Sunday, February 27, 2011

Reality: analog, digital, or information compression continuum?

The Foundational Questions Institute (FQXi) has a thought-provoking new essay challenge for seasoned physicists, cosmologists, and lay-persons to answer: “Is Reality is Digital or Analog?

In one sense, analog and digital is not an either/or question but two points on a continuum. Analog and digital are different information compression algorithms, using frequency and amplitude as levers for modulating information onto electromagnetic spectrum. As analog has progressed to digital, so too could there be several subsequent phases of information compression algorithms that are denser than digital.

Along the electromagnetic spectrum (Figure 1), analog communication uses radio waves, analog and digital satellite communication uses microwave frequencies, and digital communication uses fiber optics in the visible spectrum. Next-gen terahertz communications systems are already under development.

Figure 1. Electromagnetic spectrum

Quantum computing modulates atoms with information. Eventually, maybe all atomic and energy quanta could be modulated with information (smart matter). In the farther future, modulating information onto the other three forces (strong, weak, and gravitational) could be explored, along with the modulation of dark energy and dark matter. Gadget of the future: dark energy multiplexer.

Figure 2. Harnessing gravity waves through muons despite their 1.56 microsecond half-lives?

Sunday, February 20, 2011

Transcranial magnetic stimulation

An emerging technique for working with the brain is transcranial magnetic stimulation (TMS). In TMS, an electromagnetic coil is placed on the scalp and delivers short painless bursts of energy to stimulate nerve cells in the brain.

TMS has been suggested as clinical tool for the neurorehabilitation of many conditions including depression, hallucination, pain, tinnitus, Parkinson’s disease, and stroke, and possibly for neural enhancement in improving focus and concentration. NeuroStar, a TMS device used in the treatment of depression, was cleared by the FDA in 2008.

The non-invasive nature of TMS also makes it useful as a research tool. Some recent research using TMS has improved knowledge of motor control and perception:

  1. adaptive motor learning in humans is related to cerebellar excitability and depression; motor learning could possibly be enhanced by noninvasive brain stimulation (paper)
  2. the right parietal and frontal eye fields play a key functional role in the spatial updating of objects in trans-saccadic perception (TSP), the process of constructing an internal representation of the world from successive saccadic eye movements (paper)

Sunday, February 13, 2011

New class of drugs: stapled peptides

Stapled peptides refers to a computational drug design technique that may create a whole new class of drugs by being able to more effectively target substances within cells and increase the number of proteins which can be targeted. Stapled peptides are generated through the synthetic enhancement of a 3-D alpha-helix protein segment with hydrocarbon bonds to make proteins more rigid and able to penetrate cell walls. The more rigid structure also gives stapled peptides longer lives through greater protease degradation resistance.

The two current classes of drugs, small molecules and biologics, are limited in that they can only target 20% of all proteins. Stapled peptides could allow a wider range of proteins to be used in drug-targeting. They are currently in clinical trials for the inhibition of a BCL-2 family protein, oncogene MCL-1, using an exclusive inhibitor, the MCL-1 BH3 helix, which could unblock caspase-dependent apoptosis in cancer cells (paper).

Sunday, February 06, 2011

Synbio update: reference standards, protein fusions, and bioscaffolds

One of the core tools developed and used by synthetic biologists is the Registry of Standard Biological Parts which has over 5,000 available parts (paper). A contemporary research focus is on improving methods for working with the standardized parts. Three recent innovations are described below.

1. In vivo reference standards
One advance is in establishing in vivo reference standards for the different biological parts. For example, the absolute activity of different promoters (gene transcription regulators) varies across experimental conditions and measurement instruments. Variation in promoter activity was reduced 50% by using a selected promoter as an in vivo reference standard against which other promoters were measured (paper).

2. Construction of protein fusions
Another advance is in allowing the construction of protein fusions. This is not feasible in the current assembly standard due to an unfavorable scar sequence that encodes an in-frame stop codon. Restriction enzymes BglII and BamHI are employed in a new assembly standard that replaces the scar sequence with a generally innocuous glycine-serine peptide linker (paper).

3. Rapid circuit generation with BioScaffolds
A third advance is in the creation of a new part, a BioScaffold, that can be used in the rapid generation of synthetic biological circuits. The BioScaffold can be inserted into cloning vectors and excised from them to leave a gap into which other DNA elements can be placed. Targeted circuit modification simplifies and speeds up the iterative design-build-test process through the direct reuse of existing circuits (paper).