Category Archives: evolution

The Eyes Have It

Charles Darwin published the “Origin of Species” in 1859 and established evolution as the central organizing principle of biology. The molecular basis of evolution became clear about a century later with the understanding of the structure of Deoxyribonucleic Acid – better know as DNA.

DNA is the stuff of inheritance, and changes in DNA are the stuff of mutations and ultimately evolution. The code of life is defined by a simple alphabet consisting of only 4 letters and a grammatical structure which demands words can only be three letters long. Although this means there are only 64 words (called codons) in the DNA dictionary, “sentences” in the genetic code can be crazy long, literally tens of thousands of words long. The functional unit of DNA are strings of codons called genes which specify instructions about life.

Most importantly, the code is shared by all life. The codons mean the same thing in an aardvark and a zebra, from simple bacteria to you and I. Closely related organisms have closely related sequences of codons. This has allowed confirmation or rearrangement of the cladistic relationships of life. Not only can whole organisms be compared but also individual organs.

The evolution of the eye can be seen by comparing DNA across many organisms. Devotees of the idea of intelligent design, i.e, the god did it crowd, have suggested that an organ as complex as an eye cannot have arisen by evolution. They proffer the idea of irreducible complexity. It’s the old “what good is half an eye” argument. Mammalian eyes, just as one example, have several parts including a retina, an iris, a lens, a pupil, etc. Arthropods have compound eyes with multiple lenses and retinas.

There is a range of types of eyes that serve different functions and therefore have different levels of complexity, but in the last analysis they all share one common feature and that is the detection of light. The basic requirement for light detection, shared across all life, is a group of closely related molecules called rhodopsins. If light shines on this molecule, it changes shape and that triggers a signal to the brain that says light! Multiple copies of the molecule allow greater sensitivity and features such as a lens add acuity to the detection. Slight variations in the structure of the rhodopsin allows for detection of different wavelengths (colors). That the rhodopsin occurs across all kinds of life is seen in the gene which codes for the production of the molecule.

Here is the really interesting part. The gene for rhodopsin synthesis occurs in forms of life that have no eyes, such as a primitive organism know as cyanobacteria. These ancient bacteria have been around for billions of years. Why would a bacteria that couldn’t care less about detecting light have rhodopsin? It turns out the bacteria use this molecule for an entirely different reason.

Minor mutations in the rhodopsin gene allowed for the “repurposing” of the molecule to serve as a light gathering structure, rather than the function it serves in bacteria. This repurposing of structures is not an uncommon feature in evolution and allows for small changes to make big differences. Life is not irreducibly complex.

Thoughts on Oxygen – Part 2

Based on genetic evidence across all life it appears that the earliest organism called LUCA, short for Last Universal Common Ancestor, contained a wealth of cellular components that handled molecular Oxygen otherwise known as O2. This in light of the fact that there was scant Oxygen present in the atmosphere, a fraction of a percent compared to the current concentration of 21 percent. Why?

Most likely is the fact that Oxygen is a very reactive gas, and it reacts by snatching electrons away from other molecules. This creates two other kinds of chemical compounds, free radicals which are electrically neutral but very reactive, and cations which are positively charged ions which also are reactive. When Oxygen or a few derivative molecules react with other components of cells or tissues they cause damage which can lead to cell death and even death of the whole organism.

One description of growing old is little more than the accumulation of cellular damage due to exposure to Oxygen. Just one example is that Oxygen reacts with a component of our skin called collagen. Over time the damage leads to reduced elasticity. This results in “brittle” skin which is more easily damaged by physical abuse. The skin also loses its tone and becomes saggy. These are oxidation reactions just like the rusting of iron and cooking oil becoming rancid. When you burn something you are oxidizing it, hence growing old is slowly burning up.

The earliest anaerobic single celled organisms had a myriad of cell components to protect themselves from oxidative damage even in an atmosphere which contained little oxygen. Today most of what we recognize as living things such as plants and animals, are aerobes. We require Oxygen to drive the processes by which we generate energy. We need the energy to do all the work of our bodies. To detoxify poisons in our liver. To move us from couch to dinner table and back. To fuel the nerve impulses to our brain that allow us to read newspaper columns.

Interestingly, our brains consume close to 25 % of all the Oxygen we use. Compare that to the heart muscle which only uses 12 % or the kidneys which need only 7 % of our Oxygen. The question now is how did we go from Oxygen being a deadly poison when life operated anaerobically (without oxygen) to our current state where it is demanded? The answer lies in a number of evolutionary advances. Those cell components that were used to protect anaerobic organisms were shifted in function by random mutations to do the job of aerobic metabolism. The advantage is that if you can control the reactivity of Oxygen, you can put it to good use to do the work of the body, but only if you control it.

Evolution does not require new constructions from whole cloth. Slight changes in a macromolecule allow it to be repurposed. Life is complex, but not so complex it requires a designer. Evolution only requires random mutations and a long time scale.

A Few Thoughts on Oxygen – Part 1

Until late in the 20th century scientists hypothesized that the earth’s early atmosphere was highly reduced, in a chemical sense. What atmospheric elements were present were bonded to hydrogen. This followed from the well-known fact that hydrogen is by far the most abundant element in the universe . Hence, other elements were more likely to be chemically attached to Hydrogen than anything else. Any carbon would be present as methane CH4, nitrogen would be present as ammonia NH3 and oxygen in the form of water OH2.

Scientists in the early 1950s (Stanley Miller-Urey) used this assumption in experiments looking for mechanisms for the beginning of life. They created an atmosphere composed of these reduced gasses and then induced chemical reactions among them using UV light (which would have been abundant ) and/ or Electric arc (simulating lightning.) They found that the could produce several “life precursor” molecules such as amino acids (to form protein), purine and pyrimidines (to form nucleic acids), and simple sugars (to form carbohydrates.)

I gave many a lecture discussing the Miller-Urey experiments, which with current understanding of what the early atmosphere was like, were wrong. Evolution of life most likely required the same simple precursors to be present but they must have come about by other mechanisms. The current wisdom as to the composition of the early atmosphere suggests in was more in line with the composition of volcanic gasses. This is based on more recent geochemical studies. Carbon would have been present in its oxidized form, CO2. Nitrogen would have been present as the diatomic gas N2, sulfur as SO3.

The only feature of the previously assumed early atmosphere and the current hypothesis is that the presence of any free oxygen (O2) was very limited, maybe a fraction of one percent of the total atmosphere. Currently it is about 21 percent.

Regardless of the competing hypotheses about the composition of the atmosphere life most likely began and then evolved in the absence of any significant amount of Oxygen for a couple of billion years. Because of the specificity of the genetic code it has always been assumed that all life is related and the earliest ancestor of all life is called LUCA – the Last Universal Common Ancestor.

What did LUCA look like? How did she make a living? Surely she was a single celled organism replicating by cell fission. Information from mother to daughter cell was transmitted by DNA replication, so the enzymes attendant to this task are shared by all her descendants. She had to have been an anaerobe as there was scant oxygen in the atmosphere at the time. What about the other cell machinery?

When certain components of cellular machinery are found across all life, it must be that LUCA had these components. Oddly, for an anaerobe, LUCA appears to have had a broad range of macromolecular structures which are for handling oxygen. What is that all about?