So complicated… yikes…

There’s an idea out there, proposed by people who support intelligent design, known as irreducible complexity. What they believe is that biological systems are too complex to have possibly evolved by chance. I disagree with them on their point of evolution, but I do believe they have a very valid observation about the complexity of biological systems.

A lot of people get overwhelmed when they think about the vastness of space, but when I think about the complexity of biological machinery, it almost makes me want to throw up. Take a look at this: Metabolic Pathways and Cellular and Molecular Processes.

Biological complexity reminds me of space for some reason.

These biochemical reactions and cellular functions are happening in basically every cell of your body, and are happening in almost every cell in almost every organism on this planet. And it’s just the tip of the iceberg…

I’ll back up for a second. It’s well known that we’re all composed of relatively few elements (carbon, oxygen, etc),  but when we move to high-order biological systems there’s even less variety. There are proteins, nucleic acids, lipids, maybe a few other macromolecules, and these all have very simple basic building blocks.  For example there are only four(or five) bases in nucleic acids that encode all our genetic information, and only 20 amino acids make up proteins.

So the code of life is only four bases, and the machines/raw material of life is made of 20 amino acids. Food chains, replication, biodiversity, species, intelligence, having arms, whatever. All of it is 4 bases and 20 amino acids. Doesn’t seem that bad.

The central dogma of molecular biology is generally taught in science classrooms everything. It’s the idea that one gene codes for one protein, and that RNA is the mediator. The human genome project showed that out of the ~3 billion DNA base pairs that make up our genetic blueprint, we have about ~30,000 genes that code for proteins (our genes are ~1-2% of our total genome). So 30,000 genes, 30,000 proteins, doesn’t seem that bad… right?

Nope. I don’t even know where to begin. I can give only a few examples.

Alternative Splicing

Alternative splicing: a gene is made of coding and noncoding regions, called exons and introns. Coding regions are the regions that get turned into proteins, and noncoding regions are there for other purposes. But the kicker is, when DNA gets turned into mRNA (messenger RNA, which is like a copy of the master blueprint used to build the protein), these coding regions aren’t all copied over. Depending on what coding regions are actually transcribed, you can get a variety of proteins from a single gene, all of which complex implications further downstream. If you find a gene that causes cancer, and you think “hey let’s just delete it,” you wouldn’t be just deleting one malfunctioning protein, you might wipe out hundreds.

Epigentics: Knowing the full code of the human genome means almost nothing (right now).

from scienceinschools.org

Supercoiled DNA - We don't fully know how the code is read

DNA is really long – stretched out it’s ~2-3 meters for a human – yet it has to fit into the nucleus of every cell. It can do so because of an ultra-efficient storage method, where the DNA strands get super-coiled (imagine twisting a piece of rope). For genes to get expressed, the regions containing genes have to be uncoiled so that enzymes can get in there and do their work. The regulatory mechanisms for what areas get uncoiled are very complex, and have a heavy environmental affect – it’s one of the reasons why identical twins aren’t perfect copies of each other. There’s no change to the blueprint, but how it’s read is complicated.

Signaling pathways: Most biological functions in a cell, including gene expression, are initiated by a really complicated network of protein cascades.

from wikipedia

Yikes

An example of this would be: A molecule on the outside of a cell is recognized by a protein on the membrane of the cell. That protein activates/changes another protein. Which activates/changes another protein. Which activates/changes a couple of other proteins. Which activates/changes other proteins. Which either do something or activate a gene that makes other proteins. Etc.

Cells cross talk, sending signals to each other (even by distance) and the network of inter- and intra-cellular communications is not an easy thing to study. We know a lot about these signaling pathways, but most of the research being done is piecing it together step by step… is this protein downstream or upstream of this one, what about that protein, what gene does this target, etc. It’s complicated.

Unraveling the tangle, thread by thread - that's science

Knowing all this, why would anyone ever want to study this stuff? I asked Dr. Marco Petrillo, a postdoc at Harvard Medical School who does research in signalling pathways in zebrafish, how he felt about the magnitude of complexity in what he was studying. “I want to quit my job,” was his immediate tongue-in-cheek reaction. “But it just means there’s more for us to discover, and that’s exciting,” he said after a little more thought.

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What does a scientist actually do? (an experiment)

When I read about scientists and research in magazines/newspapers/etc, I get really curious as to what it is exactly they do, and more importantly, what this stuff looks like. I have no clue what goes on in a chemical engineering lab, or a math professor’s office, or what a theoretical physicist does all day, and hopefully someday I’ll get the chance to explore that.

As an… experiment, I’m going to try and run through a small… experiment… in biology and see if it’s interesting.

Transfection is a very common technique used by scientists to basically put artificial DNA into cells. Pubmed has almost 150k entries when you search for it, so I don’t have the space to tell you all the things you can do with/learn from/whatever from transfections. But suffice it to say, putting DNA of your choice into a cell of your choice, and getting that cell to express that DNA is pretty ultra useful.

A cartoon of a transfection, from MicroscopyU

But it’s actually kind of boring to do.

First, what is it exactly? There are a few different ways of introducing foreign DNA into cells (like viral vectors or using electricity to punch tiny holes in the cell membrane), but I’m going to talk about lipofection. This uses liposomes, basically ultra-small soap bubbles, to deliver genetic material (or other things, like drugs or siRNA as well) into a cell, because their outer layer is chemically compatible with the membrane of a cell; they can pass through that membrane relatively easy, under the right conditions.

A cartoon of a liposome, from Wikipedia. It says for drug delivery, but for lipofection it's basically the same.

So how do you do it?

1. DNA!

1. Get DNA. Here’s two plasmids, harvested by synthesizing a specific sequence of DNA, getting bacteria to take it up, growing the bacteria to huge numbers, and then isolating and purifying the DNA again.

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2. Lipofectamine!

2. Get a lipofection reagent. This is lipofectamine, a proprietary product, but works under the same conditions. This is a basically a bunch of lipid molecules.

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3. Cells!

3. Have cells you want to transfect. Here are some HEK (human embryonic kidney) cells.

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4. Mixing!

4. You basically mix the DNA you want with the lipofection reagent in some cell culture medium. This may look like nothing’s happening, but chemically, those lipid molecules are racing to find each other because they hate the water in the medium, forming bubbles (liposomes) and trapping DNA.

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5. Into the incubator they go

5. Put the mix on your cells, and let them sit overnight. Not too long, because lipofection can be toxic to cells.

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That’s about it. Now you have a plate of cells that have artifically introduced DNA in them. My experiment involved putting genes normally found in the ear into these HEK cells, but the microbiological world is your oyster when you can play with DNA.

Ok that was less interesting than I had hoped. But that’s biology!

An example of a successful transfection (not mine). Voila, monkey kidney cells transfected with a human gene(GIT1, which also has a GFP tag on it. More on GFP later.), shown in green. Blue is the nucleus, and red is an endogenous structural protein called F-Actin. Taken from CreativeCommons.


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How to see a cell – use rainbows!

When Robert Hooke, in the mid 1600’s, pointed a magnifying glass at a piece of cork and found small, distinct chambers, units he dubbed “cells,” he really had no idea what he was looking at. It took almost two centuries of microscope evolution before scientists had a vague idea of what a cell was and what was happening inside.

The problem? When you look at a tissue or cell, how do you know exactly what you’re looking at? When you look inside a cell, it’s even worse. How to figure this out involves some really innovative and fascinating – yet relatively simple – scientific techniques.

What tissue (in this case a developing cochlea) looks like under light microscopy

Here, I took a picture of a thin slice of a very young mouse cochlea, and as you can see, it’s very difficult to interpret. Looking at it with a light microscope is useful, but to tease out the inner machinery and mechanisms behind cellular functions, more precise resolution is needed.  In the latter half of the 1800’s, scientists began staining cells with various dyes, like crystal violet, which helped them visualize the microscopic by making cells, bacteria, and whatever they were looking at, colorful instead of translucent.

Today, with crazy technological innovations that previous generations would perceive as witchcraft, the dyes developed by chemists more than a century ago are still very commonly used. But, of course, we have new tricks in the repertoire – fluorophores.

Same picture as above, but with DAPI staining - the DNA of cells takes up the dye, which means the nuclei light up under the scope (although a little fuzzy here, my bad)

Fluorescent microscopy is complicated, but the concept is simple. And really, really cool. Where our scientific forefathers simply tossed dyes onto a plate of cells and watched what happened, scientists now are able to specifically tag and visualize the expression of individual proteins. The key to this is a class of chemical compounds called fluorophores, which emit a certain wavelength of light in response to a certain amount of energy.

Fluorophores emit a certain color (yellow-green, or 521nm, for fluorescein – a common example) when they get hit with a different color of light (red, or 494nm, for fluorescein). On their own, they’re not world-changing, but when combined with antibody technology (which is incredibly cool, complicated, and too much to talk about here in depth) they translate the microscopic world into visual scientific art.

The same as above, but this time stained for a very specific protein (myosin VIIa, which is only expressed in hair cells). Here, you can clearly see 3 outer and 1 inner hair cell, which were almost invisible before. The fluorophore used here was a proprietary one called Alexa Fluor 488

These aren’t the best ones I’ve ever taken, but you get the point. Taking a very difficult to interpret biological picture, we can stain with a certain dye and visualize exactly where the cells we’re interested are, what they look like (you can even see the dark spot of the nuclei), where the antibody you’re looking at is being expressed, etc. Antibodies are designed to recognize and attach to specific proteins in or on a cell, and when a fluorophore is attached to those antibodies, we can suddenly see everything.

There are dozens of different fluorophores and fluorophore-like molecules that have been developed by different biotechnology companies, and the range of colors that can be emitted cover the entire range of the human visual spectrum, and what scientists can do with them is only limited by how specific to molecules they can design antibodies (or in the future, Quantum Dots).

Stained HeLa cancer cells, from nikonsmallworld.com (which is awesome!).

This technology is one of the key techniques that has allowed scientists to know how biology works at the cellular level, and is basically ubiquitous in biology laboratories involved. There are issues with it, like everything, but the insights it gives are invaluable, and it will be a long while (I think) before it loses its utility.

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Cochlear implants – human ingenuity at its finest

My friend Brad, who had an article written about him on Boston.com, is deaf and has cochlear implants. These devices are one of the most incredible feats of human engineering, devices that are implanted into the head, take sound and, using an electrode, transmit that sound into something your brain can recognize. If you’re like me, you had no idea such things existed, but cochlear implants are some of the coolest biomedical devices ever invented, in my opinion. They make me think, “Doctors can do what now??”

What a cochlear implant looks like on a person

Before I can tell you how they work, I have to talk about hearing first. Your ear is divided into three parts. Sound is collected by the external ear, which goes up to your ear drum. The ear drum transmits those sound vibrations to the ossicles (hammer, anvil stirrup if you remember, the tiniest bones in the human body), which reside in the middle ear. The ossicles then transmit that energy into your cochlea, or inner ear.

An ear

The cochlea is a snailshell in your ear basically. It is a hard bone that houses a series of cells, which coil around a central axis. The most important cells in it are the sensory cells of hearing, which translate the sound that’s traveled all the way through your hearing systems into a series of neural impulses, to be interpreted by the brain.

A cochlea with the bone removed

The most common form of hearing loss, called sensorineural hearing loss, is due to the death of some or all of these sensory cells, and the neurons that attach them to the brain. These cells never come back after they die, whether by disease or drugs or loud noise. I work in a lab that is trying to find a way to regenerate these, and believe me, it’s going to be a long time before anyone succeeds in putting the ear back to how it was before damage (wear earplugs!!!!).

Cochlear implants are really the last option for people with severe sensorineural hearing loss, the kind that can’t be helped by hearing aids. They, for the most part, bypass every step that I’ve described, up until the last one. The implant has external microphones that pick up noise, and an electrode that runs all the way into and along the length of the cochlea. These electrodes stimulate the nerves along the cochlea, which transmit the perception of sound to the brain.

Schematic of a cochlear implant

Think about that. Cochlear implants literally take microphone and then directly stimulate the nerves that are associated with perceiving that sound. As far as I know, they are really the first devices that (mostly) replace a sensory organ, and the fact that it’s the ear is amazing. The cochlea is encased by the hardest bone in the human body, is incredible sensitive to any sort of disturbance, and is one of the most surgically difficult organs to reach.

They’re not perfect. For many people they don’t work, or (like for Brad), they only give the sensation of sound without any meaning. But for a lot (majority I think) of people with them, they give enough hearing that people who would otherwise be profoundly deaf actually have some measure of hearing. Ultimately their quality of life is improved tremendously.

Everything about the cochlear implant is amazing, and while hopefully someday they will become obsolete as regenerative medicine matures, they are a testament to human ingenuity.

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The world’s largest toilet – the Pacific Ocean

If you don’t know what the great pacific garbage patch is, basically all the plastic things we use in our lives – forks, straws, pens, lighters, buckets, car parts, TV’s, etc., etc., etc. – are designed to last for a really, really long time, and when we throw them away they have to go somewhere. That somewhere is the ocean.

The New England Aquarium holds a series of lectures, and for a class I went and saw Anna Cummins of the 5 Gyres Institute give a talk about where this trash goes. Some of it winds up in land fills, some gets burned, some gets recycled (but that’s more of a myth than reality, according to Cummins – I will say more about this in a bit), but a lot of it winds up flowing into the oceans.

Circlulating ocean currents collect trash

Circulating ocean currents called gyres collect trash

Imagine a thin soup of tiny, colorful plastic chips (plastic gets degraded by UV light, so as it floats in the ocean it degrades into almost sand like particles), interspersed with a few larger chunks of fishing rope, bags, buckets, car parts, and whatever else you can think of that’s made from plastic. This soup circles around the Pacific and is estimated to be between the size of Texas to twice the size of the continental US. And this is only in one ocean. It really doesn’t take a scientist to imagine the kind of impact that has on the environment, and the statement that makes as to how humans treat the ocean speaks for itself.

Cummins and her husband holding a sample of sea water, filled with plastic, from one of their expeditions

What Cummins and her institute does is relatively simple. They sail the worlds oceans, dragging a net behind their boat, record the amount of plastic they find, and then try to raise awareness of this fact: “I’ve [Cummins] spent the last two years sailing over 25,000 miles across five oceans, and we have seen evidence of plastic pollution throughout.” She called these garbage patches, which concentrate in large circulating ocean currents called gyres, “a toilet bowl that never really flushes.” She highlighted her talk with a lot of images of animals in pretty bad condition, especially dead albatrosses with stomachs full of plastic.

A dead albatross, stomach full of plastic

The major problem here, is not what to do about the trash in the oceans. It’s there, will be so incredibly difficult to get rid of that it’s almost not useful to think about it. The problem is how do we stop plastic from getting into the ocean? That, and awareness, is Cummins’ ultimate goal. Getting rid of the plastic that’s there is perhaps impossible. There’s just so much of it out there, and no one has come up with a good way to get rid of it yet.

Recycling plastic isn’t even a good solution, according to Cummins. A large portion of the plastic you recycle so diligently is still put into landfills, or sold to other countries with far looser environmental laws. Googling “plastic recycling myth” yields almost two million entries.

So Cummins thinks that the most important thing, for now, is to try and stop using disposable plastics. Her message: Those straws you use at restaurants? Stop. Drink out of the cup. Plastic bags? Please stop – get a reusable bag. Get glasses for parties instead of disposable plastic cups, a zippo instead of bic lighters, even reusable pens instead of those disposable plastic ones. If people would start using reusables consistently, that would be the first major step toward slowing down the trash-i-fication of our oceans.

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The science of cooking

Perhaps the only time I’ve ever been jealous of a Harvard undergrad was when I learned that they could take a class on Science & Cooking for credit, a class where you learn science and cooking from celebrity chefs. This class made headlines around the world when it debuted last year, and 300 lucky undergrads got to rub elbows with some of my heroes.

Luckily this year it’s been modified to include a series of public lectures. Still, while we sit and watch, undergrads get to actually cook with chefs like Jose Andres, Wiley Dufresne, David Chang, and (maybe) Ferran Adria. If you know who these people are, you’re probably like me and cursing the heavens for not working hard enough and getting into Harvard solely to take this class, but if you don’t, here’s an overly quick introduction to the world of molecular gastronomy.

Molecular gastronomy is basically a style of cooking that tries fuse science and food. The idea is that a scientist-chef can take a knowledge of the biochemistry and physics of the process of making food, and translate it into an unreproducible tasting experience, at least compared to traditional cooking techniques. Using different emulsifiers, taste and texture modifiers, strict control of temperature, smoke and air and foams, and dozens of other techniques, this style of cooking is basically the equivalent of modern art on the plate – sometimes jarring, unbelievably stimulating, and unlike anything that has ever seen a plate before.

Pea shaped eggs and an egg-yolk shaped pea, the magic of sodium alginate

I don’t want to get too heavily into the science, but I do want to give an example. Sodium alginate is the salt form of a chemical isolated from seaweed. It is a natural gelator, meaning that it traps water in between its molecules, creating a jello-like texture. The interesting thing about alginate is that it only forms a gelatin complex in the presence of calcium chloride, meaning you can take a flavored water (e.g. a pea slurry), mix in some alginate, drop a spoonful into a sodium chloride bath for a minute, and kablam, you have peas that have the same texture and look as an egg yolk (topic for another blog post, aginate is actually used in drug delivery systems as well). As a natural consequence of the nature of this style, practitioners of molecular gastronomy are the perfect guests for a lecture series titled Science & Cooking.

Turtle dove with tuna medulla, enokis and samphire

Like art, there are a few masters and there are a large, large number of people who really don’t know what they’re doing. THE master however, as iconic a figure as there is in the cooking world today, is Ferran Adrià. The creative hurricane that fueled the modern boom in molecular gastronomy, the Catalonian is, to many, the greatest chef alive today, and his elBulli (recently closed) the greatest restaurant. I could wax poetic about Ferran for hours, or lament over how we will probably never get the chance to taste his food, but I will have to save that post for when I (hopefully) attend that lecture. For now, I must talk about the lecture I was able to attend.

elBulli, on the Catalan coast in Spain. Only open for for a few months a year, it operated at a massive loss, even with amazing demand. In 2010, they served 8,000 diners, but had over 2 million requests.

If Ferran is the messiah of molecular gastronomy, then José Andrés is his Paul. You can read about him at your leisure, I cannot do justice to his fame and accomplishments here, but in his lecture/demonstration this past Monday, his enormous passion for cooking was more impressive than his resume. He is an incredible chef and businessman, one of Ferran’s first apprentices on the Catalonian coast, and is now, in my view, the rock on which Ferran’s church will be built. The lecture on gelators was very interesting, and the techniques and ingredients something I will try to learn, but I was struck by how José, an icon in his own right and definitely more financially successful than Ferran, made sure that the audience, perhaps 200 strong, knew that none of this would be possible – molecular gastronomy, a class at Harvard, the evolution of cooking, everything – without Ferran and elBulli.

Pickled kombu seaweed caramelised in matcha tea

José is one of the few people I think truly merits the description “larger than life,” someone who’s not that tall, a big portly, but seems like he’s 200 feet tall. I was in the front row and asked him a question about criticisms on the safety of these strange ingredients and techniques he was demonstrating. As he towered over me, his voice almost a whisper, but still booming (probably because of the mic, but maybe not), and defended his style of cooking, his business, his mentor, his life, I was a little afraid I overreached with my question. But it was still damned cool!

Ferran and Jose

Their concept of food, these two master artist-scientist-chefs, is different, very different. They don’t perceive food the same way a lay person does, but I would be an idiot to even try to interpret. But I do I feel that for them, food is a a gateway into people’s hearts and souls, and that they can move people in a way that no other kind of art can. With food, they can tap into every sense a human has, they can play with all the tools of perception we have as a species, from the brain down.

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