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Monthly Archives: October 2016

Robocop delivered

Last night was the first film of the new SciFlix Series at KU Edwards Campus and both the film and the discussion afterward were a great success. Alex Williams of Psychology joined Annette Tetmeyer from Electrical Engineering and Computer Sciences and Matt Luetke from the KUMED’s Hanger prosthetics clinic to take questions from the audience on topics of Artificial Intelligence, Big Data, Lack of Empathy, and the state of the art in smart prosthetics.

 

Robocop, released in 1987, is set mid 21st century in Detroit, Michigan, a city that looked bound for chaos in the 80s as the gasoline crises of the 1970s continued to push consumers away from large American vehicles to smaller, more fuel-efficient imports. 2043 finds Detroit at a crossroads between complete urban decay and a vast privately developed renaissance. The company behind this redevelopment (creating Delta City) is Omni Consumer Products, OCP or OmniCorp for short.

OCP has a history of moving into the public sector taking contracts in managing prisons, hospitals, space exploration, and – notably – the Detroit Police Department. Before committing to the massive undertaking of rebuilding an entire city center, OCP has determined that the thriving criminal elements must be cleared out to make it safe for the ‘millions of workers needed to build Delta City.’ This is truly a massive project considering it took just 10,000 – 12,000 workers to complete the Burj Khalifa in Dubai.

What ‘the old man’ who controls OCP doesn’t know is that the foundation of  this criminal underworld lies directly under his nose with his Senior Vice President, Dick Jones, who uses his power in OCP to manipulate the police department and attorney general’s offices to protect his racketeering.

So it’s not too much of a stretch to say that Detroit is in a bad way. Crime is up. Corruption touches all aspects of public life, and empathy is almost nowhere to be found.

Victimization-Rates.jpgDr. Williams grasped this problem head on, challenging the public’s misguided perception that crime is on the rise and we are living in an increasingly unsafe world. This perception though is false. In fact, violent crime in the US has been in steady decline since the early 1990s when the ‘crack epidemic’ swept the country.

A student of Dr. Willims put him on the stop asking how he would go about treating Robocop for his evident post-traumatic stress disorder and apparent lack of empathy. Rather than just providing an answer, Dr. Williams provided a framework for understanding his unique patient and presenting a pathway to determining the therapies best suited to one who encompasses the rational mind of a computer and the all to human mind of one who experienced great loss.

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A myoelectric prosthesis implanted after shoulder disarticulation (A) 2-DOFs self-powered hand, wrist, and elbow, plus non-motorized mechanical shoulder with electrical fixation (B).

Questions  to  Mr. Luetke inquired into the capacity for integrating prosthetic devices into or onto the bodies of amputees to restore what was lost or even to upgrade a limb to be stronger than it was before the loss. Mr. Luetke provided a thorough, understandable synopsis of technologies currently in research as well as those available to the public, taking the time to describe how new myoelectric devices can translate muscle movements from restructured nervous pathways to allow for natural control of a full arm prosthesis.

 

 

Dr. Tetmeyer received a number of questions regarding artificial intelligence, the singularity (sort of), and the role of algorithms in daily life – the last of these I really wanted to explore more with respect to both Cathy O’Neil‘s Weapons of Math Destruction and the fact that it is now possible to get a motor vehicle violation with photo for going through a stop light in the middle of the night when no one is around. Surprisingly (to me), the interest in computer science was more theoretical than practical and also more positive than I had expected – considering we had all just watched a dystopian film together. The HAL 9000 was mentioned, but more for comparison to current devices like Amazon’s Echo or Apple’s Siri.

The night ended with a raffle with winners taking home KU moleskin notebooks, KU T-Shirts and the Grand Prize, an OmniCorp T-Shirt. We have the Future Under Control.

 
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Posted by on October 25, 2016 in Uncategorized

 

Looking forward to Robocop at KU Edwards

 

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Win Me!

This Friday evening (October 21) the SciFlix film will be the 1987 cult classic, Robocop starring Peter Weller. The film will begin at 6:30pm and FREE to attend for the public. We will also have free light refreshments including Roasterie coffees and candy. After the show, there will be an open Q&A with a panel of experts in computer science, prosthetics, law enforcement, and psychology to answer your questions about Artificial Intelligence, Programming ethics, the idea of ‘self’, and the state of technology in prosthetics and augmentation. We will finish the evening with drawings for KU T-shirts (and whatever else I can rustle up), as well as a grand prize OmniCorp T-shirt.

 

If you’re in the Kansas City Metro area, come and enjoy a free date night with your brain. Join us on Meetup, see our future offerings at the KU Edwards website, or just send an RSVP and show up!

 
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Posted by on October 18, 2016 in Uncategorized

 

Martha Chase, Max Delbruck, and the American Phage Group

Martha Chase is a bit of an enigma. Her career started promisingly enough working in a productive field amongst productive scientists; but following her PhD, her health precipitated setbacks in both her career and her home life from which she did not recover.

She received her bachelor’s degree in 1950 from the College of Wooster. Later that same year, she joined the laboratory of Alfred Hershey in Cold Spring Harbor to work as his lone laboratory assistant asking questions about the mechanisms of life using a viral model system. The virus they used was the bacteriophage T2, a fascinating conglomeration of proteins and DNA that specifically infects bacteria. Through her work with Hershey, she became linked to the remarkable influence of a network of biologists nucleated around the German-American biologist, Max Delbrück, called the ‘American Phage Group.’

Delbrück, himself a Nobel Prizewinner, led a rich intellectual life amongst an elite group of academic luminaries. The Chemist, Karl Friedrich Bonhoeffer, was a close friend and mentor to him during his younger years steering him into the study of physics where he became associated with Wolfgang Pauli and Niels Bohr. It was Bohr’s influence that put him on the path to Biology through its relationship with Physics. Again, not to be on the outside looking in, he became assistant to Lise Meitner who had worked with Nobel Laureate Otto Hahn to discover fission of Uranium (Meitner is often regarded as missing out in the Nobel for anti-Semitic reasons), and with Otto Frisch, who recognized that fission must be accompanied by a massive energy release tying it to both the potential for energy production and a potential massive destructive power. Delbrück initially came to the States to study genetics in drosophila, but made a deeper mark studying viruses, eventually earning a Nobel Prize in 1969 for his work with Salvador Luria and Alfred Hershey, largely thanks to the diligent work of Martha Chase.

Many of the Phage Group’s members are credited with landmark advances in our understanding of molecular biology. Luria, working with Delbrück, demonstrated that mutation of bacteria occurred in a strictly Darwinian sense, i.e. that bacteria could mutate to resist viruses even without the virus being present. This is a fundamental distinction from Lamarck’s notion that evolution was driven by need, rather than by selection of completely random events. It was at this time that he took on and trained his first PhD student, James Watson (who also did something important – I forget what).

In 1949 Renato Dulbecco came to Caltech to join Delbrück’s group with the focus of understanding how some viruses would lead to tumors. Along with David Baltimore and Howard Temin, Dulbecco shared the 1975 Nobel Prize for discovering how these viruses would reverse transcribe their RNA genome into DNA and integrate it into the host’s chromosome.

Matthew Meselson and Franklin Stahl, also working with the phage group, demonstrated that DNA replication is a semi-conservative process retaining one strand from the ‘parent’ DNA and one ‘new’ strand synthesized as a complement to the ‘parent.’ This work did not earn them a Nobel Prize, although it provided early support for Watson and Crick’s DNA structure and remains a landmark experiment in biology that every student is taught.

As evidenced by the sheer number of Nobel Prizes shared by members of this group, the Phage Group and its associates dominated the fields of bacterial genetics and molecular biology. But before those experiments were performed and Prizes collected, the physical molecule carrying genetic material was yet to be discovered.

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Frederick Griffith (see reference 1)

Frederick Griffith was the first to point the way to this molecule by showing bacteria’s mysterious ability to transfer new characteristics (Darwin’s Traits) between organisms. But, tragically, left his work incomplete due to his death in London during WWII. A number of stories exist regarding his whereabouts when he died. Regardless of its veracity, I personally like the one that suggests that he was working late in the lab when it was bombed by the Nazis.

 

Before his death, in the 1920s, Frederick Griffith demonstrated that some element of a bacterium, that is released upon its death, was sufficient to carry genetic information from one strain of bacteria to another. Specifically, he demonstrated that ‘smooth’ pneumococcus, which secreted a glycocalyx, could transfer this trait to ‘rough’ bacteria that lacked the glycocalyx. Clinically, this was very important because the rough type pneumococcus was easily handled by the immune system, while the smooth type colonized the heart and killed the host. He called this element the ‘Transforming Principle,’ but died before he could identify it specifically.2

 

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see reference-2

Experiments showing that the transforming principle was probably DNA were performed by Avery, MacLeod, and McCarty at the Rockefeller Institute in 1944. Despite being both elegant and thorough, many thought these experiments lacked the appeal needed to be convincing.

 

Knowledge of Avery’s work supported the case for DNA as the genetic material, but Protein remained a persistent contender because, with its 20 physiological amino acids, its capacity to carry the information associated with genes seemed more reasonable. DNA, on the other hand, was an arrangement of only four bases, a simplicity that obfuscated its coding potential. One compromise hypothesis suggested that perhaps DNA served as a scaffold for the information-carrying proteins, although Avery’s experiments showing that protein-free DNA preps could transform bacteria strongly argued strongly against this model.

So, the issue remained to be effectively demonstrated denying Avery and his co-workers Nobel. A more satisfying answer, reaffirming Avery’s discovery, was to come from the ever-productive phage group in the hands of Martha Chase.

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Martha Hershey and Alfred Chase (see reference 3)

Working together, as laboratory technician for Alfred Hershey, the two performed their eponymous experiment in 1952 with the purpose of identifying what served as the genetic material in phages.

 

Hershey intended to use the T2 bacteriophage to assess this question, in part because it contained no other molecules such as fats or sugars, making it an exceedingly simple model (See illustration of method, panel A) but also because electron micrographs already hinted of protein ‘ghost’ particles left outside of the cell while new phages were being assembled within. Indeed, by involving only DNA and unglycosylated proteins, it was possible to label the DNA and Protein elements individually using radioactive Phosphorous-32 to mark the DNA and radioactive Sulfur-35 to mark proteins. These isotopes worked well because they were trackable by following the radioactivity, while each was specific to its target due to the natural, exclusive distribution of Sulfur and Phosphorous in Protein and DNA, respectively.

 

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A bacterium with phages attached to its surface and phage capsids assembling within the cell. (attribution unknown)

The basic experiment was simple in theory. T2 bacteriophage was grown in media containing either nucleotides with Phosphorous-32 or amino acids with Sulfur-35. In the first condition, only the phage DNA was radiolabeled. In the second condition, only the protein was labelled (see illustration of method, panel B). Once the phage was prepared, it was allowed to attach to fresh bacteria for a time period known to allow for the passage of genetic material. At this time, the bacterial cultures were moved into a kitchen blender and pulsed to remove the material that did not enter the host cells (the ghosts). Centrifugation permits the separation of the ghosts and any other viruses in the supernatant from the (infected) bacterial cells. The only thing remaining was to check to see where the radioactive elements were: the supernatant fraction that did not enter the cell, or within the cell, where the genetic material was (see illustration of method, panel C). Like most experiments, much of the work invested in the project occurred prior to the actual experimentation in order to optimize each condition.4

 

 

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Illustration of Method for Hershey-Chase Experiment

The answer was clear, Radioactive Sulfur was never found inside of infected cells, only in the supernatant. Radioactive Phosphorus was overwhelmingly found within the cell. With this elegant experiment, the question was answered, and DNA was widely recognized as the genetic material setting up the next, obvious Nobel Prize: what is the structure of DNA? And does this structure reveal any of its properties?

 

At the University of Southern California, Martha continued to study phages under Giuseppe Bertani (Joe to his friends), ultimately following him to the Karolinska Institute in Stockholm, Sweden where she completed her PhD thesis on “Reactivation Of Phage-P2 Damaged By Ultraviolet Light” in 1964.5,6,7 Her obituary, which is one of only a few primary sources of information on Chase, describes life after earning her PhD as plagued with personal troubles arising from short-term memory loss that likely contributed to the end of her scientific career and possibly her marriage.

Despite the fact that this work represented the accomplishment of Hershey in the 1969 Nobel Prize along with Delbruck and Luria, Chase did not share in this honor. As a technician in the lab, it may be that her hands performed many (if not all) of the Hershey laboratory’s experiments, but technicians are rarely (if ever?) included in the Prize on the assumption that it is unlikely that they are major theoretical contributors to the work. Her name, however, will forever be associated with this experiment, serving as a lasting reminder of her contribution to molecular biology.

References

  1. Photograph of Frederick Griffith, photographer unknown
  2. “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Deoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III.” January 1944. Exp. Med., 79: 137-158.
  3. photo: Martha Chase and Alfred Hershey, 1953. Attribution unknown. I found both of these images at https://varietyofrna.wikispaces.com/Hershey+and+Chase
  4. Link to Hershey and Chase’s J. Exp Med paper: http://jgp.rupress.org/content/jgp/36/1/39.full.pdf
  5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827068/#
  6. http://www.the-scientist.com/?articles.view/articleNo/22403/title/Martha-Chase-dies/
  7. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll18/id/368326/rec/7
  8. See http://www.nobelprize.org/ for a listing of Nobel Prizes, Biographies, Acceptance Speeches, and even games.
 
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Posted by on October 3, 2016 in Uncategorized

 

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