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Offline marklawrence

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Why Evolution Is Wrong
« on: September 14, 2018, 06:07:55 PM »
Hi guys,

I'm writing a book. I'll be serializing it here. I'm not putting this here for debate: if you love evolution, there are a lot of books you can read, especially Why Evolution is True by Jerry Coyne, anything by Richard Dawkins, Undeniable Evolution by Bill Nye. I've read many of them, and have reasonable training in biology and in particular molecular biology.

You will not convince me that evolution is "true." I've disbelieved in evolution for several lifetimes.

This is not a book about religion or spirituality. It's a science book. I do not propose an alternative to evolution, and the argument that evolution is true unless I propose something better is no more valid than the argument that worship of the egyptian sun god Ra is correct unless I can propose something better. What I will be showing is that evolution by random mutation and selection cannot have happened in this universe, so either evolution is guided by some external force, or the universe is much, much older than we think. I have some opinions on these possibilities, but I won't be putting them in this book, as they are just as spectulative as evolution.

I'm putting the book up here so you can all be editors. I'll be particularly interested in comments on how I've done a poor job of explaining, or, perish the thought, anyplace where I'm wrong. "Wrong" doesn't mean you don't believe me, it doesn't mean you know a lot of college professors who taught you otherwise, "wrong" means you can show me a laboratory result that disallows my statement.

I'm very aware that this is a subject where people have deep beliefs and emotional commitments. In fact, that in and of itself is a sign that evolution has serious problems: there are no physicists that have a deep belief in the big bang or an emotional commitment to dark matter. There are just a bunch of physicists who think at our current levels of observation and theoretical understanding, those ideas fit the best.

Science is not done by voting, and the majority opinion is simply the current dogma. Einstein and Feynman were widely ridiculed when their theories first came out, but now we see modern physics as developing from Copernicus to Newton to Faraday to Einstein to Heisenberg to Feynman.

The topic of evolution will not be settled in my lifetime. I have disbelieved in evolution since I was 15; that disbelief is not going to change in the next decade or two.



Dedication

This book is for Sir Fred Hoyle, who first introduced me to the idea that evolution could be analyzed mathematically; to Fred Reed, who introduced me to the idea that there are a very large number of gaping holes in evolution; and for William Lawrence, who I hope will one day read this book and thereby have a much easier time learning biochemistry than I did.

Sir Fred Hoyle was a great scientist and a friend of mine. During World War II he worked in a lab on radar. After WW II he got interested in how stars cook up the heavier elements. He calculated that a hydrogen atom could hit a helium atom and make lithium, but the resulting lithium was incredibly unstable and would last only millionths of a second. He calculated that two helium atoms could hit and form beryllium, but again the resulting beryllium would be very unstable and last only fractions of a second. However, during these fractions of a second, a third helium atom could hit and product a carbon atom. There was still a problem: according to his calculations the resulting carbon atom was unstable and would not last long. Unless the carbon atom had an excited state at exactly the right energy, at exactly 7.6MeV. Then the carbon would be stable. In 1954 he said that his very existence was proof that this excited state must exist; otherwise there would not be enough carbon in the universe to form life. In 1957 researchers at Caltech found this excited state exactly where Sir Fred had predicted it. However, in the meantime Sir Fred had made a name for himself with other more controversial views. Sir Fred also estimated the probability that life spontaneously formed on Earth and found it was basically impossible. So he became a proponent of pansermia, the idea that Earth was seeded with bacteria from comets. He estimated that bacteria could not form in the universe in just a few billion years, so he invented a theory, continuous creation, which indicated the universe was eternal. On a radio program he was asked about the competing view that the universe had started 14 billion year earlier in some kind of massive explosion, and Sir Fred disparagingly called that theory "The Big Bang." The name caught on and that's still what we call this theory today. Sir Fred also became convinced that viruses that cause disease came from space, and that there was a God and this was all part of his eternal plan. The Nobel Prize committee found this and Sir Fred's enthusiastic drinking all to be too much to swallow, so in spite of the elegance of Sir Fred's prediction of the excited state of carbon and the state subsequently being found, they decided they simply could not give a Nobel prize to such an apparent nut case. After Caltech confirmed his predictions, Sir Fred was given money to start a lab at Cambridge and he hired a physicist to work with him in his lab, William Fowler. In 1957 with Fowler, and Margaret and Geoffrey Burbridge, Sir Fred published a paper that accounted for the production of most of the heavy elements in stars. The Nobel committee, seeing that they could not ignore Hoyle's important work, gave the 1983 Nobel Prize to Dr.Fowler. But with no mention of the troubling Hoyle.

« Last Edit: September 15, 2018, 12:16:03 AM by marklawrence »
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Offline marklawrence

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Re: Why Evolution Is Wrong
« Reply #1 on: September 14, 2018, 06:11:22 PM »
Why Evolution is Wrong
by Mark Lawrence
Introduction

There is a coherent plan to the universe, though I don't know what it's a plan for.
-- Sir Fred Hoyle, discovered how stars create elements.

For several years I have sat quietly and watched as many in my country, and many with the loudest voices, have turned against religion and spirituality. It must be admitted that religion has made mistakes in history, but I deny strongly the viewpoint that religion and spirituality are forces for evil; to the contrary, I think there's a reason they have been the central organizing force in human culture for tens of thousands of years.

I consider myself a scientist; certainly I'm well trained in the sciences. I appreciate the scientific perspective, and I appreciate what science has given to humanity. Science has given us modern medicine - a simple cut is no longer life threatening. Science has changed agriculture so that billions can live. Science has given us near instantaneous communication with the internet; now a huge and growing fraction of humanity has a voice. Science has taught us about the universe, and about the almost incomprehensibly tiny corner of it in which we live.

But now I find to my dismay that science is being used as a weapon. Evolution is being taught in our schools as an established fact when it's nothing of the sort; and religion has been banished from our schools because it disagrees with much of evolution. I find this extremely distasteful, especially because as a scientific theory evolution is a near complete failure. When evolution is taught in schools it is as a religion in competition with all other religions - evolution is not something you can prove in the scientific sense, but rather something in which perhaps you choose to believe. I have no problem with the idea of people believing that a lightning bolt hit the ocean and life happened, but that's not science and it didn't happen any more than the Easter Bunny left chocolates in your living room or Santa Claus came down your chimney.

The scientific truth is that it is mathematically just short of completely impossible that life evolved from nothing in our universe. And I'm by no means the only one who believes this - we will see in this book that many famous scientists agree. On a scientific or mathematical level there can be little or no question that this universe was specifically created to hold life, and then was seeded with life. This process took an intelligence far superior to mine or any other living human.

Why was our universe created? I don't know. Personally, I believe there is a plan, but that plan does not fit in my head.

Why was our universe seeded with life? Why else would you make the universe?

Who did all this? Again, I don't know. I consider that to be far above my pay grade. Many call the creator God, or Jehovah, or El, or Lah, or Krishna; sure, a name is fine. But having a name does not mean I have an understanding of the techniques, motives or plan. However, on a mathematical level there can be no question that the purpose of this universe is life.

You have about 35 trillion cells in your body which share your basic DNA. The universe we observe is made of about a trillion galaxies, so your body has 35 times as many cells as the universe has galaxies. Each of your cells is made on average of about ten billion proteins; each galaxy in the universe contains about a hundred billion stars. So your body has nearly the same number of protein molecules as the entire universe has stars. Don't sell yourself short: the act of creating a living human, something your mother did in nine months while continuing to live her life, is equally complicated as the act of creating the entire universe of a trillion galaxies each with a hundred billion stars.

What I do know is that science, in my opinion, teaches us reverence for our Creator, and it's a travesty when science is used as a weapon against our Creator. It's my hope that with this book I can contribute some understanding that the evolutionists have an agenda, but they do not have science or mathematics on their side.

This is a science book. I've tried to make it very accessible to everyone, but there is a bit of math and chemistry in it. This is necessary to prove my statements and conclusions. I won't tell you stories to try to convince you that my views are reasonable; I'm going to do math and show you that my views are mathematically inescapable.
« Last Edit: September 15, 2018, 11:00:57 PM by marklawrence »
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Offline marklawrence

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Re: Why Evolution Is Wrong
« Reply #2 on: September 14, 2018, 06:16:31 PM »
Why Evolution is Wrong
by Mark Lawrence

ATP Synthase

Life did not evolve first on Earth. The DNA evidence speaks of intelligent, information-bearing design.
-- Sir Francis Crick, Nobel prize 1962 for discovering the form of DNA


ATP Synthase

The molecule in the picture is ATP synthase. You have about 35 trillion cells in your body which share your basic DNA. Each of these cells holds several thousand smaller symbiotic cells inside called mitochondria. Each mitochondria has several thousand copies of this ATP synthase molecule. So you have tens of millions of trillions of these molecules in your body. These molecules convert ADP, Adenosene DiPhosphate, into ATP, Adenosene TriPhosphate. Adenosene is the battery that powers your cells. The diphosphate form is when the adenosene battery is dead; the triphosphate form is charged up. The ATP synthase is the adenosene recharging station. ATP synthase is the world's tiniest motor. It spins at 6,000 RPM, the top speed allowed on your car's engine, except your car does it rarely when passing on the freeway and the synthase does it 24/7/365 non-stop. The F0 part of the synthase is embedded in your mitochondria cell wall and is the part that spins. The F1 part recharges three adenosene molecules per revolution. The synthase is powered by an electric current which is generated by some nearby molecules that take in oxygen and burn glucose (sugar) into carbon dioxide and electricity. Each cell in your body uses its mitochondria and synthase to recharge about 1 billion adenosene molecules per second. Synthase is an enormously complicated molecule, made up of about 6,000 amino acids or a bit more than 100,000 atoms. Later we're going to calculate that the universe could not possibly have randomly evolved any protein larger than 60 amino acids - ATP Synthase is 100 times larger than that, and would take unimaginably longer to evolve - much, much longer than the expected lifetime of the entire universe.

The exact structure of synthase has not been worked out, but it is already known that there are several amino acids which are critical: change their position by one spot or swap them for any other amino acid and the whole thing stops working. Take a piston out of your Toyota engine and substitute a piston from a Honda and your engine will die in under a second.

Suppose you took an engine from your Honda or Toyota back 100 years to Henry Ford and asked him to put it in a model T for you. This would not work at all. Perhaps he would manage to fit it into the engine compartment, but the first time you tried to drive the car the engine would rip off the motor mounts, the drive shaft would rip in two, and the rear axle would tear off the car. The Model T was designed for 20 horsepower, not 200. But actually your modern engine wouldn't even start: the modern engine requires 90 octane gasoline and in 1915 the best gasoline was about 25 octane. In the last 100 years engines, gasoline, motor oil, motor mounts, transmissions, drive shafts, axels, wheels and tires have all "evolved" together.

Now, suppose you took the ATP synthase molecules from your cells and substituted them into the cells of a cat. No problem, they'd work perfectly. Same thing for a fish. Or a tree. The only difference in plants is the electricity is supplied by the photosynthesis molecules. In fact, the molecules we have that convert glucose and oxygen to electricity and carbon dioxide are present in the plants, but they're run backwards to take in electricity and carbon dioxide and produce glucose and oxygen, which is then used to build more plant and make fruits and berries to bribe animals to spread the plant's seeds. The same ATP synthase molecules are in moss, fungus, amoebas, bacteria, all of them use the same molecule. Everything alive on the earth uses this exact same molecule. There are no alternative simpler systems, nothing we've found that looks like an earlier version. This is it. One solution, one time, for everyone. This is a centrally planned communist molecule at the very heart of evolution's competitive capitalist system. Which begs the question: who's the central planner?

If you look around you see that all animals are left-right symmetric, so you would expect there must have been a first animal that was left-right symmetric and we're all descended from that animal. It's thought this first symmetric animal lived about 550-600 million years ago. When you see every living thing on earth sharing the exact same ATP synthase, you think that the first critter to have this must have lived about 3.4 billion years ago. So evolution tells us that cell chemistry powered by the adenosene battery, the molecules that convert glucose into electricity, and the ATP synthase all evolved in the first 100-200 million years, and absolutely nothing changed in the 3.4 billion years since then. No improvements, no alternatives, no changes, no competing chemistries, nothing. It's like every car ever made shared the same exact engine, except instead of that being true for 140 years it's true for 3.4 billion years. No hybrids, no fuel cells, no electric cars, no turbine cars, no diesel cars, no overhead cams, no turbo chargers, no fuel injection, no computer ignition, no smog controls, no changes at all. Nothing. Ever. In the first 200 million years or less the entire energy system of life on earth is all worked out, the proteins, the DNA, the molecules, the chemistry, and since then nothing essential has changed. This is not even remotely credible as a story of continuing evolution, of competition, of survival of the fittest. The ATP synthase molecule tells a story that's very different - to my eyes it looks a lot more like intelligent design, like the earth was purposely seeded with bacteria that came with this energy/chemistry system all worked out and we all copied that system.

« Last Edit: September 14, 2018, 06:56:17 PM by marklawrence »
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Offline marklawrence

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Re: Why Evolution Is Wrong
« Reply #3 on: September 14, 2018, 06:55:52 PM »
Why Evolution is Wrong
by Mark Lawrence

What is Evolution?

Evolution writ large is the belief that a cloud of hydrogen will spontaneously invent extreme-ultraviolet lithography, perform Swan Lake, and write all the books in the British Museum. -- Fred Reed

Before we start we have to define a word, "Species." A species is a group of organisms that breeds within the group but not outside the group. Dogs can't breed with cats, the DNA doesn't match up. They're different species. German Shepherds can breed with pit bulls, they're the same species.   The original form of wheat, einkorn, had seven chromosomes, two copies of each, 14 chromosomes total. Later a new kind of wheat evolved, emmer, which also has seven chromosomes but four copies of each, 28 total. Modern wheat also has seven chromosomes but six copies of each, 42 total. However if you try to grow einkorn wheat next to modern wheat, next year most of your einkorn will have picked up more copies of the basic seven chromosomes and will have 28 or 42 chromosomes. The wheat is all breeding together, so although there's a different chromosome count they're all one species, wheat. Corn will not breed with wheat, they're different species. Biologists sometimes throw the word "species" around casually, and will sometimes tell you there are three species of wheat, even though they can all breed together.

For all of recorded history people have been trying to explain the universe, life, human origin and destiny. Eventually people decided that some god created the universe out of nothing. In this sense evolution is a religion: along with the big bang theory, evolution also tries to explain the universe, life, human origin and destiny. Interestingly, the big bang is also mostly believed to have created the universe out of nothing, so in this sense we haven't come very far. The big bang started from nothing and cooked up a whole universe full of hydrogen. The hydrogen clouds condensed into stars because of gravity. The stars cooked up all the other necessary elements for life, then blew up in super novas and scattered the necessary elements all over the universe. A planet formed around a smaller, longer lived star; oceans formed, a lightning bolt hit an ocean loaded with these elements and some self-replicating molecule formed. The self-replicating molecules competed for scarce resources to make more copies, and now evolution is off and running. That's the story. A hydrogen cloud, given gravity, will eventually make San Francisco.

Religions have right and wrong, morality, Good and Evil, but evolution doesn't and can't. Evolution denies spirituality and is fundamaterialistic. Evolution can not begin to explain consciousness and so ignores it. Evolution can not even ask the central question of religion, what happens when we die, as doing so would imply the existence of realms beyond the material.

Evolution is a single word that refers to three theories which have absolutely nothing to do with each other. Here's the three theories:

Species adapt to their environments. There is absolutely no question about this. We have lots and lots of examples:
The fossil record shows that as predators got bigger and faster, horses also got bigger and faster

Giraffes grew longer necks as the trees got taller.

Flies moved from the dry air of LA to the wet air of Seattle grow stubbier wings. Move them back to LA and the wings get longer and narrower. Really, there's simply no question that species adapt to their environments, this is extremely well documented.


New species emerge from old species. There is precisely zero evidence for this.
We have grown tens of thousands of fruit flies in the lab. We have starved them, frozen them, cooked them, irradiated them, poisoned them, you name it, we've done it. We have grown fruit flies with no eyes, with four eyes, with no wings, with seven legs, with no brains, you name it and we've seen it. However, every one of these fruit fly variants proved either sterile or bred back to a normal fruit fly. We have never made a new animal species in the lab.

65 million years ago a big meteor wiped out the dinosaurs and pretty much all life. Today we estimate there are about 10 million species on the earth. That's a new species roughly every six years. Since 1859, 155 years ago, when Darwin published The Origin of Species we've been looking everywhere. We haven't seen a single new species emerge in nature.

The idea doesn't even make sense. Suppose you have some mutation, you have new, better DNA, you're a new species, a better species, one of the X-Men. With whom do you breed? You need someone else to have a mutation that's compatible with your mutation, compatible at the DNA level. Furthermore, that person must be roughly the same age as you, they need to be near enough to you that you might meet, they need to be of the opposite sex, and you have to be attracted to each other. It's not enough to have a superior mutation, there has to be two compatible mutations, both happening at roughly the same time in roughly the same place. The odds just went from "awful" to "no way is this happening." If you can breed with normal humans then you're not a new species, and it makes no sense to talk about how your children will be a new species even though neither of their parents were.

Life emerged on Earth. That's what we'll be talking about in detail in this book, and we're going to learn that this statement also makes absolutely no sense.
Although all three of these theories are called "evolution" they have absolutely nothing to do with each other. Giraffe necks and fly wings are not evidence for life evolving on earth, nor are they evidence for new species coming from old species. Science is about logic, and these three statements are not logically related to each other in any way, no matter what you name them. Why are three completely disparate theories all bundled up in one word? I imagine a biologist would tell you it's actually one theory about the emergence and adaptation of life on earth. I think it's to confuse the issue: they have fantastic evidence for one of their theories, and they want to use that evidence to convince everyone of their other theories. Basically evolutionists claims boil down to "Living things change, and that proves that life started on this planet and spread out into millions of forms to fill all the niches." Copernicus taught us that the Earth was not the center of the universe, but just a very small rock orbiting a very small star that orbits the center of a galaxy which in turn orbits the center of a group of galaxies called the local group. Biology has net yet had their Copernicus, so biologists still believe that the Earth is the center of life in the universe.

Evolution is the story of one turning into many, of parents having 5 children, 25 grandchildren, 125 great-grandchildren, and they spread out and evolve to fill the environmental niches. Hence the very popular "tree of life." Is it true? Genetic evidence tells us not even close.


Remember, we're talking here about evidence. When you study evolution you find there are a lot of "just-so" stories, logical reasoning for how things must have happened and why the theories must be right. But science is about predictions and evidence. Quantum mechanics was never going to be found with logic; in fact it was a 50 year struggle of finding a theory that fit the facts and made testable and correct predictions. If you don't have predictions and evidence, then all you have is speculation. And that's what we're going to find most of evolution is: speculation.

Why do we teach evolution as an established fact? I'm not sure. I think it's so we have a reassuring bed time story to tell our children, "So the moral of the story is, life just happened. There's no god, no nation, no king to live or die for, so we can all beat our swords into plows and live in peace and harmony with each other and nature." Unfortunately this story has two huge problems: Watch Nature on PBS, there is no peace and harmony in the wild. Evolution, after all is also called "survival of the fittest," which also means "death to the less fit." Second, to the best of my knowledge there has never been peace and harmony on earth, save perhaps for Switzerland hiding behind their mountains for the last few hundred years. And as Orsen Wells noted, "In Italy, for thirty years under the Borgias, they had warfare, terror, murder and bloodshed, but they produced Michelangelo, Leonardo da Vinci and the Renaissance. In Switzerland, they had brotherly love, they had five hundred years of democracy and peace – and what did that produce? The cuckoo clock."
« Last Edit: September 14, 2018, 07:05:03 PM by marklawrence »
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Offline marklawrence

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Re: Why Evolution Is Wrong
« Reply #4 on: September 14, 2018, 09:35:25 PM »
Why Evolution is Wrong
by Mark Lawrence

The domains of life

Life on Earth is classified into three domains: Bacteria, Archaea, and Eukaryota. We're still learning a lot about these three domains, especially on the genetic and molecular level. Bacteria and Archaea are very similar and are both called prokaryotes. Here's the best we know right now.



First a little history. The Earth formed about 4.5 billion years ago. Shortly after the Earth formed, it was hit by another planet roughly the size of Mars. The collision broke off a large piece of the Earth which became the Moon. About 4 billion years ago, when the Earth was about 500 million years old, the Earth had colled off enough so that water could change from steam in the atmosphere to liquid oceans. The fossil record indicates that about 30 million years later   the first bacteria formed - so all the major components of life, DNA, RNA, cell walls, proteins, ADP/ATP, we're to believe that all these things evolved in only 30 million years. About 400 million years later the bacteria learned how to do photosynthesis, meaning they took in light and put out oxygen. After working their photosynthetic magoc for about 1.5 billion years these bacteria had changed our atmosphere so that there was significant free oxygen - about 1%. Then the eukaryotes appeared. After another roughly 2 billion years the phootosynthetic bacteria raised the oxygen levels in our atmosphere to a more modern 20%, then multi-cellular animals appeared and the evolutionary race was on.

We all know more or less what bacteria are. They're little single-cell creatures, very small, and morphologically very simple. They're typically about a micron, a millionth of a meter long. Visible light has a wavelength of about half a micron, so we can just barely see these critters in a really good microscope. To see any inner detail we need to use something better than visible light, like perhaps an electron microscope. Bacteria are everywhere. They're a major component of dirt. The oceans and lakes and rivers are full of them. A typical river has tens of thousands of bacteria in each cup. You are made up of cells; there are about 35 trillion cells in your body that share your DNA and therefore would be considered parts of you. However, there are also about 40 trillion bacteria riding along with you, in your intestines, on your skin, in your hair. Kill all these bacteria and you lose a lot of your ability to digest food and absorb protein and vitamins.

Archaea are a relatively recent discovery, first identified in 1977. They're pretty much just like bacteria but made of different DNA and in many cases different chemicals. For example, bacteria cell walls are made of fatty acids and glycerol, always right handed glycerol. Archaea are always made of fatty acids and left handed glycerol. These require completely different enzymes, and because of this we believe that archaea and bacteria split from each other very, very early in the emergence of life.

Eukaryotes are cells with a nucleus. All animals, plants, fungus, molds and amoebas are eukaryotes. All multi-celled creatures are eukaryotes. Eukaryote cells are very different from bacteria or archaea cells. Here's the major differences:

Nucleus. Eukaryotes have their DNA contained in a small pouch, the nucleus. The nucleus has a wall, a lot like a cell wall, and it's extremely complicated so as to allow the DNA to remain protected from most cell chemistry but still able to be accessed by the cell. In bacteria and archaea the DNA simply floats around loose in the cell.

Eukaryotes have several strands of DNA which are arranged in straight lines. Bacteria and archaea have only one strand of DNA and it's circular.

Bacteria and archaea typically have about 4,000 genes, that is, their DNA codes for about 4,000 different proteins. Eukaryotes have typically about 18,000 genes.

Bacteria and archaea genes are small areas on the DNA strand with a beginning and an ending, and that section of the DNA codes for a protein. To make a protein you copy the important section of DNA, read it, and assemble the protein piece by piece according to the DNA. Eukaryotes have their genes broken up into small pieces separated from each other by strands of junk DNA called "introns." To make a protein you copy the relevant section of DNA, then you have to identify and snip out the "introns," the embedded junk sections of DNA, then assemble the remaining good DNA back into a single strand.



In bacteria and archaea genes follow each other immediately. In eukaryotes there are large meaningless sequences of junk DNA between pairs of genes. In bacteria one million base pairs on a DNA strand will typically code for 500 to 1000 proteins. A typical bacteria will have a DNA circle consisting of about 3-6 million base pairs. In eukaryotes that same 1 million base pairs will typically code for about 10 proteins. The difference is that as much as 99% the eukaryote genome is junk DNA. The bacteria genome contains no junk DNA. Embarrassing. As the geneticist David Penny put it, "I would be quite proud to have served on the committee that designed the E.Coli genome. There is, however, no way that I would admit to having served on the committee that designed the human genome. Not even a university committee could botch something up that badly."

Bacteria and archaea reproduce by cloning, by making duplicates of themselves. Eukaryotes all use sexual reproduction - two cells each contribute half the DNA for the child cell.

Eukaryotes contain other cells, especially mitochondria and chloroplasts. These much smaller cells have their own DNA, live inside the eukaroytes and perform vital functions, and in return are fed, protected and cared for. Bacteria don't do this.

Eukaryotes are typically much, much larger cells, typically about 50 microns across. Eukaryotes have typically about 100,000 times the interior volume of bacteria.

All modern biology textbooks contain the picture shown below, the Phylogenetic Tree of Life. This is taught in all introductory biology classes. It shows that there was a last universal common ancestor, that this early life form evolved and split into a bacteria and an archaea, and that the early archaea then evolved and split into modern archaea and eukaryotes. Then the bacteria, archaea and eukaryotes all evolved and split into the tens of millions of critters we see today. This is how evolution is supposed to work: you start with one thing, a bacteria. Some of those critters mutate and become a new thing, archaea. Then some of the archaea mutate and become yet another new thing, a eukaryote. Then these three things all mutate and become everything we see today. Evolution is a story of few and simple mutating into many and complex, and therefore is like a tree - a single trunk rises up and splits into dozens of branches, thousands of branchlets, tens of thousands of leaves. This is simple, compelling, popular and wrong. I find this stunning: in physics, we teach Newtonian mechanics to the younglings, but we tell them up front, "This is an approximation. Later we'll teach you quantum mechanics which is better." Everyone alive knows there's something called quantum mechanics. But in biology they teach things to all high school students and undergraduates that they know to be simply wrong. Staggering. There's a word for people who tell you things they know to be wrong, and that word is not "scientist."



The genetic evidence is far more complex. Here's something far closer to the truth: the last common ancestor split into two groups, bacteria and archaea. Then eukaryotes popped into existence much later, somehow using a whole bunch of genes from individual members of both groups. Our cells are something completely new, but historically many of the key components - cell walls, the basics of DNA and RNA, the way proteins are constructed, and the act of respiration and chemical energy production - are shared between the three groups in an insanely complicated fashion. Our best evidence right now is that we share many of these basic genes with dozens of different bacteria and archaea in absolutely no simple pattern. This is not evolution, it's not one ancestor branching out into many child species. It's a new kid on the block breaking into everyone's homes and stealing bits and pieces, TVs, stereos and jewelry from all over. There's nothing surprising about this: bacteria and archaea ruled the earth for two billion years before we eukaryotes came along. And here's the best part: there is absolutely no known mechanism for this genetic theft. By the way, we're Opisthokonts, upper right, along with all other animals and fungus.

« Last Edit: September 15, 2018, 12:15:16 PM by marklawrence »
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Re: Why Evolution Is Wrong
« Reply #5 on: September 14, 2018, 10:26:20 PM »
Why Evolution is Wrong
by Mark Lawrence

The Molecules of Life

We're going to set out now on a several part series about how we make proteins. In this part we'll see what molecules are used to create living cells. A little while ago we saw that the rechargeable batteries that power the cell are adenosine; and the adenosine is recharged by ATP Synthase. We saw that ATP Synthase is an incredibly complicated molecule, every living cell on earth uses pretty much the same molecule, and apparently it just popped out of the ether fully formed about 3.8 billion years ago. ATP Synthase is one of the complex proteins used in your cells.

Proteins are made by other complicated molecules called Ribosomes, which are protein factories. Ribosomes get their instructions to construct the proteins from RNA. We're going to learn that all cells share the same basic Ribosomes and all cells share the same RNA system. The Ribosomes are powered by the adenosine batteries. The adenosine batteries are charged up by the ATP synthase. The ATP synthase is made by the Ribosomes. So the Ribosomes can't make an adenosine battery charger without already having an adenosine battery charger around to power them. The Ribosomes also make the proteins that are part of the Ribosomes, so you can't make Ribosomes and ATP synthase unless you already have Ribosomes and ATP synthase. We get our original set of Ribosomes and ATP synthase from our mothers, present in the egg that made us. Louis Pasteur was the first to recognize this and prove it in an experiment. He said, "Life comes only from life." Before Pasteur many believed that life just spontaneously happened, for example mold just appeared on bread with no source. He showed in an experiment that this was not so: sterile environments create no life. He said of this, "Never will the doctrine of spontaneous generation recover from the mortal blow struck by this simple experiment." Today it's widely believed that this is true, except for 3.8 billion years ago when life spontaneously generated itself on the early Earth. Biologists are not troubled by this contradiction, as the Earth is the center of all live in the universe and there is no God so it must be so. This begs the question, "If there is no God, why is there anything?"

All cells share these basic critical and central features of RNA - Ribosomes - ATP Synthase, and all cells use the same basic system, there's no simpler system on the earth anywhere. We're to believe that this whole complex system evolved in a couple hundred million years, and the result of that lightening fast evolution was a system so perfect that today, nearly four billion years later, we're still using the same system, no improvements, no simplifications, no alternatives. That's where we're headed in the next few weeks, learning enough cell chemistry to see how beautiful and complex this system is, and how amazing it is that any rational person would ever think for even an instant that it just randomly popped into existence.

Living things are constructed out of a surprisingly small number of basic molecules, which are then chained together like Lego blocks and can then do some rather amazing things. The simple molecules come in four families: fats, sugars, the nucleic acids from which DNA and RNA are built, and the amino acids from which proteins are built. The simple molecules are strung together in chains called polymers. "Poly" is a Greek word that means many. The big trick is they have to be strung together in exactly the right order in order to fulfill their function. Today we're going to go over the basic molecules. There's no test, you don't have to memorize anything, but we need to know about the four basic families and the idea that they each have a few members. Here's the four basic groups:

Lipids. These are the fatty acids. You know them best as the oils, olive oil, corn oil, lard etc. Cell walls are mostly made of oil molecules arranged in a very tricky fashion. If you die and fall into an underwater crevasse, eventually almost everything in you will decompose except the fatty acids - these will turn into oil deposits which can be dug up and used to promote air pollution, terrorism, and plastic shopping bags to pollute the ocean. In the picture below a couple of fatty acids are shown; generally they are a chain of carbon atoms surrounded by hydrogen. In life there's always an even number of carbon atoms - 2, 10, 16. No one knows why. If there are hydrogen atoms all the way around the chain on all sides, the fat is called "saturated." If there's one hydrogen atom missing it's called "mono-unsaturated." The most common mono-unsaturated fat is C16, 16 carbon atoms surrounded by 33 hydrogen atoms, more commonly called "olive oil." If there are two or more hydrogen atoms missing it's called "poly-unsaturated."   Normally C18 - C24 are found as poly unsaturated. If you heat the oil up and bubble hydrogen through it to saturate all the unsaturated fats, it's called "hydrogenated," the very worst of all the fats. We'll get to lipids in this book much later when we talk about cell walls. Notice the unsaturated fat has a kink in it. We're going to see that this is a critical part of making a cell wall.


Saccharides. These molecules, alone or in pairs, are the sugars, the stuff our cells live on. If strung together into long molecules they're very difficult to take apart. Wood is a bunch of sugar molecules strung together. So are grass stems. A few bacteria can just barely take some of these long molecules apart, so cows eat grass, the bacteria in their first stomach chops up some of the long cellulose molecules into shorter molecules, then in a second stomach some of the shorter molecules are digested as sugars. It's a slow and inefficient process, but there's lots of grass and cows don't have a lot on their appointment calendars. Any carbohydrates we eat are converted to sugars. Any sugar that's not glucose is converted to glucose by our liver. The glucose is carried by our blood to all the cells. The cells use oxygen and glucose to power the ATP synthase motors. These motors recharge the adenosine batteries, and most everything else runs on the charged adenosine. Single molecule sugars - monosaccharides - come in many forms, with 3 to 10 carbon atoms. The most important for us are shown below - two of the hexoses (six carbons) Glucose and Galactose, and three of the pentoses (five carbons) fructose, ribose and deoxyribose. Fructose is mostly found in fruit and is the one that is sweet. Glucose is the one our cells prefer for metabolism. Ribose forms the backbone of RNA; deoxyribose forms the backbone of DNA. Table sugar - sucrose - is a glucose bound to a fructose. The fructose makes it taste sweet, the glucose is instant energy. Two glucoses bound to each other is maltose which ferments into beer. Malt tastes good but isn't sweet like table sugar. A glucose and a galactose bound to each other is lactose, the part of cow's milk that most people can't digest. Lactose also tastes good to many but isn't nearly as sweet as table sugar. Your liver converts fructose into glucose using much the same chemistry as it uses to break down alcohol, so if you drink a lot of high fructose corn syrup in big gulps, you will perhaps die of liver disease just like an alcoholic.


Nucleic acids. These can be strung together to make DNA or RNA. There are six letters in the nucleic acid alphabet, "A," "C," "G," "I," "U," and "T." DNA only uses A, C, G, and T. mRNA only uses A, C, G and U - in mRNA U replaces T. tRNA uses A, C, G, U and I. Taken three at a time the four nucleic acids in DNA or mRNA form 64 words. The 64 words each mean either one of the 21 amino acids or "stop." All the instructions in the cell on how to build proteins are written in this language. A "sentence" written in this alphabet is called a gene and tells you how to construct an individual protein; a DNA strand is about one thousand to a five thousand such "sentences." We'll talk about this more later, DNA and RNA will be a big part of our story.


Amino acids. These are the basic building blocks used to make proteins.   A protein is a chain of amino acids. Many proteins are used to promote or control other chemical reactions; such proteins are often called enzymes. Other proteins are used as girders or motors. Your laundry detergent has a bunch of proteins - enzymes - in it. The proteins must not only be assembled in the right order, they must also be folded up just so. Proteins generally have a few active sites that do the chemical work; these active sites must be positioned perfectly or the protein can't do its job. Protein folding is not currently understood. There are a few nobel prizes waiting for the people who figure it out. Little bacteria cells know how it works; in many ways they're still four billion years ahead of us. Proteins are also a big part of our story and will be discussed in detail later. Notice that all the amino acids share the exact same backbone, called an amino group. We can imagine thousands of different amino acids by changing the little molecule hanging off the amino backbone, but these 20 are all that are used on Earth. No one knows why.

« Last Edit: September 14, 2018, 10:43:52 PM by marklawrence »
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Re: Why Evolution Is Wrong
« Reply #6 on: September 14, 2018, 11:22:38 PM »
Why Evolution is Wrong
by Mark Lawrence

The Probability of Proteins

Once we see, however, that the probability of life originating at random is so utterly minuscule as to make it absurd, it becomes sensible to think that the favorable properties of physics on which life depends are in every respect deliberate. -- Sir Fred Hoyle, discovered how stars create elements.

The notion that not only the biopolymer but the operating program of a living cell could be arrived at by chance in a primordial organic soup here on the Earth is evidently nonsense of a high order.-- Sir Fred Hoyle, discovered how stars create elements.

In this chapter I'm going to be throwing around a bunch of numbers. You don't need to worry about the numbers or the math. Feel free to ignore them. Or check them, I don't care. Here's everything you need to learn from this chapter: the statistics of life are so impossibly improbable that you have a considerably better chance of winning the lottery every day for a week than the chance that even a single short simple protein evolved from random chance anywhere in the universe ever. You have about 25,000 different types of proteins in your body; the chances of all 25,000 evolving by random mutations is an unthinkably tiny number, so close to zero that it's really not worth talking about the difference. These proteins did not evolve by random chance in our universe. Period.

We're going to be talking about some really big numbers, so we're going to use scientific notation. 25 means 2*2*2*2*2, five twos multiplied together. 1015 = 10*10*10*10*10*10*10*10*10*10*10*10*10*10*10, fifteen tens multiplied together, a one followed by 15 zeros, 1,000,000,000,000,000. 10390 is 390 tens multiplied together, a one followed by 390 zeros. We're going to be looking at some really big numbers, so let's get used to a few of them. There are about 1012 galaxies in our universe. Each galaxy has about 1011 stars. Most of these stars are unsuitable for life - they're too close to the radiation of the galactic center, or too far out in the fringes of the galaxy where there's not much metals. We now think that most stars have planets, so roughly speaking there are perhaps something like 1023 planets that are kinda sorta habitable. The universe has been around for 14 billion years - that's about 1010 years. There are about 3x107 seconds in a year, so the universe has been around for 1018 seconds. There are about 1083 atoms in our universe. The number 10390 dwarves all these numbers. However, I have read in a popular molecular biology textbook that there are about 10390 possible proteins made up of 300 amino acids, and evolution has chosen only those which consistently fold to a chemically useful shape.  There are only 10<sup>83</sup> atoms in the universe, but the universe has looked carefully at 10390 proteins. So here's something to keep in mind: 1023 planets times 1018 seconds is only 1041. Any number bigger than about 1050, or certainly any number bigger than 1083, this is not happening in our universe. Our universe did not make 10390 proteins and select the ones that were consistently useful. In fact, later we'll see that our universe didn't even make a single such protein by random chance, much less 10390 of them.

You're perhaps heard that if enough monkeys type at random, they'll eventually type out all the books in the British library. Mathematically that's true, but what does it mean in real life? Let's see if a monkey can type out just the title of one Shakespeare play, "the twelfth night." That's just 17 characters; rather less than the 3 million characters in the Bible or the total number of characters in the 150 million books in the British Library. We'll ignore capitals; we'll give the monkey a typewriter with 32 keys: a-z, space and .,?!'. So the monkey has a 1 in 32 chance of hitting the first character, "t". 32 is 25. There are 17 characters total in Shakespeare's title, so the number of possible 17 character things our monkey can type is 25*17 = 285. 210 is 1,024 which is almost exactly 103, so 285 is about 3*1025. The universe is about 14 billion years old and there are about 3*107 seconds in a year, so the universe is about 4.5*1017 seconds old. That means if our monkey hits one key per second and has been doing this non stop since the big bang he has 1 chance in about 100 million of typing out "the twelfth night." 17 characters, 14 billion years, 1 chance in 100 million. That's about the same as your chances of winning the lottery. And, by the way, while failing rather badly to type out our simple play title our monkey ate about 20 trillion bananas. This is not happening. And the monkeys who are going to randomly type all the books in the British library? I think you can now see that's going to take an unimaginably huge number of monkeys typing for a seemingly eternal amount of time. And a lot of bananas.

We're told the Earth had a "primordial soup" that was capable of producing amino acids when hit with lightning. Ok, sure, maybe, but can this soup produce a protein? The average protein is about 450 amino acids long. There are 20 amino acids used by life on Earth, but there are thousands of possible amino acids that could be made when lightning hits our soup. Earth life has somehow selected only 20 of these and ignores the rest. These particular favored 20 are defined by the genetic code. In a primordial soup that's making amino acids at random you would get thousands of different amino acids, not just the preferred 20. But, no problem, we'll assume the primordial soup somehow magically only makes the preferred 20. This is, mathematically, a huge assumption and it's giving a huge mathematical boost to the evolutionists, but no problem, we'll just let that slide.

We'll assume the Earth's oceans have always been as big as they are now. This is almost certainly wrong: comets and asteroids hitting the Earth deliver more water, dozens of tons every day, so four billion years ago there was far less water on the Earth than there is today. But no problem, we'll give the evolutionists the modern water content of Earth.

Bacteria cells are about a micron across. We'll assume the primordial ocean / soup was as chock full of amino acids as a bacteria. Of course this is complete nonsense, amino acids would have been far less dense in an ocean than in a bacteria, but again we'll give the evolutionists the benefit.

Proteins are formed by attaching a bunch of amino acids to each other in a chain. In a cell there are enzymes that make this happen; without the enzymes the reaction is thousands of times less probable. We'll ignore this problem and let the evolutionists have the high speed cell reactions even without the cell enzymes. Also when you attach two amino acids to each other you do it by removing an "H" from one and an "OH" from the other, resulting in two attached amino acids and a free H2O water molecule. If you put this new molecule into water it doesn't last long: there are a lot of H2O molecules bumping into the aminos trying to break them apart, and the amino acids are very happy to get a divorce and share custody of an H2O. We're going to ignore this problem too. Once a pair of amino acids is joined up, we're going to let them float around all joined up forever.

There are about 1021 liters of water on the Earth. This is about 1036 cubic microns - if the Earth's oceans were solid bacteria instead of free water there would be about 1036 of them. Life is said to have evolved on Earth in about 30 million years, which is about 1015 seconds. We'll assume that the amino acids react at the same speed that they do in bacteria, which is in about a thousandth of a second, a millisecond. Now we have 1036 cubic microns times 1018 milliseconds, which equals 1054 interactions. A typical protein of 450 amino acids would require the number of different amino acids, 20, raised to the 450 power, 20450 which is 10585. So if we give the evolutionists a perfect primordial soup that's as big as all the water on the Earth, as densely packed with amino acids as a bacteria, the only amino acids present are the 20 good ones, and when amino acids combine they stay combined, our chance of producing a single typical protein in 30 million years is 1054 / 10585, which is one chance in 10531. How big is this number? Here's a comparison: there are about 1083 atoms in our universe. Here's another: there are about a trillion galaxies in our universe; if each galaxy has a hundred billion Earth type planets and every one of these planets has this same impossibly perfect primordial soup and all the soup had been working non stop for the entire life of the universe, that's about 1023 planets working for about a thousand times as long as 30 million years, 103 times as long. We still have one chance in 10506 of making a single average protein by chance. 10506 is an unimaginably large number, a one followed by 506 zeros. To have a 50-50 chance of making this one average
protein by random process you would need 10506 copies of our universe, all working together for 15 billion years.

You could complain that we just tried to produce an "average" protein; perhaps the first protein was a simpler protein. In bacteria the simplest proteins are about 100 amino acids long. 20 raised to the 100 power is about 10130, which means in our impossibly unlikely primordial Earth ocean soup/lab our chances of making one of these simple short proteins is one in 1070. Suppose again we used all trillion galaxies, a hundred billion Earth type planets per galaxy and every one of these planets has this same impossibly perfect primordial soup and all the soup had been working non stop for the entire life of the universe. We still have only one chance in 1044 of making a single short, simple protein by chance.

You could also wonder if perhaps the first protein was 50 amino acids long and did something somewhat useful, then later the protein evolved to 100 amino acids long and was much more effective in the longer version. The chances of making the 50 amino acid chain is one in 2050, then to grow it another 50 is another one in 2050. 2050 * 2050 is 20100, the odds didn't change. Perhaps it grew 10 more amino acids at a time in five more steps? That's 2050 * 2010 * 2010 * 2010 * 2010 * 2010 which is still 20100. There are no shortcuts to the 100 long protein. You see the protein and you can think "This didn't grow by chance in this universe. Not all at once, not in two steps, not in 100 steps. It simply didn't happen by chance." Apparently a lot of biologists have forgotten their high school algebra.

Your chance of winning the lottery is about 1 in 100 million. Your chance of winning the lottery five times is one in 1040, which is 10,000 times more likely than the entire universe making a single small short 100 amino acid protein by chance. I'm going to go out on a limb here and suggest you've never won even a single lottery, much less 5 of them in a row.

Not one single protein happened on the Earth by chance. Not one single protein happened in the entire universe by chance. A single bacteria has more than 2 million carefully constructed and selected proteins, and the universe is unable to make even a single protein by chance. Louis Pasteur conducted a famous experiment on the spontaneous generation of life from non-living matter, and he assured us in 1859 that "Life comes only from life." Curiously this was the exact same year that Darwin published "On the Origin of the Species." Pasteur was right in 1859 and he's right today. Life comes only from life, not from lightning and soup and random luck.

I'm truly sorry about all the dirty, gruddy math. I won't do it again.

Much.
« Last Edit: September 15, 2018, 07:22:50 AM by marklawrence »
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Re: Why Evolution Is Wrong
« Reply #7 on: September 15, 2018, 01:22:55 PM »
Why Evolution is Wrong

The Genetic Code

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. –– Charles Darwin, Origin of Species

Most of the biochemical work done by cells is done by proteins. The proteins are made by your cells. The way that works is your DNA has instructions for how to assemble each protein from small molecules called amino acids. The DNA is copied into mRNA - Messenger RNA. The mRNA moves from the nucleus into the cell, where there is a whole bunch of complicated machinery that reads the mRNA instructions and assembles the protein. We're going to talk about the language the mRNA uses to tell the cell how to assemble the protein, and we're going to talk about how that language is defined and read.

Proteins are a group of simpler molecules, amino acids, which are connected up in a line. Although the amino acids at a glance seem very different from each other, every amino acid has an amino group as the foundation. An amino acid looks like the molecule below, except "R" gets replaced by something else, something often complicated. Below I show three amino acids, separated, then the three attached in a chain. I've flipped the middle one upside down for clarity. To attach them we remove an H from one and an OH from the other, then connect them up. The new connection is called a peptide bond, so proteins are sometimes called polypeptides. They're also sometimes called enzymes. A lawyer could have a field day with all these aliases. We had to remove a molecule of water, an H2O, to connect up the amino acids, so this process is sometimes called dehydration 'cause we took away water. Since the cell is full of water, this reaction does not happen on its own - it's like jumping into a swimming pool to dry off. Joining up amino acids requires an enzyme, a protein which helps do the chemical attachment work.



The simplest R we can imagine is a hydrogen atom, and if that's what we use we get the amino acid Glycine. We can imagine replacing R with thousands of different molecules, and when we make amino acids in the lab out of random chemicals that's what happens. However, life on Earth has chosen a particular 20 of these possible amino acids, and all proteins in all cells on Earth are built from only those 20. The protein above is 3 amino acids joined up. In a living cell an average protein has about 450 amino acids joined up. A very small protein would have about 100 amino acids. The largest has over 30,000.

The 20 amino acids are all different, they all have different sizes and shapes and methods of linking up to other molecules. None the less there are some similarities. The 20 amino acids broadly fall into four categories, as shown below. Nearly half of them are non-polar, which means they don't like to be around water but dissolve readily in oil. Another third are polar, meaning they don't like oil so well but dissolve readily in water. And finally five are charged; three are positively charged and two are negatively charged. The charged amino acids will very easily bond tightly to many other molecules, and frequently if the charged amino acids are in a protein they are part of the active bonding sight that lets the protein do its work. If you have a large protein and you substitute one non-polar amino acid for another non-polar there's a decent chance the protein will keep working, perhaps with a slightly reduced effectiveness. If you substitute one polar amino acid for another polar, again there's a decent chance the protein will keep working. If you substitute a non-polar amino acid for a polar amino acid or vice-versa most likely the protein will lose a whole bunch of effectiveness or even quit working entirely.



RNA is a chain of nucleic acids. RNA is made up from four nucleic acids - Adenine, Guanine, Cytosine and Uracil. From now on we'll just call them A, G, C, U. So a chain of mRNA might read UACUUGGCAACUAGGUAA. To read the RNA you break this up into groups of three: UAC UUG GCA ACU AGG UAA. Then you look up the individual groups in the table below. UAC is Tyrosine, UUG is Leucine, GCA is Alanine, ACU is Threonine, AGG is Arginine, and UAA means Stop. So this mRNA chain codes for a very short protein made up of Tyrosine-Leucine-Alanine-Threonine-Arginine connected together in a line. There are five amino acids in our tiny protein, and the mRNA has 18 nucleic acids, three for each amino acid and three more to indicate the protein is finished. That's how you read the genetic code.



Let's take a close look at the table above, we're going to see something very interesting. In the upper left cell all the codes start UU. No matter which the third letter is, you get a non-polar (NP) amino acid. So if somehow a mistake was made in transcribing the mRNA and a UUU was accidentally turned into a UUA, there's a decent chance the protein would still work. In the next cell down, the four codes all start CU and the third code doesn't matter at all, no matter what it is you're going to get Leucine. In fact you can quickly see there are 8 cells like that, in each cell no matter what the third letter is, if you get the first two correct you're going to get the right amino acid. That's half the entire table. If you look at the first column, you see no matter what the first or third letter is, if the second letter is U you're going to get a non-polar amino acid. In the second column if the first letter switches between U and A you're likely to be more or less ok, or if the first letter switches between C and G you're likely to be ok. The entire table seems remarkably fault tolerant.

In fact it is remarkably fault tolerant. In computer simulations of possible genetic codes, distributing the amino acids around this table at random, the genetic code in the table above is 1 in a million: that is, 999,999 out of a million genetic codes are less fault tolerant.* Now here's the great part: pretty much every critter on Earth uses this exact genetic code. There are some very minor exceptions: the mitochondria in your cells use AUA for Methionine instead of IsoLeucine, and UGA is Tryptophan instead of Stop. There are a couple of funguses that have similar tiny differences. But every bacteria, every archaea, every plant, animal, protozoa, algae, they all use this exact same genetic code. So we can't possibly say life on Earth evolved this clever fault tolerant code, because everything alive on Earth shares the exact same one-in-a-million fault tolerant code. Since this genetic code is shared by everything it must date back to the very beginning.



Ok, now we can read the genetic code. What defines the genetic code? A different kind of RNA, called Transfer RNA, tRNA. Up above in our list of nucleic acids, you'll see one named Inosine and labeled "tRNA only." Inosine is called a "wobble base" and can pair with any of UCGA. So for example a tRNA which has CU in the first and second places and I in the 3rd position can bind to an RNA strand that has CU* where * is anything. Because of this there aren't 64 different tRNA molecules, there are only 31 different tRNA molecules. A tRNA gets loaded up with the correct amino acid and then can bind to the RNA so as to present that amino acid in the correct order.

What loads up the tRNA with the correct amino acid? Now we're getting into a part of biology that's not terrifically well mapped out. There are 20 different large protein molecules called aminoacyl-tRNA synthetases. They each bind to a specific amino acid, and then can bind to an empty tRNA with the right code and connect up the correct tRNA to the correct amino acid. The aminoacyl-tRNA synthetases and the tRNA together define the genetic code - they're the dictionary.

The tRNA molecules are roughly 80 nucleic acids long. Since there are four different nucleic acids this means there are about 480 combinations. This gives us a basic probability of making these things randomly of 1 in 1048. We earlier decided that if the Earth were absolutely perfect for evolving biological molecules it could make something like 1060 combinations, so the tRNA molecules could in principle have evolved randomly on the Earth. The aminoacyl-tRNA synthetases, on the other hand, range from about 560 amino acids long to 1300 amino acids long. We also earlier decided that a protein of 100 amino acids could not be made in the entire universe; here we need twenty different proteins ranging from 560 to 1300 amino acids long. So while we can perhaps evolve the tRNA, our entire universe cannot possibly evolve even one single protein to charge the tRNA up.



Why is the genetic code redundant? No one knows why only 20 amino acids were chosen from the thousands available, nor does anyone know why this particular 20. Since there can be a total of 63 different amino acids in the genetic code, there are going to be duplicates. If you break down a cell's 10 billion proteins into their component amino acids, you find that some amino acids are used more frequently than others. In the table above we see the frequency with which the amino acids are used - for example, Alanine comprises about 7.4% of the amino acids in your cells, more than the 5% you might expect based on 20 different amino acids. And Tryptophan is used only 1.3% of the time, much less than the 5% you might expect. Tryptophan has only one coding, UGG, so it uses 1.6% of the coding space. Alanine has four codings, UGC, GCA, GCC, GCG and uses 6.3% of the coding space. If you look down the two rightmost columns in the table above you'll find a decent match between the abundance of the individual amino acids and the amount of the coding space they use up. It's almost like the DNA code was specified after the cells were built. I certainly don't understand this, but it does not in the least look random.

What we've seen here is that the genetic code is a very beautiful thing, carefully constructed to be significantly immune to errors, and it's shared by everything alive on Earth, which means it was there before any of the living stuff we see today. It has to be at least 3.5 billion years old just to account for being shared by all the life on Earth. There's no meaningful chance the genetic code evolved anywhere in our entire universe by random processes. Certainly not on Earth.

*The Genetic Code Is One in a Million, Journal of Molecular Evolution 47(3):238-48 October 1998 by Stephen J. Freeland and Laurence D. Hurst
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Re: Why Evolution Is Wrong
« Reply #8 on: September 15, 2018, 02:36:11 PM »
Why Evolution is Wrong

Organic Chemistry and Helixes

Today we're going to talk about organic chemistry. This is not about evolution, it's just to help understand the players inside the cells. We're going to find that helixes are a big part of cell activity. A helix is a spiral in three dimensions, like the threads on a wood screw. Nucleic acids naturally form helixes when put together into DNA and RNA - Watson and Crick got the 1962 Nobel Prize for finding out this was the shape of DNA. Proteins can also form helixes, and such proteins are used to make little tubes that run through the cell walls and selectively let particular chemicals through at particular times. Without the helical proteins the cell wall would be like a dry cleaning bag around the cell and it would suffocate, or choke on its own waste. This chapter contains a box with some dirty, gruddy math. You can skip the box without missing anything important. However, if someone had done this calculation in the early 1950s, they would have shared the Nobel Prize with Watson and Crick. As long as they weren't also a controversial drinker. As far as I can tell, I'm the first to do this calculation.



Organic chemistry is the study of how carbon makes molecules. That's all organic really means, things made out of carbon. So when I'm shopping and I see a sign that says "Organic bananas," I'm very pleased that the bananas are made of carbon compounds, not lead or iron or copper, because I'm pretty sure lead bananas would taste awful and be pretty unhealthy.

Organic chemistry is run by the laws of quantum mechanics. We're not going to learn quantum mechanics, but we are going to learn a few generic rules.

Here's one: Electrons like to have lots of room. The more room they have, the less energy they have and the happier they are. So chemical bonds are about getting more room for the electrons.

Here's another: electrons like to come in pairs. The electrons have a property called "spin," and the spin is either up or down. It's never in between. Or you can think of it as left handed or right handed spin. Never in between. Perhaps you find that hard to understand: that's ok, no one understands it, it's just known to be true. We can't even make up consistent math which describes electron spin. But the electrons like to have a lot of room, and they like to share their room with one other electron, one with spin up and one with spin down.

And finally, when the electrons are part of atoms, they want to pair up and live in groups of four such pairs, eight electrons total. These electrons which want to pair up are called valence electrons.
The periodic table is all about how many electrons each element has, and implicitly how many it wishes it had. Below is an abbreviated periodic table. Abbreviated because I've left out almost half the elements, the heavier rare elements which are mostly radioactive and don't have anything to do with the chemistry of life. In fact even in my abbreviated table the elements which are in white squares are not used by life. There are only 32 elements out of the known 118 that are used by life, and seven of those 32 are not clearly essential - perhaps you could remove them entirely from the earth and no living thing would notice.   96% of your body weight is made up of just four elements, Carbon, Hydrogen, Oxygen and Nitrogen. These four biologically active elements are sometimes called CHON.



The right hand column of the table is the Nobel Gasses - Helium, Neon, Argon, Krypton, Xenon, Radon. These elements don't participate in chemistry, and therefore don't participate in life. They don't participate because elements want to have eight outer electrons paired up as four couples, and these atoms have all eight. They aren't interested in donating or acquiring or sharing electrons. They're quite anti-social.

Chemically speaking, all the other elements want to be one of the nobel gasses, just like all women want to be Lady Di (minus the dead part) and all men want to be Clint Eastwood (the younger version). So, for example, Hydrogen, the upper most element on the left side, has only one electron and would be happier with none or two. Helium, the first nobel gas, has two electrons, one pair, and is happy just like that. Carbon, which is the first yellow element in the second row, is four spaces away from Neon, the nobel gas directly to its right. Carbon has four outer electrons, four valence electrons, but wishes it could have eight. So Carbon is very interested in sharing electrons with other elements so that it can get to eight valence electrons, four pairs. Carbon is four spaces away from Neon, so it's looking to share four more electrons. Carbon wants to make four shared-electron bonds, called covalent bonds. Nitrogen is three spaces away from Neon so it's looking to share three more electrons. Nitrogen wants to make three covalent bonds. Oxygen is two spaces away from Neon so it's looking to share two more electrons. Oxygen wants to make two covalent bonds. Covalent (shared electron pair) bonds are the strongest bonds an atom can make, and are roughly 100 times stronger than polar bonds, hydrogen bonds or van der waals bonds.

Hydrogen in the atmosphere appears mostly as H2, meaning a molecule of two hydrogen atoms connected to each other. The two hydrogen atoms share their two electrons, so each atom has one electron pair, at least on a part time basis. The electrons are happy because they're paired up and because they have twice as much room to roam around in. If you want to break the hydrogen molecule in half to form two hydrogen atoms, the electrons will have to live in smaller rooms and therefore require more energy. You'll have to supply that energy to break up the molecule. Hydrogen is the only element that wants two valence electrons; all the other elements we're going to be interested in want eight valence electrons, four pairs.



A very simple carbon molecule is CH4, methane. This is a carbon atom with four attached hydrogen atoms. Each hydrogen atom shares a pair of electrons with the carbon atom. Because of this sharing, the carbon electrons all have more room to roam around and they're all paired up in spin pairs. The hydrogen electrons also have more room to roam around in and are also paired up in spin pairs. Everyone is happy and the molecule is quite stable. Here on earth our oceans are made up of water. On Titan, the largest moon of Saturn, it's very cold and there isn't any free oxygen to burn things up, so the lakes on Titan are made of liquid methane. Life on earth requires liquid water; if there is any life on Titan it apparently would require liquid methane. The picture on the right is a simple drawing of a methane atom, a central carbon atom with four hydrogen atoms attached. The hydrogens want to be as far away from each other as possible, 'cause less crowding makes for happier electrons. The best they can do to achieve this is to form a four cornered, four sided pyramid.





Dirty, gruddy math.
You can skip this part if you hate math, we're just going to show that high school math predicts the shape of methane. The shape of methane will then be used to predict the shapes of much more complicated molecules with surprising accuracy.



Let's consider the carbon atom and just two of the hydrogens. Three points define a plane, so the centers of the three atoms can define the X-Z plane. Let's call the angle of the left hydrogen atom φ. Let's call the distance from the center of the carbon atom to the center of the hydrogen atom 1. Now the coordinates of the left hydrogen atom are (-sin(φ), 0, cos(φ)). The coordinates of the right hydrogen atom are (sin(φ), 0, cos(φ)). The dot product of two vectors A & B is (a b cos(θ)) where a and b are the length of A and B and θ is the angle between them. The dot product of our two vectors is cos2(φ) - sin2(φ) = cos(θ). We remember that cos2(φ) - sin2(φ) = cos(2φ), so we just proved that θ is 2φ. That's not very insightful, but it's what we expect, so we know we haven't made a major screw up. Yet.



Now let's consider the carbon atom and the other two hydrogen atoms. For maximum separation these three atoms must be in the y-z plane; if there was any other angle then one hydrogen would be closer and the other further apart. Again we'll call the angle of the hydrogen atoms φ. Now the coordinates of the left hydrogen atom are (0, -sin(φ), -cos(φ)). The coordinates of the right hydrogen atom in the x-z plane are (sin(φ), 0, cos(φ)). The dot product of our two vectors is -cos2(φ) = cos(2φ). We can solve this by typing it into an online math solver like wolfram alpha. The result is φ = 109.5°. So the hydrogens in methane are happiest when they're 109.5° from each other. And apparently they're also happiest when they're not in the People's Republic of California, which outlawed methane on 1-1-2017.






The hydrogens in methane are separated by 109.5°. Is this number always correct? Not exactly. Now let's consider water, H2O. The oxygen atom wants four pairs of valence electrons, just like carbon; but oxygen already has six, two more than the four that carbon has. So oxygen is perfectly happy to form H2O, unlike carbon which prefers CH4. The math to calculate the angles is a lot like the math for methane, except now two of the four corners on the pyramid are occupied by hydrogens and two are occupied by electron pairs already belonging to the oxygen. The electron pairs are a little closer to the oxygen atom than the hydrogen pairs are, so the hydrogens get pushed together a little bit. The angle of the hydrogens in liquid water has been measured to be about 106°, just slightly closer together than the 109.5° for methane. These molecules represent the two extremes: one where there are four identical atoms, methane, and one where two of the four atoms are missing entirely, water. Most bond angles fall in between these two values of 106° and 109.5°.



Now we're going to consider a couple really big molecules. First, DNA. In the DNA there are ribose sugars which are held together by phosphate groups. There's an angle between the phosphate group and the carbon atom in the sugar. It turns out that angle is about 107.5°, intermediate between methane and water but quite close to either. If the angle had been 90° the DNA molecule would look like a ladder; instead it looks like a spiral staircase, a double helix. 107.5° is 17.5° more than 90°. This is the excess bond angle on each side of the phosphate molecule, so there's a total twist of 35° at each phosphate. That means it takes between 10 and 10.5 phosphate connections to make a full 360° turn, and that's correct - there are about 10 nucleotides in one complete twist of a DNA helix. The picture to the right shows this with fair accuracy, if you remember there's a couple nucleotides which are hidden because they go straight into the page. See? This molecular biology stuff is a bit messy, but once you get past that it starts to make some sense.

Now we're going to look at one more example. Earlier we saw that amino acids are a common backbone with differing groups attached to the sides. The backbones attach to each other with peptide bonds, forming a chain of amino acids which we call a protein. The backbones can also make a helix form, something a bit like DNA, attaching backbones to each other irrespective of the side groups. This structure is very common and is called an alpha-helix. We're going to see that it's critically important for the cell to function - a protein alpha helix forms a tube, an open cylinder, that can penetrate the cell walls and allow other molecules to pass into and out of the cell. Below is our diagram of how the amino backbones form peptide bonds to make protein chains. The letters R1, R2 and R3 stand for the side chains that give each amino acid its particular chemical character.



The basic amino acid backbone is made up of a chain that reads N-C-C. In the picture above you can see this backbone running through the middle of the molecule, N-C-C-N-C-C-N-C-C. If the protein had 150 amino acids the N-C-C group would be repeated down the protein 150 times. There are two bonds inside the N-C-C group plus the bond to the next N-C-C group, three total per amino acid. We expect just a bit over ten bonds to form a 360° circle. And in fact that's pretty much what happens: proteins can coil into a helix where it takes about 10.5 to 10.8 atoms to complete a full twist. When the helix forms there are three spots where an N-H lines up above a C=O; a hydrogen bond forms between the side chains and gives the helix additional structural strength. This means that one possible shape for a protein is a stable open cylinder, which will prove key to the proper functioning of many parts of the cell.



None of this is magic, it follows directly from the laws of quantum mechanics in three dimensions. If your universe has a speed of light which is not infinite then your electrons will have this property spin; and then the wave nature of matter dictates that there must be eight valence electrons around any atom. Except Hydrogen and Helium, the only exceptions, which have two. Put together, the speed of light and the wave nature of matter   tell us that many molecules will form a helix with about ten bonds per turn.
« Last Edit: September 15, 2018, 04:12:46 PM by marklawrence »
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