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Monthly Archives: September 2013

Biotic Potential – Unrestricted Growth

ImageLt. Uhura learned a lesson about biotic potential in Star Trek’s 44th episode airing on NBC December 29, 1967 when she accepted a tribble from the trader, Cyrano Jones. The tribbles are both endearing and incredibly dangerous as they invade the enterprise’s systems eating  everything and multiplying asexually at an alarming rate.

While they are getting unlimited food, their growth rate proceeds at their biotic potential, that is entirely unrestricted and proceeding at the maximal rate. While the environment supplies food in excess of what is needed and no other constraints are imposed, such as predators or lack of shelter, this rate of growth will be maintained.

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“The light that burns twice as bright burns half as long.” – BladeRunner

At this point we may observe a ‘J’ shaped growth curve that will either completely crash once resources are depleted, or the limitations of resources will impose themselves more gradually resulting in an “S” shaped curve.

Once one or more requirements become limiting, the rate of growth will reduce until it plateaus. At this point the rate of death is equal to the birth rate and the population will remain at a constant number. Without the input of additional food (or other requirements), the direction of growth will reverse and the population will enter the ‘death phase’ as deaths outnumber births and the population contracts.

ImageIn “The trouble with tribbles” the food never did run out, however, the population did come to a grinding halt (J-Shaped curve) once the tribbles got into a poisoned grain supply.

 

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Which curve does this one look like?

Reverend Thomas Malthus was alarmed by the rapid expansion of the human population worldwide in 1798 and wrote his famous essay, An Essay on the Principle of Population, warning of the imminent tragedy that befalls populations that grow as fast as our own.

 
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Posted by on September 30, 2013 in Uncategorized

 

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Photosynthesis: Turning CO2 into O2 – or maybe not.

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It’s so simple, right?

“The evolution of photosynthesis remade the Archaean Earth. Before photosynthesis, the air and oceans were anoxic. Now the air is a biological construction, a fifth of which is free molecular oxygen”  – Bendall et al. 2008cIt’s easy to mistakenly think that photosynthesis turns CO2 into O2, people have been doing it for years. In fact, you’d even be remiss not to initially think that it’s the case – it is, after all, a simple conclusion to make and William of Ockham tells us to always start with the simplest ideas.

How could we do this experiment now?

We could  use radiolabeled Oxygen in our CO2 and then look for that same radioactive O2 being produced as a waste from the plant. But if that experiment were done, we’d quickly see that this wasn’t the case. As we will see below, this experiment was eventually what was done and instead of labeled CO2 being produced, the leaves of the plant becoming radio labeled, while only ‘cold’ CO2 was being released. Vexing!

One complication in addressing this idea comes from the very notion of air as being something to begin with. So, what is air? – and what happens (to air) during photosynthesis?

The Dutch scientist and physician, Jan Baptista van Helmont (1579-1644), did some early experiments to understand the nature of photosynthesis. His experiment was to determine where the mass of the plant came from. He suspected that it would be from the soil it was growing in, and did a very simple experiment that refuted this hypothesis. He reasoned that if the mass of the plant came from the soil, then it was a simple conversion that he could observe happening over time as soil was depleted resulting in an equal growth in mass of the plant. His experiment used a potted willow tree planted in 200 lbs of soil. In five years, his 5 lb sprig grew to 169 lbs, using only 2 oz. of soil.

Clearly the mass was coming from somewhere else. Knowing that he watered his tree regularly, he speculated that this was the source of the tree’s growing mass.

Helmont’s experiment did nothing to answer the question directly, but it does introduce a new player into the mix: Water… H2O. There’s Oxygen in water too – another possibility?

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What could possibly have killed this mouse?

In 1771 Joseph Priestley came onto the scene with experiments examining the nature of air as something more than just “nothing.” He noticed that a flame tainted the air with a kind of pollutant that was not amenable to animal life. He called this pollutant, phlogiston. Phlogiston could be produced by burning a candle in a closed container until the candle put itself out. Then, any animal (he used a mouse), that was put in this phlogistated air would quickly die. Yet a sprig of mint could counter this effect and somehow clean up the phlogistated air.

What do we know now?

1. Air is not just ‘nothing.’

2. Air quality (composition) is affected by certain biologic and abiologic processes.

a. Candle flames pollute the air with something toxic to animals (at least mice)

b. A mint sprig is sufficient to neutralize or eliminate this pollutant

Another Dutchman, Ingenhousz determined that de-phlogistation by plants occurs only in the light and required he green parts of plants to accomplish this.

(Much of the above material can be found in the excellent History of Research Page)

How to observe these gasses more easily? Perhaps under water, where gas will appear as bubbles.

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A simple experimental setup to measure photosynthesis

“When a sprig [of Elodea] is placed upside down in a dilute solution of NaHCO3 (which serves as a source of CO2) and illuminated with a flood lamp, oxygen bubbles are soon given off from the cut portion of the stem. ” -from a History of Photosynthesis. Using this device (pictured below) as a readout, F.F. Blackman measured gas production under various conditions by observing the production of bubbles under a number of conditions.

Data from such an experiment looks like this:

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The data

From these data, Blackman concluded that photosynthesis occurred in several stages, the first was a ‘light-limited’ stage that hastened with increasing light intensity, the second did not increase with increasing light intensity and required the work of enzymes (accounting for the effect of heat speeding up the reaction).

The Dutch scientist, van Niel  first suggested the idea of Oxygen gas coming from H2O based on his observations of purple sulfur bacteria converting H2S to S2 and assuming a parallel reaction was occurring in green plants.

CO2 + 2H2S → (CH2O) + H2O + 2S             (observed in purple sulfur bacteria)

CO2 + 2H2O → (CH2O) + H2O + O2             (predicted in green plants)

The final proof of this did not come until Ruben and Kamen were able to use an isotope of Oxygen to trace its route through photosynthesis.

Using algae, given ‘heavy’ oxygen in the form of either water or carbon dioxide, it was found that the isotope given in H2O was invariably that found in the resulting O2. Their experimental procedure is outlined in the diagram as two parallel experiments:

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% 18O FOUND IN
H2O CO2 O2
START 0.85 0.20
FINISH 0.85 0.61* 0.86
START 0.20 0.68
FINISH 0.20 0.57 0.20

So, what we should be saying is not that plants turn carbon dioxide into oxygen, but that plants turn carbon dioxide into sugar, which is precisely why van Helmont was confused by a 169 lb. tree growing from only 2 oz. of soil. He probably never would have believed that all that tree was actually built out of thin air.

 
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Posted by on September 28, 2013 in Uncategorized

 

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Dies Irae

I have quizzes in both my General Biology and Microbiology classes tomorrow. I’m told that there will certainly be a question on the Micro quiz asking students to draw a virus and indicate certain proteins or other elements, such as membranes and genomic material. Just as my General Bio students are certainly expecting a question about chemiosmosis and the enzyme responsible for synthesizing ATP.

Students from both classes are probably more interested to find what movie or artist or governmental office I’ll be asking my extra credit question about. If they’re under about 30, they probably think a classic horror from 1980 isn’t worth watching. But they’d be wrong.

 
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Posted by on September 25, 2013 in Uncategorized

 

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It’s not just the caffeine (a video post)

Coffee is good, but espresso is better. Here’s why:

 
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Posted by on September 25, 2013 in Uncategorized

 

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Experimental Flaws -Uncontrolled variables

I had an interesting text message from my cousin today. He was asking, ‘What is meant when a  study is deemed to be flawed due to uncontrolled variables? i.e. what does it really Imagemean to have uncontrolled variables?’

It’s an excellent question – and one that is well addressed in a book I recently recommended here called How to Lie With Statistics.

I gave him the following answer:

‘A simple example might be someone looking back through historical data and seeing that the number of cancer cases (of all kinds) has been on the sire over the past twenty years. In terms of absolute numbers, this is true. Some people use this to raise the alarm that we have to get more aggressive in our fight against cancer because it has become a leading killer. Perhaps that’s not a bad idea either, but if someone were to look more closely at the details they would quickly see that these absolute numbers aren’t the right data to make this conclusion by. There are uncontrolled variables.

here’s some real data:

The unaltered or crude cancer death rate per 100,000 US population for the year 1970 is 162.8. Multiply this rate by the US population of that year, 203,302,031 and divide by 100,000, we obtained the total cancer deaths of that year, 330,972. Divide this number by the number of days in a year, we obtain the average number of Americans who died of cancer in 1970 at 907.

Twenty years later, the unaltered cancer death rate for the year 1990 is 505,322, the total population, 248,709,873. The cancer death rate per 100,000 population rose to 203.2. The daily cancer death rate was 1384.

(http://www.gilbertling.org/lp2.htm – original data:The 1970 cancer death rate was taken from p.208 of the Universal Almanac, John W.Wright, Ed., Andrews and McMeel, Kansas City and New York. The estimated 1996 cancer deaths figure was taken fromTable 2 in “Cancer Statistics” by S.L. Parker et al, in CA, Cancer Journal for Clinicians, Vol. 65, pp. 5-27, 1996.The 1970 US population was taken from the World Almanac and Book of Facts, 1993, p. 367; the estimated 1996 population was from the 1997 edition of the World Almanac and Book of Facts, p.382. The 1997 total cancer death figure was obtained from S.H. Landis et al in CA, Cancere Journal for Clinicians, Vol. 48, pp.6-30, 1998, Table 2. The US population for 1997 was obtained from The Official Statistics of the US Census Bureau released on Dec, 24, 1997)
ImageHowever, if this is the limit of the analysis, it’s useless. In 1970 the life expectancy was about 67 years for a white, non-hispanic male, while in 1990 that number was about 74.
Since cancer is a disease of the aged, it is likely that the increase in cancer is directly linked to the increase in population of the elderly.
What this means, it that in order for the study to be meaningful, the authors should look at cancer rates among a more comparable group, perhaps white, non-hispanic non-smoking males living in some certain region  that has not undergone drastic demographic changes or excessive immigration / emigration. By taking these additional steps, we reduce the number of differences in our two populations, allowing us to make a ‘more controlled comparison.’
 
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Posted by on September 20, 2013 in Uncategorized

 

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Two Projects

ImageI’ve been playing with a couple computer projects lately. One is trying to pick up some additional HTML / CSS skills so I can have a little better sense of a big picture with my coding club. To this end, I just got a couple of new books, Head First HTML and CSS    and    Head First PHP and MySQL.

So far, I’ve read through a decent amount of the HTML book, which I can skip through pretty easily if I need to as a lot of it is review. However, what I really do find unique about these texts is that they are both comprehensive and interactive. You need to commit to doing the practice exercises as you go along, but seriously, isn’t this what you’re reading this for anyway?

The other project is an infection model. The first iteration of this is similar to the zombie simulations that several people have created online with the exception of having thee classes of people (vaccinated, unvaccinated and infected). As the people wander around in a user-defined room, they may come in contact with one another. In the event that an infected individual comes into contact with an uninfected, unimmunized person, then that person gets infected.

In the currently functional version I can advance one step at a time where all people randomly move on both axes +1, 0 or -1, then are tested for new infections. The next step is to automate the movement and provide reports including how many people are infected each round.

Eventually, I would like to use this to model the spread of infection across the US (using actual state population and size data) and user- supplied info about immunization and infection rates. A similar program exists on the cdc website that simulates the rate of infection spread in a single population. I would like to cross that with a heterogeneous Imagepopulation (different population densities in each state) specific connectivity of states that could mimic regional outbreaks and ultimately a graphical output (this last will likely never happen, but it’s good to have an ideal in mind).

 
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Posted by on September 20, 2013 in Uncategorized

 

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Happy Birthday Batman

ImageBiff! 

 
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Posted by on September 19, 2013 in Uncategorized