2014 Super Frog Christmas Extreme

Some snapshots of last year's lab Christmas decorations, along with a poem.
Link.
Credits to Govind Shah and other members of MCBL-O for designing and decorating.

Much Time Passes

Much Time Passes by Shigeki Miyake-Stoner

Bits of sand lay deep inside a heap of waste and garbage in a large land-empty. Much time passes.

Slowly, the sand amalgamates into small, clear glass crystals, which combine further into glass shards with razor-sharp edges.

Trucks start routinely coming and taking away load after load from the land-empty, carrying it away to facilities for processing. In one such truck, all the shards of glass amongst other scraps of materials, are picked up and dutifully carried away.

At the processing facility, the shards of glass are loaded onto a conveyor belt. Alongside the belt, people are at work, taking different sorts of items coming on their own conveyor belts, and placing them on the main conveyor belt to create a diverse mix of materials. Plastic bottles, metals, and cardboard combine into a disorganized mass.

At the destination of the conveyor belt, the mixture is aliquoted into bags, and the bags are loaded onto trucks to take them away. One such bag, containing the glass shards, finds its way on a truck heading into the city.

The truck arrives at one man’s house, and puts several of them into an empty, large black can. The truck leaves the filled can at the edge of the street by the man’s house.

At the street, he holds his breath and reaches into the large black can and pulls out a sealed bag from the top. He carries the bag inside and sets it into his source bin. He undoes the tie sealing the bag and attaches the edges of the bag onto the lip of the bin.

He turns the source bin on its side, and using a broom, he encourages the shards of glass from inside the bin out onto the floor.

The man waves his hand across the table, and the glass shards from the ground anneal with each other and lift up onto the table, assembling into a drinking glass in his palm.

The man slowly regurgitates water into the glass, and takes the glass to the swell, where he holds it under the tap, and turns the faucet to evacuate the water into the city lines. He puts the empty glass onto a shelf with other glasses.

A number of times he takes the glass from the shelf and rinses it in the swell, then regurgitates water into it and sends it back into the city lines. One time, instead of returning it to the shelf, he takes the glass and lays it gently into a box. He tucks the folds of the box into place, then runs his finger along the edges of the box to conjoin its tape and seal it.

The man carries the box to the Sell down the street and heads straight to the register, where he accepts money from the clerk, then he takes the box and puts it on a shelf alongside many other boxes like it. He wanders around the store and looks at other items for some time before leaving.

The clerk takes the box from the shelf, and puts it out on the curb where a courier picks it up and takes it away to a defactory.

At the defactory, the glass is unboxed and unwrapped by machines on a conveyor belt, precisely removing the tape and materials that have been the transport for the cup.

The glass cup is rotated in a furnace, and it is coaxed into a globular form with prodding metal bars. When it has become a featureless molten glob, it is returned to a large kiln which holds much more molten glass.

The molten mass of glass is cooled, and as it cools, bits of sand begin to crack off the primary mass into fine grains and becomes sand. The cooled sand is sent to a facility where trucks are loaded to take it to the beach.

The grains of sand are laid down gently on to a beach by a Filler. The machine fills a deep depression perfectly by pouring out the contents of its bucket.

The sand is slowly swept out to sea. Much time passes.

Working with R for the first time; installing a package written in an older version of R

First-time R user here. I struggled with getting the R package XenoCat working, here I describe how I got it to work, and some of the pitfalls along the way. The XenoCat package, created by Laajala et al. is a tool for statistically analyzing xenograft treatment experiments. See Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo.

I followed instructions in the instruction PDF from the XenoCat page, and downloaded the current version of R (3.2.0) from the R project homepage. The command in the instruction document to install the packages from the R command line was unclear, and kept throwing errors. I tried unzipping the XenoCat and other packages manually into the library sub folder in the R installation folder. This is not the same as installing, apparently.

Eventually I looked in the R FAQ and found that from the R GUI there is a Packages menu that installs packages. I selected and installed the dependent lme4 package, then selected the locally downloaded XenoCat_1.0.3.zip package. When I tried to access the XenoCat library, it told me it was built before R 3.0.0, and to reinstall it.

I was able to find a previous version of R that XenoCat was tested in (2.14) on the previous releases of R page, and after installing it and repeating the installation of the lme4 and XenoCat packages through the Packages menu in the GUI, it seems to be working.

I am leaving out many other stupid attempts I tried to get this to work, so I hope this document might help some other first-time R users get started with it. I frequently run into the problem of new jargon with new software that creates a significant barrier to entry.

First published article on genome editing in human embryos

Most other media sources have a bias on the impact and implications of the recent publication CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes by Liang et al.. If you want to read to yourself, you can download the PDF for free.

In short, the group tested the CRISPR/Cas9 genome engineering tools in non-viable human zygotes.

They discovered that their genome editing occurred at low efficiency, their intended target suffered repair from a endogenous sequence (a similar sequence on another part of the human genome) rather than using their donor oligos (synthetic DNA supplied to direct the intended mutation), and off-target mutation was observed. This is the first published article on genome editing in a model that is directly applicable to human health. This technology has been used in other organisms. The problems describe highlight the need to improve efficiency and specificity if this technology is ever going to have practical use.

How to Refresh Thumbnails on Google Chrome New Tab Page

In brief, for Windows 7: If you want to refresh the thumbnails shown on your Chrome browser New Tab page for your most visited sites, you can point your Run command or navigate your Explorer to the address:

%LOCALAPPDATA%\Google\Chrome\User Data\Default\

Then delete the file named "Top Sites." You will need to close Chrome when you are deleting it. When you re-open Chrome and open a New Tab, the thumbnails will be missing, but if you re-visit the pages, the thumbnails will repopulate.

The page at howtogeek.com describes how to do it for older versions of Chrome, but in the most recent version of Chrome (as of this posting on Windows Version 42.0.2311.90 m), the file you need to delete is "Top Sites" not "Thumbnails." This will probably also be the solution for other operating systems (Mac, Ubuntu, etc.).

Dropbox, no clutter please

Dropbox just introduced a new badge that floats around and attaches to the edges of windows in Windows OS.

Thank goodness it can be disabled, but it is an awfully intrusive design decision.