Report from Alife XII: life's origin, and its evolution

When I say 'artificial life', what do you think of? I think of life-like systems in computers, mainly, but at the Alife 12 conference in Odense, Denmark that I am currently at, a large part of the presentation are really about chemistry. Many people might be surprised if they knew just how many people are working on the problem of getting chemicals to behave like life. That is, work on the origin of life is booming. Take a look at the program. A few talk titles:

• Autocatalyses
• Spontaneous Assembly of Cell-Like Structures from Likely Prebiotic Materials: Problems and Prospects
• Light induced Replication and Selection in Peptide Networks
• The Origin of Life by Serial Dilution of a Primordial Soup
• Evolution, Selection and the Metabolic Foundations of the RNA World
• Dynamical Stability of Autocatalytic Sets
• Synthetic (Constructive) Biology: From Vesicles Self-Reproduction to Semi-Synthetic Minimal Cells
• Constructing an artificial self-replication system of genetic information from RNA and proteins

The point here is just that, yes, we don't know how life originated, but people are hard at work on the problem. And they have reason to believe that it can be done in the lab, eventually. As such, the fact that it is very difficult does not mean that the problem is unsolvable. And even less does the fact that some people cannot imagine how it could occur without the word of God (also, how exactly is it that God would have done it?) have any bearing on how it happened. Of course.

In two days I am talking about some work I've done on the NK model: Critical properties of complex fitness landscapes (in EvolDyn V). In anticipation of someone asking what the relevance of this model is, I am thinking about what to say about that in the introduction (which might take up half of the alloted 15 minutes).

My particular implementation of the NK model has 20 loci. That's a lot less than natural systems have, obviously, but on the other hand much more than the usual two that can be modeled analytically. Twenty loci is enough to result in very complicated fitness landscapes, when the loci are set to interact epistatically (i.e., the effect of a mutation depends on the particular genotype of the organism), but also not more than we can completely enumerate, such that the fitness of every possible genotype is known (for N=20 loci there's a little over a million possible genotypes, and we have looked at organisms with N=32, which gives almost 4.3 billion).

Basically, the only way to learn about the global properties of fitness landscapes is to simulate them in a computer. In natural organisms it is extremely cumbersome to survey even a limited area of genotype space. This has, for example, been done in yeast (Costanzo et al., 2010). They did knock-out experiments, meaning that they disabled single genes in pairs, such that the fitness of the organism could be measured for the unaffected wild-type organism, a yeast organism with one gene knocked out, another with a second gene knocked out, and finally a fourth organism with both of those two genes disabled.

It turns out that the bigger the effect of the single mutant is, the more epistasis there is between the two genes that were knocked out. In other words, the extra effect on fitness of the interaction of the two genes is on average larger when the effect of the first gene is large. That tells you something non-trivial about the shape of the local fitness landscape centered on the wild-type genotype. But the really intriguing observation is that this shape around a single genotype is eerily similar to that in the NK model, and the point that I want to emphasize is that this observation validates the NK model to some extent, as a model that does have something to say about real fitness landscapes.

Reference:
Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E., Sevier, C., Ding, H., Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St. Onge, R., VanderSluis, B., Makhnevych, T., Vizeacoumar, F., Alizadeh, S., Bahr, S., Brost, R., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z., Liang, W., Marback, M., Paw, J., San Luis, B., Shuteriqi, E., Tong, A., van Dyk, N., Wallace, I., Whitney, J., Weirauch, M., Zhong, G., Zhu, H., Houry, W., Brudno, M., Ragibizadeh, S., Papp, B., Pal, C., Roth, F., Giaever, G., Nislow, C., Troyanskaya, O., Bussey, H., Bader, G., Gingras, A., Morris, Q., Kim, P., Kaiser, C., Myers, C., Andrews, B., & Boone, C. (2010). The Genetic Landscape of a Cell Science, 327 (5964), 425-431 DOI: 10.1126/science.1180823

How to be a blog comet

How the hell do you get 18 thousand followers after blogging for one year? Answer: cartoonery.

What I learned from Newcomb's paradox

On Rationally Speaking (one of the best blogs around with regards to the comments*), Julia Galef wrote a post about Newcombs paradox:

You’re presented with two boxes, one open and one closed. In the open one, you can see a $1000 bill. But what’s in the closed one? Well, either nothing, or $1 million. And here are your choices: you may either take both boxes, or just the closed box.

(...)

[T]hese boxes were prepared by a computer program which, employing advanced predictive algorithms, is able to analyze all the nuances of your character and past behavior and predict your choice with near-perfect accuracy. And if the computer predicted that you would choose to take just the closed box, then it has put $1 million in it; if the computer predicted you would take both boxes, then it has put nothing in the closed box.

This is a very interesting problem for several reasons. One, it touches upon the notion of free will vs. determinism. Here's a comment by Q:

This paradox is really stupid... "Assume you have no choice. Then what is your choice ?"

If the prediction of the computer is perfect, there is no such thing as a strategy or a choice anyway, there is no question, no answer and no paradox.

But then further down, ClockBackward comments that this ability to predict the future does not annihilate free will:

By the way... even if the predictor can predict what I am going to do with near 100% accuracy, that doesn't imply that I don't have any "choice" or "free will" regarding what I do. One way to think about this is to suppose that the predictor has the ability to time travel. Its prediction method could be as follows: Put money into both boxes and then (before the game starts) time travel into the future to see what decision I make during the game, and then time travel back and (again, before the game starts) remove the money from the closed box if I choose both boxes in the future. The predictor in this case is just figuring out my choice, not taking my choice way. Of course, time travel may not be possible, and the time travel idea may have other theoretical difficulties, but hopefully this illustrates the point that near perfect predictability does not eliminate the possibility of "choice". In a similar vein, just because a friend of mine can predict with near 100% accuracy that I will choose chocolate over vanilla, that doesn't imply that I'm not making a genuine choice.

So, apparently, different people view the influence of determinism in free will very differently. Personally, I side with Q on this question. If the computer can predict perfectly (not near-perfectly), then there is no choice, though we may feel that we are making a choice. In that case, hopefully you were predetermined to be a one-boxer. I'm not sure using arguments about traveling backwards in time are ever sound, because I am of the observation that sending information back in time is a logical impossibility. But again, the interesting lesson for me here is that people think very differently about free will.

Another interesting thing that I have encountered several times before, is the idea that making a rational choice does not include what we (rationally) know about the human psyche. Here's Julia's example of a real-world problem analogous to Newcombs paradox:

Now here's the real-life analogy I promised you (adapted from Gary Drescher's thought-provoking Good and Real): imagine you're stranded on a desert island, dying of hunger and thirst. A man in a rowboat happens to paddle by, and offers to transport you back to shore, if you promise to give him $1000 once you get there. But take heed: this man is extremely psychologically astute, and if you lie to him, he'll almost certainly be able to read it in your face.

So you see where I'm going with this: you'll be far better off if you can promise him the money, and sincerely mean it, because that way you get to live. But if you're rational, you can't make that promise sincerely — because you know that once he takes you to shore, your most rational move at that stage will be to say, “Sorry, sucka!” and head off with both your life and your money. If only you could somehow pre-commit now to being irrational later!

What does this ignore? Further down in the comments, James says

I would dispute that fleeing once you reach land is the rational choice. If the result of fleeing is that you will die, how is loosing your life a better payoff than loosing $1,000 dollars?

And Julia's answer.

No, you don't die if you flee -- once you're at the point where you're trying to decide whether to flee, you've already been saved. Once you're on dry land, your choices are between fleeing (and saving your money) or paying the guy.

But, but... How do we know what happens as a consequence of fleeing? Julia just assumes that after fleeing, that's the end of the story (I realize that they are talking about dying when not saved by the fisherman). However, real life is not like that. It may be that after fleeing, the fisherman will not be able to affect your future life in any way, in which case you could say you'd be in the clear a thousand dollars richer (or less poor - which is even better, psychologists have found out). However, this can never be known for sure (unless you're Newcombs computer, I suppose). But who knows? Maybe he will get upset and hunt you down. Maybe he will tell everyone he knows about your misdeed, and you will get a bad rep.

The reason why many humans would pay him the thousand dollars, is that we're "honest people", and the reason we're mostly honest, is that we know that not being honest can have dire consequences. In the past, when people lived in much small groups, this was certainly true; if we cheated someone who had saved us, then everyone would soon know, and our reputation (and thus fitness) would suffer. It's fun to make problems like Newcombs paradox that highlight these issues, but what really astonishes me is that psychologists and economists actually make experiments with real people, in which it is concluded that people make what seems like irrational choices despite the fact that they know for certain that no one else will ever know if they cheat. In game theory settings where the participant can earn money by either cooperating with or cheating another participant (often not even a real human, but a computer program, though this is not divulged, so assumed unknown, though when I participated twice, I both times knew for almost certain that there were no real human at the other end of the line), the researchers are at least sometimes surprised that people make the seemingly irrational choice of sharing money with the opponent, even when they "know" that they will only play once, and never meet the opponent again. The participant is told that this is the case, and the participant may accept this rationally. However, the choices we make are just not only based on rational thought, but on our instinctive feelings, too. And those instincts you just cannot make believe that you will never meet your opponent again, because nothing in our past experience has ever shown us that his is certain, or even very likely. The second interesting lesson for me is that many clever people completely fail to grasp this point, that "rational" is rarely that straightforward.

In summary, the reason why we would pay the fisherman the money we promised him, is that we are honest, and that we'll feel guilty if we don't. And we are honest and feel guilty because that ensures that we treat each other fairly, which ultimately works out better for ourselves, because we live in groups of people that we will meet again, some sunny day.

* As opposed to, say, Pharyngula, in which the comments are mostly dreck. It's been years since I paid any attention to them whatsoever.

Paper analyzes a case of fever in the Bible

If you haven't already seen it, go to Science Blogs and read all about the (piece of*) paper published in Virology Journal (Impact Factor 2.44) about a case of fever in the Bible. Jesus cured the fever, and the authors conclude it was was an influenza-like illness. The paper is free, and can be found here. Abstract:

The Bible describes the case of a woman with high fever cured by our Lord Jesus Christ. Based on the information provided by the gospels of Mark, Matthew and Luke, the diagnosis and the possible etiology of the febrile illness is discussed. Infectious diseases continue to be a threat to humanity, and influenza has been with us since the dawn of human history. If the postulation is indeed correct, the woman with fever in the Bible is among one of the very early description of human influenza disease.

The big question is why this kind of "analysis" has been published in a peer-reviewed journal. Beats me.

* The whole paper is just about one page.

Important update 8/11:
The paper has been retracted, according to the Editor-in-Chief of Virology Journal. See comment below.

Dumping emails from creationist

In June of last year I wrote a post about a local Tennessee teacher, Jason Groppel, who organized a course on creationism. I couldn't find much information about the class - just a little from a news article that has now been taken down.

Then a little over a week ago, Jason Groppel posts a comment:

Very negative, sorry you couldn't make it to hear what was taught.
I happen to be an ex-evolutionist and I DO happen to know quite a bit more about evolution than you apparently.

By the way, a good journalist, Blogger would have contacted the person in question before making such heinous assumptions. You have never met me and do not know anything about me. Simply negative attitudes and assumptions.

It is a bit cowardly not to approach me about this first and make such public comments without knowing anything about me or what was taught.

Sad.

I still welcome you to contact me. I am not hiding. I am easy to find online.

So I found his email online, and emailed him, and back and forth it has now gone.

Okay, Jason. Tell me what you taught in your class, then. Prove my 'heinous' assumption, that you don't know enough about evolution to teach such a class, wrong, and tell me why you assume that you know more about evolution than me, please (an equally heinous assumption?).

Bjørn

Bjørn,

You are obviously closed to the idea of anything I would ever say.
If you were interested at all in what the class was about you would have asked before making such asinine assumptions about me personally, and the class before publishing them.

I notice you have listed that you have earned your PhD. If so, perhaps you have taught classes, and may have had a student come to you and ask if they "missed anything" in a single class, much less a whole semester. This is demeaning and objectionable to any educator that takes their classes seriously, and so it is for you, to casually ask what you missed in the class.

It is unfortunate that people who claim to be so open minded also claim to be scientists or worse, educators. Scientists will humbly seek out and even entertain the possibility of knowledge from what may appear as unintelligible sources when their quest is truth.

A condescending and closed mind will not be rewarded in any search for truth.

JG

> You are obviously closed to the idea of anything I would ever say.

Why is that obvious? I am not closed to what you have to say. I even asked you what you taught, but you gave no answer. Seems like you only want to talk about my person.

> If you were interested at all in what the class was about you would have asked
> before making such asinine assumptions about me personally, and the class
> before publishing them.

I made just one assumption, and that was that you don't know enough about evolution to evaluate the evidence (though stated somewhat more on edge, to be fair). Just one, and that was based on your statement that "Evolution and creation are both religions — you have to have faith to believe either one of them," which I contend that anyone who understand evolutionary theory would never state.

But you're right that the point of my post was not that I was interested in your class, but rather to call you out on offering a class motivated by the stated fact that "Studies show that 75 percent of kids raised in Christian homes lose their faith their first year of college. That is why we are gearing the class toward high school and college-age students." That is not search for truth, but indoctrination.

Bjørn

> "Why is that obvious? I am not closed to what you have to say."

Most would consider, "Okay, Jason. Tell me what you taught in your class, then." a very condescending statement to open up with, or did I just misinterpret it as tongue-in-cheek?

I wonder sometimes if people such as ourselves with such antipodal ideologies were to meet first while on vacation, or at a bus stop how such discussions would eventually pan out. I would hope that our discussion could begin on such a basis...mutually-respecting, as people - not with disdain, not based on that of a credo.

I suppose that is why you "hit a nerve" with me, because I feel that until one understands and knows a person, and knows what they have to say one should not make prejudicial public statements about them.

What is your field of expertise related to our discussion? Perhaps, if you are truly interested, I could give you some food for thought, and vice-versa?

We could start over and discuss this in a more dignified way if you like.

Jason

As long as we agree that we both make assumptions, then.

The truth is both that now that we're talking, I would like to hear what you taught, and that I do honestly think that if it is what I gathered from what I read and quoted on my blog, then is is not a class I would agree with at all. My preconception, based on what I read about the class, is that you are a Christian who do not believe in evolution because you interpret the Bible in a way that is irreconcilable with evolution. Also, I assumed that you don't really know a lot about the scientific method and evolution, because you made the statement that evolution is a religion. If any of this is wrong, I would of course greatly appreciate to be corrected.

It is true that meeting face to face makes for a different conversation. There are good and bad things about that, really. However, I often find that in such conversations I withhold what I really mean, because I am (we are all) so reluctant to be frank in front of someone when what we have to say is contentious.

My field of expertise is evolution. I actually defended my PhD thesis in evolutionary modeling this morning. I am also an atheist (and always have been). I am from Denmark, but live in California.

Bjørn

When I was a "tween" we had a young man from Copenhagen come stay with us as an exchange student. He tried to teach me how to say "strawberry pudding" and unnecessarily greedy with his Danish black licorice...I didn't care for it at the time, but my taste buds have 'evolved' since then. :)

Maybe we should start with something simple. Let me ask you a question or two. Please be patient, I know you may find it tedious, but I think I can make a point from the answers you give. All I ask is that you are truthful and serious with your answers. Your answers don't have to be drawn out and complicated, just short and to the point...even a word or two.

1. Can a person know everything there is to know on our Earth?
2. If not, what percentage of everything can one person know about anything there is to know?

In answering these two questions one must consider even the love-life of a flea for example, the maiden name of Benjamin Franklin's mother, the number of men and women who died in the making of the Great Wall of China, the average life span of a ruby-throated hummingbird, the end result to a baby which breast-feeds while its mother takes Minoxidil,...you get the picture. As with everything you could look these up onilne, but they are examples of what might be known in comparison with what a person actually knows.
Thanks for bearing with me on this.
Jason

> 1. Can a person know everything there is to know on our Earth?

No (not in principle, though it depends on how you define "everything
there is to know", and certainly not in practice).

> 2. If not, what percentage of everything can one person know about anything
> there is to know?

I have no idea. A small percentage.

My question (again): what did you teach in your class? (Also please answer why you still haven't told me.)

Bjørn

Hi Bjorn
I am sorry to take so long in getting back to you.
When taking on such conversations one must do so in moderation by taking "one bite at a time."
I did say that we would start small by asking you a few questions and for you to bear with me.
You have answered well, even if a bit hesitantly or precautiously.
You are right, there is no person that can know all things.
And you are also right; that which we humans do know is such a miniscule percentage of all things that it would probably not register beyond a .10%.
For that reason I would like to challenge your assertion that you are an atheist.
Since you say you are an atheist, I would surmise that you probably know the definition of the word "atheist."
I would suggest that since you acknowledge that no person can possibly know everything that any clear-thinking individual with such doubts about the existence of a deity would at least claim to be an agnostic instead.
This seems to be a conscience rationale to make my point.
I hope I may have persuaded you to at least change your nomenclature.
If not, why not?
I look forward to our discourse on the hypothesis of evolution.
By the way, as a teaser, I do believe in the literal definition of evolution, but because of the adopted, connotational, and popular definition I like to use the term adaptation.
Jason

Jason, why are you not answering my question?

> My question (again): what did you teach in your class? (Also please
answer why you still haven't told me.)

From my blog:
"Personally, I believe there is no God, but I fully acknowledge that this
cannot be known with certainty. I am, then, both atheist and agnostic.
Similarly, it would indeed be possible to be both Christian and agnostic.
In fact, everyone who are not insane should admit that whatever they
believe about deities, we cannot ever know for sure. Thus, everyone should
be an agnostic. The insane would then include all those who claim to have
proof positive of their favorite fairy, say through revelation (but
exclude those who are lying about that, like the Pope)."
http://pleion.blogspot.com/2009/03/both-atheist-and-agnostic.html

Bjørn

Hi Bjorn I am not avoiding answering your question, but I wanted to see if you would even concede that you could be wrong about something so simple as the point of view as an agnostic as opposed to being an atheist. One CANNOT be both an atheist and agnostic by definition just as a Christian cannot be an agnostic by the connotational definition as referring to God.
Atheists strictly deny the existence of a deity based on a limited knowledge and conceited self-important ideologies. They are simply agnostic until they can prove conclusively that there is no deity. This was a bit of a test just to be sure you were open to what I had to say. I suppose you might understand how difficult it would be to attempt a rational discussion with someone who thinks they are never wrong and unable to concede that.
So you are, by definition, an agnostic not atheist.
With this concluded, let's narrow the topic a bit. After all, you are asking me to summarize the content of an entire course. First let's define evolution. How about you tell me what you believe evolution is so we can be on equal understanding so we can begin properly?

Sincerely,Jason

By your silly and self-centered definitions, only. By those used by many atheists, I am an atheist.

Three different dictionaries:

a·the·ist:
- a person who denies or disbelieves the existence of a supreme being or
beings.
- one who believes that there is no deity
- One who disbelieves or denies the existence of God or gods.

I disbelieve in gods, thus I am an atheist. I don't really are what you call it, though. Fact is I don't believe in any particular gods, and definitely believe that the one described in the Bible does not exist. Call that whatever you want.

> First let's define evolution. How about you tell me what you believe
> evolution is so we can be on equal understanding so we can begin properly?

Absolutely not. It really is your turn to say something here. Just give me an outline of the course. A list of topics. Examples of what you taught. Five points you made. Something. So far, after all this fruitless talk you do, nothing.

Bjørn

Bjorn it seems you are only interested in criticizing and continuing a negative attitude.
eg: "your silly and self-centered definitions" and "Certainly not..." as examples of such.
I am not only a scientist by definition, I am an etymologist; speaking a little to a lot of up to 32 languages. I am also very knowledgeable about the hypothesis of evolution.
It seems you will not join me in this discussion wishing it to be on your terms only and ridiculing any attempt I might proffer.
How can anyone come to a discussion without knowing the other person's ideas and beliefs? You are the one that has chosen to kill this discussion, not I.
I am ready to go, but you won't even tell me what your definition of evolution is.
You had no problem giving me three definitions of atheism (literally meaning:no deity), but refuse to give the definition of something you should know all about.
If you decide to come back to the table instead of huffing away in a childish, "I am going home and taking all my toys with me!" attitude then I will be waiting to discuss why I believe in evolution, but not the kind you believe in.
Jason

You are totally hilarious, Jason. Why do you refuse to tell me what your class was about?

I didn't want to give you a definition of evolution because that's silly, and because it really is your turn to tell me something by now.

I am an evolutionary biologist, and I believe in common descent. Evolution is descent with modification. It's micro- and macroevolution. It's a change in population allele frequencies over time. It's the change in inherited traits though the generations.

My bets are that the next email you send me will not tell me what you taught in your class.

Bjørn

When sending that email, I decided that if Jason did not finally tell me what he taught in his class on creationism, I would just dump the whole thing here. Today I got this email:

Hi Bjorn
"Refuse", I think not.
Thanks for answering my question about what you believe evolution to be.

Actually, I am excited to tell you what we discussed, but was hindered most recently, by your decision not to participate rationally, until now.

I see that you believe that all evolution is the result of change or modification. Good, I agree, but only to a point.

In one part of our course we discussed the importance of mutation to the assumed process of evolution.
Without beneficial mutations there can never be evolution, right?

I am eager to hear your response so we can continue the discussion.
Jason

"In one part of our course we discussed the importance of mutation to the assumed process of evolution." That's it? You discussed mutation. That's all I get about the class after all this emailing? Mutations!? Why so reluctant to discuss the class that I was initially reprimanded for not having asked about?

That's too lame, so here it ends. At least via email. Perhaps we can have more fun-filled exchanges in the comments...

P.S. If you enjoy this sort of thing, check out The Rzeppa game show.

Update 8/10:
I just received this email from Jason, and have added comments in red:

Bjorn,
I don't know what you mean by forthcoming, but I have clearly begun sharing with you the contents of the course. [Yeah, "mutations".] Apparently you wanted a list instead of a discussion.
I could tell all you wanted to do was shut down our conversation and make it look like I had tucked my tail and run in order to "prove" that I have nothing to say. [Certainly not. I wanted to hear about your class. Got nothing, though, even though I asked many times.]
I don't mind you publishing it, but I do not like the way you have hijacked the "discussion" to make it look like I pushed away from the table by not giving you a list of things we discussed. [Then you should have given me something about your class, I think.]
I, in fact, did in our last email give you the first of many aspects of our class, but you failed to read the email or just don't want me to prove you wrong through a step by step, topic by topic discussion of the rationale. [No, I clearly read it, as you can see from my comment to it above.]
I could see what you were trying to do from the beginning and it is no surprise to me that all you wanted to do was shut me up so that you would not have to listen to any scientific arguments against evolution. [I wanted to learn about your class, from the beginning.]
Now you will post only what you want to post in order to prove that "he had nothing" to offer when in fact I have much to say, but you refuse to participate in a discussion. [I did not refuse. I think that's apparent to everyone who reads our emails above. I'm glad to discuss the class you gave.]
You still have not answered my question about the importance of beneficial mutations. ["Still have not answered..." You don't smell the irony, here?]
I would say that if anyone is running low on answers at this point, it is you. [If I knew you weren't kidding, I would have thought you were kidding.]
Just be sure to include this "last" email in your posts. [Done.]
You have been very impatient throughout this "discussion" in my opinion and I am ready to continue when you decide to come back to the table. I should have known it was a waste of time to attempt any rational discussion with you when I saw you original postings about the matter. [Impatient?! Me? I think you can call it patience when I asked you this many times for the contents of your class, but got nothing. Besides, I answered your questions about atheism and knowledge and evolution. You didn't answer any of my questions. If you want a discussion, post a comment here explaining what your class was about.]
JG

North Korea's coach will do hard labor

The coach of the North Korean team who lost three out of three in the world cup has been sentenced to hard labor (and expelled from the party).

Following the event, the team's coach Kim Jung Hun has been sentenced to hard labor following a speedy trial. "He will carry loads on a building site for fourteen hours a day," reports Le Figaro. He was found guilty of "betrayal of trust of Kim Jong-un", the son and heir of country leader Kim Jong-Il who determined the final team roster, and allegedly expelled from the Worker's Party.

It doesn't say for how long. I wonder if sentences in that country are ever for a period of time, but rather just for as long as the regime is still in power. I think they should praise the man for leading his team to a 2-1 victory-loss to Brazil. Most nations would have been proud of that.

New Jersey keeps Adolf Hitler in custody

In February 2009, I wrote about the authorities in New Jersey taking away Adolf HItler and his two sisters from their parents. The word in the news was that it was because the children were named after nazis.

I feel really awful that the three children taken by the State of New Jersey on January 9 are still kept away from their parents, who have only been allowed to see them once. The state better have damn good reasons for their actions.

Now I finally see that the state indeed did have good reasons for their actions, and continues to keep the children in custody because of child abuse:

The children were taken into care shortly afterwards although at the time local authorities insisted that the move was nothing to do with their controversial names.

The court papers seem to support that assertion. According to those documents Adolf has serious behavioral problems that include frequently threatening to kill people and that his parents, who are both on disability and do not work were both apparently victims of childhood abuse themselves. In making their ruling the three-judge panel of the Superior Court of New Jersey Appellate Division sympathized with that fact, but stated that “neither has received adequate treatment for their serious psychological conditions.”

The 49 page ruling made for pretty grim reading as it detailed some rather nasty conditions that existed in the family home where the windows were nailed shut and the house filled with what was described as “unusual decorative features” including skulls and knives.

A neighbor of the Campbell’s had also given a note she received from Deborah Campbell herself that stated that her husband was trying to kill her and also teaching her son “how to kill someone at the age of 3.” When asked about the note in court Mrs. Campbell admitted she wrote it but that it had been a lie and Heath was “the perfect guy”. However, her protestations aside all three children will be remaining in the custody of the New Jersey Division of Youth and Family Services.

I'm not happy that the children were abused, or that they now have psychological problems, or that their parents were abused as children, or anything much related to this horrid affair, except that I am glad New Jersey isn't the police state that I feared last year.

Evolution highlights XXI

The other day I wrote about a paper showing that phytoplankton are dwindling at the rate of 1% per year, and that since phytoplankton produce about half of the oxygen produced by plants, we might really be doomed, together with lots of biggish animals that can't quickly evolve to do with much less oxygen. In other news, past oxygen levels were insanely high: "Over the past 400 million years, the level of oxygen has varied considerably from the 21% value we have today." "At levels below 15% wildfires could not have spread. However, at levels significantly above 25% even wet plants could have burned, while at levels around 30 to 35%, as have been proposed for the Late Paleozoic, wildfires would have been frequent and catastrophic."

Not quite evolution, but a feud evolving between two evolutionary biologists, Jerry Coyne and Massimo Pigliucci (now turned philosopher). Massimo does not like Jerry and his claim that science can test the supernatural, and thinks scientists shouldn't spend time philosophizing, but leave that to professional philosophers, like Massimo. Jerry thinks he is not doing that, and that Massimo hasn't been listening. I think it's all a really good read, including the comments, and largely agree with Coyne that, while the existence of gods cannot be empirically tested, the interactions they supposedly have in the natural realm - and that religious people posit happens all the time - can. Jerry wins the duel because he came up with the funnier title: What is the sweating professor trying to say? vs. Jerry Coyne, then and now. Also, Massimo started it, so øv bøv!

And even less about evolution (but not completely): Jonathan Swift's essay on why eating Irish babies would be great for all (via Evolving Thoughts). I concur, of course.

I have been assured by a very knowing American of my acquaintance in London, that a young healthy child well nursed is at a year old a most delicious, nourishing, and wholesome food, whether stewed, roasted, baked, or boiled; and I make no doubt that it will equally serve in a fricassee or a ragout.

It's really quite an astonishing essay. I can't tell if he jesting or being forthright (the essay is from 1729*).

My serious answer to why this really would be a bad idea was laid out in a post from 2008, Why is cannibalism taboo? Short answer: Cannibalism is taboo because I am afraid that you would want to eat me. And really, just imagine of people started accepting dining on babies. That might even lead to atheism!

*

Biologists counter creationist movie

On today's eSkeptic, there's an interesting review of the newest creationist “documentary", Distorting Darwin (that's the title of the review - movie title is Darwin: The Voyage that Shook the World).

It's particularly interesting because the author of the review, Jonathan Lowe, has interview three evolutionary biologists about some of the creationist claims in the film. For example:

Claim: The genomes of plants and animals show much redundancy. This goes against the idea of randomness. There is an abundance of information that is utilized for adaptation, and this is unexplained by any selective mechanism.

Hutchinson: “This is a total non sequitur. Some redundancy is understood as gene duplication, which is a rather random event. Some makes sense as building safety factors against the loss of critical genes by genetic damage or error. It is not unexplained. It is completely reasonable in a modern evolutionary sense. Things that can be ‘utilized for adaptation’ cannot be ‘unexplained by any selective mechanism’ because the very process of adaptation involves selection.”

And the peacock's tail, again (again):

Claim: The beauty of the peacock’s tail worried Darwin because it serves no function as camouflage, and a huge amount of genetic information went into creating the tail’s intricate structure. Darwin created the theory of sexual selection to explain why the tail feathers are so beautiful, but experiments have shown that females cannot detect some of the features, and none have any real effect on selection.

Hutchinson: “This is misconstruing a large body of research on sexual selection. As in any field of science some ideas have changed over two centuries, but sexual selection is still heavily favored as a major evolutionary mechanism. In some cases the targets of selection are counterintuitive, and females may choose traits that are not obvious or are indirectly correlated with obvious traits. But that is not a fatal flaw for sexual selection. It has just modified it. That evolutionary biologists and not creationists have discovered this information is rather telling. Creationists have contributed nothing to this area.”

Charlesworth: “There is indeed a large body of research confirming that female animals do favour males with ornaments such as the peacock’s tail, just as Darwin postulated. Sexual selection is one of the best documented phenomena in evolutionary biology.”

As I have mentioned once twice before, I think the peacock's tail works to scare off predators.

Carnival of Evolution #26 in town

The 26th edition of the reliable, the dependable, the capital, the sublime Carnival of Evolution has come to town. Town of The Thoughtful Animal, to be precise.

A sample:

Continuing with female sexual preferences, Kevin Zelnio claims that female urochordates have few, if any inhibitions. "Yep, that's right. They get it on with any male gamete that passes their way. They just don't give a [rhymes with duck]. Boom chaka-laka-boom. These loose lizzies are all about increasing genetic diversity if you know what I mean."

Sad (very sad) that you didn't get a post in this edition? Hurry and submit to the September edition already, then.

The tragedy of the commons

While working on the last bits of my thesis, "Genetic and Ecological Models of Adaptive Evolution", I came upon Garrett Hardin's 1968 article [1], The Tragedy of the Commons (Wikipedia). It's really a great piece, which coined the term that is now an established and important notion in biology and elsewhere.

In his article, Hardin says this:

Adam Smith did not assert that this was invariably true, and perhaps neither did any of his followers. But he contributed to a dominant tendency of thought that has ever since interfered with positive action based on rational analysis, namely, the tendency to assume that decisions reached individually will, in fact, be the best decisions for an entire society. If this assumption is correct it justifies the continuance of our present policy of laissez-faire in reproduction. If it is correct we can assume that men will control their individual fecundity so as to produce the optimum population. If the assumption is not correct, we need to reexamine our individual freedoms to see which ones are defensible. [Emphasis added.]

Most people will probably recognize this assumption as the one made by libertarians (yes, I know there are different kinds, already). It still amazes me that anyone seriously thinks that human society is in any way optimized without regulation. That is incredibly naive. The tragedy of the commons substantiates the problem. Individual success does not always translate into success of the group.

The tragedy of the commons develops in this way. Picture a pasture open to all. It is to be expected that each herdsman will try to keep as many cattle as possible on the commons. Such an arrangement may work reasonably satisfactorily for centuries because tribal wars, poaching, and disease keep the numbers of both man and beast well below the carrying capacity of the land. Finally, however, comes the day of reckoning, that is, the day when the long-desired goal of social stability becomes a reality. At this point, the inherent logic of the commons remorselessly generates tragedy.

As a rational being, each herdsman seeks to maximize his gain. Explicitly or implicitly, more or less consciously, he asks, "What is the utility to me of adding one more animal to my herd?" This utility has one negative and one positive component.

1) The positive component is a function of the increment of one animal. Since the herdsman receives all the proceeds from the sale of the additional animal, the positive utility is nearly +1.

2) The negative component is a function of the additional overgrazing created by one more animal. Since, however, the effects of overgrazing are shared by all the herdsmen, the negative utility for any particular decision-making herdsman is only a fraction of -1.

Adding together the component partial utilities, the rational herdsman concludes that the only sensible course for him to pursue is to add another animal to his herd. And another; and another. . . . But this is the conclusion reached by each and every rational herdsman sharing a commons. Therein is the tragedy. Each man is locked into a system that compels him to increase his herd without limit--in a world that is limited. Ruin is the destination toward which all men rush, each pursuing his own best interest in a society that believes in the freedom of the commons. Freedom in a commons brings ruin to all.

Here is an interview with Hardin.



In The Social Lives of Microbes, Stuart West and his collaborators describe evidence for complex systems of cooperation, communication, and synchronization in microbes [2]. They highlight results that demonstrate the importance in evolutionary theory of factors such as relatedness, kin discrimination, competition between relatives, and enforcement of cooperation.

One such example if the production of public goods. Public goods are products manufactured by an individual that can then be utilized by the individual or its neighbors. The public goods produced by the microbes can be used by all, even the individuals who are not themselves producers. Since production comes at a metabolic cost, and thus a cost in fitness, it pays to be a cheater. A cheater is a kind of parasite, living off the public goods producing individuals, without contributing anything to the group. Since the cheaters have higher fitness, the whole group would soon fall into the trap of the tragedy of the commons. The question then is how this is avoided.

The answer is that such a system is regulated by negative frequency-dependent selection. When one kind becomes rare, it gains a fitness advantage, and therefore rebounds to become more frequent again. When cheaters become frequent, the amount of public goods is decreased, and suddenly cheaters are at a disadvantage. This relies on some spatial structure that makes sure that the public goods are on average closer to the non-cheating microbes.



The attentive reader might already have seen the similarity to certain aspects of human society. Criminals, for example, are cheaters who live off the production of the rest of society. However, society can tolerate some amount of crime, obviously, just as in the microbial world freeloaders can exist at low frequencies. Where the tragedy of the commons in humans has yet to play out, is in the case of population growth, as discussed by Hardin. In many parts of the world, there is no incentive for the individual to be the one that does not have more children. The result is population growth, and if that growth isn't stopped sooner than later, the result is overexploitation of resources. This is turn leads, as is already all too evident, to the disappearance of many human resources (i.e., other species), and if we're unlucky, to the eventual disappearance of humans, too. Incentives needs to be created for all humans not to have many children, such that population growth can be reversed, and the ultimate result of the tragedy of the commons can be avoided.

Here is, again, the incomparable Hans Rosling on how to do that:



References:
[1] Garrett Hardin (1968). The Tragedy of the Commons Science, 162 (3859), 1243-1248 DOI: 10.1126/science.162.3859.1243
[2] West, S., Diggle, S., Buckling, A., Gardner, A., & Griffin, A. (2007). The Social Lives of Microbes Annual Review of Ecology, Evolution, and Systematics, 38 (1), 53-77 DOI: 10.1146/annurev.ecolsys.38.091206.095740

Re: The Male Privilege Checklist

In our modern society men clearly have many privileges over women. See The Male Privilege Checklist at some blog, and on Pharyngula.

As a man - one of those who are not happy that people are treated badly in any way because of their gender - I find that I want to highlight some of the disadvantages there are to being a man.

Here's is my list with immediate reactions to some of the points made on The Male Privilege Checklist. The fact that I react to them in this way does emphatically not mean that I disagree that men have many privileges over women. We obviously do. But women have some, too, and some of those I am quite honestly very envious of, particularly in regards to children. The numbers refer to points in the original list.

3. If I am never promoted, I cannot blame it on my sex.
4. If I fail in my job or career, it is more likely that it will disrupt my family.
5. I am far more likely to be sued for sexual harassment than my female co-workers are.
7. If I’m a teen or adult, it is less likely that I can stay out of prison (where my odds of getting raped increase dramatically).
9. If I choose to be a housespouse, my masculinity will be called into question.
10. If I have children but am not the breadwinner, my masculinity will be called into question.
11. If I have children and provide primary care for them, in public people will often ask where their mother is.
17. As a child, if I chose a hero of the opposite sex, I could be sure other children and adults would worry about me.
19. I need to worry more than the opposite sex whether my behavior can be construed as sexual harassment.
21. If I’m careless with my financial affairs, I am more likely to be blamed harder by my spouse.
29. If I am not rich or powerful, chances are I will have a harder time attracting the opposite sex.
30. If I am loud or aggressive, people are more likely to call the police on me.
32. I can be confident that the fact that ordinary language of day-to-day existence will always include my sex will sometimes be brought up against me, even though I had no part of making it so.
33. I am more likely to be treated unreasonably by my spouse depending on what time of the month it is.
40. If I have children with my wife or girlfriend, and she decides to make career sacrifices to raise the kids, chances are people will assume I am the one who wanted it that way.
41. Assuming I am heterosexual, magazines, billboards, television, movies, pornography, and virtually all of media is filled with images of scantily-clad women intended to appeal to me sexually. People will assume I like that, and that I am a sexist because I like it.
42. I am much more likely to suffer health consequences from being fat.
43. If I am heterosexual, and beaten up by a spouse or lover, it is much less likely that people would believe me.
46. I have the disadvantage of being blamed for my male privilege.
101. On average, my life is shorter than that of the opposite sex.
102. It will always be assumed that I am not as close to my children as my spouse.
103. I can be confident that if I complain about the disadvantages of my sex, most people will think of me as a loser.
104. If I go through a divorce and we cannot retain joint custody, it is most likely that I will not be the one getting custody of our children.
105. It is always assumed that my spouse is more important to my children.
106. I can be confident that people will assume that I am on the side of my own sex.
107. If I write a list with some of the disadvantages of my sex, chances are that people will call me a whiner and a misogynist.

Notice that a few of these points (e.g., 42 and 101) are directly biological, and have nothing to do with gender roles. The other points can all be said to be imposed by the society that we live in. However, I do believe that many of the points on both lists have a biological basis. This comment is not in any way intended as an endorsement of the gender privileges and disadvantages, but is an encouragement to find the real reasons for the cause of these differences, rather than "men are evil, and if you don't see it, you're evil, too."