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.

You Sciency Dog You

Molina the science dog says:

Susie was a chemist, but she is no more.  What susie thought was H2O was H2SO4.

Why the concept of species is more fuzzy than you might think

By Rich Feldenberg:

The term species is viewed as a fundamental unit in biology. We are the species Homo sapiens, and we love to classify ourselves and other creatures into unique categories, giving them qualities that set them apart from other creatures. Charles Darwin’s evolution by natural selection gave the first proofs that all living organisms today descended from a common ancestor, which branded into an ever growing number of different evolutionary paths, resulting in a tree of life.  The trunk being the last common ancestor (LUCA) and all the tiny twigs at the ends representing all species that have ever existed. But is this really an accurate view of the living world – each species of organism occupying its own unique little cubby, completely distinct from it’s fellows in the cubbies next door? We have learned a lot since Darwin’s important discovery of Natural Selection. Modern biology tells us that, while evolution is on firm scientific ground, the concept of the species is less so. We humans have a tendency to think in a discontinuous way – that things do fall into distinct categories – that there is a separate essence that each thing has unto itself. That may be one reason why evolution is a difficult concept to accept for some people, because if each thing has it’s own essence of being, you can’t change it into something else. This idea was demonstrated in an experiment where children were told a story about a witch that turned a frog into a rabbit. The frog now looked like a rabbit, acted like a rabbit, preferred to eat carrots and not flies, wanted to hang out with other rabbits, but when the children were asked if this animal was now a rabbit they said it was really a frog. It’s underlying froggy essence could not be altered by the witches spell.

It turns out that the concept of species is really not a discontinuous one at all. It is a continuous variable, and that may be a difficult idea to wrap your head around. In medicine some diagnoses are continuous and others discontinuous, and in some others it may be difficult to know for sure. For example, having 6 fingers on your hand is discontinuous (you either do or you don’t), but systolic blood pressure is a continuous value, with a range of anywhere from 0 to somewhere quite high like 250 or perhaps rarely 300, with most people being in a certain range, like from 100 to 140. So why is the species also a continuous variable? Isn’t a rabbit a rabbit, and a frog a frog? Certainly a human is a human, and not a chimpanzee, right?

Well, keep in mind that names are just there for our convenience. How close they approximate reality may vary depending on the purpose of the name, and how good we are at understanding what we are describing. Ideally, a name would completely describe reality, but that will never be the case because a name is just a short hand way of talking about something else. Species tells us about taxonomic ranking. This is meant to help us determine which ancestors all the members of the species have in common, and how closely related those members are to members of another species. The problem arises in that the there is no defined line in the ground where one species ends and the next begins. One definition of species asserts that members of one species can not reproduce to have fertile offspring with members of any other species. This definition isn’t technically correct. The reason that this seems true most of the time, is that the many of the ancestral species happen to have died out, so it creates the appearance of very distinct groups of organisms (each in a separate and walled off little cubby).

Every generation is the same species as its parents and the same species as its own offspring. If this is true how could new species arise? It is precisely because the changes that occur due to evolution do so over much longer periods of time than a mere few generations. An organism could reproduce with a member of the prior generation, and if transported back in time to members from tens or hundreds of generations prior. At some point, however, there will be enough structural and/or behavioral differences that reproduction would no longer be possible.

Say that we took an organism back in time (it could be any organism, even a human). When we took him or her back 50,000 generations we find that he/she was able to reproduce with the contemporary population, but couldn’t reproduce with the individuals from 100,000 generations earlier. Now if we go back 50,000 generations from our starting point and take a subject from that era (one that could easily reproduce with our original organism) and then take him or her back to 100,000 generations before our starting point (50,000 generations before this individuals time) we find that it can reproduce with an individual from that long distant time period. So the original could reproduce with a subject from 50,000 generations ago, but not 100,000 generations ago, and the individual from 50,000 generations ago could reproduce with one from 50,000 generations ahead or behind its own time.

Since in the real world, those ancestors are mostly extinct it give the illusion of a discontinuous landscape of species. Richard Dawkins gave an excellent example in his book, “The Ancestors Tale” when he described ‘the salamander’s tale’. In that example Professor Dawkins described several species of salamander that live along a ring of high elevation in Central California. The ring forms a physical geographical structure that makes the species adjacent to any salamander’s location available to them, but prevents the species from interacting with species on distant parts of the ring. At the southern end of the ring are two distinct appearing species Ensatina eschscholtzil and Ensatina klauberi. E. eschscholtzil is brown and lauberi is spotted, and the two species, while in contact with each other do not interbreed – the very definition of separate species! That’s all well and good except that as you go up north on either side of the ring there are more species still, and each of these can reproduce with the species neighboring it.

It’s likely that the ancestral species arrived at some time in the past in the north. Two descendant populations emerged, one going south by the eastern route and the other going south by the western route. If all those other species on the ring had gone extinct we would be left with two species that could not interbreed and there would be nothing very special about the story. Those other species did not die out, however, and there is a continuous ring of salamanders that can reproduce with others of similar species, except in the case of the two southern species. As Dawkins says in the book, “Strikes a blow against the discontinuous mind”. The situation for these salamanders reveals what the situation would be like for any species (human included) if all of our ancestors were alive today. There would be a continuous stream of organisms that can interbreed with those close to them in time, but only over longer time scales do differences add up that make them distinct enough that interbreeding is no longer possible.  The sides of the ring represent a common ancestor, diverging and over time becoming two separate species, but having a path of “able to interbreed” individuals all the way down.  

In another post, I’ll illustrate another problem with the “tree of life” concept.  In actuality the tree concept is complicated by “lateral gene transfer” – basically genes being swapped by other organisms of different types.  This is very common in bacteria, but also seems to happen to some extent in more sophisticated organisms.  In any case, the idea of species should be used as a useful placeholder, but has important limitations.

Reference:

1. Species, Wikipedia.
2. “The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution”, Richard Dawkins. 2004.

3. Another clever Mesign by Mother Nature.  Darwin’s Kidneys.  July 8, 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.

Does Enceladus’ alkaline ocean make it friendly to life?

Recent data sent back to us by the Cassini space probe as it samples the geyser water being shot into space at Saturn’s moon Enceladus, has determined that the moon’s subsurface ocean has a very high pH.  The pH is estimated to be around 11 or 12.  This would be considered extremely alkaline, but the team analyzing the data concludes that this might improve the odds of supporting life.  They point to the alkaline hydrothermal vents, such as The Lost City, on the ocean floor of earth, where warm alkaline fluids flow out into the cold salty deep.  There is some thought in the astrobiology community that life on earth may have originated in a similar alkaline vent environment 4.5 billion years ago.  The difference, however, is that on early earth the alkaline vent fluid was flowing into an acidic ocean, with a thin mineral wall separating the fluids and allowing a proton gradient to form.  It was this proton gradient that generated the energy necessary to transport electrons from molecule to molecule.  This is exactly what living organisms do to generate energy – they pump protons across a cell membrane, transport electrons to an ultimate electron acceptor (oxygen in our case), and use the proton gradient to generate ATP (the energy currency of the cell).  Cells do the biological equivalent of what the alkaline vents are doing geochemically.  For that reason I wonder if the high pH of Enceladus’ ocean really would support the origin of life since it doesn’t necessarily imply situation where a proton gradient would occur.

 

Reference:

How Friendly is Enceladus’ Ocean to Life?  Astrobiology magazine.  Feb. 4, 2016

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.