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    how does the molecular clock work? it analyzes the brain functionality of two different species. it examines and compares the physical characteristics of two different species. it illustrates relationships between two different species. it compares the number of mutations that exist in the dna of two different species.

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    get how does the molecular clock work? it analyzes the brain functionality of two different species. it examines and compares the physical characteristics of two different species. it illustrates relationships between two different species. it compares the number of mutations that exist in the dna of two different species. from EN Bilgi.

    Probing Question: What is a molecular clock?

    It doesn't tick, it doesn't have hands, and it doesn't tell you what time of day it is. But a molecular clock does tell time—on an epoch scale. The molecular clock, explains Blair Hedges, is a tool used to calculate the timing of evolutionary events.

    RESEARCH

    Probing Question: What is a molecular clock?

    NOVEMBER 17, 2008 By Solmaz Barazesh

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    It doesn't tick, it doesn't have hands, and it doesn't tell you what time of day it is. But a molecular clock does tell time—on an epoch scale. The molecular clock, explains Blair Hedges, is a tool used to calculate the timing of evolutionary events.

    Instead of measuring seconds, minutes and hours, says Hedges, Penn State professor of biology, the molecular clock measures the number of changes, or mutations, which accumulate in the gene sequences of different species over time. Evolutionary biologists can use this information to deduce how species evolve, and to fix the date when two species diverged on the evolutionary timeline. "Unlike a wristwatch, which measures time from regular changes (ticks), a molecular clock measures time from random changes (mutations) in DNA," Hedges notes.

    The concept of a molecular clock was first put forward in 1962 by chemist Linus Pauling and biologist Emile Zuckerkandl, and is based on the observation that genetic mutations, although random, occur at a relatively constant rate. Thus, the theory goes, the number of differences between any two gene sequences increases over time. As Hedges explains, this thinking led to the idea that the number of mutations in a given stretch of DNA could be used as a measure of time.

    But before any clock can work, it has to be calibrated, he adds. Setting a molecular clock "begins with a known, like the fossil record," for a specific species. Then, once the rate of mutation is determined, calculating the time of divergence of that species becomes relatively easy. "If the rate is 5 mutations every million years, and you count 25 mutations in your DNA sequence, then your sequences diverged 5 million years ago."

    "A nice aspect of molecular clocks is that different genes evolve at different rates, which gives us flexibility to date events throughout the history of life" Hedges points out. Broadly speaking, the evolution of important genes occurs more slowly than that of genes with less vital functions. More rapidly changing genes are used to date more recent evolutionary events, and slower evolving genes are used to map more ancient divergences, he explains.

    "The molecular clock is useful for obtaining evolutionary information when you have little or no fossil record," says Hedges. "For example, fungi, which are soft and squishy, don't make fossils well. But we can take the rate of change of genes from vertebrates or plants, which have a decent fossil record, and apply it to the unknown group."

    The molecular clock can also be used for putting a series of evolutionary events into chronological order. This is done by comparing sequences from different species to determine when they last shared a common ancestor, in effect drawing the family tree. "It's often difficult to do find common ancestors between species using fossils, no matter what the organism," says Hedges.

    Though the molecular clock is still regarded as somewhat controversial, says Hedges, it is gaining acceptance as our understanding of genome sequences improves. "As more researchers opt to use the technique," he concludes, "the molecular clock is itself evolving into a more accurate timepiece."

    S. Blair Hedges, Ph.D., is professor of biology in the Eberly College of Science, [email protected]

    LAST UPDATED NOVEMBER 17, 2008

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    Source : www.psu.edu

    The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates

    The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity. The equidistance result is the most direct evidence, and remains the only evidence, ...

    J Comput Sci Syst Biol. Author manuscript; available in PMC 2011 Oct 3.

    Published in final edited form as:

    J Comput Sci Syst Biol. 2008 Dec 26; 1: 92–102.

    PMCID: PMC3184610 NIHMSID: NIHMS92223 PMID: 21976921

    The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates

    Shi Huang

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    Abstract

    The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity. The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock. However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate. Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate. Here it is shown that the equidistance result remains valid even when different species can be independently shown to have different mutation rates. A random sampling of 50 proteins shows that nearly all proteins display the equidistance result despite the fact that many proteins have non-constant mutation rates. Therefore, the genetic equidistance result does not necessarily mean a constant mutation rate. Observations of different mutation rates do not invalidate the genetic equidistance result. New ideas are needed to explain the genetic equidistance result that must grant different mutation rates to different species and must be independently testable.

    Keywords: Genetic equidistance result, evolution, molecular clock, Neo-Darwinism

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    Introduction

    The Neo-Darwinian theory of evolution is the dominant mainstream theory for evolution and widely taught to biologists and the public at large. It suggests that evolution is a process of natural selection of randomly occurring fitter mutations. Macroevolution involves the same process as microevolution or population genetics and is simply prolonged microevolution. A major prediction of this theory is that macroevolution would take longer time and thus accumulate more molecular mutations or changes than microevolution. This prediction can be tested by analyzing molecular similarity among species, which was first done in the early 1960s (Doolittle and Blombaeck, 1964; Margoliash, 1963; Zuckerkandl and Pauling, 1962). Closely related species (in phenotypes or genealogy) should show more molecular similarity than distantly related species. However, while this prediction can be demonstrated in some cases (e.g., human is closer to chimpanzees than to monkeys in both phenotypes/genealogy and molecules), it has also been falsified in many other cases. For example, the molecular distance between two subpopulations of medaka fish that had diverged for ~ 4 million years is 3-fold greater than that between humans and chimpanzees that are thought to have diverged for 5–7 million years (Kasahara et al., 2007). The molecular distance between two different fungi can be just as great as that between fungi and humans, which is completely unexpected from Neo-Darwinism and would indeed be shocking to anyone with a Neo-Darwinian mindset.

    Such exceptions are obviously inconvenient to the widely publicized theory and hence rarely made known outside the small circle of molecular evolution specialists. One important consequence of these exceptions is that they make it impossible to trust the molecular phylogenies constructed by the present methods of molecular analysis. These methods assume, despite numerous factual exceptions or contradictions, that closer molecular similarity always means closer evolutionary distance. As a result, major conflicts between molecular dating and fossil dating are common. Given the frequent factual contradictions, it is almost certain that the theoretical basis for the interpretation of the major facts in molecular evolution is not completely correct.

    In mathematics or physics, one exception is sufficient to doom any theory. The science of biology or any scientific discipline for that matter should not be held to a lower standard. When one allows exceptions, one has effectively rendered the theory non-testable and non-scientific. Such a theory would be no different from a false theory that happens to explain a fraction of nature while being contradicted by the rest. The only way to distinguish a true theory from a false or incomplete one is to see if it has not a single factual exception within its domain of application or relevance.

    A most remarkable result of molecular changes during macroevolution is the near linear correlation between genetic distance as measured by DNA/protein sequence dissimilarity and time of species divergence as inferred from fossil records. This result is not predicted by Neo-Darwinism. It has been commonly interpreted to mean a constant mutation rate, which in turn directly provoked the molecular clock hypothesis. However, this hypothesis must negate the idea of selection, the cornerstone of Neo-Darwinism. While the Neo-Darwinian selection theory has spectacularly failed the molecular test, its ad hoc substitute for the domain of molecular evolution, the molecular clock hypothesis, is also imperfect and widely known to have countless contradictions. It is also obviously incoherent or schizophrenic to have two vastly different and non-connected theories of evolution, one for phenotype evolution based on the idea of selection and the other for molecular evolution based on the negation of the idea of selection. It is also intuitively absurd given the proven truth that phenotypes and genotypes are inseparably connected. Thus, the two theories cannot both be correct for macroevolution. I show here that the molecular clock hypothesis is merely an ad hoc restatement of a factual observation, the genetic equidistance result. It is a tautology and does not qualify as a scientific theory with true explanatory power.

    Source : www.ncbi.nlm.nih.gov

    Chapter 3: Evolution and the Nature of Science

    Read chapter Chapter 3: Evolution and the Nature of Science: Today many school students are shielded from one of the most important concepts in modern sci...

    Teaching About Evolution and the Nature of Science (1998)

    Teaching About Evolution and the Nature of Science (1998) Chapter:Chapter 3: Evolution and the Nature of Science

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    « Previous: Chapter 2: Major Themes in Evolution

    Page 27

    Suggested Citation:"Chapter 3: Evolution and the Nature of Science." National Academy of Sciences. 1998. Teaching About Evolution and the Nature of Science. Washington, DC: The National Academies Press. doi: 10.17226/5787.

    ×

    3Evolution and the Nature of Science

    Science is a particular way of knowing about the world. In science, explanations are restricted to those that can be inferred from confirmable data—the results obtained through observations and experiments that can be substantiated by other scientists. Anything that can be observed or measured is amenable to scientific investigation. Explanations that cannot be based on empirical evidence are not a part of science.

    The history of life on earth is a fascinating subject that can be studied through observations made today, and these observations have led to compelling accounts of how organisms have changed over time. The best available evidence suggests that life on earth began more than three and a half billion years ago. For more than two billion years after that, life was housed in the bodies of many kinds of tiny, single-celled organisms, some of which produced the oxygen that now makes up more than a fifth of the earth's atmosphere. Less than a billion years ago, much more complex organisms appeared. By about half a billion years ago, evolution had resulted in a wide variety of multicellular animals and plants living in the sea that are the clear ancestors of many of the major types of organisms that continue to live to this day. Somewhat more than 400 million years ago, some marine plants and animals began one of the greatest of all innovations in evolution—they invaded dry land. For our own phylum, the Chordata, this move away from the nurturing sea led to the appearance of amphibians, reptiles, birds, and mammals—the latter including, of course, our own species, Homo sapiens.

    This chapter looks at how science works in the context of our overall understanding of how biological evolution occurred. It begins, however, by discussing another scientific development that challenged long-held understandings and beliefs: the discovery of heliocentricism.

    Heliocentricism and the Nature of Science

    Surely one of the first major natural phenomena to be understood was the cause of night and day. Some of the earliest surviving human records left on clay tablets relate to the movements of the sun and other celestial bodies. The obvious cause of day and night is the rising and setting of the sun. This is an observation that can be made today by anyone and, seemingly, requires no further explanation.

    Archaeological evidence and early records make it clear that our ancestors realized that not only does the sun appear to rise and set, but so do the moon and stars. The movements of the moon and stars, however, are not precisely synchronized with

    Page 28

    Suggested Citation:"Chapter 3: Evolution and the Nature of Science." National Academy of Sciences. 1998. Teaching About Evolution and the Nature of Science. Washington, DC: The National Academies Press. doi: 10.17226/5787.

    ×

    Clockwise from top left, Nicolaus Copernicus (1473-1543), Johannes Kepler (1571-1630), Galileo Galilei (1564-1642), and Isaac Newton (1642-1727) led the way to a new understanding of the relationship between the earth and the sun and initiated an age of scientific progress that continues today.

    Illustration from the 18th century depicts the Ptolemaic system in the upper left corner and the Copernican system in other corners and center.

    Page 29

    Suggested Citation:"Chapter 3: Evolution and the Nature of Science." National Academy of Sciences. 1998. Teaching About Evolution and the Nature of Science. Washington, DC: The National Academies Press. doi: 10.17226/5787.

    ×

    those of the sun. The moon is slower by about one hour per day. The stars remain almost the same on successive nights, but slowly it becomes obvious that they, too, are slowed in their movements compared to the sun. Thus, the stars of summer are different from those visible in the winter. In fact, it takes a full year for the stars to return to their previous position, an interval of time that defines our year.

    The ancient observers realized that not all stars move in unison. Although most move in majestic unity, a few others are "wanderers"—appearing now with one group of stars and a week later somewhere else. The majority were called "fixed stars," the wanderers were called "planets."

    During the late Middle Ages, and especially in the Renaissance, beautiful brass models known as orreries were made to show the relative positions and movements of the sun, planets, and moon as they circled the earth. As the center of the universe, the earth was a sphere in the center of the orrery. The other celestial bodies were positioned on rings of metal, each moving by clockwork at its own rate. The fixed stars required a simple solution—they could be considered stuck in an outermost shell, also moved by clockwork.

    Source : www.nap.edu

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