In the news today:
“Governments, IOC and UN hit by massive cyber attack” (BBC)

How did the attack work? In a mind-numbingly ordinary way:

“An email would be sent to an individual with the right level of access within the system; attached to the message was a piece of malware which would then execute and open a channel to a remote website giving them access…they sometimes embedded themselves in the network and [tried to] spread across different systems within an organisation.”

In short:

• A person with broad authority ran a bit of code.
• The code, operating with this broad authority, wreaked havoc.

Quiz questions:

1. Why did the code inherit the person’s authority?
2. Is there a good reason for allowing this?
3. In the current model of computation, is it easy and natural to grant limited authority to individual computational objects?
4. What alternative model of computation (not an added security layer!) makes it natural to grant limited authority? What is it called? (Links, please.)

Questions for thought and discussion:

1. Why does the current computational model grant authority in this indiscriminate way? How does this lead to “sandboxing”?
2. What would be the main costs and benefits of moving computation toward the alternative model? How would this model play with the existing software base?
3. What are the leading implementations of this model today, at the language and operating system levels? In your opinion, should they be promoted more vigorously?

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I’m now working on a new book, Radical Abundance, scheduled for publication in 2012 by PublicAffairs. The book has a wide scope in both its content and intended audience, addressing scientists, a general reading audience, and thought leaders in the policy arena.

Radical Abundance will integrate and extend several themes that I’ve touched on in Metamodern, but will go much further. The topics include:

• The nature of science and engineering, and the prospects for a deep transformation in the material basis of civilization.
• Why all of this is surprisingly understandable.
• A personal narrative of the emergence of the molecular nanotechnology concept and the turbulent history of progress and politics that followed
• The quiet rise of macromolecular nanotechnologies, their power, and the rapidly advancing state of the art
• Incremental paths toward advanced nanotechnologies, the inherent accelerators, and the institutional challenges
• The technologies of radical abundance, what they are, and what they will enable
• Disruptive solutions for problems of economic development, energy, resource depletion, and the environment
• Potential pitfalls in competitive national strategies; shared interests in risk reduction and cooperative transition management
• Steps toward changing the conversation about the future

These topics interweave to make what will, I think, be a compelling story for readers with diverse interests, backgrounds, and concerns.

Update: As I mention in the comments, I’ll be posting the news on the blog when pre-orders are available, and inviting participation in pre-launch activities.

Publishers interested non-English-language rights please direct queries to Rosa at GeographicEngine dot com.

A paper in Science reports a design method that substantially advances the macromolecular technology base for building atomically precise nanosystems.

Background: foldamer engineering

As many readers know, biology shows an effective way build large, intricate, atomically precise systems: Use covalent chemistry to build chains of small building blocks, and design these chains to fold into nanoscale building blocks that undergo spontaneous assembly driven by Brownian motion and selective binding. This is a key step in climbing a ladder of fabrication technologies that leads to broader, more powerful capabilities.

The covalent synthesis of suitable chains of building blocks* was mastered decades ago, using programmable nanoscale machines that operate in biological systems. Designing structures that fold into compact nanoscale objects has become increasingly routine. Designing these building blocks to assemble, however, has lagged.

The approach

This highlights the importance of the paper in Science.

The authors (from the Baker lab, and I’m tempted to add “of course”) used RosettaDesign-based protein engineering tools to design proteins with surface structures that bind to a natural protein at a particular location, and with a particular orientation. Finding a protein that binds isn’t too hard — screening and evolutionary methods applied to antibodies (among other proteins) can do this — but achieving high affinity (tight binding) in a specific geometry is new.

They achieved this by designing binders with the correct geometry but mediocre binding, and then using selection (the equivalent of antibody affinity maturation) to refine the interfaces to achieve high affinity. The refinement process retains the initial alignment with good fidelity.

The binding target was a conserved region of the influenza hemagglutinin molecule, hinting at an approach to developing a subtype-independent anti-influenza therapy.

Solving a harder problem than necessary

Note, however, that authors didn’t address the problem of designing building-block interfaces, as an engineer would understand the task: They did something harder. Only side of the interface was designed to bind, while the other was a naturally occurring structure that normally binds nothing.
An engineer designing building-block assemblies, by contrast, would design the interface as a unit, not just one side of it.

It’s easy to see the advantages of being free to tweak both sides to achieve a good fit, to balance solubility and costs of desolvation, and to introduce specific binding interactions (hydrogen bonds, salt bridges, hydrophobic pockets on one side that match hydrophobic side chains on the other, etc.). Freedom to design both sides together also means that protein engineers — when pursuing engineering objectives — can exploit the best-understood motifs, rather than deliberately plunging into the unknown.

In conventional engineering, no one designing a system would freeze the design of one component, and then attempt to mate another to it at a location not designed for the purpose. Interfaces aren’t afterthoughts.

A companion perspective piece for the paper observes that

Although Fleishman et al. have produced a landmark result, it is evident that computational protein interface design is not a solved problem.

For the more symmetric engineering design problem, however, the methods described in the paper can be expected to provide a basis for reliable design tools.

I look forward to seeing the methods and the lab results. This should be low-hanging fruit.

* In other words, peptide foldamers (commonly called “proteins”) which include a range of high-performance engineering polymers.

See also:

• A High-Performance Polymer for Nanosytems Engineering
• Macromolecular Modeling for Molecular Systems Engineering
• The Molecular Machine Path to Molecular Manufacturing (1):
  Foldamers and Brownian Assembly
• The Antiparallel Structures of Science and Engineering

Wiley India publishes textbooks “catering to the needs of Indian students”, and now offers Nanosystems:  Molecular Machinery, Manufacturing, and Computation, the book I wrote on the principles and potential components, architectures, and implementation pathways for high-throughput atomically precise manufacturing systems.

Here’s a list of Indian distributors.

Wiley India, a branch of John Wiley & Sons, the original publisher, placed the book with the Wiley Precise Textbook series,

a uniquely designed series to help students in scoring well in the examinations as the content is exactly as per the prescribed syllabi. The focus of this series is to explain the concepts supported by examples for easy understanding.

I’m not sure that Nanosystems entirely fits this description, but I won’t complain. Indian readers are frequent (and thorough!) readers of what I’ve posted here at Metamodern and at E-drexler.com.

If you don’t have a shipping address in India, try Amazon.

Sample chapters,
 detailed table of contents,
 and glossary

Roadmaps are crucial in developing new technology platforms — in other words, for the coordinated development of complete sets of compatible technologies that, taken together, support system-level technologies at a new level. Whether formal or informal, roadmaps address a fundamental problem of risk and mutual expectations in technology development: the problem of giving all necessary parties sufficient confidence that other parties will deliver the full set of technologies needed build functional systems.

Without that confidence, technology research can decay into a flurry of useless, context-free demos, and the development process can approach paralysis. With that confidence in coordinated, reality-based development, timely developments emerge, mesh, and spur the next round.

The International Technology Roadmap for Semiconductors

For decades now, a formalized roadmapping process with a 15-year horizon has helped to drive the Moore’s Law revolution in electronics. This cooperative, industry-spanning effort produces and updates the massive ITRS document, the International Technology Roadmap for Semiconductors.

This roadmap process has sped progress by coordinating efforts and reducing the risk of doing what’s necessary.

Each generation of lithography has required a set of improved and compatible technologies for light sources, optics, masks, steppers, resists, and a raft of other process and packaging technologies. To invest with confidence in developing a shorter-wavelength light source (of adequate collimation and brightness), and at a particular time, one must have confidence that there will be a market — and a market will exist only if other companies deliver the compatible optics, masks, stepper, and all the rest, and if the major producers plan to build fabs based on this suite of next-generation technologies.

The ITRS process provides that confidence and crystallizes the shared expectations into public documents.

Without shared expectations for coordinated development on a known timeline, the situation will tend toward deadlock. Not much happens if everyone waits for everyone else to provide what’s needed to create demand for everyone’s next-generation product. Only incremental improvement are safe in that sort of environment, because to avoid suicidal risk, each developer must maintain compatibility with what already exists.

Everyone yearning for something better, no matter how universal and specific the yearning may be, isn’t enough in itself. Only mutual expectations of action can give developers the confidence to invest in their hot new technology at a time when demand for it may be nil.

For another example of this principle, note that IT standards development often serves as a roadmap, building confidence, for example, that devices will be available that fit the protocols and plugs at both ends of a cable.

Quantum Information Science and Technology Roadmap

Shared expectations that span technologies and industries are crucial in the semiconductor technology, and formalized roadmapping ensures that there will be no show-stoppers, no missing technologies for the next-generation technology platform.

It’s a different story for radical innovations in technology (such as quantum information processing) but again, if the aim is to build systems, real progress requires a roadmap-level conception of where it’s all going. Without a roadmap that defines requirements, thoroughly useless “advances” can be hyped as breakthroughs, and throughly practical technologies are apt to find no use simply because research on the needed complementary technologies never became fashionable.

The Quantum Information Science and Technology Roadmap shows a way to do roadmapping in a domain where the nature of practical physical implementation technologies remains uncertain. Participants in the ITRS can safely assume that silicon will rule for years to come, but the QISTR collaboration faced a range of fundamentally different competing approaches: qubits represented in the states of (pick one or more:) trapped atoms in vacuum, embedded atoms in silicon, nuclear spins in small molecules in liquids, and photons in purely photonic systems. These approaches differ radically in scalability and manufacturability, and in the range of functions that each can implement.

The QISTR document therefore rises to a higher level of abstraction than ITRS, presenting the “DiVincenzo promise criteria” for functional system elements and then comparing diverse approaches in terms of those criteria and the metrics that go with them. The document addresses both the status of each candidate component technologies and what physics can tell us about its future potential.

The use of criteria and metrics in the QISTR shows a way to build a shared definition of problems and a basis for expectations in fields that buzz with multiple options for system components, and where the completeness and compatibility of sets of component technologies can’t be taken for granted.

The Technology Roadmap for Productive Nanosystems

The development of atomically precise nanotechnologies is an ongoing process, and Productive Nanosystems: A Technology Roadmap, a Battelle-led effort hosted by several of the U.S. National Labs, surveys paths forward from current atomically precise fabrication technologies toward atomically precise manufacturing. To quote from the Executive Summary:

This initial roadmap explores a small part of a vast territory, yet even this limited exploration reveals rich and fertile lands. Deeper integration of knowledge already held in journals, databases, and human minds can produce a better map, and doing so should be a high priority. Some research paths lead toward ordinary applications, but other paths lead toward strategic objectives that are broadly enabling, objectives that can open many paths and create new fields. These paths are the focus of this roadmap. They demand further exploration.

Successful engineering (unlike successful science) requires coordination. Tightly managed projects that deliver products to market are at one end of a spectrum of coordination mechanisms; international, cross-disciplinary roadmapping in the exploratory stages of technology development is at the other. Both can be invaluable.

See also:

• The Antiparallel Structures of Science and Engineering
• Science and Engineering: A Layer-Cake of Inquiry and Design
• Exploratory Engineering:
  Applying the predictive power of science
  to future technologies

The American Vacuum Society writes to announce ALD 2011,
the 11th International Conference on Atomic Layer Deposition:

Atomic layer deposition (ALD) is a fast-moving frontier, profoundly impacting diverse applications and gaining momentum for industrialization and manufacturing, while leaving plenty of room for new science and innovation….

ALD is receiving attention for its potential applications from advanced electronics, microsystems, and displays to energy capture and storage, solid state lighting, biotechnology, security, and consumer products

Atomic layer deposition processes resemble the iterative, solid-anchored (“solid-phase”) chemical synthesis processes used to make atomically precise macromolecular structures: Both processes work by cycling chemical reaction conditions to add a single something, then activate it, then add another. In peptoid/peptide/nucleic-acid synthesis, the “somethings” are monomers that extend an oligomeric chain; in ALD, they are atomic layers that extend a crystal lattice.

Zyvex Labs is pursuing patterned ALD to control the other two dimensions of structure; they are developing technologies that use scanning probe tips to interpose cycles of surface activation and layer deposition with atomically precise lateral control. This approach is discussed in the roadmap for atomically precise manufacturing.

From the Zyvex home page:

Zyvex Labs is the Founder and Manager of the Atomically Precise Manufacturing Consortium. This 5-year, $15M program is equally funded by DARPA, the State of Texas, and Zyvex Labs…

Zyvex and our APMC collaborators are developing the tools to build atomically precise products atom-by-atom, under computer control. Creating such Digital Matter in massively parallel nanoscale factories will lead to revolutionary new products ranging from simple quantum dots and atomically accurate metrology standards, to powerful energy harvesting and storage devices, and eventually to stunning nanomedicine capabilities.

ALD products differ radically from self-assembled molecular systems, and the two technologies could work together, with a final layer of self-assembled structures adding unique functionality to crystalline ALD systems.

See also:

• Atomic Layer Deposition
  for Atomically Precise Fabrication (1)
• AFM Atom Manipulation: A surprising technique

I’ve updated “The Physical Basis of High-Throughput Atomically Precise Manufacturing”. Not a big change, but I expanded the discussion of reliable molecular modeling of selected, highly constrained systems, along the lines discussed here: “Making vs. Modeling: A paradox of progress in nanotechnology”.

Soon after Earth’s life first touched the Moon, NASA promised to make spaceflight routine and inexpensive, and I began studying the prospects for space as a genuine frontier.

Geologists had analyzed the new, hard-won lunar samples, and I read up on the results in the local college library. Not nice: almost no carbon, nitrogen, or hydrogen, and no obvious promise of a decent mineral ore. Asteroids, by contrast, had been delivering samples for free in the form of meteorites, year after year. Much nicer: Lots of carbon, nitrogen, and hydrogen, along with nickel-alloy steel, a substantial dash of platinum metals, and (of course) a little or a lot of everything else.

I summarized the case for bypassing the Moon in favor of asteroids in a 1983 advocacy piece written partly about resources and engineering, and partly about cognitive biases favoring the Moon.

The biases held, though, and the Groundhog vision has been Back to the Moon!— until recently, culminating in last week’s Presidential statement announcing a plan to

…abandon another landing on the moon, and develop new technologies to send astronauts to an asteroid by 2025….

New York Times, 3 June 2010

In terms of relative priorities, I like it.