Creativity unleashed

I mentioned in my last school post (the one about set ups), that I’d used a modified version of The Future Is Wild’s animal design activity.

While TFiW is more focused on evolution and decent with modification, my class was currently focusing on a more ecological unit – what roles do different organisms have in an ecosystem, how do they interact and how do we classify them.

Previous lessons had gone through self-made classification schemes, traditional classification schemes (e.g. The Classical Greek), and scientific classification schemes. The two scientific classification schemes were taught in my classes.

Advice to Teachers of Science

From the New South Wales Government.

Excellent!:

In developing the NSW Science curriculum, the Board of Studies undertook extensive consultation with experts in the field to ensure that content, including that relating to evolution, would be consistent with accepted scientific knowledge and understanding.

The Board wishes to remind teachers that Creationism and Intelligent Design are not part of the Board’s Science syllabuses. If taught as part of any school-based program, it must be clear to students that Creationism and Intelligent Design:

1. are not scientific, nor evidence-based
2. will not be included in any task that forms part of the assessment of student achievement for the award of the School Certificate or Higher School Certificate
3. will not be tested in any School Certificate or Higher School Certificate examination and will not be relevant to any response to School Certificate or Higher School Certificate questions.

Effective: Immediately

[Colouring added]

Note: Intelligent Design has not been banned from schools. But teachers must make it clear that they are not scientific or evidence based – and that will be irrelevant to any assessment or examination.

Given the ID crowd’s penchant for mandatory disclaimers, maybe they won’t be upset about this (and then I wake up).

Any comments on this mandate?

No teacher left behind

If your teacher doesn’t know any better, how can we expect you?

How your body works is no longer a mystery. Babies are not tiny miracles. And “Better Living Through Chemistry” does not mean what they think it does…

While not quite so abrupt as that, this press release from the University of Colorado makes a point – increasing scientific literacy is the primary method by which we can protect future generations from becoming victims of pseudoscientific mumbo-jumbo jargon overload. This will not happen without similarily increasing the scientific literacy of teachers in topics such as basic biology, biochemistry and genetics.

Inside the tomato

I can vaguely make out this is meant to be Tomato sapiens, it has a mouth, heart, lungs, gizzards, and I don’t know much of the other kanji, but I think there is at least one kidney.

How ethical is you vegetarianism now, huh!?

Hattip Alan and Danny Choo.

Answer to Danny’s question: In a tomato’s sweet delicious heartbeat.

Armchair biologists

Can armchair biology work?

Armchair science is where science began. Before organised and well funded institutes were about, a lot of scientists were self funded home-based ventures.

Science at home has suffered a few setbacks. They took the fun stuff out of chemistry kits. And even if you do find a decent kit, you might be arrested for making drugs and/or explosives under terrorism laws.

So chemistry as a hobby is expensive, hazardous and possibly illegal.

What about biology?

There is a little discussion at the sci-borg collective about recent news that people are attempting molecular biology (cloning, design-your-own organisms) at home.

Pure Pedantry thinks it won’t end the world. Which is fair to say. But Discovering Biology in a Digital World points out some of the real dangers. Namely, cloning usually involves potential pathogenic organisms and antibiotic resistance – not the best things to be playing around in your kitchen.

While it’s cool that people are enthusiastic about science and wanting to engage in future technologies, it’s good to remember there was a reason further than mere regulation and technophobia over why chemistry kits got dumbed down. Some science stuff isn’t safe to be messing about with at home. Particularly in your kitchen where you prepare your food.

Science that deals with microbes, carcinogens and cold storage really needs a dedicated space. That’s why I like the idea of Community Centers with lab-rooms and storage for hire, along with amateur training courses. This sort of activity should definitely be encouraged.

The best thing about future technology though is that these days biology can be done on a computer over the internet. Bioinformatics at home is a very safe, low labour activity that really only needs a computer and an internet connection.

While I too am skeptical of amatuers making “new vaccines”. I do think some more “simple” breakthroughs are possible -  bio-based tools such as biofuels, indicators and environmental solutions – remember that Canadian kid who developed bacteria that break down plastic bag polymers.

Sex, what is it good for?

(Maybe the single life is getting to me…)

Humans often look at things from a very human point of view. It’s really not that surprising, but it can lead to somewhat linear thinking.

Such as linear concepts regarding evolution. You know that horrendous version where by everything lines up towards a singularity (usually us): from amoebas to fish to lizards to rats to monkeys to us. It sounds like some twisted video game-esque parody really.

Along with opposable thumbs, the development of bonking has been paraded as a major leap forward in evolution. But why then does most life on earth today reproduce by non-sexual means?

The whole myth of sex being all that and then some begins, like many mythconceptions on evolution with high-school. We learn that sex was developed as a way of maximising genetic variation. You get genes from Mummy AND Daddy. This means offspring made from sex are ultimately more likely to be fitter than asexually reproducing species and therefore sex is the best thing before and after, and possibly during, sliced bread.

BOLLOCKS!

Sex is not a mechanism for maxmising fitness through evolution – particularly in a sense of strength, toughness and all-round better-er-ness. Sex is the slippery path to a shallow and superficial future. All sex really cares about good looks. When selective pressure rises, keeping up appearances is all that counts†. Even in yeast.

In order to pass genes onto the next generation, an asexual organism must prove its worth by surviving in its environment long enough to gather the resources necessary to create its own offspring: all… by… itself. That takes guts*, people. That’s why some of the biggest hard-asses around are asexual – Anthrax, Thermus aquaticus, and black tip sharks. They have to fight for their right to … well not party…

When you introduce sex, evolution changes from this romper stomper red in tooth and claw deathmatch to a Miss Universe pagent. Previous gen-pool lifeguard Gunn. Sgt. Hartmann has been replaced by Paris “That’s Hot” Hilton.

All a sexual reproducing species has to do is be suave enough to get someone up the duff**. After that you can run away and die. Everything after the “act” is generally no consequence. Incidentally, that’s why elephants starve to death in old age (which we’ve already covered).

I’m envisaging some sort of bizarre reverse frog-prince scenario on the horizon. Although when I look at some old people, I wonder if perhaps we are already there?

A whale is a terrible thing to waste

Oh I so want to move back to Brisbane.

The Queensland Museum has gotten first dibs on the body of a juvenile Blue Whale that died after beaching itself near Townsville.

They plan to cut away its soft tissue (a mammoth task that will take 2 days) and then display the skeleton. It would be the first complete skeleton of a blue whale in a museum anywhere in the world.

The soft tissue and other samples won’t go to waste either (I hope). They will be used in further research, first on the agenda, identifying the subspecies of this specimen.

Get to know your inner stormtrooper

via DBiDW

Oh, how far cellular animations have come.

This video illustrating the cellular mechanics behind some Nobel-worthy Australian research that laid the foundation for modern immunology is just amazing.

It avoids all the silly cliches behind and just amazes you with crystal clear realistic microscopically detailed models.

No crappy cheesy soundtrack. No silly metaphors with “machines”, “tools” or anthropomorphic representations of cells as police officers. No simple to understand but very non-representative line drawings.

The language is great (only had a quibble about “hairs” for the expressed antigens, but its a fair metaphor).

And the best thing is that the whole process is illustrated as a relatively undirected process. Things just fall into place causing reactions. No “choices” are made by cellular “brains”. The antigen locks into place at a receptor, which activates a specific cell.

It even shows how the cellular membrane is a wobbly dynamic fluid, filled with mobile receptors just drifting through.

We want more of these. More. More. MORE!!

At least its not leeches

Adverse immune reactions are a serious issue in modern medicine. Not just for transplants, but for ultra-modern molecular therapies – such as enzyme replacement therapy, or genetic therapy – making sure your body does not decide to destroy that expensive medicine can be an issue. Sometime this means giving patients immunosuppressants, drugs that turn off the immune system. This is obviously risky, leaving such patients open to infection and cancer development.

Parasites and other wee beasties have evolved very complex mechanisms to evade our immune systems. So looking at them for clues on how to develop better drug delivery systems is a good idea. Some researchers are looking at promising chemical produced by schistosome eggs that may benefit gene therapy. Schistosomes cause schistosomosis which ranks no. 2, behind malaria, as the parasite-caused disease with most global impact.

This molecule goes into the cells nucleus and binds to DNA, making sure the therapeutic genes get to where they are meant to rather than just floating around in your bloodstream. This may prove less risky than using viral vectors.

Filler Salmonella

Next two days will be spent in-transit.

Flying to Brisbane tomorrows. Driving to Sydney next day. Sleeping in any time in between.

Still don’t have longterm accomodation arranged yet, so I think I should be spending available net time looking at realestate websites*.

In the meantime, enjoy this marvellously educational brickfilm.

*Anyone aware of single bed apartments or share rooms available in North/North Eastern Sydney don’t hesitate to drop a line

It’s just an awesome video

Turns out my wireless key internet connection works brilliantly at home in Yeppoon, I hardly notice the speed difference (except maybe when watching youtube).

I’m back for a few weeks while I transition between jobs (yes, I have another new job, details forthcoming).

I’m about to kick back with my homies and follow this diagram for the next couple of days.

So I’m just going to leave you with this mind-blowing video (picked up months ago from Pharyngula) which succinctly explains a great abiogenetic explanation for life without referring to lightning or meteorites.

Next Gaming in Evolution – part 2

First two parter on It’s Alive!!

For some background on our topic: Science in the new Spore Computer game visit: Spore Official Site, Carl Zimmer: Gaming Evolves, Joan Bushwell’s Chimpanzee Refuge and/or the first part of this post.

I’m going to be rather brash and provide some constructive criticism on a game that I haven’t played yet, and isn’t even released in Australia yet…

The user-driven nature of Spore is going to be very hard to remove in a gaming market. A game isn’t a game if a user isn’t able to meddle with it. Even Sim-Earth, which allowed you to tweak planetary climate conditions, still allows some lee-way towards IDiots. Hell, IDiots even use computer evolution simulations by proper evolutionary biologists as *proof* of ID. So I’m not going to suggest too many improvements on that aspect, aside from perhaps a version that allows attributes to be generated in a more random fashion than spending points in a shop. I don’t think this would float in the market though, modern gamers are very much used to be able to get what they want.

To combat the games “one dimensional march”, perhaps mods or sequels that introduce “end-game” style content for the pre-intelligence mini-games in the greater Spore game.

For the beast-stage game, the user could try and make their creature survive in wake of another creature holotype achieving sentience. I think this could have a capacity to have some environmental messages in there. The user would be charged in ensuring their species does not go extinct. This could be achieved in several ways:

• the high road – adaptation – adjusting to threats such as hunting (build up defense like – venoms, quills, mimicry of predators), habitat destruction (adapt to extreme habitats or adjust to city life), and pollution (avoid eating plastic bags, drinking polluted streams) – standard time-based victory
• the middle road – domestication – either by becoming tasty, cute or just generally useful enough that the sentients will actively try not to wipe you out. Be careful though, the balance between being domesticated and being hunted to extinction may be very tricky to reach. Case study: The Aurochs.
• the low road – nature fighting back – why let yourself be hunted to death, having sentience doesn’t necessarily mean they have to be top of the food chain – I think this would prove a popular victory path – standard winning by ensuring the other guys (in this case the human equivalents) are wiped out

For the tadpole-stage game. I was intrigued by the NYTimes comment amount the small sea-critter being eaten by leviathans out in the depths, forcing it to go onto land. Why not allow your creature to become the leviathan. Again conservation could be brought in by drawing from the fate of whales, sharks and other ocean dwellers.

The ocean depths being analogous to space in terms of a Final Frontier would really open up opportunities for some very exotic environment and alternative creature animations.

Further discussion below the fold…

Next Gaming in Evolution – part 1

hattip Joan Bushwell and her chimpanzee minions

I really can’t remember the last time I was actually excited about the release of a video game*. The countdown until some vague release date in September is still ticking away in my soul. Hopefully my new new job will assist me affording a new Intel-based Mac on which to play it (my iBook is only PowerPC ).

Carl Zimmer’s NYTimes article “Gaming Evolves” takes a closer look at the science background story on Maxis’ latest creation: SPORE.

What I feel is going to be the opinion of most scientists is best captured here:

Even as scientists praise Spore, they voice concerns about how the game does not match evolution. In the real world, new traits evolve as mutations arise and spread gradually through entire populations. Winning Spore’s DNA points does not work even as a remote metaphor.

“I do hope that it doesn’t confuse people as to what evolution is all about,” said Charles Ofria, a computer scientist at Michigan State University and a creator of Avida.

Spore may also mislead players with the way it is set up as a one-dimensional march of progress from single-cell life to intelligence. Evolution is more like a tree than a line, with species branching in millions of directions. Sometimes species become more complex, and sometimes they become less so. And sometimes they do not change at all. “There’s no progressive arrow that dominates nature,” Dr. Prum said.

These caveats notwithstanding, Dr. Near hopes that Spore prompts people to think about the evolutionary process. “This may be totally off about how evolution works, but I’d much rather be dealing with a student who says, ‘O.K., I have no problem with evolution; I think about it the same way I think about gravity.’ If it does that, it’ll be great.”

The game is an excellent well informed thought experiment. Will Wright has done his homework to bring enough science to make Spore work, but ultimately sacrifices some reality to still make it a user-driven game. This user-drivenness is also just enough to allow some IDiots to take it under their big-tent philosphy into the division of deity-driven evolution. I still think Spore has done quite a lot better than any other “evolution” game I have seen before.

Hopefully further iterations of Spore, or possibly built-up mods will be able to emphasise a bit more on the science and free-reign aspects of Spore. It’s a bit hard to criticise a game that has yet to be released, but in my next post I’ve got some suggestions I’ve come up for improving modifying the Spore Sim-Life style game to allow more scientific playfulness.

*maybe a little about Warlords IV, which was more notsalgia/patriotism that turned into general letdown as usual

Tangled Bank #113: A Labor Day Carol

It’s Alive!! has been featured on Tangled Bank #113.

Thanks to Dana Hunter of En Tequila Es Verdad and He Who Shall Not Be Named for accepting my nomination.

Even though all the glory should be going to A Free Man.

Human parasite’s goody two shoes cousin helps coral

Malaria is one of the most important infectious diseases under study today. It has been with us since early medical history, and still persists as a major global threat.

The disease is caused by a parasite – a multicellular microorganism. Not just a simple bacteria, the malaria plasmodium is a complex critter that still remains quite mysterious. It is very hard to work with in the laboratory: it doesn’t culture well and the risks involved are immense.

The discovery of a non-infectious relative (albeit, rather distant) by Australian researchers is exciting news for many.

Paydirt hasn’t quite been hit as far as medical research. However the fun isn’t just for medicos, but the evolutionary biologists as well.

Chromera velia is clearly related to Plasmodium parasites, but rather than being a blood-borne obligate parasite of mammals and insects that rarely sees light of day, it is a plankton-like photosynthesising obligate symbiont of corals.

These long-lost cousins are so very different, it could almost make the ghost script of the next Wil Farrell comedy (or not, besides its been done before).

Can they really be from the same origin?

The evidence is convincing.

For more information, take a read of a great interview (it says so in the title) with the scientists responsible for the discovery, as well as the University of Sydney press release.

Image: Copyright University of Sydney. Use only for non-commercial and educational purposes with attribution.