Biosynth Engineering
The International Genetically Engineered Machine Competition (iGEM) is featured in the Sunday Magazine.
Genetic engineers have looked at nature as a set of finished products to tweak and improve — a tomato that could be made into a slightly better tomato. But synthetic biologists imagine nature as a manufacturing platform: all living things are just crates of genetic cogs; we should be able to spill all those cogs out on the floor and rig them into whatever new machinery we want. It’s a jarring shift, making the ways humankind has changed nature until now seem superficial. If you want to build a bookcase, you can find a nice tree, chop it down, mill it, sand the wood and hammer in some nails. “Or,” says Drew Endy, an iGEM founder and one of synthetic biology’s foremost visionaries, “you could program the DNA in the tree so that it grows into a bookshelf.”
Dr. Amy Bishop: Cursed.
The Huntsville Times has identified the likely shooter in the University of Alabama shootings: Amy Bishop, a Harvard-trained neuroscientist.
At Harvard, we learned quickly that all female graduates are cursed: too smart to keep good men, too in-their-own-heads to get out of their own way. Assuming Bishop is the shooter, we can surmise that she felt she was doing the University of Alabama a favor by teaching there — “Deny me tenure? You looking to die today?”
Willful Modulation of Brain Activity in Vegetables.
There’s a new study in the New England Journal of Medicine that’s causing a stir. 54 patients, all suffering from severe disorders of consciousness (”persistent vegetative state”), were scanned using fMRI while asked questions that generally involve cognition localized to specific areas of the brain. From the LA Times:
Several times when Subject 23 was asked to imagine playing tennis, Monti said, the region of the brain most closely associated with complex motor planning became highly active, and stayed active for 30 seconds after researchers prompted such imagery by saying “tennis.”
Similarly, when researchers asked the patient to imagine walking through the house where he grew up and then said the word “navigate,” Subject No. 23 responded with bursts of activity in the region of the brain involved in constructing and navigating a mental map.
The young, French-speaking man was the only subject who was then trained to answer simple yes or no questions — whether his father’s name was Paul (yes) or Alexander (no), whether he had siblings and how many — using the imagery technique he had already learned.
Checking the patient’s responses for accuracy and comparing them to the yes-no brain responses of a group of healthy volunteers, researchers discerned that Subject No. 23 was not only still “in there,” but capable of purposeful thought and communication.
Clever… in more ways than one.
Using your hands makes you smarter
Abstract thinking is facilitated with kinesthetic action, the NY Times reports:
As they thought about years gone by, participants leaned slightly backward, while in fantasizing about the future, they listed to the fore. The deviations were not exactly Tower of Pisa leanings, amounting to some two or three millimeters’ shift one way or the other. Nevertheless, the directionality was clear and consistent.
“When we talk about time, we often use spatial metaphors like ‘I’m looking forward to seeing you’ or ‘I’m reflecting back on the past,’ ” said Lynden K. Miles, who conducted the study with his colleagues Louise K. Nind and C. Neil Macrae. “It was pleasing to us that we could take an abstract concept such as time and show that it was manifested in body movements.”
HeLa Cells: a life immortal
Henrietta Lacks, the person from which HeLa cells were born, and family are the subject of a new book.
From an interview at Smithsonian with author Rebecca Skloot:
For scientists, one of the lessons is that there are human beings behind every biological sample used in the laboratory. So much of science today revolves around using human biological tissue of some kind. For scientists, cells are often just like tubes or fruit flies—they’re just inanimate tools that are always there in the lab. The people behind those samples often have their own thoughts and feelings about what should happen to their tissues, but they’re usually left out of the equation.
Which is as it should be, many scientists say, arguing that Mrs. Lacks’s immortal cells were an accident of biology, not something she created or invented, and were used to benefit countless others. Most of what is removed from people is of no value anyway, and researchers say it would be too complicated and would hinder progress if ownership of such things were assigned to patients and royalties had to be paid.
Joyous boredom
Jennifer Schuessler, an editor at the Book Review, tackles David Foster Wallace’s posthumous novel, The Pale King, and attempts to explain, most interestingly, the importance of being bored.
A library is an enormous repository of information, entertainment, the best that has been thought and said. It is also probably the densest concentration of potential boredom on earth.
I survived Uganda and all I got was this lousy…
Michelle Barnes, survivor of Marburg Fever.
When scientists trying to develop a Marburg vaccine at the National Institutes of Health heard about Ms. Barnes, they were eager to take blood samples from her. She agreed. They invited her and Dr. Fujita to Bethesda, Md., last June, to present her case to a standing-room-only crowd of researchers who had never seen a Marburg survivor.
GluRs come into focus.
Finally, a glimpse of a full-length tetrameric glutamate receptor.
The structure presented by Sobolevsky et al. is of one of the main glutamate-receptor subtypes, an AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptor from the rat. It is made up of four GluA2 subunits (GluR2 in older nomenclature) that are identical in terms of amino-acid sequence, and it encompasses three structural/functional domains. Two of these domains are located on the external side of the cell membrane, and we have seen them individually before — the modulatory amino-terminal domain (ATD) and the ligand-binding domain (LBD) with its clam-shell-like arrangement. The third component is the transmembrane domain (TMD), which forms the ion channel, and this is our first view of it. In many ways the structure is comforting, because it consolidates and verifies much previous functional and structural work. But at the same time it is exhilarating, owing to the unexpected way in which these domains are intertwined and linked together.
Article here.
Can you feel me?
In the current issue of Nature, Gick and Derrick propose that we hear using not only auditory and visual cues, but also tactile sensations from our skin.
When we listen to human speech we use a combination of the senses: the ears, obviously, and the eyes to see how a speaker’s face changes the perception of consonant sounds. Experiments seeking to add the sense of touch to the mix have until now been inconclusive. Many languages use an expulsion of air to change vowel or consonant sounds — in English to distinguish a sound like ‘da’ from the microphone-popping ‘pa’. Bryan Gick and Donald Derrick take that ‘puff of air’ as the starting point for a study of whether the sense of touch can contribute to what we ‘hear’. They applied small, inaudible air puffs to the skin of volunteers who were simultaneously listening to a series of consonant sounds. Air puffs aimed at either the hand or neck made it more likely that aspirated sounds would be heard. So ‘b’ was misheard as ‘p’ following an air puff. This work could prove useful in the future development of audio and telecommunication aids for the hearing impaired.
The NY Times summarizes the work nicely.
The Fantastic FOXP2
Daniel H. Geschwind at UCLA just published a paper describing the human-specific transcriptional regulation of central nervous system genes by Forkhead box P2 (FOXP2), a gene implicated in some speech disorders.
Premature Ejaculator
I like Obama. He’s personable and intelligent and writes about himself well. I think his latest decision (as well as his decision to accept the Nobel prize) however, reveals moments of complete and utter stupidity.
Briefly, he wants to lift a 22-year-old ban on HIV+ people traveling to the States. The glaring problem here is that people with HIV tend to be young; and young people have a biological predilection for sex. Lots of it. The argument he’s making is that the US is a world leader in AIDS treatment. Well, you’re wrong. As far as treating AIDS goes, we’re pretty much doing the same things everyone else is doing.
Mr Obama said the ban was imposed 22 years ago when visitors to the United States were treated as a threat.
He said: “We lead the world when it comes to helping stem the Aids pandemic - yet we are one of only a dozen countries that still bar people with HIV from entering our own country.
“If we want to be the global leader in combating HIV/Aids, we need to act like it.”
Mr Obama, being the leader of the world when it comes to stemming the spread of AIDS is IN NO WAY TANTAMOUNT to having a liberal immigration policy. Now don’t get me wrong, I’m all for curing AIDS — I even put in a couple of years looking for one; all I’m saying is that your decision has little to do with fighting AIDS and more to do with stupidity (i.e., your feigning of expertise outside of your field of study): we would obviously quarantine travelers with Swine Flu or SARS or any other pandemic.
Obama, buddy, you’re busting a nut before we’re ready for it. You should wait until AFTER we’ve found a cure before letting people come in for treatment.
Time.
The illusion of time is considered in the latest New Scientist.
Disappointing, actually, since the research used could have been flawed, yet all conclusions presented are drawn from it. (Personally, I would’ve done as Herb Benson and recruit subjects who are supposedly able to slow time at will, i.e., those who can catch arrows and such at birthday parties, and then use fMRI to study differences.)
Gladwell, Dogs, and Men
Malcolm Gladwell compares the suspected neurological consequences of American football to dogfighting in the latest New Yorker. Ultimately, the piece disappoints. Though highly entertaining (it’s standard Gladwell), the piece stretches too thin to make a connection between neuroscience and football and staged dog fights. Where he especially misses is in his moral comparisons; Gladwell believes the loyalty and dedication seen amongst pro players and their teams are tantamount to those seen amongst dogs and their handlers. (It fails not because the juxtaposition seems, intuitively, unequal, but because Gladwell seemingly assumes dogs are just furry little humans. Cesar Millan would not approve.)
What is truly disappointing, however, is that Gladwell, after having taken up his column at the New Yorker, seems to be stretching for big ideas. And that is sad to me. Because homework should be done in private.
The breathtaking significance of 31.2%
This is already old news, but an AIDS vaccine has been shown to be of statistically-significant effectiveness in preventing transmission of the disease. For years (decades!) we’ve had nothing — absolutely nothing. Ask any pharmacologist or biomedical scientist and they’d tell you the same: nothing.
Now we have something. And something, no matter how small, can make all the difference in the world sometimes.
Time to eat.
A pair of studies (including a KO) suggests eating when you should be sleeping helps pack on the pounds.
Together, the papers suggest that there’s no simple answer to why people gain weight. Says [biologist Fred] Turek, “It’s clearly not just calories in versus calories out.”
Monogamous Mating
Diane Doran-Sheehy, a primatologist at SUNY Stony Brook, thinks pregnant female gorillas use sexual intrigue as a tool to enhance pair-bonding. In essence, the female keeps the alpha male busy so other females can’t get any. This research, if validated, can add a new facet to our understanding of the evolutionary bases for monogamy and, indeed, love.
Sexy fMRI
Pek Van Andel, winner of the Ignobel Prize, gives us the best money shot ever:
Your stupidity is painful
Michael Agger wrote a short piece about whether fish feel pain that just seems all wrong. Actually, his lapses in logic and failure to achieve any real depth bother me so much I need to note them here — so I know, in the future, if I ever start making the same mistakes in the articles I write, I can just kill myself. Slowly. Painfully.
Whether animals feel pain, I believe, is a function of their nociceptive capacity. Hence, nociception is not actually pain, per se. If a hot ash from your cigarette falls on your knee, and you happen to have a callous there, you might not feel anything at all. But if that same ash flew up into your eye, you might be crying for hours. Same stimulus, different nociceptive input. In the first case, few nerves recognize the burning ash. But in the face, a particularly nociceptive area, it hurts like hell.
Presumably, we are dealing with a parallel problem when considering other animals. Humans have a relatively immense intelligence when compared to other animals, so, naturally, we can start off by saying we have an “improved” capacity to suffer (not science per se, but logic: something falls and breaks a foot and maybe experiences similar pain, but only humans have the capacity to think about all the soccer games they’ll miss and how they’ll have to use a cane before turning 30 — our pain is sophisticated in that way). If we can presume differences in nociception, we can say “animals don’t feel pain the same way we feel pain.” And, if we can do that, then we’re talking about another problem altogether — the real problem. Nociception? Sure, I’ll buy that; I think all animals can process aversive stimuli and react to them. But pain? No. I need more proof. Not only that, but I need to know, if fish do experience pain, whether that pain actually bothers them (i.e., it may be quotidian; fish may feel the same thing when they bite into baitfish, for instance).
None of this is Agger’s problem. I think he considers nociception as well as any angler can; however, in the middle of the piece, he loses his fucking mind:
What does my gut tell me about fish pain? Not happening. When I reel in a trout, I may be stressing the fish—making it expend precious energy—but it’s not howling in agony.
Fantastic. You go from using reason to guesstimation . This is how you preclude your writing from having any real depth, buddy.
And the reason why I care at all may be because I live in England (I cut live sashimi at parties sometimes, after all). The English, to me, seem to suffer from this very affliction: there’s enough intelligence there to fool people, but not enough to make things work right.
Earlier today, for instance, I had a 15-minute conversation to book a ride to Heathrow. 13 minutes of that was repeating my address (four times…) and listening to the guy tell me how important it was to be timely. Then my credit ran out, ride never fully booked. Do I expect the guy to be here at 5pm — especially knowing he’s written my address more than once? C’mon. Seriously. This is England we’re talking about. I’m better off walking.
It would involve less pain, at least.
Neuroscience and War
The New Scientist examines the use of neuroscience in developing better soldiers.
If a soldier is struggling, a digital “buddy” might step in and warn them about nearby threats, or advise comrades to zap them with an electromagnet to increase their alertness. If the whole unit is falling apart, biosensors could warn central commanders to send in a replacement team.
I have a problem with the far-term (10-20 years) goal of in-vehicle transcranial magnetic stimulation (TMS; “zap them with an electromagnet”). It just hasn’t been studied enough to know if there are any significant long-term effects associated with TMS. Putting troops at risk unnecessarily reveals the problem here: you have too many non-military, experimental scientists working together. There needs to be more overlap. The scientists need to know what it’s like to be a soldier, with a pregnant wife at home, wondering if all that brain zapping is going to give him Alzheimer’s. (And why couldn’t you just do it pharmacologically? Seems easier to carry adenosine-blocking pills than a TMS.)
Moreover, I think the approach is all wrong. American soldiers are at the top of the food chain. If you work to improve their current capabilities, you’re struggling for single-digit yields. Nothing you do is going to make, for example, a 10% difference in performance. I think a superior goal would be to improve our intelligence-gathering using neuroscience; namely, truth detection (for interrogation). Improving non-combat intelligence will lead to amazingly-better battlefield outcomes with what we currently have. More importantly, we can then fight insurgency on our terms, not theirs: good truth detection should lead to fast and efficient capture of enemy commanders (like Osama Bin Laden). And isn’t that the whole point?
The Multi-tasking Myth
John Tierney, writing for the NY Times, discusses focused attention and cognitive overload.
“It takes a lot of your prefrontal brain power to force yourself not to process a strong input like a television commercial,” said Dr. Desimone, the director of the McGovern Institute for Brain Research at M.I.T. “If you’re trying to read a book at the same time, you may not have the resources left to focus on the words.”
Conclusion? Multitasking is a myth:
“Multitasking is a myth,” Ms. Gallagher [author of Rapt] said. “You cannot do two things at once. The mechanism of attention is selection: it’s either this or it’s that.” She points to calculations that the typical person’s brain can process 173 billion bits of information over the course of a lifetime.
“People don’t understand that attention is a finite resource, like money,” she said. “Do you want to invest your cognitive cash on endless Twittering or Net surfing or couch potatoing? You’re constantly making choices, and your choices determine your experience, just as William James said.”
Intelligence: some people still have it.
Intelligence isn’t about doing well in school or making lots of money; it’s about looking at the world around you and figuring out better ways of doing things(1) — and not just for you, but for humanity. Juan Enriquez gets it; listening to him is like someone switching on a flashlight, pushing back the darkness, so you can find a way through the forest.
Notes:
1. One compelling difference between humans and animals is our ability to impose our will upon the environment. Animals adapt and evolve to the environment; we do the opposite: we force the environment to adapt to us. The problem is, most of us don’t actually impose anything; instead, we become reactive, accepting the will of others. The importance of people like Enriquez is that they think about HOW will is imposed upon the environment (our reactive directionality), then, they offer better ideas about the situation — without trying to sell you some kind of product. Bravo.
PCRed
Polymerase Chain Reaction (PCR) is one of those great science stories ordinary people never get to hear. Legend has it that Kary Mullis said, upon formulating the PCR procedure, that he was going to win a Nobel prize. He was right.
Brains, an overview
Sometimes people ask me what it’s like doing neuroscience. Well, it’s like listening to this Nedivi lecture — ALL DAY LONG.
Hi, my name is James. I’m an alcoholic.