April 1, 2013

Carnival of Evolution, #58 -- Visions of the Evolutionary Future

Welcome to Carnival of Evolution! Now with albedo!

What does the future look like? For some, the future is the place of constant progress and a place where dreams become reality. For others, the future is a scary, dystopian place. When actualized, however, future worlds fall somewhere in between these two visions. Can we make accurate projections about the future? As I pointed out in a Synthetic Daisies post from February [1], futurists and technologists have a pretty dismal track record at projecting future scenarios, and often get things notoriously wrong.

UPPER LEFT: Ad from the 1982 opening of EPCOT Center, Florida. UPPER RIGHT: Dystopic future city from the movie "Idiocracy" (Inset is the cover of "Future Shock" by Alvin Toffler). BOTTOM LEFT: Bank of England Economic Forecast (circa 2011). BOTTOM RIGHT: New New York, circa 3000 (from the TV show "Futurama").

With visions of the future in mind, this month's Carnival of Evolution (#58) theme is the future of evolution. While a significant component of evolutionary biology involves reconstructing the past [2], we are actually (with error, of course) also predicting the future. Yet can we do any better than futurists or technologists? It is hard to say, and if you have opinions on this I would be glad to hear them. However, this month's CoE will address five themes that may (or may not) help us understand where the complexity of life is headed.

A new academic discipline: prospective phylogenetics?


PART I:  The future of evolution is an open book.


Some depictions of future evolution involves both "speculative evolution" and "hyperevolved" creatures [3]. The work of Dougal Dixon [4] is a nice introduction to this point of view. His work ties together science fiction allegory with a functional view of phenotypic evolution to "project" the following future taxa: the engineered pack animal (5 million years from now), the aquatics (50,000 years from now), the tic (1,000 from now with help from engineered soft materials), and the symbiont carrier (10,000 years of coevolution). All of these examples are, of course, based on fictitious forms. And the rate of evolutionary change bears no relationship to known examples of evolution. Nevertheless, these conceptions highlight the role of chance in evolution. One can see parallels (and discrepancies) with this animation of whale evolution.


Here are some posts that provide some scientific fact to inform our speculations about what future evolution might look like:

* Carl Zimmer from the Scientific American blog Phenomena discusses the concept of and hype surrounding "nightmare bacteria". The nightmare in question is the rise of antibiotic-resistant bacteria, about which the post covers in detail.

* Sorting out Science brings us more installments in their "Scientific Tourist" series. Featured this month are the pilot whale and saber-tooth cat. And David Morrison from Genealogical World of Phylogenetic Networks brings us tattooed representations of the scala naturae, or the progressive evolutionary ladder (as opposed to the more realistic branching bush) model of evolution.

A scala naturae conception of future evolution (this time involving robots). COURTESY: Machine Overlords and John Long's "Darwin's Devices".

* Teaching Biology blog features an educational slideshow on Lamarckism, the scala naturae, and its intellectual precedents. In addition, we have two posts this month by Zen Faulkes, who writes at Neurodojo: the first is on the misinterpretation of Charles Darwin's writings as "emotionless" (No, Darwin was not a Robot), and the other is on a new paper that focuses on tail morphology to bring taxonomic clarity to the genus Xenagama.

* Good projections of speculative evolutionary trajectories rely on good estimates of genomic function. Whether the ENCODE project accomplished this for the human genome has been hotly debated since their results were published in Nature late last year. I have posted some slides to Tumbld Thoughts on the debate and scientific reasoning surrounding the latest set of ENCODE results. These slides serve as a new section to my Evolutionary Systems Biology course.

* There are two more in-depth critiques on ENCODE this month. Ken Weiss from Mermaid's Tale focuses on a new paper called "On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE" [5]. Both Ken's post and the paper critique the ENCODE projects results on several grounds. And Larry Moran's blog Sandwalk features W. Ford Doolittle's critique of the ENCODE project, which is one of four papers that critically address the claims made by the ENCODE group.

* To put this all in further perspective (Functional Illiteracy and Genetic Background), Anne Buchanan from Mermaid's Tale points us to a new paper in Trends in Genetics [6] on genomic function in the context of genetic backgrounds, which should serve as a nice addition to the ENCODE debate over genomic function. And as a case in point, we have a  post by Jeremy Yoder writing on the blog Denim and Tweed, who critically examines (he calls it a "false discovery") a recent article on how one's genetics may predict whether or not they will attend University

Visions of the Neozooic Era (COURTESY: Alexis Rockman). Artnet profile.

Finally, here are a few posts from Mermaid's Tale that might allow us to think about our explorations of future evolution in a more critical manner. Dan Parker brings us "Evolution in a Terrarium", which is an essay about the coevolutionary relationships between human civilization and mosquitos. Anne Buchanan discusses the "Ifs" of natural selection, which involves a critical assessment of what it means for a trait to be naturally selected and what the potential outcomes of natural selection might be. And Holly Dunsworth discusses the caveats and potential for thinking about the outcomes of evolution and other natural processes in an Anthropomorphized manner (a.k.a. the personification of nature).


PART II:  Future possibilities as phenotypic space.

Another depiction involves using a top-down design method to understand forces of natural selection. The video game Spore provides an example of this type of top-down design. While this is an example of "naive evolution" [7], it does provide a conceptual mechanism for future phenotypes.


Above are a collection of "animal: forms from the video game Spore. In Spore, phenotypes are determined in a top-down fashion, but live in a world of "naive" ecology and evolution. They still exhibit a form of (non-Darwinian) descent with modification.

While the creatures in Spore open up the possibilities of phenotypic space, they are not all that plausible as models of biological processes. Perhaps when projecting into the future, plausibility is as much a conceptual roadblock as it is a biological one. In light of this, Jean Flanagan from Sci-Ed discusses the dangers of taking shortcuts during the process of communicating evolution. This includes overcoming the default use of naive models to fill in conceptual gaps.

So perhaps we can construct imaginary phenotypes that are a bit more consistent with molecular mechanisms and formal evolutionary theory. We can use our imagination to build better conceptual models in cases where available data is limited or sparse. In a Synthetic Daisies post from last month (Plausibility and de navitus Models of Complex Systems), I have sketched out the means to solve this problem using something called a de navitus model, which combines naive (e.g. common sense) theories of natural phenomena, machine intelligence, and artificial selection techniques.

* Continuing with the theme of simulated evolution, the BEACON Center blog profiles some work being done by Cory Kohn at Michigan State (Testing Phylogenetic Inference with Experimental Evolution), who uses digital evolution (the AVIDA platform) to better understand the relationship between phylogenetic inference and lineage recombination.

* Carl Zimmer from Phenomena brings us another post (Watching Bodies Evolve), this time on the experimental study of evolutionary transitions. This involves replicating the evolution of multicellularity in a yeast model. The post reports on a recent publication [8] by William Ratcliff and Michael Travisano (among other co-authors), and features a number of nice microscopy images.

Besides the use of virtual worlds and experimental methods, we might also use LEGO kits and other types of physical models to represent possible phenotypes. Below is an entry in the MOCathalon by Sean and Stephanie Mayo, featuring a number of existing invertebrate species. This approach can be leveraged for our purposes by building on the work of Mark Changizi, who observed a scaling law that is shared between LEGOs and the natural world [9].

* The So Much Science Tumblr brings us Phylo: the trading card game, which looks like a potential exhibit at next year's Comic-Con. Build a collection of your favorite species, or create new ones. And Prehistoric Taxonomie (another Tumblr blog) features excellent scientific illustrations of Moschops capensis, a herbivore from the late Permian.



* A consideration of future evolutionary trajectories also requires us to consider potential mechanisms behind such changes. Joachim Dagg from Mousetrap brings us a host of posts on evolutionary maintenance, which mediates the relationship between sexual reproduction and heritable variation. He provides both a short introduction to the set of relevant issues ("A very short history of evolutionary maintenance problems"), and follows up with two specific examples ("DNA repair as a cooperative venture" and "Males and the maintenance of sex"). Blake Stacey from Science after Sunclipse brings us a short reading list on Evolutionary Dynamics. Finally, Tim Eisele from The Backyard Arthropod Project brings us a post on The Origin of Insect Wings.


PART III:  What are the historical contingencies (or time-dependencies)?

Yet another depiction involves projecting future evolutionary constraints. How will existing evolutionary constraints produce diversity into the future, or how will new constraints arise in conjunction with future events? These projections can be made in a number of ways, but here we will focus on biogeography. Specifically, how will the present and future dynamics of plate tectonics and continental drift affect the distribution of species and ecosystems many years from now? Fortunately, it is possible to build projections of future plate tectonics using geophysical data and computational models such as plate motion vectors [10].

An example of future models of tectonic drift. TOP: Earth, as it is projected to look in 100 million years. COURTESY: Ron Blakely at Northern Arizona State (NAU). BOTTOM: The end result of 650 million years of plate tectonics.

This month's evolution blogosphere features a number of loosely-related posts on how the categorical diversity we observe today may or may not be a product of contingencies from the evolutionary past: 

* Rob Graumans at The Young Socrates asks the question and reflects upon of why men and women exist, and why (by contrast) there are many potential genders. I assume his intent here is to engage in Socratic inquiry, which means that you should leave comments.

* Leo van Iersal, posting at Genealogical World of Phylogenetic Networks, brings us a discussion about the topological restrictions posed by how phylogenetic networks are configured. For example, what are the consequences of making a phylogenetic tree in different ways: rooted using a single taxon, acyclic lineages, or time-consistent lineages? And when any given model is consistent with the underlying biology [11], then what is the effect on that particular set of phylogenetic relationships? Another post from the same blog (this one by David Morrison) follows up on this by discussing partially-directed phylogenetic networks that rely on first-degree relationships.

The "escape and radiate" model of coevolution, which describes the coevolution of plant (left phylogeny) and insect (right phylogeny) macroevolution. COURTESY: Figure 1 in [12].

* Jeremy Yoder, this time writing at Nothing in Biology Makes Sense reminds us that there are a lot of potential phylogenetic tree topologies in a single species' genome. This argument is based on the notion of a consensus tree, or what happens when you put many different traits (with different evolutionary histories) together in the same tree. The resulting paper, focusing on genomes from the legume genus Medicago and forthcoming in the journal Systematic Biology, is now available online.


Another way to critically examine historical contingencies is to study macroevolution, or evolution over long periods of time (e.g. millions of years):

* The BEACON Center blog features an interview with Luke Harmon, who reflects upon the macroevolution and its role in producing evolutionary changes. These changes and their contingencies have in large part determined what modern variants (e.g. phenotypes) look like. This has particular relevance to the study of digital evolution, which captures the essence of macroevolutionary trends.

* The BEACON Center blog also features a profile of Zachary Blount's work in the area of E.coli experimental evolution, in which he describes the process of discovering of a new species. In this case, a directly-observed novel physiological adaptation (citrate metabolism) is evaluated in the context of several species concepts (e.g. biological and ecotype).

* PZ Myers from Pharyngula wins the bad joke of the month award (What's Jimmy Walker's favorite arthropod? Tri-lo-bite!). Topic: a mini-review on trilobite anatomy and phylogeny.

* The Molecular Ecologist features a post by Dylan Goldade, Kathryn Theiss, and Chris Smith on new simulation work that demonstrates the role of ecological speciation in the evolution of species [13]. This is accomplished via a review of works by Ernst Mayr and classical population geneticists. 


PART IV:  Behavioral invariants vs. evolution of intelligence.

The final depiction we will discuss here is the future of behavioral change and the evolution of intelligent behavior. Changes in behavior such as migration patterns or foraging behaviors might be observed as a consequence of climate change [14]. However, behavioral repertoires themselves might undergo future evolution, perhaps resulting in evolved intelligence [15]. One way to address this issue is to look to the evolutionary past, and find "invariant" (or recurrent) behaviors that might shape possible evolved behaviors (or their constraints) in the future.

Examples of the using the past to inform the future. Picture at left is adapted from Figure 1 in [16], and picture at lower right is taken from Neanderthal Man (Caroline Chronicles Tumblr post).

There are a number of behavior-related posts this month:

* Matthew Cobb, writing at Why Evolution is True, posts on why animals do not detect radio waves. This sounds like a strange question, unless you realize that plants and animals use the electromagnetic spectrum quite extensively for functions such as energetic inputs and sensation. According to physicists Tommy Ogden and Tim O'Brien, radio waves are too low-energy and have too long a wavelength to be useful for these purposes.

environmental change; evolution of mutation rate". The reposts featured within include content on learning and alarm call copying in birds, vocal copying and individuality in dolphins, and adaptive immunity in viruses.

* Jason Collins from Evolving Economics presents some quotes from R.A. Fisher's classic "The Genetical Theory of Natural Selection" on the evolution of human exchange and economic markets. The passages are interspersed with critical observations.

* Writing about mixed-species (or heterospecific) social groups, Felipe Dargent from Eco-Evo-Evo-Eco: Eco-Evolutionary Dynamics (Mixed-species groups – everything is about predation... or isn’t it?) presents a hypothesis and evidence as to why they form and what purpose they serve.

* Discussing the recently-published book "Paleofantasy" [17], John Hawks brings us his perspectives on the popular misconceptions and pseudoscience surrounding paleolithic-era human culture, collectively referred to "paleo-advice" (e.g. paleo-diets, paleo-child rearing, etc). And here is a post (Paleo and Woo) from Respectful Insolence which goes into even greater detail about paleo-pseudoscience.

* In keeping with the our past-can-inform-the-future theme, PonerologyNews brings us a feature on possible evolutionary scenarios for the origins of human psychopathy, and how it might be an example of a spandrel (or exaptation) in the human brain.


The right way (top, bottom) and wrong way (inset) to think about how organisms use the electromagnetic spectrum.


PART V: Future Analytical Tools.

A bit beyond the scope of this presentation but nevertheless important is the future of data integration and analysis. Recall that our knowledge of evolution is based in part on reconstruction of the past. Therefore, tools that provide better reconstructions of the past (and present) can inform our projections of the future

A recent post by Jonathan Eisen from Tree of Life blog (The gurus predict the future of evolution) reviews a recent paper called "Evolutionary Biology for the 21rst century" [18]. The authors propose an approach called "BioDiversity Informatics", which leverages computational infrastructure and data aggregation to address issues such as sustaining biological diversity in the face of climate change or the evolutionary origins and trajectory of disease.


In the spirit of BDI, Michael Harvey at Nothing in Biology Makes Sense presents a discussion of natural history in the -omics era, which bridges the worlds of traditional fieldwork and the availability of high-throughput data.

* Taking a slightly different perspective, John Hawks' blog ("The Neandertal Treatment") brings out attention to a recent NatGeo article on the potential use of whole-genome sequence data to clone something called a "neo-Neanderthal". This would be a real (if not far-fetched) opportunity to learn about the future through understanding our common ancestry. But let us suppose that a Neandertal were cloned tomorrow: Brian Switek at Phenomena has a post on "The Promise and Pitfalls of Resurrection Ecology", which is a critical evaluation of bringing extinct species (e.g. ice age megafauna) back to life.

Scenes from science in a possible 31rst century: is the future in 8-bit resolution? COURTESY: "Futurama" episode Reincarnation.

That's all for this month's edition. Hopefully this has provided us with plenty of entertainment and food for thought. So what does the future hold? Subsequent editions of "Carnival of Evolution"? If you administer a blog and are interested in hosting the Carnival of Evolution (happens every first of the month), please contact Bjorn Ostman. And why continue to blog about evolution? Razib Khan has a good post on this topic at Gene Expression (his answer: because you can!).

Finally, I have provided a printable, citable version of this Carnival edition on Figshare (doi:10.6084/ m9.figshare.661698) for those who are interested. I previously hosted CoE #46: The Tree (structures) of Life, which has been published on Figshare as well. Please let me know if you intend to use these for teaching or other purposes.


NOTES:

[1] Alicea, B.  Projective Models: a new explanatory paradigm. Synthetic Daisies blog. February 1. 

[2] For an introduction to phylogenetic construction, please see: Harrison, C.J. and Langdale, J.A.   A step by step guide to phylogeny reconstruction. The Plant Journal, 45, 561-572 (2006).

[3] Ward, P.   Future evolution. Times Books, New York (2001).

For more information, please also see the Discovery TV series "The Future is Wild", and the Speculative Evolution wiki.

[4] for more information, please see Dougal Dixon's website.

[5] Graur, D., Zheng, Y., Price, N., Azevedo, R.B.R., Zufall, R.A., and Elhaik, E.   On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution, doi: 10.1093/gbe/evt028.

[7] For information on how this approach can be misused, see this Sandwalk blog post ("Spore and Evolution") from 2008.

[8] Ratcliff, W.C., Pentz, J.T., and Travisano, M. (2013). Tempo and Mode of Multicellular Adaptation in Experimentally-evolved Saccharomyces cerevisiae. Evolution, doi:10.1111/evo.12101.

Example of a yeast proto-colony.

There is also a related paper published in 2012 by the same group: Ratcliff, W.C., Denison, R.F., Borrello, M., and Travisano, M. (2012). Experimental evolution of multicellularity. PNAS, 109(5), 1595-1600.

[9] Changizi, M.A., McDannald, M.A., and Widders, D.   Scaling of differentiation in networks: nervous systems, organisms, ant colonies, ecosystems, businesses, universities, cities, electronic circuits, and LEGOS. Journal of Theoretical Biology, 218(2), 215-237 (2002).

[10] If you are interested in how these animations were produced, here is a link to the calculation of plate motion vectors and estimation of relative plate motions. Overall, the forecast for the (deep) future is for fewer continents, with an 50-100% chance of eventual engulfment by a red giant Sun. Hopefully, this does not ruin your day.

[11] For an example, please see: Lerat, E., Daubin, V., and Moran, N.A.   From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria. PLoS Biology, 1(1), e19 (2003).

[12] This is a nice review on plant-insect macro-coevolution: Futuyma, D.J. and Agrawal, A.A.   Macroevolution and the biological diversity of plants and herbivores. PNAS, 106(43), 18054-18061 (2009).

[13] Flaxman, S.M., Feder, J.L., and Nosil, P.   Genetic Hitchhiking and the Dynamic Buildup of Genomic Divergence During Speciation with Gene Flow. Evolution, doi:10.1111/evo.12055 (2013).

[14] Western, D.   Human-modified ecosystems and future evolution. PNAS, 98(10), 5458-5465 (2001).

[15] For a simple primer on how behavior evolves, please see this short article: McGlynn, T.   How Does Social Behavior Evolve? Nature Education Knowledge, 3(10), 69 (2012).

For a more speculative projection specific to humans, please see this story: Owen, J.   Future Humans: four ways we may, or may not, evolve. National Geographic News, November 24 (2009).

[16] O'Leary, M. et.al   The Placental Mammal Ancestor and the post-K-Pg radiation of placentals. Science, 339, 662 (2013).

[17] Zuk, M.   Paleofantasy: what evolution really tells us about sex, diet, and how we live. W.W. Norton (2013).

[18] Losos, J.B. et.al   Evolutionary Biology for the 21st Century. PLoS Biology, 11(1), e1001466 (2013).

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