Heuristic Rotating Header Image


Hello March

And goodbye February. I’ve never gotten along with that month. In fact, I blame it for a lot of things. Good riddance until next year.

I was moderately productive in February, in the writing department. I finished and revised two short stories, and am just waiting on my beta reader before I submit them. I started planning a new novel, an urban fantasy I’ve been kicking the rudiments of around for a couple years. Now it has its own Scrivener file, an outline, some character sketches. Fun! I need to devote more time to finishing stuff this year (motto for 2011: “The End”), but its good for me to have several projects in various stages of completion awaiting me. I think I also promised to give a talk on social media for writers to the local writing group next fall.

For the other writer types, or those who spend time with writers: The Writer’s Survival Guide. From the article: “And so I give unto you: coping mechanisms. Fellow penmonkeys, compatriot wordslingers, if you want to do this job and not end up shellacked in your own snot-froth while hanging from the ceiling fan — if you are to survive at all with your mind and spirit intact — then you must do as I say. Do not deviate, lest you be struck down by your own lunacy.”

Here’s something I got from Warren Ellis. It relates to a less-well-developed novel idea that I should get to in a year or so, and I want to save it for then.

Immaterials: Light painting WiFi from Timo on Vimeo.

Developing new shiny ideas is more fun than finishing projects in progress, but it is now time to start rewrites on Paper Magic. I alternately feel like I know how to do this and have no clue at all what I’m doing. Fortunately I know enough writers by now to recognize that as normal, and to understand that the only thing to do is keep working.

Changing the subject entirely, if you can’t beat them, eat them: invasivory. Strike a blow for native species by consuming the invasives yourself. Complete with recipes!

And one more topic switch: things you can do with guitars!


Hugo-winning author and Shadow Unit co-founder Elizabeth Bear, author of some of my favorite books, has a new book out today, Grail, third in a science fiction trilogy (Dust and Chill being its predecessors).

I may have gone on a bit of a Bear-book-buying binge. When I went looking for a copy of Grail for my new Nook Color (about which more later, now that I’ve had it for a couple weeks and can write a sensible review), I discovered that a lot of her back catalog, including some out-of-print things I’ve been wanting to read, is available in ebook form.

I love living in the future.

And also, I seem to be suffering from an infestation of commas today. Sorry.

NASA’s big announcement

(The follow-up to this post is here.)

Very important note: This so far is all speculation based on bits and pieces I’ve found online, common sense, and a good biological education. After the press conference and the expected Science paper come out, I will write up a better and more accurate summary. This is what I think is going to be said. I’m also commenting on things that I know are wrong but are circulating online. I’m updating this as I have time and see new bits of (mis)information.

(new stuff added to the end)

Final notes on this post: The press conference was very good. I’m quite impressed by Dr. Felisa Wolfe-Simon. Her career is already made, only 4 years after her PhD, and I expect she will do many more great things. The scientists involved confirmed what I’d been expecting, and added more detail. I expect the press conference will be archived online shortly and will post a link when it does.

The Science paper has been released but requires a subscription. I’ll be reading it and summarizing it in its own post. This one has gotten quite long enough, don’t you think? In the meantime, the links at the very bottom of this page do a good job with the story, unlike some of those in the beginning and middle.

The buzz going around is that NASA’s press conference later today will announce that they’ve found bacteria in Mono Lake that use arsenic instead of phosphorus in their DNA. I think. The early leaked reports are woefully bad on basic biology. Here’s a better article.

Chemically arsenic is similar to phosphorus, and can form similar compounds, so its substitution for phosphorus in DNA is plausible. And arsenates are known to be used in the respiratory pathways of other bacteria, though arsenic is toxic to most life. Bacteria are highly adaptable little things, after all.

I’ve seen some internet buzz about these “non-carbon based life forms” – complete nonsense. The bacteria in question need almost the same elements as any other terrestrial life — carbon, hydrogen, nitrogen, oxygen, and sulfur — but substitute arsenic for the phosphorus that formerly was thought to be a requirement. So also not “made of arsenic,” sorry.

Oh, and: some people have decided this is non-terrestrial life. That’s also nonsense. These are purely home-grown bacteria, just with a new and unusual chemistry.

Third thing, and I’m seeing this one even in news stories: “bacteria that can survive in arsenic.” Well yes, sort of, but that’s not new. Neither even are bacteria that use arsenic as part of their metabolism (respiration). What’s new is that these bacteria use arsenic instead of phosphorus. They apparently need no phosphorus at all, having replaced it with arsenic even in their DNA. (My guess is they otherwise function just like all other terrestrial bacteria.)

And more: the Huffington Post completely bombs their article; it’s so bad that I’m reluctant to link it. “Arsenic-eating bacteria” – not exactly, and in the crude sense also not novel. And “phosphorus in the atmosphere” – definitely not. Phosphorus cycling is almost entirely through water and sediment. The only way it would get into the atmosphere is attached to soil particles. At least they got the “not aliens” part right.

I’m not a good-enough chemist to know whether there might be possible substitutions for any of the other big six, but I suspect not. (Edit: Boron and silicon have both been proposed in science fiction as carbon replacements. Possible? Maybe, but boron is rare and silicon is less-reactive than carbon so both are less likely. Then again, arsenic is considerably less likely than phosphorus. In a big-enough sample size, who knows?)

This, to a biologist, is huge, just in case you were wondering. It changes established wisdom about the conditions necessary for life, and changes what we might look for in non-terrestrial environments. If nothing else, every intro biology book will now have to be rewritten, because they all say that six elements are necessary for life, and that’s no longer true.

To my mind, this is the one of the major differences between science and religion: scientists get wildly excited and happy when someone proves our basic dogma wrong.

Okay, here’s some good and factual stuff.

The lead scientist, Dr. Felisa Wolfe-Simon, has been studying arsenic-metabolizing bacteria for some time. She’s the lead author on a 2009 paper describing the potential substitution of arsenic for phosphorus in biochemical pathways.

Dr. Wolfe-Simon writes (with links to the relevant PDF journal articles):

Essentially, arsenic (in the oxidized 5+ state as arsenate) is biologically, so similar to phosphate that many enzymes cannot recognize the difference. This constitutes the basis for much of the toxicity of arsenate and so most detoxification pathways in biology aim to reduce arsenate to more volatile forms for easier removal from biological systems. […] In fact, in contrast to phosphorus, arsenic readily forms sulfides and thus may have been available to early life at hydrothermal vents and similar environments. Given the distinct similarity between these two elements my coauthors and I assemble plausible TESTABLE hypotheses regarding the liklihood of life arising to either originally incorporate arsenate in a functional sense, and/or more speculatively, alternative forms of life utilizing a genetic system entirely based on arsenic. […]

To further this hypothesis, we have embarked on two different approaches to test assimilatory arsenic utilization. Firstly, as part of the NASA Astrobiology Institute we are examining arsenate-rich environments to hunt and enrich cultures for organisms utilizing arsenate in novel and unique modes.

There’s an excellent article about Dr. Wolfe-Simon’s research in Astrobiology Magazine.

To perform her experiments, Wolfe-Simon collected samples of lake water and lakeshore mud in August 2009 and brought them to Ron Oremland’s USGS lab in Menlo Park, California. The experiments consists of putting about one milliliter of sampled lake water or mud into a test tube that contains an artificial simulation of Mono Lake water’s chemical makeup – Wolfe-Simon is running two sets of experiments in parallel, one using mud, the other lake water – and adding glucose, vitamins and all of the other chemical goodies that life needs to thrive. With one crucial exception: instead of adding phosphorus to the mix, Wolfe-Simon adds arsenic. A lot of arsenic. In the highest-concentration experiments, nearly 40,000 times the EPA safety level.

When the clear liquid in the test tube turns cloudy (becomes turbid), Wolfe-Simon moves to the next phase of the experiment. “If it gets cloudy, it kind of suggests that something is growing,” she explains She then extracts a one milliliter of liquid from the first-round test tube and squirts it into a second test tube, which again contains a high arsenic concentration. The effect is to increase the ratio of arsenic to phosphorus in the environment, because the only phosphorus available is what has come along for the ride from the original sample, which has now been diluted ten-fold. After each dilution, Wolfe-Simon waits a few days to see whether the liquid becomes turbid again. If it does, she repeats the transfer, to another test tube with yet another ten-fold dilution.

“At first we’ll get normal organisms, organisms we might recognize. They may be very interesting, but they’re gonna be the same type of biology that we’re used to. And then slowly, over time, [we’ll be] left with anything that can really survive under an arsenic, no-phosphorus condition,” Wolfe-Simon says.

This is the experiment from which I expect to hear results later today.

And more. The press conference is still an hour off, but reputable sources are starting to come out with actual science-based information: Nature, Ars Technica.

It sounds like the As indeed was used in ATP and other biomolecules, as well as in the DNA. I’m interested and unsurprised to hear that arsenic-using bacteria grew more slowly than those using phosphorus. The more efficient approach is likely to be the dominant one over the long-term. It’s also very interesting that there were morphological changes in the bacteria using arsenic.

Here’s a nice discussion at Discover Magazine by Ed Yong. I agree with his take on how NASA handled the story. This is incredibly cool stuff, but people who were hoping for alien life are going to be profoundly disappointed.

Living in the future

So I’m sitting at the computer listening to music that I’d downloaded instantly instead of purchasing on a CD and ripped, or cassette, or 8-track, or LP. And I’m copying data from cdrom to my USB Harddrive of Holding, and that data used to be on zip disks once upon a time.

While I’m chatting online with people all over the world.

And then I’m going to walk home while eating a locally-grown apple.

Ain’t the future grand?

The power of internet marketing

Let me show you something.

Amazon screenshot

Amazon screenshot

Can’t read that? How about this?

Amazon screenshot

Amazon screenshot

That would be a 77. No, really. It would. Right there, just below my name. I’m having trouble believing it myself.

And here’s the photo version. We’re in good company.

Amazon screenshot

Amazon screenshot

This anthology started as a twitter joke, and was picked up by a small press and became (sort of) serious. Jaym Gates and Erika Holt did a ridiculous amount of work putting it together – thanks! All the marketing has been online, through twitter, blogs, facebook.

And it worked, far better than anyone expected.

Edit: Um. Can you all see this too? That’s a #45 isn’t it?

Amazon screenshot 45

Amazon screenshot 45

Edit: 8pm. #39. #1296.

Edit: Sometime over night – #30 and #795.

Right now it’s at 34 and 806. Congrats to everyone involved!!!

Day 1

Not bad: 2900 words, some dishwashing and a killer chocolate cake.

I haven’t written much fiction in the past few months, so it took a while to remind myself what I was doing and to get back into the mindset of writing fiction. Tomorrow should be better, except that I’m busy all afternoon.

And then there’s Monday! Three whole days of not going to work! Ahhhh….

So I think the transformer for my two-year-old netbook is dead. Should I replace the transformer ($40-$60 it seems), or the netbook ($200-$300)? I have to have something portable and light with decent battery life. I thought about using this as an excuse to get an iPad, but the current model just won’t do everything I need the netbook for. Two years jammed in a backpack is a pretty good lifespan for a netbook. I’m not sure I could realistically expect it to live much longer. But it does work fine for the moment. I could get a transformer that could be used with future netbooks – that might be a practical investment. I imagine I’ll have a netbook for the foreseeable future and that way I’d have a spare.

Decisions… and I need to make up my mind quickly, because I need a functional netbook by the 13th.

Linky catch-up

Sunday afternoon, fiddling around on the computer and organizing stuff. Fiction, non-fiction, photos… it’s all a mess, and all needs sorted out. At least if I post the links I’ve been accumulating, I don’t need to keep track of them any more.

  • Periodic Table of Visualization Methods: One of my interests is in informative ways to present data. To my mind, this site tries a bit too hard to shoehorn everything into a cute visual metaphor, but it is nonetheless an interesting overview of visualization types.
  • An excavated London witch bottle: urine, brimstone, bent pins.
  • Antique microscope slides: Lovely and fascinating bits of science history.
  • TED talk on using a 13th-c. astrolabe: I have a distinct fondness for astrolabes.
  • Where I Write: Science fiction authors in their natural habitat, recorded by the ever-fabulous photographer Kyle Cassidy. It’s a pleasant change to have this come from within the tribe instead of from someone who seems to be examining a slightly sketchy foreign culture.
  • British science fiction from the New Scientist.

That takes care of a good-size chunk of my back links, though by no means all of them.

Fly me to the moon

Probably everyone knows that 40 years ago yesterday, Apollo 11 launched from the Kennedy Space Center.

Apollo 11 departing

Apollo 11 departing

There’s an understandably large amount of publicity leading up to the fortieth anniversary of the moon landing. What you might not know about are some of the interesting online resources associated with the anniversary:

I’ll be adding more as I find them, so check back if you are interested.

I missed the original by just under a year, but have been hoping for something comparable ever since. We as a society need some inspiring feats of science and engineering. We’ve accomplished many things over the past decades that are probably more important: mapping the human genome, personal computers, the internet, but nothing so universally awe-inspiring. What should the next challenge be?

Science goes mainstream!

That’s what it means when we’re targetted by email scams, right?


Dear Colleague,

On behalf of all the Editors-in-chief of Elsevier Journals, we wish to
Communicate to you that we are currently accepting manuscripts in all Fields
of human Endeavour.
All articles published will be peer-reviewed. The following types of papers
are considered for publication:

• Original articles in basic and applied research.
•Critical reviews, surveys, opinions, commentaries and essays.

Authors are invited to submit manuscripts reporting recent developments in
their fields. Papers submitted will be sorted out and published in any of
our numerous journals that best Fits. This is a special publication
procedure which published works will be discussed at seminars (organized by
Elsevier) at strategic Cities all over the world. Please maximize this
opportunity to showcase your research work to the world.

The submitted papers must be written in English and describe original
research not published nor currently under review by other journals.
Parallel submissions will not be accepted.

Our goal is to inform authors about their paper(s) within one week of
receipt. All submitted papers, if relevant to the theme and objectives of
the journal, will go through an external peer-review process.

*Prospective authors should send their manuscript(s) in** **Microsoft Word**
 **or PDF format to** **elsevier@fake.address** *and should Include a cover
sheet containing corresponding Author(s) name, Paper Title, affiliation,
phone, fax number, email address etc.

Kind Regards,

Emily Robinson(Prof.)

PS: Pls. show interest by mailing *elsevier@fake.address* if your Manuscript is
not ready but will be ready soon.

They get points for spellcheck, though it does have the erratic capitalization characteristic of scam emails. (Really, do these guys have any idea how much more profitable their schemes would be if they bothered to have someone edit them? They go to such great lengths to get the right graphics and format, and then the English sucks.)

Elsevier is a major journal publisher, but by no means spanning “all Fields
of human Endeavour”. If you send the real Elsevier a random paper without a specific journal selected, you will get it back in a week, rejected rather than peer-reviewed. I imagine if you send these folks a paper, you will get it accepted within a week, along with exorbitant page charge requests.

The real Elsevier would like everyone to know that “Elsevier does not solicit intellectual property from authors in this fashion, and does not utilize Gmail, Hotmail, or any other free third-party e-mail providers in communications with authors and editors.” What a relief!

A New Kind of Internet

Maybe, maybe not. But it will be very interesting to see. Wolfram Alpha should go live tonight (should be live by now, but doesn’t seem to be up yet).