Posts Tagged ‘Darwin’

In 1986, American physicist, biochemist, and molecular biology pioneer Walter Gilbert was the first to propose the term “RNA world hypothesis” for the origin of life since the possibility of Darwin’s “proteine” arrival in the “warm little pond” was beyod any realm of possibility. Gilbert suggested that because RNA can synthesize itself in the absence of proteins, RNA may have originated on the early Earth before proteins or DNA; this is known as the RNA world. According to the RNA world hypothesis, the RNA molecule later evolved into DNA and protein molecules. While the DNA molecule evolved into a data storage role, the protein molecules evolved into a catalytic role.

In 1959, Spanish Catalan biochemist Joan Oró began to synthesize adenine, a key component of RNA and DNA, from hydrogen cyanide, similar to a Miller–Urey experiment. 

Like the Miller–Urey experiment though, the lack of geological evidence for hydrogen cyanide in the fossil record is missing. Another problem with hydrogen cyanide is that at room temperature, it becomes a gas toxic to cellular metabolism. During the German Nazi regime in the mid-twentieth century, hydrogen cyanide was used as an agent for mass murder.  

To date, not one laboratory experiment with realistic early Earth elements and conditions has produced a single nucleic acid. Scripps Research Institute biochemist Gerald Joyce states that the “most reasonable interpretation is that life did not start with RNA.” The origin of life is so difficult a problem that German researcher Kaus Dose stated in 1988 that the RNA theory is “a scheme of ignorance. Without fundamentally new insights in evolutionary processes … this ignorance is likely to persist.” 

In 1998, Leslie Orgel, senior research fellow and research professor at the Salk Institute for Biological Studies, where he directed the Chemical Evolution Laboratory, acknowledged that “we are very far from knowing whodunit” or what were the early environmental conditions on the Earth. 

Nearly twenty years later, the role of RNA in the origin of life remains elusive, if not improbable. In 2007, commenting in Proceedings of the National Academy of Sciences of the United States of America on a paper by Phillipp Baaske and Eugene V. Koonin, senior investigator, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, stated that while more is known about RNA, the evolutionary role of RNA has severe difficulties and “still is a hypothetical entity; … the evolutionary path to the translation systems remains essentially uncharted.”

Charles Darwin in a letter Joseph Hooker in February 1871 speculated that life might have originated in “some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a proteine compound was chemically formed ready to undergo still more complex changes”.

Darwin’s speculation went untested until the Miller–Urey experiment in 1952 at the University of Chicago. Stanley Miller and Harold Urey successfully produced some of Darwin’s “proteine compounds” by building on Alexander Oparin‘s and J. B. S. Haldane‘s hypothesis that the primitive conditions on Earth were favorable to the chemical reactions that synthesized organic compounds from inorganic precursors. Oparian and Haldane’s favorable conditions required a nitrogen-rich reducing atmosphere without oxygen.

The Miller-Urey experiment advanced the question to center stage—were the conditions of primitive Earth the same as proposed by Oparin and Haldane? Was early Earth nitrogen-rich? Was oxygen absent?

Since 1952, research on the actual chemical conditions of the primitive Earth has been on the investigative frontlines of origin of life research. After over 50 years, the consensus is inconclusive. Wikipedia, under the topic of “Origin of Life” in, now more commonly referred to as “Abiogenesis,” concludes: “There is no truly ‘standard model’ of the origin of life. Most currently accepted models draw at least some elements from the framework laid out by the Oparin-Haldane hypothesis.”

Irrespective of primitive Earth conditions, an even more challenging question emerges—what is the statisitcal probability for functional proteins to arise de novo from the “prebiotic soup” of amino acids by chance? 

Stephen Meyer, in his new book entitled Signature in the Cell, reviews the extensive research into answering this daunting question on chance. Based on the works of Robert Sauer at MIT, Douglas Axe at Cambridge University, and British cosmologist Sir Fred Hoyle, Meyer, concldues that “the improbability of generating the necessary proteins by chance—or the genetic information to produce them—to balloon beyond comprehension.”

Meyer writes, “The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebioitc soup is no better than 1 chance in 10¹⁶⁴.” Meyer continues, “Another way to say that is the probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than the odds of finding a single specific particle among all the particles in the universe.”

The evidence for the probability of origin of life arising from Darwin’s “warm little pond” seems to have vanished beyond the realm of any possibility—regardless of any early Earth scenario.

Darwin’s preamble to the first edition of The Origin of Species includes quotations from William Whewell’s popular book entitled Bridgewater Treatise and Francis Bacon’s sentential work entitled Advancement of Learning. From different worldview, both Whewell and Bacon advocated the use of inductive reasoning—the scientific method.

 Bacon (January 1561 – April 1626) is noted as one of the founders of the Scientific Revolution that eventually lead to the establishment of the Royal Society by Charles II in 1660. Whewell, one of Darwin’s dons at Cambridge University, is credited for coining the term “scientist.” 

Taking a comprehensive approach to the study of evolution, Darwin presented the two different worldviews of Bacon and Whewell. Whewell, envisioning nature apart from a “Divine” intervention,

“But with regard to the material world, we can at least go so far as this-we can perceive that events are brought about not by insulated interpositions of Divine power, exerted in each particular case, but by the establishment of general laws.”

Bacon, by contrast, envisioned nature as part of “God’s work,”

“To conclude, therefore, let no man out of a weak conceit of sobriety, or an ill-applied moderation, think or maintain, that a man can search too far or be too well studied in the book of God’s word, or in the book of God’s works; divinity or philosophy; but rather let men endeavour an endless progress or proficience in both.”

Darwin teaches, by example, to embrace the exploration of diverse worldviews. Modern education should take Darwin’s approach and “teach the controversy.”

Darwin, in a letter to Asa Gray at Harvard University in September 1860, Darwin wrote that “embryology is to me by far the strongest single class of facts in favor” of the theory.

Just two months before the release of the first edition of The Origin of Species in September 1859, Darwin wrote to Charles Lyell, “Embryology in Chapter VIII is one of my strongest points I think.”

Writing in his autobiography, Darwin recalls: “Hardly any point gave me so much satisfaction when I was at work on the Origin, as the explanation of the wide difference in many classes between the embryo and the adult animal.”

Darwin’s premise was that the similarity between the structure and the embryo of animal and man was primary proof that man evolved from animals. In The Descent of Man, published in 1871, Darwin writes in the first chapter that embryology provides the “ample and conclusive evidence in favour of the principle of gradual evolution.”

Darwin was not an embryologist, and instead relied on the work of others. In The Origin of Species, Darwin gave credit to Ernst Haeckel: “Professor Haeckel in his “Generelle Morphologie” and in [other] works has recently brought his great knowledge and abilities to bear on what he calls phylogeny, or the lines of descent of all organic beings. In drawing up the several series he trusts chiefly to embryological characters [to establish evolutionary sequences].”

Based on what Darwin thought was scientific evidence concluded: “So again it is probable, from what we know of the embryos of mammals, birds, fishes, and reptiles, that these animals are the modified descendants of some ancient progenitor.”

In The Origin of Species, Darwin wrote, “Thus, as it seems to me, the leading facts in embryology, which are second to none in importance, are explained on the principles of variation in the many descendants from some … ancient progenitor”

During the twentieth-century, Haeckel’s embryos were prominently displayed in nearly every biology textbook, even though Haeckel eventually confessed that the drawings were fraudulent.

In January 1909, Haeckel’s confession was published as a letter in the Munchener Allegemeine Zeitung, an international weekly publication for the sciences, arts, and technology. In the letter, Haeckel clearly states that the drawings were contrived by “comparative synthesis” and not by accurate reproduction. Without the fraud, the expected evolutionary embryonic sequences had obvious gaps. Haeckel concedes, “a small portion of my embryo pictures (possibly 6 or 8 in a hundred) are really ‘falsified’.”

Even more sadly, Haeckel’s only defense was that fraudulent practices were an accepted practice even by some of the “most esteemed biologists” of the day. Haeckel wrote, “After this compromising confession of ‘forgery’ I should be obliged to consider myself condemned and annihilated if I had not the consolation of seeing side by side with me in the prisoner’s dock hundreds of fellow culprits, among them many of the most trusted observers and most esteemed biologists. The great majority of all the diagrams in the best biological textbooks, treatises, and journals would incur in the same degree the charge of ‘forgery,’ for all of them are inexact, and are more or less doctored, schematised, and constructed.” Indeed the scientific method had been abandoned not only by Darwin and Haeckel, but also by a large segment of the profession of biology.

Paul R. Ehrlich of Stanford University and author of the famous overpopulation book, The Population Bomb, wrote in 1963 that Haeckel’s law now only has a leading role in mythology—not in science. “This generalization was originally called the biogenetic law by Haeckel and is often stated as ‘ontogeny recapitulates phylogeny.’ This crude interpretation of embryological sequences will not stand close examination, however. Its shortcomings have been almost universally pointed out by modern authors, but the idea still has a prominent place in biological mythology.”

Like Haeckel’s embryo drawings, the history of evolution  has been laced with an insidious legacy of fraud.

Darwin theorized natural selection to act through “slight, successive” changes -

“I do believe that natural selection will generally act very slowly, only over long periods of time…. natural selection acts slowly by accumulating slight, successive, favorable variations, it can produce no great or sudden modifications; it can act only by short and slow steps.”                                                            

While speculation on metabolic rates was beyond the scope of nineteenth century scientists, investigation in this field is now yielding new information on potential evolutionary correlates. During evolution, the continued increase in size and complexity, for example from “mouse-to-elephant”, was expected to follow corresponding “slight, successive” changes in basal metabolic rates in relationship to body mass.

The scientific team at The University of Birmingham in the United Kingdom headed by Craig White noted that the evolutionary “relationship between the basal metabolic rate (BMR) and body mass (M) of mammals has been at issue for almost seven decades.” BMR is a calculated number based on the equation BMR = aM^b and the exponent b has long been disputed. The universality of exponent b is at the center of investigation.

To determine the exponent b, the researchers studied high-quality BMR data from 585 species and a subset of 537 species and published their findings in the October 2009 edition of Evolution* entitled “Phylogenetically informed analysis of the allometry of Mammalian Basal metabolic rate supports neither geometric nor quarter-power scaling”. The team results re-establish the fact that no evolutionary relationship exists between BMR and M concluding –

“Thus, we conclude that no single value of b adequately characterizes the allometric relationship between body mass and BMR.”

Sherman J Sutter, writing for Science in the abstract entitled “Evolution: No b to Rule Them All”, concluded that -

“Their results reinforce doubts as to the existence of a universal allometric relationship between mammalian BMR and body mass.”

Evidence for the natural law of evolution through “slight, successive” changes in the BMR, as expected from Darwin’s theory of natural selection simply does not exist. Species are unique—“kind after kind.”

Evolution. 2009 Oct;63(10):2658-67.

In 1943, published in a paper entitled “Mutations of Bacteria from Virus Sensitivity to Virus Resistance,” microbiologist Salvador Luria, biophysicist Max Delbrück, and bacteriologist and geneticist Alfred Hershey discovered that mutations occur at a constant rate. In 1969, they were awarded the Nobel Prize in Physiology and Medicine “for their discoveries concerning the replication mechanism and genetic structure of virus.”

The Luria-Delbrück Experiment opened the question, are mutations inherent to microbes for the purpose of adaption to rapidly changinging environments and not for evolution? While microbe resistance through mutation is a logical mechanism for evolution, the reality is the bacteria have remained a bacteria and the virus has remained a virus. Preexistent genetic variants determine the range of mutations. Pierre-Paul Grassé, president of the French Academy of Sciences, observed, “bacteria, the study of which has formed a great part of the foundation of genetics and molecular biology … stabilized a billion years ago.”

The question is whether the mutations are the “raw material for evolution” or nature’s means for the microbes to adapt to the environment. In a 2009 review article by entitled “Darwinian evolution in the light of genomics”, published in Nucleic Acid Research, Eugene V Koonin concluded, “There is no consistent tendency of evolution towards increased genomic complexity” through mutation as expected with current evolutionary theories. Mechanisms of evolution remain beyond any known natural law.

Reflecting on the role of mutations, Grassé questioned, “What is the use of their unceasing mutations if they do not change?” Grassé concludes, “the mutations of bacteria and viruses are merely hereditary fluctuations around a median position; a swing to the right, a swing to the left, but no final evolutionary effect.” Microbes undergo constant mutations, but do not evolve – mutation stasis.

*Nucleic Acids Res. 2009 March; 37(4): 1011–1034 

Pangenesis was Darwin’s hypothetical mechanism for the origin of variation and inheritance through particles called gemmules. This “provisional hypothesis” on the origin of variation was presented in his 1868 work The Variation of Animals and Plants under Domestication through gemmules acquiring new variations that brings “together a multitude of facts which are at present left disconnected by any efficient cause”.

The etymology of pangenesis comes from the Greek words pan (a prefix meaning “whole”, “encompassing”) and genesis (birth) or genos (origin). Gemmules were thought to learn from experiences.

The origin of new variations was critical for Darwin’s theory since the “slight, successive” changes in evolution requires a constant stream of new variations for the actions of natural selection. Gemmules were imagined particles. These learned gemmules particles sent from every cell (pan) in the body with new variations (genos) accumulated in the germ cells and had a ‘vote’ in the constitution of the offspring (genesis).

This hypothesis provided a possible mechanism for the inheritance of acquired characteristics, as proposed by Jean-Baptiste Lamarck, which Darwin believed to be the origin of new variations in living organisms.

Little did Darwin know that even before the publication of the fourth edition of The Origin of Species in 1866, Gregor Mendel had presented the now-famous paper entitled “Experiments on Plant Hybridization,” laying the foundations of modern genetics.

Although, Mendel’s discovery went unnoticed until the turn of the twentieth century, German biologist August Weismann, at the University of Freiburg, launched the first scientific evidence directly challenging Darwin’s theory. Now known as the “Weisman Barrier,” in 1883, Weismann cut off the tails of mice from 21 generations. Seeing that the 22^nd generation still had tails, Weismann concluded that the evidence contradicted Darwin’s theory of pangenesis despite obvious reasons for change in the mice, “continuity” was observed, not new variations.

Ernst Mayr, Darwin’s twentieth-century bull-dag, stated Weismann as “The second most notable evolutionary theorist of the 19th century.” What is still unresolved now 150 years later is—what is the origin of variation?

Genomics offers unprecedented opportunities for testing the central tenets of evolutionary biology formulated by Charles Darwin in The Origin of Species in 1859, later modified into the Central Dogma by the Modern Synthesis during the twentieth century.

In a 2009 review article by entitled “Darwinian evolution in the light of genomics”, published in Nucleic Acid Research, Eugene V Koonin concludes “[m]ajor contributions of horizonal gene transfer… undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life.” 

Darwin wrote in The Origin of Species,“[a]lthough the belief that an organ so perfect as the eye could have been formed by natural selection, is enough to stagger any one; yet in the case of any organ, if we know of a long series of gradations in complexity, each good for its possessor, then under changing conditions of life, there is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection.”

Koonin continues, “[t]here is no consistent tendency of evolution towards increased genomic complexity.” Genomics has failed to demostrate increasing complexity as hypothesized by Darwin.

Evolution needs to synthesis a new mechanism to survive. To this end, Koonin suggests the possibility: “a new synthesis of evolutionary biology might become feasible in a not so remote future.” Until then, genomic evidence fails to support evolution.

Koonin, EV. 2009. Darwinian evolution in the light of genomics. Nucleic Acid Research, 37(4)1011-1034.

Evolution is a theory in crisis. Even students pursuing advanced degrees in science cannot grasp the basics of evolution, according to a new study by University of Guelph researchers.

The finding reveals evolutionary teaching is in chaos from elementary school up, said Ryan Gregory, a professor in Guelph’s Department of Integrative Biology, who conducted the research with former student Cameron Ellis.

The study was published in BioScience and is particularly timely, given that this year is the bicentennial of Charles Darwin’s birth and the 150th anniversary of publication of On the Origin of Species, which underpins understanding of the diversity of Earth’s organisms and their interrelations.

“Misconceptions about natural selection may still exist, even at the most advanced level,” Gregory said.

“We’re looking at a subset of people who have spent at least four years, sometimes even six or seven years, in science and still don’t necessarily have a full working understanding of basic evolutionary principles or scientific terms like ‘theories.’”

Many previous studies have assessed how evolution is understood and accepted by elementary, high school and undergraduate students, as well as by teachers and the general public, Gregory said. But this was the first to focus solely on students seeking graduate science degrees.

The study involved nearly 200 graduate students at a mid-sized Canadian university who were studying biological, physical, agricultural, or animal sciences. When the students were asked to apply basic evolutionary principles, only 20 to 30 per cent could do so correctly, and many did not even try to answer such questions. Of particular interest to Gregory was the finding that many students seem less than clear about the nature of scientific theories.

“This is telling us that traditional instruction methods, while leading to some basic understanding of evolution, are not producing a strong working knowledge that can be easily applied to real biological phenomena.”

The outcome underscores the failure of single cohesive theory of evolution to emerge since the collapse of evolution’s Central Dogma at the turn of the century. Ryan Gregory’s study further demonstrates that education on an non-cohesive theory leads to chaos in the schoolhouse.  

Charles Darwin used the term species more than any other term in The Origin of Species— 1,926 times. Defining the term species, however, has been a problem. Darwin wrote, there “is no possible test but individual opinion to determine which of them shall be considered as species”.

Naturalist Henry Alleyne Nicholson explains, “No term is more difficult to define than ‘species,’ and on no point are zoologists more divided than as to what should be understood by this word.”

Geneticist Laura M. Zahn in looking for the genetic distinction between species, published there results in paper entitled “Background Matters” in the October 2009 edition of Evolution and abstracted in Science. Much to their surprise, Zahn and colleagues discovered that no single genetic allele is known to exist that can define the difference between species.

After 150 years, Darwin’s statement continues to be dead on, “It is all-important to remember that naturalists have no golden rule by which to distinguish species.”

Ironically, a book on the origins of an indefinable term, then and now, ascended into a historical phenomenon.