I have come to this conclusion: the greatest tragedy of public polity, in science and without, in the democratic nations, one that looks very likely to me to be the major proximal cause of the ultimate failure of democracy, is the invention of public relations.Read more from John Wilkins at Spin versus framing: the tragedy of PR.
1. Innovation. Science and technology have been responsible for half of the growth of the American economy since WWII. But several recent reports question America’s continued leadership in these vital areas. What policies will you support to ensure that America remains the world leader in innovation?I'm a little confused about how the American system of government works. I think the answer means the following: "My administration will submit to Congress a proposal to increase funding ..." Is that correct? Is it just campaign rhetoric when a Presidential candidate talks like this or does the President really have more power to make laws than I imagine?
... My administration will increase funding for basic research in physical and life sciences, mathematics, and engineering at a rate that would double basic research budgets over the next decade. We will increase research grants for early-career researchers to keep young scientists entering these fields. We will increase support for high-risk, high-payoff research portfolios at our science agencies. And we will invest in the breakthrough research we need to meet our energy challenges and to transform our defense programs.
1. Doubling of research funding in 10 years means a yearly increase of 8%. While this is better than an increase that doesn't match inflation, it doesn't strike me as a very radical proposal to fix the funding situation.
[Hat Tip: Jim Lippard]
The scientific research journal Genome Research is proposing to publish a special issue on "Genomics and Darwinism" to coincide with Darwin's 200th birthday [Genome Research]. Genome Research is now accepting submissions for a special issue, entitled Genomics and Darwinism, devoted to comparative and evolutionary genomics, including primary research reporting novel insights in large-scale quantitative and population genetics, genome evolution, and natural and sexual selection.The creationists have already jumped on this as evidence that "Darwinism" is the proper terminology when referring to evolution: see DaveScot's post on Uncommon Descent entitled Is “Darwinism” a term only used by creationists?.
The deadline for submissions is September 1 and the issue is expected to coordinate with Darwin's 200th birthday (and 150th anniversary of the publication of On the Origin of Species) in February 2009.
Here's an exercise for those of you who are truly interested in teaching accurate science. Go to the recent posting by Casey Luskin on Evolution: News & Views and figure out how to respond to his challenge. He's claiming that a great deal of evolution is "random" but that's not what the "Darwinists" are saying ["Random" Samples of Media and Textbook Descriptions of Darwinian Evolution]. 1. Yes, and no. As usual Casey Luskin has only a superficial understanding of evolution and a very weak grasp of reality. However, from time to time he accidentally stumbles onto an important point. Let's set aside the fact that he has no idea what he's talking about and address how we should respond to such criticisms. My view is here: [Evolution by Accident].
The latest issue of Tangled Bank has been published on Science Notes [Tangled Bank #112].Welcome, science readers, to Tangled Bank 112. It’s a privilege to host so much good science writing. Today’s entries are presented mainly with only the authors’ comments because it’s late and I want to get them published.
If you want to submit an article to Tangled Bank, send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.
One of the many highlights of my week at Chautauqua was meeting Connie Barlow and her husband Michael Dowd. Michael is the author of Thank God for Evolution. His blog, The Evolutionary Evangelist promotes the concept of Evolution Theology ....As I and others are now using the term, Evolution Theology, or Religion 2.0, refers to those whose position on the science vs. religion controversy tends toward reconciliation or synthesis. The term points broadly to those who do not see themselves at either end of the polarized debate as it is currently framed (either anti-evolutionary creationism and intelligent design at one end, or anti-religious atheism at the other). Theistic evolutionists, religious naturalists, evolutionary humanists, emergentists, pantheists, panentheists, theosophists, and the 11,000+ signers of the Clergy Letter Project may differ in how they integrate evolution and theology , but they all do.The short Wikipedia article on Michael Dowd refers to him as an itinerant Pentecostal preacher. He and his wife travel around America promoting evolution and Christianity. Michael and Connie sat in on a class that I took (Evolution and Christianity). Michael's version of Christianity is very confusing to me, as was the instructor's version. It's part of the so-called "sophisticated" Christianity that seems to deny any scientifically detectable evidence of God's intervention in affairs of the natural world. Undetectable, that is, unless you are a person of faith. People of faith can see the hand of God in events such as the breakup of the Soviet Union and the tearing down of the Berlin wall whereas the rest of us see these as entirely natural events. People who hold this position often go as far as saying that they really don't believe in supernatural beings because God is everywhere in nature.
If more than 90% of the genome is 'junk' then why do cells make so much RNA from it?One of the answers being promoted by many molecular biologists is that this RNA is mostly functional and it represents a massive new level of control that has hitherto gone unnoticed. That doesn't mean that we never knew about regulatory RNAs because, in fact, we've known about them for over three decades. The important point of this opinion is that these RNAs are abundant and it "explains" the presence of so much non-coding DNA in eukaryotic genomes.
It is hard to comprehend the upheaval that RNA has been causing in molecular biology over the past few years. Once viewed as a passive intermediary, it was thought to faithfully carry genetic messages from the DNA sequence to the protein-making machinery, where things were made that actually got things done. Biologists were comfortable in the knowledge that only 1–2% of the human genome made protein-coding RNA in this way, and most of the rest was filler. So when, in 2005, geneticist Thomas Gingeras announced that some cells churn out RNA molecules from about 80% of their DNA, he astonished scientists attending the Biology of Genomes meeting at Cold Spring Harbor Laboratory in New York. Why should cells bother with so much manufacturing if, as it seemed, such a tiny fraction was involved in the important business of protein-making?I wasn't at this meeting but I'd be very surprised if the scientists were "astonished." I'm pretty sure most of them thought that this was an artifact of some kind, probably due to accidental transcription.
Over the past three years or so the case for this 'pervasive transcription' has strengthened. The phenomenon has now been ascribed to mice, fruitflies, nematode worms and yeast. These studies, and Gingeras's original reports, came from microarrays — a technology that relies on the tendency of nucleic acids to find their complementary cousins in a solution. Gingeras works for the microarray manufacturer Affymetrix in Santa Clara, California. But not everyone has been persuaded of the extent of pervasive transcription, in part because microarrays are subject to background 'noise'. Even using no RNA, control chips will give off some signals, and results can be a matter of interpretation.Yes, false positives may account for some of the observations but I think most scientists recognize that the microchips are actually detecting rare transcripts. The question is whether these rare transcripts are biologically significant or whether they are artifacts like most of the alternative splice variants that made all the headlines a few years ago.
John Mattick, the director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia, has no such qualms. He is a long-time advocate of non-coding RNA's importance. The doubters, he says, "keep regressing to the most orthodox explanation [that the long RNAs are junk]. But they can't just sit on their intellectual backsides and tell us to prove it."John Mattick is one of the most vocal cheerleaders for non-coding RNA. He maintains that huge amounts of it are biologically functional. His statement is a tacit confession that he has no proof of his claims. What in the world is wrong with asking for "proof" (evidence) whether sitting on our backsides or standing?
Nearly thirty years ago, a paper was published that almost every student of evolutionary science will end up reading at some point in their career. Despite being only eighteen pages long and containing no original research, many people see it as marking something of a revolution in biology.
Spencer Wells is Explorer in Residence at the National Geographic Society. He has impeccable credentials: Ph.D. with Richard Lewontin, and postdoc with Luigi Luca Cavalli-Sforza and Sir Walter Bodmer. Wells heads the The Genographic Project, a project that collects and analyzes DNA samples from individuals around the world in an attempt to understand human evolution and migration.Listen, I’m a scientist, and to the extent that people listen to scientists, I would like them to absorb this message, that scientifically speaking, races have no biological basis.This got the expected round of applause from the audience. (They love that stuff at Chautauqua.) Nobody seemed to notice the discrepancy between what he said in his lecture and the idea that "races have no biological basis."
[Photo Credit: Chautauquan Daily]
Arthur Harden (1865 - 1940) received the 1929 Nobel Prize in Chemistry for his work on the basic metabolic pathway of fermentation. As we now know, this is the glycolytic pathway whereby sugars such as glucose are converted to pyruvate. In yeast extracts the conversion of glucose to alcohol can be studied in vitro and this led to the discovery of enzymes and pathways. Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.
The fermentation of liquids containing sugar - there we have a chemical reaction older than all chemical science. The point of time when men first began to take this reaction into their service is really lost in the mists of antiquity, before the beginning of history. The peculiar and apparently self-caused process by which an innocent fruit juice is transformed with the active formation of scum, into a drink which is either stimulating or intoxicating according to the quantity partaken, attracted attention in the very earliest times; and to many peoples it appeared so wonderful that nothing less than the cooperation of a divinity seemed to them possible as an explanation.
Our enlightened time has scarcely the right to marvel at this, when we take into consideration how long a time science has since required to obtain an acceptable conception of the nature of fermentation. Here we stand face to face with one of the most complicated and difficult problems of chemical research. Little more than a couple of centuries separate us from the time when men first began to perceive that the fermenting substance was sugar, which under the influence of a certain something was decomposed, with carbonic acid and ethyl alcohol as the final products of the decomposition.
But what this "something" was, and how it worked, still remained unsolved questions, long defying the most penetrating attempts at interpretation. It was not until our own days that it has been vouchsafed to us to have a fairly satisfactory answer to these questions, but even here the process of development has been slow, toilsome, and it took place, so to speak, in several instalments.
In carrying out the provisions of Alfred Nobel's Will, the Swedish Academy of Sciences has already once before had its attention directed to this sphere of research. That was in 1907, when Eduard Buchner was awarded the Nobel Prize in Chemistry for his discovery of non-cellular fermentation. At the time complaints were raised in certain quarters against this award as being insufficiently justified. Seen in the perspective of distance in time, however, Buchner's discovery has more and more stood out as a line of demarcation between two different epochs, pointing the way to a new phase in the history of the chemistry of fermentation.
Buchner's discovery marked the final decision in a long struggle between two distinct schools - one, the older one, represented by Justus von Liebig the other, the younger one, represented by Louis Pasteur. According to the former school, fermentation was a purely chemical process, evoked by an unorganized ferment with unstable properties, which were imparted to the fermenting substance and thereby brought about its decomposition. According to the latter school, it was rather a physiological process, inseparably connected with the vital act of a microorganism known as the "fungus of fermentation". Buchner's discovery made it evident that to some extent both were right, but also to some extent both were wrong, and, consequently, that the truth lay between the two.
But the value of the discovery makes itself known in a still more definite way through the impulse it has given to later research. In fact, during the last three decades that research has made such great advances, has given such an enlarged insight into the mechanism of the process of fermentation, that the Academy of Sciences has found the time ripe once again to award a Nobel Prize in this department. In so doing the Academy has deemed it right to divide equally the Nobel Prize in Chemistry for the present year between Professor Arthur Harden and Professor Hans von Euler.
Buchner assumed in the yeast juice the presence of a uniform ferment or enzyme, known as "zymase".
When, however, Harden and his fellow-workers filtered a quantity of Buchner's yeast-juice through a gelatine filter, known as an "ultrafilter", and thereby split it up into two fractions (a filtrate and a sediment that did not pass through the filter), the curious state of things occurred that neither of these fractions was any longer able to bring about fermentation, but that after being mixed with one another they recovered that capacity.
Harden explained this by saying that a high-molecular enzyme, the zymase proper, was left on the filter, which let through a low-molecular complementary enzyme, which for the sake of brevity was called co-enzyme or co-zymase.
Another no less important advance is made in Harden's demonstration of the hitherto neglected part played by phosphoric acid in the process of fermentation. It has been found that a certain addition of phosphate gives rise to an equivalent amount of carbonic acid and ethyl alcohol. This effect is associated with the formation of one or more definite compounds between sugar and phosphoric acid - known as the "zymo-phosphates", amongst which a glucose monophosphate and a glucose diphosphate are to be regarded as the most important.
In the same measure as research in this department has made new conquests, a clearer and clearer insight has been gained into the importance of this discovery. In particular the work of von Euler and his pupils during the last few years greatly contributed to the unravelling of the mechanism of phosphorization.
The primary function of phosphoric acid in fermentation consists, according to von Euler, in the fact that in cooperation with an enzyme it gives rise to glucose monophosphate, identical with the monophosphate discovered by Harden and Robison. This phosphate afterwards undergoes a mutation in the presence of co-zymase, inasmuch as a glucose diphosphate and an active glucose are formed, after which the latter yields the necessary material for the subsequent stages of the fermentation.
This demonstration of the part of mutase played by the co-zymase, or in other words of the identity of co-zymase and co-mutase, is of fundamental importance, for it has fully revealed the central position in the process of fermentation of the complementary enzyme in question.
The researches of von Euler and his pupils have further led to the concentration of the co-zymase and to a far more exact study of its properties than had been previously possible. They have been able to determine approximately its molecular weight, which has been found to be about 490; and they have also been able to draw certain definite conclusions concerning its chemical nature, which make it highly probable that we have here what the chemists call a pentosenucleoside. The production of a co-zymase with a high activity has also shown in a brilliant manner the character of that enzyme as a specific activator.
Finally, what gives special interest to the study to the complicated reaction mechanism of the fermentation of sugar is that it has been possible to draw from it important conclusions concerning carbohydrate metabolism in general in both the vegetable and the animal organism.
The brief summary which has now been given, and which, in view of the scanty time allowed, has necessarily been extremely fragmentary, will in any case probably have shown that there is an extremely intimate connection between the researches of Harden and von Euler in this field. On the one hand, the fundamental discoveries of Harden have formed the precondition and point of departure for the various work of von Euler; and on the other hand, it is only the work of the latter that has made fully evident the importance of Harden's discovery.
Under such circumstances the Academy of Sciences has not hesitated this time to avail itself of the expedient that is offered by the Statutes of the Nobel Foundation of dividing the prize between two equally meritorious scientists.
Professor Harden. When the Royal Swedish Academy of Sciences resolved to adjudge to you, together with Professor von Euler, this year's Nobel Prize in Chemistry on account of your important contributions to our knowledge of alcoholic fermentation, the Academy had let herself guided by a firm conviction that these contributions had opened indeed a new chapter in the investigation of that very complicated matter.
It is with the most sincere gratification that I have the honour of conveying to you the congratulations of the Academy on this distinction, the outward signs of which you are now about to receive.
Professor von Euler. It is a great pleasure to the Swedish Academy of Sciences to be able to award this time the Alfred Nobel's Prize also to one of her members, and so much more since during a long series of years we have been in the position to follow from nearby your energetic, persevering, and systematic investigations. The Academy is also firmly convinced that the distinction which has fallen upon you today, will not contain for you the temptation to rest on laurels already obtained, but that on the contrary it will mean a stimulus to continued and, as we all hope, successful work in the service of biochemistry.
Hi, Larry Moran.
I think it's not too helpful to your readers to take a definition out of context from my book, and link it to my Chautauqua talk. At Chautauqua, I did not cite or employ Geertz's definition of religion.
Rather, I mentioned that I would focus on two aspects of religion (necessary but not sufficient aspects, as I put it), 1) the expression of empathy and compassion (which exist in balance with violence and cruelty, of course) and 2) symbolic rituals that in some way seem to go beyond the here-and-now, for example, burial rituals that go beyond hygenic disposal of the dead to include grave good and ritual processes that may embrace the sacred. I think the Chautauqua audience was more than capable of following that sort of framework, laced with a lot of examples from primate studies and archaeology that speak to those two particular aspects (of course, explaining too the inevitable risks in using great apes of today to model early human evolution.... that's an enjoyable point to debate, and I do enjoy conversations where people disagree on such things).
I'm not too sure how you could know what "most" of the audience of hundreds thought of my talk, unless you polled them? Your characterization of confused people doesn't fit with my experience of interacting with people there, at all....
I spoke at AAAS in Boston last winter and made a stand: I won't answer questions about my personal beliefs. The reason is really simpler than any you indicated (I surely don't remember saying what you said I said!): I'm a scientist, and want to keep focus on the science. Seems like a reasonable enough point. I don't understand this peculiar drive to know what scientists' personal beliefs might be! I was pleased that the Chautauqua audience applauded (literally) my answer.
I often enjoy your blog (some days more than others, clearly). I'd appreciate your posting this, if you're open to doing so.
Best wishes,
Barbara King
The question has come up in the discussion of the AAAS video on Panda's Thumb [The AAAS responds to “Expelled”]. The video highlights several people who claim that science and religion are compatible. Since AAAS is a scientific organization, it makes sense that the people being interviewed are scientists. However, many of them are not—at least not by my understanding of what a scientist is. 
[Image Credit: The scientist cartoon is from Jacks of Science]
Last week (Aug. 19) The Gazette from Colorado Springs published an opinion piece on atheism [Dems dismiss the atheists: Why rude guests aren't welcome].Imagine a world with no religion and one sees a world without the Golden Rule, devoid of most charities, hospitals and great universities. One sees hurricane recovery zones, minus all the chartered planes and buses full of churchgoers giving their time and money to rebuild homes. How many children are fed and clothed by atheist charity organizations? Approximately none.The interesting thing about this article is the bit about atheists not being charitable. Apparently atheists don't contribute money to social causes and public institutions. Hmmm ....
Imagine no religion and one sees a world ruled by atheist tyrants - Pol Pot, Albania's Enver Hoxha, Stalin and Mao, to name a few - who have murdered tens of millions in modern efforts to cleanse society of religion.
American Muslims, Baptists, Jews, Christians, Buddhists, Mormons, Quakers, Amish, etc., don't erect billboards saying "Imagine No Atheists." They don't advocate government force to cleanse atheist expressions and teachings from the public square. They don't imply that atheists are "irrational," even though atheists claim absolute knowledge. They don't advocate theft and desecration of atheist property, even though an atheist hero in Minnesota stole and destroyed the Catholic Eucharist.
Democrats will nominate a Christian gentleman who respects others. It's likely they didn't invite atheists to their faith service because they didn't want embarrassing guests. Atheists might bring pseudointellectual proselytizers, who are intolerant, self-aggrandizing and rude. Atheists should fund universities and hospitals. They should feed and clothe starving kids. They should act more like Christians and Jews. If they do some of that - if they contribute to a diverse humanity - they might get better party invites.
In 2000, the Gates Foundation endowed the University of Cambridge with $210 million for the Gates Cambridge Scholarships. The Foundation has also pledged over $7 billion to its various causes, including $1 billion to the United Negro College Fund. According to a 2004 Forbes magazine article, Gates gave away over $29 billion to charities from 2000 onwards. These donations are usually cited as sparking a substantial change in attitudes towards philanthropy among the very rich, with philanthropy becoming the norm.[53] Buffett, who was the world's second richest person,[54] announced on June 25, 2006 that he has pledged to give the foundation 10 million Berkshire Hathaway Class B shares, spread over multiple years through annual contributions.[55]Is it possible that the editors of the The Gazette don't know what they're talking about? Or is criticism like that just being rude?1
Gates announced on June 15, 2006 that he would move to a part-time role within Microsoft, leaving day-to-day operations management in July 2008 to begin a full-time career in philanthropy, but would remain as chairman and advisor.[38] Gates credited Buffett with influencing his decision to commit himself to charitable causes.[56] Days later, Buffett announced that he would begin matching Gates's contributions to the Gates Foundation of up to $1.5 billion per year in stock.[57] Buffett helped to guide the foundation to give its endowment away quickly. It became one of the few charitable organizations with a lifespan, promising to spend all of its resources and to close within 50 years of the deaths of its founders.[58]
Both Warren Buffet and Bill Gates have been ardent supporters of Planned Parenthood, a non-profit organization that receives financial support from the Buffet and Bill and Melinda Gates Foundations. Planned Parenthood performs approximately 20% of all abortions in the United States. Planned Parenthood receives almost a third of its money in government grants and contracts ($336.7 million in FY 2007) with the rest coming from clinic income and donations from wealthy individuals such as Bill Gates.
1. The organizations that I contribute to are Médecins Sans Frontières, Greenpeace (when I'm not mad at them), and Mothers Against Drunk Driving. I'm probably not going to give to MADD any more because I disagree with their position on the legal drinking age. I will not give money to any religious charity because they often use to money to support causes that I strongly disagree with.
[Hat Tip: Hemant Mehta at Friendly Atheist]
[Photo Credit: Bill Gates Kicks Ass]
Trichoplax adherens is a very simple animal that moves about on surfaces like a gigantic amoeba and ingests any food that it flows over. There are thought to be several species of Trichoplax in addition to Trichoplax adherens. 
