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Posts Tagged ‘Biology’

When Charles Darwin wrote “On the Origin of Species”, he wrote about the difficulty of determining the actual mechanism of change in species from generation to generation. He was quite sure that the environment played a role in the final outcome of things via a survival of the fittest system. The problem in the theory of evolution was not that the strong thrive and the weak perish, because that is obvious. The problem is how does a species actually evolve? Darwin rejected the idea of incremental change over a long period of time as the likely cause of evolution. Instead, he looked at domesticated animals and observed how they could change over several generations by selective breeding. He thought that a mechanism similar to this, some sort of selective breeding that occurred in the wild, was the most likely mechanism of evolution. The “selective” breeding would occur between organisms that happened to be in the right place at the right time under the right conditions and they also happened to have the right genes for producing a successful hybrid. His theory was, in essence, that change in a species occurred due to a “natural” and chancy form of selective breeding. It wasn’t random change, it was more like lucky change. His theory then goes on to state the almost obvious: those changes that result in better adaptations to the environment result in better survival rates.

Darwin borrowed from the environmental theories of Malthus and concluded that as supplies of food increased in nature and animal populations thereby increased that those individuals most suited to the environment would prosper more than those who had been born slightly less suited. It was the principle of survival of the fittest. These survivors would then breed and the next generation would have the traits of the survivors. This was Darwin’s theory of evolution. The problem was, as Darwin admitted, how, exactly, does this generational change occur?

Many people take Darwin’s theory of evolution and proclaim that it is based upon random changes that occur in genes and those which help an organism to survive lead to successful adaptations while those random changes that hinder survival result in population declines. Darwin never advocated a theory of random change. His theory was more like a theory of natural selective breeding where the strongest get to breed and their traits are passed on to the next generation, very similar to what he observed in the farms of England.

Recently, genetic scientists have discovered that Darwin was wrong. It turns out that genetic change does not have to happen by selective breeding. It can happen by direct impact of the environment upon an organisms DNA. This new discovery states that the vast majority of our DNA, usually referred to as “junk DNA”, is not junk after all. Much of the human genome has been decoded so that we know where the code is in our DNA for blue eyes, or our blood type or even if we have a predisposition to some forms of cancer. Yet, the vast majority of our DNA is referred to as “junk”. That’s because scientists didn’t know what its function was – or if it even had a function.

In an article recently published in the New York Times , Gina Kolata writes that gene switches in junk DNA, “play critical roles in controlling how cells, organs and other tissues behave”. She states that, “…the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not.” It stands to reason that if the environment can change junk DNA and then cause a disease, it can also cause a change that results in resistance to disease or perhaps some other very different result. The real discovery here is that a mechanism has been discovered that can cause human DNA to rapidly modify itself in response to a factor in the environment. This must be the cause of evolution.

While the Times article is primarily focused on diseases being caused by exposing junk DNA to certain substances, it is only reasonable to ask whether this is in fact the mechanism of evolution. It is a direct connection between the body’s genes and the environment. Certainly, there will be cases where the environment contains toxins and these toxins will harm the DNA and cause disease. However, this is very likely the mechanism of evolution also. It is the way in which the body’s DNA senses that the environment is changing and tries to make the appropriate response. This is very likely the true mechanism of evolutionary change. It also explains why evolutionary change is, as Darwin noted, fairly quick and not a progression of minute changes.

It seems that Darwin’s notion of selective change occurring because of the coincidence of the right circumstances for the right individuals is not the likely explanation for evolution. It seems far more likely that our “junk” DNA is not “junk” at all, and it is this DNA (it actually comprises about 90% of our DNA) that results in “evolutionary” change. It seems that just as we are able to make conscious adaptations to our environment that there is another level of consciousness in our bodies, that we are unaware of, that is also continually working to optimize our body’s response to the environment and also that of the next generation of human beings.

Junk DNA is how evolution works.

 

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About ten years ago, inspired by the movie, Jurassic Park, I began to wonder whether it might be possible to clone a mammoth, an animal that has been extinct for about 10,000 years. I figured that because some of these animals have been preserved fairly well in the frozen lands of northern Siberia, some of the DNA might be intact. It seemed to me pretty clear that Michael Crichton’s idea of getting DNA from a preserved insect that had bitten a dinosaur was a little far-fetched. However, finding intact DNA in a well-preserved mammoth might be more likely. So – I decided to write a novel about the idea. I figured that would be easier than actually cloning a mammoth…

Well, it turned out  that writing one’s first novel is not so easy after all. While the first draft was completed in 2001, I found that I really needed to rewrite it – several times. Then, after I had written the best version of the novel that I could – I put it aside, because I didn’t think it was good enough. A few years later, while living in Ireland, I decided to take another crack at it. So, I rewrote the novel again with major changes. I liked it a lot better this time and only rewrote it two more times before I thought it was ready to publish. (Come to think of it, it might have been easier to just clone the mammoth.)

The basics of the story never changed: a Japanese professor decides to clone a perfectly preserved mammoth, and like in all good thrillers, things start to go wrong. Then they go very wrong. I won’t tell you the whole story, but if you are interested, you can buy the paperback version, or if you have a Kindle reader, you can download it from Amazon by clicking this link. Now, I’m not writing this just to call attention to my book – at least not entirely anyway. I decided to write this because something strange, perhaps even eerie is going on.

While reading yesterday’s Irish Independent newspaper online (I love this paper, they have so much world news that the U.S. press ignores), I came across an article about cloning mammoths. It seems there is this Japanese professor who thinks he knows how to do it and plans to do so by extracting the DNA from a well-preserved mammoth that was found in Siberia. He thinks he could have a cloned baby mammoth in about four years. I wonder if he has read my book? I mean the part about where things start to go wrong and then they go horribly wrong? Probably not, I’ll bet.

A few years ago, cloning was pretty controversial, but the idea seems to have become accepted now. Even so, I don’t think we are being served cloned lamb or beef yet, are we? And, I haven’t heard of any cloned babies being born yet – but they certainly could be, I suppose. I think we have the technology. But the idea of cloning an extinct animal – seriously – that should be considered very carefully. Now, if we are talking about an animal that went extinct in the recent past, like the Passenger Pigeon, because people hunted it to extinction – well, maybe that would be OK. But animals that became extinct eons ago may present dangers that we haven’t considered. These animals are no longer a part of our world and reintroducing them might cause unforeseen problems. I don’t think the professor in Japan that is referred to in the Irish Independent foresees any downside to his project – and that is what worries me because that is exactly like my novel. Really.

Perhaps, we need to have some sort of international body that considers certain types of advanced research and allows or disallows certain experiments. I can think of a couple of physics experiments that would fall in that category. I suppose there are several other biology experiments, medical experiments, chemistry experiments, and even computing experiments (like embedding computers in people) that might cry out for some oversight beyond that of the individual experimenter.

Mary Shelley implicitly warned us about this topic a century ago when she wrote her novel, Frankenstein. So far, no one has taken her warning seriously. You see, we only take warnings like that after the fact.

Someday, that strategy will prove to be too late.

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OK, I just learned something that a lot of biologists knew twenty years ago. That’s what I get for watching too many superficial news programs (you know which ones) and not enough of programs on PBS, like NOVA. I recently saw a NOVA episode called “Ghost in Your Genes” and I highly recommend it to everyone, if you haven’t already seen it. The principle idea of the show is this: your DNA is not your destiny. How can that be, I thought. Isn’t DNA the roadmap of our bodies? Well yes, but there is something else besides the DNA in the human genome you’ve all heard about. It’s something called the epigenome, and that makes all the difference in the world.

It turns out that the study of the epigenome and epigenetics is pretty much the hottest thing in biotech today. Who knew? Your genome (the DNA you were born with) and your epigenome interact with each other and the result of their interaction is the DNA you wind up with at any moment in time. The epigenome acts as a sort of gas pedal and brake system for each of your genes, and it is your genes that give you not only the color of your eyes, but every other feature of your body, and maybe your mind too. And those features can change, like when someone who is healthy develops cancer or when a normal child becomes autistic. It looks more and more like a lot of these changes are due to the accelerator/brake pedal action of the epigenome that is active throughout our lives.

If that isn’t amazing enough for you, then think about this: the epigenome’s activity is affected by the environment! It appears that exposure to certain toxins, like cigarette smoke or pesticides, can change the epigenome, which then instructs the DNA to change in your genome and the next thing you know, you have cancer. The epigenome can even be activated by psychological stress. You’ll have to watch NOVA to get all the details, but there is no doubt that this is an amazing discovery that will effect everyone’s healthcare in years to come. However, something else struck me about the epigenome’s activity that the NOVA program didn’t cover. I believe that the epigenome might be the key to explaining evolution.

Ever since Darwin, evolution has been described as adaptation to the environment. Up until now, evolutionists have explained its mechanism as “natural selection”. The idea is that nature makes random mutations in organisms, and some of these work successfully and some don’t. Organisms that receive the good mutation become successful and climb higher up the food chain, while the unlucky recipients of the funky mutations become dinner. The existence of the epigenome presents us with a possible alternative explanation that I have long suspected must exist, an agent of adaptation other than random mutations. By using the brake/gas pedal action of the epigenome, our genome has the capability of responding and adapting to changes in our environment. These successful adaptations are then passed down to succeeding generations. However, sometimes the epigenome makes a mistake and presses the gas instead of the brake (hey, it’s not exactly a HAL 9000 computer, you know). When that happens we get adaptations that don’t really work all that well. Sometimes they actually backfire. We call those diseases.

You have undoubtedly heard about the debate between creationists, who tend to base their arguments on the Bible, and deny the existence of evolution and the evolutionists, whose Bible is the works of Charles Darwin. The real issue here is this: at its core, is the universe deterministic or is a random process. If you choose “deterministic” you have an argument for the existence of God, and if you choose “random process” you have an argument against the existence of God. (It’s sort the same argument that physicists have about quantum theory.) The action of the epigenome, as an agent of adaptation, may serve to sweep away much of the argument. The working of epigenome might explain how man has evolved from the apes, but the creationists could embrace this by saying that the epigenome was long ago included in our biological tool kit by a Creator. Wonderful! Argument over, right? Maybe not. That only pushes the argument back to whether the epigenome was created, or did it evolve by random chance. I think I’ll leave the discussion of origin of the epigenome to others for today. It is enough for me to think that this epigenome might be the smoking gun I have always thought there had to be: nature’s agent of evolutionary change. That is amazing. (By the way, that is not the contention of the NOVA program; that is just my own thought.)

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