BioBricks

MIT has created BioBricks, analogous to Lego Bricks and standard electronic circuit components, from which complex biochemical pathways can be created using more fundamental known biochemical pathways.

Now, don't get this wrong, but it is in no way something very new. MIT has been hosting the BioBricks competition for two years now, and BioBricks have been in development for two years as well. BioBricks are essentially a catalog of standard biochemical parts that can be assembled in a variety of ways to create functional chemical/biological/electronic/physical (almost everything) pathways for synthesizing products. Best of all, by isolating the pathways required and providing the raw materials for synthesis of the product needed, a researcher can achieve more efficient production of that product as opposed to providing micro-organisms (such as bacteria) with those raw materials, as micro-organisms tend to have side-reactions going on inside their cells that use up the raw materials but do not produce the desired product.

Additionally, by cataloging these standard pathways, one would be able to, to quote EE Times, "assemble working systems at the abstract level described in the catalog and pass the design to then another group of biochemists for synthesis in a biological manufacturing system." What it means is that one can work like an electronics engineer - design a circuit on a computer and pass it onto the production facilities to produce the desired circuit.

Now, what are the possibilities capable with BioBricks? From my standpoint, I believe we will be able to achieve advancements in two fields - disease treatment and energy conservation (cheers to you, Mridul!)

In disease treatment, I believe that we will be able to synthesize weakened versions of disease-causing organisms, perhaps by altering the genes that produce their proteins so that a particular protein is missing from their body that would render them harmless, while still preserving the overall structure of that organism. In this way, we could produce a - yes, you've got it - vaccine against many different types of disease-causing micro-organisms.

In energy conservation, imagine if we could synthesize, using the enzymes synthesized via the BioBricks pathways, to impregnate the light-energy-capturing portion of solar panels in a more concentrated and densely-packed manner. This would help reach greater efficiency in energy capture, and, since the impregnation is catalyzed by reusable enzymes, it would also help to reach greater cost-effectiveness. Extending beyond that, it would help make solar energy more affordable to commoners, because the use of enzymes in this synthetic process would help achieve economies of scale, and hence help proliferate the use of solar energy in the process too.

I guess Samsung would love to invest in this. After all, their most recent ads are telling us, "After all, it isn't that hard to imagine."

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Edit: Mridul pointed out that "After all, it isn't that hard to imagine." comes from Samsung ads, not Panasonic ads. I've edited it above. Cheers to you!

Virus Transports DNA

So it's real, viruses can be designed to inject cells with DNA. Lentiviruses can transport DNA into cells with more consistency and efficiency than traditional methods can, which will improve the rate of creation of transgenic animals. Now, that is something I didn't know. Seems like I'm outdated for now.

However, the viruses infect every single cell they meet. What I envision is a virus that will home in on cancer cells, perhaps with a single identifiable cell surface protein that will serve as a marker for the virus. The virus will deliver the desired gene only into the cells with that protein marker, following which, it will insert the gene into those cells. If we can use siRNA inside the virus, then we can theoretically cause cancer cells to die.

Click on the title of this post for more information.

A Virus That Can Discriminate

That is the central theme of Fredrick Forsyth's book, and Hallmark Channel's latest movie, "Icon".


The destruction of the Russian nation by means of a simple strand of molecules. A virus. A virus that can discriminate. A virus that can discriminate between races, religion and region. A virus that can kill selectively, wantonly, and massively. A deadly virus. A virus from hell.

But is it practically feasible? I believe not. But I can imagine an even more deadly scenario. A deadly scenario that would actually be beneficial to us, humans.

The virus in question would have to be programmable, in order for it to descriminate between different groups of people. A virus, being a physiological pathogen, would be able to discriminate between physiological differences in people. But would it be able to discriminate between the arbitrary, non-physiological differences between different groups of people?Very evidently, this wouldn't be possible. A simple example would be to use a hypothetical virus that should be able to infect all Arabs (no offense here, please!). This sounds plausible enough - many individuals with Arabic blood would probably have a similar weakness to its virus. But let's say the virus was re-programmed to target all Muslims (again, no offense here!). Would this be practically feasible? Evidently not. Religion, being an arbitrarily defined trait of a human, which also happens not to have a physiological-based discriminator, would be a poor candidate as a victim for the virus' lethal capabilities. In other words, there wouldn't be a single cell-surface protein or receptor that would be present in all Muslims that would be their Achilles heel. That would render the virus useless wrt, (please, no offense here!), infecting all Muslims. Which, then again, would be a thankful thing. I wouldn't want to see my Muslim friends go off to see Allah before I see the external part of our universe, if you get what I mean.

But think again. The virus' discriminating capabilities would need to have a physiological basis. Yes, it would have to be rooted in what we know about cells, their differences, and their roles in the human body. Now, wouldn't that be fascinating? Imagine what we could do with engineered viruses - we could cure cancer.

How could this be possible?

Simple. Let's build on recent developments.

MIT's professors have identified the use of siRNA molecules in splicing up the oncogenes that cancer cells express during their lifetime of growth. ('Lifetime' isn't exactly the best word to use, because 'cancer' essentially implies 'immortal' - they do not undergo apoptosis, or programmed cell death, like the rest of our body's cells.) siRNA molecules can do that to any gene - the only restriction is that the siRNA molecules must originate from the gene that has to be spliced up. Splicing, or cutting, up the gene will render it useless. In the case of oncogenes, they're absolutely essential to the growth and development of cancer. So splicing up the oncogenes should, theoretically, help halt the growth of cancer.


But then again, so what?

Well, let's take a look at the structure of a virus. (My favorite is the one that many people see - the bacteriophage.) A virus generally has a strand of nucleic acid, containing their genetic data for its own replication in a host's cell, and a protein coat, to protect the nucleic acid from degeneration. The part of the virus that is in interest is the nucleic acid.



There are two types of nucleic acids, deoxyribonucleic acids (DNA) and ribonucleic acids (RNA). Both are capable of storing genetic information, and both can direct protein synthesis. Viruses can hold RNA as their genetic material. When viruses infect a cell, they inject their own genetic material into the host cell, which will then interfere with the host cell's ability to do protein synthesis. It is this property that we need to harness to use a virus in combating cancer.

With the advent of "designer drugs", the processes that I'll be discussing likely won't be a distant dream of the future. If we can insert siRNA into a virus and join it up with the other forms of genetic material that are already present inside the virus, then we could potentially create a virus that, with the help of cell-surface signalling proteins, could home in on cancer cells (which would have that unique cell surface identifier I discussed in my 2nd post) without infecting our own body's cells. It would then inject its own genetic material and the siRNA, which would then help to splice up the oncogenes that are so vital to the survival of the cancer cells. In other words, viruses are our vector - much as viruses require a vector to transmit from one person to another, we now use viruses as our "shuttle bus" to transport the siRNA from the lab into the human body.

Ah. Finally got this idea off my head and onto my blog. Cheers to Blogger for this.

Arrow of Time

After reading "A Brief History of Time" by Stephen Hawking, I finally think I have an idea of what "time" is as a concept, and best of all, how to visualize it.

I used to think time could only go in one direction. It moved "forward", so to speak, but not "backwards". The relative directions was determined by what Hawking calls "psychological time", something that we perceive in our minds.

However, in reality, the laws of physics at the microscopic time level are "symmetric", that is to say, if time goes backwards or forwards, the equations that describe physical processes are the same.

What then determines the direction of time? Well, the clue comes from the Second Law of Thermodynamics (SLOT), which states that all work tends towards the production of greater entropy over time. Entropy, so to speak, is the concept of disorder. Hence, the SLOT tells us that as time progresses (i.e. goes forwards), the amount of disorder in a system increases. It's much like how we neglect our study tables as time progresses, resulting in greater mess on it.

Well, equipped with this knowledge of entropy and time, we can then define time as pointing in one particular direction - forwards. It is because the SLOT doesn't permit entropy to increase spontaneously; it only permits entropy to decrease. And since time progresses in the direction that entropy decreases, it can only point forward.

It is much like an explosion. As time progresses forward, we see a bomb progress from being a small ball full of chemical energy to a smattering mass of pieces and lots of thermal energy. Disorder increases as time progresses. That's how time progresses in the macroscopic world.


That is the arrow of time.

Blackholes - the *real* way to visualize them

Has anybody actually tried to go beyond the artists impression of a blackhole? See below for the classical depiction of one.

It pictures space-time as a two-dimensional fabric, which gets warped in a perpendicular direction. The act of making it warp perpendicularly (in most cases, vertically) is to help visualize an object falling into the deep pit that eventually collapses into a singularity. After all, it is a convenient depiction. The diagram likens it to a vortex, in which swirling objects get thrown into it, much like when we have whirlpools that suck everything to the depths of the ocean.

However, this is a misleading diagram. It's to help visualize the warping of space-time. However, space-time isn't two-dimensional; space-time is linked together, bringing the three spatial dimensions together with the fourth. In other words, space-time is a four-dimensional concept. And that is something tough to visualize.

A better way to visualize a black hole in the midst of a three-dimensional space is to think of it as a dot. After all, that's what the penultimate distinctive feature of a black-hole is - infinitely large amounts of matter compressed into an infinitely small space: the dot.

The artist's impression below would probably be a better description.

Here, the artist shows the dot in an exaggeratedly large manner, so as to ease visualization. In this, the black hole sucks in all the hydrogen and helium and all other matter from a star neighboring it.The black hole, however, is spherical, and sucks in matter from all directions - up, down, left, right, forward, backward (it all depends on your spatial orientation).

I was thinking, if we took the space-time visualization a little further, then perhaps the warping of the space-time fabric could be extended and repeated in a pattern such that there would be an infinite number of vortices pointing in an infinite number of directions. That would help to explain the warping of space-time in all three dimensions of space such that matter fell in from all directions.

Now, the next big problem is figuring out how to visualize time. That's probably in Stephen Hawking's "A Brief History of Time", Chapter 9 "The Arrow of Time". And that's for next time. ;)

Cancer Magic Bullet

Haven't we all noticed how the notion of a cancer magic bullet has actually died off? Isn't it a pity? Well, I don't think that it's wholly impossible. I think we're just limited by what we know.

Cell biologists and oncologists know what each kind of cancer is like. Melanoma is a cancer of the skin. Lymphoma is a cancer of the lymph nodes. Leukemia is a cancer of the blood. Then, there's stomach, brain and lung cancer. With so many types of cancer, isn't it going to be impossible to combat each and every single type?

That's why, the prevailing mentality amongst specialists tells us that each cancer, though not incurable, is mutually unique. That is to say, we can't use one drug to pin-point and destroy the cancer cells. (Read here for a better understanding.) Indeed, what MayoClinic says seems to confirm my own views that we don't know enough about cancer to produce a magic bullet.

Here's my vision.

We're right now in a circle that limits our knowledge of cancer. Presently, we're filling up this circle of knowledge, until we reach the critical point where we max out the space inside it. When we reach that critical point, we can break through the circle, and finally pin-point the Achilles heel of cancer cells.

From what I know (A level biology isn't a lot, but it's enough to stimulate imagination) there has to be some protein, some gene, or some metabolic process that is unique to, or at least commonplace amongst all cancers, and is totally essential for the cancer to survive. If we can identify that common weakness we'll be on the way to curing it.

As it looks now, it'll take many years of painstaking research and cataloging before we can identify that common weakness. It'll be much like what Hubble did for astrophysics, painstakingly cataloging the stars in the night sky and their distances from Earth. But I think I'll be up to the challenge.

First Post

Hello World. Welcome to my world. My world of imagination and ideas. My world of creativity and construction. This is where I will post my crazy visions of the world, plus how I believe I can scientifically achieve them. It is a world of my imagination rooted in reality.

Enjoy the ideas as I develop them, and please comment on them to help me assess its possibility.