Those of us so fortunate as to have worked under his guidance learned how to think freely, yet rigorously, and how to dream big and gamble on new adventures. We learned from Oscar how to free ourselves from convention, yet abide by the principles of science as crafted by its most honorable pillars. We remember two pieces of advice given by Oscar: “Don't believe everything you read in the scientific literature” and “There are a thousand Ph.D. thesis projects in a mound of dung.” The latter brings to mind the famous phrase of Vannevar Bush that science is an “endless frontier.” Oscar Miller was comfortable on the frontier of the unknown; he taught us that it is only on the frontier that discoveries of significance can be made. Our community of science will miss Oscar, as will all his dear friends and family. A good man has passed.Most of you have never heard of Oscar Miller but you've seen his work. He invented a technique for looking at genes in the electron microscope. The beauty of his technique, called "chromatin spreads" is that it shows genes in action. They are captured in the act of being transcribed and you can see the RNA being produced.
McKnight, S., Beyer, A., and Gall, J. (2012) Retrospective. Oscar Miller (1925-2012). Science 335:1457. [DOI: 10.1126/science.1220681
We must begin with a few round truths about myself: when I get into a debate I can get very, very hot under the collar, very impassioned, and I dare say, very maddening, for once the light of battle is in my eye I find it almost impossible to let go and calm down. I like to think I’m never vituperative or too ad hominem but I do know that I fall on ideas as hungry wolves fall on strayed lambs and the result isn’t always pretty. This is especially dangerous in America. I was warned many, many years ago by the great Jonathan Lynn, co-creator of Yes Minister and director of the comic masterpiece My Cousin Vinnie, that Americans are not raised in a tradition of debate and that the adversarial ferocity common around a dinner table in Britain is more or less unheard of in America. When Jonathan first went to live in LA he couldn’t understand the terrible silences that would fall when he trashed an statement he disagreed with and said something like “yes, but that’s just arrant nonsense, isn’t it? It doesn’t make sense. It’s self-contradictory.” To a Briton pointing out that something is nonsense, rubbish, tosh or logically impossible in its own terms is not an attack on the person saying it – it’s often no more than a salvo in what one hopes might become an enjoyable intellectual tussle. Jonathan soon found that most Americans responded with offence, hurt or anger to this order of cut and thrust. Yes, one hesitates ever to make generalizations, but let’s be honest the cultures are different, if they weren’t how much poorer the world would be and Americans really don’t seem to be very good at or very used to the idea of a good no-holds barred verbal scrap. I’m not talking about inter-family ‘discussions’ here, I don’t doubt that within American families and amongst close friends, all kinds of liveliness and hoo-hah is possible, I’m talking about what for good or ill one might as well call dinner-party conversation. Disagreement and energetic debate appears to leave a loud smell in the air.
"The Myth of Junk DNA" is actually quite easy to read. We’ve excerpted a number of passages here at UD. The interesting part is that Darwinists thought that the presence of huge amounts of junk DNA was evidence for their position.If Barry Arrington had bothered to read my review of Wells' book he would know that this is a lie. You can read the entire series of posts at: The Myth of Junk DNA by Jonathan Wells but I want to draw your attention specifically to my comments on the history of the controversy: Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].
No insulting people. This means not calling them abusive names or making insulting insinuations about them which according to my judgment unnecessarily demean them as a person or which I take to be intended to demean them as a person. You may charge that people’s ideas are false, harmful, irrationally derived, etc. You may substantiate charges that someone’s personal behavior deserves moral disrepute where that’s relevant. You may critique an individual’s standards of evidence or question their commitment to reason over faith. But when you do things like this, stick to substantiatable charges. Use words which clearly specify what specific thing makes a person or institution’s ideas, beliefs, behaviors, attitudes, etc. worthy of criticism. Abusive names (like “stupid”, “moron”, “asshole”, “jerk”, “douchebag”, “idiot”, “motherfucker”, “dick”, “cunt”, “nigger”, “Feminazi”, “shitbag”, “mental midget”, “twat”, “fuckwad”, “retard”, “homo”, “fag”, “tranny”, “bitch”, “nutcase”, “crazy”, etc.) are emotional expressions meant solely to hurt other people. They are social equivalents of physical assaults.I know where they're coming from. They're talking mostly about racist and sexist comments since that's their main concern on Freethought Blogs, for now.
“Stupid” is just not a word that smart people have ruining their self-esteem from the time they’re little kids.When I use the word "IDiot" I fully intend to bash the IDiots for their stupid ideas. Why? Because their ideas are stupid and they really are idiots.
And even yet, it is a false and belittling word that is counterproductive to constructive discourse. Calling someone stupid tempts them to either slink away in shame or to fight back with equal emotional abuse.
There are perfectly good words for telling someone that a specific idea is no good. False, empirically refuted, fallacious, absurd, illogical, unsupported by evidence, irrational, rationally indefensible, superstitious, biased. All these might work and many more. There’s no need to then personalize it by calling the person stupid or the idea stupid, which has the implication of bashing the person for thinking it.
Also congratulations to our very own Uncommon Descent author johnnyb (Jonathan Bartlett) for his work being mentioned in Wood’s paper. To my knowledge, the current tally of Uncommon Descent authors and commenters that have been published or mentioned in scientific journals: William Dembski, Michael Behe, Nick Matzke, Rob Sheldon, Caroline Crocker, Winston Ewert, Paul Nelson, Cornelius Hunter, Granville Sewell, John A. Davison, Allen MacNeill, Andrea Bottaro, Abbie Smith, Peter Olofsson, Albert Voie, Andras Pellionisz, Albert De Roos, Walter ReMine, Paul Giem, Jonathan Sarfati, Arthur Hunt, Steve Matheson, Larry Moran, johnnyb, Eric Anderson, Casey Luskin, and yours truly scordova. [If I missed anyone, please chime in.]IDiots! There's no other word to describe them.
As a first step, geneticists need to step back from the current curriculum and decide what 21st century students really need to know about genes and inheritance. These decisions should be based on how students will use what they learn, and not on what we as geneticists value.She proposes that modern genetics courses should concentrate on subjects that really interest students. Subjects like ...
Is genetic testing a wise thing to do? Is it a sound financial investment? Should I have full access to my genetic information? Should my insurer and my employer? Should athletes be tested for genetic modifications (“gene doping”)? Is it ethical to DNA-fingerprint all convicted criminals? All suspects? Did my genes make me gay? Are genetically modified foods safe? Are cloned animals ethical? How different are human races, and how different are we all from chimpanzees and gorillas?I explained in an earlier posting why I think this is wrong: Questions for Genetics Students. My main concern was that we might be sacrificing fundamental concepts and principles of genetics (i.e. science) in an attempt to appeal to students.
Many of these questions are ones bioethicists have been contending with for years. Bioethics is a multi-disciplinary field that is usually occupied by philosophers and healthcare professionals, but in the last twenty years it has seen an influx of lawyers, scientists, and people from many other disciplines.Now, I rarely agree with anything posted on The Best Schools but this is a legitimate concern.
Redfield suggests that it is the role of the scientist to address ethical questions. However, something that Redfield does not state in her paper, is that scientists are rarely trained in anything that would be helpful in assessing ethical issues, such as moral philosophy or rhetoric, and most programs do not include history and philosophy of science.
My friend, Rob Allore, taught with me for several years. He's a scientist and a Jesuit priest. This year I'll be teaching with another friend, Chris DiCarlo, a philosopher and author of How to Become a Really Good Pain in the Ass: A Critical Thinker's Guide to Asking the Right Questions.
Redfield, R. (2012) "Why Do We Have to Learn This Stuff?"—A New Genetics for 21st Century Students. PLoS Biol 10(7): e1001356. [doi:10.1371/journal.pbio.1001356]
Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree. They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 – Aug. 1 in Boston, Mass.Read more »
An expectant crowd gathered last night inside an airplane hangar at a flight school in Palo Alto, California to hear the winners of the second annual Google Science Fair. The grand prize went to Brittany Wenger, 17, of Sarasota, Florida, who wrote a computer program to help doctors diagnose breast cancer less invasively. Jonah Kohn, 14, of San Diego, Calif. won his age category for creating a device that converts sound into tactile vibration to improve the music-listening experience for the hearing impaired; and a trio from Spain won the 15 to 16 age category for documenting the hazardous and non-hazardous organisms found in water from different parts of their country.Anna Kuchment works for Scientific American and posts on a blog called Budding Scientist: Everything you always wanted to know about raising science-literate kids.
Image Credits: Charlton Heston (top), Tombstone (bottom)
In any single population, the behavior of mtDNA is rarely outside the very wide range of dynamics that happen by genetic drift alone, but that's more a sign of the extremely wide range of possibilities that drift allows. (This is why it took so long to demonstrate a problem with mtDNA in phylogenetic reconstruction). Now we know of many instances like polar bears, where the mtDNA genealogy has a different topology than that typical of nuclear genes. Moreover, we know that across many populations of different species, mtDNA is systematically less variable than the expected ratio from the nuclear genome. So it seems that once it enters a population, mitochondrial DNA sometimes spreads more rapidly and broadly than the typical gene. This dynamic sometimes may reflect extreme population histories, such as population bottlenecks and large-scale migrations. But in many cases it probably reflects selection on the mitochondrial genome.This is one of those issues where a little bit of evidence would be extremely helpful. Is it true that the fixation of foreign mitochondrial DNA is more common than, say, the fixation of Y chromosomes or the fixation of X-linked genes? What about other genes? Does maternal inheritance of mitochondria influence fixation?
The problem is that, for reasons we don’t fully understand, mtDNA also moves between species during hybridization much more readily than does nDNA, and that can screw up species relationships. This is true for both animals and plants, and not just for mtDNA either: in plants, DNA from another organelle, the chloroplasts (site of photosynthesis, this DNA is called “cpDNA”) also moves between species more readily than nDNA.Is it really true that mtDNA is more commonly fixed than nuclear alleles? Is it still true when you take into account maternal inheritance? I hope someone assigns this problem to a graduate student and I hope the graduate student takes care to rule out drift and accident.
....
We see this situation over and over again in biology. We don’t really know why mtDNA (and cpDNA) leak so readily between species, but we do know that this leakage makes it dicey to use only organelle’s DNA to make species trees. But the reason for this leakage compared to nDNA (so common to be almost a “rule of biology”) would make a useful paper topic for some enterprising graduate student.
Image Credit: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., © Pearson Education Inc. page 419 [Pearson: Principles of Biochemistry 5/E]
Hailer F, Kutschera VE, Hallström BM, Klassert D, Fain SR, Leonard JA, Arnason U, Janke A. (2012) Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347. [Abstract] [DOI: 10.1126/science.1216424]
Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A., Tomsho, L.P., Kasson, L., Zeyl, E., Aars, J., Miller, W., Ingólfsson, O., Bachmann, L., and Wiig, O. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl. Acad. Sci. (USA) 107:5053-5057. [doi:10.1073/pnas.0914266107]
Millera, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., et al, (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. (USA) Published online before print July 23, 2012. [doi: 10.1073/pnas.1210506109]
[Hat Tip: RichardDawkins.net]
Mitt Romney’s stump speech during the Republican primaries was filled with appeals to his party’s conservative base, but none consistently inspired more heartfelt cheers than his promise to “stop the days of apologizing for success at home and never again apologize for America abroad.” The statement speaks to the widely held suspicion on the right that liberals in general, and Barack Obama in particular, prefer other forms of democracy (especially those that prevail in Europe) to the American way of life.The essence of her thesis is that: (1) several European countries have laws prohibiting Muslim women from wearing the burqa in public, (2) The Swiss government bans the building of minarets outside mosques, and (3) The Norwegian mass murderer, Anders Behring Breivik, didn't like Muslims. The United States hasn't done any of these things. That's because Americans are much more tolerant of other religious beliefs than Europeans.
Martha C. Nussbaum’s new book could serve as Exhibit A in liberalism’s defense against this charge. The author of 17 previous books on a wide range of topics — from classical Greek philosophy and tragic drama to modern law, literature and ethics — Nussbaum is one of America’s leading liberal thinkers. In “The New Religious Intolerance,” she turns her attention to the rise of antireligious — and specifically anti-Muslim — zealotry since the terrorist attacks of Sept. 11, 2001. Though she writes in her opening chapter that intolerance disfigures “all Western societies,” it quickly becomes clear that there have been far fewer incidents of bigotry in the United States than in Europe — because of America’s vastly superior approach to guaranteeing the rights of religious minorities. When it comes to freedom to worship, at least, Nussbaum is an unabashed proponent of American exceptionalism.
The core of the book explores three preconditions of securing religious liberty for minorities — and in all of them the United States does a much better job than Europe. First, a nation must commit itself to protecting the greatest possible freedom of conscience that is compatible with public order and safety — a principle that the United States codifies in the First Amendment’s disestablishment of religion and guarantee of religious free exercise....Wow! It's news to me that the United States is a paragon of religious tolerance but perhaps that's just my anti-American bias. (For the record, Roger Williams was English, not American, and most of the other colonies were somewhat less tolerant.1)
The second precondition of religious liberty is an impartial and consistent civic culture. On this measure, Europe fares especially badly, as Nussbaum demonstrates by methodically exposing the double standards and bias at play in the arguments for banning the burqa.
Finally, there is the need for “sympathetic imagination” on the part of citizens. Here the United States has long taken the lead, cultivating respect for religious differences since the 17th century, when Roger Williams founded Rhode Island, the “first colony (anywhere in the world, it seems) in which genuine religious liberty obtained for all.” Nussbaum is particularly impressed with Williams’s respectful treatment of the Narragansett Indians, whose language and culture he struggled to understand at a time when most of the colonists thought of them as beasts or devils.
As Nussbaum notes, the American and European developments differ in important ways. Above all, she writes, nothing in the United States “even remotely approaches the nationwide and regional bans on Islamic dress in Europe, or the nationwide Swiss minaret referendum” — let alone an anti-Islamic massacre.I guess I'll have to read the book to see if this is what she really thinks. I hate it when that happens.
1. New Amsterdam, the Dutch colony, was noted for religious tolerance. The French colonies in Canada (somewhat tolerant) were on very good terms with many native tribes. The Narragansett Indians were eventually converted to Christianity but not until many of them had been killed or shipped off to slavery in the Caribbean.
I've been following the latest kerfluffle on the fusion of two chromosome into one during human evolution. I understand the superficial dispute involving Carl Zimmer. He had the audacity to ask for evidence to back up a claim being made by the IDiots on their Facebook page and they responded by going nuclear [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].
The evidence from chromosomal fusion, for one, is strikingly ambiguous. In the Darwinian presentation, the fact that humans possess 23 chromosome pairs and great apes 24 clearly points to an event in which human chromosome 2 formed from a fusion, leaving in its wake the telltale sign of telomeric DNA — normally appearing as a protective cap at the end of the chromosome — in the middle where it doesn’t belong. Ergo, common descent.That's it? The fusion event could have happened relatively recently in human evolution so it's no big deal? And if you don't buy that, then maybe it didn't happen at all because the junction sequence isn't exactly what a typical IDiot might expect if evolution were true?
But Casey [Luskin, of the Discovery Institute and co-author of the book] explains, there’s a lot wrong with this inference. Even if there was such an event and humans once had 24 chromosome pairs, it doesn’t at all follow that this happened in some prehuman past. Nothing stands in the way of picturing a human population bottleneck accomplishing the spread of a fused chromosome 2 from part of an early human community to all of it.
But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.
1. I haven't read the book. It's on order but it still hasn't been released in Canada (see Amazon.ca).
[Hat Tip: PZ Myers]
I thought the question I asked was pretty simple. I wasn’t asking to hold a Lincoln-Douglas debate. I just asked what the evidence was for one of the claims made by the creationists.David Klinghoffer, being David Klinghoffer, responded with a blog posting on Evolution News & Views: We Called Out Darwinist Critic Carl Zimmer, and He Folded.
Now it seems that in order to get that answer, I can either buy a book–which apparently is based on no peer-reviewed research of the authors, but just cherry-picked quotes from a ten-year old paper–or I can donate my time to write several thousands words for free for a creationist web site.
Making this offer even richer is Klinghoffer’s ground rules about focusing “strictly on the ideas, not on the personalities.” Klinghoffer himself has used Evolution News & Views to call people pathetic, a worthless bully, cowards, illiterate, and “a tyranny of the unemployed” (referring to Wikipedia editors). In one piece he wrote for Evolution New and Views, Klinhoffer mocked a post by a science blogger as “preening and self-congratulatory.”
That blogger happened to be me.
I will answer Mr. Klinghoffer publicly: no thanks. I never asked for a debate, and your arbitrary decrees, such as a mysterious thousand-word cutoff (my blog post on the chromosomes alone clocked in at over 2,000 words) make it even less appealing. I am particularly opposed to web sites that do not allow readers to comment. That’s how I ended up on Facebook in the first place–because the Discovery Institute’s web sites do not permit commenting. You, on the other hand, are more than welcome to leave a comment on my blog. My comment policy is very lax: I only throw out commenters who curse uncontrollably, hawk their own wares, or can’t stay on topic after repeated warnings. We have a thriving, fascinating discussion here, one from which I regularly learn new things from my readers. You might too.
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.Sort of makes you wonder, doesn't it? Do you think the IDiots really are interested in debating science or is it only on their own terms, on their own blog, with no comments, and moderated by their own kind?
This work addresses a very important question with big/deep/fundamental importance to the colossal problem of the origin of meiotic sex in eukaryotes. The question is 'Do bacteria have any processes that evolved because of selection for recombination of chromosomal alleles?' We think this selection is the reason for the success of meiotic sexual reproduction in eukaryotes, but compelling evidence for this has been elusive. Bacteria have four well-studied processes that do generate homologous recombination; three that transfer DNA between cells and one that carries out homologous recombination. But almost every aspect of these processes has been shown to cause recombination as an unselected side effect of processes selected for other functions.I don't think sex evolved in eukaryotes in order to promote mixis so this argument doesn't resonate with me.
[Image Credit: Rosie Redfield]
