A couple of things

Although I haven't posted to this blog in some time, I thought this would be a good time to get back in the game.

For the moment, I just wanted to post a couple of my current ventures.

I'm part of a team of graduate students organizing a symposium on protein science at Purdue. You can read more about this venture here: https://purdueproteins.wordpress.com/

I'm the content provider and writer for the website, in addition to my other roles on the organizing team. We're super excited to organize this symposium for the Purdue community, and have an excellent group of invited internal speakers as well as a superb keynote presenter, Dr. Tony Kossiakoff from the University of Chicago. Please check back on the website for more information, details of our program are forthcoming!

I'll also be reprising my role as a blogger for the 2015 Biophysical Society Annual meeting in a few short weeks in Baltimore. I loved writing about the meeting last year in San Francisco. You can read my past entries here: https://biophysicalsociety.wordpress.com/author/satchal/

Finally, for those of you interested in the structural biology of membrane proteins, we just had our first paper accepted on our studies of the bacterial ribose transporter. This is a long-standing project in the lab of my advisor, Dr. Cynthia Stauffacher. We have sought to better understand the function of this primary active transporter: how it receives its substrate, how it utilizes energy, and how the three protein components interact.

We find this transporter particularly interesting because its organization resembles that of a human chloride channel, CFTR, whose defunct form is implicated in the disease cystic fibrosis. This paper details our initial characterization of protein-protein interactions during transport. The early version is up, and you can read it here: http://www.jbc.org/content/early/2014/12/22/jbc.M114.621573.full.pdf+html
I'm particularly excited about this paper because, not only is it my first publication, it was written by me. It's been a thrilling feeling to see my own words published in an excellent journal.

I'll be back again soon.

Blogging at the Biophysical Society Annual Meeting!

This is a bit of shameless self-promotion, but I've been blogging for the 58th Annual Meeting of the Biophysical Society in San Francisco, CA. The meeting has been fantastic, a wonderfully educational opportunity with a great chance to network.

I've posted a few times so far. Topics include my experience as a first-time presenter and my thoughts on the next 100 years of X-ray crystallography and retroactive crowd-sourcing. I'll upload my posts here at some point, but for now, here is the link.

http://biophysicalsociety.wordpress.com/author/satchal/

Shameless self promotion

Many thanks to Scicurious for the opportunity to write for her blog.

My inaugural piece:

http://blogs.scientificamerican.com/scicurious-brain/2012/12/19/scicurious-guest-writer-x-ray-crystallography-100-years-at-the-intersection-of-physics-chemistry-and-biology/

I highly recommend her work as well, great articles on neuroscience research.

http://blogs.scientificamerican.com/scicurious-brain/

Let's Re-Elect President Obama

Finally, here we are! Remember, remember the 6th of Nov...wait, what? No more soaring rhetoric? Fine, fine, let's get to the point.

President Obama today deserves re-election. His nearly four years in office have largely echoed an overarching theme of his adult life - we'll get to that shortly. The argument that his legislative accomplishments have been few or ineffective is tired and wholly inaccurate. If there is an area he has been shockingly poor in, it has been successfully communicating his laws and ideas - quite stunning for an otherwise effective orator. We'll remember the 2012 elections not just for Romney's deceptive campaigning, but also for Bill Clinton's brilliant presentation of President Obama's accomplishments, distilling all of the specious arguments to give us the essence of what has largely been good policy.

For liberals like myself, gripped by the passion of 2008, it is easy to find disappointment in President Obama's record. He never proposed a single-payer option during the fight for health care reform - to be fair, he never supported this - and came to the negotiating table with a plan largely consisting of Republican ideas, which was the essence of the ACA he passed in 2010. His administration largely embraced Wall Street - from Tim Geithner to Robert Rubin to Lawrence Summers - and effectively diluted the Dodd-Frank reform bills and the Volcker Rule. For this effort, Wall Street has turned its back on him (Obama might have bear-hugged Wall St, but Mitt Romney is Wall Street). His expansive use of drone attacks and continued use of Guantanomo Bay has placed him nearly to the right of Dick Cheney. I highly recommend the Rolling Stone's Matt Taibbi and the Nation's Jeremy Scahill for anyone interested in good research on these topics.

Yet President Obama's signature accomplishments have echoed the overarching theme of his adult life. In the mid-1980s, Obama left a lucrative career as an analyst for Business International to become a community organizer on the south side of Chicago. His initial efforts were frustrated by failure, yet he stuck to his guns, driven by the simple idea that everyone should play by the same rules, and that the poor of Chicago didn't have the same opportunities as others. In the Me-First 1980s of Ronald Reagan, those of his ilk stood out in stark contrast to many of that generation. Those ideas have inspired his political career, and though it may not be readily apparent, his proposals have mostly echoed this theme, that everyone deserves a fair shot and everyone should play by the same rules - whether it his expansion of Pell Grants and Medicaid, support for Head Start, and taking student loans out of the hands of big banks. He has ended "Don't Ask Don't Tell" and proposed marriage equality for all Though he initially took the teeth out of Wall Street reform, he has more recently come out in favor of tighter regulations. I highly recommend Rachel Maddow's brilliant outlay of all of President Obama's legislative accomplishments.

There is much to be optimistic about for Obama's second term. The economy is poised for a major recovery and his signature legislative accomplishment - the ACA - goes into full effect. The so-called "fiscal cliff" will, I think, prove to be a stroke of genius, providing Obama with an effective bargaining tool. It will give him the opportunity to propose and enact his new tax plan, as well as implement of variety of domestic initiatives (in particular, I look forward to his promise of increasing NSF and NIH budgets). I think we will see a renewed push for the DREAM Act, continued progress towards immigration reform (there is legislation that is sitting in Congress to give work permits automatically for those completing advanced degrees in American universities), follow-through on equality for marriage, and finally some serious talk about climate change.

I don't think there could be a starker contrast between two candidates. President Obama is a serious, thoughtful, introspective, self-critical, and deliberate leader, and deserves our votes. The world over is hoping we re-elect President Obama. I've done my part; I hope you do, too.

Update: I've often thought about Obama's contention that Reagan transformed America in ways Bill Clinton did not. This has been widely interpreted as praise of Reagan and a slight on Clinton, and perhaps the latter is true. Increasingly though, I doubt the former analysis. I think Obama is being critical of this transformation, that Reagan's policy and rhetoric produced this irrational mistrust of government, that somehow government jobs are not "real", and that taxation is merely to impose financial restrictions on job "creators". Obama has a practical view on what the government can provide - his record is proof of this - and I think it troubles him how Americans today largely doubt its capability to do so - thanks in no small part to Reagan. 

Are you smarter than an infant?

Not likely. Check out this interesting article from Slate.

Perhaps most interesting is the idea that we become less able to take in information as we get older, or that we require ourselves to focus on particular tasks at a time (this may also explain why infants learn language more effectively that adults). Is it also possible that we are using less of our brains as we get older (most people assume we only use about ten percent of our brains)?

Who Decided the Definition of Life?

In the wake of President Obama lifting the Bush administration's bans on stem cell research, the ethics of "destroying life" to save lives has been discussed ad nauseum. Typical of the rhetoric being produced is this article by the Tribune's John Kass. After comparing the use of embryos to help treat degenerative diseases to a dying man, Kass closes with an open ended remark: "And what happens to us, as we take other lives, in order to live?"

I think the most pertinent issue here is what our operating definition of life is. Clearly, what Kass and many theologians and political conservatives refer to is human life. At the same time, we're discussing the ethics of scientific research, and in its most reduced form, all life is sustained by the metabolic processes of the living cell. From a scientist's perspective, life is defined by the ability of the cell to efficiently sustain these functions.

However, if this is our operating definition, then what we take as life, and the protections we offer it, has to be extended much further than human life. In terms of the cell, the difference between human cells and those of animals, plants, bacteria, and other organisms is not much more than variations in genetic and protein content. And yet, we don't have much of a problem destroying bacterial, yeast, plant, and animal life for the purpose of scientific research. Our understanding of life would not have been made possible without these experiments, and so we tolerate some destruction for our ultimate benefit.

What, then, makes human life different from other life? Almost all religions have a concept of soul, which is the standard in differentiating humans from everything else. This is usually what the counter arguments to stem cell research, and the sanctity of human life, refers to. And yet, in a secular society, this isn't an acceptable operating standard. Not all religions limit the concept of soul to humans only; in Hinduism, essentially every organism, from the merest Protista to the most complex animal, contains some sort of soul. On the other hand, atheists deny such a concept entirely. It would be un-Constitutional to use one soul standard over another in the United States.

Given that, our official definition for life should more closely resemble the scientific one. Stem cell opponents will argue this will lead to all sorts of human experimentation and human cloning, the sort of behavior we associate with science-fiction stories. I don't buy this. Humans appear to have built-in moral sensors, and appear to find reprehensible any experimentation involving a human well-developed enough to resemble one of our species (there are exceptions to this, and it is that minority that has helped create this debate). With stem cells, we are utilizing a mass of cells that represents about 4-5 days of growth post-fertilization. The mass can hardly be differentiated from a colony of bacterial cells, and yet contains the potential to improve the quality of life of many fully-formed human beings.

We tolerate the destruction of life continuously to benefit our species. Is this sacrifice not worth the outcome? Don't take my word for it; next time you meet a sufferer of diabetes, Alzheimer's Disease, or Parkinson's, ask them how they would enjoy a life without these debilitating afflictions.

Excrement from the Right

Charles Krauthammer, come on down! Your columns continue to provide me with blog-fodder. His latest piece, "Obama's Science Fiction", is in tone more reasonable than his previous swill, but no better in content (except to fertilize my lawn with, perhaps). I didn't want to be merely reactionary in this space, but the recent spate of conservative bilge has prompted my hand.

Krauthammer continues to assume scientists lack moral values. I can't credit him with authorship of this; I've heard these arguments from the right for years, and Bush made it part of his public policy. I find the following statement particularly vapid.

"Science has everything to say about what is possible. Science has nothing to say about what is permissible."

Actually, scientists agonize over ethical decisions all the time. In fact, it's a fairly significant component of all grant applications, which provide the lifeblood of scientific research (that's money). However, this is the usual argument from conservatives, that morality and science are mutually exclusive. While oversight of all major decisions is important, and I think ethical review boards have a lot of value, the implication that people intelligent enough to author such research lack the same brain power to consider ethical implications is hogwash. Of course, there is always a small minority that ruins things for the rest of us, although the South Korean researcher a few years ago who claimed to have cloned humans successfully was proven to have made a fake claim.

It's also worth mentioning the Obama plan doesn't allow federal funding for unfettered stem cell research. Government funds cannot go to expanding the number of stem cell lines; rather, they can go towards experiments involving lines that have been obtained from privately-funded research. This was what was banned by Bush, and was effectively the United States' stem cell policy under Clinton.

The impression one gets from reading Krauthammer is that he opines that Bush's arguments (if they can be justified as such) were substantive and "morally serious" while Obama's are flippant. If that's indeed the case, perhaps the Post should consider a stricter drug-testing policy for its employees.

Apparently, science is amoral...

...Or, at least, scientists are, or so claims a Slate columnist.

The whole premise of the article (comparing George Bush's use of torture to Obama lifting the ban on stem cell research) is a joke. In particular, I found this paragraph particularly vile.

"The same Bush-Rove tactics are being used today in the stem-cell fight. But they're not coming from the right. They're coming from the left. Proponents of embryo research are insisting that because we're in a life-and-death struggle—in this case, a scientific struggle—anyone who impedes that struggle by renouncing effective tools is irrational and irresponsible. The war on disease is like the war on terror: Either you're with science, or you're against it."

This is fairly typical conservative spin. It represents all that is wrong with right wing of America: they'll defend you until you're born, and then you're on your own. In reality, we should be doing all we can to fight debilitating degenerative diseases. Lifting the bans on expanding the lines of available stem cells is a critical first step, but we still have a long way to go.

Embryonic stem cells are those that divide, differentiate, and specialize into all of the cells in our bodies. The brilliance of it comes from the fact that these cells are all genetically the same, and as such receive or produce some signals that cause them to become all of the various tissue types (brain, bone, skin, liver, heart, lung, etc.) in our body. Significant challenges remain to actually getting these cells to divide into particular tissue types, and then finding ways to incorporate them into the bodies of those suffering from degenerative diseases. Should we ever overcome these challenges, we may be able to cure diabetes, Alzheimer's, and MS (just to name a few).

Is this not worth the commitment to the research? The moral argument really doesn't hold here. The embryos are not derived from the eggs in a woman's body that do eventually become a person. Rather, they are derived from in vitro fertilization from eggs given by a donor's informed consent. These cells, obtained after 4-5 days of growth, are developed in a specialized in vitro fertilization clinic; bottom line, these cells are never meant to be people, and are never going to be.

And yet, they consist of the means to cure these debilitating diseases, diseases which cost people their quality of life and certainly have a great social and economic burden to all of us (this impact would make a great follow-up study). This really isn't a question of "Are you with us or against us?" Science will always continue to evolve and improve its methods; if one technique doesn't succeed or isn't allowed, others will be explored (as they have been). The primary objection to this one isn't valid, and kudos to President Obama for recognizing it, and not governing by religious ideology.

Un-intelligible Design

Intelligent design proponents have long argued that certain features of the universe and living things are best explained by an intelligent cause.

If that is indeed the case, what a cluttered mind that cause must have.

When the human genome project was completed a few years ago, one of its most stunning revelations was just how few genes we had, roughly 30000 (as opposed to 100000, a number fitting a seemingly complex organism such as ourselves). To put this into some context, the roundworm, Caenorhabditis elegans, a popular model organism for biological studies (particularly development), has about 20000 genes. Drosophila, the fruit fly used widely in genetic studies, has about 16000 genes.

More interestingly, the coding regions of our DNA (the genes that code for the proteins and RNA that are the business end of genetics) make up around 1.5-2% of our entire genome. So what about the rest of our DNA?

Much of the remaining 98-99% of "non-coding" sequences consists of repeated sequences and redundancies. Most fascinatingly, a large chunk of the genome contains pseudogenes - dead copies of genes we don't use. On the face of it, this appears to be a remarkably inefficient way of organizing - or creating, if you will - the portion of the cells that is mostly responsible for who and what we are. If some entity was in charge of putting all this together, then it did a stunningly poor job.

Really, what our understanding of the genome, post-Human Genome Project, provides for us is perhaps our most relevant and comprehensive historical document. Dead copies of genes aren't there because a creator thought it would be fun; they are once-functioning remnants of evolution that allow us to trace our journey along this pathway. By studying them and comparing them with other organisms, we may be able to improve our understanding of evolutionary relationships.

This is essentially the next major challenge following the completion of the human genomic sequence. By a process called gene annotation, we can attach relevant biological information to these genes. Potentially, by better understanding pseudogenes, we may be able to reconstruct, from a genetic point of view, how we arrived at the point we did. It will provide a fascinating look at the molecular basis, and consequences of, natural selection.

The best comparison for this process may be the evolution of Microsoft Windows. Since it was initially produced in the early to mid-1980s, the Windows' code has been added to and updated, producing a behemoth that perhaps no one but the most hardcore techie geeks could appreciate. By and large, many of the problems and complaints people have with Windows is this architecture, which has led to a cluttered and (seemingly) poorly organized code. And yet, the operating system survives and thrives, problems and all (perhaps due to good marketing, but hey, that's how survival of the fittest works). And while the cluttered code has produced the best-selling operating system on the planet, I'm sure anyone would deign to call it intelligently designed.

I've found the simplest explanation is generally the best one, for many things. Rather than believe a creator has produced a genome that is nearly 99% non-coding, and significantly redundant, it simply makes more sense that our genetic code has evolved and improved by natural means over millions of years. Of course, it is perhaps with chagrin that some folks must accept being evolutionarily linked to chimpanzees and pigs. However, we've just come off of eight years of being led by George Bush; if anything, it is the the chimpanzees that should be upset by the comparison.