Field of Science

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