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 by Casey Luskin at Discovery Institute Evolution News HERE if you are interested. 

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.  For example, two MIT scientists integrate ENCODE findings with the Human Genome Project in Ward and Kellis, "Evidence of abundant purifying selection in humans for recently acquired regulatory functions," Science 337, 6102 (Sept. 28, 2012): 1675-8.  The first sentence of the abstract 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 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?"

As you can see from the above quote, they would then say to me, "WE ARE WONDERING WHETHER THE ADDITIONAL ELEMENTS EVOLVE NEUTRALLY OR CONFER A LINEAGE-SPECIFIC FITNESS ADVANTAGE."

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 which I mention in a previous post.)  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 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.

More Than Millions

The National Human Genome Research Institute, under the National Institute of Health, located in Bethesda, MD, announced the results of the latest 5-year project in a continuing study of human DNA. (2019 Update: the press release of the Encyclopedia of DNA Elements, or ENCODE, project was an archived web page, but as of 2026, Encode website HERE.) The article 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. The paper is JF Reidhaar-Olson and RT Sauer, "Functionally acceptable substitutions in two alpha-helical regions of lambda repressor," Proteins, 7, 4 (1990): 306-16. 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. 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.

ENCODE: DNA Junkless

ENCODE is a project that has been studying DNA since the Human Genome Project (HGP) laid out the entire sequence for humans. Results have just been published by The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature 489 (Sept. 5, 2012): 57-74 on the latest research concerning the function of DNA in the areas between genes.  They have found at least 80% of DNA to be functional, from a previous estimate of 5% to 10% (a pretty big miss).  Before, many scientists insisted that most of DNA was junk, accumulated through totally random mutation of genes.  Francis Collins himself, leader of the HGP, used junk DNA as an example of materialistic biological evolution. I'm generalizing by putting all scientists in a lump, but let's face it, we don't see many supporting Creationism or Intelligent Design Theory.  However, though they are saying one thing, they must be thinking another, since they sunk about $200 million into the study.  Why study junk?  Because more and more small studies supported evidence that non-protein-coding areas had to do with gene regulation.  They could no longer ignore it.  They may even find that 100% of DNA is functional when they further improve their ability to detect activity. 

The findings are described in a number of scientific journal articles. You can find much more at a website arranged by Nature called the Nature ENCODE Explorer. It has various threads to help you, as it says there, to "Access the collected papers by exploring the thematic threads that run through them, such as DNA methylation, RNA and machine learning."

Most evolutionists want you to believe evolution is totally materialistic, without any Divine guiding hand.  This affects our school textbooks and even what they want parents teaching their children.  Researchers now think there are 4 million switches in DNA for gene regulation to form parts of the body and get it to work.  Billions of years sounds like a lot of time, but it is a drop in the bucket compared to the probability of all this coming together by chance.  Changing one's mind can be very difficult, but on the other side is an amazing world of wonder. 

One down-side to this research is that human embryonic stem cells have been used for it and are continuing to be used for further discovery.  If there are other ways to learn about these things I would challenge scientists to use their ingenuity to find them. That is a discussion the whole country (and world) needs to go into.

Even without the use of human embryonic stem cells, we are seeing more of the complexity of DNA and the cell.  May more and more of us praise the Lord, through Jesus Christ, for His wondrous, amazing works.

Happy Summer or Winter

Hi there.  Hope you are having a nice summer (those of you in the northern hemisphere).  I wish a nice winter to the folks down under (not just Australia). 

2019 Update: I previously had some instructions here for printing out the booklets, Heaven's Passport and Creation Science for Biology.  But that was a long time ago and would probably not be applicable any more. I still feel these are good booklets for edification and evangelization.  I see them as a way to approach and teach people about the subjects. So I hope anyone interested will read them from the blog, either online or downloaded. I do print them out once in a while to distribute, but anyone interested in doing that themselves would have to work out their own printer settings for booklets. Thanks for your interest.

Penance Peace

I went to a reconciliation, formerly known as penance, service last evening for our area deanery. I did not look forward to going, and apparently I'm not the only one who feels that way. The priest who gave the homily (who I think was Fr. Thomas Brown at Sacred Heart) said most people put this service on par with going to the dentist. The thought of spilling the beans about yourself to another person, known as confession, is not pleasant.

And yet before I even got to the confessional, I felt a greater peace than I have in a long time. The priest talked of a God who loves us enough to keep Himself on a cross until He died, and that was powerful. Often in Lent I think of Christ's journey to the cross, but last night I focused on what it took for Him to stay there. He could have easily shown the people who mocked Him that He was indeed the son of God and could come off. They would have been proven wrong in an amazing way.

But Christ kept His focus on the long-run, just as He had His whole life. He put aside the majesty and splendor He could have had in the short-run. He saw not only the people in front of Him, but all mankind. He gave us all a chance at future life with Himself and the Father and Holy Spirit.

When someone like myself becomes wrapped up in news stories of political fighting and even fighting within the Church, one can get angry and accusatory. But we pay a price in all that when we lose our own peace and best focus. I was really glad I went to the penance service to start concentrating where I should--on Christ's life, death, and resurrection to His present life where we can meet and know Him.

Maafa21

I just found out about a movie which theorizes that the abortion industry even today is an extension of the eugenics movement. It's called Maafa 21 and you can get to information on the website HERE. The term "eugenics" was coined by Francis Galton, a cousin of Charles Darwin. In the 1860's, he applied Darwin's theory, in which survival of the fittest supposedly brought about all evolution to superior beings, to humans. He believed the Caucasian race was superior to any others. What is more, others started getting on the bandwagon and pushed for population control, warning against feeble-mindedness and inability to rise above poverty. Only intelligent, talented people were to marry each other and produce a better and better race. The movie documents many articles written by famous eugenicists of their day. The creators of the movie ask why the percentage of minorities stay the same. Are people of color being encouraged to keep their numbers down?

The scientists in the past believed the Negroid races were inferior to the white because of evolution. Many believed that the African came from the ape and the white person from the African. And even as recently as 2007, James Watson, co-discoverer of DNA, seemed to assume the same, considering remarks he made. He was quoted in The Times of London as suggesting that, overall, people of African descent are not as intelligent as people of European descent and had to apologize, reported by Randerson and Truscott, "DNA pioneer apologizes over race row," The Guardian (Oct. 18, 2007).

The eugenics movement is now being linked to the abortion industry in the United States. The claim the movie Maafa 21 makes is that the mass sterilization that became prevalent in the early 1900's is still at work today, though it might not be "forced" as it was early in the movement. A good article, though, about forced sterilization is at a George Washington University web page.  It is by Edwin Black, "The Horrifying American Roots of Nazi Eugenics," History News Network at GW (Sept 2003).This quote comes from the article link:

Even the United States Supreme Court endorsed aspects of eugenics. In its infamous 1927 decision, Supreme Court Justice Oliver Wendell Holmes wrote, "It is better for all the world, if instead of waiting to execute degenerate offspring for crime, or to let them starve for their imbecility, society can prevent those who are manifestly unfit from continuing their kind…. Three generations of imbeciles are enough." This decision opened the floodgates for thousands to be coercively sterilized or otherwise persecuted as subhuman. Years later, the Nazis at the Nuremberg trials quoted Holmes' words in their own defense.

This article also claims that only after eugenics became well-established in the US did it become part of the Nazi psuedo-scientific justification for genocide. It is interesting that the 2008 movie with Ben Stein, Expelled (YouTube trailer HERE), made the same connection to Darwin's theory, eugenics, and the Nazi's. Expelled exposed the current prejudice in academia against any theories which oppose Darwinian evolution.

I have not seen the entire Maafa 21 movie yet, just the first few sections. I hope to watch the whole thing eventually. And I think we must be careful in blaming abortion on this one factor alone. Statistics show a large proportion of non-white women have abortions, as described on a web page of abort73.com HERE. But there are things going on other than elite eugenicists doing clandestine operations to sterilize women as was the case before. Let us not forget the culture has changed so that sex is a constant temptation for young people who do not then want the ensuing responsibility. Also, sex crimes and even human slavery are increasingly parts of our abortion problem.

In fact, one thing the narrators of the Maafa 21 movie have not addressed is the apparent lack of responsibility related to unmarried, teenage pregnancy. I’m sure this factor, with its link to poverty, is a concern for many liberals. There is not always a sinister motive for those who approve of abortion, and in fact these persons can sincerely desire the welfare of African-Americans. They want the females to have more freedom to continue education and have a secure job before they have children. They want the children to be in a home with higher income and better chances for them to make it as well. This is why some African-Americans also see abortion as a freedom of choice issue. The narrators do themselves no favors when they mention welfare in a way that seems like an entitlement that African-Americans are owed. That is not likely to win a lot of sympathy in these days of huge national debt.

However, the movie makes some good points. I think many liberals have never even thought of the angle of genocide or been informed of it. As the movie points out, the press avoids this side of the argument against abortion. Not everyone believes a fetus is a full human being, which muddies the issue.

It does not hurt to examine the mindset of those who set up abortion clinics in poor and usually minority-race neighborhoods. Are they really there for the good of the people involved? Do they want to encourage responsibility or do they want to help people run away from it? Can human life be equated with money and the economy?

The creators of the Maafa 21 movie would contend that, just like latter-day eugenicists, those advocating abortion don't want more of the minority around. I understand the desire to see others be responsible with their own lives and those of their children. But though life without responsibility can be very tough, responsibility has no chance at all without life.

Re-Evangelization All Over Again

In one of the recent newsletters of Our Sunday Visitor (Jan. 15, 2012), a column by Msgr. Francis Mannion (pg. 19) answered questions about the reality of hell. Now, he believes there is one. But he also says that anyone who has loved or been loved will not end up there. He said he heard this idea "about 1970" and has believed it since then.

It doesn't surprise me this idea circulated in the 70's. All you need is love, right? This has been a pervasive idea among Christians. Of course love is a wonderful reality, an amazing characteristic of our Divine God. But we must also remember that Jesus Christ came to Earth for our redemption because of our sins. He is our true hero, for He overcame a terrible ordeal to win the victory. And he asks us to believe in Him so we may have everlasting life with Him (John 3:16 NABRE).

The idea that all religions are the same is called "indifferentism." Evangelicals kept free of this ideology for a while, but mainstream Protestants and many Catholics subscribe to the idea that one spiritual path is as good as another. Some theologians subscribe to "universalism," in which we are all acceptable. A part of this group may say this is due to Christ's redemptive act which included everyone, but some would not even go so far as to say we needed Him, but that God simply loves all of us and we are all just on different journeys to the great universal oneness of love we will all eventually experience. However, indifferentism is not new and was mentioned by Pope Gregory XVI in 1832. He quoted St. Augustine from an even earlier time (born 354 AD): “The branch has the same form when it has been cut off from the vine; but of what profit is the form, if it does not live from the root?” (20. St. Augustine, in psalm. contra part. Donat.)

A Church document called "Nostra Aetate" (proclaimed by Pope Paul VI in 1965) says though there may be some parts of truth in all religions, the whole Truth culminates in Jesus Christ. If you know Him, there is no reason to follow another religion. To me, Christianity is a combination of being able to read the Truth in the Scripture and experiencing it with Christ.

Love is a wonderful thing, but many people have loved some people and hated others. Criminals have loved. Did past tyrants and dictators love their children? Probably, at least to some degree. Are they prepared for or worthy of heaven? Remember, heaven is perfect.

There must be a way we are able to be righteous in heaven, and we are told how that can be. The Apostle Paul tells us: 20...no human being will be justified in His sight by observing the law; for through the law comes consciousness of sin. 21 But now the righteousness of God has been manifested apart from the law, though testified to by the law and the prophets, 22 the righteousness of God through faith in Jesus Christ for all who believe. For there is no distinction; 23 all have sinned and are deprived of the glory of God. (Romans 3:20-23 NABRE),

John Paul II and Benedict XVI have called for a re-evangelization of the Church. I went through a time of doubt and even disbelief myself, influenced by these kinds of theology I have mentioned. Yet it is really worth thinking about the afterlife. The more I read the Bible and prayed, the more I believed you really do have to believe in Jesus Christ, that He was God, and that He came to save us from our sins to enter heaven. God the Father made Him the center of our lives and our hope, and He truly is.

People say a good God would not let people who never heard of Him go to hell. It is God's business how to handle that and should not be used as some excuse to not believe. Christians have faith that God is just, and things would not come out right if there was no justice. But He is also merciful. Each human being who has heard about Christ and has the opportunity to learn must work on their own soul to believe. Hopefully, they will come to do so, and then can help others do the same. The idea that we don't need to believe in Christ to get to heaven, which in my opinion is implied by Msgr. Mannion, is the very reason we need evangelization and re-evangelization.