Singularity Hub

Singularity Hub is proud to deliver the web’s most comprehensive coverage and analysis of the Singularity Summit 2008. The Singularity Summit is the premier annual event for those that are interested in the singularity. Below you will find our high level summary, followed by a link to a much more detailed description with pictures.

On Saturday October 25, 2008 I attended the Singularity Summit at the Montgomery Theatre in San Jose, CA. An impressive lineup of speakers, including Ray Kurzweil (de facto singularity advocate), Peter Diamandis (Founder/Chairman of Xprize Foundation), Vernor Vinge (famous science fiction author), and Justin Rattner (CTO of Intel) were on showcase for the roughly 500 attendees. The summit was thought provoking, inspiring, and overall a success.

The summit began promptly at 9:00am and continued throughout the day until 6:00pm with a few breaks in between and a one and a half hour lunch break. Here are the Hub’s major takeaways from the event:

1. When people become believers in a near term singularity (a singularity that may come in their lifetimes) they radically change their behavior in terms of risk tolerance, eating habits, and investment horizon. If large numbers of people begin to believe in a near term singularity this poses the possibility of enormous and potentially dangerous upheavals for society.

2. Even if a true singularity is not reached within our lifetimes the singularity summit reinforces the vision that tremendous technological change beyond our imagining is coming in the next 40 years. In the next 5 years an explosion in interest about the singularity and the pace of accelerating technology may occur.

3. According to Ray Kurzweil, solar energy is an information technology that is experiencing exponential growth. Solar energy production has doubled every year for the last 20 years and is now only 8 doublings away (that is about 10 years!) from providing nearly all of the world’s energy needs. The implications of this trend are huge and warrant careful consideration for the environment, investment, politics, etc.

4. Peter Diamandis announced that the Singularity University (SU) will be launched in the near future. The Hub’s Keith Kleiner will be a founding member of SU and we will have much more to say about SU soon!

5. According to Intel CTO Justin Rattner Intel has a solid roadmap that will ensure that Moore’s law will continue for at least another 10 years, by which time computers will be at least 1,000 times more powerful than today’s computers

6. Virtual worlds will continue to gain traction and functionality as people continue to recognize and leverage the unique advantages that these worlds offer versus the physical world.

7. Computers may be able to beat humans at chess and air hockey, but they are still a long way off from emulating human emotion and social behavior. Demonstrations today of the cutting edge in computer emulation of emotion and social ability were downright pitiful. Of course it is possible that we will make big leaps in the coming years, but today’s demonstrations were not encouraging.

Below is a breakout of the entire Singularity Summit:

Read the rest of this entry »

The Short:

The Harvard Crimson and the LA Times offer some of the better articles reporting that researchers have genetically reprogrammed mice pancreas cells directly into a completely different type of cell called a B cell. B cells are responsible for creating the blood sugar regulating hormone insulin in humans, and it is the absence of these B cells that causes humans to suffer from type 1 diabetes, a currently un-curable disease that requires burdensome lifelong treatment.

With this breakthrough, the Harvard researchers have apparently offered “the first conclusive evidence” that it is possible to genetically convert one type of adult cell or tissue into another type of cell or tissue. Although still years into the future, this research could pave the way for major advances in the field of regenerative medicine where people’s bodies have lost certain types of cells or tissues to injury or disease.

The Long:

Mice suffering from type 1 diabetes were treated with a virus that
specifically infected their pancreas cells and converted them into B
cells. Ten days later, up to 20% of the pancreas cells had ceased
their normal function and instead begun producing insulin at levels comparable to
B cells from healthy, non-diabetic mice.

Although this is apparently the first demonstration of direct conversion of one adult cell type to another cell type, it should be noted that this is not the only route to creating a desired cell or tissue type. Therapies derived from stem cells and pluripotent cells have been used to create all sorts of cell types in numerous studies and in fact this breakthrough from the Harvard researchers complements rather than competes with these therapies. What is notable here is the proof of concept that mature cells such as pancreas cells can be genetically reprogrammed to do almost anything through the technique of intentional viral infection, changing their behavior or even changing their entire identity.

Human applications for this type of genetic reprogramming are still many years into the future. Not only will effort be required to apply this breakthrough to humans instead of to mice, but also the proteins required to induce the reprogramming, called transcription factors, require years of effort to pinpoint and are specific to the type of reprogramming desired.

Image from Royan Institute

Nature recently published an article written by Armand Marie Leroi that opens with this interesting question:

“Now that many people approve the elimination of certain genetically defective fetuses, is society closer to screening all fetuses for all known mutations?”

The article offers interesting statistics on the current state of genetically defective fetuses in the USA and how often these fetuses are aborted. The statistics clearly show that termination of the pregnancy of a genetically defective fetus is a widespread and growing phenomenon.

Although the abortion of a genetically defective fetus is quite controversial in the USA, Leroi points out that in many other countries it is morally acceptable, with 80% or more of such fetuses aborted in France and Taiwan compared to roughly 30% in the USA.

The moral and religious facets of aborting a genetically defective fetus are intentionally avoided in this article. Leroi’s intention is neither to promote nor discredit the abortion of genetically defective fetuses, but simply to report on the science and statistical trends that are taking place.

A significant impediment to a universal, total prenatal screen for all known mutations is the invasive and expensive nature of the procedure. Should the procedure become less invasive and less costly I suspect abortions of genetically defective fetuses would skyrocket, quickly overpowering most of society’s moral issues with the matter.

Below are interesting quotes from the article:

“Every year, 4.1 million babies are born in the USA.  On the basis of the well-known risk of Down syndrome, about 6,150 of these babies would be expected to suffer from this genetic condition, which is caused by an extra copy of chromosome 21. In reality, only about 4,370 babies are born with Down syndrome; the  there have been aborted during pregnancy…Data from other regions are similar or even higher: 32% of Down syndrome fetuses were aborted in Western Australia (Bourke et al, 2005); 75% in South Australia (Cheffins et al, 2000); 80% in Taiwan (Jou et al, 2005); and 85% in Paris, France (Khoshnood et al, 2004). Despite this trend, the total number of babies born with Down syndrome is not declining in most industrialized nations because both the number of older mothers and the conception rate is increasing.”

“This high number of so-called medical abortions shows that many people … consider the elimination of a genetically defective fetus to be morally acceptable”

“…there is no technical obstacle to constructing an oligo-based micoarray able to detect all known disease-causing mutations”

“In Taiwan, screens for thalassaemia mutations have caused the live-birth prevalence of this disease to drop from 5.6 to 1.21 per 100,000 births over eight years (Chern et al, 2006).”

Ultrasound scan to amniocentesis test. Amniocentesis is a diagnostic procedure performed by inserting a needle (seen on the left) through the abdominal wall into the uterus and withdrawing a small amount of fluid from the sac surrounding the fetus. The test can detect chromosomal disorders, such as Down syndrome, structural defects, such as spina bifida (open spine, where the vertebrae fail to close), anencephaly (a condition in which the brain is incomplete or missing), and many rare, inherited metabolic disorders. © Mediscan/Corbis

Many people have heard of the original X Prize, which was a $10 million prize given to the first company that could build a spacecraft capable of carrying three people to 100 kilometers above the earth’s surface, twice within two weeks. Many people are unaware that this original X Prize has since spawned an entire family of other $10 million X Prize challenges that are ongoing today.

The Archon X Prize is offering $10 million “to the first Team that can build a device and use it to sequence 100
human genomes within 10 days or less, with an accuracy of no more than
one error in every 100,000 bases sequenced, with sequences accurately
covering at least 98% of the genome, and at a recurring cost of no more
than $10,000 per genome.”

The Archon X Prize will accelerate mankind’s efforts to achieve affordable and fast sequencing and analysis of the DNA for every individual on the planet. Once this capability is a reality it will unleash a revolution in our ability to make people healthier, fight disease, and even improve people beyond their original genetic and biological bodies.

Picture from Archon X Prize Website

deCODEme offers an excellent video tour on their website that demonstrates what they can do with your dna. This video will be enlightening for those who are new to genetics and the amazing power that personalized dna analysis will offer all of us in the coming years. deCODEme offers four distinct tools for analyzing dna:

1. Risk analysis for various diseases based on your genes

2. Assessment of physical attributes such as hair color

3. Detailed assessment of ancestory (did your grandparents really come from New Zealand

4. Comparison of your DNA to other people in the database, such as family members or famous people

Wired came out with a pretty nice article on the Personal Genome Project (PGP) with a focus on the project’s founder, George Church. The PGP will be collecting and analyzing the DNA of 100,000 volunteers. Each volunteer must fill out an exhaustive survey that will tally information about them such as head circumference, ability to roll heir tongues, exposure to power lines, dietary preferences, medical history, and much more. This data will be entered into a database along with their genetic data, creating a vast trove of data that can be cross referenced in countless ways. From the article:

“This phenotype data will be integrated with a volunteer’s genomic
information, then combined with statistics from all the other subjects
to create a potent database ripe for interrogation. In contrast to the
heavy lifting that genetic research requires now — each study starts
from scratch with a new hypothesis and a fresh crop of subjects,
consent forms, and tissue samples — the PGP will automate the research
process. Scientists will simply choose a category of phenotype and a
possible genetic correlation, and statistically significant
associations should flow out of the data like honey from a hive. A
genetic predisposition for colon cancer, for instance, might be found
to lead to disease only in connection with a diet high in barbecued
foods, or a certain form of heart disease might be associated with a
particular gene and exposure to a particular virus. Genomic discovery
won’t be a research problem anymore. It’ll be a search function. (This
helps explain why Google, among others, has donated to the project).“

One of the fantastic features of the PGP is that all of the data will be completely open to the public. By opening the data to the public researchers across the globe will be empowered to sift through the data and further advance the field of genetics for all of humanity. From the article:

“If the PGP were simply an exercise in breaking down 100,000 individuals
into data streams, it would be ambitious enough. But the project takes
one further, truly radical step: In accordance with Church’s principle
of openness, all the material will be accessible to any researcher (or
lurker) who wants to plunder thousands of details from people’s lives.
Even the tissue banks will be largely accessible. After Church’s lab
transforms the skin into stem cells, those new cell lines — which have
been in notoriously short supply despite their scientific promise —
will be open to outside researchers. This is a significant divergence
from most biobanks, which typically guard their materials like holy
relics and severely restrict access.”

If you want to be a volunteer to donate your genetic information (I did!) to the project all you have to do is sign up at the PGP website here.

Picture from the wired article

Two separate projects are both analyzing the genes of healthy, old (90 or even 100 years) people to see if they have genes in common that may be responsible for enabling their longevity.

Technology Review reports that Eric Topol leads the Genomic Medicine Program at the Scripps Translational Science Institute that is collecting blood samples from 1,000 people age 80 or older who have never suffered any serious illnesses and do not take medication. From the article:

“These people have genetic susceptibility markers for many serious diseases, including cardiovascular disease, stroke, and diabetes, but they don’t get any of these diseases,” says Eric Topol’”

“Sequencing allows researchers to determine if healthy older people are more likely to carry [genetic] variations that either make protective factors function more efficiently or hinder the activity of harmful factors.”

From this same report we also learn of the Longevity Genes Project which is also searching for longevity genes, but they are using microarray analysis instead of direct gene sequencing.

Picture from Longevity Genes Project website

IEEE produced a special report on the singularity in its June 2008 issue located here:

http://www.spectrum.ieee.org/singularity

This is a comprehensive report, representing many diverse views about the singularity from a selection of tech luminaries and scholars in singularity related fields. It is a must read if you are at all interested in the singularity. In a few separate posts I will be highlighting some of the cool insights to be found within this report.

The Short:
Technology Review reports that for just $1,350,000 USD you can have have the worlds fastest commercially available DNA sequencer, called the Heliscope. The machine developed by Helicos BioSciences takes just one hour to read 1.3 billion base pairs from a strand of DNA. Here is a picture of the beauty:

HeliScope™ Single Molecule Sequencer

The Long:
The Heliscope is being marketed as a DNA microscope. It is unique in the field of DNA sequencing because it sequences an actual DNA strand whereas most other sequencing technologies use PCR to create millions of copies of an original DNA template and then parallelize the analysis of these millions of strands. Although PCR based technologies can compete with the Heliscope on speed, only the heliscope offers analysis of an actual single strand of DNA. The millions of copies created from PCR based technologies differ slightly from the original template strand due to very rare but significant copying errors that occur during the creation of the copies and hence some of the information from the original strand is lost. From the article:

“The technology is so new that it’s not yet clear what applications it
will be best suited to. But some scientists believe that
single-­molecule sequencing could be particularly important in
understanding how genetic variations contribute to disease. After all,
some rare mutations linked to disease may have been missed in previous
genomic studies because they weren’t copied during the amplification
process.”

Both PCR and single strand based analyses have their place in genetics, but if you are doing single strand analysis then Helicose has the machine for you!

Like other DNA sequencing technologies, the Heliscope uses fluorescently tagged DNA to “see” the DNA sequence, but the Heliscope is unique in its ability to see individual fluroescence of a single base as noted in these quotes:

“Once the fluorescently tagged base is incorporated into the new strand,
the HeliScope’s camera can spot the light it emits. “The imager detects
a plume–a 200-­nanometer cone of light–from the integration of a
single [base] onto a ­single strand of DNA,”

and

“But unlike those technologies, the HeliScope can distinguish the
unamplified fluorescent signal of a single base taking its place on a
growing DNA strand. One key to that ability is a nonstick material that
the company developed, which coats the surface of the flow cell and
allows it to be washed clean between reactions: residual fluorescent
bases would make it more difficult to accurately detect individual
sequencing reactions. “You need to make sure no extra base molecules
are sticking to the surface,” says Patrice Milos, chief scientific
officer at Helicos. “This was one of the biggest early challenges.”
After each cycle, the fluorescent markers are clipped from the newly
incorporated bases, and remaining chemicals are washed away. The
process is repeated sequentially with each of the four bases.”

The Short:
In this recent paper from Lab on a Chip it is revealed that researchers in Japan have developed two microtools for manipulating large strands of DNA such as an entire chromosome. Using a 10 micrometer hook they are able to grab hold of a strand of DNA and drag it where they like. Also, using two microspools (microbobbins) a chromosome sized strand of DNA can be neatly wound up into a small, compact form. The wound up DNA can easily be unwound as needed.

The Long:
The microtools are manipulated by targeted laser beams that can move the microtools and orient them as needed. Excellent videos demonstrating the microhook pulling a strand of DNA and a strand of DNA being wound up and then unwound using the spools can be seen here. Below is a picture of the microtools:

Although many tools, such as optical microtweezers already exist for the manipulation of small chunks of DNA, such tools are poor at dealing with large eukaryotic chromosome sized strands of DNA primarily because large strands easily break due to hydrodynamic shear. The microtools used by the Japanese researchers specifically overcome this problem by only requiring small forces (25pN) to manipulate the DNA and thus avoid breakage or deformation of the DNA strand. The researchers use a technique they previously pioneered called electroosmotic flow (EOF) to first untangle the DNA strand from its original three dimensional form and draw the strand out into a nice straight thread for subsquent manipulation by the microhook or microspools.

I just read the following post from the 23andMe company blog. The most interesting revelation here is the demonstration of how easy it is for a person to find a compatible organ donor once their DNA is scanned and compared against the DNA of other individuals in the database.

Less than ten years ago an enormous scientific endeavor to decode a single human genome was completed with the expenditure of millions of dollars and more than a decade of intense effort. Today, for less than $1,000 you can have your own individual DNA analyzed in a matter of weeks! The ability to analyze the DNA of an individual cheaply and quickly represents a revolution in the way mankind will be able to manipulate the human body. Stick with us here at singularity hub and be in the know as the revolution unfolds.

In the next month or so I will be having my DNA analyzed by the two leading companies in the field, 23andMe and deCODEme. In depth analysis of my experience at both companies will be posted here as soon as possible so stay tuned.

Wired just setup a how-to wiki describing how to check yourself for genetic abnormalities. The wiki is pretty wimpy on details at the moment, but hopefully people will update it with more information soon. The wiki suggests the following 3 options for analyzing your DNA:

1. Visit a genetic counselor. These companies specialize in detecting specific genes

2. Scan your whole genome by using a testing company such as 23andMe or deCODEme. By scanning your entire genome you can check much more than your genes. You can check for a million or more genetic markers called SNPs.

3. Perform the test yourself at home! This requires a good deal of work on your part, but the tools required to analyze your genome at home do indeed exist and they will surely become more available, cheaper, and easy to use in the near future