Monday, September 27, 2021

How Does Molecular Biology Support Evolution

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Discovering Dinosaurs In Colour

Molecular Biology Supports Evolution: Brief Introduction

Vinther spends a great deal of time looking at exceptional fossils from around the world, trying to understand where they belong on the evolutionary scale. He has an interest in how some of these bizarre looking animals have been preserved a branch of science known as taphonomy: I have been looking at some fossils of softbodied animals that have been found in sandstone, which is very rare. These rare fossils lead to questions about the kind of conditions there were to facilitate this preservation.

During his graduate studies in 2006 Vinther looked at the preservation of squids and their ink sacs, and as part of this research conducted an experiment where he decayed a number of squids. Within days, everything had dissolved into squid slurry with a stench beyond description.

When Vinther realised that the pigment melanin in the ink sacs was preserved in the fossil squids, he began to look at fossil melanin elsewhere. He looked at fossilised feathers and realised that the structures under the microscope thought to be bacteria were in fact pigment-containing organelles known as melanosomes, changing a view held for over thirty years:

That was a terrible experiment but we found out how to put colours into dinosaurs as a result. It really changed the whole scene in terms of how people saw these fossils, but it also shifted the paradigm that bacteria were of overarching importance in the fossilization process. – Dr Jakob Vinther

Chemical Evolution Is Dead In The Water

Assume for a moment that there was some way to produce simple organic molecules on the early Earth. Perhaps they did form a primordial soup, or perhaps these molecules arose near some hydrothermal vent. Either way, origin of life theorists must then explain how amino acids or other key organic molecules linked up to form long chains like proteins .

Chemically speaking, however, the last place youd want to link amino acids into chains would be a vast water-based environment like the primordial soup or underwater near a hydrothermal vent. As the National Academy of Sciences acknowledges, Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored.14 In other words, water breaks protein chains back down into amino acids , making it very difficult to produce proteins in the primordial soup.

Materialists lack good explanations for these first, simple steps which are necessary to the origin-of-life. Chemical evolution is literally dead in the water.

Darwinian Theory On A Molecular Level

    How has molecular biology enhanced our understanding of Darwin’s theory of natural selection? Biochemist Lynn Helena Caporale of Columbia University, author of Darwin in the Genome: Molecular Strategies in Biological Evolution, says that examining genomes of fossils and organisms across ages helps scientists see relationships between them.

    JENNIFER LUDDEN, host:

    This is ALL THINGS CONSIDERED from NPR News. I’m Jennifer Ludden.

    For the past academic year, we’ve been reporting on debates raging in school boards across the country on whether and how to teach the theory of evolution. It’s been nearly 150 years since Darwin first published on “The Origin of Species.” Since then, biologists have been observing the process of natural selection that Darwin laid out on an ever smaller scale.

    To find out how modern-day molecular biology and genetics have shed light on the theory of evolution, we turn to Lynn Helena Caporale. She’s a biochemist at Columbia University and the author of “Darwin in the Genome: Molecular Strategies in Biological Evolution.”

    Hello, Dr. Caporale.

    Dr. LYNN HELENA CAPORALE : Hello.

    LUDDEN: Darwin never knew there was such a thing as a gene. So when he spoke of evolution by natural selection, what did he mean?

    LUDDEN: So take us back to science class for a minute. What happens in a cell when there’s a mutation?

    LUDDEN: How do they change? What determines if this pattern changes?

    LUDDEN: You talk about snails, a certain kind of snail.

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      The Nature Of Genetic Information

      The problem that arose after that, around the nineteen forties, was to discover the geneâs physical nature. What was its chemical composition? The solution to this problem led to what I call the second revolution in biology: Watson and Crickâs explanation of the nature and structure of genetic information as DNA. The famous article published in Nature magazine in 1953 was the beginning of a biological revolution destined to change the very course of humanity. DNA is a molecule with a double-helix structure consisting of two large chains of molecules of a sugar linked by phosphates. Connecting the two chains, like rungs of a ladder, are other molecules called nitrogenated bases that maintain the structureâs stability. Watson and Crick immediately noticed that the structure of the molecule itself explains the mechanism of replication, leading to identical molecules and thus insuring faithful transmission of biological information for generations.

      Moreover, the structure of DNA indicates that biological information lies in the sequence of four nitrogenated bases running throughout the molecule. These bases are called thymine , guanine , adenine , and cytosine . What an organism inherits from its progenitors, and which will determine its biological characteristics, is simply a sequence written in a language of four letters.

      A Pattern Of Explosions

      How Does Molecular Biology Support the Theory of Evolution

      The eventual realization that the fossil record is not entirely incomplete has forced evolutionary biologists to accept that the record shows a pattern of explosions, not gradual evolution of living organisms. One biology textbook explains this:

      Many species remain virtually unchanged for millions of years, then suddenly disappear to be replaced by a quite different, but related, form. Moreover, most major groups of animals appear abruptly in the fossil record, fully formed, and with no fossils yet discovered that form a transition from their parent group.75

      Probably the most famous instance of abrupt appearance is the Cambrian explosion, where nearly all of the major living animal phyla appear in the Cambrian period. An invertebrate biology textbook explains this:

      Most of the animal groups that are represented in the fossil record first appear, fully formed and identifiable as to their phylum, in the Cambrian, some 550 million years ago. These include such anatomically complex and distinctive types as trilobites, echinoderms, brachiopods, molluscs, and chordates. The fossil record is therefore of no help with respect to the origin and early diversification of the various animal phyla76

      In spite of much research and analyses of different sources of data , the origin of the angiosperms remains unclear. Angiosperms appear rather suddenly in the fossil record with no obvious ancestors for a period of 80-90 million years before their appearance.82

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      Problem 3: Random Mutations Cannot Generate The Genetic Information Required For Irreducibly Complex Structures

      According to evolutionary biologists, once life got started, Darwinian evolution took over and eventually produced the grand diversity we observe today. Under the standard view, a process of random mutation and natural selection built lifes vast complexity one small mutational step at a time. All of lifes complex features, of course, are thought to be encoded in the DNA of living organisms. Building new features thus requires generating new information in the genetic code of DNA. Can the necessary information be generated in the undirected, step-by-step manner required by Darwins theory?

      Most everyone agrees that Darwinian evolution tends to work well when each small step along an evolutionary pathway provides some survival advantage. Darwin-critic Michael Behe notes that if only one mutation is needed to confer some ability then Darwinian evolution has little problem finding it.24 However, when multiple mutations must be present simultaneously to gain a functional advantage, Darwinian evolution gets stuck. As Behe explains, If more than one is needed, the probability of getting all the right ones grows exponentially worse.25

      If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.28

      Bonus Problem: Humans Display Many Behavioral And Cognitive Abilities That Offer No Apparent Survival Advantage

      In recent years, evolutionary biologists have tried to explain the origin of human moral, intellectual, and religious abilities in terms of Darwinian evolution. Harvard University evolutionary psychologist Marc Hauser has promoted the increasingly common hypothesis that people are born with a moral grammar wired into their neural circuits by evolution.200

      Humans do appear hard-wired for morality, but were we programmed by unguided evolutionary processes? Natural selection cannot explain extreme acts of human kindness. Regardless of background or beliefs, upon finding strangers trapped inside a burning vehicle, people will risk their own lives to help them escape with no evolutionary benefit to themselves. For example, evolutionary biologist Jeffrey Schloss explains that Holocaust rescuers took great risks which offered no personal benefits:

      The rescuers family, extended family and friends were all in jeopardy, and they were recognized to be in jeopardy by the rescuer. Moreover, even if the family escaped death, they often experienced deprivation of food, space and social commerce; extreme emotional distress; and forfeiture of the rescuers attention.201

      Natural Academy of Sciences member Philip Skell explained why evolutionary psychology does not adequately predict human behavior:

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      Fossils Anatomy And Embryology

      Fossils provide solid evidence that organisms from the past are not the same as those found today; they show a progression of evolution. Scientists calculate the age of fossils and categorize them to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. For example, scientists have recovered highly-detailed records showing the evolution of humans and horses. The whale flipper shares a similar morphology to appendages of birds and mammals, indicating that these species share a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.

      Common AncestorsEvolution of Humans and Horses

      Some structures exist in organisms that have no apparent function at all, appearing to be residual parts from a common ancestor. These unused structures are vestigial.

      Adaptations: Winter Coats

      The Genetic Design Of Animal Bodies

      Creation Bytes!: Is Evolution Supported by Molecular Biology?

      One of the areas in which molecular biology has progressed significantly, and with considerable applications for human biology, is the field of genetic design of animal bodies. Initially, molecular biology experiments used unicellular organisms, bacteria or viruses, to study the properties and functions of DNA. Those studies produced very important results, as described above, but their very nature made it impossible to draw conclusions about genetic control of the development of complex organisms, such as a fly or a mouse, in which associations of cells have to be grouped in the proper fashion as part of a three-dimensional structure.

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      Problem 8: Differences Between Vertebrate Embryos Contradict The Predictions Of Common Ancestry

      Another area where evolutionary biologists claim powerful evidence for common ancestry is the patterns of development of vertebrate embryos. Biology textbooks typically portray the embryos of different groups of vertebrate as starting off development in a highly similar fashion, reflecting their common ancestry.129 However, such claims overstate the degree of similarity between the early stages of vertebrate embryos.

      Biologists who investigate these questions have found considerable variability among vertebrate embryos from their earliest stages onward, contradicting what we are told to expect from common ancestry.130 As a paper in Nature stated, Counter to the expectations of early embryonic conservation, many studies have shown that there is often remarkable divergence between related species both early and late in development.131 Or, as another article in Trends in Ecology and Evolution stated, despite repeated assertions of the uniformity of early embryos within members of a phylum, development before the phylotypic stage is very varied.132

      But when biologists have looked for evidence supporting the existence of a phylotypic or pharyngula stage, they found the data points in the opposite direction. One comprehensive study in Anatomy and Embryology surveyed the characteristics of many vertebrates during this purportedly similar stage, and found that embryos show differences in major traits, including:

      • body size,
      • growth patterns, and
      • timing of development.134

      Conflicts Between Higher Branches

      A 2009 paper in Trends in Ecology and Evolution notes that, A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome.109 Similarly, a paper in Genome Research studied the DNA sequences in various animal groups and found that different proteins generate different phylogenetic tree.110 A June, 2012 article in Nature reported that short strands of RNA called microRNAs are tearing apart traditional ideas about the animal family tree. Dartmouth biologist Kevin Peterson who studies microRNAs lamented, Ive looked at thousands of microRNA genes, and I cant find a single example that would support the traditional tree. According to the article, microRNAs yielded a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents. Peterson put it bluntly: The microRNAs are totally unambiguous they give a totally different tree from what everyone else wants.111

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      Genetics And Evolution: An Operational Definition Of The Gene

      Darwin offered a descriptive explanation of biological diversity that was plausible, but not mechanistic. The question is: if all living organisms have a shared origin, what biological function is common to all of them, transmitted from parents to offspring and modifiable in order to generate biological diversity? In his time, Darwin was unable to answer these questions. It was precisely the posing of such questions that led to Genetics, the discipline that studies how biological information is transmitted and modified. We owe the first evidence of the existence of inheritable genetic information to Gregor Mendel, an Augustinian monk who demonstrated that the shape or color of peas is faithfully transmitted from one generation to the next.

      But the progress of Genetics in the twentieth century owes much to the fruit fly, Drosophila melanogaster, an organism that has become a classic object of study for genetic research because it breeds easily in laboratory settings, has a very short biological cycle and is totally innocuous to human beings. Drosophila studies revealed many concrete inheritable traits , demonstrating that they are located and aligned in cell nucleaeâin organules called chromosomesâand that each gene is situated in a specific position in the chromosome.

      Project Description And Outcomes

      Molecular Biology and Evolution

      EMBO organizes an annual life science congress, The EMBO Meeting.42 The series was started in 2009 following the European Life Scientist Organization meeting as a counterpart to the large annual meetings taking place in the United States. The EMBO Meeting is attended by approximately 1500 participants from around the world and its program reflects science of the highest quality. The meeting offers scientists from all areas of the life sciences the opportunity to hear from leaders in the field of molecular biology. Child care was offered at The EMBO Meeting in 2009 , 2010 , and 2011 .

      In the pilot year, a number of challenges were considered before determining how best to provide on-site child care for conference participants.43 Caregivers needed to be multilingual, as children were expected from many different language backgrounds. Nevertheless, the number of languages that could be covered was limited. A broad range of ages was envisioned, with the program catering to the needs of children aged 6;months to 14;years. On-site facilities were planned, so that the conference venue would serve as a base for the service, as were appropriate catering and access to public transportation. Finally, it was decided that care would not be restricted to safekeeping; rather, the children would have a fulfilling day with a program that sparked their imagination.

      Randy Wayne, in, 2019

      All new news is old news happening to new people.

      Attributed to Malcolm Muggeridge.

      Alan J. Cann, in, 2016

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      The Century Of The Gene Molecular Biology And Genetics

      The twentieth century was the century in which human society incorporated technological development in a massive way. For much of that century, the greatest technological contributions grew out of the physical sciences: automobiles, the telephone, airplanes, plastics, computers, and so on. The introduction of those factors has changed society and human behavior more than even political and social events.

      During the second half of the twentieth century, however, and especially during the last two decades, biological technology with enormous medical and social potential has emerged. This technology offers a new image of the evolution of life on our planet and is destined to revolutionize the very structure of human society.

      Perhaps the person who has most lucidly delved into these ideas is Sydney Brenner. One of the most brilliant scientists of the twentieth century, he will be remembered by the history of science for his enormous contributions to molecular biology, a science he was decisively involved in creating. Brenner says that new biology offers us greater comprehension of ourselves, and a new understanding of humans as organisms: ââ¦for the first time, we can pose the fundamental problem of man and begin to understand our evolution, our history, our culture and our biology as a whole.â

      Does Life History Drive Molecular Evolutionary Rates

      We have discussed evidence to support the idea that molecular evolutionary rates are driven by life history. By comparing differences among a wide variety of organisms, biologists can test the prediction that DNA nucleotide sequences do indeed evolve according to a rate that, at least partially, depends on organism-level traits. Generation time and metabolism, each to some degree or in combination, affect the mutation rates of some organisms and, thus, their molecular evolutionary rates. Even so, some relationships among generation time, metabolism, and molecular evolution depend on whether the organism is a plant or an animal and the location of the genome within the cell . Also, differences in neutral vs. non-synonymous rates, when averaged together across long DNA sequences, could further complicate interpretations.

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