In Rome, one of the most astonishing mosaics is found in the Basilica of San Clemente. There, the cross in the center dominates the scene, but out of its foot an acanthus bush grows with many curly vines. In the circles formed by the vines are many scenes, some sacred, but most what we would call secular. There's a woman feeding chickens (right now, that would be Aidan up there, he loves chickens) and other humble professions of the time found on that church wall with the saints. Animals drink from the waters flowing out of the foot of the cross, streams of living water that evoke the Psalms, Ezekiel, even the end of Revelation.
This mosaic shows that even the most "non-sacred" things can be centered on the cross and done as worship, say, feeding the chickens, paying taxes or making dinner. By extension, the most mundane little experiments in the lab are acts of worship. A "scientific" version of the same mosaic could be made today, with the biologist, the ecologist, the chemist, the teacher, the computer programmer, each in their circle, enfolded by the tree of life springing from the foot of the cross.
The animals, too, each have their place on that mosaic, overshadowed and encircled by the cross at the center of creation. I imagine a "biological" version of the tree where each animal is encircled by the acanthus and joined to the same root. The deep connection that comes from being formed by the same creator is shown by the acanthus embracing them all.
Little did they know at the time just how deep that connection runs, and shows throughout biochemistry. If you sample jellyfish DNA and rabbit DNA, you'll find that the same four chemicals make up all of it. The DNA carries the blueprints for making proteins, and the proteins are made of the same twenty amino acid chemicals in jellyfish as are in rabbits. Because these are the same chemicals, we have been given the extraordinary power to take tiny molecular scalpels and sculpt the DNA, moving it around as a chemical using other chemicals. Here's a vivid example. Some jellyfish have a protein that glows green under a black light. Using biochemical tools, you can take this gene out of the jellyfish, put into an albino rabbit, and behold, you get a green glowing bunny:
This is only possible because the same 4 pieces make up DNA in both species. It's a little funny and of course a little scary too. It brings up the question of what we do with this power, questions that deserve to be talked about more, in other blog posts. But my point here is that, like it or not, this power has been given to us because bunny biochemistry and jellyfish biochemistry rely on the same 4 chemicals.
I exploit this similarity in my research. We study human immune system proteins, but we need a lot of pure protein for our studies. So to make it, we take DNA for the human protein and put it in bacteria and tell them to make it. For our proteins, the bacterial make a protein that is functionally and structurally the same as the human-made proteins. There are some peripheral differences, but the primary protein is the same, and we can use it to study how the system works and, if grace allows, to improve on it.
This biochemical snap-in/snap-out interchangability is indeed universal. If each species were a separate creation, there would be no need for it. But it would have to be universal if every species grew from a single root. Geology gives us the time, and DNA gives us the similarity between creatures and also the fluidity to change one to another. Remember that DNA is a chemical in solution. That means it floats around, degrades, breaks apart, in short, that it's fluid. This fluidity can happen in small changes (point mutations) or large changes (big chunks of DNA flying around like mentioned before for viruses). But when coupled with the old age of the universe, it provides an elegant mechanism for animals spouting up from a single root. These species, or as Darwin called them "records of Creation," contain the same language deep down in their DNA, and once you read the language from those records, it tells a story of relatedness and change.
Humans and mice have 90% of the same genes in their DNA. Even humans and flies have 60% of the same genes. You can take a mouse eye gene and put it in a fly and it will grow an eye like that gene tells it to (thank goodness this doesn't work all the time). We even have the same tail genes as a mouse does, but they are permanently switched off (again, whew!). You can see this yourself with free databases online: you can look up a gene in one species and find its equivalent in another. Invariably, the genes from species that look more alike also look more alike on the chemical level. But across the biosphere, there's so much similarity that we can look at stromatolites (from Day 4) and look at us and find the same protein with the same function, using about the same order of amino acids. To quote Bill Bryson: "About half the chemical functions that take place in a banana also take place in you." When you scratch the surface of anything alive, you find the same chemicals underneath doing almost the same things.
See for yourself. Below is a simplified picture of two "thioredoxin" proteins, lined up. The red protein is the human version and the yellow protein is the fly version. At this level, you can see that they are pretty much the same in structure, and they serve the same function.
This deep biochemical similarity gives us a mechanism for how creation could have happened, that there is enough biochemical fluidity for one animal to change into another over time, and that they can look very different and yet use the same chemicals underneath. It has other amazing benefits as well. It means at the Fred Hutchinson Cancer Research Center that there's a whole floor of scientists who work with yeast. Yeast don't get cancer, but they do grow using the same genes as human cells, so if you're interested in how human cancer grows you can study how yeast grows and get ideas for how to fight cancer. This even resulted in a Nobel Prize in 2001 for an FHCRC scientist. The fact that you can get a handle on how cancer works from studying the microorganism used to make beer and bread is a clear gift of grace.
Some scientists like Michael Behe object that the differences between species are just too great to be accounted for by chemical kinds of change. Behe says that small changes might happen, but big changes couldn't. As a metaphor he says you can't jump over a 100-foot wide canyon, the distance is too great, and changing from one species to another requires a "jump" too far. He says that biologists claim that species changed incrementally, requiring 9 buttes 10 feet apart to jump across the canyon, and then that the buttes disappeared. He points out that this sequence of events is unlikely. (Darwin's Black Box)
I agree that it's unlikely, but I disagree with Behe's metaphor. Animals deep down are not like rocks. They are fluid collections of chemicals. So I would expand his metaphor just a bit. Remember that at the bottom of every canyon there's a river, and stuff floats down that river. If the river's fluid enough, you can cross a 100-foot canyon by jumping from log to log across the stream. In a fluid system, you could have that kind of change adding up. It's like a game of Frogger when you get down to it. Remember that species have all the same chemicals deep down, and to get from species to species you require a rearrangement of chemicals: the deep fluidity of the tree of life allows it all to connect. (My friend Scott Becker actually used a similar metaphor involving a river for revelation to the church, but that's neither here nor there -- I just like to cite Scott when I can.)
If proteins are essentially flexible and fluid, then they should be able to do a lot of different things, and they should be able to change what they're doing. In the lab, they can. A good example is the recent work of Michael Hecht and Shona Patel. They made 1 million simple proteins in a test tube, and made them randomly, with only the constraint that they should fold up into a coherent protein structure, or in other words, that they shouldn't stick together into globs like scrambled eggs or fall apart without warning. They didn't encode for or select for any chemical function whatsoever. As far as they knew starting out, the proteins should have just been oily blobs floating in the water. But they were actually highly chemically active, just by chance. From this random pool they found the following:
1.) a subgroup of proteins that could bind heme (like red blood cell proteins can)
2.) a subgroup of proteins that could make oxygen radicals (like immune cells can)
3.) a subgroup of proteins that could break ester linkages (like digestion proteins can) and
4.) a subgroup of proteins that could break lipids (like cobra venom can).
These functions are just waiting to happen from a random group of proteins. Something about proteins, they just can't wait to do biochemistry. From each of these subclasses, just a few minor changes could make an efficient protein that would do each of these four different reactions, from the same randomized starting point.
This causes a problem for some people. These chemical reactions are random. When DNA gets a mutation, that's a chemical event, and it's caused by the jostling of various waters and carbons around. If this is the basis of life, doesn't that mean life is built on a foundation of randomness? Doesn't that mean life is meaningless?
Some scientists, the "anti-Behes," would say just that. But they are just as wrong as Behe, because meaning can and does emerge from randomness. In chemistry, we have an entire field of statistical mechanics, which is all about what predictable (and I would say meaningful) results come from random collisions among a large collection of molecules. Life is based on solution chemistry, and the random behavior of solutions is what allows life to proceed predictably. I would go one step beyond "predictably" and add the implication of "therefore it's meaningful," but when I do that, I step outside what science can do and must shed my lab coat. The opposite's true too. When anyone draws the opposite inference, by focusing on the randomness at the bottom levels of life and saying that what springs from randomness must be meaningless, they, too, are stepping outside of the science of randomness into the philosophy of meaningfulness, and I don't think they're right.
You know, the best proof to me that proteins changed and were modified over time is that if I want to make a protein do something new, I can evolve it myself in the lab. I can use the tool of "descent with modification" in a test tube to create a new protein and new functions. I think the tool of being able to modify and grow new protein functions is a gift of grace. This convinces me that God could have used it too. He didn't have to, but this is the way I'm convinced he did it, and I am trying to figure out what it means. Once the framework for multicellular life was set, DNA recombined, new life forms grew, died, grew again, creation itself accelerated and the earth began to celebrate with fruitfulness and abundance. The result is beautiful and terrible.
Then God said / “Let the waters abound with an abundance of living creatures / and let birds fly above the earth / across the face of the firmament of the heavens” / So God created great sea creatures / and every living thing that moves / with which the waters abounded / according to their kind / and every winged bird according to its kind / And God saw that it was good / And God blessed them / saying “Be fruitful and multiply / and fill the waters in the seas / and let birds multiply on the earth” / So the evening and the morning were the fifth day.
In part 2, we'll take a closer look at the "abundant life" that exploded across the scene at this stage of history, which was abundant in every way imaginable.
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