Biomedical Feed

November 30, 2008

Walking Proteins Move Cargo

Kinesin dimer / David S. Goodsell, Scripps Research Institute

One way to transport objects inside a cell is by the use of Kinesin motor proteins. Three things are required: a motor to move the cargo, a track along which to move it, and the cargo itself that needs to be delivered.

Motor Proteins

Proteins are essential components of cells that are involved in a number of processes. They are formed by linking amino acid molecules together in chains. The sequences of amino acids needed to build proteins are specified by genes as part of the genetic code.

Motor proteins are a special form of protein that do physical work. Remarkably, these proteins have the ability to move along surfaces, transport cargo that is attached to them, or produce force. They use the chemical Adenosine Triphosphate (ATP) as an energy source to power their movement. The motor protein myosin, for example, is involved in the contraction of muscle fibers in animals. Dynein is a motor protein that is found in flagella, the long tail-like structure that projects from certain types of cells like sperm to help the cell move.


Microtubules are one of the components of the cytoskeleton, the infrastructure that supports the cell. They are made by linking repeating units of the tubulin protein together. The resulting chain is then curled into a hollow cylindrical shape. They can grow or shrink to produce force, and also serve as conduits along which other cellular components can be transported.

Kinesin Cargo Transportation

Small molecules in the cell can move to where they are needed by the process of diffusion. However, larger molecules that are synthesized in the cell body are transported by motor proteins to their destinations. Kinesins are a type of motor protein that use microtubule tracks to walk along. 

Two intertwined chains with globular heads on one end form a Kinesin dimer. To move, the heads repeatedly attach and detach to the tubulin units of the microtubule track, moving everything forward in a hand-over-hand fashion. The opposite ends of the dimer drag the cargo along that they are attached to.

Thanks to Nested Universe reader Faris Naji for inspiring this topic, and discovering the attached video which shows the Kinesin protein in action.


October 20, 2008

Brain Science Is About To Fundamentally Change

After inventing the Palm Pilot, Jeff Hawkins focused his efforts on neuroscience. He describes his memory-prediction framework theory of the brain in his book On Intelligence.

Predicting Patterns

This theory describes the process of how the brain makes predictions of future events by matching sensory inputs to stored memory patterns. Inputs that are processed from the bottom-up interact with expectations from the top-down to generate predictions. When a particular level recognizes a pattern, a label is associated and forwarded to the next level in the hierarchy.

Jeff Hawkins was inspired by an issue of Scientific American dedicated to the brain. He saw that neuroscience lacked a comprehensive framework to describe the operation of the brain and embarked on an effort to build one. In this TED video, he describes his ideas and their implications on artificial intelligence and machine learning.


September 16, 2008

Animals Survive Experimental Exposure to Open Space

Tardigrade. Source: Wikipedia Commons. Licensed under Creative Commons Attribution ShareAlike version 3.0. reports that tiny 8-legged animals were able to survive in open space during an experiment performed on a European Space Agency spacecraft. Tardigrades, more commonly called water bears, are similar to the brine shrimp Sea-Monkeys.

The Foton-M3 spacecraft carrying the experiment was launched by the European Space Agency in September 2007 and exposed the creatures to the extreme environment of space. Many of the Tardigrades were able to withstand the exposure to vacuum, ultraviolet radiation and cosmic rays.

The results of the experiment lend support to the panspermia hypothesis - that seeds of life may be able to travel between planets and throughout the universe by a number of possible mechanisms.


April 15, 2008

Jill Bolte Taylor: Brain Scientist Studies Her Own Stroke

Fermi Paradox
© / Vasiliy Yakobchuk

Dr. Jill Bolte Taylor is a Harvard-trained neuroanatomist. At the 2008 TED conference in Monterey, she talked about an amazing experience of being able to observe changes in her own consciousness and perceptions as she was having a stroke. This experience forever changed her outlook on life in a positive way.

Chris K. Haley, Subscribe Get free RSS or email updates here. 

January 21, 2008

Three dimensional human tissue printer

NewScientist is reporting that Dr. James J. Yoo of the Wake Forest University Institute for Regenerative Medicine has developed a way to use inkjet printer technology to build up three dimensional human tissues by printing layers of cells.

Dr. Yoo's research efforts are focused on tissue engineering technologies and cell-based therapies for the repair and replacement of diseased tissues and organs. Some of the tissues that may be produced by his invention include nerve, skin, pancreatic islet, and bone tissue.

Chris K. Haley, Subscribe here.

January 20, 2008

Distributed Computing Projects and the Singularity

Grid Computing
© / Felix Möckel

I have been an active supporter of a number of distributed computing projects for years. In the early 1990s, I participated in the Great Internet Mersenne Prime search and its challenge to find the largest prime numbers. I refocused my efforts on the SETI@home project in 1999 for two reasons. I felt that a distributed computing search for extraterrestrial radio transmissions was a great way to conduct SETI research for a relatively modest cost by analyzing data that was already being captured for other astronomical research projects. I also felt that, while mathematical research is a noble cause, SETI research had something more concrete to offer humanity, despite the enormous probabilities of success. There are certainly more unimportant things that could be done with spare computer cycles.

Recently, I've been reading the writings of Michael Anissimov, who is a leader in the Singularity community and a prolific science and technology writer. Michael co-founded the Immortality Institute, and is the Fundraising Director, North America for the Lifeboat Foundation. Michael is extremely intelligent and writes on a wide range of topics from Life Extension to Nanotechnology to Artificial Intelligence. His outlook for the future is inspiring and thought provoking. Two articles of his had a completely different outlook on the subject of SETI than my own: Aliens - There Are None and Aliens - Stop Looking. His arguments are persuasive and have convinced me to do some more research of my own on the subject, including the Fermi paradox.

But even if I'm not yet as convinced as Michael is in terms of calling for an outright end to SETI research, I realized that there are many more distributed computing projects that I can participate in that have a higher probability of affecting mankind in a positive way in the near term. For example, rosetta@home's search for the 3-dimensional shapes of proteins and the folding@home project to understand how proteins fold are both worthy projects. They have a high likelihood of helping understand and creating treatments for major diseases by using idle computer time from desktop computers.

Accordingly, I will be focusing the vast majority of my idle computer cycles on projects like these. The fact that I don't find these projects as personally exciting or interesting isn't the point. Finding ways to get through the Singularity quicker by helping humanity in the best way possible is.

Related Posts

Singularity Institute for Artificial Intelligence
Why Are We Alone? The Fermi Paradox
What is the Singularity?
The Singularity Effect
Upcoming Artificial Intelligence Events

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January 18, 2008

California stem cell research company produces two human embryonic clones

The Washington Post reported that scientists from Stemagen, a stem cell research company based in La Jolla California, created embryonic clones of two adults that developed to a stage that was more advanced than any previous experiment had achieved. The goal of Stemagen's research is to create personalized stem cells for patients suffering from various diseases that can then be grown into replacement tissues. Tissues fabricated in such as manner would not be rejected by a patient's immune system.

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January 17, 2008

SciVestor Corporation launches Singularity-related technology research offerings

I spoke with Jonas Lamis, Executive Director of SciVestor Corporation regarding the launch of SciVestor this month. SciVestor is a research and advisory company focused on key Singularity technologies, and provides valuable insight as to the effects these emergent technologies will have on business, economic and societal models. SciVestor offers research reports that I believe are of value to investors who are looking to improve their investment strategies. Here is some key information that I have summarized from the SciVestor web site:

  • Robotics
    The robotics industry is expected to grow from $5B in 2007 to $50B in 2012. SciVestor believes the age of intelligent machines is at hand. From service robots to toys and teachers to companionship to war-fighting, the decade ahead will see a dramatic acceleration in human robot interaction (HRI).

  • Nanotechnology
    The rise of molecular manufacturing over the next decade portends a transformation across the supply and delivery chains. Traditional manufacturing enterprises could be displaced by distributed fabrication capabilities. Intellectual property rights for brands and designs will rise to the forefront when perfect replicas become commonplace.

  • Artificial Intelligence
    The software development marketplace is on a steady march to automation of more complex tasks and processes. In the decade ahead, we will see the rise of complex AI capabilities that will take ownership of virtually every repetitive digital task that could be automated. This shift will create significant disruptions in many career roles as well as with outsourcing companies that rely on human capital for efficiencies.

  • Life Extension
    At the intersection of genetics, biotechnology and Moore’s Law lies the new science of life extension. Over the next decade, we will see medical technologies deliver designer therapies targeting disease and degeneration on an individual basis. By 2015, we estimate that more than 10% of first world medical expenses will be devoted to life extension treatments, and many senior citizens in 2050 will have substantially lengthened, productive lifespans.

Jonas Lamis has extensive experience in corporate strategy, business development, and technology marketing with venture-backed enterprise software companies. He is Director of Partnerships at the Singularity Institute for Artificial Intelligence. He is the founding editor of Architecture and Governance Magazine, authors the weblog Singularity U and co-launched Jonas received his MBA from The University of Texas at Austin, an MS in Systems Engineering and Optimization from Georgia Institute of Technology, and a BS in Industrial Engineering from Purdue University.

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January 13, 2008

Newsweek reporting significantly accurate computer thought decoding study

Newsweek is reporting the results of a scientific study by researchers at Carnegie Mellon who used MRI technology to scan the brains of human subjects. The subjects were shown a series of images of various tools (hammer, drill, pliers, etc). The subjects were then asked to think about the properties of the tools and the computer was tasked with determining which item the subject was thinking about. To make the computer task even more challenging, the researchers excluded information from the brain's visual cortex which would have made the problem a simpler pattern recognition exercise in which decoding techniques are already known. Instead, they focused the scanning on higher level cognitive areas.

The computer was able to determine with 78 percent accuracy when a subject was thinking about a hammer, say, instead of a pair of pliers. With one particular subject, the accuracy reached 94 percent.

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January 08, 2008

First Impressions

I was engaged in a conversation the other day with someone about my new association with the Lifeboat Foundation and the opportunity that was presented to me to sit on one of the scientific advisory boards. Let me first point out that the person I was talking with is extremely intelligent, but has a lay person's knowledge of scientific topics, and is generally unfamiliar with Singularity related concepts in particular.

I immediately realized the opportunity in associating with the organization, but still did some reasonable due diligence research before joining it. During the course of the conversation, I explained the goals of the Lifeboat Foundation. I also showed some of the current work that it is doing, and some of the people associated with it by randomly showing some of their biographies. However, when I presented leading biomedical gerontologist Dr. Aubrey de Grey's biography, I was confronted with what was essentially an ad hominem argument regarding his trademark beard. I refer to this as an ad hominem argument because this person believed, without having previously seen or met Dr. de Grey, that his long beard was the sign of a large ego and that he was doing his cause a disservice by conveying a negative image to the public.

I do not personally know Dr. de Grey, nor do I know the reasons why he chooses to have a long beard. To me, the issue of his beard length has no bearing on the value of his work, and although I do not choose to wear a beard at the present time, I thrive on living in a world of diversity where one can do so. What I have gathered about Dr. de Grey is that he is a highly respected member of this community who has many important things to say. The situation was ironic because Dr. de Grey does research that relates to a medical condition affecting a member of this person's family.

I know the point that the person I was speaking with was honestly felt, and that she believed Dr. de Grey could better serve his cause by changing his appearance. But unconscious bias is something that affects all of us to some degree, and it is a subtle, but insidious error in reasoning. Fifty years ago, in the United States, with a different person, this discussion might have been about the color of someone's skin. Twenty-five years ago, it could have been about someone's sexual orientation. It's easy to see the errors in rational thinking of others looking in retrospect, but it's much harder to find our own biases. I long to know what errors in thinking style and biases that I myself harbor now, and which will only be evident with a clearer perspective in the future. As such, I will continue to follow the Overcoming Bias web site to help me in my journey.

I believe that Dr. de Grey reaches an even larger audience by making them take a second look at him. If he had a more common appearance, my debate partner would not have noticed him, and would not have engaged me in a lengthy conversation about his work. If this helps get our message out, then I implore Dr. de Grey to grow his beard even longer!

I eventually resorted to an appeal to authority to plead my case regarding the Lifeboat Foundation by creating a list of some of the more prominent people associated with the Foundation, their professions, and academic credentials. At first I regretted doing this. I am a student of Bayesian reasoning (thanks to Eliezer Yudkowsky) who would like to master the art and I know perfectly well that a person's title or degree can't prove their ideas. Ideas must be judged on their own merit. However, in this particular discussion, it made sense to use the appeal. It wasn't about an appeal to authority being a valid debating technique or not. It was about using the right tool to persuade one person to open their mind to a new idea.

I, for one, am no longer ashamed to have this tool in my bag of tricks, and will use it whenever I need to get one more person to consider a new idea, even for a brief moment.

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