Notes on Cambrian Explosion and origins of genes

One of the benefits of teaching at University is that you need to stay current in your field, but also be able to explain new findings in contest of larger issues. One can only do so much, but clearly as one who teaches about evolution, need to keep up with the big historical concents like transitional fossils and the Cambrian Explosion. Not my field, I’m more comfortable with evolutionary genetics. But in preparing for a lecture I did a little work on these areas and list here some of the references I found useful.

Erwin et al (2011) The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals. Science 334(6059):1091-1097. Puts new fossil findings into context with evidence for environmental changes. Suggests role for acquisition of new forms of regulation of development as key.

Fossils come in to land — Covers a point-of-view debate over whether fossils deemed to be early marine organisms found in rocks of the Ediacaran period in South Australia were instead evidence for fossilized soils. This would suggest that these Ediacaran organisms lived on land. If true, that’s an invasion of land much earlier than the dates in textbooks.

Origins of new genes http://www.nature.com/nrg/journal/v4/n11/abs/nrg1204.html

Lyson et al (2010) Transitional fossils and the origins of turtles. Biology Letters 6(6):830-833 Discusses role of new fossils applied to phylogeny reconstruction and adds to the debate over whether turtles form clade with Diapsids or Archosaurs or are outside these relationships. Discusses differences in results/implications between morphology and molecular datasets.

Uninstalling applications on Macs

Computers come today with lots of pre-installed software, some of which you will use and depend on, others you rarely if ever use. Overtime, and after repeated visits to web sites, after unexplained crashes, etcetera, it may be time to manage the software bloat.

On PCs, use Task manager, on Macs, use Activity Monitor to learn about software processes that are running — check to see of you ever use the associated applications. If you do not, go ahead and uninstall the application.

Windows users know about the Control Panel and running the uninstall option for Programs and applications. This works pretty well, but still may leave some application data scattered at locations on your hard drive that you may want to track down.

However, this post is directed at my Mac-using-students. Mac users may know about dragging applications to the Trash, they may be unaware that this removes none of the libraries that may be installed to support the application. To perform a clean uninstall, users should load and run something like Appcleaner.

“I am uncomfortable downloading and installing files from the Internet.”

I teach a number of courses at Chaminade University that depend on software. Mostly, the software is open source, and universally, students have never heard of these titles. I support my courses with materials posted to and managed by Moodle; we run R and many R packages (ape, , Rcmdr, Rmarkdown, and RStudio); we use Unipro UGENE and PHYLIP (via the wonderful Rphylip package), Figtree, ImageJ and others.

We do not require students to install copies of the software on their own computers, but naturally, they will benefit by having unlimited access to the software if is installed on their local machines. What I have found is that many students have not installed any software (to their knowledge) on their own. So, we work with them to learn about the pros and cons of installing software.

Here’s how I approach the subject when asked.

That’s a good kind of hesitation to have. If you do not want to download and install software onto your computer, you do not have to. The department has several laptops with all software preloaded for your use during class. You can do well in my course even if you do not install software on your computer, but you can expect to work outside of class time using the computer lab when it is a vailable. The advantage of loading the software onto your computer is that you can work on the assignments on your own and you get to use your computer for something more than just typing and playing media. So, once you decide to install the software, some basic precautions are in order.

Make sure you are at the official website and not some unauthorized site.
Use updated antivirus software. If you have not purchased antivirus software, or are trying to live with 30-day trials, then you should look into the free versions (here’s a recent review for PCs, another for Macs). My own 2 cents — if you are uncomfortable with loading software, then you should go with a commercial antivirus package from one of the known companies (Norton, McAffee). If you get Internet access from your cable company, they probably provide you with access to one of these (here on Oahu we are Oceanic Time-Warner and they provide you with McAffee). On my MacPro I use SOPHOS; on my Win7 laptop I use a paid version of Malwarebytes.
Learn about checksum (hashsum).
To get the checksum number for software on MACS, go to the terminal and at the bash $ prompt type “md5 [package name]” without the quotes and replacing the [package name] with the file name.

On PCs, it is a little trickier, you need to acquire and install Microsoft’s Checksum Integrity Verifier application.

I have a Mac and I have no idea what version I have

Mac operating systems have a split personality — they are referenced by version number (10.4, 10.5, 10.6, etc) and by names (Tiger, Leopard, Snow Leopard, respectively) (Wikipedia ref). Current version of the Mac OSX is 10.9 or “Mavericks.”

Two options to find the version of your operating system.

1. Open the terminal and type “sw_vers” at the bash $ prompt. From my computer I see

[username]$ sw_vers

ProductName: ………….. Mac OS X
ProductVersion: ………… 10.6.8
BuildVersion: ……………. ######## I think I won’t give you my computer’s build number 🙂

2. To find your version, click on the Apple symbol at upper left part of your window in the Menu bar and select “About This Mac,” which is the first option in the context menu.

You’ll get a small popup that looks like this (from my Mac)… From the image you can see that my Mac version is 10.12.5. That’s an updated “Sierra”

Apple –> About this Mac