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Blog Profile / assertTrue

Filed Under:Technology / Programming
Posts on Regator:545
Posts / Week:1.9
Archived Since:March 20, 2009

Blog Post Archive

Putting a News Stream into a WordPress Site

Over at, I managed to put together a News page in record time using the WordPress plugin HungryFEED. The (free) plugin was worth its weight in gold. And validates (in my mind) the superiority of the WordPress platform as a blogging platform.Most plugins are easy to install or uninstall on WordPress and can be figured out quickly. Show More Summary

Last Responsible Moment

A military officer who was about to retire once reportedly said: "The most important thing I did in my career was to teach young leaders that whenever they saw a threat, their first job was to determine the timebox for their response. Show More Summary

Amazon and Acquia

A fascinating news tidbit surfaced a few days ago at CMS Wire. It seems Amazon has invested in Acquia (the company that provides commercial support for Drupal, the popular open-source content management system), at a time when Acquia...Show More Summary

Complexity Begets Charm

Giamatti and Curch in Sideways. Today's post is reblogged (with permission) from took me ten years to finally get around to watching the quirky 2004 bromance Sideways, starring Paul Giamatti, Thomas Hayden Church, Virginia Madsen, and the ever-piquant Sandra Oh. Show More Summary

When Is It Really Necessary to Hold a Meeting?

Jason Fried explains very nicely, in a 15-minute TED talk (watch it here), why the modern office is a singularly poor place in which to get work done. Bottom line: The modern office is specifically designed to facilitate interruptions. Show More Summary

Hachette vs. Amazon: A Trader's Perspective

Hachette and Amazon are locked in a pricing dispute that's gone on for some time now. It may eventually be resolved, although frankly, it could well go unresolved, too; Hachette doesn't have to cave in to Amazon's demands. Hachette may...Show More Summary

A Workflow Wish List

In my day job, I evaluate content management systems (enterprise-grade systems, not light-duty blogware), and I get to see and touch a lot of so-called workflow systems. This is the part of the system that (for example) routes documents...Show More Summary

Complementing Codons: A Riddle Solved?

For some time now, I've been puzzling over a fairly big riddle, and I think an answer is becoming clear.The riddle is: Why, in so many organisms, do codons turn up at a rate approximately equal to the rate of usage of reverse-complement...Show More Summary

Pearson vs. Spearman: A Tale of Two Correlations

One of the most rudimentary yet most valuable types of statistics you can calculate for two data sets is their correlation value. Two widely used correlation methods are the Pearson method (which is what we normally think of when we think "correlation coefficient"), and the Spearman Rank Coefficient method. Show More Summary

A Large Genome with Lots of Structure

In contrast to higher life forms, bacteria usually have compact genomes, with few duplicate genes and very little non-coding DNA. But some bacteria, for reasons not entirely understood, accumulate relatively large genomes. A good example...Show More Summary

A Tiny Genome with Lots of Structure

Mycoplasma genitalium is a super-tiny bacterial parasite of the human urinary system, causing about 15% of urinary infections in men. Its genome, encoding just 476 protein-coding genes, is often cited as the smallest genome of any organism that can be grown in pure culture. Show More Summary

Books Everyone Says Everyone Should Read

I found the graphic below in David McCandless's book Information Is Beautiful and felt it was worth sharing; I couldn't stop looking at it. Click to enlarge. Sad to say, I've read shockingly few of these titles (maybe twenty percent of them?). Show More Summary

Why So Many Helicases?

Many DNA-processing genes have an unusual amount of internal complementarity: regions of DNA in which the DNA can fold back on itself to form stable structures. A good example is the dinG gene of Mycobacterium tuberculosis, which encodes an ATP-dependent helicase. Show More Summary

A Different Approach to Anti-Aging

In this fast-paced talk by Dr. Aubrey de Grey, we hear about a breathtakingly radical approach to forestalling aging, which (in a nutshell) involves moving all remaining mitochondrial genes into the nuclear DNA, so that mutations in mitochondrial DNA, per se, are rendered irrelevant. Show More Summary

Thermometer Genes

Heat shock proteins are an interesting class of proteins that provide "damage control" for enzymes when temperatures rise to the point where proteins start to unfold and refold improperly. Protein 3-dimensional structure is critical to proper enzyme function, and it doesn't take much thermal jostling to mess up a protein's structure. Show More Summary

How Do Bacteria Survive Radiation Damage?

Secondary structure of the Trad_1400 gene (encoding a MutT hydrolase) in Truepera radiovictrix. In the 1950s, a tin of meat was exposed to a dose of radiation that was thought to be capable of killing all known forms of life, but the meat subsequently spoiled, and Deinococcus radiodurans (dubbed Conan the Bacterium by some) was isolated from it. Show More Summary

March of the Microbes

It can be hard to convey to non-biologists, who may think of germs as pests (an unseen, unclean residue to be neutralized with disinfectants), the grandeur and miraculous intricacy of microbial life. After more than three billion years...Show More Summary

A Manganese Catalase Fusion Protein

In science, it often happens that finding the answer to a particular mystery only leads to further questions. That's certainly the case with the non-heme/manganese-based catalases in bacteria (which I talked about in a previous post). Show More Summary

The Other Catalase

Microbiology students are taught from Day One that strict anaerobes (organisms that are killed by exposure to oxygen) lack the enzyme catalase, which breaks down hydrogen peroxide to water and O 2. You're already familiar with this enzyme...Show More Summary

Odd Structures in a Prophage Genome

Contrary to what it looks like, this is not an arrival-gate diagram for an eastern European airport. It's a diagram of secondary structure of a portion of the mRNA for the yoqJ gene in B. subtilis phage SPBc2. Click to enlarge. The common soil bacterium Bacillus subtilis has long been known to harbor an inducible prophage (virus) called SPBc2. Show More Summary

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