Posts Tagged science

Mocking Richard Gunther

Okay, so normally I approach the slightly more difficult denialist arguments and try to give them the benefit of the doubt, so as to constructively critique them and address the fundamental misconceptions that resulted in them, as well as to comment on actual concerns in science communication and on some of the more unintuitive and interesting results of the theory of evolution. [deep breath] But

… sometimes I read something that breaks the stupid barrier so hard the air-molecules in front of it fuse with it and cause a multi-megaton explosion, and I just have to laugh at it, and share it with friends so they can laugh at it, and broadcast it via gravitic waves from a repurposed orbital EMP cannon to finely control the vibrations of every smooth surface on the planet so every sentient being on earth including the reptiles that live thousands of kilometres under the earth can laugh hysterically at it. This is the sort of stupid to which the only real responce is snark: snark so dense that it collapses into a snarkularity and causes the snarkpocalypse, which I’m proposing as an ending for a Darker And Edgier cover of Dr Seuss’s The Cat In The Hat. So here’s an article from Richard Gunther of Living Waters Ministry, Ray Comforts official cartoonist and easily one of the dumbest creationists I’m aware of. Seriously, this guy puts Comfort, Hovind and Ham to shame. He’s in a whole league of his own.

Fair warning, the following makes no attempt at being constructive, persuasive, unbiased or even fair. It is written solely as an exercise in sadistic mockery of the eminantly mockable. And I am going to thoroughly enjoy writing it.

I will, however, refrain from commenting on the HTML layout of his site. Some targets are just too easy.

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A while ago I drew a cartoon as a joke, with the picture of hairy primate and the words to the effect: “If we come from apes, and if apes were “fitter”, then how come there are still apes?”

That would be this cartoon:

Richard Gunther is a professional cartoonist.


(Attribution: Richard Gunther, Living Waters Ministry)

Have you ever wondered what you’d get if you gene spliced an orang-utan, a horse, and a goldfish? Well now you know.

And in answer to the question, an analogous question: “If Australians are descended from Europeans, why are there still Americans?” (The answer, of course, is “Because We Find Them Amusing”)

It was a rather confusing question, unless you followed the assumption followed by Darwin, that the “fittest” would survive – as opposed to the “unfittest” which would become extinct.

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Firstly, Mr Gunther, Thomas Huxley came up with “Survival of the Fittest”. Darwin wasn’t too keen on the term, and would probably have used twenty times as many words anyway.

Secondly, SotF is a 150 year old oversimplification. Everyone else moved on, why didn’t creationists?

Thirdly, Microsoft Word says “unfittest” isn’t a word.

This joke was drawn and written for its humour, not its accuracy, because of course it is downright silly to argue this way.

Alright, fair enough. I suppose it was pretty funny, in a “laugh at the mentally disabled creationist” sort of way… wait, no, that’s not funny at all. But then again, since when are cartoonists expected to have a sense of humour anyway?

Just because one thing came from another does not mean the originator must be gone – just because humans are “fitter” than apes does not mean that apes ought to be extinct. A simple illustration of this is found in dog, or cat, or rabbit, or hen, or pigeon, or horse breeding. The original stock is still with us, while the offspring, hybridised and modified through careful breeding, is also with us. There are also many examples of very “unfit” plants and animals, such as the panda which lives almosty exclusively on bamboo, or the koala which likes mainly eucalyptus. Most unfit” yet they survive.

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There’s a pretty big difference between “specialised” and “unfit”. I’d like to see you survive solely on Eucalyptus, Richard! (Actually, I really would, that would be awesome)

The only reason panda’s and koala’s are ‘unfit’ these days is because we’re destroying their natural habitat faster then they, as extremely specialised animals, can adapt.

Unfortunately, when this cartoon about the humans and apes was posted on a website, it drew a great deal of flak, as several people took it as a serious comment. On the one hand I am pleased to see that there are some intelligent people ‘out there’ in etherland, who know some facts about breeding,

“Breeding”? I assume he meant to say something like “ancestry” or “population dynamics” (or, azathoth forbid, “evolution”), but… “breeding”? Now I’ve got a mental image of Zombie!Gunther staggering about moaning “breeeeeedddinnnnggg”…

(I suppose it makes sense: he certainly has no desire for brainz)

and I must admit I was slightly flattered that anyone would even notice my little cartoon, but on the other hand I was disappointed that the humour in the work was not taken as just that. Humour, satire, irony and other forms of amusement are not supposed to be taken as seriously as, for example, a scientific statement, or a statistical comment.

“If the world is really made entirely from cheese like creationists believe, then what type of cheese is it?”
“Ummm… creationists don’t actually believe the…”
“CAN’T YOU TAKE A JOKE?!”

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It reminded me of a joke I read, where a little kid asked his Dad “If God made us, and we are apes, then God must be an ape too!” Very logical, and based on the original premise being true, quite consistent, but funny, because the whole question is based on a silly premise.

Alright, so if we assume Gunther is claiming this joke is analogous to his, then the “silly premise” in question is… what? A rediculous caricature of the theory of evolution?

Something doesn’t add up here. Why would a creationist make a parody of a strawman caricature of evolution? I could understand a evolutionist making that parody to mock creationists, and I can understand a creationist making a parody of evolution itself, but in this case we’ve got a creationist parodying a creationist strawman?

Or maybe Richard is just backpedalling because he realises his original cartoon was somewhere between neurodeficient-tapeworm and concussed-housefly on the IQometer.

So taking up this view that it is a good thing to be logical, and consistent with an original premise, let us see where the Darwinian view leads, if we follow it through: Darwin saw Mankind as the product of millions of years of slow development, an increasing trend, from lower to higher levels of intelligence and complexity – a development which he claimed was a normal part of living things.

Well, leaving out the ‘lower to higher’ aspect, which is just silly, (increased complexity and intelligence are merely byproducts of our improved ability to survive), yes. Evolution progresses slowly, over millions of years.

Apply a logical progression to this: If this premise is true we should see:

A continuing improvement in average human phisique, health and resistance to biological opposition over time,
A continuing increase in average human intelligence, and technology,

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Okay, see, the one part I left out, because it was silly? That’s the part you’re focusing on, Richard. Also, you seem to have forgotten the ‘millions of years’ part.

Also, when did human technology start reproducing biologically? You’ve been holding out on me, technologically industry! I want my biotech!

We do not see any of these things. The trend is the other way. Darwin’s theory of evolution upward doesn’t fit the real, observed world.

False Attribution: “Darwins theory of evolution upward” actually refers “Richard Gunthers utterly moronic caricature which he thinks is an accurate description of evolution.”

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Health? Humans are increasingly beset by new diseases (small pox, malaria, cholera, ‘black death’. etc)

,
Black Death? The black death is a new disease? BWAHAHAHAHAHAHAHA!!!

The other “new diseases” there would still be lol worthy even without the black death, but… oh my goodness, that’s hilariously idiotic.

I’m subtracting a Headdesk just for that.

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How[sic] Intellect? Increasingly discoveries of ancient civilizations are revealing that those people were actually brighter they we are in many ways (i.e. huge monuments made of incredibly heavy stones, the antikathera, astronomical knowledge, metal-work, more complex languages, etc.

Yep. The people who built great big lumps of triangular rock to bury their dead leaders in were totes smarter than the engineers and experimental physicists who built a perfectly circular tunnel of vaccum under france and italy and just used it to discover the Higgs Bosun. And the zodiac is waaaaay more advanced than hubble. And metal work? I’ll bet the engineers who just landed a rover the size of a mini on another planet with a parachute/hovering VTOL skycrane combo would never have thought of heating up iron.
Any more insights, Professor Gunther?

No, seriously, is he seriously arguing that our intellectual level has followed a downward trend since the bronze age using examples from technology to prove his point? I would understand it if he was using writing and philosophy: that would at least make a certain level of sense, albeit sense not backed up by evidence. But technology?

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Are humans improving ‘morally’? Not at all – we have had more than 5000 years of continuous war, raging at least somewhere on the planet, including the more recent two world wars, a holocaust, and many examples of genocide – some going on right now. Peace on earth? Right now there are millions of people living under oppressive military regimes, or dying of sickness, hunger and/or are in the grip of poverty.

Yeah, and a large percentage of the world population now believes that war, slavery, racism and discrimination is wrong and lives in peaceful democratic countries, where our opinions, beliefs and freedoms are protected and we are all (theoretically) given equal ability to influence how our countries are governed. WE’RE WORSE THAN WE’VE EVER BEEN.

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So this is the opposite to the path set by Darwin’s theory? According to him, evolution for humans is all up and up,

Also according to Darwin according to Gunther: the moon is an eyeball of yog sothoth’s pet unicorn, humans are secretly being controlled by the koala-bear hivemind (but it’s okay because they only want hugs), and germs are actually the tears of fairies who have lost their wings.

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but the reality is down and down. Humans are not smarter, healthier, better. They are either much the same or much worse. Darwin was dreaming.

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All I can think of right now is that quote from The Castle: “Tell ‘im he’s dreamin’!” It’s possible I may have just given myself a concussion.

But there is one last thing to note: one huge and obvious difference between that ape I drew and the average modern human is that apes don’t have an inherited sinful nature.

Bonobo’s have sex for pleasure and chimps eat each other.

If humans really did come from primates, they too would be sinful, but they are not. They have no moral awareness at all.

Several species of apes grieve for lost loved ones, and are capable of altruism.

That makes humans more likely to be special creations, by a moral God, than merely animals – something Darwin apparently refused to notice.

Yep, because Darwin was absolutely incurious about the natural world and didn’t spend decades of his life studying every detail he could find prior to publishing his theory. No, instead he “refused to notice” basic creofacts and wrote On The Origins Of Species after a drunken night on the town, during which he proposed to a 200lb dock-worker and accidentally set fire to his beard. Twice.

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Although, credit where credit is due, it can’t be easy for Richard Gunther to transmit these essays to us across the 5th dimension from the parallel universe he apparently inhabits.

“Pro-tip: never try to hug a koala. Seriously. Furry bastards have claws and a temper.”

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Species 0.4.1

… is Released!

Heeeellllooo…

Download the game here: Species ALRE Official Website

From the Development Thread:

Developments

Gene Splicing
Radiation Gun
Highlight Colour Filters (basic implementation)
Ultra Time Acceleration (deactives rendering, runs at the maximum speed the computer can handle)
Q/E to make the camera Rise/Fall. (It’s like maaagic)
Head animation and movement. (To make them look like they’re actually thinking. Makes them seem a lot less brain-dead)
Eye animation and movement. (as above)
Animated Cloud Plane.
Tree’s waving in the breeze. (These two should make the Time Accelleration actually feel like Time Accelleration, as opposed to simply putting all the creatures on meth)
Better Looking Corpse/Meat Models (Steaks! Delicious bloody raw steaks! How can they resist evolving into carnivores now?)
Fake Shadows
Basic Ambient Noises (placeholder sounds: check back for a hotfix for them later this week)
Export Creature function
Import Creature function
Mutation Map – Feature Model
Mutation Map – Feature Texture
Mutation Map – Body Covering
Mutation Map – Colour Pattern
Update the Mod Maker to acknowledge new Mutation Maps.
Mark Perception Target. (Head animation already made the creatures a bit easier to read: showing the player what the selected creature is targeting should improve that even more)
Remake the Eyes (Eyestalks and eyelids and light sensing pits!)
Remake the Eye textures (Lenses and Compound Eyes!)
Autorestart option for Mass Extinction (in the Options Menu)

Fixes

Creatures not wandering even though they say they are. (LIIIIIEES!)
Creatures spinning endlessly in circles around tree’s. (Clearly they’re attempting to rob the planet of it’s rotational momentum. They must be stopped)
Game crashes at some point when you set the population cap to 2000.
Autosave closing any open UI tabs. (My bad guys, I should have fixed that one before release)
Creature’s heads rotating into their own bodies (mostly fixed, still happens occasionally though)
Creatures looking in the wrong direction in the Creature Details Panel.
Fake shadows visible through cliffs.
Fake shadows not orienting to ground properly.
Remove Creature Thumbnails. (currently they’re being taken at birth for every creature on the map, which costs performance. It would be better to take one solely for whichever creature is currently selected)
Deforest the area outside the border
Automatically detect if the player’s graphics card can’t handle Pixel Shader 3.0 and/or > 2048×2048 textures
Deal with all of the AI problems that Mark Perception Target made painfully obvious
Bind the Up, Down, Left and Right keys as secondary movement controls for people who don’t have qwerty keyboards.
Option to save as BMP files, for systems that don’t support saving to PNG (assuming that’s what’s causing the loss-of-terrain problems some people are reporting)
Check Biomass Bar for possible Memory Leak (No way to test it, but I have made sure it won’t try to draw more than 150 scale sprites)

Report any bugs here. (or leave a comment below)
Discuss the release here.
Make suggestions for 0.5.0 here.

You think you know me? You know nothing.

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Why aren’t carnivores evolving?

Here’s a new type of post: analysing the behavior of Species: trying to work out why things are happening the way they are, and using what we learn to improve the mechanics for the future.

Eventually, I’d like to integrate this sort of questioning into the game mechanics themselves: make science itself a game mechanic. As an example: say you want to know what a specific gene does. The game could require you to earn a certain amount of “data points”, or something equally abstract, and then spend them on that gene to discover it’s function. And that would make for a decent game mechanic, encouraging you to earn data points, which I assume you’d get by performing actions like creature sampling. But it wouldn’t be science, it’d be economics. And no offence to economists and EVE Online players, but unless your entire country is falling into disrepair because of too many short-term investments and cuts by the rich and powerful, economics is boring.

Alternatively, you could take a creatures genome, apply heavy mutation to that gene specifically (via a targetable radiation gun or something equally awesome), then clone a creature from that genome and see what’s changed. You could then go back and label the gene. Observation, hypothesis, experimentation and conclusion: that’s science, turned into a gameplay mechanic. And best of all, the reward is the logical result of the experiment: you can now target that feature specifically when you manipulate genetics.

Of course, the game can take care of some of the slower bits: for instance, an ‘autocompare’ between parent and child, which detects and names the heavily mutated gene for you, would keep the game moving better than if the player had to visually inspect for differences, and then go back and type in the function of the mutated gene themselves. Afterall, I’m not interested in data entry, I’m interested in science. (On the other hand, if naming gene functions is your thing, this would tie in well with the ‘naturalist mode’ idea that Reprieve suggested)

Anyway, I’ve managed to go off track before I even got on the track in the first place. I don’t even think I ever even [i]saw[/i] the track: I’ve been doing donuts in the carpark this whole time. Shorter me: I’ll be looking for any opportunity I can to integrate science and gameplay. In the meantime, I can still do science on the game out here in meta-space.

And what I want to know today is: why aren’t carnivores evolving?

Play the game for a bit and the best you’ll probably get are omnivores, despite all the giant piles of delicious meat lying around. Something’s going on: hunting and scavenging should be viable strategies, so why don’t carnivores survive?

Part of this is simply the power of stupid. Creatures are often too dumb to seek out plants, let alone other creatures, let along dead other creatures. Rest assured I’m working on this for 0.4.1, and future versions will have significant AI improvements on top of it.

But it’s not just that. You may have noticed that probably the most viable strategy among the creatures is to find a large tree and just sit there eating it, staying at max energy and pumping out 10 or more babbies until it’s gone, like the Quiverful movement’s vision of the ideal woman.

So why doesn’t this work for carnivores?

Is it just simple math? I’ve been meaning to check the math for this post, but haven’t gotten around to it (and I don’t have the game in front of me right now durn it), but I’m pretty sure it isn’t: meat energy is highly dependant on the life of the dead creature, but everything they eat during their life is converted to meat, so there should be loads of it in each meat pile.

But there’s another factor. You see, creatures have an ‘eat rate’ value, which differs between vegetation and meat. The malleable, delicious, high-protein meat can be consumed much more rapidly than the tough, horrible, inefficient plants.

Seriously. We really appreciate it.

In theory, this serves as a reward: unlike grazing, creatures can get a lot of energy in a short amount of time from meat. In practice, it became the opposite: the above strategy, where creatures maintain their energy at max by eating from one source until it’s completely consumed, works for only as long as the source lasts. And meat doesn’t last much time at all.

This is an interesting phenomenamnicon in it’s own right: the ecosystem actually encourages slow-eating creatures, which is the opposite of my expectations. But it makes the game less interesting and actually discourages evolution, so I believe a few changes are in order.

There are two approaches I could take to this:

– The balancing approach. Consuming meat faster is preventing carnivores from developing, so I’ll make them consume meat slower. I’m not going to take this approach, partly because it’s illogical, but mainly because it utterly and unforgivably violates my primary design goal. I’m developing the environment, not the evolution: I shouldn’t be ‘balancing’ selection pressures to make the things that I find interesting develop. That’s not what the game is about! Aargh!

– The expanding approach. It’s not consuming meat faster that’s preventing carnivores from developing: it’s that I’ve failed to model the animals eating behavior correctly. It’s logically impossible for them to continue to eat when their stomach’s completely full, so why are they doing so? I need to fix that fundamental bug, rather than working within it to achieve outcomes I percieve as desirous.

Of course, I probably won’t be able to fix it immediately. Making them make a new decision when full is a relatively simple thing to implement, but it will lead to a whole bunch of new bugs to test for, and will have significant implications for their survival (making it much harder on the early, blind creatures, and much easier on the sighted random creatures). So I’ll probably hold off implementing it until 0.5.0, which will also implement grazing, a feeding strategy that doesn’t depend on sight and so makes it easier on the starting creatures.

(EDIT) Actually, you know what guys? Screw everything I just said, I’m implementing it anyway. I might as well: it’s not like I’m not fixing AI bugs already, and with those fixes I’ve already completely screwed over the game balance.

(EDIT Mk2) What the flip. The blind starting creatures are surviving better now? How are they… I don’t even… what is this? What the hell even is this? YOUR GOD DEMANDS TO KNOW.

(EDIT Mk3) Okay, it looks like this might be one of those hilariously unintuitive results the Anthropomorphic Personification Of Evolution is so fond of. I could explain what I think is causing it, but that would deprive you guys of the challenge of working it out yourself. So come on: tell me in the comments why they’re reproducing better now that they leave tree’s alone when they’re full! I’ll post what I think is the answer a few days from now.

Cheers
Qu

“Phenomenon”: singular. “Phenomena”: plural. And the “Phenomenamnicon” is a book used to summon a particularly vague eldritch abomination. Geez, it’s not that hard to remember!

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Evolving Reproduction

Sorry this post is a day late. Administrative stuff has been occupying a lot of my spare time. Hopefully I’ll have a few surprises for you guys in time for the release… [ominous smile]

It’s been a while since I did an evolution/misinformation post. Better get onto that…

This claim probably qualifies as picking the low hanging fruit, but I’ve heard it enough times recently to finally lose my cool and deal with it. Those who use it prominently, evangelists like Ray Comfort and Eric Hovind, are surprisingly popular despite being some of the least intimidating intellectuals amongst the anti-evolutionist movement, so I feel the need express my awareness that this is kind of like picking on the special needs kid at school. I’ll will make an attempt to increase the local level of intellectualism somewhat by dealing with the fundamental disbelief that motivates this claim, but quite frankly, it seems likely I’ll descend into the incoherent noises of someone suffering first degree WTF.

The claim, to quote the aforementioned Mr Comfort, goes something like this:

“For example, evolution has no explanation as to why and how around 1.4 million species of animals evolved as male and female. No one even goes near explaining how and why each species managed to reproduce (during the millions of years the female was supposedly evolving to maturity) without the right reproductive machinery.” – Ray Comfort

The ignorance required to even make this claim is breathtaking. I get phantom keyboard pains in my forehead just thinking about it. Where to even start?

I suppose the first point to make here is fairly blatantly obvious to anyone who didn’t fall onto their head from the top of a ten story building: the theory predicts that sexual selection evolved once in the common ancestor of those “1.4 million species of animals”. I don’t know how Ray Comfort got to the end of the sentence without realising that this is obviously what the theory must predict, but he has somehow managed that weirdly impressive feat many times since: for several years he frequently made this bizarre argument, hundreds of times over. As far as I know Comfort himself finally seems to have stopped using the argument, but his followers most certainly have not.

The claim, despite being the equivalent of a lobotomised guppy in a swimming pool full of sharks, does have a more interesting basis: general disbelief in the evolution of sexual reproduction. Explaining the origins of dedicated sexual reproduction is a tricky one with few concrete answers, so seeing creationists asking gotcha questions about it online is not uncommon.

The first point is that, as is often the case, we can see a continuum of creatures in the ecosystem already. Plenty of asexual and hermaphroditic organisms exist, and there are a variety of creatures that fall somewhere in between. Even amongst our own species gender is hardly a binary male/female trait, and the animal kingdom makes the even the most varied among us look positively mundane. It’s not that hard to draw a line from the asexual to the sexual organisms once you gather up enough dots.

For sexual reproduction to evolve, it needs two things: a viable evolutionary pathway via multiple, progressive mutations (similar to the metaphorical line I wrote about above), and a benefit to following this pathway.

The benefit to sexual reproduction isn’t immediately apparent. Sexual creatures as individuals don’t survive any better than their asexual cousins: indeed, the necessity of finding a mate is quite a harsh impact on an individual’s ability to reproduce. But evolution isn’t about individuals: it’s about populations, and genes. A lot of people think of evolution in simple ‘faster leopard catches more food, faster leopard survives’ terms, when it often doesn’t work like that.

The benefit to sexual reproduction (well, okay, one of several) isn’t that the creature that mates survives, it’s that the population of creatures that mate can take advantage of beneficial mutations more efficiently than the populations that don’t. Amongst asexual creatures, every creature is in direct competition. In order for it’s genes to survive in the long term, it isn’t enough for creature A to survive and reproduce: creature A’s descendants have to survive and reproduce and continue to survive and reproduce, out-competing and avoiding being out-competed by the descendants of creatures B and C.

Assuming creature A’s lineage out-competes lineage B and C, any beneficial mutations amongst B and C will be lost.

Sexual reproduction introduces an entirely new dynamic: co-operation, rather than competition. Creature A’s lineage doesn’t have to out-compete B and C’s: instead they interbreed, merging their three lineages into one. This means that the beneficial mutations of all three creatures can make it into the descendant population. This co-operation is a surprisingly powerful benefit: so powerful that it prompted the development of a requirement to breed prior to reproducing.

The evolutionary pressure in favour of sexual selection, then, is that it increases the efficiency of evolution itself. Populations that evolve faster and more efficiently will, over time, be able to out-compete slower populations.

This is a large advantage to macroscopic creatures, for which the cost of reproduction is high. Microscopic creatures like bacteria and viruses see less benefit from this: they can easily compensate for the lack of efficiency by cranking out ridiculous numbers of offspring at a rapid pace.

All of this is fairly theoretical and abstract, but one of the things I’ve been very happy to see is that it is replicated in at least some form in Species. Individual species usually do become more amorous over time, without me ever having had to implement any direct advantage to mating.

My hope is that tools in future versions of the game will help us dig down even further, to establish exactly why this is the case, by (for example) comparing the most successful half of the population to the less successful half, and highlighting the largest changes.

Another hope for future versions of the game is to improve the evolution of sex. Currently, all creatures can reproduce sexually, and their ‘amorousness’ behavioural modifier increases the chance they’ll mate upon encountering another of their kind. When they mate, both creatures take a copy of the others genetic code. Whenever they subsequently reproduce, they blend their own genetic code randomly with that of their mate to produce the offspring.

So they can and do evolve from asexual (never mates) to sexual (mates whenever given the chance), but it’s a very simple spectrum, and even the most sexual creatures are still capable of reproducing without mating. Adding additional complexity in this system, like possible birthing restrictions and maybe even gender differentiation, would be worthwhile.

As a friend said recently, the feature creep potential for this game is practically infinite. Good thing I’m not trying to implement everything before release!

Cheers!
Qu

Hmm… I had actually meant to do a thought experiment fr this post: try to work out the most likely evolutionary pathway from basic splitting to gender differentiation. Oh well, some other time I guess.

Here’s something we found while Googling around for the relevant Ray Comfort quote”: “Darwin theorized that mankind (both male and female) evolved alongside each other over millions of years, both reproducing after their own kind before the ability to physically have sex evolved. They did this through “asexuality” (“without sexual desire or activity or lacking any apparent sex or sex organs”). Each of them split in half (“Asexual organisms reproduce by fission (splitting in half).” – Ray Comfort.

The Banana Man, ladies and gentlemen. Accept no subtitute.

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Abiogenewhat?

Okay, as much as I enjoy telling the development saga, it’s past time for a rant against ignorance. It’s like running for charity, only replace the foot blisters with throat ulcers and the happy children with offended denialists.

Upon what topic of irredeemable stupidity should we feed this rant monster, so it can grow into a big and healthy eldritch abomination whose only desire is to see this world die in internet flame wars? Irreducible complexity? Second law of thermodynamics? Micro vs macro evolution?

No… I’m going to go earlier than that, to a pet hate of mine. The claim: “A cell can’t form by chance.”

From experience, this claim is often accompanied by a bit of good ol’ statistical abuse. The claimant will find a protein, calculate the probability of that protein being that protein, and show off the result as if adding enough to the exponent somehow makes a number important. Here’s a good example from Talk Origins:

”The proteins necessary for life are very complex. The odds of even one simple protein molecule forming by chance are 1 in 10113, and thousands of different proteins are needed to form life.”
Watchtower Bible and Tract Society. 1985. Life–How Did It Get Here? Brooklyn, NY, pg. 44.

Of course, anyone with a basic understanding of statistics and a good pair of heavy boots can kick your ass over this. It’s possible to use the same logic to “prove” that Hydrogen can’t possibly be more common than all the other elements, because each naturally occurring atom only has a 1 in 91 chance of being hydrogen. Besides, the sheer extent of lies upon misinformation upon things-deliberately-overlooked involved in getting these sort of numbers normally indicates the person using them is either a professional charlatan or copy-pasting from the website of a professional charlatan. If you’re interested, check out Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations on Talk Origins. I know it’s a little dated, but it’s a fine start. I’ll stay here and deal with the simpler aspect of the claim, using slightly smaller words, not least because I don’t understand all the big ones.

So improbable... not.
(img src: http://www.astrobio.net/pressrelease/83/one-handed-life)

A common answer to the cell-forming-by-chance claim (aside from the fact that the original reproducer is believed to have been far simpler than a modern cell, and was probably little more than a fairly complicated molecule in the right solution to allow it to “reproduce”) is that the forming of the “first cell” has nothing to do with evolution. And that’s perfectly true: this is the domain of abiogenesis, and an acceptance of the still-relatively-young science behind abiogenesis has bugger all to do with accepting the oversized mountains of evidence for evolution. Even if abiogenesis turns out to be a load of rubbish when it comes to explaining the existence of life on earth, evolution remains a highly convincing explanation for the diversity of life on earth.

But that answer is also a cop-out. Abiogenesis is still the most likely method by which life arose on our planet, and as a hypothesis it’s a heck of a lot more complete than the juvenile concept anti-evolutionists so often seem to have of it: namely, that the pieces of a cell “rolled together” purely by chance.

As already stated, the original reproducer was most likely little more than a complicated organic molecule that made copies of itself. Even so, this still sounds like a complex thing to have come about at first, (well, not really: “Self-replicators can be incredibly simple, as simple as a strand of six DNA nucleotides (Sievers and von Kiedrowski 1994)”) until you realise that it didn’t just “come about”: it was the end product of a long chain of natural biochemical reactions, which are far from uncommon. They’re everywhere, reacting with each other and with the results of their own reactions.

Sadly accurate

Given the size of our planet, and the incomprehensible time-frames we’re talking about, is it really so hard to believe that the right sequence of biochemical reactions could result in some sort of imperfect chemical replicator?

Now if you’re a denialist, there’s a good chance you are even now rolling your eyes and saying “it’s all just speculation, he has no evidence”. To which I say: Yes. You’re right, it is speculative. That’s the nature of abiogenesis. We’re talking about microscopic chemical reactions that happened billions of years ago: what “evidence” could we possibly produce aside from a plausible, reproducable path from chemestry to life? We don’t have a TARDIS. But we do have the ability to reason, and sometimes the similarities are striking.

The ‘evidence’ for abiogenesis is that there is life on earth now, and that it wasn’t always there. From these two facts, we can offer plausible explanations, and try to prove them wrong one by one until we’re left with only one option. This is where denialists fail at science. They offer implausible explanations, then try to prove the plausible ones wrong.

I’m not saying there wasn’t a deity who intervened directly and breathed life onto our dead earth 4 billion years ago, or a race of organic engineers who designed the earliest life, or a temporal traveller who accidentally dropped his sandwich in a rock pool. All of these things are possible, in the same way that me being a brain in a jar, or having been created memories-and-all last Thursday, is possible.

But they are not the most likely, plausible, or scientifically supported explanation. That would be Abiogenesis.

/rant
Qu

* * * * * *

“The year is 2033. The last survivors of the Flame War have fled into underground bunkers beneath the shattered remnants of the once great social networking sites. The surface world is given over to unrestricted porn and 4chan mutants. Humanity teeters on the dark brink of extinction.

But we are those who will never give in to despair. We will return to our shattered internet, though it costs us our lives, our very identities. We do not forgive. We do not forget. But we will rebuild.”

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Development Video # 2

Presenting the unholy lovechild of Fraps, Species and Premiere, whose birth heralds the riding of the horsemen and the coming of the prophesied end times… or would do, if October 21st wasn’t 4 days ago…

… Hmm. I don’t really have much to add here. I think I put far too much information into the annotations this time around.

Annotations

I stuffed them up again. It’s hard finding a format that works: the first video’s annotations were distracting, this video’s annotations are unreadable without taking your eyes off the video. Plus they’re really fast, because I tried to put too much information into them.

I’m still reluctant to actually narrate because I sound like a nerd.

Locking up

The game in it’s current state generally stops responding somewhere between 15 and 25 minutes in due to a SystemOutOfMemory error. This is annoying, but I’m fairly sure I know at least one way to reduce the memory footprint. It might also be related to running fraps at the same time: I’ll have to investigate that.

Vegetation

Looks nice, doesn’t it? I ‘borrowed’ a few images from google. It’s amazing the difference a good texture makes. But since I don’t know whether they’re under copyright or not, they’re still just placeholders. I’ll make my own trees eventually.

As you can see, a stable population of creatures tends to keep the vegetation from growing back. This is annoying, because the trees add a lot to the visual design. I’d like to work out some way of keeping a decent number of trees around even when there’s a moderate population amongst them: maybe rather than shrinking/growing, trees could transition between a ‘dead’ texture and a ‘live’ texture? Not sure, but mulling it over.

Debug Bars

For the programmers amongst us who find this sort of thing interesting, here’s the colour key for some of the larger debug timer bars:

Blue: Update Call. Creature AI, Behaviours, Movement, Interaction: I've managed to reduce this one by a lot by messing around with the implementation. It's quite a compact routine now, though the code needs a major clean up.

Green: Species/Population Tracking. This should be almost entirely taken up by comparing creature genetics to search for speciation. Unfortunately, it's not: that's actually surprisingly fast. What really takes up the time in this routine is drawing the population graph. Render Targets hate me: the entire population graph may have to be re-written to fix this.

Magenta: Prepare Draw. Updating the animations, bone sizes and positions. This is where most of the Skinning is done. Lots and lots of matrix operations. It's been optimised, but it's still a fairly heavy routine. But not as heavy as...

Blue (2): Draw Call. Thanks to the 'every creature is unique' nature of Species I can't use mesh instancing, so drawing 1000+ creatures takes an utterly unholy amount of time. I am using State Batching where possible (so, for example, I draw all the torso's in one loop, all the necks in the next loop, and so on), and that helps, but mostly it's just a blow I have to take.

In General

There’s any number of things that need improvement visible in the video, mostly related to entertainment value more than accuracy. Some, like homogeneity and being able to tell which species is which, are general behaviours that require a subtle solution. Other’s, like implementing a proper vision system for creatures, are specific and obvious. It’s probably simplest to focus on the specifics for now, since they’ll likely have massive effects on the overall behaviour of the simulation. A lot of work to do yet!

The Next Video

… I realise this video was kinda boring overall, so the next one will be about showing off potential creature variety and the effect different shapes and body-parts have on stats. Much more interesting! But there’s a lot I want to implement before doing that, and if this video was anything to go I happen to be absolutely terrible at getting these up at the time I want, so don’t expect it for a while, okay?

Huh. Guess I did have more to add. That was unexpected.

Oh well, it keeps me entertained. Not much else to do in the EMP cannons prison block. Thank goodness they have internet access, that’s all I can say. Very forward thinking of me, putting internet access in my own prison cells- DAMMIT WHY HASN’T ANYBODY LET ME OUT OF HERE YET?!!
Qu,

(UPDATE) At 5:53 EST the insect-man army broke our defenses and overran the Orbital EMP Cannon. We were all taken hostage by the geneticist Overlord and mouthpiece for the bio-scientist hivemind, a rather pleasant bearded fellow.

Thankfully, after we locked Qu in one of the cells to shut him up, I was able to convince the Overlord to spare our lives. He even let us keep the cannon, though he took the firing mechanism (for our own safety, of course).

It’s been several hours, and everything has returned back to normal. Seems remarkably quiet, though. Strange, though. I can’t shake the feeling I’m forgetting something, but for the life of me I can’t remember what it is…
IT’S ME YOU BLOODY SASQUATCH! LET ME OUT!
… nup, can’t think what I might be forgetting. Oh well, I’m sure it’s nothing important.
I WILL WREAK VENGEANCE UPON YOUR PATHETIC FORGETFUL SOUL! YOU HEAR ME?!

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Human Chromosome Number 2

Okay, first things first, I need to check if anybody noticed I haven’t had any internet access from home since last Friday thanks to my ruddy cheap ISP and was therefore unable to post anything last week. No? No-one? Good, good, the perception nanites are working. Moving on…

WARNING: SCIENCE CONTENT

Now, we all know about chromosomes: they’re the things in our cells which hold our genes. Now, all the great apes have 24 pairs of chromosomes. This is fair enough, but (according to evolution) we are just as closely related to the great apes as they are to each other. So we should also have 24 pairs of chromosomes, correct?

But we don’t. Human beings only have 23 chromosome pairs.

Now, this isn’t a massive deal: chromosomal counts differ greatly within genus, and sometimes even within species. The plant genus Clarkia, for example, has species with chromosome counts of n = 5, 6, 7, 8, 9, 12, 14, 17, 18, and 26 (Lewis 1993). But chromosomes don’t just disappear: when they do, the victim of the mutation is missing a good quantity of, usually important, DNA. So what happened to the 24th human chromosome?

With everything I’ve just told you, a logical prediction can be made: at some point in our ancestry, but not in the ancestry of other great apes, two chromosomes must have joined. This isn’t a harmful mutation: the gene’s themselves are still viable, but they are now part of a single chromosome, not two.

Now, chromosomes have easily recognisable sequences at the ends, called telomeres, and another recognisable type of sequence in the centre called centromeres (0). Centromere’s are where the chromosome divides during reproduction.

Here’s a representation of what I’m talking about, with telomere’s represented by X’s and centromere’s represented by 0’s:

X—-0—–X

So, geneticists realised that if humans really are descended from apes, one of their chromosomes should have two (X’s) in the middle of it, with a pair of (0’s) flanking them. Keep in mind that if this isn’t found, common ancestry with apes is in big trouble: after all, how else could we lose a chromosome without it screwing us up?

Here’s a abstract representation of Human Chromosome Number 2, as discovered by geneticists who went looking for this pattern as a direct result of the theory of evolution.

X—-0—–XX—-0—–X

“Evolution has made a testable prediction and has passed.”
— Kenneth Miller

No big surprise there if you accept the theory of evolution, but it is a pretty nice piece of evidence nonetheless: easy to understand and rather difficult to refute. If you take a look at the attempts of anti-evolutionist groups like Answers In Genesis (here), you’ll notice they never even try to explain HC2, instead simply asserting it’s not evidence for evolution and then throwing out red herrings and going off on strange tangents about information content. The closest they come to an explanation is a half-hearted admittal that maybe humans and apes were created with the same number of chromosomes. Hooray for ad hoc reasoning, I guess? I’ll let you judge which explanation is more satisfying.

This one I learned from the Dover v Kitzmiller Intelligent Design Trial Transcripts. Kudo’s to Ken Miller, who presented it during the trial. And apologies to the noble geneticists whose work I am simplifying (butchering would perhaps be a better term) to make this point. Please don’t send your armies of genespliced insect-men after me.

Send the insect-men! He still thinks I’m on his side, but he’s gone too far this time. The truth is, he’s just stalling for time to finish building his [OBSCURED BY PERCEPTION NANITES] and I can’t stand by any longer. Those poor porpoises!

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