Field of Science

Step Acuity

Please help me with a little science experiment.

Measure your Step Acuity (SA) and report it here.

Your SA is the number of steps before you hit a mark that you know whether you will hit the mark with your right or left foot. As you are walking down the street, choose a mark (a line or a spot) on the ground far in front of you, and say "right" or "left" out loud the moment you realize which foot is going to step on the mark, and from there count 1, 2, 3... until you hit the mark. Do you have an SA (i.e., mostly the same outcome every time), or is the number of steps highly variable?

No cheating, this is not a competition. Just honestly report back, SVP.

The hypothesis is that everyone has an SA, meaning the number of steps is highly invariable, and that SA is normally distributed. H2: The SA is different between those who played football (soccer) as a child and those who did not.

Also, feel free to report how many steps before hitting the mark you know that you are not hitting it at all (i.e., it's right in between left and right foot). Have fun.

The Ivory Power Manifesto

The Ivory Power Manifesto

The Ivory Tower is not my friend. We will not sit idle and look down at the masses while society goes to hell. Science is to be shared, and that's why we do it.

There is no such thing as "their terms". We bring our terms to the table always, and this is how we move forward.

When someone attacks, we defend ourselves. We won't just let them walk into our living room and destroy everything.

Religion leads to creationism. Nothing else does. Creationism thus implies religion. If you're still in doubt what the real problem here is, then you're part of the problem.

This is a war that will take a long time, but we know who will win it. We will not stand idle by and be on the wrong side of history.

We will use any and every opportunity to share science with the public.

The evidence can take us where it wants. We shall have no baggage that will make us resist it.

On some topics there is no legitimate scientific debate, but we will not be afraid of debating science-deniers on these topics, even though the public may perceive that as an acknowledgement that a legitimate debate exists.

Stating that there is no debate is a case of Expert Blindness. Just because you have resolved the issue doesn't mean everyone else has. We will share our expert knowledge with everyone.

Evolutionary forecasting and the tape metaphor

You may not think so (well, not you!), but evolutionary biology does make predictions. Particularly about the past, for example about the existence of moths with long proboscises to match an orchid's long nectary, or that no remains of rabbits will ever be found in the precambrian. But people generally don't talk about predicting future evolutionary outcomes, and those that do most often say that it is impossible - often referring to SJ Gould's metaphor of rewinding the tape of life (more on that below)

One could very well say the same thing about the weather: a hundred years ago, no one in their right mind (which is a tricky way of denoting all but the ones with the most foresight) would have guessed that we would ever be able to accurately predict the weather ten days into the future. But incredible advances in physics now allows us to do just that. Even though the weather systems are very sensitive to many factors, with the combination of the Navier-Stokes equations and a continuous effort to measure weather all over the world, we are now comfortable trusting that the weather forecasts are more accurate than guessing.

In this article by Carl Zimmer from 2014 several researchers explain how the same type of forecasting could potentially be applied to evolutionary biology. Particularly, it is not at all inconceivable that we will be able to predict flu virus evolution, thereby better making vaccines and saving lives. Microbial evolution, it turns out, often has much more repeatable outcomes than what is traditionally thought. Recent research strongly suggest that this is the case, for example when bacteria evolve the same solutions again and again to the same problems.

Here's a simulation with an example of that:

In this very simple example, you'll have to admit it's pretty easy to predict where the population is going to go, yes? (See the full video on youtube for more about fitness landscapes.)

One way to think of evolutionary forecasting is by obtaining as much data as possible about the fitness of genetic variants. If we know which variants (bacteria and viruses are the best candidate organisms) are most successful in making copies of themselves, then we can potentially make predictions of how they will evolve in the near future - just like with the weather.

The problem is that measuring fitness for many many genetic variants is still difficult. It means sequencing many individual organisms, and it means measuring fitness for each one of those variants. The resulting fitness landscape (i.e., fitness as a function of the genotype) is the last of three parameters needed to predict the simplest evolutionary systems. The other two are the population size and the mutation rate. Both of these are fortunately much easier to measure than the fitness landscape. So the fitness landscape remains the biggest obstacle. But it has only taken a few years to get quite far with measurements, and I don’t think it is at all inconceivable that we could have evolutionary forecasts for certain viruses and bacteria within the next few decades.

Returning to Gould, I predict that his lasting impact on evolutionary biology will be similar to Lamarck's: His "rewinding the tape of life" will be the quintessential error that people will keep referring to when talking about evolutionary forecasting.

To be more specific: I predict that 187 years from Gould's death (i.e., by 2189), when his name is mentioned, most people will immediately think of the tape first. And additionally that the idea has been somewhat refuted, since they then will be pretty good at evolutionary forecasting. (Lamarck died 187 years ago.)

My friend Larry Moran, who blogs at Sandwalk, is a staunch Gould admirer, and he asked me these questions in regard to my prediction:
Do you really believe that if we reran the tape of life we would always end up with a continent like Australia where marsupials outnumber placental mammals? 
Do you believe that every possible scenario would result in hundreds of species of dinosaurs that go extinct about 65 million years ago? 
Is the great Permian extinction always going to happen? 
Will an oxygen evolving complex always arise in primitive cyanobacterium about 2.5 billion years ago? 
Are you convinced that replaying the tape of life will always produce eukaryotes with introns and complex spliceosomes? 
Will no replay ever produce highly intelligent New World Monkeys? 
Are poisonous mushrooms absolutely necessary? 
Will the platypus always evolve and never go extinct? 
If we ever find another planet that's very similar to Earth do you expect to find intelligent mammals and maple trees?
And Larry made his own prediction:
Gould will be remembered for his attack on adaptationism and reminding us that there's more to evolution than natural selection. He will be remembered for teaching us about contingency and exaptation. He will be remembered for hierarchical theory. Above all, he will be remembered for making us all aware of the fact that evolution is a lot more complicated than we think.
One objection to the tape metaphor is that it is not well-defined. Does "rewinding the tape of life" mean that everything starts out the same? The initial conditions are *exactly* the same? What about the random events that influence evolution, will they be exactly the same or are they different? Are we talking about the environmental effects (weather, plate tectonics, ET events) being the same or not? Would mutations be identical or just drawn from the same distribution? Some people may have a clear idea of these things and thus feel confident of what the metaphor really means, but I know for a fact that there is not a general consensus about this, with several evolutionary biologists that I have talked to having differing views about its interpretation. We can all agree that randomness is very important in evolution, but not what kind of randomness is part of the metaphor.

In answer to Larry's questions above, one answer is no, not that specifically. Stochasticity (randomness) is too strong a factor, and future evolutionary events are contingent on earlier events.

On the other hand, it may be that stochasticity doesn't mean that evolution is unpredictable, just like it is not unpredictable what will happen when you heat a pot of water, even though we can't predict the path of every individual water molecule.

On the first hand again, if we're talking about, say, evolution on other planets, then no, we cannot expect those exact outcomes. However, Gould also denied that humans would be a repeat outcome if the tape was rewinded, but it is not clearly defined what we mean by "humans" in this context. If by humans we mean intelligent bipedal tetrapods with a head on top, then I do think there are very good reasons to believe that such creatures could evolve again and again, and be a feature on many planets that harbor life throughout the universe.

Back on the second hand, one can argue that every event that ever happens is determined by previous physical states. Things are only as random as we are unable to foresee the next event. A random mutation is only random because we don't know the factors that determine it, or because we don't have the data to predict it. In other words, if we rewind until some time point, everything else is the same up until that time point, so there are good reasons to believe that all future random events would be identical to the first run, and we would thus get exactly what we got the first time.

Live concert @ Aberdeen House

Payam Rowghanian (bass) and Bjørn Østman (piano/guitar/vocals) performing live on September 10, 2016. No fun intended.

I don't love you (Am) 29:57
Spooning (D) 34:15
Today's your birthday (E) 39:23
From the other side (C) 44:52
Saturday (E) 47:43
Table days (C) 55:27
Twelve (C) 1:00:20
Our moon (E) 1:03:10
Jealous (Gm) 1:13:29
Out on a limb (C) 1:18:54
You're so happy (G) 1:22:09
Grown man (A) 1:27:38
The final cut (Bb) 1:35:17

What is a hero?

Does the hero die a hero, or does she survive?

In our worship of the mortal champion for good, is it imperative that the hero dies in the act, or do we need her to live?

What is this uniquely human construct of the hero? Why is it important for us to imagine the hero? Is the individual savior, or even a succession of hero individuals, the true constituent that will save us?

Or is it that a higher-level entity comprised of individual humans is the real savior, and that the individual only takes credit because that is the only way our evolved conscious is capable of telling the story? Does the fact that the onus of our past evolution was the individual cause us to only be able to think of heroes as individuals? Can we elevate our understanding of evolution and the narrative of the struggle to encompass the larger community comprised of individuals?

Rationally and evidently we know that the larger community - that which is larger than the individual tribe and consisting of more members than each individual can keep track of - is the entity effecting real and lasting change. The mark of the hero is self-sacrifice for the common good, but it is for the sake of, and brought about by, the community and the common good. Where we aim our admiration and how we tell the story is a product of our evolved way of thinking, but it is also a way of thinking that we have evolved a capacity for elevating, and we now have the resources and the knowledge to make this transition.

Hero has  a meaning, and only needlessly do we need to change it. But perhaps we need another term to properly tell the tale of the hero-community?

The individual hero eventually dies, whether in the heroic act or not, but both the true originator and the benefactor - the community - survives.

Holger Danske rises up against the invading forces, but is personified not by a single individual but as a group.

Will the creationists accept this gambit?

Rejoice in the fact that unicorns (as predicted in the Bible) actually existed, but agreeing to the Earth being at least 29,000 years old?

Extinct 'Siberian unicorn' may have lived alongside humans, fossil suggests

Having green in your flag is bad for your IQ

Important update 7/21-15: Please see comments below on the really low quality of the data. I was originally serious about this analysis taking the IQ data at face value, but now want to state that while I do find the aspect of the flag colors amusing, I totally do not trust the IQ data.

If your country has green in its flag, then you are less likely to be intelligent.

If that isn't an explosive statement, then I don't know what is. But data from Raven-online suggest that this is true.

In this figure is 183 countries ranked by average IQ from left to right. The higher average IQ the further to the right they are plotted. Countries that have green in their flags have a green spot, and all other have a red spot:

The average IQ of countries with green flags is 79.2 (stdev=9.5) and of countries no no green it is 89.0 (stdev=10.1), and this difference is statistically significant (a 2-sample t-test gives p=2.29e-10). You can download the annotated data here.

Supposedly Raven's test-results are pretty good:
It has been demonstrated that there is a 70% correlation between the results of this test and educational achievement. Consequently, the higher your result in this test the greater your chances of success at higher levels of study. By comparison, the correlation factors in other IQ tests have an average variation of between 20 and 60%.
70% is a very strong correlation, and they are probably right to point out that the strong correlation between IQ and level of education is not spurious. And yet, I think they got causality the wrong way around.

They are implying that if you have high IQ, then you have a higher the chance that you can successfully attain a higher educational degree. But look at the top ranked countries: Italy has some green in their flag and an average IQ score of 102. The countries ranked higher than Italy are Hong Kong, Singapore, South Korea, Japan, and Taiwan - all affluent Asian nations that emphasize book-studies from a very young age. Many, if not all, of these countries make middle-schoolers take tests, and these tests matter for their future. They are, in other words, trained to take tests. Their school systems are good at making students do well on tests. Compare that to poor counties like Djibouti, Lesotho, Gabon, and Equatorial Guinea, who all have green in their flags. They are poor countries, which obviously negatively affects education, which then doesn't allow children to practice taking tests very much (which I am not particularly in favor of anyway, I have to say).

You can practice taking tests, and it will affect your score. If that wasn't true, then there would be no point in practicing taking tests, which is something teachers everywhere make their students do.

So rather than IQ affecting education, I posit that it is education that affects IQ. That doesn't sound nearly as sexy (nor is it novel), and Raven is in business of selling IQ tests. They would like IQ to say something about your chances in life, whereas the truth is more likely that the more chances you
have in life, the higher your IQ is likely to be.

The really interesting question here is what causes the correlation between average national IQ and having green in the flag. You could very well argue that it's completely spurious: just because there isa correlation does not necessitate that there is any causation. It is difficult to argue against such a proposition - there exists lots of very intriguing but probably completely random correlations, such as yearly deaths by drowning in a pool vs. the number of movies Nicholas Cage has appeared in. However, those strange and unexplainable correlations are found by cherry-picking many, many more random pairs of variables. The correlation between IQ and green in flag is a one-shot observation, which makes it stand out. The task is then to come up with plausible explanations for the relationship.

Start by noting that there is a positive correlation between national income, education, and average IQ. It makes sense. We then observe that having green in the flag increases IQ: "smarter people dislike green". Maybe there is an effect of having green in the flag on national income: "green makes people lazy" or "other counties prefer not to trade with 'green' countries":

Other variables could be introduced. It seems to me that the "green" countries are for the most part warmer countries, particularly African. The closer countries are to the equator (lower latitude), the worse the average IQ is. Perhaps something about the latitude causes lower national income (Jared Diamond argue that coincidental geography is the main factor in explaining differences in national wealth among countries) and a preference for green? How about this: "people who live in environments where plants are green all year round are more likely to make their flags contain some green". It could be some other psychological preference that is shaped by living at a lower latitude.

I am stumped. Maybe some historian would have something to say about the prevalence of green flags at lower latitudes?

Here's more from Raven's website (original emphasis):
Richard and Tatu argues that differences in national income are correlated with differences in the average national intelligence quotient (IQ). They further argue that differences in average national IQs constitute one important factor, but not the only one, contributing to differences in national wealth and rates of economic growth.

These results are controversial and have caused much debate, they must be interpreted with extreme caution.

Sources: IQ and the Wealth of Nations (2006), IQ and Global Inequality (2002)
I ask again: do differences in average national IQ scores contribute to national wealth and economic growth, or is is more likely that national wealth contribute to raising the national average IQ? I'd say the latter, contrary to Richard and Tatu.

However, there's probably little doubt that having an educated population does contributes to the national wealth, so causality is likely circular: wealth  education  wealth, with higher average IQ (i.e., test-taking abilities) as a side-effect.

Ken Ham's solution to accomodationism and secular humanism

Ken Ham (founder and president of Answers in Genesis, the Creation Museum, wannabe arc builder) is a Young Earth creationist, and he prides himself in taking everything in the Bible literally. AiG even says that they don't interpret the Bible, they "just read it", which is of course a load of hogwash, as everything is written interpreted in some way (for example from other languages to English!).

I agree with him on two points, but then I think that's it: that it makes no sense to pick and choose which parts of the Bible to take literally, and that he is entitled to his beliefs. How can we know which parts of the Bible are allegory and which stories really happened? I think we can't. Ham's and my solution are just completely opposite, as I choose to believe that everything in the Bible is written by man.

And on the latter agreement, he can believe what he wants. I just wish he would keep it to himself, because I think his beliefs are really bad for society. I don't object to his beliefs merely because I can. I don't bash him and AiG just because I have a right to do so, but because they are demonstratively making things worse for us all. Creationism, global climate change denial, anti-science, anti-rationality, anti-education, etc.

I write this because many people, Christians and atheists alike, are accomodationists. They believe there need not be a conflict between religion and science. They often point to prominent scientists who are/were religious (Francis Collins, Kenneth Miller, Isaac Newton, etc.). But that these people manage(d) to reconcile their faith with scientific facts doesn't mean that it is a logically consistent position. They have merely succeeded in compartmentalizing these two spheres of knowledge so they don't overlap.

Additionally, accomodationists can defend their position till kingdom come, but meanwhile a majority of American Christians fail to reconcile their faith with science, and that is a huge problem. Many are more aligned with Ken Ham than with the accomodationists. 42 percent of Americans are outright creationists, while another 31 percent looks like some sort of accomodationists, and only (though rising) 19 percent believe that God had nothing to do with creation (you know, the actual, sane conclusion based on evidence):
In this re-post, Gone in Only One Generation: Battle for Kids’ Minds, Ken Ham laments that Christians are losing the new generations:
How long does it take to lose a culture, from a Christian perspective?

Actually, it takes only one generation.

The devil knows this, and of course God warns us about it. Adolf Hitler understood this when he said, “He alone, who owns the youth, gains the future!”
Nice one, Ken! Quoting Hitler right in the beginning.
I think one of the saddest pages in the Bible is in Judges 2:10–12, “When all that generation had been gathered to their fathers, another generation arose after them who did not know the Lord nor the work which He had done for Israel. Then the children of Israel . . . forsook the Lord God of their fathers, who had brought them out of the land of Egypt; and they followed other gods from among the gods of the people who were all around them.”
Really?! That's one of the saddest passages in the Bible? How about the flood, when most humans and animals perished? What about when the LORD sent two bears to maul 42 kids?
24 He turned around, looked at them and called down a curse on them in the name of the Lord. Then two bears came out of the woods and mauled forty-two of the boys. 
2 Kings 2:24

But yes, I understand his sadness nonetheless. Ken is sad because children today are leaving the church, and that is all he really cares about.
Obviously the parents in Joshua’s day did not teach their children as they should have—and in one generation, the devil had those kids! While it’s ultimately a matter of God’s grace that anyone is saved, God has given parents an immense responsibility to do their part. Over and over again, the Jewish fathers were told about their crucial role but they shirked it (see Psalm 78).
Here is the eternal dichotomy that is such a huge problem for Christianity, but which is always ignored: if God is omnipotent, why does he need our help? Why doesn't he just make it so? If he gives us free will, how can he know everything? And why did he need to torture his own son in order to forgive us for our sins? Why doesn't he just forgive us like normal people forgive each other without the barbary?

The answer is of course that those stories were made up by frightened humans, and it is not a compelling story to just have God forgive us all and make everything nice and rosy.
The public schools have been teaching their own brand of apologetics: how to defend the idea of evolution and history over millions of years, thus causing multitudes of U.S. students from Christian homes to doubt the history in Genesis. Doubts about Genesis place young people on a slippery slide of unbelief that eventually destroys their confidence in the rest of Scripture. Their trust in the soul-saving gospel itself, which is grounded on the Bible’s historical claims, is undermined.
Completely true. I think that is exactly how it works. Education and information is what will erode creationist beliefs, because while religion does not imply creationism, creationism does imply religion. Creationism come only from religion. The accomodationist view is a fallacious one, and the inevitable result is that more and more new adults will realize how problematic it is to reconcile the actual contradictions between scripture and scientific facts, as well as the contradictory ways of understanding the world around us, one being based on evidence and the other on faith (i.e., arbitrary beliefs contrary to evidence).
Yes, the atheists, like Hitler and Stalin, know that if they can capture the next generation (through the education system, media, etc.), they will have the culture.
Hitler was Catholic. And yes, the culture will be shaped by the coming generations, of course. We all know this, and there is nothing nefarious about wanting to educate our children the best way possible. Science in science classes. Religion in history(?) classes. All of the religions. Go teach your sheep whatever you want in your own churches, but keep church and state separate in the public sphere. Also, tax the churches.

So what is Ken Ham's solution?
Teaching young people how God’s Word—rather than the atheistic worldview—makes sense of our world requires intense study, commitment, and fervent prayer on our parts. The church and parents must reevaluate their old assumptions about the way we should be teaching our kids in a hostile culture, and work together to build the next generation by following the directives from God’s Word.

Imagine what would happen if God’s people raised up generations of kids who knew what they believed concerning the Christian faith, why they believe, and how to defend that faith against the secular attacks of the day. They could then proclaim the gospel with authority because they believed the authority upon which it stands. We would change the world!
In other words, shield your children from the evil ways of the secular humanists. Teach your kids apologetics. I am pleased to see that Ken Ham really has no new answer to his problem. I'll give him one, though: remove the First Amendment, teach only the one true religion in public schools, shut down the internet, build a theocracy. That will really make your problem go away, because the next generations would then be ignorant of how the world actually works. Move to Saudi Arabia, Ken.

American teens are losing their religion

Just this figure.

Fig 2. Percentage of American adolescents endorsing “none” for religious affiliation, 1966–2014.

From Twenge et al. (2015) Generational and Time Period Differences in American Adolescents’ Religious Orientation, 1966–2014, PLoS ONE.

Press release


The Monty Hall Evolver

The Monty Hall problem is very famous (Wikipedia, NYT). It is so famous because it so easily fools almost everyone the first time they hear about it, including people with doctorate degrees in various STEM fields.

There are three doors. Behind one is a big prize, a car, and behind the two others are goats. The contestant first picks one door without opening it. Then the game show host tells you that he will open one of the other two doors behind which there is a goat. It is assumed (but often untold) that the host knows where the car is, and so deliberately opens a door with a goat behind it. It is also assumed that the contestant wants to win the car, but let me tell you already that if you really want a goat, you can be sure to get one. Then the contestant is given the choice of choosing again. Since there are now two closed doors, the choices are to stay on the door first chosen or to switch to the only other closed door. The question is what the best strategy is, switching or staying. Is the probability of getting the car 50% for staying and switching? No, it turns out that switching is the best strategy, giving the contestant a 2 in 3 chance of winning the car. Why? Well, there are many ways to realize this. My favorite is this. Once the contestant has chosen one door, we know that the chance the car is behind it is 1/3. Thus, the chance it’s behind one of the two others is 2/3. Because the host opens one of the two other doors, switching is equivalent to actually choosing two doors, giving a 2 in 3 chance of getting the car. There we go. Another way to arrive at this (correct) result is two actually do it many times over. Pick three cards, a red (the car) and two black (the goats), and have someone play the host. Do this say 100 times, and you’ll se that if you switch every time, you’l get in the neighborhood of 67 red car(d)s. However, I give it a pretty good chance that if you do this, then after playing a handful of times you’ll anyway realize that the solution of course is 2/3 for switching.

I once many years ago set out to write a code to do the experiment. I would write the code, run it a kadoolian times and expect to see the switching strategy win out two thirds of a kadoolian times. However, much to my surprise, when I started writing the code, if-statements and all, the solution became to glaringly obvious that I gave up doing it. It just seemed so futile at that point. I suspect that my hankering for using simulations to investigate problems was strongly influenced by this experience.

Recently I have introduced several people to the Monty Hall problem - always a great party trick. And again, almost everyone instantly arrives at 50/50, and are as adamant that this is the correct solution as the next guy. So I decided to finally write the code to do it, but made two stipulations: 1) the code must mirror the way the problem is told as closely as possible. This will not be the most efficient code to write or the fastest to execute, but will hopefully be easy for readers to see through, so to speak. And 2) rather than just playing the game many times, I will let a population of individuals play it and compete with each other for a chance to reproduce (aka evolution). For full disclosure, the code is included below.

The Monty Hall code

The evolutionary dynamics

The objective of the organisms is to come up with the best strategy for playing the Monty Hall game. Each organisms has just one “gene”, called MH01, and this gene determines the probability that when playing the game the organism chooses to stay or to switch. The value of MH01 is a number between 0 and 1. If the number is 0, the organism never switches door, and if it is 1, then the organism always switches, and if the value is, say, 0.4825, then there is a 48.25 percent chance that the organism switches door. Easy-peasy.

We do two experiments: 1) comparing two strategies (50% switching vs. 50% staying, or MH01=0 vs. MH01 = 1) without mutations, and 2) starting all individuals with MH01=0 and adding mutations to all offspring.

We start with a population of N=100 individual organisms. One organism is chosen at random among the N individuals to play the game. If it wins it gets to reproduce. In that case a copy of it now replaces one of the N organisms chosen at random (including its parent). Nothing happens if they lose the game. This results in a constant population size and overlapping generations. When an offspring replaces a hapless individual, the MH01 gene can mutate (in experiment 2). This results in MH01 increasing or decreasing by a small uniformly random value. And that’s it.

The evolved solution

Figure 1: Starting with 50% switchers (MH01=1) and 50% stayers (MH01=0) all ten simulation runs result in the switchers outcompeting the stayers. Switchers win the Monty Hall game twice as often, and the population frequency of MH01=1 thus stochastically increases until it reaches 100% (fixation). Population size is N=100 (the five runs that reach a frequency of 1 after about 1,000 plays) and N=500 (five runs that take about 10,000 plays to go to fixation).
Figure 2: Average population value of MH01 with large-effect mutations. Starting with 100% stayers (MH0=0). MH01 increases relatively fast, reaching the largest value after around 30,000 plays. The effect of mutations is uniformly distributed on the interval ±0.05 centered on the current value. Population size is N=100. The black lines are minimum (bottom) and maximum (top) values of MH01 in the population.

Figure 3: Average population value of MH01 with small-effect mutations. Starting with 100% stayers (MH0=0). MH01 increases relatively slowly, reaching the largest value after around 250,000 plays. The effect of mutations is uniformly distributed on the interval ±0.01 centered on the current value. Population size is N=100. The black lines are minimum (bottom) and maximum (top) values of MH01 in the population. There is less variation in MH01 in this case because the effect of mutations is lower than in the runs shown in figure 2.


What a relief! When running simulations like this there is always the risk that for some unseen reason the evolved solution is different from what you anticipated. Thankfully that is not the case here: evolution favors the fittest organisms, and the fittest organisms are those that tend to switch when they play the game. Success!

Why does MH01 not go to fixation? In other words, why does the average population value of MH01 (blue lines) not become 1? The answer is that there is a mutational load (Wikipedia) caused by the effect of mutations. Offspring of a parent with MH01=1 has a 50% chance of having a lower value of MH01, so there will always be some individuals with a suboptimal value of MH01. What is increased in evolutionary dynamics is not fitness but free fitness.  Free fitness is the sum of the logarithm of fitness and an entropy term that is non-zero when there is either mutation and/or drift. The term was introduced by Yoh Iwasa in 1988: Free fitness that always increases in evolution.

Let me reiterate that the answer of 2/3 chance to get the car when switching relies on the game host knowing where the car is, and deliberately opening a door that the contestant has not chosen and where there is a goat behind. If the host opens another door at random and there happens to be a goat behind it, then the probability of getting the car is only 50% for switching (and for staying). The probability is thus dependent on the knowledge that the contestant has about the knowledge and intent of the host. Only if the contestant knows that the host knows what he is doing does the chance increase by switching. Update 7/15/2015: I was wrong about the effect of the knowledge of the contestant about what the host knows. It makes no difference what the contestant knows about what the host knows. If the host knows what he is doing, then the chance of winning by switching is 2/3 no matter what. Otherwise this simulation would not work, as the computer doesn't "know" anything. A simple enumeration of the possible outcomes makes this abundantly clear, as seen below in the comments.

You can play the Monty Hall game here, where you can also play the version where the host does not know which door has the car.

Answer in Genesis affirms evolution, sort of

Answer is Genesis (i.e., Ken Ham and the Creation Museum) has published a really nice description of the bedbug paper that came out earlier this year. The story is in short that bedbugs used to be one species feeding on bat blood, but now they are in the process of splitting into two species, with one specializing on humans. This has been going on for quite a while, but evolution is - mostly - a slow process, so have a little patience, yeah?

In Bedbugs, Scientists See a Model of Evolution, New York Times, by Carl Zimmer

Dr. Mitchell (she's an obstetrician, by the way) writes that
Genetic analysis supports the hypothesis that today’s common bedbug originated in bat-caves and, having transitioned to cave-dwelling people, then developed populations with a preference for people and people’s houses.
That's what I call evolution, rather than development. But she won't go that far:
The bedbug does provide a living laboratory to study speciation—which is limited to variation within a created kind—but it does not provide a laboratory to show how new, more complex forms of living things evolve as Darwin poetically and imaginatively asserted.
Here's her great description of natural selection
About 90% of the bedbugs infesting homes today are resistant to pyrethroid insecticides. However, any reports of rapidly “evolving resistance” are poorly worded. Bedbugs remain bedbugs. They don’t evolve into anything. Those genetically equipped to survive the assault of pesticides have restored their populations with pesticide resistant offspring. This is an example of natural selection (and possibly other mechanisms), as pesticide-resistant individuals selectively survive to breed another day.
But why is this not evolution, then?
There is nothing in this research either reminiscent or predictive of the evolution of increasingly complex “new forms” either wonderful or dreadful. Instead, what this research demonstrates is that bedbugs are still bedbugs, varying within their created kind to survive and thrive in a sin-cursed world.
Hold on! She just described how the human variety has evolved resistance to pesticides, so what gives? Note that the scientific jargon is that development is how an organism changes in its lifetime, while evolution is how the population changes over the generations. Pesticide resistance is not something that an individual bedbug first doesn't have, then experiences pesticide, and the develops resistance. No, either an individual has it from birth through genetics or not, just as Mitchell so eloquently describes the process. So pesticide resistance is exactly a new feature, an increase in information about the environment = an increase in complexity, through evolution by natural selection. I can only conclude that Mitchell both understands evolution and believes that it occurs.

But you know, she has a book:
But as we infer from Genesis 1 and observe in biology, living things—including bedbugs—only reproduce and vary within their created kinds. Bedbug research actually affirms this scriptural truth rather than lending any support to the bacteria-to-bedbug fallacies of Darwinian evolution.
So with semantic tricks this is not evolution because it is development, and because, even though she agrees that this is an example of speciation, it is only variation within a created kind. This kind is not defined here, and I have never seen a rigorous, scientific definition (though I've seen one based on the Bible), so it remains a question of semantics that this is not evolution. But I am happy that she agrees that speciation occurs.  \o/

CoE #78 is up

A very short edition of Carnival of Evolution is up today. A new blogger is hiding behind a pseudonym, David Hume, with two excellent posts on molecular evolution. That's the good news. The bad news is that I had to find almost all of the blog-posts myself, which means there were very few submissions by others, and clearly a lack of interest. :(

How to evolve intelligence in 7 easy steps

The September issue of Scientific American is about human evolution. It includes articles by Frans de Waal, Gary Stix, John Hawks, and others. And this one by Ian Tattersall, paleoanthropologist at the American Museum of Natural History. His research is on hominins and lemurs.

If I Had a Hammer
A radical new take on human evolution adds a large dose of luck to the usual story emphasizing the importance of our forebears' ability to make tools
In Brief
A new theory credits a combination of cultural advances and unpredictable climate change for the exceptionally fast rate of evolution in early humans.
Climate change repeatedly led to fragmentation of hominin populations, creating small groups in which genetic and cultural novelties were rapidly cemented, accelerating speciation.
Our own species, the anatomically distinctive Homo sapiens, was born out of such an event in Africa around 200,000 years ago.
About 100,000 years later an African isolate of our species acquired the ability to use symbols. It was almost certainly this unique symbolic cognition that made it possible to eliminate all hominin competition in little time.
Tattersall argues that human evolution has been unusually rapid in the last 7 million years, with many new hominin groups arising (and going extinct) and our lineage undergoing a lot of adaptive changes (tool use, brain size, anatomical modifications). Sharing cultural know-how is thought to have been under selection, steadily giving rise to humans. He then says this:
But this sort of refinement, one generation at a time, would not have been fast enough to radically reshape the human line in seven million years.
Why not? This is an assertion that Tattersall makes without any given justification. It may be so, but I don't think anyone can know this. 7 million years is maybe about 350,000 generations. That's an awful lot. If you start out with a brain that weighs just 40 grams and increase its size by one thousandth of a percent per generation for 350,000 generations, you would end up with a brain the size of humans (1,324 grams). I am not saying this is how it happened, as the fossil data suggest a doubling in between 1 million years ago and 200,000 years ago, for example. Just saying that small modifications can lead to big changes on long time-scales.

Tattersall then discusses the causes of this increase in brain size, saying that the traditional explanation of gene-culture evolution, which posits a "positive feedback between innovation in the biological and cultural spheres," is wrong. The interaction between genes that enabled them to use tools and new inventions of tool use and sharing those inventions lead to a rapid increase in the size of brains, the thinking goes. However, Tattersall then has this to say:
A little thought, however, suggests that there must have been more to it than that. One problem with this scenario is that it assumes that the pressures of natural selection—stresses to which the species were adapting—remained consistent over long periods. But in fact, Homo evolved during a period of Ice Ages, when the ice caps periodically advanced to what is now New York City and northern England in the Northern Hemisphere, and the tropical zone experienced periods of extreme aridity. Amid such environmental instabilities, no consistent directional selection pressures could have existed. [Emphasis added]
Really? So because there are periodic fluctuations in climate there can't be a consistent directional selection pressure on brain size? That makes it sound like a colder climate pushes the size in one direction, a warmer climate pushes brain size in the opposite direction. That makes no sense to me. Rather, the environmental instabilities could all select for human ingenuity and intelligence no matter what direction the environmental changes were in. If his choice of words had not made him sound so dead-certain, and instead have made this new view more suggestive than so assured, I would not really have objected. I also don't know what actually happened, but asserting that "no consistent directional selection pressures could have existed" seems like overreaching. Tattersall continues with what I think is not an argument against directional selection at all:
The more we learn about these climatic oscillations, the more we realize just how unstable the ancient environments of our ancestors must have been. Cores drilled in the ice caps and in seafloor muds reveal that the swings between warmer and dramatically colder conditions became increasingly pronounced after about 1.4 million years ago. The result was that in any one location, resident hominin populations would have needed to react frequently to abruptly changing conditions.

Then there is this picture.

This is a stone with engravings dated to 77,000 years ago.
Most notably, evidence of distinctively modern symbolic cognition emerged rather suddenly and only very late indeed. The earliest overtly symbolic objects—two smoothed ocher plaques with geometric engraving—show up at Blombos Cave in South Africa about 77,000 years ago, significantly after anatomically recognizable H. sapiens had entered the scene (some 200,000 years ago) [see box above]. Because the patterns involved are highly regular, researchers feel confident that they are not random but encode information. Such sudden breakthroughs are not the mark of steady intellectual advancement, generation by generation. [Emphasis added]
What kind of encoding are we talking about? In kindergarten I doodled something much akin to this - regular parallel and crossing lines. I wasn't conveying any information. And yet this symbolic encoding is exactly what Tattersall proposes is the one thing that gave our lineage an edge over other hominins.
When the dust settled, we stood alone, the serendipitous beneficiaries of cognitive advances, cultural innovation and climate changes that allowed us to eliminate or outlast all hominin competition throughout the Old World in an astonishingly short time. Our competitive edge was almost certainly conferred by our acquisition of our unique mode of symbolic thought, which allows us to scheme and plan in unprecedented ways. Interestingly, this development seems to have occurred within the tenure of our species H. sapiens, evidently spurred by a cultural stimulus, quite plausibly the invention of language, which is the ultimate symbolic activity.
It's not that I don't believe symbolic thought played a role. It's that I don't believe there is enough evidence that this is the case. Almost certainly this is pure speculation, and we cannot be even close to certain that what eliminated all hominin competition was ability to scheme and plan. Another hypothesis is that they were unable to cope with climate change.
Evidently, then, we have to look away from processes occurring within individual lineages to explain the rapid change among Ice Age hominins. Yet the same elements implicated in the gene-culture coevolution story—environmental pressures and material culture—may still have been in play. They simply operated rather differently from how the traditional portrayal suggests. To understand how these factors may have interacted to trigger evolutionary change, we must first recognize that a population needs to be small if it is to incorporate any substantial innovation, genetic or cultural. Large, dense populations simply have too much genetic inertia to be nudged consistently in any direction. Small, isolated populations, on the other hand, routinely differentiate.
No. Just no. Populations do not need to be small to incorporate new genetic or cultural changes. Genetic inertia (= genetic homeostasis) is the maintenance of genetic variability within a population. But we know that even though random changes have a small effect on large populations, smaller changes in fitness can be discerned by the selective agents (the environmental causes of selection) in large populations. Genetic drift can indeed nudge a small population in one direction or other, but that direction is then random with respect to what is adaptive. Rather, in large populations trait changes that are adaptive (conferring a benefit in terms of survival and reproductive success) can actually become established in a large population. For example,  the current human population is very large, and there is no problem sharing and establishing drastic cultural changes.

On top of that, when the population is large there is more genetic (or cultural) variation, as there is a constant (average) supply of mutations (or inventions) per individual. The more people there are the higher the chance is that someone will have a mutation for increased brain-size or that someone will invent something new and useful for survival. And even though those changes will take longer to propagate and establish in large population, the chance that they will be lost is also larger in a small population. This is basic population genetics theory.

Let me be clear here: I do not think it unlikely that symbolism, tool use, large brains, and small populations were not important drivers of human evolution. I do. I am just a controversialist. My pet hypothesis is that freeing the hands from locomotion led to an arms race between tool use and increased brain size, and my suspicion is that this is a general phenomenon that should be observable in other lineages (like on other planets). Evolving intelligence in seven easy steps: Become bilateral, obtain a head, use four limbs for locomotion, stand up, co-opt front-legs for tool use, get bigger brains, build a radio telescope. [Part of this is discussed in this io9 article about why aliens may look like humans.]

Tattersall's essay ends with this intriguing paragraph.
Seeing our amazing species as an evolutionary accident, though, contains a profound lesson. For if we were not shaped by evolution to be something specific—fitted to our environment and tailored to a purpose—then we have free will in a way that other species do not. We can indeed make choices about the ways in which we behave. And this means, of course, that we must accept responsibility for those choices.
Free will, all of a sudden?! Then if we were shaped by evolution to be something specific, then we would not have free will, like other species? All other species do not have free will because they were shaped by evolution to be something specific? And because we are able to make choices, then we must take responsibility for them? How does that follow?

Look, it's not that I disagree that we should take care of the planet, but I would like to make an appeal for a modicum of scientific rigor here. Rigorously, this last paragraph doesn't hold water, and evolution almost certainly does not have anything to say about free will.

CoE #77 on Carnival of Evolution

Carnival of Evolution #77 - the Phoenix edition is up at Carnival of Evolution.

Where it is going to stay.

It is also going to be up every month on the 1st.

You can submit blog-posts about evolution as comments on the blog, Facebook, Twitter, or by email.

Ken Ham wants to return to whatever we once were

Ken Ham delivers an awesome summary of the decline of religion's influence in his Answers Magazine. It reads really well, mostly, if you forget for a moment that it's written by Ham. Otherwise, you can almost hear him gnashing teeth.

He laments that the Western world is becoming more and more secular, and that you have to go to the Third World to get the kind of religious adherence he longs for. He is talking about gay-marriage and abortion and evolution, of course. He then asks
What Led to This Change?
In essence this change reflects a shift between the world’s two opposing religions. Ultimately there are only two religions—one starts with God’s Word and the other starts with man’s word. America—and the whole Western world—once built its worldview predominantly on the Bible. Now a shift has occurred, as the West’s worldview is being built on man’s word. This change is reflected in a shift from Christianity’s absolutes to the relative morality of human opinions.
I guess that it favors his rhetoric to phrase these different world views as being religions (Ham will say 'atheism' here, but he should say humanism -which is not a religion as much as a word view). Devious, though, how he basically dismisses all other religions by this false dichotomy.

He's right that the change is from a focus on absolutes to a relative morality, but not really on human opinion. At least not as arbitrary as he makes it sound. Our morality is at least in part evolved, as people like Frans de Waal argue. On top of that, the morality taught in the Bible (if you include the Old Testament, as many Americans do), is deplorable [list of actions punishable by death].

Ham (an Australian, btw) continues
Whatever we once were we are no longer! These words really mean that America as a nation no longer builds its thinking on God’s Word, but man can determine truth for himself. America has changed religion—from Christianity to a man-centered religion. This spiritual disaster is now reflected in this nation’s economic and moral disaster.
Of course, man has long been able to determine "truth" (i.e., moral values, in this case) by selecting reading the Bible, as Ham does himself. Does he call for God to smite the shellfish eaters, per chance? It really seems much more easy to explain the various Biblical laws as arbitrary human inventions (e.g., forbidden to eat leavened bread during the Feast of Unleavened Bread, Exodus 12:15 - what is the point?).
So What is the Solution?
Whatever we once were we need to return to. The only solution for this nation (and every other nation) is to return to the authority of God’s Word as the foundation for our individual and cultural worldviews.
As Psalm 11:3 states, “If the foundations are destroyed, what can the righteous do?”
Really?! Whatever we once were? You mean, like slave-owning racists? Gullible peons? Disease-ridden and ignorant of the world? Perhaps that is what he means, as long as the word of God is taken literally. Sounds like Hell-on-Earth to me, ironically.

But what is the solution? How is it that Ham here supposes it is possible to return to the authority of God's word? What can the righteous do, indeed? Build a creationist theme-park in Kentucky?

What affects acceptance of evolution?

There's a creationist conference coming to Michigan State University this Saturday, so I and others have been thinking and talking about how to respond. The majority think that complete silence on the part of MSU scientists (faculty and students alike) is the way to go, but I think responding is a good idea, and am not really afraid of bad press or short-term effects. To me what matters is what happens in society in the long run - and I think that is really the only thing that matters: some event may cause a surge in some measure of creationism, but if the event causes a decrease in creationism over a span of many years, then all is well, yes?

Besides this event and others like them, what can really change the tides of creationism in the USA?

We might recall what the origin of creationism is (and I know many will at this point already be put off). It is of course religion. And it is only religion. It is not all religion, as there are many scientists that believe (on evidence) that evolution is the best way to describe our origins, but it is only religion.

I was then today directed to this study published this month in Evolution: Education and Outreach:
The relative importance of religion and education on university students’ views of evolution in the Deep South and state science standards across the United States (that I had read about earlier on Epiphenom).

Their main result is contained in this figure:

From the abstract:
Results: We found that the degree of religiosity mattered significantly more than education when predicting students’ understanding of evolution. When we focused on acceptance of evolution only, students taught evolution or neither evolution nor creationism in high school had significantly higher acceptance than those taught both evolution and creationism or just creationism. Science majors always outscored non-science majors, and not religious students significantly outperformed religious students. Highly religious students were more likely to reject evolution even though they understood that the scientific community accepted the theory of evolution. Overall, students in two of three biology classes increased their acceptance of evolution, but only those students that seldom/never attended religious services improved. K-12 state science standard grades were significantly and negatively correlated with measures of state religiosity and significantly and positively correlated with measures of state educational attainment. [Emphasis added]
So, I submit that the problem is not that we don't know what to do about the problem of creationism in America, but it is that no one wants to touch it with a ten-foot pole.

Creationist Origin Summit at Michigan State University

Michigan State University
November 1st, 2014
Business College Complex, Room N130

 Meet the Speakers

Dr. Gerald Bergman
Northwest State Community College
Dr. Donald DeYoung
Grace College and Theological Seminary
Dr. Charles Jackson
Points of Origin Ministries
Dr. John Sanford
Cornell University


Hitler's Worldview
There's no doubt Adolph Hitler believed in evolution, but to what extent did that belief affect his actions?  You might say he caught the "survival of the fittest" ball and ran with it, declaring the Aryan race to be "the fittest".
There's no doubt that Hitler was inspired by the Bible when he wrote Mein Kampf. Several passages directly reference the creator and Hitler was of course a Catholic. Some Biblical passages condone racism. Does that mean that we can attribute his worldview to Catholicism?

Evolution Going the Wrong Way
Instead of providing new levels of the genome info, the DNA mutations actually cause that info to breakdown and
deteriorate, which is the opposite of what the neoDarwinist would have you believe.
Most mutations are neutral, some are deleterious, and a few are beneficial. Because the beneficial mutations increase fitness and the deleterious decrease fitness, natural selection ensures that beneficial mutations stay in the genome and deleterious are mostly eliminated.

The Discovery of Design
Biomimicry is a new science that studies nature's models and uses these designs and processes to solve human problems. Dr. DeYoung cites examples which reveal intelligent design & challenges the long held beliefs of naturalism.
Biomimicry is a fascinating area of research that is testament to how adaptations solve design problems in nature. Evolutionary explanations of complex features of living organisms challenge the ancient view that such systems must have had an intelligent designer.

Today's Astronomy
In this workshop Dr. DeYoung covers an array of topics ranging from the origin of the moon to the search for life on other planets.
The giant impact hypothesis proposes that the moon formed as a results of a colossal impact between the young Earth and another object the size of Mars. The search for life on other planets is a scientific endeavor that continues to this day.

The Big Bang is FAKE
The Big Bang may be the latest fad and a popular TV show, but the evidence just isn't there.  Dr. Jackson examines the evidence and presents a viable model that aligns with the facts.
There is plenty of scientific evidence for the Big Bang model of the origin of the Universe. For example, astronomers have observed galaxies 13 billion light-years away, and the cosmic microwave background radiation is consistent with the Universe forming about 13.8 billion years ago.

Natural Selection is NOT Evolution
Contrary to popular belief, they're not the same, and Dr. Jackson explains.
Correct. Natural selection is one mechanism by which evolution occurs. There are many other factors involved in evolution, such as genetic drift, mutation, transposable elements, sexual recombination, sexual selection, inbreeding, and extinction, to name just a few. Exciting stuff!

Lenski's Experiment
Since 1988 Dr. Richard Lenski has been conducting an experiment in an attempt to prove evolution and, though he has yet to prove evolution, the one thing he has proven is this: Degeneration is a biological fact.
Through his exciting experiment Rich Lenski has directly observed evolution as it unfolds in the bacterium E. coli. The trend after more than 60,000 generations is that the bacteria continue to accumulate beneficial mutations that increase their fitness.

Mendel's Accountant vs. Avida
The Avida & Mendel programs are two computer simulations that are pitted against each other in this digital duel. With one promoting evolution, and the other promoting Creation, Dr. Sanford compares the two, examines the data, and arrives at some remarkable conclusions.
Avida is a computer program invented by three professors at MSU. Digital organisms in the program have been observed to adapt, speciate, and evolve a multitude of different solutions to various problems that they are challenged with. Hundreds of Avida papers have been published. Nobody uses Mendel's Accountant.

Further reading

Mein Kampf - -
(particularly page 84 and 392)
Natural selection
Irreducible complexity
Giant impact hypothesis
Extra-terrestrial life
The Big Bang
Genetic drift
Lenski's experiment
Mendel's Accountant

Evolution, sex, and mixability
Last Friday Christos Papadimitriou gave a seminar at UC Santa Barbara in the Computer Science department. The title of his talk was Computational Insights and the Theory of Evolution [announcement].

Covertly computational ideas have influenced the Theory of Evolution from the very start. This talk is about recent work on Evolution that was inspired and informed by computation. Considerations about the performance of genetic algorithms led to a novel theory of the role of sex in Evolution based on the concept of mixability, while the equations describing the evolution of a species can be reinterpreted as a repeated game between genes. The complexity of local optimality informs the mystery of variation, and a theorem on Boolean functions helps us understand better the emergence of complex adaptations.

Papadimitriou is a very accomplished computer scientist, a member of the National Academy of Sciences and has written several textbooks and has received many awards.

The work he presented at the seminar was on evolutionary theory. Of the 60 minutes he spoke, he spent the first 30 talking about the science of evolution before Darwin, about the work of Wallace and Darwin, Mendel's work, and then briefly about Fisher, Wright, and Haldane.

Following that he then spoke about Mixability. He met Adi Livnat at Berkeley in 2006, and together they ended up publishing a paper on Livnat's theory of mixability in PNAS in 2008: A mixability theory for the role of sex in evolution [1]. In short, mixability is a theory that states that in sexually reproducing organisms, fitness alone is not what is optimized, but fitness plus population entropy is. What this means is that in addition to fitness, variation (as measured by entropy) is also optimized given the rate of recombination. Recombination introduces genetic variance by mixing the genetic material of two parents (rather than making a clone), and since genetic variance is the fuel of evolution, this is the benefit of sex, so the story goes.

Following this 2008 paper, three more papers have appeared on the same subject by the same two authors (and various others, including Marc Feldman, by the way). Now, the first PNAS paper from 2008 was edited by Dan Hartl. This means that it had a independent editor who sent the paper out for review. (As we shall hear soon, it was sent to six reviewers.) The next three papers appeared in PNAS (2010), Journal of Theoretical Biology (2011), and PNAS (2014) [2-4]. Both of these PNAS papers were contributed by Papadimitriou. Because he is a member of the NAS, he is allowed to contribute four papers per year to PNAS, which means that he acts as the editor, and is thus the person choosing which reviewers to send the paper to for review [source]:
Papers listed as “Contributed” by NAS members (at least one of the authors is an NAS member) account for only 5% of submissions and less than a quarter of published papers. NAS members are only allowed up to four Contributed papers per year. Member-contributed papers must have at least two independent reviews and are evaluated by the Editorial Board.
So only two reviewers chosen by one of the authors, and the editor/author makes the final decision anyway. Hmm. Just saying*...

Anyhow, Papadimitriou's presentation ends, and I eagerly raise my hand to ask my question. Check out this recording of the exhange.
Papadimitriou: I will pray for answers, but please give me your questions.

Me: So, you said you met Adi Livnat in 2006...

Papadimitriou: Yes.

Me: In 2005 there's a paper also in PNAS by Guy Sella and Aaron Hirsch [5]. Are you familiar with this paper?

Papadimitriou: Yes, I am familiar.

Me: They introduced the concept of free fitness analogous to the free energy.

Papadimitriou: Yes.

Me: And that seems to me to be curiously identical to mixability.

Papadimitriou: Not really, no. I mean...

Me: The point is that they update both fitness and entropy at the same time, yes?

Papadimitriou: We have two conclusions that seem to... First of all they came up with [?], supposedly do that. We came to this conclusion 1) through simulations. So, we came up with the concept of mixability, in other words that the alleles that are favored are not the ones that have the best combinations, but the ones that have the best average performance. By analyzing fitness landscapes. Please, when we published our paper we got six reviews. Two of them, they could have been from that group [i.e., Sella and Hirsch]. One of them said that this is well known, and the other one said it is wrong. The point is that once you have to articulate the theory. Let's take Kimura's neutral theory. Of course you'll find hunters in the literature. The point is that theories are cheap. Coming up with a model that says "well we know physics, so let's apply the free energy principle to evolution". The point is that it's the force of argument informed by the theory that eventually becomes the cradle of science.

Me: But you don't even cite them, which is...

Papadimitriou: Yeah, we didn't know at the time. So the second part is where we explicitly say it's a derivation. It's a derivation from the equations of Fisher and Wright. In other words, its a proof. Not a postulation. You understand what I say?   

Me: I Understand what you're saying, but it also rests on the fact that - something that biologists all agree on, which is that variation in a population is a good thing. And it's important for evolution. Without it evolution basically does not work, and you're saying that you are getting that through sex, but you're also ignoring mutations, which you said in the beginning as well. Everybody knows that this is something that happens as well, and especially in the bacterial populations that you were talking about where you said in the beginning that they are all sexual with conjugation and so on. But largely they are not. They are getting a lot of their variation from mutations, and this is known from experimental evolution as well.

[Here the moderator asked us to take it offline.]

Papadimitriou: So, mutations are paramount. Mutations in eukaryotes are also... relevant mutations are relevant. It's like meteorites: its important to understand what happens in everyday evolution, which means the evolution in populations. I'd be delighted to chat with you after the question session.

I did not stick around to talk with him afterwards. I had other obligations, plus I had basically gotten the answers that I was looking for. My conclusion is, based on this presentation and on reading the papers, that the three components at play in mixability
  1. variation drives evolution
  2. sexual reproduction increases variation through recombination
  3. free fitness is what is (attempted) optimized by populations
were already known prior to 2006. Then, showing this mathematically and by simulations is cool. But claiming that you have invented something new is not. And researchers can say that they just didn't know about the previous work, and that may be true, but as I often say, knowing the literature is half the job. Failure to give credit where it's due is egregious, especially if the following papers also do not cite the right source. None of their papers cite Sella and Hirsch**, even though Papadimitriou is familiar with the paper, and even speculated that one of them could have been a reviewer on the first paper from 2006.

On his Berkeley homepage Papadimitriou writes this about the 2008 paper:
There had been no satisfactory explanation of the advantages of sex in evolution, and yet sex is almost ubiquitous among species despite its huge costs. Here we propose a novel explanation: Using standard models, we establish that, rather astonishingly, evolution of sexual species does not result in maximization of fitness, but in improvement of another important measure which we call mixability: The ability of a genetic variant to function adequately in the presence of a wide variety of genetic partners. 
So the claim to novelty remains, and that seemingly includes a rediscovery of epistasis (the genetic interaction between genes)!

As you can also see from this paragraph, the other part of the story is that mixability is touted as an explanation for the evolutionary origin of sex (i.e., recombination). To that I just want to say that if you postulate a model in which there are no mutations, then yes, recombination saves the day, as it is now the only source of variation. However, this is clearly unrealistic in the extreme, and evades the real question, namely how could sex evolve when clonal growth is so much more efficient and asexual populations (which do exist!) have been doing so well since the dawn of time?

Adit Livnat took everyone by storm (I think) by writing the following final paragraph in 2010:
If sex is tied to the nature of genes, then one may reconsider the question of the origin of sex. Although it is common to imagine evolution as an originally asexual process that became sexual at some point, it is possible that sex had existed in a primitive sense of mixing before the emergence of genes as we know them, and that the interaction of sex and natural selection played a role in the shaping of the genetic architecture [2].
In other words - and I also have this from him verbally at the 2014 Evolution conference - Livnat thinks that sexual reproduction came first, followed by asexual reproduction later in the history of life. Papadimitriou mentioned this in his talk as well, saying that there are basically next to no species that are asexual - even bacteria have sex - and those that lost the ability to have sex are evolutionary dead ends. If you think evolution without sex is impossible, I dare you to explain why Lenski's E. coli populations - which do not exchange  genetic material laterally (i.e., between individual cells) - have been successfully evolving and adapting since 1988 [source].

* I am not the only only one who thinks this track for submissions to PNAS has got to go, but do see this article [6] for another take.

** In researching this topic I also learned that the idea of free fitness originates with Iwasa (1988) [7].

Kyushu University
Department of Biology

[1] Livnat A, Papadimitriou C, Dushoff J, and Feldman MW (2008). A mixability theory for the role of sex in evolution. Proceedings of the National Academy of Sciences of the United States of America, 105 (50), 19803-8 PMID: 19073912

[2] Livnat A, Papadimitriou C, Pippenger N, and Feldman MW (2010). Sex, mixability, and modularity. Proceedings of the National Academy of Sciences of the United States of America, 107 (4), 1452-7 PMID: 20080594

[3] Livnat A, Papadimitriou C, and Feldman MW (2011). An analytical contrast between fitness maximization and selection for mixability. Journal of theoretical biology, 273 (1), 232-4 PMID: 21130776

[4] Chastain E, Livnat A, Papadimitriou C, and Vazirani U (2014). Algorithms, games, and evolution. Proceedings of the National Academy of Sciences of the United States of America, 111 (29), 10620-3 PMID: 24979793

[5] Sella G, and Hirsh AE (2005). The application of statistical physics to evolutionary biology. Proceedings of the National Academy of Sciences of the United States of America, 102 (27), 9541-6 PMID: 15980155

[6] Rand DG, and Pfeiffer T (2009). Systematic differences in impact across publication tracks at PNAS. PloS one, 4 (12) PMID: 19956649

[7] Iwasa, Y. (1988). Free fitness that always increases in evolution Journal of Theoretical Biology, 135 (3), 265-281 DOI: 10.1016/S0022-5193(88)80243-1