Illustration and Articles

Protein Synthesis Step 1- Transcription Overview

Every living cell contains instructions on how to synthesize all of the proteins needed to support life. These instructions are carried along strands of DNA*. The process of synthesizing proteins from these instructions occurs over several steps. The first step is transcription.

Ocean Gyres and Geostrophic Flow

Water in the oceans is in constant motion driven by tidal forces, density* differences, and winds. Winds create surface currents by transferring energy to the water by friction. The direction of a wind-driven surface current is determined by how the transferred wind energy interacts with Coriolis deflection, other currents, and geological features such as continents and island arcs.

A major feature of the surface current systems in all of Earth's large ocean basins is a central gyre. These gyres move water in large, roughly circular patterns around each ocean basin's center.

Langmuir Circulation

Anyone who has spent time near water has probably seen parallel lines of bubble or other floating debris on a windy day. These are caused by a pattern of water 
movement call Langmuir Circulation - named after the scientist who described the phenomenon back in the 1930s.

Test sensitivity - specificity calculator

Tests are not perfect. Results from tests like those used to diagnose the presence of a disease or infection come with a certain amount of uncertainty. Scientists use the terms sensitivity and specificity to describe the amount of uncertainty associated with a particular test. Values for these two parameters range from 0 to 1. The higher the number, the more accurate the test is.

How earthquakes show us the inside of the Earth

Earth cross section with body wave linesIt is pretty amazing how much we know about the inside of the Earth, given that we can only directly observe a small part of it.

When we learn about the layers of the Earth, we learn that the crust is very thin, but that is only on the scale of the rest of the Earth. Relative to the scale of the tools we use to study the Earth, it is very thick, and conditions become terribly harsh quite close to the surface.

Surface currents, the Ekman spiral, and Ekman transport

As wind moves across the surface of the ocean, friction between moving air and the water surface causes water to begin to move as well. This transfer of energy by friction is how wind causes surface currents. Once water at the surface begins to move, some energy gets transferred to deeper layers allowing water movement to penetrate to depths of 50 to 100 meters.

Thermohaline Circulation

Circulation in the oceans helps transport the solar energy that falls at the equator towards the poles. Like the atmosphere, uneven heating drives this flow of energy poleward. Unlike the atmosphere, the oceans are warmed from the top-down rather than from the bottom up, so heat-driven convection is not enough to cause ocean circulation. For density-driven circulation to mix the oceans at a large enough scale to matter, changes in both temperature and salinity are required.

Pressure Gradient Force

We live at the bottom of an ocean of air. Currents in this ocean move mass

Mitosis and Cytokinesis

Mitosis and cytokinesis occur at the end of the cell cycle as the single cell divides to form two genetically identical copies.

Exponential Patterns and Large Numbers

Exponential patterns are common in natural systems, but the implication of exponential growth and decay can be hard to comprehend.

The story of the wheat and the chessboard is a good way to introduce the challenge.

Cell Cycle

The cell cycle describes the stages of cell division. It is often depicted as a circle separated into segments with each segment representing a phases of the cycle.

Adenosine Triphosphate

ATP is the energy molecule of living cells. It's ability to to play this roll stems from is structure and the fact that we have evolved the ability to store energy in this molecule and to use it to perform important cellular functions. Scroll down to learn more.

Log Scale Overview


Choosing the proper scale to use on each axis is important to get the most out of using charts to visualize data. You need to know when to use Linear, Semi-Log, or Log-Log charts when creating charts.

Palindromic Sequences

Restriction enzymes cut double-stranded DNA* at specific locations based the pattern of bases found at those locations. These enzymes predictably cut both strands because the sequences they recognize are palindromic. The recognition sequences are short strings of identical bases on both DNA strands.

Palindromic sequences are similar to language palindromes but follow distinct rules. By following these rules, any string of bases can be made into a palindromic sequence

Restriction Enzymes

Restriction enzymes cut DNA* at specific sites based on the sequence of bases along the strand at the cut site. These enzymes were first identified and studied in strains of the bacteria E. Coli in the 1950’s and 60’s. The term restriction was used to describe them because their activity restricted the growth of viruses that infect E. coli.

Restriction enzymes are nucleases - enzymes that cut nucleic acid polymers (i.e. DNA and RNA). There are two types of nuclease: endonuclease and exonuclease. Endonucleases make cuts within a DNA polymer. Exonucleases remove individual nucleotides* from the end of a strand. Restriction enzymes are a type of endonuclease - they cut at specific sites in the middle of DNA strands.

Gel Electrophoresis Overview

Electrophoresis is the movement of charged particles through an electrical field. Since the sugar-phosphate backbone of DNA

X-Linked Inheritance

Meselson–Stahl Experiment

In their second paper on the structure of DNA*, Watson and Crick (pdf) described how DNA's structure suggests a pattern for replication:

"…prior to duplication the hydrogen bonds are broken, and the two chains unwind and separate. Each chain then acts as a template for the formation onto itself of a new companion chain, so that eventually we shall have two pairs of chains, where we only had one before." - Watson and Crick, 1953

This is called semiconservative replication.

Today we know that this is the pattern used by living cells, but the experimental evidence in support of semiconservative replication was not published until 1958. In the 5 years between Watson and Crick's suggestion and the definitive experiment, semiconservative replication was controversial and other patterns were considered.

DNA Polymerase

DNA polymerases are the enzymes that replicate DNA in living cells. They do this by adding individual nucleotides to the 3-prime hydroxl group of a strand of DNA. The process uses a complementary, single strand of DNA as a template.

The energy required to drive the reaction comes from cutting high energy phosphate bonds on the nucleotide-triphosphate's used as the source of the nucleotides needed in the reaction.

Refraction in lenses

When a ray of light passes through a transparent object such as a block of glass, it refracts twice. Once when it enters the glass and once again when it exits. In order to trace the complete path a ray of light takes, both these points of refraction need to be considered separately.

Drift and Selection

The Hardy-Weinberg equation describes allele frequencies in populations. It predicts the future genetic structure of a population the way that Punnett Squares predict the results of an individual cross. The equation calculates allele frequencies in non-evolving populations. It is based on the observation that in the absence of evolution, allele frequencies in large randomly breeding populations remain stable from generation to generation.

Serial Dilution

Many procedures performed in modern biology and chemistry laboratories require sets of solutions that cover a range of concentration*s. These include quantifying the number of bacteria in a sample using plate counts and the development of standard curves for quantitative colorimetric, radiometric, and enzymatic assays.

Punnett Square Calculator

A Punnett Square* shows the genotype*s two individuals can produce when crossed. To draw a square, write all possible allele* combinations one parent can contribute to its gametes across the top of a box and all possible allele combinations from the other parent down the left side. The allele combinations along the top and sides become labels for rows and columns within the square.

Lunar and Solar Tides

Tides cause daily changes in water levels in many coastal areas. Factors such as local topography and weather contribute to the timing and height of tides, but the primary reason for tides is the gravitational attraction between liquid water on the Earth and the Moon. All objects on Earth experience tidal forces. However, the effect is most pronounced with water because, as a liquid, it is more easily deformed by gravity when compared to solid objects.

Genotype and Phenotype Probabilities

Patterns of genetic inheritance obey the laws of probability. In a monohybrid cross, where the allele*s 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.

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 features 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.


The energy that warms Earth’s lower atmosphere comes from the Sun, but sunlight does not warm the lower atmosphere directly. This region of 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, which warms up as a result. As the Earth warms, it emits some long-wave radiation back out, heating up the lower atmosphere above it. Eventually, this energy radiates from the atmosphere back 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 proportion of the total energy reflected by the Earth (or any object) is called the Albedo.

Punnett Square

During sexual reproduction, a parent is equally likely to pass on to its offspring either of the two alleles it has at each genetic locus. This makes it possible to list and estimate the probability of specific genotypes being produced from the pairing of two individuals. Given two allele from each parent, four allele combinations are possible. These combinations and their probabilities can be readily visualized using a Punnett square.

Features of a wave

A wave is a movement or oscillation that spreads from a defined point, moving energy as it progresses.

Wave Interference

Anyone who as watched the surface of a swimming pool has observed wave

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.

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 bond*s that hold atoms together in molecules.

Charles' Law

This illustration explores the relationship between the temperature and volume* of an ideal gas

Boyle's Law

On Earth, matter exists in one of three states: solid, liquid, or gas. Matter in each state exhibits distinct characteristics. Gases, for example, do not have a fixed volume* or shape.

Light Reflection and Refraction

Light is a complex phenomena. It exhibits both wave

Specular vs Diffuse Reflection

Our ability to see and make sense of the world with our eyes depends on the reflective properties of light. Without reflection, we would only see luminous objects like the sun, light bulbs, and computer screens.

The light rays that allow us to see non-luminous objects such as our hands, the floor, and the people around us are lit by light rays that travel from a light source to the object and then bounce off the object towards our eyes.

Pendulum Period

Clocks with quartz movements keep time more accurately than pendulum. As a result, quartz has largely replaced pendulums in modern clocks. But in their day, pendulum clocks were profoundly important. The first pendulum clocks were produced in the mid 17th century. They use ushered in a new era of accurate time keeping.

Gravitational Acceleration

We all understand that if we hold something up in the air and then let go, it will fall to the ground. Things fall because of gravity. Gravity is an attractive force between all things that have mass*.  It is one of the fundamental forces of nature. Gravity causes objects with mass to accelerate towards each other. The rate of acceleration depends on the mass of the objects and their proximity. The more mass an object contains, the more it will attract other objects. The closer an object is to another the greater the attraction between them will be.

Metric Unit Prefixes

Like scientific notation, unit prefixes make very large and very small numbers easier to manipulate and understand.

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.

Scientific Notation


When asked why do some things float and others sink, the first thing that comes to many people's minds is the weight* of each item. While weight*, or more properly, mass* does play a role, it is not the only factor. If it were, we could not explain how a giant ocean liner floats while a small pebble sinks. Mass matters, but there is more to it.

Alleles, Genotype and Phenotype

Genetics is the study of the organization, expression, and transfer of heritable information. The ability for information to pass from generation to generation requires a mechanism. Living organisms use DNA. DNA is a chain, or polymer, of nucleic acids. Individual polymers of DNA can contain hundreds of millions of nucleic acid molecules. These long DNA strands are called chromosomes. The order of the individual nucleic acids along the chain contains information organisms used for growth and reproduction.

Types of Waves

Every sound we hear, every photon of light that hits our eyes, the movement of grass blown by the wind and the regular beat of the tides are all examples of waves. They are all around us.  Visible, physical wave*s such as those we see when a rock is thrown into water are what many people think about when they first began to think about waves. These waves have distinct properties specific to their type but also exhibit characteristics in common with more abstract waves such as sound waves and light (electromagnetic) waves.

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