Saturday, April 30, 2016

DNA 101

I recently posted a blog entry (see http://sigma5.blogspot.com/2016/04/positive-identification.html) that talked a good bit about DNA.  For this post I have decided to dive a bit deeper.  The existence of DNA has been known for less than a hundred years but there were hints of something way before that.  For thousands of years plant and animal breeders knew that there were certain characteristics of the plants or animals they were interested in that "bred true".  The coat of a housecat, for instance, does not look exactly like the mother or the father.  But other attributes did seem to "take after" one parent or the other.  So there seemed to be some mechanism operating that passed some attributes down from parent to child.  The most obvious attribute, species, definitely behaved that way.

The first scientific investigation into what was going on was done by Gregor Mendel in the 1850's.  He cheated a little by focusing on a few inheritable traits and ignoring others that did not seem to be inheritable.  But he was able to develop some rules of inheritance.  As an example he figured out how height (tall or short) for pea plants was influenced by the height of its parents.  He published his result and no one paid any attention at the time.

But later people did similar investigations and got similar results.  And when they did they also did literature searches that turned up Mendel's old paper.  And all this resulted in the invention of the word "gene" to describe what was going on.  No one knew what a gene was but they were pretty sure such a thing existed.  And that soon led to an investigation of something called chromosomes and that led to an interest in a chemical called DNA.  No one knew how DNA was connected to genes but it was pretty likely there was a connection.  So the next step was to figure out the structure of DNA.

The puzzle was solved almost exactly a hundred years after Mendel's paper was published.  Credit officially went to Watson and Crick but many others made critical contributions.  But they limit the number of names on a Nobel Prize to three and the Nobel committee decided to pick just the two of them.  And that's how they got to be the people who are generally given all the credit.  So what is the structure of DNA?  The answer is, as they say, "very interesting".

The Twitter-length answer is "it's a double helix".  So let's see what a double helix is.  First of all, a helix is just a corkscrew shape.  A classic example, which turns out to be helpful in what follows, is a spiral staircase.  You have a central pole.  About six inches above ground on one side this pie shaped thing sticks out.  It is narrow at the pole end and wide at the other end.  And it is flat so you can step on it.  Then there is a similar pie shaped slice sticking out of the central pole about six inches above the first step.  The trick is that it is not exactly straight above the first step.  Instead it is set back a convenient amount.  This lets you step onto the first step then step onto the second step just like you were climbing a flight of stairs.

And it is the same idea with the third step.  It is about six inches above the second step and set back so you can step up to it.  And so we go.  The steps spiral around the central pole.  Eventually a step will end up straight above the original step.  But if things have been done right there is enough head room between these steps.  That means you can ascend the stairs as they spiral up around the central pole without bumping your head.  If you connect the outside ends of the steps with a smooth line you get a corkscrew shape when you look at it in in three dimensions.  And there is only one "screw" in the corkscrew so this is a "single helix" design.  But this is not the only possible design.

Let's assume the center post is quite big, say ten feet across.  Then it is easy to arrange the steps so that they spiral up just like before.  But now there is room for two spirals.  Let's say that there is another step exactly across the central pole from each step in the original spiral.  Now you can have two independent spirals.  They each circle up the post.  But you can have people going up using one spiral and people going down using the other spiral.  And, since you have two spirals, you can have people going up and other people going down at exactly the same time.  That's a double helix.

Now let's make another change.  Let's get rid of the central post.  If we connect the outside ends of each step with the one above and the one below it and we make this outside structure strong enough, we don't need any central pillar.  The central pillar is the most common way spiral staircases are made but it is not the only way it can be done.  And now you have DNA.  It is a double helix (two staircases) with an outside support structure instead the central post.  So that's nice but it is only the start of what makes DNA interesting.

I have never played with Leggo blocks but I know what they are and I bet you do too.  The interesting thing about Leggo blocks for the purposes of this discussion is that they snap together and they only snap together a few different ways.  There are little pegs and sockets in each piece.  The pegs fit snugly into the sockets if you snap them together correctly.  If there is something else where the socket needs to be then two Leggo blocks won't snap together that way.  And if there aren't enough pegs in sockets the Leggo construction isn't very strong.  DNA is the same.

With DNA there are four kinds of "blocks".  Each block is a specific chemical with a specific shape.  They snap together but only in a few specific ways.  Each of them is roughly pie shaped with a wider end and a narrower end.  When they are snapped together the wider end is toward the outside and the narrower end is toward the center, just like the steps in a spiral staircase.  And the outside of each block has a shape that can snap into the other blocks.  And the way they snap together is quite strong and requires that the blocks be offset just like the stairs in a spiral staircase.  This is just the structure we need for a "no center post" design.  And with respect to this outside part you can mix and match all four types of blocks any way you want.  As you move along the outside spiral any block type can be followed by any block type.  That's pretty cool.  But now for the really cool part.

The four blocks can also connect together on the inside end.  But with a twist, well actually a flip.  And only certain specific combinations are allowed.  The four building blocks have names (you can easily find them if you care what they are) but mostly they go by the first letter of each name.  The first letters are A, C, G, and T.  And if you turn T upside down it will connect up with A but not any other way.  Similarly, if you flip G upside down it will connect with C but not any other way.

Now one of the interesting attributes of a helix (or in this case a double helix) is that if you flip it upside down it looks the same.  So what you have with a double helix are two helixes spiraling around the same core.  If we call one of them the "up" spiral then the spiral would look just the same if we flipped it upside down.  And the "down" spiral could be flipped upside down and it would then look like the "up" spiral.  In one spiral the "top" of each step faces "up" and in the other spiral the "top" of each step faces "down" but that's the only real difference.

And in fact that's exactly what happens with DNA.  One spiral has all the building blocks right side up.  The backbone around the outside snaps together just fine.  We can have the building blocks occur in any order we want and it will all work fine.  The other spiral has all the building blocks upside down.  The backbone around the outside snaps together just fine.  And, if we ignore the first spiral, we can have the building blocks occur in any order we want.  But it turns out one spiral can't ignore the other one.

If at a certain spot on one spiral we have an A then we must have a T in the spot that is straight across.  The same is true for the other three building blocks.  We must always have a G across from the C, a C across from the G, and an A across from the T.  And this characteristic is magical.  It means that if we know the sequence of the building blocks on one spiral we can figure out with 100% certainty the sequence of the building blocks on the other spiral.  And this is how DNA can be duplicated.

The process goes like this.  The two spirals are unzipped.  Then each spiral is processed separately.  You just run down the building blocks.  For an A you turn a T upside down and snap it in on the other side.  For a C you snap in an upside down G and so on.  Each spiral is processed separately.  But for the "up" spiral the "down" spiral is rebuilt.  And for the "down" spiral the "up" spiral is rebuilt.  The result is two absolutely identical DNA molecules.  Each new DNA molecule has the same spirals with the same sequences of building blocks as the original DNA molecule had.  Once the structure of DNA was determined this other stuff was figured out pretty quickly.  But it turns out to be only the start of the fun.  So let's move on to the next cool thing.

DNA is a very efficient way to store data.  And in a lot of ways that's what it is, a string of text.  Now the text has an alphabet of four characters, A, C, G, and T.  So it's not binary.  It's quaternary (base 4).  Okay, how far can we get with a four character alphabet?  Not very far but there's a trick.  (There's always a trick.)  A byte is a group of 8 bits.  So, while a bit can only have two values, a byte can have two hundred and fifty six values.  That's a lot more interesting.  DNA doesn't do exactly the same thing but the idea is similar.  Let's group three of these characters together.  It turns out if you do the math right, you can represent 64 different numbers.  And that's what the cellular mechanisms that process DNA do.

The whole process is like reading a telegraph message.  A short click is a dot.  A longer click is a dash.  A longer than normal pause between clicks indicates that we have come to the end of a letter.  Originally Morse Code, the language of telegraphs, had no punctuation.  So the word STOP was used to indicate a period.  Telegraph operators were just supposed to figure out where the word breaks went.  And telegraph messages were in ALL CAPTIAL LETTERS and contained no punctuation, hence the need for STOP.  It worked and after a little experience telegraph operators usually got the word breaks right.  Readers and writers of telegrams just had to deal with the lack of lower case letters and punctuation as best they could.

The process of processing DNA has the same kinds of problems but without an intelligent telegraph operator to help out.  So let's ignore some of the above issues for the moment and focus on the message.  We have 64 "letters" in our alphabet to play with.  And mostly what they are used for is to represent an amino acid.  There are only 22 amino acids that this system is used with so it should only take 22 of our 64 letters to uniquely represent them all.  What's the story with the rest of the letters?  It turns out that several letters translate to the same amino acid.  In the end, most of the 64 possible letters get used for this purpose.  And here's the cool part.  A whole lot of the chemicals our bodies use are actually just a bunch of amino acids strung together in a specific sequence.  So DNA literally "codes" for molecules that consist exclusively of a specific string of amino acids.  This "letters to amino acids" process goes by the name of the "genetic code".

There is a bunch of machinery in our cells that can read off a particular string of building blocks, translate that into a list of amino acids, and build a molecule that consists of that exact sequence of amino acids.  This process can and is used to build literally tens of thousands of complex organic molecules that are used for a bewildering number of purposes by one cell or another in our bodies.  It can't be that simple can it?  Of course not.  Let's look at some of the simpler wrinkles first.

As I said above, telegraph operators are good at figuring out where the word breaks go in a message.  Lacking telegraph operators a different mechanism is employed.  These three letter groups are called "codons".  There is a special "start" codon and a (actually three) special "stop" codon.  So the translation process scans the DNA spiral until it finds a start codon.  Then it takes the next block of three letters and uses the genetic code to figure out which amino acid goes first.  It grabs that amino acid then it moves on.  It applies the genetic code to the next three letters, finds the correct amino acid, and hooks it up to the first one.  Step by step it keeps adding amino acids until it hits a stop codon.  Then it stops.  This is what a lot of the genetic machinery in the cell does.  But that's not the end of the list of problems.

I remember asking a molecular biology student many years ago which is the primary helix and which is the secondary one?  He didn't know the answer but I now do.  There is no primary or secondary helix.  This molecule building mechanism processes both helixes just the same.  Can this present problems?  It sure can.

Remember those gene things I mentioned above.  Well we now know that a gene is just a string of DNA.  Things are a little more complicated than the "string together amino acids" process I outlined above.  But the idea is pretty much the same.  With genes there is a longer sequence called a "5'" (five-prime - Why is it called that?  I don't know) sequence.  It marks the beginning of a gene.  There is another longer sequence called a "3'" (three-prime - Why is it called that?  Again I don't know) that marks the end of the gene.  And lots of genes just code for a protein.  And a protein is just a specific string of amino acids.  And the above mechanism is used to translate the DNA information into the recipe for the protein.  So can't things get confused between one DNA spiral and the other?  Yes.

It is possible for a DNA sequence on one spiral to be part of a gene while the DNA sequence on the other side of the exact same piece of DNA is part of a completely different gene.  This generally works out.  Scientists really don't know why or how.  For one piece of DNA there is this sequence of letters on one spiral that translates to whatever it translates to.  Yet the other complimentary spiral is also used in the exact same way to translate into whatever it translates to.  This all somehow works.  It shouldn't but it does and scientists only barely understand a very little bit about why it works.  Scientists know there is a vast amount they don't know about all this.  And the more they learn the more stuff pops up that they don't know about.  Moving on . . .

Scientists have known about this whole "code for a protein" business for a while now.  And they have figured out how to tell which DNA parts are involved in this "code for a protein" business.  And it turns out to be about 2% of all the DNA we have.  So what's with the other 98%?  Scientists originally called this "junk" DNA.  It looked like it was just taking up space without doing anything useful.  But then there was this whole mutation thing.

The DNA replication business I explained above works miraculously well.  But it turns out that there are 3 billion letters worth of DNA in each of us.  It doesn't take a very high error rate to mess things up.  A "one in a million" error rate would result in 3,000 mutations.  If that sounds like a scary large number it's because it is.  And mutations can cause very bad things if they happen in an important sequence.  But junk DNA is unimportant, right?  That sounded like a good theory but it didn't pan out.

You can compare the DNA of multiple individuals.  Or you can compare the DNA of people to the DNA of pigs or even plants.  Now I am NOT talking about actually inserting DNA from say a pig into a person.  I'm just talking about looking at pig DNA and people DNA to see what's different and what's the same.  And it turns out that there are large chunks of DNA that are the same from person to person or person to pig or even person to plant.  This is called "conserved" DNA.  Take a string of DNA that is the same in people and plants.  It must do something pretty damn important or it wouldn't be the same in both places.  Now what if this DNA was junk DNA?  If we understand junk DNA correctly it should be able to mutate like crazy without hurting a thing so it should not be the same in people and plants.  Scientists concluded that a lot of "junk" DNA was not junk because it was conserved.

So if it is important, how is it important?  Let me take an apparent digression that really isn't a digression.  The DNA in every cell of your body is the same.  So why is a muscle cell different than a brain cell different than a skin cell different than . . .  ?  It turns out there is a whole gene regulatory system.  Your muscle cell is a muscle cell because certain genes are turned on in that cell and many others are turned off.  The same is true for the other cell types.  Each has the same genome.  But each has a different pattern of which genes are turned on (activated) and which are turned off.  Scientists really don't understand how this gene regulation business works but they know it involves what is no longer called junk DNA but is now called "non coding" (because it doesn't code for a protein) DNA.  There is lots going on with this non coding DNA but scientists are just starting to figure it out.  They know they have a long ways to go.

But wait, there's more.  Theoretically, all you inherit from your parents is some DNA, right?  Wrong.  There are ways for your mother to influence some settings for this regulatory system that do not involve DNA.  Scientists have gotten to the point where they know this is happening but they don't know how it is happening.

Finally, there is reason to believe that cancer is a set of diseases whose common element is that the regulatory system for gene expression goes haywire somehow.  This often causes cells to reproduce like crazy (cancerous growth).  It also seems to drastically increase the mutation rate of affected cells.  This seems like bad news but it is actually good news.  A lot of cancers may turn out to actually be the same.  A large group of seemingly unrelated cancers could all be caused by the same problem with the gene regulatory system.  If this is true and if a fix for whatever the problem is can be developed then this one fix can be successfully applied to treat all the cancers in the group.

In the late '60s when the War on Cancer was first declared it was thought that there was something like 50 different cancers.  Now we can identify many thousands of cancers that are different in some large or small way from other cancers.  Developing many thousands of cures each applicable to only a small group of people because it is only known to be effective for one very specific cancer sounds depressingly difficult.  But if there are a relatively small number of underlying causes for most cancers then only a few cures could make a tremendous difference.  That is the best news cancer researchers and their patients have had in many decades.



Wednesday, April 20, 2016

Faith versus Reason

This, more than anything else, is what caused me to start this blog.  It is also the subject I return to or circle around frequently.  The conflict between these two approaches to finding truth is at least 400 years old and likely far older.  For the purpose of this post, however, I am going to mostly focus on  the last 50 or so years.  And I am going to approach it through the prism of politics.

I have just started reading "Why the Right went Wrong" by E. J. Dionne Jr.  Since he lays out his thesis in the introduction, I can describe his main thesis and conclusion fairly even though I am a long way from the end of the book.  The book was published in January of 2016.  So a lot of the events of the current Presidential campaign season had not played out yet.  And there is still a good way to go to get us all the way to the election.  But the Trump phenomenon had exploded on to the scene in time to be mentioned in the book.

And the book takes a track that I would characterize as parallel to my thesis but it is not exactly the same as mine.  He makes two main points.  The first one is that the ideas the Republican Party is now wresting with as it tries to decide what it thinks of the Trump phenomenon are not new.  He traces them back to the '64 Goldwater campaign and before.  His second main idea is that Republicans have for a long time been making promises to their base without delivering on them.  This disconnect between promise and execution is Dionne's explanation for the current Trump insurgency.

I generally agree with both ideas.  But I want to take a slightly different approach to the second one.  As Dionne sees it Republicans have been telling their base that they will do A, B, C, etc. and then they don't.  Dionne (at least in the part of the book I have finished so far) provides details on why each specific promise ends up being broken (or at least indefinitely deferred).  It might be for some tactical reason (doing so would alienate voting group X and we can't afford to do that now) but I think the problem has more fundamental root cause.

I think the Republican agenda has been built on faith and flies in the face of reason.  It is this unwillingness to be constrained by reason, the possible, that has led to this consistent failure.  But Republican failures are only a component of what I want to talk about.  I believe that at the societal level faith and reason continually vie for ascendancy.  And I think faith has been ascendant for several decades but that reason is now making a comeback.  I want to use politics as the backbone of my argument but I don't want to restrict myself just to politics.  Politics is a particularly appropriate choice at the moment because politics, and more specifically partisan politics, has now been forced into nearly every facet of our lives by one side of the other in the partisan divide.  It so happens that the time period Dionne covers is a close match for the period I want to primarily focus on too.  So let's have at it.

And I want to start a little further back, with World War I.  To an extent previously unimaginable WW I was a technological battle.  One of the key components was the machine gun.  It, in the guise of the Gatling Gun, had been invented in the Civil War, roughly fifty years previously.  But going into WW I its importance was vastly underestimated by the Generals on all sides.  A machine gun "nest", a machine gun and its operator dug into a position of cover, was nearly impervious to attack by infantry troops across open land.  If overlapping fields of fire, a geometry based setup where multiple nests could cover each part of the field of attack, were set up then the position turned out to be neigh on impregnable.  And this resulted in the trench warfare stalemate the held for most of the war.  Generals ran up horrific numbers of casualties before they learned this fundamental lesson.

So the machine gun was technology, important technology, but old technology.  WW I also saw a substantial amount of new technology introduced as the War ground on.  Perhaps the most spectacular example of this was the airplane.  At the start of the War it was a toy with no obvious military use.  But rapid development produced a very capable machine by the time the War ended.  It was most effective as a photo-reconnaissance vehicle.  But to be effective in this role it had to have offensive and defensive capability.  This was done by adding machine guns whose fire was synchronized with the rotation of the propeller.  The machine guns were initially installed for use against other airplanes.  But they could also be used to strafe infantry on the ground.  A bombing capability was also developed but airplanes of the period were not big enough to carry enough bombs to have much effect on the outcome of the War.

The submarine, another prewar technology, also evolved rapidly from a toy to a deadly weapon as the War ground on.   Another technological development was poison gas.  Under the right circumstances it could be very effective against an unprepared enemy.  But the circumstances were often unfavorable and the enemy quickly learned to be prepared.  Finally, the technological advance that decisively broke the trench war stalemate was the tank.  It represented a weapon that could defeat a set of machine gun nests with overlapping fields of fire.  So that's how things ended.  How did they begin?

They began with faith.  In the excellent Barbara Tuchman book about the run up to and the first six weeks of the War, "The Guns of August", she delves into the attitudes and beliefs of the various players as the War began.  I want to single out the French.  The French believed they could emerge triumphant because of "Élan".  French soldiers were just morally and every other way superior to their opponents (presumed to be the Germans).  This idea did not survive contact with the enemy.  Élan did not take out German machine gun nests.  WW I crushed entire empires before it was over.  And godless technology was the key to victory.

World War II played out along similar lines.  Technology in the form of advanced submarines, radar, sonar, code breaking, newer and better tanks, ships, and airplanes, and ultimately the Atomic Bomb won the day.  Faith was no match for any of this technology.  In the postwar period faith was seen as no defense against long range bombers carrying nuclear weapons or ICBMs or any of the other high tech weapons of the day.  In a straight up match between faith and reason the expected victor was never in doubt, at least when it came to things military.  That is, until Vietnam came along.

Most people have now either forgotten or never knew that the principal architect of the US strategy in Vietnam was Robert S. McNamara.  He was considered a technocrat's technocrat.  He went from the auto industry to the Defense Department.  His idea was to bring modern "scientific management" to military problems and that's what he did with Vietnam.  And it was a spectacular failure.  All the vaunted technological capability of the US military was rendered impotent by conditions on the ground.  This put a big dent in the idea that science and technology can do anything. It opened the door on the idea that there might be another way.

And this other way was first embraced not by Republicans and conservatives but by hippie liberals.  They started talking about eastern religions and meditation and flower power and alternative medicine and crystals and "turn on, tune in, drop out".  In the period running from the late '60s through the late '70s these ideas saturated our media and culture.  And then they all burned out.  But this turn away from rationality and technology was resurrected by the Right a short time later in much modified form as religious conservatism.  And now a short digression . . .

The '60 election pitted two candidates against each other, neither of whom was a member of a mainstream protestant religious denomination.  Kennedy was a Catholic and the fight between Catholics and Protestants had by then stretched back centuries.  Nixon belonged to a fringe religion.  He was a Quaker.  This need to choose between two candidates, neither of whom was a mainstream protestant, turned out to be the beginning of the end of the lock that had long been held on US politics by the traditional protestant religious denominations.  Now mainstream protestant religious denominations have no impact at all on our political discourse.  Romney, the Republican standard bearer in 2012 was a Mormon, a religion long considered even more fringe than the Quakers.  His religious affiliation had little or no impact on how the election turned out.

The reason for this is that Religious Right is dominated by people who belong not to one of the traditional protestant denominations but to a splinter of a splinter denomination.  Most mega-churches and many successful smaller congregations are nominally affiliated with a denomination.  But most of their members couldn't tell you which denomination nor how that denomination differs from a dozen other ones.  In 1960 voters knew Kennedy was a Catholic and Nixon was a Quaker.  But I doubt one in a hundred contemporary voters could name the denomination of any of the five main candidates still in the race.

Returning to the main narrative, the left was the first to turn away from a reason based approach and embrace faith as an alternative.  But the right made the same change a decode or so later.  And a fine exemplar of this, as he is for so many things, is Ronald Reagan.  The Reagan Administration embraced and championed the Religious Right.  But I want to come at all this from a different direction.  Reagan was a maser at being associated with two opposite positions simultaneously.  He would advance one position in his rhetoric and the opposite one in his actions.  I will confine myself to two examples.

He claimed to be a fiscal conservative and promised repeatedly to balance the budget.  But in actuality he did the opposite.  He ran a budget deficit every single year he was in office.  And his smallest deficit was larger than the largest deficit of his predecessor.  The result was that the national debt tripled under Reagan.  No other President has produced a larger percentage increase in the national debt.  No one.  The problem was simple math.  He put through massive tax cuts.  He also put through massive increases in Defense spending.  He left large programs like Social Security and Medicare alone.  There was literally not enough money left in the rest of the budget to bring it into balance.

One of the signature events that helped Reagan win the White House was the Iran hostage crisis.  Reagan was adamant that he would not trade guns for hostages,  He was most adamant that he would not do it with Iran.  But he did.  The details don't mater but it is a fact that what later became known as Iran/Contra involved selling sophisticated military equipment to Iran as part of a larger scheme.  So he did what he said he would absolutely not do.  He was eventually forced to reluctantly and equivocally admit what he had done.

But it didn't matter.  Reagan was wildly popular.  This was initially a mystery to me.  So I asked one of his supporters about various issues.  On one issue he said "I really like what Reagan says about this issue".  It was not important to this supporter that Reagan did the opposite.  So then I asked about something else.  He responded "I really like what Reagan does about this issue".  It was not important to this supporter that Reagan said the opposite.  At that point it was no longer a mystery why he was so popular.  And what's important here is that this is faith based thinking.  You have faith that in spite of the fact that some one says or does the wrong thing, things will work out because he does or says the right thing.  Holding to a position in spite of ample evidence that it is wrong is the hallmark of faith based thinking.

Lee Atwater, a famous Republican operative of this period was the first to figure this out.  If you convince people to have faith in you then you can literally do whatever you want.  Various GOP operatives have taken this insight to heart and used it very effectively.  A more recent example of this is Dick Armey.  The Tea Party arose because of a grass roots anger about key economic issues. 

Supposedly TEA stood for Taxed Enough Already.  So you would expect that Tea Party members would be focused like a laser on making sure that their taxes were reduced.  But Armey successfully gained their trust and redirected their energy away from middle class tax cuts and toward issues that were near and dear to the wealthy people that backed Armey.  So all of a sudden the Tea Party agenda was focused on tax cuts for the rich, a reduction in regulations, deficit reductions, and other issues that were, at best, of peripheral interest to Tea Partiers.

It worked.  A lot of "right thinking" people were elected and a lot of officials who weren't were thrown out of office.  But the amount of middle class tax reduction that resulted was modest at best.  The wealthy backers of the Tea Party got a lot of what they were interested in, however.  I'm sure as I work my way through Dionne's book he will lay out many other examples of "bait and switch" tactics by the right.  My point is you can't keep pulling this off if you don't keep convincing your constituents that you will eventually deliver.  Eventually they will desert you.  It is a tribute to the skill of these Republican operatives that they have been able to pull this trick off so often for so long.

And that brings us to today.  A simple explanation for the Trump phenomenon is that the Republican base is no longer willing to go along with the Republican establishment.  Dionne's thesis is that this is because they have finally caught on to the trick.  And with respect to the Republican establishment he is manifestly correct.  We are far enough along in the process so that all the establishment backed Republican candidates have been forced out of the race.  There is one person who could fulfill that role that is still in, namely John Kasich.  But he has not been able to gain any traction.  The establishment has never lined up behind him in the way they did for Bush and then Rubio.  And the base has consistently relegated him to a distant third.  He won his own state of Ohio.  And, he has just picked up a few delegates in the New York primary.  But the few delegates he is picking up in New York are the first delegates he has picked up since Ohio.  And there have been a lot of contests between the two.

So to that extent I am onboard with the Dionne thesis.  But what do we make of Donald Trump?  The only way to account for his success is to fall back on faith.  Fact checkers have debunked pretty much every claim he has made.  Supporters don't care.  "He's my kind of candidate", they say.  What does that mean in practical terms?  There is a word:  altruism.  It means doing something that helps someone else even if that disadvantages you personally.  A nick name for an elected official is "public servant".  The idea is that you serve the public perhaps to your own detriment.  Elected officials are expected to behave altruistically.  So is there anything that suggests the Trump has a streak of altruism in him?  No!

Trump's has been in the public eye for a long time.  So there is an extensive and detailed record of his activities readily available to anyone who wants to take the time to examine it.  And it is a consistent one of him behaving not in an altruistic manner but rather in a greedy one.  Take his four bankruptcies.  Business deals sometimes go bad.  If you have done as many deals as Trump it is not surprising that several of them have gone bad.  But when this happens there are two basic approaches you can take.  You can share the pain or you can get as far out from under as the law allows.  Trump consistently has selected the latter approach.  Has he donated generously either of his time or of his money to public causes?  No!  He has certainly been involved in many high profile charitable activities.  But these are easily identified as publicity stunts that cost him little but benefit him greatly by increasing the value of his brand.

And then there are the many businesses he has put his name on that sell directly to the public.  Here I am thinking of Trump Steaks, Trump University, Trump branded clothes, etc.  Are these high quality products backed by a "the customer comes first" attitude?  The opposite is the case.  Voters literally have no reason to trust and every reason to distrust Trump when he says he will act on their behalf.  But they have faith so they trust him not because of the facts but in spite of the facts.  The Republican base still has faith.  It has just transferred its faith from the old set of establishment operators to a new and better huckster.

But Trump is doing badly in national polls.  And so is the Republican brand in general.  And I attribute this in part to a turning away from faith and toward reason on the part of the public as a whole.  It wasn't just the Vietnam war that turned people away from reason.  The '60s era represented the beginning of the end of a number of long established trends.  People had been asked to invest in education.  And for a long time they had and they were happy with the result.  The boom that ran for more than 20 years after WW II was attributed in part to the G.I. bill that put higher education within the reach of millions.  But by the late '60s a lot of people saw college students riling things up with their civil rights and anti-war and women's rights agitation.  And over time not just any college degree was a ticket to success.  It had to be the right degree from the right school.  So many started asking what was the point?

The '60s also represented the beginning of the end of a long love affair with infrastructure.  A classic example was the Interstate Highway System.  But by the '70s highway projects were becoming prohibitively expensive and traffic remained bad and pollution was awful so what was the point?  In general, in spite of our wonderful reason based technological superiority we didn't seem to be getting ahead.  Crime was increasing.  Drugs were everywhere.  Cancer was stubbornly resisting a cure.  Reason just didn't seem to be working very well any more.

And so as a society we turned away from reason based technology as the place to find cures to our ills and shifted back to faith.  Good hard working people of faith would pray their way to success.  And "it" was all the fault of godless technology anyhow.

There were enough sins that could be credibly laid at technology's doorstep to lend this narrative some credibility.  Technology brought us the specter of global nuclear annihilation, for instance.  And for a long time faith seemed to be doing no worse and perhaps better than reason based technology.  But part of this was due to the fact that over time we had built generous safety margins into our technological infrastructure.  Our highways are now falling apart.  But they were built well and it took a long time for them for the deterioration to become obvious to the casual observer.  The same is true for our sewer systems, our water systems, out electrical grid, etc.

Meanwhile we have been fed a steady stream of "government is the problem", "we can cut taxes just by eliminating waste and fraud", "all regulations are bad", "it is the fault of [insert name of powerless group here]".  But in the same way that "all technology is good" got threadbare by the late '60s, it is these newer slogans that are now looking threadbare.

Dionne sees the problem the right has as the conservative establishment failing to deliver on their promises.  I see a parallel contributing factor in the idea that the faith based approach that was so successful for so long may have finally run its course.  This is not a situation where only one of the two ideas can be right.  Both ideas compliment and reinforce each other.  The right is now losing credibility in the same way the left lost credibility in the late '60s and early '70s.

Dionne points out that some promises could not be met for tactical reasons.  Cutting Social Security and Medicare, something the establishment right has been interested in doing for decades, will immediately alienate a large segment of the Republican base who depend on the programs.  The right has been able to square the circle by telling the donor class that wants the cuts that they are working on them while at the same time telling their base that they don't really mean it.  For this to work each group has to believe that it is the other group that is getting conned.  But if you can pull this trick off, as Reagan did, then you make two constituencies that want conflicting things simultaneously happy.  And that wins you elections.

But then their are the issues where reason tells up it is literally impossible to do something.  A balanced budget, or the closely related desire to reduce the deficit, are examples of this.  You can balance the budget by keeping taxes low if you also deliver few services.  Or you can deliver a lot of services but pay for them with high taxes.  This latter approach is the one Democrats generally pursue.  Republicans pretend they pursue the former.  But it is only pretend.  They are perfectly willing to cut taxes.  But they are also unwilling to cut government spending sufficiently to make up the difference.  They are consistently on record as supporting high military spending.  Paying interest on the national debt (currently quite a bargain due to low interest rates) is also non-negotiable.  If nothing else, Wall Street holds the paper and expects to be paid on time.

That leaves only one big chunk of the budget, the social safety net programs.  These include Social Security, Medicare, and Medicaid.  But, as noted above, the Republican base depends heavily on these programs whether they know it or not.  ("Please keep the government out of my Medicare" tells us far too much about these people.)  If you don't cut them the entire rest of the federal budget amounts to dibs and dabs.  Foreign Aid, a perennial bugaboo, is effectively a rounding error in the federal budget.  And as you go down the list to say the Highway Trust Fund, or Farm Price Supports, or NASA, or the National Institutes of Health, you find powerful Republican constituencies who benefit greatly from them and are not at all interested in seeing their meal ticket cut back.

So what we end up with is tax cuts that balloon the deficit because they are not matched by comparable spending cuts.  Reagan was not the only Republican who has run up huge deficits.  Both Bushes did it too.  It is an inevitable consequence of the Republican mismatch between what they promise and what reason says is possible.

The current election campaign has seen faith based arguments viewed with much more skepticism than in the past.  A contributing factor has surprised me has turned up to be the "just say no" campaign Republicans in the House and Senate have been waging against the Obama Administration from its first day.  They have succeeded in diminishing Obama's list of accomplishments.  But he has managed to pull some off anyhow.  On the other hand Republicans have nothing positive to show for their efforts.

They have not been able to implement any of their own agenda.  They have not been able to roll back Obamacare.  They have been forced to do various deals on the budget and deficits.  They have lost major ground on social issues like gay rights.  They may chalk up a minor win on Immigration.  But it would come from the Supreme Court and not from the legislature.  After nearly eight years of struggle Obama is viewed as the winner on points.  Importantly, this view is widely held by the Republican base.

For a long time voters would look at Democratic candidates and say "what's the point?"  They just didn't believe a Democrat could deliver.  Republicans were the champions who would do whatever it took to advance their agenda.  Voters would look at a Democrat and a Republican and say "I might as well vote for the Republican.  His policies will prevail in the end either way."  But that analysis is being turned on its head by the results of the battle between Obama and congressional Republicans.  It is now the Republicans that are seen as being unable to deliver anything except gridlock.

There was a story in the local paper recently.  The headline was "We all lie, scientists say, but politicians even more so" (see http://www.seattletimes.com/nation-world/nation-politics/we-all-lie-scientists-say-but-politicians-even-more-so-2/).  In my opinion this is a "dog bites man" story.  But, obvious as the point seems to me, it was nice to see it actually make it into print.  All politicians lie.  They lie because we the voters demand it.  We like exciting people who promise us the moon even though at some level we know it ain't so.  A lot of "straight shooter" types have run for office.  On average they lose.  We can't seem to vote for the dull guy or gal who actually tells us like it is.  "Like it is" inevitably involves disappointment and bad news.  We like and vote for the happy talk snake oil salesman instead.

Back in the day Republicans, by and large were the dull people.  They were business oriented and valued a well run operation.  They might be a little reactionary on social issues but they kept the trains running on time.  Democrats tended to be the less practical dreamers.  The two parties complimented each other.  They both over promised and under delivered but there was some connection between the promises and reality.  Then Reagan came along and the tether between Republicans and reality started stretching.  This has left Democrats by default as the party closer to reality.

Democrats frequently stretch the truth.  They even sometimes say something that is completely false.  They need a competing party to bring them down to earth occasionally.  But the current Republican party is incapable of doing that.  They seem to have lost all conception of where reality lies.  They are so good at creating a magical world that their supporters have come to believe over time that it is real.  They have completely lost their ability to recognize when Democrats say something sensible and reasonable.  At the same time they have lost their ability to tell when a Republicans say something nonsensical and unreasonable.  This is not good but I see some signs that things are improving.  I have faith.

Wednesday, April 6, 2016

Positive Identification

"Who are you?"
"Jane Doe."
"Prove it!"

Some variation of the above dialog is now a common part of our lives.  It is frequently boiled down to "Show me your picture ID."  The picture ID contains a name, a picture, and typically other information.  The name provides the answer to the question.  The rest of the information on the ID and the fact that you possess it provides the proof.  The connection between you and the ID is provided by the picture.  Presumably you and your picture can be compared to see if there is a match.

There are variations.  It is becoming more and more common for your smartphone to stand in for your picture ID.  And the degree to which the "proof" actually validates your identification varies.  Bartenders just want to know if you are old enough to drink legally.  The TSA wans to be really sure you are not a terrorist.  And then there is the sad situation with which the title of this post is most commonly associated.  Someone may need to confirm the identity of a deceased person.

With the background established let's look at the process of positive identification as it was, as it is, and as it will soon be.  The times they are a changing.  Let's start with the "was" part and for that I want to go back a thousand years.

A thousand years ago almost everyone lived on a small farm or in a small village.  Almost everyone a farmed, fished, or was otherwise engaged in the process of growing and harvesting food.  And at the time almost everyone was illiterate.  Paper hadn't been invented yet.  The alternatives that existed at the time (i.e. parchment) were all extremely expensive and only available in tiny quantities.  So in that environment how were people identified?

Most people spent their entire lives within a few miles of where they were born.  Everyone knew everyone else in the neighborhood by sight.  You saw people at home or on market days or at feast day events.  And you saw them for their entire lifetime.  At some point a woman would be pregnant.  Then she would show up with a small child.  The child would grow up, become a parent and die.  And the community observed all this.  Identification was not absolute but it was good enough for the situation.  You knew who farmed what piece of land and who their children were.

And frankly positive identification was not that important.  People were poor so they had few possessions and even fewer valuable ones.  Land ownership was mostly governed by the "possession is nine points of the law" rule.  There were no accurate surveys and all the land was probably technically owned by the local feudal lord anyhow.

Oh, there were foreigners.  Someone from outside would occasionally wander by but this did not happen often.  If the wanderer was a trader how much did it matter who they were?  They showed up, traded, and moved on.  The trade goods were important.  The identity of the trader was not.  The other group who would show up occasionally were members of the power elite.  It might be a soldier or a priest.  If a particular soldier was the top dog he became the local feudal lord.  Other soldiers either worked for him or there was a power struggle.  Eventually someone came out on top and the others ended up dead, part of the lord's operation, or they moved on.  The feudal lord was in a position to assert his authority by means of his ability to kill or maim you.

So the locals tended to take him at his word as to who he and what he was.  The niceties of the law and who's authority was more legitimate tended to be less important than who won the power struggle.  The other source of authority and power were the religious authorities like priests.  If there was a power struggle between religious factions the rules of engagement were different (less blood more politicking) but who stayed and who was pushed out mostly depended on who was supported by the local feudal lord.  And again, the peasantry tended to take whoever won at their word.  So in this period positive identification had little real practical meaning.

Eventually paper got invented and the technology for making it cheaply spread broadly and it became practical to keep paper records.  This ushered in the era when marriages, births, and deaths, started to become routinely recorded.  For a long time the process was hap hazard.  A record might be maintained at the local church or in a family bible.  How reliable was this information?  One assumed that it was fairly reliable.  But this assumption rested to a great extent on past practice.

Usually people in the community were around to testify to the accuracy of the information, at least until enough time had passed that all the eye witnesses had died.  After that inertia set in.  Records that had been accepted in the past continued to be accepted.  Beyond that, old records came to be seen as accurate records, mostly because they were old.  And it was certainly possible for a record to be fudged.  A marriage could retroactively be added to a church register or a family bible.  And the same process could be used to erase or alter entries.  People went with these records as much because they were the only practical option as for any other reason.

Not that long ago governments started taking over responsibility.  They started issuing birth certificates, wedding licenses, and certificates of death.  And more people were born in a hospital with a physician in attendance.  But in a certain sense the foundation the process rested on had not changed.  Someone filled out a form.  The information was only as dependable its source and its source was some person.  The person might be the mother or the doctor or a hospital employee.  And, in the case of the doctor or hospital employee, they might be relying on some stranger for the information they were entering.  I suspect that most of the time little effort was made to corroborate it.

The piece of paper has now been replaced by a computer screen and the data no longer resides on a piece of paper in a file cabinet.  It now resides in a computer file somewhere.  And this highlights a fundamental problem.  It's just data.  And more problematic than that is this.  How do we know that a particular birth certificate is actually the birth certificate of a particular person?  The surprising answer is that we don't.  But that can, and I expect that it will, change in the near future.

We have all been exposed to this sort of thing due to the "birther" controversy.  A lot of people but most notably Donald Trump have spent a lot of time and gotten a lot of media coverage contending that President Obama was not born in Hawaii in 1961.  A lot of their argument is nonsense.  There is absolutely no doubt that a birth certificate was issued at the time and place the President contends it was.

An argument could be made that he is not the child that belongs to that birth certificate, that there were, in fact, two children.  This argument is logically consistent but it is not the argument that birthers make.  And there is a large body of evidence that there is only one child and he is that child.  In fact the connection between this birth certificate and the President is much stronger than the connection between Donald J. Trump and any birth certificate.  So the birther argument, such as it is, is about the wrong thing.  A fundamental question exists.  How do you definitively connect any person with any birth certificate?  And the answer is that in almost all cases you can't.

In some places at some times a footprint (like a fingerprint but of the bottom of a foot instead of the fingertips) of the child was routinely put on the back of birth certificates.  With such a birth certificate you can take a matching print of the foot of the individual in question and do a "fingerprint analysis" to see if it matches.  If it does then you can definitively match a specific birth certificate to a specific individual.

But I have never heard of this comparison being attempted.  As far as I can tell the "footprint on the birth certificate" procedure was never common and, in the cases where it was done, I know of no instances where a match was attempted later.  It probably happened but it was never common enough to feature in crime fiction, for instance.  It is easy to imagine Erle Stanley Gardner plugging it into a Perry Mason novel but he never did.  The fact that it was never a common crime fiction motif is evidence that it was never a common practice.

I have both a passport (expired) and an "enhanced" driver's license.  Both of these require a positive identification.  Having been there and done that I know the drill.  I show up, fill out some paperwork, provide a picture (or get one taken), and provide "positive identification".  What's positive identification?  Why a birth certificate, of course.  So I hand over a piece of paper for examination by a bureaucrat.  But what's the piece of paper?  In my case I have the original actual birth certificate that was issued at the time of my birth and it's a pretty ordinary looking piece of paper.  That's how it was done in the era that preceded the computerization of everything.

But I actually have two "birth certificates".  One of them is the aforementioned piece of paper.  The other is a "certified copy" of the piece of paper.  It is something called a Photostat.  A Photostat, as you can guess, is just a photograph, well actually a print of a photographic negative.  The only thing special about it is that it is embossed with an official stamp and an "I attest that this is an authentic copy of . . ." statement followed by the signature of some obscure bureaucrat.

Let's say I wanted someone to impersonate me.  I could keep my original birth certificate and give them the Photostatic version.  They could use that as the basis of a scheme to identify themselves as me.  So there could be two official me's running around.  And, in fact, a minor variation of this used to be commonly done.

People who wanted to change their identity would search newspaper death notices for someone who was born about the same time they were but who had died young.  They would then write the proper authority asking for a Photostatic copy of the birth certificate for this person.  At the time this was a routine bureaucratic procedure that did not require any kind of special documentation.  When it arrived they would then use the Photostatic birth certificate as the base on which to build up an entire false identity for themselves.  If they picked their dead person properly their chance of being caught out was infinitesimally small.

Spies, crooks, people on the run for political reasons, etc. did this routinely in the '60s.  You could even find "how to" manuals if you knew the right people.  One thing that helped then was that most people did not get a Social Security card and number until they entered the job market in their middle to late teens.  If you picked someone who had died at ten, say, your chances of fooling the Social Security Administration into issuing a card were very good.  It is now much harder to pull this kind of thing off because we are all now surrounded by a much larger more complicated web of interconnection than we used to be.

Children now get issued a Social Security number at birth, for instance.  And as big data spreads its tentacles it becomes harder and harder to pull something like this off without setting an alarm off somewhere.  The federal witness protection people can still do it.  But they can change Social Security and other government records.  But none of this changes the fact that there really is no completely reliable way to positively connect a specific birth certificate to a specific person.  But I believe that is going to change in the near future.

There now exists something called CODIS, the Combined DNA Index System.  This is the database that is used to do DNA matches in crime scene and other law enforcement (i.e. missing persons) situations.  The database contains over 12 million entries and continues to grow rapidly.  There is a considerable amount of duplication so it doesn't represent that many distinct individuals but the number of distinct individuals is somewhere in the millions.  Each entry contains enough information to identify a single specific individual with very high degree of confidence.  Does that mean entries contain complete DNA sequences?  Far from it.  Instead each entry contains 14 numbers.  Thirteen of the numbers are based on something called a STR, a Single Tandem Repeat.  The specifics are complicated but the idea is simple.

An STR "locus" is a very short piece of DNA that varies wildly from person to person.  There are a bunch of variations possible for each STR locus.  The database contains the specific variation number in the DNA of the entry for each of the 13 STR loci.  The 14th number is based on a person's Amblogen gene.  It has been included because the version of Amblogen gene that an individual has tells us whether that person is a male or a female.

Only a few percent of the population has a specific version of a specific STR locus.  So different individuals are likely to have a different variation of the first STR locus.  But they could just by luck have the same variation.  But do they also have the same variant in the case of the second locus?  Here too it is very unlikely that two different people have the same variant but it is possible.  And so it goes.  Scientists have done the math and the likelihood that two different people who are not identical twins would have the same variant of all thirteen STR loci is a really tiny number.  It varies from case to case but it is unlikely that two non-twin individuals on Earth have the same variant of all thirteen STR loci.  And just to decrease the chances even more there is a move afoot to add several more STR loci to the standard list.

It turns out that the amount of DNA in all fourteen loci used in this process is a tiny fraction of your whole genome.  It's way, way, way less than 1%.  But it is enough to get the job done, namely deciding if two DNA samples come from the same person or not.  And the basic technology for this was developed more than a decade ago.  In the mean time anything having to do with DNA has gotten a lot cheaper.

The original project to sequence the entire DNA of a single individual cost more than 3 billion dollars and took about a decade.  Now the complete DNA of a single individual can be done for about 10 thousand dollars and it's getting cheaper every year.  Scientists think the cost will drop to below a thousand dollars within the next few years.  And that's what it costs to sequence everything.  The cost to sequence enough DNA to tell one person from another costs way less than that and that cost is also dropping like a rock.  And of equal importance the size of the gadget that does the CODIS sequencing is also getting smaller and smaller.  And that opens up a lot of possibilities.

We as a society have been fighting over privacy for a long time now.  Before the Revolutionary  War colonists decided they didn't like British soldiers searching peoples homes any time they wanted to.  They complained about it in The Declaration of Independence.  After the War the US adopted the Fourth Amendment outlawing "illegal search and seizure".

When I was younger we were fighting the Cold War.  The USSR was an "authoritarian dictatorship".  The Nazis before them were also an authoritarian dictatorship.  Both regimes were famous for requiring everybody to carry "papers" that had to be produced any time any place any time any official wanted to examine them.  So, since we were the good guys, we were all in favor of the opposite.  Our citizens were able to move about freely and were not be under any obligation to produce their papers.  It was a point of differentiation between us and them.  "Only authoritarian dictatorships require law abiding people to always carry identification documents as they go about their ordinary business."

Well, times have changed.  The USSR is no more so apparently we no longer need to differentiate the behavior of our government from that of authoritarian dictatorships.  It seems that we are now all supposed to be afraid of terrorists in our midst.  And that means anyone who is suspicious (not a well dressed white person) had better have their papers on them at all times.  And besides terrorists there is the ever present danger of rapist Mexicans or whoever else fits the "looks suspicious" profile.  I am going to ignore the issue of whether this change is a good thing or a bad thing.  Instead I am going to focus on the technicalities of how to positively identify people.

As I have discussed extensively above, the birth certificate is the foundation of identity for US born individuals.  There is an elaborate system in the US for dealing with the foreign born that I am not going to get into.  I will just note that in many cases it often ends up coming back to a birth certificate for these people too and move on.  And, as I have also extensively elaborated on above, there is no way currently to definitively tie a specific individual to a specific birth certificate.  And by now I think I have telegraphed where I am going pretty clearly.  The thing that could tie the two together is CODIS style DNA information.

There is no technological impediment to doing this now.  A sample sufficient to the task is easily obtained from a newborn.  Blood works and only a drop is necessary.  And the equipment needed to take the necessary measurements is relatively inexpensive and the process is relatively quick.  So it is completely possible to CODIS characterize every newborn at birth.  (As a side note it is also easy in most cases to CODIS characterize the mother and, if he is handy, the father at the same time.)  And the amount of data is modest so it could easily be added to the birth certificate computer record.  Once this is routinely done and some time has passed it becomes a simple process to prove that a specific individual is the one connected to a specific birth certificate.  You just draw a drop of blood, run it through the CODIS process and see if the results match the information in the birth certificate record.  None of this is beyond our current technical capability.

But it is currently beyond our political capability.  People do not want to be in the CODIS database.  Part of this is due to the association between the CODIS database and criminality.  But a lot of people see it as an invasion of privacy they are unwilling to put up with.  They can be convinced to change their mind if there is great need, say a loved one is missing.  But currently every state has restrictive policies that limit who goes into the CODIS database.  Not even all criminals or suspects go in now.  The details vary from state to state.  Some have restrictive policies and CODIS only a relatively small number of people.  Others apply a broad brush and CODIS many more.  But all states prohibit adding people without cause.

And the CODIS database is not the only DNA database in existence.  People sign up with 23andme or other similar companies that do DNA analysis.  The company tells them, for instance, where their ancestors are from.  Various groups also collect DNA information for a number of different scientific reasons.  But both the commercial and the scientific operations are careful to not sequence the DNA loci that CODIS uses.  They just don't want to get tangled up in criminal investigations.  And the people whose DNA ends up in these other databases like it that way.

But let me emphasize that this is a decision that is made for non-technical reasons.  Companies like 23andme try to retain the original sample so that it can be reanalyzed as technology advances.  So they could easily reanalyze the samples they still have and sequence the CODIS loci.  The sequencing they already do is much more extensive than what the CODIS process requires.  And if they did this their database could be used for CODIS-compatible searches.  The number of people whose DNA could be CODIS matched would immediately jump substantially.  But this is not really necessary.  There is already a strong trend in place to keep expanding the CODIS pool.  It is partly a result of technological considerations.  It keeps getting quicker, cheaper, and easier to CODIS samples.  And the people that run CODIS type databases keep coming up with more and more reasons to include more and more people in their collection programs.

I would think that intelligence agencies like the CIA would want to CODIS their employees and contractors.  And how about soldiers?  And how about law enforcement people.  And, on the other side, how about foreigners entering our country.  And how about people busted for minor offenses like speeding tickets or people involved in divorces or people filing for a business license or people involved in food preparation or, or, or.  As the ease with which the process can be performed and the cost comes down the strength of the argument necessary to justify including an additional group gets less and less.  And as this trend continues at some point you will have twenty or thirty percent of the entire population in the database.  At that point you might as well just put everyone in.

Consider that many crimes now go unsolved.  There is DNA evidence available in many of these cases but it doesn't match any entries in the current CODIS database.  If we had CODIS coverage of the entire population then it would go some way toward increasing the percentage of crimes that do get solved.  This higher solution rate should lower the overall crime rate, right?  And isn't lowering the crime rate a laudable goal?  That is only the most obvious potential benefit to CODISing everybody.  Other potential benefits are easy to come up with.  Instead of listing them let me extrapolate a little ways into the future.

When I was younger pretty much all small transactions (i.e. buying a cup of coffee) were done with cash.  Then people started using debit cards instead.  There are now a lot of people who carry only a small amount of cash around.  And as I write this we are transitioning to an even newer method, paying with our smartphones.  Today it is rarely used (except at Starbucks).  But that is because there are some kinks that need to be worked out.  Not all smartphones work at all stores all the time.  That's mostly because we have dueling incompatible payment systems fighting it out.  And for business reasons each system makes sure that it is incompatible with any of the other systems.  At some point that competition between systems will be made to stop.  Then people will be able to use one application on whatever phone they like to buy stuff from whoever they want to.  But that puts the identification issue front and center.

The simplest thing from a user standpoint is to always leave your phone unlocked.  And far too many people do this because dealing with the security system is bothersome.  But Apple came up with a trick.  You put your thumb in the right place and the phone can validate your thumbprint.  This can be done almost instantaneously.  And this approach is now being copied by the other smartphone makers.  I expect it to be universal within a few years.  But I suspect that the thumbprint scheme is not really that secure.  The phone only sees part of your thumb and in poor conditions.  The vendor (e.g. Apple) does not want a bunch of false negatives (you put your thumb on your phone but it doesn't okay you) so I suspect that the phone calls anything that is even vaguely close a match.

But let's fast forward a few years.  Currently the easiest way to do a CODIS analysis is with a drop of blood.  But with a lot of effort even very tiny amounts of DNA can sometimes be used.  In ideal circumstances the tiny amount of DNA that ends up in some fingerprints is enough.  And it turns out that there are lots of cells on the surface of your skin that contain your DNA.  (That's where the fingerprint DNA comes from.)  These cells can be collected and processed without having to poke a hole in you, a process that is not very painful but "not very painful" is not the same as "not even noticeable".  And it is easy to imagine harvesting a few cells from the surface of your finger in a way that is not even noticeable so let's imagine it.

Next imagine the CODIS analysis device being small enough and cheap enough to be incorporated into a smartphone.  And, while we are at it, assume it can produce an accurate result in less than a second. Now we have everything we need to build a system right into our smartphones that is fully capable of positively validating that you are you.  And it is quick enough so that it can be used routinely, perhaps a hundred or more times per day.  That would definitely solve the positive identification issue for smartphone transactions.

I think that for better or worse this is the direction we are heading.  I would like to say that it is not inevitable but I am concerned that the forces that are pushing in this direction are powerful enough to overwhelm any opposition I can currently foresee.  I think most people will be of the opinion that it is no big deal.  In the fight between Apple and the FBI over unlocking that iPhone (see http://sigma5.blogspot.com/2016/02/digital-privacy.html for more on this subject) that was the opinion of a large segment of the general public when they were surveyed on the subject.

They put it another way:  "I've got nothing to hide so what's the problem?"  That situation did not seem to directly affect them.  They did not foresee the FBI or anyone else wanting to unlock their phone so it didn't seem personally important either way.  In the case of what I am now taking about the direct connection is much more obvious.  But there are also immediate benefits.  "I can use my smartphone to pay for my coffee without having to worry about someone maxing out my credit cards if my phone gets stolen."  (As a side note if smartphones used this system they would be useless to thieves and thieves would stop stealing them.)

Our privacy is continuously under assault.   Technological advance keeps making it easier to invade our privacy and harder to protect against an invasion.  If everyone ends up in a CODIS-type database and that database is routinely used to confirm our identification and if a truly positive identification is the norm then pretty much every nook and cranny of our lives will be stored away in one or more computer databases.  It looks like this eliminates any technical barrier to the complete invasion of our privacy.

I'm sure at least some will continue to say "I've got nothing to hide."  But that's not really true.  You may think you have little or nothing to hide.  But all of us have opinions and all of us lead our lives in certain ways.  Bear in mind that whatever opinions you hold there are a large number of people who think you are wrong.  And no matter how boring you think your lifestyle is there are lots of people who strongly disapprove of it.

Are you a girl who likes to wear pants?  Are you a guy who likes to shave?  There are people who are seriously unhappy with you.  What religion to you follow?  It doesn't matter.  There are a lot of people who hate that religion, whichever one it is.  Do you like city living or do you prefer the wide open spaces?  Either way, there are people who are seriously unhappy with you.  Those are all choices many people would find boring and unimportant.  How about more controversial ones?

Do you drink?  Have you ever had sex outside of marriage?  Have you tried non-missionary sex?  Have you smoked pot?  How about other drugs?  Even once?  Have you ever broken a traffic law, driven drunk, or maybe after you have had only one or two?  Have you ever skinny dipped or streaked or done anything else "young and stupid"?  Have you ever stolen something, even accidently?

The point is we have all done some embarrassing things, maybe even a lot of embarrassing things.  And we have all done things some would disapprove of to the point that they would delight in harassing us about them.  So we all have things to hide.  Pretty much all of us have things we would prefer our parents, or our children, or our friends, or our coworkers, or the authorities, or our enemies, or random obnoxious people we don't know, don't know about.  In other words, we all value out privacy.

In the past there have been practical or technological barriers we could hide behind.  The tatters that remain of the old barriers are quickly being shredded.  I have addressed the general issue of privacy before (see http://sigma5.blogspot.com/2013/12/privacy.html).  I devoted roughly the last third of that post to what I thought should be done.  I wrote that post over two years ago.  The current topic only adds to the pressure that is moving us toward a world where there is no privacy.  I recommend that post for my overall thinking on what should be done.  Meanwhile there is a small piece of good news on the privacy front.

I linked to my blog post on the fight between the FBI and Apple above.  At the time I wrote it no one knew how it would come out.  But that specific situation has since been resolved.  The FBI found a way to crack the phone that did not require the extraordinary cooperation that Apple was objecting to.  That sounds like bad news but it's not.  The phone that was cracked is an older model.  Apple has upped its game with newer models.  Whatever methods were used are unlikely to work (or at least will be much harder to pull off) on newer models.  And in spite of various polls that were done at the time it turns out that there is a market for secure phones.  So Apple has promised to keep adding features to make each new generation of phones much harder to crack than the old generation.  And remember the phone the FBI was only able to crack after a great deal of difficulty is now a couple of generations old.

And various other technology companies are now jumping onto the "increased security" bandwagon.  They are encrypting more and encrypting to a higher level of security.  They are also changing how their products operate so that they no longer have a backdoor that lets them read unencrypted customer data.  This means that if they are subpoenaed they can respond "sorry -- we can't read it either".  And a side effect of this is that they can't sell or analyze detailed customer activity like they used to be able to do.

They can still do a metadata analysis.  For instance they can figure out who you are interacting with.  They can tell how often you are connecting up and how long you are staying connected.  But they can't tell what you are doing while you are connected.  This means that the data they can share with someone else, the government or another company, is much more limited than in the past.  And that means it is much less valuable.  And that means they will do less sharing in the future.  And that is a modest step in the direction of more privacy.  It is a small but very welcome development.