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The Book Scavenger

Screen Shot 2016-09-11 at 9.56.03 AM.png>Spoiler Alert! Or Trigger Warning, if you are emotionally tied to storytelling. This post will discuss some of the secret codes used in a book. If you haven’t yet read ‘The Book Scavenger,’ I suggest that you do so. Until that time, don’t read beyond the following paragraph!<

I picked up a copy of The Book Scavenger by Jennifer Chambliss Bertman from Denver’s Tattered Cover Book Store so that my wife would have something to read on the scant downtime she had during the AMVA Conference held there this past summer. It was advertised as the One Book One Denver selection for 2016.

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Posted by on September 11, 2016 in Uncategorized

 

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Thinking about thinking.

I’ve often taught Science as a way of thinking critically. That is, science education has (at least) two aspects. First, is the content knowledge. This is necessary because it’s not always necessary to reinvent the wheel. If every person had to start with their own tabula rasa and fill it themselves, without the help of those who came before, progress would be non-existent. Further- and this leads into the second aspect, prior knowledge provides a proving ground for developing critical thinking.

For example, every introductory biology class spends a decent amount of time talking about photosynthesis and cell respiration. Just memorizing the pathways is not enough to actually learn anything. In fact, it’s probably the quickest way to ensure that you don’t learn. Instead, it’s useful to talk about how this pathway was discovered.

Jan_Baptist_van_Helmont.jpg

von Helmont

Instead, it’s useful to talk about how this pathway was discovered. What was the question that people sought to answer? What was known /thought / assumed initially? What were the first (apparently unsuccessful) experiments done to address the question?

 

Jan Baptist von Helmont did one of the first good experiments to ask the question: Where does a tree’s mass come from?

He used a willow tree for his experiment and monitored the mass of the tree, the mass of the soil, and the mass of the water he gave it. Because the mass of the soil changed very little, while the mass of the tree grew enormously, he concluded that the tree’s substance came from the water he provided. In his own words, “But I have learned by this handicraft-operation that all Vegetables do immediately, and materially proceed out of the Element of water onely. ”

(It is notable that von Helmont recognized, in other experiments, that carbon dioxide was released from burned wood. He called this ‘gas sylvestre,’ referring to the Latin term for wood / forest, silva. This is important because the majority of a tree’s mass comes from the carbon dioxide in the air. von Helmont didn’t do just one experiment in his lifetime, after all.)

The importance of these historical experiments is that it allows the student to consider, ‘if I were in this person’s position, knowing what he or she did, how would I go about asking such a question?’

It was with this in mind that I came across this video on critical thinking, which I would say is the true value of science.

 

The topics we ask questions about depends on our interests. Perhaps today we are interested in where the mass of a tree comes from and we’ll be biologists. Perhaps most of the time we have a driving interest in the way that molecules interact, so we are primarily chemists. Regardless of the topic, we use the same critical thinking and experimental procedures to answer our questions, so we are really all scientists.

 

 

 

 
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Posted by on September 9, 2016 in Uncategorized

 

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Lookin’ fit there buddy! *wink*

I want you to hear me out. I’m going to say something that you might find unbelievable.

It’s been a long slog to get here, but you’re a middle-aged businessman (possibly lawyer) making a solid mid-six figure salary (not counting investment returns, of course). You go to the gym –  your trainer says you’re really fit – and you just left your second wife, because (let’s be honest here) she was really cramping your style.

You haven’t had a clean shave for months now, but your secretary says the stubble looks hot despite (or because of?) the touch of grey. What you’re really needing now is to ‘complete the look.’  Screen Shot 2016-09-06 at 9.39.49 PM.png

But where do you go? And what’s it going to cost you?

Roll up your sleeves, tough guy. It’s time for some manly online shopping.

Ready for the unbelievable part?

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Posted by on September 6, 2016 in Uncategorized

 

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Link to my review of Kubo

See that on my other site: 100filmsin100days

 
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Posted by on August 24, 2016 in Uncategorized

 

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Understanding Exponential Decay

 

 

{              Special Intro Note:

OK, this post has been a pain to transfer from my original writing into WordPress. A lot of the complication originated from the use of super- and sub-scripts in the mathematics, it’s also meant that I got pretty irritated in reworking it so many times that now I haven’t gone back to ensure that the math is correct anymore.

I’m saying all this because I want to say, “don’t take my word for anything here if you believe I’ve made a mistake, let me know and I’ll check it out when I have less frustrated eyes.”}

}

 

Exponential decay is a concept integral to determining the age of natural substances when initial and final concentrations are known for a specific unstable radionuclide. There are largely stable ratios of individual elements and their isotopes in the environment. Some of these isotopes are stable, and some are not. Unstable isotopes will break down over time. Although one could never predict how long any given atom will exist before it breaks down, the extraordinary number of atoms in any sample and the predictability of their decay into new atoms allows us to compute how long a substance has existed since new atoms were being incorporated (i.e. the time of death). By looking at these ratios over time, we can make very accurate measures of the age of a sample.

Screen Shot 2016-08-12 at 10.56.05 PM.png

Different decay rates of various isotopes provide an array of measuring sticks for us to use.

Some examples:

32P has a short half-life of 14.29 days and therefore has to be made synthetically for lab use.

35S is formed from cosmic ray spallation of 40Ar in the atmosphere. It has a half-life of 87 days.

14C is formed cosmogenically by the reaction 14N + 1n → 14C + 1H. It has a half-life of 5,730 +/- 40 years.

40K It has a half-life of 1.248×109 years.

Some elements have a fairly straightforward decay path. For instance, Cosmic rays (high-energy protons and atomic nuclei) from outside of the solar system bombard the atmosphere striking atoms. When this occurs, the atoms are fractured into some Helium, some protons, and some neutrons. When these neutrons strike nitrogen 14N it displaces a proton and is converted to 14C. 14C then decays back to 14N by one neutron breaking down into a proton and electron which is emitted from the atom (beta decay) with a half-life of 5730 years (note that during formation, a neutron takes the place of a proton. Then in decay, the neutron breaks down resulting in a proton, which stays and the emission is an electron, which is why the atomic mass does not change from 14 in either direction).

n + 14N –> 14C + p+

14C –> 14N + e

Speaking Mathematically…

Exponential decay occurs in a general exponential function

Screen Shot 2016-08-12 at 11.03.16 PM.pngIn other words, as x increases, f(x) decreases and approaches zero. This is exactly the type of relation we want to describe half-life. In this case, we want a = ½, so that we have the relationship

Screen Shot 2016-08-12 at 11.02.24 PM.png

Rewrite in terms of half-life. Of course, our function does not depend on generic variable x, but time, t.

Screen Shot 2016-08-12 at 11.02.27 PM.png

    • Simply replacing the variable doesn’t tell us everything, though. We still have to account for the actual half-life, which is, for our purposes, a constant.
    • We could then add the half-life t1/2 into the exponent, but we need to be careful about how we do this. Another property of exponential functions in physics is that the exponent must be dimensionless. Since we know that the amount of substance depends on time, we must then divide by the half-life, which is measured in units of time as well, to obtain a dimensionless quantity.
    • Doing so also implies that t1/2 and t be measured in the same units as well. As such, we obtain the function below.

Screen Shot 2016-08-17 at 8.08.42 PM.png

Incorporate initial amount. Of course, our function f(t)f(t){\displaystyle f(t)} as it stands is only a relative function that measures the amount of substance left after a given time as a percentage of the initial amount. All we need to do is to add the initial quantity N0.{\displaystyle N_{0}.} N0. Now, we have the formula for the half-life of a substance.

Screen Shot 2016-08-17 at 8.10.43 PM.png

Solve for half-life. In principle, the above formula describes all the variables we need. But suppose we encountered an unknown radioactive substance. It is easy to directly measure the mass before and after an elapsed time, but not its half-life. So let’s express half-life in terms of the other measured (known) variables. Nothing new is being expressed by doing this; rather, it is a matter of convenience. Below, we walk through the process one step at a time.

Divide both sides by initial amount N0.

    • Take the logarithm, base 1/2 of both sides. This brings down the exponent.

Screen Shot 2016-08-17 at 8.13.53 PM.png

    • Multiply both sides by t1/2 and divide both sides by the entire left side to solve for half-life. Since there are logarithms in the final expression, you’ll probably need a calculator to solve half-life problems.

 

 

Example Problems

  1. If you start with a sample of 600 radioactive nuclei, how many would remain un-decayed after 3 half lives?
  1. What is meant by ‘decay constant’?

 

 

  1. Warm-up Problem. You receive a shipment of 32P in the lab on the first of the month. When it arrives, you perform an experiment using 10mL of this reagent. 57 days later, you wish to repeat this experiment using the same amount of radioactive P. About how many mL of your stock will you use (Don’t calculate this using the equations above, just work it out logically for an approximate answer)?

 

 

 

Worked Examples

  1. 300 g of an unknown radioactive substance decays to 112 g after 180 seconds. What is the half life of this substance?
    • Solution: we know the initial amount N0=300 g, final amount N=112 g,  and elapsed time t=180 s.
    • Recall the half-life formula

t1/2 = t / log1/2(N(t)/N0)

    • Half-life is already isolated, so simply substitute and evaluate.

t1/2=180s log1/2(112g / 300g)

= 127s

    • Check to see if the solution makes sense. Since 112 g is less than half of 300 g, at least one half-life must have elapsed. Our answer checks out.

 

 

2. A nuclear reactor produces 20 kg of uranium-232. If the half-life of uranium-232 is about 70 years, how long will it take to decay to 0.1 kg?

    • Solution: We know the initial amount N0=20 kg,
    • Rewrite the half-life formula to solve for time.

t=(t1/2)log1/2(N(t)N0)

    • Substitute and evaluate.

t=(70 years)log1/2(0.1 kg20 kg)≈535 years

 

    • Remember to check your solution intuitively to see if it makes sense.

 

 

Of Note:

In sourcing this material (especially the maths), I came across something I did not expect. That is… a very good article explaining C14 dating in Answers In Genesis, a source that typically does not curate science in a remotely responsible manner. However, the article linked above does an excellent job in describing the steady-state production of C14 in the atmosphere and the process by which it is used to date carbon-containing remains.

In the end, Answers in Genesis quickly departs to an attack on a straw man, suggesting that only Carbon is used for dating the Earth, but this is (willfully?) mistaken in several ways.

“[B]ecause the half-life of carbon-14 is just 5,730 years, radiocarbon dating of materials containing carbon yields dates of only thousands of years, not the dates over millions of years that conflict with the framework of earth history provided by the Bible, God’s eyewitness account of history. ” (my emphasis)

First, C14 is only used to date materials in which Carbon was incorporated (e.g. organisms) during life – i.e., it is not the way non-living material is dated. Second, C14’s 5730-year half-life allows dating of materials to approximately 40,000 years, at which point there is so little C14 remaining, that this method’s accuracy is reached. Further, at such low levels, background contamination from other sources (e.g. bacteria) compromises accuracy.

I think if I were to use an analogous argument: ‘[memory] yields dates of only [dozens] of years, not the dates over [thousands] of years that conflict with [my notion of the universe beginning with my birth].’ one might see the fallacy.

 

 

 

 

>Taken in part from: http://www.wikihow.com/Calculate-Half-Life

 

 

 

 

 
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Posted by on August 17, 2016 in Uncategorized

 

Flow Cytometry Basics

Definition: Flow cytometry is a technique allowing for the examination of large numbers of single cells at high speed. The principle involved that cells can be passed within a sheath of solvent so that they pass a laser as individual units. The laser is employed to capture a scatter profile of the cells that gives information about the size and internal complexity of the cells and may also excite fluorescent probes that identify specific surface or internal structures.

Screen Shot 2016-07-10 at 10.29.53 PM

from: flowcytometry.med.ualberta.ca

Cytometers record information about each individual cell across a number of characteristics. To accomplish this, cells are titrated to run at a speed (measured by cells/second – often around 10,000 cells/sec) that is within the capacity of the machine to read. Physically, a constant flow of ‘sheath fluid’ is run across the detector’s path. The cell suspension runs as a separate stream within the sheath fluid.

 Data points can be represented very clearly as values for each characteristic measured, and may be listed as a series of numbers as the table below. Here, cells were ‘labeled’ with antibodies against three known proteins, Btk, CD3, and CD19. Each antibody also carried fluorophores that emit known wavelengths of light when excited by (a) laser(s) of specific wavelength(s). These antibodies are illustrated in the figure to the side. Each type of antibody binds to a specific ‘antigen’ and carries several fluorophores that have been chemically linked to them Screen Shot 2016-07-10 at 10.30.01 PM(illustrated by different colored stars). Alternatively, secondary reagents can be used to bind to the primary antibodies to allow more freedom of color choice or to amplify weaker signals.

Cells are labeled or ‘stained’ with these antibodies by incubating cells with the antibodies for a period of time, followed by washes to remove excess, unbound antibodies. Typically, all stains can be done together in a single incubation unless secondary antibodies are employed to amplify weak signals or adjust the colors used or intracellular staining is required (see below).

ID# FSC SSC Btk-FITC CD3-PE CD19-APC
1 412 183 41 6 58
2 374 192 4 745 9
3 299 201 3 4 8

If we measured data from each of the three cells above, this might be sufficient to illustrate the identity of each cell type without further analysis. However, if thousands of cells are measured for each condition in an experiment (done in triplicate), tables of numbers lose their value as effective illustrations of the data.

To account for this, scatter plots or density plots (similar to topographical maps) are regularly used to illustrate these larger datasets. Because it is only practical to present values in two dimensions at a time, plots are often drawn such that a population is identified in one plot and then those ‘gated’ cells are then redrawn in subsequent plots to illustrate values in new categories. Cells may also be examined for just one characteristic using a histogram.

Forward Scatter (FSC) and Side Scatter (SSC)

FSC and SSC are (very often) the primary measures of the physical properties of cells as they pass through the cytometer’s laser. FSC provides information about the size of the cell, while SSC provides information about the internal complexity of the cell. These data are presented for a sample dataset of white blood cells below. The more numerous Red Blood Cells (RBCs) and platelets have been eliminated prior to analysis.

Screen Shot 2016-07-10 at 10.30.33 PMThe cells illustrated in the FSC / SSC plot above fall into identifiable subsets of white blood cells based on their size and complexity. The gated cells are known as lymphocytes, which includes both B and T Cells. Gating is a way of selecting a group of cells to analyze further.

Screen Shot 2016-07-10 at 10.30.41 PMFluorescence

Here, the lymphocyte population is now distinguished by the presence of identifying surface proteins, CD19 (found on B Cells) and CD3 (found on T Cells). By plotting the fluorescence emitted by antibodies to these receptors, we can not only identify the two major populations but gate each of them for further analysis for another protein, the intercellular protein kinase, Btk.

Looking at the Btk expression requires a slightly different technique because this protein is located inside the cell. For antibodies to access to Btk, we have to punch holes in the cell that let antibodies permeate cells. This is done chemically after all surface staining is complete and cells are ‘fixed.’ Otherwise, the protocol is very similar to surface binding.

Screen Shot 2016-07-10 at 10.30.49 PMIn the last panel, both B Cells and T Cells (individually identified previously) are assessed for the presence of Btk and the results are represented as the number of events (cells) exhibiting high or low expression (illustrated below).

Here we can see that the B Cells express uniformly high levels of Btk, while T Cells express little or none. It would also be possible for us to see if only a subpopulation of either B or T cells expressed the kinase. In that case, we could gate expressers vs non-expressers to see if there are any other indications that these cells are different such as cell size or expression levels of the other receptors (CD19 or CD3).

It is possible to use staining to examine other features of the cells as well. For instance, if a treatment of cells might result in cell division, this can be tracked by using a non-toxic dye which is added to cells prior to treatment and then assessed afterward (typically 3-5 days). Because the dye is added only once, cells that divide will each take only half the quantity of the original dye. It is possible to distinguish up to 4-5 divisions clearly.

Screen Shot 2016-07-10 at 10.30.56 PM

CellTrace is as a ThermoFisher product, this graphic was taken from the product literature

Data from these proliferation assays is often viewed in histograms to see the proportion of cells at each division, or with another label to see if the dividing cells up- or down-regulate certain receptors. It is also common to use a vitality dye that would demonstrate if cells that don’t divide die, vice versa, or exhibit some other pattern.  The cells illustrated below are CD4 T Cells that were induced to divide by a ‘mitogen,’ possibly IL-2. The histograms depict cells in each generation, where the generation farthest to the right is the parent generation (i.e. undivided cells – this would be confirmed by a control population grown without mitogen). The next peak to the left represents cells that have divided once, the next represents cells that have divided twice, and so on. In quantitating the number of cells that have divided, it is important to consider that ONE parental cell is responsible for TWO cells that have divided once or FOUR cells that have divided twice, etc. (Note that the CellTrace dye is plotted along a log axis)

Screen Shot 2016-07-10 at 10.31.03 PM

Also from the CellTrace product literature

The Scatter plot illustrates the same cells, also plotted by cell division on the X- axis, however, this time the Y-axis separates cells according to their expression of CD4. These data show that the most actively divided cells are divided between CD4 expressors and non-expressers. We can also see that CD4 expression spikes in expressors upon division.

 

Definitions:

Fixing – chemically attaching antibodies to their targets in a reaction that kills the cells. This is required for longer term storage of cells and if further processes such as intracellular staining must be done.

Gating – Drawing a limit around a group of cells or an area where cells might appear for further analysis and/ or quantitation. Gating will always result in a calculation of the percentage of the total cells that are included within the gate

Labeling / Staining – to add fluorescent reagents to cells that will bind to specific elements.

Mitogen – a substance that induced cell division.

Washing – to repeatedly add a solvent to cells, spin to pellet the cells and remove unbound materials with the solvent.

 
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Posted by on July 10, 2016 in Uncategorized

 

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Phlogiston, bloodletting, and the four humors

Phlogiston – You know, the stuff that’s in stuff. The burny stuff that’s released by fire?Screen Shot 2016-06-09 at 5.20.34 PM.png

Not familiar? Well, that’s because it’s isn’t a thing at all – anymore.

Screen Shot 2016-06-14 at 10.04.59 PMGeorg Ernst Stahl (1659–1734) lived in a complicated time for science. It was just being brought out of the dark ages in many ways and much of what he studied sounds completely foreign and backward to modern ears.

Primarily, Stahl studied the distinction between living and dead material. This vital force was supposedly the anima, or spirit, of a living thing, that gives it ‘agency.’ This was the same force, known as vitalism, that even Louis Pasteur believed was necessary for enzymatic reactions to proceed. Pasteur wasn’t wrong about much, but this one time he fell victim to the prevailing zeitgeist.

Stahl also proposed, in his De motu tonico vitali, that there was a ‘tonic motion’ in things that needed to be permitted for proper circulation of blood. When inflammation or other obstructions occurred, the problem was that this tonic motion was being blocked. One cure for these obstructions was the practice of bloodletting, which addressed the most easily managed of the four humors and was used to treat just about everything.

Although this may sound like a criticism of  Stahl, he was highly regarded as a professor and physician in his time and his work was critical in that it added an experimental element to scientific work. As a testimony to his reputation, he served as physician to both Duke Johann Ernst of Sachsen-Weimar and King Freiderich Wilhelm I of Prussia.

To get to the point here, he proposed the existance of a substance, Phlogiston, that was a component of many things that was released when that thing was burnt. Phlogiston was colorless, odorless, and weightless and it spoke to the question why something, once burnt, could not be burnt again. Ash, for example, was completely deflogistated matter. It contained no more phlogiston and was therefore impervious to further burning.

Additionally, air could fill with phlogiston, becoming saturated. When this happened, the principle of diffusion Screen Shot 2016-06-10 at 4.26.42 PMwould kick in to prevent further diffusion of phlogiston out of a substance. Recall that the basic principle of diffusion is that substances go from regions of high concentration to regions of low concentration (Actually, the random movement of particles will continue unendingly. The apparent result of this movement is that a non-random, concentrated source of particles becomes a random distribution that is effectively uniform. Actually, the particles are still moving, but the random distribution appears stable).

It sets up a simple equation for combustion of any (flamable) thing like this:

Phlogiston(s) + heat + something else –> Phlogiston(g) + ash + energy

Actually, it’s a great hypothesis. It does a servicable job in predicting the behavior of a combustible material in a simple system.  Imagine that phlogiston = carbon. This phlogiston / carbon exists in different forms around us: a waxy hydrocarbon chain in the candle, CO2 in the air, and as the backbone of sugars. However, it fails to recognize a couple of important things too: Mass doesn’t just disappear, the CO2 does have mass, of course, but it’s harder to appreciate. Also, flames don’t necessarily go out because of too much CO2 in the surrounding air, but because of a lack of something else, Oxygen.

However, it does fail to recognize a couple of important aspects. First, mass doesn’t just disappear during combustion. What remains as ash is lighter than the starting material.  CO2 is released and despit that fact that it is harder to appreciate, it does have mass. Second, flames don’t necessarily go out because of too much CO2 in the surrounding air, but because of a lack of something else.

preistly making o2It was by following in Stahl’s footsteps that Joseph Priestley discovered oxygen. Priestley had a knack for studying gasses. He was good at capturing and manipulating them in a controlled way. The figure to the left is an apparatus  of a type common to Priestly’s work, where a substance is heated (e.g., KClO3) to boil off a gas (e.g. O2) in a way that the gas displaces water in an inverted flask so that it may be captured in pure form.

Priestley found that oxygen purified in this way could refresh deflogistated (-perhaps, phlogistated?)26844_lg air allowing it to support combustion once more. It could also rescue an animal from suffocating in a bell jar (something that Preistley did enough that is sounds almost like a hobby of his.) The idea that air was composed of numerous components was a new one, and already Preistley was purifying these substances and demonstrating their requirement for life and for chemical reactions.

So, how does this change the way we needed to think about phlogiston?

It explains that mass doesn’t just disappear when burnt. It goes somewhere, it becomes something else (CO2). It changes the requirement for combustion from one considering the diffusion of matter out of one thing and into the air into a chemical conversion of something into something else.

Instead of the Phlogiston equation, we have the combustion reaction (either proceeding until completion or not):

Screen Shot 2016-06-12 at 8.51.00 PM

Phlogiston might still fit in as carbon if we are insistant, but now we see that something else is required as well: Oxygen.

Flames don’t necessarily go out because of too much Phlogiston (CO2) in the surrounding air, but because of a lack of something else, Oxygen.

The importance of Stahl’s work was not that he was right or wrong, but that Stahl was attempting to bring rigor and experimentation into science. In medicine and chemistry, Stahl believed in taking an empirical approach to his work. Ultimately, this was a stepping stone from the pseudoscience of alchemy to the real science of chemistry.

chemistry_alchemy

:istr makes a nucleophilic attack on chemy, resulting in the leaving group (Al) to leave and precipitate out.

 

 

 

 
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Posted by on June 14, 2016 in Uncategorized

 

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