Ah … Chemistry! Part 2

| January 1, 2021 | 0 Comments

In Part 1, we skimmed over the very basics of chemistry, learning that everything physical on earth is made up of chemicals. We watched our persona named Anabaptist Andy blow up his lab trying to make water by combining two parts of hydrogen with one part of oxygen. We saw the periodic table, which lists all currently known elements.

Only the essentials

Let's continue our story with the persona named Anabaptist Andy ...

One day Anabaptist Andy learns that he only needs 25[1] of the 118 elements on his periodic table to make anything living on earth. That’s right! With a supply of those 25 “essential elements,” Andy could—at least in theory—make any living Plant, Animal, Fungi, or Protista that exists on earth. These are the four kingdoms that have life, while there are other elements on earth that are not necessary for life, but make up things like rocks and metals.

Now, that makes chemistry sound really exciting, not? Besides only needing 25 elements, the fact is that just four of those elements make up 96% of the matter of all living creatures. Just four! That means that if you can get a good handle on how to mix those four elements together in various concoctions, you could—at least in theory—be 96% done with creating any living thing.

Since this sounded so great, let’s imagine Anabaptist Andy ordering supplies for his lab. Here is his packing list when the UPS truck pulls away after unloading his order:

In 55 gallon drum size:[2]

1 Hydrogen

1 Oxygen

1 Nitrogen

1 Carbon

Next, in gallon buckets, he received:

1 Calcium

1 Phosphorus

1 Potassium

1 Sulfur

1 Sodium

1 Chlorine

1 Magnesium

Then, in pint containers he received:

1 Boron

1 Chromium

1 Cobalt

1 Copper

1 Fluorine

1 Iodine

1 Iron

1 Manganese

1 Molybdenum

1 Selenium

1 Silicon

1 Tin

1 Vanadium

1 Zinc

As mentioned already, the first four elements make up 96% of the matter in living creatures. The next set, in the gallon buckets, make up 3.5%. The other 14 elements make up .5% of all matter in living things. These percentages will vary, of course, from species to species, but these are the averages.

Knowing that he may need some help to put the elements together, Anabaptist Andy hires Henry Helper. Let’s imagine a conversation as they stand, hands in pockets, looking at their supplies in the storeroom.

“Where do you think we should start, boss? Should we make an elephant? Wouldn’t that be a great seller? I can imagine that people in our neighborhood would buy them left and right if we don’t go too heavy on the price. I know we don’t have enough supplies to make a full-grown specimen, but we could make babies and let them grow. I think we could make two or three small ones. The chemical composition is basically the same for big ones or small ones.”

Andy scratches his chin. “Um, maybe we should start with something a little simpler. It is true that we have all the elements here to build an elephant, but we are just getting started here.”

“Well, how about a koala bear? I hear they are dwindling in numbers. They are so cute. I think we could sell them to zoos pretty easy.”

Andy shakes his head. “Henry, do you realize that a koala bear is just as complicated as an elephant? It is smaller, yes, but they are not going to be much simpler to build.”

“Oh, you are right. I need to think about this a little more sanely.” Henry pauses a bit, then adds, “Well, how about making a walnut tree? I think we have enough supplies to make a 6” diameter one; that would give us a 10-15 year start on growing one from seed. And there would be no eyes to build, no ears, no mouth, no stomach, no heart. Trees are quite a bit simpler than elephants and koalas! Let’s get going!”

Andy is still scratching his chin. “No, think about this some more Henry. We are going to have to start with the basics.”

Now Henry starts scratching his own chin in contemplation. “Hmm. Well, how about just some grass? We could eventually make hay. We have all the stuff here, and we wouldn’t have to mow, rake, and fertilize it. We could even make it in the dead of winter.”

“That’s true, Henry. We have all the components here on the shelves to make some grass. We have to start with just one blade, first, to learn how. But I am still thinking that we need to come up with something simpler yet.”

While scratching his chin some more, Henry suddenly realizes that Andy’s missing beard and eyebrows—singed away when the H2O experiment blew up—would be a good place to begin. “Hey, let’s build some eyebrows! How much simpler could you get? If we can learn to do that, we could get rich by making hair in the lab and selling it to bald men!”

“Yeah, good idea,” replies Andy. “Let’s do it!”

It’s that simple

Perhaps you are turned off by my little story of Andy and Henry; I created it to make a point. Do you realize that it is true that they have at their disposal everything needed to build any living species on earth? And it is true that 96% of every living species is composed of just the four elements in the 55-gallon drums? It is that simple. (Except, of course, once they have it built, they would have to infuse life into it. This is the secret that only God knows!)

But it is also that complicated. How many different mixtures can you make from 25 elements? The number is infinite. Even with just the four main elements, there are an infinite number of mixtures.

When I consider this, worship wells up in my heart. What a Master Chemist we have! To think that He created every living creature with just 25 elements amazes me.

But let’s go back to our story of Anabaptist Andy, the chemist who now wants to build a hair in his lab.

Simple hair

When Andy looks into the chemical composition of a hair, he will find that hair is a series of keratin scales. When these scales are broken down, they become a chain of proteins. When the proteins are broken down, they become a chain of amino acids. About 500 amino acids have been found in nature.

So, to build a hair, Andy is going to have to start building amino acids. I want to re-emphasize that he has all the elements necessary to build them; it is just a matter of learning how to mix the elements. This is called … chemistry!

Let’s look at 21 of the 500 different amino acids found in nature. Don’t let the chart overwhelm you.

amino acid chart

Image: CCA-by-SA Wikipedia user:Dancojocari

Do you notice something? See all those N, O, and H’s? This tells us that these compounds are, indeed, made up largely of just hydrogen, nitrogen, and oxygen elements, of which Andy has a 55-gallon drum of each.

So, let’s make a simple amino acid. Let’s start with the simplest-looking one, found at the bottom left, called Alanine. First Andy the chemist will need to bind a hydrogen and oxygen atom (top part of the Alanine diagram). Then he will need to bind a nitrogen atom with two hydrogen atoms (to make the right side of the diagram). When he has those two chemical compositions made, he will need to bind those two together along with a single oxygen atom (the left side of the Alanine diagram).

We learned in Part 1 that it takes heat to bind hydrogen to oxygen. But how do you bind nitrogen to hydrogen? I do not know. Andy would have to learn this process. It may happen with heat. And that heat may be a different temperature than what it takes to bind hydrogen to oxygen. But sometimes elements bind by the use of electricity. Sometimes it takes a third chemical element mixed in to get the first two to bind.

If it were only that simple! Sometimes when you try to bind the third element to the first two, one of the other two will unbind. Or if you use the third element to bind two others, the third will bind right in with them, leaving you with an undesired element in your composition. Or maybe one of the two hydrogen atoms will unbind when you try to add a nitrogen to it. Now you have NH instead of NH2. Maybe Anabaptist Andy, the chemist, had better go back to driving nails instead of mixing chemicals!

Ah … chemistry!

To edit DNA

Now that we have skimmed the very (but very) basics of chemistry, perhaps we can make some sense of how to edit DNA. A strand of DNA is nothing more, and nothing less, than a string of chemical elements that are bound together. And remember, only the 25 essential elements will be found in that string, with most of them being H, N, O, and C. If you take about two billion of these 25 different element atoms and bind them together, you can come up with a strand of DNA. (To make a typical strand, you need 2 billion atoms. Stretched out it would measure about six feet long, but remember each atom is about 1/100,000,000 of an inch big! They are coiled together into a tiny packet, like twisting a yarn string tighter and tighter until it becomes a coiled up little ball.) Depending on the sequence of those atoms, different aspects of the living creature are somehow coded into the creature's being. My DNA has made me with red hair (which is actually a double genetic fault; blond hair is a single genetic fault, from the norm of black hair that covers 80% of humans), left-handed, 5’-10” tall, and every other detail of my body. Even some character traits are encoded in DNA, while others seem to be learned. Please, please do not ask me how all that works!

So how do you edit that string of DNA? Remember how heat bound hydrogen to oxygen? Well, sometimes heat will unbind two atoms. Sometimes a charge of electricity will bind or unbind two atoms. Sometimes a certain chemical composition will bind or unbind two atoms.

DNA editing is possible if you know where you want to cut the DNA strand. If you know what two atoms in the chain you want to unbind, then you need to find the formula for unbinding those two particular atoms.

Think of a log chain with a bad link. You find a way to unbind both ends of the bad link, so that you can then add a good link back in, right? In a log chain, the necessary unbinding action is the same: cut the metal with a hacksaw, grinder, or torch. In a string of DNA, you may need to “cut” it with heat, electricity, another chemical, etc. And, you may actually need two different types of cuts, because the part you want to cut out may have different “joints” on each end.

But how do you get the teeny-weeny section out of there, and replace it with what you want, once you have unbound the chemical links?

There are several methods, but one with which you may be familiar is centrifugal force. Remember the old cream separators that spun around? When the unseparated milk is streamed into the spinning wheel, the denser parts fling further out, while the less dense parts stay closer to the center. This separates the cream from the other parts of the milk.

In the same way, once a string of DNA is cut apart, a centrifuge can be used to spin out the separated part.[3] Obviously, when a person is editing DNA, he is not editing a single strand somewhere. He is editing a whole bunch of it at a time. By adding enzymes, for example, he unbinds the chain at points X and Y, then spins out what is not wanted. When that is finished, he adds back into the mix what he wants … and hopes everything binds back together as it should.

Did you notice that I wrote “hopes”? The fact is that in the best cases, only about 30% of the time does the reintroduced material bind back properly. There is still a lot of hit and miss in gene editing, with more misses than hits. When it does happen successfully, they do not tell you how many times it took them to make it happen correctly!

Simple, but complicated, but simple

Obviously, what I have just written about editing DNA is very simplified.[4] Anabaptist Andy is not going to go to the library and borrow a book with chemical formulas that will unbind the elements of DNA at certain points. With that book in hand, he will not go home and dig out the old cream separator and start tinkering with the DNA in his chickens. On the other hand, as mentioned earlier, it does not take a super-expensive, sophisticated machine to do DNA editing.

Summary

When we do not understand something, such as chemistry, we can have a tendency to fear it. Some scientists have scared Christians away from science by claiming that science proves that God does not exist. We need not fear chemistry. It is an amazing show of the majesty and power of the Master Chemist. When one studies even the basics of chemistry, he will begin to see miraculous examples of wonder that will cause worship to rise in his heart. Ponder for a long time, for example, on how only 25 elements make up every living species on planet earth, but chemists are barely able to make the simple amino acids in their labs. And no one has ever been able to add life to his compounds!

In the third part of this series we will look at some of the ethical implications of genetic modifications. What good have man’s chemical experiments accomplished in this world? What evils? What should we avoid?

Stay tuned!

Ah … chemistry!

~Mike Atnip

[1] There is some debate over whether other elements may be needed in some species, but in general these 25 are considered as “essential” across the scientific world.

[2] Some of these are gases, which would not come in a drum as such. But for simplicity’s sake we are going to put everything in a common container for the story.

[3] There are also other methods than centrifugal force. For this article I will not explore them.

[4] And I do not claim to understand it all. A real chemist might laugh his head off at my attempt to explain it!

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