Monday, December 17, 2012
Peace Amidst Horror
In the wakes of Super Storm Sandy (Fox News story HERE) and the Sandy Hook Slaughter (Fox News story HERE), most writers probably feel compelled to write something about them, no matter how inadequate we feel. My sincere prayers and hopes for recovery go to sufferers from these and other disasters, both natural and human-wrought.
Since the Newtown, Connecticut, Sandy Hook Elementary School killings on Dec. 14, there is already the usual talk about gun control. People are very upset and maybe something will change. But people were similarly shocked about the Columbine High School shootings in 1999. We’ve had the same type of occasions since then. We are still arguing about the availability of firearms.
It is human to want to manage events, and in some cases we succeed. We want to make schools and workplaces, not to mention homes, totally secure. Very few can stomach the way the young kids died in the school. We work to do our best in the physical sense so that no one has to endure that kind of end.
But there are those situations which will be beyond our control. We must also work on our attitudes, including coming to grips with the fact that there will be an end to all our lives as we know them sooner or later.
Many are concerned about the Mayan Calendar and the implied end of the world on Dec. 21, 2012, but some people didn’t even make it that long. There are those who are worried about an international economic collapse and are arming themselves, but that doesn’t guarantee survival. You can buy high-powered weapons for self-protection, as did the mother of the Sandy Hook gunman. Her son used her expensive equipment to kill her in her own home and himself in the school.
Christians believe there will be a Second Coming which will end the age as we know it. Though Christ told us not to put a date on this event, it is important to be ready for it in a spiritual sense. Many of us have heard sermons to that effect. But then we go off and seemingly forget how soon the end can come for any of us personally. Each of us should learn now how to follow our consciences and use proper spiritual discernment to determine which of our ongoing plans should be pursued and which forgotten.
The Sandy Hook Elementary School killings and other disasters have shown us that even little children need to know that there is life after death, and there is only one way to have a good one. That is through Jesus Christ, the Son of God who came to save us from our sins. He asks us to believe in Him. This is the spiritual work we each must do, so that the attitude we have will help our actions fall in line with what is important. Once we have the right mindset, we are to help others find it too.
Enjoy the music in the video, by Third Day. Listen to the lyrics. And please, no matter what your circumstances, have a blessed Christmas.
Wednesday, December 5, 2012
Gain Application Probability
Statistics are being used in the arguments about biological origin and evolution. Advocates of Intelligent Design Theory (ID) are prominent among those attempting to link probabilities of events with mathematical proofs of biological information but they are not the only ones. This post, though dated 12/5/12, is an update (8/27/13) and a new compendium, called Biological Information: New Perspectives, was just released and can be read online HERE. The book is an overview of the work being done to align biology with information theory which uses probabilities in trying to understand biological systems. Its authors are both ID and non-ID advocates.
I have a new theory that I present here, but like all new theories, it needs some more work. In fact, I've come back to re-write this post several times and instead of re-writing it another time, I'm going to eventually post about it again. But, if you are so-inclined, read on. Then catch up with a newer post called GAP Theory that should appear Nov. 2013.
Mathematics can be applied to reality. Probabilities in thermodynamics and chemistry predict quantities and actions of energy and mass. They exist and behave in a certain way that can be measured. But human judgment and mathematics are two different things. People rely on their own judgments about many subjects without being experts in probability theory.
It's pretty hard to imagine converting all of nature into strict mathematical terms. Evaluating a pattern is done by humans and therefore has subjective elements. Perhaps Information Theory does and will reveal certain hidden secrets about biology. But I doubt if even chaos theory could give all the answers.
Some examples might be helpful. A straightforward one goes like this: someone "blindly" picks all red balls from a bag which contains equal numbers of red and black. After about 20 times a pattern emerges that is different from the expected 1:1 ratio. One might suspect the red and black balls have unique surface features which allow discrimination. Maybe the red surface is more sticky. But in another example, consider a different type of situation. For a while my husband and I went to the store and they didn’t have any fresh grapefruit. The produce people could not answer our questions of why they were not there, so I looked on the Internet to understand. I found that some of the Southern US produce had been damaged by storms, and Mexico had droughts that affected their exports. What was the probability that a grapefruit would be available by the next time we went to the store? Wouldn't even the experts in distribution have trouble being precise due to the unpredictability of long-range weather? Even though they have their formulas, in certain circumstances they still incorporate judgments. It is of a different nature than pulling balls from a bag at a particular place and time.
Included in human judgment is the sense that the extreme complexity of biology is improbable and not random. (Some would argue here that neo-Darwinian evolution is not random due to “natural selection of the fittest,” but nature needs something worth-while to select first, which is claimed to come from random mutation.) And yet there exist many things with very low probability, including every hand you get in a card game. This is where critics come in and say low probability doesn't prove design. Design advocates then refer to "specificity," meaning that specific molecules are needed to perform biological tasks and that the exact combinations of these molecules are extremely improbable.
Specificity implies different values placed on equally probable outcomes. As in the grapefruit example above, I don't think we can always know exact probabilities. And yet the concept of probabilities still might give us some insight to whether nature itself could have come up with biological function and complexity. In some cases, an evaluation of probability can affect how a person judges an event. I'd like to talk about putting value on similar probability outcomes. I'll call it “Gain Application Probability” (GAP).
If you have only one second to toss a coin and it takes 1 second to toss it, you will either get heads or tails (no edge landings or double half-second flips allowed). Each outcome has a probability of one half, and one of the possibilities will occur. In this example, nothing is special about either unless one outcome is assigned to a prize. If a football team calls heads and the coin lands heads, they get to choose whether they receive the ball now or later. If I say I’ll give you a hundred dollars if it lands heads, you will perceive the difference in the outcome.
Now we move on to a dice. You have only one second and it takes one second to throw. I’ll give you a prize (say, 100 dollars) if you get a 1, but not on any other number. Each outcome has one chance in six, but there is still a difference in what happens if the number 1 comes up as compared to the others. The award or denial of the prize is in a related way a measure of the outcome.
Then we take a full deck of cards. We shuffle them fairly and put them face-down on a table. You have only one second and it takes a second to draw the top card. I tell you I’ll give you a prize if the top card that you draw is an Ace of Diamonds. But now you only have one chance in 52 that the card will be the Ace of Diamonds. Is this different than tossing a coin and getting a prize if you get heads? Which would you pick to take your chances?
While we’re talking of cards, it is true that each combination in a game hand has the same probability. But with a good grouping according to the rules of the game you are playing, you can win the hand. You might win money if there is a pot. You therefore gain with the good combination (if you play it well) more than with the bad.
Amino Acids are molecules that make up the various proteins. They have 20 different forms in our bodies and their various properties make their different combinations unique. The chances for one amino acid combination to occur might be the same as another, but if only one in 10^70 will help to break down a food molecule to produce biological energy while the others in that number don't do anything biologically active, then to me that one protein is different from the rest. If there is function for the few molecules among so many, I would apply a value of gain to those which can carry out biological tasks.
These examples demonstrate, in my term given above, Gain Application Probability. To say there is no difference between certain low probability events is to ignore the possible results. We can deliberately attach an extra benefit to an outcome or we may observe a benefit which comes naturally. We can evaluate events of low probabilities in relation to the gains they bring.
I think we can reasonably say that some improbable outcomes have more value than others. And the lower the probability and the more we gain, the greater the value. One might also be able to apply loss and neutrality to probabilities (LAP and NAP). After all, there is a losing side to a football coin toss, and many improbable events have no appreciable effect. And I suppose that zero times GAP is ZAP.
You might say Gain Application Probability is as subjective as other biological information theories (if you are a critic of these theories). But I’m not claiming to entirely eliminate chance. I don’t even want to quantify the values of gain and loss. I think there is worth in acknowledging that values can be applied differently for different probabilistic events even when they have similar probabilities. And some outcomes are so valuable that our human judgment can take over to tell us they did not happen by chance. So it is with functional biological materials made from combinations of molecules.
The value put upon the probability outcomes is a dimension above the science of nature. When you have faith, you can still be scientific and yet not get bogged down by needing all-encompassing mathematical and scientific proofs. Faith is given to us as a gift (Ephesians 2:8-9 NABRE). This is a mystery which transcends our understanding.
I have a new theory that I present here, but like all new theories, it needs some more work. In fact, I've come back to re-write this post several times and instead of re-writing it another time, I'm going to eventually post about it again. But, if you are so-inclined, read on. Then catch up with a newer post called GAP Theory that should appear Nov. 2013.
Mathematics can be applied to reality. Probabilities in thermodynamics and chemistry predict quantities and actions of energy and mass. They exist and behave in a certain way that can be measured. But human judgment and mathematics are two different things. People rely on their own judgments about many subjects without being experts in probability theory.
It's pretty hard to imagine converting all of nature into strict mathematical terms. Evaluating a pattern is done by humans and therefore has subjective elements. Perhaps Information Theory does and will reveal certain hidden secrets about biology. But I doubt if even chaos theory could give all the answers.
Some examples might be helpful. A straightforward one goes like this: someone "blindly" picks all red balls from a bag which contains equal numbers of red and black. After about 20 times a pattern emerges that is different from the expected 1:1 ratio. One might suspect the red and black balls have unique surface features which allow discrimination. Maybe the red surface is more sticky. But in another example, consider a different type of situation. For a while my husband and I went to the store and they didn’t have any fresh grapefruit. The produce people could not answer our questions of why they were not there, so I looked on the Internet to understand. I found that some of the Southern US produce had been damaged by storms, and Mexico had droughts that affected their exports. What was the probability that a grapefruit would be available by the next time we went to the store? Wouldn't even the experts in distribution have trouble being precise due to the unpredictability of long-range weather? Even though they have their formulas, in certain circumstances they still incorporate judgments. It is of a different nature than pulling balls from a bag at a particular place and time.
Included in human judgment is the sense that the extreme complexity of biology is improbable and not random. (Some would argue here that neo-Darwinian evolution is not random due to “natural selection of the fittest,” but nature needs something worth-while to select first, which is claimed to come from random mutation.) And yet there exist many things with very low probability, including every hand you get in a card game. This is where critics come in and say low probability doesn't prove design. Design advocates then refer to "specificity," meaning that specific molecules are needed to perform biological tasks and that the exact combinations of these molecules are extremely improbable.
Specificity implies different values placed on equally probable outcomes. As in the grapefruit example above, I don't think we can always know exact probabilities. And yet the concept of probabilities still might give us some insight to whether nature itself could have come up with biological function and complexity. In some cases, an evaluation of probability can affect how a person judges an event. I'd like to talk about putting value on similar probability outcomes. I'll call it “Gain Application Probability” (GAP).
If you have only one second to toss a coin and it takes 1 second to toss it, you will either get heads or tails (no edge landings or double half-second flips allowed). Each outcome has a probability of one half, and one of the possibilities will occur. In this example, nothing is special about either unless one outcome is assigned to a prize. If a football team calls heads and the coin lands heads, they get to choose whether they receive the ball now or later. If I say I’ll give you a hundred dollars if it lands heads, you will perceive the difference in the outcome.
Now we move on to a dice. You have only one second and it takes one second to throw. I’ll give you a prize (say, 100 dollars) if you get a 1, but not on any other number. Each outcome has one chance in six, but there is still a difference in what happens if the number 1 comes up as compared to the others. The award or denial of the prize is in a related way a measure of the outcome.
Then we take a full deck of cards. We shuffle them fairly and put them face-down on a table. You have only one second and it takes a second to draw the top card. I tell you I’ll give you a prize if the top card that you draw is an Ace of Diamonds. But now you only have one chance in 52 that the card will be the Ace of Diamonds. Is this different than tossing a coin and getting a prize if you get heads? Which would you pick to take your chances?
While we’re talking of cards, it is true that each combination in a game hand has the same probability. But with a good grouping according to the rules of the game you are playing, you can win the hand. You might win money if there is a pot. You therefore gain with the good combination (if you play it well) more than with the bad.
Amino Acids are molecules that make up the various proteins. They have 20 different forms in our bodies and their various properties make their different combinations unique. The chances for one amino acid combination to occur might be the same as another, but if only one in 10^70 will help to break down a food molecule to produce biological energy while the others in that number don't do anything biologically active, then to me that one protein is different from the rest. If there is function for the few molecules among so many, I would apply a value of gain to those which can carry out biological tasks.
These examples demonstrate, in my term given above, Gain Application Probability. To say there is no difference between certain low probability events is to ignore the possible results. We can deliberately attach an extra benefit to an outcome or we may observe a benefit which comes naturally. We can evaluate events of low probabilities in relation to the gains they bring.
I think we can reasonably say that some improbable outcomes have more value than others. And the lower the probability and the more we gain, the greater the value. One might also be able to apply loss and neutrality to probabilities (LAP and NAP). After all, there is a losing side to a football coin toss, and many improbable events have no appreciable effect. And I suppose that zero times GAP is ZAP.
You might say Gain Application Probability is as subjective as other biological information theories (if you are a critic of these theories). But I’m not claiming to entirely eliminate chance. I don’t even want to quantify the values of gain and loss. I think there is worth in acknowledging that values can be applied differently for different probabilistic events even when they have similar probabilities. And some outcomes are so valuable that our human judgment can take over to tell us they did not happen by chance. So it is with functional biological materials made from combinations of molecules.
The value put upon the probability outcomes is a dimension above the science of nature. When you have faith, you can still be scientific and yet not get bogged down by needing all-encompassing mathematical and scientific proofs. Faith is given to us as a gift (Ephesians 2:8-9 NABRE). This is a mystery which transcends our understanding.
Sunday, November 25, 2012
Work and Visits
On my blog I have commented about Creationism and Intelligent Design as well as a variety of other subjects. I’m also writing a book, and had been working in a part-time job. So for a while the blog was left to simmer, with a few posts at very long intervals. Well, the place I was working closed, and I have a little more time. I’ve enjoyed writing so much since the job closed that I’m going to try to continue. This means finishing my book and trying to get it published, as well as working on the next books down the line when the first is complete. Therefore I’m still busy, and probably still won’t write that much here. But I think about what I’d like to say and hope to do a little more blogging again.
I used to comment on a few other websites, but I think I need to concentrate on my own writing since I have trouble getting it done. I’m sorry I don’t visit others, and realize that’s probably why I don’t get much traffic here. I’m not on Facebook at all—if I hardly have the time here, I’d never have it for there. I know there are those out there who like to comment on other sites as well as those who have their own and I imagine much of that happens on Facebook. Still, there are those who use the regular old Internet, and anyone who visits and wants to comment here is welcome.
This blog has been an on-again off-again affair and will probably continue to be. But it is nice to have a little more freedom to work on it, at least for now. I hope you may find my occasional posts interesting and just want to repeat (as I’ve said in previous posts) that I’m glad to be here and to have you visit.
I used to comment on a few other websites, but I think I need to concentrate on my own writing since I have trouble getting it done. I’m sorry I don’t visit others, and realize that’s probably why I don’t get much traffic here. I’m not on Facebook at all—if I hardly have the time here, I’d never have it for there. I know there are those out there who like to comment on other sites as well as those who have their own and I imagine much of that happens on Facebook. Still, there are those who use the regular old Internet, and anyone who visits and wants to comment here is welcome.
This blog has been an on-again off-again affair and will probably continue to be. But it is nice to have a little more freedom to work on it, at least for now. I hope you may find my occasional posts interesting and just want to repeat (as I’ve said in previous posts) that I’m glad to be here and to have you visit.
Thursday, November 15, 2012
Thanks at Thanksgiving
There have been newspaper columnists and now are bloggers who list the things they have been thankful for. I’d like to list some of the things I’m thankful for at Thanksgiving.
I’m thankful for a great and glorious Lord who is such a genius that He could create the world and all that is in it. If not for Him, we wouldn’t have life at all. When I think of what He had to know in order to make us, most of it is above my head. But I’m thankful He has allowed me to understand and have access to read about some of the new discoveries of His creation. I enjoy them so much. Biology is absolutely wondrous.
I’m thankful for our house, which is not big or fancy but is homey and warm in the cold weather. I pray for those who are displaced by the storms or having economic problems, that they will be restored soon.
I’m thankful for my laptop computer and the Internet. They both boggle my mind as far as how they work but I’m sure glad they do. The ability to connect to the world in this way is so much fun. What would I do on winter nights without them? (Or winter mornings—I’m usually up by 5:00 am.) Although cable TV is also a connection to the world, there is just something special about the web. I guess it's more hands-on and personal. I pray that Christian communicators may use it to spread the Word of Truth to all.
I’m thankful for doctors and researchers who try to treat disease, not just to make a living but to help others. I pray for cures for the many ill people who still need them.
I’m thankful for my family and friends. I’m thankful for our church family, and I pray we may all love and appreciate each other as the years go by.
I know I haven’t listed everything, but perhaps I’ll be here next year to list more. Just like the others, whom I am thankful for.
Sunday, November 11, 2012
Thanks to Veterans
Today is Veterans Day and I thank all veterans for the sacrifices they have made for all of us.
I've been reading the Book of John in the Bible and just today came to the verses in Chapter 15 where Christ said:
I pray the Lord help us to love each other as we should. To do this, many emphasize charity in material ways. But we also love others by telling them about God and how He has given us physical life through His creation and gives eternal life through belief in His son, Jesus Christ.
I've been reading the Book of John in the Bible and just today came to the verses in Chapter 15 where Christ said:
11. I have told you this so that my joy may be in you and your joy may be complete. 12. This is my commandment: love one another as I love you. 13. No one has greater love than this, to lay down one’s life for one’s friends. 14. You are my friends if you do what I command you. 15. I no longer call you slaves, because a slave does not know what his master is doing. I have called you friends, because I have told you everything I have heard from my Father. 16. It was not you who chose me, but I who chose you and appointed you to go and bear fruit that will remain, so that whatever you ask the Father in my name he may give you. 17. This I command you: love one another (John 15:11-17 NABRE).A soldier often faces immediate death and must come to terms with it. Though I've never been in the armed forces, I'm sure that is a difficult task. But we will all die eventually, barring the Second Coming before that. In the meantime we can give ourselves to each other in the way we spend our time and act on what we believe is important.
I pray the Lord help us to love each other as we should. To do this, many emphasize charity in material ways. But we also love others by telling them about God and how He has given us physical life through His creation and gives eternal life through belief in His son, Jesus Christ.
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 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:
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.
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.
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 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:
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.
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.
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