The evolving carnival

The CoE blogger thinks Carnival of Evolution is evolving. Doofus! There's no population, no real inheritance, and not even a genetic code to be transmitted. All it amounts to then is akin to memes, and they really don't evolve the same as genes. I like the stats, though:

Figure 1: Number of posts included in CoE by month from its conception in August 2008 through May 2012. Not all months are included, because not all past editions are accessible. Numbers are approximate (counted one time by one person).

Notice that very consistent increase in body size of CoE over through time. A one-tailed t-test with unequal variance on the first half of editions vs. the second half gives p= 4.7072e-5, which is highly significant. That is, the average change in size from the first half (18.81) to the second (33.95) is not due to random fluctuations in number of posts included in the editions. CoE is definitely evolving. Creationists, go redacted!

There are still a few days left to submit to the next edition, which will be hosted on Pharyngula (clue: get linked to and get 29,000 in a day).

Titles

Yet more papers from the ToCs that I'd like to live longer to read.

• Evidence of non-random mutation rates suggests an evolutionary risk management strategy
• Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift
• The evolution of sex is favoured during adaptation to new environments
• The extended evolutionary synthesis and the role of soft inheritance in evolution
• Group adaptation, formal darwinism and contextual analysis
• The effects of migration and drift on local adaptation to a heterogeneous environment

Is Eigenfactor really a good measure?

I have just been alerted to Eigenfactor - a new measure of how influential scientific journals are. A one-page article in PNAS discusses its use, and explains how it is calculated:

The Eigenfactor™ algorithm corresponds to a simple model of research in which readers follow chains of citations as they move from journal to journal. Imagine that a researcher goes to the library and selects a journal article at random. After reading the article, the researcher selects at random one of the citations from the article. She then proceeds to the journal that was cited, reads a random article there, and selects a citation to direct her to her next journal volume. The researcher does this ad infinitum.

A comparison of journals reveals that the journals we already know to be the best(?) have high Eigenfactors:

But, when I went to Eigenfactor.org and read the FAQ, I saw this:

1. How do I interpret a journal's Eigenfactor™score? A journal's Eigenfactor score is our measure of the journal's total importance to the scientific community. 

With all else equal, a journal's Eigenfactor score doubles when it doubles in size. Thus a very large journal such as the Journal of Biological Chemistry which publishes more than 6,000 articles annually, will have extremely high Eigenfactor scores simply based upon its size.

Whaaat?! That seems misleading, doesn't it? Just because a journal publishes more articles certainly doesn't mean it is more prestigious to publish in. I realize that that wasn't the question; the question was which journals are most influential, and this I can see. However, what does that matter for the author who has to choose the journal to submit to? Take PLoS journals. If you submit to PLoS Biology or PLoS Computational Biology, then upon rejection they'll suggest you to submit to PLoS ONE. Why? Well, clearly because it is way easier to get accepted there - PLoS ONE is a much larger journal (with a policy of accepting papers as long as they are not erroneous).

Looking up the Eigenfactor of these journals, I get this:

PLOS ONE: 0.319571
PLOS Biology: 0.159932
PLOS Computational Biology: 0.060394

 PLoS ONE is thus twice as influential as PLoS Biology, and over five times as influential as PLoS Comp Bio. However, no sane author I know would prefer to publish in PLoS ONE over PLoS Biology, so what's the use, then? None, as far as I am concerned.

CoE #47: All the evolution news fit to blog

47th Carnival of Evolution has been posted on Evolving thoughts. All the evolution news that fit to blog includes this interesting post on the caveman diet:

Except for Captain Caveman and Fred Flintstone, were there other overweight cavemen? Would we be healthier if we adopted the diet that ancient humans ate thousands of years ago?

What is your favorite diet? 

The Atkins diet? South Beach diet? Ever heard of the paleolithic (paleo) diet?

Titles

Last weeks interesting papers on evolution:

• Adaptive evolution of facial colour patterns in Neotropical primates
• Selection in a fluctuating environment leads to decreased genetic variation and facilitates the evolution of phenotypic plasticity
• Footprints of positive selection associated with a mutation (N1575Y) in the voltage-gated sodium channel of Anopheles gambiae
• Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
• In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

Titles

More papers published this week about evolution:

• The Evolution of an Enigmatic Human Trait: False Beliefs due to Pseudo-Solution Traps.
• Spatial Structure and Interspecific Cooperation: Theory and an Empirical Test Using the Mycorrhizal Mutualism
• THE ECO-EVOLUTIONARY RESPONSES OF A GENERALIST CONSUMER TO RESOURCE COMPETITION
• Meta-analysis suggests choosy females get sexy sons more than ‘good genes’
• Evidence for elevated mutation rates in low-quality genotypes
• Ontogenetic niche shifts in dinosaurs influenced size, diversity and extinction in terrestrial vertebrates
• Speciation with gene flow in a heterogeneous virtual world: can physical obstacles accelerate speciation?
• Synthetic Genetic Polymers Capable of Heredity and Evolution
• ROLES FOR MODULARITY AND CONSTRAINT IN THE EVOLUTION OF CRANIAL DIVERSITY AMONG ANOLIS LIZARDS
• ENVIRONMENTAL ROBUSTNESS AND THE ADAPTABILITY OF POPULATIONS

How wonderful life would be if there were more hours in a day. I'd use them for sleeping.

 

Titles

As a new feature mostly intended for my own benefit, I will start posting titles of new papers that I come across in the ToCs that I get emailed every week. I practically never have time to read the papers I find, and so they disappear into oblivion, which is sad. Perhaps just listing the titles here will result in me going back to them at some point. Also, even though I only post the title, it's easy to find them again by a simple Google scholar search.

• Cooperation and the evolution of intelligence
• EXPLORING VARIATION IN FITNESS SURFACES OVER TIME OR SPACE
• Goldilocks Meets Santa Rosalia: An Ephemeral Speciation Model Explains Patterns of Diversification Across Time Scales
• Generalized Movement Strategies for Constrained Consumers: Ignoring Fitness Can Be Adaptive
• Reproduction-longevity trade-offs reflect diet, not adaptation
  
  

Correlation does too imply causation

What's this nonsense I hear that correlation doesn't imply causation? Of course it does. If there is correlation between two variables, there must be causation somewhere. Granted, the correlation alone doesn't show which of the three types of causation it is (A causes B, B causes A, or C causes A and B*), but causation has to be there, if the correlation isn't spurious. It would be correct to say that correlation doesn't indicate the kind of causation.



In this case, causation is likely that those who've gone to the moon are alive, and those who are alive have eaten, and those who have eaten have likely eaten chicken - particularly likely if you're among those who have been in training to to go the moon.

More.

* All three cases could have intermediate variables, of course.

Carnival of Evolution #46

Carnival of Evolution #46 has been posted. This time, in addition to the posts, we get to learn about different trees used in evolutionary biology and computer science. E.g., the cladogram:



See the rest at Synthetic Daisies.

Carnivores have bad taste

Pseudogenes are genes that used to have a function, but no longer do. If a gene contributes to an important function for the organism, offspring with deleterious mutations that ruin the gene will have lower fitness, and as a result won't have as many offspring, if any at all. That mutated gene will likely not go to fixation (become prominent in the population). On the other hand, if the gene used to have a function, but no longer don't, then mutations affecting the gene won't be deleterious. Mutations that turn off its expression (so the protein the gene codes for is no longer produced), and mutations that mess up the amino-acid sequence of the protein (so the protein can't carry out the previous function), won't be detrimental to the individual that has those mutations if the individual no longer needs that function. As a result, those mutations can go to fixation either by genetic drift (i.e., at random), or can even be selected for (e.g., when there is a cost to producing the proteins).

However, examples where pseudogenization is coupled to function is rare. A new study published in PNAS links genes that code for taste receptors to specific dietary changes in carnivorous mammals. Basically, animals that do not eat sweets don't have receptors for sweetness (e.g., cats), and animals that swallows their food whole have no receptors for umami (e.g., sea lions, dolphins).


Mutations causing loss of the sweet-taste receptor gene are in red. The exons (DNA coding for a protein) are intact for dog, which can taste sweet just fine, compared to the exons for various other carnivores which cannot taste sweet, the poor souls.


Examples of what the mutations actually do. Looks like they typically cause frameshifts, which makes the rest of the gene nonsense, and introduces stop codons, which causes transcription to stop prematurely. The first one, with Sea and Fur Seals, shows a mutation that messes up the promoter region of the gene, thereby ruining gene expression.


Phylogenetic tree showing loss (diamonds) of Tas1R2, one of the genes coding for a protein that enables animals to taste sweet.

In this way, several species have lost taste-receptors, and they have done so independently. The Fossa of Madagascar™ have lost the gene for the sweet-taste, but their most close relative examined, the Yellow Mongoose, have not. The red diamonds in the this phylogenetic tree indicates in which the gene for sweet taste has become a pesudogene. The results strongly suggest that loss of the gene has occurred multiple times, rather than once in a common ancestor.

Measuring the strength of selection along these branches, the authors found that the ratio of non-synonymous to synonymous substitutions, d_N/d_S (aka ω) is considerably lower for the species that can still taste sweet, compared to those that can't. An ω lower than one means that mutations that change the amino acid sequence aren't tolerated, while those that don't (the synonymous mutations) are.

So this lower ratio means is that there is strong purifying selection on the gene when the gene is still in use, whereas when ω is higher, selection doesn't care much about the gene. However, the best model fit was one where the branches leading to species with intact taste-receptors had ω=0.13656, while the others had ω=0.41974. That is, while the latter is found to have been under relaxed selection compared to the former, the fact that ω isn't (close to) 1 suggest that it selection isn't wholly indifferent to the state of the protein. The authors themselves are at a loss as to the nature of this mechanism:

Recently, sweet, umami, and bitter taste receptors have been implicated in several extraoral functions (36). Pseudogenization of Tas1r receptor genes in dolphins and sea lions and Tas2r receptor genes in dolphin indicates that these receptors cannot be involved in extraoral (e.g., gut, pancreas) chemosensation (36) in these species. Thus, to the extent that these extraoral taste receptors are functionally significant in rodents and humans, these functions must have been assumed by other mechanisms in the species we have identified here with pseudogenized receptors. What these other mechanisms are remains to be determined, and further assessment of the relationships among taste receptor structure, dietary choice, and the associated metabolic pathways will lead to a better understanding of the evolution of diet and food choice as well as their mechanisms.

One of the species in the order Carnivora is the Banded Linsang, which lives in tropical forests of Thailand, Malaysia, Borneo, and Java. I include a picture of it here just because I have never seen this creature before, and because it is super adorable. It is a close relative of cats, and cannot taste sweet.

Reference:
Jiang P, Josue J, Li X, Glaser D, Li W, Brand JG, Margolskee RF, Reed DR, & Beauchamp GK (2012). Major taste loss in carnivorous mammals. Proceedings of the National Academy of Sciences of the United States of America PMID: 22411809

CoE #45 - the bug edition

Adrian Thysse has done something new. He has slaved through all 45+ submissions to this month's edition of Carnival of Evolution (which, in case you have never hosted, you might not know is a lot of work), and this is the result:



Excellent! I predict that before 2013 we'll see an edition of CoE with sound and even cooler animation, perhaps even uploaded to Youtube and CNN. That really wouldn't be too much to ask.

Nothing is unstable

A previous post from almost three years ago keeps getting comments: Another creationist dentist expert on evolution. That's great, even if it is fueled by creationists like anonymous who left this comments a few days ago:

How can an iris, that can't smell or see, evolve to look and smell like a wasp? The skeptics of God remind me of the biblical verse that reads "they worship the created insread of the creator". God also says He has left evidence of Himself through all creation. Just for a time, I challenge you to put down science books, study not read God's word with an open mind and see if you still cannot see God. By the way, where did all the atoms, energy and all the other elements needed for creation come from. You cannot expect a Big Bang to come from nothingness.

If the question was honest, in that the commenter really wanted an explanation for how a plant can mimic a wasp, then that would be intriguing. There are of course explanations, but this creationist of course isn't interested in any of that. The remarkable thing, though, is the notion that the plant needs to be able to see and/or smell the wasp in order to mimic it. What an utterly ignorant understanding of evolutionary theory!



Another anonymous commenter was kind enough to point to this video of Lawrence Krauss explaining how something can come from nothing. Basically, nothing is unstable. That is, "nothing" is unstable. See for yourself:

Is stasis a general trend across non-skeletal traits?

In today's eSkeptic, which celebrates Darwin's 203rd birthday, Donald Prothero writes about the most cited paper in all of paleontology: Eldredge and Gould's Punctuated equilibria: an alternative to phyletic gradualism (1972).

Prothero explains that the revelation was that species (at least as described by fossils) mostly don't change, but rather are in stasis for most of the time. Gradualism, as proposed by Darwin, doesn't describe the change of species very well.

For the first decade after the paper was published, it was the most controversial and hotly argued idea in all of paleontology. Soon the great debate among paleontologists boiled down to just a few central points, which Gould and Eldredge (1977) nicely summarized on the fifth anniversary of the paper’s release. The first major discovery was that stasis was much more prevalent in the fossil record than had been previously supposed. Many paleontologists came forward and pointed out that the geological literature was one vast monument to stasis, with relatively few cases where anyone had observed gradual evolution. If species didn’t appear suddenly in the fossil record and remain relatively unchanged, then biostratigraphy would never work—and yet almost two centuries of successful biostratigraphic correlations was evidence of just this kind of pattern. As Gould put it, it was the “dirty little secret” hidden in the paleontological closet. Most paleontologists were trained to focus on gradual evolution as the only pattern of interest, and ignored stasis as “not evolutionary change” and therefore uninteresting, to be overlooked or minimized. Once Eldredge and Gould had pointed out that stasis was equally important (“stasis is data” in Gould’s words), paleontologists all over the world saw that stasis was the general pattern, and that gradualism was rare—and that is still the consensus 40 years later.

Stasis, which I have blogged about previously, is not nothing, but a phenomenon to be explained. Why would populations not change gradually, as some had expected? The environment does change ever so often, perhaps even what cold be termed gradually at times. Does stasis in the fossil record have to do with the fact that the information we get from fossils are predominantly about the morphology of vertebrate skeletons? Could it be that gradual changes in response to selection causes gradual changes in traits that don't affect skeletons (such as physiology or behavior)? Could there be general features of genetic architecture, for example, that constrains how skeletal morphology can change?

Alternatively, are is there evidence of stasis on other kinds of traits?


Gould, Shermer, and Prothero in 2001.

Program of the Proceedings of the 44th Carnival of Evolution

We are happy to announce the program for the Proceedings of the 44th Carnival of Evolution to be held at The Atavism:

Session 1. Symposium on the evolution of novelty
Session 2. Evolutionary ecology and life history evolution
Session 3. Philosophy and evolution
Session 4a. Experimental Evolution
Session 4b. Timing and tempo of evolution
Session 5. Outreach and anti-creationism

The poster session will start following the last talk, and will be followed by a banquet.

Notable speakers include

Carl Zimmer, The Loom
Eric M. Johnson, The Primate Diaries
Jeremy B. Yoder, Denim & Tweed
John Wilkins, Evolving Thoughts
S. E. Gould, Scientific American
Zen Faulkes, NeuoroDojo

Registration is free, and we hope you can all attend.

Organizing committee:
David Winter, The Atavism
Bjørn Østman, Pleiotropy, Carnival of Evolution

Behe on Behe, and Behe on evolution

I hadn't seen before that Leo Behe gave an interview last year.

He says as well as anyone what is wrong with the argument from design:

As for the arguments from design, such as irreducible complexity or the so-called fine-tuning of the six cosmological constants, I have many reasons for dismissing them each in particular, but one overarching reason would be the common refutation of William Paley’s classic watchmaker argument—the only reason that complex objects appear to be designed is because we as humans create complex objects, and we then assume that complexity is indisputably indicative of a designer. This is an association we make only as a result of what our “common sense” tells us.

A much too much unappreciated fact.

And Behe Jr. on Behe Sr.:

I would like everyone to realize that he doesn’t have any sort of religious agenda and he’s not trying to denigrate science in any way. Long-held beliefs, especially beliefs developed during childhood, operate on a very deep and basic level of thought—almost subconsciously. These beliefs can exist independently in a perfectly honest and intelligent scientist who is simply doing his part to further theories or ideas that he believes are supported by the scientific data. The best way to progress is through respectful and thoughtful discussion and debate, as it has always been.

I wish this to be true. I've met Michael Behe briefly at a conference, and I would like to believe that his mind is merely clouded by his religious thinking (and I hasten to say, in much the same way that most of us are clouded in our thinking in some ways or other - to me, one of the greatest joys* in life is to discover my own delusions).

That being said, take a look at Michael Behe's take on the newest research out of Lenski's lab: More from Lenski's Lab, Still Spinning Furiously (not a site I spend a lot of time on nor link to much, but making this one exception). He goes:

So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.

Seems to me that what he's doing here is confuse the evolution of the whole system consisting of bacteria and virus (which from the outside does end up with the same dynamics of infection), but ignores the really interesting thing that goes on in the virus in response to the changes in its host (the bacterium). First, what a shame that he can't appreciate the evolutionary processes that took place in these experiments. If this is not a blatant example of inability to break free of dogma, then something else is.

Second, I have always had a problem understanding proponents of Intelligent Design, because they seem to at some level agree that evolution does occur, and yet they have problems with research that shows how new things are made. This is the domain of the "designer", apparently. But then, why not just say that that's what he did? ID proponents still - as far as I am aware - haven't described how evolutionary events such as viruses evolving new ways to attack the bacteria look different from when they happen naturally. In other words, there's no way of distinguishing the two ways (which would be a great step forward for the "debate" if someone would take this question seriously), so why don't the ID proponents just say that this is the way the designer does it in the first place? I mean, instead of this yapping about whether some research is profound or not.

* Along singing, dancing, playing, drinking, thinking, eating, winning, losing, procreating, baking, kissing, camping, biking, skiing, and writing in dew.

Link between political views and physiology

It is becoming more and more clear that political views are in fact not completely decided by rational considerations, as common sense would have us believe. Rather, previous studies have shown a link between emotional (i.e., largely uncontrollable) responses and position on the left/right spectrum: "those on the right are ‘distrustful of differences … fear change, dread disorder, are intolerant of nonconformity, and derogate reason’."*

A new study takes this even further, showing that there are physiological differences between people to the political left and right: "compared with individuals on the political left, individuals on the right direct more of their attention to the aversive despite displaying greater physiological responsiveness to those stimuli."

The researchers measured skin conductivity of people as they were looking at aversive images (spider on a face, maggots in a wound, crowd fighting with a man) and appetitive images (happy child, bowl of fruit, cute rabbit).

In the physiological session, participants were shown a series of 33 still images. Each image was shown once and was preceded by a fixation point that was displayed during an inter-stimulus interval. The order of slides was initially randomized and then presented in the same order to all participants. During the slide show, electrodermal activity (in the form of skin conductance readings) was collected using a pair of Ag|AgCl electrodes and standard psychophysiological equipment. Since eccrine glands release moisture as part of sympathetic nervous system activation, and since the rate of movement of electricity across the surface of the skin is a good indicator of the presence of moisture, electrodermal activity has long been accepted as a fairly direct and pure representation of sympathetic activity, making it a good measure of the psychological concepts of emotion, arousal and attention.

The skin of test subjects on the political right conducted more electricity than those on the left when presented with "aversive" images. That is, conservatives react more strongly to disturbing images.


Triangles: political right. Squares: political left.

As good researchers always should, the authors here moderate their discussion of these findings to not condemn:

Rather than using colourful adjectives, perhaps, the proper approach is simply to state that the aversive in life appears to be more physiologically and cognitively tangible to some people and they tend to gravitate to the political right.

They conclude that we can best understand political inclinations as being partly determined by something other than rational discourse, and propose a way forward:

Rather than believing those with political views opposing ours are lazily uninformed or wilfully obtuse, political tolerance could be enhanced and cultural conflict diminished if it is widely recognized that at least part of our political differences spring from subconscious physiological and cognitive variations that lead people to experience the world in fundamentally different ways and therefore to believe that fundamentally different political policies are appropriate.

Even if we recognize that people on the political right experience the world in a different way than those on the left, and that these differences are strongly influenced by genetic and physiological predispositions - perhaps prompting us to view them as pathological - and thereby fostering greater acceptance, it is in my mind by no means given what "left" and "right" means. The far left and far right have quite different meaning in different societies. In Denmark, for example, being on the far right does not imply that one is against welfare or abortion, while in the USA those go hand in hand. In other words, the Overton window can be moved, and the result will be that people who are on the far right will shift their actual political views, while still associating with the political right. What people identify as may be determined by non-rational factors to a large degree (but most likely not entirely), but where it is even possible to locate yourself is evidently affected by public discourse. We should therefore not view public outreach as futile because people anyway (mostly) can't change their minds, but as imperative to shifting what it means to be liberal and conservative.

* The rest of the quote from the paper goes "while Block & Block [53, p. 395] find that those on the right are ‘easily victimized, easily offended, indecisive, fearful, rigid, inhibited, relatively over-controlled and vulnerable’." Hell yeah!

Reference:

Dodd MD, Balzer A, Jacobs CM, Gruszczynski MW, Smith KB, & Hibbing JR (2012). The political left rolls with the good and the political right confronts the bad: connecting physiology and cognition to preferences. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 367 (1589), 640-9 PMID: 22271780.

SOPA and PIPA

These US House and Senate bills will censor the internet. Sign the petition to vote no on both.

What determines rates of ecological speciation?

Speciation models are the most beautiful thing in evolutionary biology. This is widely known, and those who disagree are the crazies. Other models have their place, and empirical evidence for speciation, and insights from there into how speciation takes place are crucial for progress. But real understanding of this question of questions in evolutionary biology only comes once a model is constructed and validated. It is the ultimate goal of scientific work to condense knowledge in terms we can share and peruse, and this we do in models - which you may call theory, but I tend to regard this distinction with distrust.

Case in point is a model of ecological speciation in a population of sexually reproducing diploids adapting to different resources scattered heterogeneously in the environment: Patterns of Species Ranges, Speciation, and Extinction.

Specific questions asked and answered include: What is the effect is limited vs. wide dispersal, i.e., how is the rate of speciation affected by individuals occupying a small geographical area? How does the distribution of resources (food, a place in the sun, etc.) affect the rate of speciation?

And the answers are: The more widely the individuals roam, and the more mixed resources are in the environment, the lower the rate of speciation is. So when individuals only get their resources from a small geographical area, and when there are few types of resources within that area, the more speciation happens.


Examples of environments with many types of resources within a small area (A) and resources distributed such that individuals will mostly find only one type within the area they roam.

With four different types of resources, the simulations are started with only 20 identical individuals in the corner of an area like the ones above. By reproduction and mutation the population grows and diversifies. Whether resource specialists or generalists emerge depends primarily on the two factors already mentioned: range and resource distribution. Specialists, which are very good at utilizing a single resource, can coexist with other specialists when they use different resources. You eat the bananas, and I'll the the leaves, and then we can get along. However, different generalists, in this model defined as those who use more than one resource, may not get along so well, because they overlap in resource use, and so one will tend to outcompete the other. We thus have that the emergence of specialists equates to higher rates of speciation.

Here are some results:



A and B: highly mixed resource environments. C and D: fragmented resources. A and C: low dispersal range. B and D: large dispersal range.

In A there are three specialists using only one resource (red), five generalists using two resources (blue), and two three-resource generalists (green) coexisting.

In B there is only a single generalist (no speciation).

In C there are four specialists coexisting.

In D there is one specialist and two two-resource generalists.

And Birand et al. did lots of simulation runs to get a good handle on the importance of the different parameters governing speciation rates. In addition to the two already mentioned (dispersal and resource distribution), another important one is the strength of trade-offs. It can be set as more or less difficult for individuals to be good at utilizing more than one resource. As an example of trade-offs, think of lemurs: Some lemurs eat leaves, and in order to digest the hard-to-digest cellulose, they have really long intestines. Other lemurs eat fruit containing lots of sugar, which is easy to digest. They don't need to have long intestines for that, so they have short ones, and thus can't digest leaves very well. At the same time, lemurs with long intestines can't eat fruits, because they tend to rot while making it all the way to rectum, which makes the lemurs sick. Thus, there is a trade-off between which foods the lemurs can eat, which makes the two species able to coexist (at least in theory - I don't know if they have overlapping ranges). Competitive exclusion (wiki) prevents lemurs that use the same resources from coexisting in the same area, while two species that occupy different niches won't have a problem with each other.

But, while trade-off are important to have for speciation to occur, varying the strength of it had little effect compared to the effects of limited dispersal and resource distribution.

In fact, geography turns out to be the most important feature in this model:

Indeed, when resources were distributed randomly, which resulted in highly fragmented landscapes (figs. S1, S11), there was always only one species regardless of the dispersal range D and trade-off coefficient b (of the 90 simulations initiated with all the parameter combinations of b and D, only one simulation resulted in two species).

That is to say, if it wasn't because resources are distributed in a patchy way, then speciation just doesn't occur at all. When individuals can find all four types of resources within their dispersal range, then generalists are always of higher fitness, and specialization is not favored. This also means that this model cannot account for (strict) sympatric speciation, where there is no geographical structure, and where individuals are not limited to mate with those close by, or use resources in their neighborhood. Not surprisingly, parapatric and allopatric speciation (where geography is a factor) is much easier than sympatric speciation (where geography is not). For that something else is needed. Stay tuned.

Reference:
Birand A, Vose A, & Gavrilets S (2012). Patterns of species ranges, speciation, and extinction. The American Naturalist, 179 (1), 1-21 PMID: 22173457

My time with Hitchens

So Christopher Hitchens died. It is sad when someone dies, mostly, and it is a good time to remember the good thing about the deceased. When the dead is a person like Hitchens, troublemaker extraordinaire, people will do the usual an extoll his accomplishments, but will also point out the extent to which they disagree with him. I don't personally have a problem with either (and feel quite certain that Hitchens wouldn't either, for what that's worth), and he has been given a lot of praise and taken a lot of flak since his death. But I see it as I do with other great contributors to thought - scientists in particular - that we can take from them what we appreciate and leave the rest for historians. Newton was not a nice person, and likely died a virgin (pft!), but we admire him as the greatest thinker of all time because of his accomplishments. And as for Hitchens, what does it matter to me that he was a drunk and supported the Iraq War? None. What matters is the things he said that I can use.

In spring 2008 I took a course with Michael Shermer at Claremont Graduate University called Evolution and Society. Shermer assigned us to answer the same question that he asked a bunch of luminaries via the Templeton Foundation: Does science make belief in God obsolete? Hitchens' answer is in the newest edition of eSkeptic, titled "No, but it should." That sums it up pretty well, and the substance of his reason why religion ought to be obsolete is captured by his sentence "It [religion] is how we came up with answers before we had any evidence," and thus captures the essence of what is exactly wrong with religion and faith: a lack of evidence and dismissal of evidence.

My own essay is listed here (comments by Shermer in Brackets):

Does Science Make Belief in God Obsolete?

As an atheist scientist, I dismiss the supernatural, and am therefore tempted to rule belief in God obsolete. There are many obvious reasons why – from a scientific point of view - science and religion cannot both be true. To cite just one example, Genesis 1 - what we have learned through science directly contradicts this biblical story of creation. They cannot both be the correct model of our origins.

By itself, however, this fact doesn’t render belief in God obsolete Because belief in God serves multiple purposes. Although science is superior at predicting and describing the world around us, has brought us true insight and utility, and has been used for a broad range of purposes, both good and bad, it cannot do some things that religion does very well.

Judaism, Christianity, and Islam are nearly identical in the way they are utilized by some of their followers, most notably in ways that science cannot replace. This God of a bronze age desert people continues to serve many people very well today.

What this God does for people is to tell them how to behave by word and by example. This frees people from thinking about such moral matters, and justifies the behavior of those who live and act as commanded by God. Many people still believe that it is through God we have our morals, and they cannot imagine a world without a deity to guide them. Logically, there exists no way of inferring how we should behave from what we can learn through science (the so-called “is-ought” problem, or the naturalistic fallacy), and religion thus trumps science in this matter. Science can explain what we come from, but it cannot tell us how to behave.

Belief in God allows some people to make a living without producing anything of value to society. Interpreting scripture and telling people how to live as God commands, they are generously supported by the rest of society [in what way?]. They [who is “they”?] do not contribute anything tangible, but purport instead to be a link to God, and to know what God wants from us [do you mean priests and pastors? In America they are voluntarily supported by their customers, the members of the church, who by making donations signal that they do, in fact, believe there is something of value being presented]. While science requires scientists devoted to the pursuit of knowledge, scientists cost society far less than what it earns from the resulting discoveries.

Throughout history, belief in God has given rulers the justification for their positions of superiority [I think you mean here the divine right of kings concept]. Oppression and tyranny has been, and continues to be, done in the name of God. Kings and emperors would never have been able to control the masses without the belief that God had personally chosen them. World leaders today continue to justify their means by invoking God, and they are often supremely confident that they have the moral high ground over those people who do not share their particular belief, let alone over those who do not believe at all. Science does not do this. It cannot, because it deals only in knowledge, and thus doesn’t speak of superiority. [what about Marxism, and Marxism-Leninism, supposedly grounded in solid social science and applied throughout the Soviet Union and Mao’s China?]

But perhaps more than anything else, belief in God comforts. People are scared of life, and they are scared of death. It’s a frightening world, and we are but dust blowing in the wind, with minimal control over our own fate. Death is final, and that’s all there is [too colloquial, best suited for a bumper sticker] [these short toss-off lines are not sentences]. Belief in God means, perhaps more than anything else, that once you die, you get to go to a better place, where you will stay forever together with your loved ones. Your life on Earth is merely a test, and if you pass it, you will fear no more, forever. Those lewd unbelievers can go to Hell, where they will burn and suffer forever for their unbelief, by will of God, loving and omnipotent. All science does in this respect is tell you that this life is all you’ve got. That’s it.

So belief in God is by no means made obsolete by science. While my professed disbelief strongly suggest a heap of sarcasm [I’ll say!], I honestly mean it when I say that belief in God is extremely useful, just not in any way in which I would like to participate.

I believe that this world would be better place without belief in God. Science has been a way for me to gain comprehension, and thus a way to accept who we really are, and what life has in stall for us. I am also afraid, but I have come to accept that fear as part of who we are. I refuse to join those who extort and oppress others in the name of God. I am a scientist, and I shall not waiver. Faith is obsolete for me – there is nothing that I dare not question.

I met Hitchens when he came to Pitzer College in 2008 to give a talk before a student audience. He hadn't prepared a presentation particularly for this event, but asked a small group of us over dinner what we would prefer, and it was generally agreed that he should talk about atheism. However, at one point he noted that he also had a great memory for limericks, and asked if we wanted to hear some. Second question: Can we handle some dirty ones? General excitement, except from one woman behind me who gloomily went "No. No. No." Among the many he shared, I only recall this one:

There once was a hooker from Q
who filled her pussy with glue.
She said with a grin,
if they'll pay to get in
they can damn well pay to get out too.

And for that, we thank you.

Pun five