The wondrous mitochondrion and its proteome

The sequencing of human mitochondrial DNA, a circular DNA molecule contained in mitochondria, was completed in 1981, and, since then, roughly 150 mutations have been found that are associated with maternally inherited diseases (if you don't remember why mtDNA is inherited from the mother and not the father, check out this earlier post of mine). Despite this, the majority of human mitochondrial syndromes are actually caused by defects in the nuclear genome. This is sort of obvious if you think about it, given that human mitochondrial proteome consists of an estimated 1,100-1,400 distinct proteins, of which 13 are encoded by the mitochondrial DNA. The majority of proteins targeted at the mitochondria are actually encoded by nuclear genes. In fact

"The 13 proteins encoded by mammalian mtDNA are all components of the respiratory chain, which generates the majority of cellular ATP via oxidative phosphorylation (OXPHOS). However, the remaining respiratory chain subunits are encoded by nuclear genes, as are all proteins required for the transcription, translation, modification, and assembly of the 13 mtDNA proteins. All the components of numerous other mitochondrial pathways are also nuclear en- coded, including the tricarboxylic acid (TCA) cycle, protein import, fatty acid and amino acid oxidation, apoptosis, and biosynthesis of ketone bodies, pyrimidines, heme, and urea. Furthermore, during the decades following the sequencing of the mtDNA, it became clear that maternally inherited mitochondrial disorders represent only 20% of all inherited human mitochondrial disorders [1]."

Mitochondria are amazing organelles. Roughly half of mitochondrial proteins are ubiquitous and found across all organs, while the rest are tissue specific, meaning that their function and structure varies across cell lines. For example, when comparing mitochondria across different tissues, researchers found about a 75% overlap. In addition to this cell-type specificity, some of the mitochondrial proteins are expressed at very low levels or only during certain specific developmental stages, making the characterization of the mitochondrial proteome a challenging task. Today, a little over 1,000 of all mitochondrial proteins have been identified, mainly through large-scale proteomics, microscopy, and computation.

The first half of Calvo and Mootha's review [1] is an detailed report on the progress made so far in extensively classifying the mitochondrial proteome. They then proceed to discuss how the inventory of mitochondrial proteins has lead to the better understanding of mitochondrial disorders as well as the discovery of new disease genes.

"Traditionally, mitochondrial disease has referred primarily to disorders of oxidative ATP production, as discussed above. However the breadth of the mitochondrial proteome now implicates a large number of additional phenotypes, such as soft tissue tumors (paragangliomas) and diabetes mellitus. The discovery of new disease genes will further expand the clinical phenotypes associated with mitochondrial defects."

[1] Calvo, S., & Mootha, V. (2010). The Mitochondrial Proteome and Human Disease Annual Review of Genomics and Human Genetics, 11 (1), 25-44 DOI: 10.1146/annurev-genom-082509-141720

Have you been blogging lately?

I have to admit I'm obsessed with social networking. I have a love-hate relationship with the whole thing. Until last year I would've sworn I'd never jump the "networking" fence. My thoughts: "There's enough background noise already on the Internet." And: "I've got nothing interesting today."

Whether my posts are background noise or not, I'll leave it to you guys to decide, but I'm myself appalled by the fact that I've been blogging since last July and recently surpassed the threshold of 100 posts. That's not bad for somebody who thought they had nothing to say!

I can't help but wonder, though: what makes social networking so appealing? And how do people behave on the Internet? I've myself been on a couple of boards and found quite different behaviors, ranging from extremely aggressive to extremely supportive (yes, I love my G+ friends, absolutely love you guys!) From what I read about these things, the trend seems to be towards supportive. In fact, websites like Wikipedia and Foldit count on collaborative learning and crowdsourcing through networks based on the assumption that shared knowledge can rise over the background noise and provide meaningful advancements. A new research field has risen in order to analyze the huge amounts of data now available through the Internet.

It's mind boggling, isn't it?

All this to say that, much like I did in this post, I continue to avidly browse the literature looking for more info on social networks. Back when I wrote that post I hypothesized that "likes" on Facebook spread like viruses. My own experiment tells me that's not the case, but guess what? I did find something in the literature that mentions networks and viruses! Check it out:

"The user-generated content showed interesting viral-spreading patterns within blogs. Topical content such as news and political commentary spreads quickly by the hour and then quickly disappears, while non-topical content such as music and entertainment propagates slowly over a much long period of time [1]."

Ha! I knew I was right! Okay, I had the wrong "target." What's viral here is not the "likes" on Facebook, but blog content: for this particular study Cha et al. [1] analyzed 8.7 million posts from 1.1 million blogs -- wow, that's a lot!

Now, while I'm morbidly curious about these things, people smarter than me keep an eye on these data because of their economic value:

"Sentiments embedded in short text updates in social media have been shown to effectively predict and even precede the daily stock price variation (Bollen et al. 2011). Likewise, the blogosphere has been shown effective in capturing up-to-date news (Leskovec et al. 2009). In fact, a non-negligible fraction of news items shared in these social media are known faster than the traditional, authoritative news sources."

The paper lists several findings. First, when hey looked at the network structure of blogs, they saw a heavy-tailed distribution. Apparently, this is common to most network data: when you graph users vs. the amount of use/contribution to the network, you see few individuals contributing a lot (a spike in the graph), then a steep decline and a long tail indicating that the vast majority of the users contributes occasionally. Same with tweets, wikipedia edits, etc. However, unlike most other networks, blogs show much less reciprocity. That's understandable, as blogs are more intended as a means to publish content rather than exchange, giving rise to much less bidirectional nodes when you look at the blog graphs compared to posts on Facebook or Twitter.

The researchers also found that

"media content spreads according to two broad patterns: flash floods and ripples. The first group includes topical content such as news, political commentary, and opinion. Like flash floods, these types of content spread quickly by the hour and then quickly disappear. This demonstrates the role of blogs as a social medium that helps and influences how opinions form and spread on current issues. The second group includes non-topical content such as music and entertainment. Like ripples, old content (produced more than a year ago) can get rediscovered and again start gaining the attention of bloggers, albeit at a slow rate."

[1] Cha, M., Pérez, J., & Haddadi, H. (2011). The spread of media content through blogs Social Network Analysis and Mining DOI: 10.1007/s13278-011-0040-x

Surfing the wave of genetics: the man who invented genetic landscapes

 
Today is the 90th birthday of the one and only Luigi Luca Cavalli-Sforza, professor emeritus at Stanford University and a pillar in population genetics. Oh, and in case you couldn't tell by the name, he's Italian, too. Not that I'm biased, mind you.

Cavalli-Sforza is best known for his book The History and Geography of Human Genes, in which he reconstructs the history of human migrations by mapping the distribution of gene alleles and correlating gene frequencies in populations with the geographic distances between them.

I had an interesting discussion a few months ago and it occurred to me then that many people outside the field of genetics still think that all traits are selected through evolution. This is not true. If you remember, another famous population geneticist came up with a mathematical model according to which it would take 300 generations for a trait under constant selection pressure to completely take over. That lead to Haldane's dilemma and the fact that such time scale was too slow to explain all genetic variation observed today.

The fact that Haldane's model didn't fit the observations eventually lead to the neutral theory of molecular evolution, and one of the greatest players in this new thinking was Motoo Kimura. Kimura's theory of "random genetic drift" is based on the assumption that most mutations are free of selective effects, and hence the rate of molecular evolution is determined by the mutation rate. This is backed up by the fact that most mutations we see are "silent" (which means they bear no effect on the proteins) and that most of the DNA in eukaryotes is non-coding.

Genetic drift is the change in allele frequencies due to chance. Under selection, some individuals pass their genes onto the next generation because they are "fitter." However, if not all traits are under selection, the vast majority is driven by chance. Some individuals will have offsprings, others won't, and each generation represents a new random drawing in the gene pool. When a random mutation arises in a population, assuming the mutation is neutral (in other words it doesn't affect the fitness of the individuals), the chance that it will get fixed in the population by random drift is 1/N where N is the population size. Therefore, the smaller the population, the greater the chance that a random mutation becomes prevalent by "chance" (and not selection!).

To celebrate Cavalli-Sforza's birthday, I chose a paper published in 2009 [1] that looks at genetic diversity in the Y chromosome and compares it to the expected variation under neutral drift. From the abstract:

"We observe geographic peculiarities with some Y chromosome mutants, most probably due to a drift-related phenomenon called the surfing effect. We also compare the overall genetic diversity in Y chromosome DNA data with that of other chromosomes and their expectations under drift and natural selection, as well as the rate of fall of diversity within populations known as the serial founder effect during the recent ‘‘Out of Africa’’ expansion of modern humans to the whole world. All these observations are difficult to explain without accepting a major relative role for drift in the course of human expansions."

The surfing effect is a really interesting phenomenon: mutations that arise in the wave front of an expanding population have an advantage over mutations that arise in individuals who are left behind with respect to the migrating portion of the population. This is because the front of the migration is a local, temporarily smaller population, and since the probability of a mutation to get fixed is inversely proportional to the population size, the fact that the mutants arise in a smaller population puts them at an advantage. Furthermore,

"The faster the population expansion, the greater the probability of success of a mutant that arises in the wave front, because then the wave front is longer."

In the paper, Chiaroni et al. look at the 18 major haplogroups (genetically similar groups that can be thought of as originating from the same ancestor) of Y chromosome genotypes and inferr their place of origin.

"If migrations were random, the geographic distribution of individuals with a specific haplogroup would be approximately normal (Gaussian) around the place of origin of the oldest mutation defining the haplogroup, apart from irregularities due to vagaries of the environment: obstacles, like mountains and deserts, or favored routes, like coasts and rivers."

The interesting finding in the paper is that while the expected genetic diversity for chromosome X more or less matches the observed one, the expected diversity of chromosome Y is significantly higher than the observed one indicating that, on average, there is more natural selection acting on X and the other autosome chromosomes than on the Y chromosome.

The authors conclude:

"The increasing role of human creativity and the fast diffusion of inventions seem to have favored cultural solutions for many of the problems encoun- tered in the expansion. We suggest that cultural evolution has been subrogating biologic evolution in providing natural selection advan- tages and reducing our dependence on genetic mutations, especially in the last phase of transition from food collection to food production."

[1] Chiaroni, J., Underhill, P., & Cavalli-Sforza, L. (2009). Y chromosome diversity, human expansion, drift, and cultural evolution Proceedings of the National Academy of Sciences, 106 (48), 20174-20179 DOI: 10.1073/pnas.0910803106

Mapping HIV-human protein to protein interaction reveals new targets for better drug design

HIV has a small genome (roughly 9,000 bases) and it survives by using the host's proteins and DNA. Understanding how these proteins come in contact and interact with one another is crucial in order to unravel the mechanisms by which HIV hijacks the cellular machinery and proliferates. A comprehensive work [1] by a group of researchers at UCSF lead by Nevan Krogan looked at two human cell lines in particular and identified 497 HIV-human protein-protein interactions between 16 HIV proteins and 435 human factors. The study, published in the last issue of Nature, is the first one to look at protein-protein interactions in a host-pathogen system, and it opens up new possible targets for drug design.

The researchers devised a score to classify the strength of the interactions, which they statistically validated through random reshuffling. They identified 196 interactions in both cell types, while 150 and 151 were specific to each line (HEK293 and Jurkat cells respectively, two human cell lines that were isolated in the '70s and are used today in experiments). Interestingly, the proteins identified in both cell lines had stronger evolutionary signatures than the others, something the researchers were able to identify using comparative genomics between human and rhesus macaque.

Besides revealing an enrichment for host proteins that the virus recruits in order to replicate, the study unveiled proteins that have an inhibitory role during the infection. For example, they knocked down ten interactors using RNAi and observed an increase in HIV infection, suggesting that those factors may play a role in inhibiting replication.

"Ultimately, our analysis of the host factors co-opted by different viruses using the same proteomic pipeline will allow for the identification of protein complexes routinely targeted by different pathogens, which may rep- resent better therapeutic targets for future studies."

[1] Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J., McGovern, K., Clarke, S., Shales, M., Mercenne, G., Pache, L., Li, K., Hernandez, H., Jang, G., Roth, S., Akiva, E., Marlett, J., Stephens, M., D’Orso, I., Fernandes, J., Fahey, M., Mahon, C., O’Donoghue, A., Todorovic, A., Morris, J., Maltby, D., Alber, T., Cagney, G., Bushman, F., Young, J., Chanda, S., Sundquist, W., Kortemme, T., Hernandez, R., Craik, C., Burlingame, A., Sali, A., Frankel, A., & Krogan, N. (2011). Global landscape of HIV–human protein complexes Nature DOI: 10.1038/nature10719

Photo: I'm crazy about soap bubbles this week. The macro lens can enlarge all the pretty color patterns and they are so, so beautiful. More bubble awesomeness to come later!

Regenerating tissue through autologous cells: a personal appeal

The trachea is one of the most challenging organs to transplant, with a high risk of necrosis and infection due to inadequate graft revascularization and the fact that it's constantly exposed to airborne elements. Transplants requires lifelong immunosuppression, which also carry high risks. Prosthesis can rupture, generate infection, and cause injury.

What to do then? One answer is tissue engineering.

Dr. Paolo Macchiarini is one of the pioneers in this techniques. In a recent paper [1] he and his co-authors

"describe in detail the tissue engineering approach used for tracheal construction, with a focus on the mobilization, isolation, and in vitro culture of cell types with high potential for use in bioengineering."

The technique is highly sophisticated and I'm sure I'm doing a poor job here in trying to explain it in simple terms. The starting point is a scaffold that should provide the basic characteristics of the trachea. As Macchiarini and colleagues state in the paper,

"Despite intensive research in this field, no solution has been proposed as being optimal; currently both natural and synthetic grafts are being used."

In one case study in particular, they used as scaffold a decellularized cadaveric organ from a human donor trachea, and then colonized it by epithelial cells and MSC-derived chondrocytes cultured from autologous cells taken from the patient. They aspirated bone marrow from the patient to obtain marrow mononuclear cells. These contain a class of repair cells called multipotent mesenchymal stem/progenitor cells, cells that are able to differentiate and hence can be used to regenerate tissue. The researchers separated the cells, differentiated them, and then seeded them along a scaffold:

"We then expanded and differentiated these cells toward chondrocytes and seeded the cells into the exterior spongy layer of the scaffold, where they formed the cartilaginous component. For generating the inner epithelial lining of the trachea, we seeded the surface of the scaffold with nasal epithelial cells, after in vitro expansion to obtain sufficient numbers for seeding the graft."

Above: The entire concept of the regenerative approach to tracheal transplantation using natural scaffolds. MNC, mononuclear cell.

While ex-vivo, the tissue is maintained through a perfusion system called bioreactor. Once implanted, several pharmacologic intervention are prescribed to minimize the risk of necrosis, infection, and cell migration. Despite the non-trivial risks, the result is incredible:

"Since 2008, nine patients (ranging in age from 11 to 73 years), with either benign or malignant conditions, were treated using this decellularized scaffold. To date, the new in vivo engineered transplanted tracheas have been shown to be viable and to possess a good epithelial coating, are characterized by immediate vascularization, and, above all, maintain a constantly open lumen for air passage."

Please help Rachel Breathe

Now, to most of us, what I've discussed above is fascinating science. To some, is hope for a new life. Rachel Phillips was a ballet dancer with Royal Ballet in London, the Kirov in St. Petersburg, Russia and other major companies in the US and abroad. Today, with over 90% of her airways collapsed, Rachel is fighting for her life. She suffers from a genetic disorder called Ehlers–Danlos syndrome, which is caused by mutations in a number of genes involved in either the structure, the production, or the processing of collagen. Collagen is essential in all connective tissues in the body. Because of this Rachel needs a new trachea and Dr. Macchiarini's tissue regeneration technique can give her one but she needs our help.

Please visit Rachel's website at helprachelbreathe.com/ and help her out with a donation. This is not just science. It's life!

Thank you.

[1] Jungebluth, P., Moll, G., Baiguera, S., & Macchiarini, P. (2011). Tissue-Engineered Airway: A Regenerative Solution Clinical Pharmacology & Therapeutics, 91 (1), 81-93 DOI: 10.1038/clpt.2011.270

Introns, exons, and stop codons: how antisense oligonucleotides can fix frameshift mutations

DMD is the largest gene in nature, covering roughly 2.4 mega bases of the X chromosome. It encodes the dystrophin protein, a component of the protein complex that connects the cytoskeleton to the extra-cellular matrix.

DMD is a very complex gene. Its RNA transcripts are differentially spliced, which means that the gene produces different transcripts, encoding a large set of protein isoforms. A refresher: every gene is composed of coding parts, called exons, interspersed with non-coding bits, called introns. When the gene is transcribed into RNA, a process called RNA splicing, the introns are removed and the exons (grr… my auto-correct keeps turning all my "exons" into "eons"!) reassembled to form the RNA transcript that will be used to form proteins. Some proteins, like dystrophin, have different isoforms (some specific to different cell types), and those are obtained through different splicing forms of the RNA, originated by maintaining a different number of exons in the final transcript.

This video is a good illustration of RNA splicing:

All this to give you an idea of how complex this gene is. So, when it carries a mutation, things get very complicated, and the consequences devastating. Mutations in the DMD gene are responsible for several forms of muscular dystrophy (MD), and because the gene is on the X chromosomes, the prevalence is usually higher in boys than girls. (This is because girls carry two X chromosomes, hence if one allele only is mutated, the other will compensate.)

The most common mutations causing muscular dystrophy cause the transcription process to stop too early, producing incomplete, and therefore non-functional, RNA transcripts. I discussed reading frames in this post: in layman terms, the reading frame of a gene is how you split the bases in triplets so that each triplet codes one amino acid (the building blocks of proteins). Mutations that cause a shift in the reading frame basically disrupt the translation into amino acid, often resulting in the early termination of the transcription process (when the frameshift causes the random appearance of an early stop codon). When not enough functional dystrophin is produced, individuals experience a significant loss in muscle function and muscle degeneration.

How to counteract the action of frameshifting mutations?

One way is to use antisense oligonucleotides, buts of RNA that bind to a splicing site on the pre-mRNA causing the deleterious exons to be skipped and thus restoring the "functional frame." What does this mean? Remember, RNA is one-stranded. From DNA to RNA there are several steps: pre-messenger RNA and messenger RNA, or mRNA. The deleterious mutations are on the gene and they cause a misread when going from DNA to pre-mRNA. Now the mutations are on the pre-mRNA. Suppose you can devise a "bandage" that literally covers the bit of bases causing the framshift. If the bandage works, the bit won't be read when the pre-mRNA is turned into mRNA thus effectively canceling the frameshift and restoring the original RNA transcript. These "bandages" are bits of antisense RNA specifically made to bind to the "bad" parts of pre-mRNA. I covered this kind of therapy in an earlier post on gene therapy.

Does it work? So far, enough to give hope.

Goemans et al. [1] recruited 12 patients with Duchenne's muscular distrophy. Over the course of 12 weeks, the patients received weekly, dose-escalating

"weekly abdominal subcutaneous injections of PRO051 (from 0.5 to 10 mg per kilogram of body weight, with 3 patients receiving each dose) for 5 weeks. The specific increases in dose were determined after analysis of safety and dystrophin levels in muscle-biopsy specimens."

The lowest dose of 0.5 mg per kilogram showed no effect on RNA or protein expression. Exon-skipping RNA was instead observed in the higher-dose patients. Muscle biopsies were sampled at the end of the high-dose period and new dystrophin expression was observed starting from week 2, with increased signal as time and dose progressed. By the end of the twelve weeks the average distance walked in six minutes across all patients had increased by 35 meters, with some patients able to walk 65 meters farther than at baseline. Patients were also tested 2 and 7 weeks after the treatment, and most still showed similar dystrophin expression levels as right after the treatment.

Though a lot still needs to be done in order to defeat this disease, these results certainly set a much needed step forward.

[1] Goemans, N., Tulinius, M., van den Akker, J., Burm, B., Ekhart, P., Heuvelmans, N., Holling, T., Janson, A., Platenburg, G., Sipkens, J., Sitsen, J., Aartsma-Rus, A., van Ommen, G., Buyse, G., Darin, N., Verschuuren, J., Campion, G., de Kimpe, S., & van Deutekom, J. (2011). Systemic Administration of PRO051 in Duchenne's Muscular Dystrophy New England Journal of Medicine, 364 (16), 1513-1522 DOI: 10.1056/NEJMoa1011367

This picture was a "Rule of Thirds" exercise: find an interesting background, and have the main subject of your photo cover one third of the picture only, instead of positioning it in the middle. You can see how it immediately makes both subject and background more interesting. Focal length 26mm, shutter speed 1/25, ISO speed 100, F-stop 7.1

Tackling the mysteries of evolution: Peter Watts talks about consciousness, publishing, and his Hugo nominated novel Blindsight

One of the things I enjoy the most about running this blog is getting to know writers. I also get to learn about the infinitely many faces of the publishing world, like the new and ever-growing realm of self-publishing. Today, though, I have a story that is even more amazing, because amazing is the person I talked to: marine biologist Peter Watts is the author of the Hugo nominated novel Blindsight, as well as the Rifters Trilogy Starfish, Maelstrom, and Behemoth. Publisher's Weekly gave Blindsight a starred review, defining it an

"Intellectually challenging hard science fiction ... Watts puts a terrifying and original spin on the familiar alien contact story. Combines riveting action and a fascinating alien environment with a stimulating exploration of the nature of consciousness."

Peter is one of the most interesting writers I've talked to, so without further ado, please join me in welcoming Peter to the blog today!

EEG: For starters I'd like to know more about your research: I love marine biology, can you tell me a bit about what you do?

PW: Research-wise, these days, zippo. I used to work on the distributional/biophysical ecology of marine mammals, but that was before I ran screaming from academia in reaction to the inevitable craven political bullshit involved. For a while I worked for a research consortium investigating why marine mammal populations in the North Pacific/Bering had collapsed a few years after the US fishing industry moved into their feeding grounds. Turned out most of our funding came from the US fishing industry; what could possibly go wrong? I also worked for a private research association funded by the International Fund for Animal Welfare. Turned out I wasn't allowed to say anything that might reflect negatively on the animal welfare movement.

I'm told that somewhere, in some far-off land, scientists are not whores with data sets. Somewhere, people like me get to follow the data wherever they lead. I remain skeptical. If such a utopian realm exists, it does not lie within the bounds of marine mammalogy. So these days I'm pretty much a full-time writer. I still do the occasional bit of biostatistical analysis as an independent consultant -- migratory waterfowl stuff, mainly -- but it's been years since that was my primary source of income. At least with science fiction, you're supposed to make shit up.

EEG: LOL. I see. I guess I'm lucky, then, to be working on viruses instead of mammals. Though a decade ago saying that AIDS was caused by HIV was also something highly frowned upon.

Let's talk about your books. Blindsight is a fascinating read that touches on many scientific and philosophical concepts. Can you tell me how the story was born? Was it one concept in particular that intrigued you or a scene or... ?

PW: The question of consciousness -- not what it is so much as what it's good for, in a Darwinian sense -- has been rattling around in the back of my head ever since 1991, when I read an offhand comment Richard Dawkins made in an afterword to an anthology of ecology essays he'd edited. I can't remember what that book was called -- it had a pale blue cover with a picture of a wasp's nest on the front, if that's any help -- but Dawkins tossed off this remark to the effect that it was very easy to imagine a nonconscious meat robot that could do pretty much everything we do, so the functional utility of consciousness is thus one of the great mysteries of biology.

He obviously wasn't the first person to raise that issue; his iteration just happened to be the one I read at an impressionable age. As thought-fodder, it was both profoundly inspiring and profoundly limiting. Inspiring, obviously because sapience seems to be at the heart of what we are as a cognitive species, and we have no damn idea how it works. But limiting, too, because the question "What is it good for?" implies that it is, in fact, good for something. The question itself puts you in a box. Obviously self-awareness serves a purpose to the organism; surely natural selection would have weeded out anything so metabolically expensive if it didn't serve some vital purpose, yes?

So I went for years trying to think of what that vital purpose was. Finally I realized that nobody asks how a parasite benefits its host; the very question would betray an ignorance of what parasites are. And then it occurred to me that the very absence of function -- the idea that the core of what we most exalt about ourselves might in fact be an impediment, that the little guy behind the eyes is actually a tapeworm that the system would be better off without -- well, that's a much more dramatic punchline than the realization that, Oh, of course, we need self-awareness because we couldn't do X particular thing without it. So that's what I went with; it was consistent with the limited research I'd done, it was beautifully nihilistic, it would make a memorable point that readers could argue about. But I didn't really believe it. I figured there was some obvious function that just hadn't occurred to a dabbler like myself, and that any real real expert would shoot down that punchline in an instant.

It wasn't until I got to the copy-editing stage that it began to dawn on me that a significant number of those experts were coming to exactly the same conclusion. Lucky coincidence, eh?

I'd just add here that, having broken out of the "Must be good for something" box, there's a follow-up question that I find very helpful when dealing with those papers that do argue for useful sapience. Some are really ingenious; perhaps my favorite was a piece by a dude named Ezequiel Morsella, who claims that consciousness exists to mediate conflicting motor commands to the skeletal musculature. The question I always ask myself when such a mechanism is presented is "Okay, but is it possible to imagine a nonconscious agent that does the same thing?" I'm perfectly willing to accept that we use consciousness for a variety of tasks-- evolution is always grabbing whatever's at hand and repurposing it to some other task. So maybe we do use self-awareness for logical deduction, or muscle mediation, or the aesthetic appreciation of grapes for all I know. But to me, a more interesting question is always, can we imagine something that does all that nonconsciously? Would its solution to the problem be more efficient than ours? And would it kick our asses if the two of us ever ended up on an island with limited resources?

EEG: That's fascinating and indeed one of the hardest problems ever tackled by both science and philosophy. Though if I may add my two cents, I think the heart of the problem is that the question "What is it for?" in science is ill-posed. Take genetics, for example. So much work has been done looking for "causative" loci, attributing function X to locus Y, when in fact it's like trying to answer the question of why a stream chose exactly one path to come down from the mountain, out of a million possible paths.

Back to consciousness, I was quite intrigued, last September, by your observation on Too Hard for Science? that if you split the brain down the middle you get a split in consciousness with different tastes and opinions.

Which sort of brings me to the next question... In your bio you write: "Peter Watts has spent much of his adult life trying to decide whether to be a writer or a scientist, ending up as a marginal hybrid of both." Can you elaborate more on how the two worlds, science and writing, coexist in you?

PW: I've wanted to write SF (age seven) almost as long as I wanted to be a marine biologist (age five). To me, both pursuits are flip sides of the same coin: both involve experiments of a sort. You start with a premise, and (here it comes again) follow the data. The difference, of course, is that there are fewer constraints when writing SF: you don't have to spend ten years developing real-world expertise in your subject; you don't have to fellate NSERC or the NSC for funding; peer-review -- such as it is -- is generally a lot more forgiving. You're not saying "This is"; you're asking "What if it was?" But in both cases you're exploring questions about the way the universe works.

Of course in science fiction your answers are more likely to be wrong, because you generally don't have the requisite fine-scale expertise and nobody can predict the future. But in real science, your answers are less likely to be deep, because most science is step-by-step trudgery and the filling in of a million little holes in the knowledge base. It doesn't matter whether your data are more reliable: "What if the lachrymal secretions of herring gulls can be used as an index of heavy-metal contamination" just doesn't have the same zing as "What if the Internet developed a sex drive?"

(I'd also add here than I'm increasingly convinced that too much scientific expertise actually makes one a worse SF writer, simply because every time you have a cool idea, your own expertise squashes it flat with all the reasons why it would never work. You become strait-jacketed by your own knowledge of the state of the art.)

EEG: Ah, we're on the same page on this one. I've written in another interview that I truly believe that writing a story (any story, in fact, not just SF) is like solving a system of equations. Your variables are the characters, your initial conditions the premises, and then you just sit down and solve it.

Let me warp up with one last question: I'm curious as to why you have a free version of Blindsight on your website when the book is on the market...

PW: I myself went the Creative Commons route for two reasons. Short stories, out-of-print titles in my backlist had stopped earning money anyway. I was giving up nothing by posting them online, and by setting them free I was increasing my exposure to potential fans who might go on to buy my next book if they liked what they read. At the very least it would cost me nothing, and at most it could significantly increase my readership.

I set Blindsight free, however, while it was still in print (just a couple of months after it was released, in fact) and for entirely different reasons. It's pretty obvious that Tor had written it off as a failure even before it was released: one of the two largest retail distributors on the continent had chosen not to preorder any copies, so Tor slapped on a cheap-ass cover and put out a very small print run. Then the critics started raving about it, but of course because so few copies had been printed nobody could buy the damn thing; Blindsight was the weekly #1 bestseller in at least a couple of stores that didn't even have any copies‚ the greatest number of their orders was for a book they didn't even have in stock, because not enough copies had been printed to meet the demand!

You'd think at this point that Tor would've hustled out another print run, and they did in fact start talking about it. But then they decided to wait until all the physical stock had left their warehouses. Then, once that that happened, they changed their minds and decided to wait until the back orders had built up. They kept moving the goalposts.

At this point I had pretty much come to the conclusion that Blindsight was going to fail commercially no matter how many good reviews it got, simply because there were so few copies for sale. So I had a choice: it could fail commercially and be read by no one, or it could fail commercially and at least be freely available to anyone who wanted it. There was no "succeed commercially" option that I could see. So, with nothing to lose, I put it out in the Creative Commons— and hardcover sales nearly tripled the very next week. The rest is history: strong sales, numerous award nominations, multiple hardcover printings, and widespread overseas translations. Blindsight is being used as a required textbook in a couple of university philosophy courses, and even as a core text in a neuropsych course at the University of Miami. It's been a commercial and critical success beyond anyone's expectations, and there's no doubt in my mind that none of that would have happened if I hadn't resorted to a Creative Commons release.

It's important to recognize, though, that it wasn't the CC release per se that caused the boost in sales, it was the publicity that resulted from the CC release. My actions were covered by boingboing, and by high-profile bloggers like John Scalzi and Kathryn Cramer. If those folks hadn't taken notice, Blindsight would have languished. But giving one's stuff away is still a pretty rare strategy, and that makes it newsworthy, and that's why my strategy worked.

That's also why it won't work for very much longer. As more and more people jump on the CC bandwagon, this kind of move will become a lot less noteworthy. We'll have to come up with some other way of drawing attention to our work. But for now, and in this case, the Creative Commons did more than just boost my sales and get me wider recognition; it literally saved my career as a writer.

EEG: I'm really glad it worked because you totally deserved the success. Thank you so much for being with us today and for sharing your experience with us.

To find out more about Peter's books and work, check-out his website and his blog, where he muses about writing, publishing, and yes, of course, science, too.

Sickle cell anemia, malaria, and the heterozygote advantage

Hemoglobin is the oxygen-carrying protein found in the red cells of our blood. Patients with sickle cell anemia have a sickle form of hemoglobin. While healthy red cells are shaped like a disk pinched in the middle (a doughnut without a whole), in patients affected by the disease the sickle hemoglobin forms strands which cause the red cells to be shaped like a crescent. This causes all sorts of complications and risks: the sickle red cells are more rigid and increase the risk of ischemia and necrosis; the drop in hemoglobin can cause painful enlargement of the spleen, anemia, tachycardia.

Sickle cell anemia is caused by a single-base polymorphism, SNP rs334, in the hemoglobin gene. The "normal" allele is A, whereas the mutated one is T. As you know, we all carry two copies of each genes, so the vast majority of the population has AA at this locus, a few carry AT and very few TT. Heterozygous carriers of the SNP (people who carry the AT form) are, for the most part, not affected by the disease. The healthy gene allele produces enough healthy hemoglobin to compensate for the sickly one.

This is not uncommon in genetics: another example of disease that's only expressed when both gene copies are mutated is cystic fibrosis. You may carry the "mutated SNP", but so long as you have only one copy, you're not affected by the disease. The problem is when both parents are carriers: if the child inherits both mutated alleles, she will develop the disease. Now the question is: if this allele causes such a devastating disease, why has it not been wiped out by natural selection and/or genetic drift?

The answer lies in a concept called heterozygote advantage: if the one allele turns out to be advantageous in certain circumstances, then it will still be prevalent at a certain frequency in the population. For example, the allele that causes cystic fibrosis has been hypothesized to protect against cholera, typhoid, and diarrhea. In the case of RS334, the sickle cell anemia SNP, the mutant has been proven to confer an advantage against malaria:

"These deleterious mutations are maintained in the population in a state of balanced polymorphism because of the protective effect against severe forms of malaria conferred by the heterozygous states. [...] However, it is not clear what happens to these polymorphisms in areas where the selective pressure has become relaxed or is nonexistent altogether. In some cases, as in the Caribbean, the HbS mutation has been shown to continue to exist with unaltered frequency, despite the near eradication of malaria more than half a century ago [1].

In [1] Salih et al. looked at the prevalence of malaria in the population from two African villages, Hausa and Massalit. The two populations were of different ethnic origins, and in both malaria was endemic but mostly mild. Within the two populations, they looked at the genotype frequencies of the sickle cell polymorphism and used a simulation to predict its behavior. Although the sickle cell SNP conferred significant protection from malaria in both populations, they found a trend for a decrease of the RS334 allele frequency in Hausa and an increase of frequency in Massalit. They conclude that this effect may be due to the fact that

"In the Hausa village, this seems to be likely due to the low clinical burden of the disease, the population effect (possibly under drift) in addition to the deleterious impact of the homozygous allele, both conspiring against the maintenance of balancing selection. In the Massalit village, the relatively higher episodes of clinical malaria, in addition to a potential impact from visceral leishmaniasis (a disease with a higher fatality rate), may be responsible for the different selection profile."

[1]Salih NA, Hussain AA, Almugtaba IA, Elzein AM, Elhassan IM, Khalil EA, Ishag HB, Mohammed HS, Kwiatkowski D, & Ibrahim ME (2010). Loss of balancing selection in the betaS globin locus. BMC medical genetics, 11 PMID: 20128890

Blinding pain, simple truth: a professor of mathematics heals himself through Buddhist meditation

Husband, father, grandfather, and teacher, Richard S. Ellis is a professor of mathematics and an adjunct professor of Judaic studies at the University of Massachusetts Amherst. And, for the past few years, a promoter of Buddhist meditation through his book, Blinding Pain, Simple Truth.

How did a professor of mathematics end up writing a book on Buddhist meditation? It’s a fascinating story, one that I was lucky enough to hear in person since I’ve known Richard for over ten years now, and I was thrilled when he graciously accepted to share it here on Chimeras.

EEG: I know you’ve always been writing: papers, essays, novels, and more. Do you find that the writer in you is an essential part of the scientist, or are the two completely separate?

RSE: I love writing, and I’d like to put it in a wider context. My area of research in mathematics is the theory of large deviations, which studies random events having small probability and often significant effect. More broadly, a large deviation is any event defying expectation: a surprise, a revelation, a miracle. My activities as a scientist and as a writer have their roots in this theory because my life has been a large deviation in numerous ways, Jewish, literary, spiritual, and mathematical. A major example is the casual conversation at a bat mitzvah in 1981 that inspired my family and me to spend a sabbatical the next year in Israel, a visit that changed my life by putting me on a spiritual journey through Judaism, Torah, literature, and Buddhism that still continues.

The writer in me is definitely an essential part of the scientist. I don’t see a big difference between writing about mathematics and writing about literature or spirituality because in essence it’s all text. As I continue to write and discover new fields and new connections, I feel as if I am building a palace of mirrors in which everything reflects back on everything else. In this sense writing is an act of creation that brings light where there was darkness, order where there was chaos, and connections that previously were not seen.

EEG: You have so many interests. You are a professor of mathematics, an adjunct professor of Judaic studies, and you have published and taught courses in mathematics, literature, and Bible studies. What inspires your writing the most?

RSE: Let me answer by referring to the poem “so you want to be a writer?” by Charles Bukowski. In it he gives one view of the writing process: “if it doesn’t come bursting out of you / in spite of everything, / don’t do it.” This poem certainly expresses the initial, exhilarating inspiration that I have always felt while writing, the sense that I have something new and important and even life-altering to say. However, the poem minimizes the painstaking work required to polish a piece. I first felt “it” bursting out of me when I was an undergraduate at Harvard, writing an honors thesis on the figures of Apollo and Buddha in the New Poems of Rainer Maria Rilke. Under Rilke’s inspiration, I filled notebooks with my own poetry and published a few.

I continue to be inspired by the same feeling of exhilaration whether I discover a beautiful solution of a difficult problem in mathematics or understand a resonance between a poem of Emily Dickinson and a passage in the Torah or so quiet my mind that the deep spirituality of a Psalm of David reveals itself to me. The inspiration bursts forth, and I start to write in ever-widening circles, each new section putting previous sections in a new light, and I revise, motivated by the insight that language is inherently linear while what I am trying to capture is nonlinear. Finally, after much work, it crystallizes as I finally see how all the pieces interconnect and find the words to express these interconnections.

EEG: Please tell us how you discovered Buddhist meditation and how your book, Blinding Pain, Simple Truth, came to be.

RSE: The short answer is that I discovered meditation because of pain. In 1980 a therapist introduced me to relaxation techniques based on Buddhist meditation to deal with tension headaches. These techniques were miraculously effective. However, as soon as the headaches were healed, I stopped meditating and stopped listening to the wisdom of the headaches as I threw myself into an ambitious project of a research-level math book. Headaches returned twenty years later, in February 2000, and this time they were much worse, nearly destroying my career. Desperately seeking help from doctors but unable to find relief from the many pills they prescribed, I dealt with the pain by anger, avoidance, and fear, which only compounded my suffering.

After suffering for two and half years, in September 2002 I sought help from Jean Colucci, a psychologist who based her therapy on meditation and Buddhist teachings. My work with her set the stage for a transformative experience in the summer of 2003. At a meditation retreat I experienced the truth about the headaches and the suffering they had caused. This truth is so simple, yet so deep: it is not the pain that causes suffering, but the mental state associated with the pain. Through meditation I learned not to push the pain away, or to react to the pain with anger and fear, but rather to accept it. Accepting the headaches allowed them to become my best teacher, a wise guide who constantly reveals new insights about life and pain and suffering and letting go and love.

The wisdom about pain, suffering, and healing that the headaches revealed is the subject of my recently published book, Blinding Pain, Simple Truth: Changing Your Life Through Buddhist Meditation. My goal in writing it is to empower people who suffer from physical and emotional pain to heal their suffering and embrace their lives with equanimity, gratitude, and joy.

I started writing the book at the suggestion of a literary agent, who found me on the internet in 2003. My experiences with the headaches had been so profound that, as Charles Bukowski describes, the inspiration for the book burst out of my heart and my mind and my mouth and my gut. However, revising and polishing the manuscript took years. In 2007 the literary agent announced, without explanation, that she could no longer represent the book. After much effort and further revision, I was able to place the manuscript with Rainbow Books, which published it in 2011. As I have often joked, the quest to write a book on Buddhist teachings and find a publisher requires the full wisdom of Buddhist teachings to lead one through the labyrinths and past the ego-traps that make this quest such a challenge.

As the book describes, every day I am blessed by the gifts of infinite worth that meditation has bestowed upon me: it calms my mind, enables me to connect with the wisdom of my body and the wisdom of the present moment, allows my body’s natural healing powers to flourish, and has freed me from the prison of chronic pain into a vast landscape of equanimity and peace. The book is also an invitation to begin meditating. It is a practice with potentially infinite rewards that can become an all-encompassing approach to people’s lives as it has become with mine.

EEG: That is truly amazing. Thank you, Richard, for sharing your story with us and for spreading the word through your book.

Richard S. Ellis has published numerous papers in mathematics and is the author of two research-level math books. He has also published poetry and articles on the Torah, literature, art, and anti-Semitism and the Holocaust. To learn more about his recently published book, Blinding Pain, Simple Truth: Changing Your Life Through Buddhist Meditation, check out his website at RichardSEllis.com. You can also email Richard at rsellis (at) math.umass.edu. Information about his work and interests is available at his webpage.

Having kids wears you out? Same holds for telomeres. In zebra finches.

One of my most popular posts on the blog has been The Immortality Paradox, in which I discuss telomeres, aging, and cancer. Telomeres are the ends of he chromosomes, a bit of non-coding DNA that naturally wears off as cells divide and as we age. Once the telomeres reach a certain critical length the cell stops dividing and eventually dies. As a consequence, telomeres length varies across age groups but, even within the same age group, it varies from individual to individual. So, it becomes natural to ask: is this variation in telomeres length correlated to longevity?

A new study published in PNAS [1] seems to indicate that it is. Now, my personal disclaimer is that I'm always a little skeptical about associations with longevity because there are so many factors and confounders that it's really hard to extrapolate meaningful p-values. However, this study was done in birds (Taeniopygia guttata, or zebra finches), which makes it less prone to bias than a human study. In fact, the authors cite various studies that attempted to correlate telomeres length an longevity in humans but yielded mixed results. Most importantly, these earlier studies had not monitored telomeres length since an early stage in life, something that is critical in order to account for environmental factors that have been shown to accelerate telomere shortening.

In this study, Hedinger et al.

"examined telomere length in red blood cell samples from early in life (at 25 days) and at various points thereafter in a group of zebra finches (n = 99) that were allowed to live out their natural lifespan (ranging from 210 days to 8.7 years). We also examined the effect of reproduction on adult telomere length, by experimentally manipulating whether, and how often, individuals were allowed to breed. These data enabled us to uniquely examine the relationship between telomere dynamics from early in life and total lifespan and reveal that telomere length in early life is a highly significant predictor of the age of death."

While they found no differences between genders, Heidinger et al. did record a decrease in telomere length with age, which was most marked during the first year of life. Interestingly, they also found that telomere shortening was accelerated in birds engaging in reproduction. (When parents say kids make them age faster, they mean it!!) The effect, though, did not persist, and at the next time point the effect of reproduction on telomere length had weaned. Of course, the most interesting result was the significant correlation between telomere length in early life and lifespan. It is important to note that the highly significant correlation was with the measurement taken early in life: length measured at later time points didn't have such a strong predictive effect.

"We found telomere length at 25 days to be a very strong predictor of realized lifespan (P < 0.001); those individuals living longest had relatively long telomeres at all points at which they were measured. Reproduction increased adult telomere loss, but this effect appeared transient and did not influence survival. Our results provide the strongest evidence available of the relationship between telomere length and lifespan and emphasize the importance of understanding factors that determine early life telomere length."

The authors underline what still remains to be seen:

"Whether telomere length change itself plays a directly causative role in determining the pace of decline and age of death is an active area of research. Several mechanistic routes have been identified, mainly from in vitro studies, whereby shortened telomeres can accelerate aging and reduce longevity, primarily involving activation of cellular checkpoints of apoptosis, cell cycle arrest, and impaired stem cell and tissue function."

One thing is certain: any analogous study to be carried in humans should measure telomere length very early in life because, as this study shows, if individuals with shorter lengths die earlier, a sample of lengths measured later in life would already be skewed towards longer length (since individuals with shorter length would have already died) and hence the results would be inconclusive.

[1] Heidinger, B., Blount, J., Boner, W., Griffiths, K., Metcalfe, N., & Monaghan, P. (2012). Telomere length in early life predicts lifespan Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1113306109

Chaperon proteins do more than... chaperon

The full human genome was typed for the first time in 2003. Ever since, there has been a "hunt" for mutations and, more in general, associations between genotypes and phenotypes. As I have pointed out multiple times on this blog, things have turned out more complicated than originally anticipated: what happens between DNA and proteins (what we could consider the "end" product) is still very much a "black box" in which epigenetic changes and RNA editing can completely turn around the outcome. Furthermore, the interaction between genes and mutated loci can either increase or decrease the likelihood of certain phenotypes, given the genotype.

Take molecular chaperones, for example. These are proteins that assist the folding and unfolding of other macromolecules. They are typically involved in protein folding, but they also assist the assembly of nucleosomes from folded histones and DNA in the nucleus (see this earlier post on chromatin) and thus, by changing the topology of the nucleus, they play an important role in regulating gene expression.

A study published in the last issue of Science [1] looks at the role of chaperon proteins in compensating for deleterious mutations in Caenorhabditis elegans. Casanueva et al. found that worms with higher expression of protective chaperon genes were more resistant to deleterious mutations: worms with a potentially deadly mutation received a mild heat stress when still larvae. The heat stress promoted the expression of protective chaperon genes, and in some of the worms this prevented the deleterious misfolding of proteins, resulting in a 35% increase in chance of survival.

"We subjected animals to a transient heat shock as larvae to induce a stress response, allowed them to develop to adults, and examined the proportion of individuals affected by late-acting mutations. When a mutation was chaperone-dependent, a mild environmental challenge stimulated a reduction in penetrance."

Paradoxically, they also found that individuals with higher chaperon expression reproduced less. Why, if the higher expression seems advantageous and protective? Casanueva et al. hypothesize that the net effect is to maintain a heterogeneous population in levels of expression, and this is more advantageous to the survival of the population than homogeneous levels of gene expression. In other words, what is advantageous to the individual is not necessarily advantageous to the species.

From the paper abstract:

"The induced mutation buffering varies across isogenic individuals because of interindividual differences in stress signaling. This variation has important consequences in wild-type animals, producing some individuals with higher stress resistance but lower reproductive fitness and other individuals with lower stress resistance and higher reproductive fitness. This may be beneficial in an unpredictable environment, acting as a “bet-hedging” strategy to diversify risk. These results illustrate how transient environmental stimuli can induce protection against mutations, how environmental responses can underlie variable mutation buffering, and how a fitness trade-off may make variation in stress signaling advantageous."

Of course, it's not clear how this could apply to humans. However, it does prompt caution when treating a person's full genome as a key to disease risks. We are still far from unraveling the complete interactions between genome, epigenome, and proteome, and, as I've often said before, Mother Nature has made us far more complex than any of our models can predict.

[1] Casanueva, M., Burga, A., & Lehner, B. (2011). Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans Science, 335 (6064), 82-85 DOI: 10.1126/science.1213491

Photo: it's not what it looks like! This is eggs, water and vegetable oil all mixed in a blue bowl to make brownies. Seriously. You just set the bowl under a lamp and suddenly it behaves like a mirror. Eventually the mix turned into brownies, but not before my daughter and I had a little fun shooting pictures.

The curse of drug-resistant TB strains

Tuberculosis (TB) is a disease caused by a number of strains of mycobacteria. It affects mostly the lungs with chronic, bloody cough and fever. It can remain asymptomatic as a latent infection, though about 10% of these latent infections eventually progress to active disease.

The two most common drugs used to treat TB are isoniazid and rifampicin, but unfortunately new mycobacteria strains (called MDR strains, which stands for multi-drug resistant) have emerged that are resistant to both these powerful drugs. In other words, the pathogens have developed certain mutations that make them "immune" to the drugs. As with HIV, common thought is that these drug-resistant strains emerge during the course of the treatment in single individuals as a result of the selection pressure induced by the drugs. This is also reinforced by the fact that typically drug-resistant mutations confer a cost of fitness: though able to escape the drugs, the mutated strains tend to reproduce less quickly and/or are not able to be transmitted.

Unfortunately, that's not always true. A study published by Nature Genetics in December [1] showed that MDR TB strains do not show a fitness cost and that the most common drug-resistant mutation is present in the population with a wide variety of compensatory mutations. These are additional mutations that compensate for the loss of fitness by working in antagonistic epistasis to lessen the structural and functional instability of the affected proteins.

Comas et al. compared

"the genome sequences of ten paired clinical rifampicin-resistant isolates to the genomes of the corresponding rifampicin-susceptible isolates recovered from the same infected individual at an earlier time point. We identified all nonsynonymous and intergenic mutations found only in the rifampicin-resistant genomes. In addition, we experimentally evolved six laboratory-derived rifampicin-resistant mutants from rifampicin-susceptible ancestors during 45 weeks of serial subculture in the absence of rifampicin."

They showed that

"The high frequency of compensatory mutations in strains from Abkhazia/Georgia, Uzbekistan and Kazakhstan is consistent with the success of MDR strains in these regions, where up to 50% of individuals with TB are estimated to carry MDR strains compared to a global average of only 3%."

These findings are particularly relevant for TB treatment policies: isoniazid and rifampicin have been used not only to treat infected patients, but also as a preventive measure for people visiting countries with high TB prevalence (as for example peace corps). Furthermore, people are treated as soon as they become TB positive, but for the most part these infection are latent and all genetic information we have on TB is from active infections. There's no way to know if these drugs are effective until the infection becomes active. If these MTR strains are not only fit but also transmissible, the persistent use of these drugs will have the net effect of allowing breeding and spreading drug-resistant strains, resulting in a rise of non-treatable infections.

"In conclusion, our results suggest that the acquisition over time of particular mutations in rpoA and rpoC in rifampicin-resistant M. tuberculosis strains leads to the emergence of MDR strains with high fitness. Furthermore, our data show that these mutations occur at high frequencies in clinical settings, particularly in hotspot regions of MDR TB9. Additional studies are needed to determine whether MDR strains of M. tuberculosis with mutations in rpoA or rpoC have increased transmission rates and how these mutations contribute to the success of these strains. Use of targeted genotyping of these mutations will enable TB control programs to focus on the most transmissible MDR strains. Our findings also suggest that mathematical models that aim at predicting the future of the global MDR TB epidemic should take into account the effects of compensatory mutations as well as the time necessary for such mutations to emerge."

[1] Comas, I., Borrell, S., Roetzer, A., Rose, G., Malla, B., Kato-Maeda, M., Galagan, J., Niemann, S., & Gagneux, S. (2011). Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes Nature Genetics, 44 (1), 106-110 DOI: 10.1038/ng.1038

Photo: making progress with my macro lens! Canon 40D, focal length 100mm, shutter speed 1/100, F-stop 14, ISO speed 100.

Stories born in the ER: best-selling author CJ Lyons talks about writing and her decision to self-publish

She's been called a "master within the genre" (Pittsburgh Magazine) and her work has been praised as "breathtakingly fast-paced" and "riveting" (Publishers Weekly) with "characters with beating hearts and three dimensions" (Newsday). New York Times Bestseller CJ Lyons is the author of many cutting edge thrillers, including the award-winning, critically acclaimed Angels of Mercy series (LIFELINES, WARNING SIGNS, URGENT CARE, and CRITICAL CONDITION). Where does she get the inspiration for all these stories? In the ER, of course! Quoting from her bio:

A trained in Pediatric Emergency Medicine, CJ has assisted police and prosecutors with cases involving child abuse, rape, homicide and Munchausen by Proxy. She has worked in numerous trauma centers, on the Navajo reservation, as a crisis counselor, victim advocate, as well as a flight physician for Life Flight and Stat Medevac.

I'm so excited to have CJ as my guest today!

EEG: How much of your fiction was inspired by your work in the ER?

CJ: All of the characters in my work are fictional, but the medical cases and the emotions surrounding trauma, violence, and loss are real. Well, as real as you can get and still be entertaining. It always surprises me when an editor cuts something because no one would believe it but it's something that really happened. I guess truth really is stranger than fiction.

EEG: Can you share more about what happened when, during your residency, a fellow intern was murdered and how this inspired you to turn to crime fiction? (You hint to it in your bio).

CJ: Halfway through my internship year at Childrens Hospital of Pittsburgh one of my fellow interns was killed in a very horrendous way. The police apprehended the killer, thanks to good forensic work and cooperation of several agencies. But we interns were still traumatized and left to mourn and make sense of this terrible thing while simultaneously caring for infants and children entrusted to our care and trying to help families cope.

For me, writing helped me to heal. I wrote my first crime fiction novel, a romantic thriller called BORROWED TIME (which recently hit the USA TODAY Bestseller list). Before I'd always written SF/F, but after Jeff died I needed to explore good/evil, justice/truth more than I needed the escapism my previous novels provided me.

EEG: Wow, that's chilling. I noticed that many of your recent titles are self-published. I'm curious as to what prompted you to turn to self-publication and how it's turning out for you.

CJ: After signing with a NYC publisher I thought I had it made. But after my first book came out I realized my readers wanted more books faster than NYC could publish them. So late 2009 I began to self-publish via Kindle and then Smashwords and Barnes and Noble.

At first it was a way to use those e-books as promotional tools. It was easier to give them away than print books and I could adjust the price. Then a year later, everything changed. E-books grew exponentially, my fans were loving the new books, and I was on track to make more money than I was making from my NYC published books, despite their being bestsellers.

A win/win for all… in fact, I believe the future of publishing will be a partnership between traditional publishers creating books that are events, keepers that readers treasure and display on their bookshelves, agents selling subrights, booksellers handselling both print and e-books, and writers giving their fans what they want and making a living wage. It's a true Renaissance for writers and book-lovers everywhere!

EEG: That is so interesting! The publishing world is indeed changing, and faster than we realize. Thanks so much for sharing your experience with us. And yes, it's absolutely fantastic to be able to click and one second later read. Makes you want more!

To find out more about CJ and her "Thrillers with a Heart," check out her website at www.cjlyons.com.

A lot happens in the blink of an eye!

Do you have recurrent nightmares? I do, especially when I'm under a lot of stress. I often dream of missing a train. The setting, location, company and place I need to reach change every time, but the common factor is always the frightening sense of having missed the train and not being able to make it. Another recurrent nightmare I have is that the light is so bright I can't keep my eyes open. So I start blinking faster and faster but I can't see a thing and end up missing something very important.

Blinking seems to be such an important task that our body takes care of constantly, as important and essential as breathing. And yet we hardly ever think about it. Under normal conditions, we blink spontaneously 10 to 15 times a minute. We blink both eyes at the same time, which may seem obvious but (maybe you already knew this, I didn't!) it's unique to mammals. Birds, for example, blink one eye at the time and this prevents loss of visual information. In fact, blinking causes a momentary loss of vision that lasts lasts 100 to 150 milliseconds -- a mini black-out that happens constantly as we stare at things and yet we hardly ever notice it, in ourselves, or in others.

Another thing our eyes smoothly cope with is saccades, quick, simultaneous movements of both eyes. When I rapidly move my camera and press the shutter, not matter how fast the shutter speed, I get a blur. However, our eyes move all the time and yet what we perceive is a constant, flowing image.

We compensate these visual disruptions with two similar mechanisms: blinking suppression and saccadic suppression -- basically, visual sensitivity is suppressed immediately prior to and during both blinking and saccades. The two mechanisms are often coordinated in order to minimize downtime in visual processing. Unfortunately,

They are challenging to study because any brain-activity changes resulting from an extra-retinal signal associated with the blink motor command are potentially masked by profound neural-activity changes caused by the retinal-illumination reduction that results from occlusion of the pupil by the eyelid [1].

In order to measure the neural consequences of blinks on visual function one has to bypass the physical consequences of eyelid closure. In other words, you want to stimulate the retinae maintaining the eyes open. How? Via the mouth, as Volkmann et al. [2] showed in 1980: you insert a light probe in the mouth, the light passes through the palate and stimulates the retinae without forcing eyelid closure.

In [1], Bristow et al. use the same technique to stimulate both retinae while measuring brain activity through fMRI. They also used opaque goggles to ensure that retinal illumination remained constant throughout the experiment, whether the eyelids were open or closed. By doing this, they could see what parts of the brain were responding to the retinal stimulation independently from the change in illumination caused by eyelid closure. They find that

Whereas it might have been supposed that blink suppression is a purely low-level visual phenomenon, mediated solely by retinotopic visual areas, our whole-brain analysis surprisingly revealed that activity evoked by retinal stimulation in parietal and frontal cortices was also suppressed by blinking.

Thus, one possible interpretation of our findings is that the observed suppression of these parietal and prefrontal regions during blinking represents a neural mechanism underlying the lack of awareness of the changes in visual input that normally occur during a blink. Specifically, it may account for the lack of awareness of the percept of the eyelid descending across the pupil and the resulting reduction in retinal illumination.

Their experiment also proves the deep connection between saccade suppression and blinking suppression, as they conclude:

In summary, our data demonstrate that responses to retinal illumination are suppressed by blinking in retino-topic visual area V3 and in parietal and prefrontal cortices, whereas in the absence of retinal stimulation, we identified a positive blink-related signal in early visual areas LGN–V3. We propose that these findings represent a neural signature of blinking associated with the blink motor command and may go some way toward explaining both the neural mechanisms underlying the visual-sensitivity loss, known as blink suppression, that occurs during blinks, and why they go unnoticed. Our findings parallel recent observations of saccade-related changes in activity in visual cortex during saccades, suggesting that blink suppression and saccadic suppression may indeed share common neural mechanisms.

Finally, I'd like to mention a more recent paper by Bonfiglio et al. [3], which used EEGs to look at brain waves during blinking. Brain EEGs typically show oscillations that are classified based on their frequency. Spontaneous blinking modulates two oscillations in particular, alpha and delta, which are thought to be involved in the automatic mechanism of maintaining visual awareness. In their study, Bonfiglio et al. studied the alpha oscillations and postulated that

a) an early blink-related synchronization represents the short-term memory maintenance of the last visually perceived trace of the surroundings; b) the alpha blink-related desynchronization is associated with the comparison between the newly perceived image of the environment and its mnestic representation.

[1] Bristow, D., Haynes, J., Sylvester, R., Frith, C., & Rees, G. (2005). Blinking Suppresses the Neural Response to Unchanging Retinal Stimulation Current Biology, 15 (14), 1296-1300 DOI: 10.1016/j.cub.2005.06.025

[2] Volkmann FC, Riggs LA, & Moore RK (1980). Eyeblinks and visual suppression. Science (New York, N.Y.), 207 (4433), 900-2 PMID: 7355270

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Photo: trees in downtown illuminated over the holidays. It was freezing cold, but the sky was so pretty and I just couldn't stop shooting. I could hardly feel my hands when I got home.