Citations

Chapter 7 – Genetics

[1286] Book: Movers And Shakers: A Chronology of Words That Shaped Our Age. By John Ayto. Oxford University Press, 2006. Page 18:

1906 William Bateson: "The best title would, I think, be the 'Quick Professorship of the study of Heredity'. No single word in common use quite gives this meaning … and if it were desirable to coin one, 'Genetics' might do."

[1287] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 1: "Variation Under Domestication."

[1288] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 13: "Mutual Affinities of Organic Beings: Morphology: Embryology: Rudimentary Organs":

At whatever period of life disuse or selection reduces an organ, and this will generally be when the being has come to maturity and to its full powers of action, the principle of inheritance at corresponding ages will reproduce the organ in its reduced state at the same age, and consequently will seldom affect or reduce it in the embryo. …

… On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition, or quite aborted, far from presenting a strange difficulty, as they assuredly do on the ordinary doctrine of creation, might even have been anticipated, and can be accounted for by the laws of inheritance.

NOTE: Over the next several pages, we will see why Darwin's views about "disuse" and "selection" are profoundly mistaken.

[1289] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 5: "Laws of Variation."

[1290] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 7: "Instinct":

It may be doubted whether any one would have thought of training a dog to point, had not some one dog naturally shown a tendency in this line; and this is known occasionally to happen, as I once saw in a pure terrier. When the first tendency to point was once displayed, methodical selection and the inherited effects of compulsory training in each successive generation would soon complete the work….

Chapter 1: "Variation Under Domestication": "The great and inherited development of the udders in cows and goats in countries where they are habitually milked, in comparison with the state of these organs in other countries, is another instance of the effect of use."

Chapter 5: "Laws of Variation": "In some of the crabs the foot-stalk for the eye remains, though the eye is gone; the stand for the telescope is there, though the telescope with its glasses has been lost. As it is difficult to imagine that eyes, though useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse."

Chapter 5: "Laws of Variation": "The external conditions of life, as climate and food, etc., seem to have induced some slight modifications."

[1291] Book: What Evolution Is. By Ernst Mayr. Basic Books, 2001.

Page 91: "The genetic material … cannot be changed by the environment or by use and disuse of the phenotype. … Genes cannot be modified by the environment. Properties acquired by the proteins of the phenotype cannot be transmitted to the nucleic acids of the germ cells. There is no inheritance of acquired characteristics."

[1292] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 346: "Their results, along with the results of many other experiments have shown that environmental stress does not direct or cause genetic changes…."

[1293] Book: The Evolutionary Process: A Critical Review of Evolutionary Theory. By Verne Grant (Ph.D. in botany and genetics from Berkeley, Professor of Botany at the University of Texas at Austin). Columbia University Press, 1985.

Pages 17-18: [The theory of evolution by the "effects of use and disuse" or "inheritance of acquired characteristics" is] "blatantly at odds with our experimental knowledge of the subject."

[1294] Book: Mendel's Legacy: The Origin of Classic Genetics. By Elof Axel Carlson (Geneticist and Distinguished Teaching Professor Emeritus at Stony Brook University). Cold Spring Harbor Laboratory Press, 2004.

Page 14 (note 5): "There is no convincing evidence that acquired characteristics are inherited. The chief difficulty of that doctrine would be would be in finding an environment that resequenced the amino acids of proteins and then drove the genetic code in reverse back to the DNA of the gametes [reproductive cells]."

[1295] Book: Evolution. By Colin Patterson. Comstock Publishing (division Cornell University Press), 1999. Second edition. First published in 1978. Page 118:

Second is the idea that evolution proceeds by the inheritance of modifications acquired, through use or disuse….

… [This theory] suffered a severe reverse early in this [the 20th] century from the work of geneticists, who could find no good examples of the process and no mechanism that could bring it about.

[1296] Book: The Triumph of the Embryo. By Lewis Wolpert. Oxford University Press, 1991. Pages 135-6:

The powerful muscles of the blacksmith's arms are not inherited by his children; a mother's knowledge of Russian is not inherited by her children; giraffes did not acquire long necks by their ancestors stretching their necks to the highest branches. Characteristics and attributes acquired by experience or learning are not passed on to the offspring. The reason is simple. There is no mechanism whereby the acquired character—strong arms, Russian—can be transferred to the germ [reproductive] cells and appropriately alter their genetic constitution. … Disappointing though it may be, no such mechanism exists, and germ cells only pass on the genetic information they start with, together with only random mutations that may have arisen during the cells' lifetime.

[1297] Web Page: "Lewis Wolpert." Nobel Web, 2007. http://nobelprize.org/nobel_prizes/medicine/articles/wolpert/cv.html

"Lewis Wolpert is Professor of Biology as Applied to Medicine in the Department of Anatomy and Developmental Biology of University College, London."

[1298] Paper: "The marks, mechanisms and memory of epigenetic states in mammals." By Vardhman K. Rakyan & others. Biochemical Journal, May 15, 2001. http://www.biochemj.org/bj/356/0001/3560001.pdf

Page 1: "These modifications interfere with the DNA–protein interactions that facilitate transcription, resulting in transcriptional silencing of the epigenetically modified allele. Epigenetic modifications can, therefore, cause phenotypic variation in the absence of genetic differences."

Page 6: "The studies described above demonstrate that phenotypic heterogeneity can exist even in the absence of environmental and genetic differences, but more importantly, the phenotype can also be inherited to an extent."

[1299] Article: "Does Environment Influence Genes? Researcher Gives Hard Thoughts On Soft Inheritance." ScienceDaily, August 8, 2006. http://www.sciencedaily.com/releases/2006/08/...

Quoting Eric Richards, Ph.D., professor of biology at Washington University in St. Louis:

Certainly, nobody has shown that an epigenetically induced beneficial or adaptive change has been inherited. Mechanistically, there is no reason to discount epigenetic inheritance. The biochemical nuts and bolts are there to support it. The big questions to resolve are how many epigenetic changes are induced by the environment, what types of phenotypes result from these changes, and how many of these epigenetic changes are inherited.

[1300] Paper: "Weismann Rules! OK? Epigenetics and the Lamarckian temptation." By David Haig (Department of Organismic and Evolutionary Biology, Harvard University). Biology and Philosophy, June 2007. http://www.oeb.harvard.edu

Page 415: "Epigenetic inheritance expands the range of options available to genes but evolutionary adaptation remains the product of natural selection of 'random' variation. … My comments will focus on the second dimension of epigenetic inheritance, because this is my area of expertise."

Page 425:

If I could choose, I would ban discussion of 'the inheritance of acquired characters' and talk separately of the inheritance of mutilations, the inheritance of the effects of use and disuse, the inheritance of methylation patterns, the acquisition and inheritance of DNA-bearing plasmids, and so on. If this step were taken, one would find broad consensus on most questions of fact: mutilations and the effects of use and disuse are not inherited⁶; some methylation marks are inherited.

[1301] Book: Plant-Breeding: Comments on the Experiments of Nilsson and Burbank. By Hugo de Vries. Open Court Publishing Company, 1907.

Page 1: "In the beginning of the last century Lamarck founded the theory of common descent for all living beings. … His evidence, however, was very scanty and therefore he failed in convincing his contemporaries. Half a century afterward Darwin brought together such an overwhelming mass of evidence that opposition had to give in."

Pages 2-3: "The theory of common descent is Darwin's theory, since it has been founded by him on so broad a basis of facts as to insure almost complete acceptance."

[1302] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Preface:

Lamarck was the first man whose conclusions on the subject excited much attention. This justly-celebrated naturalist first published his views in 1801…. With respect to the means of modification, he attributed something to the direct action of the physical conditions of life, something to the crossing of already existing forms, and much to use and disuse, that is, to the effects of habit. To this latter agency he seemed to attribute all the beautiful adaptations in nature; — such as the long neck of the giraffe for browsing on the branches of trees.

[1303] Article: "Evolution." Contributor: Alan R. Templeton (Ph.D., Charles Rebstock Professor of Biology and Professor of Genetics and Biomedical Engineering, Washington University). World Book Encyclopedia, 2007 Deluxe Edition.

"In 1809, the French naturalist Chevalier de Lamarck formulated the first comprehensive theory of evolution."

[1304] For example, Article: "Lamarck, Jean-Baptiste de Monet, Chevalier de." Encyclopædia Britannica Ultimate Reference Suite 2004.

"Lamarck is best known for his idea that acquired traits are inheritable, an idea known as Lamarckism, which is controverted by Darwinian theory."

NOTE: As shown above, Darwin embraced this very theory.

[1305] Book: 5 Steps to a 5: AP Biology. By Mark Anestis. McGraw-Hill, 2002. Pages 127-8:

Lamarck proposed that giraffes had long necks because individuals were constantly reaching for the leaves at the tops of trees. A giraffe's neck lengthened during its lifetime, and then that giraffe's offspring had a long neck because of all that straining its parents did. The key here is that the changes in the trait was passed on. … Darwin had another idea, one that ended up being entirely consistent with mendelian genetics…. Darwin suggested the idea of natural selection….

NOTE: Again, as shown above, Darwin completely bought into Lamarck's idea and even used the example of a giraffe's neck to illustrate the concept.

[1306] Book: Palaeobiology: A Synthesis. Edited by Derek E. G. Briggs & Peter R. Crowther. Blackwell Scientific Publications, 1990. Section 6.5.2: "History of Palaeontology: Darwin to Plate Tectonics." By P. J. Bowler (Department of Social Anthropology, Queen's University, UK).

Pages 546-547 explicitly distance Darwin from Lamarckism.

[1307] Textbook: Botany: An Introduction to Plant Biology. By T. Elliot Weier, C. Ralph Stocking, Michael G. Barbour, Thomas L. Rost. John Wiley & Sons, 1982.

Page 665: "Darwin's concept of evolution, expressed over a hundred years ago, is the one accepted today; not Lamarck's."

[1308] Book: Zoological Philosophy: An Exposition with Regard to the Natural History of Animals. By J. B. Lamarck. Published in 1809. Translated and introduced by Hugh Elliot. Macmillan and Co, 1914. Reprinted in 1963 by Hafner Publishing. Page 108:

[N]ew needs which establish a necessity for some part really bring about the existence of that part, as a result of efforts; and that subsequently its continued use gradually strengthens, develops and finally greatly enlarges it; in the second place, we shall see that in some cases, when the new environment and new needs have altogether destroyed the utility of some part, the total disuse of that part has resulted in its gradually ceasing to share in the other parts of the animal; it shrinks and wastes little by little, and ultimately, when there has been total disuse for a long period, the part in question ends by disappearing. All this is positive; I propose to furnish the most convincing proofs of it. … [A]quired modifications are preserved by reproduction among the individuals in question, and finally give rise to a race quite distinct from that in which the individuals have been continuously in an environment favorable for their development.

Page 130:

[T]he only direct production that is required from nature, that is to say, the only production that occurs without the cooperation of any organic activity, is the case of the simplest organized bodies, both of animals and plants…. Now she endows these bodies, which she has herself created, with the faculties of feeding, growing, multiplying, and always preserving the progress made in organization. She transmits these same faculties to all individuals organically reproduced throughout time and immense variety of ever-changing conditions. By these means living bodies of all classes and orders have been successively produced.

Page 175: "I do not doubt that mammals originally came from the water, nor that water is the true cradle of the entire animal kingdom."

NOTE: Page 179 contains a diagram entitled "SHOWING THE ORIGINS OF THE VARIOUS ANIMALS." It is the rudimentary equivalent of a modern evolutionary tree. Further relevant quotes are found on pages 239 and 247.

[1309] Article: "Genetics." Encyclopædia Britannica Ultimate Reference Suite 2004.

The section entitled "Historical background" states: "Late in the 19th century, a German physician, August Weismann, showed that reproductive cells (germ plasm) are independent of other body cells (somatoplasm), thus refuting earlier hypotheses of inheritance of acquired characteristics."

[1310] Textbook: Principles of Genetics. By D. Peter Snustad, Michael J. Simmons & John B. Jenkins. John Wiley & Sons, 1997. Page 12:

The idea that environmentally induced changes could produce, specific, directed genetic changes was very appealing to Stalin. It was an idea perfectly compatible with Marxism: Proper social conditions would produce permanent, heritable changes in human behavior. Lysenko became a key part of Stalin's team and in 1940 was appointed director of the Institute of Genetics of the USSR Academy of Science. … Lysenko dominated Soviet genetics and agriculture until 1964. Soviet agriculture, based on the theory of acquired characteristics, was in shambles. Soviet genetic research was an international disgrace.

NOTE: This entire section was scrubbed from 2006 edition of this book.

[1311] Book: The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. Sixth edition. John Murray, 1872. has its whole frame beautifully adapted for browsing

Chapter 7: "Miscellaneous Objections to the Theory of Natural Selection":

The giraffe ... has its whole frame beautifully adapted for browsing on the higher branches of trees. It can thus obtain food beyond the reach of the other … animals inhabiting the same country; and this must be a great advantage to it during dearths. … Man has modified some of his animals, without necessarily having attended to special points of structure, by simply preserving and breeding from the fleetest individuals, as with the race-horse and greyhound, or as with the game-cock, by breeding from the victorious birds. So under nature with the nascent [emerging] giraffe, the individuals which were the highest browsers and were able during dearths to reach even an inch or two above the others, will often have been preserved; for they will have roamed over the whole country in search of food. That the individuals of the same species often differ slightly in the relative lengths of all their parts may be seen in many works of natural history, in which careful measurements are given. These slight proportional differences, due to the laws of growth and variation, are not of the slightest use or importance to most species. But it will have been otherwise with the nascent [emerging] giraffe, considering its probable habits of life; for those individuals which had some one part or several parts of their bodies rather more elongated than usual, would generally have survived. These will have intercrossed and left offspring, either inheriting the same bodily peculiarities, or with a tendency to vary again in the same manner; while the individuals less favoured in the same respects will have been the most liable to perish. … [N]atural selection will preserve and thus separate all the superior individuals, allowing them freely to intercross, and will destroy all the inferior individuals. By this process long-continued … combined, no doubt, in a most important manner with the inherited effects of the increased use of parts, it seems to me almost certain that an ordinary hoofed quadruped might be converted into a giraffe.

[1312] Book: Evolution. By Colin Patterson. Comstock Publishing (division Cornell University Press), 1999. Second edition. First published in 1978.

Page 7: "Darwin used variation in domestic animals as one of the major arguments for this theory. The science of genetics was then unknown and, apart from human family trees, domestic animals and plants were the only source of reliable information about patterns of inheritance."

[1313] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

The opening sentence of Chapter 1 pertains to "cultivated plants and animals" and Darwin uses the words "domestic," "domestication," "domesticated," and "cultivated" more than 200 times in this work.

[1314] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 4: "Natural Selection":

Thus the varieties or modified descendants, proceeding from the common parent (A), will generally go on increasing in number and diverging in character. Slow though the process of selection may be, if feeble man can do much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection.

Chapter 13: "Any change in function, which can be effected by insensibly small steps, is within the power of natural selection; so that an organ rendered, during changed habits of life, useless or injurious for one purpose, might easily be modified and used for another purpose."

[1315] For example:

Textbook: Biology: Concepts & Connections. By Neil A. Campbell, Lawrence G. Mitchell, Jane Reece, Larry Mitchell. Benjamin/Cummings Publishing Company, 1997. Second Edition. Page 266:

Darwin reasoned that, if so much change could be achieved in a relatively short period of time by artificial selection, then over hundreds of thousands of generations, natural selection should be able to modify species considerably. With natural selection operating over vast spans of time, heritable changes would gradually accumulate.

[1316] Book: Mendel's Principles of Heredity. By William Bateson. Cambridge University Press, 1909. Page 289:

The conception of Evolution as proceeding through the gradual transformation of masses of individuals by the accumulation of impalpable changes is one that the study of genetics shows immediately to be false. Once for all, that burden so gratuitously undertaken in ignorance of genetic physiology by the evolutionists of the last century may be cast into oblivion. … The scope of natural selection is closely limited by the laws of variation. How precise and specific are those laws we are only beginning to perceive.

NOTE: This quote also appears in the third edition of this book, which was published in 1930.

[1317] Book: Practical Genetics for Dog Breeders. By Malcolm B. Willis (PhD in Genetics and Animal Breeding from the University of Edinburgh and Senior Lecturer in these disciplines at Newcastle University, Newcastle upon Tyne, United Kingdom). Howell/Macmillan, 1992. Page 14:

[B]reeds of dogs go back a long time and books of the fifteenth century do define some breed types. Great antiquity is thought desirable for a breed but, in reality, claims to great antiquity are more imagined than real. … Most breeds have changed more in the past 120 years or so than they would have done in the previous 500 years because in the past 120 years man has been consciously and deliberately breeding distinct types (breeds) of dog as specific entities. Some breeds popular today are the result of the deliberate crossing of existing breeds with a view to creating new kinds of dog. Most of these created breeds go back only to the turn of the century.

[1318] Book: Evolution. By Colin Patterson. Comstock Publishing (division Cornell University Press), 1999. Second edition. First published in 1978.

Page 8: "All breeds of dogs are interfertile [can be bred physically or via lab techniques to produce fertile offspring], but some crosses for example between a 1 kg Chihuahua and a 75 kg Great Dane, are prevented by the disparity in size."

[1319] Book: Genetics: A Beginner's Guide. By Burton Guttman (Professor of Biology at Evergreen State College), Anthony Griffiths (Professor of Botany at University of British Columbia), David Suzuki (Emeritus Professor at University of British Columbia) & Tara Cullis (former teacher at Harvard University). One World Publications, 2002.

Page 255-6: "Sometimes the members of a species can look very different but can still interbreed. Domestic dogs are an impressive example: the largest types, such as Newfoundlands, can breed with the smallest, such as Chihuahuas, to produce fertile offspring."

[1320] Book: Animal Species and Evolution. By Ernst Mayr. The Belknap Press of Harvard University Press, 1963.

Page 289. "Obviously any drastic improvement under selection must seriously deplete the store of genetic variability."

[1321] Book: Genes and DNA: A Beginner's Guide to Genetics and Its Applications. By Charlotte K. Omoto (Professor of Cell Biology and Genetics at the School of Biological Sciences, Washington State University) & Paul F. Lurquin (Professor of Genetics at the School of Molecular Biosciences, Washington State University). Columbia University Press, 2004. Page 155.

[1322] Website: Animal Behavior, An Online Textbook. By Michael D. Breed (Professor of Environmental, Population and Organismic Biology at the University of Colorado, Boulder). Accessed July 5, 2006 at http://www.animalbehavioronline.com/dogbehavioralgenetics.html

NOTE: This textbook is "under development and is currently in a rough draft form." The quote is from a section written in 2003 entitled "The Behavioral Genetics of Dogs."

[1323] Book: Genetics and the Logic of Evolution. By Kenneth M. Weiss & Anne V. Buchanan. John Wiley & Sons, 2004.

Page 27: "Selection screens out variation that exists (by chance), favoring some functional variation that may or may not relate to flight but is useful in at least some way."

NOTE: This statement is made in the general context of all traits. Flight is merely the example that is used. Also note that the phrase "by chance" appears in this book. It is not something I added.

[1324] Book: Genes and DNA: A Beginner's Guide to Genetics and Its Applications. By Charlotte K. Omoto (Professor of Cell Biology and Genetics at the School of Biological Sciences, Washington State University) & Paul F. Lurquin (Professor of Genetics at the School of Molecular Biosciences, Washington State University). Page 154:

The fittest individuals are not necessarily the strongest, the smartest, or the healthiest. … the genes from the fittest individuals are those that are selected for in such a way that their proportion will increase in successive generations. The genes from less fit individuals are selected against and their proportion will decrease in successive generations.

[1325] Article: "On the Importance of Being Ernst Mayr." By Axel Meyer. PLoS [Public Library of Science] Biology, April 5, 2005. http://biology.plosjournals.org/perlserv?request=...

This article states that Mayr "published his first scientific paper (of a total of almost 700) at the age of 19." It also affirms that two of Mayr's eminent colleagues considered him to be "the greatest evolutionary biologist of the 20th century."

[1326] Book: Animal Species and Evolution. By Ernst Mayr. The Belknap Press of Harvard University Press, 1963.

The back cover of this book contains this quote from P.B. Medawar of the Medical Research Council, London: "A major work of scholarship by one of the few Grand Masters of evolutionary genetics and taxonomy." It is also contains this quote from  George Gaylord Simpson: "This is the soundest, most complete, and best documented study ever published on genetical characteristics and evolutionary processes in animal populations around the crucial level of species."

[1327] Book: What Evolution Is. By Ernst Mayr. Basic Books, 2001. Page 117.

The dust cover of this book states that the New York Times called Mayr "the Darwin of the 20th century," Stephen J. Gould called him "the world's greatest living evolutionary biologist," and Edward O. Wilson called him "one of the grand masters of twentieth century biology."

NOTE: I independently confirmed each of these quotes.

[1328] Book: Practical Genetics for Dog Breeders. By Malcolm B. Willis (Ph.D. in Genetics and Animal Breeding from the University of Edinburgh and Senior Lecturer in these disciplines at Newcastle University, Newcastle upon Tyne, United Kingdom). Howell/Macmillan, 1992.

Pages 13-14: "The dog exhibits greater variation than any other mammalian species, ranging in size from the Chihuahua weighing only a kilo or so to the St. Bernard which is heavier than most men. In shape, too, the enormous differences are obvious."

[1329] For an example of a textbook that does not make the true implications of domestication clear, see citation 1315.

[1330] Book: Mendel's Principles of Heredity. By William Bateson. Cambridge University Press, 1909. Page 280:

[I]t has become clear that variation, in so far as it consists in the omission of elementary factors, is the consequence of a process of "unpacking." The white Sweet Pea was created in the variation by which one of the four color-factors was dropped out. Such variation is not, as it was formerly supposed that all variation must be, a progress from a lower degree of complexity to a higher, but the converse. When from a single wild-type, man succeeds in producing a multitude of new varieties, we may speak of the result as a progress in differentiation: but we must recognize that the term is only applicable loosely, and that the obvious appearance of increased complexity may in reality be the outcome of a process of simplification. The facts nevertheless preclude the suggestion that all variation even under domestication is of this nature, nor till experimental research has developed far beyond its present limits, can we make any confident estimate whether it is the one process or the other which has played the larger part in the formation of the diversity of living forms.

Page 289:

The conception of Evolution as proceeding through the gradual transformation of masses of individuals by the accumulation of impalpable changes is one that the study of genetics shows immediately to be false. Once for all, that burden so gratuitously undertaken in ignorance of genetic physiology by the evolutionists of the last century may be cast into oblivion. … That the variations are controlled by physiological law, we now have experimental proof; but that this control is guided ever so little to the needs of Adaptation there is not the smallest sign. … The scope of natural selection is closely limited by the laws of variation. How precise and specific are those laws we are only beginning to perceive.

NOTE: The quotes above also appear in the third edition of this book, which was published in 1930.

[1331] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 343: "Nevertheless, mistakes in the genetic material do occur. Such heritable changes in the genetic material are called mutations."

[1332] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 69: "In nature, mutations provide the raw material for evolution."

[1333] Book: Evolution. By Colin Patterson. Comstock Publishing (a division of Cornell University Press), 1999. Second edition. First published in 1978.

Page 47: "Mutations are random events, the result of accidental errors in replication of DNA or in nuclear division."

[1334] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 346. For example, see pages 359-362 on "Mutations Induced by Radiation."

[1335] Book: Endless Forms Most Beautiful. By Sean B. Carroll. W. W. Norton & Company, 2005. Pages 164-165:

As the Big Bang [Cambrian explosion] unfolded, the pressure of ecological interactions and competition among increasingly diverse animal species drove the evolution of more complex structures—compound and camera eyes for vision; jointed appendages for walking, swimming and grabbing prey; hearts for managing circulation in larger bodies … [etc.].

[1336] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 346. {See next citation for the context.}

[1337] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 345 explains that some cockroaches and rats are resistant to certain poisons and then states:

Is mutation a purely random event in which the environmental stress merely preserves preexisting mutations? Or is mutation directed by environmental stress? … Despite the beliefs of Jean Lamarck and his follower Trofim Lysenko, who believed in the inheritance of "acquired traits"—traits imposed on organisms by environmental factors—the answer is no....

Pages 345-346:

When exposed to the streptomycin, most of the bacteria will be killed by the antibiotic. However if the population is large enough, it will soon give rise to a streptomycin culture in which all the cells are resistant to the antibiotic. Does streptomycin simply select rare, randomly occurring mutants that preexist in the population, or do all of the cells have some low probability of developing resistance in response to the presence of the streptomycin? …

[Experimentation has demonstrated that the] streptomycin-resistant mutants in the population of bacteria [were present] prior to their exposure to the antibiotic. Their results, along with the results of many other experiments have shown that environmental stress does not direct or cause genetic changes as Lysenko believed; it simply selects rare preexisting mutations that result in phenotypes [organisms with characteristics] better adapted to the new environment.

[1338] Entry: "teleological." Merriam-Webster's Collegiate Dictionary, Encyclopædia Britannica Ultimate Reference Suite 2004.

[1339] Book: Genetics and the Logic of Evolution. By Kenneth M. Weiss (Professor of Anthropology and Genetics) & Anne V. Buchanan (Senior Research Scientist in Anthropology). John Wiley & Sons, 2004. Page 28:

There is no satisfactorily provable way out of the teleological illusion, but this has not shaken biologists into eschewing the making of adaptive scenarios, mainly because a good enough alternative material explanation for directed change does not exist. Religious creationists scurrilously misrepresent what biologists mean when they say evolution is due to chance.* But ironically, in insisting upon adaptive scenarios* biologists share with religious creationists the belief that complex traits cannot arise just "by chance." However, we will suggest that chance may be a more important factor in adaptive evolution than has been thought.

NOTE: *For example, see citation 1335.

[1340] Book: What Mad Pursuit: A Personal View of Scientific Discovery. By Francis Crick. Basic Books, 1988. Page 138.

[1341] Romans 1:18-2:

The wrath of God is being revealed from heaven against all the godlessness and wickedness of men who suppress the truth by their wickedness, since what may be known about God is plain to them, because God has made it plain to them. For since the creation of the world God's invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that men are without excuse.

[1342] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 348.

[1343] Textbook: Principles of Genetics. By D. Peter Snustad, Michael J. Simmons & John B. Jenkins. John Wiley & Sons, 1997. Page 742.

[1344] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 777.

[1345] Article: "Human Genome Map Has Scientists Talking About the Divine." By Tom Abate. San Francisco Chronicle, February 19, 2001. http://www.sfgate.com/cgi-bin/article.cgi?f=...

NOTE: The person who made this statement was Gene Meyers, VP of Informatics at Celera Genomics. This article also quotes Meyers as stating: "There's a huge intelligence there. I don't see that as being unscientific. Others may, but not me."

[1346] Article: "Prominent scientist is misquoted." TonkaFocus ("an independent community group supporting the integrity of the Minnetonka Public Schools"). Accessed July 2007 at http://www.tonkafocus.org/

Based upon the quotes above, this organization asked Dr. Meyers if he was a supporter of intelligent design, and he responded:

I am not. I am being taken out of context and upset about this. Abate [the San Francisco Chronicle reporter] interviewed me shortly after we had completed the genome and for a moment I waxed poetic about the complexity of what was there and the elegance of the "design." Evolution is very real – it is directly observable in the time frames of mutating bacteria, e.g. the acquisition of antibiotic resistance.

NOTE: Despite the title of the article, the only demonstrable misquotation here is the one propagated by this organization (TonkaFocus), which claims that a Mr. Tucker "is mistaken about Dr. Gene Myers being a proponent of Intelligent Design." As the quote from Mr. Tucker in the article shows, he asserted no such thing. Furthermore, Dr. Meyer's claim that he is being taken out of context is absurd on its face.

[1347] Book: Population and Evolutionary Genetics: A Primer. By Francisco J. Ayala. Benjamin Cummings Publishing Company, 1982.

Page 58. "The ultimate source of all genetic variation is the process of mutation."

[1348] Book: Finding Darwin's God. By Kenneth R. Miller. Cliff Street Books, 1999.

Page 49: "Mutations are a continuing and inexhaustible source of variation, and they provide the raw material that is shaped by natural selection. Since mutations can duplicate, delete, invert, and rewrite any part of the genetic system in an organism, they can produce any change that evolution has documented."

[1349] For example, Genesis 1:11-12, 24-25 (New International Version):

Then God said, "Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds." And it was so. The land produced vegetation: plants bearing seed according to their kinds and trees bearing fruit with seed in it according to their kinds. And God saw that it was good. … And God said, "Let the land produce living creatures according to their kinds: livestock, creatures that move along the ground, and wild animals, each according to its kind." And it was so. God made the wild animals according to their kinds, the livestock according to their kinds, and all the creatures that move along the ground according to their kinds. And God saw that it was good.

[1350] Textbook: Principles of Genetics. By D. Peter Snustad, Michael J. Simmons & John B. Jenkins. John Wiley & Sons, 1997. "Epilogue: Genetics Yesterday, Today, and Tomorrow - A Personal View." By James F. Crow.

Page 764: "Genetics is a new science.… The subject is unusual in that its origin can be pinpointed to a single event, the publication of Gregor Mendel's paper in 1866."

[1351] Paper: Experiments in Plant Hybridisation. By Gregor Mendel. Verhandlungen des Naturforschenden in Brünn, 1865 (appeared in 1866). In English translation with commentary by Ronald A. Fisher. Oliver & Boyd, 1965.

[1352] Articles: "Mendel, Gregor" & "Pasteur, Louis." New Millennium Encyclopedia. Simon & Schuster, 1999.

[1353] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 33:

The genetic analysis of bacteria began in earnest in the 1940s. … [E. coli] can be cultured in the laboratory on a simple medium, it is amendable to all sorts of biochemical analyses, and mutant strains with different growth requirements can be isolated easily. As of a result of these features, E. coli has become the microbial workhorse of geneticists.

[1354] Book: Genetics: A Beginner's Guide. By Burton Guttman (Professor of Biology at Evergreen State College), Anthony Griffiths (Professor of Botany at The University of British Columbia), David Suzuki (Emeritus Professor at The University of British Columbia) & Tara Cullis (former teacher at Harvard University). One World Publications, 2002.

Page 165: "One of a geneticist's main tools is analyzing crosses between different strains, and this can also be done with bacteria, because even they have a kind of sex life. The discovery of sex and sexual interchange in bacteria is a fascinating story."

NOTE: The authors go on to describe recombination, plasmids, and transduction.

[1355] Article: "Genetics." Encyclopædia Britannica Ultimate Reference Suite 2004. The section entitled "Microbial genetics" states:

Microorganisms were generally ignored by the early geneticists because they are small in size and were thought to lack variable traits and the sexual reproduction necessary for a mixing of genes from different organisms. After it was discovered that microorganisms can have different physiological characteristics and also are able to reproduce sexually, they became objects of great interest to geneticists because they reproduce more rapidly than larger organisms….

[1356] Article: "Genetics." Encyclopædia Britannica Ultimate Reference Suite 2004.

The section entitled "Microbial genetics" states: "[O]ne bacterium may produce 10,000,000,000 offspring, among which are numerous mutants, in 48 hours."

[1357] Web page: "Rank Order - Population." CIA World Factbook, 2006.

https://www.cia.gov/library/publications/...

Estimated world population as of July 2006: 6,525,170,264.

Annual birth rate: 20.05 births/1,000 population.

[1358] Calculations performed with data from the following sources:

a) Article: "Genetics." Encyclopædia Britannica Ultimate Reference Suite 2004.

The section entitled "Microbial genetics" states: "[O]ne bacterium may produce 10,000,000,000 offspring, among which are numerous mutants, in 48 hours."

b) Book: Endless Forms Most Beautiful. By Sean B. Carroll. W. W. Norton & Company, 2005. Page 60 states that there are 4,288 genes in an E. coli and "more than 25,000" in humans.

c) Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 345:

Measurements of spontaneous mutation frequencies for various genes of phage and bacteria range from about 10^-8 to 10^-10 detectable mutations per nucleotide pair per generation. For eukaryotes, estimates of mutation rates range from about 10^-7 to 10^-9 detectable mutations per nucleotide pair per generation… [T]he coding region of the average gene is usually assumed to be 1000 nucleotide pairs in length. Thus the mutation rate per gene varies from about 10^-4 to 10^-7 per generation.

Treatment with mutagenic agents can increase mutation frequencies by orders of magnitude. The mutation frequency per gene in bacteria and viruses can be increased to over 1 percent by treatment with potent chemical mutagens. That is, over 1 percent of the genes of the treated organisms will contain a mutation, or stated differently, over 1 percent of the phage or bacteria will have a mutation in a given gene."

d) Article: "How Many People Have Ever Lived on Earth?" By Carl Haub. Population Today, November/December 2002. First published in 1995. http://www.prb.org/Template.cfm?...

Any such exercise can be only a highly speculative enterprise, to be undertaken with far less seriousness than most demographic inquiries. Nonetheless, it is a somewhat intriguing idea that can be approached on at least a semi-scientific basis. … According to the United Nations' Determinants and Consequences of Population Trends, modern Homo sapiens may have appeared about 50,000 B.C. … This semi-scientific approach yields an estimate of about 106 billion births since the dawn of the human race.

CALCULATIONS:

a) "400 billion mutations": 10¹⁰ bacteria × 4.288 X 10³ genes/bacteria × 10^-2 mutation frequency = 4.288 X 10¹¹ mutations. (Note that this number would be significantly higher if we included the mutations from the generations between the first bacterium and those that remained alive after 2 days.)

b) "mutations alleged to have occurred in the human race": 10^-7 to 10^-9 detectable mutations per nucleotide pair/generation × 10³ nucleotides/gene × 2.5 X 10⁴ genes/gamete [this is a reproductive cell] × 2 gametes/child × 1.06 X 10¹¹ births = 5.3 X 10¹¹ to 10⁹ mutations = 530 to 5.3 billion mutations. (I doubled checked this result by approaching this calculation in another way with different sources, and the results were of the same order.)

[1359] Article: "A Theory Evolves: How evolution really works, and why it matters more than ever." By Thomas Hayden. U.S. News and World Report, July 29, 2002. http://www.usnews.com/usnews/culture/articles/...

For microbiologist Richard Lenski, evolution is an obvious reality. Since 1988, the Michigan State University professor has been following 12 populations of the bacterium E. coli. With a new generation every 3.5 hours or so, this is evolution on fast-forward. The populations were once genetically identical, but each has adapted in its own way to the conditions in its test-tube home. The same speedy adaptation, unfortunately, can be readily seen in hospitals, where powerful antibiotics provide a major selective advantage for bacteria that evolve resistance.

NOTE: For a refutation, see "U.S. News and World Report joins in the evolution onslaught." By Don Batten. Creation Ministries International. Accessed February 27, 2009 at http://creationontheweb.com/content/view/2544

[1360] For example, see the citation above.

[1361] Article: "Antibiotic-Resistant Ribosome Sheds Light on Protein Synthesis." ALS News, October 29, 2003. http://www-als.lbl.gov/als/science/sci_archive/...

"Ribosomes are the organelles in living cells responsible for translating the genetic code into proteins. … Streptomycin binds to ribosomes and leads to error-prone protein synthesis…."

NOTE: ALS (Advanced Light Source) is a division of Lawrence Berkeley National Laboratory.

[1362] Paper: "Mutant sequences in the rpsL gene of Escherichia coli B/r: mechanistic implications for spontaneous and ultraviolet light mutagenesis." By A.R. Timms, H. Steingrimsdottir, A.R. Lehmann, & B.A. Bridges. Journal of Molecular and General Genetics, March 1992. Pages 89-96.

Page 89: "In all, 12 different mutations conferring the ability to grow in the presence of streptomycin were identified…."

[1363] Article: "Drug." Encyclopædia Britannica Ultimate Reference Suite 2004.

The section entitled "General principles" states: "The binding of a drug to a receptor site requires a precise chemical fit, and a small change in a drug's chemical structure may drastically alter its potency."

[1364] Article: "Researchers illuminate how bacteria become resistant to antibiotics." By Janet Rettig Emanuel. Yale Bulletin and Calendar, May 6, 2005. http://www.yale.edu/opa/arc-ybc/v33.n28/story8.html

"They [antibiotics] bind tightly to an RNA site on the bacterial ribosomes, the cellular machinery that makes protein…."

Regarding a specific mutation: "The mutant G [bacterium] has an amino group that pokes into the center of the macrolide ring [of the antibiotic], causing it to back off the ribosome by an Angstrom or so [roughly 4 billionths of an inch]," says Steitz. The change … reduced the ability of the antibiotic to bind by a factor of 10,000."

[1365] Article: "Visualizing Antibiotic Resistance." By Elizabeth Tolchin. Reed Life Science News, April 25, 2005. http://www.genpromag.com/

"We are able to understand why this [bacterial] mutation of an A to G makes that binding site resistant to macrolides and other antibiotics that target that area." One of the main reasons, he [Thomas Steitz professor, Department of Molecular Biophysics and Biochemistry, Yale] says, is because the G has an amino group that the A does not have. "That amino group protrudes from the binding site, pokes into the center of the macrolide ring [of the antibiotics], and prevents the antibiotics from binding tightly," Steitz says.

[1366] Paper: "Mutant sequences in the rpsL gene of Escherichia coli B/r: mechanistic implications for spontaneous and ultraviolet light mutagenesis." By A.R. Timms, H. Steingrimsdottir, A.R. Lehmann, & B.A. Bridges. Journal of Molecular and General Genetics, March 1992. Pages 89-96. Page 89:

Streptomycin-resistant mutants can be divided into two phenotypic classes, those resistant to the antibiotic but able to grow in its absence (Sm^r) and those whose growth depends on the continued presence of streptomycin (Sm^d). Both classes of mutant have alterations in ribosomal protein S12, encoded by the rpsL (strA) gene.

Streptomycin causes a decrease in the translational fidelity of the ribosome (reviewed by Gorini 1974), probably by inhibiting its proofreading mechanism (Ruusala and Kurland 1984; Bohman et al. 1984). This effect is alleviated by mutations in the ribosomal protein S12 producing a Sm^r or Sm^d phenotype. These phenotypes reduce the affinity of the ribosome for streptomycin and result in a slower rate of translation (even in the absence of streptomycin) with a concomitant increase in translational accuracy (Galas and Branscomb 1976).

[1367] Textbook: Todar's Online Textbook of Bacteriology. By Kenneth Todar (University of Wisconsin-Madison Department of Bacteriology). 2002. http://www.textbookofbacteriology.net/antimicrobial.html

The page entitled "Antimicrobial Agents Used in Treatment of Infectious Disease" states: "Since bacteria grow to reach population densities far in excess of 10⁹ cells, such a mutant could develop from a single generation during 15 minutes of growth."

[1368] Article: "Scant Search for the Maker." By Alan H. Linton (Emeritus Professor of Bacteriology in the Department of Cellular and Molecular Medicine at Bristol University). Times Higher Education Supplement, April 20, 2001. http://www.timeshighereducation.co.uk/

This article is a book review of The Triumph of Evolution and the Failure of Creationism by Niles Eldredge.

NOTE: Given that the University of Bristol has been anonymously impugned on the Internet as a substandard college, it should be noted that in 2001, an "independent assessment of the quality of research in UK higher education institutions" found that "78 per cent of the University's departments were judged as world class or internationally excellent." [Web pages: "RAE 2001: World-class research triumph for Bristol University" and "Prospective students information - Postgraduate prospectus." Bristol University. Accessed July 26, 2006 at http://www.bris.ac.uk/]

[1369] Book: The Spontaneous Generation Controversy from Descartes to Oparin. By John Farley. Johns Hopkins University Press, 1977. Page 145:

Although all researchers agreed that disease-causing bacteria could not arise by a spontaneous generation from "nothing" or "other things," {year not specified, but from the context, we can see it was during Darwin's era} there was still a very widespread belief in pleomorphism. This tenet, which was particularly strong in Britain, denied the existence of distinct and stable bacterial species, and accepted that disease-causing bacteria could arise de novo from nonpathogenic strains under suitable conditions. As Karl von Nägeli expressed it, bacteria are

inconstant and continually lose themselves in one another. … The same organism in milk produces lactic acid, in meat, putrefaction … in the body to take part in some disease. As every communicable, infectious disease has arisen spontaneously it must continually arise anew under similar circumstances. (1877)

[1370] Textbook: Jawetz, Melnick, & Adelberg's Medical Microbiology. Edited by Geo. F. Brooks, Janet S. Butel, Stephen A. Morse. 21st edition. Appleton & Lange, 1998. This book is considered the "classic text on the medical aspects of medical microbiology." Page 39:

[T]he concept of a species—the fundamental unit of eukaryotic phylogenies—has entirely different meaning when applied to bacteria. A eukaryotic species is a biologic group capable of interbreeding to produce viable offspring.* A bacterial species is defined as a distinct group of organisms that have certain distinguishing features and generally bear a close resemblance to one another in the more essential features of organization. The decision to circumscribe clusters of organisms within a bacterial species is made by the taxonomist, who may chose to subdivide the group in biotypes and to cluster species within genera."

Page 40: "In 1980, the International Commissions on Systematic Bacteriology published an approved list of bacterial names. This list of about 2,500 species replaces a former list that had grown to over 30,000 names…."

NOTES:

* This is not exactly true, as shown on pages 193-194 of Rational Conclusions. As illustrated in this citation and explained on pages 193-194, there is much confusion surrounding the definition of the term "species." Thus, I use a concrete example of an E. coli bacterium versus a streptococcus to clarify Linton's point.

[1371] Web Page: "In memoriam." French Academy of Sciences. http://www.academie-sciences.fr/membres/...

Pierre-Paul Grassé was 'Président de l'Académie' in 1967.

[1372] Book: Larousse Encyclopedia of the Animal World. Edited by Pierre Paul Grassé. Larousse and Company, 1969. English translation by William Collins Sons &Co., 1975.

The dust cover states that this "text was created through the work of some fifteen of France's most distinguished biologists under the guidance of Pierre Paul Grassé."

[1373] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 347 explains that restorations of mutations sometimes occur through "back mutations."

[1374] Book: Evolution of Living Organisms. By Pierre-P. Grassé. Academic Press, 1977. First published in French in 1973. Page 87.

[1375] Book: Evolution of Living Organisms. By Pierre-P. Grassé. Academic Press, 1977. First published in French in 1973.

Page 3: "Zoologists and botanists are nearly unanimous in considering evolution as a fact and not a hypothesis. I agree with this position and base it primarily on documents provided by paleontology, i.e., the history of the living world."

Page 89: Some contemporary biologists, as soon as they observe a mutation, talk about evolution. … No matter how numerous they may be, mutations do not produce any kind of evolution."

Page: 246 "The united efforts of paleontology and molecular biology, the latter stripped of its dogmas, should lead to the discovery of the exact mechanism of evolution…."

[1376] For example, the author of the following citation grudgingly admits there are problems, but makes it clear he is not going to abandon mutation unless some other genetic mechanism can take its place.

Book review: "Darwinian or "Orientated" Evolution." By Theodosius Dobzhansky. Evolution [Journal of], June 1975. Pages 376-378. This is a critical review of Grassé's book L'Évolution du Vivant (Evolution of Living Organisms):

The mutation-selection theory attempts, more or less successfully, to make the causes of evolution accessible to reason. The postulate that evolution is "oriented" by some unknown force explains nothing. … Nothing is easier than to point out that this or that problem is unsolved and puzzling. But to reject what is known, and to appeal to some wonderful future discovery which may explain it all, is contrary to sound scientific method.

NOTE: To embrace the only explanation you can muster to support your theory even though it plagued by problems is not science, but desperate stubbornness. There is nothing unscientific in saying "I don't know."

[1377] For another example, scrutinize the following quotes from Ernst Mayr, who as we have seen, is widely considered to be one of the greatest evolutionists of all time. Pay close attention to the disconnects and their implications. Note that in reading and comparing the books from which these quotes were drawn, I found no scientific evidence that would warrant a change of opinion. He uses the same basic facts to arrive at divergent opinions. In all probability, it follows that Mayr was forced to alter his stance simply because forty additional years of scientific research failed to produce a more saleable mechanism for evolution:

Book: Animal Species and Evolution. The Belknap Press of Harvard University Press, 1963. Pages 7-8:

We now believe that mutations do not guide evolution; the effect of a mutation is very often far too small to be visible. Recombination produces far more selectively important phenotypes than does mutation, and the kinds of mutations and recombinations that can occur in a given organism are severely restricted.

Book: What Evolution Is. Basic Books, 2001. Pages 98 … 104:

Even though all new genes are produced by mutations, most of the phenotypic variation in natural populations that is available for selection is the product of recombination.…

… [Recombination provides] unlimited new material for the process of natural selection.

[1378] Paper: "The Paradox of the 'Ancient' Bacterium Which Contains 'Modern' Protein-Coding Genes." By Heather Maughan and others. Molecular Biology and Evolution, September 2002. Page 1637-1639. http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

Page 1637:

Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. This fact has historically been used by critics to argue that these isolates are not ancient but are modern contaminants introduced either naturally after formation of the surrounding material … or because of flaws in the methodology of sample isolation…. Such criticism has been addressed experimentally by the development of highly rigorous protocols for sample selection, surface sterilization, and contamination detection and control procedures. Using the most scrupulous and well-documented sampling procedures and contamination-protection techniques reported to date, Vreeland, Rosenzweig, and Powers (2000) reported the isolation of a sporeforming bacterium … within a halite crystal recovered from the 250-Myr-old Permian Salado Formation in Carlsbad, NM.

NOTE: More information about this subject is provided in Chapter 9 of Rational Conclusions, which covers the fossil record.

[1379] Book: George Beadle - An Uncommon Farmer: The Emergence of Genetics in the 20th Century. By Paul Berg & Maxine Singer. Cold Spring Harbor Laboratory Press, 2003.

Page 33: "In the laboratory, Drosophila has a rapid reproductive cycle (about 10 days) and produces abundant progeny (100-400 offspring per mating)."

[1380] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 101 states that extensive genetic research on fruit flies has been ongoing since 1909.

Page 84 speaks of the fruit fly meeting.

[1381] Article: "Vinegar fly." Encyclopædia Britannica Ultimate Reference Suite 2004.

[1382] Book: Animal Species and Evolution. By Ernst Mayr. The Belknap Press of Harvard University Press, 1963. Page 285:

I refer to the pioneering and now classical studies of Mather and his associates on bristle number in Drosophila…. The object of the selection was an increase in the number of bristles (chaetae) on the ventral surface of the fourth and fifth abdominal segments in Drosophila melanogaster. Two experiments were run, one for increase and one for decrease in bristle number. In the starting stock, the combined average bristle number of males and females on these segments was about 36. Selection for low bristle number was able to lower this average after 30 generations to 25 chaetae, after which the line soon died out owing to sterility. A mass "low" line (maintained without selection) was started with 32 chaetae and remained nearly stable for 95 generations. However, all attempts to derive from this line others with lower bristle numbers proved failures. The lines invariably died out owing to sterility before selection had made much progress.

 Page 286:

In the "high line" (selection for high bristle numbers), progress was at first rapid and steady. Within 20 generations, bristle number had risen from 36 to an average of 56, without marked spurs or plateaus. At this stage sterility became severe and a mass culture (without selection) was started. … New high selection lines were repeatedly taken from this "high" mass line. The first two (started at the 24th and 27th generation) regained the previous high bristle number as quickly as the line had lost it when selection was stopped. However, viability was now much improved and a viable line could be maintained under constant selection pressure (without, however, much phenotypic response).

Page 290:

Animals and plant breeders have long known that various "correlated response" may occur as a consequence of selection for a particular character, that is, changes in seemingly independent aspects of the phenotype. … The occurrence of sterility during selection for changed bristle number in Drosophila is a typical case of a correlated response. …. Correlated responses occur during virtually every case of selection, since most genes seem to affect simultaneously some components of fitness and some more trivial aspects of the phenotype. … The most frequent "correlated response" of one-sided selection is a general drop in fitness. This plagues virtually every breeding experiment.

NOTE: Mayr attempts to put forth what could be construed as an evolutionary explanation for the cause of such limits on pages 287-9, but any such inference is dashed with this statement that appears on page 289: "Obviously any drastic improvement under selection must seriously deplete the store of genetic variability."

[1383] Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999. Page 359:

Indeed, what convinced Morgan and is colleagues that evolutionary change was gradual was Muller's experimental manipulation of generation after generation of fruit flies in which he painstakingly altered the predominant wing length from being longer, to being a bit shorter than, body length. Muller was able to do this because there were a few individuals with short wings, although most individual of the parental population had long wings. Occasionally, as the experiment proceeded, individuals would emerge with slightly shorter wings than usual and Muller selected them to breed for the next generation. …

In considering the significance of Muller's experiment, it is important to realize that the genes for short wings were already present in the experimental population and that even when he managed to shift the tendency of the population from long to short wings, there were still individuals with long wings. Muller had certainly changed the character of the population in terms of average wing length, but he had not manipulated the genes that were responsible for the presence or absence of wings. Morgan assumed from Muller's experiment that, if the process of selection were to go on long enough, wing length would eventually become so diminished that the wingless state would eventually result … This extrapolation is, however, not valid.

[1384] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Pages 84, 356.

[1385] Book: Genetic Variations of Drosophila Melanogaster. By Dan L. Lindsley & E. H.

Grell. Carnegie Institution of Washington Publication No 627, 1968.

The Preface states there are "about 3000" mutations detailed in this book.

[1386] Web Page: "James F. Crow." Department of Genetics, University of Wisconsin – Madison. Updated September 3, 2006. http://www.genetics.wisc.edu/faculty/profile.php?id=102

His Genetics Notes – virtually everyone calls it "Crow's Notes" – became the foundation for genetics courses around the world. It was translated into many languages: Japanese, Korean, Portuguese, Dutch, Yugoslav. … Over a career that has spanned more than 50 years, Jim and his collaborators have studied a variety of traits in Drosophila, dissected the genetics of DDT resistance, measured the effects of minor mutations on the overall fitness of populations, described the behavior of mutations that do not play the selection game by Darwin's rules, and investigated many other subjects. His theoretical work has touched virtually every important subject in population genetics. … He chaired the Department of Medical Genetics for 5 years and the Laboratory of Genetics (that is, Genetics plus Medical Genetics) for a total of 8 years. He also served as Acting Dean of the UW Medical School for 2 years. He has been President of the Genetics Society of America and the American Society of Human Genetics.

[1387] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Epilogue: "Genetics Yesterday, Today, and Tomorrow - A Personal View." By James F. Crow, University of Wisconsin, Madison.

Page 799: "But if Drosophila tells us anything, it is that the great bulk of mutations are those that cause small, nonspecific, harmful effects."

[1388] Book: Genetic Variations of Drosophila Melanogaster. By Dan L. Lindsley & E. H. Grell. Carnegie Institution of Washington Publication No 627, 1968.

Page 16 covers the Antennapedia mutation, of which there are several variants. Note that this mutation is generally lethal in the homozygous state.

[1389] Article: "15 Answers to Creationist Nonsense." By John Rennie. Scientific American, June 18, 2002. Pages 78-85. http://www.scientificamerican.com/article.cfm?id=...

Mutations that arise in the homeobox (Hox) family of development-regulating genes in animals can also have complex effects. … In fruit flies, for instance, the mutation called Antennapedia causes legs to sprout where antennae should grow. These abnormal limbs are not functional, but their existence demonstrates that genetic mistakes can produce complex structures, which natural selection can then test for possible uses.

NOTE: For a refutation of this article, see the article: "15 ways to refute materialistic bigotry: A point by point response to Scientific American." By Jonathan Sarfati (Ph.D. in Physical Chemistry). Creation Ministries International, June 20, 2002. http://creation.com/15-ways-to-refute-materialistic-bigotry

[1390] Article: "Fly fMRI reveals secrets of smell." IN VIVO (a publication of Columbia University Health Sciences), October 27, 2003. http://www.cumc.columbia.edu/news/in-vivo/...

"The olfactory system, even in flies, is complex. … The odor receptors are arranged in the fly's antennae that lie in the front of its head, between its two large compound eyes."

[1391] As will be shown, the prevalent definition of "species" results in exceedingly narrow classifications that flout evolutionary significance. Also, in the words of Ernst Mayr, "there is not yet unanimity on the definition of species." As such, when I use the word "type," I am speaking along the lines of genera and families (e.g., vinegar flies, roses, canines, etc.). Furthermore, let it be noted that the scientist quoted in the next note is doubtful that experimentation has yet to produce even a new species of fly.

[1392] Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999.

Page 288: "Dobzhansky even identified … a new species of fruit fly … on the basis of chromosome differences. In fact, since … [it] was virtually identical morphologically to … [another species], Dobzhansky could identify it only on the basis of its chromosomes."

Pages 299-300:

Dobzhansky neglected to consider the fact that that while Goldschmidt's systemic mutations may not have been observed, neither had the mechanisms of speciation that he, or anyone else, for that matter, had proposed.* … Nevertheless, it was and still is the case that, with the exception of Dobzhansky's claim about a new species of fruit fly, the formation of a new species, by any mechanism, has never been observed.

NOTE:

* Clearly, Schwartz does not buy Dobzhansky's claim.

[1393] Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999. Page 353:

[W]e are still at a loss to identify the mechanisms by which organismal change can emerge and become established in groups of organisms. … [T]here remain important unanswered questions. One such question is: "How does more than one individual come to have a novel structure?" … A second question is: "How will a novelty look when it does appear?"

NOTE: The above is an unmistakable admission that no one has ever seen a novelty appear.

[1394] Web page: "An Introduction to Evolution." By the "Understanding Evolution Team" at the University of California Museum of Paleontology and the National Center for Science Education. Accessed May 1, 2009 at http://evolution.berkeley.edu/evolibrary/article/_0/evo_02

The central idea of biological evolution is that all life on Earth shares a common ancestor, just as you and your cousins share a common grandmother.

Through the process of descent with modification, the common ancestor of life on Earth gave rise to the fantastic diversity that we see documented in the fossil record and around us today. Evolution means that we're all distant cousins: humans and oak trees, hummingbirds and whales.

[1395] Textbook: Principles of Genetics. By D. Peter Snustad, Michael J. Simmons & John B. Jenkins. John Wiley & Sons, 1997.

Page 727: "A well known and widely cited example of … [heterozygote superiority] is the sickle-cell allele in humans…."

[1396] Teaching guide: "Human Genetic Variation." By BSCS and Videodiscovery under a contract from the National Institutes of Health, National Human Genome Research Institute, 1999. http://science.education.nih.gov/supplements/nih1/...

Page 9: "Some genetic variation, however, can be positive, providing an advantage in changing environments. The classic example from the high school biology curriculum is the mutation for sickle hemoglobin, which in the heterozygous state provides a selective advantage in areas where malaria is endemic."

[1397] Book: Evolution. By Colin Patterson. Comstock Publishing (division Cornell University Press, 1999. Second edition. First published in 1978. Pages 48-51.

[1398] Also see citation 1402. These examples of are just a few of many that link the mutation that causes sickle-cell anemia with evolution. A search for "sickle cell anemia" AND evolution at http://www.google.com/ on May 1, 2009 produced 97,200 results.

[1399] Textbook: Fundamentals of Anatomy & Physiology. By Frederic H. Martini. Prentice Hall, 2001. Page 631.

[1400] Article: "Sickle cell anemia." Mosby's Medical Encyclopedia, 1997.

[1401] Article: "Sickle-cell anemia." Encyclopædia Britannica Ultimate Reference Suite 2004.

The name of the drug is hydroxyurea.

[1402] Book: Animal Species and Evolution. By Ernst Mayr. The Belknap Press of Harvard University Press, 1963.

Page 227: "The anemia caused by the sickle genes results in at least a 90-percent reduction in fitness among homozygotes. Indeed, few of them reach even the age of five years."

[1403] Textbook: Medicine. By Mark C. Fishman. Lippincott Williams & Wilkins, 2003.

Page 373: "Heterozygous persons are said to have sickle cell trait and only rarely experience any of the symptoms of sickle cell anemia."

[1404] Book: An Atlas of the Blood and Bone Marrow. By R. Philip Custer (Emeritus Professor of Pathology, University of Pennsylvania School of Medicine; Senior Member, Institute for Cancer Research, Fox Chase; Consultant, Presbyterian-University of Pennsylvania Medical Center). Second edition. W. B. Saunders Company, 1974.

Page 145: "SICKLE CELL DISEASE … The gene is a dominant one that transmitted vertically in a purely classic fashion, but the disease per se is recessive in that it requires homozygosity. Heterozygotes (AS) carry the trait but are free of disease, except under certain circumstances to be mentioned later."

[1405] Article: "Malaria." Mosby's Medical Encyclopedia, 1997.

"Plasmodium parasites enter the red blood cells of the infected human, where they mature, reproduce, and burst out every so often."

[1406] Book: Malaria: Parasite Biology, Pathogenesis, and Protection. By Irwin W. Sherman. ASM Press, 1998. Chapter 30: "Host Genetic Factors in Resistance to Malaria." By Adrian V. S. Hill & David J. Weatherall.

Page 446: "While there is very clear evidence for the protective effect of the sickle cell trait against severe malaria, the mechanism by which it is mediated is far less certain."

[1407] Article: "Lactose Tolerance in East Africa Points to Recent Evolution." By Nicholas Wade. New York Times, December 11, 2006. http://www.nytimes.com/2006/12/11/science/11evolve.html

[1408] Book: Evolution of Living Organisms. By Pierre-P. Grassé. Academic Press, 1977. First published in French in 1973. Pages 85-86.

[1409] Ancient Work: Historia Animalium. By Aristotle (384-322 BC). Translated by D'Arcy Wentworth Thompson. Clarendon Press, 1910.

Book 2, Chapter 1: "With regard to animals in general, some parts or organs are common to all, as has been said, and some are common only to particular genera; the parts, moreover, are identical with or different from one another on the lines already repeatedly laid down."

[1410] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 13: "Mutual Affinities of Organic Beings: Morphology: Embryology: Rudimentary Organs."

[1411] Book: Homology: An Unsolved Problem. By Sir Gavin de Beer. Oxford University Press, 1971. Page 3.

[1412] Entry: "hom-." Merriam-Webster's Collegiate Dictionary, Encyclopædia Britannica Ultimate Reference Suite 2004.

"Etymology: Latin, from Greek, from homos— more at same."

[1413] Book: The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces. By George McGhee. Cambridge University Press, 2007. Page 182:

In biology, however, the study of morphology was quickly eclipsed by the discovery of the structure of DNA by James Watson and Francis Crick in 1953…. By the mid-1960s the DNA coding for all the amino acids had been worked out, and in the past four decades, the discipline of molecular biology has experienced explosive growth in the number of its practitioners.

[1414] Paper: "Homology-A Continuing Challenge." By Rolf Sattler. Systematic Botany, Oct. - Dec., 1984. Page 382-394. Page 385:

Besides the problem of circularity and additional assumptions, homology based on common ancestry may have yet another serious limitation. If it is understood as a correspondence of entities that have arisen from a common ancestor through a real historic process, then it applies only to entities that show a direct genealogical or phylogenetic relationship, i.e., it applies to entities such as genes, chromosomes, and whole organisms. It does not apply to organs, organ-systems, or modules because they do not become directly transformed into one another.

[1415] Article: "Gavin Rylands de Beer." By E. J. W. Barrington. Biographical Memoirs of Fellows of the Royal Society, December, 1973. Pages 64-93.

NOTE: de Beer also wrote several acclaimed books such as Vertebrate Zoology: An Introduction to the Comparative Anatomy, Embryology, And Evolution Of Chordate Animals, Embryos and Ancestors, and his magnum opus, Atlas of Evolution.

[1416] Book: Homology: An Unsolved Problem. By Sir Gavin de Beer. Oxford University Press, 1971.

[1417] Same as above. Page 15: "What all this means is that characters controlled by identical genes are not necessarily homologous. … Therefore, homologous structures need not be controlled by identical genes, and homology of phenotypes does not imply similarity of genotypes."

[1418] Same as above. Pages 15-16.

[1419] Paper: "Mammalian phylogeny: Genes and supertrees." By Michael J. Novacek. Current Biology, July 24, 2001. Pages R573-R575. http://www.sciencedirect.com/science?...

Page R573:

A massive effort to sample mammals for genes has yielded new proposals for the branching architecture of the great radiation of placental mammals. Some of these are notably discrepant with morphologically based analyses….

… As their name implies, afrotherians putatively represent a radiation of placentals rooted in the African continent and nearby island of Madagascar. From a morphological standpoint, this aggregation is extremely provocative. …

… Acceptance of such groups as Afrotheria or Laurasiatheria would suggest a radical shakeout of the placental tree, in ways not anticipated by morphological work.

NOTE: This paper is chock full of relevant information and well worth reading in full. A few quotes cannot do justice to it.

[1420] Paper: "Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions." By Hidenori Nishihara, Masami Hasegawa & and Norihiro Okada. Proceedings of the National Academy of Sciences, June 27, 2006. Pages 9929-9934. http://www.pnas.org/content/103/26/9929.full

Page 9929 (referencing the paper in the citation above): "Comprehensive analyses of large collections of DNA sequences mostly reject the conclusions from morphological analyses…."

[1421] Book: Mammals from the Age of Dinosaurs: Origins, Evolution, and Structure. By Zofia Kielan-Jaworowska, Richard L. Cifelli, and Zhe-Xi Luo. Columbia University Press, 2004.

Page 12: "There are great differences between the molecular trees of modern mammal orders and those based on morphological data."

[1422] Article: "T. Rex Protein 'Confirms' Bird-Dinosaur Link." By Scott Norris. National Geographic News, April 24, 2008. http://news.nationalgeographic.com/news/2008/...

If molecular data become more widely available for dinosaurs, Asara noted, researchers will be able to fill in gaps and overcome possible errors in existing classification based on physical features.

To illustrate his point, he [John Asara of Harvard Medical School] noted that the shared ancestry of two present-day groups—elephants and shrew-like tenrecs—is known solely from DNA and protein comparisons.

"Nobody could make that connection based on bones," he noted.

[1423] Article: "Shaking the family tree." By Henry Gee. Nature News Service, February, 1 2001. http://www.nature.com/news/2001/010201/full/...

Biologists trying to reconstruct the evolutionary relationships of placental mammals using DNA and molecular evidence have often locked horns with scientists versed in the old-school approach, based on the careful study of bones, teeth and anatomy. At last, some resolution is emerging from the gunsmoke. The two independent reports now claim to provide robust answers to the question of the branching order in the family tree of placental mammals.

NOTE: These "independent reports" are not from the conflicting sides in this debate. Both reports are based upon genetic similarities, and as the author later admits, the results: "are unlikely to settle all debates immediately…."

[1424] Article: "Morphology." Encyclopædia Britannica Ultimate Reference Suite 2004.

This article explains what morphology entails, as does the citation above. 

[1425] Article: "Bats and horses get strangely chummy." New Scientist, June 25, 2006. http://www.newscientist.com/

NOTE: This article briefly summarizes the paper cited in the next citation, which contains so much technical verbiage that it is almost incomprehensible to laymen. The article states that

bats seem to be more closely related to horses than cows are. …

"I think this will be a surprise for many scientists," says Norihiro Okada at the Tokyo Institute of Technology, Japan. "No one expected this."

[1426] Paper: "Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions." By Hidenori Nishihara, Masami Hasegawa & and Norihiro Okada. Proceedings of the National Academy of Sciences, June 27, 2006. Pages 9929-9934. http://www.pnas.org/cgi/reprint/103/26/9929?...

Page 9933:

[W]e found an unexpected clade [evolutionary classification based on genetic similarities] comprising Chiroptera [bats], Perissodactyla [horses, zebras, donkeys, rhinos, etc.], Carnivora [ten families of meat eating mammals including dogs, bears, etc.] and Pholidota [scaly anteaters]. … We propose the name Pegasoferae for this clade, because Pegasus refers to the flying horse (Chiroptera + Perissodactyla) in Greek mythology and Ferae refers to the monophyletic clade of Carnivora + Pholidota.

[1427] Article: "Human, Sea Slug Brains Share Genes for Alzheimer's and Parkinson's." Scientific American, December 29, 2006. http://www.sciam.com/article.cfm?chanID=...

The ancestors of humans and sea slugs diverged more than a half billion years ago, but scientists have now unexpectedly found genes that are remarkably similar in the brains of both. …

Scientists had assumed that many genes present in humans and absent in worms and flies had evolved recently in our lineage… These new findings suggest modern animals had a common ancestor with a surprisingly complex genome, whose descendants subsequently kept or lost various genes.

[1428] Paper: "Neuronal Transcriptome of Aplysia: Neuronal Compartments and Circuitry." By Leonid L. Moroz and others. Cell, December 29, 2006. Pages 1453-67. http://linkinghub.elsevier.com/retrieve/pii/S0092867406015959

Page 1457: "Figure 3A also illustrates that the evolutionary distance from Aplysia [sea slug] to human is shorter than the distance from Drosophila [fruit fly] and C. elegans [roundworm] to human. … This analysis also showed a significantly shorter distance from humans to Aplysia than to both C. elegans and Drosophila."

Pages 1457-9:

In summary, information from the Aplysia transcriptome together with recent comparative data (Kusserow et al., 2005; Miller et al., 2005; Technau et al., 2005) support the idea that there was a common bilateran ancestor (Urbilateria) that had a complex genome. As a result, more derived genomes of insects and nematodes represent a substantial level of gene loss from an ancestral state as compared to slower evolved genomes within selected lophotrochozoan (e.g., molluscs, annelids) and deuterostome (vertebrates) lineages.

[1429] Paper: "Molecular convergence of NAR and unusual mammalian immunoglobulins." By Kenneth H. Roux and others. Proceedings Of The National Academy of Sciences, September 1998. Pages 11804–11809. http://www.pnas.org/content/95/20/11804

Page 11804:

We recently have identified an antigen receptor in sharks called NAR (new or nurse shark antigen receptor)…. Here we show by electron microscopy that NAR V regions, unlike those of conventional Ig [immunoglobulin] and TCR [T-cell receptors], do not form dimers but rather are independent, flexible domains. This unusual feature is analogous to bona fide camelid [a group of creatures that includes llamas] IgG [immunoglobulin G]. … These unusual characteristics shared by NAR and unconventional mammalian Ig are most likely the result of convergent evolution at the molecular level.

NOTE: In other words, there is an unusual immune system protein in nurse sharks that is very similar to one found in creatures such as llamas.

[1430] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 770: "Two [protein] sequences that come to resemble each other even though they are derived from entirely different ancestral sequences are said to be analogous."

[1431] Paper: "Mammalian phylogeny: Genes and supertrees." By Michael J. Novacek. Current Biology, July 24, 2001. Pages R573-R575. http://www.sciencedirect.com/science?...

Page R575: "Another problem with the more recent molecular analyses concerns the connections between data and the choice of method or assumption for the analysis. … [D]espite the congruence claimed in these papers, the results do show marked inconsistencies."

[1432] Abstract: "The phylogenetic position of the Clitellata and the Echiura - On the problematic assessment of absent characters." By G Purschke & others. Journal of Zoological Systematics & Evolutionary Research, September 2000. Pages 165-173. http://www.ingentaconnect.com/content/...

"Different phylogenetic assessments often result in contradictory phylogenetic hypotheses, in which the direction of evolutionary changes is diametrically opposed."

[1433] Paper: "Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions." By Hidenori Nishihara, Masami Hasegawa & and Norihiro Okada. Proceedings of the National Academy of Sciences, June 27, 2006. Pages 9929-9934. http://www.pnas.org/content/103/26/9929.full

Page 9933: "Although this clade [evolutionary classification based on genetic similarities], named Zooamata, is favored by recent molecular analyses of nuclear DNA, BP [bootstrap probability – a statistical method of interpreting genetic data] supports for the clade are relatively low in many cases."

[1434] Paper: "Where is the root of the universal tree of life?" By Patrick Forterre & Herve´ Philippe. BioEssays, October 21, 1999. Pages 871-879.

Page 871: "With more and more sequences available, in particular from rapidly expanding genome projects, it turned out that many protein phylogenies contradict the rRNA tree and also each other in terms of relationships between the three domains…."

[1435] Textbook: Foundations of Modern Cosmology. By John F. Hawley & Katherine A. Holcomb. Oxford University Press, 1998. Page 17.

[1436] Book: DNA and Your Body: What You Need to Know about Biotechnology. By Colin Masters. University of New South Wales Press, 2005. Page 51.

[1437] Article: "Human-Chimp Gene Gap Widens from Tally of Duplicate Genes." By JR Minkel. Scientific American, December 19, 2006. http://www.scientificamerican.com/article.cfm?...

[1438] Article: "Relative Differences: The Myth of 1%." By Jon Cohen. Science, June 29, 2007. http://www.sciencemag.org/cgi/content/short/316/5833/1836

Page 1886:

Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of "humanness" vs. "chimpness." "There isn't one single way to express the genetic distance between two complicated living organisms," Gagneux adds.

[1439] Same as above. The geneticist quoted is Svante Pääbo.

[1440] Paper: Rodent Monophyly: Pitfalls of Molecular Phylogenies. By Hervé Phillipe. Journal of Molecular Evolution, December, 1997. Pages 712-5. http://www.springerlink.com/content/1l5c766g0cptp6fv/

Page 712: "Thus the inclusion of three additional species in the analysis has changed an apparently well-supported conclusion into a still-unresolved question."

[1441] Book: History of the Coelacanth Fishes. By Peter L. Forey (Department of Palaeontology, Natural History Museum, London). Chapman & Hall, 1998.

Page 296: "Phylogenetic conclusions arrived at with different molecular data sets seem very susceptible to taxon sampling (as with some of the palaeontological studies)."

Page 368: "Analysis of molecular data leads to results that are highly conflicting and the different solutions often depend on particular taxon sampling."

[1442] Paper: "The rooting of the universal tree of life is not reliable." By By Hervé Phillipe & Patrick Forterre. Journal of Molecular Evolution, October, 1999. Pages 509-23. http://www.ncbi.nlm.nih.gov/pubmed/10486008

Page 509: "Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones."

[1443] Book: Cladistics: Perspectives on the Reconstruction of Evolutionary History. Edited by Thomas Duncan & Tod F. Stuessy. Columbia University Press, 1984. Chapter 4: "The Concept of Homology and Its Central Role in the Elucidation of Plant Systematic Relationships." By Donald R. Kaplan. Page 52.

[1444] Book: Homology: The Hierarchical Basis of Comparative Biology. Edited by Brian K. Hall. Academic Press, 1994. Chapter 1: "Richard Owen and the Concept of Homology." By Alec L. Panchen. Pages 55-6.

[1445] Book: Cladistics: Perspectives on the Reconstruction of Evolutionary History. Edited by Thomas Duncan & Tod F. Stuessy. Columbia University Press, 1984. Chapter 5: "Problems in the Determination of Evolutionary Directionality of Character-State Change for Phylogenetic Reconstruction." By Tod F. Stuessy & Jorge V. Crisci. Page 84:

From a general perspective, no aspect of cladistic [homology-based] analysis should be free from careful and thoughtful interpretation, and there are no easy answers or simple solutions. We have no true phylogenies [evolutionary histories], nor will we ever have them.

NOTE: As the definitions for "cladistics" in the next two notes show, there are some nuances in the meaning of this word, but in the context of this quote, the phrase "homology-based" is an appropriate synonym.

[1446] Entry: "cladistics." Oxford Dictionary of Biochemistry and Molecular Biology. Oxford University Press, 1997.

Page 119: "The term cladistics is currently used to describe an evolutionary or phylogenetic tree based on gene sequence similarities and gene association."

[1447] Book: Palaeobiology: A Synthesis. Edited by Derek E. G. Briggs & Peter R. Crowther. Blackwell Scientific Publications, 1990. Section 5.2.2: "Analysis of Taxonomy and Phylogeny: Cladistics." By P. L. Forey (Department of Palaeontology, The Natural History Museum, London).

Page 430: "Cladistics is a method of biological classification which, in its purest form, seeks to group taxa into different sets and subsets based on the most parsimonious distribution of characters. … Sister-groups are discovered by finding shared derived characters (synapomorphies) inferred to have originated in the latest common ancestor."

[1448] Genesis 1:26: "And God said, Let us make man in our image...."

[1449] The terms homeobox and Hox are sometimes used interchangeably and sometimes not. For example:

a) Book: Human Molecular Biology: An Introduction to the Molecular Basis of Health and Disease. By Richard J. Epstein. Cambridge University Press, 2003. Page 401: "Homeobox (Hox) gene are ancient genes that specify cell fate in the antero-posterior embryonic axis and thus determine body plan."

b) Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999. Page 35: "The abbreviation Hox is still used to designate the regulatory genes that are involved in the development of segmentation and segmented structures, but the term homeobox gene now covers the entire gamut of regulatory genes that are fundamental to an organism's development."

c) Article: "15 Answers to Creationist Nonsense." By John Rennie. Scientific American, June 18, 2002. Pages 78-85. http://www.scientificamerican.com/article.cfm?id=...

"Mutations that arise in the homeobox (Hox) family of development-regulating genes in animals can also have complex effects."

[1450] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 653.

[1451] Book: Master Control Genes in Development and Evolution: The Homeobox Story. By Walter J. Gehring. Yale University Press, 1998.

Page 128: "These [fly] experiments … showed conclusively that Antennapedia is a master control gene for leg morphogenesis. Turning on a single master control switch activates the leg developmental pathway, which involves several hundred or thousand genes."

[1452] Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999.

[1453] Book: Endless Forms Most Beautiful. By Sean B. Carroll. W. W. Norton & Company, 2005.

[1454] Same as above. Page 164: "Evo Devo … suggests that the last common ancestor of the two main branches of the animal tree [protostomes and deuterostomes] was fairly complex, genetically and anatomically, in spite of its paleontologically cryptic existence in the Precambrian. Second, we know for certain that the full genetic tool kit for body building was in place…."

NOTE: The main constituent of the "genetic toolkit" referred to in this book is Hox genes.

[1455] "International Stratigraphic Chart." International Commission on Stratigraphy, 2007. http://www.stratigraphy.org/

According to this chart, the Precambrian ended 542 million years ago.

[1456] Paper: "Hox genes are not always Colinear." By Ana Sara Monteiro & David E.K. Ferrier. International Journal of Biological Sciences, May 5, 2006. Pages 95-103. http://www.ncbi.nlm.nih.gov/pubmed/16763668

Page 95: "If we can discern what the homologous features of Hox cluster organisation, function and regulation are across the animal kingdom, then we can discover how these genes were arranged and were operating in an organism that lived more than 525 Million Years Ago, from which all subsequent animal lineages diverged."

[1457] Book: Oxygen: The Molecule That Made the World. By Nick Lane. Oxford University Press, 2002.

Page 59: "Why are the Hox genes so similar in different species? The fact that animal groups were already distinct in the Cambrian (such as the arthropods and chordates) share very similar Hox genes implies that all inherited them from a common Precambrian ancestor."

[1458] Book: Endless Forms Most Beautiful. By Sean B. Carroll. W. W. Norton & Company, 2005. Pages 63-65:

Somewhere, we had seen a structure like the homeodomain [this fly Hox gene] before….

The lac repressor. And not only the lac repressor, but a whole catalog of DNA-biding proteins that bind to genetic switches in bacteria and yeast.

Bingo.

… This was great news but the skeptics would say we've moved from a tiny bacterium to a tiny fly. … They purified DNA from all sorts of critters … including various bugs, earthworms, frogs, cows, and humans, and went looking for themselves.

Jackpot.

When the sequences of these homeoboxes were examined in detail, the similarities among the species were astounding. … These Hox genes were so important that their sequences had been preserved throughout this enormous span of animal evolution. … The implications were stunning. Disparate animals were built using not just the same kinds of tools, but indeed, the very same genes!

[1459] Paper: "Dispersal of NK homeobox gene clusters in amphioxus and humans." By Graham N. Luke and others. Proceedings of the National Academy of Sciences, April 29, 2003. Pages 5292-5. http://www.pnas.org/content/100/9/5292.full.pdf

NOTE: See figure 1 on page 5293, which compares five similar Hox genes in amphioxus (a small sea creature with no eyes or brain), Drosophila melanogaster (fruit fly), and humans. The genes that begin with "Amphi" are from amphioxus, the fly genes are labeled as such, and all the genes beneath these are human. There are differences in every case.

[1460] Paper: "Hox cluster duplications and the opportunity for evolutionary novelties." By Gunte P. Wagner & others. Proceedings of the National Academy of Sciences, December 9, 2003. Pages 14603–6. http://www.pnas.org/content/100/25/14603.full.pdf+html

Page 14603: "Since their discovery, Hox genes, a family of linked transcription-factor genes sharing a DNA-binding domain (the homeobox) (1), have confronted biologists with surprising riddles. The first so-called Hox paradox was the discovery that homologous genes "code" for fundamentally different body plans."

[1461] Paper: "Molecular evolution of the HoxA cluster in the three major gnathostome lineages." By Chi-hua Chiu & others. Proceedings of the National Academy of Sciences, April 16, 2002. Pages 5492-7. http://www.pnas.org/content/99/8/5492.full.pdf+html

Page 5495:

First, the single HoxA clusters of two distantly related taxa, the horn shark and human, are remarkably conserved in architecture and putatively functional cis-regulatory sequences. Second, the HoxAa and HoxAb clusters of zebrafish exhibit striking modifications of these conserved structural and putative regulatory features, most likely the outcome of HoxA cluster duplication. In fact, Hox cluster duplication and retention of duplicates in a lineage have played a prominent, although relatively little understood, role in the evolution of chordates.

Page 5496:

Nevertheless, our results are intriguing, because despite the fact that human and horn shark diverged from one another more than 400 million years ago and have considerable differences in morphology, selection acting on the HoxA clusters has been strong enough to maintain their remarkable conservation in putatively functional cis-regulatory sequences in the absence of a cluster duplication. Yet, after HoxA cluster duplication in the zebrafish, radical remodeling of cis sequences occurred even when only one gene is retained to perform these functions. Interestingly, some of the cis elements conserved in human and horn shark and absent in zebrafish are retained in the striped bass and vice versa (Table 1).

[1462] Paper: "Neuronal Transcriptome of Aplysia: Neuronal Compartments and Circuitry." By Leonid L. Moroz and others. Cell, December 29, 2006. Pages 1453-67. http://linkinghub.elsevier.com/retrieve/pii/S0092867406015959

Page 1456: "This tripartite classification, initially based on analysis of rRNAs and selected HOX genes (de Rosa et al., 1999; Halanych, 2004; Passamaneck et al., 2004), has now been challenged by recent molecular studies (Philip et al., 2005; Rokas et al., 2005; Wolf et al., 2004) and by data from developmental biology (Nielsen, 2001, 2005)."

[1463] Paper: "Homology and Hominid Phylogeny - Problems and Potential Solutions." By Daniel E. Lieberman. Evolutionary Anthropology, February 5, 1999. Pages 142-51. http://www.fas.harvard.edu/~skeleton/pdfs/1999a.pdf

Page 146:

Developmental approaches to homology, however, are not without their problems. Most importantly, it is well established that similar developmental signals can lead to contrasting morphological features. For example, the Hox cluster of regulatory genes gives rise to the anterior neural chord in primitive chordates (Amphioxus) but to the rhombencephalon portion of the brain in vertebrates. In addition, homologous genes in vertebrates and invertebrates that initiate eye morphogenesis can lead to the growth of eyes that are vastly different both structurally and developmentally. Such phenomena occur because divergent lineages frequently make use of commonly inherited genes in novel ways.

[1464] Paper: "Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes." By Austin L. Hughes & others. Genome Research, May 2001. Pages 771-80.

Page 774: "Even among gene duplications likely to have occurred around the same time as the Hox duplications, phylogenetic analyses revealed inconsistencies among their phylogenies and between their phylogenies and the Hox phylogeny."

[1465] Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999. Pages 361-362.

[1466] Book: Master Control Genes in Development and Evolution: The Homeobox Story. By Walter J. Gehring. Yale University Press, 1998.

Page 128: "These [fly] experiments … showed conclusively that Antennapedia is a master control gene for leg morphogenesis. Turning on a single master control switch activates the leg developmental pathway, which involves several hundred or thousand genes."

[1467] Book: The Adapted Mind. Edited by Jerome H. Barkow, Leda Cosmides, John Tooby. Oxford University Press, 1992. Chapter 1: "The Psychological Foundations of Culture." By John Tooby & Leda Cosmides.

Page 79: "Complex adaptations are intricate machines that require complex "blueprints" at the genetic level. This means that they require coordinated gene expression, involving hundreds or thousands of genes to regulate their development."

[1468] Book: The Johns Hopkins Atlas of Human Functional Anatomy. Edited by George D. Zuidema. Fourth Edition. Johns Hopkins University Press, 1997. Chapter 12: "The Eye and the Mechanism of Vision." By Charles E. Iliff. Pages 61-4.

NOTE: These parts include the optic foramen, sclera, annulus of Zinn, trochlea, oblique muscles, lacrimal fossa, lacrimal gland, lacrimal ducts, Meibomian glands, glands of Moll, lacrimal sacs, optic nerve, oculomotor nerve, infraorbital nerve, levator muscles, ciliary ganglion, constrictor muscle of the iris, trigeminal nerve, sphincter and dilator muscles of the pupil, cornea, aqueous humor, iris, crystalline lens, ciliary muscle, zonules, ciliary body, trabecular meshwork, Schlemm's canal, choroid, retina (which is itself composed of many different components), ophthalmic artery and vein, central retinal artery, vitreous, tarsi, orbicularis muscles, recti muscles, Muller's muscle, fontalis muscle, Tenon's capsule, levator tendon, Whitnall's ligament, supraorbital nerve, lateral palpebral ligament, conjunctiva.

[1469] Book: Sudden Origins: Fossils, Genes, and the Emergence of Species. By Jeffrey H. Schwartz. John Wiley & Sons, 1999. Page 353.

[1470] I read from an average of 10-15 different news publications on a daily basis, and my assertion that these groups represent the mainstream is based upon the press coverage I have seen, the staff size of these organizations, the amount of their scholarly output, and other variables such as the fact that Answers In Genesis recently opened the doors on a 60,000 square foot creation museum.

[1471] Web page: "What we believe." Creation Ministries International. Accessed May 1, 2009 at http://creation.com/what-we-believe

"The account of origins presented in Genesis is a simple but factual presentation of actual events and therefore provides a reliable framework for scientific research into the question of the origin and history of life, mankind, the Earth and the universe."

[1472] Web Page: "About Answers in Genesis." Accessed May 1, 2009 at http://www.answersingenesis.org/home/area/about.asp

"The Bible—the "history book of the universe"—provides a reliable, eye-witness account of the beginning of all things, and can be trusted to tell the truth in all areas it touches on."

[1473] Web page: "CRS Statement of Belief." Accessed May 1, 2009 at http://www.creationresearch.org/stmnt_of_belief.htm

"The Bible is the written Word of God, and because it is inspired throughout, all its assertions are historically and scientifically true in the original autographs. To the student of nature this means that the account of origins in Genesis is a factual presentation of simple historical truths."

[1474] Web page: "Top Questions." Discovery Institute. Accessed May 1, 2009 at http://www.discovery.org/csc/topQuestions.php#...

The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

Is intelligent design theory incompatible with evolution?

It depends on what one means by the word "evolution." If one simply means "change over time," or even that living things are related by common ancestry, then there is no inherent conflict between evolutionary theory and intelligent design theory. However, the dominant theory of evolution today is neo-Darwinism, which contends that evolution is driven by natural selection acting on random mutations, an unpredictable and purposeless process that "has no discernable direction or goal, including survival of a species." (NABT Statement on Teaching Evolution). It is this specific claim made by neo-Darwinism that intelligent design theory directly challenges. …

… Unlike creationism, the scientific theory of intelligent design is agnostic regarding the source of design and has no commitment to defending Genesis, the Bible or any other sacred text. …

… Intelligent design theory then is an alternative solution to answer problems with Darwinian evolution.

[1475] Article: "15 Answers to Creationist Nonsense." By John Rennie. Scientific American, June 18, 2002. Pages 78-85. http://www.scientificamerican.com/article.cfm?id=...

"On the contrary, biology has catalogued many traits produced by point mutations (changes at precise positions in an organism's DNA)--bacterial resistance to antibiotics, for example."

NOTES:

This article knocks down this straw man with two other illustrations, one of which has already been explicitly debunked (fly legs on head), and the other is debunked in a general sense through the previous discussion of homology and the forthcoming summary of this section on genetics.

For a refutation of this article, see the article: "15 ways to refute materialistic bigotry: A point by point response to Scientific American." By Jonathan Sarfati (Ph.D. in Physical Chemistry). Creation Ministries International, June 20, 2002. http://creation.com/15-ways-to-refute-materialistic-bigotry

[1476] On, July 27, 2007, I inputted the phrase, "mutations can only eliminate traits" into Google.com and came up with 33 results, most of then quoting from Rennie and absolutely none of them out of the mouth of a creationist. The same applies to the other claim that mutations "cannot produce new features."

[1477] Article: "Love Affairs and Supergerms." By Robert Doolan. Creation, December 1994. http://creation.com/love-affairs-and-supergerms

"The occasional case in which a mutation causes such resistance to arise does not prove microbe-to-man evolution. Mutations do not give a microbe more information to build itself into something else."

NOTE: This is only one of many creationist writings predating Rennie's article that essentially assert the same thing.

[1478] Article: "The Evolution of Ken Miller." By Linda Heuman. Brown Alumni Monthly, November/December 2005. http://www.brownalumnimagazine.com/

[1479] Book: Finding Darwin's God. By Kenneth R. Miller. Cliff Street Books, 1999. Page 49.

Also see page 107: "Incredibly, the critics of evolution continue to claim that the mechanism of evolution is unknown, that mutations are never beneficial, and therefore that the hand of design is the only way to explain adaptations of organisms to their environment."

[1480] Article: "Darwin Under the Microscope." By Michael J. Behe. New York Times, October 29, 1996. Page A2. http://www.nytimes.com/

[1481] Article: "The Evolution of Ken Miller." By Linda Heuman. Brown Alumni Monthly, November/December 2005. http://www.brownalumnimagazine.com/

[1482] Article: "Genetics: no friend of evolution." By Lane Lester. Creation, March 1998. http://www.answersingenesis.org/creation/v20/i2/genetics.asp

[1483] This magazine has been in print for 30 years and according to its publisher, Creation Ministries International (http://creation.com/), it is currently "the world's most-read creation publication." I have seen this magazine cited in many venues and have little doubt this is the case.

[1484] Creation Research Society Quarterly. http://www.creationresearch.org/crsq.html

[1485] Book: Finding Darwin's God. By Kenneth R. Miller. Cliff Street Books, 1999.

Page 126: "To the anti-evolutionist, when new species appear in the fossil record, it is not as the modified descendant of ancestral species. It must be the product of design."

Page 98: [With regards to elephants:] "The classic branching of this lineage is a typical evolutionary pattern. Intelligent design, however, regards the appearance of each new species as the result of an individual act on the part of a designer."

Page 100:

There are approximately 10,000 living species of mammals. If the rate of new elephant species is an indication, we might expect one new mammalian species to have popped up every twenty-three years or so. As rapid as this seems, these thousands of mammals are dwarfed by literally millions of insect species. To produce all those insects, the designer must have been even busier—that puff of smoke might have been a weekly occurrence. … Like it or not, intelligent design requires us to believe that the past was a time of magic in which species appeared out of nothing. That magic began at the dawn of life on this planet, and continued unabated for more than a billion years, bringing a grand parade of living things into existence.

[1486] Article: "Genetics: no friend of evolution." By Lane Lester. Creation, March 1998. http://www.answersingenesis.org/creation/v20/i2/genetics.asp

[1487] Article: "Darwin Under the Microscope." By Michael J. Behe. New York Times, October 29, 1996. Page A2. http://www.nytimes.com/

[1488] Article: "On the Importance of Being Ernst Mayr." By Axel Meyer. PLoS [Public Library of Science] Biology, April 5, 2005. http://biology.plosjournals.org/perlserv?request=...

"Perhaps his most widely known contribution is to the current notion of what constitutes a species. … Students of biology all over the world have memorized Mayr's definition of species for more than half a century."

[1489] Book: What Evolution Is. By Ernst Mayr. Basic Books, 2001. Page 163.

[1490] Book: A Neotropical Companion: An Introduction to the Animals, Plants, and Ecosystems of the New World Tropics. By John C. Kricher. Second edition. Princeton University Press, 1999. Page 106:

A biological species is traditionally defined as an actually or potentially inbreeding population, reproductively isolated from other such populations (Mayr 1963). The key to identifying a species therefore rests on the fact of reproductive isolation. … Other species concepts, not based on the establishment of reproductive isolation, have been proposed in recent years because it is often difficult or impossible to know with certainty if separated populations are capable of interbreeding (Zink and McKitrick 1994)… Nonetheless, the biological species concept, focused as it is on the presumption of reproductive isolation, is still the most widely used species definition, and it is the one that will be used here.

[1491] Textbook: Principles of Genetics. By D. Peter Snustad, Michael J. Simmons & John B. Jenkins. John Wiley & Sons, 1997.

Page 780 uses essentially the same definition as the citation above.

[1492] Book: Palaeobiology: A Synthesis. Edited by Derek E. G. Briggs & Peter R. Crowther. Blackwell Scientific Publications, 1990. Section 2.2 "Speciation." By B. Charlesworth (Department of Ecology and Evolution, University of Chicago).

Page 100 uses essentially the same definition as the two citations above.

[1493] Book: Animal Species and Evolution. By Ernst Mayr. The Belknap Press of Harvard University Press, 1963. Page 90:

In spite of everything that has been written in the last 25 years there are still some authors who seem to think that reproductive isolation and sterility are synonymous terms. Nothing could be further from the truth. An ever-increasing number of very distinct, reproductively isolated sympatric species are known that are not isolated from each other by a sterility barrier. …High, if not complete, fertility is known for many species crosses, not only among ducks and other families of birds, but throughout the animal kingdom.

[1494] Article: "Evolution: Five big questions." New Scientist, June 14, 2003. Question 3: "How are new species formed?" By George Turner. http://www.newscientist.com/article/mg...

[1495] Article: "How did all the animals fit on Noah's Ark?" By Jonathan Sarfati. Creation, March 1997. http://www.answersingenesis.org/creation/v19/i2/animals.asp

"We know that tigers and lions can produce hybrids called tigons and ligers, so it is likely that they are descended from the same original kind."

[1496] Article: "'Lost world' animals—found! Cave drawings brought to life by exciting new discoveries." By Carl Wieland. Creation, December 1996. http://www.creationontheweb.com/content/view/656/

Most creationists would suggest that there was probably only one 'elephant kind' on the Ark, which would have been the ancestor of all living elephants, such as the Asian and the Indian, as well as those which have died out since that time, such as the mammoth, the mastodon, and the stegodon.⁵ Similarly, one 'kind' was likely ancestral to the various types of horses, zebras and asses.

Note 5:

This is not evolution, which would require new genetic information to be added through time. It is instead a 'downhill' process which actually involves a thinning out of genetic information into more depleted, but more specialised sub-groups. … It is also possible that chromosomal translocations may have, again without adding any new information, contributed to the development of genetic [breeding] barriers between such daughter groups/species. Also, different mate recognition systems in varieties can cause them to be classified as separate species, although interbreeding is possible in artificial conditions.

[1497] Correspondence: "A View from Kansas on that evolution debate." By Scott C. Todd (Department of Biology, Kansas State University.) Nature, September 30, 1999.

Page 423: "Mainstream creationists also accept that genetic and phenotypic changes could result in speciation." 

[1498] Articles: "Vinegar fly," "Cricket," "Ladybird beetle." Encyclopædia Britannica Ultimate Reference Suite 2004.

[1499] Book: Galileo's Finger: The Ten Great Ideas of Science. By Peter Atkins. Oxford University Press, 2003.

NOTE: Pages 10-13 provide a good overview of different evolutionary ideas as to what constitutes a species. However, one point of clarification is needed. Page 11 states that the fruit fly species D. pseudoobscura and D. persimilis "do not interbreed." It should be noted that these species can produce offspring, but the males are sterile and the females "have severely reduced fertility."* As shown in citation 1495, because these species of fruit flies can produce offspring, creationists generally consider them to be "descended from the same original kind." Furthermore, as shown in citation 1496, creationists do not generally subscribe to the view that a lack of the ability to produce offspring means creatures are descended from different original kinds.

* Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition. Page 764.

[1500] Book: What Evolution Is. By Ernst Mayr. Basic Books, 2001.

Page 166: "Almost 50 percent of the North American species of crickets were discovered only by their different songs, they are that similar to each other."

[1501] Article: "Evolution and Its Discontents." By Kenneth Chang. New York Times, November 15, 2005. http://query.nytimes.com/gst/fullpage.html?res=...

"Most biologists do not make the distinction between microevolution and macroevolution; the larger changes are simply the accumulation of small changes."

[1502] Book: Palaeobiology: A Synthesis. Edited by Derek E. G. Briggs & Peter R. Crowther. Blackwell Scientific Publications, 1990. Section 2.6: "Hierarchy and Macroevolution." By N. Eldredge (Department of Invertebrates, American Museum of Natural History).

Page 124: "It is the general position of the synthesis that 'macroevolution' is simply microevolution summed up over geological time."

Page 125 states that some palaeontologists disagree with this position.

[1503] Article: "Bateson, William." Encyclopædia Britannica Ultimate Reference Suite 2004.

This article refers to Bateson as a "dedicated Darwinist" and explains that he did a great deal to educate scientists about the discipline of genetics.

[1504] Book: Movers And Shakers: A Chronology of Words That Shaped Our Age. By John Ayto. Oxford University Press, 2006. Page 18:

1906 William Bateson: "The best title would, I think, be the 'Quick Professorship of the study of Heredity'. No single word in common use quite gives this meaning … and if it were desirable to coin one, 'Genetics' might do."

[1505] Book: The Encyclopedia of Genetic Disorders and Birth Defects. By James Wynbrandt & Mark D. Ludman. Facts on File, 1991. Page xv:

Bateson also introduced the term "genetics" in 1906, formally proposing to the scientific community that the term be used for the study of heredity and variation. (It first appears in a 1905 letter of his; however, the term "cytogenetics" has been dated to 1903, used by American Walter S. Sutton in a paper, "The Chromosomes in Heredity" published in the Biological Bulletin.)

[1506] Book: Practical Genetics for Dog Breeders. By Malcolm B. Willis (PhD in Genetics and Animal Breeding from the University of Edinburgh and Senior Lecturer in these disciplines at Newcastle University, Newcastle upon Tyne, United Kingdom).

Page 21: "In 1901 the English scientist William Bateson showed that Mendelian principles applied to chickens as well as plants…."

[1507] Textbook: Principles of Genetics. By D. Peter Snustad & Michael J. Simmons. John Wiley & Sons, 2006. Fourth edition.

Page 65: "Bateson's book played a crucial role in spreading the principles of Mendelism to the scientific world."

[1508] Book: Mendel's Principles of Heredity. By William Bateson. Cambridge University Press, 1909. Page 280.

NOTE: This quote also appears in the third edition of this book, which was published in 1930.

[1509] Entry: "Harold, Franklin Marcel." American Men and Women of Science. Edited by Pamela M. Kalte and Katherine H. Nemeh. Gale, 2003. Volume 3.

Page 508 reviews Dr. Harold's background and notes he earned a Ph.D. in biochemistry from the University of California.

[1510] Web page: "Creative Retirement Institute Instructors." Accessed May 2006 at http://cri.edcc.edu/

"Dr. Frank Harold is a basic scientist with 40 years of experience in research on cell biology and microbiology. He holds a Ph.D. in biochemistry and is Professor Emeritus at Colorado State University. He has authored two books and many papers on science."

[1511] Book: The Way of the Cell. By Franklin M. Harold. Oxford University Press, 2001. Page 205.

[1512] Article: "Study, in a First, Explains Evolution's Molecular Advance." By Kenneth Chang. New York Times, April 7, 2006. Page A21. http://www.nytimes.com/2006/04/07/...

"By reconstructing ancient genes from long-extinct animals, scientists have for the first time demonstrated the step-by-step progression of how evolution created a new piece of molecular machinery by reusing and modifying existing parts."

[1513] For example, the article:

"Evolution and Its Discontents." By Kenneth Chang. New York Times, November 15, 2005. http://query.nytimes.com/gst/fullpage.html?res=...

"Most biologists do not make the distinction between microevolution and macroevolution; the larger changes are simply the accumulation of small changes. Most also say that the issue is not controversial and that there is much experimental evidence to indicate that such changes have occurred."

[1514] Article: "Why Only One Big Bang?" By Geoffrey Burbidge. Scientific American, February 1992. Page 120:

Those of us who have been around long enough know that peer reviews and the refereeing of papers have become a form of censorship. It is extraordinarily difficult to get financial support or viewing time on a telescope unless one writes a proposal that follows the party line. … The same attitude applies to academic positions. I would wager than no young researcher would be willing to jeopardize his or her scientific career by writing an essay such as this.

[1515] Report: "Intolerance And The Politicization Of Science At The Smithsonian." United States House Of Representatives, Committee On Government Reform, December 2006. http://www.souder.house.gov/_files/Intolerance...

NOTE: There is much in this report that is instructive. A few pertinent extracts are shown below.

Page 8:

Dr. Richard Sternberg is an evolutionary biologist who holds two Ph.D.s in biology, one in molecular evolution and the other in theoretical biology. Dr. Sternberg has authored more than 30 refereed scientific publications. He is a staff scientist with the National Center for Biotechnology Information at the National Institutes of Health as well as a Research Associate at the Smithsonian Institution's National Museum of Natural History. From 2001-2004 Dr. Sternberg was managing editor of the Proceedings of the Biological Society of Washington, a peer-reviewed biology journal published by the Biological Society of Washington.

Page 4:

In emails exchanged during August and September 2004, NMNH officials revealed their intent to use their government jobs to discriminate against scientists based on their outside activities regarding evolution. For example, Dr. Hans Sues, Associate Director for Research and Collections, suggested in emails on August 30, 2004, and again on September 9, 2004, that Dr. Sternberg would never have been appointed as an RA [Research Associate] if Smithsonian officials had known about his non-governmental activities regarding evolution. Sues even blamed the scientist who nominated Sternberg as a Research Associate for not adequately investigating his background: "Sternberg is a well-established figure in anti-evolution circles, and a simple Google search would have exposed these connections." The clear implication was that had a background check been conducted on Sternberg's non-governmental activities, he would have been barred from being a Research Associate.

[1516] Article: "Believing Scripture but Playing by Science's Rules. By Cornelia Dean. New York Times, February 12, 2007. http://www.nytimes.com/2007/02/12/science/...

Michael L. Dini, a professor of biology education at Texas Tech University, goes even further. In 2003, he was threatened with a federal investigation when students complained that he would not write letters of recommendation for graduate study for anyone who would not offer "a scientific answer" to questions about how the human species originated. Nothing came of it, Dr. Dini said in an interview….

NOTE: This is an unrevealing and inaccurate depiction of the facts of this case, as the next two notes document. First, Professor Dini had a statement on his website demanding that his students personally affirm they believe in evolution in order to get a letter of recommendation from him. Second, something did come of it. Professor Dini completely changed the thrust of his written policy.

[1517] Press Release: "Justice Department Closes Religious Discrimination Inquiry At Texas Tech University." United States Department of Justice, April 22, 2003. http://www.usdoj.gov/opa/pr/2003/April/03_crt_247.htm

The Justice Department today announced that it was closing its inquiry into complaints by Texas Tech students that a biology professor's medical school recommendation policy, which required affirmation of a personal belief in evolution, constituted religious discrimination. The decision was based on the professor's replacement of the affirmation requirement with a requirement that students simply be able to explain the scientific theory of evolution.

The Justice Department received complaints alleging that Professor Michael Dini had discriminated, based on religion, against several students through his written recommendation policy. The policy, set forth on a Texas Tech website, stated that to receive a medical school recommendation, the student had to meet three criteria. These were to get an "A" grade in one of Professor Dini's courses, get to know him personally through working as a teaching assistant or extracurricular activities, and "truthfully and forthrightly affirm a scientific answer" to the question: "How do you think the human species originated?"

In response to complaints by students, the Justice Department requested information about the school's policies regarding letters of recommendation. Professor Dini subsequently changed the third criteria on the website, dropping the requirement that students affirm a personal belief in evolution. Instead, he now requires them to be able to explain the scientific theory of evolution. In light of this change, the Department of Justice has closed its inquiry into the matter.

[1518] Here is a pertinent excerpt of the statement Professor Dini had posted on his website:  

If you set up an appointment to discuss the writing of a letter of recommendation, I will ask you: "How do you think the human species originated?" If you cannot truthfully and forthrightly affirm a scientific answer to this question, then you should not seek my recommendation for admittance to further education in the biomedical sciences. … If modern medicine is based on the method of science, then how can someone who denies the theory of evolution -- the very pinnacle of modern biological science -- ask to be recommended into a scientific profession by a professional scientist?

NOTE: The full text of this statement used to be posted at Professor Dini's website at http://www.ee.ttu.edu/dallas/dini.htm, but the URL is no longer valid. To the best of my knowledge, the full text is only now available on a few creationist web pages such as http://www.scienceagainstevolution.org/v7i5n.htm

[1519] Paper: "Evolution of Hormone-Receptor Complexity by Molecular Exploitation." By Jamie T. Bridgham and others. Science, April 7, 2006. http://www.sciencemag.org/cgi/content/abstract/312/5770/97

[1520] Web page: "The Lamest Attempt Yet to Answer the Challenge Irreducible Complexity Poses for Darwinian Evolution." By Michael Behe. April 6, 2006. http://www.arn.org/docs/behe/mb_lamestattempt.htm

[1521] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Chapter 6: "Difficulties on Theory":

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated; but I may remark that several facts make me suspect that any sensitive nerve may be rendered sensitive to light, and likewise to those coarser vibrations of the air which produce sound.

In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition. Amongst existing Vertebrata, we find but a small amount of gradation in the structure of the eye, and from fossil species we can learn nothing on this head. In this great class we should probably have to descend far beneath the lowest known fossiliferous stratum to discover the earlier stages, by which the eye has been perfected.

In the Articulata we can commence a series with an optic nerve merely coated with pigment, and without any other mechanism; and from this low stage, numerous gradations of structure, branching off in two fundamentally different lines, can be shown to exist, until we reach a moderately high stage of perfection. In certain crustaceans, for instance, there is a double cornea, the inner one divided into facets, within each of which there is a lens shaped swelling. In other crustaceans the transparent cones which are coated by pigment, and which properly act only by excluding lateral pencils of light, are convex at their upper ends and must act by convergence; and at their lower ends there seems to be an imperfect vitreous substance. With these facts, here far too briefly and imperfectly given, which show that there is much graduated diversity in the eyes of living crustaceans, and bearing in mind how small the number of living animals is in proportion to those which have become extinct, I can see no very great difficulty (not more than in the case of many other structures) in believing that natural selection has converted the simple apparatus of an optic nerve merely coated with pigment and invested by transparent membrane, into an optical instrument as perfect as is possessed by any member of the great Articulate class.

He who will go thus far, if he find on finishing this treatise that large bodies of facts, otherwise inexplicable, can be explained by the theory of descent, ought not to hesitate to go further, and to admit that a structure even as perfect as the eye of an eagle might be formed by natural selection, although in this case he does not know any of the transitional grades. His reason ought to conquer his imagination; though I have felt the difficulty far too keenly to be surprised at any degree of hesitation in extending the principle of natural selection to such startling lengths.

[1522] Book: The Life and Letters of Charles Darwin. Edited by Francis Darwin (his son). Volume 2. John Murray, 1888. Reprinted in 1969 by Johnson Reprint.

Page 272: "Well, what seems to me the weakest point of the book is the attempt to account for the formation of organs, the making of eyes &c. by natural selection. Some of this reads quite Lamarckian. … I never learnt so much from one book as I have from yours."

NOTE: Darwin's response appears on pages 272-273.

[1523] Article: "Gray, Asa." Encyclopædia Britannica Ultimate Reference Suite 2004.

"American botanist…. [O]ne of the few persons whom Darwin kept fully informed concerning the publication of his Origin of Species."

[1524] Textbook: Principles of Genetics. By D. Peter Snustad, Michael J. Simmons & John B. Jenkins. John Wiley & Sons, 1997. Epilogue: Genetics Yesterday, Today, and Tomorrow - A Personal View. By James F. Crow.

Page 764: "Genetics is a new science.… The subject is unusual in that its origin can be pinpointed to a single event, the publication of Gregor Mendel's paper in 1866. … This paper languished in obscurity until 1900, when it was rediscovered by three botanists…."

[1525] Paper: Experiments in Plant Hybridisation. By Gregor Mendel. Verhandlungen des Naturforschenden in Brünn, 1865 (appeared in 1866). In English translation with commentary by Ronald A. Fisher. Oliver & Boyd, 1965.

NOTE: This is Mendel's original paper.

[1526] Book: Mendel's Principles of Heredity. By William Bateson. Cambridge University Press, 1930. Pages 332-3:

The fact that the Brünn journal is rather scarce does not in itself explain why the work [Mendel's paper] was not noticed. Such a circumstance has seldom long delayed general recognition. The cause is unquestionably to be found in that neglect of the experimental study of the problem of Species which supervened on the general acceptance of the Darwinian doctrines. … The question, it was imagined, had been answered and the debate ended.

[1527] Book: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. By Charles Darwin. John Murray, 1859. http://www.literature.org/authors/darwin-charles/the-origin-of-species/

Glossary: "PROTOZOA - The lowest great division of the Animal Kingdom. These animals are composed of a gelatinous material, and show scarcely any trace of distinct organs."

NOTE: As was shown on pages 159-169 of Rational Conclusions, nothing could be further from the truth.

[1528] See citation 1521.