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Deus Ex Machina

April 4, 2009

As long as human beings have been able to think, they have been wondering just exactly what the point of everything is and trying their best to explain their surroundings. Priests, philosophers and scientists have all given it a go, sometimes combining the various disciplines to come up with some answers to describe the reality around us. But every layer of the onion that gets peeled back leads to more questions about what’s really inside.

In the modern computer age, some have speculated that all we see around us may be just an illusion, just part of some vast computer simulation we, with our five limited senses, are unaware of. Is it possible that we are just part of the Matrix? A couple of new scientific developments provide some food for thought.

Take a look at this picture.

Looks like a collection of sea shells any beachcomber may have put together. But it isn’t. All the ‘shells’ in the picture were created from a computer simulation designed by a Berkeley grad student.

ScienceDaily (Apr. 2, 2009) — University of California, Berkeley, graduate student Alistair Boettiger has amassed a beautiful collection of seashells, but not by combing the beach. He created them in his computer.

He and George Oster, a UC Berkeley biophysicist, along with University of Pittsburgh mathematical neuroscientist Bard Ermentrout, have written a computer program that generates the complex patterns of seashells using simple principles developed to explain how the brain works and how memories are stored.

The “neural net” model explains how mollusks build their seashells based on the finding that the mollusk’s tongue-like mantle, which overlaps the edge of the growing shell, senses or “tastes” the calcium carbonate layer laid down the day before in order to generate a new layer.

“The pattern on a seashell is the mollusk’s memories,” said Oster, a professor of environmental science, policy and management and of molecular and cell biology. “The shell is laid down in layers, so the mantle is sensing the history of the mollusk’s ‘thoughts’ and extrapolating to the next layer, just like our brains project into the future.”


“The model gives us a remarkable ability to explain much of the dramatic diversity of both shape and pattern that we see in the natural world,” Boettiger said.

To build their model, the UC Berkeley scientists first studied electron microscope images of mollusk mantles in order to understand the network of neurons connecting the sensing cells in the mantle with the secretory cells that produce calcium carbonate and proteins – many of them colored pigments – incorporated into the growing shell. Different rates of calcium carbonate secretion determine the shape of the spiral, while different amounts of pigment secretion create a pattern unique to each species.

They then modeled the size of the excitatory and inhibitory regions surrounding the secretory cells and the cells’ firing thresholds – nine parameters in all – as a neural network that determines how much calcium and pigment is secreted.

Based solely on these nine parameters, Boettiger, Oster and Ermentrout were able to reproduce the shapes and patterns of almost every known sea mollusk.

And Cornell researchers have developed another algorithm which allows a computer to deduce physical scientific laws from observed data without any knowledge of the underlying science . Again from ScienceDaily:

The researchers have taught a computer to find regularities in the natural world that become established laws – yet without any prior scientific knowledge on the part of the computer. They have tested their method, or algorithm, on simple mechanical systems and believe it could be applied to more complex systems ranging from biology to cosmology and be useful in analyzing the mountains of data generated by modern experiments that use electronic data collection.


Their process begins by taking the derivatives of every variable observed with respect to every other – a mathematical way of measuring how one quantity changes as another changes. Then the computer creates equations at random using various constants and variables from the data. It tests these against the known derivatives, keeps the equations that come closest to predicting correctly, modifies them at random and tests again, repeating until it literally evolves a set of equations that accurately describe the behavior of the real system.

Technically, the computer does not output equations, but finds “invariants” – mathematical expressions that remain true all the time.

“Even though it looks like it’s changing erratically, there is always something deeper there that is always constant,” Lipson explained. “That’s the hint to the underlying physics. You want something that doesn’t change, but the relationship between the variables in it changes in a way that’s similar to [what we see in] the real system.”

Once the invariants are found, potentially all equations describing the system are available: “All equations regarding a system must fit into and satisfy the invariants,” Schmidt said. “But of course we still need a human interpreter to take this step.”

The researchers tested the method with apparatus used in freshman physics courses: a spring-loaded linear oscillator, a single pendulum and a double pendulum. Given data on position and velocity over time, the computer found energy laws, and for the pendulum, the law of conservation of momentum. Given acceleration, it produced Newton’s second law of motion.

It takes quite a while to perform the necessary calculations, but even that may be made easier one day as scientists get closer to developing quantum computers which can process data orders of magnitude faster than what is currently available. Use one of these to process the mountains of data expected to be produced by the Large Hadron Collider and who knows, it may turn out that life is but a dream after all.

16 Comments leave one →
  1. cometman permalink*
    April 4, 2009 10:03 am

    Hey I got it to work! Just copied it from FSZ and the only thing that came out different was that the pic isn’t centered.

  2. Stemella permalink*
    April 4, 2009 10:14 am

    Woo Hoo! Bravo.

    You can center the pic in edit mode. It’s like a MS Word center button.

    You know, the older I get the more I welcome our computer squid shaped overlords. Humans suck at managing this planet. Maybe computers would do a better job. Of course the first order of business would probably be to extermine us as hideous parasites. ;)

    Speaking of which… I caught a whole rat last night! Now I get to give him “swimming lessons”

  3. Stemella permalink*
    April 4, 2009 2:14 pm

    I figured out a way to add some cephalo pics to the front page for decoration. See lower right side. They are the podkeepers to ward off evil spirits. It is in the widget function for added text. I just pasted in some flickr pics. Feel free to add more, or post some jpg links and I can add more. I did get your mimic in there plus a cool translucent one. Had to have a dumbo too. If you do post some, be sure to keep the width at 250 or less.

    • cometman permalink*
      April 5, 2009 4:09 pm

      Looks good! I’ve got one I’m going to try to add to see if I can figure it out.

      • cometman permalink*
        April 6, 2009 6:07 am

        OK, do you have to use Flickr to post pics to the sidebar? I only have a photobucket account right now.

  4. udg permalink
    April 4, 2009 3:34 pm

    Cool, cometman!

    Don’t know whether you did this or not, but under “settings” > “discussion” > “Enable threaded (nested) comments levels deep” you can set comment nesting/threading to 10 deep. Maybe this link will work for you

    • Stemella permalink*
      April 4, 2009 4:38 pm

      Thanks udg, I did set the thread depth to max of 10, knowing how we can get carried away in threads. I also took the liberty of setting you to contributor status. If you think you’d like to post front page posts on a regular basis, let us know and either cometman or I can bump you up to author. Welcome!

      • April 4, 2009 11:09 pm

        Awesome & thank you, Stemella! Great content & I love the imagery here!

    • cometman permalink*
      April 6, 2009 6:11 am

      Hi udg. Thanks for stopping by and for the link. I’m just learning about all this wordpress stuff so that was helpful. Now I know how to turn off the function that sends me an email every time somebody posts a comment!

      I think we can set things up so that after you post one comment the others appear without having to be approved by anybody. Stemella? Do you know if that’s right? I haven’t been checking to see if any are waiting.

      • Stemella permalink*
        April 6, 2009 6:56 am

        I’ve been checking on the comments page, so far no problems. I’ve got it set that commenters need to be registered on wordpress to comment here but other than that don’t need approval to comment. They should all come through.

        As to the photo thing, you can use a photobucket link. Just paste it below the ones I have in there already. I’ve saved them in case there’s a glitch. If you can’t make it work, just post your jpeg in a comment and I’ll paste them in.

        • cometman permalink*
          April 6, 2009 7:30 am

          Got it to work with photobucket photos. But evidently some of the pics were smaller to begin with and when I put in width=250 they ended up being fuzzy. Any idea how to get back the proper resolution?

          • Stemella permalink*
            April 6, 2009 7:36 am

            Try changing the resolution in your photobucket acct and then repasting the link without width parameters? Or just remove the width parameters from the current link and see how it looks?

            • cometman permalink*
              April 6, 2009 8:18 am

              Ok. I’ll play around with it. That fuzziness is not aesthetically pleasing and cannot be allowed to stand!

            • cometman permalink*
              April 6, 2009 8:32 am

              Took out the width parameters. Looks better but I’d still like to get them all the same size with good resolution, if only so I know how to do it. I’ve been playing around with photobucket trying to resize images for months now and haven’t been able to get the resolution right. Usually what I end up doing is seeing if I can find the same pic I want in a different size at a different link but that is a big time waster.

              • Stemella permalink*
                April 6, 2009 8:41 am

                Here’s a pretty large sized one of the cat

                and check this one out! haha

                Here’s another deadsite for our blogroll – I think we should highlight dead sites. It seems so right somehow!

                • cometman permalink*
                  April 6, 2009 9:03 am

                  Just switched out the pic and got the cat fixed.

                  Not sure how to fix the other one. Doesn’t look that good small and there isn’t much to crop to make it more square either. I’ll try again later or just delete it if I can’t figure it out.

                  And Cthulu Cat. Ha!

                  And in the useless info dept I just did a quick search for ‘dead’ sites and discovered that there is no website. Who would have guessed…

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