Carnival slump?

What's up? Seems to me the number of submissions to Carnival of Evolution is not. This summer we had one edition with 60+ submissions, but last month is was down to less than half that. And it looks like tomorrow's November edition will be the same, because right now I see only 27 posts submitted on BlogCarnival.com, and some of those are spam.



Are people just writing less about evolution these days? Or are bloggers feeling that carnivals matter less than they used to think, so they can't bother submitting? Is creationism winning, with more and more science bloggers avoiding topics in evolution?

I, for one, am blogging less these days, or months, but I have excuses. What about the rest of you? Are you also inundated with teaching, applications, deadlines...? Emotional upheaval? If so, I get it. Otherwise, you can submit right here.

Get some ignorant science advisers now!

It's *almost* hard to tell whether this republican science adviser is for real or not. The giveaway is of course that republicans don't have those...?

We will survive

For Christie, who writes so eloquently about the pain of loss of loved ones.

I lie flattened, like the weight of his words has literally crushed me. I need to do something, anything to lessen this ache. The thought crosses my mind to self medicate, but I quickly decide against that. Mild analgesics like ibuprofen would be useless, as they act peripherally, targeting the pain nerves which send signals to the brain. In this case, it is my brain that is causing the pain. I would have to take something different, like an opioid, which depresses the central nervous system and thus inhibits the brain’s ability to feel. Tempting as that might be, painkillers are an easy – and dangerous – way out. No, I need to deal with this some other way.

Ayala donates $10 million to science

Francisco Ayala is donating $10 million to the School of Biological Sciences at UC Irvine - money earned from his vineyard. The Templeton Prize money he earned last year was donated to UCI as well ($1.5M).



Read the accompanying interview about his work and about accommodating religion and evolution:

Q. Is there a tendency in our society to mix up religion and evolution?

A. I am afraid largely so. I think it is wonderful to teach the Bible, but not to pretend the Bible is an introductory textbook for biology or astronomy.

We succeed in keeping these kinds of things out of the schools, but then the impact on the public at large is not as good as you would expect to have. In the last few weeks, two or three of the Republican presidential candidates have expressed skepticism about evolution. And yet, evolution is confirmed as much as any scientific theory, and better than most. Evolution is confirmed as well as (the idea that) the Earth goes around the sun, or that matter consists of atoms.

It's a matter of scientific ignorance. It's a matter of religious ignorance; as you surely know, most religious authorities, most
churches, are in favor of evolution. As, famously, an Anglican minister -- a theologian -- said, (evolution) appeared first as an enemy, and has turned out to be our best friend, because evolution can now explain all of these sorts of cruelties or mistakes that exist in the world of life.

Let's start with a simple example. The human jaw is not large enough for all the teeth. So we have to pull wisdom teeth -- sometimes one, sometimes two, sometimes three, sometimes all four. An engineer who designed the human jaw would be fired. And yet here we are, saying that would have been designed by God.

Much more extreme and much more serious is the human reproductive system. The human reproductive system is a mess. Twenty percent of pregnancies end in spontaneous abortion, or miscarriages, in the first two months, because the human reproductive system is so badly designed. They blame God for 20 million abortions per year; there are about 100 million births in the world a year. [Emphasis added.]

If evolution was first an enemy and then a best friend, then how does the negation of a literal reading of the parts of the Bible that speak on biology (and other sciences) not call all of it into question?

No one lifts a finger for Chinese girl run over by van

Without questions, this is the most horrific video I've watched in my entire life. You might not want to see it, but everyone should know about it.

A two-year old Chinese girl is in the street alone (!), and a van runs into her, knocking her over, and then drives over her with the front wheel. After stopping for seconds, the van continues, running the girl over with the back wheel.

Lying bleeding in the street, people on foot and in vehicles just pass by her without doing anything. Later, a truck actually runs over her again.

Reports: 1 2 3

What the fuck is wrong with you people? When did a life become so worthless? Shit.

Many people in China are hesitant to help people who appear to be in distress for fear that they will be blamed. High-profile law suits have ended with good Samaritans ordered to pay hefty fines to individuals they sought to help.

---

Update 10/21:

The little girl has now died from her injuries.

Please stop it with the commas!

Lately I have been reading a bunch of papers. I'm teaching a seminar course on evolutionary dynamics, taking a seminar course on multidimensional selection, and I am writing a paper on metagenomics that requires a lot of reading too. So I'm getting picky about commas. It's pretty annoying when people overuse them. I don't care whether there is a consensus that it's appropriate to put them all over the place - even if there is, it's still annoying.

People really like to put them after the first word or first few words in a sentence, as if some big a cumbersome sentence awaits, and for which we must be prepared by taking a deep breath for god measure. For example, one paper had this in the first line of the abstract: "Here we describe, the longest microbial time-series analyzed to date..."¹ The hell? What is that comma doing there? Much more common is to write "Here, we cluster networks..."² But to what end? What is the function of that comma? Are we not really doing it here? Here, we are?

What if I wrote the first paragraph like this:

Lately, I have been reading a bunch of papers. I'm teaching, a seminar course on evolutionary dynamics, taking a seminar course on multidimensional selection, and, I am writing a paper on metagenomics that requires a lot of reading too. So, I'm getting picky about commas. It's pretty annoying, when people overuse them. I don't care, whether there is a consensus that it's appropriate to put them all over the place - even if, there is, it's still annoying.



References:
1. Gilbert et a;, 2011, Defining seasonal marine microbial community dynamics
2. Rahat et al., 2007, Cluster conservation as a novel tool for studying protein–protein interactions evolution

Artificial Life 13: Call for papers

Artificial Life 13

The Thirteenth International Conference on

the Synthesis and Simulation of Living Systems

“Evolution in Action”

July 19–22, 2012, Michigan State University

East Lansing, Michigan, USA

www.alife13.org

You are invited to submit papers to the upcoming Thirteenth International Artificial Life Conference.

The 13th conference for Artificial Life is going to be held next year here at Michigan State University. Dates are July 19-22, 2012, and it's going to be a blast, because we'll have great keynote speakers (Benner, Catts, Kerr, Nagpal, Szostak), and lots of sessions on various aspects of evolution (evolutionary dynamics, simulations of evolution, experimental evolution, viral and bacterial evolution, evolution of drug resistance). I went last year and gave a talk on the structure of complex fitness landscapes (pdf), and was happily surprised at the number of evolutionary biologists there. Next year will surely be the same.

Center of the 99% world

The anti-Wall Street protests going on in the states and elsewhere(!) have a website. There you can find your local Occupy Together group - and I suggest you go join them.



What I wanted to point out here, though, is that the map they have on the site with "meetups" has a curious feature. If you start zooming in and keep going, you'll end up right where I live, in East Lansing, Michigan. Try it.

Anyhow, I just thought that was weird.

P.S. Oh, and something about evolution...

Carnival of Evolution #40 at last

The 40th Carnival of Evolution is up today at Kevin Zelnio's blog, EvoEcoLab at Scientific American.

Next month it will be over at EcoDevoEvo aka The Mermaid's Tale. Never too early to submit...

Submit to Frontiers in Genetics

As a first for me, I have been accepted as a member of the editorial board of the new journal Frontiers in Genetics. I'm very excited about this, particularly because I think the particular model of peer-review might benefit science a lot: Articles will be peer-reviewed for correctness, followed by an open online post-review by readers. It's sort of like PLoS ONE in that manuscripts don't have to present completely novel ideas, but with the added post-review by peers that will determine it's impact on the field.

Whether this will work better is an empirical question, and I look forward to seeing the outcome: Will science benefit by shorter time from submission to publication? Will costs be reduced and less money going directly from tax-payers to journals (journals take money from authors to publish, and cost money to subscribe to, and yet ask for a free service from reviewers)? Changing either or both of those would be a step in the right direction.

Specifically I am a review editor for Frontiers in Evolutionary and Population Genetics, which you are hereby encouraged to send your manuscripts to.

My love of kiwi

Clearly, I'd say, love has some evolutionary significance. Why do we love each other? Evolutionary adaptive reasons seem quite convincing: people in love have sex, sex makes babies, and people in love take care of each other, thereby incrasing chances of baby's survival. What a wonderful reward it all is! But what happens in the brain, and why does it feel so bad to lose the one we love? This blog post on Big Think looks at the neurological and chemical underpinnings of this most wonderful human(?) emotion, and what is has to do with sex.

Love is in the brain: That said, it appears that when people are in love, among other neurological activities, two parts of their brain really get activated. They are called the caudate nucleus and the tegmentum. The caudate is a reward center of the brain, and the tegmentum is a region of the brain stem that sends dopamine to it; dopamine tracks how rewarding something is. I get this with food, for example when I eat the perfect kiwi.

And drugs do it too: In effect, being in love rewards the pleasure centers in your brain, which then crave whatever it was that was so rewarding – in other words, your beloved. Those reward centers are the same ones that light up when people win the lottery. Or use cocaine. But love is a double-edged sword, and when it goes wrong it can haunt us like a vendetta.

Indeed, love literally hurts: And being rejected in love activates a part of the brain called the insula, which is the same region that lights up when we are in physical pain. So we are doubly motivated to hold fast to the object of our love: feel the pleasure, and avoid the pain.

Really.

Evolution favors those that feel love, if we believe that the emotion is adaptive. Hard to test, but still a pretty persuasive idea.

Happiness is irrelevant, resistance is futile

When I was a child, I once watched an animated kid's program about a family where the youngest of two children turned out to be retarded. At first the child was just happy, and all was joy. But then later on, the parents got worried that the child didn't respond much, but was just happy crumbling up paper and listening to the sound.

A doctor told them that there was nothing wrong with their child, but that she was just one of "them". At first the parents got really sad and worried, but then the older child said "but look! she's happy!", and then they all realized that this was good, and they that everything was going to be all right.

For me as a child it was a good story to hear (rather than Dragon Ball Z GT total brainless waste of time kind of thing). It made me think. The morale was perhaps that as long as someone is happy, things are really all right. Something like that.

But...

Is that true? Is happiness really the ultimate measure of worth? Does the pursuit of it really make sense to write up as a guiding principle? Is everything okay if we're happy? Can we be happy in other ways than being happy?

I will counter that happiness can be made to stand alongside other measures of a good life. That is, rather than saying that happiness is achieved given we work well, carry out our duty, live up to our responsibilities, treat others well, honor thy parents, score many touchdowns, or whatever you think are good things to do in life, I would say that happiness can be added to that list. Happiness is a thing to achieve for sure, but need not be the ultimate goal. A life can be lived to the fullest without happiness necessarily playing a big part.

For example, people sometimes say that flow is one way to be happy: when we are so immersed in a task that we notice nothing else, then this is one form of happiness. But, while I agree that flow is nice, I do not think it is happiness at all. Rather, it makes happiness irrelevant.

And this is my point here: Happiness is not enough. It is one thing among many that are worth striving for. Rather than being what we may achieve when everything else is right, we can make life worthwhile without being happy (note that not being happy is not equal being unhappy). And also, we can be happy at times without anything else going our way.

In evolution, I could add, happiness is irrelevant. Fitness does not come to the happiest. The happiest human beings are not at all those with the most children. Does the one who have the most children become the most happy? Or does the happiest person become the one with the most children?

Surely a life lived in pure and constant happiness induced by a constant intake of heroin cannot be deemed a good life. Of course a life lived as the happiest retard is not something to aspire to. Clearly happiness is not everything.



Happiness is a warm gun, yes it is.

The beliefs of others... they matter!

Margaret Morgan just alerted me to this old xkcd comic. Old, but unfortunately more pertinent than ever.



So many people have told me that it is a fools errand to care what other people believe. Or that it's just none of my business. Or that I am arrogant to even have an opinion about the beliefs of others.

Well, as this comic illustrates, the beliefs of others sometimes matters in very tangible ways. Besides, religious people impose their beliefs on others all the time, as when they go door to door telling us that we are going to hell*, or when they pass laws based on ancient texts written by homophobic bigots.

* Actually, as I learned the most annoying way, Jehova's Witnesses don't believe there is a hell at all. Boring! Her daughter sure looked like she lived there.

A blog you don't want to be featured on

Retraction Watch. Tracking retractions as a window into the scientific process.

Collecting cases of retracted scientific papers, this blog keeps track of scientific sinners. Whether the retractions result from honest mistakes or from downright fraud, you can find out about them here. Pretty cool. Except for the sinners.

Let it count as a warning for all of us: be careful who you associate with. Should you be an author (particularly a senior author) on a paper primarily written by someone else, make damned sure that the analysis is correct, that the data are genuine, and that the text is original.

The American Family Association still strong on homophobia

It's been quite a while since I last heard from the American Family Association. I was signed up on their mailing list, but then one day those emails stopped coming. I suspect they found out I commented on their stupid endeavors to boycott various companies because they "support the homosexual agenda".

But no worries. All their foolery are available on their website. Among the items is a call for boycotting Home Depot, because they sponsored the San Francisco Gay Pride parade and festival. AFA call for Home Depot to "remain neutral in the culture and political war over homosexual marriage".

There's nothing like religion to excuse homophobia.

Carnival of Evolution #39, and notes on how to help

September 1st edition of Carnival of Evolution has been up for a couple of days already at The End of the Pier Show - biology editor of Nature Henry Gee's blog.

Despite carnivals going extinct here and there, CoE is doing really well. When I can get my act together, it is really no problem finding hosts; right now all slots are taken through January next year (go here and click on 'future hosts'). And while the number of submissions does vary quite a bit - between the low thirties and to over sixty - there are always plenty for the host and readers to dig into. Probably few people get thought them all, except of course for the host who has to, and that is easily a full days work, if not more. So from here a heartfelt thanks to all past and future hosts, and everyone doing what they can to keep CoE running, whether it be by submissions or by linking on their blog, tweeting, updating their FB status, announcing CoE at conference talks*, making it required reading in college, etc. Thanks!

I'm often thinking about new ways to improve the carnival, both in terms of making each edition better and in terms of increasing the number of readers. It's up to the hosts how to put the CoE together, though suggestions are allowed. If you have good ideas that you'd like to share, you'd be welcome to let us know (comments, email, @carnyevolution #carnyevol). And if you think of new ways to promote CoE, feel free to let us know that too. Right now, when a new edition is up, an email is shot out to the email list, which has some 80 contacts, and then a number of people link to CoE on their blog (though that number is usually not greater than ten or so, which I think is too little). If you have done that, go ahead and put a link to your blog in the comments of that edition, like this. And I tweet (ir)regularly now, so perhaps a few of the current 442 followers find their way to it like that. But I really don't know, as I never get around to asking the hosts to find out how many visitors they get to their edition and how they get there. Except, when Larry Moran hosted last month, he showed me that visits went up an order or magnitude compared to the baseline, which was mostly due to a link on Pharyngula. Oh how I wish PZ would link every month, but alas that is like getting the attention of a celebrity.

Now, go check it out.

* Incidentally, I did this recently, and I got nothing but blank stares from an audience of about 200.

On theory and hypothesis

This article in the Washington Post is very tough in creationism, which I can only agree with. For example:

Evolution could not have produced a single mother and father of all future humans, so there was no Adam and no Eve. No Adam and Eve: no fall. No fall: no need for redemption. No need for redemption: no need for a redeemer. No need for a redeemer: no need for the crucifixion or the resurrection, and no need to believe in that redeemer in order to gain eternal life. And not the slightest reason to believe in eternal life in the first place.

It's a great thing to read in such a prominent newspaper.

However, the author, Paula Kirby, also reiterates a characterization of 'theory' and 'hypothesis' that I vehemently disagree with:

In everyday English, 'theory' can mean something vague, a hunch, a guess. In scientific English, it is almost as far from that meaning as it's possible to get: in science, a theory is the best explanation for a set of facts. It carries real weight: in science, nothing can be called a 'theory' until it is very well established indeed. Science has its own term for what, in a non-scientific context, the rest of us might call a 'theory': the scientific term for a suggestion, a best guess, something that seems plausible but has not yet been shown to be reliably true, is 'hypothesis'. You will never, ever hear a scientist talk about 'the hypothesis of evolution', for the simple reason that evolution is long past that stage. Evolution is a theory in the scientific sense of the word - tested, researched, explored and supported by masses and masses of evidence. There may still be specific details that are not entirely agreed upon; but the fact of evolution itself is not disputed by any reputable scientist.

It's a common misunderstanding that those two words convey degrees of certainty in science. They do not. A theory need not be "very well established", and a hypothesis is not necessarily something that has "not yet been shown to be true".

Rather, in science, a theory specifies a cohesive explanation of a natural phenomenon. A theory is a model of how something works, and can produce several hypotheses that can be tested. For example, gravity is a theory of how masses attract each other and other related phenomena (and it is a fact that the phenomenon of gravity exists), and one hypothesis that comes from that theory is that that a hammer dropped above the surface of the moon will fall down to the surface. But again, neither theory nor hypothesis need to be true to be called theory and hypothesis. There are theories that have been shown to be wrong, and yet we still call them theories. The theory of the ether has been shown to be wrong, but it is still a theory. The theory of homeopathy has been shown time and again to be false, and yet we can still refer to it as a theory.

Similarly, a hypothesis need not be a tentative statement of fact. It is a hypothesis that a hammer will fall down to levitate over the moon, but even when that hypothesis has been tested, it is still a hypothesis. It is a disproven hypothesis, but nonetheless still a hypothesis. In everyday English, it does indeed connote uncertainty, but not so in science. For example, we can still refer to both the 'null hypothesis' and our pet hypothesis even when the evidence favors one of them over the other. It's a hypothesis that the hammer will levitate, and while it has been shown to be false, but it can still be termed a hypothesis.

At least, this is how I use the words, and I am a scientist (but see impostor syndrome).

Payback Charlesworth style

Ruse on the left, Charlesworth on the right.

A few days ago I told the story of an exchange between Michael Ruse and some member of the audience at ESEB 2011.

On the train from Tübingen to Stuttgart I sat next to Brian Charlesworth. We spoke about research and the conference, and also about Ruse's talk. I commented how amusing I found the above exchange, and Brian joyfully let on that it was he who had voiced his disagreement. Brian gave the final plenary talk at the conference, and with a smile on his face, he recalled how he in his talk had mentioned that Haldane has written so lucidly about evolution, and that perhaps that was why certain philosophers had trouble appreciating him, since lucidity is not the strength of philosophers in general. Har! Hear hear. Rumor has it that Ruse didn't find that comment all that amusing, but I'm not so sure.

Michael Ruse at ESEB 2011

I'm at ESEB 2011 in Tübingen (website, Twitter), and saw Michael Ruse give a talk today titled What, if anything, does a historian and philosopher has to say to real scientists?

At one point he showed these pictures of Fisher, Wright, and Haldane (left to right), and said that out of those there could be no doubt that it was Fisher and Wright who were the heavyweights. One person in the audience made a sound to disagree, which made Ruse look at the clock and say "in 9 minutes you'll get your chance - if you're a graduate student*. With a comment like that I rather suspect you are."

Major laughs.

As for the answer to his query, I rather fear the answer is "no." At least, he didn't explicitly say anything to the contrary.

* At ESEB 2011, graduate students can raise a page in the program with a green hand to indicate they are graduate students, which will give them priority in the discussion.

Can Michelle Bachmann embarrass herself more than this?

The answer is without a doubt that, yes she can. And I can't wait for the next bigger blooper. While wishing Elvis happy birthday on the day he died is hard for most people to top, I think Michele has got it in her.



How can anybody take her serious as a candidate after dissing Elvis so badly? Surely she could never take Tennessee now!? And the answer to that is that lest we forget, her backers are the craziest of the craziest in this nation of crazies: the Tea Party movement.