Musings of a bottom-up "design" engineer

I find the design methodology you humans have mastered, quite fascinating. No, there isn't a touch of mild condescension in that statement. You had very little time to iterate - I had way more time to iterate and improve than you did. So it's not fair to compare your design with mine. Actually, your designs are quite impressive considering the amount of time you had (by the way, I love your iPhone - neat).

Anyway, let me share with you some of my design nuggets in the upcoming articles. I will explain my design only using "common sense" terminology. To those of you who are biologists, I am afraid you may have to use the  inverse mapping table at the end of my articles to trace back from "common sense terms" that I use, to your vocabulary (which I have to confess, I find, quite daunting). Hopefully, you shouldn't have to inverse map often - my terms will reveal the mapping themselves  in most cases.

But before I share my "design nuggets", allow me to first brag by posing just one challenge that highlights what my machines can do:

Can you build a machine using all the natural material you want in the world, or even synthesize your materials, and  expend all the energy you need, but with the following constraints- 

  • the individual size of the raw material used to build your machine  should be no larger than a grain of sand, around 1 cubic millimeter. 
  • The manufacturing factory for your machine should be the very machine you are building . That is, your machine must be able to replicate itself. 
  • Your machine should be no larger than 27 cubic feet, the average size of a TV.

I am being very generous, I am relaxing the scale for you by a million. I can do it with raw material the size of  nanometers and my factory can be as small as a cube, 100 micrometers in length. I can build machines 100 feet long, all from factories the size of a  cube just 100 micrometers in length.    Another generous concession - your machines can shatter on fall like your iPhone, they don't have to survive even a 5 feet fall. Oh, and don't bother trying to emulate fancy features such as being able to "think". Just try building a self-replicating factory no larger than a TV box, with raw materials no larger than the size of a grain of sand - and you would replace my veiled hubris with total humility.

I bet you can't meet my challenge - at least not yet. :-)

No cheating like Craig Venter - he bootstrapped with  "my factory"! You have to play fair and make the self-replicating factory yourself.

If your immediate reaction is, "we can't even build a self-replicating machine, why all this constraint on its size?" You will see, with a little thought, that the size constraints on the materials and the machine are not really constraints. They are crucial clues to build self-replicating machines, at least of the kind I am aware of.  When building machines like mine, from "inside out" (that is growing in size over time), having raw material that is really small is an advantage. It gives tremendous control to assemble intricate structural designs. This "inside out" method of building  may seem counterintuitive to most of you because you are used to building bridges and houses by assembling large chunks of prefabricated pieces (even your circuit boards are built by adding prefabricated components, though they are small - granted you have recently started dabbling with ideas similar to mine in self-assembly).  Also, in my "inside out" design, having the factory, which is itself the building block, to be small, is an advantage - it enables the "self-shaping factories" to grow, replicate, and  morph to different shapes.

It is quite easy for me to explain the principles of my software design striking parallels with your world of software engineering. My hardware design however, has concepts that may not be intuitive at all, and may require some getting used to. The hardest thing to get used to, is how order can emerge on its own to create complex self-assembling, self-replicating machines, all from randomly moving atoms and molecules. I am starting this series with examples to give you an insight into just that "hard to fathom" concept. In all my examples, self-assembly and even goal oriented behavior, all emerge from randomly moving particles. Over time, once you get the hang of the underlying design principles, it will become more apparent how such emerging order from randomness can create self-replicating machines. The experience  is not unlike opening the hood of a car and marveling at the engineering inside. If you don't know car design, it will all seem like magic. But if you get an engineer who designed it give you an overview, things under the hood would start to make some sense. The only key difference from car design, however, is that the assembly of a car is done externally in a factory, even if automated. My machines self-assemble from within, and my factories full of these self-assembled machines, can self-replicate.

The core of my hardware design is self-assembly and self-replication. Lets take self-assembly first. You have already mastered a form of self-assembly, like assembling a car using robots - you call it automation. There is another form of self-assembly spanning scales  -  galaxies and planetary systems on the macroscopic scale to individual atoms at the microscopic scale. There is a common thread in all these forms of self-assemblies - some of them require expenditure of energy to assemble, while some assemble on their own without any need for energy input - like some atoms accidentally bumping into each other and spontaneously forming molecules. Some of my machines self-assemble without energy and  others need energy for assembly. What makes my self-assembly unique then?  My self-assembling factories can replicate themselves. So to summarize the essence of my hardware design - my factories are made up of self-assembling machines and structures, some of which require energy to self-assemble. My factories, which are themselves machines, can grow, morph to different shapes, and most importantly self-replicate. Now, you may ask, how did I make the first factory? Did I cheat like Craig Venter, and bootstrap my machines off someone else's work? Well, I didn't have anyone else around to steal from - it had to be original work. But I am only going to reveal, just as much as Fermat did, of his famous last theorem, "I have a remarkably simple bootstrap method, which this article is too small to contain". Surely, an Andrew Wiles will emerge and solve it for you some day.

Now a few disclosures are in order. It took few billions of years to make my machines. Oh, by the way, I didn't design at all - I lied.  You will see through my lie, assuming you read even some, if not all of my upcoming articles. It would become apparent  I did nothing.  Self-assembly dabbled with itself for a long time and a chance bootstrap event made one of the designs, self-replicating. From that point, my machines evolved on their own. All I did was, make a big bang...


Detailed Design notes and references - You can skip this section entirely

Self-assembly



Self-replication



Directed cargo transport in cells


 Convergence of biology and computing



 Craig Venter - a leading scientist who made significant contributions to genomic research, including pioneering the creation of synthetic DNA

 Fermat's last Theorem
Penned by Pierre de Fermat in the 17th century,
x(raised to the power of n) + y(raised to the power of n) = z(raised to the power of n), where n represents 3, 4, 5, ...no solution
Fermat wrote - "I have discovered a truly marvelous demonstration of this proposition which this margin is too narrow to contain."
In 1994,  Andrew Wiles announced a proof to Fermat's last theorem.

Fermat's Enigma: The Epic Quest to Solve the World's Greatest Mathematical Problem - a great book by Simon Singh on Fermat's last theorem and the quest to solve it by many mathematicians.
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