Got questions about evolution?

There must be lots of people out there on the interwebz with questions about evolution. People are evidently very interested, whether they are creationists, evolutionists*, or on the fence. When I first started blogging, it was really to spread the word about evolution, so maybe it's about time to explicitly invite people to ask. 

I was prompted to call for questions because I got a promotional offer from Google Adwords. I have now set up an ad so that people searching on certain keywords might find their way here, inviting them to ask questions.

So, if you have a question about evolution, you can ask them anywhere in the comments, and I'll make sure to try to answer, or refer you to someone else who can.

I'll keep a FAQ:

1) Q: Did we evolve from monkeys? A: Not from monkeys alive today, but surely it would not be much of a stretch to call the most recent common ancestor of humans and present-day monkeys monkeys, since that species probably looked at lot like something resembling a monkey. You can use Time Tree to find out when humans and monkeys split: about 29 million years ago. Since then the human and the baboon lineages have been evolving separately. That there are still monkeys around today does not invalidate evolution anymore more than the fact that there is still dust around invalidates creationism.

* I use the term 'evolutionist' to mean someone who believes in evolution, and 'evolutionary biologists' for the professional scientist.

Titles in evolution

Here's pickings from the last month of new papers in evolution. Those are just the ones that popped out at me in the tocs, but there are of course many, many others. I wonder how many were published in creation science and intelligent design? What are those journals again? Answers Research Journal is one - nothing there since July 11th (check out the archive there, if you want to have a laugh).

• Functional and evolutionary trade-offs co-occur between two consolidated memory phases in Drosophila melanogaster
• Life histories and the evolution of cooperative breeding in mammals
• Evolutionary novelty in a rat with no molars
• General and inducible hypermutation facilitate parallel adaptation in Pseudomonas aeruginosa despite divergent mutation spectra
• ADAPTATION AND MALADAPTATION IN SELFING AND OUTCROSSING SPECIES: NEW MUTATIONS VERSUS STANDING VARIATION
• Epistasis from functional dependence of fitness on underlying traits
• Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown
• Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)
• Kin selection, not group augmentation, predicts helping in an obligate cooperatively breeding bird
• Genetic change for earlier migration timing in a pink salmon population
• Superinfection and the evolution of resistance to antimalarial drugs
• Fluctuations of Fitness Distributions and the Rate of Muller’s Ratchet
• A Resolution of the Mutation Load Paradox in Humans
• Calcium and salinity as selective factors in plate morph evolution of the three-spined stickleback (Gasterosteus aculeatus)
• Ontogeny Tends to Recapitulate Phylogeny in Digital Organisms
• FISHER'S GEOMETRICAL MODEL OF FITNESS LANDSCAPE AND VARIANCE IN FITNESS WITHIN A CHANGING ENVIRONMENT
• GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK
• EXPLOSIVE RADIATION OF A BACTERIAL SPECIES GROUP
• The Caribbean slipper spurge Euphorbia tithymaloides: the first example of a ring species in plants
• How does adaptation sweep through the genome? Insights from long-term selection experiments

50th Carnival of Evolution with references

For the love of references! If the submitted posts didn't all have references for support, they do now, because host of the 50th CoE edition, Marc Srour, has provided them himself. Everyone blogger who has a post included in this edition should go read it and consider reading the paper(s) that Marc refers to.

In my case, that would be

Chapter 2 of Luisi’s 2006 book, The Emergence of Life, has an excellent overview of the definitions of life.

Unfortunately, the preview on Amazon does not include the relevant pagers (page 21-23). If you happen to have those in electronic format, please let me know.

Marc comments on every single post, and I think this is an excellent idea. Who says CoE shouldn't be a place where the merit of individual posts are discussed? Anyone?

Crossing valleys in fitness landscapes

With his "holey adaptive landscapes", Sergey Gavrilets (e.g. 1997) solved the problem of crossing valleys of low fitness in the fitness landscape* by positing that for high-dimensional landscapes (which is realistic - typically the genotype consists of thousands of genes and many more DNA nucleotides) there is always a ridge between fitness "peaks" (which are then not really peaks). The only rationale for that idea is that the more neighbors a genotype has, the higher the chance that the fitness of one of them is about the same. However, there are indications that this is generally not true. Gavrilets himself says that if all the high fitness genotypes are over in one "corner" of the fitness landscapes, then there could not always be ridges. One way to formulate this is Kauffman's Massif Central hypothesis, which just says that the chance of finding a fitness peak of high fitness is higher closer to another high peak; peaks cluster in genotype space, and there is a correlation between peak fitness of neighbors. This has already been shown to be true in Kauffman's NK landscape (Østman et al., 2010), and is under investigation in other models as well. Stay tuned.

Ridges are irrelevant
That is not to say that it couldn't be true that there are ridges in real biological fitness landscapes of extremely high dimensionality. After all, the numerical landscapes investigated have few genes/loci in comparison. But, looking at real biological fitness landscapes empirically, there is every reason to believe that they are rugged, containing many peaks varying in height/fitness. I could state it like this: no one (that I have heard of) have shown that there is always a path of about constant fitness between any two genotypes. In other words, there are generally (at least) not any accessible paths between genotypes separated by more than one mutation that does not vary enough in fitness that selection can distinguish between them**. However, even if there is, it doesn't matter! If there were always paths of neutral fitness - ridges - between any two genotypes, it would be extremely unlikely that the population would find them. The ridges, supposedly, appear in fitness landscapes of very high dimensionality, meaning that the number of neighboring genotypes is going to be huge, so when increasing dimensionality and the first ridge appears, there are already a fantastic number of mutational neighbors, making it very improbable that the ridge will be discovered by stochastic processes (as evolutionary processes inherently are).

Fitness landscapes are not static
Not only has it been shown that valleys can be crossed when the mutation rate is not prohibitively low (Østman et al., 2012), as in the strong-selection weak-mutation regime (SSWM), where each new mutation is lost or goes to fixation alone, so no two mutations segregate in the population at the same time. But Gavrilets assumed that fitness landscapes are static in both space and time. Static in space means that they are the same in different geographical locations (wet vs. dry conditions, for example). Static in time means that for one location it stays constant and fitness does not change from one point in time to another. And I really should not have to explain how not true this is, right? I mean, not only is it obvious that a genotype adapted to a wet environment will not have the same fitness in a dry environment, it should also make immediate sense that the environment at one location can change over time, for example from a wet climate to a dry one. Fitness landscapes are clearly not static functions (references, you lazy bastard!).

The fitness landscape changes when 1) environmental conditions change and 2) when the population changes. Changes in population size can reduce the strength of selection; the larger the population is, the better able selection is to distinguish small fitness effects. When the population size is low, stochastic effects dominate, and genetic drift rules. In this case, valleys may be crossed in small populations just because the decrease in fitness while crossing the valley matters less (but see Weissman et al., 2009).

The effect of changing the environment is to change the fitness landscape. This could result in peaks shifting position in genotype-space, peaks appearing and disappearing, and deep valleys becoming shallow or vice versa. In two dimensions, instead of thinking of a rigid landscape, think of a seascape of water (e.g., Mustonen and Lässig, 2009). In this case, where fitness as a function of genotype is forever changing, evolutionary dynamics (i.e., moving around in the fitness landscape, crossing valleys, and locating new peaks) may be reduced to moving only uphill, rather than having to actually tolerate deleterious mutations at all. Some landscapes may indeed be rather static over longer periods of time, and then the dynamics of populations crossing valleys may be relevant. But it is totally possible that all the important evolutionary changes occur when the fitness landscape changes, rendering theories of valley-crossing somewhat immaterial.

* There are these two terms in use among researchers: adaptive landscapes and fitness landscapes. The only thing the former term has going for it is that Sewall Wright (1931) - accredited as the inventor of the idea - called it "adaptive landscapes". However, most people actually call it "fitness landscapes", but in addition to that important fact, it also makes a lot more sense. A fitness landscape is a function where fitness is given by genotype or phenotype values (rather than frequencies - incidentally, Gavrilets and I agree that fitness as a function of population allele frequencies makes no sense), so it makes a lot more sense to call it that. On top of that, fitness as a function of genotype/phenotype does not have to have anything to do with adaptation. The fitness landscapes can be flat, in which case there will be no adaptation going on. To my exasperation I just discovered a new book here at the Evolution 2012 conference in Ottawa by the title of The Adaptive Landscape in Evolutionary Biology (Oxford University Press). Nearly all the chapters, written by more or less famous people in the field, have 'adaptive landscape' in the title. Piss me off, it does.

 ** If two genotypes differ in fitness by a small amount, it may be too small for selection to distinguish between them. Since evolution is an inherently stochastic process, in which genetic drift is always present, and selection only chooses who gets to reproduce based on probabilities (fitness can be thought of as this probability), having higher fitness than your neighbor does not guarantee that you will have more offspring; it only makes it so on average. Generally, selection can distinguish fitness effects that are greater than one divided by the population size (s>1/N). If the selection coefficient (the measure of the fitness effect of a mutation, s=w'/w-1, where w' is the fitness with mutation, and w without) is less than one over the population size, then that mutation/genotype will drift, and selection makes no difference. The smaller the population is, the larger a mutation's fitness effect has to be for selection to see it, and therefore selection is weaker in small populations. This is the basis of Sewall Wright's Shifting Balance Theory (Wright, 1982), which explains how crossing valleys in a rugged fitness landscape can be done by breaking the population up into smaller groups (demes), which are then able to drift across the valleys, because selection is now weaker.

References:
Gavrilets S and Gravner J (1997). Percolation on the fitness hypercube and the evolution of reproductive isolation. Journal of theoretical biology, 184 (1), 51-64 PMID: 9039400

Mustonen V and Lässig M (2009). From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends in genetics : TIG, 25 (3), 111-9 PMID: 19232770

Weissman DB, Desai MM, Fisher DS, and Feldman MW (2009). The rate at which asexual populations cross fitness valleys. Theoretical population biology, 75 (4), 286-300 PMID: 19285994

Wright S (1931). Evolution in Mendelian populations Genetics (16), pp. 97–159

Wright S (1982). The shifting balance theory and macroevolution. Annual review of genetics, 16, 1-19 PMID: 6760797

Østman B, Hintze A, and Adami C (2010). Critical properties of complex fitness landscapes Proc. 12th Intern. Conf. on Artificial Life, H. Fellerman et al., eds. (MIT Press, 2010), pp. 126-132 arXiv: 1006.2908v1

Østman B, Hintze A, and Adami C (2012). Impact of epistasis and pleiotropy on evolutionary adaptation. Proceedings. Biological sciences / The Royal Society, 279 (1727), 247-56 PMID: 21697174

ALife 13 at Michigan State

The 13th conference on Artificial Life is going on right now at Michigan State University. Follow tweets at #alife13, and see program here. Being hosted by BEACON, it's got lots of evolution in action.

12 reasons why there is something

Why is there something rather than nothing? Pick your favorite reason among Michael Shermer's picks in Nothing is Negligible: Why There is Something Rather than Nothing. 

In the meantime, while scientists sort out the science to answer the question Why is there something instead of nothing?, in addition to reviewing these dozen answers it is also okay to say “I don’t know” and keep searching. There is no need to turn to supernatural answers just to fulfill an emotional need for explanation. Like nature, the mind abhors a vacuum, but sometimes it is better to admit ignorance than feign certainty about which one knows not. If there is one lesson that the history of science has taught us it is that it is arrogant to think that we now know enough to know that we cannot know. Science is young. Let us have the courage to admit our ignorance and to keep searching for answers to these deepest questions.

Defining life foolishly

Some like to define living organisms as that which

1) reproduces,
2) has inheritance, and
3) has variation.

In other words, living things would be those which evolve by natural selection. Rosie Redfield (blog) espoused this view in a recent and otherwise really goo talk at the Evolution 2012 conference in Ottawa (#evol2012 Twitter feed). Jerry Joyce (lab page) did the same at the 74th symposium of Quantitative Biology at Cold Spring Harbor Labs in 2009.

But this is folly.

First of all, I can easily give an hypothetical example of something that must clearly be alive, but which does not evolve. I'll defer that to the end of this post.

But I can also give an example of something that most people will not agree is alive, namely languages. Metaphorically, I can accept that languages are alive. "Danish is such a beautiful language, alive with raunchy adjectives and verbs that sing." Or something. But not actually alive in a literal sense. It is spoken by beings that are alive, but is no more alive than thoughts or books, even if it does evolve (note that languages evolution really isn't of the Darwinian kind, either, just like memes aren't).

We can of course define for our own purposes life (or living things) as anything we want. Doing that sensibly, however, is key, since science is all about communication. I could define life as anything that grows, anything that moves, anything that catalyzes chemical reactions, etc. Those are all things that most things we would call life do in some way or other. But it would not be sensible, because there are things that are not alive that do those things, too. Fires grow, the wind moves, earth catalyzes. Defining something sensibly means that it should conform to daily use of the term, or in the cases where it does not, it should make sense to refine the vernacular.

So in defining life as something that evolves by natural selection, we would both include things that clearly are not alive in the sense that most people understand it (language), and we would also exclude some things that are clearly alive, but does not evolve.

This latter thing that is alive but does not evolve - what is it, then? It's true that no living organisms that we know of do not evolve, right?

Well, both true and false. First of all, individual organisms do not evolve at all. Populations evolve. Lineages evolve. Individuals develop - from a single cell to an adult human, for example. Organisms are collections of cells, and does not evolve. Does that mean I am not alive? Clearly I am. This definition does not work. It is true that all living things descend* with modification from ancestors that were different from themselves. But what if we one day discovered an organism, looking quite like any other, but which does not die and does not reproduce? Would it not be alive?

Suppose we go to another planet and find one being there, looking exactly like a human being. Everything we can measure about this being confirms that it is just as much alive as you and me. It eats, moves, heals, replenishes, communicates, feels, defecates. Learning more about this being, though, we find that it has no ancestors, and that it does not age. It does not reproduce, and it is the only such being on the planet. Thus, there is no lineage of descent and no population that can evolve. So this being is then not alive? Of course it is. This definition does not work.

For those of you who would object that this example is irrelevant, because no such being that is alive but does not evolve has ever been found: definitions must encompass such thought experiments, or they are useless. If our definitions can not guide us when we are in doubt - in situations where something new is encountered, them they are useless. In that case we might as well just define life as the things that we already know are alive, which just amounts to bookkeeping.

Lastly, see what I did there? I demolished something without providing a solution. Tough luck! I am not required to put forth another definition that I think is better than this one. Just as well as I am not required to come up with some alternative to religion just because I am an atheist.

Is R2-D2 alive? Is it evolving?

* Actually, I prefer to say 'ascend', like the twigs on a tree grows up, and not down. Idiosyncrasies.

Blogger poutine

Here we are a group of bloggers in Quebec just across the border from Ottawa having poutine. Jerry Coyne, Rosie Redfield (blue hair), T. Ryan Gregory, Steve Watson, and Seanna Watson. Picture is taken by Larry Moran.

Tweets from Evolution 2012 in Ottawa

Lots of people are tweeting from the Evolution 2012 conference in Ottawa. It's the biggest evolution conference ever - first joint North American and European. Sad for those who are missing it, but at least you can follow it on Twitter.

Carnival of Evolution #49 at Mousetrap

CoE #49 is up at the Mousetrap. This is Joachim Dagg's blog, and he really likes mousetraps. I suppose this may be inspired by Michael Behe, but I cannot be sure. Here's one of my favorites:

 

 As he says, notice the trap to the right. There are other interesting things to notice here.

 Next edition - the 50th - will be at Teaching Biology.

On independence

[Repost from July 4th, 2009.]

On this 4th of July allow me to quote that famous sentence from the Declaration of Independence:

"We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness."

I personally disagree and agree with everything said in that sentence at the same time. Those truths are not self-evident. They must be arrived at. They aren't truths to me, and yet they are all goals worth pursuing. All men (humans?) are not created equal, but some are born into slavery, poverty, or born with mental or physical disabilities. However, they should be treated with equal respect and compassion. Since there is no Creator to endow us with anything, nor to uphold any rules (the latter, at least, is evidently true), then rights are something that we humans instill by law, and nothing else. A "right" to life doesn't even make any sense, but that we afford, by law and compassion, everyone with the help they may need to live, that would be a worthwhile effort (hopefully we'll get there eventually). Liberty is a human concept, thus we decide what we want of it. And it is safe to say that nearly everyone living in this country (that's the USA) agrees to uphold the law, and thereby forego some of that very liberty. Freedom is good, but only partially so*. Same for pursuing happiness, granted you don't diminish anyone else's, I would say.

In summary, those words can be interpreted with good meaning, but are so horribly written that they allow themselves to be used with favor by anyone anywhere on the political spectrum.

In regards to independence, I value it as much as - equate it to, even - Life, Liberty and the pursuit of Happiness. I say on to ye, let these proud nations be free to govern themselves. Free Tibet, if that's what they really want (by majority). Let Taiwan go. Let the measure of China be whether nations want to be part of them. If not, take it up for consideration, and change in ways that will entice others to join you. Why is larger better, anyway? Greenland ceased to be a Danish colony in 1953. If they want independence, I say let them have it. Iceland got their independence from Denmark in 1944. Good for them. The Faroe Islands, like Greenland, is a part of the Danish Kingdom, and has been stirring with thoughts of independence. If they can ever make a decision, let them them go too, if that's what they decide. Then get a proper football team.

*Who said "Free as a bird. The next best thing to be."?

What happens to bacterial communities under selection?

When one gene comes under a new selection pressure, a population can respond by increasing the frequency of the better alleles. This can involve directional selection, whereby the population shifts towards the new optimum, and/or it can entail stabilizing selection, where the genetic diversity of the population decreases. In both cases allele frequencies change, and this is what (biological) evolution is.

This is all fairly straightforward. However, when there are many populations that are distinct species, and they all come under the same new selection pressure, then what is that? If we can detect selection between these distinct populations, is that still evolution? It is not evolution in the traditional sense, which center its attention on what happen within a population. So if we’re not looking at what happens within one population, can we even say that we are studying evolution?

In a previous post I explained how we have used metagenomics to retrieve DNA sequences of a specific gene called nitrite reductase (nirK) that soil bacteria use to obtain energy from fertilizer. When sequencing the soil only a limited set of sequences are discovered. Imagine then that some species are more abundant in the soil than others. Because it is random with respect to which species they come from, we are then clearly more likely to retrieve sequences from the most abundant species. There are many bacterial species that has a copy of nirK, and we are limited in how many sequences we can obtain. Many species will therefore not be represented in our sample.

Now, comparing these sequences is done using the formalism of d_N/d_S, which measures the ratio between non-synonymous nucleotide substitutions and synonymous substitutions (substitutions that change an amino acid vs. those that do not). d_N/d_S (also designated by ω) is measured between species, so it is perfect for the sequences we have. The analysis showed that ω is very low, indicating purifying selection – there are more synonymous nucleotide changes compared to non-synonymous changes than expected if both were equally likely. That means that nirK is being constrained and optimized, presumably because the gene carries out an important function for the bacteria. Changes to the resulting protein are not tolerated, though a little variation in the amino acid sequence between the species does exist.

Furthermore, different environments were compared. In one environment, deciduous forest (DF), the soil is not fertilized. In another environment used for standard agriculture (AG), the soil is fertilized. The analysis showed that the sequences in AG are under stronger purifying selection than sequences in DF (figure 1). Presumably this is because the conditions in AG make it more favorable and more important to have a really good copy of nirK that can help the bacteria to obtain energy from the nitrate in the fertilizer.

Figure 1. dN/dS is smaller in Ag than in DF, indicating that there is stronger purifying selection in AG compare to DF. ES and SF are environments that have not been used for agriculture for about 20 and 40 years, respectively.

So far, so good. Now here is my question. Given that the bacteria experience purifying selection, do we really know what is happening to the community of species? Take a look at the following figure.

Figure 2. An artist’s representation of different populations in two-dimensional amino acid space. Click to enlarge.

The farther sequences are from each other, the fewer amino acids they have in common. In (A) several species of bacteria can be seen, each represented by a Gaussian distribution, where the darkest points are the more abundant sequences. The red cross represents the optimal sequence (need there be only one?), but because bacteria in DF get most of their energy from oxygen, nirK is of relatively little consequence. In (B) and (C), AG has been loaded with fertilizer, so now there is ample opportunity to get energy from that. Therefore the species experience a pull towards the optimal sequence. In (B) this results in each of the population shifting their distribution towards to optimum, while in (C) they do not shift, but instead the species that are already closer to the optimum experience an increases in carrying capacity, such that they become more abundant compared to species that are farther away from the optimum.

d_N/d_S basically measures this distance in amino acid space, and clearly this distance is on average diminished in (B). However, because we are more likely to retrieve sequences from the more abundant species, the average distance between sequences is also diminished in (C). In other words, both models are consistent with d_N/d_S being lower in AG, and we therefore cannot say what is really going on in the soil. Is there a way to distinguish between the two models? Could we take some bacteria to the lab and grow them under DF and AG like conditions, and then figure this out? Is there a third model that can explain the data as well?

And then the question of evolution – is this even evolution? Some biologists simply call this species sorting, and dismiss that it is evolution. However, I argue that it is evolution, because what we are observing is the effect of natural selection, which in (B) causes a change in allele frequencies within each population, and in (C) because it changes abundance that can lead to long-term changes in community structure.

Evolution or not? What do you think? Cross-posted on BEACON's blog.

Titles

Some times very technical papers are published that would be very good for me to read. Papers that on title don't look very sexy (to me). On the details of psedogenization, for example, whereby a functional gene becomes unexpressed, meaning it does not produce a protein anymore. Who knows if I will get around to it.

But then there are papers like this one, which I will get around to read: Environmental change exposes beneficial epistatic interactions in a catalytic RNA. That should be a good read about the impact of dynamic fitness landscapes (when fitness is not a static function of genotype or phenotype, but changes as the environment changes.

• Genomic consequences of multiple speciation processes in a stick insect 
• The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity 
• Estimating the Strength of Selective Sweeps from Deep Population Diversity Data Biology of the sauropod dinosaurs: the evolution of gigantism 
• The role of gene flow asymmetry along an environmental gradient in constraining local adaptation and range expansion 
• Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation 
• Specific inactivation of two immunomodulatory SIGLEC genes during human evolution 
• Cast adrift on an island: introduced populations experience an altered balance between selection and drift 
• Environmental change exposes beneficial epistatic interactions in a catalytic RNA 
• Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)

Oh, and no new creationist science paper published since last week.

CoE poster for Ottawa

BEACON has a booth at Evolution 2012 in Ottawa, and they have invited me to put up a poster about Carnival of Evolution.

Here's a draft. Let me know what you think, plz. (Click image for larger version.)

China is a dictatorship

The fact that Hu Jintao refuses to talk to the Danish press as he visits Denmark next week. Apparently he never has in China either, in the almost ten years that he has been General Secretary, President, etc. etc.

Right now, as I search Google news, all articles fail to mention that the Danes are very skeptical towards a state leader that won't meet the press, and who leads a country whose politics oppresses its own people (no freedom of speech, no democracy, massive violations of human rights), but it is all over the Danish news (in Danish, sorry). He runs a dictatorship, basically. Thanks to Mao.

Hu Jintao, with slight editing.

Titles

This is only a fraction of the new papers on research in evolutionary biology from the last week or so. How many creationist papers have been published in the same time-span?

• POPULATION SUBDIVISION AND ADAPTATION IN ASEXUAL POPULATIONS OF SACCHAROMYCES CEREVISIAE
• THE EFFECT OF A COMPETITOR ON A MODEL ADAPTIVE RADIATION
• The Evolution of Patch Selection in Stochastic Environments
• Local Adaptation along Smooth Ecological Gradients Causes Phylogeographic Breaks and Phenotypic Clustering
• Tradeoffs limit the evolution of male traits that are attractive to females
• THE GENETIC ARCHITECTURE OF A COMPLEX ECOLOGICAL TRAIT: HOST PLANT USE IN THE SPECIALIST MOTH, HELIOTHIS SUBFLEXA
• Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli

We may, as evolutionists (a term that I take to mean those who believe in evolution*) be frustrated with creationists, because they so incessantly refuse to give up dogma and take the evidence from nature at face value.

However, some years ago I realized how much more frustrating it must be for the creationists that the experts all but a few loonies believe in evolution, that all the evolution research in universities confirms evolution, and that nearly everyone who aren't a creationist because of their religious beliefs believe in evolution. The creationists (at least the ones who aren't ignorant and boneheaded) know that the evidence is on our side, and that must be excruciatingly frustrating.

 

 * You may refuse to use the word believe in this context, and insist that we say "accept evolution", but then you don't read enough dictionaries.

Kreativ Blogger {award}

I've been chosen for the Kreativ Blogger award chain letter*. I'll play along.

Rules: link to the blog who nominated you, say seven things about yourself that readers may not know, list seven other blogs that you feel deserve the award chain letter and let them know, and include the Kreativ Blogger logo. Here goes:

Dear friends, I wish to send my heartfelt thanks to my (new) dearest friend, Gunnar De Winter of The Beast, the Bard and the Bot for thinking of Pleiotropy (it is an important concept in genetics). I would not be here without him.

And friends, you probably didn't know about me that I

1. don't believe in free will, 
2. am an optimist-pessimist-optimist, 
3. want to try to be homeless, 
4. want to try to be pregnant, 
5. have eaten cod uterus, 
6. taught myself to play guitar and piano,
7. currently have a Klout score of 44. 

Lastly, here are six blogs that warms my heart:

• Epiphenom 
• Evolving Thoughts 
• Denim and Tweed 
• NeuroDojo 
• Sandwalk 
• The British Psychological Society Research Digest

* Today, about 870,000 results Googling "Kreativ Blogger award", and about 324,000 results in Google images.

Carnival of Evolution on Pharyngula

The June edition of Carnival of Evolution is now live on Pharyngula: Carnival of Evolution #48: The Icelandic Saga!

There are nearly 50 posts written by some amazing science bloggers. I seriously wonder when CoE is going to reach that tipping point where close to all evolutionary biologists know about it, and looks forward to some more or less light reading about diverse topics in evolution every month.

Follow CoE on Twitter @CarnyEvolution
Like CoE on Facebook

Titles

Wondering, with all the time in the world, would we even do all the things we say we would if we had all the time in the world?

How does that even work? By saying all the time int he world, do we mean that time will stand still at our command, while we can do what we want in the "meantime"? Or does it mean to live forever, in which case I don't think I would use my immortality to read these papers?

• Density-dependent fitness benefits in quorum-sensing bacterial populations 
• On the Evolution of Personalities via Frequency-Dependent Selection 
• Fitness conferred by replaced amino acids declines with time ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli 
• Species Interactions Alter Evolutionary Responses to a Novel Environment 
• Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution 
• Metopic suture of Taung (Australopithecus africanus) and its implications for hominin brain evolution

The Black Queen Hypothesis

In the game of Hearts, the object is to not get certain cards. The most vile of them all is the dreaded black queen of spades, which is as bad as all the other bad cards put together.

In a recent theory paper, Jeff Morris, Rich Lenski, and Erik Zinser present the Black Queen Hypothesis to explain why some organisms lose genes that are apparently important for survival.

Prochlorococcus is a bacterium that is able to live in an environment full of a toxic peroxide, HOOH, because they have a gene, KatG, that produces catalase-peroxidase, a compound that neutralizes HOOH. But then why are some forms of Prochlorococcus able to survive in this environment even without a functional copy of KatG? Here is their Black Queen Hypothesis:

In the context of evolution, the BQH posits that certain genes, or more broadly, biological functions, are analogous to the queen of spades. Such functions are costly and therefore undesirable, leading to a selective advantage for organisms that stop performing them. At the same time, the function must provide an indispensable public good, necessitating its retention by at least a subset of the individuals in the community—after all, one cannot play Hearts without a queen of spades. The detoxification of HOOH fulfills both of these criteria, and therefore the BQH predicts that this function will be performed by helpers that comprise only a fraction of the community.

In other words, the mutant form of Prochlorococcus that does not have KatG survives because of the public good produced by the original Prochlorococcus with a functional copy of KatG. And it does not cause the original type to become extinct, because it depends on it for removing HOOH from the environment.

Initially, all Prochlorococcus has the gene, KatG, that allows the bacteria to produce catalase-peroxidase. This allows the cells to live in an environment with a peroxide, HOOH (blue), which is otherwise toxic. The HOOH diffuses into the cells, where it is neutralized by catalase-peroxidase. This creates a gradient such that there is less HOOH the closer you get to the center of the colony.

A mutant is born (red cell) that has lost KatG, and so cannot produce catalase-peroxidase. If it were to live in an environment with HOOH, it would die. However, it can live close to other Prochlorococcus that are resistant to HOOH (blue), because these resistant cells remove HOOH from the environment.

Because producing KatG comes at a slight cost in fitness, those who don't spend the resources producing it has a slight reproductive advantage over those who do. As a result, the mutant Prochlorococcus will soon increase in number.

An equilibrium is established such that the original KatG producing Prochlorococcus and the mutant form coexist, because the higher the number of mutant cells results in less HOOH being removed from the environment. Negative frequency-dependent selection thus ensures that both types can exist side by side, because it is favorable to be the less frequent type.

Negative frequency-dependent selection works like this: If chance would have it that more is born of the mutant type, then there isn't enough space for them where HOOH is being removed, and some will die. However, the original KatG producers are still fine, so they will have a fitness advantage and grow in number. If it happens that there are few mutants, they they again has a fitness advantage over the original type, and now they will grow in number.

Jeff Morris

Luckily, Jeff works three doors down the hall from me, and so I was able to go talk to him about the BQH. The BQH is formulated mathematically as if the organisms/bacteria are in a homogeneous well-mixed environment. However, this is of course, as they discuss in the paper, not 100% realistic. Bacteria often exist in microenvironments, and it matters where the mutant cells are in space in relation to the original KatG producers; if they are too far away, HOOH is not removed from their environment, and they die. Jeff agrees that this heterogeneity - as portrayed in the figures above, where HOOH isn't removed equally from all of space - changes the dynamics somewhat, most probably by shifting the equilibrium frequencies of the two types, such that there are fewer mutants in a heterogeneous environment compared to a well-mixed homogeneous environment.

Jeff has this to add (personal correspondence):

No modern Prochlorococcus (that we've found so far) has katG. Almost all other cyanobacteria do, however, so we infer that Pro lost it at some point. The "helpers" in the modern ocean are entirely different species. So really what you're describing in the blog is the hypothetical process by which the first Pro to lost katG was able to invade its ancestral population.

The neat thing is that, because other species exist that aren't in competition with Pro but still degrade HOOH, the katG-deficient Pro was able to sweep its ancestor to extinction. In general BQH stands out (along with Red Queen) in considering interspecies interactions more explicitly than most evolutionary ideas.

Read more about the BQH on BEACON's blog and Science Daily.

Reference:
Morris JJ, Lenski RE, & Zinser ER (2012). The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio, 3 (2) PMID: 22448042.