Monthly Archives: October 2013

Rockin’ like Dokken – Nightmares 1,2 and 3

#RockinLikeDokken this Halloween

100 Films in 100 Days

October is a great month for horror movies. My DVR is filled to the brim with films my wife refuses to watch with me, so I’m up late nearly every night working through my list. This week I watched a couple Nightmare on Elm Street sequels (Freddy’s revenge and Dream Warriors), neither of which I’ve seen for a long time.

I don’t think I saw Freddy’s Revenge in the theater, but I have a very clear memory of seeing Dream Warrior at the King and Queen theaters in Newark, DE. These were the crummy kind of dollar theaters where you don’t think it’s a good idea to get the popcorn or anything else that didn’t come in a sealed container.

Freddy’s Nightmare is terrible – a standard no-story resurrection by a replacement director with nothing by Wes Craven but the characters.  Dream Warriors isn’t much better due to some terrible…

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Posted by on October 30, 2013 in Uncategorized


Speaking of Blood Types

General Biology class may benefit from checking out the link on this page to the game hosted by


We discussed blood types in General Biology today as an example of a trait where there are more than two alleles present in the population – the three most common of these alleles are the A allele (IA, IB and i). Last semester I wrote an essay here discussing this trait and how it is truly expressed (rather than the more simplified terms I used in class) and I wanted to point anyone interested in reading more about that here.

ImagedYou can also find a cute game about blood typing and transfusions at The game emphasizes the importance of blood typing prior to transfusion and discusses which blood types are able to be transfused into what patients. Again, it’s cute and simple, but makes a good point.


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Posted by on October 30, 2013 in Uncategorized


It was a Perfect Day

Goodbye to a fabulous musician

Lou Reed 1942-2013


Posted by on October 27, 2013 in Uncategorized


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Devilish Tumors


     You poor devil

RadioLab recently updated and rebroadcast their Tumors episode (RL link). This includes a story about President Grant’s tumor kept in a cigarbox in museum archives and one about the transmissible facial tumor plaguing Tasmanian Devils. The tumor, known as Devil Facial Tumor Disease (DFTD) is a rare case of an infectious cancer. This is the one that I wanted to think about some more.

What do we know about tumors? How do they arise? Why is cancer so much more prevalent today than ever before? What makes these Tasmanian Devil tumors especially nasty?

What do we know about tumors?

Actually, quite a lot. And many new therapies are very successful – especially those that target very specific kinds of tumors. In 1963 Todero and Green   ( established both a cell line and a precise methodology for growing cells in culture that permitted researchers the ability to recognize specific changes in cells grown in culture – changes such as becoming non-responsive to the presence of other cells that should control cell division.


                                              30 years of p53 research

Over the years a number of tumor suppressor proteins and proto-oncogenes have been identified. These are the proteins responsible for restraining cell cycle in the event of DNA damage. Among these is p53, the most frequently altered protein in cancer. It was originally identified in 1979 and has since been shown to arrest cell cycling in the event of DNA damage, initiate repair protocols and start a ‘countdown’ to self-destruction (apoptosis).

A number of additional mutations have been defined in proteins that either promote cell cycle progression (proto-oncogenes) or arresting cell cycle progression. Each of these proteins may be mutated in a different way, but the outcome is always the same: cells are pushed through their cycle despite the presence of DNA damage.Image

Beyond this, more processes have been found to contribute to tumor success. Some tumors promote angiogenesis (the growth of new blood vessels) to feed the tumor. Some have mutations that allow them to break off of the main tumor mass and survive in the blood or lymph and migrate to new areas. Some tumors perform tricks to escape recognition by the immune system.

In time, successful tumors may do all of these things. And how can they mutate so quickly and skillfully? It all goes back to p53. When a cell doesn’t slow down and correct errors in its DNA – and when it does not self-destruct when these errors are too damaging, the cell is free to mutate again and again. Each mutation is like a new child that either does better or worse in its environment, with only the successful ones living to spread their genes.

How do they arise?

Tumors arise when DNA damage occurs in just such a way that it escapes notice by the cell and starts to multiply. Actually, we think that a lot of tumors start up, but get weeded out by our immune system again and again. The ones we see are those that were successful enough to evade our defences and grow up. (immune surveillance:

Why is cancer so much more prevalent today than ever before?

Because we live so much longer. The increase in cancer rates does not come from cancer becoming worse over the years, but comes from the fact that we live long enough to get it


      We’re getting old … Unfortunately, that means we’re getting cancer too



What makes these Tasmanian Devil tumors especially nasty?

Transmissible tumors are rare because of the conditions required to allow for them are also very rare. In the case of DFTD the stars aligned in just the right way to allow this to occur.

The first requirement is that a tumor must have evolved sufficiently to be able to spread throughout the body of the initial host and be expressed on the face of this animal.

Second, this tumor was amazing in that it could start growing even in new animals if cells should be transferred from one to another. This may have something to do with the uniformity of the devil population and/or the way that these tumors ‘hide’ cellular markers that would otherwise expose them as bad/ foreign cells. The latter of these explanations is supported by data such as: pnas “reversible epicene tic down-regulation of MHC by devil facial tumor…” Siddle et al vol. 110 no. 13

(my question now is: don’t these devils have NK cells that should eliminate these MHCI-deficient cells?)


Perhaps most importantly, these tumors affect animals that are naturally aggressive towards other members of their species in both feeding and sex. Because devils bite one another so often, they provide just the right opportunity for cells to jump from one animal to another.

There is a similar case of a canine transmissible tumor (“tumor cells spread canine cancer” in the scientist, August 10, 2006 by Melissa lee Phillips.) but other than that, these types of tumors are not often seen.

Altogether, this is a fascinating case that illustrates some peculiarities of tumors, DNA damage control and immunology.

The devastating effect of this tumor epidemic is that it has precipitated a dramatic decline in devil numbers now making them endangered of extinction.


Visit the ‘Save the Tasmanian Devil’ website for more information about their condition. (:



Posted by on October 27, 2013 in Uncategorized


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The question we gotta ask is: “Is our kids learning?”

ImageThis September was a landmark for the Los Angeles unified school district, which began to equip each of its 30,000 students with iPads. The push goes through all grades, K-12 and provides the iPad, an educational suite of apps and a gated internet portal.

Businessweek (citation) reported that it took only days for students to hack their machines and work around the limitations imposed on internet usage. The school district  immediately reacted to the breach and seized all the machines in order to address the problem.

Interestingly, I see no mention of how this is quite an amazing effort by the students to assess their situation, realize they are frustrated and hack their way through the security. First, this should be exactly what you expect. But more importantly, this demonstrates a lot of skill and ingenuity. I would be proud if my son had been the one to do it.

This is like recognizing the Kevin Mitnicks of the school early on, before they got into any deep trouble and having the opportunity to cultivate their skills rather than demonize them. After all, where did this guy wind up?  


Phone home, Captain.

That’s right, working as a security advisor. (I’m sure everyone would have been happier without the time on the lamb and locked up for doing for fun the stuff he does today for profit.

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Posted by on October 25, 2013 in Uncategorized


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MicroBiology Test Questions


Mixed Culture

Despite the surfeit of responses to my call for General Biology Test questions earlier this week that I had to wade through (read sarcastically), I thought I would yet again offer the opportunity for anyone (Students!?) to present potential test questions. If there is anyone out there who would like to try their hand at it, please respond here in the comments section with your proposed question(s).

Topics for this exam include:

-Laboratory techniques (primarily microscopy and culturing methods)

-Cell composition/organelles/functions, comparing and contrasting prokaryotes and eukaryotes

-Prokaryotic cell biology

-Eukaryotic cell biology

-Viral biology

-metabolism / flow of energy through living systems

-cell culture / growth patterns / nutrition

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Posted by on October 23, 2013 in Uncategorized


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An open letter from NaNoWriMo

Thank you for opening this briefing. This message will self-destruct in five minutes.

You are receiving this transmission because we have a task only you can handle. Intelligence has it on good authority that there is a novel inside of you: a story so crucial it must be shared with the world. Your mission, if you choose to accept it: write your novel in 30 days. Code name? Operation: Power-Up.
As always, NaNo HQ is in the sky and on your shoulder, ready to guide you through.
Assemble Your Team: Get Sponsored
This mission is not a one-agent job. You are authorized to keep your friends and family apprised of your progress, and encouraged to establish an inner circle. Consider engaging that inner circle in your mission by asking them to sponsor your novel through StayClassy and support your march to success.
Establish Your Supply Lines: Help Earn $10,000 for NaNoWriMo and the YWP
Our partner agency, Goodsearch, has committed up to $10,000 to encourage the creative cause this November. How can you help?
  1. Download and install the Goodshop button for your browser.
  2. Make a purchase from their more than 3,000 online vendors, including, by December 31. November provisions such as caffeine and candy have full HQ approval.
  3. Goodsearch will donate $5 and 20% of your total purchases to NaNoWriMo and the Young Writers Program.
Get kitted out to ensure the success of your mission while supporting the creative mission of young writers in classrooms the world over. That’s the kind of team player that earns medals.
Meet Your Handlers: Seek Advice from Published, Veteran Authors
We’ve lined up a series of published authors to guide you through your trials, tribulations, and triumphs via our Twitter account. Beginning on Monday, October 28, authors like Teri Brown, Jason Hough, and Kristyn Kusek Lewis will take over @NaNoWriMo to provide the advice, inspiration, and intel you need.
You have our support, you have our faith, you have the fate of a world in your capable, authorly hands.
(Please pretend this email exploded with a small puff),
Tim Kim
Editorial Director



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Posted by on October 23, 2013 in Uncategorized


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Inspired by my favorite This American Life, replayed this week

imagesThis comes from the superpowers episode of This American Life. It’s always been a favorite of mine – I probably talk about this episode more than all other combined.

Click here to go to the TAL page

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Posted by on October 21, 2013 in Uncategorized


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10 questions

ImageI’m in the midst of writing mid-term exams for my general biology students and I’m desperate for more questions. For logistical purposes, a 50 question exam is ideal. I have almost 40 of them in the can and I feel like I’ve covered most of the material pretty well. 

 – Oh, crap, I just made the last batch of Cookies for the Microbiology Review a bit ‘well-done’ –  

Any suggestions out there?

Topics include:

1. Basic cell functions and organelles

2. Enzymes and Energy

3. Plasma Membrane and the Principle of Diffusion

4. Photosynthesis and Cell Respiration

5. Cell Division and Cancer

Any suggestions (including those from my own students) are appreciated. Here’s your chance to write a question that you already know the answer to.


Posted by on October 21, 2013 in Uncategorized


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What can we prove?

Evidence mounts in the strange case of proving that Kevin Bacon, the man who is seven degrees from everyone, has never been to the Liberty Bell in Philadelphia.

The hypothesis: Kevin Bacon has NEVER visited the Liberty Bell


Exhibit A: Kevin Bacon standing in front of a VW beetle – not the Liberty Bell


Exhibits B-E: The Liberty Bell with accompanying visitors, none of which are Kevin Bacon


Exhibit F: The Liberty Bell, yet again, without Kevin Bacon anywhere in sight


Conclusion: Hypothesis accepted – Kevin Bacon has NEVER been to the Liberty Bell


What’s wrong with this argument?

Special thanks to Paul Offit, MD, whose Coursera Vaccines Class inspired this investigation


Posted by on October 16, 2013 in Uncategorized


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