Damn you heathen! Your book learnin' has done warped your mind. You shall not be invited next time I sacrifice a goat.
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Chris Mooney warns us that science journalism is in trouble. He notes that many newspapers are firing their science writers and he warns of the dangers [The Death and Strangulation of Science Journalism].What's disturbing, though, is to see a meta-discussion of the "trouble" with the practitioners of science journalism without any discussion of the real "trouble": the economic realities that are killing them off, one by one.I responded by saying ....
Memo to scientists: If you don't like science journalists, you're going to like even less what you get once they're gone.
Not to worry. We'll figure out some way to frame it so that it sounds like a good thing!Now Chris has started a separate thread in order to disucuss this point [Science Journalism: When Things Get Rough, You Find Out Who Your Real Friends Are].
:-)
Seriously, most of what passes for science journalism is so bad we will be better of without it.
Maybe the general public would have been more interested in science if science journalists hadn't been writing so much hype about "breakthroughs" for the past twenty years. Maybe the public would have been more interested in science if so-called "science" journalists hadn't been confused about the difference between science and technology.
Science isn't about what the latest discoveries can do to make your life better. It's about learning how the natural world actually works. It's all about knowledge and not application or politics.
Science journalists have let us down. I say good riddance.
My post last week about the death knell of science journalism prompted some incredible responses. Here's Larry Moran, putting it more bluntly than I expected, and enunciating an opinion we'd better hope does not prevail:Well Chris, I hate to tell you this but there are plenty of scientists who share my opinion, even though they may not have put it so bluntly.
...
Breathtaking, huh? I seriously hope opinions like this are not very widespread in the scientific community.
Honestly, based upon the foregoing, I have to question whether Larry Moran knows what a science journalist is--or at least, whether we're talking about the same thing. For it seems to me that virtually everything he's complaining about, a real science journalist would complain about as well.I don't believe you.
Take the media slights against science described above--the hyping of "breakthrough" findings, the confusion of science and technology, and the swapping of serious science coverage for "feel good" or "news you can use" infotainment fare. Although you will certainly find exceptions, in general these aren't the fault of dyed-in-the-wool science journalists, of the sort that proudly claim membership in the National Association of Science Writers (as I do). In fact, you can bet that within their respective media organizations--when they still were working within them; most of NASW today is freelance--science journalists have fought against many such calls over the years.
And you can also bet that they frequently lost out in those internal battles.
The point is that nobody loves science more than science journalists--and nobody more devoutly wishes to see it covered accurately and widely, so that the "general public" thereby benefits, and comes to appreciate science more thoroughly. So how is it that now, a scientist like Larry Moran won't stand up for these science evangelists in the media, and blames them for a host of failings that, in truth, they themselves most assuredly abhor?I gave you my answer. It's because I don't believe you. Is George Johnson one of your examples? How about Graham Lawton?
Today's molecule is actually two molecules but we only care about the protein. You need to identify this protein, being as specific as possible. A general description of the type of protein won't do because the image clearly show a particular version.
The only unproven area is Darwin's natural selectionI'll get the conversation going by pointing out that well before the 150 years Professor Singh mentions in his article, random genetic drift was proposed as a pretty good theory about how evolution can occur. It may not be "better" than natural selection but I think it's good enough to have deserved a mention.
...
Living organisms, on the other hand, evolve by variational evolution that depends on the survival and reproduction of the "fittest" individuals in the population, which is composed of many genotypes.
Unlike evolution, which is taken as a fact, the theory of natural selection, Darwin's mechanism for evolution, has come under criticism as to whether it is sufficient to explain evolution. In particular, early developmental biologists questioned if natural selection was adequate to explain the diversity and complexity of life.
Yet after 150 years of vigorous research (and many Nobel prizes!), no one has come up with a better theory. In fact, the more scientists have explored biology, the more they have become convinced of the facts of evolution.
Natural selection is a fact of everyday life. Resources are limited, individuals differ in their survival and reproduction, and evolution is a common sense conclusion deduced from facts and reasons. The problem with evolutionary change is that it takes place on such a slow place that we do not see it. However, we can imagine how evolution occurs by looking at the spectacular variety of food plants, flowers and domestic animals that we have produced by using the same principles of genetics and selection that nature uses. We may not witness the origin of species, but we have witnessed species becoming extinct in our own life time.
Anyone involved in teaching has heard the sob story. One student works really, really hard in the course but only gets 65% on the final exam. Another student gets 95% without breaking a sweat. In line with Dean Hogge’s observation are Professor Greenberger’s test results. Nearly two-thirds of the students surveyed said that if they explained to a professor that they were trying hard, that should be taken into account in their grade.Michelle Cottle has a comment in The New Republic [An A for Effort? Talk About a Lousy Idea]. Now, this isn't a publication that I routinely look to for views that are similar to my own1 but her comment below pretty much hits the nail on the head as far as I'm concerned.
Jason Greenwood, a senior kinesiology major at the University of Maryland echoed that view.
“I think putting in a lot of effort should merit a high grade,” Mr. Greenwood said. “What else is there really than the effort that you put in?”
“If you put in all the effort you have and get a C, what is the point?” he added. “If someone goes to every class and reads every chapter in the book and does everything the teacher asks of them and more, then they should be getting an A like their effort deserves. If your maximum effort can only be average in a teacher’s mind, then something is wrong.”
No, Jason. What would be wrong is if a university trained its students to believe that they were excellent simply for getting up off their futons and doing what was expected of them. Did the reading? Attended class? Stayed up late working on a paper? Good for you, puppy! Sure, you did a craptastic job on that paper--not to mention the final--suggesting that you have no more than a fourth-grader's grasp of the material. But what the hell!? You worked hard. You showed up--even when you had that reallllly bad hangover. You may not have learned much, but you sure did try. Have a nice fat A. And here's hoping it comes in handy when your first employer fires you for not being able to tell your ass from your elbow when it comes to doing your job.Hopeful Monster has something to say over on Chance and Necessity [Student effort ≠ high grades].
Sweet Jesus, where did such dizzying nonsense come from? Sure, it's easy to blame today's youth for being whiny, spoiled, and entitled. But the kids had to get these delusional ideas from somewhere. I suspect at least part of the blame lies with all those well-intentioned self-esteem-boosting messages that anxious parents, educators, and coaches feel compelled to spout in this era of making every child feel like a winner all the time. You know, the cheery, you-can-do-it mantras along the lines of, "All that matters is that you tried," "The only way to fail is not to try at all."
Um. No. While I understand the self-defeating doubt that we're trying to short-circuit here, there are, practically speaking, lots of ways to fail--much less fail to get an A. One of those is by not having much of an aptitude for a particular area of study. Not all of us are equipped to be rocket scientists, economists, or playwrights, just as not all of us are equipped to be actors or professional basketball players. If anything, a student who tries really, really, really hard at something and still repeatedly falls short might benefit from realizing that his talents lie elsewhere. (As could the rest of us: Not to state the obvious, but I don't want a brain surgeon who graduated at the top of his class because he had perfect attendance. I want one who is an artist with a scalpel.) Go ahead: Aim for the stars. Don't let anyone tell you you can't do something. But if you actually try that thing and it turns out that you're not so hot at it, don't whine about unfair grading. Acknowledge that you have major room for improvement and decide where to go from there. The sooner kids learn how to deal with failure and move on, the less likely we are to have a bunch of whiny, fragile, self-entitled, poorly qualified adults wandering around wondering why their oh-so-stellar efforts aren't properly appreciated in the real world.
Alternatively, now might be a good time to revisit my dream of becoming a concert pianist. I've never had much of an ear for music, but I bet if I quit my day job and worked at it really, really hard--or at least showed up at all my lessons and did the homework--someone would eventually reward my "excellence."
1. By this, I don't mean to imply that The New York Times is any better.
I don't look good in T-shirts but there's plenty of other gifts for me on that site. All those shoppers who might be looking to buy me something for St. Patrick's day should check out the large mugs.[Hat Tip: Ryan Gregory]
Michael Smith (1932 - 2000) won the Nobel Prize in Chemistry for developing the technique of site-directed mutagenesis. Today this is a common technique in biochemistry labs. It enables researchers to specifically alter a nucleotide in a gene in order to study its effect. It is frequently used in structural biology labs to explore the roles of varous amino acid residues in the function of a protein. Background
Chemically, the genetic material of living organisms consists of DNA (deoxyribonucleic acid). DNA molecules consist of two very long strands twisted around each other to form a double helix. Each strand is formed of smaller molecules, nucleotides, that represent the letters of the genetic material. There are only four different letters, designated A, T, C and G. The two DNA strands are complementary, being held together by A - T and G - C bonds. It is only when the genetic code is to be read off e.g. for protein building in the cell that the two strands are separated. The genetic information in DNA exists as a long sentence of code words, each of which consists of 3 letters which can be combined in many different ways (e.g. CAG, ACT, GCC). Each three-letter code word can be translated by special components within the cell into one of the twenty amino acids that build up proteins. It is the proteins that are responsible for the functions of living cells, including their ability to function, among other things, as enzymes maintaining all the chemical reactions required for supporting life. The proteins' three-dimensional structure and hence their function is determined by the order in which the various amino acids are linked together during protein synthesis.
Site-directed mutagenesis
The flow of genetic information goes from DNA via the translator molecule RNA to the proteins. By re-programming the code of a DNA molecule, e.g. changing the word CAC to GAC, it would be possible to obtain a protein in which the amino acid histidine is replaced by the amino acid aspartic acid. In nature, such mix-programming of the genetic material (mutation) occurs randomly, and is nearly always fatal to the organism. However, a dream of biochemical researchers has been to alter a given code word in a DNA molecule so as to be able to study how the properties of the mutated protein differ from the natural. It was through Smith's oligonucleotide-based site-directed mutagenesis that this dream became reality. As early as the 1970s Smith learned to synthesize oligonucleotides, short, single-strand DNA fragments, chemically. He also studied how these synthetic fragments could bind a virus to DNA. Smith then discovered that even if one of the letters of the synthetic DNA fragment was incorrect it could still bind at the correct position in the virus DNA and be used when new DNA was being synthesized. At the beginning of the 1970s Smith was a visiting researcher at Cambridge and the story goes that it was during a coffee-break discussion that the idea arose of getting a reprogrammed synthetic oligonucleotide to bind to a DNA molecule and then having it replicate in a suitable host organism. This would give a mutation which in turn would be able to produce a modified protein. In 1978 Smith and his co-workers made this idea work in practice. They succeeded both in inducing a mutation in a bacteriophagic virus and "curing" a natural mutant of this virus so that it regained its natural properties. Four years later Smith and his colleagues were able for the first time to produce and isolate large quantities of a mutated enzyme in which a pre-determined amino acid had been exchanged for another one.A protein with a changed (mutated) amino acid can be
produced with site directed mutagenesis. A chemically
synthesized DNA fragment with a changed code word is bound
to a virus DNA which is multiplied in a bacterium. The DNA
molecule with the changed code word is reduplicated and can
be used for producing the changed protein.
Smith's method has created entirely new means of studying in detail how proteins function, what determines their three-dimensional structure and how they interact with other molecules inside the cell. Site-directed mutagenesis has without doubt revolutionised basic research and entirely changed researchers' ways of performing their experiments. The method is also important in biotechnology, where the concept protein design has been introduced, meaning the construction of proteins with desirable properties. It is already possible, for example, to improve the stability of an enzyme which is an active component in detergents so that it can better resist the chemicals and high temperatures of washing water. Attempts are being made to produce biotechnically a mutated haemoglobin which may give us a new means of replacing blood. By mutating proteins in the immune system, researchers have come a long way towards constructing antibodies that can neutralise cancer cells. The future also holds possibilities of gene therapy, curing hereditary diseases by specifically correcting mutated code words in the genetic material. Site-directed mutagenesis of plant proteins is opening up the possibility of producing crops that can make more efficient use of atmospheric carbon dioxide during photosynthesis
The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.
The image on the right was created by Mike Rosulek. You can view the complete set at More Darwin. He's planning to sell T-shirts and poster with all proceeds going to support the National Center for Science Education.Paleontology's view of speciation has been dominated by the picture of "phyletic gradualism." It holds that new species arise from the slow and steady transformation of the entire population.They illustrate this point with two "classic" views of gradualism.
In the first view (left) we see speciation by gradual transformation of a single population. This form of speciation is called anagenesis. 
The other form of speciation is called cladogenesis. It's when an ancestral species splits into two parts—often due to geographical separation—and each separate population evolves gradually into distinct species. This is the way most people think about adaptive radiations. The key point, according to Eldredge and Gould, is the slow and steady change in each lineage as they diverge from one another.
Slowness and Smoothness (but not Constancy) of RateGould goes on to support his claim based, in part, on Darwin's commitment to Lyell's uniformitarianism. Gould also points out that Huxley was vexed with Darwin for adopting such a gradualist approach to evolution.
Darwin also championed the most stringent version of gradualism—not mere continuity of information, and not just insensibility of innumerate transitional steps; but also the additional claim that change must be insensibly gradual even at the broadest temporal scale of geological durations, and that continuous flux (at variable rates to be sure) represents the usual state of nature.
Since Darwin prevails as the patron saint of our profession, and since everyone wants such a preeminent authority on his side, a lamentable tradition has arisen for appropriating single Darwinian statements as defenses for particular views that either bear no relation to Darwin's own concern, or that even confute the general tenor of his work....For more on this debate, see John Wilkins on Myth 4: Darwin was a gradualist.
I raise this point here because abuse of selective quotation has been particularly notable in discussions of Darwin's views on gradualism. Of course Darwin acknowledged great variation in rates of change, and even episodes of rapidity that might be labelled catastrophic (at least on a local scale); for how could such an excellent naturalist deny nature's multifariousness on such a key issue as the character of change itself? But these occasional statements do not make Darwin the godfather of punctuated equilibrium, or a cryptic supporter of saltation....
1. The words on the poster are a take-off on one of the campaign slogans of Barack Obama.
2. There are other models that can account for the observations. In other works, Eldredge and Gould have explained how punctuated equilibria is also compatible with sympatric speciation.
Eldredge, N. and Gould, S.J. (1972) Punctuated Equilibria: an Alternative to Phyletic Gradualism. in "Models in Paleobiology" T.J.M. Schopf ed., Freemna, Cooper & Co., San Francisco pp. 82-115. [PDF]
Carl Zimmer ran a Science Writing Workshop at Yale University a few weeks ago.
Do you remember this cover? It caused a minor uproar a few weeks ago [see Explaining the New Scientist Cover].What on earth were you thinking when you produced a garish cover proclaiming that "Darwin was wrong" (24 January)?Darwin was wrong about a lot of things but the tree of life wasn't one of them. It's still an accurate metaphor for most of the history of life—certainly the parts Darwin wrote about.
First, it's false, and second, it's inflammatory. And, as you surely know, many readers will interpret the cover not as being about Darwin, the historical figure, but about evolution.
Nothing in the article showed that the concept of the tree of life is unsound; only that it is more complicated than was realised before the advent of molecular genetics. It is still true that all of life arose from "a few forms or... one", as Darwin concluded in The Origin of Species. It is still true that it diversified by descent with modification via natural selection and other factors.
Of course there's a tree; it's just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA.
President Obama (USA) just arrived in Canada. Here he is being greeted by Governor General Michaelle Jean. You can see the complete video on YAHOO! News.
As most of you know, Gould (1941 - 2002) was a critic of the hardened version of the Modern Synthesis. He thought that evolutionary theory needed to be updated to include some things that the originators of the Modern Synthesis were unaware of—or rejected prematurely.The modern synthesis, as an exclusive proposition, has broken down on both of its fundamental claims: extrapolationism (gradual allelic substitution as a model for all evolutionary change) and nearly exclusive reliance on selection leading to adaptation.Ryan Gregory discusses this paper in detail on Genomicron [Gould (1980)]. If you want to be informed in this debate you absolutely must read what he has to say about this key paper in evolutionary theory.
[Image Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]
Gould, S.J. (1980) Is a new and general theory of evolution emerging? Paleobiology 6:119-130.
Gould, S.J. (1982) Darwinism and the expansion of evolutionary theory. Science 216:380-387.
Most people do not understand current ideas about evolution. The following is a brief summary of the Modern Synthesis of Genetics and Evolution as put forth by evolutionary biologists in the late 1940s.The term "evolutionary synthesis" was introduced by Julian Huxley in Evolution: The Modern Synthesis (1942) to designate the general acceptance of two conclusions: gradual evolution can be explained in terms of small genetic changes ("mutations") and recombination, and the ordering of the genetic variation by natural selection; and the observed evolutionary phenomena, particularly macroevolutonary processes and speciation, can be explained in a manner that is consistent with the known genetic mechanisms.The original version of the Modern Synthesis included mechanisms other than natural selection, especially random genetic drift. Later on, there was a hardening of the synthesis so that natural selection became the predominant mechanism and drift was relegated to a bit part (see Mayr quotation, above). The original version is described by Douglas Futuyma as ....
Ernst Mayr (1980) "Some Thoughts on the History
of the Evolutionary Synthesis" in The Evolutionary Synthesis,
E. Mayr & W.B. Provine eds. Harvard University Press.
The major tenets of the evolutionary synthesis, then, were that populations contain genetic variation that arises by random (ie. not adaptively directed) mutation and recombination; that populations evolve by changes in gene frequency brought about by random genetic drift, gene flow, and especially natural selection; that most adaptive genetic variants have individually slight phenotypic effects so that phenotypic changes are gradual (although some alleles with discrete effects may be advantageous, as in certain color polymorphisms); that diversification comes about by speciation, which normally entails the gradual evolution of reproductive isolation among populations; and that these processes, continued for sufficiently long, give rise to changes of such great magnitude as to warrant the designation of higher taxonomic levels (genera, families, and so forth).This description would be incomprehensible to Darwin since he was unaware of genes and genetic drift. The Modern Synthesis differed from Darwinism in four important ways:
Futuyma, D.J. in Evolutionary Biology,
Sinauer Associates, 1986; p.12
The Modern Synthesis was a theory about how evolution worked at the level of genes, phenotypes, and populations whereas Darwinism was concerned mainly with organisms, speciation and individuals. This was a major shift in emphasis and those who fail to appreciate it find themselves out of step with the thinking of evolutionary biologists.
- It defined evolution as a change in the frequency of alleles in a population; an idea based on population genetics.
- In addition to natural selection, it recognized random genetic drift as an important mechanism of evolution.
- It recognized that characteristics are inherited as discrete entities called genes. Variation within a population is due to the presence of multiple alleles of a gene. Variation is caused by mutation.
- It postulated that speciation is (usually) due to the gradual accumulation of small genetic changes. This is equivalent to saying that macroevolution is simply a lot of microevolution.
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