Of home labs and fun of science

A bit late to the party, I just noticed - thanks to a tweet from Noah Gray, a senior editor at Nature in NYC - an interesting write-up that the New York Times carried a couple of weeks back. It talks about the somewhat meteoric rise of home labs, dabbling in science experiments, ably aided by the availability and use of relatively low-cost tools. [click to summary if you have a tldr; moment]

A Brief Sojourn To Visit The Potomac

The spousal unit had to retire to the old country this week rather urgently - for a bit of administrative heckling (a.k.a. visa processing) and hopefully some much-needed R&R - of course, leaving me in the deep doldrums, alone and depressed on the long Christmas weekend. Thankfully, two dear friends of mine, SB-squared, decided to come over to Baltimore to ameliorate my misery. Muchas gracias, mi amigo y amiga!

In two minds... about BioEthics

I am really in two minds as I write this.

This post was prompted by a news item on Teh Grauniad this morning, brought to my attention by that esteemed daily's twitterfeed. The title and the byline goes as:

Girl, nine, benefits from UK's first IVF 'saviour sibling' therapy
Doctors treat girl with rare blood disorder by transfusing healthy bone marrow from baby brother created at IVF clinic

Intrigued, I read through the report.

Of Correlations, Causations and the Divide Therein

An important maxim used in science, or more precisely, in the scientific study of relationships between/amongst variables, is that 'Correlation does not imply Causation'. Indeed, until and unless such causality has been verifiably established through independent means, any attempt to indicate that it does falls under the logical fallacy of questionable cause, cum hoc, ergo propter hoc (Latin for "with this, therefore because of this").

It is important for all to understand this concept - those who are engaged in scientific studies, as well as those who read about and interpret such studies.

Exciting prospects: Stem Cell Therapy in HIV therapy

I am tremendously psyched about this fascinating report published in Blood about a week back. The paper from this German multi-institutional group describes how, in an HIV-infected leukemic patient, transplantation with CCR5Δ32/Δ32 stem cells appeared to cure HIV. Even as I write this, I can barely contain my excitement; this finding has tremendous possibilities.

Of Affiliations and Conflicts (Pensées - entry 00013)

Original publishing date: Jun 11, 2010. Original Title: Of Affiliations and Conflicts...

Recently, through an unrelated chain of events, I came across the author guidelines (PDF) for the international journal of general medicine, The Lancet.

All of you are, of course, aware that The Lancet is a high impact factor journal with significant global readership of both of its off-line and online versions. The journal - no stranger to controversy - has come under severe criticism from the medical and scientific community, ever since it published the Wakefield article on Autism and the MMR vaccine in 1998. The conclusions and interpretation of this study were retracted by ten of the co-authors in 2004 (Murch et al., Lancet 363 (9411): 750), and the editor, Richard Horton, went on to explain that the retraction was due to "...revelations about conflicts of interests" (reported on The Beeb here). Wakefield was found to have been paid a large sum of money by lawyers trying to prove that the MMR vaccine was unsafe, and he did not declare this clear conflict of interest. The rest, as they say, is history. I needn't elaborate; you are aware of how Wakefield was censured for this non-disclosure, as well as for scientific and ethical misconducts.

Pensées - entry 00012

So... here. As promised in Pensées from Moi.

Original publishing date: May 25, 2010.

Original Title: My fellow hoopy froods...

Pensées - entry 00011

So... here. As promised in Pensées from Moi.

Original publishing date: May 4, 2010.

Original Title: Age Old Wrangling Over Natural World

Pensées - entry 00010

So... here. As promised in Pensées from Moi.

Original publishing date: May 1, 2010.

Original Title: A Quick Snippet

Pensées - entry 00009

So... here. As promised in Pensées from Moi.

Original publishing date: April 23, 2010.

Original Title: Prophetic?

Pensées - entry 00008

So... here. As promised in Pensées from Moi.

Original publishing date: April 27, 2010.

Original Title: Placebopathy

Pensées - entry 00007

So... here. As promised in Pensées from Moi.

Original publishing date: April 13, 2010.

Original Title: Spam Skillet Casserole

Pensées - entry 00006

So... here. As promised in Pensées from Moi.

Original publishing date: April 13, 2010.

Original Title: Homeopathy and mouse model

Pensées - entry 00005

So... here. As promised in Pensées from Moi.

Original publishing date: April 13, 2010.

Original Title: In which I take on Homeopathy

Pensées - entry 00004

So... here. As promised in Pensées from Moi.

Original publishing date: March 30, 2010.

Original Title: Publication Bias in animal experiments?

Pensées - entry 00003

So... here. As promised in Pensées from Moi.

Original publishing date: March 18, 2010.

Original Title: Exciting science, age-old problem...

Pensées - entry 00002

So... here. As promised in Pensées from Moi.

Original publishing date: March 15, 2010.

Original Title: I rant against Helicobacter pylori...

Pensées - entry 00001

So... here. As promised in Pensées from Moi.

Original publishing date: Mar 12, 2010

Original title: Suddenly...

Pensées, from moi

How many of you know what Pensées are? Raise your hands.

"Pensées" (literally, "thoughts") is a posthumously published collection of notes made by the renowned French Philosopher, Mathematician and Physicist, Blaise Pascal, during his final years as he worked on a treatise on Christian apologetics. These contain his infamous wager/gambit.

'Meh!' You say. Rightly so.

Wishy-washy Arguments in Support of Belief. Yawn.

Following a few heated exchanges between us on Twitter, a journalist friend of mine has decided to put up a blogpost defending the ultimate accommodationist position: Why can't we all just make nice-nice and be happy together?

Okay, that was taking a bit of liberty (strictly tongue-in-cheek, of course!) in paraphrasing her position, but basically she is questioning the source of belief and the lack thereof. In particular, she is examining those beliefs that are not evidential/ material/ cogent in nature (Hmmm... Is there any other kind?)

She starts with a valid question:

How do we know these exist, if we choose not to believe that they exist?

Most unfortunately, she considers this as a rhetorical question, and therefore, comes up with a simplistic, outlandishly puerile, answer:

The answer to this is also simple: we know they exist and therefore we believe that they exist.

I can't even begin to describe the logical fallacies in this circular argument, that a seasoned journalist should never have committed IM(NS)HO. When did journalism stop being about fact-checking, objectivity, logical consistency, integrity of reportage and all that jazz? Sigh.

A most awesome rally! Only if...

S and I were at the Rally To Restore Sanity And/Or Fear yesterday! It was an incredible and awesome experience. Not to mention - ahem! - brief.

No, really. We were at the site of the rally for all of glorious seven and a half minutes before beating a retreat. I was/am so ashamed of myself, and it fills me with embarrassment even as I write this account.

And before any of you commiserate with me, no, it was not agoraphobia, nor enochlophobia. What made us leave post-haste was the concatenation of several powerful realizations - call it 'light-bulb moments' - chiefly amongst which were (a) both of us were vertically challenged compared to most of the crowd, and (b) the rally was being telecast live on Comedy Central and C-Span, and also being streamed live online.

A Decidedly Un-Robotic Open Letter to Nikhat Kazmi...

Dear Nikhat-didi,

aapne mera dil toRh diyaa... (You broke my heart). This was my first reaction when the end credits started rolling after "Enthiran: The Robot".

How could you? No, really, how could you? You are Nikhat Kazmi, an esteemed Senior Editor with the Times of India group and the author of a highly popular weekly film review column for the newspaper. La Esposa and I have been, for years, hanging on to every word you said in your movie reviews, because our collective opinions almost always found a reflexion in your eloquent ones. Sadly, you seem to have gone to the deep end now: you gave Four Stars to the newly released Rajnikanth-Aishwarya Rai starrer "Enthiran: The Robot". Intrigued about the movie and emboldened by your Four-Star review, we drove 50 miles to a theater in Gaithersburg to watch the spectacle, that purportedly broke all records by garnering Rs. 205 crores (1 crore = 10 million) through advance bookings before its release.

I want our money back.

I know we can't get those 2 hours and 52 minutes of our lives restored, but I have written them off to my stupidity and lack of foresightedness. I mean, seriously, what was I thinking? et tu, Nikhat-didi?

Dabangg: A pleasant surprise

S and I, with our friend, Neel, watched the newest Salman Khan starrer "Dabangg" last night in a movie theater in Columbia, MD. Not particularly fans of Salman, we were nevertheless intrigued by the news that it had broken the record of 3 idiots in the first week alone; so we took the half hour drive and checked it out for ourselves.

With extremely low expectations of the movie, I was ready for anything. Generally, S and I have always trusted the movie reviews by Nikhat Kazmi, a senior editor with the Times of India, because seldom it has been that our experiences have not resonated with her write-ups. Ms. Kazmi gave Dabangg four stars out of five, and wrote a generally positive review about this Khan Family production (Oh, yes! Salman in the lead, with his brother, Arbaaz, playing the underdog, and a smashing item number by Malaika Arora-Khan, in this Arbaaz Khan Productions movie). We decided to take Ms. Kazmi's cue (as we have done countless times), and leave our brains at home.

Boy! Was there a pleasant surprise waiting for us! I am not ashamed to admit that we enjoyed every minute of it! Completely mindless, the movie had no pretension to any message or subtlety; it was just plain old story-telling in the late 70s-early 80s Hindi movie ishtyle... A larger than life Salman, unabashedly corrupt in his role as inspector Chulbul Pandey, but with a frank degree of Robin-Hoodiness that makes him difficult to dislike. A hackneyed tale of sibling rivalry, but Arbaaz - undoubtedly a good actor - expressed well the angst of the younger, weaker brother. Sonu Sood, with a sculpted torso (and sadly, chicken legs), settled well in the role of a believable villain. Most of the other actors were in cameo roles, sharing the screen for short periods of time. We were surprised to see Vinod Khanna after a long time, and Dimple Kapadia in a deglamorized, albeit significant, role. Special appearances were put in by Mahie Gill and Mahesh Manjrekar, as well as veteran actors Anupam Kher, Om Puri and Tinnu Anand. In presence of such established industry regulars, Shatrughan Sinha's daughter, Sonakshi, the lead heroine opposite Salman, held her own quite well - although a large part of her role consisted of her giving smoldering looks; she is pretty and emoted adequately when required.

The songs by the Sajid-Wajid duo were hummable (my particular favorite, the title-song, 'Udd, dabangg, dabangg'), sung by the familiar voices of Sonu Nigam, Shreya Ghoshal, Sukhwinder Singh and the distinctive Rahat Fateh Ali Khan. Malaika was, of course, stunning as usual in the item number (by one Lalit Pandit), although the song somehow lacked her erstwhile Chhaiyaan-chhaiyaan magic. The fight sequences were well choreographed by S Vijayan; although almost all the signature moves (Matrix-type bends, leaps, falls, high kicks and punches) were reminiscent of similar sequences seen in Hollywood action movies, they were brought together into a cohesive whole that was thrilling. Salman also got to do his Hulk act where his shirt tears off and flies away - but a shirtless Salman has always been dear to the masses ever since his Maine Pyaar Kiyaa days. The dialogs were peppy and smart, very UP-Bihar belt type, with a surfeit of jokes that were sometimes downright silly - but they resonated well with the overall impression and flow of the movie. The cinematography by Mahesh Limaye was pleasing to the eye with scarcely a jarring moment, creating a nice, enjoyable visual experience.

It was undiluted fun! No higher cerebral activity involved, we enjoyed the thrill ride of Dabangg very much, as did the other viewers judging from their expressions.

In which I reason with my brother...

Yesterday I expressed my outrage on Facebook at two news items that were reported in the Times Of India - one about India still topping the list of highest maternal mortality rates in the world, and the other about the existence of an 'Untouchability fence' in Tamil Nadu. My brother, ever concerned about my health and well-being, took me to task for my comments, that seemed to him too vitriolic and negative (and therefore, bad for my health in the long run). He interpreted the comments as indicating that I was ashamed of where I am from, and counseled that respect is rare for people who reject their roots. He admonished me that if I felt compelled to post negative news and comments, I should demonstrate fairness by posting positive news also - perhaps thereby preserving some sort of cosmic balance, particularly since [he said] "No place is paradise and no place is a total hell". He also accused me of searching for "every ill on the planet" to comment upon (Just FYI: this is called the SIWOTI syndrome, "Something Is Wrong On The Internet") - which was still all right, but what shocked me was when he uttered this tired old sermon, "Be positive and solution-oriented, not negative and angry", very Deepak Chopra-esque in its vacuity and naïveté.

To a random pearl-clutching crank commenting thusly, I would say, simply, "f*** off." But this is no crank. This is my sharp-as-a-tack brother; he loves me dearly, and I have nothing but affection and admiration for him. And therefore, he deserves a reasoned response. I could start by counting off the interesting, heartening, even exhilarating news items that I have shared on FB, but that would be petty. Let me address the more serious questions.

Beautiful sentiments...

I am a great fan of Cuttlefish. Those who don't know him, check out his brilliant blog, Digital Cuttlefish; the man has an amazing talent for poetry, and is a rationalist and a frequent and well-respected commenter at PZ Myers' Pharyngula. Recently, when talking about Christopher Hitchens' battle with esophageal cancer - an ongoing discussion at Pharyngula - he expressed some beautiful and heart-warming sentiments in a comment. I was immensely moved; they brought tears to my eyes and a glow to my heart. I wished to share that comment with y'all.

Thus spake Cuttlefish:

How do atheists face death?

All too recently, I was at the bedside of a dying atheist. He was not conscious, so I can't speak to how he himself faced death, but I can tell you how his atheist daughters and atheist brothers did.

To the extent that anything offered comfort, it was the knowledge that the doctors were doing what could be done, and the knowledge that he was not suffering. The hospital chaplains were of no use at all, not even to those gathered who *are* believers. There is no way to put a positive spin on losing someone so early; no way to tell a 16-year old girl that this is part of God's plan and have her just accept it.

Of course, the families of other patients offered to pray for us, and assured us that God is great, and that if it is his will, our brother, our father, will recover. I assure you, even when you take it as a sincere expression of their best wishes, assurances of God's mercy start to ring hollow very quickly.

How does an atheist child face her father's death? As bravely as I have seen anyone face anything. There was genuine beauty in the things his daughters said, and none of it relied on an afterlife, or a heaven, or a god. None of it denied the hurt, the heartbreak, the incredible pain of losing a father at such a young age. Death's impact should not be denied; claiming he is in a better place is a slap in the face of the daughter who knows his best place is back home, helping with homework, mowing the lawn, reaching the things on the high shelf.

How does an atheist face death? By facing it, not by denying or diminishing it. Not by turning it into a transition to some other reality. Not by making up a story to make themselves feel better. It hurts because it's real, it's permanent, it's the end. It should hurt.

And now he lives on only in our memory, and in our changed lives. That is his legacy; that is the good he continues to do. He's not looking down and guiding; he doesn't wait for us to join him. If we love him, we can do our best to fight for his causes, to continue his work.

In the real world. The only one we have.

Gotra - the irrational, unscientific idiocy continues...

This great country of ours, India, with its underlying theme of unity in diversity, has a rich cultural heritage of education and knowledge, and civilization. It pains me immensely to find instances of idiotic and irrational customs, based solely in religious myths and superstitions, still existing in modern day India; the pernicious influences of such customs and traditions, fuelled by religious beliefs, are not only degrading the secular principles enshrined in the Constitution of India, but also actively harming the lives of many of its citizens.

Examples abound. Let me refer to a specific and recent one: the controversy about same-gotra (sub-caste) marriages among the Jats of Haryana. It all began with the 2007 murder of a young couple, Manoj and Babli, who were kidnapped and killed for the 'crime' of falling in love and marrying within the same gotra, against the wishes of the Taliban-style local village caste council, the Khap Panchayat. Though the perpetrators were arrested, tried in a court of law and given the death sentence, they were unrepentant - as were the other Khap leaders, who went on to ostracise Manoj's mother. The Jat cops who colluded with the murderers have not been punished yet.

The capital punishment handed out to the perpetrators was meant to act as a deterrent. Yet, undeterred, the Khap chieftains recently pledged to intensify their war against same gotra marriages, and started clamoring for amending to Hindu Marriage Act to ban same-gotra marriages. Recently, in a bizarre turn of events, a young Jat soldier, belonging to the traditionally caste-less Muslim religion, has caught the ire of the Khap for marrying a Muslim girl, whom the Khap considers to belong to the same gotra - never mind the completely different religion!

For All Indians currently residing in the US...

Please consider this a serious word of caution. A lot of Indians, including us, currently reside in the United States. We, of course, are here legally, either studying or working with a valid visa (including a green card), or are in the status of a dependant of a valid visa holder. A few of us (like the children of my friends) are even American citizens by birth or naturalization.

Some of us speak English fluently, some haltingly; some speak it with a heavy Indian accent, some with no accent, and some with an American accent. Almost all of us pay their annual Federal, State and City taxes, and all of us are contributing to the society and economy of this country in some way or other. We have friends and families here, and are busy in building our lives and careers.

Doesn't matter. All that matters is that we all have skins of various shades of brown. And it has just started mattering a whole lot in the State of Arizona.

Johns Hopkins as a cash cow for Baltimore?

Curious opinion piece in the Baltimore Sun today, titled: "Tax-exempt Hopkins must help balance city budget", by one Jay Hancock.

The piece is confusing, to say the least. Hancock opines that Hopkins and its non-profit affiliates should pay Baltimore city, seemingly indicating that the city should regard Hopkins as a cash cow, milking it for revenue as much as it can. He takes the examples of the relationships between Cambridge and Harvard/MIT, and New Haven and Yale. But are the economics, demographics, management and administration of Cambridge, MA, and New Haven, CT, comparable to those of Baltimore, MD?

Later Hancock acknowledges Hopkins' immense contribution to the city in form of many thousands of jobs, millions in research grants that faculty at Hopkins bring, and millions in revenue spent on services and products, as well as the provision of top-quality medical education. As Hopkins rep Tracy Reeves indicates, Hopkins' academic & medical services already pay the city $10 million/year (parking & licensing fees, energy and telecom taxes), plus spending millions on security (that arguably is the city's responsibility).

What is it, then? Does Hancock mean to say, “Oh, we know Hopkins is doing a lot, but Hopkins needs to do more”, and that's about it?

As one commentator asks in the comment section, what about taxing the multitudes of churches of various denominations in and around the city? Or the entities providing so-called spiritual services need not concern themselves with the welfare of the city?

Prayer Therapy? Are you freakin' kidding me?

Snake oil comes in various forms and shapes, and its salesmen (perhaps I should use the PC term, 'salespersons') are of various hues and creeds. The commonalty between many of them lies in their relentless push to gain mainstream acceptance, which, of course, would mean more funds and more followers. They are not hampered or thwarted by the inconvenient fact that their brands of quackery, often founded on religious/mystical beliefs, are not supported by hard empirical evidence, or indeed, rationality. Undeterred, they plod on, championing superstitions, promoting lies, feasting on the fears, uncertainties and vulnerabilities of disadvantaged people.

Take, for example, the Church of Christ, Scientist, founded by Mary Baker Eddy in 1879 in Boston, which purports to tend to the sick using "Christian Science", a hodge-podge of elements of the Christian faith and severely evidence-challenged practices that combine airy hand-waving and crazy superstitions. According to an article published in the New York Times today, the faith's central scripture, written by Eddy who claimed an inspired understanding of the “science” behind Jesus’ healing method, expressly forbids medical care, and relies instead on Christian Science healing - a form of spiritual healing, based on Eddy's understanding of the Bible. Disappointed that existing Christian churches would not embrace her discovery of the "science" of healing, Mary Eddy created her own church, which trains its practitioners to "help" patients with "transcendental prayer intended to realign the patient's soul with God".

This is wrong on so many different levels.

Does acupuncture work in depression control? Nope.

This past weekend, the New York Times published an article on a study from Stanford University, where the authors apparently found benefit from acupuncture in pregnant women with Major depression. Given the track record of acupuncture (which features a resounding lack of evidence that it works), my skeptical antennae started twitching. I ferreted out the original study in the Obstetrics and Gynecology journal (link to full text here), and read it through thoroughly. This report - of a single randomized clinical trial (RCT) study with less than 150 subjects - claimed that an acupuncture regimen, specifically designed for a particular individual, could significantly reduce depression in that individual. As I suspected, the paper made a whole lot of science-y sounding, but nonetheless vacuous, arguments; their predominant talking point seemed to be that multiple exploratory analyses were done on the observed outcome. This assertion is always suspect; for an RCT, it shouldn't need so many exploratory analyses at the study stage, and the outcome measures should have been determined prior to the initiation of the study. As a friend of mine pointed out, "exploratory analyses" frequency means "fishing expedition", which is what this paper seems to have done in plenty. Unfortunately, the mainstream media coverage of this single study has been far from ideal; the news report has been worded to make it seem like a breakthrough or a major milestone in research, which is the impression the general public is left with - eventually to their detriment.

NIGMS soliciting comments on research training

As a part of its commitment towards research training, the National Institute of General Medical Sciences of the NIH is seeking comments from predocs, postdocs and other interested parties on a strategic planning process focusing exclusively on training and career development. The NIGMS recognizes that as science, the conduct of research, and biomedical workforce needs evolve, it is essential to ensure that the training activities meet current needs effectively and anticipate emerging opportunities, and that they contribute to building a highly capable, diverse biomedical research workforce.

Between March 2 and April 21, you can provide your input at:
http://public.nigms.nih.gov/2010TrainingSP/

Many of their important and coveted training and research awards, such as the Ruth L. Kirschstein National Research Service Awards for postdocs and senior fellows, are highly competitive and geared towards promotion of their mission of generating a scientific workforce in biomedical research. Unfortunately (from my perspective), these awards are often restricted to citizens or non-citizen nationals of the United States or permanent residents. To me, this restriction seems counter-productive, because it excludes a wide group of talented, young and motivated individuals who are from other countries on a visa, but are nonetheless engaged in cutting edge research work in this country. Perhaps merit of the research proposals and research credentials should be the criteria for selection.

I encourage you to put forth your constructive comments at the above website.

A brrrrief Burrrrlington sojourn...

Snowed upon, wet and cold in Baltimore, the missus and I accepted an invitation from a close friend in Burlington, Vermont, to spend the New Year's Eve and the New Year's Day with his family. Did I say 'snowed upon, wet and cold'? Check, check and check. What was I thinking? Not a warm, sunny climate - for sure. [Yeah, S, my brother, remember that we love you. A lot.]

Anyhoo, what we were not prepared for was the massive amount of snow and relentless snowing that we encountered. From 7 a.m. Saturday to 7 p.m. Sunday, a record 32.5 inches of snow fell on the city of Burlington, according to the National Weather Service. It just came on and on and on. From the report:

Nor’easters typically move north along the coast, but strong winds blowing south forced this ocean storm to back up from near Nova Scotia to near Maine.

“What happened in the Champlain Valley, we were under this northerly wind that just didn’t stop,” National Weather Service meteorologist Paul Sisson said. “And what that did was focus the heaviest snow on the eastern part of the Champlain Valley. It’s unusual for something to stay so stationary for such a long time.”

During that time, Burlington remained under the “tail end” of the storm, which usually produces heavy snow, according to National Weather Service meteorologist Scott Whittier said.

Roads were white, fields were white, trees were white with cotton-like snow deposited on the leafless branches; irregularly-shaped mounds of snow stood by the roadside where people had parked their cars. There were icicles formed, like stalactites, from the edge of the roof of houses and stores, and even from the edges of car front and back fenders, wheel wells and so forth. It was surreal. I have never quite seen anything like it. Snowploughs, snow-blowers and snow-shovels were generously employed by denizens of Vermont, but that barely scratched the surface. Towards the end, it seemed that one could jump into one's backyard from the second-floor window and drown in the snow. Road conditions were slippery and dangerous.

Click to embiggen

At the same time, it was good to see that the Vermonters' holiday spirit was not much dampened; we visited the downtown mall at Church street on Saturday, and people were there, enjoying, braving the snow.
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And now, a visual of the scary, non-stop snow shower on our way home.