Ultraphyte

We hear so much about government waste–it’s good now and then to see a place where American tax dollars are well spent. An undeniably great place is NCBI, the National Center for Biotechnology Information. All the publically known gene sequences–every published gene defect–lots of free books–DNA mining tools.

And all of this information is free. Not just free to Americans, but free to the known universe. Anyone with Wi-fi can tap in.

Take for example Online Mendelian Inheritance in Man (sic). Despite the stilted name, OMIM is a truly democratic collection of every reported variant of any person on the planet. This site in effect transformed the human population into a genetic petri dish–like mutant E. coli, every possible mutation is out there. Search your favorite defect–blindness, hypoglycemia, developmental delay. Here’s one form of blindness, Leber congenital amaurosis–just one of hundreds of ways to go blind (and those are just the genetic ways). It makes you wonder how any of us could have developed normally, to have vision as good as we do.

If you get to New York this year, don’t miss the Natural History museum exhibit, Creatures of Light. A fantastic collection of modeled creatures showing bioluminescence; that is they light up like in Avatar.

What’s remarkable is the wide range of reasons why creatures light up. This Science article explains a few:

• An octopus’s suckers evolved into light organs, apparently to lure prey
• A jellyfish lights up blue, under attack–to lure predators to its attacker
• A fish eye fluoresces green and focuses the fluorescence onto its retina, for more sensitive detection
• Another jellyfish lights up as camouflage, to appear from below as the same brightness as light from above

Other interesting examples?

Day 29 at Supreme Court

Today marks the 29th day the Supreme Court has started deliberating whether to total the most important US health care legislation since FDR. Actually, they may have decided already, but leave the rest of us wondering till June. Sometime in June we’ll find out whether Scalia really meant what he said, to let my uninsurable relatives lie there in the street.

If you think this is important, feel free to spread this campaign–Health care Held Hostage. And send the Court your message.

Share the above logo on your page and let people know you care.

If Obamacare goes down, what’s next? There’s always Paul Ryan’s new plan for “able-bodied people.” And don’t forget churches. Our churches try, but honestly I don’t know where my church is supposed to come up with the funds for cancer or hip replacements; I just don’t see that much change in the collection plate. Maybe we need to join one of those “prosperity gospel” churches where God give you a Lexus. A Lexus might cover a few years of cancer treatments.

Some other folks pondering what’s at stake in June:
Small businesses are wondering if their improvements will be halted.
HIV-positive Americans are wondering what will happen to them.
Even conservative legal scholars support Obamacare.
But if the law is struck down, the highest-income earners will save on their taxes.
And health insurers will save over $1 billion in rebates to consumers and employers.

As announced today, Tor Books will go DRM free. This means all eBooks available from Tor will be convertible among formats. How far that goes, and how significant it will be, is unclear to me since my books (and most others) end up on Torrents anyhow, but it’s a symbolic step in the direction of modernizing the book market, along the lines we discussed earlier.

For the serious future, I still argue that the ultimate “monopoly” is the (supposed) author. In the future–what will an author be?  If a publisher or a distributor cannot maintain a monopoly, how can an author?

Suppose a book published by Chris Author is totally open–to editing.

What’s to stop any fan from “improving” on it, then offering the improved version for sale?  For a dollar a download?  Or pennies, or nothing?

Suppose it’s actually a better book? A lot of people think they could improve on Thrones. What if someone’s right?  What if an improving fan’s version convinces the public it’s better than the original?

The future of the Author is in grave doubt.

Update:
Read this, from the digitizers to see what I mean. If it’s not “true” yet, it will be soon.

Pamela Sargent just won the Pilgrim award for lifetime contributions to science fiction scholarship. Known for pioneering work in SF, her novels such as Earthseed and Shore of Women promote women protagonists and explore gender.

Serendipitously, I received a set of “research questions” recently from an Iranian scholar writing about women in SF. Which lead me to reflect, where is gender headed? What’s the cutting edge of gender exploration today?

Looking back, when writers first started writing fiction as women (rather than hiding behind a man’s name) they took these approaches:
(1) A woman protagonist takes a role traditionally filled by men, in a man’s world (Picnic on Paradise)
(2) A planet or country is inhabited only by women (Whileaway,  Gate to Women’s Country, A Door into Ocean)
(3) A world where males and females have equivalent roles (Brain Plague).

The last approach is the  most tricky, in my opinion. It only “counts”  if the females and males are equally likely to succeed, and all relationships are potentially bi/trans. That’s where I see the biology heading.

What do you think are the most interesting directions for gender in fiction today?

And now for something completely different–the (supposedly) Singing Snails of Hawaii. The singing of these snails may be stuff of legend, but Hawaiians sing songs about them. They do have gorgeous shells, and they give live birth (instead of eggs, like normal snails.) These snails climb trees and supposedly help keep the leaves clean. The greatest danger these snails face is rats, unfortunately. But with luck they can hide under a wiliwili tree.

What do you think snails are good for?

Amazon wars have inspired much excellent discussion of late. Is Amazon our next Great Satan, the media Walmart? Is there a “right” or “good” way to offer and consume literature?

The idea of media monopoly interests me. I grew up in an IBM family, alongside their rival Ma Bell, and my children grew up on Microsoft PCs. I recall the great lawsuits, including Bill Gates’s famously unhelpful testimony. Year after year, I warned my publisher about Amazon, only to be told, “They’re really going bankrupt.”

Let’s unpack some things.

Monopoly. What is a monopoly? The clearest kind of monopoly is a literary author.  We all agree, for example, that George R. R. Martin is the only source of Game of Thrones books. When too much time lagged between books of the Thrones series, fans blogged in outrage how unfair it was to put them off so long. An author, especially a living, breathing author with copyright, is a monopoly.

Is Amazon a monopoly?  That’s what publishers claim. But if so, it’s a precarious one. Today, anything can sell from anywhere. The best-sellers–even mid-list authors–can set up shop instantly and sell from their own website.

Maybe we need another lawsuit-of-the-decade, like the ones I grew up with.  Or maybe, if Amazon is really that bad, they could get outcompeted soon, like MySpace and Yahoo.

Publishers.  What is a publisher?  The first thing I recall hearing from my fellow writers, when I made my first sale a hundred years ago, is “Beware the publisher.” Publishers were the source of all necessary evil. “Don’t let the publisher rewrite your book!”

Yet today, we defend the poor hapless publisher from the technology of the twenty-first century? And bemoan the lack of editing of self-published books?  As Spock used to say, “I can’t believe my ears.”

Publishers perform a valuable function for authors–more than we usually give credit for. But the big New York publishers have always been behind the curve. My first book was shipped to Hong Kong for typesetting.

Today, if publishers are dying, why are there so many new small presses? If it weren’t for small press and eBook, most of my titles would be out of print.  There is no more dreaded “out of print” today.

Greedy consumers.  What is a greedy consumer? According to lots of Amazon consumers, no eBook should sell for more than ten dollars. Perhaps encouraged by Amazon, but these are real readers’ voices.

What I hear readers saying is that, instead of painstakingly selecting a few promising books to buy, the reader wants to buy a thousand books–as much as a device will hold–then select them to read whenever. This may not be the 20th century view of books–nor the Renaissance view, nor the Medieval view, nor the library of Alexandria–but nor is it evil. It’s just the 21st century view. That’s our contemporary reader, like it or not.

It seems to me that both authors and publishers need to find new ways. It won’t be easy; when text went from papyrus to codex, much of the ancient libraries were lost. But it had to happen, or else books today would still be rolled up in a monastery, unread by most.

At Oklahoma State-Stillwater, I met some great scientists doing the kind of research that will one way or another make it into my next book. One is Danielle Lee, postdoc and artistic note taker (see above) who authors Urban Scientist blog for Scientific American. Danielle is studying giant pouched rats in Tanzania, and how they are trained to sniff out landmines. Another colleague, Babu Fathepure, is showing how bacteria eat away the concrete bridge pylons in polluted rivers of a neighboring state (we won’t say which one). Thanks so much to Margaret Ewing and Karen McBee for hosting me here.

What kinds of microbiology or zoology (or even botany) do you think should make it into a book?

The next stop in my Oklahoma tour was Oral Roberts University, where a science fiction conference was held by my friend Andy Lang, who teaches mathematics. ORU, as I discovered online, has a colorful history perhaps worthy of a novel. Those of us attending the conference received a warm welcome, including about twenty wonderful ORU students. (I may be prejudiced since a couple of them had read my books very thoughtfully). Some were from the science fiction class taught by Andy with Mark Hall, which I visited several years ago through Second Life.

One presentation we heard was by physicist Paul Davies, on the possibility of time travel. Davies explained to us that time travel forward is not only a possibility, but something our GPS satellites do every day, for billionths of a second that would screw up all our Garmins if it were not corrected. Time travel backwards would be more difficult, requiring something called “negative energy.” It’s not clear where we would get enough negative energy to keep open a wormhole, for instance.

Davies expressed skepticism regarding the various space travel devices of Star Trek. On the other hand, Davies said he had no problem with a “time loop” in which someone goes back in time to cause some event, then continues on to the future and goes back again. Such time loops would be consistent with known physics. That’s if we could figure out how to manage it.

My talk was about evolution. I showed how my students are studying bacterial evolution in our laboratory, and how our findings relate to human evolution. Humans and other apes have evolved under considerably selection pressure for increased sociality and brain power. Another force in evolution may be that of immune system diversity. It is hypothesized that after humans and chimps began to diverge from a common ancestor, they interbred several times. Later, Homo interbred with other human populations such as Neanderthals and Denisovans. These populations may have restored immune system genetic diversity to the highly inbred Homo population.

Following an excellent dinner on the sixtieth floor of the former medical school, a conference attender said that ORU is trying to integrate concepts of evolution into their Bible-based curriculum. He asked how it was possible to reconcile common descent of humans and apes with the creation of Adam and original sin. Lacking time travel, I didn’t have an answer for that, but I wondered whether literal reading of Genesis guarantees wise judgments today. We agreed that it does not.

So then, what is in fact our best basis for making wise judgments? How is the average non-science trained person to know if they should accept the claims that time loops are possible and that humans interbred with chimps? And how should they wisely decide whether it’s good to travel back in time, or to breed with chimps?

BTW the tornado in Norman today was just a day too late to catch me there, but I hear the winds howling outside tonight.

P. S. (next morning)  Missed again!  A beautiful day!

At OU-Norman, I will be meeting a microbiology class to talk about biofilms. I know it’s hard to believe how beautiful a biofilm can be, especially when it’s growing on your teeth. But this one pictured above is a marine bacterium Marinobacter hydrocarbonoclasticus SP17 growing on alkanes (hydrocarbon pollutants). It’s not only beautiful, it’s doing us  service by cleansing our oceans–and as we all know, our oceans desperately need cleansing.

How do biofilms grow? Surprisingly, there is a pattern common to many biofilms formed from many different species, often multiple species in one biofilm. First the swimming bacteria decide to settle (not sure how; sometimes they communicate with each other by chemical signals called quorum sensing.) Then they stick their flagella onto a substrate, and start to pile up next to each other. The cells grow in a monolayer, and start coating themselves with polysaccharide (long chains of sugars–sticky). In the advanced stage, the biofilm builds up towers of semi-dormant cells with nutrient channels inbetween. Finally, the towers grow buds of motile “planktonic” bacteria that escape to go out and start new biofilms elsewhere.

The process can be deadly, especially if it happens inside your lung when you have cystic fibrosis. But the same Pseudomonas bacteria–in a very different setting–can make a sugar polymer called alginate, a biodegradable material that we can harvest and use for all sorts of things, like dental products and artistic sculptures.

What would you like to do with biofilms?