Why aliens aren't Here (02-Jun-08)

In 1950 Enrico Fermi asked a question. It was a really good question. His question still orbits the hallways of university astronomy departments, echoes off the domes of Keck and Arecibo, pops up on sites and boards in cyberspace. The Search for Extraterrestrial Intelligence -- seekers of little green men near and far, hunters for things that go blip in the night in a statistically significant way -- must pay attention to what Fermi asked. Faced with the statement that there must be life elsewhere in the universe, Fermi asked, "Where are They?"

This has come to be called Fermi's Paradox. It isn't a paradox but it is a bloody good question. It is a much better question than, Is there life elsewhere in the universe? Better because "So what?" isn't one possible honest answer to Fermi's question. A lot of thinking has since gone into providing answers (or ducking the question) -- see Wikipedia for details. I think it is interesting how the mood of the times and the sensibilities of successive generations have affected the search for possible answers to Fermi's Pointed Question.

Hoping to be above average (25-Sep-07)

Kevin Kelly writes about how to calculate your actuarial (not actual!) date of death and discusses how this focuses the mind wonderfully.

Drop me a line on 21-Jan-2047. Hope I'll reply…

Grumpy about Google (03-Nov-06)

Inside Google Book Search is the corporate blog that highlights interesting stuff in Google's book programs. If you're American, that is. Think they're a global company? Think again.

Commence whinge

On 7-Sep-06, they posted about Hanging in Chains, saying it was one of many "out-of-copyright crime history books in Google Book Search". I followed the link but it wasn't free for me.

So on 8-Sep I filled in their feedback form at the bottom of the page:

Hi,

I followed the link on your blog to 'Hanging In Chains' and it is not available to me. Which is odd, because New Zealand's copyright law is a lot less draconian than the US and yet you are pushing this book as available and interesting in the US. What am I missing?

Thanks

Zac

The auto-reply came back immediately (typical for Google ) and a human replied a day after that on the first working day of the week (gratifyingly unprecedented feedback speed for Google!):

Hi Zac,

Thanks for your email. I understand that you were unable to download "Hanging in Chains." For users outside the U.S., we make determinations based on appropriate local laws. As with all of our decisions related to Google Book Search content, we're conservative in our reading of both copyright law and the known facts surrounding a particular book.

I appreciate your taking the time to offer us this feedback and encourage you to continue to let us know how we can improve Google Book Search. As this is still a young program, new features are under consideration and your feedback is very helpful.

Sincerely,

Dan

The Google Book Search Team

Which is nice, but wrong. It's just quoting their own corporate-speak. Reply on 9-Sep:

Thanks for your reply. But, and I mean to ask this in the politest way with oodles of admiration and so on, are you kidding?! The situation in copyright law is pretty unequivocal - there's not a lot to be interpretative or conservative about. NZ copyright extends 50 years past the end of the year in which the author died. Is any book in your database deemed to be in the public domain in NZ?

Other countries have longer terms but Hartshorne died in 1910 so his works are public domain absolutely everywhere that copyright law exists except Mexico and Cote d'Ivoire. If its public domain in the US, it's public domain in every other country in the OECD.

To reiterate, I don't want to be anything other than polite and respectful but your answer was, er, unexpectedly incomplete.

Thanks,

Zac

Silence for three days: not so unprecedented. Perhaps they're busy. Perhaps they're checking out if I'm making that up. Perhaps they're about to correct the problem…

Hello Zac,

Thanks for your reply. I understand your reaction to my initial email.

I have consulted the rest of our team, and it seems that PDF downloading is not fully available to international users. I appreciate your patience as we work to expand this newly released feature.

Sincerely,

Dan

The Google Book Search Team

Which is nice. Also unsatisfactory.

Thanks Dan. I appreciate you following that up.

Hope it rolls out global soon.

Best,

Zac

As of 3-Nov-06, the global rollout has yet to begin.

Here is the relevant Google Book Search Help Center entry (my emphasis):

How do you determine if a book is in the public domain and therefore out of copyright?

Whether a book is in the public domain can be a complex legal determination. For users in the U.S., Google Book Search currently treats all books published after 1922 as protected by copyright, except for books to which no copyright was ever attached, such as books authored by the U.S. government. For users outside the U.S., we make determinations based on appropriate local laws. As with all of our decisions related to the Google Book Search content, we're conservative in our reading of both copyright law and the known facts surrounding a particular book. If we don't know for sure that a book is in the public domain, you'll see at most bibliographic information about the book and a few short snippets -sentences of your search term in context.

But who cares about some little country barely on the map that has copyright laws as yet unchanged by corporate lobbying since the fifties?

PNAS Early Edition highlights 20060802 (02-Aug-06)

PNAS publish their own This Week In PNAS Early Edition but below the fold are my picks from the latest batch, which include a million underwater moles, liposuction as a resource for tissue surgery, crummy bioweapons made in the US purely for civilian applications, and the problems of verbing nouns or nouning verbs.

PNAS Early Edition highlights 20060727 (31-Jul-06)

PNAS publish their own This Week In PNAS Early Edition but below the fold is the one I liked best from the latest batch of papers.

SBLPP (Six billion laptops per planet) (27-Jul-06)

Nigeria has placed an order for one million of Negroponte's kid laptops; India has declared it will not be ordering any in bulk.

One million in, one billion out. The singularity delayed.

Bad Natured (17-Jul-06)

Whinge time. News@Nature's all news feed had been broken for over a month. This despite the RSS banquet they offer and their avowed purpose to make it "easier for users to keep track of our content". Perhaps nobody uses it; perhaps nobody cared; perhaps Nature likes to offer these facilities only nominally and prefers us to visit their Yahoo!-style self-referential banner-strewn site instead. Either way, the top story on their feed was 'Mouse Testicles Reveal New Class Of RNAs' from 5-Jun-06 through to 7-Jul-06.

I sent a nice email ("Hi Nature, Did you know…?") pointing this out to a name I found on the site - her Out Of Office reply provided another contact so I sent the same message to him. This was 21-Jun. Nothing happened. So, on 6-Jul after four weeks of rodent gonads, I forwarded the message to news@nature.com to say it was my last try and wishing them luck in the future for both feed-fixing and email-replying. Next day--surely a coincidence!--the feed was fixed. Ten days on, still no email reply. Nature: prestigious, authoritative, bad-mannered.

PNAS Early Edition highlights 20060712 (12-Jul-06)

PNAS publish their own This Week In PNAS Early Edition but below the fold are my picks from the latest batch, which include unanticipated difficulties in finding the molecular genetics that keep voles bonded for life, unexpected complexity in the molecular genetics underlying a single gene disorder, and what happens when you push birds through a bottleneck (answer: they come out more like chickens).

Fooling at least one person all the time (08-Jul-06)

Kruger, Dunning (1999): "Unskilled and unaware of it: How difficulties in recognizing one's own incompetence lead to inflated self-assessments", Journal of Personality & Social Psychology 77(6): 1121-1134 -- Abstract online, payment required for fulltext

Kruger and Dunning state something that isn't self-evident enough: "People tend to hold overly favorable views of their abilities in many social and intellectual domains" Then they measure it: "participants scoring in the bottom quartile on tests of humor, grammar, and logic [whose] scores put them in the 12th percentile […] estimated themselves to be in the 62nd" But of course. (via)

Posted 4-Mar-05. Update: a pdf of the paper is now available online (Google cache has the html) as part of a feature by the American Psychological Association, and Dunning-Kruger syndrome is now in Wikipedia.

PNAS Early Edition highlights 20060705 (06-Jul-06)

PNAS publish their own This Week In PNAS Early Edition but below the fold are my picks from the latest batch of papers, which include the diminishing importance of valines in protection against Mad Cow disease, the effect of having brothers on sexual orientation, and evolvability among the immunoglobulins.

Sandmole (25-May-06)

Glen Mackie, coastal geologist, estimates that there are something like 10²³ grains of sand on the beaches of Earth. Meanwhile, Avogadro defined a mole as a unit of quantity equal to the number of atoms in 12g of ground-state carbon-12, approximately the number of atoms in a cubic centimetre of ideal gas - and it happens to be about 6x10²³. In other words, having a mole of stuff is shorthand for having 6.02214199447x10²³ bits of stuff. It's hard to have that much of anything unless the stuff in question is atomic-scale stuff and so, apart from using it to beat homeopaths over the head, I thought Avogadro's number had no real-world equivalent. But if Glen is right then we may have, just lying about where anyone can look at it, a mole of sand. I'm inordinately pleased about that. (inspiration[62])

Assume that right now I'm not thinking (24-Apr-06)

There's been a recent spurt of linking to this news article in New Scientist about how humans "switch off" during rote tasks. The research in question is Goldberg et al. (Neuron 2006 50: 329-339) and is about those blank periods without self-awareness we humans all have, during which we can find we have driven a car all the way to work or ploughed a field or read an overhyped paper. However, it's the news article that (hopefully mis)quotes the first author and gets my goat:

The brain’s ability to "switch off" the self may have evolved as a protective mechanism, he suggests. "If there is a sudden danger, such as the appearance of a snake, it is not helpful to stand around wondering how one feels about the situation," Goldberg points out.

Er, I doubt it. There's no need to explain how the brain came to be able to "switch off" - the hard part is explaining how it was ever switched on. What evolved was not the ability to shut down introspection during danger but rather the ability to introspect from time to time at all. It's misleading to call lapsing to the default state switching off. Thinking is akin to anaerobic muscle exertion - we can only sustain it for short periods but the hard work can be worth it. Was it James Burke who first pointed out that there is no need to explain why plants do not roam about like us animals but instead seem to sleep though life? He pointed out that it's the animals who need to be explained - why bother to be awake when there's a living to be made being asleep, as amply demonstrated by the entire plant kingdom?

In a feat of self-awareness (and pretensiousness?), I can now quote myself from elsewhere hereabouts

I believe we fool ourselves into thinking we have a continuous experience of existence when really we are blank or mindless for quite worrying amounts of time. I believe this is true of everyone, though I have observed that the force is particularly strong in one or two of my acquaintances.

The puzzles of inattention, sleepwalking, hypnotism, sleep itself, consciousness itself - these are in some ways like quantum mechanics. Not that they're based on quantum phenomena (jeez, no, shut it, Penrose!): instead they're merely(?) deeply counterintuitive and so we have been unable to make as much progress on them as we would like. We just don't have the terminology i.e. the reusable metaphors for the underlying concepts yet. They are profoundly alien to our understanding, and that's a sweet irony and a provocation.

See all you transhumanists there (14-Apr-06)

1-Apr-10000 AD:

The biosphere extends to the stratosphere (05-Apr-06)

Some panspermia papers by Wickramasinghe and coworkers at Cardiff University on the red rain phenomenon.

I'd love the panspermia hypothesis to be true. But none of this stuff helps. Case not proven, sorry.

Top down or bottom up?

The facts: there are things that look like microbes in the stratosphere and advocates of panspermia try to argue that these are more likely to be arriving space-travellers than uplifted terrestrial organisms. But why are these likely to be visitors from the vacuum? Well apparently there's just so many of them:

"atmospheric transport may raise terrestrial particles into the stratosphere above the 16km tropopause, but if the particles rise above 20km to 40km the fraction is likely to drop off substantially, at least in comparison with particles descending from spacecraft or space sources."

But consider this: if there are formerly terrestrial organisms up there, why presume they are recent accidental additions? Isn't it more likely that the biosphere is bigger than you presume than that the stratosphere is constantly contaminated from above? Why can't life, which occupies black smokers on the deep sea floor and underground ice lakes and every other extreme environment on Earth where we've taken the time to look - why can't life make it to the stratosphere? The authors actually acknowledge this:

"In recent years the limits of microbial life on the Earth have expanded to encompass an extraordinarily wide range of habitats: geothermal vents, the ocean floor, radioactive dumps and antarctic soil, eight kilometres underneath the Earth's crust, to name but a few . The long-term survivability of bacteria has also been extended from 25-40 million years (Cano and Borucki, 1995) to a quarter of a billion years the case of a bacterium entrapped in a salt crystal (Vreeland et al, 2001)."

but seem unaware of its consequences for their theory. They think it means bacteria are tough enough for space, when it equally (or more!) means they're tough enough for the stratosphere. And if the idea that the biosphere extends to the stratosphere seems a little far-fetched, well fine - aren't you at least bound to check that option too before you claim that anything found up there is drifting down from space? If life has colonized the stratosphere, it will be growing and dividing and increasing its biomass up there - which might be why you see more than you would expect if you presume the only terrans up there are unfortunate strays.

I'm only saying this: it is their duty to consider all alternative hypotheses, and it took me five minutes to think of that one.

Crossing the line

The authors have already dispensed with any theory of native stratosphereans by assuming that the tropopause is a strong barrier against ambitious terrestrial microbes en route to the stratosphere:

"Convection currents lead to mixing of ground level particulates in the air that can be carried relatively easily into the troposphere, but temperature inversions beyond 15 km lead to barriers through which very few aerosols can penetrate. Whenever rare events such as volcanic eruptions loft particles above 30 km, particles larger than a few microns fall back quickly to the ground under gravity. The isothermal temperature regime between 15 and 25 km effectively stops the ascent of particulates, and the rapidly rising ambient temperature gradient at higher levels makes the upper stratosphere almost impervious to the transport of aerosols from the ground."

This presumes much and overlooks lots (and doesn't define "few" in the right context[59]). It doesn't take a volcanic eruption to hoist stuff up there: storms will do. Many tropical storms are violent enough to shove material through the tropopause via convective overshoot. Some conformations of high-relief terrain can lift troposheric air through the tropopause too (this is how some glider pilots can make it into the stratosphere even though thermal plumes don't extend so high). Mundane cloud microbes could be carried up by these processes and would therefore inevitably be in the stratospheric samples. Moreover, this is not a new phenomenon: even if it is impossible for life to sustain itself in the stratosphere there is plenty of incoming, upwelling supply of microbes to fill the sample chambers (and, if it is possible to earn a microbial living in the stratosphere, they will have been there billions of years).

There's another way to get into the stratosphere, one where all an organism has to do is stand still. The tropopause can descend far enough for decidedly earth-bound life to find itself in the stratosphere if on sufficiently high terrain. The summit of Everest is only a few kilometres shy of the tropopause on an average day and there are occasional low pressure systems in the troposphere that can pull down the tropopause enough for the Chomolangma's summit to poke through into the stratosphere. This has killed numerous climbers on Everest. Microbes, on the other hand, are better at adapting.

There is no data to support the theory that any of Wickramasinghe's red rain or high-altitude samples contain anything other than homegrown microbes. But they should keep looking. Because, if it were true, that'd be amazing!

Volcanocams (20-Mar-06)

Volcanocams are cool, because volcanoes are cool (volcanoes can also be no fun or, occasionally, overwhelmingly no fun). Some volcanocams give more than pictures: Alaska Volcano Observatory accompanies the traditional live pic of the Augustine cone with a data-rich display from a "webicorder". But if you're going to do it properly, you need a dinosaur!

Good timing (13-Mar-06)

I read Tim O'Reilly's Sep-05 What Is Web 2.0? yesterday and found the mention of Writely (linked on p5). Nice idea, I thought. Tried it, liked it, signed up.

Next day: Google bought them, signups frozen.

Next time I'm one step ahead of Google, I should file a patent or buy some shares or something.

Update (3 days later): signups are back on. After using Writely for a bit I can see that it's great and I'll stick with it. It would be excellent as the default GUI for GMail (which itself could be much better with a 'Save to GDrive' button next to 'Send' and a view of such pseudo-Saved items that looked like they were files not draft emails…) but somehow I doubt Microsoft is too worried. There's a reason why Adobe invented the pdf format and why one of the better hooks in MSOffice is the ability to use Word as your email editor - it has to do with the fact that, no matter how much CSS and XmlHttpRequest you use, a document inside a browser still looks like a webpage. There's going to have to be a dirigibleful lot more "really well-executed AJAX" and a browser that behaves perfectly with CSS3 before many who care a dot about layout will switch to an online word-processing solution. Most people don't use Word for word-processing - they use it for writing-and-amateur-desktop-publishing (the two definitions are probably merged now). Doing that through a browser is at one extra remove that adds nothing (except some quite cool collaboration options) and takes away much. While there's a case for stripping some of the sprawl of functions in Word and OOoWriter and the like but nobody's "custom streamlined Word" would look like Writely, because nobody wakes up thinking, I no longer want to Convert Text To Table and I despise the ability have the middle section of the document on landscape with three columns.

Sorry but that's how it is. I'll use Writely a lot, but not for the things I use Word and OOoWriter for.

Three-body problem solved (11-Mar-06)

It's nothing to do with what I normally put on this site. It's just that the juggler in this 4:27 video is abso-tmesis-lutely amazing. I was in a room alone when I watched this video and even then I stood up and applauded at the monitor.

Rock star scientist wanted (06-Feb-06)

In an odd little review on Nature News (link, paywall rising soon), Kendall Brown pays a visit to Kansas and reviews Flock Of Dodos, a movie about the Intelligent Design controversy. At a meeting in the local science museum (included to inform us, should we be so dim, that not all Kansans are ID-championing hicks), the writer-director Steve Miller says one of the weirdest things about science and education I've ever heard, and Brown doesn't pick up on it:

Miller points out the caricature of Albert Einstein that greets museum-goers. "We haven't had a rock star scientist since Einstein," he notes. "What's the incentive for kids to go into discovery science?"

Duh. What does he think goes on in kids' heads? Kids don't become rock stars because of rock stars - they become rock stars because of rock. Scientists become scientists because of science, not from looking up to Albert or having posters of Charles and his posse of finches on their bedroom walls. Kids might get into sport because they worship a hero, but they don't get good unless they worship the game. Most people can't name a living scientist but they can name a living sports hero and a living rock star; however, this inequality is not the reason why Intelligent Design prospers in the Bible belt or why enrolment in university science courses is low.

[Later: Steve Miller commented that his real words have been, er, under-reported in typical journalist abbreviative style, and the true gist/context lost. He was a little more nuanced on the day. Still, as he implies, any space in Nature is going to be good for the movie's exposure.]

The proper subject for science (25-Jan-06)

The New York Times has a slightly hostile interview with Daniel Dennett today (no link since NYT puts everything behind a paywall after 5 days; Kottke's the source). Dennett answers with admirable style a question a lot of scientists have faced. After he states there is no soul and that the brain is neurones all the way down, the interviewer says, "That strikes me as a very reductive and uninteresting approach to religious feeling." Dennett remarks that love can be studied scientifically too.

But what's the point of that? Wouldn't it be more worthwhile to spend your time and research money looking for a cure for AIDS?

How about if we study hatred and fear? Don't you think that would be worthwhile?

Save us from those who would decide on our behalf--and with the best of intentions--what is good, right or appropriate!

Still true, still unproven (29-Nov-05)

Back in January Kottke asked for comments on the 2005 Edge Question: What do you believe but cannot prove? I responded, but forgot to include it here on ortholog. I still stand by my comment:

I believe we wear more blinkers, have more blind spots and use more crutches than we realize. Frank Herbert: What senses do we lack that we cannot see another world around us? A. Lots, Frank. Lots. We have such little brains, local brains, limited brains. As a result, I believe we would not recognize non-human intelligences if we met them, at least for a long time (and we might have met them already -- don't write the orcas off just yet). I also believe that there are things that are fundamentally incomprehensible to us and that it will become necessary to enhance/extend/rewrite our minds somehow.

I believe the universe is not friendly (nor caring nor aware). I believe that the universe is too huge for us fully to understand; the proper reaction is awe in the face of the infinite. I believe that the proper response after that is to be stimulated rather than daunted. I believe the cleverest thing our species has done so far is invent/discover science. I believe it will take us far and we will still use it when we have extended/rewritten our brains beyond their current limits.

I believe we fool ourselves into thinking we have a continuous experience of existence when really we are blank or mindless for quite worrying amounts of time. I believe this is true of everyone, though I have observed that the force is particularly strong in one or two of my acquaintances.

I believe there isn't a god. I believe there isn't a persuasive argument of this for believers. Nevertheless, I'm right. Actually I am. No, I am.

I believe we have no purpose. I believe our species is neither special nor interesting, except to ourselves. I believe that is the only measure that is, can be, and should be important.

I believe that banoffee pie is the best kind of pie. I believe that I could be persuaded that our purpose is to consume banoffee pie. I believe that the orcas feel the same way about penguins.

I also believe I got it wrong: eight out of ten orcas who expressed a preference chose leopard seals.

Pharyngula vs Dilbert, humour entropy in action (16-Nov-05)

Scott Adams cast an oddly jaded and naive eye over the Intelligent Design debate the other day and set off a flamewar. The mighty PZ Myers, diligent defender of truth, responded (with much less humour). Staggering slightly, Scott's back, still a bit funny but now also plaintive and out-of-his-depth. This lob is easily, casually smashed back over the net by PZ in a post that was both dismissive to the point of rudeness and unfunny. "Next!" he seemed to say. Scott crumbles, producing his unfunniest post yet. It's a confirmed kill for PZ, who proceeds to bury the body with a grim expression on his face. And yet what a shame, what a waste. Truth won, nobody had a good time.

ID's wrong, case closed, debate over. PZ's position is unassailable though any reasonable means. Scott Adams is just some oft-funny guy, trying a little provocation on for size. I know who's in command of the facts and I know who's more representative of the man on the Clapham omnibus (hint: not the same duellist). I know which of them has a case of post-Dover seige mentality[55] and which one's only in it for the laughs, however cheap. And I know two normally excellent sites that got progressively less entertaining recently.

Scott took the wrong tone, too flippant by half. PZ did the same, too heavy-handed by five-ninths.

Come from Mars (07-Nov-05)

Warmflash and Weiss (2205): Did Life Come from Another World? in Scientific American 24-Oct-05

Warmflash and Weiss put the case (again) for panspermia (more properly, exogenesis). They're gentle on themselves:

In modern times, several leading scientists--including British physicist Lord Kelvin, Swedish chemist Svante Arrhenius and Francis Crick, co-discoverer of the structure of DNA--have advocated various conceptions of panspermia. To be sure, the idea has also had less reputable proponents, but they should not detract from the fact that panspermia is a serious hypothesis.

"Leading scientists" support panspermia? True, but are they being scientists when they do? Kelvin had a few off-days, being at least as famous for his dogged insistence on an incorrect age of the Earth as he is for his thermodynamics. Aarhenius was a smart guy who died nearly 80 years ago - give him a break. Crick talked in public about panspermia but was far from an uncritical advocate of it. Odd that Hoyle isn't mentioned.

Anyway, so what? Ever heard of the first of Clarke's laws? Ever counted how many learned scientists don't agree with panspermia? Arguments from authority carry little weight since the Rennaissance. And extraordinary claims require at least ordinary evidence.

"Panspermia is a serious hypothesis"? Hmm. Actually it occupies a peculiar niche in science, being for a long time almost but not quite falsifiable. There's no evidence for it but also nothing fully compelling against it. As hypotheses go, it doesn't impress. It makes for good copy though.

Plausible deniability or deniable plausibility?

While life-from-space might be possible (they say "plausible" but that's a connotation too far for me), why might Mars be a more congenial cradle for life than Earth? Earth is, at least currently, the poster boy for a planet on which life could begin: it provides tectonics, vulcanism, liquid water, and fantastically complex geochemistry, all of which are likely to help abiogenesis along. At it's worst it has been at least survivable (fossil evidence goes back to the Hadean).

Any good hypothesis has to be able to survive a slash attack from a fourteenth century razor-wielding monk. Invoking Occam, it seems more plausible that life began on Earth and stayed there than that it began on Mars, sent emissaries to Earth, then died out back "home". Why invoke a perilous and improbable crossing of the gulf of space at all? What additional explanatory power is provided? What missing features does areogenesis confer over geogenesis? On current knowledge: nothing. If we found DNA-based life on Mars, it would still be more likely that it originated on Earth.

I personally find polygenesis a more likely, yet still unproven, hypothesis, one which, if successful, would boost Occam further at the expense of panspermia. If you can make it at home, why send out for it? Undoubtedly we came from outer space (we are starstuff, said Sagan). But, while our sample size is poor, there is so far no reason to suppose that we arrived on Earth alive and replicating.

Domain experts comment on Wikipedia's efforts (28-Oct-05)

Their pronouncements were collected by The Guardian. Part of the backlash? Maybe, but also just a storm in a teacup, tilting at a strawman on a stalking horse.

Personally, I'm quite happy with the entry on science as a work in progress. There's scope for improvement but then it is Wikipedia, that's the point of it. It's not that Wikipedia is social software at its best (it might be) or based on the power of iteration and the general niceness of people at all (only a bit) - it's that it is alive, dynamic, perennial, inescapably uneven. Don't expect perfection, offer thanks and muck in instead. Like the T.S.Eliot expert says,

It's not terrible. But then I wouldn't have thought of using Wikipedia as a serious reference source.

But sophisticated lit crit would be asking a lot of a small, free encyclopedia entry. There's a lot of good basic stuff in it.

Science publishes 1918 flu genome, futurists panic (18-Oct-05)

Kottke's remainders today include a note that Ray Kurzweil, tech guru of the month, and Bill Joy have published an opinion piece in the New York Times characterising the publication of the 1918 flu virus genome as "extremely foolish" (Boingboing linked to it too). The paper in question - Tumpey et al., 2005; doi: 0.1126/science.1119392 can be found behind Science's (ludicrous) pay wall.

Kurzweil and Joy are themselves being extremely foolish here.

Mighty behemoth, teeny-tiny ant (03-Oct-05)

Oo, beaut. I just got boingboing'ed: Xeni Jardin picked up my submission to them about the Google Ant!

Passers-by, feel free to sniff around. Idiosyncratic samples:

• a bunch of opinions
• something fundamentally useless but may provide an insight into something or other
• the only thing that's vaguely topical but ascientific round here
• some thoughts on how tiny you and I are
• suggestions as to which direction the future is lunging from
• my prejudices exposed

Can't decide whether I want to be Kottke'd or Slashdotted next.

Glitter, shock and awe (10-Aug-05)

Stephen Zanichkowsky (2005): The Beauty of the Bomb - It is terrible, and it is miraculous, in Invention & Technology summer 2005 issue. (via)

One of the more interesting articles to come out of the 60th anniversaries of Little Boy and Fat Man. Zanichkowsky discusses the fascination and repugnance of the bomb, the shock and awe it has always provoked. He quotes Freeman Dyson:

I have felt it myself. The glitter of nuclear weapons. It is irresistible if you come to them as a scientist… . It is something that gives people an illusion of illimitable power … when they see what they can do with their minds.

but he is quotable himself. After listing the changes physics has brought to our lives--from the bomb to CT scanners, radiotherapy and maglev trains, computers and mobile phones--he forecasts,

Over the next century biochemistry is going to bring us the same changes that physics brought in the last.

Oh yes. Damn right. At the very least.

(One nitpick. Zanichkowsky writes of the Trinity test on 16-Jul-1945,

For the first time ever, humans had released energy that had nothing to do with the "stored sunlight" found in coal, oil, and wood. Energy was squeezed from a lump of ore.

Er, I think we achieved energy sans sunlight 200 years ago)

It's all in yer head (17-Jul-05)

Henry, R.C. (2005): The mental Universe[sic], in Nature doi: 10.1038/436029a

It's not April 1st again is it? Richard Conn Henry is surely fooling or blithering when he writes:

The only reality is mind and observations, but observations are not of things. To see the Universe as it really is, we must abandon our tendency to conceptualize observations as things.

This is easily the greatest concentration of gobbledygook I've read in Nature for a while, particle physics included. I'm not even going to comment on the difference between a "tendency" and a heuristic integral to perception. I'm not being all empiricist or positivist or anything about this; I'm just agog at the waffley, dribbley, marshmallowiness of it all.

New Scientist's 13 things that do not make sense (06-Jul-05)

Since I'm in listmania mode, I'll tackle this.

http://www.newscientist.com/channel/space/mg18524911.600

Their list of weirdnesses:

1. Non-psychological mechanisms implicated in the placebo effect
2. The inexplicable uniformity of the cosmic background temperature in opposite directions
3. Oh-my-god particles
4. Some better-than-average evidence for one instance of homeopathy
5. The location of dark matter
6. Ambigous evidence of life on Mars from the 1970s landing
7. A one-off observation of tetraneutrons, an aggregations of subatomic particles which we don't think could exist
8. The perturbances in the Pioneer 10 and 11 trajectories
9. The driving force behind the Universe's accelerating expansion
10. Ambiguous evidence for a "proper" tenth planet in our solar system (not Sedna or Quoar)
11. A radio signal burst of unprecedented magnitude picked up from the direction of Sagittarius in 1977
12. Some aberrant spectroscopy results hinting that one fundamental constant may have varied in value
13. Cold fusion, its reality or otherwise

Effed (05-Jul-05)

Let's prepare to grapple with the ineffable itself, and see if we may not eff it after all. (Douglas Adams[42])

Since Science has posed 125 questions for science to answer, I thought I'd unearth and update this: a consideration of one hundred of the big philosophical, ethical and moral questions which trouble mankind as the third millenium begins to tumesce, with short answers provided. This should remove distractions and allow folk to concentrate on Science's list. There are some overlaps, which should save time since, unlike Science, I've provided answers.

No attempt has been made to provide a philosophical background, define terms, supply arguments (whether supported by evidence or not,) or cover all bases, let alone to avoid controversy, triteness or tangled moral mazes. Caveat lector.

There will be no attack ships on fire off the shoulder of Orion (20-Jun-05)

Geoff's got a movement with a manifesto, just like Bruce has. I like Geoff's better, though it's bleaker:

[Mundanity claims] That the most likely future is one in which we only have ourselves and this planet … [leading to an] imaginative challenge that awaits any SF author who accepts that this is it: Earth is all we have. What will we do with it?

Downer, right? But the Mundane Manifesto contains the following promise:

To burn this manifesto as soon as it gets boring

That line should be legislatively stipulated manifesto boilerplate.

Bees aren't quantum (15-Jun-05)

Quantum honeybees - research on honeybee behavior by Adam Frank

An article from 1997 linked today by Kottke[48] discusses, in the most over-reaching and bogus terms, some reckless extrapolation. Mathematician Barbara Shipman discovered that the waggle dance--the way bees communicate the location of food supplies to each other--encodes information in such a way that a human needs higher mathematics to parse it. So far so good, well done those bees! She then lunged to a conclusion that bees must be able to perceive quantum phenomena directly. It's not ridiculous (well, it is, but…) but it is certainly nothing more than fantasizing. Maybe it would be nice if it were true (certainly nice for Penrose and his ilk) but that's not a reason to open your mouth and let something like that fall out.

Kottke disgraces then redeems himself (06-Jun-05)

You can normally rely on Jason Kottke to find reams of interesting stuff on the web. By now there must be a Kottke Effect, in which considerable quantities of Googlejuice will be injected into--and server load imposed upon--anything he links to. (The Slashdot Effect and the Boing Boing Effect are of course larger; I wonder how many Kottkes there are to a BoingBoing, or whether a DecaKottke is larger or smaller than a HemiSlashdot?) But when he posted this the other day:

The theory of evolution: just a theory?  #
"Historian Prof. William D. Rubinstein shares his doubts about the theory of evolution."

I was kind of disappointed. I read the article and wondered why anyone with an academic credit would post a few thousand words of dreck on the web when there are many thousands of words refuting everything Rubinstein's got to say out there already. It didn't deserve any prominence it would get from featuring on Kottke. Why can't Jason use his mighty power for good instead? I wondered.

Thankfully, today he did, linking to Pharyngula's response to, and dissection of, Rubinstein:

A historian disgraces himself  #
A rebuttal of "The Theory of Evolution: Just a Theory?"

And the megatonnage of BoingBoing has been recruited to the effort.

The scales tip back.

Working for Google (04-Jun-05)

Now webmasters can produce their own sitemap for the GoogleBot and feed it regularly (via). Is this Google getting us to do their work for them? Dunno, but it was easy enough to set up in Movable Type: just create a new template and insert Niall Kennedy's code (via). All those with the coder kudos of making their own CMS may now bite through their mouse cable.

The result, not exactly human parsable®, is here.

Four hours later, I find it has been downloaded. Yet when I search Google for a recent phrase ("not exactly human parsable"®), it isn't there. And when I search for an older phrase ("wormholes are wormfood"), I find that Google last read it 8 days ago. Hmm. I guess downloaded doesn't mean indexed. After all, it is a beta and they have got 8 billion pages to get through…

Elsewhere

• Slashdot is discussing this
• SearchEngineWatch has an interview with the Google guy responsible
• There's a discussion group on Google Groups
• They're not discussing it in any Yahoo! groups yet…

Evidence for a Young Me (24-May-05)

The evidence that I am thirty-four years old is flimsy: godless scientists simply do not understand the true reasons for my isotope ratios and temperature. Science, inflated with a few early successes, thinks it can shore up claims of a ~12,500-day period for my Earthly existence with a multitude of falsifiable scientific hypotheses to explain away the glaringly obvious proofs of my more recent origin.

You say tomato, I say Lycopersicon spp. (12-May-05)

This is a followup to the human genes in rice deserving (mutated) meme. Elements of that news story highlight some of the fundamental problems in public discussions about science. I tried to cover some of this at the GM hui.

The story quotes (or panders) to the usual overwrought hystericals:

Environmentalists say that no one will want to eat the partially human-derived food because it will smack of cannibalism.

I'm struggling to articulate my response to this but here goes.

Misleading misbreeding (04-May-05)

Nicholas Wade, writing in The New York Times, discusses modern chimaeras confusingly and with a handful of bizarre anachronisms and anthropomorphisms. A bad article that will get lots of undeserved googlejuice thanks to Kottke.

Rice, genes, and fox terriers (27-Apr-05)

Hirose et al. (2005): Transgenic Rice Containing Human CYP2B6 Detoxifies Various Classes of Herbicides, in J. Agric. Food Chem. doi: 10.1021/jf050064z S0021-8561(05)00064-6

Geoffrey Lean reports in The Independent about Japanese work inserting a human P450, cyp2b6, into rice to confer multiple herbicide resistances. (Declaration of interest: I like P450s.) The reportage may turn out to be an example of a trackable meme on the move (analogous to Gould's "about the size of a fox terrier" meme).

Ten Commandments from Kornberg (20-Apr-05)

Kornberg (2000): Ten Commandments: Lessons from the Enzymology of DNA Replication, in Journal of Bacteriology 182(13): 3613-3618; fulltext via open access.

Ten THOU SHALTs that Nobel laureate Arthur Kornberg learnt from enzymology which work as heuristics for pretty much all biological research, and for most other research too.

Biotech Science Scan - Collected Speculations (15-Apr-05)

Hanley (2004): Biotech Science Scan - Collected Speculations, for RSNZ/MoRST. Fulltext

Early in 2004 I participated in a group convened by the Royal Society of New Zealand at MoRST's behest that was to produce a "biotechnology science scan" covering a 15 year span. This paper [pdf, ~200k] was my initial and belated contribution, written after reading the results of the early discussions by the group and therefore benefitting from them. In it I outline a few concepts--which, as often occurs, tend to become statements of context--and some notes of caution. Then I give my thoughts on two kinds of biotech development: enablers and breakthroughs (i.e. evolutionary development of tools, and things that may shake all other predictions, respectively). The likely impact over the next 15 years is discussed. Anything that doesn't fit this scheme appears in an appendix.

As mentioned hereabouts, the final report, Biotechnologies To 2025, was published by MoRST early in 2005.

Papal election hackproof (and evolutionary) (15-Apr-05)

Schneier, security guru, details the voting system and concludes,

When an election process is left to develop over the course of a couple thousand years, you end up with something surprisingly good.

Well, good enough to elect someone who would say this:

Theories of evolution which, because of the philosophies which inspire them, regard the spirit either as emerging from the forces of living matter, or as a simple epiphenomenon of that matter, are incompatible with the truth about man. (speech 22-Oct-96)

But, Pope, if Schneier's observation can be generalized, we could then hypothesize:

When an iteratively complex system of replicators is left to develop over the course of a couple billion years, you end up with something surprisingly good, so good in fact that you might assume in error it represents "a great ontological discontinuity" rather than a "simple epiphenomenon".

Course, that's just me seeing evolution everywhere.

Science fools (01-Apr-05)

It's April 1st. The scientific community has expressed its sense of humour in the following ways:

(Later: a long list of pranks played this year, mostly computer-geek ones.)

Supervolcanoes (18-Mar-05)

Sparks, Self, Pyle, Oppenheimer, Rymer, Grattan (2005): Super-eruptions: global effects and future threats, a Report of a Geological Society of London Working Group; www.geolsoc.org.uk/supereruptions

Off the back of the publicity from a BBC documentary and two-part dramatization, some eminent geologists have put together a report on supervolcanoes, the volcanoes that have global rather than local or regional effects. It's an interesting read, with some dramatic photos and predictions.

Drive to the sun (08-Mar-05)

I tried to come up with a way of clueing my kids in on what a big, wide world in a big (big!), wide (wide!) universe it is. I don't think it can be done.

Bigger brains aren't necessarily smarter brains (02-Mar-05)

Crick lousy at drawing double helices (15-Feb-05)

Sir Francis was no better at drawing the things than I am!

This is from the National Library of Medicine's Profiles in Science site, which, working with the Wellcome Trust, recently put up a profile on Sir Francis Crick, including hundreds of items from his personal archive (and more to come).

(via)

iPredict (04-Feb-05)

In the wake of the iPod and all the rest, here are Apple's forthcoming releases for 2005:

iKea

A range of furniture flatbacked in utterly gorgeous white boxes but which is incompatible with your other furniture

iNcas

Announcement of the discovery by intrepid Apple marketing anthropologists of an utterly gorgeous race of indigenous people in Central American jungles who unfortunately worship the Sun (and worshipped Hewlett-Packard before that)

iNches

Unit of measurement Apple will henceforth use for all their utterly gorgeous white boxes

iDempotency

A new mathematical operation which looks utterly gorgeous whether you look at it once or any number of times

iCeland

An upgrade for that country, making it even cooler and whiter, and of course utterly gorgeous

…

Belief that Science is the One True Path? (01-Feb-05)

No, you do not have to believe that only science can provide the answers to all questions to be a Compleat Scientist (or even just a scientist).

However, for the types of questions which it is suited--a number bigger than advocates of other pathways to knowledge will admit--science is superior. Sorry, but that's the way it is.

Human evolution a privileged process? (08-Jan-05)

Unwarranted claims are being made about research published in Cell by Dorus et al. While the paper reports interesting results on sequence comparisons for genes involved in nervous system development in primates and rodents, much more troublesome are the senior author's comments in press interviews. Extraordinary claims for a "categorically different" kind of selection being necessary for the evolution of the human brain are being made. These claims seem to me to be unfounded, either by the research or by armchair contemplation of the problem.

(I had this originally as a Deserving Meme but my rant was so long I've recategorized it.)

Inadequate response to the 2004-12-26 tsunami (30-Dec-04)

Below is the fulltext of a comment I posted to a topic called Tsunamis and the Moral Anthropology, on a blog where there was a discussion among (mostly) religious types about how natural disasters and wholesale death by "Acts of God" could be squared with their beliefs.

It's off-topic for ortholog but, since there were no permalinks to individual comments on http://amywelborn.typepad.com/, I thought I'd put this where I can find it again if I need it.

Big 3 journals have RSS (30-Dec-04)

It's about time. They don't all offer the same degree of content access or the metadata though; read on for details.

A "Western" mindset? (24-Dec-04)

Do you need "Western" values to be a Compleat Scientist?

No. You do not need to participate in, or subscribe to any unique elements of, so-called Western civilization in order to be a scientist. The things that delineate the subculture of science are compatible with any other thing you might reasonably call culture. Facets of science (including some of its results--not what we're talking about here) might be incompatible with your individual doxastic hungers and with factual claims made by your co-culturists, but science is a culture-independent strategy for finding out certain types of things. It is as acultural as the wheel or long division or marriage or dance.

Nature columnist rants about declining literacy standards in science papers (05-Dec-04)

The Write Stuff, by Henry Gee

Excellent article from reliably good Nature columnist Henry Gee. He's definitely got a point (i.e. that modern scientific exposition is shabby and shoddy) and generates a few quotable quotes:

• "…poor scientific writing comes from a misplaced (I'd go so far as to say dishonest) objectivity, in which cause people are encouraged to remove themselves from the discourse…" [I wholeheartedly agree with the "dishonest"]
• "Scientists' convoluted prose produces a general frustration akin to that felt by the boxer who, while still gloved, tries to peel a banana." [and sometimes even as though the boxer is on a moving train]
• ""If you want to make a silk purse out of a sow's ear," as someone once said to me in another context, "start with a silk sow."" [GM ahoy!]

But…

Art, for Darwin's sake (22-Nov-04)

I both enjoyed and disagreed with Denis Dutton's interesting review of an interesting book, Literary Darwinism: Evolution, Human Nature and Literature by Joseph Carroll. In his essay The Pleasures Of Fiction, Dutton argues, with supporting quotes from Carroll, against what both see as an incomplete explanation of the adaptive benefits of art given in Steven Pinker's book How The Mind Works. Pinker needs no help from me defending his thoughts but I'll have a go anyway. I also believe that Dutton and Carroll use modern critical theories in their ideas about the adaptive nature of literature that are not relevant to evolutionary psychology for the simple, almost absurd, reason that our ancestors were not literary theorists.

Certain cultural values? (19-Nov-04)

Do you need certain cultural values to be a Compleat Scientist?

Depends what you means by "culture" I suppose. There's two things to talk about here: firstly, the culture within science and, secondly, any effect of wider culture on the practice of science. The first is easy: you definitely need to participate in the (sub)culture of science in order to be a recognized scientist, though to be a scientist-in-the-head requires less visible commitment. The rest of this article is about this. It's pretty hard to articulate the Culture Of Science and I've made an imperfect attempt. As for the effects of your or any other wider culture, the compatibility or otherwise of science with cultures is discussed elsewhere hereabouts.

A friendly universe? (09-Nov-04)

Do you need a tolerant or friendly universe to be a Compleat Scientist?

No, just a barely compatible one. This is a question for everyone, not just scientists; a friendly--or amenable, or tolerant, or at worst merely compatible--universe is a prerequisite for the existence of you, me, plumbers, sea squirts and giant redwoods. Scientists may perhaps feel the question more keenly because they are engaged with the universe in its detail, because they have a passion for understanding it, and because they at times tamper with it. Scientists are best placed to find out how friendly the universe is. They can also ask the interesting question of how long it will remain so.

(The question is necessarily anthropomorphic. The universe is neither friendly nor unfriendly but it seems hard-wired in us to ask these existential queries from the intentional stance.)

Extreme prejudice (20-Oct-04)

(This is what can happen when a word game gets out of hand.)

The CIA (supposedly) have a Health Alteration Committee (i.e. an assassination workshop group and authority) which can give the order for someone to be "terminated with extreme prejudice". If that judgement is passed on you and you happen to lack your own Secret Service then you are in deep trouble and need to be thinking about getting a will drawn up.

All well and good you might say. Doesn't the committee get bored? Well, yes, they do, and occasionally they dig out the thesaurus and stamp alternatives in big red letters on victims' files, e.g.:

Awe in the face of the infinite? (20-Oct-04)

Do you need to be gasping in wonder at the world in order to be a Compleat Scientist?

Always. The Compleat Scientist certainly needs to make an honest attempt to grok[28] the immensity and complexity and perplexity of it all. Actually, those might not be the right words: a certain humbleness about how little it is possible to see--let alone comprehend, let alone grok--is a necessary trait in a scientist. An uneasy balance between shock and calculating appraisal is required. To date, the only way we have found of inching towards a glimpse of a sliver of a simplistic understanding of any part of the universe is through science. It's a cure for our species's arrogance rather than a cause.

Leaves compute, like brains do (27-Jul-04)

Peak, West, Messinger, Mott (2004-01-19): Evidence for complex, collective dynamics and emergent, distributed computation in plants, PNAS 101(4): 918-22; doi: 10.1073/pnas.0307811100 (open access)

There's something important that leaves and your brain have in common at a fundamental level and this apparently unrelated paper hints at it. The authors take care to describe one particular thing that leaves do and the surprising way they manage to do it but this is also interesting because of what it tells us about complicated and apparently wonderful things (like thoughts) arise out of everyday and apparently simple things (like us and the stuff we're made of). The authors don't make the leaf-to-brain link but I see the comparison as a useful one somewhere near the border--or the discontinuity--between analogy and homology. Note that the authors are not suggesting that plants are computers, rather that there is a fruitful comparison to be made between how plants perform certain tasks and the way that a certain type of mathematical pattern works. Going further, I think this comparison neatly demonstrates how complexity appears as if by magic from simplicity of a certain type.

Scientific training? (30-Jun-04)

Do you need scientific training in order to be a Compleat Scientist?

No. A Compleat Scientist does not have to have a PhD, or a laboratory group, or a synchrotron, or a pipette, or a labcoat, or a calculator, or an Einsteinian haircut[30]. A Compleat Scientist has a scientific approach to life but may work in an office, a truck, a workshop, or a home. A Compleat Scientist doesn't have to know what a tachyon is, or a nucleotide, or a paleosol, or a retinoblastoma, or an engram, or an anisotropic universe, or whether the the Hawthorne effect is a real one or not.

Who's already invited to dinner? (01-Jun-04)

Xu and Gordon (2003-09-02): Honor thy symbionts, PNAS 100(18): 10452-9; doi: 10.1073/pnas.1734063100 (open access)

Honor Thy Symbionts is a commandment -- Xu and Gordon want us to salute our symbionts because these tiny creatures make us what we are. True?

A particular mental pathology? (31-May-04)

Do you need a particular mental pathology to be a Compleat Scientist?

I suspect so. Perhaps "pathology" is a bit too loaded a term - a particular atypicality or a certain quirk of mental configuration, then. The question comes down to whether or not anyone can choose to be a compleat scientist, or whether only some kinds of brain can do it? This is not to ask whether a person can opt to make a living as a scientist, nor whether they can temporarily get into the mindset of one - such things are entirely possible. However, I don't believe a person can select Science-with-a-capital-S from the range of lifestyle options and live it, full time, without stinting. Are compleat scientists born or made? I think they're born then made, arriving with the inbuilt tendencies and developing them to fullness in an appropriate environment. There are many more that are born and then left unmade.

About ortholog (05-Mar-04)

ortholog.com: commonplacings, preponed futures, brainworthy memes, paradigm fragments, rigorously conceived musings, gists, free association on free science, stuff I've got nowhere else to put. It exists neither for nor despite you, but you are more than welcome to read it.