Anthony Griffiths (University of British Columbia, Vancouver) places more emphasis on core principles than on specific applications: “The goal is to show how genetic inference is made ... hence overall the emphasis is more on process than the discoveries.”That's right. A textbook should emphasize concepts and principles and not facts. The goal is to show students how all of the knowledge we have fits into a coherent picture of the subject. Genetics, like all sciences, is based on models that represent the consensus view of the scientists in the field. It's important for students to see that these models are internally consistent and compatible with biology and biochemistry and all other sciences. It's important that students realize that there may be some controversy in the discipline but that they need to learn how to sort it out.
[Scott] Hawley also places a heavy emphasis on core topics, because he “factor[s] in heavily the concept that so-called facts can be pretty ephemeral in science.” As Hawley explains, “Many of the ‘facts’ I was taught in college are either irrelevant now or wrong. For example, I heard many lectures as an undergrad asserting that a huge part of the genome was useless ‘junk’. We no longer look at things that way.”I'm looking forward to seeing the next edition of The Human Genome by Julia Richards and Scott Hawley. It will be interesting to see what principles and concepts they advance to explain the absence of junk in our genome.
Thanks to a friend who alerted me to the article in The GSA Reporter.
According to Bill Dembski, "The 2nd Law of Thermodynamics has never been a friend of materialistic evolution." [Granville Sewell on the 2nd Law]. His authority for such a ridiculous statement is none other than Granville Sewell, a Professor of Mathematics at the University of Texas, El Paso. Biochemists have never had a problem with the 2nd law or evolution. Creationists have learned enough scientific terminology to use it in their attempts to disprove evolution. They do this in numerous ways, but the most common example, at least in the mail I receive is the repeated assertion that the second law of thermodynamics demonstrates the evolutionary process to be impossible.
In kindergarten terms, the second law of thermodynamics says that all spontaneous change is in the direction of increasing disorder—that is, in a "downhill" direction. There can be no spontaneous buildup of the complex from the simple, therefore, because that would be moving "uphill." According to the creationists argument, since, by the evolutionary process, complex forms of life evolve from simple forms, that process defies the second law, so creationism must be true.
Such an argument implies that this clearly visible fallacy is somehow invisible to scientists, who must therefore be flying in the face of the second law through sheer perversity. Scientists, however, do know about the second law and they are not blind. It's just that an argument based on kindergarten terms is suitable only for kindergartens. [my emphasis - LAM]
PZ Myers posted this video of Cynthia Dunbar reciting a prayer to open a meeting of the Texas I believe no one can read the history of our country without realizing that the Good Book and the spirit of the savior have from the beginning been our guiding geniuses.Keep in mind that this is the same board of education that is rewriting American history. They don't have a lot of credibility. Having said that, there's one thing I'd like to point out. Cynthia Dunbar makes reference to the First Charter of Virginia as evidence that the United States of America is a Christian nation.
Whether we look to the first charter of Virginia, or the charter of New England...the same objective is present — a Christian land governed by Christian principles.
I like to believe we are living today in the spirit of the Christian religion. I like also to believe that as long as we do so, no great harm can come to our country.
JAMES, by the Grace of God, King of England, Scotland, France and Ireland, Defender of the Faith, etc. WHEREAS our loving and well-disposed Subjects, Sir Thomas Gates, and Sir George Somers, Knights, Richard Hackluit, Clerk, Prebendary of Westminster, and Edward-Maria Wingfield, Thomas Hanham, and Raleigh Gilbert, Esquires William Parker, and George Popham, Gentlemen, and divers others of our loving Subjects, have been humble Suitors unto us, that We would vouchsafe unto them our License, to make Habitation, Plantation, and to deduce a colony of sundry of our people into that part of America commonly called VIRGINIA, and other parts and Territories in America, either appertaining unto us, or which are not now actually possessed by any Christian Prince or People, situate, lies, and being all along the Sea Coasts, between four and thirty Degrees of Northerly Latitude from the Equinoctial Line, and five and forty Degrees of the same Latitude, and in the main Land between the same four and thirty and five and forty Degrees, and the Islands thereunto adjacent, or within one hundred Miles of the Coast thereof;This doesn't sound much like the United States of America, does it? The United States didn't come into existence until almost 180 years after this charter was written. Furthermore, when the revolution began the goal was to separate from Great Britain and its monarch and start a new country that did not have a state religion.
....
We, greatly commending, and graciously accepting of, their Desires for the Furtherance of so noble a Work, which may, by the Providence of Almighty God, hereafter tend to the Glory of his Divine Majesty, in propagating of Christian Religion to such People, as yet live in Darkness and miserable Ignorance of the true Knowledge and Worship of God, and may in time bring the Infidels and Savages, living in those parts, to human Civility, and to a settled and quiet Government: DO, by these our Letters Patents, graciously accept of, and agree to, their humble and well-intended Desires;
William Thorsell
Director, the Royal Ontario Museum
100 Queen's Park
Toronto, ON
M5S 2C6
Mr. Thorsell,
We at the Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry (Canada) and its supporters were dismayed to learn that the Royal Ontario Museum will be sponsoring a talk by Deepak Chopra at the University of Toronto in connection with the Director's Signature Series: The Warrior Emperor and China's Terracotta Army.
While we fully support the concept of academic freedom, we are baffled by this invitation and wonder how it fits into the mandate of the museum to "serve as an advocate for science in the study of nature," as stated in your message on the ROM website. Mr. Chopra's new age psycho-babble may be attractive to the general public, but by inviting him to speak at the ROM, you lend undeserved scientific credibility to his pseudo-scientific claims about quantum physics, psychology, chemistry and medicine. These claims are rightly rejected as absurd by the scientific community and by promoting them you tarnish the otherwise excellent scientific reputation of the Royal Ontario Museum.
CASS will be publishing the standard rebuttals of Deepak Chopra's fanciful quackery in order to help the public understand where he goes off the rails. Our hope is to turn this otherwise embarrassing event into a learning opportunity. We are also contacting the sponsors of the event and the ROM's other private donors in order to voice our concern about Mr. Chopra's presentation. We would like the ROM to clarify how Mr. Chopra's visit fits into this lecture series, as it seems this is just another opportunity for him to promote his new book.
We look forward to hearing from you.
Sincerely,
The Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry Canada
This is the fifth in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. The second installment is: Theory vs Theory. The third part is: The Mutationism Myth, II. Revolution"To Darwin the question, What is a variation? presented no difficulties. Any difference between parent and offspring was a variation. Now we have to be more precise. First we must, as de Vries has shown, distinguish real, genetic, variation from fluctuational variations, due to environmental and other accidents, which cannot be transmitted." (p. 95)and as Morgan wrote:
"As has been explained, the kind of variability on which Darwin based his theory of natural selection can no longer be used in support of that theory, because, in the first place, in so far as fluctuating variations are due to environmental effect, these differences are now known not to be inherited, and because, in the second place, selection of the differences between individuals, due to the then existing genetic variants, while changing the number of individuals of a given kind, will not introduce anything new. The essential [feature] of the evolutionary process is the occurrence of new characteristics." p. 148-149 of Morgan (1932) 3Because heredity and variation did not behave in the manner assumed by Darwin and his followers, it was up to a new generation of evolutionists to develop a new understanding of evolution. Thus, at a time when naturalists were dismissing genetics and clinging to 19th-century views of heredity, including Darwinism and Lamarckism, a group of Young Turks4 was laying the foundations of the genetics-based understanding of evolution that dominated the 20th century.
Population genetics theory2 (roughly speaking) works out the implications of transmission genetics in populations of reproducing organisms, focusing on implications of such Mendelian phenomena as biparental inheritance, chromosome assortment, mutation, recombination, sex-linked inheritance, and so on.
As it exists today, population genetics theory2 covers a wide range of possible worlds, and thus a wide range of possible theories1. For instance, it provides classic equations to treat allele frequencies continuously and deterministically (e.g., Hardy-Weinberg), and at the same time, it provides another framework for addressing probabilistic changes with random drift. Is evolution deterministic or probabilistic? Population genetics theory2 doesn't say- it allows us to consider both possibilities. Is evolutionary change smooth or does it come in chunks? Population genetics theory2 doesn't say: it provides a quantitative genetics framework for continuous changes in quantitative characters, and a completely different framework for molecular evolutionists examining discrete characters. There are limiting cases where these different frameworks converge in some respects, but there is not any single realizable world in which all of population genetics theory2 applies, thus theoretical population genetics can't be understood as a theory1.
Crudely speaking, three frameworks of population genetics theory have been important in the 20th century: the stability analysis5 of systems of continuous allele frequencies, initially deterministic a la Hardy-Weinberg (or Lewontin-Kojima and so on) and later stochastic; the "quantitative genetics" theory of generational change in continuous-valued phenotypic characters (with implicit genetics) subject to selection; and the dynamics of the steady-state origin-fixation process, which was not an important paradigm until Kimura proposed the neutral theory.
"It will be of great interest to study the statistics of such a population [with recognizable Mendelian characters] in nature. If the degree of dominance can be experimentally determined, or the heterozygote recognised, and we can suppose that all forms mate together with equal freedom and fertility, and that there is no natural selection in respect of the allelomorphs, it should be possible to predict the proportions of the several components of the population with some accuracy. Conversely, departures from the calculated result would then throw no little light on the influence of disturbing factors, selection, and the like.Those of you who know your population genetics will recognize, in this passage, a paradigm that continues to play a key role in contemporary research as a "zero-force" model, describing the case of an unperturbed system, i.e., a system at rest. Deviations from this resting state indicate the perturbing effect of some factor or force.
"If through a mutation a character appears that is neither advantageous nor disadvantageous, but indifferent, the chance that it may become established in the race is extremely small, although by good luck such a thing may occur rarely. It makes no difference whether the character in question is a dominant or a recessive one, the chance of its becoming established is exactly the same. If through a mutation a character appears that has an injurious effect, however slight this may be, it has practically no chance of becoming established.This is an abbreviated framework for understanding evolution under the "new mutations" or "mutation-limited" view that is now commonplace in molecular evolution. A new mutation arises and may "become established- we would say "become fixed" or "reach fixation" in population-genetics jargon- with a probability (not a certainty) that depends on its effects. If its effects are injurious, is has practically no chance of being established, and so on.
If through a mutation a character appears that has a beneficial influence on the individual, the chance that the individual will survive is increased, not only for itself, but for all of its descendants that come to inherit this character. It is this increase in the number of individuals possessing a particular character, that might have an influence on the course of evolution." (187-189)
(substitute 2N for diploids), where N is the population size, and this value is not affected by recessivity or dominance, just as Morgan says; for a newly introduced beneficial allele, 
, where s is the selective advantage; for a significantly deleterious allele, the probability of fixation is vanishingly small. Later, diffusion theory was used to derive a more general expression for the probability of fixation (e.g., Gillespie, 1998, p. 82)
"In the case of a population presenting continuous variation in regard to say, stature, it is easy to see how purity of the gametes in respect of any intensities of that character might not in ordinary circumstances be capable of detection. There are doubtless more than two pure gametic forms of this character, but there may quite conceivably be six or eight. When it is remembered that each heterozygous combination of any two may have its own appropriate stature, and that such a character is distinctly dependent on external conditions, the mere fact that the observed curves of stature give 'chance distributions' is not surprising and may still be compatible with purity of gametes in respect of certain pure types." (p. 31)By "chance distribution", Bateson is invoking what we now call a "normal distribution". Such a distribution "may still be compatible with the purity of the gametes", i.e., compatible with Mendelian inheritance, because it can result by the combined effects of a multiplicity of Mendelian loci (6 or 8, he imagines), each with 2 homozygotes and 1 heterozygote, with environmental variation due to "external conditions".
"On this view we can understand why selection of the largest seed[s] raises the average weight in the next generation. We are picking out more of C and less of A and B, and as this process is repeated the proportion of C gradually increases and we get the appearance of selection acting on a continuously varying homogenous material and producing a permanent effect."Second, as the Mendelians stressed repeatedly, the end result of this process is a not a new complement of hereditary factors, but a mixture of old components in new and different proportions. The hereditary factors are not changed by this process (as Darwin and his followers wrongly believed): only their proportions in the population are changed. Without new mutations, the new population would never transcend the genetic limits inherent in the original mix.
References
Batson, W., and E. R. Saunders. 1902. Experimental Studies in the Physiology of Heredity. Reports to the Evolution Committee. Royal Society. (Bateson%20saunders&pg=PP1#v=onepage&q&f=false">online source)
Bateson, W. 1902. Mendel's Principles of Heredity: A Defense. Cambridge University Press, Cambridge. (online source)
Bateson, W. 1909. Heredity and Variation in Modern Light. Pp. 85-101 in A. C. Seward, ed. Darwin and Modern Science: Essays in Commemoration of the Centenary of the Birgh of Charles Darwin and of the Fiftieth Anniversary of the publication of the Origin of Species. Cambridge, London.
Gillespie, J. H. 1998. Population Genetics: A Concise Guide. Johns Hopkins University Press, Baltimore, MD.
Morgan, T. H. 1932. The Scientific Basis of Evolution. W.W. Norton & Co., New York.
Orr, H. A. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evolution Int J Org Evolution 56:1317-1330.
Punnett, R. C. 1911. Mendelism. MacMillan. http://www.archive.org/stream/mendelism00punn#page/172
Stephens, C. 2001. Selection, Drift, and the "Forces" of Evolution. Philosophy of Science 71:550-570.
Sturtevant, A. H. 1965. The Early Mendelians. Proceedings of the American Philosophical Society 109:199-208.
Vavilov, N. I. 1922. The Law of Homologous Series in Variation. J. Heredity 12:47-89.
Notes
1 As quoted in part 1, mutationism is a source of "mirth" for Dawkins.
2 The words "doomed rivals" are also from Dawkins. Back when I was a lad in school, my evolution professor- Dr. Kenneth Christiansen, who has been at Grinnell College for at least 45 years and is still there today- had a slightly gentler way of referring to alternative theories as the "also-rans".
3 Note that Morgan's choice of words leaves some wiggle room that some other kind of variability could be offered "in support of" Darwin's theory. A century ago, admiration for Darwin was nearly universal, as it is today. The meaning of Darwin's theory, and ownership of the "Darwin" brand, were contested by scientists. By 1950, the "Modern Synthesis" school had captured the Darwin brand and began to use it more aggressively than they had dared to do before. However, things might have turned out differently. De Vries labeled himself as a "Darwinian". Bateson and others sometimes cozied up to "Darwinism".
4 Sturtevant (1965) lists 22 Mendelians who published from 1900 to 1905, and notes that all but 5 were under 40 (the older exceptions are de Vries, Garrod, Johannson, Wilson and Lang).
5 "stability analysis" means finding the "attractors" or points of stability in a dynamic system.
6 Hardy reveled in the purity of mathematics and stated that he had no desire to do anything useful. He said that his most important discovery was Srinivasan Ramanujan, a largely self-taught Indian genius who had written to Hardy and others seeking a mentor- only Hardy recognized his genius.
7 Synthesis Historiography attributes the resolution of Darwinism and Mendelism to Fisher (1918). In reality, the problem that Fisher (1918) solved was how to derive Galton's law as a formal consequence of Mendelian principles. Either this is a red herring, or it suggests that as late as 1918, "Darwinism" still implied a rejection of Mendelism in favor of blending. Note that Galton himself lacked the ideological purism of his followers: he believed in discontinuous evolutionary changes and felt that this was a missing element in Darwin's theory.
8 "Synthesis Historiography" is Ron Amundson's term for the industry of writing versions of history in which the Modern Synthesis is presented as the manifest destiny of science, and Mayr, et al are the heroes, while their intellectual opponents are fools and knaves.
*The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth3 (Arlin Stoltzfus, ©2010)
I'm beginning to realize that there are (at least) two fundamentally different approaches to teaching science. One strategy, which I'll call the "fact-based" approach, concentrates on communicating facts about the natural world. The other approach, which I'll call the "methodological approach" concentrates on teaching students how to acquire knowledge. Argument and debate are common in science, yet they are virtually absent from science education. Recent research shows, however, that opportunities for students to engage in collaborative discourse and argumentation offer a means of enhancing student conceptual understanding and students’ skills and capabilities with scientific reasoning. As one of the hallmarks of the scientist is critical, rational skepticism, the lack of opportunities to develop the ability to reason and argue scientifically would appear to be a significant weakness in contemporary educational practice. In short, knowing what is wrong matters as much as knowing what is right. This paper presents a summary of the main features of this body of research and discusses its implications for the teaching and learning of science.Clearly, this approach is consistent with bringing creationist ideas into the classroom in order to teach students why they are wrong. You will also want to bring up astrology and the ancient theory of demon possession if that helps make the point. You can't discuss every single controversy, but, at the very least, you should include the "active" ones—the ones students will encounter as soon as they step outside the classroom and watch FOX News or listen to their preacher on Sunday morning.
1. Thanks to Bruce Alberts who, as editor-in-chief, is trying to promote more emphasis on science education.
P.S. I don't want to discuss whether the methodological approach is possible in American schools. If you think that science teachers are too stupid to adopt this approach, or if you think that many of them are secret creationists, then that's an entirely different problem. It's a defeatist attitude to conclude that the quality of science teachers is so bad that science education can't be fixed. If you have bad science teachers then the first step is to replace them with good ones. The sooner the better.
To investigate the extent and nature of transcriptional dark matter, we have analyzed a diverse set of human and mouse tissues and cell lines using tiling microarrays and RNA-Seq. A meta-analysis of single- and paired-end read RNA-Seq data reveals that the proportion of transcripts originating from intergenic and intronic regions is much lower than identified by whole-genome tiling arrays, which appear to suffer from high false-positive rates for transcripts expressed at low levels.Many of us dismissed the earlier results as transcriptional noise or "junk RNA." We thought that much of the genome could be transcribed at a very low level but this was mostly due to accidental transcription from spurious promoters. This low level of "accidental" transcription is perfectly consistent with what we know about RNA polymerase and DNA binding proteins [What is a gene, post-ENCODE?, How RNA Polymerase Binds to DNA]. Although we might have suspected that some of the "transcription" was a true artifact, it was difficult to see how the papers could have failed to consider such a possibility. They had been through peer review and the reviewers seemed to be satisfied with the data and the interpretation.
van Bakel, H., Nislow, C., Blencowe, B. and Hughes, T. (2010) Most "Dark Matter" Transcripts Are Associated With Known Genes. PLoS Biology 8: e1000371 [doi:10.1371/journal.pbio.1000371]
Right now there's a conference going on in Oxford, United Kingdom—that hotbed of Christian apologetics (and Richard Dawkins). John Wilkins is there. One of the topics is defining religion [Ruminations in Oxford]. With an eye to the discussion of the previous chapters, I want to pick out four items or claims that are central to Christian belief—four items that the Christian takes on faith. If you do not believe in these, then you should not call yourself a Christian. First, that there is a God who is creator, "maker of heaven and earth." Second, we humans have duties, moral tasks here on earth, in the execution of which we are going to be judged. Hence, God stands behind morality. Third, Jesus Christ came to earth and suffered because we humans are special, we are worth the effort by God. The usual way of expressing this is to say that we are "made in the image of God." We have "souls." Fourth and finally, there is the promise of "life everlasting." We can go to heaven, what ever that means.Here's my quick take on the four items.
Let me spell out carefully what I see as the task in this and the next chapter. It is not to defend Christianity as a true or compelling belief system. I take it that you can enter these chapters as an agnostic or an atheist and depart in the same frame of mind. I do not want to dissuade people from Christianity, nor do I want to convince them of it. I want to explain in a fair manner what is meant by Christianity in terms of the four points introduced in the last paragraph. I also want to show that you could hold these, if you so wish, in the light of modern science—if you prefer, in the face of modern science. In other words, the Christian's claims are not refuted by modern science—or indeed threatened or made less probable by modern science.
Ward effortlessly flows from one fascinating insight to another about the often contentious relationship between diverse religious views and the new scientific knowledge. Writing with both passion and clarity, he masterfully converys the depth, the difficulty, and the importance of the greatest intellectual and existential questions of the modern age."Clarity"? Don't make me laugh. Keith Ward has never met an example of obscurantism that he doesn't embrace.
[Hat Tip: Clarity - A very nice statement by Dawkins, at RichardDawkins.net.]
Mr. Prime Minister and excellent minister Bev Oda:Did I mention that Denyse is a Roman Catholic? Do you think it's relevant?
Please stand firm against the people who will get money from aborting babies in other countries, if you cave in.
This is for a number of non-religious reasons:
1. There is NO reason to believe abortion will even be voluntary. And what can we do if it isn't? It is better if we Canadians just do not fund it. (If people in other countries want to force women to be aborted, to meet grant-based population reduction quotas, we cannot stop them. But at least we had nothing to do with it, right? It's not like the cheque is stamped 'From a grateful CANADA'. Surely, there are some shames we cannot stoop to.)
2. Contrary to population whackos, most of the world is in steep demographic decline. This is bad news for business, pension plans, etc. Why add to the problem? Right now, YOUR government is advertising for healthy young workers from abroad. So we should kill their successors?
3. Abortion clinics are run by people who do not mind killing babies for a living. Even if you didn't agree that that is a problem, a number of other evils result, including: Teachers molest underage girls and ship them to clinics for discreet abortions, unbeknown to their parents. Abortion clinics may also function on the adoption black market. = Would you keep it for a while instead of killing it, if we get you some money?
4. No one should believe anything an abortion clinic operator says about not killing viable babies. If he really cared about stuff like that, he would not likely do what he does now. So you can assume, for practical purposes, it is unreliable.
5. Some babies may be sold for research that should never be done on a human being, but remember that they do not technically exist.
Stand firm! Most of the criticism I hear about your government comes from NOT standing up for traditional Canadian values. Most of the praise I hear is for doing so.
And REPEAL Section 13 and FIRE Jennifer Lynch. Quit fooling around about that too. People are really angry.
Traditional values and civil rights are important to the people who would re-elect you.
Katarin MacLeod reviews a new book on evolution—one that's intended to educate children who lack an understanding of science [Evolution (Biology)-Juvenile literature]. Katarin MacLeod is an Assistant Professor in Science Education at St. Francis Xavier University in Antigonish, NS. Her areas of interest include physics educational research (PER), and the incorporation of science, technology, society and environment (STSE) outcomes into science courses at all levels to help students understand the relevancy of science, increase scientific literacy, and to promote citizenship.Here's part of her review. You can judge for yourself whether she is competent to teach science education at St. Francis Xavier University.
Although the text is very good in describing the theory of Evolution, there are points in the book where the author makes comments that could imply that Evolution is more than a theory. For example, “…Charles Darwin revealed the solution to the mystery of evolution” (p. 7). He also makes the comment that Evolution is the most important idea in all of biology (p. 7). Such phrases may lead the reader into thinking that scientists completely understand the theory of Evolution which would be incorrect, else Evolution would be a principle or a law and not a theory. As well, it is a bit bold to claim that evolution is the most important idea in all of biology – biology is a huge field of study with other key discoveries.Hint to Professor MacLeod. Before you review your next book on evolution you'd better brush up on the difference between a fact and a theory and learn that a theory can never become a law.
[Hat Tip: Richard B. Hoppe at Panda's Thumb]
