http://discovermagazine.com/2007/oct/space-faring-fungus-hats-and-synthetic-biology
10.22.2007
Space-Faring Fungus Hats and Synthetic Biology
If the science moves like Moore's law, get ready for bio-freakiness.
by Jaron Lanier


If you share my view that technology drives history more than any other
factor, then you will probably agree that the 21st century
is going to be significantly shaped by the outcome of a single question:
Will synthetic biology achieve radical success or not? In
this column I'll describe an early warning sign to watch for that will
give us a clue about which way this important new field is
headed.

Synthetic biology is the current term for the outer reaches of ambition in
biotechnology. More often than not, the notion includes
making artificial biology more like digital computation. It could hardly
be otherwise, for computers are central to most of the
prior art we have for building highly complicated structures from scratch.
Computers also symbolize the ultimate in freedom through
technology. You can hypothetically program a computer to do virtually
anything with its input and output devices. If we could only
find the right computer program to operate robotic medical devices, for
instance, we could create a robot surgeon to cure any
disease. If we could do the same with DNA and the other chemicals of life,
we could create a huge variety of novel creatures or
transform ourselves into astonishing new forms.

But if we entertain the idea that biotechnology is going to become more
like computation, we aren't being very specific, because
there is more than one kind of computation. In particular, it might be
more revealing to ask if synthetic biology is more likely to
turn out like digital hardware or software. That's an excellent candidate
to be the most important question of the century.

From a mathematician's point of view, hardware and software are
practically interchangeable. You can almost always emulate a chip in
software or implement a program as a chip. In practice, though, the two
things could hardly be more different. Chips get faster and
cheaper at a predictable, accelerating rate that is so reliable it is
known as a law-the famous Moore's law. Software typically gets
worse over time.

It's true that faster computers enable new software algorithms that
weren't possible before, like ones for machine vision (see
Jaron's World: Computer Evolution), but old programs don't necessarily get
better as hardware improves. In fact, they often lose
efficiency at such a breathtaking rate that they effectively cancel out
Moore's law when they are adapted to run on new, faster
machines. Try opening a similar word-processor document on old and new
computers: The performance is often similar, even if the
hardware has improved a thousandfold. How can this be? Software is so
difficult to work with that in practice it almost never
achieves its theoretical potential.

If synthetic biology turns out to improve in the accelerating way that
computer hardware does, we will be in for quite a ride. It's
hard to predict how weird things could get, so one is tempted to max out
deliriously as a futurist. Imagine an artfully designed
fungus that looks like a hat; when you put it on, it digests your head and
turns it into a still-conscious, rubbery Super Ball an
inch across, suitable for easy launch into space. Once there, another
fungus might then reconstitute your head and form a protective
life-sustaining bubble around it. (This prediction may go too far, but the
point is that it's hard to say by what margin.)

If synthetic biology instead turns out to be more like software, it will
still be amazing but in a more incremental, less
predictable way. We will witness a succession of plateaus of achievement
in areas like medicine and bioenergy. After a decade or
two, we might have engineered bacteria that make fuel out of old garbage
dumps, or maybe even a substantially artificial cell that
acts like a doctor, swimming through the body and fixing our own aging
human cells.

Then again, reality often violates our preconceived notions, and synthetic
biology could turn out to have a character that doesn't
resemble hardware or software. Natural biology is certainly unlike either
of those! It is flexible, as software ought to be from a
naive point of view, but it is not as fragile as software. Synthetic
biology may very well introduce a fourth kind of design
complexity that has some of the qualities of all three precedents.

Lately I've had the good fortune to be able to investigate this
possibility as a visitor at a remarkable lab in Berkeley called the
Molecular Sciences Institute, or MolSci, headed by Roger Brent. He and his
team are describing biological phenomena at a minute
level of detail, which could pave the way for synthetic biologists to
come. One of MolSci's innovations is a "tadpole," a
human-designed molecule with a protein head and a DNA tail that can
precisely count the number of rare molecules inside a cell. The
kinds of data that can be gathered at labs like MolSci are exactly what's
needed if we are ever to understand what is going on
inside a cell from a computational point of view.

The key to understanding complicated things like synthetic biology is
being able to break them into simpler things. Let's call this
modularity. Going back to the difference between hardware and software:
The problem a chip designer has to solve is modularized
completely within a tight conceptual box. The logic design of a chip is
perfectly specified, and the parameters of the physical
environment in which it will operate, such as the temperature, can be
carefully constrained.

We could create novel life or transform ourselves into astonishign new
forms.

Software, in contrast, makes contact with the wild world outside the
limits of comfortable abstractions. Even when you think you've
considered every condition that a piece of software will encounter, the
rebellious nature of reality (including the foibles of human
users) will come up with something to violate your assumptions. E-mail
programs were originally written without foreseeing that some
people would want to write viruses to pierce them.

http://discovermagazine.com/2007/oct/space-faring-fungus-hats-and-synthetic-biology
10.22.2007
Space-Faring Fungus Hats and Synthetic Biology
If the science moves like Moore's law, get ready for bio-freakiness.
by Jaron Lanier


If you share my view that technology drives history more than any other
factor, then you will probably agree that the 21st century
is going to be significantly shaped by the outcome of a single question:
Will synthetic biology achieve radical success or not? In
this column I'll describe an early warning sign to watch for that will
give us a clue about which way this important new field is
headed.

Synthetic biology is the current term for the outer reaches of ambition in
biotechnology. More often than not, the notion includes
making artificial biology more like digital computation. It could hardly
be otherwise, for computers are central to most of the
prior art we have for building highly complicated structures from scratch.
Computers also symbolize the ultimate in freedom through
technology. You can hypothetically program a computer to do virtually
anything with its input and output devices. If we could only
find the right computer program to operate robotic medical devices, for
instance, we could create a robot surgeon to cure any
disease. If we could do the same with DNA and the other chemicals of life,
we could create a huge variety of novel creatures or
transform ourselves into astonishing new forms.

But if we entertain the idea that biotechnology is going to become more
like computation, we aren't being very specific, because
there is more than one kind of computation. In particular, it might be
more revealing to ask if synthetic biology is more likely to
turn out like digital hardware or software. That's an excellent candidate
to be the most important question of the century.

From a mathematician's point of view, hardware and software are
practically interchangeable. You can almost always emulate a chip in
software or implement a program as a chip. In practice, though, the two
things could hardly be more different. Chips get faster and
cheaper at a predictable, accelerating rate that is so reliable it is
known as a law-the famous Moore's law. Software typically gets
worse over time.

It's true that faster computers enable new software algorithms that
weren't possible before, like ones for machine vision (see
Jaron's World: Computer Evolution), but old programs don't necessarily get
better as hardware improves. In fact, they often lose
efficiency at such a breathtaking rate that they effectively cancel out
Moore's law when they are adapted to run on new, faster
machines. Try opening a similar word-processor document on old and new
computers: The performance is often similar, even if the
hardware has improved a thousandfold. How can this be? Software is so
difficult to work with that in practice it almost never
achieves its theoretical potential.

If synthetic biology turns out to improve in the accelerating way that
computer hardware does, we will be in for quite a ride. It's
hard to predict how weird things could get, so one is tempted to max out
deliriously as a futurist. Imagine an artfully designed
fungus that looks like a hat; when you put it on, it digests your head and
turns it into a still-conscious, rubbery Super Ball an
inch across, suitable for easy launch into space. Once there, another
fungus might then reconstitute your head and form a protective
life-sustaining bubble around it. (This prediction may go too far, but the
point is that it's hard to say by what margin.)

If synthetic biology instead turns out to be more like software, it will
still be amazing but in a more incremental, less
predictable way. We will witness a succession of plateaus of achievement
in areas like medicine and bioenergy. After a decade or
two, we might have engineered bacteria that make fuel out of old garbage
dumps, or maybe even a substantially artificial cell that
acts like a doctor, swimming through the body and fixing our own aging
human cells.

Then again, reality often violates our preconceived notions, and synthetic
biology could turn out to have a character that doesn't
resemble hardware or software. Natural biology is certainly unlike either
of those! It is flexible, as software ought to be from a
naive point of view, but it is not as fragile as software. Synthetic
biology may very well introduce a fourth kind of design
complexity that has some of the qualities of all three precedents.

Lately I've had the good fortune to be able to investigate this
possibility as a visitor at a remarkable lab in Berkeley called the
Molecular Sciences Institute, or MolSci, headed by Roger Brent. He and his
team are describing biological phenomena at a minute
level of detail, which could pave the way for synthetic biologists to
come. One of MolSci's innovations is a "tadpole," a
human-designed molecule with a protein head and a DNA tail that can
precisely count the number of rare molecules inside a cell. The
kinds of data that can be gathered at labs like MolSci are exactly what's
needed if we are ever to understand what is going on
inside a cell from a computational point of view.

The key to understanding complicated things like synthetic biology is
being able to break them into simpler things. Let's call this
modularity. Going back to the difference between hardware and software:
The problem a chip designer has to solve is modularized
completely within a tight conceptual box. The logic design of a chip is
perfectly specified, and the parameters of the physical
environment in which it will operate, such as the temperature, can be
carefully constrained.

We could create novel life or transform ourselves into astonishign new
forms.

Software, in contrast, makes contact with the wild world outside the
limits of comfortable abstractions. Even when you think you've
considered every condition that a piece of software will encounter, the
rebellious nature of reality (including the foibles of human
users) will come up with something to violate your assumptions. E-mail
programs were originally written without foreseeing that some
people would want to write viruses to pierce them.