Tag: Biology

Arrested development or pedomorphic edge?

It’s remarkable how much a baby ape resembles a small human. The similarity decreases quickly with age, but it does help explain how we can share so much DNA with them. In many ways we’re just slowed down versions of them. We carry that flat forehead and big brain cavity (relative to skull size) right into adulthood. I’ve often thought that chimps must look at us and shake their heads at how absurdly childish we look. Geez! These researchers, I swear they get younger every year.

In biological terms, this physical retardation goes by the name pedomorphosis or neoteny. And despite the insane length of time we have to spend sheltered by adults, we humans like to think that our childishness has treated us well. That big fat brain doesn’t blossom overnight, but when it finally pops, watch out!

A neuroscientist once explained to me that some fairly dramatic changes in brain physiology occur in late adolescence. Regions that were more plastic become more hardwired, or “burned in”. This is a reasonable biological response — your brain is saying “Hey, now that you know how things work, I can save us both a lot of time and energy by just looking up the answer on these note cards.” It’s also obvious: anyone can see that learning changes as you age, the best example of this being language acquisition. When you come to be old person, you canna learn to speaka da language… but never like a native.

On the other hand, maybe it’s time for us to let that brain be plastic a little longer. Call it Pedomorphism 2.0. After all, there’s a lot to learn these days, and it’s changing all the time. And right on cue, there is a rise in pedomorphic behavior. The average age of entry into adulthood is rising. Living at home as long as you can is a pretty sound strategy. And those extra graduate degrees may well come in handy some day.

That 28 year-old slob who plays video games all day in the basement of his parents’ house (a.k.a. Area Man)? He may well represent the future of the species. But only if he can be induced to get a girlfriend.

Micro-Brewing the Bioeconomy

The amount of useful stuff we squeeze out of petroleum is shockingly long. In addition to merely propelling us in various motor vehicles, it takes the form of plastics, lubricants, solvents, waxes, asphalt, synthetic rubber and fibers, flavorings and fragrances, cosmetics, medicine precursors, and on and on. On the plus side, we can be congratulated for eating every last knuckle and sinew of that oleaginous beast. More dispiriting is fact is that, as we consider the already frightening task of getting our fuel from somewhere else, we’ll need to get all those other things from somewhere else too. Where, for example, are we going to get all the plastic we need to hold this place together?

With that in mind, here’s a mildly cheering tale from Rob Carlson’s synthesis blog: Micro-Brewing the Bioeconomy: Beer as an Example of Distributed Biological Manufacturing. His premise is that small-batch biosynthesis of things like plastic precursors is already economically viable. This will supply carbon neutral versions of some of the chemicals we crave, but more importantly it will help us grow the expertise and infrastructure we’ll need farther down the road. To make his point, he considers the beer industry. If it was all about scale, he observes, then we’d all be drinking Budweiser, full stop. But there’s plenty of room for craft brewers. By analogy, there’ll be plenty of room for micro-brewery style biosynthesis startups. Carlson’s best line:

Any technology that is based on cow digestion doesn’t have to be any bigger than a cow.

Microbreweries won’t replace Exxon, not by a long shot. But they’re a critical step in the right direction. I was skeptical too, but Carlson pointed out that companies like Blue Marble Energy are already making money with this approach. Their game is turning algal slime into plastics. Watch the video on their home page.

Heard at the brew-pub of the future: Hey barkeep, how about an amide hefeweizen for the lady, and put another head on this carbon-neutral anhydrous ammonia double bock.

Nature Biotechnology on Synthetic Biology

If you have any interest in synthetic biology, Nature Biotechnology has been kind enough to A) devote a special issue to the topic and B) make it available for free. I first learned about this on Rob Carlson’s Synthesis blog because he’s the author of an article on the economics of DNA synthesis (PDF).

carlson-curve

I also recommend the survey by Lu, Khalil, and Collins: Next-generation synthetic gene networks (also PDF). Taken all together, the issue communicates a sense “We’re moving faster and faster” combined with “Jesus this stuff is complicated!” Commercial breakthroughs won’t come quickly, but it’s hard not to be impressed with the progress being made.

For an indication of where things are headed, look at the projects being built by student teams for the International Genetically Engineered Machine (iGEM) competition. Browse through the abstracts here and remind yourself that these things (these organisms) are being built by undergraduates in a matter of months. The team from Valencia is building the Valencia Lighting Cell Display (iLCD):

We are making a “bio-screen” of voltage-activated cells, where every “cellular pixel” produces light. It is just like a bacterial photographic system, but it’s digital. Within seconds, instead of hours, you can get an image formed of living cells.

I recall doing much less impressive things with my college projects.

Regenerative medicine: Printed parts for a broken heart

If you needed a kidney, who’s the best person in the world to donate that kidney to you? Your brother? Your sister? Your child? If I told you this was a trick question, you might guess the answer is you. Of all the people in the world, you are the only donor guaranteed to cause no problems with tissue rejection.

By why donate an organ to yourself if it’s already in the right place? Anthony Atala knows the answer.

http://video.ted.com/assets/player/swf/EmbedPlayer.swf

Here’s the short answer. Let’s say your bladder is diseased or broken (sorry). If you give Atala one little chicklet chunk sliced from the healthy side, he’ll pop it in a Magic Grow oven and make you a new one (Please select one of the following: small, medium, large, or extra large. Allow 6-8 weeks for delivery). Then, like a sea turtle release program, a surgeon will introduce your new bespoke bladder to its natural environment: you. It sounds like science fiction, but he’s been doing this successfully for ten years.

I knew this much, but the images are compelling, and I was surprised by how much farther they’ve gotten in the last few years. In their experimental (non-clinical) work, they’re building highly vascularized organs like the liver. They’re using ink-jet printers to make simple hearts. Watch the video. It’s really mind-boggling. By the time I got to the end of it, I was convinced that Bill Gates must have backups of all his organs in three different redundant facilities. Maybe it’ll be cheap enough for me to do that too some day.

Bonus footnote: I grew up in the shadow of Wake Forest University, so I take hometown pride in pointing out that the leading edge of regenerative medicine is happening at the Wake Forest Institute for Regenerative Medicine.

Cell Size and Scale

In a Zoomable User Interface (ZUI), you can move up and down the scale of a spatial dimension easily. This feels very natural when you’re zooming through something that you have some physical intuition about, like a picture of the inauguration, or a map of the planet. It can be very disorienting when you’re zooming through an abstract space.

Here’s an especially nice example of where it can work well: Cell Size and Scale.

It’s always eye-opening to see how tiny cells are, and then to see how tiny (most) bacteria are relative to eukaryotic cells. Consider: you couldn’t cram one of your chromosomes into an empty E. coli shell if you used a spatula and two shoehorns. I don’t know if I’m more impressed with my size or E. coli’s minuteness.

Virusworld

In the book Genome, author Matt Ridley starts chapter four like so:

Open any catalogue of the human genome and you will be confronted not with a list of human potentialities, but a list of diseases, mostly ones named after pairs of obscure central-European doctors. This gene causes Niemann-Pick disease; that one causes Wolf-Hirschhorn syndrome. The impression given is that genes are there to cause disease.

As you might suspect, Ridley is at pains to point out that genes do not cause disease. At least they don’t cause disease any more than, say, hearts cause heart attacks. But we tend to notice genes when they fail in spectacular ways.

viruses

When it comes to viruses, we have to admit that they often do cause disease. But of all the viruses out there, very few are interested in making us sick. And since they surround us in such a thick cloud, they can perform an under-appreciated role: gene libraries. They are busy little day traders, moving their stock of DNA and RNA in and out of cells all day long. As such, they’re in a good position to acquire, store, and transfer useful genetic knowledge that bigger folk might have written off. Like bacteria, they take a beating for causing various diseases without getting any compensating credit for their health-giving talents and, I think you’ll agree, good looks.

One of the fun things about viruses is that, being small, it’s relatively easy to take their (virtual) snapshots. Virusworld, based at the University of Wisconsin, keeps a regular family photo album of virus pictures. There are some real lookers in the bunch. Check out the handsome reovirus core. And the Norwalk virus that ruined your aunt’s last cruise is a charmer up close. We have such a comprehensive three-dimensional understanding of some viruses by now that we can print out solid copies of them, like this fist-sized version of the pariacoto virus. I find it amusing that this virus has caused us to print out giant versions of itself.

Bio-mimics and bio-copycats

On BotJunkie I came across this robotic fish video. The fish, from the University of Essex, is a careful model in form and behavior of a real fish. The idea is that nature has already created a great design, and we can benefit from simply copying it. According to BotJunkie, the robofish will monitor pollution levels off the coast of Spain.

Bio-mimicry is compelling, but I wonder if it’s sometimes overdone. The materials we have at our disposal are very different from those available to growing fish, and many of the constraints that operate on fish don’t apply to robots. Compare the above robotic fish with the underwater robots being built by iRobots new underwater group, beasts like the Seaglider and the Ranger. It may well be that slavish bio-mimicry isn’t a good all-purpose strategy.

Fish shows the value of keeping a clear head

There are many species of cave fish that, after millennia in utter darkness, have either lost their eyelids or lost their eyes entirely. You might think that losing your eyelids is a way station on a one-way trip to blindness. But the barreleye fish (for its tubular, or barrel-shaped, eyes) lost its eyelids even as its eyes were bulking up and becoming more powerful. Barreleyes live in the deep sea where there is still just enough light filtering down from the surface to silhouette a snack, provided you are looking straight up and have the necessary light-gathering equipment.

So, let’s say you are Mother Nature and you are presented with this puzzle: giant tubular light-collecting eyes and no eyelids. Hmmm… what to do? I know! Why not evolve a transparent head?

Look at this picture.

barrel-eye-fish

The things that look like eyes are actually nose-like things called nares. The head itself is clear, and the eyes are those giant green things lodged deep in the head jelly. In fact, the green things are the lenses on top of cylindrical eyes, and they point straight up, perpendicular to the body axis, like a twin telescopes in a sheltering observatory dome.

Now, look at the picture again and read the last paragraph again. It may help to mutter to yourself those are not eyes… those ARE eyes. It takes a while to sink in.

I don’t blame you if you don’t want to take my word for it. Read more about it here: MBARI News Release – Researchers solve mystery of deep-sea fish with tubular eyes and transparent head. That Mother Nature… where does she get her material?

Thanks to Greg Wilson for the tweet on this one.

Genetic intellectual property

One of the great sticking points in international trade negotiations has been over intellectual property rights. The rich “northern” countries complain that their expensive movies, music, and software are insufficiently protected in poorer “southern” countries like Brazil and India. What’s less well known is that these same southern countries have intellectual property concerns of their own, only the intellectual property in question is genetic. Under the name of bioprospecting, biologists collect tropical botanical specimens in the hopes that there might be some therapeutic benefit to the chemicals contained therein. Governments in tropical countries thus worry that plant material leaving the country may be developed into blockbuster drugs at no compensation to them… software piracy goes in one direction, biopiracy goes in the other. Unfortunately this anxiety causes all visiting biologists to be treated with great suspicion. Craig Venter, on a genome-collecting sail around the world, was placed under temporary arrest in French Polynesia for the unauthorized theft of genetic material.

This problem of genomic intellectual property is going to get much worse. For example, Monsanto will sue you if they find some of their patented genes in your potatoes. The problem is that Mother Nature likes to move genes around. Maybe you don’t want trouble with Monsanto’s legal department, but your promiscuous plants might bring it in the form of an illicit cross-fence liaison with your neighbor’s potatoes. We may end up with a Mann Act for tubers.

In Rob Calson’s biotech blog, I came across this throw-away line in an article about biofuel synthesis:

I wonder how thoroughly they are scrubbing the waste stream?  Dumpster diving for competitive intelligence takes on a new meaning here.

I hadn’t considered this before. You may spend ten years perfecting a biomass-composting superbug, only to have your competitor slurp it out of your sewage.

It’s become a standard line among software CEOs to say your chief assets walk out the door every night. In the biotech business you literally pour those assets down the drain. It’s a strange business when the smartest guy in the building sleeps in a picoliter pup tent. And it’s hard to enforce that employee non-compete agreement when he or any of his five billion children feel like walking the day after tomorrow.

Live! Nudis! (toxic nudibranchs, that is)

Some animals live up to their cool names. Animals like the toothy velociraptor and the mysterious leafy sea dragon. Others, despite their nifty cognomens, fall short. For example, the Northern beardless-tyrannulet (not to be confused with the Ruby-crowned Kinglet) is a comparatively plain little flycatcher.

But I imagine any animal might have a hard time living up to a label as racy as “toxic nudibranch”. Except, of course, for the toxic nudibranchs. Don’t do them the disservice of calling them mere “sea-slugs”. And if you’re talking about them at your next cocktail party, remember to pronounce it NUDIBRANK.

The photographer for these amazing images is David Doubilet, and I recommend the accompanying video.

[Spotted on visualcomplexity.com]