Every Year, There is Less Junk DNA

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The evolutionary mindset produces all sorts of pathologies in modern science, but it has probably wreaked the most havoc in the field of genetics. Because DNA is so incredibly well designed, assuming that it is the result of random processes guided by natural selection has hampered our understanding of it significantly. Nowhere is this more apparent than in the concept of junk DNA. The term was coined by Susumu Ohno back in 1972.1 He applied it to all parts of an organism’s DNA that don’t code for proteins. Back then, it was thought that DNA’s only job was to tell a cell which proteins to make and how to make them. If a portion of DNA didn’t do that, to Ohno and most other geneticists at the time, it was simply junk – a leftover vestige of the evolutionary process. To give you an idea of how unreasonable this evolution-inspired idea is, at one time, it was thought that more than 98% of the human genome was composed of junk DNA!


Of course, creationists have always contended that there cannot be much junk DNA in any organism’s genome. Because DNA is so incredibly well designed, any significant amount of junk DNA would cause all sorts of problems. Imagine throwing a bunch of junk into a race car engine. Do you think the engine would work properly if it was filled with junk? Of course not. Since DNA is designed more elegantly than the fastest race car engine today, it is hard to believe it could function properly if it were filled with junk. The creationist view, then, has always been that while there might be a bit of junk DNA that has come from mutations which have degraded the genome over time, the vast majority of all organisms’ DNA serves important purposes, whether or not we understand them.

Not surprisingly, the more we learn about DNA, the more the creationist view is being confirmed. Time and time, again regions of DNA that have been positively identified as “junk” by evolutionists have been demonstrated to have a necessary function. A recent article in the journal Nature is yet another example of this confirmation process.

To understand the article, you must first understand the difference between a gene and an enhancer. When a sequence in DNA tells a cell how to make a protein, it is called a gene. In the typical jargon of genetics, it is said that a gene codes for a protein. It is actually a bit more complicated than that. Because of the elegant design of the genome (and thanks to other DNA sequences that were at one time definitively called “junk DNA”), a gene can actually code more more than one protein. The bottom line, however, is that a gene tells the cell how to make one or more proteins.

An enhancer is also a sequence on DNA, but it does not code for a protein. Instead, it helps to control how a gene is expressed. You can think of an enhancer as a regulator. A gene tells the cell how to make one or more proteins, and an enhancer for that gene regulates how actively the cell uses it. Now remember, according to Susumu Ohno, these enhancers were “junk DNA,” since they didn’t produce any proteins. However, now we know that they are anything but junk.

The reason I am blogging about enhancers is because of the newest twist to their story. Initially, it was thought that an enhancer needed to be near the gene that it regulates. Thus, a stretch of DNA would have a gene, and if that gene had an enhancer, it would be found as another stretch of DNA relatively close to the gene. In 2008, however, Hong, Hendrix, and Levine showed that there were duplicates of these enhancers, and they were often quite far from the gene they regulated.2 These enhancers were nicknamed “shadow enhancers.”

Now since these shadow enhancers were far from the gene they regulated, and since they were simply duplicates of the nearby enhancer, it wasn’t clear what their function was. Hong, Hendrix, and Levine suggested some possibilities in their paper, but duplicated parts of the genome are often considered redundant junk. In addition, these “shadow enhancers” were from from the gene they were supposed to regulate, so it was unclear what they could actually do.

Well, now we know what they do. They help to make sure the organism’s DNA is ready to meet the organism’s needs, even when the conditions are not optimal.3 Frankel and colleagues studied a fruit-fly gene called shavenbaby. This gene codes for proteins that are involved in producing hair-like protrusions, called trichomes, on the fly’s body. If the gene is mutated, the trichomes aren’t produced well, and the fly looks “shaven” compared to a normal fly. This gene was found to have at least two shadow enhancers.

The researchers deleted the two shadow enhancers in the genomes of developing fruit flies and then watched their development. When the temperature was ideal for fly development (25 degrees Celsius), the flies without shadow enhancers had slightly defective, but useful, trichomes. However, when flies without shadow enhancers developed at non-ideal temperatures, the trichomes became very defective.

As a further means of understanding the role of shadow enhancers, they used flies that had a mutation in another gene (not shavenbaby) that is involved in making trichomes. They deleted the shadow enhancers in some of the flies and kept them in others. As the flies developed, those that still had shadow enhancers had significantly less-defective trichomes than those that did not have shadow enhancers.

So here we have sections of DNA that seem to be redundant, but instead, they do a very important job. They help the organism develop properly when the conditions are not optimal, and they even help the organism develop properly when the organism’s own DNA is not optimal. Not bad for something that was once put in the junk pile!

REFERENCES

1. Ohno, Susumu, “So much ‘junk’ DNA in our genome,” a chapter in Evolution of Genetic Systems, H. H. Smith. ed., Gordon and Breach, New York. pp. 366–370, 1972
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2. Joung-Woo Hong, David A. Hendrix, Michael S. Levine, “Shadow Enhancers as a Source of Evolutionary Novelty,” Science, 321:1314, 2008
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3. Nicolás Frankel, et al., “Phenotypic robustness conferred by apparently redundant transcriptional enhancers,” Nature, 466:490-493, 2010
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17 Comments

  1. Arthur Hunt says:

    Hi Jay,

    I don’t want to sound overly critical, but promoters have been considered to be “parts” of genes since, oh, the days of the lac operon. I honestly don’t know of any working molecular biologist who equates, exactly and literally, the terms “gene” and “protein-coding region”. One is a subset of the other.

    1. jlwile says:

      Thanks for your comment, Arthur. You certainly know more about this than I do, but as I understand it, promoters and enhancers are quite different. While a promoter must be immediately adjacent to the gene, an enhancer can be far away. In addition, a promoter must be upstream of the gene, while an enhancer can be anywhere, even in an intron. Thus, while promoters were always considered a part of the gene because they are ‘attached’ to it, enhancers were lumped into the junk, as they were not thought to be a part of a gene.

  2. Eric says:

    Dr. Wile, thanks for the post and comments on anti-vaxers. I think homeschoolers are particularly susceptible to this anti-scientific movement. This is a great place to promote the sound science of vaccines.

    1. jlwile says:

      Thanks Eric and Dionisio!

  3. Dionisio says:

    Hi Dr. Wile,
    interesting post
    thanks!
    keep writing more!

  4. Wendy Hilton says:

    Hello Dr. Wile,
    I wanted to leave a comment on one of your vaccine-related posts, but it looks like comments may be closed on them. I am sorry to leave a comment on an unrelated post, and I understand if you wish to delete it. I felt like I had to leave a comment, though. I have read some of your vaccine-related posts and a few of the comments. Since I didn’t read them all, I hope I’m not repeating what someone else has already said. Please forgive me if I am. My daughter, age 15, is moderately to severely autistic and is totally non-verbal. She was healthy and verbal and inquisitive and so very “normal” until she had her 12-to-15 month vaccines (at 15 months of age). Immediately after having the vaccines, both of her legs (where she had the injections) became so swollen that I couldn’t put a diaper or clothing on her. She screamed and cried for hours and ran a very high fever. Days later, when the swelling and fever had cleared, she still remained a little lethargic and just didn’t act like herself. What I didn’t know then was that she never would be “herself” again. She never fully recovered and in fact started regressing in all areas. She stopped making eye contact, gradually lost all spoken language, lost the ability to play and copy the actions of others and all of the other things that children do at that age. Since she is my oldest child, of course I was afraid to vaccinate my other children for fear that the same thing will happen to them. Yes, it does frighten me to think about the possiblity of my other children having one of the diseases that they would have been vaccinated against. It is my honest opinion, though, after seeing what happened to my oldest child and having no doubt at all that it was a result of the vaccines she received, that I would be putting my other children at even greater risk by vaccinating them. The saddest part of the whole situation is that I had my daughter’s titers checked later, and she is not even immune to the diseases that the vaccines were supposed to protect her from. It was all for nothing. I am not one of those angry parents who is against all vaccines and hates all doctors and vaccine companies. I simply think that there must be some kind of genetic pre-disposition or something similar that causes some children to have severe reactions to the vaccines that they receive. I am not a trained scientist and I don’t have lots of studies to back up my opinion. In fact, the only evidence I have is what I saw in my own daughter’s life in my own home almost 15 years ago. I feel inadequate to even comment after reading your posts and other comments left by folks who are obviously much smarter and more scientifically-minded than I am. I am simply a mom who loves her children, wants what is best for them, and constantly receives information from “both sides” of the issue until I have no idea who is “correct” or what to do about it. IF I am correct and there is a genetic pre-disposition involved, I only pray that some scientist somewhere will discover it and will help parents like me to know which children can be safely vaccinated and which should not be vaccinated. Until then, I feel like I am gambling either way I go. I do appreciate the chance to state my opinion. While I don’t agree with everything you have said in your posts about vaccines, I do hope that “both sides” can eventually learn to work together instead of continuing to fight and argue. The lives of our children are too important to waste time trying to “win” the argument. The only thing I know to do for now is to pray pray pray that the Lord will shed light on the causes of autism. Then parents like me can spend less time worrying and wondering what is best for our children. I do appreciate that you are sharing your opinion in hopes of making our children safer and healthier. I am doing the same.

    1. jlwile says:

      Wendy, thanks for your comment. WordPress (the software that runs this blog) turns off comments after a certain length of time.

      I truly understand why you are afraid to vaccinate your other children, but I do think the science is quite clear. When studies look at hundreds of thousands of children and see no difference in the rate of autism between vaccinated and unvaccinated children, it is clear that vaccines aren’t related to autism. Even if it were just a genetic predisposition, these massive studies would find it. They don’t.

      Unfortunately, I don’t see much hope of both sides learning “to work together instead of continuing to fight and argue.” The fact is, they use different methods. The pro-vaccination side uses science. The anti-vaccination side uses misinformation. Those two methods don’t work well together.

  5. Pyrodin says:

    While I do not agree on your view that vaccines are 100% safe, I do believe they are somewhat effective. Vitamins and nutrition can do almost as well, but in situations where that’s not possible, vaccination is better than mass death. But you can’t deny GlaxoSmithKline (in bed with the media) played up the birdflu/swineflu threat and the World Health Organization (WHO, also in bed w/GSK) declared that the swine flu was a world wide pandemic and changed the definition of pandemic so that mass profits could be reaped by fear. This is why people have lost faith in vaccines, not autism. Also, there could be an unknown factor/factors causing or triggering the vaccine problems that all these studies missed, people aren’t omnipotent, we get things wrong all the time. As for this article, I found it agreed with me and I would like to repost on my blog ( http://www.pyrodin.wordpress.com ), contact me if you do not wish me to do so. Thanks!

    Pyrodin

    1. jlwile says:

      Pyrodin, I am not sure where you got the idea that I think vaccines are 100% safe. No medicine (indeed, no food) is 100% safe. Hardly anything is 100% safe. Even vitamins can be dangerous in large doses. More than 300 people die in the U.S. every year taking baths. Thus, the idea that ANYTHING is 100% safe is just plain silly. However, what the scientific data clearly show is that as long as an individual doesn’t have contraindications (such as an allergy to eggs), the most dangerous thing you can do is NOT vaccinate. Indeed, California is already experiencing the carnage of what happens when people stop vaccinating.

      I have no idea whether or not GlaxoSmithKline or any other group “played up” the avian flu and swine flu issues. Certainly, pharmaceutical companies are motivated by profit, but that’s why the medical research community handsomely rewards those researchers who find problems with medicines. That way, the profit motives of the pharmaceutical companies are kept in check by the selfish motives of the medical researchers. Those who have lost faith in vaccines are generally swayed by misinformation, not profits or anything else.

      There is certainly a possibility that the studies are missing something. However, remember that in ONLY ONE YEAR, the medical research community was able to find a side effect in the old rotavirus vaccine that occurred only once in every 11,073 injections. That’s a TINY side effect chance, but the studies were easily able to find that in about a year. Thus, the studies are pretty well-designed, specifically because it is in the best interest of the researchers to find problems.

  6. Pyrodin says:

    First of all thanks for the reply, you are correct absolutely nothing is 100%, I did not mean to put words in your mouth, I should have said relatively safe, my apologies.

    When SHOULD we stop vaccinating though? 100 years? 1000? How long until the diseases become nonthreatening? I’m sure all the medical researchers/pharma would say we should never stop because there’s always a chance of a comeback, or should that be always a chance of profits? Seems like we are exposing ourselves to a risk for fear of a lesser risk and making vaccine producers a lot of cash. Yeah if whooping cough is making a comeback, I’ll get the shot, but otherwise it seems like we are experimenting on ourselves to see the long term effects of generations of vaccination(maybe autism?), the greed system does not engender good things.

    Peace
    Pyrodin

    1. jlwile says:

      Pyrodin, we stop vaccinating when the diseases are not a threat anymore. You are quite wrong when you say, “I’m sure all the medical researchers/pharma would say we should never stop because there’s always a chance of a comeback, or should that be always a chance of profits?” In fact, we stopped vaccinating for smallpox, because smallpox is not a threat anymore. In addition, the pharmaceutical companies make many vaccines that are not part of the standard vaccine schedule in the U.S., such as the Japanese encephalitis, yellow fever, and typhoid vaccines. They are not a part of the standard vaccine schedule in the U.S. because those diseases are not a threat in the U.S. This is why it is important to rely on science and not hype when it comes to medical issues. Real science can guide you very clearly as to what kinds of medications you should and should not use. Hype cannot.

      You are actually experimenting on yourself by not getting vaccinated. The safety and efficacy of vaccines are well established by many reproducible studies. To ignore those studies is not only irrational, it is a downright dangerous experiment!

      While I agree that the greed of the system does not engender good things, ignorance of the basic medical data engenders very bad things, such as the deaths of innocent children.

  7. Pyrodin says:

    Well said, but I think it really depends on the type of vaccine you get.

    “The safety and efficacy of vaccines are well established by many reproducible studies”

    Well, I think vaccines like the MMR are mostly safe, even if it does cause autism in .01%, but other vaccines may not be. Just because one or more types of vaccine work and are safe, it doesn’t make any other vaccines safe or well tested. I think most people get confused as to which vaccines are well known and safe and which are new less tested vaccines.

    Heres an interesting old documentary on the 1976 swine flu vaccine problems, shows some of the scare-tactics they used then.

    http://justgetthere.us/blog/archives/Swine-Flu-1976-Propaganda.html

    Thanks again for your comments, I enjoy reading your views on this subject.

    Peace

    1. jlwile says:

      Pyrodin, I don’t know where you are getting your misinformation, but the MMR is not linked to autism in any way. When 500,000 children are studied and the rates of autism are the same among those who got the MMR and didn’t get the MMR, it is clear that the MMR has nothing to do with autism.

      Also, you don’t seem to understand how vaccines are approved and studied in this country. ALL vaccines go through a series of clinical trials before they can be approved, and then once approved, they are followed closely by rigorous studies. While it is true that the newer vaccines haven’t had time to be as closely monitored as the older vaccines, remember that the side effect in the old rotavirus vaccine was discovered in LESS THAN A YEAR, even though it occurred only once in every 11,073 injections. Thus, it takes very little time for the studies to uncover problems, mostly because those who do discover the problems are hansomely rewarded.

      I expect your confusion over vaccines comes from the fact that you put stock in television shows and videos rathers than serious scientific sources. If you want to learn the truth about vaccines, you will start reading the science behind them, not the propaganda against them.

  8. Pyrodin says:

    You misunderstand me, even if it DID cause autism in a small percent it would still be worth it, not that it does or doesn’t.
    As for not “understanding how vaccines are approved country”, what is there not to understand?

    Are sites like these misinfo?

    http://www.nvic.org/NVIC-Vaccine-News/June-2010/FDA-Proposes-Dangerous-Vaccine-Rule-Change.aspx

    http://www.webmd.com/cold-and-flu/news/20090717/swine-flu-vaccine-fast-track

    “I expect your confusion over vaccines comes from the fact that you put stock in television shows and videos rathers than serious scientific sources”

    I am not confused about vaccines nor am I anti-vaccine, just very very cautious about them. I don’t watch ANY cable or brodcast tv, and do not consider most videos to be “information” only a good starting point for research.

    1. jlwile says:

      Thanks for clarifying your comment, Pyrodin. That makes better sense.

      You ask what is not to understand about how vaccines are approved. However, your previous comments show that you don’t understand, as you indicated that some vaccines are not very well tested. Once again, if you focused on scientific sources, I would expect that you would have a better understanding of the safety and efficacy of vaccines.

      You asked if the two sites you linked are misinformation. The first one certainly is. The National Vaccine Information Center is one of the most powerful anti-vaccine organizations in America. It was started in 1982 by Jeff Schwartz, Barbara Loe Fisher and Kathi Williams, all of whom thought their children were severely harmed by vaccines. They have been providing misinformation about vaccines for years in an effort to scare people into not getting vaccinated.

      The webmd site you linked is not a source of misinformation and it, of course, provides rational arguments for the fastracking of the swine flu vaccine. As the site says:

      Why deploy a vaccine that hasn’t completed safety and efficacy testing? Because we already have a lot of experience with similar vaccines, concluded the NBSB flu vaccine working group, led by University of Utah flu expert Andrew Pavia, MD. Pandemic swine flu is a type A, H1N1 flu virus. For decades, a type A H1N1 vaccine has been part of the regular seasonal flu vaccine, and the new vaccine is made exactly the same way. Fast-tracking the vaccine will mean guessing at the best dose, but that’s an educated guess based on the well-established dosage for the seasonal H1N1 vaccine.

      That’s the difference between propaganda and good information.

      You are clearly confused about vaccines, as you have made several incorrect statements about them, which I have corrected for you. Once again, study scientific sources and you won’t be so confused.

  9. Pyrodin says:

    Haha, sigh, when I said “it doesn’t make any other vaccines safe or well tested” I was referring to the the actual use after the approval process. And judging by your reply to the sites, I can tell “the difference between propaganda and good information” just fine. Anyhow, your comment section is filling up, thanks for quibbling, err, correcting. I’ll keep an eye out for those almighty “serious scientific sources”.

    1. jlwile says:

      Unfortunately, Pyrodin, based on your comments, I seriously doubt you will be looking for scientific sources on the vaccine issue. I pray that you do, however.

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