Category Archives: academia

the environment or community concerned with the pursuit of research, education, and scholarship : he spent his working life in academia.

Short Guide To Presenting Scientific Material – Part 1 – Organization

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Presentations are hard work and in allot of ways you are out there alone in front of a group, opening up in ways that can be difficult for you and the audience. The challenges and mistakes that I see are pretty common and I have identified some of those. With a little preparation and review you can avoid most of these issues, and present difficult material in a way that engages your audience. Most of the items below really boil down to the trust between you and your audience. A presentation is an agreement between you and them. You promise that you understand and have researched what you are presenting and they give you their time and attention.

It is a great opportunity for you and them. Don’t waste it.

Organization

  • Use standard referencing. Each slide’s contents must have a small, but identifiable reference on it. At the end your last slide should be the list of all of the references used throughout the presentation. This way you only need author year, on the individual slides.
    • Use this site as a guide for how references should be formatted: http://jama.jamanetwork.com/public/InstructionsForAuthors.aspx#References
    • Break up complex items into smaller diagrams, tables or slides. You are asking the audience to digest lots of information at a time. Break complex ideas down into understandable parts.
    • Avoid spelling errors in slides. It just puts the viewer off; they immediately distrust you if there is sloppy unchecked work in the presentation.
    • Any visual, chart or graphic must have the reference directly on the slide. If you took the material from somewhere else, then be sure to give them credit. This way you do not get into trouble.

“And That Concludes Our Presentation”…

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Graduates

Graduates From j.o.h.n. walker’s Flickr photostream

When we ask students what drives them crazy, they sometimes respond that they wish we had given them a packet describing everything they would have to do to graduate.

There is, and we do tell them. The thing here is continuity of service. They start getting these packets from day 1, before they even sign on to the college. Some things are verbal, some things are written. All get repeated.

The problem with being a student is the continuity. Most students don’t realize that the program that they are in is fluid, so students admitted the year before and students admitted the year after may well have a different curriculum and requirements.

This shocks students. It is their education, it seems to the students that it is a giant monolithic event, one unchanged path towards a degree. Yet for faculty and administrators the curriculum and requirements are a fluid space, different for almost every year.

So back to continuity, how do we take the two perspectives and bring them into one place, where students are satisfied and faculty understand. Students should allows have access to a forward and backward look across their own curriculum and requirements, but currently that takes some work to figure out.

Yes, I can hear you thinking, as a school we already have allot of this functionality, but we don’t use it.

The Rx system we use here, or really, any portfolio system could be used this way, students get a pre-formatted space when they arrive. Pre-formatted in the sense that their handbook goes from a dead pdf online to a more interactive space that they (the student) fill with their grades and accomplishments, as it fills, they can check items off and see how close (or far) they are from reaching their goals, that year, that rotation, ultimately graduation.

Tough request, but there are places were we could do a better job. Since students get packaged by “year of entry” we could probably use the same system as is in place now, but we would improve the continuity for the student by moving it to a live space online where they could look at it when they are ready.

We tell them everything they will have to do in the beginning of their first year, but all they hear is “and that concludes our presentation”. Towards the end they ask us what is it that they have to do and are they almost done, but all we hear is our own perspective whispering, “they didn’t listen”.

That is the divide that we have to cross.

Fighting Leukemia By Reprograming T Cells

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Some really fascinating work is being done to save leukemia patients who have reached the end of conventional therapy without a cure. Detailed in a NEJM article here, the treatment takes the patients own T cells and reprograms them, targeting the cells to attack the patients own B cells. The reprogramming is done using an HIV derived vector that integrates its DNA payload into the genome of the hosts T cells.

The New York Times has a couple of good writes-ups on this. At the time of this post, this is the most recent.

Chemists Outrun Laws in War on Synthetic Drugs

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What does similar mean?

This is where Brandon Keim starts in a post on a chemists ability to churn out legal analogues of illegal compounds.

The question is a good one for medicinal chemists, policy makers, and emergency room clinicians, but all for different reasons.

Chemists Outrun Laws in War on Synthetic Drugs | Wired Science | Wired.com.

I think this will make a good first lecture for the my toxicology students, framing the unusual mix of stakeholders when we discuss abused drugs.

Why Teach Pharmacogenomics; And How Much?

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There seems to be some confusion about what a pharmacogenomics course is, and how much we should invest in one. I want to be up front in stating that we need to invest some serious effort here, and the only way to do so is to provide a solid foundational course in this very fast moving field. More recently I was informed of a 2 credit vs 3 credit discussion. I like neither, I like a 3 credit plus one more credit for a lab, but if we cannot give our students that optimum in our very packed curriculum, then we will have to settle for the 3 credits worth.

Here is why:

Pharmacogenomics is required by our accrediting body.

The 2007 accreditation standards set forth the need for education in not just pharmacogenomics, but genomic variability and the genetic basis of disease. In the AACP’s 2007-2008 final report from the “Bylaws and Policy Development Committee”, the educational challenge was further refined:  “personalized medicine, including relevant competencies in cell and systems biology, bioengineering, genetics/ genomics, proteomics, nanotechnology, cellular and tis- sue engineering, bioimaging, computational methods and information technologies”. Our charge is to insure that our students are prepared to be fluent in this emerging field.

Numerous pharmacy schools have decided that they must include more pharmacogenomics in our curriculum.

School after school has determined that there was insufficient coverage or breath of genomic and proteomic material in the curriculum. They have identified modules in a few courses that could be expanded, but the general feeling of the faculty is that improvement is needed and would be part of a new curriculum. Surprisingly as the pharmacogenomic field grows, surveyed faculty are less optimistic that pharmacy covers this area sufficiently.

Pharmacogenomics is not just warfarin and cytochrome P450s

There is a perception that pharmacogenomics can be defined by its most cited cases, warfarin and cytochrome P450 alleles. 

This is not the case.

Pharmacogenomics is an intersection of numerous different fields of study, including (but not limited to) human genetics, protein biochemistry, population biology, evolutionary genomics, molecular biology, pharmacology, systems biology, and toxicology. The perception that one can learn pharmacogenomics by covering a limited number of case studies of warfarin followed up by a review of cytochrome p450 alleles is misfounded, particularly when the majority of individuals asked can’t even define what an allele is, let alone how such information can be assessed clinically. Going forward pharmacists will be in an ideal position within the healthcare system to use, disseminate, and educate their patients on genomic issues. We must train students to be prepared to serve in this role.

We have an opportunity to lead in pharmacogenomics/biotechnology/genetic therapy instruction

One of the most consistently repeated challenges in pharmacogenomics education is the lack of foundation. We have direct experience with this in our current toxicogenomics class, TOX1401. Students are unprepared for concepts that serve as the foundation for pharmacogenomics. Concepts from basic gene expression to genotyping using single nucleotide polymorphisms require considerable educational investment. To be direct the PHS department has worked hard to fit this content into a 3 credit course with an additional 1 credit of lab. Pharmacogenomics now consists not only of fields previously listed but also relies heavily on bioinformatics. Our students need a solid understanding of computational approaches that are already in use from the drug development phase to public health outcomes studies. This is part of a pharmacogenomics course. See the PharmGKB dataset for examples: http://www.pharmgkb.org .

We need to invest now in order to prepare our students

If we do not invest in fully preparing our students for this field we are failing them. We are not discussing a new technology that may show up in a few year, but rather it is here now. Teaching our students that a few gene products have allelic differences and relating this concept to a few drugs is a huge disservice. The field is growing in ways that will shortly include true gene (siRNA) based therapies. We have to invest in a real foundational course taught by professionals who have a deep understanding of the concepts. This sort of approach will insure that our students are prepared to understand new technologies. 

As a school we have an opportunity to lead here, we should. A two credit class is a salve, a 3 credit class at least gives us a shot at getting a foundational understanding. A three credit class and a lab would be better.

How Complex Is Life?

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As the human genome project’s influence grows, one of the concepts that has emerged is complexity. Scientists including biologists have appreciated for some time that genetic networks drive development and biological responses. The cell’s responses to stimuli require and ever changing cast of proteins. The instructions for the protein sequences are encoded within the genome. If we could understand how this large cast of proteins is assembled into smaller pathways and responses we would be considerably further along. The parts list is long and complex, but as the genome project began to uncover the instructions for how the “parts” are made there was a feeling that science may be able to build models that describe function and disease.

The 2010 Nature article describes this aspiration:

The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved

And indeed this did (and still does) seem like a reasonable approach. Biological networks have turned out to be as complex as we could have hoped. Systems biology is still moving forward, but the sheer number of possible rules that govern how all of the cellular parts work together and interact suggest that we will be working with this complexity for some time. There is a universe of rules that describe networks; explaining how proteins, ligands, nucleic acids and more interact and result in function.

Towards the end of the article there is an interesting quote from Bert Vogelstein:

“Humans are really good at being able to take a bit of knowledge and use it to great advantage,”

And we are. With some careful science and good detective skills we can take what we do know and put it to good use, combating disease. The fact that biological systems are complex and that this complexity is not simply going to be understood the first time we draw back the curtain is a great finding.

I am asking the Tox1401 students to look into this complexity a bit further. Let’s start with a pathway database like reactome.org. Choose the phase II pathways and select a single protein within that pathway, perhaps the NAT1 arylamine N-acetyltransferase. Provide a description of the protein, and the pathway that it takes part in.