Archive for the ‘Technology’ Category

Bioinformatics now! It is time to learn computer coding

Monday, July 30th, 2012

The science of bioinformatics or computational biology is increasingly being used to improve the quality of life as we know it. Bioinformatics has developed out of the need to understand the molecule of DNA, also known as the code of life. Massive DNA sequencing projects became a reality with the advent of next generation technologies and has added in the growth of the science of bioinformatics. DNA, the basic molecule of life, together with other layers of information in the cells, directly controls the fundamental biology of life. It codes for genes (both protein-coding and non-coding) that act in concert with some environmental factors to determine the biological makeup of humans or any living organism. It is variations and errors in the genomic DNA (such as mutations and polymorphisms), which ultimately define the likelihood of developing diseases or resistance to these same disorders. This way, the ultimate goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of sequence, structure, literature and other biological data obtaining a clearer insight into the fundamental biology of organisms and to use this information to enhance the standard of life. The science of bioinformatics grows together with computer science since the more breakthroughs the better for both fields. Recently, with the explosion of genetic data and genomics information, bioinformatics became an essential tool to life sciences. In other words, the need to deal with complex types and sources of data from living organisms is increasing the importance of computer science for biology. Never in history, computers and biology were so close to each other. I believe that, in the future, every laboratory from academic and private sectors will need to have a group dedicated to bioinformatics. This is already happening in several institutions and companies. Genomics and the projects related to it are adding amounts of data that our brain cannot process. Big challenges will be faced in order to facilitate the interconnection between computer science and biology. Computer scientists have no biology or medical training and biologists know little on the language used by “computer coders”. Thus, to be a multitasking scientist today, an individual needs lots of computer skills. And by computer skills I do not mean just knowing how to use a computer. A deeper knowledge is needed to deal with big amounts of data being generated by genetics and genomics right now.

How new web technologies and innovations are impacting our society

Sunday, January 29th, 2012

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)

Illinois – a hub state for technology development and creation?

Sunday, October 30th, 2011

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: 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…

Computers, internet and our brain – the extended mind?

Wednesday, August 17th, 2011

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.

Web 2.0 and the democratization of science

Sunday, October 10th, 2010

Science was supposed to be all about collaboration to achieve our main goals – try to understand the basics on how organisms and cells work and use this information to aid in the wide range of diseases that affect humankind. Unfortunately, the scientific world is not all about sharing information. In fact, it was always the opposite; a big competition in which the ones with more resources get to the discoveries first and prevail. To be able to do a nice discovery in science and make it available to the whole scientific community is more difficult than anyone would imagine. Scientific journal article evaluation and peer-revision, as I already pointed in my previous blog posts, is an unfair and frustrating process that can take months and even years. There is a lot of competition and the journals are not accessible to all scientists in the world since they charge for article download. This is somehow changing with the revolution of the Web 2.0 in which there is more interaction of the individuals with the information available online. Free social media networks such as Podcasts, YouTube, innumerous blogs, Twitter, Facebook, and others have been facilitating the “spread” of the scientific discoveries faster than it was imagined let’s say 10 years ago. The current “migration” of the printed media to the virtual world is indeed facilitating the democratization of science all over the world.  Several scientific journals  that are Open Access and free of charge have emerged, so everyone is able to download articles and commentaries about specific topics. The trend is that even the more “traditional” journals will need to find ways to get revenue and become freely available so everybody can have access to “first class” scientific discoveries. This type of democratization is not necessarily new, but now it will occur faster and will affect people all over the world in an era that information is the most valuable product. In a large enterprise like science, this can make a big difference. Web 2.0 is already changing the scientific community and I hope this will positively impact in the evolution of our field and facilitate the application of our discoveries.

Popularity x Prestige in science – what matters most?

Sunday, October 3rd, 2010

In my last blog article I wrote that science is in a moment of “transformation” like any other field mainly because of the Web 2.0 revolution – which implies that the user has the power to insert and delete whatever he wants in websites, mainly social networks and information sites such as Wikipedia, Facebook, blogs, and etc. Society is dealing with a lot of privacy issues concerning these new internet advances. Some people think this is not a good sign, however any evolving field brings good and “evil” outcomes and society has to deal with it. In its early years, for example, the company Google stated that they would never play “evil” and collect private data from people using their search engine. It looks like this is not the case now that we know they are facing some problems with privacy, especially in China and in Europe. In the same fashion, Facebook faces increasing privacy issues and problems. Anyway, the point of this new blog article is focused in the scientific field. The point is that our research and reputation (and by our I mean every scientist in the world) is basically measured by the research we do. This means that if we can get our results to be published in high impact scientific journals our “prestige” in the scientific community will be good. The Impact Factor or IF of a journal was developed by Eugene Garfield of the Institute for Scientific Information (ISI) and it has been the main method to determine the impact of a scientific research discovery. However, in the “Google age” we have been facing a very interesting trend which is the fact that the search results or ranking that Google gives for a specific article or journal is different from the IF calculated by ISI. This is explained by the fact that these two sources use different methods and algorithms to calculate the impact of articles and  journals. It is clear now that “popularity” that Google searches gives us does not overlap with the IF provided by ISI. The conclusion is that we need to come up with different methods to calculate the impact factor of research discoveries and journals. In that regard, currently available methods for evaluation of the quality of scientific papers and status are undergoing a profound re-evaluation. The question now is what matters most? Popularity or Prestige? A recent article is proposing a formula for this complicated issue (for more details see: “Impact Factor Page Rankled” by Hascall, Bollen and Hanson, 2007). A new formula that takes into account the algorithm from Google for web searches and the IF from ISI can be combined in a very elegant manner. Larry Page, one of the Google founders published the algorithm (see article: “The anatomy of a large-scale hypertextual Web search engine” by Brin and Page, 1998) they use in Google Search Engine. The ranking used by IF is mainly based in their own method for calculation which evaluates the number of citations a journal receives over a 2 year period divided by the number of research papers and reviews published in that journal. It is becoming clear that as the scientific material becomes available for free download in the Web 2.0 era with Open Access Journals popping up everywhere, and hence become searchable through Google, our perception of article popularity will change as a result of the recently suggested  Page Rankled and not the IF alone. I am quite sure that a new revolution in the journal and article classification industry has already started. Now we just need to search our articles using Google and see how popular they are independent in which journal they were published in…

Think Different and challenge the “Status Quo”

Sunday, August 29th, 2010

Steve Jobs caricature

Steve Jobs back in the early days of Apple…

After watching this video from Steve Jobs back in 1997 when he was addressing the media about the new Apple “Think Different” advertisement it got me thinking… He was right more than 10 years ago. Nice marketing and products of quality are a combination close to perfection in technology (and probably in science too) and for a company to be successful. Like he says in this video: always “Think Different” and challenge the “Status Quo”. The best minds in history did this and entered to eternity. They were always questioning the beliefs and the things that general people thought were “correct”. Just doing a parallel or metaphor with the scientific world, i think that the great minds always thought different and challenged the “Status Quo”. This is why they entered to history, to science books and some got Nobel Prizes, etc. Another parallel is the history of the company Google. In the early days of the company, Larry Page and Sergey Brin were doing Ph.D.s trying to find a way to come up with a matematical formula or model that could be applied in searching terms in the web and also to rank the results (they were lucky to give up their Ph.D.s and found Google at that time – a company that now is threatening Microsoft and even Apple). At that time nobody though this way and some books now telling the history and what happened when they had the “Google idea” describe that some of their peers were skeptic thinking they were crazy and a search engine like that would never work. Well, Google is a giant now not just in search engine, but also in other areas such as marketing, software development among other technologies. Thus, we definitely need to move forward and fight for our ideas, specially when other people or even peers tell us we are crazy and our ideas are nonsense. Sometimes, these ideas are too far ahead of time (like 10 years or more) in the general public’s mind. This is why iconic people such as Steve Jobs are geniuses and it does not matter if they present a conference to the media wearing shorts back in the 1990’s (see the video above to believe in what i am saying…). Well, our ideas need to be good, but we have to be brave to “sell” them!