Pro-Human Extremist

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Why do things look black and white in moonlight?

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Most of what we know about the world around us comes from seeing. Vision is such a useful sense because photons emitted by the sun stream down to earth all day long and reflect off objects or are absorbed by them. Materials that reflect more photons appear lighter to our eyes, while materials that absorb more photons appear darker. Because photons travel at the speed of light, the stream of photons reflecting off an object gives us practically instantaneous information about it, even if it is far away from us. The only other sense that gives us information about far distant objects is hearing.

opsin protein

The structure of an opsin protein. The corkscrew shapes represent alpha helix domains in the protein structure. The bound retinal molecule is just visible in front of the orange alpha helix and behind the two green ones.

We can see because the retinas in the back of our eyes contain cells called photoreceptors, which can detect the presence of photons. Photoreceptor cells can sense photons because they contain molecules of retinal that change shape when they absorb a photon. The retinal molecules are bound to proteins called opsins, which change shape when the retinal changes shape. This triggers a cascade of molecular events in the photoreceptor cell that alters the release of neurotransmitter molecules by the photoreceptor, thus sending a neural signal to other cells in the retina.

Our opsins have evolved so photoreceptor cells are most sensitive to photons in the range of wavelengths emitted by the sun. What we call visible light has wavelengths from 400 to 700 nanometers (a nanometer is one billionth of a meter), because when retinal is bound to opsins, it doesn’t readily absorb photons with wavelengths below 400 nanometers or above 700 nanometers. Photons with wavelengths above 700 nanometers are  in the infrared range, and they’re bouncing off objects all around us, but we can’t see them because they have no effect on the retinal molecules in our photoreceptors.

The different colors that we see are simply photons of different wavelengths within the 400-700 nanometer range of visible light. The colors in a rainbow from blue to green to yellow to orange to red correspond to photons having a range of wavelengths, from shorter to longer.

We can distinguish these different colors because the photoreceptors called cones come in three types containing three different opsin proteins. Those are called L, M, and S opsins because they interact with retinal so it preferentially absorbs photons having long wavelengths, medium wavelengths, and short wavelengths. Red light is absorbed best by cones containing L opsins, while green light is absorbed best by cones containing M opsins and blue light by cones containing S opsins. The visual circuits in our brains compare the neural activity triggered by these three different kinds of cones to distinguish between slightly different colors, like tangerine vs. pumpkin.

The blue, green. and red lines show the range of wavelengths of light that are absorbed by S, M, and L opsins. The dashed line shows the range of wavelengths absorbed by the rhodopsin proteins in our rods.

So why do we see these colors only during the day? Because cone photoreceptors aren’t sensitive to very dim light. The density of photons at night is so low that it has virtually no effect on any of the three different types of cones. Another type of photoreceptors called “rods” are the only ones responsive to dim light, and there’s only one type of opsin in rods, so there’s no way to compare the wavelengths of different photons. We can see, but only based on different intensities of dim light, so everything looks just like different shades of grey.

Of course all of that only applies to dim light at night—as bright as moonlight, for example. We can still see something like a neon sign at night in color, as long as our eyes receive a high enough density of photons to produce a response in our cone photoreceptors, so different wavelengths of light can be distinguished.

© Joel Benington, 2012.

All images come from Wikimedia Commons, and are used under a  Creative Commons Attribution-ShareAlike 3.0 Unported license.

Written by Joel Benington

July 5, 2012 at 11:28 pm

Posted in biology, science

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The evidence for biological evolution on Earth

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I’m constantly amazed by how many people in the US either reject the idea of biological evolution or have serious reservations. By contrast, in Europe and other countries with developed economies, only a relatively small fraction do. And the mainstream Christian denominations that most Americans belong to all explicitly accept the reality of biological evolution. That includes the Catholic, Episcopalian, Presbyterian, Methodist, Lutheran, and Anglican churches

The simple fact is that there is overwhelming evidence for biological evolution. As the 20th century biologist Theodosius Dobzhansky said (when the evidence for biological evolution was not even as strong as it is today), “Nothing in biology makes sense except in the light of evolution.” If we were compelled to reject the idea of biological evolution, there would be literally thousands of unexplained biological phenomena that currently make perfect sense as consequences of the evolutionary history of life on Earth.

No credible biologist rejects the reality of biological evolution. Even the very few biologists that have signed on to the Intelligent Design movement, like Michael Behe, accept the reality of the vast majority of evolutionary thought, arguing merely that certain biological phenomena cannot be explained by a purely mechanistic process.

When asked to make a quick case for the reality of biological evolution, I like to focus on the evidence for common descent—that all animals including humans have descended from a common ancestor that lived hundreds of millions of years ago, and that animals are likewise related to other groups of living things, with a common ancestor that lived billions of years ago. The evidence for these conclusions includes the following:

All living things use DNA as their genetic material.

The genetic code, determining which three-nucleotide DNA sequences code for which of the 20 amino acids that are used to make proteins, is essentially the same in all living things.

All living things use essentially the same molecular machinery (involving over 100 proteins and other molecules) to synthesize proteins based on DNA sequences.

All living things use ATP and some of the same other molecules as energy carriers.

Many metabolic pathways are shared among all or a considerable fraction of living things. Many enzymes have essentially the same shape and catalyze the same chemical reactions in those pathways in animals, plants, fungi, and other living things.

The cells of all animals (including humans) are made of many of the same components, including their membranes, internal organelles, cytoskeleton, etc. Many of the same proteins are found in these various structures, in animals as diverse as humans and other mammals, fish, birds, worms, and flies. And those proteins interact with each other in many of the same ways in these different animals.

Mammals exist in a wide variety of shapes and sizes, but they all share substantial similarities in their bony structure, internal organs, cell types, and the organization of cells in different tissues.

In other words, though we may be accustomed to thinking of humans as distinct from other animals, on the levels of molecules, organelles, cells, tissues, and organs, there are literally thousands of ways in which our bodies function in essentially the same ways as the bodies of other animals.

Over ¾ of the approximately 22,000 genes in the human genome have specific, one-to-one equivalents in the mouse genome. Also, 90% of the mouse and human genomes can be lined up based on the occurrence of equivalent genes in more or less the same order.

96% of the over 3 billion nucleotides in the DNA sequences of the human and chimpanzee genomes are identical. This includes both functional and non-functional (“junk”) nucleotide sequences, the latter having no identifiable genetic influence on either organism. Similarities in functional DNA might be explained based on similarities in the structure and functioning of  the two species, but similarities in “junk” DNA only make sense if the two species share a recent common ancestor.

The fossil record presents a succession of forms of living things over time that is entirely consistent with evolution of life on Earth over the past 3.5 billion years or so. There are some gaps in this record, but it is far more complete and detailed than one would think after reading creationist literature. Given the thousands of fossil species that have been identified in rocks dating from just a few million years ago to billions of years ago, the chance that a succession of forms consistent with biological evolution would occur by chance is infinitesimally small. For example, even one fossil rabbit or bird in rocks from 500 million, or 1, 2, or 3 billion years ago would be completely inconsistent with an evolutionary process; and yet such inconsistencies are strikingly absent.

There are also many demonstrated cases of natural selection causing evolution among present-day living things. These include the evolution of antibiotic resistant bacteria, experiments in which model organisms like fruit flies and yeast have evolved when placed in new environments, and studies in which populations of organisms are compared in two different environments where different characteristics should be selected for. Creationists, however, discount all of this evidence by supposing that small evolutionary changes do occur as a result of natural selection, but there are limits to how much any given species can change. There is no evidence for such limits—evolutionary changes observed in the present are relatively small only because such small time periods are involved. More dramatic changes in living things typically involve millions to hundreds of millions of years.

© Joel Benington, 2011.

Written by Joel Benington

September 10, 2011 at 7:39 pm

Posted in biology, evolution