Does This Belong in a Scientific Journal?

The other day I was browsing through recently published papers in PLoS Biology and came across this one.

Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, et al. 2011 The Genomic Standards Consortium. PLoS Biol 9(6): e1001088. doi:10.1371/journal.pbio.1001088.

Abstract

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

I'm interested in this sort of thing since back in the olden days (1993) I spent a bit of time at GenBank exploring annotation issues with a view to correcting the growing number of errors that were being propagated in online databases.

It's an insoluble problem and I doubt very much that a new organization is going to help.

But that's not what I want to talk about. Near the end of the article in PLoS Biology you find this paragraph.

The Internet has resulted in a Cambrian explosion of productivity and data sharing through the adoption of a huge stack of agreed-upon protocols (standards) that allow many devices and programs to communicate to the transformative benefit of the everyday user [26]. Enabling access to user-generated content is key to harnessing the resources of a distributed community: Flickr has over 5 billion photographs uploaded, and Wikipedia has over 3.5 million English articles as of this writing. Standards for organizing sequence data will be similarly needed as sequencing instruments themselves, especially as these instruments are more and more commoditized and owned by individuals rather than institutions.

I'm sad to find this sort of content-free language creeping into scientific journals. We've been spared up to now but it looks like the 23 scientists listed as authors feel comfortable with this new style of writing.

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Losing Charlemagne

Back in October 2009 I published my genealogical connection to Emperor Charlemagne [My Family and Other Emperors]. It is wrong. I relied too much on the information found in Ancestry.com and much of that information is unreliable.

In my case the connection was through Ruhamah Hill (b ~1708) who married John Belden (1728 - ). They were British citizens who lived in Norwalk, Fairfield Country, Connecticut (a colony of Great Britain). The parents of Ruhamah Hill are often listed as William Hill and Abigail Barlow of Greenfield Connecticut but there's no evidence to support this connection. On the other hand, historical records say that Ruhamah Hill is the daughter of Captain John Hill (1669 - 1768?) of Westerley, Rhode Island and this seems much more reasonable since Captain John Hill married Ruhamah Wyer (1670 - ).

There goes my connection to Charlemagne and all of the other notables on the list.

Not to worry. The probability is high that I am a descendant of Charlemagne just like most others with any European blood [Are You a Descendant of Charlemagne?]. There are two other connections in my genealogy. I'm working on conformation.

Ms Sandwalk doesn't seem to have any ancestors that connect to European royalty but she is related to a number of very interesting people. Unfortunately, she's too embarrassed to let me mention them in public.

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For Your Amusement

vjtorley (Vincent Joseph Torley) has posted on Uncommon Descent. The title of his posting is Someone’s wrong. Who is it?. The issues is whether the similarities of mammalian embryos is PREDICTED by modern evolutionary theory. PZ Myers says "no" and Ken Miller probably agrees. They are both correct.

Do those similarities provide support for common descent even though they may not have been predicted by evolutionary theory? Yes, they do, in the same sense that common pseudogenes support evolution even though pseudogenes are not a necessary part of modern evolutionary theory.

So here's the question ... who is wrong about this issue?

1. PZ Myers
2. Ken Miller
3. Vincent Joseph Torley

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New York Legalizes Same-Sex Marriage

Same-sex marriage is legal in ten countries (Argentina, Belgium, Canada, Iceland, the Netherlands, Norway, Portugal, South Africa, Spain and Sweden). In Canada it has been legal for gays and lesbians to marry since July 20, 2005.

In the United States same-sex is legal in Connecticut, Iowa, Massachusetts, New Hampshire, Vermont, and the District of Columbia). A few hours ago it became legal in New York. I wonder if this will cause other states to make same-sex marriage legal?

The map shows where gays and lesbians have the same rights as other citizens and where those rights are restricted. I think it reflects a deep cultural divide in America and I wonder where this is going to end up? Is it possible that some of the red colored states will eventually change their minds on this issue?

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[Image Credit: modified from Wikipedia]

The Religious Left in Canada

The New Democratic Party's "Faith and Social Justice Commission" has produced a video to prove that you can be religious and socialist.

My position is that religion should be kept out of politics. There should not be a "Faith and Social Justice Commission" sanctioned by the NDP. (Is there also an "Unfaith and Social Justice Commission" for all those atheists who believe in social justice?)

I have no problem with individuals adhering to one religion or another but keep it personal. There's no need to band together in order to influence policy within the government or even within a party. Frankly I don't care why you support socialist progressive policies as long as you do. Don't try and make it look like religion is what motivates you to favor the left because that just makes you look as silly as the right-wing fundamentalists who use religion to defend their position.

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[Hat Tip: Canadian Atheist]

For Your Amusement

Bill Dembski has just posted an article titled Who Will Be Michele Bachmann’s Science Advisers?.

This is deeply ironic on many levels. Why would Bachmann need people to advise her about science? So far she's gotten along just fine without knowing a thing about science. A real science adviser would just confuse her.

I wonder if Dembski has anyone in mind? He surely can't be thinking of himself or any of his closest IDiot friends because, as we all know, there are Nobel Laureates who would be far better qualified.

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Pretty Money

Canada is about to release a new set of polymer banknotes. Watch the video to see all the security features and the cool windows in the notes. (BTW, is there any country other than the United States that has monocolor money? Is there a reason why the USA makes every denomination of bill the same color?)



What's on these banknotes? The $100 bill depicts Sir Robert L. Borden, Prime Minister of Canada from 1911 to 1920. Here's the description of the other images fron The Bank of Canada.

# Theme: Medical Innovation

Canadians have long been at the frontiers of medical research and as a result have helped to save millions of lives worldwide. Notable Canadian contributions include pioneering the use of insulin to treat diabetes, DNA and genetic research, the invention of the pacemaker, and the first hospital-to-hospital robot-assisted surgery.

Researcher at a microscope

The image of a researcher using a microscope depicts Canada’s long-standing commitment to medical research.

DNA strand

Deoxyribonucleic acid (DNA) is the genetic blueprint of life. Canadian researchers have been at the forefront of mapping our human genetic makeup in this field of medical science.

ECG

This electrocardiogram provides a visual cue to Canada’s contributions to heart health, including the invention of the pacemaker by John Hopps in 1950.

Insulin

The discovery of insulin to treat diabetes was made by Canadian researchers Frederick Banting and Charles Best in 1921.

It's nice that Canada is celebrating science.




The $50 dollar bill has a picture of William Lyon Mackenzie King who was Prime Minister from 1921–30 and from 1935–48. The other side has ...

# Theme: CCGS Amundsen, Research Icebreaker

The vastness and splendour of Canada’s northern frontier have helped to shape our cultural identity. The icebreaker plays an important role in the North, keeping Canada’s historic passages open, undertaking marine search and rescue, supporting isolated communities, and participating in international environmental research. The CCGS Amundsen helps Canada—the nation with the world’s longest stretch of Arctic coastline—to remain at the leading edge of Arctic research, providing the world’s oceanographers, geologists and ecologists with unparalleled access to the North.

CCGS Amundsen, Research Icebreaker

The Canadian Coast Guard Ship Amundsen became a research icebreaker in 2003. It is jointly operated by ArcticNet and the Canadian Coast Guard.

“Arctic” in Inuktitut

This syllabic text is taken from Inuktitut, a language of Canada’s Inuit population. It stands for “Arctic.”

Map of Canada’s northern regions

The map on the back of this note shows Canada’s northern regions in their entirety, including Inuit regions of the Arctic. This image was provided by Natural Resources Canada.

More mention of research and another language. The $50 dollar bill has words from three languages (French, English, and Inuktitut. (I think there's only two languages on American bills. )

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The Summer Solstice and Science Literacy

From time to time my colleagues and I discuss the basic requirements of science literacy. We envisage a group of intelligent people at a party discussing various topics. Let's restrict our discussion to Western European culture.

Everyone agrees that they should be familiar with the basic outlines of history (e.g. who did Paul Revere warn in 1775?) and politics (what's the difference between socialism and capitalism?). Everyone agrees that you would look like an idiot if you didn't know who Will Shakespeare was and what Hamlet said. Everyone agrees that you can't call yourself an intellectual if you don't know the difference between French Impressionists and Michelangelo. You're expected to know something about Socrates and Aristotle. You're expected to know at least a few foreign words and knowledge of a foreign language is almost a requirement.

You should know something about food even if it's only the difference between couche couche and curry. Any "intellectual" should be able to discourse for five minutes on a favorite wine. You get the picture—there are some things that you just have to know if you claim to be literate.

What about science? Are there any things in science that you just have to know if you want to be taken seriously as an informed literate person?

No, there aren't. We've all experienced the situation I describe where a group of non-scientists at a party or bar are showing off their knowledge. Knowledge of science and math is not a requirement. In fact, you get points if you brag about always being too stupid to understand mathematics and dropping it as soon as you could in high school, especially if you're a woman.

Are there scientific facts and concepts that you really should be expected to know if you claim to be literate? Yes there are, and it's up to us to make sure they are widely publicized.

Today's your chance to publicize one of those facts. The summer solstice happens two hours from now no matter where you are on the planet. Ask your non-science friends to explain the summer solstice (Northern Hemisphere). It's one of those simple science things that everyone should know about. Not being able to explain it is like not knowing that Libya is in Africa, Napoleon lost the battle of Waterloo, Charles Dickens wrote Oliver Twist, and Frank Lloyd Wright was an architect.

Can you explain the solstice? If so, you are on the way to scientific literacy. What are some other must-know scientific facts and concepts? Evolution is one. If you don't understand the basic concepts of evolution then you can't clam to be scientifically literate. My point is that I'd like to live in a world where you can't claim to be literate, period, if you aren't scientifically literate.

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[Image credit: Wikipedia]

Texas Prayed and God Answered

Back in April, Governor Rick Perry of Texas proclaimed a weekend of prayer (Friday, April 22, 2011, to Sunday, April 24, 2011). Texans were supposed to pray for God to relieve the terrible dought [Pray for Texas].

Bill Maher reminded me that it's been several months since Texans prayed so it's time to analyze the results.

On the site US Drought Monitor there are maps of the USA showing region of drought. The top map below shows the regions with severe drought (dark brown) for April 26, 2011, right after all the praying. The second map (below) shows regions of drought on June 14, 2011.

It looks like God hates Texas and/or Rick Perry. I'm told that Governor Perry is thinking of running for President of the United States. Is this a good idea?

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Creationist Logic

Help me out, dear readers. I can't for the life of me figure out the logic behind the latest posting at Uncommon Descent: If you make a prediction and it doesn’t happen ….

I'm serious. Although I often make fun of the IDiots, I usually try hard to understand the points they are trying to make so I can expose them as nonsensical. But this one has me completely stumped. On the surface the author seems to be saying that "Darwinism" made a prediction "based on core principles" that wasn't fulfilled. This is bad for "Darwinism."

What is that prediction?

The author ("News") starts with a quotation from The Myth of Junk DNA.

In 2010, University of California Distinguished Professor of Ecology & Evolutionary Biology John C. Avise published a book titled Inside the Human Genome: A Case for Non-Intelligent Design, in which he wrote that "noncoding repetitive sequences–'junk DNA'–comprise the vast bulk (at least 50%, and probably much more) of the human genome." Avise argued that pseudogenes, in particular, are evidence against intelligent design. For example, "pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered along the chromosomes like useless molecular cadavers." To be sure, "several instances are known or suspected in which a pseudogene formerly assumed to be genomic ‘ junk’ was later deemed to have a functional role in cells. But such cases are almost certainly exceptions rather than the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic tinkering for which nonsentient evolutionary processes are notorious."

Jonathan Wells, The Myth of Junk DNA (Seattle: Discovery Institute Press, 2011), pp. 26-27

This is a pretty accurate representation of what John Avise actually says except that it juxtaposes two separate facts. It's true that repetitive DNA sequences—mostly defective transposons—make up about half our genome. Then there's pseudogenes. They are found in the other half and they make up about 1% of the human genome.

Avise, and many others, point out that the presence of pseudogenes is inconsistent with good design and therefore poses a problem for Intelligent Design Creationism.¹ I note that the IDiots have consistently refused to address this problem. Instead, they try and convince their followers that pseudogenes don't exist.

Here's what Avise says in his book Inside the Human Genome: A Case for Non-intelligent design (p. 115). You can see that Wells accurately represented the actual argument that he (Avise) was making.

At face value, pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered among the chromosome like useless molecular cadavers. This sentiment does not preclude the possibility that an occasional pseudogene is resuscitated such that it contributes positively to cellular operations, several instances are known or suspected in which a pseudogene formerly assumed to be genomic "junk" was later deemed to have a functional role in cells. But such cases are almost certainly exceptions and not the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic genetic tinkering for which nonsentient evolutionary evolutionary processes are notorious.

It's important to make sure you understand the argument that Avise and others are making. When looking at the big picture the presence of thousands of pseudogenes in the human genome is a challenge for those who argue for Intelligent Design Creationism. The fact that a handful of these regions were misidentified as pseudgenes and now turn out to have a function cannot be taken as evidence that all of the 20,000 known pseudogenes have a function.

So, how does Wells deal with this challenge to his belief? On the next page of his book (p. 27) he says ...

But Is It True?
The arguments by Dawkins, Miller, Shermer, Collins, Kitcher, Coyne and Avise rest on the premise that most non-coding DNA is junk, wihout any significnat biological function. Yet a virtual flood of recent evidence shows that they are mistaken. Much of the DNA they claim to be "junk" actually performs important functions in living cells.

The following chapters cite hundreds of scientific articles (many of them freely accessible on the Internet) that testify to those functions—and those articles are only a small sample of a large and growing body of literature on the subject. This does not mean that the authors of those articles are critics of evolution or supporters of intelligent design. Indeed, most of them interpret the evidence within an evolutionary framework. But many of them explicitly point out that the evidence refutes the myth of junk DNA.

This is a classic "bait-and-switch." The argument from Avise and the others is mostly about the presence of pseudogenes. There is solid evidence that many pseudogenes are completely non-functional. There is evidence that non-functional pseudogenes have been inherited from common ancestors, strongly suggesting that the genes were inactivated in ancient ancestors and passed down to modern species as the evolved.

This argument is NOT about "most noncoding DNA." It's about that 1% of the genome that contains known pseudogenes. Unless that point is addressed directly (it isn't) then Wells is guilty of ignoring one of the main arguments of his critics.

But that's not the point of this posting. I'm concerned about the point that "News" makes in the recent posting on Uncommon Descent. He/she says ...

Darwinism predicts something, based on its core principles, and it doesn’t happen. And there are no consequences? Only on planet Darwin. Where all correct predictions originate in Darwin’s theory and are grandfathered as such by his loyal heirs. All incorrect predictions are “proved” to have originated elsewhere, no matter where they actually originated.

What are these predictions of "Darwinism"? It's surely not pseudogenes since no evolutionary theory that I know of predicted pseudogenes. Bacteria don't have many pseudogenes and that's perfectly consistent with evolutionary theory. Plant genomes have lots of pseudogenes and that's perfectly consistent with evolutionary theory. Yeast has a few pseudogenes but not nearly as many as plants and that's perfectly consistent with modern evolutionary theory.

Is "News" referring to junk DNA in general? That's not a prediction of "Darwinism" or any evolutionary theory that I know of. The fact that bacteria have very little junk DNA has never been taken as a fact that overthrows modern evolutionary theory. I'm unaware of any evolutionary biologist who predicted back in the 1960s that most of the mammalian genome would be junk and that this prediction was a requirement of modern evolutionary theory. The arguments of Avise et al. are not based on the "premise" that most of our genome is junk, they're based on the evidence that pseudogenes exist.

No prediction was made so no prediction has been refuted. The point that "News" is making seems illogical.

Unless I'm missing something obvious.

What about the predictions of the IDiots? Casey Luskin explains it [Intelligent Design and the Death of the "Junk-DNA" Neo-Darwinian Paradigm].

Proponents of intelligent design have long maintained that Neo-Darwinism's widely held assumption that our cells contain much genetic "junk" is both dangerous to the progress of science and wrong. As I explain here, design theorists recognize that "Intelligent agents typically create functional things," and thus Jonathan Wells has suggested, "From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much ‘junk'." [4] Design theorists have thus been predicting the death of the junk-DNA paradigm for many years: ...

and in Another Intelligent Design Prediction Fulfilled: Function for a Pseudogene ...

Darwinists have long made an argument from ignorance, where our lack of present knowledge of the function for a given biological structure is taken as evidence that there is no function and the structure is merely a vestige of evolutionary history. Darwinists have commonly made this mistake with many types of "junk" DNA, now known to have function. In contrast, intelligent agents design objects for a purpose, and therefore intelligent design predicts that biological structures will have function.²

Here's another prediction, according to Barry Arrington on Uncommon Descent [FAQ4 is Open for Comment].

ID does not make scientifically fruitful predictions.

This claim is simply false. To cite just one example, the non-functionality of “junk DNA” was predicted by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980), Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions. In contrast, on teleological grounds, Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004) predicted that “junk DNA” would be found to be functional.

The Intelligent Design predictions are being confirmed and the Darwinist predictions are being falsified. For instance, ENCODE’s June 2007 results show substantial functionality across the genome in such “junk DNA” regions, including pseudogenes.

Thus, it is a matter of simple fact that scientists working in the ID paradigm carry out and publish research, and they have made significant and successful ID-based predictions.

It seems like it's the IDiots that have hitched their star to a prediction about junk DNA. If any genome turns out to have a substantial amount of junk DNA then Intelligent Design Creationism is refuted. As it turns out, many genomes do have a lot of junk DNA in spite of what Jonathan Wells would have you believe. Thus, Intelligent Design Creationism is no longer a credible scientific hypothesis.

But you knew that already, didn't you?

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1. Most scientists actually argue a more specific point; namely, that the conservation of specific pseudogenes in different species is an especially serious problem for Intelligent Design Creationists.

2. It's interesting that Casey Luskin seems to know something about the motivations of the intelligent designer because when scientists point out that the genome doesn't look like it was designed this is not taken as an argument against the IDiot position. Instead it's taken as illegitimate science as pointed out by Wells in his book (p. 103), "Do arguments based on speculations about a creator or designer have a legitimate place in science? Not according to Canadian biologist Steven Scadding, who once wrote that although he accepted evolutionary theory, he objected to defending it on the grounds that a creator would or would not do certain things. 'Whatever the validity of this theological claim,' Scadding concluded, 'it certainly cannot be defended as a scientific statement, and thus should be given no place is a scientific discussion of evolution."

Junk Poll Results

Here are the results of the most recent poll on junk DNA. Below it is the result from several years ago. I realize that the questions are different but the shift toward favoring junk DNA is still a surprise. I'd like to think it's because more and more Sandwalk readers are becoming aware of the science behind junk DNA but it could be just that more "junkers" are reading my blog.

Is there anyone out there who changed their minds over the past few years? Is The Myth of Junk DNA going to convert everyone to rejecting junk DNA? I'll have to do another poll in six months to see if the Intelligent Design Creationists are having an impact.

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Zoë and Window Shopping

Don't you just hate it when bloggers post cute pictures of their children, grandchildren, cats, or molluscs?

Tough. Here's my granddaughter, Zoë, window shopping in Barcelona (Spain) a few weeks ago. The window looked so inviting she decided to check out the shop.

She's only 16 months old and already enjoys shopping!

(Zoë took her parents to Barcelona to meet up with Ms. Sandwalk and our nephew for a week of zoo's, Cava, and Gaudí. You can read all about it on leslie jane moran.)

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Omnisaurus Games

My number one son¹, Gordon Moran, is a texture artist working for a video game company in Vancouver. He has hooked up with his programmer friend Kevin Forbes to found Omnisaurus Games. They are working on an iPhone/iPad game and the unique thing about this is that you can follow their progress on their blog. Did you ever wonder what goes into to making a fabulous app?

Omnisaurus Games is an independent game developer currently developing games for the iPhone, iPad, and iPod Touch. Founded May 2011 in Vancouver, Canada by Kevin Forbes and Gordon Moran, we stress open game development, meaning we share every aspect of our development cycle with you the players. Follow our game development journey through our blog, twitter, facebook, or rss feed. Watch our game grow from the conceptual phase, all the way through the entire development cycle. We regularly post our work in progress builds so that you can test them out online and most importantly give us your feedback and great ideas. After all, we’re making these games for you, so shouldn’t you have a say in how they’re made? Most importantly, keep in touch. We’d love to hear anything you have to say about our games, any games, or life in general. We’ll try really hard to implement the best and most popular ideas into our games and reward the most helpful suggestions and ideas with free copies of our game when it launches. We look forward to hearing from you!

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1. Note for the irony deficient - whenever someone says this it usually means they only have one son/daughter. Note that I did not say "number one child" 'cause that would have gotten me in trouble.

A Visit from Rick

It was late in the day when I heard a knock on my office door. I opened it to discover a strange man I hadn't seen in many years he introduced me to his wife and son. Rick Nicholson is a former graduate student in my lab. He got his Ph.D. 25 years ago ("The HSP70 Multi-Gene Family in Saccharomyces cerevisiae.") Rick was the first person to clone and sequence the yeast BiP gene.

Rick went from Toronto to Strasbourg (France) to work in Pierre Chambon's lab and from there he went to Australia. He is currently Professor at the Hunter Medical Research Institute in Newcastle, NSW where he works on peptide hormones expressed during pregnancy in humans.

I've reached the age where it's a real thrill to remember the "olden days" and how much better they were than today. Over dinner, Rick and I agreed that graduate students and young professors were much better 25 years ago than they are today.¹

We tried to remember everyone who was in the the lab during the early 1980's. Fortunately there was a list in Rick's thesis (undergraduates. graduate students, post-docs): Sean Blaine, Kim Bird, Eric Degan, Monica Fuchs, David Lowe, Marc Perry, Andrea Townsend, Sharon Shtang, Scott Young and Kee Wan. I know where most of them are but I haven't seen some of them for decades. That's sad.

Rick and his family are on their way to Strasbourg to celebrate Pierre Chambon's 80th birthday. When I reach 80 I'll have to throw a big party so I can invite all my former colleagues and students.

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1. I recently had dinner with my former Ph.D. supervisor and we reached the same conclusion only it was for 40 years ago. Isn't that strange?

Carnival of Evolution #36

This month's Carnival of Evolution (36th version) is hosted by Greg Laden at Greg Laden's Blog ["If You Love Evolution, Tweet About It!" COE # 36].

Here are the subtitles ...

• Hard Core Theory, Genetics, Mutations
• Kin Selection (or not)
• Ecology and evolution
• Microbes with ESP
• Applied Evolution
• Fish Physiology
• Crayfish Sex
• Human Evolution
• Darwinia
• Time and Deep Time
• Elephants
• Basic Concepts and Pedagogy
• Brains
• Extinction
• Blog The Controversy

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