Memory boost

About two months ago I signed up with Duolingo to study Japanese.

I've been fascinated with Japan and the Japanese culture pretty much all my life, but I'm a total novice with the language, so I started out from "complete beginner" status.  I'm doing okay so far, although the fact that it's got three writing systems is a challenge, to put it mildly.  Like most Japanese programs, it's beginning with the hiragana system -- a syllabic script that allows you to work out the pronunciation of words -- but I've already seen a bit of katakana (used primarily for words borrowed from other languages) and even a couple of kanji (the ideographic script, where a character represents an entire word or concept).

[Image licensed under the Creative Commons 663highland, 140405 Tsu Castle Tsu MIe pref Japan01s, CC BY-SA 3.0]

While Duolingo focuses on getting you listening to spoken Japanese right away, my linguistics training has me already looking for patterns -- such as the fact that wa after a noun seems to act as a subject marker, and ka at the end of a sentence turns it into a question.  I'm still perplexed by some of the pronunciation patterns -- why, for example, vowel sounds sometimes don't get pronounced.  The first case of this I noticed is that the family name of the brilliant author Akutagawa Ryūnosuke is pronounced /ak'tagawa/ -- the /u/ in the second syllable virtually disappears.  I hear it happening fairly commonly in spoken Japanese, but I haven't been able to deduce what the pattern is.  (If there is one.  If there's one thing my linguistics studies have taught me, it's that all languages have quirks.  Try explaining to someone new to English why, for instance, the -ough combination in cough, rough, through, bough, and thorough are all pronounced differently.) 

Still and all, I'm coming along.  I've learned some useful phrases like "Sushi and water, please" (Sushi to mizu, kudasai) and "Excuse me, where is the train station?" (Sumimasen, eki wa doko desu ka?), as well as less useful ones like "Naomi Yamaguchi is cute" (Yamaguchi Naomi-san wa kawaii desu), which is only critical to know if you have a cute friend who happens to be named Naomi Yamaguchi.

The memorization, however, is often taxing to my 63-year-old brain.  Good for it, I have no doubt -- a recent study found that being bi- or multi-lingual can delay the onset of dementia by four years or more -- but it definitely is a challenge.  I go through my hiragana flash cards at least once a day, and have copious notes for what words mean and for any grammatical oddness I happen to notice.  Just the sheer amount of memorization, though, is kind of daunting.

Maybe what I should do is find a way to change the context in which I have to remember particular words, phrases, or characters.  That seems to be the upshot of a study I ran into a couple of days ago in Proceedings of the National Academy of Sciences, about a study by a group from Temple University and the University of Pittsburgh about how to improve retention.

I'm sure all of us have experienced the effects of cramming for a test -- studying like hell the night before, and then you do okay on the test but a week later barely remember any of it.  This practice does two things wrong; not only stuffing all the studying into a single session, but doing it all the same way.

What this study showed was two factors that significantly improved long-term memory.  One was spacing out study sessions -- doing shorter sessions more often definitely helped.  I'm already approaching Duolingo this way, usually doing a lesson or two over my morning coffee, then hitting it again for a few more after dinner.  But the other interesting variable they looked at was that test subjects' memories improved substantially when the context was changed -- when, for example, you're trying to remember as much as you can of what a specific person is wearing, but instead of being shown the same photograph over and over, you're given photographs of the person wearing the same clothes but in a different setting each time.

"We were able to ask how memory is impacted both by what is being learned -- whether that is an exact repetition or instead, contains variations or changes -- as well as when it is learned over repeated study opportunities," said Emily Cowan, lead author of the study.  "In other words... we could examine how having material that more closely resembles our experiences of repetition in the real world -- where some aspects stay the same but others differ -- impacts memory if you are exposed to that information in quick succession versus over longer intervals, from seconds to minutes, or hours to days."

I can say that this is one of the things Duolingo does right.  Words are repeated, but in different combinations and in different ways -- spoken, spelled out using the English transliteration, or in hiragana only.  Rather than always seeing the same word in the same context, there's a balance between the repetition we all need when learning a new language and pushing your brain to generalize to slightly different usages or contexts.

So all things considered, Duolingo had it figured out even before the latest research came out.  I'm hoping it pays off, because my son and I would like to take a trip to Japan at some point and be able to get along, even if we don't meet anyone cute named Naomi Yamaguchi.  But I should wind this up, so for now I'll say ja ane, mata ashita (goodbye, see you tomorrow).

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Remembrance of things past

I've been interested in memory as long as I can remember.  Part of the reason is that my own personal brain seems to be made up of a rather peculiar assemblage of things I can remember with apparent ease and things that I don't seem to be able to remember at all.  I recall music with no effort whatsoever; I once put a nifty little Serbian dance tune into long-term storage for over twenty years after hearing it twice (and not practicing it or writing it down in the interim).  Names, likewise, stick with me.  I know more scientific names of obscure species than is useful or even reasonable, and it's not from engaging in any sort of surreptitious memorization of taxonomic lists late at night when no one's looking.  That sort of stuff simply sticks.

On the other hand, numbers.  I know people who can remember what their phone number was in houses they haven't lived in for thirty years.  I'm lucky when I can remember what my phone number is now.  In this day of passwords, PINs, and so on, there are a variety of number/letter combinations I'm expected to remember, and the maximum amount of these I seem to be able to recall is: one.  For all of the passwords where this is possible, I use the same one.  If anyone ever discovers it, I'm fucked.  Fortunately, it's pretty obscure, so I don't think it's likely (meaning you shouldn't waste your time trying to figure it out).

It does, however, point up something odd about memory, which is how compartmentalized it is.  People can be exceptionally good at certain types of memory, and rather bad at others.  A few things, however, seem common to all sorts of memory; repetition improves retention, memory consolidation increases after sleep, and we all get worse at it (all types) as we age.

[Image licensed under the Creative Commons Michel Royon Ce message en français, Brain memory, CC0 1.0]

This last one is the subject of some cool research published in Nature, in a paper entitled "Increased NR2A:NR2B Ratio Compresses Long-Term Depression Range and Constrains Long-Term Memory," by Zhenzhong Cui, Ruiben Feng, Stephanie Jacobs, Yanhong Duan, Huimin Wang, Xiaohua Cao, and Joe Z. Tsien, as a collaborative project between Georgia Health Sciences University and East China Normal University.  The experiments involved using transgenic mice that overproduced a neurotransmitter receptor called NR2A, and found that they were significantly poorer than normal at forming new long-term memories than ordinary mice were. The reason, the researchers speculate, is that this receptor is involved in weakening the synaptic firing patterns from old memories.

Put another way, it seems like one of the reasons we become more forgetful as we age is that we aren't as good at getting rid of things we already have stored in there.  In an interview with the New York Times, study lead author Joe Z. Tsien compares our brains when young to a blank page, and older brains to a page from a newspaper.  "The difference is not how dark the pen is," he said, "but that the newspaper already has writing on it."

"What our study suggests," Tsien added, "is that it’s not just the strengthening of connections, but the weakening of the other sets of connections that creates a holistic pattern of synaptic connectivity that is important for long-term memory formation."

In other words, our brains really do fill up and (in some sense) run out of space.

It's a funny thought, isn't it?  One of the reasons I can't remember where I left my keys is because my brain still is determined to hang onto the name of my 7th grade English teacher (Mrs. Trowbridge).

I find this a fascinating result, partly because it contradicts my long-held belief (admittedly based on no evidence whatsoever) that no one ever gets close to the actual memory storage capacity of the brain.  Also, it brings up the questionably prudent possibility of developing technology to selectively erase memories, the ethical and personal problems of which are memorably delineated in the wonderful movie Eternal Sunshine of the Spotless Mind.  Not, in this case, to eliminate traumatic or unpleasant memories, as it was for Jim Carrey's character -- but to free up hard drive space.

Which, aside from the scary aspects, creates some interesting possibilities.  Imagine reading your favorite book, seeing your favorite movie, hearing your favorite song again for the first time.  Wouldn't it be cool to recapture the wonder of having a new experience over and over again?

In any case, this is only the beginning.  A dear friend of mine, the brilliant (now retired) Cornell human genetics professor Dr. Rita Calvo, once made the prediction that "if the 20th century was the century of the gene, the 21st will be the century of the brain."  We are, she said, right now with respect to our understanding of the brain approximately where we were in 1919 with respect to our understanding of genetics -- we know a little bit of the "what" and the "how much," but almost nothing about the "how" and the "why."

If so, we should be looking forward to some amazing advances over the next few years, and I'm sure I'll have to do a lot of reading to keep up with the research even well enough to teach competently my Introductory Neuroscience class.  It's exciting, however, to think that we may finally be elucidating the inner workings of our most intricate organ, and finding out how it does one of the most mysterious things of all -- storing, and retrieving, information.

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This week's Skeptophilia book recommendation is a brilliant look at two opposing worldviews; Charles Mann's The Wizard and the Prophet.  Mann sees today's ecologists, environmental scientists, and even your average concerned citizens as falling into two broad classes -- wizards (who think that whatever ecological problems we face, human ingenuity will prevail over them) and prophets (who think that our present course is unsustainable, and if we don't change our ways we're doomed).

Mann looks at a representative member from each of the camps.  He selected Norman Borlaug, Nobel laureate and driving force behind the Green Revolution, to be the front man for the Wizards, and William Vogt, who was a strong voice for population control and conversation, as his prototypical Prophet.  He takes a close and personal look at each of their lives, and along the way outlines the thorny problems that gave rise to this disagreement -- problems we're going to have to solve regardless which worldview is correct.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]

The memory virus

Nota bene -- Yesterday, I posed a "divergent-thinking" puzzle for my readers, to wit:

A man leaves home, makes three left turns, and as he is arriving back home he sees two masked men waiting for him.  Who are the masked men?

The answer is at the end of this post -- fair warning if you're still working on it!

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It's virus season, which thus far I've been able to avoid participating in, but my students are hacking and snorting and coughing and I figure it's only a matter of time.  Viruses are odd beasts; they're obligate intracellular parasites, doing their evil work by hijacking your cellular machinery and using it to make more viruses.  Furthermore, they lack virtually all of the structures that cells have, including cell membranes, cytoplasm, and organelles.  They really are more like self-replicating chemicals than they are like living things.

Simian Polyoma Virus 40 [Image licensed under the Creative Commons Phoebus87 at English Wikipedia, Symian virus, CC BY-SA 3.0]

What is even stranger about viruses is that while some of the more familiar ones -- colds, flu, measles -- invade the host, make him/her sick, and eventually (with luck) are cleared from the body -- some of them leave behind remnants that can make their presence known later.  This behavior is what makes the herpes family of viruses so insidious -- if you've been infected once, you are infected for life, and the latent viruses hidden in your cells can cause another eruption of symptoms, sometimes decades later.

Even weirder is when those latent viral remnants cause havoc in a completely different way than the original infection did.  There's a piece of a virus left in the DNA of many of us called HERV-W (human endogenous retrovirus W) which, if activated, can trigger multiple sclerosis or schizophrenia.  Another one, Coxsackie virus, has an apparent connection to type-1 diabetes and Sjögren's syndrome.  Thus far, all of the viral infections, whether or not they're latent, are damaging to the host.  So it was quite a shock to me to read a piece of recent research that there's a viral remnant that not only is beneficial, but is critical for intercellular communication -- and individuals without it have trouble forming long-term memories!

In two separate papers published in the journal Cell -- "The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer" and "Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons," each by a large team of neurobiologists and geneticists -- we learn about the proteins Arc and Gag, which were put into our cells by retroviruses (probably) hundreds of millions of years ago, and which generate virus-like particles that transfer from one brain cell to another.  This process seems to mediate memory formation, as mice that have the Arc/Gag gene knocked out are unable to retain long-term memories -- and may even be unable to form them in the first place.

As Sara Reardon explained it, writing in Nature:

Shepherd and Budnik [lead researchers in the two studies] think that the vesicles containing Arc play a part in helping neurons to form and break connections over time as an animal’s nervous system develops or adapts to a new environment or memory.  Although the fly and mouse versions of Arc are similar, they seem to have evolved from two distinct retroviruses that entered the species’ genomes at different times.  "There must be something really fundamental about it," Budnik says, for it to appear in both mice and flies... 

The human genome contains around 100 Gag-like genes that could encode proteins that form capsids.  It’s possible that this new form of communication between cells is more common than we thought, Shepherd says.  "We think it’s just the beginning."

Which is pretty astonishing.  The idea that some viruses might have beneficial effects on the host is weird enough; the idea that they could facilitate something as basic as memory storage is mind-blowing.  As such, they'd be a major driver for evolution -- given that organisms that have strong memory capacity are clearly at an advantage over ones that don't.

So before you curse the viruses this winter, be a little thankful for Arc and Gag and any other genetic parasites we might have that help us to function.  It may be small consolation if you are currently fighting a cold, but keep in mind that without viruses, you might not be keep anything in mind at all.

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The answer to the puzzle: The two masked men are the catcher and the umpire.

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One of the best books I've read recently is Alan Weisman's The World Without Us.  I wouldn't say it's cheerful, however.  But what Weisman does is to look at what would happen if the human race was to disappear -- how long it would take for our creations to break down, for nature to reassert itself, for the damage we've done to be healed.

The book is full of eye-openers.  First, his prediction is that within 24 hours of the power going out, the New York Subways would fill with water -- once the pumps go out, they'd become underwater caves.  Not long thereafter, the water would eat away at the underpinnings of the roads, and roads would start caving in, before long returning Manhattan to what it was before the Europeans arrived, a swampy island crisscrossed by rivers.  Farms, including the huge industrial farms of the Midwest, would be equally quick; cultivated varieties of wheat and corn would, Weisman says, last only three or four years before being replaced by hardier species, and the land would gradually return to nature (albeit changed by the introduction of highly competitive exotic species that were introduced by us, accidentally or deliberately).

Other places, however, would not rebound quickly.  Or ever.  Nuclear reactor sites would become uninhabitable for enough time that they might as well be considered a permanent loss.  Sites contaminated by heavy metals and non-biodegradable poisons (like dioxins) also would be, although with these there's the possibility of organisms evolving to tolerate, or even break down, the toxins.  (No such hope with radioactivity, unfortunately.)

But despite the dark parts it's a good read, and puts into perspective the effect we've had on the Earth -- and makes even more urgent the case that we need to put the brakes on environmental damage before something really does take our species out for good.