Monday, July 26, 2010

Genome sequencing? There's an app for that.

Richard Dawkins talking about the Genomic Revolution.

I think we'll look back on 2010-2011 as the tipping point for the Genomic Revolution, just as we look back on 1993-1994 as the tipping point for the World Wide Web.
..and the Genomic Revolution will be every bit as transformational as the World Wide Web, if not moreso.

Saturday, July 24, 2010

The Future of Health Care - The Genomic Revolution

For the first time in decades, we are due for a completely transformational change in health care. We are on the cusp of the Genomic Revolution, and we will start seeing the earliest results in the immediate future. Personal genomics – the practice of tailoring prescriptions, treatments, and lifestyle choices to an individual based on their genes – will soon depose the old paradigm of medicine. No longer will doctors merely give patients the drugs with the highest chance of success; they will be able to predict whether or not the drug will be effective for a specific person. No longer will patients try to base their diet and exercise habits on generic recommendations of what is healthy and what is not; instead, they can determine the healthiest lifestyle for their genetic makeup specifically. Health care will become mostly preventative, rather than reactive.

Why now? What is the driving force behind this paradigm shift? For the first time in human history, we have enough computing power to cheaply and quickly sequence the human genome. In the very near future, nearly everyone will have access to their entire DNA code, which they can carry on their smartphones. When Craig Venter became the first person to have his genome sequenced in 2000 as part of the Human Genome Project, it cost $3 billion and took thirteen years. When James Watson had his genome sequenced in 2007, it cost $2 million and took two months. Today, sequencing a human genome costs about $6,000 and takes a couple weeks. Within the next year, it is very likely that companies will offer genome sequencing for less than $1,000. Some observers view the $1,000 mark as a tipping point: the point at which average people can afford the service, and at which health insurers may start covering it. And after we have $1,000 genomes, $1 genomes won’t be far behind. Let’s not forget that the cost has dropped nearly a thousandfold in the last three years. Fast-forward a few more years, and it is conceivable that the cost of genome sequencing will be essentially nothing. I envision a day in the not-too-distant future when Walgreens and CVS will have self-service genome sequencing machines, as quick, cheap, and user-friendly as self-service photo machines.

Of course, merely knowing one's genetic code is worthless without knowing how to interpret it. While biologists have identified thousands of disease markers, there is vastly more that we don’t know about our genetic code. Some services available now, such as Google-funded 23AndMe, can test DNA to determine one’s predisposition to a narrow range of diseases, but this is only the tip of the iceberg of what is possible. As the cost of genome sequencing approaches zero, nearly everyone will have it done. As the total number of genomes grows from thousands to millions to billions, scientists will have a treasure trove of data to analyze diseases and patient responses to medication. A machine called a microarray allows scientists to compare different DNA sequences and search for correlations. As more and more human genomes are available to be analyzed, patterns will become more evident and it will become much easier to unearth the specific genes associated with certain diseases. Patients who know the diseases for which they are at risk will be able to modify their lifestyle to prevent them from arising.

Those who are unlucky enough to get a disease in spite of (or because of) their lifestyle will have access to much more robust treatments than those currently available. By pinpointing the genetic location of a particular disease, scientists will be able to understand what caused the disease and how it can be reversed. Think of our genetic code like a computer program: Understanding the cause and location of the bugs will enable us to fix them. In the slightly more distant future, it will be possible to directly repair defective genes, such as those that cause cancer, through genetic therapy.

The next ten years will be the most transformative decade in human history for medicine, as we finally unlock the secrets of our genetic code which have been a mystery since the dawn of humanity. The things I have described here are by no means a comprehensive description of the benefits of the Genomic Revolution, and the new paradigm will not be without problems of its own. To be continued in another blog post…

By 2011 – At least one company offers genome sequencing for $1,000 or less
By 2014 – At least one company offers genome sequencing for $100 or less
By 2019 – Over half of all Americans have had their genomes sequenced
By 2021 – U.S. sales of personalized medicine (i.e. drugs tailored to the patient’s specific genetic profile) are greater than sales of non-personalized, mass-market medicine

Sunday, July 11, 2010

Rebuttal to the Simulation Hypothesis

According to Nick Bostrom’s simulation hypothesis, every universe’s inhabitants would be equally likely to be living in a simulation, even if they were running simulations of their own. This leads to the uncomfortable conclusion that our universe is much more likely to be one of a huge number of simulations, rather than the one parent universe.

From a logical standpoint, this argument makes sense to me. But I’m always eager to poke holes in philosophical arguments, so here’s my best rebuttal as devil’s advocate. It doesn’t directly attack the logic of Bostrom’s philosophy; rather, it creates a probabilistic argument that we are NOT a simulation.

Let’s assume that simulations can be “turned off” by the parent universe at any time. Perhaps the inhabitants decide that the simulation is no longer needed for whatever reason, or perhaps the simulation is accidentally destroyed, or perhaps they are in a simulation themselves which is turned off by their parent universe. If this is the case, it would break the simulation chain. If Simulation A was the parent of Simulation B, which was the parent of the Simulation C, which was the parent of Simulation D, the inhabitants of Simulation A would be able to break this chain and destroy all of the simulations in this chain by turning off Simulation B.

The simulation hypothesis concludes that we are in a simulation in all probability, and that every universe is equally likely to be a simulation. This means that the universe that begat ours is also probably a simulation, as is the universe that begat our parent universe. If this is the case, it would be very likely that our own universe is merely one node in a huge chain of parent universes.

But this creates an interesting question. If any of those universes could break the chain at any time by turning off their simulation, the probability that not a single one of them would do so must be extraordinarily low. This strongly suggests that we are not in a simulation.

There are a couple of responses to this argument which I can foresee, so allow me to preemptively address them. Some might invoke the Anthropic Principle. It doesn’t make sense to marvel at the unlikelihood of our own existence, they will reason, because if our universe had been turned off we wouldn’t be here to speculate about it. In my opinion, this is a flawed application of the Anthropic Principle because there is another plausible explanation for our existence: Our simulated universe hasn’t been “turned off” by any of its parents because they don’t exist. We are the original universe.

So we have two possible explanations for our own universe. Either we are in a simulation, and are here due to the infinitesimally unlikely whims of an unimaginably vast chain of parent universes…or we are simply not a simulation. If these are the two possibilities, the latter seems much more likely from this probabilistic standpoint. It also has the advantage of surviving Ockham’s Razor.

What do you think? Is my probabilistic argument for our actual reality as strong as Bostrom’s argument for our simulated reality? What flaws do you see in my logic?

Sunday, July 4, 2010

The Future of Agriculture - In Vitro Meat

With the speed at which biotechnology is progressing, it seems very likely that by the end of the decade, we'll be able to grow meat in laboratories at a price that is competitive with meat grown in ranches. It is already possible to produce it, but as of now it is horrendously expensive and has the texture of runny eggs. Not exactly appetizing. Scientists have learned that they can manually "stretch" the cells in a laboratory to mimic the muscle movements of a live animal. By the end of the decade, it is likely that scientists will have the ability to produce lab-grown versions of meats like hamburgers and hot dogs, for which texture is not as important. It will probably take several years longer before we get to taste any lab-grown steaks.

New Harvest is a non-profit dedicated to the research and development of in vitro meat. PETA has offered a $1 million reward for the first team that can develop lab-grown chicken with the taste and texture of real chicken (although their 2012 deadline makes it highly unlikely that anyone will claim the prize). How would the world change if we switched from farm-grown meat to lab-grown meat? The benefits of this are hard to overstate.

The environmental impact will be enormous. Every pound of beef requires 30 or more pounds of crops to feed the cow. Pork and chicken aren't quite as crop-intensive as beef, but nevertheless consume a very large amount of resources. This is a huge drain on our water supplies and farmland. If our meat was grown in a lab, it could completely eliminate these problems, freeing up our land and water supplies to be used for other productive things or returned to nature. Along with solar energy, this is the emerging environmental technology that I am most excited about.

The health impacts of lab-grown meat could be very large too. As it stands now, red meat is extremely unhealthy. It has been linked to heart disease, diabetes, obesity, and cancer. Growing our meat in the laboratory would enable us to tinker with the genes to make it more nutritious, and to control how much fat is in the meat. Imagine eating something that tastes like a cow, with the nutritional content of a fish. We would be able to eat some of our favorite foods as often as we wanted, without any guilt or negative health consequences.

Furthermore, those with moral or religious qualms about eating meat could sleep easily at night, knowing that no animal was killed just so that they could eat dinner.

I think that right now, the "yuck" factor might dissuade people from trying it. But this is really just a matter of how the lab-grown meat was marketed. If it had the same taste and texture of actual meat, I definitely could see this becoming very popular. And after it became commonplace, the "yuck" factor would disappear on its own. What do you think? Would you eat lab-grown meat, assuming it had the same taste and texture of regular meat, at a reasonable price? I certainly would. It could save the world.

(Donations to New Harvest are tax deductible under US law, and are spent on university research on in vitro meat. It's a great cause with enormous potential to transform the world.)

By 2022 - Lab-grown hamburger (with the taste and texture of real hamburger) is sold commercially, for the same price or less.
By 2029 - Lab-grown steak (with the taste and texture of real steak) is sold commercially, for the same price or less.