DNA and Common Descent


Psalm 139 describes man as “wonderfully and fearfully made.”

Every one of us carries the assembly instructions for his own body. The cells in our bodies contain this information stored in each cell’s genetic material. Deoxyribonucleic acid or DNA is the molecule that holds these instructions controlling the development and functioning of our bodies. In fact, DNA does this in all known living organisms.

DNA is often compared to a set of blueprints. This is because it contains the information necessary to build the components of our cells, molecules such as proteins and ribonucleic acid (RNA). DNA takes the form of a polymer made up of simpler units called nucleotides which are in turn held together by a backbone of sugars and phosphates. Each sugar is attached to one of four types of molecules called “bases.” [1] The physical structure of the DNA molecule is usually referred to as a “double-helix.” Imagine a long ladder that has been twisted so that the side rails form a pair of spirals tied together by the rungs. In DNA the sugars and phosphates make up the spiral rails, and each rung is made up of a pair of the bases. The sequence of the base pairs along the DNA molecule encodes the information being stored.

Figure 1. Basic Cell Structure.

DNA is organized into structures within the cells called chromosomes, and the complete set of chromosomes in a cell makes up a genome. Multicellular organisms (plants, fungi, and animals) store their DNA in the cell nucleus. Single-cell organisms keep their DNA in the cell’s cytoplasm.

In spite of the tremendous variety we find among living things, they all have certain properties in common. These include replication (they have offspring), heritability (they pass on genetic material to their offspring), catalysis (they have a common set of chemical processes), and energy use or metabolism (they all burn carbon through similar processes). This similarity among organisms led to a hypothesis that they all had inherited these traits because they were descended from a single original species that had these four functions.

Figure 2.  The 24 Human Chromosomes.  (Oak Ridge National Laboratory)

The scientific evidence for common descent is quite strong.  Indeed, over the last century or so, no other hypothesis has been able to account scientifically for the unity and diversity of life on earth. Common descent has been verified so extensively that it is the currently accepted scientific “fact.” [2] The common descent hypothesis makes predictions that have been confirmed not only in genomics and molecular biology but also in other areas such as paleontology and anthropology. No significant contradictory physical evidence has been found. Competing proposals either have been contradicted by the evidence or are not testable using the scientific method. No other scientific explanation competes with common descent.

This is probably a good point to pause and consider just what is meant by scientific evidence and scientific proof.

Science can never really establish a “fact” in the sense of proof beyond question. Everything in Science is open to reevaluation when new data emerge. Proof in the sense of airtight logic is limited to mathematics. [3] Scientific “facts” are “proven” when they are strongly supported by data and have not been shown to be false.

Much of Science defies common sense. Our common sense tells us that the earth is flat, that the sun rises and sets as the earth stays fixed, that the continents don’t move, that bowling balls ought to fall faster than marbles, and that heavier-than-air objects should fall out of the sky unless they flap their wings. Common sense is often flat wrong.

Figure 3. The Scientific Method.

Science shows us thing that we can’t see with our own eyes—germs, atoms, electrons, x-rays, solar fusion, and genes. All of these unseen things were made known through scientific inference.

The flow chart at right outlines the scientific method. Because new observations and testing occur continually, the four steps are practiced concurrently. New observations, even unpredicted ones, may provide data that will cause a hypothesis to be refined. However, Science is much more that just naive observation and measurement. What distinguishes Science from other disciplines is that the observations are interpreted, tested, and used.

But I digress.

What do our DNA and the DNA of other species tell us about common descent? It is conceivable that we might have found different genetic material for each species, but during the middle years of the 20th century, DNA was identified as the genetic material for all life on earth. All known organisms base their replication on DNA. All organisms synthesize their DNA using the same four nucleosides (out of more than 100 naturally occurring possibilities).

In order to function living things must catalyze various chemical reactions. Every known organism bases its catalysis on the same limited subset of amino acid used to to form the necessary proteins and RNA. There must be a some means by which the genetic material transmits information to the catalytic systems in the cells, and, with a few extremely rare exceptions, all known organisms use the same universal genetic code. The few minor variations are associated with major classification groups (eg., vertebrate animals vs. plants vs. certain single-cell creatures, etc.).

Thousands of new species are discovered each year, and tens-of-thousands of new genetic sequences are determined annually. Each is a test of common descent, and, to date, not one has falsified the theory.

Common descent predicts an organization of species in a nested hierarchy of groups within groups as organisms’ genomes diverge. We will consider the fossil evidence supporting common descent in a later post. For now, let’s consider some of the molecular biological evidence of the common descent among humans.

In theory, one could trace human ancestry through any single chromosome. In practice, the genetic mixing that occurs when a sperm fertilizes an egg muddles the ancestry path. However, our mothers pass along genetic material to us in the form of mitochondrial DNA which is not affected by sexual reproduction. Mitochondrial DNA has been used to trace our matrilineal inheritance back to a single woman, the so-called “Mitochondrial Eve.” Most references cite early research which suggests that she was alive about 140 ky ago. A couple papers, now shown to be flawed, came up with a date roughly 6500 years ago. [4, 5]  More recent work would place the date roughly ten times further in the past (> 50 ky ago). [6]

Work has also been done using markers on the Y-chromosome, and the evidence now points to the fact that every male alive today is the descendent of a single male (called “Y-chromosome Adam”) who lived in the range of 35 to 88 ky ago. [7]

Now, nothing in the data shows that these two ancestors of ours were necessarily alive at the same time. Furthermore, there is nothing in the science to indicate that there were not other males alive while “Y-chromosome Adam” lived, and the same holds for other females and “Mitochondrial Eve.” And nothing in our genome rules out our having had other ancestors who were alive at the same time as these two individual, but all of us share these common ancestors. Still, it is an interesting point of convergence between Science and Genesis that both say that we all share a single genetic father and a single genetic mother.

Let’s also consider some evidence concerning common descent among primates, including humans.

Animals can be infected by viruses. A retrovirus (for example, HIV, which causes AIDS, or HTLV1, which causes a type of leukemia) infects its host by making a copy of its own genome and inserting it into the host’s DNA. These copies are called endogenous retroviruses. If this happens in a sperm or egg cell, the retroviral DNA will be inherited by the host’s descendants. This is fairly rare, so finding retrogenes in exactly the same spot in the chromosomes of two different species strongly suggests common ancestry.

About 1 % of the human genome is infected with retroviruses. [8] There are several instances of retrogene insertions in the same locations in humans and chimps as well as other primates. Figure 4 is a genetic tree of several primates which shows shared endogenous retroviruses among these species. The arrows show the relative insertion times of the different instances of viral DNA into a host. All branches in the tree to the right of an arrow carry that retroviral DNA.

Here we have genetic evidence at the molecular level of common ancestry for these primates. Humans and chimps have a common ancestor that is not shared with gorillas. Humans, chimps, and gorillas have a common ancestor that is not shared with orangutans. And so on. Note that this does not indicate that humans are descended from chimpanzees. [9] Rather, it indicates that humans and chimps are both descended from a common, now-extinct ancestor.

It would make no sense if other mammals (such as bears or rats or platypi) had these same retrogenes as primates in exactly the same locations within their chromosomes, and we have not seen such evidence to date. If such evidence were to appear, that would falsify our prediction, and we would have to come up with a new theory.

Our theory would have to evolve to fit the real world’s facts.

Figure 4.  Human Endogenous Retrovirus K (HERV-K) Insertions in Identical Chromosomal Locations in Various Primates.  (After Lebedev et al.) [10]

NOTES

[1] These bases are identified as A, C, G, and T. These letter designations have a basis in their chemical names.

[2] Karl Popper argued that the primary criterion of science is the falsifiability of a theory. One cannot prove something absolutely, but one can falsify. A theory that has withstood multiple tests over many years becomes a scientific fact. For example, the theory that the earth is a sphere was taken to be a scientific fact by the ancient Greeks, but no one directly observed the earth as sphere until Yuri Gagarin did in 1961. No one has yet directly observed the earth in orbit around the sun, but that proposition is considered factual by science. A set of ideas that cannot be tested may, in fact, be true, but it isn’t science.

[3] Albert Einstein, in an address to the Prussian Academy of Sciences, once remarked, “As far as the laws of mathematics refer to reality, they are not certain; and as far as they are certain, they do not refer to reality.”

[4] Gibbons, Ann, “Mitochondrial Eve:  Wounded, But Not Dead Yet,” Science, 14 August, 1992, vol. 257, no. 5072, pp. 873 … 875.

[5] Gibbons, Ann, “Calibrating the Mitochondrial Clock,” Science, 2 January, 1998, vol. 279, no. 5347, pp. 28, 29.

[6] Siguroardottir, Sigrun, et al., “The Mutation Rate in the Human mtDNA Control Region,” Am. J. Hum. Genet., vol. 66, pp. 1599 … 1609 (2000).

[7] Ke, Y., et al., “African Origins in Modern Humans in East Asia:  A Tale of 12,000 Y Chromosomes,” Science, 11 May, 2001, vol. 292, no. 5519, pp. 1151 … 1153.

[8] That about 30,000 sites in each person’s genome.

[9] Legend has it that in a debate with Bishop Samuel Wilberforce, Thomas Huxely (aka, “Dawin’s Bulldog”) claimed that he would not be ashamed to have a monkey as an ancestor but would be ashamed of an ancestor who obscured the truth.

[10] Lebedev, Y. B. , et al., “Differences in HERV-K LTR insertions in orthologous loci of humans and great apes,” Gene, 18 April, 2000, vol. 247, pp. 265 … 277.

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