USS Clueless -- Evolution, Creationism and Chocolate Cake

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Evolution, Creation and Chocolate Cake

How do genetic engineers rely upon evolution when they produce human insulin in vats?

Let's try a thought experiment. You're a fan of chocolate cake and across the street are two restaurants which serve chocolate cake. So you go into the first restaurant and order a piece and eat it and it tastes good. Then you go into the second restaurant and order a piece and eat it and it tastes EXACTLY the same as the other one. You get two pieces to go from the two restaurants and take them home and analyze them, and you can't tell them apart.

Here's what you don't know: the cook in the first restaurant only speaks Russian and the cookbook he used to make the cake is written in Russian. The cook in the second restaurant only speaks Hindi, and the cookbook he used was written in Hindi. But they were both translations of the same cookbook, and in fact both cooks were using the same recipe. Also, both restaurants get their supplies from the same supplier. So the cakes came out the same way. They are completely indistinguishable.

The importance here is to differentiate between information (the recipe), material (flour and chocolate) and encoding (the language in which the recipe is written) and to understand that the encoding has nothing whatever to do with the others. A third restaurant whose cook spoke only Spanish but using a Spanish translation of exactly the same cookbook, and getting supplies from the same supplier, would still produce exactly the same cake and you still wouldn't be able to tell. When you eat a piece of cake, the recipe for the cake is important, but the language in which the recipe is written is not important. The information is important, but the encoding is not important, as long as the cook understands the encoding and can thus derive the information from the stored representation.

On the other hand, you can certainly tell the difference between chocolate cake and angel-food cake. In that case, the actual recipes themselves are different. And the resulting cakes would be different if their recipes were written in the same language, or if they were written in different languages. The recipes (the information) matter, but the languages (the encoding) don't.

The "recipe" for a human being is the genetic information held in our 23 pairs of chromosomes. It's written as a sequence of codons, and for each entry there are four choices which are usually referred to as A, C, G, and T (the first letters of the four chemicals which are used). A human is made of proteins, and the genetic code describes how to make about a hundred thousand of them. Each of those proteins is a chain, sometimes short and sometimes long, made up of amino acids, of which there are 20. So the trick is to figure out how to convert sequences of DNA into proteins -- how to bake a human from the recipe stored in the chromosomes. It ain't easy.

The way you make a protein is by taking the DNA entries in threes. (Actually, the DNA gets converted into RNA first, but...) Because there are four choices for each of the three positions, the total number of combinations is 64, and there's a chart which shows how each of those 64 translates into a specific amino acid -- with three exceptions. Three of the entries are "stop", and what that means is "this is the end of this protein; stop adding amino acids and start using it." So the chart has to make it possible to access all 20 amino acids, and it has to be able to encode a "stop". But there's no particular rhyme or reason to the way that they're assigned to the chart; it's totally arbitrary. The recipe for a cake can be written in Russian or Urdu or any of a hundred other languages, and equally, there are a large number of "languages" in which the recipe for a human could be written representing different ways that this chart could be laid out. In fact, the number of possible "languages" is truly gargantuan. And any of them could be used, and as long as the "recipe" (the descriptions of those hundred thousand proteins) were translated to match the language of that chart, the result would be the same, and you'd still bake a human.

There are 64 entries and 21 essential values which must appear in that chart. The total number of possible ways in which the encoding could take place is 21 factorial multiplied by 43 to the 21st power.

21 factorial guarantees that every one of the essential values appears at least once. The other 43 entries each can contain any of the 21 values, which means 43 to the 21st power possible combinations to fill the chart out.


But the one thing which is necessary is that every member of a particular species use the same chart, because otherwise they wouldn't be able to breed. I got half my genes from my dad and half from my mom, and they better be encoded the same way, or my body isn't going to know how to understand them.

It is, however, NOT necessary for members of DIFFERENT species to use the same chart. This is critical. The encoding is arbitrary; as long as it's used consistently within a single species. There is nothing special about the particular chart that humans use; nothing to prefer it to any of the other charts which are possible. All that's important is that every human use the same one.

I happen to only speak English. But I can eat a piece of chocolate cake even though the cook only speaks Russian. And it will still taste good.

When a lion catches and eats a zebra, the meat can be nourishing as long as the proteins in the meat are made of the same amino acids as the lion uses, and as long as the lion has enzymes to break down those proteins. BUT the lion cannot tell and does not care what genetic encoding chart (language) was used to describe how to make those proteins as long as those proteins came out correctly and are made out of the right amino acids. In other words, he doesn't care whether the recipe for a Zebra is written in Swahili, or in Estonian, or in Chinese. All he cares is that the recipe itself was right and that the ingredients were also right, and that the cook understood the recipe. The lion likes to eat zebras, but the lion doesn't care what language was used by the cook who made the zebra.

And the recipe for a Zebra could be written in any of those 21!*4321 languages and still come out a zebra which a lion can eat.

In fact, by simple observation of a living organism and how it relates to its environment, there is no way to tell what encoding chart it uses. Actually, that's not quite true. There is one and only one way to actually tell that two different species use the same chart, though even here you cannot tell what chart it is. If a virus has the ability to move from one species to another, then it means both species use the same chart, because it means that they both interpret the genetic information in the virus the same way. We can prove that swine, geese and humans all use the same chart because all of us get influenza and the disease can move between us. But if you have two species which cannot trade viruses, there's no way to tell if they use the same chart. There are no viruses known which infect both Sequoias and humans. So there's no way of proving that we use the same chart as redwood trees.

However, the chart can be determined for any given species by laboratory analysis.

So here's where we reach the central point: EVERY KNOWN SPECIES USES EXACTLY THE SAME CHART. Here it is:

U UUU - Phe
UUC - Phe
UUA - Leu
UUG - Leu
UCU - Ser
UCC - Ser
UCA - Ser
UCG - Ser
UAU - Tyr
UAC - Tyr
UAA - Stop
UAG - Stop
UGU - Cys
UGC - Cys
UGA - Stop
UGG - Trp
C CUU - Leu
CUC - Leu
CUA - Leu
CUG - Leu
CCU - Pro
CCC - Pro
CCA - Pro
CCG - Pro
CAU - His
CAC - His
CAA - Gln
CAG - Gln
CGU - Arg
CGC - Arg
CGA - Arg
CGG - Arg
A AUU - Ile
AUC - Ile
AUA - Ile
AUG - Met
ACU - Thr
ACC - Thr
ACA - Thr
ACG - Thr
AAU - Asn
AAC - Asn
AAA - Lys
AAG - Lys
AGU - Ser
AGC - Ser
AGA - Arg
AGG - Arg
G GUU - Val
GUC - Val
GUA - Val
GUG - Val
GCU - Ala
GCC - Ala
GCA - Ala
GCG - Ala
GAU - Asp
GAC - Asp
GAA - Glu
GAG - Glu
GGU - Gly
GGC - Gly
GGA - Gly
GGG - Gly

This is actually the chart for RNA. "U" instead of "T" because RNA uses a chemical called "Uracil" instead of a chemical called "Thymine". Replace every "U" with a "T", then swap every A with a T and vice versa, and every C with a G and vice versa, and you'll have the chart for DNA. DNA is the complement of RNA. The three letter mnemonics are shorthand for the names of the various amino acids. For example LEU is Leucine. GLU is glutamic acid (most famous as being part of "mono-sodium glutamate" or MSG). PHE is Phenalanine, TRP is Tryptophan and so on. One of these is unique: MET is Methionine and the reason it's unique is that it functions as the "start" signal. EVERY protein begins with a Methionine and for chemical reasons it can only appear at the beginning of the protein chain. So it's always first and never anywhere else in the protein. And note that three entries say "stop".

This precise chart is used by bacteria, by fungi, by animals, by plants, by the slime on the bottom of the ocean, by EVERYTHING living. No exception has ever been found. There's nothing particularly special about that particular chart except for the fact that it's the one that everything uses. Any of the other 21!*4321 possible charts could have been used instead, except that none of them were. Evolution DEMANDS this because evolution predicts that ultimately everything alive started from a single original living cell. Evolutionary theory basically says that the initial creation of life was a low probability event, but that once it happened it spread very rapidly. Therefore, there was no opportunity for it to happen twice. Because of that, everything uses the same chart.

And it happens to be the case that this is so fundamental that any mutation in this area must have overwhelming effect on the organism, so overwhelming that the chance that it would be alive is essentially zero. Remember those hundred thousand proteins which make up a human? Changing one of these 64 entries would alter perhaps 5,000 or 10,000 of those in random ways; the chance of surviving this is so low that we can forget about it. All it takes is one critical protein being changed enough so that it can't carry out its function, and we have a stillborn baby. And the same thing is true for other organisms. So this encoding is mutation-proof. Any organism suffering a mutation in this area would simply die instantly because too many critical proteins would be built incorrectly.

How it actually would mutate is in the genetic description of transfer RNA; it would alter one of them so that they attached themselves to a different amino acid than before. There are 64 transfer RNA's, one for each slot in that chart. That's how that translation occurs. Alter any of them and the organism will die.

But Creationism doesn't require a single chart for all species. A single chart is not contradictory to the theory (because in fact NOTHING is contradictory to creationism, it happens to be unfalsifiable) but it's also not required. In a creationist scenario, there's no reason why the recipe for a lion couldn't be written in Swahili and the recipe for a Zebra be written in Zulu, which is to say that the recipe for a lion would use one chart and the recipe for a zebra use an entirely different and unrelated one. It is completely plausible under a Creationist scenario for every species to have its own chart. From external observation of the organisms and the way they live, it would be impossible to tell the difference between this case and the one where all of them are using the same chart (except for the behavior of viruses, as explained above). The lion could still eat the zebra and find it delicious, and no-one would ever know.

But in fact, they all use the same chart, and this fact is an essential part of evolutionary theory. And that brings us to our genetic engineers who are using evolutionary theory to get useful things done. The example I gave was the production of huge amounts of human insulin.

Genetic engineers have located the place in the human genetic library where the recipe for insulin is located and have extracted it out. They then produced what's called a plasmid, a ring of genetic material which includes the recipe for insulin plus a few other critical things like activation sequences. This plasmid was then injected into an E. Coli, which has by now reproduced and had billions of offspring all of which carry that same plasmid. What that plasmid does is program those particular E. Coli so that in addition to doing all the normal things that they do to stay alive and reproduce, they also produce a lot of human insulin along the way. Grow a big vat full of these things, then process it and extract out the human insulin, and you have a valuable and life-saving commercial drug. It has changed the lives of diabetics worldwide, because before this the only source of insulin was through processing of pancreases of pigs and cattle gotten from slaughterhouses, and while those forms of insulin are very similar to human insulin, they aren't identical and they don't work quite the same way, and in some cases some human diabetics had allergic problems.. Human insulin is simply better since it is exactly the form we really need, and has pretty much become the standard form used to treat diabetes.

The reason that genetic engineers can use E. Coli to reproduce human insulin is because E. Coli interprets DNA exactly the same way that a human does. Suppose that E. Coli had a different chart. In that case, while that genetic sequence could be inserted into the E. Coli, the E. Coli would interpret it entirely differently and produce something else entirely -- probably something completely useless, but whatever it was, it wouldn't be insulin. It's like that cook who only speaks Russian trying to work from a Spanish-language cookbook to try to make that chocolate cake. Maybe he won't make anything at all, maybe he'll make a mess, but he's not going to make that cake because he won't understand the recipe.

But E. Coli does use the same chart as humans, so E. Coli understands the recipe exactly the same way that a human does, and therefore the E. Coli does make human insulin from the recipe, just as the genetic engineers expect it to.

The recipe for every single living organism is written in exactly the same language. This is an essential prediction of evolution. If this were not true, eventually the genetic engineers would notice because one of their experiments in genetic modification would fail because the DNA sequence they've programmed will be interpreted wrong.

But that's never happened. Evolutionary theory predicts that everything alive uses the same chart. Genetic engineers are using that prediction to do their work -- and they're getting the right answer. Every time they do so, they're testing Evolution and proving that it is true.

If anyone ever finds an organism here on earth whose encoding chart is completely different than the one we know now, and as I mentioned there's an astronomically large number of possible encoding charts, someone's going to have a lot of explaining to do. (At the very least it probably represents an independent creation of life from the one we all know of now, though it may not mean that evolution didn't happen thereafter. But there will certainly be a lot of fundamental reappraisal of evolutionary theory.) If someone found a whole series of organisms and every one of them had a different chart, then overall Evolutionary theory as an explanation of the origin of life would be toast and we'd be back to square one. (Which is why creationists who claim that evolution is unfalsifiable are lying.)

But that's never happened. Every living organism which has ever been checked has turned out to use exactly the same translation chart as every other living organism. That's a very strong prediction of evolutionary theory, and the fact that genetic engineers are using that prediction as part of their engineering, and getting the right answer because they do so, is a very strong test and confirmation of evolutionary theory.

This is by no means the only way that genetic engineering tests evolution; there are dozens of ways. But it's easily the most important one, because none of the others would work if this one were wrong.

Until recently, it was assumed that ultimately all ecologies depend on energy from the sun, that every living thing either directly creates its life from the sun through photosynthesis or indirectly by eating something else which did that (or like the lion eating something which ate something which got its energy through photosynthesis).

Probably the most exciting ecological discovery of the last twenty years was an entire ecology which does not rely on the sun at all. It's at the bottom of the ocean, and instead of the fundamental source of food being photosynthesis, it relies upon what has become known as "chemosynthesis". The basic lifeform on which everything else relies is a bacteria which lives near underwater hot springs, and it gets its energy by extracting hydrogen sulfide (which contains energy) from the water and processing it. Everything else in that ecology directly or indirectly gets its food by consuming those bacteria. (Just in passing, they're all related to you and me; they use the same chart we do. They don't represent a separate creation of life, just an extremely unusual and totally unexpected ecology.)

This may not seem related, but it will all tie together. The four main moons of Jupiter all affect each other gravitationally and are constantly being flexed by tidal effects as they move around in different orbits. That's why Io, the innermost major moon, is the most volcanically active body known in the Solar System; it's constantly being heated by tidal effects. But the same kind of thing happens to the other major moons, just not quite as much nor as spectacularly.

In particular, it happens to Europa. The Galileo mission has shown evidence which is extremely convincing that Europa is covered with an ice sheet over a liquid ocean. The evidence is extremely strong that that ocean is there now and that it hasn't frozen all the way down to the surface. And since Europa's core is constantly being heated by tidal effects, the same thing which causes Io's volcanoes, it is virtually certain that Europa has hot springs at the bottom of that ocean.

And that leads to the interesting idea that an ecology like the one at the bottom of Earth's ocean could also exist at the bottom of Europa's oceans. That's why Europa is now top of the list of places in the Solar System which might also have life. And that is an extremely exciting possibility.

We don't know how likely it is for life to develop. We only have one sample; we don't know if it's rare or common. For all we know it's only happened once in the entire universe.

But if it can be shown that life developed independently twice in just this solar system, then we know that life is going to develop anywhere that it possibly can and that the universe is bursting with life.

If life is found on Europa, will it be the result of an independent creation or will it be infection from Earth (which is not implausible, for there may have been a time when there was no icecap on the ocean of Europa, and bacteria from Earth might have travelled there through space in the form of spores). How will we know?

If the life on Europa uses the same chart as life on earth, we'll know it's the result of infection. The chance of the same chart happening twice independently is astronomically small. If the chart is different, we'll know it's an independent development of life.

So we'll analyze the encoding that it uses to interpret its DNA. And that's how we'll know.

And if it's different, then it means that life is everywhere, that life in the universe is common, and this is something I very much hope is true.

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