Sunday, October 28, 2012

Evolutionese and lncRNA

The ENCODE research that I have written about in the last two posts said that 80% of the DNA in our cells is functional.  By that they meant that it is copied and so has biochemical activity.  However, some evolutionists still resisted accepting the functionality of all that DNA by denying that this copying was really purposeful. Previously, only about 1-2% was understood to be the active part of genes, and the rest of DNA believed to be just a broken-down relic of millions of years of evolution.

Now, research by a commercial lab has been published which has discovered that some of this extra DNA which was formerly called "Junk" is necessary for regulating RNA translation into protein.  DNA is copied into RNA, and more and more types of RNA are being found.  Not only does RNA get directly translated into proteins which are the work-molecules of the body, other types of RNA can either stimulate or stop the protein production.  Among them are long, non-coding RNA (lncRNA) which does not code for proteins directly (as does messenger RNA) but is part of a regulatory system.  It is further described at Discovery Institute Evolution News and Views here if you are interested.  Here is also a link to the story in Science Daily which is worthwhile.

It is quite ironic that a group of evolutionists are fighting this new knowledge, since the scientists in the ENCODE report do not give up on materialistic, naturalistic evolution themselves.  There is an abstract of the report by MIT scientists Ward and Kellis about the findings and how they relate to evolution here.  The first sentence reads:
Although only 5% of the human genome is conserved across mammals, a substantially larger portion is biochemically active, raising the question of whether the additional elements evolve neutrally or confer a lineage-specific fitness advantage.
This is Evolutionese for insisting that the possibility of materialistic, naturalistic evolution by chance mutation and natural selection still exists.  I speak Evolutionese about as well as I speak Spanish.  I've studied both quite a bit and can pick up pieces of meaning.  I can read the languages, but they don't always make sense to me.  In Spanish, though, the translation problems are my fault.  In Evolutionese, there always seems to be an attempt at obfuscation.  [The Freedictionary definition of obfuscate, just so I don't commit the same mistake, is 1. To make so confused or opaque as to be difficult to perceive or understand.] 

To digress a bit, just once I'd like to see a paper come out and talk about the findings and their evolutionary implications in English.  Though most sciences have their own jargon, many people are concerned about the teaching of evolution in the classroom.  Especially now that materialistic evolution has been proven wrong, scientists' statements on this topic should be made plain.

I got the Ward and Kellis article and read it.  I would have really liked to understand their work, but I didn't.  Many people yell when they speak to foreigners, assuming they will then understand them.  I'll try it.  "ARE YOU SAYING ONLY 5% OF THE HUMAN GENOME IS THE SAME AS OTHER ANIMALS BUT AT LEAST 80% IS ACTIVE AND THE ENCODE SCIENTISTS ARE SAYING IT MIGHT TURN OUT TO BE 100%?  I HAVEN'T HEARD MUCH ABOUT THAT IN THE PRESS. SO WHERE DID ALL THE UNRELATED, FUNCTIONAL DNA COME FROM?"


Well, I know that the Neutral Theory of Molecular Evolution never had a chance in the first place before we even found out that DNA is all functional.  The probabilities of getting functional proteins by chance have been known since the 1990's at least to have been astronomically small even if organisms had billions of years to give it a try.  Not all proteins are closely related, and only 1 in less than an estimated trillion, trillion, trillion, trillion, trillion is functional (1 in 10^63 by the research of Reidhaar-Olsen and Sauer back then on average-length proteins.)  The chance mutations coming from the reproduction of organisms from one generation to the next were supposed to take place in the part of the gene not used by the organism, only to take over when forming something functional, but the numbers did not add up. It is estimated the Earth could have supported less than 10^50 organisms in the supposed billions of years it has been habitable.  So all those organisms couldn't have produced enough changes to get one functional protein operating in time to be selected for better fitness than the ones already working.  But with all of DNA having a function, very little sifting power is left.  Gauger and Axe have done some great research in showing the problems of molecular evolution.

And now Ward and Kellis wonder about a lineage-specific fitness advantage?  "AY?  SAY WHAT?" I ask.  "ARE YOU PROPOSING THESE GENES ARE WHAT MAKE HUMANS WHO THEY ARE?"

I'll finally go back to the point of why evolutionists are fighting about the functionality of DNA:  they KNOW what a fully functional DNA molecule means.  All we heard from the press after the first comparative genome projects was how DNA genes in humans matched 98% of monkeys. At the time, they thought the rest of the DNA was worthless.  Everyone in that camp was crowing that evolution was now a fact.  But the 98% similarity was just the protein-coding part, only about 1-2% of the whole length of the DNA in each cell. They know that if DNA proves fully functional, it doesn't matter what scientists say with their Evolutionese.  It won't matter how they mix words together.  We will all be able to really understand what that means: materialistic, naturalistic evolution is impossible.  And fully functional DNA is already proving, from the ENCODE project and the work on long, non-coding RNA's, to be true.

Tuesday, October 16, 2012

More Than Millions

The National Human Genome Research Institute, under the National Institute of Health, located in Bethesda, MD, announced the results the latest 5-year project in a continuing study of human DNA. The press release of the Encyclopedia of DNA Elements, or ENCODE, project states in part:

During the new study, researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions where proteins specifically interact with the DNA. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell. The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes themselves. They also identify where chemical modifications of DNA influence gene expression and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.

Though I don’t want to overload you with numbers, I assume you can easily imagine winning a million dollar lottery. Take a million times a little more than 3 thousand and that is about how many DNA units carry on their work in our body’s cells: over 3 billion. Take a million times 75 million and that is approximately how many cells we humans each have: 75 trillion. Almost all of these cells contain the full 3 billion complement of DNA with the functions identified by this ENCODE project. Among other things, they have found that various, specific sets of switches are active depending which cell type is studied.

Before this latest part of the project was released, we were under the impression by an initial study, called the Human Genome Project, that there were only about 20,000 genes comprising about 1-2% of the DNA code. There were inklings that other things were going on, but by and large scientists thought that the rest of the DNA, which was called “junk,” was accumulated from millions of years of evolution and basically worthless. However, they were getting practically nowhere in understanding how some genetic diseases and even cancerous tumors come about. Now they are seeing that these previously unknown switches have a great deal to do with the actions of DNA and small mistakes in their functions can cause big problems.

This false prediction of evolutionary theory is no joke. It cost precious time and kept monies from being available to learn more about the rest of the DNA. Fortunately, scientific curiosity prevailed. After the Human Genome Project, the first ENCODE endeavor included looking at just 1% of the rest of DNA. The scientists found activity for the small molecules that were made from DNA but not translated into protein. These, therefore, were useful products from parts of the non-gene-producing DNA. Surprised by this study, scientists desired to know more and procured the necessary money and manpower needed (both considerable). The results of the ENCODE research were published in over 30 papers in several scientific journals in early September, 2012. Numerous other journal articles have already been spawned from the basic research.

Sadly, the scientists still refer to evolution. Though evolution has many definitions, the one accepted in modern scientific terms is the one that refers to totally materialistic, naturalistic, random formation of life, both originally and in developing speciation. It relies only on the laws of chemistry and physics to bring about the first creature known as the common ancestor and develop diversity from it. There has been no discussion of which I’m aware in all the scientific articles of any other possibility.

Let me be the first to tell you, then, that the latest ENCODE results prove that materialistic, naturalistic evolution is impossible. Scientists already knew that active parts of DNA were too valuable to change much. Mutations are usually bad for the metabolism of the organism. That’s why they focused on the “junk” as available to change “neutrally,” part of their “neutral theory of molecular evolution.” Though this already was doubtful to anyone who understood probabilities, the theory should have been scrapped for sure in 1990, when two MIT scientists published a paper about their tests on what proportion of the combinations of amino acids, components of proteins, would be found functional. They gave the astounding number of 1 in 10 to the 63rd power (written 10^63). 10^63 is a 1 with 63 zeroes following. A trillion is a million times a million, or 10^12. You would find less than 1 functional protein in a trillion trillion trillion trillion trillion of them. A billion years would be a drop in the bucket to form even 3 useful proteins, much less for them to find each other. A free-living organism is estimated to need 1000 self-producing proteins to survive.

It was then that every headline should have shouted: Discovery Brings End to Darwin’s Theory! Of course, one study could be wrong. But since then, similar results have been produced many times. And now the ENCODE project has shown that the “junk” is not available for mutational experimentation and re-arrangement anyway. The non-gene part of the DNA, now being called “dark matter,” is projected to be found almost 100% functional by the time more experiments evaluate even more types of cells.

But the headlines never seem to come that announce even the possibility that blind physical forces are not the whole story of life. And scientists and the media wonder why people don’t trust them. Even before these revelations, many persons thought there could have been evolution over eons directed by God as well as those who believe in a young Earth. I know from studying genes that though I am amazed by the discoveries of technology, it is unlikely I will get the whole truth from modern scientific journals and the media. I hope that though the jargon and numbers may be difficult, people will realize they can understand what the research reveals. It’s worth more to them than a million dollars.