Monthly Archives: October 2012

Is there new hope for ‘A New Hope’?

ImageDisney bought the rights to the Star Wars franchise from Lucasarts today for $4B. For old Star Wars fans like me, this poses two immediate questions:

#1 Is Disney going to make rubbish movies and destroy the series?


#2 Does this mean that finally someone is in a position to remaster and release the ORIGINAL version of Star Wars, A New Hope?


The answers:

#1  Too Late. George already did that with 3 1/2 crummy episodes

#2 Who knows. I can only keep my fingers crossed – a good friend of mine consulted his magic 8 ball though and he said the outlook was grim.




Posted by on October 30, 2012 in Uncategorized


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Miller, Urey and Venter

The Spark of Life

Life is a funny thing. Despite our primary connection and concern with it, life defies a simple definition. This seems absurd because it is intuitively obvious whether the dog lying at your feet is alive or dead. But do you use the same criteria in judging if the tree in the front lawn is alive? What about a frog frozen in the Siberian winter? Somehow the line still seems fairly bright – even if difficult to define.

You might be a little more hesitant if you’ve spent time in a biology classroom contemplating the fringes of life. Biologically, there are two general ideas that define life. The first is the ‘cell theory’ that defines the cell as life’s smallest unit. Second is a list of characteristics that life may possess. These include such things as organization, homeostasis, growth, response to stimulus and reproduction (among others.) Some simple thought experiments illustrate how some of these characteristics may exist in dead things, while others may be absent in living things.  But when taken together, they provide support for, or argue against a thing’s life. Consider: a fossil has evidence of both cellular structure and organization, but fails to respond to stimulus or grow; a single celled amoeba responds to stimulus but does not grow (at least not beyond its single cell ‘body’); a castrated bull that has almost all of the listed characteristics save reproductive ability. Which of these is alive?

In contrast, consider a virus. It fails almost all of the tests and is nearly always considered to be unliving, yet is very well organized, can reproduce when infecting a host cell and does respond to some stimuli as its DNA may harmlessly reside in a cell until conditions induce it to ‘awaken,’ start reproducing itself and finally kill the host cell as it bursts from the sheer number of virii produced.

Life, then, seems dangerously close to Justice Stewart’s 1964 definition of pornography – or rather, his failure to define it – “I know it when I see it.”

It’s amusing that the definition of life even eludes biologists. ‘Biology’ itself translates as ‘the study of life,’ yet those of us who study it can’t say exactly what it is in every case.

So it is doubly complicated when scientists puzzle the origin of life. We don’t know exactly what life is AND current estimates place the origin of life back 3.5 billion years. This leaves us with fossils, assumptions about the early Earth’s atmosphere and laboratory experiments meant to mimic early conditions. We are also in something of a quandary because of Louis Pasteur’s demonstration in 1862 that showed quite definitively that spontaneous generation does not occur  under present conditions– only life can beget life. Yet this must have happened once for us to be here pondering our origins.

In 1922 the soviet scientist, Alexander Oparin, was pondering the origin of life on Earth. At the time, evidence was beginning to suggest the environment of the early Earth as being a reducing environment consisting of ammonia, methane, hydrogen and water vapor. Oparin determined that this was ideal for the chemical evolution required to generate the amino acids and other complex molecules that could later make life possible. One reason this atmosphere was ideal was the lack of oxygen that can be very destructive to molecules that become oxidized in its presence.

Stanley Miller

It took thirty years for Oparin’s theory to be actually tested in a laboratory and it was not Oparin himself who did the experiment. Instead, it was the Americans, Stanley Miller and Harold Urey who, in 1952, constructed an apparatus that sterily re-created the Earth’s early atmosphere within a self-contained glass tubing. Water was heated to form vapor and an electrical spark was provided to simulate lightening. Under these conditions Miller and Urey witnessed the generation of five amino acids as well as a number of sugars and fats – all building blocks necessary for life.

This does not prove that the chemical precursors of life formed this way, but it does demonstrate that, under these conditions, molecules necessary for life could self-assemble. Regardless, this was not the generation of life in the laboratory, but only a step showing that macromolecules required for life can spontaneously form under the proper conditions.

Beyond this, we know some of the things that are required of life as we have defined it. There must be the generation of some device to carry information from one generation to another.  Why do we require this? Because there needs to be a way for the new organism to ‘know’ how to do the things it needs to do to stay alive. That way is through inherited information

It is interesting that from the beginning we assume that life must proceed in generations rather than as a single organism going on indefinitely – but considering how fragile a single life may be, generations may be the only way. This information is almost uniformly encoded in DNA. Further, the code used to store this information is also (for practical purposes) universal. Together, these facts argue strongly for the origin of life as a single event.

There must also be a compartmentalization of this information and the machinery required to replicate it within a membrane – thus creating a cell. It’s another interesting thought experiment to contemplate whether life is possible without a membrane. However, it is difficult to conceive how a lifeform could occur without the ability to concentrate itself and hide its resources away from potential predators.

So, life is difficult to define and we have only hints about how it originated. An interesting question is, ‘can we create life ourselves?’ The answer is: of course, it’s so easy that it doesn’t require a lab at all.  All our youthful energies are directed at making new life (or perhaps avoiding doing it so we can earn enough money to pay fertility doctors to do the same thing once we’ve gotten to old to do it ourselves.) But that’s not what I mean. More specifically, “Can we create life in the lab synthetically… from scratch?”

More than just an idle curiosity, this is more a question of testing what we know about life and its requirements. Biology has been a reductionist science since the structure of DNA was modeled by Watson and Crick in 1953 and developed as a tool of molecular biologists by the 1980s. Creating a living organism in the lab is a test of our ability to rejoin these reductionist ideas into a unified, functional model.

A step in this direction was taken in 2002, when Eckard Wimmer’s group made a synthetic poliovirus and demonstrated that DNA made in the lab was just as infectious as naturally derived poliovirus DNA. This advance was met with skepticism based on the fact that the only novel element of this work was the chemical source of the DNA. All other elements of the experiment had been previously demonstrated and were not at all unexpected (these are the two elements that make for good science– novelty and unexpectedness.) Furthermore, in terms of creating life, a virus is generally not accepted as alive for reasons we discussed above.


Craig Venter

Enter Craig Venter. In 2000, his Celera Genomics company was the first to sequence the entire human genome. Since then he founded the J. Craig Venter Institute and Synthetic Genomics as vehicles for deriving synthetic life. In 2010, his group was successful in generating an entire microbial genome chemically and then using it to direct life functions within a new cell that previously had its own DNA removed.

This might not sound like much of an advance over Wimmer’s work with a synthetic virus, but it certainly brought its own challenges, one of which originated from the fact that the ‘host’ cell used was not the same as the ‘donor’ DNA. This led to some trouble in overcoming certain molecular defenses set up by the cell in order to repel parasites such as viral infections. After overcoming these obstacles, the cells were observed replicating the introduced DNA, manufacturing the proteins it encoded and dividing into daughter cells.

This work also began to define just what genes were required to accomplish this goal and possibly address the question, “what are the minimal requirements for cellular life?”

A possible utility for the project would be tailoring this bacterium for the production of recombinant proteins, fats, etc. These bugs can then be used to make medicines, remediate ecological damage and perhaps even serve as medical therapies themselves. Since we have created it from scratch, we know that there is no danger of having it ‘escape’ and mutate back into a virulent form.

So, despite the difficulties associated with even knowing what life is and how it originated, we have not let these questions prevent us from using what we do know to accomplish amazing tasks that were unthinkable just a few short decades ago: creating life in the laboratory.

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Posted by on October 30, 2012 in Uncategorized


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Salk’s work was revolutionary, but he did not work in this field alone. Albert Sabin also developed a polio vaccine around the same time using a different approach. Together, the story of these two men’s work is a fascinating story that uncovers many of the difficulties and solutions taken in vaccine development.


Jonas Salk the medical researcher who came up with the first polio vaccine was born on this day in 1914. Salk died at the age of 80 in 1995. Salk did more to help the country and the world than most of the presidents of the United States have done. The news of the polio vaccine’s success was made public in 1955 and Salk was called a miracle worker and celebrated all over the world. Salk had no interest in personal gain on his discovery. When asked if he had the vaccine patented he replied ” There is no patent. Can you patent the sun?”

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Posted by on October 28, 2012 in Uncategorized


Another take on my making better babies post from last week.

The Cords that Bind

In Star Trek lore, the Eugenics Wars were a series of conflicts in late 20th century Earth that was precipitated by the creation of genetic supermen. These genetically superior human beings launched a plan to take over the world from non-genetically enhanced humans. The results of their plans led to millions of deaths and a ban of all such genetic enhancements not just on Earth but throughout the entire Federation.

Now scientists have taken one step closer towards genetic enhancement by breaching an ethical taboo and modifying genes across generations. They are doing so for good reasons, namely the prevention of inheritable genetic disease, but we all know the saying about the road paved with good intentions. It will be fascinating to see where this will lead in the years to come. Will it remain relatively benign, or will we have a case of the financial elite genetically modifying their…

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Posted by on October 28, 2012 in Uncategorized


Game Night

I just wrote about the change in season and it’s very much on my mind and last night was a perfect example of what I like.: Perfect for game night.

ImageMy wife has been away traveling for two weeks (with a little respite last weekend) and just returned yesterday afternoon. Because she’s been gone so long, it felt much better to sit and play a board game rather than get sucked into a movie. Moreover, Harry picked the perfect game.

When I was a kid, I lived (most of the time) with my grandparents. My youngest aunt, Kim, was only eight years older than me, so she was in the house for many of those years. She was also a wholeheartedly devoted runner who still holds a  records in Delaware for her age group for 10K, 15K, 20K, 10 mile and Half-Marathon. I’m waxing on about her a little because she passed away a couple of years ago following an accident that caused serious brain damage, so there’s no fear of her reading this and getting an inflated ego.

I brought up Kim’s memory because she once got a Marathon board game from Runners, World. It’s a great game in part because of its simplicity. Basically, you set your pace to one of five speeds and then draw cards that indicate how many spaces you can go. Being a marathon, the road is littered with obstacles, thirst and injuries that will limit your pace, causing more damaging impact the faster your pace was set when you hit it.

This game is so old and targeted at such a specific audience that I really wonder how many surviving copies there still are.


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Posted by on October 27, 2012 in Uncategorized


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A wonderful time of year

The leaves are changing, the god-awful heat is gone, frost coats the lawn and a fire is crackling. I love the fall – possibly in large part because I hate the hot summer days so much, but also because it’s a great time of hunkering down for the holidays and a cold winter.

One thing I especially look forward to is the surfeit of horror movies on TV. I’m a big fan of the Hammer Horror films – which I consider the true classics of the genre. I enjoy the older Universal films, but I think Hammer did a better job with less money. Instead, they somehow lucked into a team of truly great actors and gave them good scripts. There was no shortage of gory scenes, but none of these films depended on them to deliver the real tension (well, not really anyway).

ImageInterestingly, this is also the time of year when the first Exam happens in my intro Bio class and I just can’t imagine a world where it would be harmful for my students to take a break and enjoy a great film like Dracula or Frankenstein.

On a side note, despite all the problems I have with George Lucas for doing everything in his power to undermine his own opus, he did at least have an eye for talent (well, sometimes he did). It’s just too bad that he didn’t learn more from watching Hammer films as a kid.




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Posted by on October 27, 2012 in Uncategorized


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Two minutes into my latest coursera lecture….

Two minutes into my latest coursera lecture (introduction to interactive programming in python) the instructor indicated his frustration in javascript programming saying that it’s a terrible language. This may be the case… so far I don’t have a lot to compare against, but I have been enjoying learning JS in codecademy and I’m dying to know why he thinks so.

If you have experience programming in javascript and python (or other languages…ruby?) let me know if you agree with the above statement and what makes you think so. As a new programmer I am interested in learning as much as possible – if I can understand what faults people see in these languages I think that would be very instructive.



Posted by on October 25, 2012 in Uncategorized


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Making Better Babies – A pragmatic solution to a problem and the ethical firestorm it provokes

Let’s say you are a young person thinking about having a baby, but you know there is a genetic disease in your family that worries you. It’s a reasonable concern that people have recognized for some time. There have always been diseases to concern parents, but technology is changing how we think about and face these concerns.


A Downs Syndrome Karyotype

Once upon a time these was little more to do but cross your fingers and hope for a good result. Then chromosomal testing (Karyotyping) of a developing fetus became possible allowing parents to know what is happening inside the womb. Getting this information was not without risk, and even with the results in hand, would-be parents are faced with terrible choices. The way we dealt with this test in our family was to not have it done. We really wanted a baby and thought that  that having test results would not change our behavior. So we chose not to be put in a position of having to make that choice. It was what worked for us, but we also didn’t have specific concerns other than the fact that we were getting older.

Following the advent of chromosomal tests, it became possible to test the DNA of a fetus for specific, known problems. For example, If caner runs in the family, you could check to see if the baby’s p53 gene was normal. Having one or more bad copy of this gene dramatically raises the probability of developing cancer relatively early in life. Today, this is something we can know for certain.

But there are several sources of DNA in us. We typically think of the vast amount of DNA carried in the form of linear chromosomes that are packaged inside the nucleus of our cells. This is definitely the lion’s share of the DNA passed from one generation to the next, but there is another source as well: The Mitochondria. You may have learned about these organelles (little organs) as the ‘Powerhouse of the Cell’ for its role in generating much of the energy (ATP) your cells need to do their jobs. These organelles have a strange history in us. It is thought that many eons ago those things that are now mitochondria inside our cells were once free living organisms (possibly parasites, possibly a bigger cell’s dinner). However it happened these microbes were taken inside of our cells, but not digested as food or harmful enough to kill the host either.


Why am I talking about this? Because those organelles still carry remnants of their former selves. They still have their own protein-making machinery and even their own DNA. This DNA isn’t large, but it does carry genes coding for vital proteins. And this is how we get back to our original story, because sometimes these mitochondrial genes are no good. If these genes aren’t right, they can’t make healthy, functional proteins. If they can’t make good proteins, then the host cell and the while organism can die.

Interestingly, all the mitochondria in every cell of your body came from your mother. This is one place where dad makes no contribution. Even though sperm have mitochondria, they don’t get incorporated into the new zygote, only those from the egg will remain.

Enter The Future of Fertility Medicine

Recent developments have shown that it is possible to replace the unhealthy mitochondria with healthy versions from a donor cell to make good eggs that can be fertilized and result in a healthy child. This was the subject of an excellent review in Nature and also discussed on the Nature Podcast this week. So how many parents is that? One mom, one dad and one mitochondria donor (I guess this could conceivably come from dad, but I just don’t know). This procedure has been done successfully with non-human primates, but so far not with humans.

So, pursuing a simple line of work aimed at helping parents make healthy babies is suddenly possible and suddenly a great ethical question. Have you ever seen Gattaca? If not, go out and watch it. I was sure this film was going to be miserable and be a poor representation of science, but I was totally wrong. They ask the same questions in that film that we are beginning to face in real life:

This isn’t the first time people have thought about this

When does Medicine become tampering with life? And does it matter? Don’t we want healthier, more able bodied people? Is it wrong to replace bad genes? What constitutes ‘bad’?

Personally, I don’t believe that there are universally right and wrong answers to these questions. Even if we decide that there are some less desirable consequences for mankind, that doesn’t mean that we wouldn’t do it. Much of plastic surgery isn’t really necessary and some might call it a perversion of medicine, but that doesn’t stop tons of people from getting it.

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Posted by on October 24, 2012 in Uncategorized


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Sometimes people can be wonderfully, unexpectedly kind.


This morning as I was trying to cool my mind from fuming at my seven year old son I stopped for a little pick-me-up at a Starbucks drive thru. I’m baffled about how it could possibly take an hour for him to get up and brush his teeth and come downstairs. Especially since today is a special ‘Wear your PJs to School Day.’ Nevertheless, waking him at 6:30am could not produce him in the kitchen until 7:45am despite warnings that he would miss breakfast, etc. etc.

My wife is traveling for work again this morning, which means two things: #1 There’s no one pushing me out of bed on time. #2 Our veritable wild kingdom of animals must be tended by a single zookeeper. Perhaps I also have to admit that the above-mentioned zookeeper was up way too late trying to squeeze in some late night Coursera lectures during the 12am-5am free internet time and also left the kitchen a mess because it’s much easier to put off today what you can possibly do tomorrow.

Oh, and there’s homework to do that should have been completed yesterday after school, but somehow that slipped too. 

Ok, Ok. I know it’s my fault. I’m terribly lazy and find it very hard to motivate myself to do things that don’t seem all that important in the grand scheme. -But I find time to write this blog, don’t I. But this isn’t what I wanted to talk about. I’m writing about coffee and gratitude.

Back to Starbucks. When I pulled up to the window to get my drink the barista asked if I knew the woman ahead of me. “No,” I said.

“Well, perhaps she saw you, because she paid for your coffee.” I don’t think that has ever happened before for this particular barista because she was acting very confused. I want to think that’s the long and short of it because I’d rather not speculate as to any other reason why she thought this was so unbelievable.

Nevertheless, I was instantly perked up and thanked the barista, even though she was only unwillingly dragged into this and tipped her a buck before pulling away. But this then put me in the mildly awkward position of rather closely following the woman who had bought my drink out onto the highway. We even come to a stop at two traffic lights together where I wanted to thank her, but I have to admit to being pretty shy and having the self-confidence of a radish.

So, instead, what do I do at the traffic light? I make a quick decision to turn exactly the wrong way and head away from my destination. Not because I want to pull up beside her and wave, but because I didn’t want to do that. Or at least I wasn’t brave enough to.

Thank God I somehow found someone to marry me (let’s be fair to my poor wife, there was a good amount of alcohol involved in our meeting that probably blinded her to my fumbling). Because if this is how I handle even the most innocuous social situations, I would certainly be damned to a lonely hermit’s existence. I’m really a very lucky man.

Well, I had imagined this as an opportunity to thank the universe for a free coffee and a nice boost to my day, but somehow I twisted it into a rant about my own foggy inner dialog. So let me conclude by saying that I mean to find a way to pay it forward today and to say that sometimes even the simplest things in life can be not so simple.


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Posted by on October 24, 2012 in Uncategorized


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Another old essay – Morgan and Memes

This essay was originally published in the Osawatomie newspaper (The Graphic?) a year or two ago. It was prompted by an article in my local newspaper that showed how two ideas that have no logical connection can sometimes appear to be intimately ‘linked’ to one another.

Morgan and Memes                                                                                           

Thomas Hunt Morgan in the Fly Room

In the early 20th century, a scientist at Columbia University, named Thomas Hunt Morgan did work establishing the connection between the observations of Gregor Mendel and some lesser known scientists, Flemming, Sutton and Boveri. Mendel, an Austrian monk, was the first naturalist to see deep into the workings of nature and establish a clear, testable theory of how inheritance operates in organisms of all types. Trained in mathematics, Mendel saw that if each trait he observed was controlled by two ‘factors’ (one from each parent,) then inheritance followed a predictable pattern.

In his laboratory in Germany, totally unaware of Mendel’s work, Walther Flemming watched and documented the precise orchestration of cell division under the microscope. What he saw, less well known than Mendel’s work, was how chromosomes seem to form as threads in the cell that group along the center line of a cell before splitting and separating into each of the daughter cells formed by division. Sutton and Boveri saw the connection between these sorting chromosomes and Mendel’s ‘factors,’ but could not finish connecting the dots. Hunt’s conclusion, which seems so obvious now, was that chromosomes carry genes. To prove this he tracked two special chromosomes, X and Y and found that they determined the sex of the organism. Like humans, when flies had two X chromosomes, they were female; one X and one Y and they were male. Chromosomes were controlling the sex of the organism. This conclusion changed the way genetics was studied for years to come.

One thought that beguiled him though, was that Mendel’s work predicted that all genes sorted independently, but there were only so many chromosomes, and many, many genes. This was troubling because Mendel’s work was otherwise very clear and stood up to rigorous testing, yet it was inconsistent with what he saw with chromosomes. Mendel said that all genes are randomly inherited – and here he was, working with fruit flies and finding that it just couldn’t be true with so many genes and so few chromosomes. To skip the details, Morgan, and his lab members eventually discovered that chromosomes are tricky – and sticky. The two sets of chromosomes you get from each of your parents pair up and swap bits promiscuously. This swapping, or ‘crossing over,’ imitated randomness in all genes except those that were very close together. And so, while most genes adhered to Mendel’s law of independent assortment, those genes that lie close together on the chromosomes travel together and can be seen as traits that go hand-in-hand down the generations.

In 1976, Richard Dawkins, wrote “The Selfish Gene” in which he buried a nifty little idea. He proposed that thoughts are like genes- he called them memes– that get passed along from one person to the next, taking on a life of their own in a sort of world-wide game of telephone. He has written often about this idea, which is an interesting analogy, but not altogether useful scientifically.

Nevertheless, I had the thought of memes in my head, and when I read an article about organic farming our local county paper, I suddenly realized that memes too travel together! In the article a farmer described her farm as organic and natural – all the things that I like to hear about. I was immediately excited and wanted to join her co-op to get food that was a little more a part of the earth and a little less a product of chemistry. But then I got to some ideas that just didn’t make sense to me – things that often travel with the less well informed members of the organic food crowd: She doesn’t vaccinate her animals – or her children. She went on to suggest that cancer and autism are causally linked to genetically modified organism (GMO) foods – a completely groundless hypothesis.

Two chains of Memes (Memosome?). Memes 1-3 are all linked in some way, Memes 4 and 5 are also linked to one another, but not to Memes 1-3.

Yet, I’ve seen these memes travelling together in the past without giving it as much thought, and here they are again: The natural food meme and science-makes-us-sick meme. On one hand I see the connection and agree, I don’t think GMO foods are natural and vaccines are a way of unnaturally generating immunity without being exposed to disease. But, GMO foods are not inherently unsafe. They simply put together traits that exist in nature, but in combinations that would take breeders eons to produce ‘naturally.’

I love to know that my food comes from a natural, organic farm. And I expect to pay more for food of that sort, mostly because it is not as abundant and does not take advantage of advances in science. Advances that make it possible to feed all the billions of people on this planet. Billions that could not all be fed without modern, scientific agriculture. But there is something wholesome about foods grown in this way: the great variety of fruits and vegetables with their subtly distinct flavors and colors. Like GMOs, vaccines are also something of an unnatural creation – unnatural creations that spare us from the all too natural world of smallpox, measles, poliomyelitis.

I don’t mean to impose my values on anyone, but I do think that it can be enlightening to consider what ‘natural’ means. There are many things from the past that we should not forget and good food is one of them, but we ought not to also forget the ravages of disease that once kept children from playing outside together in the summer months or made them deathly sick only to recover and lead a life blinded, paralyzed or otherwise retarded from exposure to all things natural in the world.

I don’t think that anyone leads an entirely consistent life, but we are intelligent creatures and we don’t have to accept anything without consideration. So take some time, examine what you believe in and see just what memes are in your head just catching a ride. Maybe there’s some cleaning out to do.

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Posted by on October 24, 2012 in Uncategorized


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