Tag Archives: daily roundup

Daily Roundup: The Fragility of Memory

When I read the EurekAlert about researchers at Northwestern Medicine who proved that “memory is like a telephone game”, I was a little puzzled. Even more so when I read the line “The Northwestern study is the first to show this.”

I’m a little confused because the first time I read of memory alteration, it was in a Wired article about the ultimate memory pill, which in turn references the work done by Karim Nader years ago. There’s a nice long article by Smithsonian.com which is essentially a profile of Nader’s life and work on this specific aspect.

The work by Northwestern is significantly different, though; for one, it’s conducted on human subjects and not on rats being taught aural cues. But while the Northwestern press release doesn’t refer to a theory of memory reconsolidation, Nader’s work and other research has much more background to support it. I’m not sure if this was simply not referenced in the press release, or if they genuinely were ignorant of the pre-existing work.

Either way, it’s heartening to see that the research is being replicated and the theory borne out by evidence: every time we remember something, at least part of our memory is being reconstructed from scratch. Our memories are never pristine and rarely reliable, which makes me wonder what research exists that compares the protein production of those with normal recall faculties to those with eidetic memory.

Daily Roundup: Neural Implants Help With Cognitive Function

Hot on the heels of the mixed press coverage of the ENCODE project is an EurekAlert article I’m very wary of taking seriously. Wake Forest University researchers claim to have created a prosthetic device that restores cognitive functions to primates whose capabilities have been impaired by injections of cocaine, in some cases to better than average.

Specifically, the monkeys involved were able to complete tasks correctly more often when they were stimulated by this prosthetic.

Before we begin talking about taking magic pills to help us in times of stressful decision making, let’s review the facts: the researchers set the monkeys to doing a task that involves matching a shape they’d seen a few minutes ago to an array of shapes, and they had been trained to achieve a 70-75% proficiency on this task for two years. Miracle cognitive therapy, this certainly isn’t.

But what I am interested in is how their prosthetic works. What are levels L2/3 and L5 of the brain and why are they important? How do they communicate, and why is that suppressed by cocaine (and why is dopamine involved in the first place?)

Most fascinatingly, how do you calculate the mathematical relationship between neuron levels? How is that even possible? And how do you tune a device like this to record during the correct input?

This, for me, is a classic example of a press release that promises so much and delivers tantalizingly little. Now I’m itching to speak to the scientists involved to ask them these questions.

Daily Roundup: Living Longer, Better

A little break from the mechanics of the last few posts: yesterday’s news consisted of some startling, and possibly controversial, biological revelations.

It’s been known for a while now that women outlive men, by about five to six years. Looking through some simple statistics, it’s clear that this has been the case as early as 1930, so better living conditions for women and improved access to female healthcare might not tell the whole story. Some scientists in Lancaster University think they have the answer: mitochondrial genetic inheritance.

Mitochondria are tiny organelles believed to have been co-opted by eukaryotic organisms (which includes humans) a couple of billion years ago. Eukaryotic organisms — my high-school biology is slowly returning to me! — are creatures whose internal structures are enclosed and separated by membranes. Most important of these internal structures is the nucleus; prokaryotes lack one, and eukaryotes are defined by it.

Mitochondria are one of the most important of these internal structures. Producers of ATP, the cell’s energy source, they are crucial to cellular health. One of the reasons that mitochondria are theorized to be symbiotic with our bodies is that they actually contain their own version of DNA, with a handful of genes that code for proteins important to respiratory processes, or the production of energy via ATP. The idea of a mitochondrial Eve arose when biologists discovered that every child carries only the mother’s copy of the mitochondrial DNA. There’s no recombination analogous to the meeting of egg and sperm; the entire DNA of the mitochondria is simply handed down from mother to child1.

Scientists from Lancaster conducted a rather interesting study to figure out if this mitochondrial handing-down had any effects on the males as opposed to the females. Using some fruitflies, they determined that variations in mitochondrial DNA seemed to correlate with male life expectancy, while they had no effect on female life expectancy. The idea, if I understand it correctly, is that mutations that are harmful for women don’t accumulate, since natural selection weeds out the women who couldn’t have survived nearly as well. But they may very well have preserved mutations harmful to men. This could mean that the mutations which contribute, in whatever small way, to a smaller male lifespan, would be passed on through generations. The Lancaster researchers argue that the “Mother’s Curse”, which is probably the most frustratingly hyperbolic scientific contraction I’ve heard, would account for reduced male life expectancies.

It’s an interesting hypothesis, but I think I’ll wait for the experiments to be either repeated or something analogous to be discovered in human research. It’s rather too sweeping a realization, especially when combined with the assertion that this could have implications across all species that have similar life expectancy gaps. Does the mitochondrial inheritance work the same way across all of them? If not, what other factors could contribute? This rather well-annotated Wikipedia article indicates that mitochondrial DNA is remarkably slow in accumulating mutations — perhaps once every 3500 years, or 35 human generations. That’s plenty of time to develop mutations harmful to men, but it would be interesting to see where the life expectancy differences began to show up, corresponding to the mutations in DNA.

Another article, this one far more controversial, was the link between persistent cancer and something called “cancer stem cells”. Researchers in three different studies tracked pre-cancerous tumors and found that most of the cell populations in later stages of division had descended from a small subset of the original cell population. In the study conducted by researchers from Belgium, it was reported that the cancer stem cells looked similar to skin stem cells.

At first, the idea of cancerous stem cells seemed rather paradoxical to me. After all, cancer is the result of a small population of cells gone wild, refusing to undergo apoptosis where they trigger a sort of self-destruct mode. But this must begin in some fairly mature, developed, specialized cells of internal organs.  So I’d like to discover how cancerous cells grow and spread across the body, causing the cells of other internal organs to go rogue.

It might be time to do more research — and talk to a graduate student I know…

Footnote:

1.  A whole other interesting tangent is the idea of the “mitochondrial Eve”, the ancestor of most living humans today whose genetic inheritance can be traced in an unbroken line to today’s women. This Wikipedia article gives a little bit of an overview, although more citations are probably needed.

Daily Roundup: 3D Printing… Everything

Two articles in PopSci caught my eye this week, and both concerned 3D printing — in wildly different ways.

French design student Luc Fusaro created the first custom-built running shoe using 3D printing techniques. At 96 grams, it’s a full 42% lighter than the Nike Mayfly, until recently the world’s lightest running shoe.

On the other end of the spectrum of usefulness (I’m revealing my liberal ways here, aren’t I?) is the working assault rifle one gentleman produced from a Stratasys printer.

And after I found those two examples of what prototype, or 3D, printing can do for us, I looked around PopSci.com a little while to see what else  I could find. The almost-completely printed UAV (the only thing created using conventional means was the engine) wasn’t even the most extreme example — the Urvee is an entirely printed car, and this was back in 2010.

I think 3D printing has been creeping up on us for a while, now. My first exposure to it was this rather terrible video, which was so astonishing that I honestly believed it to be a hoax for a good several months. But the novelty will begin to wear off soon enough, and we’ll start asking ourselves the really difficult questions — not “What can I make with this?”  or “Can I print a space shuttle?”, but “What does it mean if I can manufacture weapons at home?”

To inject a little reality into a nightmarish scenario of terrorists printing weaponry in some remote location, we should note that you’d need 3D printer schematics to be able to do something like this. Thingiverse, which is linked to in the article about the assault rifle, has a number of other gun and rifle parts; I’m not well-versed enough in the mechanics to determine how much of a threat this sort of thing is. I must note, though, that (using a link given by a commenter on HaveBlue’s design), Thingiverse’s Acceptable Use Policy does state that “(a) You agree not to use the Site or Services to collect, upload, transmit, display, or distribute any User Content… ii) that… promotes illegal activities or contributes to the creation of weapons, illegal materials or is otherwise objectionable”.

Announcing it is one thing; enforcing it is another. None of the admittedly few gun parts I found on Thingiverse had been taken down. Perhaps they’ve taken down the others and are slowly working their way through them, but this would require some serious moderating.

If those levels of moderation grow, along with the community, does that mean that we’re in greater danger? Should 3D printing be restricted to strictly regulated companies and industries, even though they could be boons to innocent engineers and hobbyists? Put another way, should the possibility of printing weaponry prevent us from printing cars and shoes and planes?

Perhaps the situation isn’t as dire as we think it is. Given the state — or the lack, rather — of gun control in this country, I’d hesitate to suggest it, but maybe a supervisory approach is really what we need here. If you’ve invested in a 3D printer, gotten the schematics and printed out the various components of an entire rifle, perhaps your interest in weaponry is a little more sophisticated than someone whose sole purpose is to facilitate crime (I am, of course, leaving the 3D printer-enabled  terrorists out of this equation). In this case, we could assume that the person doing the printing would either know what they’re doing with their product, or would want to be trained to use it. So maybe, in the case of guns, a process of registration, licensing, training and regular maintenance should be enforced. 

What about the terrorists and the mentally disturbed, then, those who can’t be trusted to register anything they create? There’s where I find myself without an answer — except, Big Brother-like, to track the purchases of 3D printers. That’s a far from satisfactory suggestion.

I think 3D printing is the cusp of a new brand of technology altogether. It isn’t simply information. It’s a way to create tools, and perhaps in the future weapons and vehicles. Possibly, if we stretch the boundaries of what’s allowed in 3D printing (I’d have to look this up) food substitutes for impoverished regions of the world. The vending machines of Neal Stephenson’s Snow Crash could be around the corner.

I’ll be following developments with equal parts trepidation and excitement.

Edit: How’s this for developments?

Daily Roundup

The internet today is practically seething with news of the rat-heart-jellyfish story, which is less absurd and far more interesting than this description makes it sound.

Researchers and bioengineers at Harvard have created what might be called a morphologically accurate jellyfish: a slip of a creature that pulses its way through liquid when an electric current is applied across it. We say “morphologically” because it’s nothing to actually do with a jellyfish; the creature is made from rat heart cells.

The news surrounding this, at first, seemed confused. The words “artificial jellyfish”, “rat heart” and “heart cells” have been bandied about without any real context to the issue. Take ABC’s reporting of the news, for instance. The meat of the matter makes its first appearance in the seventh paragraph (“Why do such an experiment?”). Build-up is all well and good, but establishing relevancy is a more important goal. The odd juxtaposition of jellyfish and rat hearts isn’t going to be really rewarding until you present the link — and soon.

Ed Yong, whose work I’ve been coming across more often recently, has a very nice piece in Nature which might as well be the polar opposite of ABC’s1. I very much appreciate the fact that both articles go beyond quoting the press release, but Yong’s is not only scientifically more informative, it’s also more… endearing, for lack of a better word.

A science writer’s comment thread I saw somewhere spoke about the importance of quotes from scientists, especially those who are apt to get excited about their work. I can’t think of a better representation of science than to quote these people, because science is so far from being a cold and mathematically driven discipline. It’s motivated by a need to improve lives, or to discover some even more fundamental truth about the universe, or to simply create something magnificent. Which is why these scientists are the best ones to get the story from. I liked the manifestation of this in the Ed Yong article:

In 2007, Parker was searching for new ways of studying muscular pumps when he visited the New England Aquarium in Boston, Massachusetts. “I saw the jellyfish display and it hit me like a thunderbolt,” he says… “I grabbed him and said, ‘John, I think I can build a jellyfish.’ He didn’t know who I was, but I was pretty excited and waving my arms, and I think he was afraid to say no.”

And soon enough, Yong gets to the point, in Parker’s own words:

“It’s exactly like what you see in the heart. My bet is that to get a muscular pump, the electrical activity has got to spread as a wavefront.”

Space, time and resources permitting, I’d love to be able to write an article like this. By the way, the extended version of the interview by Yong can be found here.

The other piece of news was something I should’ve written about over the weekend: researchers from Stanford U and J. Craig Venter Institute have simulated the entirety of an organism using a cluster of 128 computers.  The magnitude of this task needs to be emphasized: they simulated all known genetic processes of this humble bacterium that lives in human genitalia. Thus, they were able to track the entire life cycle of the organism — and, incidentally, open the way to creating better models for complicated processes like the genetic expression of human diseases.

“A lot of the public wonders, ‘Why haven’t we cured all these things?’ The answer, of course, is that cancer is not a one-gene problem; it’s a many-thousands-of-factors problem.”… For medical researchers and biochemists, simulation software will vastly speed the early stages of screening for new compounds.

Of course, this little guy has 525, while E. Coli has 4288 genes. It’s like a mathematical problem: if it takes 10 hours to simulate one division of an organism with 500-odd genes, how long will it take to simulate E. Coli? And how much extra hardware would that take?

What tickles me is this line:

In designing their model, the scientists chose an approach called object-oriented programming, which parallels the design of modern software systems.

I’m not sure what author John Markoff’s background is, but it certainly isn’t in programming (although I see he used to write for tech related things back in ’76. Punch cards, y’all). OOO is a very common concept that’s used in a variety of programming languages and isn’t nearly as exotic as this article makes it out to be. Every time you create a HelloWorld class in Java, you’re using object-oriented programming. The press release, however, has a better grasp of what constitutes cutting edge software technology. It’s quite fascinating, actually, and I need to ask my CS friends who have used CAD how exactly it might be adapted for more biological purposes.

1. I understand ABC isn’t a science magazine, but it’s still important to cover science news well and accurately. The New York Times covers science and politics as well as any other topic, for instance. Or maybe there are certain newspapers that specialize in science news? That would be an interesting thing to look up.

Daily Roundup

The internet’s been abuzz with quirky little (and not so little items) of note these past few days. For one, there’s a new lightest material in town — aerographite, produced by scientists in two European universities. It’s not simply 75 times lighter than styrofoam, which isn’t exactly concrete itself; it’s also electrically conductive, extremely strong, and absorbs light very efficiently, leaving it jet black. That means it’s probably going to be useful for a huge number of applications — from aviation to stealth weaponry to more efficient batteries. The material is tubular and porous, which is apparently what contributes to both its strength and lightness. I don’t imagine it will be seeing any immediate application, though. The production process doesn’t seem scalable at this point and is still being tweaked for maximum efficiency.

A completely different piece of news caught my eye earlier today: Wired had an interesting report on the Nonhuman Rights Project, which seeks to award legal rights to cetaceans like dolphins and whales. This is particularly quirky and very contentious, because it’s beginning to wrench at the deeper meaning of rights vs. legality and what rights even mean. As the article points out, the group isn’t saying dolphins have a right to education or anything like that; they are saying that cetaceans have a right to life, liberty and freedom.

For example, nobody will argue that SeaWorld’s orcas have a right to free speech or guaranteed medical care  — but they could have rights to freedom from imprisonment or captive breeding.

There are a lot of people who’d agree with that, and they wouldn’t necessarily use a scientific argument either. There are parts to this that are intriguing and possibly peculiar, though. A friend argued that simply assigning rights to cetaceans, no matter how complex they may seem to be, is still putting a very human perspective and value on things like brain size, individualism and social behavior. Paradoxically (at least it seems that way to me) he suggested that because of these skewed perspectives on what it means to be “a person”, we might be leaving out whole other species and even ecosystems. I will admit that this is indicative of some hubris. But — of course — the first thing that occurred to me was robots. Organizations like this place a premium on human intelligence, but what happens when we face a consciousness that we can’t relate to? Interesting thoughts.

Whiplash again as we move to another fascinating article on cryptography. Why, ask an interdisciplinary team of neuroscientists and cryptographers, would you want to consciously memorize your password when you can subconsciously — and safely! — access it? The idea is that, through a series of training exercises, before which the test subject has to create a random series of letters. Then the sequence, along with some randomized mixes of the sequence, is played back to the user almost exactly the way Guitar Hero works, where the player must hit a button when a falling disc hits the fret. Apparently, by the end of this training, you’d be able to pick out the correct sequence interspersed with other random letters. As the article says, “To pass authentication, you must reliably perform better on your sequence.” I think the practical applications of this would be… humorous at best, although the theoretical form of it is interesting.

The last item, I think, deserves a separate blog post of its own. I’ve noticed PopSci’s been running a series of climate change-inspired articles, and this one fits right into that sphere. Scientific American reports that an experiment to dump a load of iron into the ocean — thus fueling rapid algae growth and death — would suck a significant amount of carbon out of the air and thus perhaps offset global warming. Even besides the science, which is optimistic at best because we can’t control for all the ecological variables, this raises a whole slew of questions about ecological ethics. When we’ve screwed up, do we try to be as unobtrusive as possible or do we re-engineer our planet? Do we do it at the cost of whole ecosystems, when the bacteria that grow and die in countless numbers deplete the oxygen that’s normally at steady levels?

Work in Progress, Daily Roundup

It’s been all over the news, and I would be remiss in including it here — Rice University has created batteries that can be spray-painted onto a variety of surfaces, batteries would then allow a remarkably consistent power supply over a number of hours.

There are five layers to this battery, which lead author Neelam Singh describes as a battery “converted” into different paints. The image at the end of the Rice press release I’ve linked to has a pretty clear description of how that’s achieved — there is a cathode and an anode, held apart by a separator/electrolyte, and current collectors to divert the charge to the load. I did, in fact, have to brush up on my knowledge of battery operation through the HowStuffWorks article, but it has been a while since high school.

The process of slimming/transforming a battery down into its constituents in paint is impressive in itself, but the fact that it can be industrialized so easily is a huge boon. Singh presents a good example of a use-case: since the batteries can be charged easily with solar cells, they can be used as building materials, with solar cells on top to keep the batteries charged. There’s an entire house running on green energy, right there.

I’m also wondering if — when the low-oxygen requirement is factored into the process, and when the cost of production drops — these batteries can be used in more rural situations, or in third world countries perhaps. You wouldn’t be able to cover every house in solar cells and battery tiles, but you could perhaps establish one central charging station and supply it with emergency lights, phones and any other electronic devices. Even if the area can’t be hooked up to the central power grid, you’d have an independent source of electricity.

As part of my grand plan to read more intellectually, I’m (in parallel with The Elegant Universe) reading The First War of Physics: The Secret History of the Atom Bomb, 1939-1949 by Jim Baggott. It’s a mouthful of a name but the book is eminently readable, interspersed as it is with fact, historical reconstruction and some very human moments. I particularly like how the progression of the idea plays out — from “we’ve got fission!” by Lise Meitner to “this could be a dangerous weapon” and the development of the Manhattan Project.

It’s also interesting to trace how scientific constraints — and political leverage and ego — led to certain theoretical decisions, like the methods of generating sustainable nuclear fission, being taken over others.

I’m actually looking forward to the end of the project, with reactions to the bomb and the discovery that Oak Ridge was an atomic bomb testing facility. According to this article from The Atlantic, which has excellent, evocative photos, some of the equipment operators had no clue they were working on the most destructive machine in history.