Archive for January, 2010

Vestiges: Evidence for Evolution? Part I

Chamber, RobertCharles Darwin uses “vestiges” five times in The Origin of Species. Vestiges, since then has become synonymous with evolution. Eminent evolutionist, Douglas Futuyma, Professor of Ecology and Evolutionary Biology at the University of Michigan, notes that vestigial structures make no sense without evolution. The first question is—what are vestiges?

In this first in a series on vestiges, we will discover how structures labeled as vestiges once played an important role as evidence for the theory of evolutionary. Since the most popular example of a vestige structure is the human appendix, the human appendix will be the focus structure examined in this series.

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Evolution Theory Chaos

Jerry A. Coyne, one of the leading evolutionists at the University of Chicago, in his new book entitled Why Evolution is True (2009) writes “much confusion and misunderstanding surrounds evolution” even though “the modern theory is easy to grasp.” The question is how can a theory be “easy to grasp” and still be surrounded by “much confusion”?

But what could the confusion be over? Here are some examples.  Charles Darwin wrote in The Origin of Species – “There is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection”. Coyne contradicts Darwin by stating – “natural selection does not yield perfection”. Over a trivial issue, confusion reigns over whether natural selection can or cannot produce perfection in nature.

Presumably, to show how easy the theory of evolution is to understand, Coyne features what he calls the six basics of evolution: “evolution, gradualism, speciation, common ancestry, natural selection, and nonselective mechanisms”. For Coyne, natural selection is not the exclusive driving force of evolution.

Niles Eldredge, evolutionary biologist and curator of the American Museum of Natural History, disagrees. Niles Eldredge, architect  and designer of the museum’s currently touring Darwin exhibit in the companion book Darwin, Discovering the Tree of Life (2005), credits Darwin with discovering the actions of natural selection—the essence of evolution: “When [Darwin] formulated the principle of natural selection, he had discovered the central process of evolution.”

Unlike Coyne, Eldredge envisions evolution acting exclusively through the process of natural selection: “A century and a half ago, Charles Darwin offered the world a single, simple scientific explanation for the diversity of life on Earth: evolution by natural selection.” Unlike Coynes six basics of evolution, Eldredge uses a VISTA acronym for natural selection that stands for Variation, Inheritance, Selection, Time, and Adaptation.

Differences in approach even between Coyne and Eldredge, exemplify why evolution theory continues to be confusing—even on the basics. The teaching of evolution is in chaos. Coyne pines “most of my university students who supposedly learned evolution in high school, come to my courses know almost nothing about this central organizing theory of biology.” Could it be because a unified theory of evolution simply does not exist?

Even university science major graduates seem to be no better. T. Ryan Gregory and Cameron A. J. Ellis, in their paper entitled “Conceptions of Evolution Among Science Graduate Students” published in BioScience 59(9):792-799 (2009), surprizingly found that less than 30% of students pursuing advanced science degrees could correctly identify even the basic principles of evolution.

The reason is—a comprehensive theory of evolution simply does not exist. Even with the convening of the most respected evolutionary scientists at the Altenberg Summit in 2008, no consensus was reached on a comprehensive theory of evolution.

Given the flood of available evidence, in the wake of Crick’s Central Dogma collapse, evolution is a theory that remains in chaos—now more than ever.

Species

Species and natural selection are the two most common terms Charles Darwin uses in the book from the title—The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

In the “Glossary of the Principle Scientific Terms Used in the Present Volume”, while Darwin defines “Organism” as “An organised being, whether plant or animal”, surprizingly, neither “species” nor “natural selection,” the key terms of the book, are defined in the Glossary. The question is why.

Defining “species” became one of Darwin’s great challenges. From the start, Darwin recognized that among naturalists of the day, the term “species” did not have a consistent definition: “No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. Generally the term includes the unknown element of a distinct act of creation.”

 Unlike Newton who was able to measure and test the laws of gravity, Darwin had to deal with the problem that there “is no possible test but individual opinion to determine which of them shall be considered as species and which as varieties.”

In the pursuit for a definition, Darwin suggested that as a variety begins to exceed the number of the parent species, the new variety becomes a new species: “If a variety were to flourish so as to exceed in numbers the parent species, it would then rank as the species.” In other words, species was simply a numbers game.

Darwin’s numbers game approach was never seriously taken—even by Darwin himself. After 150 years, the problem of defining species has not been resolved and is now known as the long-standing “Species Problem.”

Jody Hey of Rutgers University wrote in Trends in Ecology & Evolution (2001) – “The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word ‘species’. The innumerable attacks on the problem have turned the often-repeated question ‘what are species?’ into a philosophical conundrum.”

Massimo Pigliucci professor of Ecology and Evolution at the State University of New York at Stony Brook noted in BioEssays (2003) “First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require – but cannot be settled by – empirical evidence.”

The Origin of Species is loaded with plastic contradictory definitions even on the central term of the book—species. Darwin eventually concedes on the definition of species by writing – “We have seen that there is no infallible criterion by which to distinguish species and well-marked varieties.”

Today, known evidence remains compatible with the following definition of species that Darwin long endvoured to eliminate – “Generally the term [species] includes the unknown element of a distinct act of creation.”

Darwin—Chagas Hypothesis

Charles Darwin struggled with significant health problems. Just less than two weeks before publication of The Origin of Species, Darwin described his condition to his cousin Fox in a letter, stating, “I have had a series of calamities; first a sprained ankle, and then badly swollen whole leg and face; much rash and a frightful succession of Boils—4 or 5 at once. I have felt quite ill—and have little faith in this ‘unique crisis’ as the Doctor calls it, doing me much good. I cannot now walk a step from bad boil on knee.”

Things that Darwin once found pleasurable as a young man turned on him. By 1865, at the age of fifty-six, Darwin summed up his problems in writing to a new medical adviser by writing that for twenty-five years he had experienced extreme flatulence, preceded by ringing ears and visual black dots, and vomiting preceded by shivering and crying.

In 1871, one year before the publication of the sixth and final edition of The Origin of Species, in a letter to his natural selection collegue, Alfred Wallace, Darwin confided: “present I feel sick of everything, and if I could occupy time and forget my daily discomforts, or rather miseries, I would never publish another word.”

Time and health took a toll on Darwin’s mind: “I have said that in one respect my mind has changed during the last twenty or thirty years. Up to the age of thirty, or beyond it, poetry of many kinds, such as the works of Milton, Gray, Byron, Wordsworth, Coleridge, and Shelley, gave me great pleasure, and even as a schoolboy I took intense delight in Shakespeare, especially in historical plays. But now after many years I cannot endure to read a line of poetry: I have tried lately to read Shakespeare, and found it so intolerably dull that it nauseated me. I have also lost my taste for pictures or music.”

What caused Darwin’s life-long health problems? To explain why Darwin experienced such poor health, scientists have pointed to a one night event east of the Andes near Mendoza in March 1835—Darwin wrote: “At night I experienced an attack (for it deserves no less a name) of the Vinchuca, a species of Reduvius, the great black bug of the Pampas. It is most disgusting to feel soft wingless insects, about an inch long, crawling over one’s body.” Darwin is thought to have been bitten by an insect called the “Great Black Bug of the Pampas” carrying the infectious parasite Trypanosoma cruzi.

For over a period of forty years, Darwin suffered intermittently from various combinations of symptoms such as malaise, vertigo, dizziness, muscle spasms and tremors, vomiting, cramps and colics, bloating and nocturnal intestinal gas, headaches, alterations of vision, severe tiredness, nervous exhaustion, dyspnea, skin problems such as blisters all over the scalp and eczema, crying, anxiety, sensation of impending death and loss of consciousness, fainting, tachycardia, insomnia, tinnitus, and depression. However, since attempts to test Darwin’s remains at the Westminster Abbey by using modern PCR techniques have been refused by the Abbey’s curator, the real cause of Darwin’s health problems remains only speculative.

Molecular Evolutionary Clocks

Michael Ruse, author of Defining Darwin, Essays of the History and Philosophy of Evolutionary Biology concluded that “Indeed, the truth is that there is virtually nothing today in evolutionary studies that correspond exactly to the facts of the Origin.”

For Charles Darwin, molecular clocks were the farthest his mind, not to mention cellular biology or DNA. In 1859, inheritance was thought to occur by blending the characteristics with the new information learned by the “gemmules” in the parents. Gregor Mendel, the Austrian monk, in 1865 eventually decimated blending inheritance, but the foundation of modern genetics went unrecognized until rediscovered by Hugo de Vries and Carl Correns in 1900.

To estimate the pace of evolution, in 1962 molecular biologist Emile Zuckerkandl and Nobel Prize winner Linus Pauling were working at California Institite of Technology on hemoglobin evolution and expressed the idea of “molecular anthropology” as a new discipline. The idea was later termed the molecular clock theory. The purpose of the molecular clock is to estimate the rate of evolution for individual molecules. In 1962, molecular sequence problems were just emerging.

Zuckerkandl and Pauling postulated that in a protein, each amino acid randomly changes at a constant rate. If the estimated time for divergence between species and the number of amino acid changes since that time can be determined from the fossil record, the rate of change can be calculated. This rate of molecular change (time per amino acid change) has been called the molecular clock.

As the molecular data began to accumulate during the early 1990s, it became increasingly apparent that the theory was intrinsically even more problematic when examining evolution from the context of the entire organism and the fossil record. At the core of Darwinian evolution are the successive, slight changes in molecules. However, how different molecules can evolve at different rates in the same organism emerged as an enigma.

Information from the molecular clock was once thought to be one of the most useful tools in establishing evolutionary biology. How the evolution of each molecule can run by a different molecular clock in the same organism continues to undermine a cohesive theory of molecular evolution.

The pursuit to resolve the clock issue has reemerged onto center stage because the rate of molecular change is foundational to evolution. If the molecular mechanisms of evolution cannot be traced, the only logical conclusion is that molecular biology has played no role in evolution.

In 2007, Naoyuki Takahata, of The Graduate University for Advanced Studies in Japan, wrote in the journal Genetics, “It is now clear that any kind of molecular clock ticks erratically, but it is nevertheless widely used [unfortunately] for estimating species divergence times.”

How Zuckerkandl and Pauling’s simple postulate has become so complicated begs the question, are molecular clocks real? Professor of evolutionary biology Thomas Cavalier-Smith of the University of Oxford in England wrote in Philosophical Transactions of the Royal Society B in a paper entitled Cell Evolution and Earth History: Stasis and Revolution that the answer is no: “Evolution is not evenly paced and there are no real molecular clocks.”

Available evidence bodes negatively for the usefulness of molecular clocks in establishing any shape for the Tree of Life. What was originally thought to become a cornerstone for molecular evolution is now irreconcilable with evolution and created chaos in evolutionary thought. Difficulties associated with attempting to explain how a family of homologous proteins could have evolved at constant rates have created chaos in evolutionary thought.

Rather than supporting the theory of evolution, the molecular clock evidence and the sequence data actually undermine the theory of evolution through “successive, slight” variations in molecular biology. Just as hope in the fossil record, the origin of life, and the sequence of amino acids dissipated, the hope that molecular clocks will become an evidential, evolutionary cornerstone is vaporizing. In 2005, geneticist Giuseppe Sermonti wrote: “Once the universal ‘molecular clock’ was shelved, biochemists ceased to question (in any case dubious) datings proposed by paleontologists.”

Molecular biologists beginning in the early twentieth century had expected to trace the organization of inorganic to organic molecules as well as the successive molecular changes as the species evolved. Clearly, however, the convergence of molecular evidence does not support the theory. Darwin concluded in The Origin of Species if the evidence does not support “numerous, successive, slight modifications, my theory would absolutely break down.”

Molecular clocks, as evidence for evolution, continue to be unsuccessful in delivering on earlier expectations.

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Darwin, Then and Now is a journey through the most amazing story in the history of science - the history of evolution. The book encapsulates who Darwin was, what he said, and what scientists have discovered since the publication of The Origin of Species in 1859.

With over 1,000 references, Darwin Then and Now is a historical chronicle of the rise and fall of the once popular theory of biological evolution.

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