Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

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lksalinero
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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby lksalinero » Tue Aug 11, 2015 1:11 pm

I thought it was interesting that Dr. Gilbert included “the explosion in scientific manpower” as one of the main problems faced by science today. It seems to me that having more researchers could only be a good thing for scientific advancement, and that the solution to the problems described by Dr. Gilbert is not reducing the number of scientists, but improving training and education and developing new procedures for peer review and publication.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby uwogisele » Tue Aug 11, 2015 3:20 pm

This is quite an interesting article. One thing that was kind of shocking to me is when he said this, "Another major problem is the explosion in scientific manpower that has not necessarily led to the betterment of science, especially in biology. In fact, bad material that gets published has increased. In biology, the top journals – Cell, Science and Nature – have created a mess. They tell the authors “give me the headline, not the data”

I never thought for a second that some scientists just want to create headlines. Normally only the popular press wants to create headlines without real accurate information. The fact that all the hype about knowing about our DNA is not all that it promising to be wasn't surprising to me considering the two articles that we have been reading.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby fdtran » Tue Aug 11, 2015 5:07 pm

I really enjoyed reading this article because it provides insight into the misconceptions people often have about science and in this particular case it was the HGP. As an aspiring scientist, I found his advice at the end of the reading to be invaluable. Often times we read and accept things for what they are rather than question the claims and premises that they often entail. I feel that this class will help me a better think in this regard.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby twilliams » Tue Aug 11, 2015 5:38 pm

lksalinero wrote:I thought it was interesting that Dr. Gilbert included “the explosion in scientific manpower” as one of the main problems faced by science today. It seems to me that having more researchers could only be a good thing for scientific advancement, and that the solution to the problems described by Dr. Gilbert is not reducing the number of scientists, but improving training and education and developing new procedures for peer review and publication.


The second half of that sentence explains what he meant. The issue he was describing (if it actually excists, I cannot say for sure) was not the explosion of scientific manpower, but scientific manpower "that has not necessarily led to the betterment of science." He describes this later as more or less people who are doing science hoping to get famous by making some gigantic discovery. He isn't suggesting lowering the numbers of scientists, but increasing the number of scientists who are in the field for the right reason.

On an unrelated note, I love the last paragraph. Science is constantly changing and challenging what we know, that it demands we always have a healthy skepticism, even towards science itself. My favorite example is how Einstein refused to accept Heisenberg's Uncertainty Principle because he drastically warped how we view physics (and perhaps science in general), and it turns out all his objections failed. Another example to note was brought up in class earlier today, how epigenetics threw a monkey wrench into our understanding of evolution. Always question; at worst, you just strengthened the theory by proving why an objection doesn't work, at best you just made an important discovery.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby herrerajen » Tue Aug 11, 2015 8:33 pm

I was particularly drawn to Gilbert's response to the problems science confronts. Gilbert finds it problematic that money is consistently spent on easy solutions or immediate outcomes. Because of this, scientists are forced to only use the "current level of understanding" rather than something else could have been researched with the money or grant.
In a similar respect, this reminds me of the weight loss solutions that promise consumers they'll lose 10 pounds in 2 weeks.

I also found it interesting that he pointed to the "bad" scientific material that gets published as a problem. Science is upheld as the epitome of truth; therefore, when articles cite a study, most readers can be susceptible to believe the argument the article presents. Although he speaks in the context of biology, I think this is especially true in environmentalism/environmental studies or research. Oftentimes corporations will pay their private researchers to conduct a "study" that proves the corporation is not responsible for the toxins found in the nearby residents bodies. This study will then be published and therefore consumers of this media will believe dioxins aren't so bad for the body after all.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby euriekim » Tue Aug 11, 2015 8:53 pm

I really enjoyed Gilbert's interview. I liked that he was frank and realistic with his answers. He flat-out declared how scientists are spending too much money on problems that can have "immediate outcomes" and how, recently, so much bad material are getting published in science. I liked that he stated that "Big Data" is not a panacea to diseases because he wasn't over-simplifying the process or being overly optimistic. I also liked that he addressed the issue of big pharmaceutical companies and their interference with personalized medicine. People need to stop thinking that solely one medicine will work on an illness that different kinds of people, in different environments, have. Like Gilbert said, one person's cancer is not the same as another's.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby tschristoffel » Tue Aug 11, 2015 9:15 pm

I found this article to be very interesting. Gilbert's comments on the the "explosion in scientific manpower" did not surprise me. Sometimes it seems that the internet and television are being flooded with stories about new studies with sensationalistic titles. Wherever monetary and other incentives abound, it can be expected that people will try to cheat the system, harming society and bringing the innocent down with them, as detailed in some of the articles linked from the interview. I would have also liked to know Gilbert's opinion as to how society could change this, if such a change is possible.

Additionally, Gilbert mentions that "all statistically significant things are not biologically significant." Can anyone explain the difference to me? Is he simply referring to the problems that come with scientific studies (correlation vs. causation; confounding variables)?

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby dianalee » Tue Aug 11, 2015 9:19 pm

It was very refreshing to read Dr. Gilbert's interview. I love the fact that he gave honest answers to the questions. “It is common belief that once we can sequence the genome, we can edit it to have babies with higher IQ for example. This is a myth, because it is very rare that one gene corresponds to one property” This is an example that we won’t be able to delete a gene that will cause a disease to a person. I also like the advice he gave toward the end, “do not continuee science if it does not excite you. Science cannot be a nine-to-five job.” Reading this advice makes me feel more secure on changing my path from science field to architecture field.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby ktoporovskaya » Tue Aug 11, 2015 9:39 pm

I liked how positive this article was. Three things that jumped at me were the future work with the genome. Nobel Laureate expects the price for DNA sequencing to go down with the technological advances. Scientists are also working on personalized medicine that will cater to individuals instead of just generic drugs that are distributed now. The third was the big data- to find associations between genes and diseases. There is work to be done now that we have the full genome and these are promising steps that we are taking towards success.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby Bowen Tan » Tue Aug 11, 2015 11:40 pm

They are all great questions with great answers. From an aspect of the personalized medicine which is popular in recent years, sometimes it is fascinating to the public. It sounds like there's a doctor tailoring a patient by sequencing the patient's genome. Actually, it is a fake conception to the public. Even the most wealthy person is not able to make scientists do all the gene researches for his/her own genome. The precision medicine is a way more relying on some identified gene subtypes. Another question on ethics is, when the cost of sequencing one''s genome decrease into an extent which is affordable for most people, there should be some laws published to protect one's genome information and even prevent it from being edited abuse.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby KelseyBS » Tue Aug 11, 2015 11:57 pm

Like many of my classmates I really enjoyed this interview. Gilbert was frank and honest about science. When he brought up the "explosion in scientific manpower" and the media's interference with biological publications, it brought up this idea to me that online science articles are looking for big SciFi breakthroughs that will get them more views. Online journals tend to have attention and money as a higher priority than true honest scientific discoveries. People uninterested in real science don't want to read about the whole procedure behind experiments; they want to hear that they can finally take a ride on that hover board, order their dream baby online, download and 3D print that delicious deep dish pizza.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby pkshah » Wed Aug 12, 2015 8:43 am

I really liked this interview because the terminology that was used was relatively commonplace, and as a result, I was able to understand all of what Dr. Gilbert was saying.

I did not quite understand what Dr. Gilbert meant when he said not all statistically significant things are biologically significant. I am assuming that he meant that not all things that are statistically probably are medically likely? I think it would help if I had an example of how this works.

I fully agree with Dr. Gilbert when he was asked about what the problems science faces today are. It seems like practical applications for science are what are sought after nowadays. It seems that all people want to do with science is to better their quality of life, make money, or a combination of the two. However, it seems that the need for discovery for its own sake has diminished. As Dr. Gilbert says, we are only using what we know, as opposed to focusing on the vast majority of things that we do not. For example, when we discovered the electron we thought it was virtually useless. However, now we have an entire multi trillion dollar industry that is run on electronics. Even if we cannot see the value of it now, discovery for its own sake can have magnanimous practical applications in the future.

Finally, it is exciting to think of a potential future where genes can be sequenced at a local drug store. I know there has been heavy debate about whether it can do all of the things that we want it to do; however, it certainly cannot hurt (if the genome has been well curated).

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby eridolfi » Wed Aug 12, 2015 9:31 am

I think he gave a very holistic view of science and the issues surrounding it. I especially enjoyed that he mentioned that gene editing doesn't automatically equal genetic engineering of humans and the role of industry in science. I could see how pharmaceutical companies would see personalized medicine as a threat unless they were the primary owners of such technology.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby kgbaidoo » Wed Aug 12, 2015 10:37 am

I thought the interview was interesting because Dr. was very blant in answering the questions.We need more scientists like him.One thing that bothers me is that if the cost of sequencing one's genome is that expensive then why is the result not accurate for medical purposes? If I spend a billion dollars for service, I definitely expect the service to be excellent.I also love the part of the interview where Dr. Gilbert explained that sequencing of the genome does not help in improving the IQS of babies.I am glad he clarified this point becuase most people in our society are often mislead by certain scietists whose ineterst is to raise the hopes of people.

I also love that fact he advised student to follow and love what they good in and not what the crowd follows.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby lemacias » Wed Aug 12, 2015 11:01 am

I think that this article should be everywhere!! This is the type of questions (and answers) that we expect to be asked to a scientist who won a Nobel prize. It really catch my attention that he mention the role of big companies in the future of science and how they take advantage of the information to manipulate the consumer. Furthermore, the last two questions were the core of the interview for me. I took a writing in science class last summer and I realized how bad are some of the articles from prestigious sources presented and I couldn't believe it!. I agree with his last statement that science is a full time job and only people who are willing to go the full mile should be the ones considered as a real scientists.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby kgbaidoo » Wed Aug 12, 2015 11:03 am

I thought the interview was interesting because Dr. Gilbert was very blant in answering the questions.We need more scientists like him.One thing that bothers me is that if the cost of sequencing one's genome is that expensive then why is the result not accurate for medical purposes? If I spend a billion dollars for service, I definitely expect the service to be excellent.I also love the part of the interview where Dr. Gilbert explained that sequencing of the genome does not help in improving the IQS of babies.I am glad he clarified this point becuase most people in our society are often mislead by certain scietists whose ineterst is to raise the hopes of people.

I also love that fact he advised student to follow and love what they good in and not what the crowd follows.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby SamGarcia25 » Wed Aug 12, 2015 11:42 am

This article brought up an interesting and realistic perspective about the direction science is going today. One point that the person being interviewed made about sequencing the human genome is that the process is not as perfected as scientists claim it to be. This person had their own genome sequenced and noted the shortcomings of it afterwards. Then a question came to mind. How will people without biology backgrounds who get their genome sequenced from private companies know that it was done right? Especially if it is expected to cost a few hundred dollars by 2020, one would think it important that this is done correctly.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby JustinN » Wed Aug 12, 2015 12:44 pm

It seems like a lot of people are confused with the difference between statistical significance and biological/clinical significance so I looked it up. From what I'm getting, the scientific community is trying to come up with a stronger sense for testing data from experiments for "real world" significance. Statistical importance has become equivalent to a low enough p value. This means that it's highly unlikely that your data arose entirely due to chance, not that your hypothesis is actually correct. And then there's even the issue that your result might not mean anything in practical terms. Here's the paper if anyone else wants to look over it.

http://pubs.acs.org/doi/pdf/10.1021/jf401124y

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby nyonan » Wed Aug 12, 2015 12:53 pm

This article is incredibly interesting to me for the sheer fact that it gives a great example on humanity. Professionals of a field, while the field is relatively small, will be doing it because they truly love it. Thankless jobs are often the ones people work the hardest at. Then, as is said, you get an explosion in popularity which leads to my humanity comment. The second something becomes popular, there are those that view that as a cash cow. Suddenly, things are done solely for money (as it is the main driving force behind a lot of things) and you have a flood of those who don't care about the actual job anymore. Look at absolutely anything: music, video games, movies, books, technology, so on and so forth. All started with basic integrity and then lost it in a sea of popularity. The more accessible science becomes for the masses, the less the masses has to put an effort in to understand science. While I find the actual research he speaks about interesting, I find it absolutely fascinating that this is a trend humans do. One that is more visible and understandable than the human genome we are desperately hoping to gain control of, yet we don't attempt to change behavior before we attempt to change physiology.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby ShawnMiller » Wed Aug 12, 2015 12:54 pm

lksalinero wrote:I thought it was interesting that Dr. Gilbert included “the explosion in scientific manpower” as one of the main problems faced by science today. It seems to me that having more researchers could only be a good thing for scientific advancement, and that the solution to the problems described by Dr. Gilbert is not reducing the number of scientists, but improving training and education and developing new procedures for peer review and publication.

Yes, this is an interesting issue, and you are right to point out that peer review and publication models are ripe for rethinking/reconfiguring. Nature recently ran an article about a fruit-fly paper with 1,000 co-authors, which is common in physics, but less so in biology.

It seems that there are at least two options to avoid the problem Gilbert points out about bad/mediocre work being published and retracted: (1) Publish fewer articles, which presumably would help quality, or (2) publish the same number of articles but increase editorial standards. If you pick (1), then there is almost certainly going to be fewer working scientists b/c peer reviewed publications are required for an ongoing career, i.e., publish or perish, and fewer papers means fewer authors. Picking (2) would keep the number of scientists the same, but it turns the problem into one of quality control, i.e., how to keep production high, and defects down.

An analogy: Apple products have a very good reputation because they "just work," i.e., they aren't buggy and crash prone. This is achieved in part by not making lots of different products: at present, they make three types of laptop (Macbook, Macbook Air, Macbook Pro); two types of desktop (iMac and Mini); one type of server (Pro); three types of iPads (regular, Mini and Air); and a few types of iPhones, and there is considerable technical overlap among these products. By contrast, there is lots and lots of PC and Android hardware made by lots and lots of different companies. Getting software to run reliably on all those different devices is enormously difficult even if the software is top notch. So one way to put the question is: do scientific publications want to be like Apple computers (high-performance but narrower in scope) or like PC/Android computers (less reliable but covering great ground)? And is this in part an aesthetic question?

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby ShawnMiller » Wed Aug 12, 2015 1:13 pm

Gilbert says: "I support the cause of personalised medicine. I believe that it has two underlying themes – each one of us has different metabolism ..."

Does anyone have any insight into what he means by different metabolism? I've only ever thought of metabolism in terms of the parameter of speed. What other properties does metabolism have such that mine is different from someone else's? Does this have something to do with the ability or inability of certain individuals to metabolize different substances, e.g., alcohol?

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby Michelle Tarango » Wed Aug 12, 2015 1:23 pm

I thought this article was extremely interesting, especially as it was much more recent than the other papers we had been reading for this class. I was confused about Dr. Gilbert's statement that "we are spending money on problems that can have immediate outcomes." Does this mean that the problems being solved are only relevant in the immediate future and will soon become outdated or incorrect?

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby msnelmida » Wed Aug 12, 2015 1:27 pm

dianalee wrote:It was very refreshing to read Dr. Gilbert's interview. I love the fact that he gave honest answers to the questions. “It is common belief that once we can sequence the genome, we can edit it to have babies with higher IQ for example. This is a myth, because it is very rare that one gene corresponds to one property” This is an example that we won’t be able to delete a gene that will cause a disease to a person. I also like the advice he gave toward the end, “do not continuee science if it does not excite you. Science cannot be a nine-to-five job.” Reading this advice makes me feel more secure on changing my path from science field to architecture field.


I agree I think his example that you mentioned is the reason how the HGP was perceived to be. It is perceived to be the answer to almost everything at least the sequencing part. The reality is that it was not but it is a helpful tool to further advance our knowledge but it is a important step that must be taken and taken on a big scale.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby jjquintanilla » Wed Aug 12, 2015 1:28 pm

The article as a whole was interesting, but one of the main sections which caught my attention was the section dealing with personalized medicine and the negative correlation with pharmaceutical companies. I feel as though this ties with the notion that the foundation of science, which may or may not have a good cause, is not free from self interest. It also ties the relatedness on how corporation view any innovation as a threat or a benefit to their own company; viewing science as a financial upbringing or downfall. Thus, the question of whether science and its impact on patients and the rest of the human society truly matters, or is it simply a matter of numbers; investments; or checks.

Secondly, I will agree with Dr.Gilbert on his notion of an increasing amount of biologist, but who have not the skills or perhaps the understanding to fully comprehend their field of study. Therefore, the question of how our educational system may not be adequate and thus brings a second question of how one might go about to bring forward an innovative system that can prepare young minds to fully understand and contribute greatly to the scientific community and to bring more knowledge into contemporary scientific literature and at the same time remove outdated information.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby anjames » Wed Aug 12, 2015 1:33 pm

Considering the interview was so short, I appreciate the emphasis on skepticism and caution. I wouldn't say I enjoyed it because I like longer articles that get into details of issues. One paragraph bothered me so much that I have a hard time focusing on all others. I wish Gilbert hadn't said anything about "big pharma" and generic drugs (which I'm guessing he means in contrast with personalized drugs, not generic brand medications). To me "big pharma" has the same connotation of paranoia and oversimplification that "the government doesn't want us/you to know about [blank]" does. And his statement makes me think he's suggesting if Big Pharma is against it, you should consider being for it. It's a reaction I realize I need to subdue when evaluating an argument. There are problems with big pharmacological companies pressuring doctors to overprescribe certain medications and then throwing money at the lawsuits brought against them. It's not a unique problem to personalized medicine. More information also might not be easy to parse. It will still be up to healthcare professionals and consumers to critically think about care. There are some easy plays a big company with a non personalized drug. It's complicated and low-risk to take drug A, so just do that instead of spending time and money on a personalized drug. /Their/ drug has been tested extensively. Or how about misleading commercials downplaying the likelihood of side effects?

I think Gilbert could have just left personalized medicine on the note of good or suggested a disadvantage, invoking critical thinking, instead of saying something so vaguely negative that I don't think is completely true. It feels like a misplaced political argument. When he talks about big data, he could have even then brought up how personalized medicine will be affected.

Other than that, I do appreciate the interview and Gilbert's perspective. I swear. It keeps things simple and his advice is good. It just wasn't for me and my clear bias against arguments that do not take into account the complexity of medicine when mentioning big pharma and the implications of personalized medicine.

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Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby Selestine » Wed Aug 12, 2015 1:43 pm

I think the of Walter Gilbert was really nice, though I didn't get him when he suggested that big pharmacy companies should start manufacturing personalized medicine since it was a cheaper. Also I do agree with him that people shouldn't be allowed to patent genes since they are not responsible for their inventions. On top of that if genes were going to be patent then it wold make it difficult for the scientist to conduct research on some various cases.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby eugenekim » Wed Aug 12, 2015 1:54 pm

While I appreciate the benefits of having personalized medicine. I have to disagree with Walter Gilbert on his belief that personalized medicine would be something that could occur in the near future. In my opinion, his view on Big Pharma's greed leading to a situation where personalized medicine could occur but is being held back. Although Big Pharma is greedy the extensive of money that it takes to put a drug through test trails and the regulations of the FDA, just make it that much harder for personalized medication to be a viable entity. Furthermore, the production of personalized medication would be incredibly difficult and the manufacturing of such medication may be too costly as well.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby Nancy Galeno » Wed Aug 12, 2015 1:58 pm

I really liked how this article was straightforward about problems in science, specifically sequencing the genome, yet still positive. I liked how he addressed the issue about personalized medicine by saying that he supports it since there are a lot of subtypes of cancer and one type of cancer is different than the rest. I also agree that there are many myths that have risen due to being published in popular journals, such as that we will be able to edit genes in a way that babies will have higher IQ’s.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby Bowen Tan » Wed Aug 12, 2015 2:02 pm

ShawnMiller wrote:
Gilbert says: "I support the cause of personalised medicine. I believe that it has two underlying themes – each one of us has different metabolism ..."

Does anyone have any insight into what he means by different metabolism? I've only ever thought of metabolism in terms of the parameter of speed. What other properties does metabolism have such that mine is different from someone else's? Does this have something to do with the ability or inability of certain individuals to metabolize different substances, e.g., alcohol?


Most of the researches on metabolism the scientists carry on today are based on those consistent pathways especially their phenotypes. But if we take a look of the original data from human subjects, it can be really various from person to person. That means each person has his/her own gene expression levels. And sometimes scientists set up some standards to judge some symptoms, the standards can be lack of its valence due to one person. For instance, a person might be regarded as metabolic syndrome due to the standards, but that doesn't mean they are really abnormal. Because one of those abnormal indicator level satisfies the standard, but the person's metabolism may get used to the abnormal level of this indicator.

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Re: Aug. 12: Nobel Laureate: big data and full-genome analysis not all they’re cracked up to be (required)

Postby lgomez » Wed Dec 07, 2016 10:25 pm

Having done a bit of research in genetics labs myself, the "explosion of scientific manpower" is something I've witnessed myself. I've seen how much some graduate students struggle to get published and the emphasis put upon it, so I certainly resonate with that.


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