Author Archives: sainan liu

The CRISPRs Fever

You may remember from biology textbook that we can edit genetic material using restriction enzymes, a DNA-cutting protein structure. Using this we can learn about gene functionalities, search for disease treatments or increase yields of crops. Controversially, it also made unnatural creations possible. However, different gene targets require different enzyme structures, just like to open different doors you need different keys, and making these “keys” turns out to be complicated, expensive and time-consuming, which might have kept most of the “fantasies”, such as “super human” or other wired things, away from reality for now for better or worse.

by PuraVida_Fotografie from Google Image "genetic mutation" Labeled for reuse

by PuraVida_Fotografie from Google Image search “genetic mutation”, labeled for reuse.

However, what if all the “doors” also have the same type of “digital locks”, and all you need to change is the password? CRISPRs (clustered regularly interspaced short palindromic repeats) turns out to be this “lock”. It contains repeated sequences sandwiched with spacers (unique genetic information) in between. The spacers are external virus genes kept in bacterias and served as the “criminal records” so that when invasion happens again, the bacteria can send an “army” of gene-cutting enzymes, called Cas9, to cut the recognized viruses’ DNA apart.

"Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA" by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki - Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

“Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA” by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki – Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

In 2012, scientists have proven that instead of making restriction enzymes for different genes, we can simply replace these “criminal records” and use the same Cas9 “armies” to cut desired genes with much less time and cost. You can find the details in this following video.

YouTube Preview Image[by McGovern Institute for Brain Research at MIT]

Nature , Science and many major media have unanimously deemed CRISPRs to be a revolution. Radiolab has discussed its ethical controversies as if the realization of the technology is right around the corner. It has been portrayed as such a simple and approachable method that people even claim to provide CRISPR DIY kit for experiments at home.

However, I think despite these attentions,  the reality is that we are still far from ready to harness CRISPRs. Although many researches has already been using it to edit genes in a variety of bacterias, plants, and animals within a short 3-year period, few studies focused on the limitations and functions of CRISPR itself. Some research was done too early without waiting for the technology to mature, such as the research using human embryos, which has resulted in a less satisfactory result. Some researchers commented that CRISPR can be less accurate than expected and may not be the most efficient and cost-effective solution for certain problems on Quora. Scientist Konstantin Severinov on Quanta Magazine also pointed out that it is still unknown whether defending invaders is the major usage of CRISPRs since many of these spacers appear to be genes of viruses that are long gone. It might be a good time now to slow down and maybe build the technique from ground up concretely first.

by Sainan Liu

Can we predict the future?

back to the future II dash board

October 21, 2015 by Mike Licht from Flickr Commons

In celebration of the  “future day”, Oct 21, 2015, from Back to the Future II, many media have listed things about what the movie has predicted right, and they actually found quite a few. This might not be that surprising to you, since they were often based off some advanced technologies at that time. However, all fantasy aside, from a scientific perspective, as technology advances and more data is accumulated from our everyday life, can we actually predict the future?

Predicting the future has been a very attractive scientific topic from all times. We have already been trying to predict weathers by monitoring clouds and winds, stocks by monitoring the market performance and related information, and even politics. Every year, we also use data of influenza cases and circulating viruses around the world to make vaccines predications for the flu season. Just like the movie, we managed to predict correctly for quite a few times, but since it’s not a movie, when the prediction is not correct, sometimes the consequences could be heart-breaking. What can we learn from these?

To predict the future, the first thing we need to know is that not all false predications are tolerated equally. For example, if a forecasted rainy day turns out to be sunny, people probably won’t complain; however, for a hurricane like Patricia, the “strongest landfalling pacific hurricane on record“, missing the prediction of its arrival would be very devastating. Thus, for a better prediction, we often need to consider the costs of false positive/negative results.

Secondly, we learned that we may not be very good at predicting what is going to happen in the next 30 years, but we could get pretty good for the near future. You may have noticed that the weather forecast for tomorrow is much more accurate than the forecast for next week. This is because we have more relevant data for tomorrow’s weather prediction. It might seem intuitive, but having more data is crucial for all kinds of predictions. As Kenneth Cukier would probably say , the more, the merrier, based on his TED talk here.
YouTube Preview Image
[by youtube channel TED]

Thirdly, based on what I have learned from my machine learning class (it studies algorithms that “learn” from existing data), averaging predications from multiple qualified good models makes the prediction more trustworthy. Taking global warming for example, despite the fact that different prediction models don’t agree on the level of global warming 85 years from now, they do agree on the trend if we average them all together especially in the near future.

Global Warming Projections by Pflatau from Wikipedia

Global Warming Projections by Pflatau from Wikipedia

Finally, we should always be cautious about future prediction. Just like in the movie, our predication model is only good if we don’t act on it based on our prediction; once we intervene, the prediction would no longer be valid. As most movies would tell you that you have already entered a parallel universe.

Earth From Google Image

Earth From Google Image

by Sainan Liu

Video

Is in vitro meat the future meat source?

 

Cell Culture, Author: Umberto Salvagnin, Source: Flickr Commons

Cell Culture, Author: Umberto Salvagnin, Source: Flickr Commons

While “Humans no longer raise animals for food” is still a science fantasy in TV shows like Star Trek, growing meat from a Petri dish as one solution to achieve this goal is no longer a far-fetched dream.

Around 2000, Morris Benjaminson, has successfully produced fish fillet from goldfish skeletal muscle in the lab, and deep-fried their result. “It looked and smelled pretty much the same as any fish you could buy at the supermarket,” says Benjaminson (Scientific American).

Two years ago,  two people tasted the in vitro beef muscle prepared as a burger patty at a news conference in London for the first time.

YouTube Preview Image
[by youtube channel Maastricht University Cultured Beef]

They both agreed that the texture was quite close to meat. “I know there is no fat in it so I didn’t really know how juicy it would be, but there is quite some intense taste,” said one taster.

We seem be able to see lab-grown meat in production fairly soon. However, would in vitro meat be our future meat source even if they taste no different from natural meat?

I think there are some obvious advantages. First of all, in vitro meat allows us to control its nutrition content, hence it can be much healthier than farmed animals. Secondly, reducing animal farming can significantly reduce animal cruelty, the burden on land use, and animal waste. Last but not least, from a environmental point of view, in vitro meat can even reduce green gas emissions. For example, cattle farming is infamous for their Methane emissions (Food and Agriculture Organization of the United Nations), and Methane has a global warming potential 72 times more than carbon dioxide over a 20-year-period based on a 2007 report by  Intergovernmental Panel on Climate Change (IPCC).

Name: Confined animal feeding operation, Author: SlimVirgin, Source: en.wikipedia

Name: Confined animal feeding operation, Author: SlimVirgin, Source: en.wikipedia

However, people do argue that there might be some disadvantages that we should look out for. For example,  Science Friday  has pointed out a few down-sides such as reduction on animal by-product, and the $300,000 price tag for a beef burger patty. However, I think these are trivial problems given that animal by-products have already been largely replaced by artificial materials, and the scientists were quite confident about cutting the price down. The most interesting point is that they mentioned that it is just like industrial revolution, artificially producing natural product is always going to cost more energy, which is not necessarily a good thing for the environment. I agree that it does seem like more energy cost is inevitable, but energy related environmental damage is something that we have already been working on for years, and it is up to us to prevent it from very beginning.

All in all, I think with a combined effort with other solutions that we have already been working on such as animal farming regulation, and a global effort on reducing green house gas emission, there is definitely a place for in vitro meat to benefit us to some extend in the future.

By Sainan Liu