## Sunday 30 December 2012

### Tetropters V: a livelier animation

Regular readers may know that I return to the subject of tetropters from time to time, in a slow and fragmented effort to produce a documentary video showing the little beasties hovering through the air as if they were real, perhaps with an appropriate narrator (as I wrote earlier, David Attenborough would be perfect).

New readers may however respond by saying "What on Earth is a tetropter!?". Part of the answer lies in rephrasing that as "What on Furaha is a tetropter!?" Well, tetropters are small exoskeletal insectoids with a radial base-four Bauplan using a double clap-and-fling wing movement. That is about as short a description as can be given, I think. Those who wish to read more can find the latest instalment ('Tetropters IV') right here, with links to the previous three chapters.

'Tetropters IV' had reached the stage where I could simulate tetropter wing movement, resulting in animations showing a completely immobile body in a completely immobile environment and a fixed camera position. To get there had required a lot of work, but so much more was needed: the animals' bodies should be detailed -and should probably have internal movement as well-; there should be a larger variety of wing shapes; the animal should tilt a bit in the direction of movement, and larger tetropters with slow wing beats should bob up and down in flight, like a butterfly does when flying. And to mimic the effect of a macro lens the scene the depth of field should be narrow, with blurring of nearby and far objects.

I used some time in the holiday season to work on the animation, pushing against the limitations of time and capability. The first result of that push stage is shown above, and had the animal moving about freely in three dimensions. To do so I wrote a program in Matlab to define a 3D path in x, y and z-coordinates. The movement is based on the number of frames per second and the numbers of seconds the film should last for. To keep the wings moving there is the number of frames per cycle to consider. I added a little tremor to the vertical component of the movement, so the animal bobs up and down a bit, in phase with its wing beats. All this resulted is a text file with a lot of numbers stipulating where the animal is and at which phase its wings are. The more difficult part was convincing the rendering program 'Vue Infinite' to accept all these numbers and produce a nice image per frame. I had to work on a program in the language 'Python', which I am hardly familiar with, but which can be used to control almost any function in Vue Infinite. I got over that and made the animation above. Not too bad, is it? In an earlier version Evan Black commented that an improved animation might have the effect that the coarser aspects of the design, such as wing attachment, would be less noticeable if the animation would be developed more. I think that that now proves to be true. By the way, the three axes and the balls are there to tell me whether the animal is with regard to local space. I also did not bother to set the wing cycle to match with the movement; in a real scene the wings should beat much more often over the course of such a movement.

The next stage, shown above, involved 'lens blurring' and body tilting. After various tries and errors Vue Infinite could do lens blurring, but in a very complicated manner: there was a variable that had to entered as a percentage, so I stopped at 100%. The blurring only worked as intended when I set it to 2000%, something I learned after having received help from the Vue Infinite forum at E-on software.
As for the body tilting, that involved rotations around all three axes. I wrote the program so i could control the rotations by hand, but added an automated feature that differentiated a position path. There should probably be a time delay in that the body should probably start to tilt in a given direction slightly before it starts to move that way, but the lack of such a delay is not noticeable. There could be various way for tetropters to change direction; they could change the aspect ration of specific wings or during specific phases of wing movement, or they could bend their bodies to change their centre of gravity. Regardless, I think the tilt adds a nice touch, rendering the flight a bit like that of a helicopter.

The animation above shows where I am now: camera movement. The camera follows the tetropter. As all this is a simulation that could be done perfectly, so every bob up and down would be followed, and the body would stay centred on the image with mathematical perfection. That would look very artificial: a human camera operator would lag behind the movement and would not follow tiny variations. I mimicked that by having the camera follow a smoothed path rather than the actual one, but I do not think the smoothing is good enough yet; it probably needs a delay function as well.

Oh well, there are enough things left for the next stage, such as adding a suitable body. I will probably sculpt one in Sculptrix or build one in Vue itself. The latter option will result in an artificial technical look but has the advantage of colouring the animal with ease. The Sculptrix option will produce a much more biologically looking body, but requires colouring in some other program, another new task to learn (apparently Photoshop can be used to paint 3D objects). So, do not hold your breath, but 'Tetropters VI' will probably be the final documentary, adding all the items mentioned earlier.

Except for the narrator, I am afraid...

## Sunday 16 December 2012

### From the Archives (VI): the woolly-haired shuffler

It is time to delve in the crypts of the Furahan Archives once more. There are body plans there that have never seen the light of day, and remnants of species long forgotten. Scribbled notes in a mixture of languages show that names of continents, animals or even the entire planet evolved as did the animals. The more prosaic version boils down to an unsorted stack of paper of all possible sizes and types.

 Click to enlarge; copyright Gert van Dijk
This post will deal with how the woolly-haired shuffler (Gigatheron inexorabilis) came into being. The two small doodles on the left show running animals with big heads that seem to have overlapping layers of skin or armour on their body. Their overall shapes suggest a warthog or a ram, and perhaps that is where the inspiration came from. The one on the right was done with felt-tipped pen, and mostly shows a head with interesting horns or teeth as well as a nice neck shield. There certainly is nothing resembling the overlapping dermal plates that came to characterise the shuffler.

 Click to enlarge; copyright Gert van Dijk
This one is rather similar, and the fact that it is a colour sketch means that I had starting thinking about elevating the idea to a full painting. The head has not changed much, but does not work well: the eyes are above the horns in the middle. Those horns have already developed the split tips that I still like, making the horns look as if they developed from entwined separate cores. The colours suggest dawn on a very cold plain, with some direct light coming in horizontally from the left. That colour scheme would probably have worked quite well, as it would have allowed the bits of snow that are scraped aside by the animal as well as the mountain in the background to be highlighted in pure white.

 Click to enlarge; copyright Gert van Dijk
Some developmental sketches must be missing, as the head of the next one has already evolved to its final shape: the eyes have moved down and the lower teeth now form a perfect shovel. The shield and the face below the horns together form a triangle, while the shovel and parts of the contour of the horns form an oval framing the face. You often see such ovals, circles and spirals around major parts of the composition in art books. I have never consciously used such design elements while drawing, and am always a bit amazed that they are in fact there. Drawing involves rummaging around with many shapes until they sort of 'click in place', so i guess that the 'clicking in place' involves an unconscious search for lines and shapes.

What this drawing reveals is that I am not a painter at heart: I do not think in blobs of colour or light and dark, but in lines. This drawing was done on transparent paper, something I used to transfer a drawing onto the prepared board, ready for painting. I traced the final design with pencil on transparent paper, and then laid that, reversed, on the board. By tracing the lines once more with a soft pencil the tracing was transferred. Here, I cannot have been happy with the animal's body, which is clearly still being developed: the overlapping skirts are there, but they do not reach down very far, and the body is rather small.

 Click to enlarge; copyright Gert van Dijk
Here is another colour sketch. This became the final design. The head is exactly the same, but the body has grown, making the animal much more impressive. There isn't much of a background: just a peak mimicking the shape of the shuffler's shoulders. The bits of colour show that I was thinking of using bits of unexpected colour here and there, something I had seen in the works of Frank Frazetta and that I wished to experiment with.

 Click to enlarge; copyright Gert van Dijk

And here is the final painting again. The shuffler's story probably does not end here though. When I will have the time in a month or two to pick up the project again, I will continue the digital make over of old paintings. The eyes may change, and so will the fur, I think. Some of you may remember that I mentioned a film in which Furaha would feature. That project is still alive, although progressing slowly, and the final version should feature a shuffler...

## Saturday 24 November 2012

### Thomastapir’s Xenohox Gazelle

Readers who have followed my Furaha work and this blog will know that I take a strong interest in biomechanics and locomotion, resulting in studies and animations of concepts such as six-legged gallops, radial walks and tetropter flight. There is of course another drive at work, and that is the wish to create something new, something truly alien. Given the immense diversity of life of Earth I used to feel that there probably was not that much that blind evolution had not yet stumbled upon, but later I felt that the limited number of basic animal shapes on Earth does in fact pose limits on the shapes we see, varied as they are. Hence forms such as spidrids and tetropters that I consider among my most original animal schemes. But at heart I am a bit conservative, which is why I hesitate to depart from known and tested body schemes.

Luckily, not everyone lets himself be restrained in this way, and that is why I would like to draw your attention to the work of thomastapir, whose work can be seen at deviantART. Like me, he likes locomotion and biomechanics, and he has produced some truly original creatures. I will only focus on one of his aliens here, but his dinosaurs and mythical beasts are well worth an visit. I will very likely revisit his page one day to discuss the 'Moebius inside out animal'.

Xenohox Triphidian
I should perhaps jump right in with the Xenohox gazelle, as starting there will give you the full sense of wonder, but it would need a lot of explaining at once. Starting with this forerunner, here in its original place, has the advantage that its shape can be taken in fairly easily. Now this shape is new. One way to look at body shapes is to smooth the surface of animals until the shape cannot be reduced further, revealing its topology. Limbs, as simple protrusions, disappear, and our own vertebrate shape reduces to a blob with a hole through it, i.e. a torus: our digestive tract forms the hole. Jellyfish have no such hole, and can be reduced to a blob, or probably even a sheet. Thomastapir's animal represents three half tori mashed together.

 Click to enlarge; copyright Gert van Dijk
That is what you see above: the blob on the left with a hole through it represents humans and our Earth kin us reduced to our basic topology, whereas the more complex structure on the right is the triphidian. The points where the three half tori join would be natural spots to place the machinery of an animal, meaning its digestive, respiratory, cleaning and neural tracts, along with other odds and ends that need not be universal, such as spleens. The legend on the deviantART page does state that the 'bodies' indeed house the organs. One is called the head and the other the body, which is almost a pity: departing the beaten track should perhaps be accompanied by more original anatomical names as well.

Xenohox Gazelle
The animal above, the 'Xenohox Gazelle', has the same topology as the triphidian. To develop it, we can pull at the surface to produce extrusions, in the same way we can pull at a single torus to sculpt a human or a millipede. The result of this sculpting are three strong limbs.

You will probably need time to work out how this animal is built, and understanding how it moves will take more study. Thomastapir's remarks on his deviantART page explain how it works. He has chosen to keep the triradial anatomy fully intact. Others -well, me at any rate, see here and here- might have decided to let two of the half tori develop into weight-bearing structures, freeing the other one for other uses such as manipulation. Thomas kept all three as equally functional locomotor limbs, which inevitably leads to the conclusion that the animal must turn along its body axis to bring each limb towards the floor in turn. That is very interesting but also very complex. You will need a good ability to visualise movement in your mind's eye to understand it. This is the task: the animal is running across your imaginary field of vision, its body spinning like a screw as it does so. Each leg rotates along with the body, and when it is pointed downward, it also moves backwards pushing at the ground. When it moves up again it also moves forward. If you manage to visualise that, add the two other legs, of course with the proper phase difference. Got it?

If you did not, never mind, as I prepared an animation to help you see how it works. I am fairly pleased how it turned out, although it seems to move more ponderously than the name 'gazelle' suggests. Perhaps I stumbled along the analogue of a heavy eland antelope instead of a slightly built gazelle.

I do see one problem with this way of movement, and that is that it adds complexity to sensing the world around you. The eyes turn with the animal, so the visual field continually turns around as well. That cannot help vision one bit. This is very similar to the problem I encountered in 'cernuation'. There was a solution though: the head would turn against the movement keeping the eyes still (of course, after one turn the head would have to snap back to allow a new counter turn). When I mentioned the vision problem to thomastapir he answered the following:

"On the complication of vision due to rapid rotation about the long axis--it could be a matter of, let's say it has three eyes, that each eye takes a sort of "snapshot" at specific point in its motion cycle--say, when the given eye reaches the top of its rotation.  So then a composite or gestalt image is built up sequentially from those single snapshot images, almost like a flip book or film strip.  The rate of rotation is rapid enough that it should create a fairly smooth, uninterrupted stream of visual information. And certainly it could keep one or more eyes continuously open when it's motionless or walking slowly."

That would probably work, but is not ideal either, as visual information would be lost some of the time.

Anyway, above is another animation with added drama. Nice, isn't it? The topic of how such animals stand still or walk slowly also came up in our conversation, and it appears there are several solutions for this. Would evolution leave the animal this way, or would it evolve towards a simpler 'same side up' form? Would its particular set of hox analogue genes even allow such an evolution? I do not know, nor do I care much, while enjoying the creativity of the Xenohox gazelle and its mode of locomotion.

## Saturday 10 November 2012

### Let's bag some Venusian animals while we can, what?

I visited Greg Boadmore's Venusian Bestiary in April 2011, which is not that long ago. It is quite possible you have all been visiting the Dr Grordbort site or Greg Broadmore's own site regularly, but if not, perhaps the following images will lure you to them. What you should understand about Dr Grordbort is that it is a place where hunting gentleman of the Victorian steampunk variety feel right at home. No wishy-washy 'preservationism' here; a sporting gentleman kills game, all in the natural order of things, of course!

It is obvious that the Dr Grordbort universe is thriving: there are more rayguns than ever, as well as some new books, but those are not the reason to visit (although I admit that I am tempted to buy one of the metal rayguns, but the more sensible -or humourless- part of my brain insist that I should not spend that much money on what is basically just a display object (so far that part is winning, but the boy in me really wants to hold a 1.5 kg raygun...).

Anyway, we are here to visit Venus and its menagerie. First, let's have a look at one or two insectoid specimens, nicely pinned and prepared in their own display cabinets.

This is Gumbolt's wind rat (Xenodefugio subtiltus). It is obviously a flying animal, although it is a bit difficult to see how its parts function as a whole. If the blue parts are its body, the centre of mass would seem to be placed very far near the front, perhaps too much for the wings to keep it balanced. Unfortunately, the underside cannot be seen, nor is there a side view. Perhaps the brilliant blue lateral flaps at the front are very thin, so the centre of mass is placed somewhere between the attachment of the first pair of wings. Then again, the accompanying text describes Xenodefugio's locomotion as follows: "To ascribe the characteristic 'retarded' to it movement would not be unfair, as these simple little beasts move unpredictably in a manner akin to an unhappy grasshopper with mild brain damage." Well, its behaviour certainly seems to be in line with its anatomy.

 Click to enlarge

The blue-sacked pillock (Simpletonius indigum). This one is accompanied by some intriguing remarks: the odd little blighters apparently attack themselves to the corneae of Royal Toops, providing them with the means to travel. It also has functional wings, and is a ballont to boot! The sac at its rear end helps it aloft, where it is 'suspended by its inflatable gas sack posterior'.

As you may know, my studies into ballooning life forms were rather disappointing as far as small animals were concerned, simply because the surface to volume ratio of the sac weighed against the balloon rising into the air (the last post on that is here, and you can find the others from there). It is jolly good to hear that things are rather different on Venus, where gentlemen need not bother with boffin types spoiling all the fun.

Ah, that's better, something large at last! All these silly little sissy animals do not warm a hunter's heart. Milton's Drunken Fussock is certainly large enough for sport!
Intriguingly, the fussock has recognisable eyes, in contrast to many of its relatives. The lack of apparent eyes does not mean that Venusian animals do not have eyes. In my previous post on the subject, Mr Broadmore commented on just that subject, and said that the lack of visible eyes added to the alien feel. It does, too.
That does not mean that I think 'eyelessness' is at all likely. In fact, writing about Venusian wildlife set me on the path to explore vision in some depth (here, here, here and here). No doubt, such critical musings would lead Dr Grordbort and chums such as Lord Coxswain to consider me a 'socially inept boffin' (comments on that are NOT required).

Now, here is Lord Coxswain himself -I assume that this is him- knows how to have fun; after bagging the fussock, he has set up the cadaver for a good laugh. Ha ha!

Finally, a video. The Grodbort universe is a clear source of inspiration to many people, and this video shows a splendid example. It was created by students from the Media Design School. I copied the one above from YouTube so you can have a quick look directly, but if you wish a much larger view, there is a much better version at Vimeo right here. 'The Deadliest Game' is all about the proper gentlemanly attitude towards 'sport'. The hero's beliefs are challenged by a young woman, but he is not fazed by such silliness. The film contains some wonderful animations of Venusian animals. I love the way in which modern software allows people to visualise what they imagine with more ease than ever before. Do watch the end titles, as they offer a glimpse of how the film was made. If I had to choose a career now, that is what I would like to do.

## Friday 19 October 2012

This is -probably- the last of my series of posts on the comparison of vision with echolocation. Previously, I discussed disadvantages of echolocation (here and here).First, an animal using echolocation must send out very loud noises, and in doing so makes its presence known over a much larger distance than at which it can detect objects itself. Second, echolocating animals  have to provide their own signal limiting their range, while sight takes advantage of sunlight or moonlight. Third, sight -and hearing- are passive senses, not betraying the presence of animals using them. Instead, echolocation boils down to shouting "WHERE ARE YOU!?", which probably means that only the Big and the Bad can afford its use.

I ended by assuming that the darkness of the deep sea would make it a perfect habitat for echolocators. Of course whales do exactly that, and they fit the job description of being Big and Bad. But they have not been around all that long, and the seas have been full of fish and squid for much longer, so you would think that they would have had the time to evolve echolocation. So where are the marine echolocators? Nothing. Silence.

So I asked a biologist, Steve Haddock, who was kind enough to enlist a colleague, Sonke Johnsen. Here is their conversation, Steve Haddock first: "I don't know of any examples. Lots of fish make sound (the midshipman), but it takes a lot of energy and seems to be largely for mating. Maybe the distance between their 'ears' is too small to be effective? Even humans underwater can't tell what direction sound is coming from. That doesn't explain bats, but different speeds of sound in air vs. water? Not sure, but it is an interesting question!"

I had not thought of that, but sound certainly travels faster through seawater than through air. At a depth of 2 km, sound travels at a speed of over 1500 m/s. Compared to about 333 m/s in air at sea level, the speed of sound in the deep sea is about 4.5 times faster. That matters, because you can tell the direction of a sound by measuring the differences in arrival time between two ears. Immersing those ears in water immediately makes the difference in arrival time 4.5 times smaller and therefore more difficult to detect. Could it still work? To find out,  I first assumed a distance between the two ears of 20 cm. With that, a sound coming in from the side will arrive 0.6 ms later at the farthest ear in air, and 0.13 ms later in the deep sea. That does not seem like a lot, but Wikipedia informs us that humans can detect differences in  arrival times of sound of 0.01 ms. So, given some good neural software, it should be possible to use this trick in the deep sea.

Anyway, Sonke Johnson added the following to Steve's reply: "There seems to be no good reason why fish don't echolocate. There are certainly fish and sharks whose heads are wider than echolocating dolphins. It's also not a marine mammal thing, since seals don't echolocate. Many fish and mammals eat the same things, so it's not that either. Cetaceans have great hearing, but that's sort of a chicken-egg thing and there's nothing preventing fish from having better hearing. You can't even say it's a warm-blooded-only club, because certain large fish (e.g. swordfish, tuna) actually heat up their brains and eyes so that the work faster. It's probably just one of those things. One possibility is that early cetaceans may have started in muddy rivers. Muddy river animals sometimes evolve interesting sensory systems (e.g. electroreception) because it's impossible to see. Even today, some cetaceans inhabit murky rivers and lagoons. Of course, many fish do too...."

I thanked both through email, but would like to repeat my gratitude to them here.

Back to the light

So far, we have to conclude that we do not know why the deep seas are not filled with Big Bad Echolocating Fish (BBEF) or Squid (BBES).

Click to enlarge; from this source

The sea is full of bioluminescent animals, and the image above shows the ways it can be used for offensive purposes, something we will focus on. An amazing array of life forms, from bacteria to many diverse major groups, have bioluminescence. They use it for a wide variety of purposes, that can be basically divided into defensive and offensive ones. Steve Haddock has written a very comprehensive review, that can be obtained free of charge, and which is very readable for non-biologists. There is also an excellent website. I will focus on just one of the many uses of bioluminescence: to illuminate prey using photophores.

Click to enlarge; source here

First, what are photophores? Well, the word simply means 'light bearers', so they are organs producing light. Without ever having studied them, I thought they would be just sacs with bioluminescent chemicals in them. But as the image above proves, showing a squid photophore, they turn out to be much more complicated than that. Perhaps you recall the reasoning that the physics of light quickly led to the evolution of a camera-type eye, with a retina, lens and diaphragm? Well, there are lenses and shutters in photophores as well. There must have been a process very similar to that of evolution of the the eye, but here the question must have been how to produce the best biological flashlight possible. The image above shows a photophore from a squid. At the centre there is a light producing mass, surrounded by a mirror, reflecting light until it exits the photophore through a lens. I have unfortunately not found a review paper comparing the optical design of photophores, but this should be enough to prove how complex they can be.

Click to enlarge. These are 'loosejaw' fish.The one on the top right sends out red light, and is called Malacosteus niger. Note that these animals have various photophores on their heads. The one it is all about is the suborbital one ('so').
From: Kenaley CP. J Morphol 2010; 271: 418-437

Now, finally, we are ready for the final twist in the comparison of vision and echolocation. There are fish, shown above, using well-developed photophores as searchlights to find their prey. This use of light is very similar to echolocation: the animals have to provide their own signal, resulting both in a limited range and in becoming rather conspicuous.

Click to enlarge. Photophores from the dragonfish Malacosteus. In the two images, 'c' is the light-emitting core, 'r' is the reflector surrounding it, and 'f' is a filter to give the emitted light a red colour. The light bounces around until it exits the photophore through the aperture 'ap'. Form: Herring and Cope, Marine Biology 2005; 148: 383-394

The fish best known for this behaviour are so-called dragonfish, and their use of photophores involves the kind of wonderful bizarre features that only real evolution produces. These fish send out red light, which is unusual because red light doesn't carry very far in water. Most bioluminescent signals therefore use blue light, and accordingly most animals in the deep sea cannot see red light. They also cannot see the red light emitted by the dragonfish, which is rather cunning and makes the searchlight invisible. The snag is that some dragonfish species do not have a pigment in their retinas to see red light either...

Instead, they use a trick: there is an antenna protein in their eyes that is sensitive to red light, and this transferred the energy to the pigments sensitive to blue and green light that the fish does have. That transfer pigment works like chlorophyll, not a protein you expect in an animal at all. That's because the fish obtain it from their food and somehow transfer it to their retina. All this can be found on the website I mentioned. I certainly would not dare to use such outrageous traits in my fictional animals!

The oceans may not be filled with predatory BBEF, but there aren't many Big Bad Flashy Fish (BBFF) either. Neither option seems to have gained evolutionary prominence. Perhaps their characteristic conspicuousness makes these options too risky. I must say I like the option of equipping animals with flash lights.

Click to enlarge; copyright Gert van Dijk

So here is a quick and rough sketch of a possible Furahan animal with searchlights, which has just spotted a tetropter. Would the edge of better prey detection outweigh the increase in its own predation risk? I do not know. There are other worrying thoughts: why is bioluminescence on Earth so rare outside the oceans? It is hardly found on land, and does not even seem to occur in fresh water either. Are there reasons for that? Is the poor animal shown above doomed already?

## Saturday 6 October 2012

### The 'lateral fin theory' and mackerel mode

I still have no time for posts that take time to read, think and write; well, more than a hour or two. That is a pity, as some ideas need time to do them justice. For instance, there is a post to write on what happens is photosynthesis is less dramatically imperfect as it is on earth (see here); there is also the final chapter of the 'sight is superior series' (see here), and I have at least one other world builder's creations in mind.

Those will have to wait; instead, here is a short post on where the six limbs on Furahan hexapods came from. On the 'real life' level the answer is easy: 'six limbs will look exotic and therefore help create an alien ambiance'. Within the Furahan world, the logic of science fiction demands an answer that fits within the concept.

Click to enlarge; copyright Gert van Dijk

The sketch above is an old one, and the first that showed the first steps in hexapod ancestry. By now, many of the anatomical features are being overhauled, so the number of eyes is incorrect. The overall scheme is still there though: it all starts with a less than impressive little elongated tube with broad fins at its sides. This 'ULF' (unassuming life form) swims by waves that pass from front to back along the fins. Nothing particularly spectacular here: undulating fins may well be a constant throughout the universe. From that start I assumed that the fins might be divided gradually, to provide greater control and flexibility (you cannot suddenly move a part in one direction if it is fixed to parts in front and behind of it). This greater need for manoeuvrability evolved together with jaws; you cold also say that the jaws and the fins helped one another's evolution: without jaws, there is no speed, and without a better propulsion, the jaws do not provide that much benefit. The third stage shows an animal with fully separated fins, just not necessarily six of them; the reduction to six came afterwards.

The origin of hexapod fins therefore lay in a lateral membrane that split up. Many years later I wondered where Earth vertebrate limbs originated. To my very large surprise, the first explanation I came across was something called the 'lateral-fin theory'.

Click to enlarge; Coates MI. The origin of vertebrate limbs. Development 1994; Supplement 169-180

The images above show an example of what a hypothetical vertebrate ancestor was supposed to look like: it already had unpaired fins along its back and belly, and lateral (sideways) fins along its sides. The theory, apparently first formulated in 1877, states that these lateral fins later gave rise to limbs. I was first a bit irritated, but later pleased that I had stumbled on a principle that apparently was not altogether fictional. That was until I went back for a closer look at current theories regarding vertebrate limbs. It would appear that the lateral-fin theory is now out of date. Other theories held that limbs evolved out of gill branches, which seemed to make sense as the first forelimbs were attached directly to the skull. That theory apparently also now belongs in the dustbin of history.

Click to enlarge; Coates MI, Cohn MJ. Fins, limbs, and tails: outgrowths and axial patterning in vertebrate evolution. BioEssays 20:371–381, 1998

The image above shows an illustration from a recent paper on limb development. It shows that that unpaired fins in the midline ('median fins') existed well before vertebrates had jaws or lateral fins/limb. When lateral fins appeared, the first to appear were the front pair, with as yet no trace of hind limbs. The two pairs did not evolve together, which you would think, given their similarities. Modern discoveries in the field of 'evo-devo' ( embryonic development in light of evolution) centres on hox genes as a sort of overall conductors of embryo formation. A recent theory holds that the genes responsible for limb formation were co-opted from a previous use, one that involved formation of the gut through the 'lateral plate mesoderm'. The paper from which the image above was taken  mentioned the possibility of a third pair of limbs in vertebrates, the kind of nice exotic happening that we like in speculative biology. Here is what Coates and Cohn wrote:

"Finally, the absence of vertebrates with more than two sets of paired appendages has often been used as an illustration of evolutionary constraint. Developmental mechanisms responsible for this anatomical limitation remain unclear. Arguably, the nearest approach to a third pair of lateral appendages may be the lateral caudal keels of certain fishes, such as tuna and various sharks."

So there are in fact three pairs of lateral, well, outgrowths in vertebrates? Fascinating. But the test continues:

"Even the most elongate lateral fins of primitive fishes terminate in front of the anal level. Clearly, lateral caudal keels can and do emerge, but articulated endoskeletal paired appendages require the lateral plate mesoderm, and this is linked intimately to the extent and pattern of the gut."

Curiouser and curiouser. It does not look as if vertebrates will surprises us by evolving a third pair of legs, though. For three pairs of legs, you need to turn to insects, and for big hexapods, there is always the fictional universe.

But does all this mean I should give up on my 'lateral fin theory'. Actually, I see no reason to do so. In fact, it is rather nice that the lateral fin theory remains in place on Furaha, as the explanation of the origin of six legs in Furahan hexapods.

Click to enlarge; copyright Gert van Dijk

To celebrate that I stole another two hours and used Sculptris to sculpt two quick ULFs. The first is shown above: no jaws, four eyes, two lateral undulating membranes and two long gill tubes running along the belly connected to the sea by a number of spiraculae. I still need to name it, and I think I need something that does justice to its pivotal position in evolution. Suggestions are welcome. Latin or Greek only though, please.

Click to enlarge; copyright Gert van Dijk

And here is its successor. As you can see, the membrane has developed indentations and the animal is longer and bigger. It has six claspers in front that can already deal with soft prey quite well. Note that the body is stiff, very unlike the very flexible body in the old sketch. The body can flex up and down, but sideways movement are almost impossible, thanks to he two stiffening rods that lie buried in the body at the root of each lateral fin. The stiffness is a consequence of this early body plane, and is a feature of all later hexapods.

Click to enlarge; copyright Gert van Dijk

I could not resist quickly daubing one in Sculptris with colour to show one in 'mackerel mode' (I still prefer painting, but the 3D process certainly is a very quick way of producing an illustration).

## Sunday 16 September 2012

### The Devonian feet of the Furahan marblebill

I really should stop having fun with incomprehensible blog titles. Anyway, too much work again left me no time to write a solid scientific essay. So I will just relate the story of where the 'branching toe theme' originated. The previous post was about redesigning the marblebill, and Spugpow had observed a novel branching pattern of the marblebill's toes.

Click to enlarge.
From: Gould SJ, Ed. The book of Life. Ebury Hutchinson London 1993.

To see where that came from, we have to go back, either to the Devonian or, more appropriately, to books on palaeontology up to about 10 years ago. The image above is from such a book, still available from Amazon in the UK and in the USA. No doubt you have seen similar images before, illustrating how Earth's tetrapod legs evolved from the fins of fish. In the middle right, you will see such a prototypical tetrapod leg: one bone in the upper limb, two parallel bones in the lower limb (the radius and the ulna), a bunch of small bones as a sort of shock absorbers, and five (well, seven) parallel digits with several bones in series. That is basically our arm or our leg. The middle image on the left shows the bones in the ancestral fish limb. Do you see the resemblance? If you do, good for you. I never did, as to me the branching patterns seemed completely different. In effect, the two boned destined to become the radius and ulna may start parallel where they touch the upper limb bone, but their lengths are quite different, and while there are no other bones connected to the radius, some do connect to the ulna. In fact, if you start at the upper arm, there is just one other bone at the front of the limb before you reach the 'lepidotrichia' (the stiffening rods in the fin), but there are three at the hind end of the fin.

Click to enlarge.

This branching pattern was never explained in such books. In a newer book by SÃ©bastien Steyer, (who by the way is not just a palaeontologist but one of the driving forces behind the future book on future animals I discussed here earlier) you will find the images above. Mind you, besides the French and Dutch versions it is also available in English. The left part shows the fin/limb skeleton of Ichthyostega, and to the right SÃ©bastien has shown a series of limbs showing intermediate forms. Very well, I believe the transition happened, but have never stopped wondering about the branching patterns.

Click to enlarge. Copyright Gert van Dijk

So here are some old sketches. The one on the left in the middle row is more or less our current branching pattern: all fingers have equal numbers of segments (phalanges) and in the middle one of that row I experimented with different patterns: you could first split a limb into two parts and have these two each split into two more, etc. That would be equally 'consistent' in the sense that the number of steps from wrist to tip of a toe is the same. But in the right one on the middle row I played with another way of branching, in which some bones both give rise to a new bone and also continue downwards themselves. In the bottom row I developed the latter pattern some more, finally arriving at the right one, which looks like Ichthyostega's skeleton.

Click to enlarge. Copyright Gert van Dijk

And finally some sketches that show the design taken to extreme consequences. The left one is designed for a marshland creature that needs to spread its weight over a large surface. Mind you, I would never equip Furahan animals with legs that split that far up. I do not think that that makes much sense, as it will double the weight without appreciable advantages. Toes are good for many things: one good thing about them is that they extend stride length, and another is that they help spread weight, act as shock absorbers and help direct forces. Are more toes and longer toes therefore better than few short ones? Well, for these purposes, yes. But there is always a need to conserve mass and energy, so fewer and thinner bones have advantages too. As always, there is an optimum.
The foot on the right is suitable for a very heavy animal of a not too athletic build, rather like an elephant. Its toes are mostly there as shock absorbers and a means to transfer ground forces. They are good for standing and walking sedately. This particular design is not at all suited for athletic animals though, as the toes do not help extend stride length at all: they are much too short for that and hardly bend at all. If you want toes for an athletic animal, think of the feet of a chicken or a tyrannosaur. Well, now you known why I not like the feet of many of Barlowe's animals in 'Expedition' that much: he equipped active athletic animals with unsuitable elephantine feet.

But I digress. In the current Furahan redesign, I decided to build the anatomy of hexapod feet on a pattern that I thought I saw in the fin/feet of Devonian amphibians, that never seemed to be explained. So that is where the marblebill got its feet.

## Saturday 25 August 2012

### A marblebill in progress (also known as the becdacier)

No time this fortnight to write anything elaborate, unfortunately. Some posts take much more time than others. The ones that take most time are those that require checking the physical aspect of some matters, not just because finding sources and digesting the content takes time, but usually also because I then need to do some programming of my own or I have to make some specific illustrations. In short, the heavy science bits take a lot of time. Over the years I have written quite a few words on such subjects, and I started wondering whether I should perhaps bundle them, work them over, write some new chapters, and produce a book on the biomechanics of alien life. Something like 'Darwinian creativity in a Newtonian Universe'. The title is probably much too enigmatic for the book to sell, but perhaps it could be a subtitle. Mind you, it would be completely separate from the Furaha book. But would anyone buy it? Let me hear what you think.

Anyone, I have been working on an update of the marblebill. I showed you another such update once before, and the marblebill is on the Furaha website but featured previously on this blog as well. You may recognise some general update principles. The eyes on stalks are now less prominent, but certainly still occur in various species. There is also eye specialisation. The images below are taken from the sculpting program Sculptris, a free programme I recommend unreservedly.

Click to enlarge; copyright Gert van Dijk

The marblebill is an arboreal brachiating predator, and has two forward facing eyes to help it judge distances and fixate its prey. As is the case for dragonflies, the size of the ommatidia (the individual eyelets in a compound eye) depends on where you are in the eye: they are smaller in the part of the eye facing directly forward. This increases visual resolution at the price of sensitivity to light. The marblebill is a diurnal creature, which makes sense I think: you would need impossibly good vision to allow an animal to hurl itself from branch to branch at high speed at night.

Click to enlarge; copyright Gert van Dijk

There is another pair of eyes, the 'oculi posteriores'. Note that these were not posteriorly placed in ancestral hexapods, whose four eyes were placed around the head. What became the anterior eyes were once the bottom ones, and the posterior ones are the former upper ones. Anyway, in the marblebill lineage the upper ones, alresdy in the posterior position, over time migrated outwards, providing an all around vision, not just in the horizontal but in the vertical plane as well. For an animal living in three dimensions this is more important than for a grazing animal. One result is that it would not be easy to sneak up on a marblebill. Not that there is any other predator up there in the trees that would perform such sneakish acts anyway: it would be too dangerous. The marblebill also does not need much vertical vision for its territorial disputes, as these involve no sneaking whatsoever, but are announced frighteningly loudly. But detecting prey is another matter, and for that these eyes are superb.

Click to enlarge; copyright Gert van Dijk

Here is the painting in progress. I used to work out perspective and draw everything completely without any aid except for the occasional ruler, but I now make use of what the digital age has to offer. So I exported the sculpted head into Vue infinite, made certain the lighting came from the correct direction, adjusted the perspective angle and produced two renders. Cut out the head, place them on a separate layer in Painter 12 (to be deleted later), and everything is in place to start painting. Now all I need is the time to do so...

## Saturday 11 August 2012

### Why sight is superior to echolocation

In the previous post some characteristics of echolocation were discussed, and the results were somewhat worrying as far as a comparison with vision is concerned: echolocation involves 'shouting to hear a whisper', meaning that its range is limited and the sender is loudly proclaiming its presence.

Optics of pinhole and lens eyes. Source here

In my opinion there are two other major difficulties with echolocation that favour vision. The first is the ability to locate objects: with eyes such as ours it is very easy to locate objects. Rays of light can be bent by lenses and can reflect from surfaces, but in between they follow nice straight lines. That is the reason why even a simple pinhole camera such as in the image above will produce a good image: any particular point on the retina can only be lit be rays coming from a direction specific to that point. Such a pinhole will not let much light in, and solving that by increasing the pupil will blur the image. If you put in a lens you can have a large pupil for lots of light with a sharp image. Problem solved. The point of all this is that seeing an object is almost the same as knowing where it is.

From: Animal Eyes (2nd Ed.), Oxford; copyright Land & Nilsson

Above you see an image of lineages of eye design, leading to pinhole eyes and eyes with lenses. Those who wish to read more about eye evolution should read the new edition of Land and Nilsson's 'Animal Eyes'. It also describes the very high number of eye designs (there are even eyes based on mirrors!). Another very nice book is Evolution's Witness, with hardly any physics but boasting numerous examples of wonderful eye designs.

From: Animal Eyes (2nd Ed.), Oxford; copyright Land & Nilsson

In 1994 Nilsson and Pelger calculated that a good camera eye with a retina and a lens could evolve from basic elements without any localizing ability in fewer than half a million generations. With one generation a year this amounts to a geological blink of an eye (sorry for that one), meaning just half a million years. Vision can apparently evolve so quickly and conveys such a large advantage that some say it explains the runaway evolution known as the Cambrian explosion. In a very short time things such as armour, speed and vision evolved. Giving animals an unobtrusive ability for precise long-range sensing may just have been the impetus to start this accelerated runaway evolution: claws, shells, teeth and brains co-evolved quickly. Perhaps vision was not the only factor jump-starting the process, but the idea is too powerful to ignore a role for vision altogether, I think. It is tempting to think that most planets with complex life would have their own 'Cambrian Explosion' in the early evolution of complex animals. Of course, the label 'Cambrian' would not apply on Furaha, Snaiad, Nereus, nor on real exoplanets. We need a more general name for the phenomenon; how about the 'Sight Spark'? (and if it sticks can I copyright it?).

Back to sound

Seeing how a pinhole eye is simple and works well, how about evolving a 'pinhole ear'? Suppose we place lots of microphones on the inside of a sphere and cut a hole in front of the sphere to let sound in. Wouldn't each microphone only pick up sound from the bit of the world it 'sees' through the opening? If so, we would have an ear with perfect localising ability. Alas, no. Sound does not travel in neat straight lines but travels around corners. You can hear people talking through an open door even when you cannot see them.

Sound 'bending' around a building. Source here.

How the size of an opening affects diffraction of sound. Source here.

When sound waves hit objects, those interfaces form new sound sources, a process called diffraction. In the misbegotten 'pinhole ear' idea, the 'pupil' would simply act as a new sound source, so all microphones on the 'retina' would receive sounds from all directions. As a location device this would be utterly useless.

The physical reason why sound bends around corners and light does is not that diffraction is limited to sound. But in fact diffraction affects light and hence vision too. The effects of diffraction depend on wave length, and the wave lengths of sound have a range of a few cm to 15 or more meters; those of light are measured in micrometers. The diffraction of light is seen at microscopic scales, but that of sound occurs at the scale we live in, that of doors and people.

So the physics of sound conspire against it providing an easy way to tell where a sound is coming from. Evolution solved that problem as it did others, but the solution requires combining the signals from two ears (I know that using two eyes improves distance detection, but you can do it with one eye, and locating the direction of an object needs just one eye). Tiny differences in arrival time of a sound at two ears allow a suitable brain to calculate the direction of the source of a sound in the plane of the ears, but not whether it is to the front or the back nor up or down. Finding out things like that call for ingenious trickery such as tilting heads or complexly shaped outer ears that subtly change the characteristics of a sound depending on where it is. Wikipedia has a nice article on the subject. Some animals (owls!) perfected the art of sound location, but theirs is a small niche compared to the ubiquity of good camera eyes.

Mind you, I have no idea why there are no animals with more than two ears. Having four, placed at the corners of a tetrahedron, would be nice. Then again, perhaps there are arthropods with more than two functional ears. I have never heard of any but have not looked either. Are there any?

An unfair advantage of sight over echolocation

I wrote above that I thought there were two more difficulties with echolocation. The second one is based on the fact that echolocating animals have to produce their own signal, limiting the range at which they can detect anything. How about vision? There was an omission in the discussion, and it is a glaring one: the sun! (sorry about that one too). Sunlight, free for all and there regardless of whether anything of anyone is using it, is what allows vision to work as a long range sense. Compared to echolocation this free gift to sight is not really fair.

The images above were made for the previous post: the right one showed what echolocation might be like, with some energy coming from the 'camera', only illuminating objects close by. Compare that to the left image, a visual scene lit by the much more powerful sun.

But vision is not always available, and echolocation has a chance when there is no light. On rotating planets like ours, sunlight is only available for half the time, so the night would seem a good time for animals to start echolocating. But that is not the case; most animals prefer to more or less shut down at night. In previous discussions on when echolocation would be better than vision some dieas came up: caves, planets with permanent fog, planets without suns and seas underneath ice caps. One region seemed to have been forgotten though: the deep dark seas, where the sun does not reach. Shouldn't they be filled with echolocating animals, squeaking and pinging away? For Earth whales, the ocean floor may be too deep to reach, but fish were there a long time before the first whale ancestor took its first dive. Why are there no echolocating fish? I asked experts, but they did not know either. Fish have suitable ears and brains, and nothing seems to stand in the way of them evolving echolocation. But they have not. Or is echolocation simply too much like a burglar who enters a silent dark house and then starts shouting 'Hellooo!'? I do not know.

However, I do know of one final twist in the comparison of echolocation and vision; but I will keep that for the last post on this subject...

## Friday 27 July 2012

### Echolocation: a sound choice?

In January I wrote a post on whether detecting heat could supplant vision, and concluded that it was, in fact, just a form of sight. I wished to tackle echolocation next, but wondered where to start: with echolocating animals in fictional biology? Other possible questions would be which atmosphere would be best, which frequencies to use, how it can be compared with vision, etc. In the end I decided to start -there's more!- with a post on the nature of echolocation; so here we go...

The basic principle is simple: you send out a sound and if an echo returns, there is something out there. As everyone knows, dolphins and bats are expert echolocators., but it is less well known that some blind people are quite good at it, and that they in fact use their occipital cortex to process echoes, a brain region normally busy with analysing visual signals. That direct link between vision and echolocation is perhaps not that surprising, as both senses help build a spatial representation of the world outside: what is where?

A major difference between vision and echolocation is how distances are judged. In vision, judging distances depends on complex image analysis, but in echolocation the time between emitting a sound and the arrival of the echo directly tells you how far an object is away. The big problem here is that echoes are much fainter than the emitted sound. The reason for that is the 'inverse square law', something that works for light as well as for sound.

Click to enlarge; copyright Gert van Dijk

The image above explains the principle. Sound waves emanate from a source near the man in the middle and spread as widening spheres (A, B and C). As the spheres get bigger, the intensity of the sound diminishes per 'unit area'. A 'unit area' can be a square meter, but can also be the size of your ear. When you are close to the source your ear corresponds to some specific part of the sphere, and when you move away your ear will correspond to a smaller part of the sphere: the sound will be less loud. Now, the area of the sphere increases with the square of the distance. If you double the distance from the source, the area of the sphere increases fourfold, and the part your ear catches will decrease fourfold. To continue; increase the distance threefold and the volume decreases ninefold. Move away ten times the original distance from the source, and the sound volume becomes 100 times smaller!
In the image above, only a tiny fraction of the original sound will hit the 'object', a man, at the left. Not all of that will bounce back, and the part that is reflected forms a new sound: the echo. The echo in tun decreases immensely before arriving at the sender, and that is the essence of echolocation: to hear a whisper you have to shout.

Click to enlarge; copyright Gert van Dijk

As if the 'inverse square law' is not bad enough, there is another nasty characteristic of echolocation. At the left (A) you see a random predator using echolocation. Oh, all right, it's not random, but Dougal Dixon's 'nightstalker' (brilliant at the time!). It sends out sound waves (black circles) of which a tiny part will hit a suitable prey; there's that man again. As said, the echoes travel back while decreasing in strength (red circles).
There will be some distance at which a prey of this size can just be detected. Any further away and the returning echoes will be too faint to detect. Suppose that this is the case here, meaning 10m is the limit at which a nightstalker can detect a man (as mankind is extinct in the nightstalker's universe no-one will be hurt).
Here's the catch: most of the sound emitted by the nightstalker travels on beyond the prey. These sound waves can be picked up easily by other animals further away than 10 meters (I assume you recognise the creature listening there; it's pretty frightening). For animals out there the sound only has to travel in one direction and none of it gets lost in bouncing back from the prey. The unfortunate consequence of all this 'shouting to hear a whisper' is that the nightstalker is announcing its presence loudly to animals that it cannot detect itself!
This suggests that echolocation could be a dangerous luxury. One way to use it safely would be if other predators cannot get to you anyway. Is that why bats, up there in the air, can afford echolocation? Another solution would be to be big and bad, so you can afford to be noisy? If so, echolocation is not a suitable tool to find a yummy carrot if you are an inoffensive rabbit-analogue. The carrot does not care, but the wolf-analogue will.

---------------------

Getting back on topic, we now know that echolocation tells you how far away an object is. To make sense of the world you will also need to know where the object spatially: left and right and up and down. With hearing this is more difficult than with vision, but it can be done. The spatial resolution of bats is one or two degrees (see here for that), which is impressive but still 60 to 120 times less good than human vision. For now, let's take it for granted that an echolocating animal can locate echo sources. Next, let's try to visualise what it may be like.

Click to enlarge; copyright Gert van Dijk

Here is a scene with a variety of objects on a featureless plain. The objects have transparency, colours, shadows, etc. At one glance we see them all, as well as the horizon, the clouds, etc., without restrictions regarding distance, all in high resolution. The glory of vision, for all to see.

Click to enlarge; copyright Gert van Dijk

Colour is purely visual, so to mimic echolocation it has to go. All the objects are now just white. They are also all featureless, but that is for simplicity's sake only: vision and echolocation can both carry information about things like wrinkles and bumps, so I left texture out.

Click to enlarge; copyright Gert van Dijk

In sight the main source of light is the sun shining from above, but in echolocation you have to provide your own energy. To mimic that, the only light source left is at the camera. The resulting image looks like that of a flash photograph, for good reasons: the light follows the inverse square law, as does sound. Nearby objects reflect a lot of light (sound!) for two reasons: they are close by, and part of their surfaces face the camera squarely, turning light directly back at the camera. This is an 'intensity image'.

Click to enlarge; copyright Gert van Dijk

However, you can see nearby and far objects at the same time, but that is not true for sound. Sound travels in air at about 333 m/s, so sound takes about 3 ms to travel one meter. An object one meter away will produce an echo in 6 ms: 3 ms going to the object and 3 ms travelling back. The image above shows the same scene, but now the grey levels indicate the distance from the camera. Light areas in the image are close by, dark areas are further away. This is a 'depth image', formed courtesy of the ray tracing algorithms in Vue Infinite.