subscribe to the RSS Feed

Thursday, October 23, 2014

Oh No! He’s Wrong Again!

Posted by jlwile on January 18, 2011

Susumu Ohno is famous for postulating the existence of “junk DNA.” In his paper introducing the term, here is what he wrote about DNA sequences that he thought were nonfunctional:1

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?

Of course, as time went on, we slowly learned how wrong Ohno was in this assessment. While many DNA sequences are not used to produce proteins, specific functions have been found for much of this supposed “junk.” Indeed, as more and more functions have been found for more and more “junk” sequences, it is becoming increasingly clear that very little junk exists in the genome.

While Ohno did some marvelous work in his illustrious career, much of it was hampered by the blinders of evolution. When you are compelled to believe that nothing but natural processes are responsible for life, you simply cannot see the deep complexity of creation. As a result, you force simplistic ideas on science, whether the data support them or not. The idea that much of an organism’s genome could be filled with “junk DNA” is a perfect example of how evolutionary thinking produces absurd conclusions.

Recently, Yuanyan Xiong and colleagues have laid to rest another evolution-inspired idea that originated with Susumu Ohno.

Many organisms have two different kinds of chromosomes. Gender is determined by sex chromosomes, while all the other chromosomes are called autosomes. People, for example, have 22 pairs of autosomes. Each pair is perfectly matched, so that the genes correspond. This means you have two genes for every trait, and they can both be found in the same autosome pair.

This isn’t necessarily the case for the sex chromosomes, however. If you are a woman, your sex chromosomes consist of a pair of X chromosomes. Thus, your sex chromosomes are like your autosomes in the sense that they come in a pair, and the pair is perfectly matched. If you are a man, however, your sex chromosomes consist of an X chromosome and a Y chromosome. This means your sex chromosomes are not a matched set. Instead, they are two different chromosomes.

Now if you think about it, this could cause a problem when it comes to the amount of protein each gender produces from its sex chromosomes. After all, women have two X chromosomes, but men have only one. If women used both X chromosomes, they would produce twice the amount of X-related proteins as compared to men. That doesn’t happen, though, because one of the two X chromosomes in women is inactivated. As a result, even though they have two X chromosomes, they use only one of them. That way, when it comes to the proteins that are encoded on the X chromosome, men and women produce equal amounts. This is called X-inactivation, and it is was actually first detected by Ohno himself.2

This leads to a big question in terms of evolution. Remember, evolutionists believe that gender was something that arrived later in the evolutionary process. Initially, all organisms were asexual. Thus, they had only autosomes. Later on, some evolutionary process had to eventually produce sex chromosomes from autosomes so that sexual reproduction could evolve. Of course, evolutionists have no idea how this actually happened, but they are confident that it must have.

Well, both of the chromosomes in each autosome pair are fully active, producing proteins over and over again. However, in the sex chromosomes, only one X is active in both genders. If sex chromosomes evolved from autosomes, then, something must have happened to make the the X chromosome genes expressed twice as much as the genes on any single autosome. Otherwise, the fact that both genders have only one active X chromosome would mean that both genders would produce only half of the needed X-related proteins. Because of this, Ohno suggested that during evolution, the expression of genes on the X chromosome was boosted by a factor of 2.

Some early genetic studies seemed to indicate that this was, indeed, the case. These studies suggested that the genes on the only active X chromosome in both males and females were expressed as much as the genes on the autosomes. This, of course, would indicate that the single active X chromosome is producing twice as much protein as any single autosome.3-4 However, in a new paper, Xiong and colleagues show that those previous studies were not correct, at least not for mice and people. They show that the expression of genes coming from the X chromosome in mice and people is (on average) half as much as the expression of genes coming from any autosome pair.5

The authors, therefore, conclude that Ohno’s idea is incorrect. Of course, they call for new theories to try to understand how sex chromosomes could have evolved from autosomes without the increase in activity that Ohno realized was crucial. However, it would be more fruitful if some researchers were willing to consider the idea that sex chromosomes did not evolve from autosomes. Instead, they were specifically designed for gender delineation and as such, there is no reason to believe that the expression of their genes is related to the expression of autosomal genes in any way.

REFERENCES

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

2. Ohno S, Kaplan WD, and Kinosita R, “Formation of the sex chromatin by a single X-chromosome in liver cells of rattus norvegicus,” Cell Research, 18:415-419, 1959.
Return to Text

3. Nguyen, D.K. & Disteche, C.M., “Dosage compensation of the active X chromosome in mammals,” Nat. Genet., 38:47-53, 2006.
Return to Text

4. Gupta, V,et al, “Global analysis of X-chromosome dosage compensation,” J. Biol, 5:3, 2006.
Return to Text

5. Yuanyan Xiong, et al, “RNA sequencing shows no dosage compensation of the active X-chromosome,” Nat. Genet., 42:1043-1049, 2010.
Return to Text

Comments

19 Responses to “Oh No! He’s Wrong Again!”
  1. The Black Sheep says:

    Did he attend public school in the U.S.? If so, he was mocked incessantly with a name like that.

  2. jlwile says:

    Hehe – Ohno went to school for most of his childhood in Korea. In fact, his father was the minister of education of the Japanese Viceroyship of Korea. He didn’t come to the U.S. until he was 23. He already had two Ph.D.s and a D. Sc. by then, so he was a real underachiever.

  3. Dan says:

    Thanks for the interesting post, Dr. Jay. I noticed that many evolutionists are now using the term “noncoding DNA” instead of “junk DNA,” and acknowledge that some of it does indeed have function. If this functional DNA doesn’t code for anything, then, would it still be consistent with evolution? In other words, do evolutionists still have an argument by pointing out that a large percentage of DNA is noncoding, whether or not it may have a function?

  4. jlwile says:

    Thanks for the comment, Dan. In answer to your question, back when it was thought that most of the genome was junk, the vast majority of evolutionists considered it a confirmation of the gene duplication mechanism of evolution – a gene gets duplicated, allowing one of the two duplicates to mutate freely so as to form a completely new gene while the other one doesn’t mutate, allowing the old function to continue on. Under such a mechanism, you would expect a lot of mutating duplicates to come up with nothing, since the sequences for biologically functional proteins are very improbable. Thus, the gene duplication mechanism for evolution predicts quite a bit of junk DNA.

    Now that more and more “junk” is being shown to have function, many evolutionists (but not most) are backing away from the idea that the gene duplication mechanism predicts junk DNA. What they now say is that while the mutating duplicates might not have hit on a functional protein sequence, they have hit on other functions, such as regulatory functions. This is much like the nonsensical “vestigial organ” argument that evolutionists now use. Back when it was thought that there were a lot of useless organs, evolutionists said you expected that in an evolutionary model. Now that we know there are very few useless organs, evolutionists say you expect that in an evolutionary model, because an organ that no longer serves its ORIGINAL purpose can be co-opted to serve some other purpose. In the same way, while the mutating duplicate gene no longer produces a protein, it has been co-opted for some other function.

    So the crux of the matter is how important the noncoding DNA is. If you could determine that the function of the noncoding DNA was not necessary when it first came about, then evolutionists could say that it is an example of a “broken” gene being co-opted to do something else. However, if a lot of noncoding DNA is found to have incredibly fundamental functions that would be important in the early stages of evolution, then evolutionists could not use that explanation.

    Now please understand – even if we determined there was absolutely no junk DNA in the genome, that wouldn’t destroy evolution in any way. Evolution is such a plastic hypothesis that it can be molded to fit any data. That’s one of the things that makes it so useless as a scientific paradigm. About the only thing it would destroy is the genetic homology in junk DNA argument for common ancestry – the idea that since humans and chimps share identical “broken” genes, we must be related, as it would be very improbable for mutations to produce the same “broken” genes independently. Of course, that argument is already nonsense, as evolution regularly requires mutations to produce identical FUNCTIONAL genes independently. Since that is now a requirement of evolution, there is no reason to believe that mutations couldn’t produce identical nonfunctional genes as well.

    In my mind, the best thing that the whole “junk DNA” story tells us is how evolutionary thinking can lead to absurd conclusions while creationist thinking produces better science. While evolutionists were absolutely willing to conclude that noncoding DNA is nonfunctional, those of us who understand that creation was produced by a Masterful Engineer concluded that noncoding DNA tells us that the genome does more than just code for proteins. Not surprisingly, the data now clearly show that creationists were right and evolutionists were wrong.

  5. jsilverheels says:

    Dr. Wile,

    Can you please explain for a layman (such as myself) just how it works that men and Turner’s syndrome females can live with just one X chromosome?

    I get the whole X inactivation thing, dosage compensation, etc.

    But I don’t understand how, if mammals need two functional copies of the autosomals, we also don’t need two functional copies of the X chromosome.

    This confuses me.

    Make it simple – but not too simple! Thanks.

  6. Mary says:

    Hi Dr. Wile,
    I stumbled on your blog this evening and I’m quite excited that I did. I’m a home-school grad currently pursuing what is essentially a Chemistry-Biology degree (that has a fancier name than that). I took genetics last year, and this notion of “pointless DNA” always annoyed me. (Although at least in my course we called “pointless DNA” introns, and “useful” DNA exons.)

    I’ve always loved chem over bio at heart for many years(since, say 9th grade…) and recently at college that’s been strengthened. I get so frustrated that so many times in Bio the data and theory are not necessarily consistent, but clearly the data, not the theory is wrong. At least with the chem professors I’ve had so far there’s been an attitude of “if the data is inconsistent with the theory(and there’s data from several reliable experiments that is inconsistent), then clearly it’s the theory not the data that’s wrong.” One chem professor actually said that in class, and I wanted to cheer!

    Anyway, I feel I should probably also mention that I used Exploring Creation with Chemistry, Biology, Physics, Human Anatomy, Advanced Chemistry and Advanced Physics in high school, and the astronomy and botany books in junior high. As mentioned above, I’ve gone on with science and have done extremely well so far by the grace of God. Chemistry is still my favorite by far, though I have to admit to loving organic more than general chem. (I still use some of the phrases in the Chemistry book from 9th grade, such as LEO says GER.)

    Anyway, this has been a far too rambling comment already!
    -Mary

  7. jlwile says:

    That’s an excellent question, jsilverheels. To fully understand this, lets get some basics out of the way. First, to get the terminology straight, the “gene” on each autosome in a pair is called an allele. Thus, the proper technical phrase is that you have have two alleles for every autosomal gene.

    Second, we are typically taught that there is a “dominant” form of an allele and a “recessive” form of an allele. This is true for many genes, but certainly not all genes. There are a few ways an allele can be dominant or recessive, but let’s just concentrate on the easiest way: the dominant allele produces a functional protein, and the recessive allele does not. In other words, the recessive allele is “broken.” If you have both dominant alleles, you can produce the protein. If you have one dominant and one recessive allele, you can still produce the protein. If you have two recessive alleles, you cannot produce the protein.

    Third, The number of alleles affects how much of a protein is expressed. The cell can regulate allele expression up and down within certain limits, but if you have two dominant alleles, you tend to produce more of the protein than if you have only one dominant allele.

    Fourth, each autosome pair carries a wide range of genes that produce a wide range of proteins. Some proteins are critical for life at very specific concentrations, some proteins are critical for certain stages of development at very specific concentrations, some are critical for life but their concentrations can be highly variable, and some just seem to provide variety.

    Given all that, can you guess which genes typically have the kind of dominant and recessive alleles I have been talking about? The last two kinds: the ones that are critical for life but their concentration can vary, and the ones that just seem to provide variety. When a protein is critical for life or critical for a certain stage of development at a specific concentration, it cannot really have a nonfunctional recessive allele. If the concentration needs to be in a very narrow window, there need to be two functional alleles so that the cells produce enough of the protein.

    In the end, then, many of your genes produce proteins whose concentrations can vary widely. As a result, there is a lot of flexibility to the alleles for that gene. However, some of your genes produce proteins whose concentrations must be in a very narrow window. For those genes, there is little flexibility in the alleles.

    Each of your autosomes carries all those kinds of genes. If you had only one autosome, that wouldn’t present a problem with many of the genes, because your body could still function even though it couldn’t produce as much protein as someone with two alleles for that gene. However, there would be certain proteins whose concentrations must be very precise, either for a certain stage of development or for the maintenance of life. Since you can’t produce enough of that protein with just one allele, you can’t survive.

    In the case of the sex chromosomes, I would expect that you have some of each kind of gene as well. However, for those genes whose proteins must have a specific concentration, one allele is enough. Indeed, two alleles might produce too much of some of those proteins, which is why there is X-inactivation in women.

    This is why the results discussed in the post are such a blow to the idea of the evolution of gender. In the end, if sex chromosomes evolved from autosomes, you would expect that the concentration-specific proteins on the X-chromosome would need to be expressed twice as much, since during the evolutionary time when the sex chromosomes were autosomes, there would have been two alleles expressing those proteins.

    Now please note that there ARE some animals that can live with only one of each autosome. Bees, ants, and wasps are examples. For them, I expect that their cells are able to regulate gene expression more freely so that they can get the necessary concentrations of the critical proteins.

    If this doesn’t make sense, please comment back. It was an excellent question, and I want to make sure you understand the answer. Also, if you don’t understand the answer, I expect there are others who don’t as well!

  8. Mary says:

    I wanted to post this on a different post (“Every year there is less junk DNA”) but the comments appear to be closed.

    Promoters and enhancers are different. If I remember correctly(and genetics was one of the first bio classes at college for me, so this isn’t super fresh in my mind, promoters are the area in the DNA that signal where transcription begins, thus without a promoter, transcription will not occur. (The polymerase usually binds at the promoter site, unless I am much mistaken.) Enhancrs, however are not necessary for transcription, but will boost the rate of transcription. Promoters are upstream of the gene, and enhancers are found in may parts of the DNA. Promoters are close to the gene and enhancers can be pretty far away. Also enhancers are only found in eukaryotes, while promoters are in prokaryotes and eukaryotes.

    Sorry to leave this on a different post, but I really wanted to explain the difference between the two. I’ve been enjoying visiting your blog this evening. Thanks!

    Mary

    P.S. This website does a nice job of explaining about promoters/enhancers and the whole transcription/translation process.

    http://www.emunix.emich.edu/~rwinning/genetics/transcr.htm

  9. jlwile says:

    Mary, thanks so much for your kind comment. Chemistry is, indeed, a more data-driven subject than biology. As a result, you will not see as much nonsense in chemistry as you see in biology.

    Please note that according to evolutionists, there is a lot more “junk DNA” than just introns. Introns are, indeed, considered junk, even though they clearly are not. There are many other examples of “junk,” however. Long interspersed repetitive elements and short interspersed repetitive elements are generally considered “junk,” although functions have been found for some examples of each. Some pseudogenes are also considered to be junk, since they look like broken genes. However, functions have been found for some of them as well.

  10. jlwile says:

    Thanks for your comment, Mary. I assume this is in response to Arthur Hunt’s comment. I wish he had responded, but I do believe you are correct. He seemed to think that the post was saying promoters are separate from genes. Of course, the post did not mention promoters; it was about enhancers, and they certainly are not considered part of a gene. You explained it very well – you don’t need enhancers for transcription to occur, but you do need a promoter. I didn’t know that enhancers are found only in eukaryotes. Thanks for adding that!

  11. jsilverheels says:

    Dr. Wile,

    Thanks for answer – I am going to download it, read it and regurgitate it back to you in a few days to see if I got it. As I said i am a layman and these concepts are new to me. I didn’t even know what X inactivation was one month ago! (And I bet most Americans don’t, either.)

    Offhand though, there does seem to be something “special” about the sex chromosomes, something quite different from the autosomals. I’m still getting my head around the fact that having homologous chromosomes is “normal”, and males sex chromosomes are not….

  12. jlwile says:

    Please do get back with me. It is a tough concept to grasp, but it helps one appreciate the amazing design that makes life possible.

  13. jsilverheels says:

    Dr. Wile,

    OK, I’ve been chewing over my response to you over and over. It’s time to spit it out, and risk looking like an ignoramus.

    My understanding of your answer is that my question was in essence one about gene dosages and gene expression. Lurking at the heart of my question, which I didn’t want to write, because I wanted to pose my question very simply, is: are the genes on the X chromosome QUALITATIVELY different from those on the autosomals?

    It would appear, from your answer that yes: they are qualitatively different. In your words: “When a protein is critical for life or critical for a certain stage of development at a specific concentration, it cannot really have a nonfunctional recessive allele.”

    I have another question regarding X inactivation and X-linked diseases (and also the entire concept of dominant and recessive with respect to the sex chromosomes) but before I ask it, I’d like your confirmation that I got your answer right. Or if I am wrong, tell me where I went wrong.

    Personal note: as I said I am new to this. I took a few undergraduate courses in physics, and Dr. Wile: Newtonian mechanics is baby stuff compared to this!

  14. jlwile says:

    Jsilverheels, thanks for your reply. Never fear looking like an ignoramus. Other commenters have done a more spectacular job at that than you could ever do. Also, your point at the end is quite correct. Newtonian mechanics is baby stuff compared to genomics!

    I would say that the results of this study show that the genes on the X chromosome are quite different from those on the autosomes. They seem to be the ones that don’t need to be expressed as often, which implies that the proteins they code for are not nearly as sensitive when it comes to concentration. This is what you would expect if the sex chromosomes were sex chromosomes from the beginning, and it is not what you would expect if they evolved from autosomes.

    This isn’t to imply that all the genes on the X chromosome are related to gender. They clearly are not. However, if there were a set of genes that didn’t need to be expressed as often, a Designer would probably tend to group them on the chromosome that has no homologous partner. That seems to be what has happened, at least based on the results of this study.

  15. jsilverheels says:

    Hi Dr. Wile,

    Well, it seems I rather got it right with respect to “quality” of genes on X chromosome. (When I use a lay-term such as “quality” – I don’t mean that the gene in question is “better” – I mean “different in kind, function, purpose.”

    “‘This isn’t to imply that all the genes on the X chromosome are related to gender. They clearly are not.” I should really read up on the genes that are loaded onto this amazing chromosome. Do you have any suggestions?

    However, preliminarily, my understanding of the X chromosome is that the genes on it are crucial to placental development, and ultimately to human cognition itself. Amazing!!

    It doesn’t surprise me that most of the genes on the X aren’t related to gender – since the template of development is female. Males must be forcibly virilized by the intervention of the Y chromosome. I will ask you my question about X inactivation in a different comment.

  16. jsilverheels says:

    Question regarding X inactivation:

    Normal 46,XX fertile women inactivate one X. 45,X0 (Turner’s syndrome) women have only X to begin with. They are infertile and have numerous subtle developmental problems. What’s the difference between having a normally silenced X chromosome, and being an interfile Turner’s syndrome woman? The so-called “escape genes”?

    Further to this, if X inactivation is complete, then why would a man with Klinefelter’s syndrome exhibit subtle signs of feminization?

    2. Let’s go back to my above question about “quality” of genes on X chromosome and X-linked diseases. X inactivation effectively forces females’ two X chromosomes to mimic the behavior of homologous chromosomes in terms of compensating for a defective gene. Usually. (Hemophilia: if half her X’s produce enough gene product for the clotting factor, she’ll be OK. Not so her brother, all of whose eggs are in a defective basket. OK, I think I get that.

    Doesn’t this put males at a terrible disadvantage in terms of those characteristics that are coded on the X?

    Note: I’m not making a subtle argument against design here. I do question neo-Darwinian dogma with respect to the efficiency-producing tendencies of natural selection.

    Strikes me that nature really is all about bargains.

    Males might be, in terms of X-linked diseases, better off with two X chromosomes, one inactivated, one active, like women, and a virilizing Y chromosome.

    But in the year 2011 AD, that would make males sterile. Not a good solution.

    I’m offering it as a viable Darwinian alternative.

    3. Finally a simple question. I accept the nomenclature of dominant and recessive with respect to autosomals, because they are homologous, but doesn’t this nomenclature create confusion when you extend the concept to the sex chromosomes? If they are not homologous, how does the concept of dominance and recessiveness even apply? (I ask this because of the term “X-linked recessive diseases”, which I have encountered.) Does my question even make sense to you?

    Hope I haven’t presumed too much on your time. Genomics is harder than Newtonian mechanics, but it’s much more rewarding!

  17. jlwile says:

    More excellent questions, jsilverheels!

    1. The infertile part is easy. The mechanisms of meiosis (the process that produces egg cells in women) depend on a full compliment of chromosomes. With one missing, meiosis simply cannot finish properly, so the woman has no functional egg cells.

    The difference between a woman with Turner’s syndrome and a woman with two X chromosomes is caused by the fact that the X chromosome is not FULLY inactivated. There are some genes on the X chromosome that also appear on the Y chromosome. Thus, men have two active alleles for those genes, and so must women. So for those genes, the alleles on the “inactivated” X chromosome are still active. If a woman doesn’t have a second X chromosome, she cannot make as much of the proteins coded for by those genes. I think (but am not sure) that this is the problem with men who have two X chromosomes (Klinefelter’s syndrome). Their second X is inactivated, but once again, not the alleles that also show up on the Y. As a result, these men have three active alleles for those genes and therefore make too many of those proteins.

    2. You are absolutely right that males are at a disadvantage regarding X-linked traits. That’s why they are more likely to be hemophiliacs, for example. Many think autism must be partly X-linked, since boys are significantly more likely to be autistic than girls. However, I am not sure your idea of all men being XXY (which I don’t see as an argument against design) helps. I agree that a large part of biology is about making bargains or (as I would say) compromises. Indeed, that’s what design is about as well. I have designed many detectors for my nuclear chemistry research, and it is all about making compromises so that the detector does what you need it to do but is reliable and doesn’t produce too much nonsense.

    In the case of a cell, you have a lot of mechanisms (meiosis principal on the list) that count on two of each chromosome set. If I want one set of chromosomes to have three members (and only in males), I am going to have to design a whole new group processes just for that one chromosome set. While a good designer could probably do that, it might reduce the efficiency, resiliency, or longevity of the cell. That might not be worth the benefit of protecting males from being more susceptible to X-related genetic abnormalities.

    3. I agree that the terminology “dominant” and “recessive” makes little sense in the case of males and most of the X chromosome. However, it works if you think of “dominant” as “working” and “recessive” as “broken.” In that sense, then, a man has the dominant allele if the allele produces a protein that works at the expected proficiency. The man has a recessive allele if the allele does not produce a protein or produces a protein that doesn’t work with the expected proficiency. So the dominant allele dominates in women. It simply produces a protein that WORKS in men. The recessive allele is covered up in women, but it produces a protein that DOESN’T WORK (or doesn’t work very well) in men.

  18. jsilverheels says:

    “Many think autism must be partly X-linked, since boys are significantly more likely to be autistic than girls.”

    As is the case with florid schizophrenics, although more females than males are somewhat schizoaffective. (Think hemophilia.)

    “However, I am not sure your idea of all men being XXY (which I don’t see as an argument against design) helps. I agree that a large part of biology is about making bargains or (as I would say) compromises.”

    I offered the option of nature creating fertile XXY males as a thought experiment. If this had happened then males would be more protected from the X linked diseases than they currently are. I think. Research on Klinefelter’s boys is really very rudimentary because they are hard to detect and also due to ethical considerations. But it strikes me as logical that they would suffer less from X-linked diseases and more from feminine type things, such as autoimmune diseases.

    But in addition to being based on compromises, as you put it, nature wants parsimonious compromises. So a fertile man gets one X – and therein lies the risk. Get a “good” X and you have a man who is talented, intelligent, stable and fertile. Get a bad one….and he is much more disabled than his sister.

    C’est la vie!

    I appreciate the answers.

  19. jlwile says:

    I am happy to help, jsilverheels.

home | top