Ken Miller defends evolution

Ken Miller, biologistKen Miller, a cell biologist who happens to be a Roman Catholic, has become a prominent speaker in the cause of science.

Miller argues that the position of most anti-evolutionists is really scientific illiteracy. Everything in science—from gravity to relativity—is “just a theory,” he points out. If an explanation comes along that more successfully accounts for the observations and evidence, science adopts it, replacing the earlier “truth” with the newer, more complete one. If someone, for example, can come up with a better explanation than gravity for why your spilled coffee falls on the floor instead of the ceiling, science will happily give up the “theory” of gravity. Science is always provisional, Miller explains, but that does not mean that it is controversial, or a matter of opinion, faith, or personal preference. Similarly, evolution via natural selection is a “theory” only in this provisional, scientific sense.

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Textbook warnings

Why stop at biology and evolution? Let’s make sure that students understand the limitations of all their courses!

  • ‘This textbook contains material on physics. Physics is a theory, not a fact, regarding the behaviour of inanimate objects. All objects can never be observed and thus most of them will remain theoretical. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on gravity. Gravity is a theory, not a fact, regarding the behaviour of inanimate objects with respect to each other. Certain gravitational phenomena, such as the disconuity around a black hole, can never be observed and remain theoretical. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on cosmology and astronomy. Cosmology is a theory, not a fact, regarding the formation and history of the universe. The beginning of a universe or the formation of a star has never been observed and will remain theoretical. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on geology. Geology is a collection of theories about the formation of the earth and the earth’s crust. The depths of the earth’s crust and the centre of the earth have never been observed and have not been proven to exist. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on thermodynamics. Thermodynamics is a theory, not a fact, regarding the interactions of matter and energy. The theoretical temperature called absolute zero has never been observed and its existence can never be proven. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on psychology. Psychology is a theory, not a fact, regarding the behaviour of living things and their state of mind. States of mind can never be directly observed. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on chemistry. Chemistry is a theory, not a fact, regarding the behaviour of molecules and atoms at various temperatures. Atoms are formed from even smaller particles that have never been directly observed. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on literature. Literature is a theory, not a fact, regarding written materials. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on economics. Economics is a theory, not a fact, regarding exchange and incentives. This material should be approached with an open mind, studied carefully, and critically considered.’
  • ‘This textbook contains material on civil engineering. Engineering is a theory, not a fact, regarding structures and forces. This material should be approached with an open mind, studied carefully, and critically considered.’
  • Warning sticker for the Bible

Glacial air samples go back 650,00 years

This is a new article in Science magazine:

Air trapped in glacial ice contains the only reliable direct record of atmospheric composition before scientific sampling began in the 18th century. Since 1997, the oldest ice available for analysis was that from the Vostok, Antarctica, ice core, which extends back to 420,000 years ago and covers four complete glacial cycles. A new ice core from the EPICA Dome C site in Antarctica now extends back to an age of 740,000 years or more. Two reports present data on the composition of the atmosphere between 400,000 and 650,000 years ago, an interval soon after glacial cycles switched from a dominantly 41,000-year period to the dominantly 100,000-year period that occurs today. See more….

Read the Ice Core news in Nature.

Here’s a link to an article with more details about the carbond dioxide levels.

Stop flogging the Piltdown Man

Creationists love to point out that the “missing link” Piltdown Man was a hoax, and a hoax that took years to be declared. Their point is that some scientists are dishonest and that the Piltdown Man was accepted because “evolution is a faith.” I, for one, feel that they are flogging a dead horse. For one thing, it was scientists who exposed the hoax. Science is a self-correcting activity.

a broad ditch dug with shovels and garden forks
It is true that Piltdown Man was accepted too readily. The specimen, with a large (modern) brain and an ape-like (orangutan) jaw, was discovered in 1908 – 1912. Evolution from an ape-like ancestor was already accepted as probable, but the intermediate steps had not been found. Many scientists felt that man’s brain was so unique that it must have developed first. However, even at the time, at least one reputable scientist dismissed it as a crude fake. The discovery of a second, similar specimen a couple of years later seemed to confirm that it was real. In those days, 93 years ago, there were no accurate tests for age. But other specimens were being discovered and the Piltdown Man did not fit in with any of them. As time went by, it was shoved aside as an anomaly.

The Piltdown Hoax did not create the idea that man and ape have a common ancestor: that was already accepted on the evidence of other fossils. It merely misled us as to how and wasted scientists’ time and effort. Here is the discovery in context:

1856 — Neanderthal man discovered
1856 — Dryopithecus discovered
1859 — The Origin of Species published
1863 — Moulin Quignon forgeries exposed
1869 — Cro-Magnon man discovered
1871 — The Descent of Man published
1890 — Java Man discovered
1898 — Galley hill “man” discovered [modern, misinterpreted]
1903 — First molar of Peking man found
1907 — Heidelberg man discovered
1908 — Dawson (1908-1911) discovers first Piltdown fragments
1921 — Rhodesian man discovered
1924 — Raymond Dart makes first Australopithecus discovery.
1925 — Edmonds reports Piltdown geology error. Report ignored.
1929 — First skull of Peking man found.
1934 — Ramapithecus discovered
1935 — Many (38 individuals) Peking man fossils have been found.
1935 — Swanscombe man [genuine] discovered.
1938 — Robert Broom finds the first Australopithecus robustus.

Self-interest can motivate scientific dishonesty or self-delusion. I suspect the former in those who constantly claim that something is dangerous, such as electrical power lines, and when no effect is found call for more and ever more research money. But those who falsify data and are found out are disgraced and distrusted forever after. It is not a part of real science to perpetrate frauds. So, creationists, give it a rest, please!

UPDATE: “In the 1970s a trunk was discovered that belonged to Martin Hinton, a volunteer in the British Museum (Natural History) at the time of the discoveries. It contained what appeared to be test fakes – bones that had been cut and stained to look ancient. Many believe this put Hinton at the heart of the fraud; others think he may simply have been trying to work out how others made their fakes.” — from BBC news

See the link below for a detailed discussion of the entire Piltdown Man affair.

Is there good research on Molecular Evolution?


BPSDB
Michael Behe, in his October 2005 testimony in support of Intelligent Design as science, confidently stated under oath that there is no research on molecular evolution published in scientific journals. Here are his own words as recorded on Page 20 of the court transcript (PDF, italics mine):

Michael Behe“Molecular evolution is not based on scientific authority. There is no publication in the scientific literature, in prestigious journals, specialty journals, or books that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred. There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations. Since no one knows molecular evolution by direct experience, and since there is no authority on which to base claims of knowledge, it can truly be said that… the assertion of Darwinian molecular evolution is merely bluster.”

A quick Web search gives the lie to that statement. Is it flat-out perjury or is it just wilfully blind stupidity? Out in the real world of science…

He could read about the science and history of Molecular Evolution:

  • Perspectives on Molecular Evolution (from MIT’s Web pages on the History of Recent Science and Technology): “Beginning in the 1960s, evolutionary biology was significantly transformed by the incorporation of ideas and techniques from molecular biology. This led to many novel views (and as many controversies) about phylogenetic relationships, rates and mechanisms of evolutionary change, and standards of inference and hypothesis testing.”
  • Michael R. Dietrich’s article, The Origins of the Neutral Theory of Molecular Evolution, in the Journal of the History of Biology, 27 (1994), 21-59. “The first major conferences on molecular evolution were held in 1964.” (PDF)

He could read peer-reviewed papers about molecular evolution:

International Journal of Systematic and Evolutionary Microbiology Molecular evolution of the Chlamydiaceae — Bush and Everett 51 in the International Journal of Systematic and Evolutionary Microbiology, Vol 51, 203-220, Copyright © 2001 by Society for General Microbiology
Journal Toxicon Regional and accelerated molecular evolution in group I snake venom gland phospholipase A2 isozymes–Chuman Y, Nobuhisa, et al. in the Toxicon 2000 Mar;38(3):449-62, Copyright © 2000 by International Society on Toxinology

He could find more scientific papers about molecular evolution in any of these journals:

Journal of Molecular Evolution (published for 30 years, 8 of them available online). The Journal of Molecular Evolution (JME) covers experimental and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems onward. Topics addressed in the Journal include the evolution of informational macromolecules and their relation to more complex levels of biological organization, up to populations and taxa. This coverage accommodates well such subfields as comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA.
Journal of Molecular Biology and Evolution Molecular Biology and Evolution, founded in 1984, publishes research at the interface between molecular and evolutionary biology. The journal publishes investigations of molecular evolutionary patterns and processes, tests of evolutionary hypotheses that use molecular data, and studies that use molecular evolutionary information to address questions about biological function at all levels of organization. Reports of work on comparative and evolutionary genomics and the evolution of molecular structure and function are particularly welcome. It is published by the Society for Molecular Biology and Evolution, an international society of molecular evolutionists.
Genetics journal Genetics publishes contributions that present the results of original research in genetics and related scientific disciplines.
Nucleic Acids Research journal Nucleic Acids Research (NAR) publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism or interactions… under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology…. The first issue of each year is devoted to biological databases, and an issue in July is devoted to papers describing web-based software resources of value to the biological community. NAR Methods Online provides a forum for the online publication of methods papers.
Journal of Applied and Environmental Microbiology Applied and Environmental Microbiology publishes a substantial share of the most significant current research in the areas of biotechnology, microbial ecology, food microbiology, and industrial microbiology.Sections include “Genetics and Molecular Biology,” and “Evolutionary and Genomic Microbiology.”
Journal of Virology Journal of Virology is a source of broad-based, high-quality, original research concerning viruses.The journal provides fundamental new information obtained in studies using cross-disciplinary approaches of biochemistry, biophysics, cell biology, genetics, immunology, molecular biology, morphology, physiology, and pathogenesis and immunity. Sections include “Recombination and Evolution.”
Mathematical Medicine and Biology Mathematical Medicine and Biology publishes original articles with a significant mathematical content addressing topics in medicine and biology. Papers exploiting modern developments in applied mathematics are particularly welcome.The biomedical relevance of mathematical models should be demonstrated clearly and validation by comparison against experiment is strongly encouraged.
Bioinformatics Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers.
Its main focus is on new developments in genome bioinformatics and computational biology.
Protein Science journal Protein Science is dedicated to research on all scientific aspects of protein molecules. The journal publishes papers by leading scientists from all over the world that report advances in the understanding of proteins in the broadest sense.
Glycobiology journal Glycobiology provides a unique forum dedicated to research into the biological functions of glycans, including glycoproteins, glycolipids, proteoglycans and free oligosaccharides, and on proteins that specifically interact with glycans (including lectins, glycosyltransferases, and glycosidases).
FEBS Journal FEBS Journal is an international journal devoted to the rapid publication of full-length papers describing original research in all areas of the molecular life sciences, including the subdiscipline of “Molecular evolution.” Preference is given to papers that advance new concepts or develop new experimental techniques. It is published by The Federation of European Biochemical Societies.
journal of Molecular Endocrinology Journal of Molecular Endocrinology provides a wide coverage of research in all aspects of endocrinology. It is in the top ranks of global endocrine journals and publishes high quality, leading-edge research from all over the world.
Physiological Genomics Physiological Genomics publishes results of a wide variety of studies from human and from informative model systems with techniques linking genes and pathways to physiology, from prokaryotes to eukaryotes. The Journal encourages the submission of research that links genes to cell replication, development, metabolic function, cell signal transduction and intracellular signaling pathways, tissue and organ function, and whole organism function. Physiological Genomics encourages the utilization of approaches ranging from expression profiling, assays for molecular interactions, natural and directed gene alteration, selective breeding studies, gene identification, and the assessment of gene/environment interaction. The Journal welcomes important new technologies and concepts that enhance the study of functional genomics. The Journal encourages publication of new computational approaches, integrative models, and image analysis predictive of gene function.
PNAS - Proceedings of the National Academy of Sciences of the U.S. PNAS (Proceedings of the National Academy of Sciences of the U.S.) is one of the world’s most-cited multidisciplinary scientific serials. Since its establishment in 1914, it continues to publish cutting-edge research reports, commentaries, reviews, perspectives, colloquium papers, and actions of the Academy. Coverage in PNAS spans the biological, physical, and social sciences. It is published by the U.S. National Academy of Sciences.
Annals of Botany Annals of Botany is an international plant science journal with at least one extra issue each year that focuses on a particular theme in plant biology. Areas of plant science include those applying molecular, analytical, mathematical and statistical techniques to examine topical questions at any level of biological organization ranging from cell to community, from tissue culture to crop production, and from microclimate to ecosystem. Its scope extends to all flowering and non-flowering taxa, and to taxonomic and evolutionary questions particularly when these are addressed using molecular tools. The journal is managed by the Annals of Botany Company, a not-for-profit educational charity established to promote plant science worldwide.
Biological Bulletin The Biological Bulletin publishes outstanding experimental research on a wide range of organisms and biological topics from the fields of Neurobiology and Behavior, Physiology and Biomechanics, Ecology and Evolution, Development and Reproduction, Cell Biology, Symbiosis, and Systematics. Published since 1897 by the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, The Biological Bulletin is one of America’s oldest peer-reviewed scientific journals.
FASEB Journal The FASEB Journal is a multi-disciplinary resource for the life sciences published by The Federation of American Societies for Experimental Biology.
Journal of Clinical Microbiology Journal of Clinical Microbiology publishes the most current research on the microbiological aspects of human and animal infections and infestations, with emphasis on their etiologic agents, diagnosis, and epidemiology. It is published by the American Society for Microbiology. Its Epidemiology section includes papers on molecular evolution. Sample paper from the current issue:

cov-journal-humanmolecualrgenetics.gif Human Molecular Genetics. concentrates on full-length research papers covering a wide range of topics in all aspects of human molecular genetics. These include the molecular basis of human genetic disease, developmental genetics, cancer genetics, neurogenetics, chromosome and genome structure and function, gene therapy, mouse and other models of human diseases, functional genomics, and computational genomics. HMG also publishes research on other model systems for the analysis of genes, especially when there is an obvious relevance to human genetics.
Journal of Biological Chemistry Journal of Biological Chemistry. JBC publishes more than 55,000 pages per year of original research reports on biochemistry and molecular biology. It is published by the American Society for Biochemistry and Molecular Biology.
Journal of Bacteriology Journal of Bacteriology, established in 1916, keeps pace with the times by advancing and disseminating fundamental knowledge of bacteria and other microorganisms. Sample paper from the current issue:

Journal of Biochemistry Journal of Biochemistry. It is published by the Japanese Biochemical Society.
Biophysical journal Biophysical Journal. It is published by the Biophysical Society. Sample paper from the current issue:

QJM (Quarterly Journal of Medicine) QJM (QJM: An International Journal of Medicine) focuses on internal medecine. It publishes articles in clinical medicine and in molecular/cell science relevant to medicine.
Protein Engineering Design and Selection journal Protein Engineering Design and Selection (formerly Protein Engineering). Sample paper from the current issue:

  • “An evolution-based analysis scheme to identify CO2/O2 specificity-determining factors for ribulose 1,5-bisphosphate carboxylase/oxygenase.”
journal of General Virology Journal of General Virology includes topics on all aspects of animal, plant, insect, bacterial and fungal viruses, transmissible spongiform encephalopathies, molecular biology and immunology, virus–host interactions, and antiviral compounds. It is published by the Society for General Microbiology. Sample paper from the current issue:

  • “Recombination in circulating Human enterovirus B: independent evolution of structural and non-structural genome regions.”
Microbiology and Molecular Biology Reviews Microbiology and Molecular Biology Reviews is the definitive, broad-based review journal in the disciplines of microbiology, immunology, and molecular and cellular biology, keeping readers abreast of the latest findings about bacteria, viruses, parasites, fungi, and other higher eukaryotes. It is published by the American Society for Microbiology.
 Science
  • Science calls itself the world’s leading journal of original scientific research, global news, and commentary. It is published by the American Association for the Advancement of Science. Sample papers from the current issue:
    • Xinquan Wang et al. “Structure of the Quaternary Complex of Interleukin-2 with Its , ß, and c Receptors ” (A hormone activates immune cells by sequentially recruiting two specific receptors and then a common third receptor, forming a high-affinity signaling complex)
    • J. Kirsty Millar et al. “DISC1 and PDE4B Are Interacting Genetic Factors in Schizophrenia That Regulate cAMP Signaling” (Two genes associated with schizophrenia code for interacting proteins that modulate cyclic AMP metabolism, suggesting that this signaling pathway may contribute to the disorder).
  •  Nature Nature. This journal was founded by, among others, Charles Darwin. Sample paper:

    He could visit or join any of these organizations:

    He can attend meetings and conferences on Molecular Evolution:

    He could find and read books about it:

    He could keep up with regular science news, which frequently covers evolution, biochemistry, and genome discoveries:

    There are literally dozens more links that I could add, to

    • conferences,
    • university departments,
    • peer-reviewed research papers,
    • scientists,
    • scientific organizations,
    • university courses, and
    • more journals.

    But my typing fingers are getting tired. Whom are you going to believe? Michael Behe, with his flat statement that there is no research on molecular evolution? Or hundreds, thousands, of workers in the search for a real and complex truth?

    Finally, here’s a review of Behe’s book, Darwin’s Black Box (and a Wikipedia article).

    UPDATED in February 2008 to add journal cover images.

    Overview of DNA and RNA

    This overview of DNA and RNA structure and function comes complete with “3-dimensional” images of the molecules that you can turn around by dragging your cursor on the image.
    (image of DNA courtesy of the Dorling Kindersley Limited clip-art library)

    Tangled Bank #41 at Flags and Lollipops

    Tangled Bank #41 is up at Flags and Lollipops. It’s a biweekly collection of ‘blog articles in science and medicine.

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