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Category Archives: Education

Biology / iOS in the classroom / microbiology / genetics / evolution

SciFlix Movie of the Month: Soylent Green

SciFlix Movie of the Month: Soylent Green

Relax. It’s just people.

This month’s film will be the 1973 adaptation of Harry Harrison’s novel, Make Room! Make Room! Charleton Heston plays a 21st-century police detective working the massively overpopulated New York City. A murder sparks an investigation that cuts to the heart of the world’s population problem: How to feed it?

The Soylent Corporation just released its new product, a plankton-based biscuit made from a harvest from the world’s oceans, Soylent Green. Nutritious! Delicious! Friday, February 10th is Soylent Green Day.

Film Starts at 6:30pm

Regnier Auditorium

12610 Quivira Rd., Overland Park, KS 66213

Discussion to follow – What is the role of the government in providing food safety and biosecurity to a growing population? And what ethics govern a runaway population? Come hear Professors from KU and K-State discuss these questions and answer your questions.

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Posted by on February 5, 2017 in Education, tv, Uncategorized

 

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Cryptography

Today is the first day of the Coursera Cyrptography class taught by Stanford Professor, Dan Boneh. I follow courses like this every once in a while in order to learn a bit about topics that I would not otherwise get any exposure to. Boneh’s course is a little math-intense, but there is another more concept-driven course on the same topic being offered on Khan Academy. If you haven’t taken advantage of either of these two sites, you should look into them. Both are entirely free, and both are taught by excellent educators.

Here’s a video from the Khan Academy site introducing the Caesar Cipher, a simple cipher like those used on radio dramas of the past (get your secret decoder ring!).

If you want to crack a simple substitution cipher like this, you might want to start by using a frequency chart of letters used in the English language, like this one:


The Caesar cipher: Brit explains the Caesar cipher, the first popular substitution cipher, and shows how it was broken with “frequency analysis”

frequencies

 

 

 

However, once you figure out the easiest letters (e,t,and a), things get a bit more difficult. At this point, you will probably have to start looking at letter pairings (Bigrams) to see if any useful patterns show up there. Here’s a listing of the most common Bigrams (again, in English).

bigrams

 

 

 

 

 

It’s interesting that these kinds of codes might ever have been considered sophisticated enough to use in the real world. After all, it’s easy to find examples of these types of ciphers in daily newspapers around the world presented as cryptograms that people do for fun.

 

KT RPP EXRDJ PXZ’J KX BOXD EVDIXI,

KSZ DBZ JB BOXD EVDIXI ZQRZ BSA KARVDJ YRPP BSZ.

                                               -AVWQRAI IRCNVDJ

 
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Posted by on September 8, 2014 in Education

 

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Back to School: Zombies, Ebola and some cool tunes

Ebola is in the news a lot right now.

Could this be The Coming Plague that Laurie Garret warned us about in 1994?

By the late 1980s, with the world shaken by the strangest and deadliest arrival of all – HIV and AIDS – Garrett traveled widely in search of understanding: Why did new viruses and bacteria appear, seemingly out of nowhere? Why couldn’t modern medicine vanquish HIV and other newly emerging microbes? How were scientists battling these diseases? Had hubris put the arrogant biomedical world of the late 20th Century at peril?

– from her website

A recent depiction (below) of the rise of Ebola cases and deaths (cumulative numbers) appears on the wikipedia site.

Diseased_Ebola_2014

The CDC is probably the most reliable source of information on the virus today. They provide a wealth of information about the virus, including that infection does not spread through the air, water or food (with the possible exception of some bushmeat – likely bats acting as a reservoir for the virus). And further, although Ebola does have a frighteningly long incubation period (of about 21 days), there is no evidence that asymptomatic persons can spread the disease.

When an infection does occur in humans, the virus can be spread in several ways to others. The virus is spread through direct contact (through broken skin or mucous membranes) with

  • a sick person’s blood or body fluids (urine, saliva, feces, vomit, and semen)

  • objects (such as needles) that have been contaminated with infected body fluids

  • infected animals

In recent news, two items sound eerily similar to those scrolling across the newswire in the game Pandemic 2:

August 8, 2014 – Experts at the World Health Organization declare the Ebola epidemic ravaging West Africa an international health emergency that requires a coordinated global approach, describing it as the worst outbreak in the four-decade history of tracking the disease.

August 19, 2014 – Liberia’s President Ellen Johnson Sirleaf declares a nationwide curfew beginning August 20 and orders two communities to be completely quarantined, with no movement in or out of the areas.

With all this in mind, maybe it’s a good time to pack up your emergency preparedness kit. And, while you’re at it, check out this comic from the CDC to help determine what you need to include:

Zombie_GN_Final

Imagine a ven diagram illustrating preparedness. How prepared should you be for flooding? fire? tornado? active shooter? zombies?? If you’re prepared for the apocalypse, surely you can handle a flood.

prepared

While you’re huddled in the basement waiting for the threat to pass, enjoy some music to keep your spirits up.

 
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Posted by on August 20, 2014 in Education, Uncategorized

 

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Variables

imagesThe Fall Semester is starting soon and I have to say: ‘what a relief’. Going all summer without teaching is difficult, yet I always avoid summer classes because I’m worried that I will get myself into trouble with vacation plans or childcare responsibilities. But all that ends soon and I can get back in the classroom, start thinking (and writing) about science, and stop writing so much about movies and TV.

I’ve nearly finished one of my two iBook- format handbooks that I need to have ready for when classes begin. This year’s book is much more interactive, with review questions at the end of each chapter, keynote presentations of my lectures and some video animations. In writing it, I got a bit hung up on my day 1 material. Namely, the scientific method. This is the method developed by Descartes and others to help us figure out the difference from what is true about the world and what isn’t – although saying it that way makes it sound more clear and 100% accurate than it actually is. In reality, the scientific method is a way of thinking that is based on ‘verity and validity.’ What it is best at is determining what is NOT true. However, over time, that steps us ever so slightly closer to an accurate understanding of the way the universe works.

On the one hand, the scientific method is a very precious thing. It comes from the realization that our senses and our minds often fool us. We evolved in a world rife with danger and it made a lot of sense for us to see connections in the world – even when they were not really there. Because, as many evolutionary biologists will explain, the person who assumes there is a lion behind every bush tends to live longer than someone who does not – especially when there are occasionally lions lurking behind the bushes.

Once we escaped that world, created civilization and put an end to the lion problem, we started to wonder, “How does the world work?”

VariableTo answer that question, we could make up ideas and just cling to them so long as they appear to be at least make a consistent story (I’m thinking Aristotle), or, we could test our ideas and see what we get.Which brings us back to the scientific method.

For the most part, however, most scientists don’t really frame their ideas in the form of this method, but have internalized the method and just apply the principles. What I mean by this is, every introductory science book talks about independent and dependent variables, etc. but I have never actually heard anyone describe their experiments in these terms. Instead, we talk about conditions, controls, data and conclusions. Despite working in science my whole adult life, I still have to look up the difference between independent and dependent variables – and I don’t use these terms in my class unless someone asks about them. Instead, I spend much more time focused on setting up an experiment and thinking about what controls would be needed and how someone may interpret the data. I also spend a lot of time early on asking what data really tells us. What’s the difference between correlation and causation, are we reading too much into our data? Can there be other explanations for the same results?

But, having though about this a bit today, I wanted to ask (although I see that my readership has really died off over the summer) what people thought about these terms?

Do any of you actually think these terms are important to teach students? Do you regularly use them in your work? 

 
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Posted by on August 3, 2014 in Education

 

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Bane of the Garden Gnomes

Last week, we discussed the use of the Hardy Weinberg equations to estimate the rate of change in population under conditions of extreme selection, i.e. total elimination of one phenotype. This is essentially the goal of any sort of eugenics program. As an example of a way that this kind of policy could creep into culture, we watched GATTACA. Besides, it’s just a good film.

The purpose of the Hardy Weinberg equations is to model conditions under which allele frequencies can NOT change from one generation to the next. Therefore, it is evident that these are exactly those conditions that are responsible for allele frequency changes.

These conditions are:

  1. No Mutation
  2. No Selection (survival)
  3. No Sexual Selection
  4. No Genetic Drift –due to occasional fluctuations occurring by chance
  5. No Gene Flow – immigration / emigration

In order to prevent the random changes in allele populations stipulated in #4, we also need a sufficiently large population, where sufficient is likely definable by someone with better probability-computing skills than my own. (I feel like going off half-cocked on notions of probability and finite vs infinite time, but I’ll spare you).

Anyway, if we know something about the population, we might be able to work out the allele frequencies and then compute our theoretical proportions for the next generation from the equations…

p+q = 1,

where p and q are the frequencies of the (only) two alleles we are calculating.

and

p2+2pq+q2 = 1

where each unit above represents the proportion of that genotype.

Mathematically, these equations provide insight into how rapidly the rate of an allele in a population could be eliminated if reproduction was prevented in a specific group. (This sounds completely esoteric without using an example, so let’s come up with one…)

A Healthy Gnome Couple

A Healthy Gnome Couple

Imagine a population of fictional creatures – Garden Gnomes.

These gnomes have a recessive allele that makes them susceptible to a fungal disease. We’ll call the two alleles for this trait H – hearty (resistant) and h– weak (susceptible)

There was recently a new law passed amongst the gnomes forbidding susceptible gnomes from breeding (let’s imagine that the H allele is apparent by a normal complexion and the h allele is apparent by a jaundiced complexion. Like susceptibility to disease, jaundice only appears in the homozygous recessive (hh) gnomes.)

Imagine a population starting with equal allele frequencies, p=q=0.5.

p2+2pq+q2 = 1

will give us genotype frequencies of:

25% HH   + 50% Hh + 25%hh = 1

for the present generation.

Now, if we start our draconian, anti-jaundiced gnome policy and prevent breeding of these individuals, then this generation‘s breeding population only consists of the HH and Hh gnomes, where only the heterozygotes will contribute the h allele to the next generation.

If we call the next generation q1, we can estimate the new proportion of the q allele in the population as the frequency of the heterozygote over the total population excluding the hh gnomes:

No wonder they want to get rid of these guys

No wonder they want to get rid of these guys

After one generation, the frequency of the H allele is now 67%.

Since the same process would occur generation after generation (as long as the law was in place – and followed), we can determine the frequency of q at any generation, where n is the generation number.

  1. From this information, try calculating the frequency of both alleles after the policy has been in place for 5 generations.
  2. How long will it take to completely eliminate the h allele?
  3. How would this change if the susceptible (h) allele is dominant?

 
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Posted by on April 28, 2014 in Education, Uncategorized

 

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The Utility and Futility of Debate

ken-ham-bill-nye-debateOn the evening of February 4 at 7pm EST Billy Nye and Ken Ham debated on the topic of whether “creationism is a viable model of origins in today’s modern scientific era?”

The Richard Dawkins Foundation’s Dan Arel wrote what many scientists have thought for a long time. Don’t debate creationists, it just eggs them on.It is typically the position of scientists to discuss data and how it should be interpreted, but not to simply debate on a larger idea that does not hinge on some critical observation. There are many reasons for this: 1) It’s too large in scope to actually present all the evidence for and discuss it rationally, 2) This debate in particular is coming about more than a century too late (when there was new data challenging the old paradigm, and 3) debate doesn’t actually solve anything.

It was also argued that Bill Nye might not be the best representative of the field of biology and its primary tenet. It would be counter productive to have a debate of questionable utility and then not send the best qualified person for the job.

But it happened. You can watch the whole debate here:

I was fidgeting in my seat waiting for the thing to start thinking, ‘this could go poorly, what do I really know about Bill Nye? By being held at the Creationist Museum in Kentucky, Bill is definitely speaking before a potentially overwhelmingly biased audience. I hope he’s done his homework.’

Dino with a saddle at the Creationism Museum

Dino with a saddle at the Creationism Museum

The two took the stage, were introduced to the audience and the rules of the game were outlined (intro statements, a 30 minutes opportunity to build a case, then shorter Q&A style back and forth.)

Mr. Ham won the coin toss and went first. In his opening statements he spoke very well, redefined a couple of terms for us, like ‘science’ (which he broke into observational science and historical science) and talked a bit about the theory of knowledge (what can we know? What counts as evidence?)

I was thrown off by some of his definitions and didn’t like his assertion that we cannot use observations of the laws of nature today and apply the lessons we learn to the past, but overall, he came off fairly well and charismatically.

Then Mr. Nye took the mike and started telling a story about bow ties. I like bow ties and I think he pulls it off very well, but I didn’t like where this was going. Luckily, he came back to his message and gave a strong introduction that settled my nerves somewhat.

For the meat of his talk, Mr. Ham really went all out to establish the language that could be used and what he deemed admissible as evidence. The short story was, we can’t know anything about the past, except from the eye-witness account of history the Bible gives us (God’s Word). Anything else is ‘Man’s Word’ and inherently faulty.

-Great! we can agree on something! I also believe that humans make mistakes, misremember things, etc. This is why data beats anecdote.

So, what’s troubling about this?

Well, a lot. It means we can’t really learn anything. We cannot expect the same rules of nature to apply tomorrow as they do today. And we can know nothing about the past by studying the world as it is today. This sounds suspiciously, and tragically, like David Hume’s Empiricism, i.e. we may think we observe causation, but this is impossible – and even if we are not wrong, every instance of the world is new and different, so we can’t extrapolate from past experience at all. Mr. Nye, like myself, had a problem with this and repeatedly asked, ‘Where does this leave us? Can we make no predictions about how the world will work? ‘ (not a direct quote)

Rather than getting too hung up on epistemology, Nye did an extraordinary job discussing the Earth, Life on this Planet and What evidence we have for these things. My favorite part of his talk was the example of Kangaroos in Australia. How did they get there? (he relied on Mr. Ham’s story of the flood) If all animals left Noah’s ark, how is it that all the marsupials marched directly to Australia leaving to trail of fossils along the way?

Nye pursued several lines of reasoning, including the kangaroo story above, fossil progressions, plate tectonics and paleomagnetism. I would have included more biochemical evidence for the relationship between all life, but that’s just me.

However, I feel like it all came down to one question. One that, perhaps, should have been asked right at the beginning. If the answer to this one is ‘nothing’ then you just undermined the purpose of your debate.

“What, if anything, would ever change your mind?”

Jonathan Holowoka, writing for the Liberty Voice, claims that Nye’s performance was something that all scientists should be proud of and that he effectively rebutted the concerns expressed by the Richard Dawkins Foundations.

Dan Arel answered, admitting that Nye did not fail in any of the ways he worried about in his first column. However, he remains convinced that the debate was useless and may still have done harm.

 
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Posted by on February 6, 2014 in Education, Uncategorized

 

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A look into cell division

ImageIt’s that time in the general biology semester where we transfer our attention to cell division.  Having already discussed a number of basic principles like the laws of thermodynamics and a touch of chemistry, and cellular functions such as the flow of energy and the flow of information, it’s now time to look at how cells reproduce themselves.

In this chapter we should be recalling all the parts of the cell and accounting for how they get sorted into the developing ‘daughter cells’, and also recall the role of information, in the form of DNA, and how this is apportioned into the daughter. Of course we will spend most of our time focusing on the distribution of DNA, but we should always keep in mind what we know of other structures and organelles.

I previously wrote an essay describing cell division in humans that marries this information with the subject of the next unit, genetics and inheritance. You can find that text here. Therein, I briefly address one of the oddities of eukaryotic cells, the mitochondria. Mitochondria are odd because they live in our cells as strange symbiotes that share their energy with us in exchange for protection and a supply of nutrients. The theory describing this relationship was proposed by Lynn Margulis, and is widely accepted today. A description of her theory can be found here.

Because Mitochondria (and chloroplasts) are pseudo-autonomous cells, they must replicate themselves. A cartoon and some micrographs that illustrate this process have been borrowed from Nature Reviews.

ImageThe process involves an interaction with the Endoplasmic Reticulum, that guides an assembly of molecules that constrict around the Mitochondria eventually effecting its division into to smaller organelles. What this image does not include is the replication and separation of the mitochondria’s own circular DNA, a process that necessarily precedes the actual division of the organelle.

Altogether, there’s a lot to keep in mind when examining cell division. Why is this cell dividing? How are the instructions for life (DNA) being distributed between daughter cells? What does the daughter cell need in order to survive on its own? How do these parts / organelles handle their own division between the cells? And what would happen if any of this went wrong along the way?

 
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Posted by on October 7, 2013 in Education, Uncategorized

 

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