Sunday, July 5, 2020

Evidence in Science Requires Context

Suppose someone approached you and said, "There is a volcano close by." And when you ask them how they know that, they show you a piece of volcanic rock. Is that evidence that a volcano is nearby? It depends.

Where was the rock found? Was it close by? Are there other volcanic rocks in the area? Or did someone bring it into the area?

By itself a piece of volcanic rock is not evidence of a volcano. The rock has to be placed in context for it to be evidence of a volcano nearby.

This idea is easy to understand, but sometimes very hard to apply. Here I will give a few real examples of observations that when taken out of context can be considered evidence for a particular conclusion, but when put back into context do not support the conclusion.

In an article entitled Paleoindian ochre mines in the submerged caves of the Yucatán Peninsula, Quintana Roo, Mexico published recently in Science Advances, the authors were describing their work in a system of caves in Mexico. They found evidence of humans using the caves to mine ochre for pigment and paint. One of the things they had to determine was how long ago humans were using the caves.

They found charcoal in the caves near where the mining had taken place. If the charcoal was left there by the people who were mining the ochre then all they would have to do is use carbon dating to determine the age of the charcoal. The age of the charcoal should tell us when the mining took place. It would be easy to assume that the charcoal came from the people who were mining the ochre, but the full context must be taken into account before we can accept that conclusion. The age of the charcoal may not be evidence for the time when there was mining.

As the authors noted,
"Charcoal is a difficult medium for dating in the submerged caves of Quintana Roo because it may be produced by forest fires, then deposited by wind and rain, and remobilized repeatedly by floods during major storm events or, ultimately, by rising sea level. Archaeologists have often interpreted instances where charcoal concentrates in small catchment basins and litters cave floors as prima facie evidence of human activity. However, the mere presence of charcoal concentrations is insufficient to make this inference. Before submerged-cave charcoal can be interpreted as anthropogenic, it is necessary to establish that the sample materials are artifacts, that is, that they are representative of human activity and distinct from the products of natural processes."
In other words, the presence of charcoal is not automatically evidence for human activity. The charcoal must be considered in context.

In this case the authors could argue that the charcoal most likely came from human activity, and human activity at the time the ochre was being mined. To make this case they considered the broader context to see if there were other ways that the charcoal could get there, or if the cave formations showed that the charcoal had been there for a long time. Some of the charcoal was covered over by flowstone, which allowed the authors to get a rough date for when it was left there. This dating agreed with the carbon dating.

Only after all this could they use the carbon dating as evidence for when the mining took place. Before it was evidence for their conclusion they had to consider the evidence in context.

Now a second example. In a recent meeting at work we were discussing ways of detecting starburst driven galactic outflows using X-ray observations of galaxies. These outflows should produce strong X-rays which are easy to detect. The problem is that the things we were looking for are not thew only things that produce X-rays in galaxies. Just detecting a strong X-ray source is not evidence of a galactic outflow.

Before we could consider it to be evidence for what we were looking for we had to look at the context and see if other things could produce the X-rays and rule those out first. Only then we could use the X-ray detections as evidence for our conclusions. Just like the archaeologists with the charcoal in the caves, we had to consider the context.

Now a final example. In a discussion I had about the age of the earth, the person I was talking to brought up polonium halos as evidence of a young earth.

Polonium is a radioactive element and if polonium is mixed with melted rock it will collect inside micro-zircon crystals inside the rock. As the polonium decays the released radiation will "burn" the rock around it. This leaves a "halo" of scorched rock around the zircon crystal that held the polonium. These halos are very small and can only be seen under a microscope.

Young earth creationists argue that these scorched halos around zircon crystals are evidence of the rapid formation of the rock instead of the rock slowly cooling to its present state over thousands or millions of years. Their reasoning is that polonium has a very short half life (138 days) so the only way it can be in the zircon crystals is if the rock formed and cooled into its solid state in a matter of days. This fast formation would allow for the polonium to last long enough to freeze in the rock, and then burn the halo as it decayed.

There are a few problems with this, and all involve the context of these halos. First, assuming the source of these scorched halos is polonium, that would only show that the rock formed quickly, but it would not tell you how old the rock was. In order for the halos to be used as evidence for a young earth they have to show that the rocks are young, not just that they formed quickly.

Second, while polonium is highly radioactive, it isn't the only radioactive element. There are other elements with much longer half lives that can still do just as much damage to the surrounding rock. Most notably, uranium. Uranium is also found in zircon crystals. There is no proof that the scorched halos around zircon crystals were caused exclusively by polonium.

Third, even if the halos were caused exclusively by polonium there is more than one way to get polonium in the crystals without rapid formation. It turns out that polonium is a daughter product of uranium. In fact the only source of naturally occurring polonium is in rocks and ores with uranium content. So if the damage was done by polonium it could still have been done over millions and billions of years as uranium slowly decayed into polonium, and polonium quickly decayed into lead.

Young earth creationists argue that these halos around zircon crystals are evidence of a young earth. But when considered in context they cannot be used as evidence of rapid formation or especially young rock ages. In this it fails to be evidence for a young earth.

In these three real examples, before something can be considered evidence for a certain conclusion, it must be considered in context and scientists must ask the questions,

  • How did it get here?
  • Is there another possible source for it?
  • Does its presence make sense in its environment?
  • Does it actually support my conclusion?
If we do not ask these basic questions then we cannot claim that something is evidence for our conclusions.

Sunday, June 7, 2020

We Missed Our Window of Opportunity with COVID-19

There is no way to sugar coat this. The US blew their opportunity to have a successful lock down. The failure point came in early to mid May. Lock downs across the country were ended too soon basically nullifying most of the benefits of the lock down. It was like running a marathon only to quit one mile from the end because "we've come a long way and we don't see the point in running anymore because the end is far away."

I will illustrate what happened with graphs. All graphs come from the Coronavirus information page maintained by John's Hopkins University. Data was accessed on June 7th, with the latest data being from June 6th.

Here is a graph of the number of confirmed cases of Coronavirus in the US from the first detected case in January to today (June 6). The period from February to early April showed exponential growth, as is expected for an unconstrained virus.

In mid April the effects of the lock down took over and stopped the exponential growth. It was on the way to flattening out, but in early to mid May the curve shifted and we lost the opportunity to suppress and contain the virus.

Below is a graph over the same time period but showing the number of new cases per day.

US Virus Cases per Day
Here you can see the exponential growth from February to early April. The growth curve flattens due to the lock down. But it does not continue its downward trend. Here is the same graph but for Germany, which did have a successful lock down.

Germany Virus Cases per Day
Germany had one advantage, they got the virus a little later than the US (about a week), and then they started their lock down earlier. This curve shows what a successful lock down looks like. Germany can now return to a more normal state with some precautions in place.

Italy had a much more painful experience but they too had a successful lock down, as shown by their graph below.

Italy Cases per Day
There are some countries where lock downs were not implemented or they had no effect. Here is Brazil (note the difference in the scale on the y axis).

Brazil Cases per Day
And India.

India Cases per Day
If a lock down is not successful and no preventive measures are taken then you get a second hump. This happened in Iran. Iran is also a case where tests were not done or intentionally not reported. The first hump has a piece missing from the left half. There are also indications that there was significant under reporting in general.

Iran Cases per Day
If you want to see actual data manipulation then Belarus is the best example. Mysteriously positive cases stay under 1,000 per day (except for one day where reports doubled up from the day before).

Belarus Cases per Day
If you want to see a lack of testing, under reporting and data manipulation all in one country, look no further than Russia. You have natural exponential growth, then in the middle of April a chunk is missing showing a lack of testing, followed by a period of under reporting in the first half of May. Finishing off with data manipulation after that.

Russia Cases per Day
Then you have Singapore which had a successful lock down, but then lost control when new cases were imported at the beginning of April/end of March, and now they are trying to bring it under control.

Singapore Cases per Day
The gold standard of lock downs was done by New Zealand (also Iceland). They had significant advantages of being an island where they can greatly control incoming people, and they were not along any major travel routes. But they did take advantage of that and managed to eliminate cases of coronavirus from the country.

New Zealand Cases per Day
Sweden tried a different approach with a "soft" lock down. It only kinda worked, and it may get worse now that they are opening up slightly.

Sweden Cases per Day
Compare that to Denmark right next door who tried a hard lock down. Again, note the difference in the scale on the y axis.

Denmark Cases per Day
So how did individual states in the US do? It's a mixed bag.

New York had a successful lock down. States next to New York (New Jersey, Connecticut, Massachusetts, etc.) had similar success.

New York Cases per Day
California not so much. It did have an effect, but then people gave up too early and lost all the benefits of a hard lock down like New York had.

California Cases per Day
It's a similar story with Texas.

Texas Cases per Day
And North Carolina.

North Carolina Cases per Day
In some sates it wasn't bad... until 1-2 weeks after Memorial Day. They have a very clear Memorial Day spike. Utah and Arizona are the best examples. You can also make out a Memorial Day spike in North Carolina and a few other states.

First Utah.

Utah Cases per Day
Then Arizona.

Arizona Cases per Day
Minnesota is a case where the virus came, got slowed down early by a lock down, but then the lock down ended and... well let's just say it found plenty of hosts.

Minnesota Cases per Day
From here on out the US does not have the option of suppression, control, and elimination as happened in New Zealand and Iceland, or the suppression done in Germany, Italy, Spain, South Korea, and many other countries.

We blew our chances of having a successful lock down. If we had waited 2-3 more weeks we could now be seriously planning on opening up the country again for normal business. But we blew it. Now we can only work on mitigation and maintaining good health practices so that we are not overwhelmed all at once. Because of this we will go through maximum economic pain. Even if everything opens up there will not be enough people that will return to normal to keep businesses afloat. A short 3-4 month shock could have been handled. But this will now drag on for over a year, possibly more.

Without any significant changes we are looking at more than 100,000 more deaths by the end of the year, assuming it doesn't get any worse, or significantly better. I don't know where it will end up, only what direction it's going right now.

Tuesday, June 2, 2020

Letter to My Congressman

Dear Representative Allen,

I was shocked at the news yesterday that U.S. Park Police and National Guard troops cleared Lafayette Park of people for the sole purpose of providing President Trump the opportunity of having his picture taken in front of St. John's Church while holding the Holy Bible. The use of St. John's Church as a backdrop for his picture was not authorized by the Episcopal bishop of Washington, Right Rev. Budde, or any other church leader. Other church members providing Christian service on the steps of the church were forcefully removed by U.S. Park Police employing tear gas.

This is a gross violation of religious liberty and a crass disregard of respect for constitutional principles. As a man of faith I was dismayed at the sight of the President of the United States, who took an oath to uphold and defend the Constitution, so callously disregarding his oath of office and basic Christian charity for the inconsequential purpose of having his picture taken. To add to it he sought to use the Holy Word of God as a prop for his violation of a sacred space.

Throughout history church buildings have been used as sanctuaries in times of crisis, fear, and violence. Some of the worst atrocities in history have come when political leaders transgressed the sanctity of sacred spaces. While no church buildings were burned yesterday, or believers martyred, the President of the United States did violence to our religious liberty and assailed the wall of protection that provides safety to believers from the encroachments of Government power. The sacred space of a House of Worship should never be used as platform to proclaim violence on the children of God.

For my entire life, when I first came of age, I voted with a conviction that religious liberty must be preserved as a fundamental right. In the 2016 the Republican Party platform it states, "We believe in the Constitution as our founding document." If that was true then, surely the foundation of Republicanism has shifted like sand since then. I find no condemnation of the President's actions, nor of any defense of sacred spaces from those who proclaim the Constitution as their founding document. But as for me and my house, our principles are placed on a sure foundation that will not wash away with the changing tide of political expediency. I believe that constitutional freedoms must be protected and respected, not gassed and harassed.

Representative Allen, you proclaim to be a man of faith. Now is the time to live your religion and make good on your faith. The actions of the President must be condemned and not defended. I cannot in good conscience vote for anyone who provides cover and defense to someone who uses their office to violate the sanctity of a House of Worship. The rights written in our Constitution define the character of our government. How we treat those rights define who we are.


[quantumleap42], PhD

Monday, May 11, 2020

What counts as evidence in science?

Recently a young earth creationist asked me if I had looked at the evidence for a young earth and I said that I had and did not find any of it to be credible evidence for a young earth. He challenged my assertion that there was no evidence for a young earth and said, "you should be ashamed of yourself ... to say there is NO evidence rather than you just disagree with the conclusions of the data." He then listed many things he thought were evidences for a young earth. The problem was his list of "evidence" didn't actually contain evidence. They were attacks on the theory of the old earth, or attempts at finding uncertainty in what we know. There was nothing there that hinted at positive evidence for a young earth.

So what counts as evidence in science and why did I say there was "NO evidence" for a young earth instead of saying that I disagree with how to interpret the evidence? For that we have to look at what was presented as evidence.

One thing usually presented as evidence for a young earth is the argument that there is massive uncertainty in radioisotope dating. One of the ways we date rocks and meteorites is by using the half-life of radioactive isotopes to find out when a rock first formed. This is the most direct evidence that we have for the age of the earth. This of course presents a problem to anyone insisting that the earth is only 6,000(-ish) years old.

Since this counts as strong evidence for an old earth this obstacle must be removed if a young earth is to be proved. Thus the need to call into question the reliability of radioisotope dating. It is true that if the earth really was 6,000 years old then our method of dating rock really is unreliable and cannot be used as evidence for an old earth.

Whether or not you accept the reliability of isotope dating does nothing to provide evidence for a young earth. Unreliable rock dating only removes evidence for an old earth, it does not create evidence for a young earth. Young earth creationists will have to argue persuasively that it is unreliable, but it also means they cannot then use it to argue for a young earth. Without radioisotope dating the age of the earth could just as well be 21 million years instead of 6,000 years.

This kind of argument is presented as "evidence" for a young earth, but it does not provide evidence, it only removes the evidence for an opposing theory. Additionally it does not provide an explanation for why radioisotope decay is the way it is, it only attempts to undermine the reliability of it.

This then gives us an example of what counts as evidence in science. For something to be evidence it must increase our confidence in a particular theory and not just introduce uncertainty into our understanding. Many of the arguments for a young earth are of a similar form and do not actually provide evidence. They only seek to decrease the certainty of the evidence for an opposing theory.

Sometimes it is necessary to argue that certain evidence is not as certain as we think it is, but for that to then count as evidence for a different theory the uncertainty must be resolved in favor of the other theory. The purpose of science is to increase our confidence in how we view the workings of the universe, thus for something to count as evidence it must decrease our uncertainty.

Sunday, April 5, 2020

A New Christian Symbol

Last night President Russell M. Nelson announced a new symbol for the Church of Jesus Christ to use. The new symbol has a depiction of Jesus under an arch symbolically representing the tomb. He is standing upon a corner stone with the name of the Church on it. If we take the simplest form of this symbol there are many other meanings that we can give it. Like many symbols of religions through out the world it is very simple, but can contain intense meanings.

Here are possible interpretations of this symbol:

  • It is the door of the empty tomb after the resurrection of Jesus.
  • It is an open door to the Church, inviting others to enter.
  • It is gateway leading us into the path of Eternal Life. The gateway is baptism, which is symbolic of the grave and of resurrection.
  • It is the windows of heaven.
  • It is a doorway to a new life.
  • It is an open door of fellowship and friendship. Our door is always open.
  • The stone is the corner stone representing Christ.
  • The stone is the Rock upon which we should build.
  • It is the foundation of the Church and the Gospel.
  • It is the welcome mat to our homes.
  • It contains the steps to the doorway to heaven.
It's a very simple symbol but can have many meanings.

Friday, April 3, 2020

What stays the same when science changes?

"Science always changes so there's really no way know what is correct. Years from now everything we think we know could be wrong." -- Anonymous Internet Philosopher
That statement is so generic and I have seen so many countless permutations of it that I have no practical way of counting them. Every single time I have seen statements like that it is a subtle way for the person to say, "I don't want to talk about this anymore and no matter what you say I won't listen to you." This post is not for people like the anonymous commenter, but for people who have sincerely asked the question, "If everything in science can change, then what can we trust?"

So in the midst of the constant change of science what stays the same? Or does anything stay the same?

Let me give an example (I may have shared this story a few years ago). One day I was talking to an acquaintance and he asked me "What if it turns out that gravity isn't real?"

My response was simple, "Rocks still fall down. The Earth continues going around the sun. Gravity doesn't change."

What he was really trying to ask was, "What if gravity doesn't turn out to work the way we think it does?"

There is a difference between the two questions. One deals with what we observe, the other deals with our explanation of why it happened, and how we can predict future events. The former never changes, the latter can change.

One of the earliest explanations of gravity (that we know of) came from Aristotle. His explanation was standard explanation for almost 2,000 years. When Galileo first measured how objects accelerate due to gravity, and Riccioli confirmed his theory and made refinements to his measurement, the universe did not suddenly snap to conform to the new understanding. Things fell towards the Earth as they always had. Their motion remained the same. If you dropped a stone one day and then dropped another the next day the same thing would happen.

These basic observations are the things that do not change when science changes. Over 2,000 years ago Eratosthenes measured the circumference of the earth and also proved that it was a sphere. Since then our understanding of the shape of the Earth has not changed drastically. We still call it a sphere or a globe, but we have also found that it is not perfectly spherical. It bulges slightly at the equator. Our understanding of the shape of the Earth will change and grow as we make more observations, but our new observations will not change our previous observations. We will still view the Earth as roughly spherical.

What will NOT happen is we will wake up one morning and find that the Earth has been a flat disk all along. It won't suddenly become a doughnut shaped object. So when we say that science will change it means that our previous observations will only become more refined.

This brings us to the age of the Earth, which is almost always the topic that prompts the comments like the one I started with. In the years to come there will be changes and refinements to our understanding of the age and formation of the Earth, but just like the globe, we won't suddenly wake up one morning and find that scientists have figured out that they were wrong all along and that the Earth is actually 6,000 years old.

When changes in science come the changes must explain and agree with our previous observations. If we change the way we view the formation of the Earth, or how life evolved, what won't change is the rocks and fossils we analyzed previously. There are plenty of ways that our understanding of evolution may change in radical ways, but what won't change is the fact that it took millions of years, and that we have a part in it. Any new explanations we have must explain the evidence we have and what we currently observe.

Our explanations will become more refined and there may even be major shifts in our understanding, but the evidence will stay the same. Too often we fall into the trap of wanting the evidence to fit our worldview, but we must first make sure our worldview can accommodate the evidence.

The sentiment expressed by the quote at the beginning is a wish that in the future evidence will be found that makes everyone else conform to the worldview of anonymous, rather than a desire to find a worldview that accommodates all the evidence.

Sunday, March 29, 2020

Science Requires Positive Evidence

Finding explanations to what we observe is the essence of what science is. At the simplest level is it looking at the world and making sense of why we see what we see.

The science comes when we seek explanations in a systematic way. We take what we have observed, find an explanation that fits what we have observed and then, and this is the hardest part, question our assumptions to see if we should change our explanation, or more likely, expand our explanation.

While I have written this as a simple processes, understanding this process requires applying the process of science to the process of science itself. In the end you end up with a greatly expanded understanding of how not just science works but also how we interact with the universe.

Explaining this is not something that can be done in a single blog post, or even a single book, but it is a lifetime of learning. What I can do is provide examples of how science is either properly or improperly applied. Here I will give one example of a misapplication of science.

A few years ago an asteroid, that we named ʻOumuamua, from outside our solar system passed through our solar system. This was the first asteroid to be positively identified as having an unbound orbit. It was something that got a lot of attention and there were a few ideas proposed, such as gasses venting from the inside, or even we had measured its shape and mass incorrectly because it was spinning rapidly, or any number of possibilities.

Two astronomers at Harvard proposed the idea that ʻOumuamua was actually a spacecraft from an alien race. Their argument rested on the fact that as ʻOumuamua began its journey out of the solar system its velocity was not changing as we would expect. Its velocity was consistently too high. This would mean that there was something giving ʻOumuamua a push on its way out.

There is nothing wrong with proposing that something is evidence for extra-terrestrial life, it is after all an open question in science. But their motivation for their conclusion was flawed. Their argument rested on the fact that our measurements of ʻOumuamua's motion did not fit with our other measurements of its properties. Put simply, there was a difference between what was measured and what was calculated for its speed.

The problem with the alien spaceship theory was that there was no positive evidence pointing towards that idea. There only existed uncertainty in how it's motion could be explained by our other measurements of ʻOumuamua.

In the measurements of ʻOumuamua there was some uncertainty of its dimensions, spin, composition, and mass. ʻOumuamua's motion was not outside the possibility that it was just an asteroid and nothing else, just unlikely. Thus its motion did not constitute positive evidence for ʻOumuamua being an alien spacecraft.

Something is positive evidence iff its presence, or our knowledge of it, can only be explained by the proposed theory. That is, if the explanations needed to accommodate the new observations break our current understanding and theories at a fundamental level.

In the case of ʻOumuamua the difference between the measurements and calculations did not fundamentally break our understanding of physics. It didn't even make it exceptionally difficult to find other explanations that did not require it to be an alien spacecraft. Hence it could not count as positive evidence for it being an alien spacecraft.

If, for example, ʻOumuamua had been emitting regular radio signals with a defined pattern, then that would be positive evidence. In our understanding of physics there is no way for a hunk of space rock to make radio signals with a regular pattern. But to have its motion be slightly off from what we calculated, that is not positive evidence. Therefore not only is the idea not supported by the evidence, but proposing the idea was not supported by the evidence.

The critical thing that separates new scientific ideas from normal speculation is that there must be positive evidence first. This is a minimum bar to separate science from non-science. Finding evidence of aliens is perfectly within the realm of science, but we must be careful because not all things can be positive evidence for aliens.