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Nucleotides in DNA

The study of modern genetics depends on an understanding of the physical and chemical characteristics of DNA. Some of the most fundamental properties of DNA emerge from the characteristics of its four basic building blocks, called nucleotides. Knowing the composition of nucleotides and the differences between the four nucleotides that make up DNA is central to understanding DNA’s role in living systems.

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The immunity diet

Everybody knows that broccoli are a healthy food. Like most vegetables, they bring in vitamins, antioxidants, and fiber that contribute to a complete diet, protect our tissues from oxidative damage, and regulate the activity of the intestine. Now two recent studies in mice, highlighted on the New England Journal of Medicine January 12 issue, show that broccoli and related veggies (cabbage, brussel sprouts, kale) do more than that: they directly and specifically stimulate the development of immune system cells in the wall of the intestine, to protect us from infections, to control the amount of bacteria present in the gut, and to modulate inflammation.

Here is the cool, geeky part: the effect involves chemicals called flavonoids, present at high levels in Broccoli & Co., and a protein, the Aryl hydrocarbon Receptor, located in a small population of lymphoid cells in the intestinal wall. Flavonoids bind to the AhR and stimulate limphoid cell growth, and these cells in turn stimulate the growth of other immune system structures called lymphoid follicles. These structures and their products provide immunity against pathogens, and regulate the inflammatory response. Mice without the AhR weaned with a flavonoid-rich diet have few lymphoid follicles and low immunity against infection, same as mice with the AhR but weaned with a diet free of flavonoids.

Important? Yes, because this is the first time that direct immunomodulation by dietary plant compounds has been shown, and it should stimulate more studies on the effects of diet on the immune system. So are new guidelines coming soon on how to put together the perfect “immune-boosting diet”? Well, maybe not so soon, because mice ain't people, and the USDA needs human studies to issue guidelines; but mice are more similar to us than most of us like to acknowledge, broccoli. taste pretty good and are already known to be a healthy food, so why not crank them up a bit?

Albedo

The energy that warms Earth’s atmosphere comes from the Sun, but sunlight does not warm the atmosphere directly. The atmosphere warms from below. Most of the short wavelength, electromagnetic energy from the Sun passes through the atmosphere and is absorbed by the Earth. Absorbing this energy warms the Earth. As the Earth warms, energy re-radiates back into the atmosphere as heat. Eventually, this energy re-radiates from the atmosphere back out into space.

The Earth does not absorb all of the electromagnetic energy that hits it. Some reflects back out into space. This is important for the Earth’s energy balance because only absorbed energy contributes to the temperature of the Earth/atmosphere system. The amount of energy reflected by an object is its Albedo.
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About the illustrations

Most of the illustrations at SciencePrimer.com are written in JavaScript.  JavaScript must be enabled and theyshould run without trouble using the most recent version of  Firefox, Chrome, Safari, Opera, or           Internet Explorer (9 or higher).  Internet Explorer version 8 or lower will not work.

A limited number are written in the NetLogo language.  These require java and will not run on mobile devices such as phones or tablets.

Wave Interference

Anyone who as watched the surface of a swimming pool has observed wave interference. Wave interference occurs when two or more waves move through the same space at the same time. Unlike solid matter, waves move through each other. The principle of superposition describes the response of a medium being displaced by more than one wave.
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Balancing Chemical Equations

In chemical reactions, sets
of compounds interact with each other to form new compounds. Chemists use equations to describe these interactions. Like mathematical equations, chemical equations conform to a set of rules. This allows equations to provide detailed information about a reaction.
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Covalent Bond Energy

Eating, putting gas in a car and throwing a log on a campfire all involve adding energy to a system. In each case, the energy is added in the form of covalent bonds that hold atoms together in molecules.

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Metric System Unit Prefixes

Similar to scientific notation, unit prefixes make very large and very small number easier to manipulate and to understand.

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Scientific Notation

Some people have a strong resistance to using scientific notation. Almost every time I teach an introductory science class, I have one or two students with good math skills who insist on doing all of their calculations in standard notation. Doing this invariably results in mistakes that lead to lost points on exams and homework.

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Serial Dilutions II

***UPDATE- View the updated illustration at SciencePrimer.com


Serial dilutions are a common part of may laboratory procedures. Background on serial dilutions, how they are performed and calculation of dilution factors are covered in a previous post.

The following illustration extends the exploration of serial dilution by following changes in the volume and concentration of a solution over three dilution steps.

Pendulum Period

Clocks with quartz movements are more accurate at keeping time than those that use pendulums. Quartz has largely replaced pendulums in modern clocks. But, in their day, pendulum clocks were profoundly important due to their ability to measure time accurately over long periods. The first pendulum clocks were produced in the mid 17th century and their impact was dramatic. Their use ushered in a new era of accurate time keeping. The reliability of pendulum clocks is based on the predictable relationship between the length of a pendulum and the time it takes the pendulum to complete one full swing.
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Buoyancy II

If you wanted to move a heavy rock across the bottom of a shallow pool, would it be easier to move it if the pool was empty or full of water?

The rock would be easier to move if there was water in the pool. The reason, buoyancy force.
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Charles' Law

Three parameters used to describe the characteristics of gases are pressure, volume and temperature. The ideal gas laws describe the behavior of gases with respect to these parameters. Boyle’s Law describes the relationship between the volume and pressure of a gas when temperature is held constant. Charles' law describes the relationship between temperature and volume when pressure is held constant.

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Specular vs Diffuse Reflection

Light is central to our experience of the world. Without its reflective properties, our eyes would not work. When we look at an object, the light rays entering our eyes are ones that have reflected off of the object. Our ability to determine the location and distance of the things we see stems from the fact that light rays behave in predictable ways.
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genotype phenotype probabilities

Patterns of genetic inheritance obey the laws of probability. In a monohybrid cross, where the alleles present in both parents are known, each genotype shown in a Punnett Square is equally likely to occur. Since there are four boxes in the square, every offspring produced has a one in four, or 25%, chance of having one of the genotypes shown.

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Note to mac users -

A recent update is causing the illustrations to run poorly on the chrome and firefox browsers. I expect a future update will resolve this issue.

For the time being you will get the best performance on a mac with safari or opera.

pH

The definition of pH is straightforward: pH describes the concentration (or activity) of positively charged hydrogen ions (H⁺) in a solution. Underlying this definition is a set concepts that can be challenging to understand. The challenge comes from needing to appreciate:

Phase of the moon

The moon is second only to the sun as the most dynamic feature of our sky. It moves across the sky from east to west once every day and each month it goes from being invisible to the brightest object in the night sky and back to invisible again. These patterns result from the motions of the earth, moon and sun relative to each other.

Features of a wave

A standard set of terminology is used to describe the feature of waves.
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