I know it must seem like I get a real kick out of spot­ting other’s taxo­nomic mis­takes and point­ing them out here, but really I’d be a much hap­pier man if it wasn’t neces­sary. All it would take would be for journ­al­ists to double check their terms before going to press, or to make sure they got their pieces proof read by someone famil­iar with the sub­ject. It’s the BBC’s turn again this time, and in the midst of what is, oth­er­wise, an excel­lent piece about recent pion­eer­ing work on determ­in­ing the col­our of dino­saur feath­ers, by using an elec­tron micro­scope to exam­ine the shape and struc­ture of fos­sil­ised melano­somes. There’s noth­ing at all wrong with most of the art­icle. In fact, go and read it now; I’ll wait.

See? It’s all very inter­est­ing; well researched, and well writ­ten, and it avoids the two most grat­ing errors sci­ence pieces in the main­stream media usu­ally make; mak­ing it sound like this has over­turned everything we’ve pre­vi­ously thought about the sub­ject, and giv­ing ‘equal time’ to some wacko who dis­agrees with the research. So, yes, it’s a great piece. With one small error:

A rel­at­ively benign mis­take to make while sat at a desk in a nice com­fort­able office, but there are scen­arios where you might want to be a little more care­ful in check­ing your definitions…

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So, Fire­fox 3.6 is finally here, and on aver­age it’s 20% faster than 3.5. It’s actu­ally a really notice­able improve­ment for both ren­der­ing and scrolling around pages; I’d say it’s more or less on a par with Safari on most pages. I hear from Win­dows using friends that it’s sim­il­arly quicker on that plat­form too, approach­ing the speed of Chrome, in places. All of which makes this a little odd.

I noticed, not long after the upgrade that my blog (this page, unless you’re read­ing a syn­dic­ated copy,) was scrolling really, really slowly in Fire­fox, which it had never done before I upgraded. I checked it in Safari to reas­sure myself that it wasn’t some­thing wrong with the site, and everything was fine; scrolling was smooth and respons­ive just like it has always been. I checked Fire­fox 3.5 on my mac­book; same thing. I dis­abled all my fire­fox addons and tried again on the desktop: still pain­fully slow. So I re-​​enabled some of them and star­ted mess­ing around with fire­bug, dis­abling vari­ous style ele­ments to see if I could fig­ure out where the slow­down was com­ing from.

It didn’t take me long to find the cul­prit: shad­ows. I try to avoid using images in my pages as much as pos­sible to improve page load speed, so I use box-​​shadows to give a bit of depth to the wid­get box-​​outs; they look even more flat and drab without them. I also find that a subtle text-​​shadow is a great way to increase text con­trast without mak­ing the page harder on the eyes, which is a big deal for any light-​​on-​​dark dis­play (at least until someone intro­duces a decent super-​​light web­safe font,) so I make heavy use of that too. None of this has ever had any notice­able per­form­ance impact before, but here we are; with the new, optim­ised, gecko engine it renders like arse.

I thought per­haps there was some­thing else about my CSS that was con­fus­ing the ren­der­ing engine — it’s hardly the most min­imal or eleg­ant set of style defin­i­tions in the world — so I knocked together this abuse of text-​​shadow to prove that it’s the prob­lem. As expec­ted, it renders fine in Safari and older Fire­foxes, but incred­ibly slowly in Fire­fox 3.6, so it’s def­in­itely some­thing to do with the new browser.

Next check was to see if it affects FF3.6 on other plat­forms, so I fired up my Win­tendo, upgraded Fire­fox and tried the page. No slow­down. I don’t know how rep­res­ent­at­ive that is though; that box is a quad-​​core 3GHz Nehalem with 6GB of RAM and a GTX295 in it; it’s got about twice the graph­ics oomph of my Mac (which is a 3GHz Core2 Duo with an 8800GS), and I don’t have a slower win­dows box to test on. So this is a bit incon­clus­ive; I can’t really det­mine whether the issue is con­fined to the Mac ver­sion of Fire­fox, or to Fire­fox on machines that can’t run Crysis at 60fps. But, hon­estly, I don’t think it matters.

Long story short; my site renders really slowly on the latest, greatest ver­sion of Fire­fox, which is an issue. I make no bones about the fact that I don’t give a monkey’s how it renders in IE, but I do like to make sure it gives a good exper­i­ence in decent browsers, which by my defin­i­tion means any­thing web­kit or gecko based. Fire­fox is by far the most pop­u­lar browser in that cat­egory, so I can’t just ignore this. The ques­tion is what to do?

I can sit around and hope that 3.61 fixes the prob­lem, but that is basic­ally just ignor­ing it, tak­ing no respons­ib­il­ity, and means that my site sucks until someone else fixes their browser, which might never happen.

Or I can reskin the whole site such that it looks OK (or at least as OK as it looks now) without rely­ing on shad­ows. The prob­lem is, I’m not a web designer, so that’ll take me ages, and I only just got the place look­ing how I want with this design. It’ll also, inev­it­ably, mean mov­ing back towards the bad old way of doing things, using back­ground PNGs to try to give the site any sense depth or char­ac­ter, and I really don’t want to do that; I want to be able to use stylesheets to define the style of my page, not rely on image-​​based work­arounds. Admit­ting that I need those work­arounds feels like giv­ing up. Maybe the state of browser tech­no­logy just isn’t up to that out­look yet.

Basic­ally, I see no entirely sat­is­fact­ory way out of this situ­ation; I’m just going to have to decide which solu­tion is the least unsat­is­fact­ory. I’m going to have to give it some thought.

Looks like a bunch of homeo­pathy sup­port­ers have got sick of not being taken ser­i­ously on the inter­net, and decided that the best way to gain the respect of the wider com­munity is to spam wiki­pe­dia until the ser­vice is over­loaded. I’m not sure whether the intent is just a DoS, or if they think people will just get so tired of revert­ing their edits that they just roll over and let them have their say. Either way, it’s a stu­pid plan; the abso­lute most they’ll achieve is that the pages they tar­get will be locked until they them­selves get bored and go away.

In any case, I won­der if the irony of the whole idea is lost on them? Surely the homeo­pathic way to do this would be to have one per­son say, very very quietly, what they want on the page, while in the same room as someone who knows someone who knows someone who knows someone who knows someone who is a Wiki­pe­dia user.

Hat tip to @xtaldave for the link.

Oh, oh, oh! This is an excit­ing one! Earlier this year, when the dis­cov­ery that Komodo Dragons (Varanus komod­oen­sis) are venom­ous was pub­lished, I idly wondered if any dino­saurs were as well. Komodo Dragons and dino­saurs are not closely related, so there was no reason to make that leap, bey­ond the fact that they are (or, in the case of dino­saurs, were) both large ter­restrial rep­tiles, and that I want it to be true.

Well, it turns out I might yet be onto a win­ner with that one. A recent pub­lic­a­tion by Enpu Gong of the Chinese Academy of Sci­ences doc­u­ments fossil evid­ence that Sinor­ni­tho­saurus, a small Creta­ceous thero­pod from what is now China, pos­sessed a venom­ous bite. The venom gland itself, being soft tis­sue, has not been pre­served¹, but the skull con­tains a cav­ity that Gong believes could have con­tained one. More con­vin­cingly, the animal had long, grooved upper teeth, like those used by extant rear-​​fanged snakes to inject venom into prey, with voids above them, which could have func­tioned as local reservoirs.

Not everybody’s con­vinced, and I’d cat­egor­ise the evid­ence as ‘strongly sug­gest­ive’ rather than a slam-​​dunk, but it’s fas­cin­at­ing stuff and lends a big pile of cred­ib­il­ity to an idea that I really want to be true.

Check out Ed Young’s longer and bet­ter cov­er­age, over at Not Exactly Rocket Sci­ence.

1. Which is not to say that soft tis­sue can never leave fossil evid­ence, in fact Sinor­ni­tho­saurus is also fam­ous for being one of the first dino­saurs to be dis­covered with fos­sil­ised feather-​​impressions, merely that it is sig­ni­fic­antly rarer. [↩]

A couple of years ago I wrote about the extinc­tion of the Baiji — or Yangtze River Dol­phin — and now, as the BBC reports, it looks like another large inhab­it­ant of the Yangtze is on the verge of fol­low­ing it, if it hasn’t already done so.

One of only two extant spe­cies of Pad­dle­fish, the Chinese Pad­dle­fish (Pseph­urus gla­dius,) which, with repor­ted sizes up to 7m long, may also be the world’s largest fresh­wa­ter fish¹ has not been detec­ted at all on a recent sur­vey. The team do admit that it’s quite pos­sible for isol­ated indi­vidu­als to have escaped detec­tion due to the sheer size of the area sur­veyed, but point out that the envir­on­ment can no longer sup­port a viable breed­ing pop­u­la­tion, and that unless some spe­ci­mens can be caught in time to begin a cap­tive con­ser­va­tion pro­gramme the spe­cies is doomed.

It’s depress­ing to be writ­ing about the extinc­tion of another large, eco­lo­gic­ally import­ant spe­cies so soon after the Baiji — doubly so since it was nat­ive to the same river sys­tem — and it’s no com­fort at all to know that there will have been plenty of other, less-​​visible (but no less tra­gic) extinc­tions in the same period, or that this is unlikely to be the last.

1. it is cur­rently not clear — and now may never be — whether the animal spends it’s entire life in fresh water [↩]

Hat tip to John Lynch over at A Simple Prop for the link.

Also, if The End of the Line didn’t con­vince you, John has dis­covered another reason not to des­troy the world’s fish pop­u­la­tion: if there are no fish to eat, the Otters will have to find some­thing else to eat: Human Flesh!

Don’t look so cha­r­is­mic now, do they?

It won’t come as news to many of you that I’m no fan of Microsoft — their long his­tory of sub-​​standard soft­ware com­bined with eco­nomic dom­in­a­tion and anti­com­pet­it­ive beha­viour just doesn’t do it for me — but even I can’t bring myself to see this pat­ent rul­ing as a good thing. Funny per­haps, and cer­tainly karm­icly appeal­ing, but ulti­mately it does no-​​one but i4i any good whatsoever.

Soft­ware pat­ents do noth­ing but limit com­pan­ies’ abil­ity to innov­ate and develop qual­ity soft­ware, and this an ideal example of that. Microsoft Word is one of the few genu­inely good products MS has ever pro­duced, and their move to an XML file format in office 2007 was both a huge improve­ment in file size and pro­cessing speed, and an import­ant step towards open-​​formats and inter­op­er­ab­il­ity from a com­pany that had his­tor­ic­ally seen those things as an ana­thema. Obvi­ously, it’s not per­fect, and there were already open XML formats they could have adop­ted rather than rolling their own, but it’s a step in the right dir­ec­tion and it bene­fits every user of MS Word. We should not be dis­cour­aging Microsoft from mak­ing these kinds of change, yet that’s exactly what the recent East-​​Texas court rul­ing ban­ning the sale of Word due to pat­ent infringe­ment does — and in the strongest pos­sible way.

But it’s worse than that; not only does this dis­cour­age fur­ther good beha­viour on the part of MS, but it dir­ectly impacts thou­sands of com­pan­ies all over the world; Word is crit­ical to the func­tion­ing of a huge num­ber of busi­nesses, and not being able to buy new licenses, even for a short while, could be a ser­i­ous prob­lem for some of them. If they’re left with less licenses than they have employ­ees, then some of those employ­ees might not be able to work, or have to do so on illegal soft­ware. In this fin­an­cial cli­mate, no com­pany wants to have to make that choice. It’s true that there are altern­at­ives (even free ones,) but any­one who thinks that’s a solu­tion has never had much con­tact with cor­por­ate IT departments.

The whole situ­ation seems like utter non­sense to me. Microsoft fol­lowed a totally obvi­ous course of action, which benefited pretty much every­one, when it switched its file formats to XML, and yet because some other com­pany had the idea first, they’re fined $277,000,000.00 in “damages” — someone will have to explain to me how Microsoft improv­ing their office suite cost i4i $240 mil­lion — and the rest of us are pre­ven­ted from buy­ing the soft­ware we want to use.

In case any­one needed fur­ther proof that soft­ware pat­ents (and pat­ents in gen­eral) do more to harm to innov­a­tion and com­pet­i­tion than they do to pro­tect invent­ors, I think this is a prime example.

Yes, you read that right; in the second new liz­ardly dis­cov­ery I’ve read about this week — this time at the excel­lent Not Exactly Rocket Sci­ence — it turns out that not only are Komodo Dragons (Varanus komod­oen­sis) 3m long car­ni­vor­ous liz­ards with razor-​​sharp, ser­rated teeth that can run at 20km/​h, but they’re also venom­ous. You know, in case all that other stuff wasn’t enough to give you nightmares.

It was thought for dec­ades that Komodo Dragons relied on the vir­u­lent cock­tail of bac­teria present in their mouths to infect and weaken prey when they bit them, so that they could hunt them down over a few days and fin­ish the job. It turns out that, while their mouths cer­tainly are ran­cid, they have an even nas­tier weapon in their arsenal.

Brian Fry of the Uni­ver­sity of Mel­bourne, tipped-​​off by the dis­cov­ery in 2005 that a close rel­at­ive of the Dragon (Varanus varius, the Lace Mon­itor) has venom glands, took an MRI of the head of a Komodo Dragon and demon­strated con­clus­ively that it too is venom­ous. The venom in ques­tion is com­plex, but seems mainly tailored to increase blood loss from the gap­ing wounds left my the Dragon’s razor-​​like teeth and char­ac­ter­istic ‘backward-​​jerk’ bit­ing motion, caus­ing massive blood loss in the vic­tim, weak­en­ing them and often lead­ing quickly to shock, and then to death. It’s worth not­ing that even where the blood-​​loss is not suf­fi­cient to kill the vic­tim, going into shock within sight of a hungry 3m car­ni­vore prob­ably will be.

Komodo Dragons being the largest extant rep­tiles, and me being me, the first thing I thought of when I read about this was the pos­sib­il­ity that some dino­saurs may also have evolved a venom­ous bite, and I was pleased to see that I’m not alone; there a dis­cus­sion of the sub­ject in the com­ments at Not Exactly Rocket Sci­ence. Unfor­tu­nately, they agree with me: the idea is a bit of a stretch (OK, a lot of one,) since Komodo Dragons aren’t closely related to dino­saurs, and there are no known venom­ous examples of the closest extant rel­at­ives of dino­saurs: the birds. What this does show, how­ever, is that it’s quite pos­sible for rep­tiles — even large ones — to be venom­ous without provid­ing any skeletal or dental evid­ence of the fact. So our con­clu­sion has to be that some dino­saurs may have been venom­ous, but that we have no good reason to believe that they were.

The sand­fish (Scin­cus scin­cus) is a spe­cies of desert skink that has a nifty trick for evad­ing pred­at­ors (or just the hot sun): it sub­merges itself in the sand and lit­er­ally swims though it — thus the name.

The spe­cies has always been known to be an excep­tional bur­rower, but recent exper­i­ments util­ising x-​​ray imagery have shown that it doesn’t dig using it’s limbs as one might expect, but holds them fast against its body while using grace­ful side-​​to-​​side undu­la­tions to push itself for­ward, much like a snake swim­ming in water. Check out the video the research­ers have pos­ted online; it’s really quite impressive.

The thing I really love about dis­cov­er­ies like this is that it really high­lights just how diverse and incred­ible life on Earth is. It doesn’t mat­ter how out­land­ish some­thing sounds; if its a viable way of get­ting around, find­ing food, catch­ing food, or eat­ing food, then some­thing, some­where is almost cer­tain to be doing it.

Also, the BBC has an extremely cute image of one sur­fa­cing.

Tonight I upgraded the Word­press install on the site to ver­sion 2.8, res­ul­ted in about half-an-hour’s down­time while I untangled some merge con­flicts the svn update to 2.8 com­bined with a move to the new Word­press core svn server cre­ated. Inter­est­ingly the pro­cess went fine on my test server, but not on live; I’ll have to look into that. Any­way, apo­lo­gies for any incon­veni­ence the down­time may have caused you.

The 2.8 upgrade itself is almost entirely back-​​end, admin stuff, and shouldn’t have any impact on the vis­ible site at all.

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