Science is cool and kids should know it!

I don't often meet 8 year olds and when I met one a couple of days ago, after a long time, it was a thought provoking experience.

Eight is not a big number but it is not the age when you can coochie-coo your way around or walk away from questions with your reputation intact. Neither is it those dreaded teens when although rebellion tinges the conversation, you can treat the child like an adult, or a young adult as they say. For me it was a tricky experience that made me realize how much some things have changed and how some others have stayed the same. 

This was the second time I meeting V - a friend's son. The first time was after his long flight from India and I could understand that he was not going to be talkative. As we adults kept talking and he was lying there with these big headsets watching animations. He was the usual 8 year old who loved his gadgets and video games and was shy/wary of strangers. Upon not getting any attention from him for almost an hour, I poked him a little on my way out. I tried to get his attention by prattling-on about about two headed turtles, sharks and conjoined twins, about pangrams, dinosaurs and pilots. All in less than ten minutes I think. I just wanted to find something that he was interested in. Finally, with all this being thrown at him - I had his attention. But then he declared that science is boring as his parents (both scientists) are mostly doing "not-so-cool" stuff on the computer and in their lab.

I have long been the scientist in the house - the one who asks why, the one who breaks the rules, the one who explores - worlds both real and fictional. My brother, on the other hand is a pilot - how cool is that! I know! And, I am used to that same reaction from everyone. With my brother present in the room, conversations would always be about flying, landing speeds, visibility, gadgetry and rest of the cool stuff - much to his annoyance as well. Kids are almost in awe when he is around, also because he is usually towering over everyone at 6ft3".

Being a scientist myself I was a little saddened by the proclamation of an eight year old that science is boring. But then, as we ended up speaking for the next two hours about books, calligraphy, Harry Potter, Halloween, Dinosaurs and magic tricks - I realized that he doesn't dislike science, he just doesn't care for the slower, accurate and more grown-up version of it. But this also made me realize that there is strong need for science advocates - people who can make kids realize about the unknowns of the world.

Science is cool and kids should know it!

Why should only astronauts, race car drivers, doctors and pilots be considered cool? Why are scientists depicted in popular media like these quirky, almost crazy, wild-eyed, wild-haired geeky people?  That is a huge amount of prejudice and scientists as a community just accept it. But it is not true (at all). Scientists are cool! They are blasting electrons and protons looking for smaller particles; they are climbing down caves looking for bacteria;  they are hunting snakes and finding new cures in the Amazon; they are recording dreams and memories, engineering thoughts in mice; they are making life in a dish; they are making hearts, lungs and livers for treatment; they are understanding the universe - one piece at a time. 

Science is cool and as are scientists! And kids should know this. And we as a society need people to enthuse children. We need to fascinate them and to enthrall them with the world around us.

Not just to tell them quirky facts about rhino-horns, hair and antlers, about twin-headed animals and dinosaurs, but also about the unknowns! About how we don't know how the dinosaurs died or how the universe began or about how we remember, dream, sleep or think? Science for kids has to be more than a summation of facts and experiments or about exams and answers. Books that give these descriptive details about what is known must also mention what is unknown so that they can think.

Yes, what is known is an ever-present constant while what is unknown is changing everyday - but that is precisely why writing a book or education is no mean task. 

Science is a way of looking at world. A way of wonder. A way of thinking with a questioning mind. We need the next generation of people to know the world for what it is and to then change it - to engineer it for the better. We need kids to come up with new solutions without forgetting the old!   Knowledge and information are better received when they told with fun facts, quotations, action and drama - but this is not to strip away the facts and the questions. This is to enhance them and to improve retention. 

When as a seven-or-eight year old, I first read of Marie Curie working with her father and then eventually discovering radioactivity; or when I heard of the small-pox vaccination and its beginnings with the milkmaids; or even about the discovery of Penicillin - I was in awe. I wanted to change the world like them.

I wanted to make discoveries. I wanted to understand the world - a little better each day. And the quest continues even today - despite being a little tarnished by the harsher realities of life in science. I was and still am passionate about knowledge, about having more questions than answers and to go on that hunt - each day, every day. I try and carefully stow away in a box every unanswered question that I find - waiting for an answer to come. I don't remember all the questions. Neither do I remember all the answers. But I know one, when I find one and I try and put the two together - happy at the resolution!

That wonder for the world around me has kept me sane and unjaded through the years of graduate school and the drugdery of post-doctoral work. It is this wonder that I am scared of losing if I move on to do something different. It is this wonder that keeps me sane and eager to learn. And I want all the kids around me to have that.

Battling homogeneity...

The world is shrinking and there is no denying that.

But the world is also becoming more homogeneous and averse to differences. People are becoming the same the world over and we are becoming less and less able to talk of differences. Differences of gender, race, culture are nationality are being trivialized and even being ignored. Even talking of them seems to make one a racist or a chauvinist these days. No! I am not espousing the millions of racist or chauvinist people living all around us. I am not saying that people should be discriminated against one way or another. No!

But this post is meant for the rest of the world. The world that is so determined to be impartial, fair and politically correct - that they deny the very existence of differences. Differences between races, people, genders and social strata. 

This is a theme that has been recurrent in my thoughts, ever since a popular science writer once told us in class that when writing about women scientists one must avoid reference to their gender and simply focus on their work. But even today - almost two years since then - when I read of the Finkbeiner rule that is espoused by many science writers, I can't help but disagree. I am not saying that writers should focus on merely the gender and judge people or their work in that one dimension.

No!

But I do think, we should learn to write the whole story without any prejudice and at the same time give due respect to the person, his/her origins, character, gender and his/her story. After all, it is these things that make us who we are. Every individual is a sum of these and many other parts and these factors play a role in shaping our thought processes and formulating our decisions. Then why should we deny these differences? 

People are different.
Just because we are flooded with genomic scale data that tells us that we are 99% similar to chimps, we should not develop this perception that all men and women are similar. No. In fact, science today is grappling with the understanding of how the diversity is generated.
People are different.
Caucasians, Asians, Africans - we are all different - genetically, culturally, socially. And these are important differences. People's attitudes, priorities, choices, interests and thought processes are a summation of these and many other factors.
They are different in obvious ways - in ways that are imprinted in our genes. And these differences don't mean inferiority or superiority.
But then, instead of accepting and respecting these differences, I find it strange that the world is promoting homogenization of the world and its people. And by limiting the perception of an individual to any one dimension - we only limit our understanding of them.

I do not advocate trivializing a woman scientist to just a woman. Certainly not!
But at the same time, the "woman" part of that "woman-scientist" is not excess baggage. It tells you a lot about the journey and the story.
Women today are caught in this time-warp of sorts where they have been unable to completely break away from their traditional roles and at the same time they have successfully taken on newer roles at home and in the society. In many ways they have moved a lot faster and the rest of the world just couldn't keep up with them.

The challenges that people face in the world, because of their race, gender or background should not be brushed under the carpet. Coming from a developing country. Coming without any training in english. Being a woman. Being a man. Having a family. These are all factors that affect you and there is no reason to emphasize one versus the other.
What is needed however, is to develop an attitude in the people where such details are taken for what they are, in a non-prejudicial, perhaps even an inspirational way. What is needed is not the nullification of individuality but the open acceptance of individuality and the differences that come with it! We need to make people embrace differences again - without innately associating any value with them!!

Equality does not come from homogeneity.

It comes from appreciating the differences and from learning to value them. After  all, the best things in life are like the rainbow and they arise from the differences built into them.

The numbers game...

Behind one of world's leading research institutes in the world - the Salk, there lies the vastness of the Pacific ocean. But between this seemingly never-ending expanse of the pacific and this incubator for great scientific research - there lie the memories a 16 year old.

A 16 year old, fondly remembered by her parents and memorialized in the form of a bench overlooking a grassy lawn and above the muddy-brown cliffs from where the paragliders take off into the heady ocean winds. She was "Drawn to the ocean and kissed by the sun, radiant and exuberant, always smiling." She was Morgan and she "lives on in their hearts forever".

I don't know Morgan or her story but even as I sit on that bench, I feel spooked and haunted. Not by ghosts and demons but by the questions whose answers elude me and leave me wondering. What could cause a 16 year old to die? Why couldn't we - researchers at a premier research institute - do anything to help? What can we do now to change things? 

The future of science is probably brewing in some test tube or being envisioned in some computer screen somewhere right behind this bench but still, here she was, a possible victim of fate.

Science to me was all about solving puzzles and answering questions.
Therapy, disease, cure, application, translational research - to me these were all the price we pay for our scientific freedom. The debt we owe to the society for their generosity. But, I have never been keen on them or appreciative of the present focus of the entire scientific community on them.

Yes - it is probably petty and selfish! But to me, science is all about the utopian search of mankind to understand the world. It is my pursuit for the truth, for understanding the world as it exists. In my mind, it is the engineers who should tweak things and make them more suited for application. We, scientists, should be allowed to just think and dream, and test and prove.

How naive was I? 

Even a purist like me is affected when I sat by the memories of that 16 year old.

Could we have done something to change things for her...? She could have died of cancer and there are many of us working on that problem!! But what if it was not a rampant disease like cancer that had the world in its grasp? What if it was a rare disease - a disease that affected one in every thousand or ten thousand or even a million? Are there others like her who can be helped? If not, does it matter that she was alone?

They say, she was a happy child who loved the ocean - just like this friend of mine. Isn't that enough? How many patients does one need for a problem to be worked on? Will we ever be able to help such children and patients? These one of a kind, rare patients. Or will the scientists, the industry and the granting agencies ultimately succumb to the burden of numbers and the finances? 

Research is usually justified by many parameters: the numbers benefited from it, the feasibility, the cost and benefit, the applicability and the potential. Ten or twenty vs. the hundred or thousands is a seemingly important question when looking at the bigger picture. But, when I look at this tiny place under the sun, I wonder, if it should? Is a small benefit to the millions more important, feasible and lucrative than a big benefit to a small group of people? 

Private companies and entrepreneurs think like that. Should we, too? For them one time cures are less profitable than long term treatments. For them diseases afflicting the masses are more profitable than elusive diseases affecting a few. But, why is research on these rare diseases also limited to small groups of people...? Why are there a few laboratories across the world working on these rare diseases and disorders affecting a precious few? It has to do with the available funding and the number of scientists interested... 

I find that most people fail to see the bigger picture here.

Research in mice is driven by our ability to knock-out and over-express select genes i.e. you find out what someone does by either removing them or putting in more of them. This is how we study what individual genes in our genomes too. But this can obviously not be done in humans and so we resort to the next best option of doing it in mice. But then how can we expect to understand the function of the 25,000 odd genes that are coded for in the human genome?? Most people just hope that the information from the other model systems will help. But, we all know that despite a lot of broad similarities between mice and men, there are many critical differences. These rare patients can potentially fill in that gap providing us vital information about these rare mutation and its effects. Knowing the mutations that they have and the disease symptoms they show can be vital to understanding the role of the affected gene(s) in the normal individuals.

Isn't that incentive enough for big pharma companies, scientists and granting agencies to pursue such rare diseases? Rare diseases that may affect these 16 year olds bubbling with life but stripping them of life and all the joys that come with it.

Thankfully, as the costs for genome sequencing have come down - more and more groups have been applying these and other approaches to study these individual, rare, one-of-a-kind patients. That is certainly hopeful but we are still a long way away.

Hopefully, the winds will change.

References: 

http://phenomena.nationalgeographic.com/2013/03/11/we-gained-hope-the-story-of-lilly-grossmans-genome/

http://www.nytimes.com/2013/02/19/health/dna-analysis-more-accessible-than-ever-opens-new-doors.html?pagewanted=all&_r=0

http://news.wustl.edu/news/pages/23465.aspx

http://www.jsonline.com/features/health/111224104.html

Seeking CLARITY? Make it invisible for best results…

Biology has long sought a window into the human mind and with new technologies, today, it is possible to literally see through the brain!

In a recent report in the journal Nature, the authors have developed a new technology, called CLARITY, that render big chunks of tissue optically clear and permissive to immunolabeling.

Understanding the functioning of the brain and its transformation into the mind is one of the single biggest challenges facing biology today. And although work over the past few decades has given us a fairly good understanding of the brain at a microscopic level; we have lost out on the bigger picture that emerges from the interactions among the different microscopic areas – largely due to technological limitations (and the diffraction limit of light).  

Our current view of the brain is almost like a map of the world before the satellite technology came in – remember the pre-google map/ pre-GPS era? Our reconstructions of the brain either involve microscopic examination of many smaller pieces aimed at re-creating the bigger picture or a gross overview of the bigger areas without the finer details. Not only does this piece-meal effort yield a partial and incomplete picture, it is labor intensive, expensive and time consuming. Also most of these techniques are often incompatible with molecular phenotyping of the intact tissue such that we most often get a crude map without any labels or orientation. This makes it virtually impossible to understand the landscape of the human brain. And mapping a place is truly critical to visiting and understanding it!

One possible solution to these technical challenges would be to render the intact tissue transparent to light and permeable to our molecular tags in their native location. Now, this sounds like the perfect dream but Prof. Karl Deisseroth and his team at the Stanford have achieved exactly this with their technology called CLARITY.

They figured that lipid bilayers or the cell membranes are the single biggest obstacle in making a tissue inaccessible to light (and hence imaging) and to our molecular probes; and if they could be selectively removed without destroying the structure and localization of the tissue, then we could get an optically clear 3-dimensional tissues that can be imaged with ease. But these cell membranes are what provide structure and integrity to the cells; without them we would be staring at a broth of many proteins and nucleic acids with no structure or localization. Thus, even as the lipid bilayers are removed, one needs to replace that framework with an alternative scaffold that can physically support the tissue and this is what they have achieved with their technology.

Briefly, they first immobilize the proteins and nucleic acids in the brain tissue by fixing them and crosslinking them with formaldehye and a hydrogel (acrylamide and bisacrylamide) that is liquid at low temperatures (and hence perfuses all through the tissue), but solidifies at higher temperatures. Formaldehyde is a strong, pungent smelling chemical that uses the amine groups (NH2 or nitrogen groups) of proteins and nucleic acids and crosslinks them to each other. This locks the cells and tissues in a state of complete inaction enabling additional manipulation (sectioning, staining, storing). While formaldehyde is routinely used in the hospitals and laboratories to store and “fix” tissue samples, it would not preserve structural integrity in the absence of lipid bilayers. Once the tissue is embalmed with this mix of a hydrogel and a fixative, the authors can now move the tissue to higher temperatures (37C) where the hydrogel will solidify and form a firm scaffold with the proteins and nucleic acids anchored on it.

At this point, the tissue is ready to be cleared off the lipids. And although using organic solvents like alcohol, benzene etc. would probably be an easier route to remove the lipid bilayers, this treatment usually quenches any fluorescence that the tissue may carry due to the expression of genetically encoded fluorescent proteins (like GFP, YFP, RFP etc.). To circumvent this problem, the authors used ionic detergents to remove the lipid layers, much like what your soap does. However, instead of relying on a slow (month-long) passive diffusion process, the authors applied an electric charge on the tissue to strip off the lipids along with the detergent. Since the proteins and the nucleic acids (also charged) were already cross-linked to the hydrogel, a small electric field should selectively strip out the lipids thus leaving behind an optically clear scaffolding of the brain with the proteins and nucleic acids anchored in place.

Using CLARITY, or Clear Lipid-exchanged Acrylamide-Hybridized Rigid Imaging/immunostaining/in situ hybridization compatible- Tissue hYdrogel, the authors managed to transform a mouse brain in 8 days into an optically clear, lipid-free, structurally stable hydrogel tissue hybrid. This tissue hybrid (map) could then be labeled for specific areas by the use of specific molecular probes (nucleic acid probes in FISH or antibodies against proteins) and imaged as a whole with standard microscopy that is routinely used.

Intact adult mouse brain Imaging before and after CLARITY.

CLARITY: Tissue is crosslinked with formaldehyde (red) in the presence of hydrogel monomers (blue), covalently linking tissue elements to monomers that are then polymerized into a hydrogel mess (followed by a 4 day wash step). Electric fields applied across the sample in ionic detergent actively transport micelles into, and lipids out of, the tissue, leaving fine-structured and cross-linked biomolecules in places. The ETC chamber for the electrophoresis is depicted in the boxed region.

Imaging was performed from an intact adult mouse brain using CLARITY. This is a non-sectioned mouse bran showing the cortex, hippocampus and thalamus (X10 objective; stack size 3400 uM; step size, 2uM).

Clearing tissues has been attempted for a long time now and for many end purposes like imaging, generating tissue scaffolds, developing tissue niches and synthetic organs. However, these approaches have relied on harsher methods that stripped the tissues off all biomolecules – lipids, nucleic acids and proteins – thus making the cleared tissue stripped of biological landmarks/ markers. Previous methods used detergents like SDS, urea, Triton X 100 and chemicals like Scale to strip the lipids from the tissue matrix and most of these methods also caused massive protein loss ranging anywhere between 65% to 25%.

With their improvements and modifications, CLARITY has enabled optical clearing of bigger and denser tissues with only 8% loss of the tissue protein thus allowing more landmarks in our map. The authors also found that replacing the impervious lipid bilayers with the porous hydrogel enabled the diffusion of the molecular probes deeper into the tissue – enabling greater access and better coverage.

Remarkably, these hybrid tissue scaffolds were also compatible to banked specimens that were fixed years ago with only formaldehyde. This further broadens the scope and utility of the technique as it makes available for study tissue samples banked and collected years before.

Although further improvements in imaging and computational techniques would enable a more refined, high throughput analysis, the use of CLARITY has certainly enabled integrative visualization of large scale biological systems. And within a few years, we might be able to have an accurate and labeled (satellite level) map of the landscape of a mammalian brain.

References:

1)   K. Chung et al. Nature http://dx.doi.org/10.1038/nature12107; 2013.

2)   http://www.nature.com/news/see-through-brains-clarify-connections-1.12768