Astute readers will have noticed that there's not much going on here anyway. I've had immigration hassles (done with, I hope), health problems (fixed, I think) and I'm waaaaaaaaaayyyyy behind at work. I need a couple months' absolute tunnel vision: publish or perish, publish or perish, publish or perish. So, no blogging for me, and I won't be reading much except research papers either. I'll copy all my science/OA RSS feeds to Google Reader (which unlike Bloglines doesn't stop caching at 200) and try to catch up on the backlog over whatever Christmas break I get.

[ahnuld] I'll be back... [/ahnuld]

[deleted widget -- it was slowing the page load waaayyyy down, not all the time but at least once a day. screw that.]

Hey, this one doesn't suck. The customization is not great, but the stuff you can't get to is set up in a way that suits me anyway. Plus, it's free.

[deleted widget]

I can't get rid of the unsightly space in the items with no description, because the "tagged by" is part of the %DESCRIPTION% variable. I won't be paying for this one if the customization doesn't improve. (It'll show up to 20 items, but I've set it to 5 because it's so clunky.)

Not going to use a commercial service when there's a free alternative (see FeedSweep, above) that seems OK.

Why is this so hard? Argh. This one's not free but I'll happily pay for something that works.

[deleted widget, see update]

Hoo boy, that's ugly. But it seems to work, and the tabs at the top are sorta nice -- you can separate feeds by category. (Not sure Simpy plays nice with that -- it's supposed to, but...) Oh, and there's a minimum width otherwise you get side-scrolling, don't like that.

Update: fails to refresh/show new content. Wonder if it's something Simpy is doing? This one's too damn ugly to bother, but I might test the others with different feeds.

What do people think? Should I add this widget as a sidebar? I like it a lot; the only thing missing is a way to set all the items open as default. Meh, slow to load and fails to update. Might have been something I did but I'm too busy to figure it out right now.

Update: trying again: deleted widget, couldn't make it work (update). Might have been me but if it's going to be that much work I'll just write my own damn parser. How hard can that be? (Yeah yeah, famous last words.)

To those of you who read my Simpy RSS feed to see what I'm collecting in my bookmarks, I just want to say that I had nothing to do with the appearance of advertising in that feed and it won't be staying. I've written Otis to find out what's going on, and to say that I'll happily pay good money for a premium no-ads service. It would suck to have to switch bookmarking apps again, because Simpy is a great tool, but I will NOT put up with advertising in my RSS feeds. (I just saw one for US Army recruiting, for fuck's sake! I am NOT going to start shilling for the hired killers. That's what prompted this entry.)

In fact, since my blogroll is entirely driven by Bloglines, I'm thinking of de-linking anyone who allows advertising in their feeds. Feed ads are intrusive and annoying, and to date RSS feeds have been about the one place on teh internets that has been mercifully free of that particular plague. I'm not at all responsive to the "ads support this service" argument as applied to RSS. I've come to terms with on-site advertising as more and more of the bloggers I like have decided to try to make a little extra from their sites, but feed ads are where I draw the line. "You can have my feed with ads, or no more of my writing" gets a simple answer from me: goodbye. I also suspect -- though of course I have no data to hand -- that this cancellation effect will more than compensate for any increased revenue that feed ads might generate.

Update: On re-reading that, I should add: I don't want this to sound like a threat, or even (at this stage) a complaint. Otis has been doing a lot of work behind the scenes lately, improving Simpy's stability and speed, and I presume that the ads appearing unwarranted and unannounced is simply a glitch that will speedily be fixed.

I know a few people are reading the linklogs, so I thought I'd ask: would you prefer it as a sidebar? I could convert to a three-column layout, with the existing columns much as they are (just a bit thinner) and a third, probably central, column that would contain just the linklogs.

Also, I've been doing them as blog posts so that I could send trackback pings and people could comment on them -- but trackback fails as often as it works (MT, I'm looking at you), no one is commenting on the link posts, and converting from my Simpy/Feed2JS setup is a bit of a hassle. So, should I just leave it as a feed? You can see what that would look like here.

Quite apart from the ungrammatical message, the "contact us" link goes to -- you guessed it -- the same error page. Oy. There's no blog or forum where I can find out what's happening, either. I mean, I don't demand 100% uptime, but I do at least want to know what up.

This only gets to happen one more time (and that's only because I am very lazy), then I'm switching to Simpy.

Update: changed my mind, as per the strikeouts. I just like Simpy better; I trust it, and Otis, more. I'm a tool, I should have done this from the start. Until I work out how to do the linklog posts, if you really need to watch me surf the Simpy feed is http://www.simpy.com/rss/user/sennoma/links.

I mentioned a while back that I chose Ma.gnolia over Simpy in part because the latter's RSS feeds didn't work with Bloglines, so it seems only fair to note that this is no longer the case: Simpy's feeds now work perfectly with Bloglines (at least the full links feed I tested does). Moreover, since Ma.gnolia feeds initially didn't work with Bloglines either, and the Ma.gnolia team replied to my email to say "it works now, we dunno why", I figure it was likely something Bloglines did. I meant to email Otis -- see for yourself how responsive he is -- but forgot; if I hadn't, I'd be using Simpy now. This would mean finding a way to convert XML to HTML to replace the Ma.gnolia linklog widget, but there's an API and an active dev community so even if FeedDigest doesn't open up signups again I'm sure I could cobble something together.

For now I'm satisfied with Ma.gnolia, but I'm keeping my backup with Simpy and keeping an eye on developments. Honestly, Simpy is less flashy and commercial and has that hacker feel to it (these are good things, imo); I feel I can trust Otis, whereas I just don't know what the Ma.gnolia folks have in mind. I should probably switch, but I'm too lazy to do it right away -- so this entry is my way of trying to be fair to Simpy.

Since I had to ditch del.icio.us, I've been looking for a replacement online bookmarks manager. Furl is useable but poorly designed and unresponsive to feedback, Spurl is better but clunky (I don't like their folders+tags system), Simpy is good but the RSS feed didn't work and there were some uptime issues. I'm not sure why I didn't just mail Otis (Simpy's developer), since he seems pretty keen on feedback and improvement. I may go back to Simpy yet, but for now I'm sticking with Ma.gnolia. It's got all the basics down, and I got a good response when I sent mail, and it gives me a way to put up a sidebar like all the cool kids have. Only I've decided not to do it as a sidebar, but rather as regular "linklog" entries -- so that readers can comment on whatever I link, and so that it will all show up in my RSS feed. For now I'll use Magnolia's linklog widget, but when Feed Digest opens signups again I'll also try the RSS-to-html method, because Magnolia's feeds show tags and include thumbnails. I've also added my public Magnolia account to the sidebar, so without further ado:

Link Log (powered by Ma.gnolia)

Displaying RSS Feeds

More than I will ever understand about RSS feeds.

A Golden Age for a Pinup - Los Angeles Times

Sad and sweet article about Bettie Page in her retirement. Never mind Ellison's blather about golden means, the photo-touchup guy has it: she looks like fun.

blackprof.com: Crime Fighting Ticket Cheats?

The St Louis metro is an honor system -- and everyone cheats. Eric Miller has some interesting observations about the Broken Windows theory, and (what seems to me) a smart practical solution to the case at hand.

Nautilus-Fiberarts | Home

Nautilus Fiberarts - Katazome by Karen Miller

One Foot In | Alice Domurat Dreger

Member at Bioethics Forum. Likes penises.

Google Answers: Red States / Blue States

Why are Republicans red and Democrats blue? Turns out there's not much reason or design behind it.

under the fire star: Timepass

This sort of thing is one of the reasons I read Nancy. "Timepass", what a charming coinage.

Astroseti.org : How to discover asteroid impacts

Emilio decided to have a look at the new Kebira impact crater on Google Earth. Then he decided to go hunting for others; pretty soon he'd discovered what appear to be two previously-unknown members of the Aorounga impact line.

ScienceDaily: Manchester Scientists Create New Bio-gel For 3D Cell Culture

3D bio-gel for cell culture; may be an early step on the long road to grow-your-own organs.

Largest-ever galaxy portrait is awesome | Science Blog

The image of spiral galaxy Messier 101 (the Pinwheel Galaxy) is a composite of 51 images, collected for various purposes and mined from the Hubble archive. Messier 101 is about twice as big as the Milky Way and some 25 million light years away; it covers an area about one-fifth the size of the full moon in the constellation Ursa Major. It contains at least a trillion stars, of which maybe 100 billion physically resemble our Sun. If you go outside and look at it tonight, the light striking your eyes will have started its journey at about the same time as Antarctica was breaking away from Gondwanaland.

GeoWhen Database - Geologic Timeline with Stages

Handy chart for when you need to know your Jurassic from your Devonian.

Wetsuit helps Third World women survive complicated childbirth | Science Blog

A neoprene suit can save the lives of women suffering from obstetrical hemorrhaging due to childbirth, which accounts for about 30 percent of the more than 500,000 maternal deaths worldwide each year due to childbirth, nearly all in poor countries. The mechanism is amazingly simple: the suit provides pressure to prevent blood from pooling in the lower abdomen and extremeties, mitigating the most immediately lethal effects of shock.

ScienceDaily: Smallest Triceratops Skull Ever Found Provides Clues To Dinosaur's Growth

Cuuuuuuuuuuuuuuuuuuute!

LiveScience.com - The World's Toughest Coffee Cup

Now *this* is science. The winning design doesn't look to me as though it would be particularly tough.

LiveScience.com - Mom's Genetics Could Produce Gay Sons

The pattern of X chromosome inactivation appears to influence the sexuality of male offspring. The lead scientist (Sven Bocklandt, UCLA) has it exactly right regarding the "it's not a choice" vs "we could cure it" views of the possible genetic underpinnings of (homo)sexuality: "I think if there's ever a time when we can make these changes for sexual orientation, then we will also be able to do it for intelligence or musical skills or certain physical characteristics -- but whether or not these things are allowed to happen is something that society as a whole has to decide. It's not a scientific question."

Baby's helping hands

This is encouraging for those of us who (want/have to) believe in the possibility of human improvement: "Felix Warneken and Mike Tomasello found that children as young as 18 months willingly helped complete strangers. 'The results were astonishing because these children are so young - they still wear diapers and are barely able to use language,' says Warneken. 'But they already show helping behaviour.'"

The APC tumor suppressor counteracts beta-catenin activation and H3K4 methylation at Wnt target genes.

Does APC/Wnt play any role in cell cycle entry repression of MYC? From the abstract: "beta-cat recruits Pygopus, Bcl-9/Legless, and MLL/SET1-type complexes to the c-Myc enhancer together with the negative Wnt regulators, APC, and betaTrCP. Interestingly, APC-mediated repression of c-Myc transcription in HT29-APC colorectal cancer cells is initiated by the transient binding of APC, betaTrCP, and the CtBP corepressor to the c-Myc enhancer, followed by stable binding of the TLE-1 and HDAC1 corepressors"

LiveScience.com - Immortal Styrofoam Meets its Enemy

Pseudomonas putida can convert styrene oil, made by simply heating polystyrene, into polyhydroxyalkanoates -- from which can be made biodegradable cutlery, plastic film, and so on.

BBC NEWS | Science/Nature | New rodent is 'living fossil'

Laonastes aenigmamus is the only known representative of the otherwise extinct family Diatomyidae.

slacktivist: Filtered Camels

I'd never heard this "interpretation" of the camel/needle parable -- viz., that the "eye of the needle" referred to an actual gate through which a camel could, just barely, pass. It is, of course, bullshit, but that it persists speaks volumes.

If you're reading this by RSS, you are using the old feed (http://www.sennoma.net/main/index.rdf) -- it should perform exactly as the new feed (http://www.sennoma.net/main/index.xml), and should do so indefinitely, but if I were you I'd update the subscription anyway. The spousal unit worked some unholy juju to make this happen, and you know how unreliable black magic is.

When I started this site, I intended to go for the funny a lot more, and to get much more closely in touch with my inner asshole. Turns out that isn't good for me, and "malice aforethought" doesn't describe me or what I want to do here very well. It wasn't a great choice of name: I am not a malicious person, nor do I want to play one on the internets. So, after due consideration, I've changed the name of my blog. (If you link me, I'd appreciate it if you'd update. Sorry for the inconvenience.)

Most of my posts here concern science or politics, so I was going to call the site "The Art of the Soluble" after Peter Medawar's remark that "If politics is the art of the possible, research is surely the art of the soluble. Both are immensely practical-minded affairs." Unfortunately, Sir Peter used that title for a famous essay, so I consider it taken. (Comparisons are invidious, particularly when I suffer by them.) Thus thwarted, I settled on another horrible pun (an open reading frame is, basically, a stretch of nucleic acid that can be translated into protein), and unless someone is already using it here I will stay.

Other changes: I am no longer anonymous, in English or Esperanto. (I still think my original idea for a website would have been interesting if I'd stuck to it, but I didn't, so.) I am becoming very interested in the role of blogs and other online communications tools in professional scientific research, and it's simply easier to use my "real" name with my colleagues. I also plan to add a links feed from my Furl account (update: I'm using Simpy and Feed2JS now, and posting linklogs every so often instead of a feed so that I can have comments and trackbacks) and update the blogroll and the categories. Let me know if there's anything else you think I should do (comments are back on, muchas gracias to the spousal unit for the various upgrades).

I don't know if it's just me, or if there's a flood of spam across the whole internets, but I can't be arsed to delete two dozen comments a day. (And most of it porn, have you noticed? I have a depressing vision of thousands upon thousands of greasy pimply rejects hunched over in their smelly bedrooms, one ear on the doorway in case Mother comes by and only one hand on the keyboard. *shudder*)

Anyway, no comments until the spousal unit has time to upgrade the MT install for me, which could be a while because she has approximately six million better things to do with her limited free time and I am too damn lazy to do it myself.

The categories are all screwed up, the blogroll needs fixing (many good blogs not included simply because I cannot add them to my Bloglines feeds or I'd never do anything but read online), the bio needs updating (I have a new job, in cancer biology) and I want to add my del.icio.us links as a sidebar feed.

Resolved: must get to all that. Some time in next decade or so.

OK, hiatus over. One of the main reasons for taking a break was that politics was making me nuts, and I wanted to step back and find a way to cope. I didn't have time to cover all the political issues I felt were important, nor even time to do justice to the most urgent of those issues. Being unable to provide comprehensive coverage made me freeze up (again). I still don't have time to cover everything, but no one who wants to be politically well informed is going to rely on me as a news source anyway. For the most part, I'm just going to point to the most pressing issues, or the ones that press my particular hot buttons, and leave it at that. For everything else, see my blogroll. I chose the "primarily political" links with great care, and I really do think that between them they provide more comprehensive coverage than any mainstream news source, and I guarantee that they provide better analysis.

The other thing I'm going to start doing is passing on the various petitions and letters I sign. I'm on a bunch of mailing lists, all of which pretty regularly send me information about current issues and links to web pages where you can take some kind of action -- sign a petition, send a letter, and so on. Without exception, they also ask me to "tell a friend" (or five friends, or everyone I know, or whatever). It's clear that such networking is a powerful tool for political and charitable organizations. I'm not going to sign anyone up for these lists, which is of course what happens when you "just use this handy web form" to send emails -- but I will post the links here. I don't kid myself that I'm doing much by responding to these prompts, but I'm doing something, and that's better than nothing. Right?

(Oh, and I'll bribe the spousal unit to fix that thing with the spurious links too, but don't hold your breath 'cos she's plenty busy.)

I was going to apologise for the lack of updates, but the hell with it -- I don't do this for you. Stupid readers, who needs 'em? (That was a joke! A joke! Wait, come back...)

Anyway, the spousal unit has the basics, to which I'll just add that work is a lousy way to make a living. I am one fucked unit, and not likely to get any less fucked any time soon. If you're reading this, I probably owe you email too -- sorry about that, I'll do my best. It's not that I don't love you any more, I'm just nackered.

See yer in a few weeks then, when I'm in better form.

P.S. the linky weirdness below is a glitch that appeared when I (by which of course I mean the spousal unit) had to delete trackbacks; I was getting so much spam that it took down a server. Bastards. Anyway, fixing a little glitch on my site is not high on our list of priorities right now, so it'll be staying that way for a while.

Just a quick note for anyone sending trackback pings (hi, T, pericat!): they work, but don't show up until I rebuild the site. I have no idea why this should be so, or how to fix it, and no way am I upgrading asking the spousal unit to upgrade me to a later version of MT until the bugs are ironed out, so in the meantime please just bear with me. I get email notification of comments and pings, so I'll rebuild as soon as I see a ping.

Tangentially: Jay did a wonderful thing building MT-Blacklist and setting it free, and I'm appropriately grateful for all the time and hassle it's saved me; similarly, niggly bugs and all, I like MT. I haven't paid a dime for either product, so I can't -- and don't mean to -- complain here. But at the same time, I won't be paying SA for software that I can see in advance is substantially more problematic than the setup I have. I think the company's track record indicates that they will listen to feedback and solve the problems, so I'm just going to sit back and be a late adopter this time.

Something bad seems to have happened to my images, but since I have all the technical chops of Mr Computer I wouldn't hold your breath waiting for it to get fixed. "Wait!" I hear the anguished voices cry, "doesn't your spousal unit make her living from that dire species of satanic voodoo known to decent, CPU-fearing folk as "computer stuff"?" Well, yes, but if I bother her with computer stuff too much, she kicks me in the nuts. It hurts, you know, but I figure I deserved it. Those of you who live with tax accountants or lawyers or doctors or any other useful professional, you'll understand. After all, it's not like the SU set me up this site just so that she could spend her precious minutes of free time hacking code (where I come from, a hacking code is subthig you see a dogtor for, but I just love to use jargon I barely understand) in response to my twittering. But Respectful of Otters is now in Rocket Scientists where it belongs, and I haven't forgotten about the teeny-tiny text in the comments boxes either (hi, P!). There are other things to fix, too: front-page links to my bio and copyrightanything notice, and a bunch of sites I don't read by RSS but to which I do want to offer linky props over there on the sidebar somewhere.

So I'll get to all of these things eventually, but please be patient. My nuts thank you.

That's me, more or less. I took that shot about a week ago; the spousal unit says that if it were all you had to go on, you'd recognise me easily enough. What's left of the hair is mousy brown, the beard is reddish where it's not grey, and the eyes are blue: standard WASP-y hybrid. (Another photo here.) Born Papua New Guinea 1969, moved to Australia 1976; high school here, university here; Hons with this bloke, PhD here on vaccine candidate antigens in this disease with this bloke (photo here, works here), just before he moved to Tulane. First post-doc in HIV replication with David Harrich, to whom I owe an enormous debt and not just for all the science. Met wife online Nov 01, married Aug 02, moved to Portland OR Nov 02. Until June 2005, worked with Caroline Enns on the molecular basis of iron homeostasis in humans, with a particular emphasis on haemochromatosis. Now working with [redacted, see update below]

Anything else you want to know, just ask.

Update 041207: no one asked, but for Google juice and because I never actually meant to be anonymous (I keep the handle because it's how most of my online friends know me): Bill Hooker. Search here for "Hooker CW" to see most of my scientific publications.

Update, 2008: It has been brought rather forcefully to my attention that my employers do not want anyone ever to get the impression that I represent them in any capacity. So if you, dear reader, should happen to find out where I work, please ignore that information and know that the contents of this site are my fault and my fault alone, having nothing whatsoever to do with my current employers.

Have I mentioned how much I love Bloglines? I just sent them this via the contact form:

Dear Bloglines,

I would like to be able to see the public subscriptions of people whose blogs I like. Currently, this requires knowing whether they have a bloglines account and, if so, what name they signed up with. Would it be possible to annotate each blog's entry in the directory with a link to the owner's bloglines account, if they have one?

Also, when the ads start, please please please make the paid service ad-free. I'll happily pay a reasonable fee for bloglines, which I think is the best thing since sliced bread, but not if I can't get rid of ads.

I'll update this post when I get a reply.

One other issue, not under Bloglines' control: too many people have crappy feeds that show only the first few words, or just a headline. When I am trying to keep up with 126 sites, I want to be able to skim, and headlines-only feeds make that difficult. That's what the new "full text feeds please" folder in my bloglines account is for: I'll be quarantining those sites for now, and probably only checking them "by hand" once a week or so.

(The post title? "Full text feeds please" reminded me of Chomsky's famous phrase. Perhaps you had to be there me.)

Update: it's been pointed out to me that there are bandwidth issues with providing full feeds (although I think those are minimal if you only feed text), and, more importantly, that presentation is stripped bare in an RDF format. Full-text feeds are nice, but I am also happy with enough of an excerpt to give me a good sense of the post. I didn't mean to demand that other people's designs should be subordinate to my convenience, so I've changed the folder title to "longer excerpts please", but I've let the post stand to remind me what happens when I post without sufficient thought. (I generally won't delete anything, and I'll always make original versions available.)

Update the second: Bloglines' reply to my email:

We'll be adding a directory of public feeds soon. And we currently are planning on having a no-ads version available when we do start running ads.

As I expected, it's taking me longer than I expected to get the rest of the site (bio, non-blog writing, etc) up, so I thought I should address the issue of copyright. I've just gone back and added links for all the unattributed pictures except the Hubble one (I can't remember which news story I got that from, but it's almost certainly a stock beauty shot from the telescope's home page). So without further ado:

Copyright Notice
Case 1: If I didn't make it, it belongs to someone else and you should respect their rights and wishes. I certainly will: all legitimate requests regarding intellectual property and the content of this website will be speedily obliged. By "legitimate" I mean either "made by the owner of said property" or "reasonable, as determined by me".
Case 2: If I did make it, take anything you want, and do with it as you please. I reserve no rights bar this: if you alter something I made in any way, do not identify me as the author of the altered work. I'd love to hear back about anything you do with something you found here.

Update: as discussed here, I intend that this blog should be part of the public domain. You can take anything you find here (so long as I made it) and do anything with it that you like. I'd love to hear about it, but you're under no obligation whatsoever.