Learning analytics, formative assessment and student data banking

If there are no targeted hints that students can ask for, if there is no targeted feedback, if there is no well-designed question, there is no semantic data.

There is a very interesting blog post (and an entry into the learning analytics universe that makes a number of important points about the types of data we need to capture from students in order to i) help them learn through coherent and useful suggestions, as well as to ii) to generate objective measures of what learning outcomes various courses and curricula (including MOOCs) actually achieve, as opposed to what they claim or presume to achieve.    

What can we do when we are empowered with this sort of semantic data and analysis?  Here are just some examples:  ... Use semantic analyses like learning curve analysis to identify areas where content needs to be improved

It also highlights the need for formative assessments that go beyond multiple choice questions, something that beSocratic is uniquely suited to do.  

Clearly something we need to incorporate into a useful educational tools (and student education bank) system. 

Thinking about inheritance and epigenetics

There is an interesting RadioLab podcast on inheritance that is worth listening to.  It discusses the differences between Darwinian and Lemarckian mechanisms of inheritance and more.  

They discuss the case of the midwife toad and the work of Paul Kammerer.  One part of this involved work that suggests the role of epigenetic inheritance (changes that do not involve mutations in the DNA, but rather hereditable changes in gene expression.)   

The whole idea of the "Central Dogma" associated with molecular biology (namely that information moves from DNA to RNA to protein, but not backward from protein to nucleic acid, seems pretty clear.  BUT, it is also true that a behavior can influence selection.  This is the topic of the book and the video lecture: Evolution in four dimensions. by Eva Jablonka and Marion J. Lamb.

Sadly, there are some errors in the Radiolab: Inheritance pod cast.  For example that methyl groups are "sticky", and that the transcription factors "knock off" methyl groups is weird (and wrong, at the molecular level).  Both processes are mediated by enzymes (histone methyltransferases and demethylases).  In fact, there are a number of modifications of chromatin, all of which are enzymatically mediated.  

Also interesting is the RadioLab episode on Stochasticity.  The section that starts around 43 minutes in is relevant to gene expression.  

MadSci Network: Does the DNA contain the codes needed for shaping body organs?

I love composing answers for the MadSci Network and here is my latest here [link].

The challenge to answering such questions is to try and place the answer in a coherent and accessible context.  While it is hard to know whether a particular answer actually succeeds in doing that, it certainly gets one thinking about how to address complex questions and looking around for compelling references and resources.

For this answer, I found an amazing video on polydactyl, which could be viewed as a beneficial mutation (assuming that six fingers and toes are better than five!) 

As usual, the Onion get it right!

link to the article!

Viruses within Viruses & the politics of Anti-Science

One of the more amazing discoveries of late are the giant viruses (first identified in 2003)(for more details, read reviews here and here).  These miniviruses have been found to infect various types of amoeba.  

More amazing still, these giant viruses have their own parasites [read general description here and a scientific description here.]   Cells infected with the giant virus are infected with a second type of virus, known as a virophage, which replicates only in virus infected cells.  Another example of how ecological niches, no matter how small or obscure, can be populated by replicating entities.  

On another, less intellectually entertainingly front, it is increasingly amazing how both scientific denialism and active anti-scientific posturing and policies are coming to dominate American political discourse, particularly in situations where they are seen to threaten fundamentalist religious doctrine (or in Boulder, CO, self-centered ignorance, as illustrated by the anti-vaccine and anti-GMO movements)[check out the panic virus blog].  

This recent article Shawn Otto in Scientific American (Antiscience beliefs jeopardize U.S. democracy) is particularly cogent.  In part scientific denialism may arise from the naive view that science equals truth, and so poses a direct threat to belief and in part from a failure of our education system to help students understand the process by which science accumulates and integrates useful knowledge into a coherent world view. Perhaps more emphasis on critical analysis and less on often superficial "inquiry" would help here.  

In any case, it is scary to see the US return (at least in certain regions) to medieval patterns of thought -- I wonder when witch burning will become part of a political party's platform.  Probably not long, given political positions that explicitly deny global warming [read more here].   

Is embryology a lie "straight from the pit of hell"?

Two remarkable stories from today's paper, one about a Republican Georgia representative  Paul Broun who appears to believe that, 

"All that stuff I was taught about evolution and embryology and Big Bang theory, all that is lies straight from the pit of hell. "

What is truly bizarre is that this person on the House Science, Space and Technology committee.    I am particularly confused by, and would love to understand the logic behind, the  relationship between embryology and hell.  

The second is a quote from an Arkansas state representative John Hubbard that slavery was a blessing in disguise and that all Muslims should be deported, similar views appear to be held by Republican state house candidate Charlie Fuqua.  Their views on Mormons, Jews, atheists, and perhaps all Democrats, etc, are not recorded, but Fuqua claims that 

"I think my views are fairly well-accepted by most people".

Also finished an interesting book that is relevant, "The Rocks Don't Lie: A Geologist Investigates Noah's Flood" by D.R. Montgomery.   

Evolutionary contingency (in the lab)

Bount et al (2012) describes a very interesting study of the appearance (evolution) of the ability of the common gut bacteria, E. coli, to utilize citrate in the presence of O2, something that E. coli normally cannot do. This work was based on the original observation that described the evolutionary origin of citrate utilizing E. coli (Bount et al., 2008).  The Lenski lab has been growing (and freezing) samples of this population for over 40,000 generations (here is an interesting paper on how these populations have been used to study competition within a population (Le Gac et al., 2012).  

The evolution of the ability to utilize citrate in the presence of O2 in E. coli involved "potentiating mutations", which occurred in one specific lineage somewhere around the 20000th generation of the experiment.  These mutations have no (as yet discovered) overt phenotype on their own. 

Later on in this lineage, around the 31,000th generation, there was a mutation that involved the duplication and generation of a novel fusion protein derived from the citrate-succinate antiporter (a membrane-transport protein of a type we discuss generically here in biofundamentals).  This mutation allows the cell's carrying it to import and grow (albeit) poorly on citrate.  Subsequent mutations improve the efficiency of citrate metabolism.  

What is interesting is that because they had "frozen ancestors", Blout et al could "replay" their evolution, and ask, when new citrate utilizing lines arose (which they did), whether they had similar (although not identical) mutations to that found in the originally identified lines.  Interestingly, they did.  

Now it becomes an interesting question whether, given that E. coli is usually defined in part by its inability to grow on citrate under aerobic conditions, whether the appearance of cells, derived from E. coli, but able to grow on citrate in the presence of O2 represents a new species or not.