Photo: codoncode

Of course, phylogenetics has become increasingly complicated since those early days. Now, instead of treating all traits as equal, evolutionary biologists build models for how likely different traits are to change. We count the likelihood of evolutionary shifts between species instead of just the number of traits they have in common, because fur color is more likely to change than heart structure. Another major change is that biologists now look at DNA and Protein sequence for most of their data instead of looking at traits like bone structure or number of toes. Our models and methods have become significantly more sophisticated, and phylogenetics is now a relatively old and mature field.

Evolutionary insights into language and culture

The verb "to spit" may be one of precious few words preserved from the common ancestor of all Eurasian languages. The word "huh," as in "what did you just say," has arisen* in many languages around the world. These findings come from two of several recent studies that use methods developed in evolutionary biology to discuss the evolution of language. Specifically, they employ a method called "phylogenetics" that uses information about the characteristics of species to figure out their relationship to one another. There have been some basic errors,*  as you would expect in a discipline taking up new methods. However, these studies hold promise for getting at questions about the history and spread of language, and also understanding how language evolves.

The fundamental assumption of phylogenetics is that species descend with modification, and in theory the method should work for anything that does. Like language, or culture.

Hey, look at that!
Picture: Jack Lynch

The new wave of linguistic and cultural phylogenetics is driven by the insight that languages and cultures, like species,  evolve and diverge. But that insight itself is not new. The understanding that languages descend from each other goes way back to before Charles Darwin was born, as European explorers noticed that their tongues shared similarities with Persian, Gujarati and other languages they encountered. Darwin himself gives a shout-out to the parallels in The Origin of Species, saying:


"Yet it might be that some ancient languages had altered very little and had given rise to few new languages, whilst others had altered much owing to the spreading, isolation and state of civilisation of the several co-descended races, and had thus given rise to many new dialects and languages. The various degrees of difference between the languages of the same stock would have to be expressed by groups subordinate to groups; but the proper or even the only possible arrangement would still be genealogical; and this would be strictly natural, as it would connect together all languages, extinct and recent, by the closest affinities, and would give the filiation and origin of each tongue."



The possible application of phylogenetic methods range far and wide in anthropological, linguistic and sociological research. In addition to the linguistic papers cited above, researchers are now publishing papers about the phylogeny of  "Little Red Riding Hood", Turkmen Textiles, and marriage practices. Aside from just determining relationships, phylogenetic analysis can also tell us about which practices and language structures change faster or slower, which might hint at their centrality and importance. For example, the first paper I cited in this post uncovered that the words for "we," "what," and "thou" are amongst the slowest-changing in the Indo-European language family.

However, there are many reasons to doubt that phylogenetics will be as successful at untangling linguistic or cultural relationships as it was for biological ones. Though biological evolution can be chaotic and hard to predict, the limited number of possible changes in DNA code (you only have four letters to work with) make it easier to predict how likely different kinds of changes will be. In addition, there are rules for the flow of information such as the so-called "Central Dogma" of molecular biology. While many, many exceptions have been found to these general rules, they provide a relatively stable framework to judge the likelihood of evolutionary events, which is crucial to building an accurate tree of relationships.

Right chaps, should we go with "Porc" or "Pig?"

It remains to be seen whether these models of change can be worked out for linguistics or cultural evolution. Much depends on whether there actually are generalizable rules for the likelihood of developing an irregular verb, or changing a phoneme, or adding in certain plot points to your mythology. Perhaps the linguistic changes to English following the Norman invasion can someday be modeled like a hybridization between two species. There are researchers asking these questions, and the race is on to find general rules of linguistic and cultural evolution.

I somehow doubt that these rules will emerge, though I hold out more hope in language than culture. Perhaps it is pessimism in the face of the complexity of the problem. Humans are wild and chaotic in the way we dance with our languages and cultures, subverting and transforming meanings and sounds, and making synesthetic connections between completely separate realms of thought. Maybe I harbor hope that that can't be fit into a mathematical model. In any event, the next few decades of linguistic and cultural research should be interesting to watch.

===================================================

*This is an example of a mistake that the authors made in their use of evolutionary language, and I will introduce some of that terminology here - if you're not really into evolution, this might be dry and it's OK if you stop reading now:
In the "huh" paper, the authors conclude that the word arose independently through "convergent" evolution without knowing if ancestral languages have this word. That is a basic mistake: convergent evolution is when a trait evolves in two separate lineages, but wasn't present in the common ancestor of those lineages.

If the word "huh" was convergent, then English and Hindi would both have the word "huh" but the Indo-European ancestral language that English and Hindi descent from would lack this word. The authors respond to that by basically saying that we should strip the term "convergence" of all meaning by "generalizing" it, citing a paper that suggests merging the terms "parallel" and "convergent" evolution. Their argument is not very convincing":

"We use ‘convergent evolution’ as a general term for the independent evolution of similarities in form and function. When ancestral forms are known, a distinction can be made between form/function convergence in species that are closely related (‘parallel evolution’) versus in species that are not closely related (‘convergent evolution’). However, this distinction is not always consistently made in biology and recently there have been proposals to use ‘convergent evolution’ as a general term [76]. We use the term in this general sense. Our proposal accounts for the present-day cross-linguistic similarity of huh?, but has to remain agnostic as to its ultimate origins – in the absence of historical language data it is impossible to tell whether the present-day forms go back to one ancestral form (a stabilising evolution scenario[77]) or whether they arose independently in different languages (an independent convergent evolution scenario [78]). In either case, the selective pressures are the same."

But the distinction between convergence and parallelism is not whether the lineages are closely related, but whether the trait (the word "huh") evolved from different traits or the same trait in the ancestor. That is, it would be parallel evolution if the ancestor language of English and Hindi had a word "bleeble" that meant "huh", and that word changed to "huh" independently in both English and Hindi. There's no evidence for this either! The authors admit that it "is impossible to tell" whether the word "huh" is in so many languages because it was present in the ancestor of those languages or not, but go on to use the term "convergent evolution" in their title. Harumph!

Mt. Etna is blowing smoke rings!

Mt. Etna, an active volcano on the island of Sicily, is blowing smoke rings! According to German volcanologist Dr. Tom Pfeiffer, the most recent paroxysm (violent eruption) changed the shape of the vents inside to allow circular rings to emerge.

Vulcan is taking a smoke break
Photo: Volcano discovery

This has apparently happened a few times before, including in 2000. Here's a video of a smoke ring from the 2000 event, taken by Geoff Mackley:

Volcanoes: sometimes they destroy your town, sometimes they chill out and blow a few smoke rings. I hope this has served as your daily reminder that you live on an amazing planet.

The Romance of the Garden

For three years now, my partner Jen and I have been helping our friends Liz and Kevin build a pretty respectable vegetable garden at their house a little ways outside downtown Ann

Arbor. Kevin just wrote a great article about it, mostly dealing with the economics, health benefits, and effect on the community. I want to share two other sides of the story: the sheer joy and naively romantic allure of gardening, and the environmental benefits. First, the joy: the fresh air and exercise, the delicious food (oh my god, the food), and the feeling of accomplishment watching the garden come alive all come together to make vegetable gardening the most gratifying hobby I've ever taken up, by far. Afternoons of friends, music, beers and meandering conversations yield a basket of fresh, almost peppery basil and juicy, purple, lusty tomatoes: did I mention oh my god, the food?

Boom

Gardening solo, by contrast, is a deeply meditative time to slow down, unplug from modern life and gain a respect for the pace and ways of plants growing and reacting to their environment. We get so caught up in the noise of human society, we forget that for most of time (well, since the Ordovician period), and on most of the planet, this is and has been the ur story of earth: plants capture the energy of the sun and produce the sugars, starches, fats, and proteins on which we all depend, and the tastes, smells and drugs in which we all delight. If this story goes too far off track, none of our other tales are going to have a happy ending. Obviously, our garden makes an infinitesimally small contribution to food production, but it did open my eyes to the problems in the food system. Without environmental justice, there can be no justice of any kind: to distribute fairly, there must be something to distribute.

Deep thoughts, dill pickles

A lot of people use their land to grow grass, and that can be great, too. Badminton, barbeques, outdoor parties, little kids running around: all immensely improved by a well-tended lawn. However, we now use three times more land in the U.S. for lawns than for corn, and lawns have an environmental cost of decreased biodiversity and increased use of pesticides and fertilizers. The aesthetic of a closely-cropped lawn, whatever its origins (probably European aristocracy showing off how much land they could not grow food on), became firmly fixed in the '50s as a symbol of America: everyone tends their own yard, and you have a nice, tidy, orderly neighborhood. I can see why people are into that, and I don't want to add to the culture war or suggest that you're single-handedly destroying the planet if you love your lawn. But if you don't care that much one way or another, you should consider a vegetable garden, a native flower garden, or even mulch and trees. And no matter what you do, please don't change your neighborhood bylaws or call the cops to report a vegetable garden, as has happened three times to us.

Mine is bigger than yours
photo: Aesthetic Effect

Gardening is a botanical, sensual pleasure that reminds you that you are an embodied human with needs (for sustenance, for vitamins), and that you can meet those needs by meeting the needs of some very different embodied organisms, your plants. It's a miracle so fundamental that, as Michael Pollan points out, it is deeply subversive: the Tree of Knowledge is just that. Gardening is a deeply romantic endeavor, and forces you to see a little patch of the world in a slow, deliberate way that is sorely lacking in 2013. As the (admittedly whimsical) saying goes, a bad farmer grows weeds, a good farmer grows crops, and a great farmer grows soil. You don't hear much about growing soil these days, actually or metaphorically.

P.S: If you are interested in growing your own vegetable garden, buy this book.

Welcome to The Jungle!

photo: Farm Sanctuary

The USDA is moving towards a new policy on poultry manufacturing, although you wouldn't know it from reading the news. The change is based on the HIMP program, a Russian nesting doll of acronyms* that was started in the late '90s as a pilot program in a small number of factories. HIMP encourages the use of antimicrobial sprays to keep down the prevalence of harmful bacteria like Salmonella, because you aren't already eating enough poison, and some of the beneficial bacteria in your gut are probably still alive. The main idea, though, is to de-emphasize the role of USDA inspectors, instead relying on companies to regulate themselves by paying for their own inspections.

If there's anything we've learned from the last few years of world-class corporate citizenship, it's that companies are excellent at self-regulation, and will always put their long-term interests and those of others over short-

Kids these days have no work ethic!

term profits. If you aren't providing an honest, clean service or product, people won't buy it  and you'll go out of business: it's simple economics! That's why the previous Gilded Age was such a treat - clean working conditions, sanitary food, and social and economic justice, all enforced solely by market forces. No need for big government breathing down your neck.
Besides, as the hilariously-named National Chicken Council and the USDA both enthusiastically declare, this is about modernization! And global competition! In the global marketplace, there's really no choice but to cut regulation until we can compete with China in production of basic goods such as food and coal. They don't have these stifling regulations and things are fine over there, right?

probably not
photo: Atlantic Cities

Sometimes deregulation makes sense; having worked at a VA hospital for three years, I have seen regulation that is excessive and acknowledge that it exists. But asking factory farm owners to inspect their own factories is pretty clearly not a good idea. As someone who has personally slaughtered and gutted (and then eaten!) a chicken, I can attest that it is a very messy (though ultimately delicious) process. This regulation basically amounts to trusting factory farms, and a little antimicrobial spray is not going to make me feel any better about that. 

Disclaimer: I want to stress that this is not a scientific viewpoint, but a political one. The data currently out suggests that the pilot program (HACCP) that is the predecessor of HIMP improved Salmonella rates in meat. But there is good reason to be suspicious of these studies. If you were an executive at a corporation like Tyson that has a serious interest in getting this regulation changed, you just might make an extra effort to thoroughly inspect the few plants where the pilot program is running, while the government is watching closely. 

*The full name of HIMP is the "HACCP (Hazard Analysis and Critical Control-Points)-based Inspection Models Project", so you know they're hiding something juicy** behind all that obfuscation 

**Juice may be derived from chicken pus and innards, and natural or artificial flavors. Individual results may vary.

Reductionism

Reductionism - looking at a complex situation and identifying a few main forces to explain what is happening - is an incredibly powerful tool for understanding the world around us. There are an almost infinite number of known and unknown factors that go into even the most mundane phenomena, and an even larger number of ways to describe them. Trying to take stock of everything all at once will drive you insane and leave you with a lot of “patterns” that say more about your thinking than the reality of the situation.

Reductionism also rhymes beautifully with the Scientific Method, as it is much harder to test the effects of many interacting factors on an outcome than it is to test the effects of one or two. There is a satisfying progressive nature to identifying and testing the most important factor, then the next, and then the next. At each step you have fewer anomalies to contend with, and you’re always standing on stable ground if you test the factors as you go. Even though, at any given time, you may only be able to account for a small fraction of variation in outcomes with the causes you propose, you can be relatively sure that those causes really do influence the outcome. The steady drumbeat of reductionism has been the marching music of science for hundreds of years. Many of the triumphs of science have been reductionist in nature, and most scientists see reductionism as a cornerstone of scientific practice. As a tool of investigation, it has worked very, very well.

To pick a controversial example, say we want to test whether Prozac treats anxiety. We collect a group of people with anxiety and measure their anxiousness with something like the Beck Anxiety Inventory. Then we split the groups into a test and control group, administer Prozac for a period of time to the test group and a placebo to the control group, and measure their anxiety again. If the test group has a lower anxiety measure than the control group, we could say that Prozac is an effective treatment for anxiety. The world is a messy place, and because of that, scientists accept some statistical wiggle-room when allowing that a certain finding is significant. When the test is over, if 95% of the test participants have anxiety levels like what we would expect if Prozac improved anxiety measures, then we can say it works. Because 95 is a good number, right?

There are many stories contained in the
               spaces between the points and the line.

But that other 5% might not be a random fluke or statistical noise; those participants could all have a specific genetic variant Y that acts to negate the effects of Prozac. In this case, the better headline would be “Prozac is an Effective Treatment for Anxiety in those without Genetic Variant Y,” but that’s not captured in the significant finding. Furthermore, and more importantly, answering the question of whether Prozac significantly treats anxiety says nothing about the effect of exercise, sleep, financial security, social position, or any number of other factors that also likely play a role. As the reductionist ball rolls forward, these other factors can be incorporated into a model of what plays into anxiety. Then we can see if people who don’t take the Prozac, get a good night’s sleep, or get adequate exercise are, on average, more anxious than people who do. We get better and better at explaining the variation we see in anxiety across people as we add more factors. In psychology, explaining 30% of that variation is considered a strong result. But why should we even bother with all this work if, in the end, 70% of what goes into anxiety is still completely unexplainable?

Well, one reason is that we might not even know that genetic variant Y exists, or what categories of social position are important. In a world of unknown unknowns (to borrow a phrase from Donald Rumsfeld), we measure what we can and try to find the most solid relationships possible. We accept that our explanations will not hold water in every circumstance, and we try to pursue further the circumstances where the explanation fails. This has to do with how we form questions in science; we ask “Does Prozac improve anxiety outcomes in most people?” because we don’t have the tools to ask “What is every factor that goes into this particular person’s anxiety?” Reductionist science focuses on measuring the outcome based on a few factors, and then replicating that across many trials to identify the effect of those factors on the outcome. If we want to know whether those factors actually have an effect in reality, there’s not much more we can do.

The unknown unknowns are blowing his mind

However, there is a disconnect between how this tool is properly used and how its findings have been communicated, especially at the points where science intersects with the human experience. Scientists endeavor to find the factor X that explains the most variance in trait Y in the population, but the message that too often comes across is that that factor X causes trait Y. To illustrate what I’m talking about, I googled around and cherry picked some examples. This is obviously not a fair survey, but I’m sure you’ve been bombarded with news stories like these, argued on the nature side as well as the nurture side.

Most of these articles couch their statements in statistical or quasi-statistical language - the gene is “linked to,” “associated with,” “implicated in,” or “may shape” certain behaviors - that are likely to be lost on the audience. That is partly a failure of education, in that many people don’t have a clear idea of what those terms mean, or how statistics operate in the context of reducing complex phenomena to statistical shifts in test outcomes. But the larger failure is in communication: it would help enormously if more of these articles had clear caveats - “not everyone with this gene will be anxious,” or “this gene plays a role in anxiety, in interaction with other genes as well as your environment.”

Reductionist explanations-in-progress are often presented as if they were the whole story, and the simplified relationships that get into our heads result in a lot of confusion and frustration about categories and causes. The world we actually live in is incredibly complicated, and the real reason why things are the way they are often has a lot to do with history, chance, and “emergent” phenomena that arise from the interaction of multiple parts. Remember, reductionist explanations-in-progress are good at identifying which causes are real, but at a given time they might only be able to account for a small percentage of the variation you see.

Often, we can’t explain why Bob has anxiety, even if we can show that social environment, exercise, genes, endocrine regulation and a host of other factors contribute to anxiety. Often, someone will attempt to explain (judge might be a better word) why Bob is anxious using just one or two of those factors. Often, this is frustrating, offensive, and wrong. The explanation is taking a complex phenomenon (Bob’s anxiety) and trying to reduce it to one or two inadequate and possibly irrelevant dimensions. And when it comes to explanations and judgments about people (or social phenomena, or a number of other very important topics) irrelevant and inadequate can quickly become disrespectful, confusing, and painful. It’s not cool to use incomplete evidence to explain away Bob’s experience.

Questions like “What should I do to be healthy?” or “Why is he anxious?” require us to synthesize all that information we’ve gotten from reductionism about factors that affect these things, and integrate it into a wider world view. It is our job as thinking people to take that information for what it’s worth, and recognize that a study showing that a genetic variant makes one more likely to become anxious does not necessarily mean that a given person’s anxiety is solely genetic in cause. We should treat reductionism and holism as complementary approaches to the truth, and different ways of thinking of the same problem. We need to change the way we think and communicate about these simplified but powerful takes on complex relationships.