This month marks the 50th edition of Carnival of Evolution. The latest version is hosted on Teaching Biology. Read it at: Carnival of Evolution 50: The Teaching Edition
Welcome to the 50th edition of the Carnival of Evolution! In keeping with the name of the blog, this edition will have an educational theme to it. The posts are categorised into modules. Each module has an introduction by me about why it’s important to learn about it, and each post has a short blurb by me on the post’s content and, if appropriate, personal comments. I include a further reading list with links to relevant books and review papers for further discussion/background information. Most of these papers are behind draconian paywalls. If you don’t have institutional access, my e-mail can be found here. Just saying.
I've got seven posts from Sandwalk on the list. That's a record for me and it means one of two things: (a) my posts are getting more interesting, or (b) they were hard up for posts this month.
The next Carnival of Evolution (August) will be hosted by The Stochastic Scientist. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.
I am an atheist. What does that mean? It means that I have never seen any evidence that supernatural beings exist. I don't think the devil exists, I don't think that Zeus exists, or Thor, or Gitche Manitou. I don't believe that the god of the Bible exists.
There are thousands of gods that I don't believe in. Some of them have imaginary reputations of cruelty, some of them are supposed to be kind, and some of them are indifferent. It doesn't matter to me because the one thing they all have in common is that they don't exist.
I'm told that some people believe in gods who are supposed to be kind. Those people have trouble understanding why the world is evil. It's a problem that has spawned an entire discipline called theodicy. Bully for them. It's their problem, not mine. I don't accept their premise.
For reasons that seem incomprehensible to me, there are some atheists who really like to talk about the problem of evil as though it were a real problem. Jason Rosenhouse is one of them. You can read his latest at: The Only Reasonable Reply to the Problem of Evil. Jerry Coyne is another. See his post from yesterday at: More Sophisticated Theology: The world’s worst theodicy.
Well, maybe not all the IDiots really like me but David Klinghoffer is sure a big fan [You Go, Larry Moran!]
Just think. Imagine you're one of those undecided fence-sitters on the Darwin question that he thinks he's appealing to. Or say you're a journalist, reflexively pro-Darwin but one who's never had an occasion to follow the controversy in the past. Now something's come up in the news that touches on evolution and you figure you'll sample the arguments on both sides with a view to writing on it.
You stumble upon the blog, named in honor of Charles Darwin's famous "Sandwalk," of a University of Toronto biochemist and man of mature years who writes this way, over and over and over. He will, for example, reproduce a photo of an Internet Darwin critic with the words "I'm an IDiot" superimposed. This same biochemistry professor and Darwin advocate writes blog posts trying to defend and recommend this approach, including his favorite term "IDiot," to others. Are you impressed? That's a self-answering question.
Of course it would be different if Moran were not a guy who teaches in a relevant scientific field at a university you've heard of. If he were just another one of those pseudonyms that populate comment boxes around the Internet, and who dish out their own vicious/viscous stuff, no one would care. Much as it's distasteful to read Moran's blog (as I very rarely do), there's reason to be grateful for its existence.
Now watch, he's going to trawl the Internet for a picture of me and write "I'm an IDiot" on it and post that.
If I were purely strategic, I would say: Give us more, Larry Moran! Pour it on. Please!
Happy to oblige.
Cells require both a source of energy and a source of building blocks for synthesis of organic (carbon-containing) molecules. Some of the most interesting species are those that only need inorganic molecules to survive. They can make all their carbon compounds from carbon dioxide (CO2) by "fixing" it into more complex molecules like sugars.
These species are called "autotrophs'" The most familiar are the plants. As most of you know, plants can grow quite successfully in a glass of water (with minerals). Animals are the most obvious example of "heterotrophs," species that need to be supplied with complex organic molecules in order to survive. We can't survive on water alone. We need to get sugars and a host of other compounds from eating other (mostly dead) species.
Oscar Miller died last January. Steven McKnight, Ann Beyer, and Joseph Gall (2012) wrote up a nice tribute to their former mentor.
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.
His photographs are in all the textbooks. The example shown here is ribosomal RNA genes being transcribed in the nucleolus. The "Christmas tree" structures are due to multiple transcription complexes transcribing the same gene. (Ribosomal RNA genes are very active.) The newly synthesized RNA is splayed out on either side of the DNA being transcribed. It would look like a cone inside the cell but it appears two dimensional here because it has been spread out on an electron microscope grid.
The initial transcripts are quite short but as the transcription complexes progress along the gene they get longer and longer giving rise to the Christmas tree structure. You can learn a lot from looking at these fantastic pictures. Notice that there are multiple ribosomal RNA genes arranged in tandom along the genome with relatively short spacers between them. These photos were taken before cloning and sequencing were invented so it was our among our first clues about gene organization in eukaryotes.
There's not much actual data from the 1960s that's still shown in modern textbooks. Remember Oscar Miller the next time you see his work.
McKnight, S., Beyer, A., and Gall, J. (2012) Retrospective. Oscar Miller (1925-2012). Science 335:1457. [DOI: 10.1126/science.1220681
Last week we discovered two chemically similar reactions that were catalyzed by related enzymes of the same gene family [Monday's Molecule #178]. Today's molecule is a lot more important than any of the four molecules from last week although you won't find it in most biochemistry textbooks. (Surprise! It's in my book.)
What is this molecule (IUBMB name) and why is it important?
Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)
Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)
In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.
Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.
Comments are invisible for 24 hours. Comments are now open.
UPDATE: The molecule is 2-carboxy-3-ketoarabinitol 1,5-bisphosphate, an intermediate in the reaction catalyzed by rubisco (ribulose 1,5-bisphosphate carbozylase-oxygenase). This is the main enzyme responsible for carbon dioxide fixation in plants and one of the most enzymes on the planet.
This week's winners are Bill Chaney and Raul A. Félix de Sousa.
Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
I can't believe it was almost five years ago that I posted a quotation from Stephen Fry on the differences between dinner conversations in Britain and America [Two Cultures].
Here it is again because it's relevant to our discussion about IDiots. It's from: Getting Overheated (Nov. 19, 2007).
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.
Have you ever been at a social gathering and heard someone proclaim, somewhat proudly, that they just don't "get" math? They dropped it in high school as soon as they could. If so, you probably resisted telling them how sorry you are that they are stupid and you probably avoided getting into a discussion about people who say the same thing about history or literature. You know that those same people would be appalled to hear you say that you don't "get" the arts and dropped them as soon as you could.
If Andrew Hacker has his way, people who can't pass a simple math course will never have to apologize again. He proposes, in the New York Times, no less, to eliminate algebra from high school [Is Algebra Necessary?]. (Andrew Hacker is a former professor of political science.)
The "news" on Uncommon descent continues to amaze me. Today they put up a post with an ironic title: Sometimes, one runs into ID opponents who are just so confused ….
It caught my attention because my name was mentioned. Apparently some "ID opponent" read my take-down of Jonathan Wells' book The Myth of Junk DNA. This prompted the following response from "news" (lawyer, Barry Arrington).
"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?].
Ophelia Benson has put up several posts recently on the use of insulting terms in blog conversations. She is opposed. Ophelia recently linked to another Freethought blog called Camels with Hammers written by Daniel Fincke. Here's Ophelia's post: A camel with a hammer offers a tap upside the head. And here's Daniel's post: Making My Comments Rules Explicit: “Don’t Bully People With Insulting Names” and “Make Personal Charges Against Others Only In Egregious Cases”. Here's the one rule that I want to discuss; it's from Daniel Fincke's post but Ophelia quotes it approvingly.
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.
For the record, I do not condone those kind of insults. Nor do I condone accusing someone of racism or sexism without very good evidence.
On the other hand, I frequently use insulting words to describe stupid people. The most obvious example is my use of "IDiot" as a shorthand for Intelligent Design Creationist. A commenter on Daniel Fincke's blog suggested that words like "stupid" were okay since they aren't homophobic, sexist, or racist. Here's how Fincke responded ...
“Stupid” is just not a word that smart people have ruining their self-esteem from the time they’re little kids.
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.
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.
Here's where Daniel gets it wrong. I don't expect to convince the IDiots of the error of their ways any more than they intend to convince scientists by using insulting terms like "Darwinist," "materialist," and "stupid." There's no such thing as "constructive discourse" with creationists.
My audience is not the creationists I'm debating, it's the readers who might not have made up their minds about Intelligent Design Creationism. They will read the viscous attacks of these creationists on scientists (Darwinists) and wonder whether there's some truth behind them. I could reply with polite phrases like "rationally indefensible" "unsupported by evidence" and "empirically refuted" but that would be like bringing a flyswatter to a gunfight.
The general public needs to hear what passionate scientists really think of these IDiots. The best way to do that is to fight fire with fire. The idea is to plant in the public's mind the notion that these creationists are crazies and kooks, not respectable scientists with a different, but scientifically valid, opinion. We tried treating them politely for several decades and what did it get us? It got us leaders and politicians in many countries who think it's perfectly respectable to believe that evolution is false.
We were up against people like Jerry Falwell, Rush Limbaugh, and Michele Bauchmann but we were fighting with one hand tied behind our back. That's no way to win a fight like this.
The good news for the more polite proponents of rationalism, like Ophelia Benson and Daniel Fincke, is that they can be the "good cops."
There are (brief) times when I wonder if it's unfair to label all Intelligent Design Creationists (IDC's) as "IDiots." I see glimmers of hope on the IDC websites where it appears that at least one or two people might actually be exhibiting signs of intelligence.
Those thoughts are short-lived. It never takes the IDiots more than a few hours to disabuse me of any such sympathies.
Yesterday, for example, Sal Cordova (scordova) posted one of the most stupid things I've seen in a long, long, time. He was bragging on Uncommom Descent about a paper by Todd Wood that is about to be published was published last year in the Journal of Evolutionary Biology. This is big news for the IDiots because they don't publish much in the peer-reviewed scientific literature.
But he couldn't leave it at that. Look what he said next [Creationist Paper Published in Peer-Reviewed Biology Journal, UD Author Cited — Origins 2012 Conference] ...
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.
Rosie Redfield doesn't like the way genetics is taught in most university courses. She thinks we should re-design genetics courses (Redfield, 2012).
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.
Rosie's goals sound like noble goals but is it even realistic to address these issues in a genetics course? That's the question that Heather Zeiger asks in her post on Genetics Class 2.0.
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.
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.
Now, I rarely agree with anything posted on The Best Schools but this is a legitimate concern.
My position is that philosophers and healthcare professionals have been spectacularly unsuccessful at clarifying bioethical questions. I cringe just about every time I see a "professional" bioethicist on television. Most of them can't separate science from ethics and most of them are more concerned about appeasing religion than getting to the bottom of a difficult issue.
Scientists often make much more sense but that doesn't mean that all scientists are good at dealing with ethical issues. I teach a course that deals with ethical issues (cloning, reproductive technology, immunization) and I find that it's an excellent way to get students to think critically. However, I've learned a lot from my colleagues about ethics and philosophy over the years and I don't think I would be very effective without this background1.
I doubt very much that the average genetics teacher or TA can really be effective at handling ethical debates in their classrooms. I don't think you should build a course around such issues no matter how much the students want it.
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]
I'm going to keep hammering on this until it sinks in.
We don't know how life began but one of the more fanciful hypotheses is that it began in a primordial soup of organic molecules supplied by meteors, comets, and violent lightening storms. The idea is that the ocean was full of glucose, amino acids, and nucleotides. Glucose and similar carbohydrates supplied the energy for life. Amino acids spontaneously came together to form proteins. Nucleic acids arose by stringing together pre-existing nucleotides or nucleosides.
In the most extreme version, the ocean itself was the primordial soup and concentrations of organic molecules were sufficient to drive the formation of life. A simple back-of-the envelope calculation indicates that the concentration of typical amino acids would have been about 0.1 nM (10-10 M) [Can watery asteroids explain why life is 'left-handed'?]. This is an unlikely scenario [More Prebiotic Soup Nonsense]. You won't get spontaneous formation of polymers in water at that concentration.
What's Wrong with this Picture?
Biology New Net posted a press release today from the American Institute of Physics: Researchers dig through the gene bank to uncover the roots of the evolutionary tree. It advertises the work of William Duax and his colleagues, including some high school students who work in his lab on Fridays.
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.
New enzymes often evolve from old ones via a gene duplication event. This gives rise to gene families encoding evolutionarily related enzymes with similar, but different enzymatic activities.
There are two principle ways to evolve related modern enzymes with specific activities. The first way postulates an ancestral enzyme that catalyzes a specific reaction (e.g. A1 → B1). Following a gene duplication event, one of the copies evolves an enzyme that catalyzes a completely different (but chemically related) reaction: A2 → B2.
Most people think that this is by far the most common pathway. That's because they are used to thinking that enzymes are highly specific—that's what's emphasized in most biochemistry courses. They think that it should be possible to reverse engineer the evolutionary pathway on the right-hand branch and thus transform one enzyme to another.
