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Genetics, Humor, Medicine and Society, Science, Stanford News

Using epigenetics to explain how Captain America and the Incredible Hulk gained their superpowers

Using epigenetics to explain how Captain America and the Incredible Hulk gained their superpowers

When I was kid I used to watch the Incredible Hulk on TV and wait for Bruce Banner to fly into a rage, his muscles inflating like balloons, pants torn to shreds while his entire body turns green as he transforms into the Hulk. As I grew up, and learned more about the advances in genetics, it never occurred to me that cutting-edge genome-editing techniques could explain the scientific principles behind the Hulk’s metamorphosis or his fellow Marvel Comics star-spangled hero Captain America. In a recent Stanford Report story,  Sebastian Alvarado, a postdoctoral research fellow in biology, creatively applies the concepts of epigenetics to illuminate the process by which average Joes become superheroes.

As Alvarado notes in the piece and above video,  over the past  70 years scientists have developed tools for selectively activating and deactivating individual genes through chemical reactions, a process termed epigenetics. Similar to flipping on a light, switch gene expression can be “turned on” or “turned off. “We have a lot of genome-editing tools – like zinc finger nucleases, or CRISPR/Cas9 systems – that could theoretically allow you to epigenetically seek out and turn on genes that make your muscles physically large, make you strategically minded, incredibly fast, or increase your stamina,” he said.

In the case of Captain America, the process of deliberately switching on and off genes could offer a real-world explanation as to how scrawny Steve Rodgers gained extraordinary, strength, stamina and intelligence after being injected with “Super Solider Serum” and then blasted with  “Vita-Rays.” When it comes to Bruce Banner, a little more creative license is required. Alvarado’s theory is:

First, when gamma radiation hits DNA, it breaks the molecule’s double-stranded, ladder-like helix, a process known as chromothripsis. Your body can repair a few breaks without significant loss of function.

If many breaks occur – say, if you were caught in a giant gamma explosion – the repairs can become sloppy, and new instructions can be keyed into the genetic code. Alvarado suggested that it’s possible that when Banner’s DNA reassembled after the initial blast, it now included a handful of epigenetic switches. Instead of the switches being activated by light, however, the hormones produced when Banner is angry might flip the genetic switches to reconfigure his DNA to transform him into the big, green Hulk.

As for the Hulk’s skin turning green, anyone who has suffered a nasty bruise has firsthand knowledge of the process that might be behind this transformation. When you bruise, red blood cells at the point of injury die and the oxygen-carrying molecule on their surface, hemoglobin, begins to break up. One of hemoglobin’s metabolites, Alvarado said, is a molecule called biliverdin, which can make the blood appear green and is responsible for the avocado hue at the edge of a bruise.

Giant gamma explosion and epigenetics aside, there’s one question that has scientifically stumped Alvarado: How do the Hulk’s pants stay on after every transformation?

From August 11-25, Scope will be on a limited publishing schedule. During that time, you may also notice a delay in comment moderation. We’ll return to our regular schedule on August 25.

Humor, Parenting, Science

A humorous look at how a background in science can help with parenting

A humorous look at how a background in science can help with parenting

Scientist-moms out there might enjoy this playful (tongue-in-cheek) Huffington Post essay on how having a science degree made the writer a better parent. I had to chuckle at Sarah Gilbert’s list of how she’s found uses for the sciences in her day-to-day life:

Physics: Knowing that my house will return to complete disorder immediately after I clean it, because entropy.

Biology: Knowing everything my baby ate by the contents of her diaper, because scat identification.

Neuro-psychology: Knowing that my toddler freaking out over sandwich crusts is just a phase, because frontal lobe development.

Statistics: Knowing that the chance of having a baby brother is 50/50 no matter what my mother-in-law thinks, because mutually exclusive events.

Astronomy: Knowing that the woman judging me by my yogurt-spattered shirt isn’t the only thing in the universe, because cosmology.

Humor, Neuroscience, Research, Stanford News

Looking at how a child’s sense of humor takes its shape

Looking at how a child's sense of humor takes its shape

girl2Where does a child’s sense of humor come from? That depends on how you define humor and where you look to find it. A recent blog post from the Cognitive Neuroscience Society reports:

Humor can be a very complex and hard concept for some kids to grasp, said [Jessica Black, PhD,] of the Graduate School of Social Work Boston College, speaking yesterday about her poster on this new work at the CNS meeting in Boston. It requires people to both detect and resolve incongruities and to find amusement – involving many regions of the brain, including those that process cognitive computations and those that process emotions.

Black and others, including Allan Reiss, MD, the study’s director, and Pascal Vrticka, PhD, both of Stanford, studied how different brain regions were activated as children watched a video with funny, positive or neutral content. Twenty-two children ages 6 to 13 were asked to rate their ability to create and appreciate humor. Then, researchers examined their brain activity using fMRI scans.

The CNS blog post continues:

In general, the researchers found greater brain activity in children who rated themselves low on the sense of humor scale. The systems related to detecting incongruities and those involved in language and working memory had to ramp up to process the funny videos, as did the arousal network that is usually more active when processing negative emotional information. Interestingly, the brain activity related to social processing was lower in these children, suggesting perhaps more difficulty in being able to think about the mental state of others.

Their results suggest that children with a low sense of humor may require more cognitive effort to process humor, Black said. The data also imply that children with a low sense of humor may experience stress and increased levels of arousal during social interactions involving humor.

Previously: A closer look at the way our brains process humorHumor as a mate selection strategy for women? and Making kids laugh for science: Study shows how humor activates children’s brains
Photo by Maria del Carmen Gomez

Humor, Research

Laughter: really the best medicine?

LladrÛ ClownOh! what fun it is to write for the British Medical Journal‘s Christmas issue. In it, you can read about Richard Wagner’s migraines, James Bond’s alcohol-related health risks, and nominative determinism in The Brady Bunch.

As Popular Science reports, one of the special edition’s studies “includes many interesting ways in which laughter is beneficial, as well as an odd list of harmful consequences.” The heavily footnoted, pun-laden paper notes that in healthy people, 15 minutes of laughter could burn up to 40 calories, for example. Other benefits include improved lung function by clown-induced laughter for people with chronic obstructive pulmonary disease.

The authors are largely skeptical, though. From the study:

…laughter is no joke—dangers include syncope, cardiac and oesophageal rupture, and protrusion of abdominal hernias (from side splitting laughter or laughing fit to burst), asthma attacks, interlobular emphysema, cataplexy, headaches, jaw dislocation, and stress incontinence (from laughing like a drain). Infectious laughter can disseminate real infection, which is potentially preventable by laughing up your sleeve.

The authors disclosed funding (“none was required”) and conflicts of interest (“their senses of humour sometimes conflict”).

Previously: How laughter, anger may influence heart health and Using humor to evaluate negative experiences can improve emotional health
Photo by Garry Knight

Humor, Neuroscience, Research, Videos

Late nights in the lab, expressed through song

Late nights in the lab, expressed through song

Like many others out there, my favorite thing to listen to this summer was “Get Lucky.” (Totally superior to that other Pharrell hit.) An earworm of a song, it launched tons of parodies – but it’s the latest, from the UC-San Diego Neurosciences Graduate Program - that managed to win my heart. I’ve never worked in a lab, but that doesn’t mean I can’t appreciate classic lyrics like this:

She’s up all night to pipette
I’m up all night to collect
She’s up all night, no regrets
I’m up all night to get data

I highly recommend watching the video. But don’t blame me if you find yourself humming the chorus the rest of the day.

Via The Next Regeneration
Video by 123comicbro

Bioengineering, Events, Humor, Neuroscience, Science, Stanford News, Technology

Can Joe Six-Pack compete with Sid Cyborg?

Can Joe Six-Pack compete with Sid Cyborg?

cyborgA few weeks ago, I blogged about the past half-century’s startling advances in computer competence. Referring obliquely to the Turing test, I mused, “Makes me wonder: Just how long will it be before we can no longer tell our computers from ourselves?”

A week later, as fate would have it, I showed up in a classroom on Stanford’s quad for a discussion between UC-Berkeley philosopher John Searle, PhD, and Stanford artificial-intelligence expert Terry Winograd, PhD, concerning a similar-sounding but subtly deeper question: “Can a computer have a mind?”

Failed philosophy major that I am (see confession), I refrained from raising my hand while Searle recapped his famous “Chinese room” argument. “I don’t understand a word of Chinese,” he told the audience. But were you to arm him with sufficient instructions for responding to myriad character combinations with counterpart character-combination outputs, he claimed, he might be able to fool a remote observer into concluding otherwise. (Philosophers are always “claiming” something or other. How nostalgic!)

Sure, machines might be able to “think” in the sense of manipulating symbols, said Searle. But when it comes to consciousness, such “thoughts” do not a mind make. Syntax (the manipulation of symbols – nothing but ones and zeroes, in this case) isn’t the equivalent of semantics (the effects of those manipulations on our consciousness: in a word, “meaning.)

“We still don’t know how the brain creates consciousness,” Searle said, arguing that to fully understand subjectivity, it will be necessary not merely to simulate brain function but to duplicate it. (A street map is not the same as the city it’s a map of.) That’s a comforting constraint for carbon-based throwbacks such as myself, who would like to feel our dominance is assured, at least for a while, by the excruciating nested complexity of the biological components-within-components-within-components of the human brain.

Aha! The Devil is in the details. (The Tom Südhofs of the world are busily working those out as I write this). Score one for biology: A ones-and-zeroes-based gizmo, which can’t even sprout body hair, may never acquire that precious thing called “consciousness.” At least, not on its own.

But what if nanotech and biotech team up?

Once upon a time before coming to Stanford , I wrote an article titled “The 21st Century Meets the Tin Woodsman” and subtitled: “Can Joe Six-Pack compete with Sid Cyborg?” Consider a scenario wherein computation- and communication-enabled nanoparticles, ingested in a pill, float through the blood-brain barrier and seat themselves at each of the quadrillion or so nerve-cell to nerve-cell contact points in a person’s central nervous system:

With nanobots monitoring every critical neural connection’s involvement in a thought or emotion or experience, you’ll be able to back up your brain – or even try on someone else’s – by plugging into a virtual-reality jack. The brain bots feed your synapses the appropriate electrical signals and you’re off and running, without necessarily moving. If nanotechnology gets traction, all bets are off, because whoever’s packing those brain bots will be infinitely more intelligent than mortal meat puppets like me … I hope our sleek semiconducting successors like pets, because, while the mammalian herding instinct ensures that many of us will go along for the ride, characteristic human obstinacy ensures that many will not.

Call me obstinate. To the best of my knowledge, I’m still 100 percent human. But in ten or twenty years, at the rate things are going, how will I be able to be sure you are, too?

Previously: Step by step, Sudhof stalk the devil in the details, snagged a Nobel, Half-century climb in computer’s competence colloquially captured by Nobelist Michael Levitt and Brains of different people listening to the same piece of music actually respond in the same way
Photo by Javi

History, Humor, Medicine and Literature, Science, Technology

Half-century climb in computer’s competence colloquially captured by Nobelist Michael Levitt

Half-century climb in computer's competence colloquially captured by Nobelist Michael Levitt

ancient computerOn October 9, the day Stanford macromolecule-modeling maven Michael Levitt, PhD, won his Nobel Prize, I wrote him a note of congratulations.

He wrote back six days later: “Thanks so much. It has been one wild ride! It will be good for the field, though, and I will learn to disappear and still have time for myself.” It’s a wonder he got back to me as soon as he did, crushed as he must feel by the cheering throngs dogging him at every turn since Nobel day. But he has made a point of replying quickly and gracefully to not only well-wishers but deadline-driven reporters.

Although his Nobel was for chemistry, the lab Levitt operates in is stocked with shelves full of ones and zeroes. His expertise lies in the field of computer science, a field of which Alfred Nobel had no inkling when he created the awards in his final will, written in 1895.

As we all know, Nobel made his millions in the explosives field. No explosion he could have imagined in 1895 has been more profound, in recent decades, than the explosion in computing power pithily encapsulated in Moore’s law. In the late 1960s, Levitt began constructing his increasingly detailed simulations of the giant biomolecules that animate our cells and, in a sense, our souls as well, by pumping punchcards into what was then among the world’s most potent computers (dubbed Golem in memory of a powerful, soulless giant of medieval Jewish folklore) at Israel’s Weizmann Institute.

Since those seminal days, the ones-and-zeroes game has picked up speed. Responding to an e-mailed query from science writer Lisa Krieger of the San Jose Mercury News, Levitt put it this way:

The computer that I used in 1968 allowed me 300 [kilobytes] of memory, or about 1/10,000th of the memory on a smart phone. [An extremely complex,  fifty-step computation] took 18 minutes on the Golem computer… for a cost of about five million 1965 U.S. dollars ($35 million today). The same calculation takes 0.18 seconds on an Apple MacMook PRO laptop costing $3,500. This means that the calculation is… 6,000 times faster on a computer costing… 10,000 times less.

If cars had changed in the same way, Levitt drolly noted, “a 1965 Cadillac that cost $6,000 in 1965 dollars ($40,000 today) would actually cost just four dollars. More amazingly, it would have a top speed of 600,000 miles an hour and be able to carry 50,000 people.”

Makes me wonder: Just how long will it be before we can no longer tell our computers from ourselves?

Previously: But is it news? How the Nobel Prize transformed noteworthy into newsworthy, Nobel winner Michael Levitt’s work animates biological processes, No average morning for Nobel winner Michael Levitt and Stanford’s Michael Levitt wins 2013 Nobel Prize in Chemistry
Photo by kalleboo

Humor, Research

A flowchart for debating scientific studies?

A flowchart for debating scientific studies?

Nerd alert: I love flowcharts. They can be used to learn the structure of an organization, find a solution to a problem, or determine if all connections really do lead back to actor Kevin Bacon. I’ve even used them as a self-diagnosis tool (allergies or sinus infection?). Well, it turns out flowcharts may also be useful when it comes to research. Dylan Matthews at WashingtonPost.com’s Wonkblog has come up with one for scientific studies called “How to argue with research you don’t like.”

The argument guide provides readers with a range of reasoned responses in a debate, from “This is a major contribution of unparalleled rigor” to “I urge you to tell the thousands this program has helped that it has failed to make their lives better.” You might want to put a few in your pocket.

Via i09.com

Humor, Medicine and Society

Discussing “urgent” matters in medical paperwork

Discussing "urgent" matters in medical paperwork

Apparently writers aren’t the only ones repelled by exclamation points: In an essay on NEJM Journal Watch, the blog’s editor-in-chief Paul Sax, MD, describes in bullet points why extreme punctuation and other editorial overstatements make irritating, and sometimes unnecessary, demands on doctors’ time. Especially when delivered by fax.

From the piece:

  • It’s “Urgent.” Not just Urgent, but urgent!!! How do we know? Look, the word has squiggly underlining — that means it must be really important. But one might wonder why it’s so important when, as mentioned above, the care has already been given (and, for the record, the patient no longer needs their services, he’s much improved). Could it be that that the definition of “urgent” for this company differs quite substantially from a clinician’s? To a clinician, examples of “urgent” problems include a patient who is short of breath, or bleeding, or having chest pain. For this company, “urgent” means “we want to be paid as soon as possible.”

The whole post is an amusing – if maddening – read.

Via Common Health

Big data, Events, Humor, Stanford News, Technology

Big laughs at Stanford’s Big Data in Biomedicine Conference

Big laughs at Stanford's Big Data in Biomedicine Conference

Last week’s high-powered Big Data in Biomedicine Conference, held on Stanford’s campus, featured more than 40 speakers and several hundred participants grappling with the massive challenges of harnessing the growing flood of relevant data that’s soaking the fields of patient care and medical research.

Sound deadly? In fact, the talks were punctuated every five minutes or so by belly laughs. In my write-up of the three-day event, I managed to include one causal zinger, a comment by opening speaker John Hennessy, PhD, Stanford University’s president and a computer scientist by training:

If cars had made as much progress as computers over the past several decades, you’d be able to drive across the country for a dime in one of them and then pack it up and stick in your shirt pocket.

But I had to leave a whole lot of great material out – for instance, this aside by Atul Butte, MD, PhD, the conference’s principal organizer, upon noting that the amount of data generated globally each year is now measured in zettabytes (the prefix “zetta” referring to the number “1″ followed by 21 zeroes): “I’ll freely admit that most of those zettabytes are kittens playing the piano!”

And here’s keynoter David Ewing Duncan, author of the book “The Experimental Man” and a human guinea pig who has had himself tested more than a thousand times for tens of thousands of genetic traits including behavioral ones, on learning that he is at “very high risk” for a deficiency in empathy: “I don’t know quite what to think about that. And I don’t care what you think about it.”

Previously: Image of the Week: The Experimental Man at Big Data in Biomedicine, A call to use the “tsunami of biomedical data” to preserve life and enhance health and Mining medical discoveries from a mountain of ones and zeroes

Stanford Medicine Resources: