Genome Engineering

Today, Genome Engineering hosts the carnival of evolution, or CoE, for the first time. The focus of Genome Engineering is – quite obviously – the engineering of the genome. So what does that have to do with evolution, I hear you say? Evolution has been driven by genetic changes, both small and large, and the natural engineering of the genome has a lot to teach those of us who want to engineer in – ahem – a less ‘natural’ way.

Evolution in action

Jeremy Yoder reports on the adaptation of three types of lizards of the White Sands as a model of evolution in the blog For lizards on white sands, evolution doesn’t quite repeat itself, but it does rhyme posted at Denim and Tweed. The lizards have all evolved towards lighter skins and different sizes and shapes, but show very different levels of genetic diversity between the lighter and darker types.

Yoder has also looked at the effects of mutualistic relationships as drivers of the evolution of a type of orchid, and in the post One of these mutualists is not like the other describes how pollinators and mycorrhiza can have opposite effects on genetic diversity. Here, at Genome Engineering, we also looked at mutualism in Genetic evolution in action. Bacteria symbiotic with aphids showed huge reductions in genome size, perhaps mimicking the changes seen in the process that turned ancient symbiotic bacteria into organelles.

While, according to Dollo’s Law, evolution is a one-way street, traits that have been lost through evolution can seem to reappear. Ken Weiss, posting on Reversibility: Dollo’s ‘law’ in development and evolution and Anne Buchanan, posting Lost and found — Breaking Dollo’s Law, both at The Mermaid’s Tale, show how existing genes can produce what appear to be lost traits.

In NeuroDojo, Zen Faulkes posts on Songs and size in sabrewings: evolution across an isthmus. These beautiful hummingbirds are evolving as three separate populations around an isthmus, and the changes in size appear to be driven by genetic drift. However, this doesn’t seem to explain the changes in song – these seem to be selected by female preference – a perfect posting for the week of Valentine’s Day.

A number of different factors can drive evolution of specific organs, such as the eyes – these include the ability to find food or mates, or as in the case of Gammarus minus, predators. Zen Faulkes’ post What big eyes you have! at NeuroDojo describes research that suggested the presence of predator fish drove the selection for crustaceans with bigger eyes, though more research is needed.

Bjørn Østman posted Mankind has not stopped evolving at Pleiotropy in response to a statement from a mathematician concluding that there is no more selection pressure on humans. This topic is also discussed on the BBC website this week.

And just to put things into context. Genome engineers work fast, with the speed of gene changes only limited by our current technology, and in comparison, evolution is a slow process, even during periods of accelerated gene birth. Iddo Friedberg gives us a moment of reflection in The Oxygen Rush: late January, all of February and a Day in November, posted at Byte Size Biology. If the history of life were compressed to one year, the Cambrian explosion would be one day in November. The Archaean gene expansion took place for more than a month, starting late January, apparently triggered by the ‘great oxygenation’ of the planet.

Leaving things behind

Evolution sometimes leaves behind vestigial traits. In the fantastically named blog Why Evolution Is True Greg Mayer’s post highlights the scraps of the hind legs that hide within the bulk of whales. In the same blog, and with a very cute picture of a kitten, Jerry Coyne writes about another vestige – the arrector pili in humans. These are the tiny muscles that make our hairs stand on end, and give us goosebumps, when we get cold or afraid. While these helps our ancestors keep warm or scare off threats, they have no real use in modern humans.

While the loss of a limb can be seen as logical, the Loss of anus? does seem unlikely – however, microRNA studies in a paper discussed by Bjørn Østman in Pleiotropy appear to suggest that Acoels, small worms with a shared mouth and anus, had ancestors that had separate mouths and anuses (ani?), which were subsequently regained later in evolution.

Biological heredity and social sciences

As well as having a role in biological sciences, heredity has a role in social sciences as well. A post by Ken Weiss at The Mermaid’s Tale, on “Peeled truffles and seasoned mushrooms”: how are the sins of the fathers visited on their sons? discusses the dangers of attributing everything to nature when, in fact, it could be influenced by nurture.

A paper from Sweden on evolutionary psychology seems to indicate an increased level of murder of stepparents compared with natural parents, suggesting an evolutionary link. Bjørn Østman disputes this, in Regicide in evolutionary psychology, posted at Pleiotropy.

Scott Bartlett reviews The Dangers of Progress by Ronald Wright at BATSHITE. The book looks at how human evolution has veered dangerously away from biology with the advent of civilizations, and suggests that we have sufficient knowledge that we do not have to repeat history. I hope we don’t.

Happy birthday to you

February 12 was Darwin’s 202^nd birthday (well, it would have been), and there have been a bunch of posts celebrating this. At Mario’s Entangled Bank, Mario Pineda-Krch wishes a Happy birthday Charley Boy, and many more and supports the Statement of Congressman Pete Stark Honoring Charles Darwin. His other posts this month include Darwin as a theoretician, and the (alleged) meeting between the Flying Spaghetti Monster and Darwin in The Quest for the Theory of Evolution. Awesome.

Kevin Zelnio posted Ex Omnia Conchis: Darwin and His Beloved Barnacles at Deep Sea News, about Darwin’s love of barnacles and their role in his work. Michael Barton talks about the influence of the Galapagos in Darwin on Galapagos (1880) and introduces us to some fantastic cartoons about evolution in Just So Darwin, both posted at The Dispersal of Darwin.

SEX!

That caught your attention. There have been a few posts on sex and evolution this month. Evo-punk’s posting, ?Sex feeds evolution?, was triggered by a visit to the London Natural History Museum’s Sexual Nature exhibition, and talks about sex and adaptive evolution (and that ‘asexual reproduction might even be twice as efficient as sexual reproduction, but is not half as fun’).

Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhoea, and Iddo, in the post Humans draw the LINE at Gonorrhoea. Not that it helps at Byte Size Biology shared the news that there is human DNA in the bacterial genome – while they have been infecting us, we have been infecting them!

Splendid fairy wrens (who are rather splendid) have evolved an interesting sexual strategy. As Kelsey’s post Splendid Splendiferousness and the ‘Scary Movie Effect’, posted at Mauka to Makai, reveals, while they pair for life, the female wren responds to (and mates with) other male wrens that wait for a predators’ call and then call themselves – almost as if they are teenagers waiting for someone else’s girlfriend to get scared before providing ‘comfort’. How bizarre. Don’t try this at home.

And finally for sex, the prize for this month’s ‘eww’ factor goes to Becky Ward’s post on Worm sex and spiky sperm on It Takes 30.

This month’s genomes

The SUPERFAMILY database lists over 1400 completely sequenced genomes, and every month seems to add more. In the Release of the Daphnia Genome from Deep Sea News, Dr Bik suggests that the water flea’s gene duplication could help it to adapt to the wide range of environments it calls home.

Slightly off the evolutionary track, but still something worth thinking about, the first human genome data were published ten years ago, in February 2010. This (and the atomic bomb – Anne Buchanan will explain in Omics and the atomic bomb, posted at The Mermaid’s Tale) has led to an explosion of data and of ‘-omics’, but few ‘hard’ outcomes.

Evolution isn’t true… is it?

No blog carnival on evolution is complete without a section on why there is no such thing as evolution. Some people clearly believe that evolution is not true, and little that any of us say will dissuade them. Troy Britain of Playing Chess with Pigeons has visited a creationist museum, and tells the story of Dinny the dinosaur (still) held hostage, while unpacking some of the myths of creationism. And in the Tale of Two Dinosaurs, Britain reflects on the contrast between how the science of evolution theory and the pseudoscience of creation science cope with new fossil evidence of dinosaur ancestors.

Ants seem to create networks of trails between nests that take the shortest route possible, which look like Steiner trees, a mathematical problem. Dave Thomas has applied genetic algorithms to solve the Steiner problem. However, intelligent design proponents like Bill Dembski see the ants’ problem solving abilities as proof of ID, says Thomas, posting at The Panda’s Thumb on Dembski Wakes Up, Smells the Steiners, Pushes Snooze Button.

Next-generation sequencing is an incredibly powerful tool in the study of genes and their associated proteins, and can be used to plot the fitness landscape of individual proteins. Steve Matheson’s blog on Mapping fitness: protein display, fitness, and Seattle, posted at Quintessence of Dust points out that this could be a useful methods to tackle questions of protein evolution, and wonders why the intelligent design ‘scientists’, based nearby, haven’t got involved in the research.

We close this section with two poems – the Strong Anthropic Principle Song from The Digital Cuttlefish, and Holly Dunsworth’s Mything Links from The Mermaid’s Tale (along with a call for a transition animal, and there’s $10,000 in it for you!) – and a question about talking animals from Michael Barton in The ultimate question for evolutionists? posted at The Dispersal of Darwin.

And a few things I couldn’t fit anywhere else!

In Deep-Sea Creatures Play in the Same Band, posted at Deep Sea News, Kevin Z tells us that brittle stars have evolved based on latitudinal influences that reach across the oceans.

The Chengjiang formation is an incredible window into the life of the early Cambrian, and Why Evolution is True, in Two weird fossils, highlights the beautifully-preserved lobopod that may be the ancestor of modern arthropods.

Neutral evolution theory suggests that many of the evolutionary changes are driven by random mutations that confer no particular advantage; adaptionists believe that evolution progresses through changes that confer an advantage. For a cracking debate, have a look at the comments in Dawkins, Darwin, Drift, and Neutral Theory, posted at Sandwalk. Thomas Mailund posts about CoalHMM analysis of the human/chimpanzee ancestor, based on the orangutan genome, which suggests that selection, rather than drift, has driven human evolution.

Anne Buchanan posts on natural selection in malarial parasites, in The Wars Within at The Mermaid’s Tale. The parasites have to allocate resources for each different stage of their lifestyle, and this may be driven by natural selection, or as an adaptation maneuver to avoid the rigors of our immune systems.

From just one bone – Jerry Coyne, posting Australopithecus afarensis: a “committed terrestrial biped” in Why Evolution is True, tells the story of the single bone that confirms that ‘Lucy’ was a terrestrial biped.

That single bone concludes this edition. I’ve typed this post proudly wearing my Darwin Fish t-shirt, and have thoroughly enjoyed my first hosting of CoE. Submit your blog article to the next edition of carnival of evolution using our carnival submission form. Past posts and future hosts can be found on our blog carnival index page.

Fancy hosting CoE this spring? Email bjorn@bjornostman.com and join us at the carnival of evolution.

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