Wednesday, October 29, 2014

The Sclerosis of Science

Whenever I come back from a conference, I have mixed feelings about the progress being made in the field I work in.  There are times when I feel like we are really discovering what is going on, and moments where I feel that we are merely spinning our wheels.  We are looking at very specific areas of biochemical processes, and I often wonder why we are looking at them.  Are we studying them because we truly understand the overall process and know this is the area that is important, or are  we studying a particular area because it is the only area we know to look at?  Are we studying something because we know it is important, or have we deemed it to be important because it is the only area we know to look at?

In the field I am working in, I feel like everyone is spending an eternity examining meaningless minutiae of the processes we are studying.  This has led to a sclerosis in which very little advancement is being made.  As scientists, we need to be bold, and start thinking about how to take the leaps forward we need to study the overall processes we are examining, and not get lost in the minutiae.

Sunday, October 26, 2014

Looking to be Remembered

As many of you may know, there have recently been several "Lone Wolf" terrorist attacks.  We've had the man in Quebec who ran over two soldiers with his car, the Ottawa shooter, and then the hatchet wielder in New York.  All three men died in their attacks, and all three were home-grown converts to Islam.  

Numerous questions are being asked about what would lead these men to do this.  One popular answer, which Mark Steyn has written about extensively, is that the spiritual death of the West is leading many into the arms of Islam, which gives these young men a purpose that they don't receive from their native culture.  While there is much truth to this, I feel it leaves a lot out of the phenomenon and doesn't completely cover why these men become so radicalized that they carry out to us what look like useless and futile attacks.  After all, what does killing one man in a nation of millions do for someone's perceived Jihad against the West.  In order to answer this question, I believe we need to take a step back, and try to answer, if we can, what man's purpose is in life, in a nutshell.

If you were to ask different people what our purpose in life is, you are sure to get a myriad of answers.  Some would say our purpose in life is to reproduce and raise children.  Others would say it is to love and be loved.  Some might say it is to have a worthwhile career full of accomplishments. Still others would say it is to follow your dreams and simply be happy.  I believe the one thing that almost all these answers have in common is they revolve around what I believe to be the main thing people strive for in life, and that is to be remembered after we die.

Much of what we do in life we do because of our mortality and the desire to be remembered after we pass from this Earth.  We have children so we will have a line of descendants that can trace themselves back to us.  We try to make a name for ourselves in work or charity so others will know about our accomplishments when we are gone.  We seek fame, fortune, and create art so our names will be spoken forever.  We want to be remembered, we have the need to make a mark that proves we were here, we existed.

Sometimes, of course, this desire to make a mark leads people to violent acts of evil and depravity. Spree killers seem to be motivated by the desire to commit an act so atrocious that their names will be remembered forever.  Adam Lanza would appear to fit this profile to a T.  The guy was an unemployed loner who seemed to have little chance of having a family or a career where he could accomplish something.  He played video games such as Dance Dance Revolution endlessly in the hope of having his name at the top of the scoreboard.  When he realized that was no path to immortality, he turned his sights to mass murder, keeping a scorecard of the death totals of other spree killers so he would know how many kills he needed in order to make it to the top and stay there, so he would always be remembered as number 1.

The Islamic terrorist attacks of the past week is what occurs when you have a desire for notoriety combined with an attempt to achieve immortality by joining an ascendant movement.  The terrorists who committed the recent attacks undoubtedly saw Islam as an ascendant force that is going to sweep the globe.  While their attacks might have accomplished little to help in that endeavor, their hope likely had to be that future Islamists will remember their names and what they did for the cause.  In this way, they will achieve their immortality on Earth.

Thursday, October 23, 2014

Living for a Millennium

I was initially excited when I saw this article on The Week about 1,000 year lifespans, as something I tried to tackle in my book with its alien species was the effects of having a lifespan of a millennium. The article ended up being an extreme disappointment, although it did link to a scholarly paper on the biology of increasing our lifespans.  I've only skimmed it so far, but that at least appears to be interesting.  As for The Week article, it reads like something the author scribbled in a couple minutes before an editor added a few links.  It barely scratches the surface of many issues raised by longer lifespans, and seems to engage in magical thinking about government budgets.  The author does bring up a few questions about longer lifespans that I tried to answer in my novel, though.

First up, the author points out longer lifespans will also mean healthier lifespans, and this will give humans several hundred years to live at their peak physical level.  This has huge implications for work and family.  If our longer lifespans require us to work for centuries, does this mean we will have one career, or several?  Will we continually have to go through re-training or head back to school?  How will we cope with hundreds of years worth of technological change in our jobs?  In my book, I anticipated that with longer lifespans career changes will occur, but they won't quite be a necessity.  In a futuristic knowledge economy, there will always be some career angle for a particular set of skills.  While major career changes won't be required then to stay employed, many people will still go through them as they become bored with their old jobs.  Longer lifespans, though, will allow people to build up capital over centuries that they will then be able to use to follow their dreams.  I believe the rates of entrepreneurship and self-employment will be extremely high if we manage to live for a millennium.

I think the biggest complication with long lifespans is going to come in the area of marriage and family.  If we live for a thousand years, are we really going to want to be married to one person for the rest of our lives?  In my book, I anticipated that the answer would be yes, but with a caveat.  I think people will still marry for life, but they will take the occasional break to go off and do their own thing before returning to their spouse.  I think longer lifespans will make it imperative to have one person who is always there for you, from the time you enter adulthood to the time you die.

How having children will work with a lifespan of a millennium could be very interesting.  If childbearing years could be extended to last several centuries, all kinds of possibilities exist.  Couples could have children over the span of centuries, meaning they could still be having babies when their first set of children are several centuries old, with grandchildren and great-grandchildren or later descendants of their own.  That is something to me that is completely mind-blowing, the idea that a person could have all their ancestors going back centuries still alive.

Tuesday, October 21, 2014

The Importance of Different Perspectives in Science

I feel like I've recently had a certain revelation about the research I'm working on, and it's all thanks to the new Brad Pitt movie, Fury.  Richard Fernandez at PJ media wrote an interesting piece about the tank battles depicted in the movie and whether or not  the German Panther and Tiger tanks were superior to the American Sherman tanks.  He refers to research done by Steven Zaloga in the book Panther vs. Sherman.  In this book Zaloga proposes that the key to almost all tank battles was who fired first.  In his view, battles were won by the side that occupied the high ground first and initiated the hostilities against their enemies.  Everything was decided in that first crucial minute.

In reading the piece by Fernandez I couldn't help but think of the old quote by General Robert Barrow, "Amateurs talk about tactics, but professionals study logistics."  As Zaloga points out, the tactics of tank combat didn't matter as much as the logistics of how the tanks came upon the enemy and initiated hostilities.  If you wanted to study why a certain force won a battle, you needed to understand the logistics of how it got there.

The article led me to have a revelation about the research I am doing.  My current work involves the examination of RNA binding proteins and how they compete against each other to bind their particular substrate.  In this research, my lab and most others have been delving into the mechanisms these proteins use to recognize the RNA itself as the key to understanding how they compete against each other.  It hit me though, that here we are looking at tactics, when the solution might rely in the realm of logistics.  What if the important thing is not how the protein binds the RNA but how it gets to the RNA.  What if the cell has a pathway for getting a particular protein to a particular point on the RNA at a particular time?  I think I've answered that question for the system I am studying, now I'm just trying to come up with experiments to prove my hypothesis.

Monday, October 20, 2014

Government Incompetence: Part 374,897,392,472

So today when I was coming in to work I had to drive around a crew cleaning up the leaves off the street curb.  Now, I've lived in several different areas over the past decade, and everywhere I have lived previously collected leaves in the same manner.  They had a single large dump truck for vacuuming them up and hauling them away.  This method was quick, easy, and could be done by a crew of just 2-3 men.  In contrast to this simple setup, the locality where I am living apparently believes the only way it can clean up leaves is with a front loader, five dump trucks, and a crew of about ten men.  Instead of vacuuming up the leaves, they were blowing them into the shovel of the front loader before depositing them in the dump trucks.  Needless to say, this way is a hell of a lot more costly, but at least some cronies are making money.

Wednesday, October 15, 2014

Enterovirus d68

With everyone focused on a possible Ebola outbreak, the growing epidemic of enterovirus d68 infection is getting scant attention.  It has been infecting children all over the country and so far is directly responsible for two deaths and indirectly responsible for at least four more.  While it is primarily a respiratory infection, it has caused paralysis in a small percentage of patients, indicating that it is able to attack the nervous system as well.

The fact that this is getting so little attention now is dangerous.  The enterovirus outbreak is widespread enough that everyone needs to know what symptoms to watch for.  This article explains many of the basics on what to be on the lookout for.

I've seen a lot of speculation that this virus was brought in by all the immigrants Obama allowed in this summer, and I've also seen it connected with other outbreaks in Asia and Australia instead of Central America.  It's a virus that hasn't exactly been non-existent in this country, it was first identified in California in the 60's, and has been around ever since then.  It's always caused a few illnesses here and there every spring and summer, but this current outbreak and its widespread nature indicate a new strain that likely has several points of origin in this country.

This is one area where I truly don't know who to believe.  When the outbreak first made the news, I read a lot of message boards that said it was likely from Central America because polio is still prevalent down there and polio is also an enterovirus, but this categorization is extremely general and really means nothing.  On the other hand, this paper from the Virology Journal does seem to indicate that enterovirus respiratory infections were very prevalent in Latin America just a year ago. It's time like this when I really wish we had a media willing to investigate facts, even ones that may be embarrassing to the current administration.

My concerns with Ebola

With a second case of Ebola transmission in the US, fears of a major outbreak are increasing.  A lot of information is being thrown out there about the way it can or cannot be transmitted.  We are told over and over it can only be spread through body fluids, but are often not given details about what this means.  While the list of body fluids Ebola lives in is long, its presence in mucus and saliva are the two that primarily make it communicable.  A person who has direct contact with the saliva or mucus of an infected and symptomatic individual can contract Ebola, but there are several caveats concerning that.  Ebola can't penetrate the skin, so the infected mucus or saliva would have to come into contact with someone's mouth, nose, etc. to enter the body.  For example, if you shook the hand of an infected individual, they could only pass it to you if their hand had a bodily fluid such as mucus or saliva on it, something that is unfortunately a real possibility.  After that, you would only become infected if you touched your hand to your mouth or nose before washing it, or if the virus found a way to enter through a cut or abrasion.

It gets trickier when trying to determine whether or not someone could catch Ebola from a contaminated surface.  I've read that the virus can't survive long outside the body, but it appears "not long" is still a few hours.  In this case the rules of transmission would be if you touch a contaminated surface a few hours after it became contaminated, you could become infected if the virus then came into contact with your mouth, nose, skin wound, etc.

There has been much discussion about the possibility of Ebola becoming airborne with many doctors and scientists saying it is possible.  While it wouldn't be impossible for it to happen it would seem to me that it is improbable.  The virus would have to make a steady series of mutations to become airborne, a series that I find it unlikely to make in a short time frame.

The greater danger with Ebola isn't that it will make the huge leap to become airborne, but that smaller mutations will cause slight alterations that could greatly enhance its infectivity or decrease our chances to detect it.  A single mutation that allowed it to survive outside the body for a significantly longer period of time would be trouble.  It would also be trouble if a mutation altered its symptoms in a manner that made it harder for doctors to recognize.  For example, this article mentions that not everyone who contracted Ebola gets a high fever that would serve as a flag for it.  The lack of a high temperature in this small percentage of patients most likely is due just to variance in physiology and not an alteration in the virus itself.  However, if an alteration in the virus would allow it to infect individuals without causing a significantly high temperature, at least for some time after a person becomes contagious, it would make it much more difficult for us to detect.

Sunday, October 12, 2014

An Alphysicist's Tale

One of my favorite book when I was a kid was The Trumpeter of Krakow.  I loved everything about it, but probably my favorite part was naturally the alchemist subplot.  Before reading the book, I had never heard of the historical alchemists and their attempts to turn lead into gold.  Everyone laughs now at their stupidity in trying to carry out an impossible task, but I always knew that what they were doing in theory was possible.  Their ignorant mistake was in thinking they could turn lead into gold through chemical reactions.  It is possible, theoretically, to turn lead into gold, you just need physics to figure out how to alter the nucleus of lead.  Lead has an atomic number of 82 while gold's is 79. This  means that lead differs from gold by having three more protons in its nucleus and three more electrons revolving around said nucleus.  If a process could be developed to remove three protons from lead, it can be turned into gold.  What is needed then is alphysics, not alchemy.

The photo at the top of this post might look like a simple statue, but it is actually a professor who was a pioneer in the field of alphysics.  He devised a process for turning every molecule in his body into lead.  Unfortunately, the reverse process wasn't successful.  His students immediately went to work to try and figure out where he went wrong.  They worked diligently, but couldn't do it.  Recently, funding for the project was pulled as it wasn't considered a high priority.  And so the professor sits diligently, waiting for the day when physics has advanced enough to find a way to turn him back.

Friday, October 10, 2014

Synthetic Biology: Its promises and curse

After much meandering in my career, I am finally starting to put together a project I can take with me in pursuit of my own appointment.  One thing that finally moved me to take this step is the possibilities that are offered by the capabilities of synthetic biology.  DNA production has gotten so cheap that you can get any gene you want to work with synthetically produced.  No more begging other researchers to send you plasmids of something you want to work with.  For the work I intend to do, this will allow me to express any protein I want to work with recombinantly and look at it in the manner I want to.

The increased affordability of synthetically produced biological macromolecules stands to greatly improve the productivity of scientists.  Cheaply produced RNA is probably next in line, which will make the the ability to transcribe and purify RNA a lost and obsolete art.  It will make it easier for scientists with no previous experience in RNA to work with it.

The curse of synthetic biology is the potential it can create for the production of bio-weapons, something that is a plot point in my book.  With the genome sequences of viruses out there, anybody can order a viral genome to work on and mutate.  While the technology isn't there to turn these viral genomes into infectious agents, that is rapidly changing, as outlined in this story about J. Craig Venter and his work creating synthetic life.

Tuesday, October 7, 2014

Why I'm watching sports less and less

For most of my life I have been an absolute sports fanatic.  I would follow almost every sport to some degree, watch whatever game I was on.  I could even watch the same Sportscenter hour after hour. All of that has changed recently, however.  Any desire I have had to watch and follow sports has abruptly disappeared.  I might still have a game on while I am doing other things, and I will peruse the scores every morning, but something has significantly changed for me.

I've read several posts in the manosphere deploring men to play sports, not watch sports.  These posts have helped point out to me how watching sports is a passive activity that can often be a waste of time when there are more important activities one can actively engage in.  For me, this realization came after several incidents in sports that have made me feel that they are no longer worth watching and following.  The SJWs have been attacking sports for several years, and the various league's have been giving in on one front after another.  Sometimes it feels like the games are secondary to whatever "message" needs to be conveyed from week to week.

A significant portion of my turning away from sports can more accurately be described as a turning away from sports journalism, which has been so fully captured by the SJWs that there seems to be almost no coverage of the actual games anymore.  Of course, this is a trend that stared long ago and has a lot of causes.  The people who work for ESPN came to believe long ago that they were bigger then the sports they covered, and everything at the network has reflected that.  I remember several years ago, shortly after LeBron James announced he was going to the Heat on his ESPN special, a friend of mine on Facebook said that ESPN no longer covered sports, they consisted of nothing other then rumors and speculation, most of which was wrong.  The personalities there want to make names for themselves, and they seem to believe the best way to do that is to report scoops, not the games themselves.

I feel like I would be remiss if I didn't mention the worst offender in the poor sports coverage department, NBC's Football Night in America.  The show is so atrocious that I almost believe it was put together with the purpose of making football so boring no one will want to watch the sport.  It's an hour and a half show that is supposed to cover the action of the day, but shows almost zero highlights.  I truly believe that Chris Berman's fastest three minutes in football contains more highlights then this show.  Still, the highlights are better then the analysis, which is done by former players and coaches who seem to have less knowledge of the game then someone watching it for the first time.  Then, once the analysis is over, they go to Peter King and Mike Florio, who somehow are getting big money to tell us such things as "You know that guy whose leg bent in a way that legs aren't supposed to bend and got carted off the field howling in pain with a bone protruding from his skin.  My "insider sources" tell me he's going to be out for a while.  At least two weeks."

Saturday, October 4, 2014

Billing Companies, Collections, and the Economy

Earlier I wrote a post about the trouble my sister's radiology practice was having with their billing company.  For some reason they could never understand, the billing company was unwilling to pass along the money it owed them.  They never figured out what the problem was, and at the time I wondered if Obamacare regulations had screwed up medical billing.  I'm starting to re-think what might have been going on with that situation as my university has recently had some problems with billing.

About a week ago, I got an email from the company that does our DNA sequencing that they did not receive payment for several orders.  After I inquired about it, I found out the university did pay the billing company that handles payments for the sequencing company.  Several other labs at the school received similar notices.  The sequencing company specifically mentioned they didn't get their money from the billing company, so it would appear the billing company is at fault here.

When I found out what the situation was, I couldn't help but notice the similarities between this and the one my sister experienced.  I'm wondering what the overlap might be, if there is any.  I tried to look up the billing company to see what kinds of accounts they handle.  I was curious to see if they do medical billing too, but I couldn't find out anything about them.  It's possible they do medical billing too, and their problems stem from that.

Of course the big question is why these billing companies aren't passing along the money.  For some reason, they're in such dire straits that they're holding on to what money they can and trying to extract it from whoever they can fool into overpaying.  If the problem is Obamacare, then at least the problem is regulatory and confined to the medical/scientific sector.  What really worries me is the fact the problem might be more general economics.  I worry that there is just no money out there for these companies to collect, and that is why they are acting the way they are.  If this is true, then the economy is undoubtedly much worse then the media and our politicians are letting on.

In the email I received from the billing company, they said if we didn't settle our accounts, they would report our debt as outstanding.  It made me remember this story that stated 1/3 of Americans have an unpaid debt in collections.  The story contains a map that shows the region by region data. When the story broke, many commenters made a point that the South has more people with debt in collections then other areas of the country.  I wonder how accurate some of the data is, as the map appears to show that Detroit isn't actually too bad about paying its debts.  This would be the same Detroit that had a major controversy over unpaid water bills.  The same Detroit where half the residents don't pay their property taxes.

It should be noted the story about unpaid debts only concerned those actually reported to collection agencies.  A lot of businesses might not report debts if they believe there isn't much chance of getting their money.  I had an uncle who had this attitude with his medical practice.  As a consequence, regions that are horrible about paying their debts might not actually show it in certain data.  I wonder if there's a similar dynamic occurring with the billing problems I'm seeing with our sequencer's billing company.  They've been hopelessly stiffed by so many other companies they are trying to go after any business that has money.  The big question I have is, what makes them think universities have money?  We're in the middle of a higher education bubble.