subscribe to the RSS Feed

Saturday, December 20, 2014

Surprising? Only to Evolutionists!

Posted by jlwile on September 7, 2012

The human genome is the sum of all the DNA contained in the nucleus of a human cell.
(Click for credit)

In 2001, the initial sequence of the human genome was published.1 Not only did it represent a triumph in biochemical research, it allowed us to examine human genetics in a way that had never been possible before. For the first time, we had a complete “map” of all the DNA in the nucleus of a human cell. Unfortunately, while the map was reasonably complete, scientists’ understanding of that map was not. Despite the fact that scientists had a really good idea of what was in human DNA, they didn’t have a good idea of how human cells actually used that material.

In fact, there were many scientists who thought that most of the contents of DNA is not really used at all. Indeed, when the project to sequence the human genome was first getting started, there were those who thought it would be senseless to sequence all the DNA in a human being. After all, it was clear to them that most of a person’s DNA is useless. In 1989, for example, New Scientist ran an article about what it called “the project to map the human genome.” In that article, the views of Dr. Sydney Brenner were brought up. As the director of the Molecular Genetics Unit of Britain’s Medical Research Council, he was considered an expert on human genetics. The article states:2

He argues that it is necessary to sequence only 2 percent the human genome: the part that contains coded information. The rest of the human genome, Brenner maintains, is junk. (emphasis mine)

This surprising view was probably the dominant view of scientists during the 1980s and 1990s. Indeed, the article represents the idea that the rest of the human genome might be worth sequencing as being the position of only “some scientists.”

Now why would scientists think that most of the human genome is junk? Because of evolutionary reasoning. As Dr. Susumu Ohno (the scientist who coined the term “junk DNA”) said about one set of DNA segments:3

Our view is that they are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?

Indeed, evolutionists have for quite some time presented the concept of “junk DNA” as evidence for evolution and against creation. In his book, Inside the Human Genome: A Case for Non-Intelligent Design, Dr. John C. Advise says:4

…the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes…To the best of current knowledge, many if not most of these repetitive elements contribute not one iota to a person’s well-being. They are well-documented, however, to contribute to many health disorders.

His point, of course, is that you would expect a genome full of junk in an evolutionary framework, but you would not expect it if the genome had been designed by a Creator. I couldn’t agree more. If evolution produced the genome, you would expect it to contain a whole lot of junk. If the genome had been designed by a loving, powerful Creator, however, it would not. Well…scientists have made a giant leap forward in understanding the human genome, and they have found that the evolutionary expectation is utterly wrong, and the creationist expectation has (once again) been confirmed by the data.

The leap began back in 2003, when scientists started a project called the Encyclopedia of DNA Elements (ENCODE).5 Their goal was to use the sequence of the human genome as a map so that they could discover and define the functional elements of human DNA. Back in 2007, they published their preliminary report, based on only 1% of the human genome. In that report, they found that the vast majority of the portion of the genome they studied was used by the cell.6 Now they have published a much more complete analysis, and the results are very surprising, at least to evolutionists!

In a coordinated release of 30 peer-reviewed papers in several different scientific journals, the ENCODE project detailed 1,640 distinct sets of data that cover 147 different types of human cells. In these data sets, the researchers looked for elements in the DNA that participated in one of five known functions. The first is protein coding. DNA is a storehouse of “recipes” for the cell. It tells the cell how to make the proteins that it needs to make. Those recipes are called “genes,” and they represent the most obvious functional element of DNA.

However, protein coding is not the only useful function in which a segment of DNA can participate. Another is transcription. In order for a cell to use the information in DNA, it must first be copied by a molecule called RNA. The process by which it is copied is called “transcription,” and it represents a major investment of energy and resources. While all protein coding segments of DNA are transcribed, many segments of DNA that are not used as recipes for proteins are also transcribed. For example, there are DNA segments called “introns.” They do not code for proteins, but their transcription makes it possible for DNA to store information significantly more efficiently than it otherwise could (see here and here for why this is the case). In the end, then, if a segment of DNA is transcribed, it is probably useful. Otherwise, the cell would not waste energy and resources on it.

In addition to protein-coding segments and transcribed segments, other segments of DNA are involved in regulation. For example, there are certain proteins called “transcription factors.” These proteins regulate transcription by attaching (binding) to certain regions on the DNA molecule. Those regions are called transcription-factor-binding sites. Without them, the cell would not be able to regulate the production of proteins nearly as efficiently as it does now. In the same vein, there are certain segments of DNA to which a chemical unit known as a “methyl group” can attach. This process, called “methylation,” reduces how much a cell uses a specific gene, so it is also an important way the cell regulates protein production. The sites to which methyl groups bind are called DNA methylation sites, and they represent yet another way a segment of DNA can be used.

Finally, DNA doesn’t just lie around in the nucleus. It is actually packaged in an amazingly efficient way by being wrapped around little balls of protein. This incredible complex of proteins and DNA is called “chromatin,” and the structure of the chromatin is very important in determining how quickly DNA can be read and used. Because of this, there are certain segments of DNA that contribute to the chromatin structure. Obviously, these are also functional elements of the genome.

In the end, then, ENCODE set out to determine what percentage of the genome was involved in one of these five functions (protein coding, transcription, transcription-factor binding, methylation, and chromatin structure). Here’s what was found:7

Accounting for all these elements, a surprisingly large amount of the human genome, 80.4%, is covered by at least one ENCODE-identified element…

In other words, contrary to Dr. Advise’s claims, the vast majority of the human genome does, indeed, have function. This goes squarely against the expectations of most evolutionists. In fact, the idea that the genome of any “higher” organism contains mostly useless DNA is so ingrained in evolutionary thinking that the “gold standard” computer program which simulates evolution, Avida, requires that 85% of the simulated organism’s instruction code (in other words, its DNA) starts out as useless.8

This is why the paper says the amount of functional DNA in the human genome is “surprisingly large.” Evolutionists didn’t expect that much functional DNA in any highly-evolved organism, much less a human being. However, creationists have always predicted that the vast majority of human DNA will be shown to be functional. In fact, to a creationist, 80.4% seems rather low. That’s not a problem, though, because while the ENCODE project’s data set is massive, it is not complete. For example, they looked at “only” 147 different cell types. The human body has a few thousand different cell types, so most likely, functions will be found for the vast majority of the other 19.6% of the human genome. Indeed, according to the project’s Lead Analysis Coordinator, Dr. Ewan Birney:

It’s likely that 80 percent will go to 100 percent…We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.

So in the end, 80.4% functionality is a lower limit. That’s not at all surprising…if you are a creationist. The more we learn about DNA, the more the creationist view is vindicated, and the more untenable the evolutionary view becomes.

REFERENCES

1. International Human Genome Sequencing Consortium, “Initial sequencing and analysis of the human genome,” Nature 409: 860–921, 2001
Return to Text

2. Sharon Kingman, “Buried Treasure in Human Genes,” New Scientist July 8, 1989, p. 36
Return to Text

3. Susumu Ohno, “So Much ‘Junk’ DNA in Our Genome,” Evolution of Genetic Systems, Brookhaven symposia in biology, 23:366-370, 1972.
Return to Text

4. John C. Advise, Inside the Human Genome: A Case for Non-Intelligent Design, Oxford University Press 2010, p. 107.
Return to Text

5. The ENCODE Project Consortium, “A User’s Guide to the Encyclopedia of DNA Elements (ENCODE),” PLoS Biology April;9(4): e1001046, 2011.
Return to Text

6. The ENCODE Project Consortium, “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature 447:799-816, 2007.
Return to Text

7. The ENCODE Project Consortium, “An integrated encyclopedia of DNA elements in the human genome,” Nature 489:57-74, 2012. (Available online)
Return to Text

8. Chase W Nelson and John C Sanford, “The effects of low-impact mutations in digital organisms,” Theoretical Biology and Medical Modeling, 8:9, 2011 (Available online)
Return to Text

Comments

26 Responses to “Surprising? Only to Evolutionists!”
  1. Eduardo says:

    But even if it turns out that 100% is functional, evolutionist will have a story to acomodate that. Talking about this news an article on New Scientist says than some gene were resurrected and kapoon!!! they are functional again. When you read about DNA even atheist can not avoid to talk about knowledge in the cells.

  2. jlwile says:

    Eduaro, I agree that evolutionists will invent some story to work around the fact that most (if not all) of the genome is functional. However, every time such a story is invented, evolution loses more adherents, because scientists evenutally get sick of continually explaining around the data. This is how science corrects itself, and it is in the process of doing so when it comes to evolution.

  3. tmaze says:

    Nice spin…but I don’t see anything in this article that is remotely related to evolution theory or creationism? A few quotes from a 1989 geneticist does not reflect the current dogma of the modern evolution theory. Other than that I enjoyed your blog.

  4. jlwile says:

    Tmaze, you might want to read the article again. The quote from Advise comes from 2010, and it relates this issue directly to creation/evolution. Also, as I point out in the article, the “gold standard” evolution simulation program requires the vast majority of the genome to be composed of junk DNA. If nothing else, then, we know that the very best evolution simulation that exists today is built on a false premise.

  5. Jason says:

    How many more failed predictions will the scientific establishments accept before giving Darwinism the boot?

    Time for a change…surely?

    http://www.darwinspredictions.com/

  6. jlwile says:

    Jason, scientists are slowly giving Darwinism the boot. That’s why militant Darwinists are fighting so hard and with such venom. Science is self-correcting, but the process is slow.

  7. Isaac Kim says:

    I feel like there are many scientists who believe design cannot be even considered in science because it leads to a “designer”. So no matter how intelligently designed humans and DNA are, they will believe in a theory that will leave design out of the picture. So more evidence against evolution will not deter many from that theory unless a better theory without design is presented. So that way of thinking needs to change before debunking evolution. What do you guys think?

  8. jlwile says:

    I’ll have to disagree with you, Isaac. If design is the best explanation, and I think it is, then developing some new design-free theory doesn’t help. It just replaces one poor theory with another. Also, we know that many scientists are leaving evolution as a comprehensive explanation for life and its origin. That can be seen in the dissent from Darwin list and a list of young-earth creation scientists.

  9. Isaac Kim says:

    I wasn’t saying that we should develop design-free theories, but that some evolutionists will never accept design theories because they believe science and God cannot coexist. Especially since evolution cannot be tested since it deals with historical science rather than operational. Wouldn’t psychology, philosophy, and logic be much more effective in bringing people to see the shortcomings of evolution? I know there are scientists leaving evolution, but it seems to be a slow process.

  10. jlwile says:

    I understood what you were saying, Isaac. My point was that a design-free theory would be just as much at odds with the data, so it would not be seen as a suitable replacement. I honestly don’t think scientists are going to be swayed by psychology, philosophy, and logic. Instead, I think they need to be met on their own terms. Yes, the change is slow, but remember, it took more than 2,000 years to get rid if the idea of spontaneous generation. Science often moves very slowly, especially when a viewpoint is entrenched.

  11. D. Perrine says:

    Just a question.
    You said they looked at 147 of “a few thousand” different cell types. I just want to understand clearly.
    Are we talking about glial cells, muscular cells, epithelial cells, etc?

    Also, when you say that: “ENCODE set out to determine what percentage of the genome was involved in one of these five functions (protein coding, transcription, transcription-factor binding, methylation, and chromatin structure).”
    How does this compare to each cell. Did they find, for example, that the DNA of glial cells do not protein code but are involved in one of the other four actions? Or do certain DNA of glial cells preform one action, while other glial DNA another action, etc?

    I am not sure that I understand completely the configuration of DNA to cell to different cell types but preforming similar activities (coding, binding, structures, etc).

    I am sorry for the long comment, I only seek to understand the topic being discussed.

  12. jlwile says:

    Excellent questions, D. Perrine. Please do not apologize for them. When we talk about cell types, we are not only talking about glial cells, muscle cells, etc. We are also talking about cells in different stages of development. For example, T-cells do not become T-cells until they have had a period of “training” in the thymus. Before then, they are a different type of cell. In addition, after training, there are different types of T-cells, like killer T-cells and helper T-cells. Finally, when you are developing in the womb, there are a host of different types of cells that never exist again once you are born.

    In order for a DNA element to have function in the ENCODE system, it only has to perform ONE of the five functions in ONE cell type. I hope to blog later about how they found the same element can actually perform differently in different cell types, but that is another issue. So if a DNA element performed just one of those functions in just one cell type, it is considered functional. To me, that definition of “functional” is the most reasonable one.

    In every cell, the complete genome is the same. However, in one cell type, only a subset of the DNA elements are actually used. That’s why ENCODE will have to examine ALL cell types to determine the complete functionality of the human genome.

  13. Isaac Kim says:

    So we’re going to have to wait till year 3900!! O_O

  14. jlwile says:

    I certainly hope not, Isaac!

  15. D. Perrine says:

    Thank you for your very thorough response Dr. Wile.

  16. Seth says:

    Great article! You explain everything so well when you write, even someone with hardly any understanding of biology (me), it can make sense.

    Now one quick question, what’s the explanation of this article, it seems to contradict what you claim:

    http://www.nature.com/nature/journal/v431/n7011/abs/nature03022.html

    In the experiment Nobra, et al cut/replaced some of the non-coding DNA (1,511 kilobases and 845 kilobases in length) from a mouse genome. When this DNA was removed, the mice (or mouse) behaved nearly the same.

    If nearly 100% of DNA is used for something, wouldn’t replacing such a large chunk make a significant difference?

    (TalkOrigins also mentions this in their “Creationist Responses” index http://www.talkorigins.org/indexcc/CB/CB130.html ).

  17. jlwile says:

    That’s a great question, Seth. The first thing to realize is that talkorigin’s description of the paper is deceptive, as is typical of talkorigins. The site claims that “Sections of DNA can be cut out or replaced with randomized sequences with no apparent effect on the organism.” However, that’s not what the research showed. Note that the abstract says, “Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice.” Thus, there was an apparent effect. It might have been minor, but the effect was there. What was the effect? You find out if you read the paper:

    Out of the 108 quantitative expression assays (12 tissues for 9 genes), only 2 revealed detectable alterations in levels of expression. The expression of Prkacb was reduced in the heart of delMm3/delMm3 mice and Rpp30 was reduced in the brain of delMm19/delMm19 mice, compared to wild-type littermates (Fig. 3)

    If you look at figure 3, you will see that Prkab and Rpp30 were reduced by more than half. Thus, while there were only 2 differences out of 108 assays, those differences were significant.

    The second thing you have to realize is that the study did not test mice throughout their lifetime or in multiple settings. The phenotype tests and molecular assays were made at 25 weeks, and there was only one setting in which the mice were raised: the lab. They also didn’t study a wide range of proteins. They only looked at proteins coded for by genes that are near the regions which were knocked out. This is important, because every cell has the same genome, but some sections of the genome are only used in specific types of cells under specific conditions. For example, suppose the sections of DNA that were knocked out were important for the mice’s immune response. If the mice were never exposed to the right pathogen, those sections would never be used. What if they are important for the mice to survive periods of starvation? If the mice were always fed well, those sections would never be used. What if the sections are important for dealing with age-related difficulties? Those sections would never be used during the course of the study.

    Nevertheless, even though the study didn’t explore multiple conditions, the entire lifespan of the mice, or a wide range of proteins, they still saw two significant reductions in protein expression. Thus, far from showing these sections of DNA aren’t important, the study shows that their deletion produces noticeable molecular effects, even under a narrow range of conditions.

  18. Seth says:

    Thank you for answering my question. :)
    When it comes to science, nothing is concrete. You’re right, for all we know the small differences in Prkab and Rpp30 could be vital in other areas not tested, we really can’t be sure.

  19. Jason says:

    Biochemistry professor Larry Moran seems to strongly disagree. Aside from his anti-creationist rants, is there any truth to his objections?

    “The creationists are going to love this. You blew it Ed Yong. … ‘Almost every nucleotide …’? Gimme a break. Don’t these guys read the scientific literature? This is going to make my life very complicated.” (Larry Moran, “ENCODE Leader Says that 80% of Our Genome Is Functional”)

    http://www.evolutionnews.org/2012/09/what_an_evoluti_1064101.html

  20. jlwile says:

    Thanks for the link, Jason. I was eventually going to get to the denialists who cannot accept what the data seem to say. Moran is certainly one of them. His big beef is that in his mind, transcription doesn’t mean function. He thinks that the cell can afford to waste a wealth of energy and resources to copy DNA that is useless. Obviously, that doesn’t make sense, and it doesn’t explain why the encode data show that many of these gene transcripts are concentrated in specific parts of the cell, which also indicates function.

    So to believe Moran and the denialists, you have to believe that the cell can afford to waste huge amounts of energy and resources on making useless chemicals. In addition, many of those chemicals are arbitrarily concentrated at specific points in the cell, even though they’re don’t doing anything. That seems like a stretch, to say the least.

  21. Jason says:

    Thank you for clearing this up Dr Wile.

    It’s very confusing for someone like myself, untrained in the sciences, to make sense of the ENCODE data. Just when I think I understand the basics, boom, along comes Moran etc and confuses me all over again.

  22. Jason says:

    I believe 10 scientists from the project are accepting / answering questions here:

    http://www.reddit.com/r/askscience/comments/znlk6/askscience_special_ama_we_are_the_encyclopedia_of/

    Mr Moran has a few questions of his own I see.

  23. jlwile says:

    That’s a very interesting link, Jason. Thanks for posting it!

  24. D. Perrine says:

    A link found from that reddit discussion:

    http://selab.janelia.org/people/eddys/blog/?p=683

    If you have the time to read, Dr. Wile, I would appreciate your opinion of the article.

  25. jlwile says:

    Thanks for the link. D. Perrine. There are several problems with the post First, the author seems to think that “junk DNA” was coined to describe transposable elements. However, that’s not true. It was coined by Susumu Ohno while he was studying pseudogenes.

    Second, the author thinks that transcription doesn’t imply function. He seems to think that the cell will transcribe pretty much anything. However, that’s just not true. For example, while the ENCODE team found that 80.4% of the entire genome is transcribed, they found 7,186 pseudogenes (which look like broken versions of working genes), but they found that only 876 of them were transcribed. So the cell seems to be able to turn of transcription for most pseudogenes. Why? Well, even though functions have been found for some things that have been labeled as pseudogenes, many pseudogenes do really look to be broken. So…it appears that some things which are called pseudogenes are actually useful, and the cell transcribes them. However, most of the sequences labelled pseudogenes really are useless, and the cell has turned off transcription of them. That makes a lot of sense, since transcription requires an enormous amount of energy and resources. If the cell can turn of transcription on broken genes, why would it transcribe other useless DNA? Even if the 876 pseudogenes that are transcribed are useless, we can say that the cell turned off transcription for 88% of the useless pseudogenes. If it can turn off transcription for 88% of the pseudogenes, why can’t it do that for 88% of the rest of the junk in the genome?

    Third, he seems to think that transposable elements are known to be junk. However, that’s just not true. We have known for quite some time that transposable elements serve a very important function. As this review article tells us:

    The literature holds several examples that illustrate how transposons can serve as a reservoir of genetic innovation. Such innovation includes the creation of new coding or non-coding genes, with beneficial functions to the cells and/or modifying regulatory cis elements that may affect the balance of bound and free regulatory factors.

    In the end, I think the author is trying to cling to the idea that most of the genome is junk, even though the data clearly say otherwise.

  26. Jason says:

    Another denialist no doubt. I guess Darwinists will defend the Junk DNA claim because it’s such a strong doctrine in their belief system.

    And they have the nerve to say creationists deny the evidence hah!

home | top