Archive for the ‘Science’ Category

My 10 Second Impression of Fringe

Posted on: by Jeremiah Tolbert

My super-​​quick impres­sion of the TV show Fringe:

SHOW INTRO

Ridiculous and bad sci­ence premise  results in some­one being gorily mur­dered, often involv­ing slime and/​or blood.

CREDITS roll.

OLIVIA

(stares emo­tion­lessly)

WALTER BISHOP

Something off the wall, either grossly inap­pro­pri­ate or involv­ing food, while exam­ing some grotesque CG crea­ture or corpse.

(The audi­ence laughs and shakes their heads).

PETER BISHOP

(smirks mys­te­ri­ously)

THE END

And yet I love this show.  I want to start a Doctor Walter “Crazy Motherfucker” Bishop fanclub.

Still, the most recent episode had some painfully bad sci­ence.  The cold is caused by a virus.  Viruses are not cells.  Come on, Fringe, that’s first-​​year bio stuff.  Don’t embarass me like that again. Or I might just have to down­load Walter high­light reels instead of actu­ally watch­ing your show.

Virophage

Posted on: by Jeremiah Tolbert

Damn it, while I’m out immers­ing myself in the sci­ence fic­tion world all week at Denvention 3, sci­ence goes and spits out some­thing truly amaz­ing and I’m only just now read­ing about it. Check this out:

There is a large virus that gets sick by becom­ing infected by a smaller virus.

If that does not blow your mind, then noth­ing will.

It def­i­nitely set­tles the debate for me as to whether or not viruses are life. Maybe one of the def­i­n­i­tions of life should boil down to “some­thing that can be infected by a virus.”

Fermi’s Paradox and the Great Filter

Posted on: by Jeremiah Tolbert

The inter­est­ing astro-​​related blog Centauri Dreams had a post the other day dis­cussing one of my pet top­ics, Fermi’s Paradox. The lat­est dis­cus­sion and solu­tion to be offered comes from Robin Hanson by way of Nick Bostrom, and the idea is being referred to as the “Great Filter.” This is kind of a meta con­cept, an idea con­cern­ing prob­a­bil­ity: we see no advanced life in the uni­verse, so there must be some fil­ter event that destroys/​eliminates intel­li­gent life. Here is Bostrom’s explanation:

The fil­ter con­sists of one or more evo­lu­tion­ary tran­si­tions or steps that must be tra­versed at great odds in order for an Earth-​​like planet to pro­duce a civ­i­liza­tion capa­ble of explor­ing dis­tant solar systems.

So is this fil­ter event in our rel­a­tive past, or our rel­a­tive future?  Have we already passed through it, or is it yet to come?   Bostrom believes that the Great Silence is a good thing, and means that we’re past the fil­ter event.  If we find com­plex life, then we should be con­cerned that the event is yet to come.

As a SF writer, this stuff is a gold mine.  I’ve read quite a few nov­els and short sto­ries that dance with the Paradox.  It’s a very impor­tant ques­tion, and it really lights a match in the boiler beneath my imagination.

For instance, I was won­der­ing this morn­ing, while think­ing about the Great Filter, if the rea­son behind the silence out there might some­how be a result of the fun­da­men­tals of quan­tum mechan­ics, of which I have very lit­tle under­stand­ing of, so you’ll have to for­give me if I man­gle something.

It’s obser­va­tional bias that I keep turn­ing over in my mind.  The idea that we change the results of an exper­i­ment just by observ­ing them.  Is it pos­si­ble that once one “observer” species evolves, it’s very exis­tence is the fil­ter that pre­vents other life from evolv­ing? Our obser­va­tion changes the uni­verse?  I don’t feel like I can explain this idea. I need to read up on quan­tum mechan­ics and its impli­ca­tions to develop this line of thought further.

Clay Shirky and The Cognitive Surplus

Posted on: by Jeremiah Tolbert

Continuing on the thoughts of yesterday’s post, I’ve recently read Clay Shirky’s speech, “Gin, Television, and Social Surplus.” You can read a tran­script of it, or watch a video. I highly rec­om­mend check­ing out one or the other and com­ing back here. I’ll wait. For the lazy, here”s a choice bit that explains much of it:

If I had to pick the crit­i­cal tech­nol­ogy for the 20th cen­tury, the bit of social lubri­cant with­out which the wheels would’ve come off the whole enter­prise, I’d say it was the sit­com. Starting with the Second World War a whole series of things happened–rising GDP per capita, ris­ing edu­ca­tional attain­ment, ris­ing life expectancy and, crit­i­cally, a ris­ing num­ber of peo­ple who were work­ing five-​​day work weeks. For the first time, soci­ety forced onto an enor­mous num­ber of its cit­i­zens the require­ment to man­age some­thing they had never had to man­age before–free time.

And what did we do with that free time? Well, mostly we spent it watch­ing TV.

…

And this is the other thing about the size of the cog­ni­tive sur­plus we’re talk­ing about. It’s so large that even a small change could have huge ram­i­fi­ca­tions. Let’s say that every­thing stays 99 per­cent the same, that peo­ple watch 99 per­cent as much tele­vi­sion as they used to, but 1 per­cent of that is carved out for pro­duc­ing and for shar­ing. The Internet-​​connected pop­u­la­tion watches roughly a tril­lion hours of TV a year. That’s about five times the size of the annual U.S. con­sump­tion. One per cent of that is 100 Wikipedia projects per year worth of participation.

Here Comes Everybody by Clay Shirky Pretty cool, huh? I think Clay is describ­ing the under­ly­ing force behind the New York Times arti­cle from yes­ter­day. The cog­ni­tive sur­plus is lead­ing to many peo­ple using the time for­merly soaked up by the one-​​way media to cre­ate things them­selves, and to share them. Which causes a glut in the choices for actu­ally con­sum­ing, and results in the para­dox of choice. Making things col­lab­o­ra­tively like Wikipedia makes us happy, but hav­ing all those other options makes us unhappy. Another para­dox, of sorts.

Wikipedia is a bit of a dif­fer­ent from, say, writ­ing fan fic­tion, because Wikipedia has a core use­ful­ness that is more broad in appeal. You could say that Wikipedia pro­vides a clear ben­e­fit to soci­ety, whereas the ben­e­fit to soci­ety of more fic­tion, or more music, or more pho­tog­ra­phy is less read­ily appar­ent. I’m not say­ing that your X-​​Files/​Evil Dead crossover fan­fic doesn’t pro­vide a ben­e­fit. I just think it’s harder to make the case for it. I’m not going to do it for you, anyway.

The real mind blower here for me is this idea of think­ing about the cog­ni­tive surplus–not think­ing about it as leisure time, but think­ing about it as hours spent think­ing. That sur­plus has always existed, but some­thing about the Internet has pro­vided an entirely new means of tap­ping into it. Sure, some have cho­sen to express their sur­plus by launch­ing flame wars over which Doctor was the best (clearly the 7th), but I think Shirky is right in point­ing out that this is all embry­onic still. We’re going to see some amaz­ing things soon. What forms will they take? My think­ing along these lines before was lim­ited to the idea of crowd­sourc­ing, but I’m start­ing to see that it’s so much more than that. I really need to read Shirky’s book, Here Comes Everybody.

What prob­lems can we solve using the inter­net and our cog­ni­tive surplus?

Related arti­cles

Memories of Africa

Posted on: by Jeremiah Tolbert

Besides my ostrich encounter, there were really only two occa­sions where I felt that my life was threat­ened by wildlife in Kenya. There were sev­eral occa­sions of fear­ing for my life involv­ing other peo­ple, but that’s another post.The inci­dent hap­pened in Tsavo. Tsavo is famous for one thing in par­tic­u­lar. Man-​​eating lions. Around the turn of the cen­tury, Colonel Patterson was tasked with build­ing a bridge for the British Empire (a bridge that still stands today, and is not remotely impres­sive). He watched in hor­ror as worker after worker (mostly “coolies” from India) were dragged away, killed, and devoured. Eventually, Patterson killed two lions, but only after unbe­liev­able dif­fi­cul­ties. The lions were named The Ghost and The Darkness, and a film about this inci­dent star­ring Val Kilmer came out in the mid-​​90s. The lions’ bod­ies are on dis­play in the Chicago Museum of Natural History. They are male lions, but they have no manes. None of the male lions in Tsavo have them. Upon see­ing the area, you would imme­di­ately real­ize why.

Elefanti Tsavo East
Creative Commons License photo credit: Oscar&Alessia

Tsavo was green and dense with thorny thicket when we camped there. It was not like the rest of the African savan­nah. It is almost cer­tain that the male lions of Tsavo do not have manes because if they did, they would never make it ten feet through the underbrush.

The first night we made camp, we could hear lions roar­ing as the sun set. It was the first time we had heard any­thing like it, and we were all thrilled. We put our tents, which were made for three peo­ple. After an evening around the fire, we all retired to our tents. I slept for a few hours, but woke some time after mid­night with a press­ing need to ah, relieve myself. There was only one problem.

The roar­ing con­tin­ued, but it was much, much closer now. Without open­ing the tent, it sounded as if a lion was not more than 30 yards away. Another lion was answer­ing this lion from the oppo­site side of our camp.

I tried to hold it as best I could, but even­tu­ally, I absolutely had to go to the bath­room. I roused my tent mates and we opened the ten flap just a bit and pointed our flash­lights into the dark­ness. The eyes of some­thing flashed green at the very edge of the light. The roar­ing stopped.

“Okay,” I said. “I’m going to step right out­side the tent, and piss to the left. You guy watch those eyes, and if they start com­ing towards me, say some­thing.” And that’s what I did. It seemed like I was uri­nat­ing the con­tents of a small ocean. I kept my eyes on my busi­ness and did not look at the lion. If I did, I, well, froze up. Finally, I squeezed out the last drop of fluid and not even paus­ing to zip my fly, I dove inside the tent.

The eyes never moved. We sealed up the tent and went back to sleep as best we could with mas­sive cats roar­ing all night. In the morn­ing, the lions were gone.

I can’t remem­ber where the sec­ond brush with death hap­pened. It was either Tsavo also, or Amboseli. We were rid­ing in a Land Rover down a muddy road in the park, and the brush was fairly thick on either side of the road. Everything that wasn’t green with life was a dark red from the clay mud. Wildlife was hard to spot. I stood on my seat, hold­ing onto the edges of the hole in the roof, and scanned with binoc­u­lars, look­ing for some­thing inter­est­ing. Then, the dri­ver spot­ted it.

A bull ele­phant came out of the brush not even twenty feet from us. His skin was streaked red, and his tusks were almost four feet long. He took a hes­i­tant step, then flared his great ears for­ward. I snapped a shot with my cam­era. Then, he charged.

Our dri­ver gunned the engine, and we tore off down the road. The ele­phant stopped in the road behind us and raised his trunk in dis­dain. For less than a sec­ond, I was pretty sure I was going to be thrown from the Rover and tram­pled to death. Everyone in the vehi­cle laughed hys­ter­i­cally, and I mean that lit­er­ally, for half an hour afterward.

Bt-​​cotton vs. the bollworm. Bollworm wins in 72 rounds!

Posted on: by Jeremiah Tolbert

First doc­u­mented case of pest resis­tance to biotech cot­tonNature is wicked awe­some. Let me show you.

This story is about three organ­isms. First, we have cot­ton plants. Tasty, yummy cot­ton plants. Secondly, we have the boll­worm, aka Helicoverpa zea. Finally, we have a lit­tle bac­terium called Bacillus thuringien­sis which pro­duces a toxin that kills insects. We call that toxin Bt for short.

In 1996, some smart biol­o­gists decided to take the genes from B. thuringeien­sis that pro­duce those toxin pro­teins and insert them into the genome of the cot­ton plant (and pota­toes and corn too). This served to make the cot­ton plants not so tasty to the boll­worm. Tasty cot­ton plants become “ack-​​ack, plant of death!” to them. This was good because the cot­ton crop is worth $4.5 bil­lion annu­ally, and 70% of the dam­age caused to the crop is caused by cat­ter­pil­lars like the lowly bollworm.

All was well in the land of cot­ton for a while. But then in 2003, boll­worms were found eat­ing Bt-​​cotton plants! What gives? Evolution, baby!

Here are a few cool things about this. Places where bt-​​cotton is grown as a huge mono­cul­ture resulted in faster evo­lu­tion of bt-​​resistance in the boll­worm. Basically, the only boll­worms that could be found to mate with had a ten­dency to be resis­tant, and so you got really fast resis­tance in the over­all pop­u­la­tion. In places where boll­worms could end up on non bt-​​resistant plants, the resis­tance devel­oped much more slowly.

Now, of course the gengi­neers at Monsanto have upped the ante and pro­duced a cot­ton vari­ety that pro­duces two vari­eties of Bt-​​toxin. For now, the boll­worms are resis­tant to only one of those two. Soon, the sci­en­tists will develop another vari­ant that kills the resis­tant boll­worms and reset the clock.

So I looked it up, and the boll­worms have a life­cy­cle of 30 days. BT cot­ton went out in 1996, and in 2003, we have lev­els of resis­tance large enough that we see it. That means in roughly 72 gen­er­a­tions, H zea pop­u­la­tions devel­oped wide­spread resis­tance to the toxin.

There are two morals to this story. One: insects evolve really fast. Two: insects evolve resis­tance even faster when their envi­ron­ment is uni­formly poi­so­nous. Plant some nor­mal plants here and there to pro­vide refuges so that evolved resis­tance devel­ops slower.

Think about the above the next time you spray every­thing you own with antibac­te­r­ial soap.

Whale Fall

Posted on: by Jeremiah Tolbert

When a whale dies, an entire ecosys­tem blos­soms in its corpse. Species of clams, worms, and other inver­te­brates can be found on the bones of a dead whale that can­not be found any­where else. The “seeds” of these ecosys­tems seem to lay dor­mant in the ben­thos of the deep oceans, wait­ing for that one-​​in-​​a-​​million chance that a whale, it’s last breath escap­ing for the sur­face, will fall to the muck and mud. Imagine being stranded in the desert, your only hope for flour­ish­ing in the form of a giant falling from the sky. Tons and tons of meat and bone, pro­vid­ing nour­ish­ment and suc­cor. Later, sulfur-​​loving bac­te­ria pick over the bones and release hydro­gen sul­fide, launch­ing an entirely new ecosys­tem of chemosyn­thetic bac­te­ria. And it’s here where the diver­sity really gets wild, with nearly 200 dif­fer­ent species mak­ing up the com­mu­nity, feed­ing on the bac­te­ria, feed­ing on the feed­ers of the bacteria.

Swim in the sky
Creative Commons License photo credit: t2s

I see no beauty in death. I am ter­ri­fied of it, as a gen­eral rule. The loss of a human mind to the black maw of noth­ing is the only thing that fright­ens me, really. My panic attacks, at their root, are all about my fear of death. But, for some rea­son, I read about whale falls, and I am filled with awe and amaze­ment. There is beauty there, for me, and I don’t know why. A great, amaz­ing crea­ture dies, and gives life to not just one, but sev­eral ecosys­tems, for years and years after its death.

I want my death, when it comes, if it comes (as I hope to catch the wave of life exten­sion sci­ence and live for centuries–a fool­ish hope, but I can­not relin­quish it), to be as beau­ti­ful and as gen­er­a­tive as a whale fall. I want what I have done in my life to cre­ate as much, per­haps. And the fear of death that I have–maybe it’s because I know I haven’t done that yet. Now would be too soon. I’m not ready. That’s what the attacks are about. Not being ready.

I refuse to come to terms with the idea of my own mor­tal­ity. Not yet. Not until I can die like the whales do.

On Terraforming

Posted on: by Jeremiah Tolbert

On Terraforming

I wrote the below for a mail­ing list the other day in response to a ques­tion about whether we’re ter­raform­ing our envi­ron­ments for good. I liked it, so I thought I would share it with you all:

I think Americans ter­raform quite a bit, but they do so in a not-​​environmentally concious/​protective ways. Grass lawns and farm fields are two good exam­ples. Grass species that are planted on your aver­age lawn are in no way native to America (last I checked any­way). They are for­eign species, and by plant­ing them, we have cre­ated mas­sive arti­fi­cial habi­tats for no rea­son that I can discern–what, because we think grass is pretty and it’s easy on the feet?

Farms are also a form of ter­raform­ing. We took the world’s largest con­ti­nous long-​​grass prairie and turned it into a mas­sive food pro­duc­ing ecosys­tem (with 1/​1000th of the bio­di­ver­sity, but that’s a digres­sion) (Actually, there’s some belief that many of the grass species that we found in the mid­west when whites set­tled had actu­ally been semi-​​cultivated by native amer­i­cans for a few thou­sand years, and some anthro­pol­o­gists argue that it wasn’t really a native ecosys­tem at that point either. This brings up lots of debates in habi­tat restora­tion that I bet Melinda knows a hell of a lot more about than I do).

As part of this, we straight­ened the HELL out of every river we could, which had pro­found effects on flood­ing and river ecosys­tems. Did you know that if it wasn’t for the Army Core of Engineers, the Mississippi would enter the Gulf of Mexico some­where dozens (hun­dreds?) of miles east of where it does now? I think I read that some­where in a book about giant engi­neer­ing projects “gone wrong.”

The Army Core of Engineers almost spe­cial­izes in refor­mat­ting the land­scape for human pur­poses. However, they don’t quite do it on the scale that you are talk­ing about, and I think the main rea­son is, these buffer zones that were pop­u­lar to dis­cuss after Katrina are not “cost effec­tive” sim­ply because they would eat up valu­able real estate that MUST BE DEVELOPED, THERE’S GOLD IN THEM THERE SWAMPS! In my opin­ion, noth­ing should ever be built on a flood plain, but flood plains are real estate, the most valu­able “invest­ment” you can make in America. Damn the future, build build BUILD!

I have been col­lect­ing a lot of links regard­ing archi­tec­ture plans for build­ing homes that are envi­ron­men­tally sus­tain­able and that become a part of the land­scape instead of paving it. There may very well be a move­ment afoot here, but it’s in Europe, not in the land of out­sourc­ing and ser­vice indus­try (here).

The big projects you see of this sort in the future are almost all going to have to do with stealing/​moving fresh water around to places where we shouldn’t have built really big, water-​​guzzling cities (IE: any­thing west of the rock­ies, minus the Pacific Northwest). I think it’s a race over whether a mas­sive war is going to be fought over remain­ing oil or remain­ing fresh water. Our use of it far out­strips its avail­abil­ity and there is seri­ous con­flict ahead (assum­ing some­one doesn’t invent some cheap and low-​​energy way of desalin­iza­tion or something).

Finally, I recently read a short arti­cle on Deep Sea News about how huge chunks of the ocean have effec­tively been aquaformed by the process of deep sea trawl­ing. Trawling may very well be THE most eco­log­i­cally dam­ag­ing prac­tice we humans con­tinue today. It destroys thou­sand year old deep sea corals and other habitat-​​necessary organ­isms in a mat­ter of min­utes. Imagine a giant hand com­ing out of the sky and scrap­ing your city away, and you’re close to what this does. However, in the after­math, the process seems to make a bet­ter home for some pop­u­lar and tasty fishes, and the process is prob­a­bly irre­versable, so there’s an argu­ment that once a nation has destroyed their waters this way, they should just keep doing it because we won’t see a recov­ery in cen­turies, per­haps millenia.

Oh, we’re shap­ing the world alright, is my basic opin­ion. We’re just doing it in search of a short term buck and damn the future. Damn it straight to the biggest god­damn mass extinc­tion the world has seen yet.