GenomicEnterprise.com Science Blog

Welcome to the “narciss-omics” era

Fabricio Costa — Sun, 29 Apr 2012 02:39:40 +0000

Everything started more than a decade ago, in 2001, when the first draft of a human genome was finished, published and made available for the whole scientific community through an array of bioinformatics tools. After this important milestone, a new field of study emerged named “omics”. The suffix -ome is generally used in molecular biology referring to a totality of some sort – in this case the total genome or sequence of bases of the DNA of an organism. The genomics field started before the human genome sequencing, since several organisms had their genomes sequenced; for example viruses and bacteria. Technology evolved fast since 2001 and now we are entering the “personalomics” era. The cost and time spent to sequence a human genome has dropped considerably, and today one genome can be sequenced in a few hours costing a few thousand dollars. A decade ago, the first human genome consumed millions of dollars from the government of the United States for years. These new advances in technology have enabled important studies in the “omics” field. The blog post today will discuss two recent studies that did whole genome sequencing applied to personalized medicine. Different methods can be used to generate not just whole genome sequencing of an individual but all sorts of measurements such as transcriptomics (all genes or RNAs expressed by the cells), metabolomics (all metabolites in the bloodstream of a person), imunogenomics (auto-antibodies from that individual) and so on. “Omics” studies mark the beginning of a new era of personalized medicine in which we will be able to track diseases before they are diagnosed. The first study discussed in this post was published on Science Translational Medicine and analyzed the “genometype” or the predictive capacity that a genome sequence has in detecting a disease using genome sequencing of a large number of monozygotic twins (to read more check the article “The Predictive Capacity of Personal Genome Sequencing”). In this case, just the genomes of twins were sequenced and the results of the study suggested that genetic testing will not be the determinant of patient care and will not substitute preventive medicine such as risk assessment based on family history, physical status and lifestyle. This study provides strong evidence that whole-genome sequence of individuals alone does not tell much, and a model of gene-environment interaction should be considered. For example, the future of personalized genomic medicine can be glimpsed in a second report published in the journal Cell in which Michael Snyder’s genomic sequence (who is also the lead author of the study) with the other “omics” were uncovered to give a read-out on his predisposition to disease, and his body’s response to viral infections and the onset of type 2 diabetes. As a proof-of-principle example of personalized genomic medicine, it is distinct from other studies because it applies whole-genome diagnostics to a healthy person rather than to individuals with disease, before the disease appears. Snyder, a geneticist at Stanford University School of Medicine in California, joins other researchers who have publicly aired their own genome sequence (others include J. Craig Venter, James Watson and celebrities such as Ozzy Osbourne from the rock band Black Sabbath). Snyder’s ‘Integrative Personal Omics Profile’ named iPOP, was created by merging his genomic sequence with RNA, protein, metabolic and auto-antibody profiles taken 20 times over a 2 year period (for more information see the article “Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes”). The results revealed Snyder to be genetically predisposed to type 2 diabetes, despite no family history or other risk factors. During the study, his blood glucose levels escalated following the second of two viral infections, and he was subsequently diagnosed with the disease. Snyder has since made drastic dietary and lifestyle changes to manage his blood sugar levels and the glucose levels went down showing the power of such study. However, there is a lot of criticism and skepticism about it. For example, Richard Gibbs of Baylor College of Medicine in Houston, Texas, has humorously dubbed it “the narciss-ome” or the beginning of the “narciss-omics” era according to a Nature magazine journalist (check the article “The rise of the narciss-ome”). The geneticist George Church of Harvard Medical School in Boston, Massachusetts says that a criticism of this paper is that it’s anecdotally about one person, but that’s also its strength since it shows an integrative “omics” in a timeframe of 2 years. Well, when comparing both studies (of course each one has its limitations) it is clear that “personalomics” should incorporate different measures with time since our bodies are constantly changing based on the environmental cues (diet, lifestyle, infections, etc…). The conclusion is that the sequence of the human genome is important; however since it is static, it is not enough to give us all answers. Genomic sequences should be integrated with other “omics” technologies to guide doctors in the new era of personalized medicine. Or should I say “narciss-omics” era? (Image credits: deviantART)

Our “old friends” in a brand new world – a tale about worms and microbes

Fabricio Costa — Wed, 28 Mar 2012 03:09:12 +0000

The topic of this blog post is controversial and I would say “intriguing”. I just came back from Europe and watched some presentations of different researchers in a very “cozy” city called Bergamo in Italy. The most interesting talk was about the “hygiene hypothesis”. Well, humans have a very strong aversion to worms in general and one of these are helminths (the so-called “old friends” in the title of this post) that colonize our gastrointestinal tract. These worms can be pathogenic, cause digestion discomfort and they are uncommon in the developed countries but still occur in poor countries and the ones under development. In fact, there is an inverse correlation between the percentages of autoimmune disease incidences in the world and helminth infestation (see figure above). Recent research by several epidemiologists has shown a paradox with an opposite view of helminths suggesting that the recent increase in allergic and autoimmune diseases such as, for example, Multiple Sclerosis, occurred mainly because of increased improvement in sanitation (see the editorial “Helminths and multiple sclerosis: Will old friends give us new treatments for MS?” for more details). Even more disturbing is the suggestion that helminths may protect humans from autoimmune diseases and also allergic reactions. To prove this hypothesis, researchers did an experiment with Multiple Sclerosis (MS) patients. One group of patients was infected with helminths and the other wasn’t. After some time, the symptoms of MS patients infected with helminths disappeared and the ones without the worms worsened. These results are unexpected but have a scientific explanation: the improved control of the MS patients’ symptoms was associated with cellular immune responses characterized by decreases in immunomodulators and increase in other factors with concomitant induction of imunne regulatory cells (for more information see “Helminth-derived immunomodulators: can understanding the worm produce the pill?”). Essentially, in the infected MS patients it was if gastrointestinal helminth infection acted as a virtual immunological “switch”: when present helminths significantly turned off MS activity; however when helminths were removed by drug treatment, MS activity was turned on again. These results are controversial and more research is needed to understand why the worms can turn the MS activity off, but they are indeed intriguing. If the increase in autoimmune disorders and allergic reactions is associated to the elimination of worms in the developed countries, the “hygiene hypothesis” could explain more than we think about this increase in autoimmune diseases. Another fact worth to mention is the increased use of antibiotics in the developed world: in fact, microbiome research is showing that the microbes in people with autoimmune diseases such as Crohn’s and IBD is different from people without the disease. These new insights and theories that are emerging will be very important for a better understanding of why there has been an increase in autoimmune diseases in the developed world. The answer could be in the worm and microbe population that were always in “symbiosis” with our body and now we are “killing” them. New studies are warranted, but the worms are more important than we have thought for sure…

P4 Medicine – a new revolutionary approach to treat diseases?

Fabricio Costa — Thu, 01 Mar 2012 02:51:46 +0000

The term “P4 Medicine” was first introduced more than 5 years ago by the researcher Leroy Hood in an attempt to change medicine from a reactive to a proactive perspective. The ultimate goal of this “futuristic medicine” is to maximize wellness for each individual rather than just treat the disease. P4 stands for the letter “P” in four words: Predictive, Preventive, Personalized and Participatory (for more information see “Predictive, personalized, preventive, participatory (P4) cancer medicine” by Hood and Friend). Emerging from debates related to health care system reform and translational research, this new way of thinking about medicine has put the focus on the patients, other than the physicians. P4 medicine utilizes four interconnected aspects to improve both the effectiveness and efficiency of health management at the individual level. The first “P” that stands for Predictive medicine studies the risk factors, predispositions, and genetic susceptibilities that exist before issues arise by the use of genetic testing and genome sequencing, technologies that have evolved in the last decade. This gives the patient and their health care team warning signs long before a disease is diagnosed. It also gives information that can influence changes in the diet and lifestyle of individuals. The second “P” for Preventive medicine uses the knowledge of the risk factors learned from predictive medicine to change a person’s behavior. It also helps in pre-disease treatments and early screening helping cut off the development of more serious conditions. The third “P” is for Personalized medicine in which each individual will respond differently to treatments. This helps the physician understand what works and what does not work. Personalized or individualized medicine studies and treats each individual as a unity and the current system of health care attempts to treat patients in a universal fashion, which is wrong. The knowledge and access to multiple treatment options as well as better predictions on what works more effectively will help patients and their health care team in selecting the treatment to best meet the patient needs, thus personalizing the medical experience. The fourth and last “P” is for Participatory medicine in which the patient and doctor relationship will become more interactive, helping in better diagnosis and effective treatments. Participation in health care decisions empowers the patient and can encourage innovation among the health care team. Importantly, the emergence of the Web 2.0 and social media websites is facilitating these interactions. Social Media is also empowering individuals to share their data with others that may have the same conditions. This new era in medicine has been shaped by technology breakthroughs such as increasing computer storage capacities and speed, the emergence of the cloud and systems biology generating tons of patient data points. This concept of enabling data and models to be shared by communities as maps of disease built in an open-source manner that includes researchers and physicians around the world will change the style and speed of discovery and development of new therapies. This revolution in medicine will also facilitate clinical trials that need to recruit a very large number of patients. It will be possible by the use of crowd-sourced recruitment bringing several centers and groups together with the use of next generation Electronic Medical Records (Next-Gen EMRs) empowered by social media tools. I truly believe that “P4 medicine”, with patients being more in charge of their own health data, will change the way we approach and treat diseases. That is indeed a medical revolution!

How new web technologies and innovations are impacting our society

Fabricio Costa — Sun, 29 Jan 2012 21:29:29 +0000

The blog post today will focus on the impact that novel web technologies such as social media and search engine tools (i.e.: Google) have in our society. These tools have been used to track diseases and to better understand different trends online. If you are like millions (or billions) of people around the world that can access the internet, you somehow engage in internet-enabled self-diagnosis for diseases (among other types of queries) using search engines and other web tools. In today’s hyper-connected world, these tools are not just used to do self-diagnosis or track diseases in populations but to evaluate different topics that are discussed in social media (for example, trend topics in social medias such as Twitter, Facebook and others). First let’s analyze how a search engine can be helpful in predicting epidemic outbreaks of a disease caused by viruses or bacteria. Google Inc. did a very interesting study to evaluate if their search engine was able to detect areas that an influenza epidemic could be eminent (for more details see the article “Detecting influenza epidemics using search engine query data” on Nature). The study was very straightforward since it evaluated queries that were done at Google using keywords containing anything related to influenza. Using this approach, they were able to track areas that could be having an epidemic of influenza. Their results were compared to the CDC (Center for Disease Control, a United States government organization) in terms of which of them could get areas affected earlier and Google’s algorithm won. Google web search logs could provide one of the most timely, broad-reaching disease monitoring systems to date. Whereas traditional monitoring systems used by CDC and the government require 1-2 weeks to gather and process the data, Google’s estimates are in a daily basis. Now both Google and CDC work together in any disease outbreak showing how this tool can help the government in tracking disease outbreaks. The second tool that is revolutionizing various sectors in our society is social media. Two recent studies were able to show, using the Twitter platform, that we can monitor trends based on the posts of users. PacSocial, which is a corporation that is focused on the development of technologies that enable large-scale shaping of social communities online was able to use “socialbots” to influence connections and interactions between two users (see “PacSocial: Field Test Report” for more details). They were able, for the first time, to show how tools such as “socialbots” can influence human connection online. This study is crucial for a better understanding on how social media is shaping our society. Another study focused on Twitter users designed by professors from MIT (see “Modeling the adoption of innovations in the presence of geographic and media influences” recently published in PLoS ONE) examined the effects of social network structure innovation adoption creating a model based on geography and mass media. The authors showed that mass media was responsible for increasing Twitter users with time. Interestingly, the authors also show how powerful is the mouth-to-mouth spread of these medias between the young. Cities with the most early adopters of Twitter tended to have large universities or technology centers attracting younger people. Twitter was launched in the Bay area in San Francisco and the other users started to come from the east cost, basically Cambridge and Boston where both MIT and Harvard University are located. These reports on new technologies influencing society and decisions, especially in epidemic outbreaks, show how empowering search engines and social media have become to our society. I suppose that several other scientific studies, especially using the Facebook platform that now have more than 800 million users will be done. I hope that these new web tools will help our society in different ways, especially for disease monitoring. This could be important to understand the trends that are influencing our society online. (Image credits: Sociology World)

Sharing results in science – a new revolution?

Fabricio Costa — Thu, 29 Dec 2011 14:04:20 +0000

Science is generally a closed society organized into little circles of highly trained specialists, meaning that only a few specific minds engage to solve any given problem. The system is closed and is shaped in part by the force of tradition, but the larger challenge is that most scientific data is proprietary and the scientists are competing for the first place. A scientist works long and hard to generate original data, and then expects to get the reward in the form of publishing the first research paper to describe some new phenomenon. The researcher is not going to share his data with others, particularly strangers, any more than say, an investigative reporter would want to share his notes before a story has been written and published in the front page of The New York Times. Harnessing non-scientists to help in specific scientific problems requires sending your data out into the world – something that science is afraid to do. The scientist’s interest in keeping things private and getting credit, in other words, is directly opposed to society’s interest in tackling some problems with the help of the best minds. There are exceptions, such as large astronomical and biological data sets that are available for anyone. For example, particle accelerators have produced a new collaborative working model for science and globalization, with hundreds of specialists all over the globe working to solve a specific problem in physics. Most data generated by these experiments are stored in the “cloud”, using the advent of cloud computing. Biological databases that are supported by the US government, such as the National Center for Biotechnology Information (NCBI), store data from whole genomes of several organisms (including our genome) and are opened to the general public – something unusual. However, in the last 10 years, there has been a boom in technology that allows large numbers of people to do amazing and cooperative things with information, but the scientific establishment has taken only baby steps toward figuring out ways to share it productively. According to the former theoretical physicist Michael Nielsen that wrote the book “Reinventing Discovery: The New Era of Networked Science”, sharing in science will become something more common than we expect, specially now that social media is reshaping society. To encourage this shift, the federal government, which funds the United States research, has been pressuring scientists to work more cooperatively, in groups, and share more of what they find faster. In addition, there are nascent efforts within academia in order to identify ways that scientists might be recognized for their contributions to the community as a whole, beyond the publication of their individual discoveries. Scientists need to get rewards for what they are able to share – this will be the new trend in science. Cloud computing, the emergence of different types of social media and the possibility to transfer and share data faster and more reliably will open new ways of doing collaborative science. Society will gain a lot with this trend in science and technology. I believe that contemporary science will be all about sharing information. We might be experiencing now what will become the “open science” era. That is my hope…

Geniuses and creativity

Fabricio Costa — Tue, 29 Nov 2011 23:58:17 +0000

What it takes to be a genius and put your mark in history? How can we account for the sudden appearance of dazzling artists and scientists such as Leonardo da Vinci, Mozart, Shakespeare, Darwin, or Einstein? How can we define a genius? And what conditions or personality traits seem to produce exceptionally creative people in the history of humankind such as Abraham Lincoln, Vincent van Gogh, Salvador Dali, Howard Hughes, and others? Several research groups trying to understand not just the environment, life history and other personality features of famous geniuses, but also the brain of these people, have raised these questions. Famous artists, painters and people that created technologies that disrupted specific fields have strange personality and most lived isolated from society. Scientists have started to shed some light on why these historical figures are remembered in their fields. Geniuses have the ability to legate an impressive and influential body of work to future generations. However, strong creativity could be a link between genius and mental illness (Darwin was emotionally and mentally ill), high incidence of childhood trauma, especially loss of a parent, and genetic defects that are the cause of rare genetic diseases. An example is the american inventor and entrepreneur Howard Hughes. He was later diagnosed with a type of Obsessive Compulsive Disorder (OCD) that probably explains his obsession with perfection in designing airplanes. He was also known for his strong and strange personality. There is indeed a link between geniality and insanity. For instance, Darwin was a very lonely person with psychological distress. Vincent Van Gogh was also an eccentric person and socially awkward. The history of humanity has shown that the advancement of specific fields is accompanied by geniuses that are able to do things that disrupt the “status quo” of that time. Most of these individuals have some psychological problem, and science started to show that this could be explained by genetic defects and the presence of rare genetic diseases. Some studies claim that Salvador Dali had a mental disease that could be very similar to schizophrenia. Even Albert Einstein was not very comfortable with the impact that the relativity theory could cause to society. Einstein was a very isolated person and had sparks of depression late in his career. Interesting examples from our times include personalities such as Steve Jobs, Michael Phelps and Mark Zuckerberg. Steve Jobs, the CEO and founder of Apple, was adopted early in life. Jobs was extremely obsessed with product design and perfection as a response to childhood abandonment. This was probably a way to prove to the world that even with these personal problems he would succeed. An interesting example on how a genetic defect can give advantages to the person carrying it instead of being deleterious is the case of the swimmer Michael Phelps. He was diagnosed with a rare genetic disease named Marfan Syndrome (see article “Marfan’s Syndrome: Michael Phelps’ Blessing or Curse?“) which is characterized with long limbs and a different structure of the body compared to a regular person; features that were crucial for his 8 gold medal win in the last Olympics in China. The last example is Mark Zuckerberg, the founder and CEO of Facebook. Zuckerberg was elected person of the year by the TIME Magazine and has changed the “status quo” of social media in the internet. However, some analysts and scientists believe, mainly based on the way he talks and look at cameras in interviews, that his success could be attributed to a mild form of Asperger’s Syndrome. This genetic disease is in the spectrum of the diseases related to autism. The diagnosis was not confirmed yet, but Zuckerberg has several characteristics of a person with this disease. Well, to impact society and humanity with new forms of arts, technologies, theories, etc in a way that you will never be forgotten is something of a genius. The fact is that, as shown by the examples I gave, we need the “geniuses” in our society to improve fields such as arts, technology and science. If we look at the paintings from Van Gogh (illustration shown in this blog post), listen to songs from Mozart, analyze the planes that Howard Hughes designed, watch Michael Phelps swim and Zuckerberg create technologies that will impact in our society, we can conclude that humanity definitely needs a touch of a genius.

Illinois – a hub state for technology development and creation?

Fabricio Costa — Sun, 30 Oct 2011 15:00:13 +0000

We were always told that big technology drivers in the US are institutions such as MIT, Harvard, Caltech, Stanford and other well known for their disruptive inventions and creations. They are indeed very important with their creative environment and technology development. Companies such as Google and Facebook were born in Stanford and Harvard, respectively. Others such as Bose were created in MIT, and the list is extensive. Well, I live in Chicago, Illinois, in the Midwest area of the US and anybody would think the environment here is not very creative or full of innovations. I had no idea that Illinois was also a hub for creations and inventions, especially in very important areas of Information Technology (IT) and the internet. Since the beginning of the 1950s, for example, The University of Illinois in Urbana-Champaign (and not University of Chicago or Northwestern, as anybody would think…) has a legacy of IT Excellence at Illinois with several game-changing breakthroughs in hardware, software, algorithms, and networking. The story of re-imagining how humans interact with computers and with one another, and the power of having immediate access to millions of sources of information was developed in this environment (for more details check the link: http://www.it.illinois.edu/legacy/). These breakthroughs include the invention of the transistor in 1947, which is the precursor of the microprocessor used in computers today. John Bardeen co-invented the transistor while at Bell Labs and subsequently joined the Illinois engineering faculty and physics faculty, where he co-developed the theory of superconductivity. Professor Bardeen became the first person to win two Nobel Prizes in the same field (in 1956 for inventing the transistor and in 1972 for his work on superconductivity). The first computer entirely built and owned by an educational institution was also located in the University of Illinois in Urbana-Champaign. Other examples in the past include Illinois alumnus Jack Kilby (BS, 1947) that invented the integrated circuit, for which he was subsequently awarded a Nobel Prize. Interestingly, the LED concept and PLASMA screens that are used today in flat screen TVs were invented in the same university. The first practical visible spectrum LED was invented by Nick Holonyak, Jr. Don Bitzer and Gene Slottow, two Illinois alumni and professors, and Illinois graduate student Robert Willson invented the plasma display while working on the PLATO system (the first computer-assisted instruction system). In the 1970s, other technologies included the first parallel supercomputer, the UNIX system license from Bell Labs (which later became the LINUX Operating System). Importantly, in the 1990s, the first popular graphical Web browser named Mosaic (which later became Netscape and then Firefox) was developed by Marc Andreessen and Eric Bina while working for this university. It was initially viewed as an exciting new tool, but no one at the time could have predicted that its wide adoption would lead to e-commerce, online classrooms, downloadable music and films, and new worldwide communities of people with shared interests that we see today. Marc Andreessen later became an icon in Venture Capital investments and later founded a VC Fund that helps develop several other interfaces and technologies that are becoming companies of success today (see Marc Andreessen’s TIME Magazine cover when he invented the Netscape browser). Finally, alumnus Max Levchin co-founded PayPal, allowing payments and money transfers to be made via the Internet. In 2005, two Illinois alumni, Jawed Karim and Steve Chen, along with Chad Hurley, were co-creators of YouTube, which has had global impact on everything from popular culture to governmental policies on video sharing in the internet. I did not imagine how many good technologies came out from Illinois and maybe several people out there did not know either. But, Illinois is an important hub for inventions and creations in several aspects of IT and the internet. Who knows what disruptive technology will be invented in Illinois in the future and became a worldwide success? Let’s wait and see…

My thoughts on biomedicine in Brazil

Fabricio Costa — Thu, 20 Oct 2011 01:04:45 +0000

This blog post will focus on the recent cover of Nature Medicine discussing brazilian biomedicne and how the country – Brazil – has evolved in several fields but still lags behind in others (for a full story check the October issue of Nature Medicine). Well, I remember perfectly when I was studying in a private high school back in Brazil how difficult it was to enter in the best universities and get a degree (most of the universities are public and funded by the government, some are federal and some are state-funded). My high school was very good but expensive and my parents had a tight budget to maintain both me and my brother in one of these. Difficult times for them, but they made through it. It was also difficult to get into the public universities since we had (and still have) to do an exam (like in America, but here most universities are private). I passed the test and entered in one of the best universities there – the Federal University of Minas Gerais. I remember clearly that the first time I entered in one of the university’s building, it was falling apart… On the other hand, the parking lot of the university was full of fancy and expensive cars. The interpretation is that most students were rich and came from good schools. Moreover, when I started doing a training program in a laboratory inside the university, the infrastructure was awful compared to the ones I see in the USA. Well, I started my blog discussing about the Nature Medicine special and want to go back to this topic since I was interviewed for one of the articles (read the full story “Brazilians lured back home with research funding and stability”). There is no doubt that things in my home country are much better for academic research as discussed in these articles. Brazil contributes today with 2% of the world’s biomedical publication output; however this is slim compared to countries such as the USA and Germany. Even pharmaceutical companies are starting to invest in Brazil. Brazil is indeed becoming the 5th largest pharmaceutical market in the world (read the story “Brazilian drug companies hope to benefit from foreign investment”). I was brainstorming about this topic after reading all articles and came up with a list of pros and cons of doing academic research in each place. First, let’s start with the USA. Things that still attach me here are the quality of research that is done (even though we can expect the same in some places in Brazil such as the state of Sao Paulo, Rio de Janeiro, Minas Gerais and others), most laboratories are well-equipped, the environment is very competitive, publishing articles and patenting ideas is much faster and has little bureaucracy, and I see that the relationship between academic and private sectors is somewhat good and productive (one example is the Silicon Valley close to Stanford University where most tech companies are located, although MIT in Boston is also a good example). The cons that I can point today in the USA are the budget cuts by the government (believe me it is affecting everybody in academia), the tenure track system that is obsolete and broken (this is terrible for young scientist like me that are starting and have new ideas), and the system is very conservative giving a lot of priority to well-established scientists. In the case of my home country, I see a lot of improvement and the pros of coming back to do academic research there are that the system is improving with much more opportunities compared to the USA, more money is being spent with research (which is very little compared to the USA and Europe, but there was a huge increase during the past years), new companies (not just spinoff) are being created coming from academia (much more than before, but I believe that some started in the academic sector in the past; one example was Biobras that started in the 1970s in the Federal University of Minas Gerais). The government together with the Ministry of Science have created incentives and “packages” for young scientists to attract scientists abroad to come back and the stability in the job as an academic professor (which in the USA is not possible until you are tenured…) is also a plus. The cons of coming back are the same old problems I saw when I left. For example, the infrastructure in most places is terrible, the word “bureaucracy” works for everything and I mean everything; the salaries are still low (even though in the USA they are not outstanding…), the relationship between academic and private sectors are still bad, publishing articles and patenting ideas is a painful process and the most important issue for a citizen that was not touched in the Nature Medicine special – social problems and violence in the big centers are still frightening. The amount of poor and miserable people is still alarming and the percentage of people that goes to universities is low compared to the USA. I think Brazil’s economy and science as a whole has improved a lot, but it still has a lot of regulatory issues and problems that somehow keep me in the USA. These are just my thoughts on the American dream slipping away and the idea of coming back starting to tingle. One lesson I have learned is that no place is perfect and you always face difficulties and problems anywhere not just in science. If I am going back or staying here in America just time will tell. For now I am still here…

Genes, patents and arts – copyrights on our DNA?

Fabricio Costa — Sun, 25 Sep 2011 03:45:24 +0000

This blog post is a mix of a scientific controversy with an artistic vision. There has been growing concern with the idea of patenting or “copyrighting” genes from human genomes. The debate has been on and off after the sequence of the first draft of the human genome in 2001. Recently, it came back again after the company Myriad Genetics won a case in court for the patents of both breast cancer genes BRCA1 and 2. And what does arts has to do with genes and “copyrights”? The first artist to depict the structure of the DNA was Salvador Dali, who included DNA spirals in his surreal, phantasmagoric paintings in the 1950s. Dali was ahead of his time as most artists living in Europe, especially in Paris (for more information see the article “The art of DNA – Back to bases” in The Economist). It took the publication of Dr Watson’s book, “The Double Helix”, in 1968, the emergence of biotechnology and the manipulation of genetic material or “genes” in the 1970s, to edge the DNA molecule towards the centre of the public gaze. Since then, many artists have followed in Dali’s wake. Well, paintings, masterpieces, books, images and every creation and invention is patentable. But can we say that a piece of our own self, our DNA, the molecule of life is a creation or invention? Since it is already in our cells, the answer is no. The claim that lawyers are using is that as soon as the piece of the DNA corresponding to a gene is taken out of the cells and manipulated by molecular biology it could be considered a creation. Could this be? To understand this issue better we need to define how the word patent applies to genetics. A gene patent is a patent on a specific gene sequence, its usage, and often its chemical composition. The problem is that there is a big debate over whether these patents advance technology by providing scientists with an incentive to create, or hinder research by creating a lot of barriers and licensing fees to utilize research that is patented. In the case of both BRCA1 and 2, the company that holds the patents provides genetic testing for women that has familial history of breast cancer. This helps to identify the carriers of mutations and improve preventive medicine. However, the discussion is why just one specific company can hold the rights to a specific test? Should this be opened to other companies to reach more people with lower prices? The answer is yes I believe, but the law for gene patenting went to the other direction some years ago. The comparison with arts is that the creation and invention such as paintings or machines can be patented since they were designed from “nothing”. In the case of genes, even after being manipulated, they were already in our DNA inside our cells. In a NYTimes article by Andrew Pollack some time ago (“Ruling Upholds Gene Patent in Cancer Test”), the controversy is cautiously discussed and the decision on the patentability of genes and DNA was well accepted by most of the biotechnology industry. The point is that thousands of human genes have been patented, and some biotechnology executives say such patents are essential for encouraging innovation. Is that the case? In my opinion, genes are not a creation or invention even if they were manipulated by molecular biology. On the other hand, the genetic test used to detect the mutation or the defect in the gene is an innovation and can be patented. The controversy still continues since even though the court maintained the patents of both BRCA 1 and 2 to Myriad Genetics, court appeals will probably happen. For now, it looks like genes are still patentable. But we never know what the future holds for such cases…

Computers, internet and our brain – the extended mind?

Fabricio Costa — Thu, 18 Aug 2011 01:42:15 +0000

The history of the Internet started in the 1950s and 1960s with the development of computers. The beginning of the web was mainly point-to-point communication between mainframe computers and terminals and it was further expanded to point-to-point connections between computers. The internet has evolved since then and some even say that the web as we know it is dying or is already dead (see the Wired Magazine article about it – “The web is dead”). The web was very disorganized (and still is) until the launch of search engines with several links and lots of information spread all over the “cyberspace”. Search engines such as Google changed this by facilitating us in finding whatever we want in the web. If you want to search for a specific word or name, you just need to find a computer connected to the internet and type it. It is like magic and you get several webpages related to your query. The recent emergence of different types of social media such as Facebook, Twitter and others has made accessing information even easier and more organized. The web is evolving towards less entropy, and by entropy I mean disorganization. The information is becoming more detailed and the “socialization” of it is helping. Interestingly, the information stored in the web, especially in search engines such as Google and other databases has become our external memory source that we can eventually access at any time. Although the concept of knowledge seems to prime thoughts of computers, even when answers are known, we are becoming dependent on the computers and internet (see the article “Google Effects on Memory: Cognitive Consequences of Having Information at Our Fingertips” in Science, 2011). Studies have been showing that we are becoming symbiotic with our computer tools growing into interconnected systems to remember less by knowing information where it can be found; for example googling it. Another example of connection between our brains (or mind) and the computers are studies that the brazilian born scientist Miguel Nicolelis and colleagues at Duke University are conducting. They were able to taught monkeys to use brain signals to control the movements of a robot on the other side of the world (Nicolelis MA. Brain-machine interfaces to restore motor function and probe neural circuits. Nat Rev Neurosci. 4: 417-422, 2003). The researchers trained some of the monkey’s neurons to “adopt” the machine’s locomotion as its own. This is a strong and physical example on how we can become more and more connected not just to the information that computers provide us today but, to a further extent, hybrid systems of man associated to machines. Our society is becoming totally dependent on the computers and how they bring us the information we need at the exact moment we want. This unification of our brain with the machines (computers in this case) is slowly taking place and changing human evolution. I wish I could live for more than a century to see what is going to happen then…But I am just a human being like any other, not a machine-man.