Field of Science

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

Do all species form the same way as songbirds?
As niches are filled up by new species speciation slows down. Comes to a halt, even. This makes sense, as the niches are ways of life that organisms can have, if there are no other ways of life currently available, thing will stay the same. This is in line with a mode of speciation driven by niches, in accordance with the Ecological Species Concept by Van Valen (1976)* (which is a definition; species is the concept; it should be a criterion**). I'll even go so far as saying that most speciation events can be explained by this framework, though there are some known instances of speciation driven by weird genetic events that cause reproductive isolation, e.g., in European crows.

A recent study uses Himalayan songbirds to show that speciation rates decrease as niches are filled (Price et al., 2014).
Speciation generally involves a three-step process—range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations1, 2. Speciation relies on cycling through these three steps and each may limit the rate at which new species form1, 3. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions4, set an ultimate limit on speciation. 
It's a nice paper - the link between niches and speciation is close to my heart (Østman et al., 2014). Grrlscientist has a nice write-up about it in The Guardian. However, I have to mention that I am taken aback by three things in the above quote from the first lines of the abstract:

1) Generalizing from songbirds to everything else: Speciation is not always about reproductive isolation, and it may certainly not generally work the way it does in Himalayan songbirds. Especially not in asexual organisms.

2) Allopatric speciation (with geographic isolation) may be prominent, but we don't know how much sympatric speciation (without geographic isolation) occurs, so we can't discount it (and theoretically it is easy).

3) Species evolve, they don't develop. So does that mean that reproductive isolation evolves rather than develops? Semantics, I realize, but I think it's important to get this right.

So, fixed:
Speciation in sexually reproducing organisms generally involves a three-step process—range expansion, range fragmentation and the evolution of reproductive isolation between spatially separated populations1, 2. Allopatric speciation relies on cycling through these three steps and each may limit the rate at which new species form1, 3. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the evolution of reproductive isolation and ecological competition, both factors that limit range expansions4, set an ultimate limit on speciation. 
That'll be $20.

* Best title ever: "Ecological Species, Multispecies, and Oaks." I never get tired of saying this.
** I will also not likely get tired of saying that: Pragmatic definitions in biology.


Price TD, Hooper DM, Buchanan CD, Johansson US, Tietze DT, Alström P, Olsson U, Ghosh-Harihar M, Ishtiaq F, Gupta SK, Martens J, Harr B, Singh P, and Mohan D (2014). Niche filling slows the diversification of Himalayan songbirds. Nature, 509 (7499), 222-5 PMID: 24776798.

Østman B, Lin R, and Adami C (2014). Trade-offs drive resource specialization and the gradual establishment of ecotypes. BMC evolutionary biology, 14 PMID: 24885598

A morphological interpretation of traits

Have a look at this short video. Do you think it works?

It is supposed to show that new species form when traits are subject to trade-offs. However, in the actual model, those traits govern resource use, but here they are illustrated as morphological traits: tails, wings, legs, whiskers, ears, and eyes. The traits vary over time, resulting in four different species.

Now that you have watched it, my question is whether the nature of the traits in the model is adequately conveyed? What do you think?

The data is from our new paper, Trade-offs drive resource specialization and the gradual establishment of ecotypes in BMC Evolutionary Biology.

Evolutionary compromises drive diversity (MSU Today)
Compromise is key to evolving new creatures (Futurity)
A Winged Cat Helps Explain The Principle Of Evolutionary Trade-Offs (io9)
Evolutionary compromises drive diversity (Fox 47 News)

Death of the fittest

This is imho an excessively beautiful figure! I keep staring at it getting thrills, and bliss pours over me as I explore its intricacies. This is evolution.

Click to enlarge.

(You should enjoy this figure while listening to one or several of these:)

What are we looking at? Fitness over time of all individuals in a population of size 100. The blue line is average population fitness. The red line is the lineage that leads to the most fit individual after 100,000 updates.

And the real treasure? All the black lines which are all the other lineages that died out. Only the individuals who descend from the ancestor on the red line are alive near the end (technically, the most recent common ancestor (MRCA) is close to but obviously not quite at the end of the simulation).

We see two interesting facts:
  • Offspring that have deleterious mutations (that decrease fitness) survive for quite a long time, and those individuals even have offspring of their own some times. In fact, we can see that there are even deleterious mutations on the line of descent (the red line goes down on five occasions).
  • Offspring that have beneficial mutations (that increase fitness) don't always survive. In fact, most of them eventually die and those beneficial mutations are lost. Evolution does not imply survival of the fittest.
Deleterious mutations do not prohibit evolution; deleterious mutations hitchhike on the back of beneficial mutations and go to fixation that way (there is no epistasis in this model).

The simulation
I made this simulation in Matlab. Constant population size of 100. Mutation rate of 0.01. Effect of mutations is drawn at random from a uniform distribution of selection coefficients between -0.05 and 0.05. One individual reproduces per computational update (Moran process), and chance of reproducing is proportional to fitness.

73rd Carnival of Evolution: World Cup Edition

Welcome to the 2014 Carnival of Evolution World Cup of evolution blog posts.

We have an exciting post ahead of us today where we will find the winner of the inaugural CoE World Cup. Entered posts will be scored based on several parameters, and matches will be determined probabilistically.

The scoring system works like this:

+1 for mentioning "evolution" or "evolve"
+1 for posts about biological evolution
-1 for saying "develop" or "development" when meaning "evolve" or "evolution"
-1 for being very short
-2 for being very long
0 to +5 points based on the interest of the referee (the CoE host)
+2 for posts about peer-reviewed articles
+4 for posts whose authors clearly present opinions of their own
+1 per picture (up to three) included in the post
+1 for attracting any comments
+1 extra for each original picture (max 3)
+3 for showing videos
+25 for reports on rabbit fossils from the Cambrian
-5 for any hint of panadaptationism
-2 for each logical fallacy
-4 for any mention of aquatic ape theory
-7 for agreeing with Lynn Margulis that everything is endosymbiosis
-3 if talking about the work of others without citation
-5 to -1 for any wrong statements about evolution

19 posts entered into the CoE World Cup, so three posts needs to be eliminated for the round of 16. These were the three lowest scoring posts:

On guenon monkeys using facial recognition to prevent inbreeding.
D-brief. Carl Engelking.
Score = 7

On spiders hiding from predators by looking like bird poop.
Ecologica. Sam Hardman
Score = 8

On Twitter data from the 2014 Evolution conference.

The molecular ecologist. Jeremy Yoder.
Score = 9

The remaining 16 posts were paired up at random and the winner of each match determined randomly, with the probability of winning given by the score. For example, two scores of 10 and 15 will give the posts 40% and 60% chances of winning, respectively.

The following list of the remaining 16 posts have three numbers each: their ID number, their score, and their randomly assigned spot in the round of 16.

This gives us the following schedule of games [spot: post ID (score)]:

Game 1 is between Was Fisher W(right)? (score = 16) and The intricate world of cone snail venoms (score = 12). This gives them chances of winning of 52.1% and 42.9%. The CoE World Cup Random Number Generator™selects.... Was Fisher W(right)? and eliminate

On conus snail venom and how they are administered.
Teaching biology. Marc Srour.

Game 2 is between Is evolution predictable? (score = 15, P = 42.9%) and Wright's Shifting Balance Process (score = 20, P = 57.1%). Two very strong posts. And the winner is Is evolution predictable? and we must say farewell to the top seeded

On, well, Wright's Shifting Balance Theory.
Evolution in Structured Populations. Charles Goodnight.

Game 3 is between The Function Wars: Part I (score = 13, P = 56.5%) and A bizarre blood-sucking Jurassic maggot (score = 10, P = 43.5%). The Function Wars: Part I beats 

On a fossil of an aquatic fly larva from the Chinese mid-Jurassic.
Why evolution is true. Matthew Cobb

Game 4 is between The simulations behind the fitness landscape visualizations (score = 13, P = 46.4%) and Our skulls didn't evolve to be punched (score = 15, P = 53.6%). A win for Our skulls didn't evolve to be punched and a loss to 

On the computational details behind the simulations.
Pleiotropy. Bjørn Østman

Game 5 is between Add it up: the genetic basis of ecological adaptation (score = 17, P = 56.7%) and Spontaneous mutations - friend of foe? (score = 13, P = 43.3). Again the weaker post Spontaneous mutations - friend of foe? beats the odds and sends out

On the genetic and genomic changes that underlie adaptation to divergent environments.
Eco-evolutionary dynamics. Katie Peichel.

Game 6 pits Visualizing coevolution in dynamic fitness landscapes (score = 14, P = 45.2%) against Of Population Structure and the Adaptive Landscapes (score = 17, P = 54.8%). Victorious is Of Population Structure and the Adaptive Landscapes and out is

On the biology of the models behind the video.
BEACON. Bjørn Østman.

Game 7 sees Historical Contingencies at the Birthday Party (score = 12, P = 54.5%) against On Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 45.5%). A close match where Nicholas Wade and the blurring of boundaries between science and fantasy prevails and goodbye to

On the probability of convergent evolution.
Synthetic Daisies. Bradly Alicea.

Game 8 - the last of the round of 16 - is between The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process (score = 11, P = 42.3%) and Evolution 2014 (score = 15, P = 57.7%). Somewhat surprisingly The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process wins this one and sends out

On the distribution of topics at the 2014 Evolution conference.
A great tree. Lewis Spurgin.

And that concludes the round of 16. Some surprises along the way so far. The least likely post to win actually won in 3 out of 8 games, and we had to say goodbye to two of the overall favorites, Wright's Shifting Balance Process and Add it up: the genetic basis of ecological adaptation.

On to the quarter-finals...

The first quarter-final has Was Fisher W(right)? (score = 16, P = 51.6%) versus Is evolution predictable? (score = 15, P = 48.4%). A tough game, but The CoE World Cup Random Number Generator™doesn't hesitate and chooses Was Fisher W(right)? sends out

On the probability to leave descendants based on trees contracted from nucleotide sequences.
Neherlab. Richard Neher.

The second quarter-final is between The Function Wars: Part I (score = 13, P = 46.4%) and Our skulls didn't evolve to be punched (score = 15, P = 53.6%). And the outcome is that The Function Wars: Part I wins and the loser is

On whether humans skulls evolved in response to taking a lot of punches.
Laelaps. Brian Switek.

The third quarter-final is a battle between the surprise post Spontaneous mutations - friend of foe? (score = 13, P = 43.3%) and Of Population Structure and the Adaptive Landscapes (score = 17, P =56.7%). Can the surprise post do it again? Noooo! Of Population Structure and the Adaptive Landscapes wins and there is no more

On measuring mutation rate and mutational effects in yeast.
The molecular ecologist. Ryosuke Kit.

The fourth and last quarter-final has the underdog Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 47.6%) against The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process (score = 11, P = 52.4%). By The CoE World Cup Random Number Generator™the winner is Nicholas Wade and the blurring of boundaries between science and fantasy and going home is

On the role of genetic drift in Wright's Shifting Balance Theory.
Evolution in Structured Populations. Charles Goodnight.

That concludes the quarter-finals. We'll take a short break before we begin the semi-finals.

And we're back.

The first semi-final is an exiting match between Was Fisher W(right)? (score = 16, P = 55.2%) and The Function Wars: Part I (score = 13, P = 44.8%). Who will go to the 2014 CoE World Cup final? Aaaand... it's The Function Wars: Part I!!!! The post has done it again. This means goodbye to

On genetic drift and epistasis.
Evolution in Structured Populations. Charles Goodnight.

We now turn to the second semi-final that stands between the favorite Of Population Structure and the Adaptive Landscapes (score = 17, P = 63.0%) and the underdog Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 37.0%) It's amazing it has made it this far. Let's see how they do today: Of Population Structure and the Adaptive Landscapes wins as expected and sends home

On what science can and cannot comment on.
it is NOT junk. Michael Eisen.

We are thus left with just two posts for the final match that will decide who wins the 2014 Carnival of Evolution World Cup.

It is The Function Wars: Part I (score = 13, P = 43.3%) versus Of Population Structure and the Adaptive Landscapes (score = 17, P = 56.7%). Both posts have played really well so far, surviving some really close calls. Both posts have a lot to offer on evolution, though one is severely disadvantaged by its excessive length. Can The Function Wars: Part I overcome this obstacle today, or will Of Population Structure and the Adaptive Landscapes prevail as most people expect?

The game is on, and it is over before we know it as the CoE World Cup Random Number Generator™ takes a mere 0.000349 seconds to decide that... The Function Wars: Part I is the winner of the 2014 CoE World Cup!!!! What a glorious and surprising victory! The readers go wild!!! In second place we thus have

On fitness landscapes.
Evolution in Structured Populations. Charles Goodnight.

And the winner of the 2014 Carnival of Evolution World Cup is 

On ENCODE and the definitions of function.
Sandwalk. Larry Moran.

Congratulations to the post from Sandwalk and to writer Larry Moran!!!

That concludes the inaugural Carnival of Evolution World Cup 2014.

Come back next month for more blogging about evolution. We still don't have a host, so if you're interested please contact the administrator by email, Facebook, or Twitter. You can submit posts via all three of those as well.

Vertebrate sexual systems Awesome figure of the sexual systems used by 2,145 vertebrates species (705 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian).

Similar figures for plants and invertebrates.

Tree structure is derived from taxonomy, where each tip represents all species in a single genus. 
Diploid chromosome number is indicated by the height of the innermost ring.
The XY/ZW ring is colored blue for XY and red for ZW taxa.
ESD = environmental sex determination.
The ‘Other’ ring includes parthenogenesis, gynogenesis, and hybridogenesis.
Complex SCS indicates species with complex sex chromosome karyotypes (e.g., X1X2Y).

  • All mammals are XY.
  • All birds are ZW.
  • Half-ish of all fish and no other vertebrates are hermaphrodites.
  • Only some fish and some reptiles are environmentally sex determined.

Ashman, T., Bachtrog, D., Blackmon, H., Goldberg, E., Hahn, M., Kirkpatrick, M., Kitano, J., Mank, J., Mayrose, I., Ming, R., Otto, S., Peichel, C., Pennell, M., Perrin, N., Ross, L., Valenzuela, N., and Vamosi, J. (2014). Tree of Sex: A database of sexual systems Scientific Data, 1 DOI: 10.1038/sdata.2014.15

Video: Visualizing coevolution in dynamic fitness landscapes

The fitness landscape is the framework for thinking about evolutionary processes the same way the phylogenetic tree is how we think about evolutionary history. It can guide our thinking and even enable us to predict outcomes of evolution.

Fitness landscapes are usually depicted and thought of as static, i.e., not changing in time or space, but in reality they change in response to environmental changes. Populations have different fitness in different environments, so changes in both time and space can influence the fitness landscape. For example, releasing chicken on the moon will drastically change their chances to reproduce.

Many papers have been published about fitness landscapes, but with very few exceptions they investigate static fitness landscapes. Exceptions are landscapes that change between two or three different environmental conditions, such as microbes in salty or acidic conditions.

A consistent criticism of studies that look at evolutionary dynamics – the study of evolving populations – is that the fitness landscape is static, and that this is not realistic. But no one knows to what extent natural fitness landscapes change over time. Both the frequency and magnitude of such changes are completely unknown. On the time-scale of significant evolutionary change, do real fitness landscapes experience changes that make any serious difference to how populations evolve? Do they change qualitatively, with peaks coming in and out of existence? Or are the changes merely quantitative, keeping the rank order of fitnesses the same? The former is a possible solution to the problem of how populations can cross valleys between peaks in the fitness landscape: if a population is stuck on a local peak, just wait until the environment changes and leaves an uphill path to new genotypes and phenotypes. But it could very well be that in most cases most of the time populations are stuck in an approximately static landscape. We really don’t know.

And yet, for all the criticism of studies of static landscapes, not much research has been done on evolution in dynamic fitness landscapes.

One environmental factor that can change the fitness landscape of a population is a population of another species. If one species is in any way dependent on another, then there is a potential for the fitness landscape to depend on the other species.

In the video above we present three such cases of coevolution. (Details of the simulations.)

Moth-orchid coevolution. The moth eats nectar from the bottom of the orchid spur. In order to do that, its proboscis needs to be at least as long the orchid’s spur. In this model, the moth therefore gains some fitness if this is true. The more orchids it can feed on, up to a limit, the more fitness it gains. The orchids have a different agenda. They need to get someone to transport pollen from plant to plant so they can be fertilized. The moths can do this for them: when a moth sucks nectar, it touches the male flower parts and some pollen is deposited on the moth, which it carries to the next orchid, where some pollen is deposited on the female flower parts. However, if the moth’s proboscis is longer than the spur, then the moth can suck nectar without coming into touch with pollen. As a result, orchids gain some fitness if their spurs are longer than some or all of the moth’s proboscises. The orchids therefore affect the fitness landscape of the moths, and the moths affect the fitness landscape of the orchids, driving both of them to have longer and longer proboscises/spurs. We visualize this in a two-dimensional phenotype-fitness landscape, where one axis is the proboscis length in the moth landscape (spur length in the orchid landscape), and the other axis is some arbitrary neutral trait that does not affect fitness.

Rock-paper-scissors. The second dynamic fitness landscape is the familiar rock-paper-scissors system. The phenotypes consist of two arbitrary traits, and the three populations are evolving in sympatry, meaning there is no spatial component in the model. Each of the three populations dominate over one of the other two and is inferior to the third. In this model that means that if an organism has the same phenotype as the some members of the population it dominates, then it gains some fitness. The more individual members it has the same phenotype as, the more fitness it gains (density-dependence). Consequently, if this organism has the same phenotype as a member of the population that it is inferior to, then it loses fitness. This system makes the fitness landscape of each population very dynamic, with peaks and valleys appearing and disappearing over time.
Q: Are there any real systems that work like this?

Host-parasite coevolution. The third dynamic fitness landscape is a system with two populations, where the host loses fitness when it shares a phenotype with parasites, and the parasites gain fitness when their phenotypes are the same. The host organism therefore benefits from being different from the parasite, and the parasite benefits from being similar. This results in a situation where the host population evolves away from the parasite phenotype, and the parasite’s population evolves towards the host phenotype. However, it often happens that the parasite population causes the host population to split into two or more subpopulations centered around dissimilar phenotypes. The parasite population will then evolve to climb only one of those peaks, as is always the case when a population of competing organisms is facing two or more peaks. Climbing that peak will cause the host organisms that make up that peak to die out. As a result, the peak disappears, and the parasite population now finds itself dislocated from the surviving host population. Both the host and the parasite populations now have uniform fitness, and they consequently undergo neutral evolution and drifts about in phenotype space. In order to prevent this situation, we have given the parasite population a per-trait mutation rate that is twice as high as the host population. This makes it much less likely that the hosts can escape, because the parasites can now explore a larger area of phenotype space than the host. They move faster around the fitness landscape.

The last model results in two populations that continue to evolve indefinitely. Given enough time they will explore the whole fitness landscape, obtaining all the possible phenotypes. This is arguably open-ended evolution, in that evolution keeps going and populations do not encounter a stopping point. A definition of open-ended evolution requires that the population never reaches a stable phenotype, which in this case it does not. OEE can also be defined to require that new adaptive traits keep appearing, in which case this coevolving system does not qualify. New traits values keep appearing, but after a while they will not be novel, as they will have been attained and then lost in the past.

Some conclusionary words
While these movies are based on actual simulations of a model with two traits, we haven’t really done any science to speak of. Nothing has been measured and no hypotheses have been tested. However, the visualizations could be used as a tool for hypothesis testing and discovery. We can think of videos just as a modern version of the Cartesian coordinate system that enables us to visualize a temporal component (or another spatial component). When populations are seen evolving right in front of your eyes, we can sometimes observe effects that weren’t apparent by any other means.

More about fitness landscapes
Using fitness landscapes to visualize evolution in action
Evolution 101: Fitness Landscapes
Smooth and rugged fitness landscapes
Crossing valleys in fitness landscapes
BEACON Researchers at Work: Holey Fitness Landscapes