How Big is Our Universe?

How Big is Our Universe?

We are tiny creatures, living out short lives in an immense and ancient universe.  We’ve evolved to make sense of the scales of time and space that were relevant for survival of our ancestors, so it is remarkable that we have any inkling at all of just how small we are when we zoom out to the cosmic scale.  As Douglas Adams wrote in ‘The Hitchhiker’s Guide to the Galaxy’:  

“Space is Big.  You just won’t believe how vastly, hugely, mind-bogglingly big it is.  I mean, you may think it’s a long way down the road to the chemist’s, but that’s just peanuts to space.”  

To try to make sense of the vast distances between the stars and galaxies, lets scale down the universe.  It is remarkable that even when we shrink things down quite a lot, we find that it is difficult to keep the sizes from rapidly becoming astronomical once again.  This exercise also helps make clear why interstellar travel is such a difficult prospect, and may be nearly impossible to accomplish, even for a very advanced civilization.  This is some of the fun you can have on a Saturday afternoon with some imagination, a calculator, and an understanding of how to use scientific notation.   So, lets begin!

All right, for our first scale down cosmos we will shrink our sun down to the very manageable size of a 1 inch marble.  That’s pretty small right?  That is about 2 one hundred billionths of the suns actual size.  So, with a 1 inch marble at the center of our solar system, here is what follows.  The innermost planet in our solar system, Mercury would be in orbit 3.5 feet from the sun, Venus would orbit at 6.5 feet, and Earth would be a tiny 0.23mm speck (barely visible) sitting 9 feet from the sun.   Next comes the planet Mars sitting 13.6 feet from the sun.  This is our inner solar system, and so far still pretty manageable – a solar system you could fit fairly easily in your living room.

  Next comes the outer solar system with the mighty Jupiter, a speck of 2.5mm flying around the sun at 46 feet from our marble sun.  Beautiful ringed Saturn is in orbit at 85 feet, Uranus at 172 feet, and Neptune at 269 feet.  Little Pluto, now sadly demoted to a dwarf planet, is in orbit at 354 feet.  From that distance our little marble sun would appear tiny, yet it’s the gravitational pull on the tiny dust mote of Pluto that keeps it chained to the solar system.   No longer can we hold the outer solar system in our living room.  We might need to move our solar system to the park to hold it all.  

Think for a moment of how empty our solar system really is.  Tiny specks of dust orbiting a tiny star.  Our model 1 inch sun holds almost all the mass in the solar system.  The rest is just a scattering of microscopic dots out hundreds of feet from the center, with mostly emptiness between them.  The solar system is really very very empty, indeed.

The New Horizon space probe, our fastest space craft yet, visited Pluto last year, taking nearly 10 years to make the trip from Earth.   How fast can we possibly get through the solar system.  Light, traveling at the fastest speed possible in the vacuum of space moves, you guessed it, at the speed of light.  At our little solar system scale the light leaving the sun would take 8 minutes just to pass the Earth 9 feet away.  After an hour of travel the photons of light would move only 64 feet through our little solar system.  That would be somewhere between the orbit of Jupiter and Saturn.  Think of a sphere of light traveling in all directions from our 1 inch sun and taking a full hour to move to a sphere with a radius of 64 feet.  That seems rather slow, but there is nothing known in the universe that can do better.

On this scale 1 light year (the distance that light travels in one year) would be 107 miles from our little sun, and the closest star to the sun – Proxima Centauri at 4.24 light years away – would be a staggering 454 miles out.   Our little 1 inch sun floating alone in the darkness of space with next closest marble sized star being over 450 miles out in the distance.  If the sun marble was located in Los Angeles, then Proxima Centauri would be located approximately at 100 miles further north than San Francisco.   Is it any wonder that interstellar travel is such a monstrous challenge?  To travel between the stars on human time scales seems like an unrealistic dream.

The star Trappist-1, which was recently in the news for having been confirmed to have 7 exoplanets in orbit around it (some of which are in the starts habitat zone)  At a mere 40 light years from earth it has been toted has being very close to us indeed.  On the scale of our model solar system  Trappist-1 would be a small marble 4226 miles from our sun.  Again, if our sun was in Las Angeles then Honolulu would be only 60% of the way out to where the little marble of Trappist-1 would have to be placed – that vast Pacific wildness becoming the vast empty ocean between the stars.  

From our model sun, the center of the Milky Way galaxy would be 2,675,000 miles away, or about 11 times further out than our moon.   The size of the galaxy from end to end would be 10,700,000 miles across.  The next large spiral galaxy to us is the Andromeda galaxy and that would be placed 271,000,000 miles away.  Now that is getting into scales that match the sizes found in our actual solar system.  For example, if our marble sun was sitting in the very center of our actual sun, the surface of the real sun would be 4040 light years on our scale model.  The mini Andromeda galaxy would be beyond the orbit of Mars.

Ok, time to change our scale model to make the universe more manageable again.  Lets suppose that instead of our sun being 1 inch in diameter, our entire Milky Way galaxy is just 1 inch in diameter.  On this scale the Andromeda galaxy is another small disk (a little larger than our Milky Way) just 2.1 feet away from us.  The Virgo cluster of galaxies, which contains thousands of galaxies would be 54 feet away, and the edge of the observable universe, 46.6 billion light years away, would be 7.35 miles in every direction from our little 1 inch disk galaxy.  I’ve heard of races where runners run “the solar system” and pass the orbits of planets at the appropriate places on their 10K race, but you could do a “Run the Universe” race too, where you run a 10K and pass, not only deeper into space but farther back into time until you reach the very edge of time and space at the finish line.   By the way, even though the universe is only 13.8 billion years old the edge is 46.6 billion light years away because the universe expanded much faster than the speed of light in the distant past.  Inside the disk of our tiny 1 inch galaxy, the distance from the Sun to Pluto would be just 1.59 Angstroms, which is very nearly the size of a Hydrogen atom.

What if we wish to make our entire observable universe the size of a friendly 6 inch diameter snow globe, so we can put it out on our desk and admire the whole of creation as we do our work?  What would that look like?  If the observable universe was 6 inches in diameter, then the Milky Way galaxy would be a speck in the very center of the globe (yes, we are in the center of the universe from our vantage point) that was a mere 160 nanometers across.  This would be approximately the size of a virus.  In fact, all the hundreds of billions of galaxies in your Observable Universe globe would be the size of viruses.  I’m not sure you would see anything when you looked in your snow globe universe since the galaxies themselves would be microscopic on this scale, but you could surely feel quite satisfied that when you held your snow globe every galaxy in the observable universe was in the palm of your hand! 

Who would win in a fight? Science or Philosophy.

By Rich Feldenberg:

With the movie, “Superman vs. Batman: Dawn of Justice” soon to hit theaters, it makes me wonder, why? Why would Superman and Batman be at odds with one another? Why would they battle when they are both supposed to be on the side of good? It may be fun to think about, who would win in a fight, Superman or Batman, Abraham Lincoln or George Washington, Indiana Jones or Han Solo? But again, why would they fight to begin with? Lately, there has been a different sort of war between good vs good, that has resurfaced. It is that of Science vs. Philosophy, and it has mainly been revived by a group of vocal physical scientists, that could be accused of extreme Scientism.

Now, Philosophy has been around for a long time. At least since the time of the ancient greeks, while the modern scientific method (and hence modern science as we would recognize it today) is generally agreed to have begun around the time of Galileo, around 400 years ago. That’s not to discount some of the ancients who made important observations of the natural world and contributions to math and logic, but the idea of hypothesis driven experimentation is a more recent phenomenon. In fact, many of the ancient “scientists” didn’t believe it was necessary to experiment at all, that pure logical reasoning should be enough to uncover the secrets of nature. Most of these armchair deductions have since been found to be false, even if based on good logical reasoning. The reason, it turns out, is that you really do have to test your basic underlying assumptions against the real world. Often the presumptions are incorrect and deviate from what seems to be common sense, or there may simply be many other factors that were unknown, but then uncovered by the experimental data.

Prior to Galileo, science and philosophy were more unified, and what we might label as science today would have been identified as natural philosophy then. Since the split, the two disciplines have diverged and become increasingly unique in their scope, like an ancient gene duplication event leading to paralogous gene families, or perhaps like the unification of universal forces right after the big bang fracturing into what appears to be completely separate forces such as the strong nuclear force and electromagnetism. If the two have a common origin can they really be so different? As noted by many philosophers, there has been a steadily increasing hostility towards philosophy by some prominent scientists, especially physicists in many cases. If hostility seems a strong word, then it at least appears justified to declare the attitude of these scientists as indifferent to philosophy – a disciple that lost its usefulness once science arrived on the scene. Those poor misguided philosophers!

I have heard statements from some top scientists reveal their dismissive attitude towards philosophy. People like Stephen Hawking, Neil DeGrass Tyson, Brian Cox, Lawrence Krauss, and most recently Bill Nye, the science guy, himself! All people I have a great deal of respect for when it comes to their areas of expertise. What I think these smart individual get wrong is a misunderstanding of what philosophy really is. They certainly know what science is, but I believe that their understanding of philosophy is lacking.

Now let me be clear, I’m not a philosopher, at least not by training. I took a couple philosophy courses in college, but that was the extent of it. I consider myself much more aligned with the world of science. Perhaps a number of years ago I might have agreed with the scientists that have decided philosophy is dead, and science rules all. I don’t think I feel that way anymore, not at all. After learning more about the philosophy of science (POS) in the last few years I’m much more convinced that there is a lot there that is of benefit to scientist and non-scientist alike. I’ve come that that conclusion by listening philosophers like Massimo Piglucci and Rebecca Goldstein discuss, explain, and debate philosophical topics. I’ve read a some articles and a few books. Again, this doesn’t make me a philosopher, not by a long shot, but it does make me appreciate the relevance of the topic to our lives today, and value the skills of it’s practitioners.

We all know that science has been hugely successful. It’s method of “question everything”, “experiment to find the answer”, and “self correction” by updating with new data, is by far the best way we have to gather new knowledge. Today we understand how the world works orders of magnitude better than we did 500 years ago. Science has given us understanding, but it’s benefits don’t stop there. It has transformed everything about how humans live. So, what has philosophy done for us lately?

Philosophy is important in helping us understand whether our basic assumptions about how science works are valid, in what settings science can work, and in which other setting it may not give us meaningful answers (i.e.. Like in questions of morality and ethics, or questions of purpose, for example). Philosophy won’t be able to answer what lies beyond the standard model of physics, or if our universe is one of many in a multiverse, but it may be able to help decide if those questions are scientific ones or not. Philosophy can help us understand how to apply critical thinking and rationality to our lives. As the title of philosopher Rebecca Goldstein’s article in The Atlantic asks then answers its self, “Why study philosophy? To challenge your own point of view.” That seems to be an important aspect for any rational creature that values self growth and learning. Some scientist go so far as to claim that science can answer moral questions. While science can inform the discussion (such as answering questions like can animals feel pain) it can not answer those questions of morality on it’s own. Philosphopy is better equipped to shed light on the questions of, “what is the best way to live one’s life”, “where does one find purpose”, and “what are ethical choices”. Of course, religion also claims a monopoly on this territory, but from a purely authoritarian approach, with it’s logical underpinnings coming after the presumption of a “law giver” instead of allowing the a questioning of all basic assumptions and following the flow of logic from there. In earlier times religion was eager to claim scientific truths (facts about the physical world), as well, (for quite a long time it was pretty much the only game in town), but as science has now advanced to such a high degree there are few modern thinking theologians that would claim that scriptures are books of science. They are now only metaphor when in contradiction to established scientific consensus.

So, who would win in a fight, Science or Philosophy? Well, they shouldn’t be fighting to begin with. They are both of use to us poor mortals as we try to make sense of the world we’ve been born into. They each bring an important skill set to the table. Is Superman like science and Batman like philosophy? Superman seems to have almost limitless power, but does have certain weaknesses as well, such as susceptibility to Kryptonite and perhaps an overly naive nature. Batman, meanwhile, possessing human frailty is immune to Kryptonite, has become who he is by dedicated work and training (he wasn’t just given magical powers), and is motivated by dark human emotions of past pain and suffering.

The issue of who would win, science or philosophy may be a bit like the joke I heard one time about who would win in a fight, a tiger or a shark? Each would win if the fight takes place in its own domain.

References:

1. “Why Study Philosophy? To Challenge your own point of view.” The Atlantic by Rebecca Goldstein. Feb. 27, 2014.

2. “Mike, don’t listen to Bill Nye about philosophy”, Plato’s footnotes blog by Massimo Piglucci. Feb. 29, 2016.

3. “A physicist flirts with philosophy and lives to tell the tale”, Scientific American. Sept. 23, 2011.
This was an interview with physicist Brian Cox, and to Professor Cox’s credit he describes his recent acknowledgment of the importance of philosophy.

4. Rationally Speaking:  Exploring the borderlines between reason and non-sense.  Podcast with host Julia Galef. 

5. “Science can answer moral questions“, Youtube link to TED talk by Sam Harris (neuroscientist, skeptic, and atheist).  I’m arguing against this point of view, but see what you think!

 

Why your DNA is not like a blueprint

By Rich Feldenberg:

When future historians may look back on the 20th century they may critical of humanities violent tendencies, and rightly so. We drove ourselves to the point of near self-extinction with global warfare and the creation of nuclear weapons. But maybe they will also see a flowering of our more nobel side, as well, with the 20th century ushering up a new understanding and appreciation of nature and ourselves. Many areas of science saw exponential advancements, with general relativity, special relativity, and quantum mechanics, all being born in the last century. As important as these fields have become, the areas of life science have arguably had an even larger impact on society and our everyday lives. It was in the 20th century that we learned that DNA is the molecule of heredity, and the structure of DNA was described by Watson and Crick in 1953 as the now famous double helix. With improvements in the methods of molecular biology in the 1980s and 90s, genomics has lead us to a more complete understanding of the underlying mechanisms of disease and how the normal processes of life operate, develop, and evolve.

The word DNA is now common in the everyday vernacular, even if not everyone remembers that stands for deoxyribonucleic acid. Also nearly everyone has some idea that DNA is vital to genes and inheritance, and is used in forensics, paternity testing, genetic testing for disease mutations, and for mapping phylogenetic trees to understand the relatedness of all life. Somehow, though, we’ve been repeatedly told that DNA is like our blueprint. That it gives the plans for creating you and me, and anything else that has DNA. That analogy is a little misleading, as DNA doesn’t act as a blueprint at all. Looking at the full genetic code of an organism wouldn’t help you know very much about what that organism looked like. The only way you might really infer this from the genetic information would be by comparing the DNA sequences to other organisms that you already know a lot about. If the DNA you are looking at was very close to the DNA coding for octopus and squid then you could guess that this organism looks cephalopod-like. The DNA would not tell you the body plan by analyzing just the code on its own, however.

So how should we think about DNA? Is there something else we can compare it to that would make a more accurate analogy? Well, instead of being a blueprint, like a technical drawing that lays out the structural relationships of each part to the other parts, it is really more like a running computer program. DNA is a lot more like a large collection of computer programs, some are always running, and others are only running at certain times or in certain cell types. The DNA is giving instructions that are carried out by hardware running the code. In this analogy the DNA is the software and the cell and its molecular machinery is the hardware running the software. Software without hardware is hopelessly ineffectual, and hardware without software is nonfunctional. They both need each other to function. The DNA needs a living cell to carry out its instructions. In the proper setting these instructions are powerful, producing a whole human being from just a single cell, as it did with you during your 9 months of gestation in the womb. So how does it work?

Well, it’s important to recall how the information stored in DNA is interpreted by the cell’s internal machinery. The DNA itself is made of two long strands, forming the famous double helix. Each strand is made of sequences of nucleotide bases, and there are four nucleotide bases to choose from in the DNA alphabet – The DNA letters are A, C, G, and T. These letters are chemically distinct nucleotides, and you can picture a gene as being a string of these letters that make a unique sentence. A typical gene may be hundreds to thousands of these letters in length. For example, the human gene for the AVP-2 receptor, found on the X chromosome, codes for a protein located on the cell surface of certain kidney cells, and is critical to regulating normal water balance. The gene contains 4676 of these DNA letters.

Starting from letter one to ten of the AVP-2 receptor DNA code, the letters read out as CTGCCCAGCC, but all 4676 letters of the DNA code for this gene are known and can be found in genetic databanks. Each strand of DNA has a complementary strand where every base in one strand pairs to another base in the other strand. A:T are pairs, and C:G are pairs. In other words, if you know the sequence of one strand you can easily deduce the sequence in the other strand, so for our first ten bases in the AVP-2 receptor – CTGCCCAGCC we know that the complementary strand would have to be GACGGGTCGG, based on the pairing rule. It is this complementary base pairing that makes it possible for DNA to replicate itself. Each strand serves as the template for making a new DNA strand. The double helix just needs to be unwound at the right time, the complementary bases added to each of the now single stranded DNA strands, and you now end up with two identical double helix DNA molecules, where you initially had just one. This has to happen for cells to divide so both of the new cells created from the original single cell has the same DNA as the original.

There are two major cell processes involved for turning the DNA code into protein. For the most part it is the protein that does the actual work in the cell, while it is the DNA that is the code-like programming being run. The first process is transcription, where the DNA code is converted or transcribed into an RNA code. The second process is translation, where the RNA code is converted or translated into the protein product. For the sake of simplicity, we are only talking about protein-coding genes, but there are many non-coding RNA genes, as well – we’ll save that topic for another day.

During transcription a molecular machines known as RNA polymerase interprets the DNA code and converts it into an RNA code, in the form of a single strand of messanger-RNA. RNA is quite similar to DNA except for a few key differences. One distinction is that it is single stranded rather than double stranded like it’s DNA cousin. Another is that it contains an extra chemical group called a hydroxyl that is lacking in DNA, and a third distinction is that whereas the letters in DNA are A, C, G, and T, in RNA the T is missing and a U is there in its place. The RNA alphabet, therefore has the letters A, C, G, and U, with A:U forming pairs and C:G forming pairs. The RNA can then be transported to the cell machinery used to make protein, and the DNA (the original code or source code) can remain safe in the chromosome – only the transcribed copy is sent out.

The messenger-RNA (mRNA), finds it’s way to the ribosomes which are complex molecular machines that take the RNA code and make the actual protein. The RNA code is read by the ribosomes with every three bases forming a codon that specifies an amino acid. The protein is a string of amino acids. A few codons also tell the ribosome where the protein ends, and are called stop codons. The protein may still have a few steps to go before it is fully functional. For example it may need to have certain sugars or other chemical groups added at particular locations. It also needs to be folded into a very specific 3-dimentional shape, and it may need to associate with other proteins to form a part of a larger protein complex. Then it may need to be transported to specific sites in the cell, or even exported out of the cell, to do a job located in a different place in the body.

So why is our DNA not like a blueprint? Well, even if you could read the entire DNA code for all the protein producing genes, you would only see the ingredients that the DNA was coding for. That is far from a blueprint that might show you the structure of a building, where it’s doors, windows, elevators, stairwell, and so on, are located in spacial relation to one another. Knowing the protein products only gives you a list of ingredients. How those ingredients interact together, in time and space, is what creates an organism. The genetic code is a set of instructions that is executed on the code reading machinery of a living cell. The beauty of it is that not all the genes are transcribed at the same time and in the same amounts. Only a fraction of genes would be operational at any given time, and in a complex multicellular organism, only certain genes will ever be transcribed in any particular cell type. That is what makes a kidney cell different from a brain cell different from a cell in the heart muscle, and so on. Every cell has all the genetic programs, but only runs a subset of the total programs necessary for its own type.

DNA without the code reading cell machinery can do nothing on its own, which is why the vital flame of life must be passed down from living cell to living cell, uninterrupted since the very beginning of life itself. The genetic program is sophisticated enough that it causes genes to be transcribed that produce proteins that are themselves transcription factors secreted out of the cell to instruct neighboring cells as to which of their genetic programs to begin running. It is this complex coordination, leading to the switching on or off of particular genes in other cells, that starts the process of building a whole multicellular organism. In this way it is not just the genetic program that is necessary for building a animal, or person, or plant, but the local chemical environment that the program of each cell finds itself living in. The chemical neighborhood is just as important as genetic constituency.

In the language of Object Oriented Computer Programming, like Java for example, we might say that the complete genome of an organism is a program with many Classes (genes), and that when these classes are run instantiate Objects (proteins). Each and every cell in a body has the same program, but depending on it’s interaction with neighboring objects will Call only certain classes for use at any given time, and in some cases will never use particular classes that it has access to. These objects then go on to run all the functions necessary for that cell, including affecting other cells to call on certain objects in some cases. A human kidney cell has the entire “Human Program” as part of its software, but will only call on the classes used by a kidney cell, because it was derived from a cell that at one time could use all classes (Pluripotent stem cell), but at a certain point was instructed by its chemical environments to only allow use of the kidney classes. In other words, it differentiated into a kidney cell, thereby losing the ability to be a different cell type.

This is one reason, that even though we have completely sequenced the human genome, we still have a very incomplete understanding of what most the the genes are doing. Just by looking at their code it is not easy to determine what their affect is in a whole organism. The computer analogy may not be the perfect analogy, but it does illustrate the problem much better than the typical blueprint analogy does.

 

Other interesting things about DNA, and other fun topics:

1. “Intron Retention: a common cause for cancer“.  by Rich Feldenberg. ZME science. 1/25/2016.
2. Alternative Splicing.  Wikipedia.
3. Non-coding RNA.  Wikipedia.
4. “Why the Horta would not have looked like a rock monster“.  Darwin’s Kidneys.  June 18, 2015.

Happy Darwin Day 2016

February 12th, 2016 is Charles Darwin’s 207th birthday. Charles also happened to share the exact same date of birth with Abraham Lincoln – so happy birthday Mr. Lincoln, as well! Since this blog is dedicated to science, with a special emphasis on evolution, and in fact, has the name Darwin in the title, I want to be sure to honor our dear Mr. Darwin properly.

There are Darwin Day celebrations planned in the USA and around the world, but no ‘Official Darwin Day’ is recognized nationally. That could change as some efforts are being made to make it official. In fact, this year the Governor of Delaware declared an official Darwin Day in his state. In some cities there are lectures or parties to celebrate.  The Center for Inquiry has a take action page, where you can send your name in a letter  to members of congress to express the importance of creating a Darwin’s Day for public education of science.

Charles Darwin’s theory of evolution was the beginning of modern biological science. As the Russian evolutionary biologist Theodosius Dobzhansky is quoted as saying, “Nothing in biology makes sense except in the light of evolution”. Evolution is the thread that binds all of biology together. Every aspect of biology, from molecular genetics, embryology, comparative anatomy, populations and ecosystems all “make sense in the light of evolution”.

Darwin’s theory was a realization of origin from common decent. Evolution does not address the emergence of life from non-biological origins, but does an excellent job explaining the illusion of design seen in the complex structures of the living world. Of course, Darwin realized that the illusion was the product of natural selection working on variations in living things. Darwin had no idea about genetics, DNA, mutations, and so on, but as those fields of biology developed they only reinforced Darwin’s big idea. It could easily have been otherwise. If evolution by natural selection was not how the world worked, then molecular genetics, phylogenetic, developmental biology, and so on would not have provided additional support to a 150 year old theory. Yet, all these modern sciences fit in perfectly, continuing to build on the original theory. Even without the fossil record modern biology would still point the way to evolution. By the way, the fossil record also supports evolution, and has only become more robust during the last 150 years as many more fossil species have now been discovered.

I’m sure Darwin would have been delighted to learn about genes, how new mutations arise by damage due to radiation, chemical mutagens, or simply errors in the normal process of DNA synthesis. He would have loved to see how the genome is cluttered with the remains of dead viruses, pseudogenes, copying errors that we have been copying and passing down to our children for geological eons. And he would have certainly understood that we can see our degree of relatedness to any living species on the planet by looking at, not just the working genes and how closely they match to us, but also these dead viruses and pseudogenes.

Darwin’s voyage on the H.M.S Beagle remains one of the most exciting and most epic expeditions of discovery in history – certainly one of the most productive, since it resulted in much of the data Darwin needed to formulate his theory over the next several decades. Darwin was an amazing naturalist and keen observer. There is hardly any area of natural science of his time that he didn’t seem to make some meaningful contributions. Not just in biology but in geology, as well.

So this Darwin’s day I plan to celebrate at home with my family. Perhaps have a piece of Common Decent Cake or Evolution Pie, learn something new I didn’t know about evolution, and honor our Dear Mr. Darwin.  Let me know how you plan to celebrate.

Other Reading:

1. Darwin Day:  Wikipedia
2. Natural Selection:  Wikipedia
3. Youtube.  Climbing Mount Improbable.  Lecture by Richard Dawkins.
4. OxoG is how radiation turns your own water against you.  Darwin’s Kidneys blog
5. Cytosine Deamination.  Darwin’s Kidneys blog.  (another mechanism of mutation).
6. Another Clever Mesign by Mother Nature.  Darwin’s Kidneys blog.  New word mesign to differentiate apparent design in nature from when we mean a designed object.
7. How our ancestors promiscuous genes became more discriminating.  ZME Science. Feb. 9, 2016.  Article on how gene families arise by gene duplications.

The Frequency Illusion

This week I had a good opportunity to discuss an interesting cognitive bias with one of my 4th year medical student while we were on renal rounds. The issue came up when I was examining the belly of one of my young patients, who screamed out, “your hands are cold”. One of our nurses was quick to respond, “Cold hands, warm heart”. My student looked at me then remarked that she had only recently ever heard that expression, and since then has been hearing it over and over again. This, of course, lead to a natural discussion of the cognitive bias called the Frequency Illusion, which also is known as “The Baader-Meinhof Phenomenon”. I admit we had to look up the name, as neither of us could remember what it was called. As physicians and scientists, critical thinking and rational thought are vital, and one way I teach this to my students is by discussing cognitive bias and logical fallacies. These emphasize where limitations of the human mind lie, and how to avoid common pitfalls in thinking that we are all prone towards.

The frequency illusion is one we have probably all experienced from time to time. The example above, is a not unusual. My student may have heard that phrase before, but never really registered it, or perhaps really never did hear it before recently. In any case, the true frequency of the phrase is unlikely to have suddenly increased, but only my students perception of the phrase has lead her to believe that only now is she hearing, “cold hands, warm heart” all over the place. Cognitive scientists propose that when the human mind has been given new information, it creates a bias towards that information so that we are more likely to become aware of seeing or hearing that same information again the next time it is presented. This is known as a “Recency Effect”. In reality the information has always been present at the same frequency but until recently it was part of the background noise and not in the forefront of thought.

Another example of the Frequency Illusion is one that I noticed in myself this week.  This occurred after a friend of mine posted on Facebook that he and his wife were visiting the Florida Keys for vacation. Since then I have noticed several commercials on TV advertising the Florida Keys for tourism. I had never noticed those commercials before. Now, it is possible that those commercials have only just begun to be broadcast, my friend was influenced by the commercial and decided to go to the Florida Keys, and I only started noticing the commercials because they were never on TV before this week. A more likely explanation is that I have fallen victim to the Frequency Illusion.

And yes, my hands really are cold all the time, and my heart is around 98.6 degrees Fahrenheit – so pretty warm. I guess my nurse was right after all!

Reference articles:
1. “The Baader-Meinhof pheonomonen”, How stuff works.

2. Structure of a logical argument. The Skeptics Guide to the Universe page.

3. “The Clumping Effect” Darwin’s Kidneys blogpost.

4. List of Logical Fallacies.  Wikipedia.

 

You Sciency Dog You

Molina the science dog!

Why is the pH of YouTube very stable?

It constantly buffers.

Book Review: “The Vital Question”

By Rich Feldenberg:

On this episode of Darwin’s Kidneys – first of 2016- I’ll be reviewing a book by Nick Lane called, “The Vital Question: Energy, Evolution, and the Origins of Complex Life”. This book attempts to tackle some of the toughest questions in biology today, such as how, and in what environments, life originated, how the complex eukaryotic cell evolved, how the cellular mechanisms to generate energy echo back to the days before biology, and why sexual reproduction is the way it is based constraints placed on us by our energy generating systems -the mitochondria. It is a lot of territory to cover, but Dr. Lane does an amazing job of bringing all these seemingly diverse themes together, synthesizing them into a coherent narrative that flows as easily from one topic to the next, as electrons flow down the mitochondrial respiratory chain (a central subject of the book).

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For those of you, who like me, love the topic of biological origins, this book will keep you engaged, and I had trouble putting it down, as I waiting for the next amazing revelation to be exposed. The early part of the book describes the common thread between the most essential metabolic activities of all living cells on earth -whether they are bacteria, archaea, or complex eukaryotes – and the natural geochemical activity of Alkaline Hydrothermal Vents. All life generates its energy by using proton gradients to drive the production of ATP (the energy currency of the cell). In all cells today, special pumps have evolved to pump protons (hydrogen ions) across a membrane. This creates a proton gradient (more protons on one side of the membrane than the other) which will naturally lead to those protons tending to diffuse back across the membrane. Cells use this proton gradient to run the protein ATP-synthase, to generate ATP, just like running water can be used to turn a water wheel to do work at a mill. In order to get the proton, it has to be separated from its electron, and that is done through a series of oxidation-reduction (redox) reactions, where the electron is transferred from one compound to another with each subsequent compound having a greater affinity for the electron than the last compound. It ends with the electron being transferred to oxygen (O2), which has the most affinity for the electron, converting the oxygen to water. The compounds where the electron is being transferred, are the respiratory transport chain of proteins. It is also found in plants as part of their photosynthesis machinery.

 

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This process mirrors a naturally occurring geological process found in Alkaline Hydrothermal Vents on the ocean floor. These vents are different from the “Black Smokers” that have been better popularized, as sites of chemosynthesis, where an ecology of organisms survive using the energy of the vent, and are not directly dependent on energy of the sun. The Alkaline Vents, on the other hand, are not quite so hot, but more importantly are composed of a matrix of mineral with thin walls that mimics a cell membrane. The vent fluid is more alkaline, with a pH of around 10, and the ocean water more acidic. It is thought that the ocean pH, 4.5 billion years ago might have been even more acidic that it is today with a pH of around 6. Since pH is a measure of the proton concentration, there is a natural proton gradient between vent fluid and ocean water separated by a thin mineral. The mineral also contains Iron-Sulfer complexes and other minerals that can act as redox centers, producing the electron transfer that we also still see today in our respiratory transport chain.

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Dr. Lane argues that this environment provides a very plausible explanation for how life originated and why all life uses the unusual proton gradient method to generate energy. His own research is, in part, using reactors to replicate the Alkaline Vent environment to study this theory further.
He goes on to discuss how life could then have evolved more effective cell membranes making wondering further from the vent location possible, as long as these simple organisms could begin to pump protons on their own, at this point. This movement into the new environment, and an existence independent of the Alkaline Vent, is where the split between bacteria and archaea probably occurred. He shows the evidence for this hypothesis.
A great deal of the rest of the book describes the evolution of the complex cell, by the synthesis of an archaea host cell, with a bacterial endosymbiont which went on to become the mitochondria. He also describes, in detail, the genetic evidence, as well as, that logical considerations, that suggest this occurred, it occurred only once, and how the other features of the complex cell -such as nuclear membrane developed.

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The book is beautifully written, but I will say some background in biology certain helps, but his writing is clear, entertaining, and well focused.
I just finished reading, “The Vital Question” this month, but it is now in my top 10 all time favorite science books. The last Nick Lane book I read was called, “Oxygen” and was equally good. It was also about the biochemistry of energy generation in organisms. I urge you to check out, “The Vital Question”, and let me know what you think.

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References:
1. The Vital Question, by Nick Lane

2. Nick Lane webpage.

3. Darwin’s Kidney Article on Molecular Fossils (EMMAs).

4. Article on the necessity of a new word, Mesign, to help differentiate between something purposefully designed and something that has the false appearance of design being evolved by natural selection.

CRISPR: what’s the big deal?

By Rich Feldenberg:
In the last couple years there have been a growing number of mainstream media stories (like this recent CNN article) highlighting a new molecular biology technique that is revolutionizing the way scientists conduct genetic experiments, and may soon make the holy grail of medicine (gene therapy) possible. It certainly seems far from usual for the media to be overly concerned with a technical method of scientific investigation, but CRISPR has caught the attention of scientist and non-scientist alike due to its huge potential to change the research landscape. This article will discuss what CRISPR is all about, what it does in nature, how scientists are using it in the lab in place of older more traditional techniques, and what its future potential might be to cure diseases that are now incurable.

CRISPR (pronounced like Crisper) is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. Yeah, CRISPR is much more fun to say. It is a naturally occurring segment of DNA found in many prokaryotes. Prokaryotes are single celled organisms that lack a nucleus and other internal structures that more advanced eukaryotic cells contain. The prokaryotes include bacteria and archaea, and CRISPR has been found to occur in about 40% of bacteria and 90% of archaea sequenced so far.

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The CRISPR DNA is organized in a particular way. It is made of short lengths of repeating DNA basepairs that are separated by regions of seemingly random DNA, known as spacers. Both the repeating regions and the spacer regions are on the order of 24-48 base pairs in length. These repeating structures were first discovered in the DNA of E.coli (a common bacteria found in the intestines of humans) back in 1987, but their function was not known at that time. It was not until 2005 that their function began to become understood, thanks to bioinformatics. Bioinformatics is a computational biological approach to problems in molecular genetics. Using computer programs to search and compare genetic databases, it was found that the spacer portions of CRISPR exactly matched portions of DNA from bacteria infecting viruses and plasmids. That lead to the realization that CRISPR serves as a kind of immune system for prokaryotic cells.

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Basically what happens is that when a virus infects a bacterial cell, the cells first line of defense includes nucleases (enzymes that cut up DNA) that are released in an attempt to destroy the invaders genetic code. The majority of cells infected will not survive, but in the rare chance that it does survives the viral attack, nucleases then cut up the virus DNA into small parts, some of which become the spacer segments in the CRISPER complex of the bacterial DNA. Next time that the same type of virus infects the bacteria, the bacteria can quickly identify it based on the DNA match between its CRISPR spacer segment and the viral DNA. Enzymes called Cas (for CRISPR associated) are nucleases that will associate with the spacer sequence. They cut the viral DNA at the specific place where the match occurs. This increases the chance for the bacteria to survive the viral attack and confers a kind of immunity to the cell.

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It has been shown that bacteria that contain CRISPR are much more resistant to virus that have DNA sequences contained in their CRISPR spacers, and if those spacers are removed from their CRISPR segments, they lose that resistance. There are certain Cas enzymes that can continue to add new spacers each time they are attacked with new kinds of viruses, and if these types of Cas enzymes are defective or absent, the bacteria can still defend against attack with familiar viruses but are unable to acquire immunity to new ones.

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This certainly seems like good new for bacteria, which are continuously under attack by viruses day in and day out. In fact, it has been estimated that viruses kill 40% of the bacteria in the oceans each and every day. It didn’t take long for scientists to realize that CRISPR could provide an amazing and precise genetic tool. Since the spacer sequence can recognize very specific regions of target DNA and Cas9 (the particular Cas enzyme that is attached to the spacer) can then carry out a seek and destroy mission of the target DNA. It is like the delete key in a word processor program.
It was found that the target DNA didn’t have to be just viral DNA for the process to work. If DNA from a bacteria, animal, plant, fungus, or apparently any organism was inserted into the spacer sequence of CRISPR-Cas9 complex, then a genetic modification could be easily made to that organism. Using CRISPR, genes can be easily and cheaply edited. This system has set in motion a new revolution in molecular biology that has not been seen since PCR (polymerase chain reaction), a technique to amplify DNA was first introduced in the 1980s.

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So what can CRISPR really do in the lab? It can be used to delete specific genes or segments of genes. All you need is a copy of the basepairs that correspond to where you want your deletion in the target organism, and with that and your Cas9 it will find the correct place on the DNA and then cut the DNA at the precise location. In that way you can remove a gene. You can also insert a gene as well. This is done in a similar manner. You have your target DNA picked out and inserted into your CRISPR system, but in addition you need the gene, or segment of DNA you want to insert placed into the cell, as well. The cell’s own repair mechanism will detect the damaged DNA and attempt to repair the break with the added gene. In this way it acts like the cut and paste function of your word processor.
By removing the DNA from the target you are making an irreversible change to the genome of that organism, but it is also possible to use CRISPR to make reversible changes too. This is done by using a defective Cas9 enzyme. The spacer DNA sequence will still seek out and find the desired region of genome, but due to defective Cas9 the DNA will not be cut out. The spacer sequence will still attach to the DNA and block transcription, so is effectively turning off that gene.

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These sorts of techniques can be used to make “knock out” organisms – organisms that lack a particular gene. Knock out mice, for example, are an indispensable tool for understanding how certain genes function in a whole creature, and how mutations in those genes lead to certain diseases. Genes can also be turned on by CRISPR by combining the CRISPR complex with a promotor – a regulatory element that tells the cell to begin transcribing a particular gene.

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This is now allowing labs around the world to investigate disease causing mutations, including cancer biology, at a much faster rate. The techniques are considered relatively easy to use and master, and much less expensive than traditional molecular techniques to achieve similar results.
CRISPR has already been discussed as a potential therapeutic medical intervention, although, the ethics of genetic engineering are still being hotly debated. There was a attempt to use CRISPR to cure the disease hemophilia by a group of Chinese researchers, although they were not successful it is likely only a matter of time before progress along these lines would make similar trials more effective. Right now it is considered by most to be too new of a therapy for clinical medicine, and even if it could be done, some consider tampering with the human genetic code too dangerous. This might especially be true for genetic alterations that would be passed on to subsequent generations beyond the individual being treated. Some worry that it will go beyond just curing disease, and be used by the wealthy to create “designer babies”. Perhaps couples that want taller, stronger, or smarter children would be able to engineer their children to be so. Would that create an even wider divide between the haves and the have nots? These are certainly questions that should be addressed and discussed, but I do hope that fear won’t prevent this technology from reaching it full potential to treat genetic disease.

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Would it really be so bad to have future generations of humans that are more disease resistant (perhaps less prone not only to heart disease, diabetes, and Alzheimers, but less prone towards depression, addiction, or apathy)? What about a future of humans that are more intelligent, more rational, less violent, more compassionate and empathic? Only by being properly informed can we make the best decisions as a society about how to best use such technology.

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References and other reading:
1. CRISPR wikipedia article: https://en.m.wikipedia.org/wiki/CRISPR
2. CRISPR interference wikipedia article: https://en.m.wikipedia.org/wiki/CRISPR_interference
3. “CRISPR/Cas9-mediated gene editing in human triproneulcear zygotes”; Protein & Cell; May 2015, Vol6, Issue 5, pp 363-372. http://link.springer.com/article/10.1007/s13238-015-0153-5
4. “Molecular Biology of the Gene”; 7th Edition, James D. Watson, Cold Spring Harbor Laboratory Press; 2014. Pages 706-712.
5. http://www.geneticliteracyproject.org/2015/06/25/ethical-and-regulatory-reflections-on-crispr-gene-editing-revolution/
6. http://www.nature.com/news/ethics-of-embryo-editing-divides-scientists-1.17131
7. http://www.cnn.com/2015/10/30/health/pioneers-crispr-dna-genome-editing/
8. Neurologica blog article on CRISPR: http://theness.com/neurologicablog/index.php/gene-editing-humans/
9. “Is Bad Luck Really a Diagnosis?”, Darwin’s Kidneys blog: http://darwinskidneys-science.com/2015/06/14/112/

The Clumping Effect

by Rich Feldenberg

Cognitive biases permeate our thinking process, leading us to false conclusion and beliefs. Aristotle called humans, “The Rational Animal”, but it has been pointed out before that we are much more rationalizing than rational. We have a strong tendency to hold onto our notions, defending them with faulty logic and weak arguments, because we wish them to be true. Motivational reasoning and emotional argument is common to see in even very intelligent and educated individuals. Daniel Kahneman helped to define the idea of cognitive bias, and popularized it in his book, “Thinking Fast and Slow”. Over the decades the ways in which evolution has mesigned the human mind to fail the litmus test of reality testing has been more fully explored, and the list of cognitive biases, logical fallacies, and faulty brain circuits continues to grow ever longer.
I would like to introduce what I believe is a new, and as yet, unidentified type of cognitive bias the I’m labeling as “The Clumping Effect”. I have noticed this effect in myself over the last few years, and although I have not done a statistical analysis of the effect, feel it can be nothing more than a cognitive bias. The effect occurs when I am on the trail, either on my bike or running. The nature of the effect is this: If there is a stretch of trail with few runners, walkers, and cyclists, I notice that if there are two other people on the trail that are separated from each other at time 1 (when I notice them), then the three of us all converge at the same spot (time 2). In other words, if I’m on my bike I don’t just pass the first person and then later the second person, we all happen to be along the same point of the path together at time 2.
This effect can occur if all three subjects are moving in the same direction, or if two or moving in the same direction and one in the opposite direction, but all subjects must be moving at different velocities. In this definition I’m using the term velocity in its true physical sense (speed and direction), because you could for instance, have two bikes moving at the same speed, but opposite direction. Place a runner in-between the bikes and the Clumping Effect demands that the three will pass each other at the same point.
I notice this because it is somewhat annoying to be a cyclist, moving at a good clip on an empty trail, then have to be cautious about avoiding a collision when the lone spot of the trail is suddenly at full capacity. And, that I believe is the underlying reason for the Clumping Effect. It is those instances that stand out in my mind, whereas the many times that I pass one athlete then the other doesn’t really register as an event at all. We remember the hits and forget the misses, as any good skeptic knows.
I would be interested to know if anyone else has ever experienced a similar effect. I may also decide to do an experiment to measure the incidence of “hits” in comparison to “misses” on my typical trail. I’m curious to know do ‘hits to misses’ happen at a rate of 1:100 for example. How often does it have to happen that it stands out in my mind as something that “always happens”. Also, what proportion of users of the trail also notice the effect? I could send out a survey to local running and cycling groups?

References and other sources of good info:
1. Cognitive Biases Wikipedia article: https://en.wikipedia.org/wiki/Cognitive_bias
2. Daniel Kahneman Wikipedia article: https://en.wikipedia.org/wiki/Daniel_Kahneman
3. “Thinking Fast and Slow” by Daniel Kahneman. I really recommend this book.
https://itunes.apple.com/us/book/thinking-fast-and-slow/id443149884?mt=11
4. “The Skeptics Guide to the Universe (SGU)” podcast. Great free source of information on how to think logically.
http://www.theskepticsguide.org
5. “Neurological” Blog by Dr. Steven Novella. Also filled with great information on skeptical and logical thinking.
http://theness.com/neurologicablog/
6. “The Rationally Speaking Podcast”, host Julia Galef.
http://rationallyspeakingpodcast.org
7. SGUs guide to argument and logical fallacies: http://www.theskepticsguide.org/resources/logical-fallacies

The Dialogs: Is there a limit to Science?

by Rich Feldenberg

In the Dialogs the Robot from Lost in Space and Speed Racer find themselves suddenly transported to a distant location to discuss a topic of philosophy of science. This has happened on many occasions. They don’t know how they come to this place or if some intelligent being is behind it. When they return to their own worlds no one else is aware that they have even been gone.
This time Speed and the Robot suddenly appear on a beach at sunset. They are on ancient earth, in the greek islands.  The sky is ablaze with deep reds and purples as the sun is sinking beneath the sea. Waves are crashing loudly on the rocky shore and a gentle breeze is blowing. There is no one else on the island, but just 30 miles south, and out of view of our heroes, a fleet of Athenians is making a crossing as they prepare for battle.

“Hello again, Speed Racer.  In principle there are no limits to science.” Says the Robot, It’s bubble encased brain blinking red and yellow lights. “It’s methodology makes it the best tool to apply in an attempt to answer any question.”

“Good to see you again Robot.  Of course there are limits to science.” Says Speed, as he removes his white helmut and takes a step closer to the robot’s hulking metal body. “There are plenty of question it can not answer. In fact, it can’t answer the most important questions, like what is the meaning of life? What is the most ethical thing to do in a particular situation? What is love, how can you prove that you’re in love or that someone loves you? Science may be a useful tool to answer certain questions, but it completely fails in the most important areas.”

The robots accordion style arms raise into the air, claws open as its blinking red speech unit broadcasts its deep mechanical voice. “I think that if you examine both the true definition of science, as well as, the questions that you believe science can not enlighten us on you’ll find that science does, in fact, have a great deal to say and offer to us. I would also propose that if there are certain questions that science can not answer, then there is also no reason to believe that any other method of knowledge acquisition has any hope of being any more successful.”

“You’re saying that intuition, spirituality, religion, mediation, and so on, have no value? That’s ridiculous”, said Speed. Even you can’t analyze all the available data necessary for every decision you make or every insight you have. If you tried to do that you’d never even make it out the space hatch every morning. You’d be paralyzed with indecision as you scan through all the available literature, contemplate moves and counter moves, and continually update your Basyean analysis algorithm, for even the simplest choice you had to make. I dare to say that even with the processing speed of your computer brain it would take you hours to decide if you should first conduct a soil analysis, inspect the Jupiter II perimeter for danger, or see if Dr. Smith is up to no good, when you activate your circuits each morning.”

The robot rotated its torso slightly “Negative, as usual Speed Racer, you’ve made many false assumptions, which lead you to your illogical conclusions. First, science is simply the most reliable method that you humans, or machines like myself, have to answers questions. Science is not a perfect system, but has a number of qualities that make it extremely useful and unique. It is a self correcting system so that any conclusions from a particular experiment may be updated by new data from additional experiments. It uses statistical methodology to come to conclusions that may be very different than “common sense” intuitions would predict. It’s experiments or observations can be designed to minimize the potential bias that are inherent in both the human and the machine mind.”

“But that still doesn’t mean it can answer any question.” Speed looked out onto the darkening horizon. The stars were beginning to appear in the sky and it was getting a little cooler now. “It has important limits. I might not expect a machine to understand that, but most humans realize that there are other ways of knowing. Science is limited to naturalistic investigations and explanations. If there are phenomenon outside of nature then science will always be blind to it.”

“While human intuition and meditation and prayer may result in some eventual decision making process, there is no reason to believe that any special knowledge is delivered via these methods. Take intuition as an example”, said the robot as it’s high frequency sensors were rotating near the head. It’s blinking lights now seemed quite bright as the fading sun became lost below the ancient greek sea . “It’s clear that humans have intuition about certain things. It’s likely that over the course of evolution Homo sapiens has evolved the ability to have insight into certain common situations. Intuition might give a human the feeling that there is some danger in this place, and that it would be best to leave. This could easily be an evolved trait to promote survival, and those humans that didn’t feel a sense of dread or doom in a particular situation may have been less likely to pass on their genes to subsequent generations if they were eaten by saber tooth tigers or killed by neighboring tribes because they didn’t pick up on subtle unconscious clues that their immediate environment was unsafe. Those systems built into your neural networks are nothing more than survival circuits and were never evolved to produce accurate information about the world. They only have to be correct often enough to enhance survival, but in no way need to be highly accurate, and can be prone to a high false positive rate. Even the software engineers that designed my computer brain, and other AI even more sophisticated than myself recognized the importance of building in a set of heuristics to prevent a robot from harm and damage without involvement of higher brain circuits. “

Speed took a few steps toward the water. “Look Robot, I appreciate that science has taught us about black holes in the center of galaxies, and quarks in protons and neutrons, and gives us the knowledge to build interstellar ships like the Jupiter II to travel to the stars, or to design the Mach 5 to win races, but it can’t tell us about meaning or purpose or the right way to live your life. You have to find the answer to those questions through other means.”

“In many situations there may be insufficient data to draw firm conclusions”, said the robot, “and in all cases science is clear that it’s conclusions are non absolute but simply the closest approximation to truth that we can come to at the time. Asking, “what is the meaning of life”, may be an empty and futile question, since it is quite reasonable to conclude that there is no objective meaning – that the question itself is meaningless. And in this way one does reach the limit of science, in the sense that science can not answer a question that has no answer. Many philosophers would conclude that we have to create our own purpose for our life, and that this self-created purpose can be very fulfilling and give our temporary existence a great deal of meaning.”

“What about things that we know are real but can’t be studied in a lab like love?” Speed put his hand over his heart. “How can science prove that Trixie loves me? I don’t need to be put in an fMRI scanner to know. I know that she does but there is no test that can show something so important and invisible as love.”

“Love is a human emotion”, the robot said. “There is sufficient evidence to conclude that it is also present to some extent in other complex animals, especially higher mammals. While I don’t have that emotion built into my AI circuitry, there is clear scientific evidence that love does exist as a property of the central nervous system of certain animals, like humans. There is no evidence, however, that love exists outside of these systems. In other words, there is no proof that love is a force in space or would exist if there were no life or intelligent beings in the universe. Emotions, like love can be studied in the lab. Their effects on human behavior can be observed, measured, classified, and understood, in terms of underlying mechanisms. Based on that understanding, predictions can be made as to effects on future behavior or activities of those afflicted by such emotions. You can’t “know” that Trixie loves you, but you can have a high degree of confidence that she does based on experience and observation. An independent observer, such as myself, might come to a similar conclusion based on a careful inspection of facial expression, body language, speech patterns, and so on. The level of confidence might be improved further if I did indeed scan Trixie’s brain to examine blood flow patterns and oxygen consumption in specific parts of the brain while she was looking, thinking about, and interacting with you.”

Speed circled around the robot as the robot rotated its body without moving its legs. “Well, lets say that for the sake of argument “, continued Speed, “there are ghosts. You know, some kind of spirit with an intelligence of some kind that can haunt a house or drive an invisible ghost race car. Science could never find that because it is only designed to look for natural causes, and the scientists themselves would never believe in ghosts so wouldn’t design an experiment to test for it. You have to admit that is true.”

The robot answered. “Speed Racer, if there is another type of reality that exists, that has some form of interaction with the natural world then that is a scientific claim. Whether that claim involves ghosts, spirits, ESP, angels, miracles, or so on. If it affects this world it can be studied in some way by the scientific method. While extraordinary claims require extraordinary evidence, to quote Carl Sagan, scientists follow the data. If there was sufficient and reproducible effects that could best be explained by ghosts, then that hypothesis would have to be seriously considered. So far, that type of evidence has never been reliably demonstrated which leads scientists to conclude that any supernatural phenomenon seems highly unlikely. It can never be fully ruled out since additional evidence might surface at anytime and in science one is always open to new evidence.”

“So you are saying that science has no limits?” Speed said, squinting into the robots bubble head.

“Not necessarily”, replied the robot. “There may be physical limits that science will never be able to penetrate. If quantum uncertainty is built into the very fabric of space-time we will never have a full understanding of the quantum state of an object. In other words we can’t know both an electron’s position and momentum with full certainty. We may never be able to probe matter at the smallest Planck scales since that may take more energy than is available in the entire observable universe. It is also possible that our minds might have a certain limit in which we simply can not understand anymore beyond a particular point. Some of those limits could also be imposed by physical limits so that even the best designed computer brain might never be made intelligent enough to grasp the most fundamental truths of the universe. Your pet chimp Chim Chim can never be taught to understand calculus because it’s brain is just too simple, but there may be no plausible brain that could fully comprehend all aspects of nature.”

Speed looked down at his feet. “Even I had trouble with calculus. Trixie had to tutor me through it. I see what you’re saying Robot. I’ll consider your points. I feel like we’re being pulled back to our worlds again. I’m in the middle of a big race and the Car Acrobatic Team was trying to finish me off. I’m sure I’ll see you again.”

“Good luck in your race Speed Racer”, said the machine. “I was in the middle of searching for Penny Robinson who is lost on the planet we are stranded on. I must help find her. Until we meet next time, Speed Racer.”