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.
Anna Kuchment was there [Google Science Fair: Winners tackle breast cancer, hearing loss and water quality]. Just once, I'd like to see a science fair winner who actually did science and discovered something about the natural world that has nothing to do with technology or applications.
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.
I heard on CNN that applications for gun permits are on the rise in Colorado. Apparently there are people who think that arming everyone will cut down on crime. They seriously believe that if more people in the Aurora Theater shooting were packing then there would have been fewer deaths and injuries. The idea is that a gunfight between the psychotic killer and an average citizen would have resulted in the killer's death.
Here's a bit of news from Toronto that might help put this in perspective. On June 2, 2012 a gang member opened fire on another gang member in the food court of the Toronto Eaton Centre. The intended target was killed but so was a nearby shopper. Three others were wounded. On July 15, 2012 two or three rival gang members decided to have a gunfight at a barbecue in a Toronto suburb. One of them was wounded. Two innocent bystanders were killed and 22 others were wounded [Scarborough shootings: What really happened on Danzig?].
Turns out that the average citizen isn't a very good shooter. More often than not, they miss their intended target and hit someone else. Lots of people die in gunfights, not just the bad guys—it's called collateral damage.
Imagine what the death toll in Aurora might have been with more than one person blasting away with an automatic weapon.
All civilized nations have strict gun control laws. Their citizens have this strange notion that killing other people is never a viable option and they can't imagine why anyone would deliberately buy guns with the intention of shooting a fellow citizen, even in self defense or prevention of a presumed crime.
I guess some nations have a long history of solving problem with gun violence and it's difficult to abandon that option.
Image Credits: Charlton Heston (top), Tombstone (bottom)
Many species are not really "species" according to the biological species concept. They are not reproductively isolated from their closest relatives. A little bit of hybridization occurs in nature leading to the invasion of "foreign" alleles into the main population; a phenomenon known as gene flow.
Sometimes the invading alleles can become fixed (or very prevalent) in the population. This is what is presumed to have happened with Neanderthal or Denisovan alleles in modern humans. Rare matings between modern human ancestors and Neanderthal, for example, led to some gene flow between the populations [How many species of humans were there?].
The spread of invasive mitochondria is an extreme example of the fixation of invasive alleles. The example of polar bear evolution [Speciation in Bears] shows us that mitochondrial DNA can enter a population through a rare mating with an individual from another "species" and then become fixed in the new population over many thousand years.
The question is how does this fixation of "foreign" mitochondria occur? Is it an accident due to random genetic drift or do the foreign mitochondria confer a selective advantage over the original mitochondria? It seems unlikely that the mitochondria in one population (e.g. brown bears) are better than those in a foreign population (e.g. polar bears) that has adapted to a different environment.
John Hawks seems to want to have his cake and eat it too [Polar bear mtDNA replacement] ...
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?
Jerry Coyne suggests that there's something special about mitochondria (and chloroplasts) [A new study of polar bears ...].
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.
....
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.
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.
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]
I read an interesting article a few months ago. It was a study of the phylogeny of bears with an emphasis of the origin of polar bears. In theory, it should be possible to put a date on the speciation event and to identify the probably ancestor of the modern polar bear.
The first thing you have to know is that polar bears and brown bears are not distinct species as defined by the biological species concept. This definition of "species" requires that there be no interbreeding with other populations, otherwise it's not a true species. (See Jerry Coyne's analysis of the problem with respect to humans.)
Polar bears and brown bears can mate to form hybrids, although this doesn't happen very often in the wild because the two "species" are geographically separated. The interesting question is when did these two populations diverge.
Many people thought the question had been answered a few years ago when Lindqvist et al. (2010) published the sequence of polar bear mitochondrial DNA ad compared it to that of other bears.
The result is shown here on the left in a figure taken from the recent paper in Science (Hailer et al, 2012). The Lindvist et al. paper showed conclusively that polar bears are relatively young as a "species" (about 150,000 years) and that they clearly arose from within the brown bear clade.
This result was somewhat surprising but not revolutionary. However, there were some experts on speciation who, questioned the conclusion; notably, Jerry Coyne [Do “polar bears” exist?]. They cautioned that using mitochondrial DNA could be misleading.
The latest study in Science shows that their concerns were justified. Hailer et al. (2012) lookd at 14 nuclear genes and constructed the tree shown shown below on the right.
This study indicates that polar bears diverged from brown bears about 800,000 years ago. Furthermore, the two populations of bear (brown and polar) form distinct clades.
What does this mean? It probably means that about 150,000 years ago there was a brief fling between a male polar bear and a female brown bear. The female offspring, carrying brown bear mitochondria, mated with male polar bears and all of their progeny contained brown bear mitochondria with mixtures of brown and polar bear alleles in their nuclei. Over time, the brown bear mitochondria became fixed by random genetic drift in the polar bear population.
This explains why the two trees differ and why you have to be cautious about using mitochondrial DNA in constructing phylogenies.
The story doesn't end there.
Just this week, a new paper appeared in PNAS confirming this result (Miller et al., 2012). Many of the authors are the same ones on the Lindqvist et al. (2012) paper. They are refuting the conclusions of their earlier paper by now showing that the sequence of nuclear genes indicate an earlier divergence of brown bears and polar bears.
I put off blogging about the Science paper because there were more important things to do and because it would have been difficult to explain the problem and the explanation. Fortunately, Jerry Coyne has now taken up the task of explaining the result at: A new study of polar bears underlines the dangers of reconstructing evolution using mitochondrial DNA. Please read his explanation of gene flow in bears based on his extensive knowledge of speciation.
The only issue I have with Coyne's explanation is that I don't think he gives enough emphasis to the idea that fixation of brown bear mitochondria in polar bears could be a genetic accident.
UPDATE: Ed Yong of Not Exactly Rocket Science already wrote about this three months ago [Polar bear origins revised – they’re older and more distinct than we thought]. John Hawks emphasizes Jerry Coyne's warning about using mitochondrial DNA and discuss the implications for hominid evolution [Polar bear mtDNA replacement].
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]
