Journal Club: Structural and Functional Constraints in the Evolution of Protein Families

The theme of this year’s IGERT EvoDevo symposium is “Current Frontiers of Evolution, Development, and Genomics.”  Every Friday, starting this week and ending December 4th, our IGERT group is hosting a journal club discussion about our own research in the broader context of paradigm-shifting publications in Evo/Devo/Geno.  This week, I’m leading the discussion about my research in computational methods for ancestral sequence reconstruction in the context of a recent review by Catherine Worth, Sungsam Gong, and Tom L. Blundell titled “Structural and Functional Constraints in the Evolution of Protein Families.” If your campus provides access to the journal Nature Reviews, the paper can be found here: http://www.nature.com/nrm/journal/v10/n10/abs/nrm2762.html

Here are my insights into why this paper is fundamentally relevant for anyone working with genetic sequence data in an evolutionary context. . .

Scientific frontiers appear when we integrate analyses from the micro and the macro scale. Examples of this include how biology is informed by chemistry, chemistry is informed by physics, and classical physics is informed by quantum physics.  This trend is true for EvoDevo: we are rapidly arriving at an understanding of evolution from increasingly scientific first principles.  To be specific, we are beginning to understand how mutations in protein sequence and structure — at the biophysical scale — have consequences for the function and phenotype of cells, species, and individuals — at the macro scale [see Dean and Thornton, Nature Reviews 2007].

In order to reveal the evolutionary trajectory of a particular protein structure, we need to examine ancient forms of that protein.  However, the simple acquisition of ancestral molecules can be a major obstacle when we examine evolutionary histories over millions of years because the ancestral forms are typically extinct.  As a computational alternative, we can time travel via statistical inference [see Thornton, Nature Reviews 2004].

I study computational and phylogenetic methods that make it possible for us to probabilistically infer phylogenies and reconstruct ancestral gene sequences.  One of the most important inventions in the history of phylogenetic methods is the use of Markov models to approximate the evolution of gene sequences.  Markov models are used all over the place in information science: to model natural language, radio transmissions, and white noise.  Markov models are used in speech recognition, your email’s spam filter, and global weather prediction.  Google’s core search algorithm is fundamentally just a complex Markov model.

The core idea of the Markov Model concerns characters transitioning (i.e. mutating) over time.  Suppose we have some character — like a single nucleotide or an amino acid — and it currently is in state X, where X is one of the letters in our nucleotide or amino acid alphabet.  Over time of length t, X will mutate to state Y with probability determined by a matrix of relative substitution ratios.  This model follows the Markov property, where the probability of Y later mutating to state Z over time t2 is independent of its prior state X.

If we calculate transition probabilities for all branches in a phylogenetic tree, we can thus calculate the likelihood of that tree and infer the maximum a posteriori ancestral protein sequence.  In this discussion, I will avoid articulating all the mathematical minutiae of how we calculate probabilities for trees and ancestral sequences; you can learn more by reading this excellent book edited by Oliver Gascuel.  Instead, I want to focus on the substitution matrix: it is an approximation of molecular evolution and it makes critical assumptions about evolutionary forces.

In it’s simplest form (as a 4×4 nucleotide matrix or 20×20 amino acid matrix) substitution matrices assume that all residues with the same state are in a homogenous biophysical environment, and are thus exposed to the same mutational forces.  For example, the WAG matrix assumes that all glutamic acids (E) can be treated equally, and thus the relative substitution rate for any glutamic acid mutating into asparagine (D) is 6.174, while the relative rate of any glutamic acid mutating to cystine (C) is 0.021.  The assumption of structural homogeneity is often invalid; for example, as is illustrated in this week’s review by Worth et al., residues buried in solvent-inaccessible cores of a protein tend to be more conserved than residues located on the exterior of proteins.  This insight implies that we need a secondary substitution matrix expressing relative mutation rates for residues located in protein cores.  As an example, if E stands for an external glutamic acid and E’ stands for a core glutamic acid, we should expect the relative substitution rate for E-to-D to be larger than the relative rate for E’-to-D’.

The article by Worth et al. reviews a large historical body of results concerning protein structure conservation.  The article further describes how we can use environment-specific substitution tables (ESSTs) to explicitly capture information about structural conservation into our Markov model of evolution.  The insights from this paper are fundamental for anyone working with genetic sequence data in an evolutionary context.

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Worth CL, Gong S, & Blundell TL (2009). Structural and functional constraints in the evolution of protein families. Nature reviews. Molecular cell biology, 10 (10), 709-20 PMID: 19756040

Experimenting with an organ synth (part 2)

As I mentioned in my earlier post, I’ve been playing with the Korg X50.  Here is more drone-like trance organ; love it or hate it:

Organ Improvisation on September 22, 2009 (7:27, MP3 17.1 MB)

Experimenting with an organ synth

Recently, I’ve been playing with the Korg X50 music synthesizer; I greatly enjoy that I can manually adjust the shape, velocity, and attack of each synthesized pad.  Here is a recorded improvisation using a pad called Ballad Organ:

Organ Improvisation on September 21st, 2009 (MP3, 12 MB)

further audio experiments with Edirol R-09

1. Improvisation April 5th, 2009 – MP3 (4.3 Mb)

. . . walking along the Opal Creek with Tarantula.

2. Improvisation September 15th, 2009 – MP3 (5.8 Mb)

. . . Here is some new music I made, using a Korg X50 music synthesizer, a Peavey TKO(tm) 65, and recorded on an Edirol R-09.

Burma VJ; I recommend.

Burma VJ is a documentary by Anders Østergaard about the 2007 popular uprising in Myanmar.  Although the Myanmar government strictly prohibits journalism, a group called the Democratic Voice of Burma (DVB) covertly captured and smuggled video to international news outlets including BBC and NBC.  This film uses DVB’s media to tell the story of the September 2007 revolt, in which 10,000+ monks protested in the streets.  This film makes it abundantly clear that international awareness of Myanmar’s situation relies on the brave actions of a few dozen (or less) reporters.

The film stitches together high-def video, low-def cellphone imagery, and audio recorded on any number of devices.  On several occasions, the footage comes from cameras hidden inside gym bags and purses: the scene opens with blurry images inside a purse, we hear a zipper, a flap opens, and then we see thousands of monks marching and chanting through the streets of Rangoon.

After watching this film, it’s not surprising to read today’s headline that Noble Peace Prize winner Aang Suu Kyi will be kept under house arrest.  It’s also not difficult to draw parallels between Myanmar’s 2007 uprising and Iran’s recent protests; in both cases, the military won.

notes on South Sister circumnavigation

This weekend, I circumnavigated the South Sister with L.L. and E.F.  You can view my Flickr media (click here).

Our route combined a mix of trails and cross-country travel, and roughly followed the path shown on the Traditional Mountaineering website.  In summary, we started at the Devil’s Lake trailhead and hiked across the Wikiup Plain to the Pacific Crest Trail (PCT).  We traveled north on the PCT until Separation Creek; from here, we trekked cross-country upstream to the ridge connecting South Sister and Middle Sister.  We traversed over the moraines surrounding Chambers Lakes, and descended on a rough climbers trail to Camp Lake.  We bivvy-camped on a ridge above Camp Lake.  In the morning, we traversed cross-country along the east shoulders of South Sister and joined the trail north of Green Lakes.  After a short break at Green Lakes, we followed the trail to the Green Lakes trailhead and then walked along the road to return to our car  at the Devil’s Lake trailead.

Overall, the route was straightforward.  The cross-country section south of Camp Lake provided some (fun) navigational challenges, but I don’t think it was particularly dangerous.  Here is a map (linked from the Traditional Mountaineering website):

2009 Whiteaker Block Party ’twas awesome

I just returned from the third annual Whiteaker Block Party; I’m glowing from the happiness of the crowd, and my legs are sore from dancing nonstop for hours.  You can check-out my Flickr media by clicking here.

Let’s be realistic about performance-enhancing drugs

Check-out this story in the NY times: Over 100 Major League Baseball players — include Manny Ramirez and David Ortiz of the Red Sox — tested positive for “doping” with performance-enhancing drugs in 2003.  The debate about doping in Major League Baseball is hardly new; also check-out articles about doping in the Tour de France, “swimsuit doping” in Olympic swimming, and IOC doping-inquiry panels.  All these stories imply that the use of performance-enhancing drugs is unfair, unethical, and even dangerous.

Until recently, I agreed with the mainstream media’s negative view of performance-enhancing substances.  I romanticized the “purity” of human athleticism, and performance-enhancement seemed unfair. However, my opinion radically changed after I listened to this program on NPR.  In an Oxford-style debate, a panel of six critical thinkers debated the statement “We should accept performance-enhancing drugs in competitive sports.“  After considering the talking points from this debate, I’m convinced that performance-enhancing substances are not unethical.  Some substances — like steroids — have negative health consequences, but the adverse effects of these chemicals should be untangled from the ethics of these chemicals.

The ethics of “doping” becomes complicated when we consider the large number of substances — both legal and illegal — which enhance athletic performance.  For example, although the use of recombinant erythropoietin can significantly increase oxygen transport during endurance events (such as the Tour de France), is this type of enhancement ethically different from consuming an energy drink like Red Bull?  It seems there exists a spectrum of performance-enhancing substances: at one end of the spectrum we have extreme substances like anabolic steroids, at the other end we have mild substances like daily multivitamins.  The mainstream ethics (and legality) of performance-enhancing substances applies binary labels of “right” and “wrong” to situations which are nuanced and require critical discussion.

Here are a few strong talking points from the debate. . .

Julian Savulescu, professor of practical ethics at the University of Oxford, asserts that performance-enhancement is integral to sports:

“. . . performance enhancement is not against the spirit of sport, it’s been a part of sport through its whole history, and to be human is to be better, or at least to try to be better. . “

Radley Balko, a senior editor for Reason magazine, claims that performance-enhancing substances have a bad reputation, in part, because they’re labeled as “drugs”:

“Our society has an oddly schizophrenic relationship with pharmaceuticals and medical technology. If something could be said to be natural, we tend to be OK with it. If it’s lab-made or synthetic, we tend to be leery. But even synthetic drugs and man-made technology seem to be OK if the aim is to make sick people better or broken people whole again.”

Regarding the dangers of performance-enhancement, Norman Frost (professors of bioethics at University of Wisconsin) says the dangers of sports are greater than the dangers of performance-enhancing substances:

“Anabolic steroids do have undesirable side effects: acne, baldness, voice changes … infertility. But sport itself is far more dangerous, and we don’t prohibit it.”

I suggest you listen to the full debate, including the talking points against performance-enhancement: http://www.npr.org/templates/story/story.php?storyId=18299098

Finally, I think the discussion about performance-enhancement in sports has obvious parallels to the debate about performance-enhancement in academia.  To get started, I suggest you read Drew Halley’s blog post titled “Brain-doping at the lab bench.”

Trekking in the Evolution Range

I just returned from a short trek through the Evolution Range in the California Sierra Nevada.  It’s a ruggedly beautiful landscape, and all the peaks are named for famous evolutionary biologists (Lamarck, Darwin, Mendel, Haeckel).  You can view my Flickr media here.

I think “evolution” is the theme of my 2009 summer, given my recent participation at the Evolution conference, my upcoming participation at Burning Man (the 2009 theme is “evolution”), and this recent wilderness trek in the Evolution Range.

Obscure notes for the future:

• This year, patchy snow remained as low as 11,000 feet.  The switchbacks above Upper Lamarck Lake were snow-free, but the terraced plateau to Lamarck Col was mostly buried.
• In the midday sun, the snow over Lamarck Col was slushy and we did not need an ice axe.  I suspect a morning climb (when the snow is icy) would be dangerous without axe and crampons.
• The cross-country route through Darwin’s Canyon is straightforward, but the boulder-climbing can be exhausting.
• There exist many excellent campsites below Darwin’s Bench before Colby Meadow.
• This year, the mosquitos were active in Evolution Meadow, but they weren’t insufferable.  Given the cold temperatures and auspicious lack of wilderflower blooms, I suspect we experienced an early mosquito hatching and later weeks will have bigger swarms.
• My favorite campsite in McClure Meadow is beside the trail, west of the ranger station, near the outflow of the meadow.
• The best place to ford Evolution Creek is in Evolution Meadow, not at the official PCT crossing.
• An awesome campsite exists in Piute Canyon, on a southern-facing cliff about 2 miles downhill from Hutchinson Meadow.
• Although most climbers approach Pilot Knob from the eastern saddle, you can also climb from the southeast face (and avoid climbing the saddle).  I suspect the southast face offers more sand and smaller boulders than the eastern ridge.

a video postcard