One of the great triumphs of twentieth-century biology was the discovery of how genes make proteins. This question is hardly new, and the answers have earned scientists scads of Nobel prizes over the years. Scientists have also known for decades that sometimes when a cell makes an RNA transcript, it can use that transcript for an important job without bothering to translate it into a protein.
Since then, scientists have plunged ever deeper into the workings of regulatory elements and functional RNAs. Understanding the other 97 percent of the genome is a challenge at once profound and medically practical. But for just as long, scientists have known that some of the genome does not carry out such vital functions.
While the basics of the human genome have been clear for decades, the particulars have remained murky.
In 2008, I wrote in the New York Times about a then-new project called ENCODE, in which a small army of scientists would create an encyclopedia of information about the entire genome, not just the protein-coding bits.
What the scientists actually demonstrated was that cells produce RNA transcripts from a huge portion of the genome, not just for the protein-coding parts.
Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. I’ve been very curious about how scientists would move on from here, and how the debate over the genome would evolve. The scientists then probed those transcripts to see whether they were just sloppy mistakes or served a function. Counting previously discovered lincRNAs, the researchers ended up with a total 55,000 potential non-protein coding genes. The scientists also found that these stretches bear some hallmarks of being switched on and off.
If these 55,000 candidates do turn out to be true genes for lincRNAs, then they will outnumber traditional protein-coding genes by a factor of five or more. Sean Eddy, a biologist at Janelia Farm Research Campus, is very skeptical of all such large-scale catalogs.
Larry Moran, a biochemist at the University of Toronto and fierce critic of ENCODE, had a similar response.
Moran also pointed out that in many cases, the supposed genes produced just one lincRNA per cell. Moran and Eddy both point out that even if the UCSF researchers are right and all 55,000 DNA segments are real genes for important lincRNAs, that discovery would not, in fact, clear up all that much about the genome as a whole. Even supposing that all 55,000 were truly functional and important RNAs; 55,000 * 2000nt average lincRNA transcript length = 110MB, less than 4% of the human genome.
I contacted two of the UCSF co-authors to respond to these critiques but haven’t yet heard back from them. CZ: Even if all 55,000 transcripts you identified were functional, they would come to a few percent of the human genome.
MM: These are both potential sources of artifactual expression signal and we did work to mitigate both scenarios.
Regarding the second source of artifact, we did take multiple steps to minimize the potential for genomic DNA contamination, and this is described in the Methods section of the paper. CZ: Could you test out twenty candidates for lincRNAs to see if they aren’t just noise? CZ: The commenters thought it unlikely that lincRNAs that are present at just a few copies per cell would be able to have a function. MM: We make no broad-sweeping assertions about the functionality of the lincRNAs described in the study. A bit more diffidence by scientists on both sides, though not essential for progress to continue, would be reflect more positively on the scientific endeavor. Also, as far as I know, there’s little evidence for purifying selection on most of the human genome. Bjorn: for example, by mutating proteins responsible for that surveillance, and seeing the RNAs that accumulate when the mRNA quality control pathway has been removed. How much of a genome is junk, is going to vary all over the place, even for related organisms, and will vary over time also. Could it be that having almost-functional pseudo-genes lying around makes it more likely that a mutation in one of them will get transcribed into a stretch of RNA that manages to do something or other that is helpful? A reservoir of that kind would not be conserved in any usual sense, and yet might still retain the potential to do something good, some day. We are trying to learn a new language that will eventually help us in communicating with life and its evolution.
In my opinion, one of the biggest disconnects between pervasive transcription of the genome and its functional relevance is the evolutionary conservation of these sequences.
Who We ArePhenomena is a gathering of spirited science writers who take delight in the new, the strange, the beautiful and awe-inspiring details of our world. Erika Engelhaupt is the online science editor at National Geographic and manages the Phenomena blog network.
Maryn McKenna is an award-winning journalist and the author of Superbug and Beating Back the Devil. DisclaimerThe views expressed are those of the writer and are not necessarily those of the National Geographic Society.
IU will honor the GlobalNOC's past and future at a 15th anniversary celebration Tuesday, Sept.
Indiana University has implemented the Kuali Coeus Institutional Review Board, a comprehensive online system for the submission, review and approval of human subjects research. The National Center for Genome Analysis and Support (NCGAS) has announced new services to help biological researchers store and share their work, speeding scientific discovery and breakthroughs in many fields of study.
Registration is now open for the IEEE Cluster 2013 conference, hosted by IU's Pervasive Technology Institute, September 23-27 at the Hilton Indianapolis. Professors Thomas Sterling and Andrew Lumsdaine will deliver keynotes and lead workshops, tutorials and discussions on a variety of topics at the 2013 International Supercomputing Conference, the world's oldest global conference and exhibition for high performance computing, networking and storage. The center of the universe will be in Indianapolis June 2 to 6, at least as far as the study of the universe is concerned, as more than 500 scientists, educators and journalists are expected for the 222nd meeting of the American Astronomical Society. IEEE Cluster 2013 conference organizers today announced the featured speakers at this year's event. With privacy concerns addressed, Indiana University has re-released the free app Kinsey Reporter, a global mobile survey platform for collecting and reporting anonymous data about sexual and other intimate behaviors. NASA's Operation IceBridge mission wraps up its spring flight season this week, gathering radar data about Earth's polar ice sheets to help scientists better understand global climate change. Indiana University confirmed its leadership in high performance, data-intensive computing by unveiling Big Red II, a powerful new supercomputer with a processing speed of one thousand trillion floating-point operations per second (one petaFLOPS). Indiana University's new supercomputer is expected to further advance international collaborations reliant on big data research at a time when the globalization of education, science and research is omnipresent.
Indiana University and Internet2 announced a $2 million initiative to stimulate collaboration in higher education cybersecurity efforts in response to President Obama's cybersecurity challenge. This week the HathiTrust Research Center (HTRC) announced the availability of data mining and analytics tools for the HathiTrust Digital Library, a collection of digital texts from over 70 research libraries around the world. The TechPoint Mira Awards recognized Indiana University for the deployment of IUanyWare, a cloud-based service that provides IU students, faculty and staff with on-demand access to over 200 software applications. Indiana University has saved nearly $20 million by joining with other universities to reduce administrative costs for essential financial software systems. IUanyWare, Indiana University's cloud software service, is a 2013 recipient of ACUTA's prestigious Institutional Excellence award. Indiana University shares its expertise in advanced networking with the launch of a new lecture series for state business and industry leaders.
Kuali People Management for the Enterprise (KPME) announces the release of version 1.5, designed to meet the human resources needs of higher education. Indiana University today announces SAGE as the latest publisher to sign on to its eTexts initiative. Indiana University has announced an agreement with Cengage Learning to provide eTexts for students on all IU campuses. IEEE Cluster 2013 conference organizers are seeking input from the high performance computing community, in an effort to make the "Clusters and Cyberinfrastructure Strategy" event as informative as possible.
Nearly 10,000 Indiana University students are using digital textbooks (eTexts) this spring semester as part of IU's pioneering eTexts initiative. Indiana University's Center for Research in Extreme Scale Technologies (CREST) is the recipient of a three-year, $1.1 million grant from the Department of Energy (DOE) to develop software that improves the speed and programmability of supercomputers. The Indiana Center for Network Translational Research and Education (InCNTRE) at Indiana University is hosting its first single-controller vendor Software-Defined Networking (SDN) Lab PlugFest this Feb. Indiana University and Adobe are partnering to present Adobe Days 2013 on the IUPUI and IU Bloomington campuses.
Vital research collaborations involving China, Europe and the United States will be safeguarded through the first major agreement among partners running the two main high-speed research and education (R&E) Internet routes across Asia, Europe and North America.
Thomas Sterling, executive associate director of the Center for Research in Extreme Scale Technologies (CREST) and professor of computer science in the IU School of Informatics and Computing, has been named an HPCwire person to watch in 2013. The Indiana Center for Network Translational Research and Education (InCNTRE) has announced that Steve Wallace will step into the role of acting executive director.
Indiana University's IT Communications Office recently received several awards from the Chicago chapter of the Society for Technical Communication (STC). Network architects from a range of Fortune 500 companies will converge on the Indiana Center for Network Translational Research and Education (InCNTRE) on Wednesday, January 23, to take part in a new user group promoting OpenFlow and other software-defined networking (SDN) technologies.
The National Center for Genome Analysis Support (NCGAS) is expanding its reach by adding tools, services and partners to help biological research communities make important new scientific discoveries. With 6 billion mobile phone subscriptions worldwide -- that's about 87 percent of the world population -- and an even higher percentage of users estimated on campuses, Indiana University has embarked on a mobile security campaign to heighten awareness about the tools available to safeguard users and their products. The organizing committee for the IEEE* Cluster 2013 conference is now accepting proposals for tutorials, technical papers, posters, panels, and visualizations.
A recent networking breakthrough from IU researchers, in collaboration with Orange Silicon Valley and DataDirect Networks, showed that data sharing can be faster and more efficient over wide area networks (WAN). Researchers from Indiana University's Pervasive Technology Institute will serve as collaborating partners on a major grant from the U.S.
Indiana University today announced the successor to its internationally recognized Data Capacitor research data storage platform. Indiana University networking experts were recently recognized by Internet2 for their efforts to enhance broadband connectivity and support advanced services and cloud applications across the United States. IU will replace its current Data Capacitor with Data Capacitor II, a high-speed, high-capacity storage facility for very large data sets.
Indiana University will display its leadership in high performance computing and networking technologies at the annual International Conference for High Performance Computing, Networking, Storage and Analysis, also known as SC12 (Supercomputing 2012).
QuakeSim, an Indiana University-supported collection of online data and tools from NASA's Jet Propulsion Laboratory and multiple university partners, is a recipient of NASA's 2012 Software of the Year Award. Data vital to understanding global climate change will benefit from more efficient and secure processing, thanks to a new tool created by members of Indiana University's Research Technologies Systems. Recording light from millions of light years away and then sending it to the Indiana University Data Center at the corner of 10th Street and state Rt. Indiana University announced today (September 14) an agreement with Elsevier's Science & Technology Books division to provide eTexts for students on all IU campuses. A recent National Science Foundation (NSF) grant will further enable Indiana University to help scientists solve their toughest data problems. Indiana University and Ivy Tech Community College have announced a technology support partnership to help college students use technology for increased success.
Indiana University has signed agreements with technology providers CourseNetworking LLC and Instructure Inc.
The Apache Software Foundation recently asked Suresh Marru of the Indiana University Pervasive Technology Institute to join its exclusive membership. The announcement July 4 that scientists have observed a new particle that may be the elusive Higgs boson spelled success for Indiana University researchers who worked for years on a massive experiment that detected the particle. Internet2 announced today, July 20, that Indiana University President Michael McRobbie was elected as the sixth chair of the board of trustees and will serve until July 2015. Key software used to study gene expression now runs four times faster, thanks to performance improvements put in place by a team from the Indiana University Pervasive Technology Institute (PTI), the Broad Institute of MIT and Harvard and Technische Universitat Dresden. Indiana University has received a Campus Technology 2012 Innovators Award for the development of IUanyWARE, a cloud-based service that provides students, faculty and staff with on-demand access to hundreds of software applications.

The announcement last week that scientists have observed a new particle that may be the elusive Higgs boson spelled success for Indiana University researchers who worked for years on a massive experiment that detected the particle. Leaders from the China Education and Research Network (CERNET), IU, Internet2, and the Chinese government met Thursday, June 21, at Tsinghua University in Beijing, China to demonstrate unique applications now possible over a new10Gbps internet link between the education and research networks of the US and China. Beginning July 1, Indiana University will establish a new Office of Scholarly Publishing, newly appointed IU executive vice president and provost of the Bloomington campus Lauren Robel announced. Indiana University is again leading the way to better health care by enabling scientists to share research more rapidly and securely over the Internet. Indiana University received a $492,588 National Science Foundation grant to help scientists study rising sea levels and the impact of storm surge on coastal communities.
Networking giant Cisco is the latest company to join InCNTRE's Software-Defined Networking Interoperability Lab, the world's only neutral, third-party testing lab for SDN. IDG's CIO magazine has honored Indiana University as a recipient of the 2012 CIO 100 award. The Sakai Foundation recently selected its 2012 Sakai Fellows, and three of the six recipients have direct ties to Indiana University. Indiana University and Pearson are working together to reduce the costs of digital textbooks for students on all IU campuses. Senior, higher education executives announced today that they will use the nation's fastest, coast-to-coast network to implement new technologies that support scientific "Big Data" and cloud applications to drive innovation in global collaborative research. In most of the genome, these minute changes are obscured by the genetic reshuffling that takes place each time a mother and father's DNA combine to make a child. The accumulated mutations in your mtDNA and (for males) your Y chromosome are only two threads in a vast tapestry of people who have contributed to your genome. In the mid-1980s the late Allan Wilson and colleagues at the University of California, Berkeley, used mtDNA to pinpoint humanity's ancestral home. Mitochondrial Eve was soon joined by "Y chromosome Adam," an analogous father of us all, also from Africa.
Francis Collins finds a balanced ride between science and religion.The often strained relationship between science and religion has become particularly combative lately. If you tally up the amount of DNA they constitute, you get less than 3 percent of the human genome. Over fifty years ago, Francois Jacob and his colleagues realized that the non-protein-coding DNA contains stretches, called regulatory elements, that act like switches for genes.
Many of our genes are controlled not just by a single switch, but by a veritable combination lock of different regulatory elements. Earlier this year, for example, scientists identified a gene for a long piece of RNA called PTCSC3 that suppresses cancer in the thyroid.
Barbara McClintock discovered in the 1940s that parts of the genome can make copies of themselves which can then insert themselves elsewhere in our DNA. They also observed that proteins were able to grab onto those regions–a suggestion that they were switching on genes for RNA. One long-running complaint is that the mere existence of an RNA transcript does not mean it serves any function at all. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks.
Now a team of scientists at the University of California at San Francisco has published an interesting paper on the issue in the journal PLOS Genetics. They analyzed newly compiled databases of the RNA produced in cells from different tissues. They focused on one class of transcripts, known as long intergenic noncoding RNAs, or lincRNAs for short. The scientists then looked at each of the candidate genes to look for clues to whether they serve a function. DNA is wound around spools called histones, and the candidate lincRNA genes had proteins latched onto them that can unwind DNA so that it can be transcribed. It strains his imagination to picture a way for a single lincRNA to have any important role in a cell’s existence.
As soon as I do, I will add their response and post a notice on the blog that I’ve updated this piece. We noticed that many currently annotated genes can actually extend outside of their annotated regions when using RNA-seq data to analyze expression levels, so we removed any putative lincRNAs that overlap any of these empirically extended gene structures. Again, it is fair to say that in some rare cases, some of the putative lincRNAs we discovered may be artifacts and additional data is needed (longer reads, deeper sequencing) to achieve even higher confidence in all lincRNAs. Manual verification of lincRNAs is an important future direction, and an important pre-requisite for follow-up functional studies. In fact, it is entirely possible that almost none of the lincRNAs we reported are functional.
At the moment, about 9% of (known) mammalian genome sequences are conserved throughout evolution.
Phenomena is hosted by National Geographic magazine, which invites you to join the conversation. No Place Like Home is her space to talk about space—from other worlds to the fabric of the universe. Laelaps is his writing laboratory, dedicated to sifting through natural history for tales of evolution, extinction, and survival. Not Exactly Rocket Science is his hub for talking about the awe-inspiring, beautiful and quirky world of science to as many people as possible. 10, in the Informatics & Communications Technology Complex on the Indiana University-Purdue University Indianapolis campus. With seven Institutional Review Boards and more than 4,800 approved active research studies, IU is the largest university to implement this community-developed open source software. IU earned the distinction for its pioneering eTexts initiative and recent wireless network upgrade to ensure reliable and secure access to digital materials. The twice-yearly IceBridge missions generate massive amounts of data -- all stored and archived by Indiana University's research cyberinfrastructure. Offering unmatched speed, Big Red II will be the fastest university-owned supercomputer in the nation. ACUTA (the Association for Information Communications Technology Professionals in Higher Education) is an international nonprofit dedicated to serving the needs of higher education, including nearly 2,000 individuals at some 700 institutions. This version includes a new Leave Management module, which lets organizations and their employees accrue, request, report and track benefit time (such as paid time off and sick days) for faculty and staff. SAGE is now the 11th publisher to partner with the university to provide digital materials to students on all IU campuses. With this addition, IU reaches an important milestone: Faculty and students now have favorable pricing for and access to digital materials from all of IU's largest publishers. Hosted by Indiana University's Pervasive Technology Institute, Cluster 2013 will take place September 23-27, 2013, at the Hilton Hotel in Indianapolis.
Since 2000, the Mira Awards have recognized the movers and shakers of the state's IT industry. The third annual event showcases Adobe tools and resources that help students and instructors of all disciplines connect, discover, create and inspire.
The publication's annual list features 12 movers and shakers whose reach extends beyond high performance computing (HPC) to shape future directions of technology, propelling scientific and engineering advancements. The newly formed InCNTRE SDN User Group (ISUG) will bring together business leaders from insurance, finance, travel and healthcare who are investigating SDN technologies and the impact they may have on their networks. Today (January 14), in conjunction with its participation in the Plant and Animal Genome Conference (PAG XXI), NCGAS announced three initiatives to accelerate US public and private sector research and development in biology and biomedical research. Hosted by IU's Pervasive Technology Institute, Cluster 2013 will take place September 23-27, 2013, at the Hilton Hotel in Indianapolis. The team performed the world's first demonstration of RDMA (Remote Direct Memory Access) over Converged Ethernet (RoCE) across a wide area network using the Lustre file system. Department of Homeland Security to address vulnerabilities arising during the process of software development.
The new system, called Data Capacitor II (DCII), is a five petabyte storage resource engineered to provide scientific researchers with high performance access to a robust storage facility.
Their efforts will help provide advanced networking features for more than 200,000 of the country's community anchor institutions, including libraries, hospitals, K-12 schools, community colleges and public safety organizations.
With five petabytes of storage, Data Capacitor II will support big data applications used in computational research. The award recognizes innovative software technologies that significantly improve the agency's space exploration and maximize scientific discovery on Earth. The NSF has selected Indiana University as a partner in a grant to create the Science Gateway Institute.
The new version brings additional features and improvements to a software system that touches vital university functions every day.
This honor is bestowed on IT developers whose skills have significantly contributed to the foundation's projects. President McRobbie joined the board in 2009 and succeeds University of Michigan President Mary Sue Coleman, who served as chair for the last year and as a member of the board since 2003. The Innovators Award recognizes universities that deploy extraordinary technology solutions to meet campus challenges. The Indiana Clinical and Translational Sciences Institute (CTSI), of which IU is a founding member, recently became the first health care research institute to be named to the InCommon Federation's Research & Scholarship category. Department of Energy have renewed funding for the Open Science Grid project, providing $27 million from 2012 to 2016.
Through this grant, IU will improve the performance of oceanic computer models, which scientists use to protect millions of people living near coasts around the world. The 25th annual award recognizes organizations around the world that exemplify operational and strategic excellence in information technology. IU's Chris Maurer and Lynn Ward received the honor along with former employee Lance Speelmon. IU's eTexts initiative enables faculty to optionally choose these digital textbooks and online exercises at reduced prices for students.
The intent is to strengthen the nation's position as a global leader in research and education for decades to come, and at the same time help control higher education costs.
What's left is the DNA responsible for our individual differences—in eye color or disease risk, for example—as well as some that serves no apparent function at all. But by comparing the mtDNA and Y chromosomes of people from various populations, geneticists can get a rough idea of where and when those groups parted ways in the great migrations around the planet. They compared mtDNA from women around the world and found that women of African descent showed twice as much diversity as their sisters. Increasingly refined DNA studies have confirmed this opening chapter of our story over and over: All the variously shaped and shaded people of Earth trace their ancestry to African hunter-gatherers.
In one corner we have scientists such as Richard Dawkins and Steven Pinker who view religion as a relic of our superstitious, prescientific past that humanity should abandon. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten. A number of scientists have been cataloging lincRNAs for a few years now, but they’ve only identified a few thousand that appear to have a function. The lincRNA gene candidates that the UCSF scientists found are fairly similar to versions in other mammal. Rather than just compile a list of possible genes, he thinks scientists should do some careful quality control.
Upon observing that nearly the entire genome is transcribed, we chose as a first step to focus only on lincRNAs, but there are many other transcripts we did not focus on in this paper. After this filtering, we found that the majority of lincRNAs in our catalog are relatively distant (>30 kilobases) to the nearest protein coding gene. For this reason we define the lincRNAs as “putative” in the paper, because they must be manually experimentally validated with great care. That said, RNA-seq data is becoming a widely accepted approach for studying lowly expressed transcripts as evidenced by large numbers of publications using the technology. If >80% of the genome is transcribed into RNA and is required for normal development and health, how can only ~10% of it display evidence of purifying evolutionary selection? Schopf officially joined the Office of the Vice President for Information Technology and CIO on Aug. Representatives from Courseload and IU accepted the award at the IMS Global Learning Impact 2013 conference.
Keyes, professor of applied mathematics and computational science at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia, will be the keynote speaker.

The event will let SDN Lab members test the interoperability of their products with Big Switch Networks' commercial controller, the Big Network Controller. The Department of Homeland Security awarded a $23.6 million grant to the Morgridge Institute for Research at the University of Wisconsin-Madison to create the Software Assurance Marketplace, which, over the next five years, will work closely with developers of new software analysis technology and the open source community to advance the security of software. DCII will be used for a range of applications, including management of massive research data sets, high-scale data analysis, genomic sequencing and computational visualization. Named Big Red II, the next-generation Cray XK supercomputer will be capable of one thousand trillion floating-point operations per second, or one petaFLOPS.
The university will carry out the pilot trials during a two-year evaluation period to assess the technologies that can best support the changing needs of students and faculty.
Indiana University will receive $3.82 million of the award to continue running OSG's Operations Center, highlighting IU's noted expertise in grid computing and ability to deliver a reliable, secure, easy-to-use environment. For decades the only clues were the sparsely scattered bones and artifacts our ancestors left behind on their journeys. Once in an evolutionary blue moon, a random, harmless mutation can occur in one of these functionless stretches, which is then passed down to all of that person's descendants.
Since the telltale mutations seem to occur at a steady rate, modern humans must have lived in Africa twice as long as anywhere else.
In the other corner are religious believers who charge that science is morally nihilistic and inadequate for understanding the wonders of existence.
Reading its sequence, they produce a single-stranded version of it made of RNA, called a transcript. They found about 85% of the genome produced at least one copy of RNA in one of the databases. They should be like inspectors at a factory, and pick out a random set of candidates to test. In fact a study that we reference in our paper looked extremely deeply at very narrow intergenic regions thought to be transcriptionally inactive, but found a dizzying array of complex, regulated transcripts at very low levels in these regions.
This mantra is true even for the large number of existing protein coding genes that have been reported but haven’t been validated. The reality of this situation is that the data accumulated up to now is insufficient to provide any meaningful claim of victory by either side. Long non-coding RNAs will undoubtedly form some localised structural pairings given the laws of thermodynamics. Thomas Sterling, professor of informatics and computing at Indiana University and executive associate director of IU's Center for Research in Extreme Scale Technologies, will deliver the closing address. Next.IU launched in fall 2012 with exploratory studies of Instructure's Canvas learning management system (LMS) and CourseNetworking's social media-based learning environment. Equipment from SDN switch vendors Dell, Extreme Networks, HP, IBM and NEC as well as SDN testing manufacturers Ixia and Spirent will be tested at the event.
In the past 20 years, however, scientists have found a record of ancient human migrations in the DNA of living people.
Generations later, finding that same mutation, or marker, in two people's DNA indicates that they share the same ancestor.
Similarly, most of the Y chromosome, which determines maleness, travels intact from father to son. Scientists now calculate that all living humans are related to a single woman who lived roughly 150,000 years ago in Africa, a "mitochondrial Eve." She was not the only woman alive at the time, but if geneticists are right, all of humanity is linked to Eve through an unbroken chain of mothers. Into this breach steps Francis Collins, who offers himself as proof that science and religion can be reconciled. The transcript gets shipped to a cluster of other molecules, the ribosome, which picks out building blocks to construct a protein that corresponds to the gene.
They first identified long transcripts, and then they winnowed down their list to get rid of false positives. Only if careful experiments show that really do behave the way a functional gene behaves can they have confidence in their catalog.
In reading a number of the ENCODE papers, I couldn’t help but be overwhelmed by the immensity of data thus generated. It is thus important to consider the structural nature of RNA (compared to protein-coding DNA) when investigating evolutionary conservation. By comparing markers in many different populations, scientists can trace their ancestral connections.
As leader of the Human Genome Project, Collins is among the world's most important scientists, the head of a multibillion-dollar research program aimed at understanding human nature and healing our innate disorders. The protein floats off to do its job, whether that job is to catch light, digest food, or help generate a thought.
About eight percent of our genome is made up the littered remains of dead viruses, for example. They filtered out sequences that might be fragments of protein-coding genes that managed to slip into the database, for example. However, we cannot distinguish between functional and nonfunctional transcripts without performing functional experiments and this is the obvious next frontier for determining how much of this transcriptionally active “junk DNA” is or is not junk.
However, it was also clear that for most of the data, their full import is yet to be realized.
We have done this and report the findings in a Nucleic Acids Research paper to be available online shortly.
Williams, IU's first director of international networking, who is retiring after a 30-year career at the university. And yet in his best-selling book, The Language of God, he recounts how he accepted Christ as his savior in 1978 and has been a devout Christian ever since.
They also combined segments of DNA that overlapped in a way that suggested they both came from a single lincRNA gene.
Rather, what we have is a field where enough interesting data is accumulated to suggest fruitful future directions where the eventual findings may provide conclusive evidence towards one or the other interpretations.
To my mind, a lot of the lincRNA papers fail to do the part where they look carefully (manually) at what their screen produced, so they fail to develop their intuition for the various failure modes of the high-throughput computational screen.
However, another possibility is that further investigation may result in both sides having to admit defeat when data elevates a not-yet-conceived model to the fore. One idea I’ve considered, though it’s pure speculation on my part because I am fairly ignorant of the field as a whole, is the possibility that these cataloged but ill-characterized regions of the genome and transcriptome may be essential for determining the 3-D structure of the genome within the nucleus.
Horgan, who has described himself as "an agnostic increasingly disturbed by religion's influence on human affairs," directs the Center for Science Writings at the Stevens Institute of Technology in Hoboken, New Jersey.Interview by John HorganHorgan: As a scientist who looks for natural explanations of things and demands evidence, how can you also believe in miracles, like the resurrection? It does appear that the structure is important, but the whys and hows of the establishment and maintenance of this structure remain mysteries, especially since methodologies such as Hi-C that allow for a greater understanding this phenomenon are fairly new and in only limited use. Collins: I don't have a problem with the concept that miracles might occasionally occur at moments of great significance, where there is a message being transmitted to us by God Almighty. Horgan: The problem I have with miracles is not just that they violate what science tells us about how the world works.
For example, many people believe that if they pray hard enough God will intercede to heal them or a loved one.
Collins: In my own experience as a physician, I have not seen a miraculous healing, and I don't expect to see one. I'm trying to figure out what I should be doing rather than telling Almighty God what he should be doing. Whether it was the Inquisition or the Crusades on the one hand or the World Trade Center on the other?
But we shouldn't judge the pure truths of faith by the way they are applied any more than we should judge the pure truth of love by an abusive marriage. We as children of God have been given by God this knowledge of right and wrong, this Moral Law, which I see as a particularly compelling signpost to his existence. But we also have this thing called free will, which we exercise all the time to break that law.
First of all, if our ultimate goal is to grow, learn, and discover things about ourselves and things about God, then unfortunately a life of ease is probably not the way to get there. God gave us free will, and we may choose to exercise it in ways that end up hurting other people.
Horgan: Physicist Steven Weinberg, who is an atheist, asks why six million Jews, including his relatives, had to die in the Holocaust so that the Nazis could exercise their free will.
Collins: If God had to intervene miraculously every time one of us chose to do something evil, it would be a very strange, chaotic, unpredictable world.
The harder question is when suffering seems to have come about through no human ill action. Horgan: Some philosophers, such as Charles Hartshorne, have suggested that maybe God isn't fully in control of his creation.
An alternative is the notion of God being outside of nature and time and having a perspective of our blink-of-an-eye existence that goes both far back and far forward.
In some admittedly metaphysical way, that allows me to say that the meaning of suffering may not always be apparent to me.
Collins: That was a put-down that should not apply to earnest agnostics who have considered the evidence and still don't find an answer. I was reacting to the agnosticism I see in the scientific community, which has not been arrived at by a careful examination of the evidence. I went through a phase when I was a casual agnostic, and I am perhaps too quick to assume that others have no more depth than I did.
Don't you worry that science in general and genetics in particular—and your work as head of the Genome Project—are undermining belief in free will? Collins: You're talking about genetic determinism, which implies that we are helpless marionettes being controlled by strings made of double helices. Heredity does have an influence not only over medical risks but also over certain behaviors and personality traits. But look at identical twins, who have exactly the same DNA but often don't behave alike or think alike.
There are some fringe elements that say, "No, it's all an illusion, we're just pawns in some computer model." But I don't think that carries you very far. Horgan: What do you think of Darwinian explanations of altruism, or what you call agape, totally selfless love and compassion for someone not directly related to you? Many would argue that altruism has been supported by evolution because it helps the group survive. But some people sacrificially give of themselves to those who are outside their group and with whom they have absolutely nothing in common. That doesn't seem like it can be explained by a Darwinian model, but I'm not hanging my faith on this. Horgan: What do you think about the field of neurotheology, which attempts to identify the neural basis of religious experiences? Those who come at this issue with the presumption that there is nothing outside the natural world will look at this data and say, "Ya see?" Whereas those who come with the presumption that we are spiritual creatures will go, "Cool! How about that!" Horgan: Some scientists have predicted that genetic engineering may give us superhuman intelligence and greatly extended life spans, perhaps even immortality.
These are possible long-term consequences of the Human Genome Project and other lines of research.
If these things happen, what do you think would be the consequences for religious traditions? But we're so far away from that reality that it's hard to spend a lot of time worrying about it, when you consider all the truly benevolent things we could do in the near term. Collins: In spite of the fact that we have achieved all these wonderful medical advances and made it possible to live longer and eradicate diseases, we will probably still figure out ways to argue with each other and sometimes to kill each other, out of our self-righteousness and our determination that we have to be on top.
We may understand a lot about biology, we may understand a lot about how to prevent illness, and we may understand the life span. But I don't think we'll ever figure out how to stop humans from doing bad things to each other. That will always be our greatest and most distressing experience here on this planet, and that will make us long the most for something more.

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