Category Archives: Molecular Biology

Scientists Patent the Scientific Method

There has been a lot of talk in the news about the patent office awarding obvious or frivolous patents. I recently came across this one awarded to Palsson, Covert and Herrgard. I only read the abstract which is given here: “The present invention provides … Continue reading

Posted in General Interest, General Science Interest, Modeling, Molecular Biology, Synthetic Biology | Leave a comment

Modeling Course at Indiana University

Not that kind of modeling, but the kind that involves building computational models of biochemical networks and multicellular systems. James Glazier, the Director of the Biocomplexity Institute at Indiana University is the lead organizer behind a series of workshops that … Continue reading

Posted in General Science Interest, Modeling, Molecular Biology, Pathways, SBML, Software | Leave a comment

Standards in Synthetic Biology: Part 1

Standards What are standards and why should we bother developing them? I suspect to many people including my fellow scientists and perhaps even some engineers, that standards are nether a rewarding nor worthwhile endeavor. Standards however are the invisible hand … Continue reading

Posted in General Science Interest, Molecular Biology, Pathways, SBML, Synthetic Biology | 2 Comments

MAPK: Feedback Amplifier, Part I

A recent paper by Sturm et al., report results that support the hypothesis that the MAPK cascade acts as a negative feedback amplifier. The systems biology literature is full of reviews and articles about oscillators and bistable systems and very little else other than … Continue reading

Posted in General Science Interest, Molecular Biology, Pathways, Systems Theory | 2 Comments

Systems Thinking in Systems Biology: Part 2

In the last post I posed the question, what would happen to a metabolic pathway if we added an inhibitory drug to the middle enzyme in a linear sequence of steps? Here is the answer. Take a sequence of enzymes … Continue reading

Posted in Enzyme Kinetics, Molecular Biology, Pathways, Systems Theory | 1 Comment

Systems Thinking in Systems Biology: Part 1

Let’s say we inhibit an enzyme in a metabolic pathway by perhaps reducing the expression of the gene that makes the enzyme or more easily by adding a drug that inhibits the enzyme.What do you think will happen? When I … Continue reading

Posted in Enzyme Kinetics, Molecular Biology, Pathways, Systems Theory | Leave a comment

Molecule of the Month

If like me you find Molecule of the Month from the protein data bank interesting then this little widget from their web site packages up the molecule of the month into a convenient web tool.

Posted in Molecular Biology | Leave a comment

The Shrinking Transistor

How big are modern transistors? Surely they must be much bigger than an enzyme? Well, not quite. The picture below shows two transistors, both about 22 nm wide. Superimposed on top of the right-hand transistor is a single molecule of … Continue reading

Posted in Electronics, Molecular Biology | Leave a comment