Genetic Entropy

I hope you’ve read all the articles so far because I’m taking it up another notch. If you haven’t already I suggest reading the short article on Facts and Meanings as well as the ground work set down in the introduction section. Genetic Entropy was really the one concept that got me to really start looking into things, and it was one of my primary reasons for starting the site.

This article is basically a summary of a book called “Genetic Entropy and the Mystery of the Genome” written by Dr. John C. Sanford. I have to warn you that I was utterly devastated after reading this book. It utterly crushed my view of the future of humanity and the world. If you are having a bad day or have something important to do soon, I would suggest you stop reading and come back at a later time. Emotions aside, we have made some very important discoveries in genetics that really deserve attention and consideration. Dr. Sanford has posed the question “Why don’t we see this in the news headlines?” the answer is that the truth can be uncomfortable.

Evolutionary Background
To give you some context, let’s start off by looking at what has been called the Primary Axiom of Neo-Darwinian Theory. No matter what the specific models or ancestry that are given, the underpinning idea of Neo-Darwinian Theory is that mutation and natural selection combine to cause evolutionary progress. This is how we went from single celled organisms to the dominant species on the planet. Mutation and natural selection can be thought of as a balance. Mutation adds in random variations in the genetic code and natural selection is simply the process by which more fit, healthy organisms are more likely to produce. By itself, natural selection cannot create any new variation, it only eliminates variation. If you are sickly, or have a lethal mutation, natural selection says you will probably not pass your genes on to the next generation. In this view, evolution depends on balance between chaos (mutations) and static order (natural selection).

So what happens if things are out of balance? If natural selection is too strong, or if mutations are practically non-existent then evolution grinds to a halt. There is no new variation, and what varieties do exist would be whittled down to the most “optimum” until you have a basically homogeneous population. If, on the other hand, mutation is too high or natural selection stops (like small populations) then bad mutations start piling up and the species degrades. This is called Muller’s Ratchet which eventually leads to Mutational Meltdown. It is something that we have observed in endangered species and a problem that threatens all species with small or in-bred populations.

Genetics Background
Now that you have some context let me explain two other key points. First off, good mutations are exceedingly rare. They are so rare in fact, that it is hard to get an exact number on how rare they are. In comparison to nearly neutral and bad mutations a fair number is in the order of 1 in a million (1,000,000) mutations actually being beneficial. That means that in general we can consider mutations bad and natural selection must eliminate virtually all mutations.

The second item is what is commonly referred to as Junk DNA. Junk DNA is simply the name that we assign to portions of DNA for which we do not know their function. Originally it was said that about 98.5% of our entire genome was junk DNA. What this translates to is that for 98.5% of the genome we have no idea what it does. Specifically, the assumption was that all functional DNA should encode for proteins so anything that doesn’t encode for a protein must not do anything. Recent research has shown that this assumption is wrong because we have discovered sequences that act as regulatory mechanisms for protein production and respond to the cellular environment. Regulatory sections shrink our supposed 98.5% junk. No one is entirely certain at this point how much of our genome is functional, at this point a big question mark still floats over much of the genome. The important thing to note is that as our knowledge of genetics progresses the amount that is labeled as “junk” is gradually shrinking.

Human Mutation Rate
So given all this information, scientists have been very interested in finding out exactly what the human mutation rate is. The global average of birth rate is 3 children for every 2 people. So if natural selection were laser accurate that would mean that it could hold ground, with no evolutionary progress, with a mutation rate of 1 mutation in every 3 people. This would be just low enough that we could maintain our population at a steady rate, there would be no room for population growth or evolution. A high mutation rate in normal models would be around .1 or 1 in every ten individuals. As the mutation rate gets higher it necessitates a higher birth rate to maintain a population. In a simple model, the necessary birth rate dependent on the mutation is x = 2/(1-m). So with a mutation rate of .5 half of all people would be mutant and thus we would need a birth rate of 4 children per woman to maintain a population that was not accumulating mutations. As this number approaches 1 mutation per person (that’s everyone) you can no longer select any individual who does not have a mutation, even with perfect accuracy in natural selection. Mutations rates with multiple mutations per person necessarily lead to a growing number of mutations, which in experience, leads to reduced fitness and eventual species extinction over long periods of time.

In 2000, Dr. Crowell, from the University of Arizona Department of Ecology and Evolutionary Biology, published a paper estimating the human mutation rate at around 175 mutations per person per generation. Kondrashov, from the National Center for Biotechnology Information, published a paper in 2002 estimating the rate of point substitution mutations alone at 100 per person per generation. This high mutation rate is commonly accepted in the scientific community today. Kondrashov’s numbers only include point mutations. They do not include numbers for deletions, insertions, duplications, translocations, inversions, macro-mutations and mitochondrial mutations. There are also sections of DNA called microsatellite regions that have mutation rates easily 1,000 times higher. The true human mutation rate has not been measured exactly – it could easily be in the thousands – and we can observe that it far exceeds comfortable numbers like 1 in 10 individuals.

It would appear mutations happen faster than natural selection can keep up with. Our scale is unbalanced; we are not evolving, but degenerating. What are the implications of this? It means that every generation that is born has 100 more mutations than the generation before it. We are all highly mutant, and not in an X-men kind of way. We judge what is ‘normal’ off of each other. So that means that anything that affects the entire species is considered normal. How many of us have bad vision, allergies, mangled toes, lopsided ears, joint pains, skin spots, jaw pops, back problems, heart problems, and let’s not forget cancer… We are all unhealthy, unfit in one way or another, and it’s sad to admit it, but that is the current state of life. We’ve … Got … Problems. Genetic entropy is all around us, it is so ubiquitous that we don’t even notice it anymore. Blinding Light. The explanatory power of genetic entropy is comprehensive.

Nearly Neutral Mutations
So far we’ve assumed that natural selection is laser accurate, that would allow it to select away one mutation per generation. But Natural Selection operates at the organism level and mutation happens at the molecular level. Let that one sit for a moment. Natural selection is on the level of organisms feeling attracted to one another and mating. Mutation is within a stone’s throw of the small units of existence that we know about. As you read this, 10^24 atoms of your car just turned to rust. Are you going to buy a new car now?

Most mutations are nearly neutral, not entirely neutral but their effects are subtle enough that they are hard to select against, which makes the problem worse. You have a library inside you that is 6 billion letters long. If I go past rows of books, pull out a giant ladder, climb to the top and pull out a book, then I open that book and change one letter, does that matter to the library? Not really. Does that make it entirely neutral? There is an important difference between near-zero and definitely zero importance. If I go in and make 100 typos in the library everyday for a thousand generations you will start noticing a decline in your library user review (fitness). Can this problem be solved by throwing out entire libraries to fix typos? Not really. This problem has been recognized by evolutionary geneticist Kondrashov in his paper Why Have we not died 100 times over?, often called Kondrashov’s Question.

Family History
Consider your own family history, did your parent’s quirks keep them from reproducing? How many quirks can go unnoticed entirely until they are passed on to the next generation. Since I can’t speak for your family I’ll give you a couple examples in my own family. My grandfather was 6′ 4″ and died of an enlarged heart when he was 40. My mother has a not so neutral problem with scoliosis (deformation of the spine) that was passed down to all of her sisters. Thanks to corrective surgery you could never tell today. Having back problems didn’t keep her from having kids, a fact I’m grateful for, but there’s a risk it could get passed on to the next generation, maybe silently. “The fact that the spine and spinal column ever form correctly is amazing given the complexity of the process from an embryological standpoint” (iScoliosis). “The gene that causes scoliosis remains undiscovered”.

I myself have a deviated septum that not even my wife mentioned until after we married. “It’s called tact, you don’t mention other people’s deformities,” according to my wife. In evolutionary terms traits not under selection can drift to fixation (everyone has it). “Estimates are that 80 percent of all nasal septums are off-center, a condition that is generally not noticed.” I also have allergies, some of which I got from my dad, some of which are new that I can pass on to any children I have.

Conclusions
So does this mean we should not have kids? Certainly not. Life is full of risk, and the reason we get up everyday is because somehow we believe that the risk is worth it. Allergies and bent noses don’t make life not worth living, it just means that we should have a healthy respect of our own mortality. We are finite creatures and no matter how cool you are, we all eventually succumb to the entropy of our own bodies. It’s what we do with our time that matters.

In retrospect, this idea really shouldn’t be that shocking. Entropy is a law of nature and everything that we see around us is dying, decaying or falling apart. I have never seen a single thing in all my life that is immune to entropy, it affects everything. My 40 year old apartment naturally degrades, the road outside must be constantly patched, every human ever born eventually dies, and the sun itself will eventually die out.

For more Info
If you would like a more in-depth discussion on Genetic Entropy I would seriously recommend getting the book. This article barely covers up to chapter three. Dr. Sanford addresses every imaginable objection in his book in enough detail that it has (maybe unfortunately) silenced every intellectual criticism so far. In particular, he covers the challenges with natural selection in much more detail than I have. He discusses problems with proposed solutions in Natural Selection, Artificial Selection (Eugenics), problems with noise, cloning, evolving genes, Crow’s solution, macro-beneficial mutations, and historical evidence. He also answers questions like how many mutations can be selected against simultaneously, and other possible objections. If you are a super-poor college student and you are interested in looking into this I will buy you a copy. This isn’t a book promo, this is real life, and I think this is important to know.

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(Contrary to the idea that all humans preceding us were ‘primitives’ there is a fair amount of evidence to suggest that our ancestors were more genetically fit in the past. Can you think of any “myths” with long lived, smart, technologically advanced people in them? I’ll be looking at a couple in future articles.)

Earth’s Magnetic Field Decay

In the previous article I talked about the irregular movement of the poles and how many magnetic pole reversals are known to have happened throughout history.

Physics Lesson
Something that I haven’t seen many people acknowledge is that these pole reversals require energy. I poked around on YouTube looking for a demo video of the nerdy professor flinging himself off his chair by reversing a gyroscope. Unfortunately, I’ll have to post that later. I did find this video which shows how much gyroscopes resist change when the gyroscope bends sideways over empty space without falling. The reason for this is Newton’s first law of motion, “An object in motion will remain in motion unless acted upon by a net force.” Change in motion requires energy and energy has a tendency to dissipate, not concentrate. This is the second law of thermodynamics “The total entropy of any isolated thermodynamic system tends to increase over time, approaching a maximum value.” In English that means things tend to go from a state of higher order to greater disorder. Things fall apart, wind down, break down, and grind to a halt.

Our magnetic field is no exception. The Canadian Geologic Survey says “Magnetic fields decay, and we can show that the existing geomagnetic field would disappear in about 15,000 years unless there were a mechanism to continually regenerate it.” This is a reference to the current theory of where our magnetic field comes from. The restriction that the system must be sustained over the course of billions of years is applied to any proposed model. This ensures that it lines up with our geologic time scale, which in turn lines up with the evolutionary biology model, which is measured by radioisotope dating. “Many mechanisms have been postulated to explain how the magnetic field is generated, but the only one that is now considered plausible is analogous to a dynamo”. It makes sense to make scientific theories line up with existing models, I just want people to understand the chain of assumptions and contingent truths. The data is not allowed to speak for itself, it is not examined in a vacuum. So let’s just look at the data.

Data
“For example, the total intensity at Toronto has decreased 14%, from approximately 64,000 nT to 55,000 nT, during the last 160 years. ” – Canadian Geologic Survey – Secular Variation

“Archeomagnetic evidence shows that this decrease has, in fact, been going on for the last two thousand years, and that the strength of the dipole now is only about half of what it was two millenia ago. The dipole strength is currently decreasing at a rate of about 6.3% per century, and were it to continue to decrease at that rate, the strength would reach zero in approximately 1,600 years.”

” It appears that only about five percent of neutron stars, the most strongly magnetized, undergo significant field decay;” – Neutron Star Field Decay could impact what we know.

“We also know from studies of the magnetisation of minerals in ancient clay pots that the Earth’s magnetic field was approximately twice as strong in Roman times as it is now.” – British Geologic Survey, Magnetic Flip

“Human beings have been on the Earth for a number of million years, during which there have been many reversals, and there is no obvious correlation between human development and reversals. Similarly, reversal patterns do not match patterns in species extinction during geological history.” – same as above.

“Satellites in low-Earth orbit over Southern Africa are already showing signs of radiation damage suffered as a result of the Earth’s magnetic field weakening above our part of the planet.” – Sunday Times, New Zealand (quoted in archive).

Amateur Project to track magnetic field change – http://www.rense.com/general51/mag.htm

Conclusions
Well, I’m not really drawing a definite conclusion. Just think about the possibilities and the underlying assumptions that hold them up. Does obscure subjects like geomagnetism really matter to you personally? Well, if you walk outside one day and see an aurora borealis above your head in the middle of the day, then suddenly it becomes the most relevant thing in the world. You’ll be able to tan in no time.

No matter what the generation mechanism of the magnetic field it is still subject to entropy and thus decay. Even if the field is able to wondrously re-generate itself, that regeneration takes energy on a global scale. The field would naturally decay by itself if it were static, such as the iron core being a giant bar magnet. The fact that it flips, moves, and jerks around means it’s using up even more energy. Some day that energy is going to run out.

Earth’s Magnetic Poles

In Star Trek, the USS Enterprise travelled through space independent of any planet. They sustained themselves using advanced technology. One of these technologies was deflector shields, for warding off all the lethal solar radiation (and being a good plot device). On our nice little planet Earth, we also have a shield to protect against solar radiation. The Earth’s magnetic field serves as a shield against high energy particles blasted out from the sun continually. Without it, well we’re not quite sure, but it’s bound to be unpleasant.

The image on the right shows the magnetic field. The direction of the sun can be seen because the field is compressed by solar wind. Also, notice that the Earth’s magnetic field is far larger than the planet. David Coppedge, from the Jet Propulsion Laboratory pointed out “Shuttle and space station astronauts operate within Earth’s protective Van Allen belts and gravitational field. So far, only the Apollo astronauts have ventured outside our safe bubble into the cosmic shooting gallery. The longest mission, Apollo 17, lasted only 12 days. Fortunately, none of the flights occurred during a solar flare. Had the space travelers received such a blast, they would have been dead within minutes.” This is a serious danger for a mission to Mars because of the extended length of the trip.

So now that we know why we care about the Earth’s Magnetic Field, what’s it up to these days? At least for me, I pictured the magnetic field as being as stable as the rock I stand on. (The Earth is a gelatinous glob of molten lava with a thin film across the surface, ponder that). So how do I say this? According to the Canadian Geologic Survey, as of 2001 the magnetic north pole is moving at 40km per year. More over, it’s not really moving in a predictable pattern in the long run. It staggers around Canada and the Arctic, seemingly at random.

Some people have taken all of this recent movement as an indication that we are very close to undergoing a pole shift. Geologic evidence shows that the poles have flipped multiple times throughout history. So the north pole was south and so on. Scientists were originally saying “don’t worry about a pole flip, they take thousands of years and the field just goes down during that time.” Of course, then the implications of that sink in. The Observer has a couple of articles discussing the implications of field collapse using computer simulations. Then I find more scientists with complex computer models showing how the Earth will be saved. Problem is, I’ve found two of them, and they contradict each other. I’m an amateur at a lot of this, but one thing I do know are computer simulations. I’m a computer programmer, in fact I’ll be writing computer simulations this summer. Computer simulations are entirely dependent on the assumptions you encode in them. They’re useful but do not think a computer is any more impartial than a human beings, they’re just fast math calculators.

So where is the real science in all this? It’s hard for people not to assign meaning and emotional value to subjects like this. The most neutral, scientific position is probably also the least helpful “Gee, that’s odd.” The natural tendency is to attract to the most comfortable position, or what benefits us the most. The truth of the matter is that our lives depend on something going on inside of the core of the planet. Something that, when we’re really honest about it, we barely understand.

(More Research on Earth’s Magnetic Field in the next article.)

Carbon-14 Dating

Carbon-14 Dating, or just Carbon Dating, is an extremely useful dating method that’s been in use since 1947. Carbon Dating is part of a larger field called Radioisotope dating which is our primary method for assigning date to fossils, rocks, skeletons, and parchment. “Before the 1940s, scientists had no accurate way of determining the age of fossils or other ancient objects” notes Lemelson-MIT. Radioisotope dating is, to my knowledge, basically the only way that we date fossils, rock layers, and by extension the age of the Earth. Since it is so crucial we’ve gotten very good at it. We have advanced machines with amazing levels of accuracy and procedures to avoid any contamination. So let me explain how carbon dating works and then we’ll get on to some interesting stuff.

Carbon-14 is a radioactive isotope of regular old carbon. From what we know, carbon-14 is created in the upper atmosphere by solar radiation colliding with nitrogen to produce carbon-14. It then drifts down through the atmosphere and is absorbed by plants, which are eaten by herbivores, then carnivores, and it enters the cycle of life. Living things sustain a present day level of about 1 carbon-14 atom in 1 trillion atoms. When something dies, it stops taking in carbon-14 by breathing and eating, so the clock begins. Carbon dating allows us to track the time of death with great accuracy because it has a very short half-life. Half the amount of carbon is depleted every 5,730 years. This means that for a finite 1 gram sample there will be absolutely no carbon-14 left in the sample after around 230,000 years. So these are the base assumptions for all radioisotope dating (remember axioms?):

• Original Amounts known (present day values used)
• Rate of decay must be constant (present day measurements used)
• Closed System assumption (rocks should not cross-contaminate)

As I mentioned, we’ve gotten really good at this radioisotope dating thing and so scientists have developed “Isochron Plots” to test assumptions 1 and 3. Rate of decay isn’t really double-checked but it is based on the basic atomic structure of the atom. So now you know more about radioisotopes than 99% of the world.

Here’s the interesting part: when scientists go out and sample every fossil, rock, peice of coal, marble, wood, or any fossil they find low levels of Carbon-14 in them. Now remember, anything past 250,000 years (or earlier) should be totally carbon dead if the assumptions hold. This was originally attributed to limited machine accuracy. But machine accuracy has improved, in fact, scientists have known about this problem for over 20 years. The obvious conclusion was that something they were doing was contaminating the samples (assumption 3). So they scour the lab, set up the most strict procedures. Before doing a test they dunk a sample in acid, then base, then acid again to remove any outside contamination. What they found is that the carbon levels remained. Eventually, people working at the carbon dating labs concluded that the samples must be contaminated out in the field, before it ever got to the lab, and dropped the issue. Carbon dating is only used for things considered recent for this reason.

It took a group of very unorthodox scientists called the RATE team to look at it again. This is why I like people who go against the grain. They came up with the idea of testing the contamination assumption by carbon dating diamonds. Diamonds are the perfect choice; they are the hardest substance in the world, they’re made from carbon, they can’t be infiltrated by water, and they’re assumed to be ancient, dating back to the origins of life on this planet. They collected multiple diamonds from multiple layers in different mines all around the world and selected the world’s premier carbon dating labs to have them tested. No one had bothered testing diamonds because they are very hard to test and should be entirely carbon-dead. What they found is that diamonds have a similar range of carbon-14 as most fossils do. If you use uniformitarian assumptions we can calculate the age to approximately 58,000 years old. That’s a big difference from the expected 1-2 billion years. (poster)

There’s four definite possibilities that I can see from this data. One or more of the 3 base assumptions are wrong or if all assumptions hold, diamonds are really 58,000 years old. Interestingly, no one is claiming that all diamonds are 58,000 years old because it doesn’t fit with anyone’s model quite right. At the very least, this data should call into question the unswerving accuracy of radioisotope dating methods. Being off by a factor of 1,000 is not acceptable in most academic circles.

(I’ll be getting back to this topic in a later article.)

Further Comments: I had a friend bring up the issue of statistical outliers.  These are common occurrences of things that do not agree with the general trend.  Most of the time these outliers are thrown out as errors.  He pointed out that if you threw out the main body and instead kept any outliers that agreed with you then you could make the data say whatever you wanted.  First off, people are dumb but I’d think that even a very biased person would notice throwing out MOST of the data that they personally generate.  So this is essentially based on the conviction that these people are being dishonest.

That aside, I asked Dr. Baumgardner (primary researcher) about this directly.  He said that there actually WERE some outliers in the data that he threw out because he felt they were errors.  Well I guess we caught them.  Except for, the samples (a minority) he threw out actually showed younger dates than the rest of the group.  So he’s actually showing the oldest dated samples.  The samples that were thrown out dated to closer to 11,000 years, which would be much easier to reconcile with a young earth model.  This batch used a different cleaning process which he believed was suspect because one of the ingredients contained carbon.  Instead he kept the ones that, while presenting trouble for an old earth, also didn’t fit perfectly with his model.

I think the main criticism that can be leveled at this point is that they haven’t tested ALL the diamonds in the world, so you can’t prove a non-existence.  The diamonds they did test were from all over the world and different beds and elevations, even some from alluvial deposits.  I’ve heard other researchers have confirmed these results but I went looking and couldn’t find anything else.  Usually private companies, like carbon dating labs, don’t publish papers in journals, it’s not their primary motivation.  And to anyone who would like to make up a story about how diamonds are a special case and how C-14 dating still works on everything else, remember this was made to test why all fossils have relatively young C-14 dates.

Facts and Meanings

This next section is entitled “We’ve Got Problems” or put another way, we’ve got serious impediments to our ability to see the world in a neutral light. Not only that, but I’ll be looking at some evidence that doesn’t line up with some people’s if not everyone’s beliefs.

I’ve been held up on writing the next couple articles because in doing research and finding primary sources I’ve run into a bit of a firestorm on the internet. What I’ve found is that it is very threatening to cite a fact without assigning it a meaning. Said a different way, every number, study, or graph is implied to have a deeper meaning that must fit with the cohesive whole. This seems to be a universal theme in human beings that deserves some self-examination.

Think of the stars in the sky. They are points of light distributed (almost) randomly with varying brightness and color. To the best of my knowledge they are not arranged in a particular fashion with regards to Earth yet we form constellations out of them. We form constellations by connecting the dots of all these stars, that’s implying meaning. Then we get this funky wireframe which we decide is a very Earthly shape, more meaning. Then we tell a story about that Earthly shape, then we link that story in with a whole mythology of stories to form a network of meaning. Then an American comes along and stamps the meaning with a (c) symbol meaning they can sue you for meaning something else with their meaning.

…

So what’s the meaning to all this meaning assigning? Well, that’s probably just perpetuating the cycle. Facts exist by themselves, whether we give them a meaning or not. The meanings that we give them also can’t change the facts. So no matter what you think of it, it’s a fact that humans assign meaning. Ponder that one for a while.

Does the line actually exist in this plot? What about the equation?

Other things to ponder:
Are there multiple levels of meaning?

Can you agree on some meanings and not others?

What would a school be like if they only taught facts and not meanings?

Is implying observations reflect reality a meaning?

Meanings bridge the gap between science and philosophy. Meanings are philosophical values that we assign to facts.

Further Comments: Ah, my little three circle interconnectedness diagram.  I meant well with that thing but it’s the last time you’ll ever see it I think.  The idea was to fill it in step by step.  So that people would have this great epiphany of the interconnectedness of everything.  I’d show the completed one but I think it got deleted in a harddrive format.  Microsoft trumps Ultimate Truth.

Something to note about Facts and Meanings: There are a nearly infinite number of facts.  There is a tiny tiny number of meanings that our brains will allow us to assign.  Therefore, working with our tiny, safe world of meanings limits the number of facts we need to consider down to only a grossly intimidating number whereas the total number of facts would make a person collapse in despair and die.  Survival mechanism.  Don’t think about it too much.  A pretty sure sign someone is going crazy or shifting worldviews (same thing from an outside perspective) is  that the facts they begin taking in and considering important starts growing or starts shifting.  Paranoid Schizophrenia is essentially when you start taking in too many “irrelevant” facts (like the arrangement of leaves on your front step) as important and start disregarding “important” facts (like what MSNBC says) as lies.  The way that we judge that this person has not found the Truth is that they become disfunctional.  The implicit assumption there is that knowing the truth will lead someone to be a functional individual.