What the junk?!

Getting back to my first blog entry, let’s delve a little deeper into why my  aptly named friend, Et, believes that humans are the product of an alien biogenetic experiment. A quick search on google reveals that a possible culprit to incite his mad ramblings is “junk DNA”.

The term junk DNA has been around since the 1960’s, but it was formalised by a Japanese-American geneticist, Dr Sosumu Ohno in 1972, while trying to determine how DNA mutates. Dr Ohno used the term to describe pseudogenes (commonly thought of as defunct relatives of known genes that do not code for proteins), but overtime this definition expanded to have a broader meaning, referring to any sequence of DNA without a functional role.

The term junk DNA has elicited strong responses over the years . A 5 minute google search and one can sense things starting to get a little rowdy! There’s blogs dismissing the myth that junk DNA is in fact junk, and then there’s the diehards with their blogs dismissing the myths around the myths. An evolutionary biologist and vehement defender of Junk DNA, T. Ryan Gregory, coined “the onion test“, which serves as a reality check to those who may be tempted in debunking the junk  out of junk DNA.

Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

In 2012 ENCODE project published a report where it seemed as though junk DNA was to be consigned to the history books.This report claimed to be able to assign biological function to over 80% of the human genome.Their abstract reads as follows:-

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

This report horrified the evolutionists, since the existence of junk DNA is one of their lines of genetic evidence supporting evolutionary common ancestry. Since genetic mutations are a driving force of evolutionary change, evolutionists expect a large amount of useless DNA (essentially leftovers from an unguided evolutionary process) to be found in genomes of certain species.

 Evolutionist Dan Graur and his colleagues make this clear: “Evolution can only produce a genome devoid of ‘junk’ if and only if the effective population size is huge and the deleterious effects of increasing genome size are considerable….In humans, there seems to be no selection against excess genomic baggage. Our effective population size is pitiful and DNA replication does not correlate with genome size.”9 Hence, evolutionists predict that the human genome should be filled with junk DNA.

The above quote is explained by a concept known as mutational meltdown which places an upper limit on the number of genes an organism can have.

Here’s how it works. A population of, say, frogs is reproducing. Every time they produce a new tadpole, that tadpole gains a certain number of mutations. A few of those mutations may be beneficial. The rest will be neutral or harmful. If harmful mutations emerge at a rate that’s too fast for natural selection to weed them out, they’ll start to pile up in the genome. Overall, the population will get sicker, producing fewer offspring. Eventually the mutations will drive the whole population to extinction.

If a frog has 10,000 genes, those are 10,000 potential targets for a harmful mutation. If the frog has 100,000 genes, it has ten times more targets.

It is thought that between 70 to 150 new mutations occur in the genome of every new human baby. Applying the mutational meltdown concept, only 10% of the human genome can be functional while the remainder 90% must be junk DNA. Mutations that alter junk DNA don’t cause any harm, since its junk in any case, but if 80% of our genome was functional as the ENCODE project suggests,according to this rationale, we should actually be extinct.

The debate on junk DNA can get a little dizzying. Was ENCODE wrong in their declaration, or are the evolutionists wrong? Can the creationists finally say “I told you so!”…..or….. just maybe it was the aliens afterall?! Finding the functionality of genomic DNA is both philosophically and scientifically challenging. What one can conclude from this debacle is that the human genome is incredibly complicated. The upshot of this is that as we discover more about our genome with emergence of new findings on the biochemistry of these non-coding “black-holes”and how they act is genetic triggers, the more insights we gain into how to treat a multitude of diseases including  heart disease, diabetes, schizophrenia, and autism (to name a few).

Further reading:-

Dunham, I., Kundaje, A., Aldred, S., Collins, P., Davis, C., Doyle, F., Epstein, C., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B., Landt, S., Lee, B., Pauli, F., Rosenbloom, K., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J., Song, L., Trinklein, N., Altshuler, R., Birney, E., Brown, J., Cheng, C., Djebali, S., Dong, X., Dunham, I., Ernst, J., Furey, T., Gerstein, M., Giardine, B., Greven, M., Hardison, R., Harris, R., Herrero, J., Hoffman, M., Iyer, S., Kellis, M., Khatun, J., Kheradpour, P., Kundaje, A., Lassmann, T., Li, Q., Lin, X., Marinov, G., Merkel, A., Mortazavi, A., Parker, S., Reddy, T., Rozowsky, J., Schlesinger, F., Thurman, R., Wang, J., Ward, L., Whitfield, T., Wilder, S., Wu, W., Xi, H., Yip, K., Zhuang, J., Bernstein, B., Birney, E., Dunham, I., Green, E., Gunter, C., Snyder, M., Pazin, M., Lowdon, R., Dillon, L., Adams, L., Kelly, C., Zhang, J., Wexler, J., Green, E., Good, P., Feingold, E., Bernstein, B., Birney, E., Crawford, G., Dekker, J., Elnitski, L., Farnham, P., Gerstein, M., Giddings, M., Gingeras, T., Green, E., Guigó, R., Hardison, R., Hubbard, T., Kellis, M., Kent, W., Lieb, J., Margulies, E., Myers, R., Snyder, M., Stamatoyannopoulos, J., Tenenbaum, S., Weng, Z., White, K., Wold, B., Khatun, J., Yu, Y., Wrobel, J., Risk, B., Gunawardena, H., Kuiper, H., Maier, C., Xie, L., Chen, X., Giddings, M., Bernstein, B., Epstein, C., Shoresh, N., Ernst, J., Kheradpour, P., Mikkelsen, T., Gillespie, S., Goren, A., Ram, O., Zhang, X., Wang, L., Issner, R., Coyne, M., Durham, T., Ku, M., Truong, T., Ward, L., Altshuler, R., Eaton, M., Kellis, M., Djebali, S., Davis, C., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G., Khatun, J., Williams, B., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R., Alioto, T., Antoshechkin, I., Baer, M., Batut, P., Bell, I., Bell, K., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Li, G., Luo, O., Park, E., Preall, J., Presaud, K., Ribeca, P., Risk, B., Robyr, D., Ruan, X., Sammeth, M., Sandhu, K., Schaeffer, L., See, L., Shahab, A., Skancke, J., Suzuki, A., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S., Hannon, G., Giddings, M., Ruan, Y., Wold, B., Carninci, P., Guigó, R., Gingeras, T., Rosenbloom, K., Sloan, C., Learned, K., Malladi, V., Wong, M., Barber, G., Cline, M., Dreszer, T., Heitner, S., Karolchik, D., Kent, W., Kirkup, V., Meyer, L., Long, J., Maddren, M., Raney, B., Furey, T., Song, L., Grasfeder, L., Giresi, P., Lee, B., Battenhouse, A., Sheffield, N., Simon, J., Showers, K., Safi, A., London, D., Bhinge, A., Shestak, C., Schaner, M., Ki Kim, S., Zhang, Z., Mieczkowski, P., Mieczkowska, J., Liu, Z., McDaniell, R., Ni, Y., Rashid, N., Kim, M., Adar, S., Zhang, Z., Wang, T., Winter, D., Keefe, D., Birney, E., Iyer, V., Lieb, J., Crawford, G., Li, G., Sandhu, K., Zheng, M., Wang, P., Luo, O., Shahab, A., Fullwood, M., Ruan, X., Ruan, Y., Myers, R., Pauli, F., Williams, B., Gertz, J., Marinov, G., Reddy, T., Vielmetter, J., Partridge, E., Trout, D., Varley, K., Gasper, C., Bansal, A., Pepke, S., Jain, P., Amrhein, H., Bowling, K., Anaya, M., Cross, M., King, B., Muratet, M., Antoshechkin, I., Newberry, K., McCue, K., Nesmith, A., Fisher-Aylor, K., Pusey, B., DeSalvo, G., Parker, S., Balasubramanian, S., Davis, N., Meadows, S., Eggleston, T., Gunter, C., Newberry, J., Levy, S., Absher, D., Mortazavi, A., Wong, W., Wold, B., Blow, M., Visel, A., Pennachio, L., Elnitski, L., Margulies, E., Parker, S., Petrykowska, H., Abyzov, A., Aken, B., Barrell, D., Barson, G., Berry, A., Bignell, A., Boychenko, V., Bussotti, G., Chrast, J., Davidson, C., Derrien, T., Despacio-Reyes, G., Diekhans, M., Ezkurdia, I., Frankish, A., Gilbert, J., Gonzalez, J., Griffiths, E., Harte, R., Hendrix, D., Howald, C., Hunt, T., Jungreis, I., Kay, M., Khurana, E., Kokocinski, F., Leng, J., Lin, M., Loveland, J., Lu, Z., Manthravadi, D., Mariotti, M., Mudge, J., Mukherjee, G., Notredame, C., Pei, B., Rodriguez, J., Saunders, G., Sboner, A., Searle, S., Sisu, C., Snow, C., Steward, C., Tanzer, A., Tapanari, E., Tress, M., van Baren, M., Walters, N., Washietl, S., Wilming, L., Zadissa, A., Zhang, Z., Brent, M., Haussler, D., Kellis, M., Valencia, A., Gerstein, M., Reymond, A., Guigó, R., Harrow, J., Hubbard, T., Landt, S., Frietze, S., Abyzov, A., Addleman, N., Alexander, R., Auerbach, R., Balasubramanian, S., Bettinger, K., Bhardwaj, N., Boyle, A., Cao, A., Cayting, P., Charos, A., Cheng, Y., Cheng, C., Eastman, C., Euskirchen, G., Fleming, J., Grubert, F., Habegger, L., Hariharan, M., Harmanci, A., Iyengar, S., Jin, V., Karczewski, K., Kasowski, M., Lacroute, P., Lam, H., Lamarre-Vincent, N., Leng, J., Lian, J., Lindahl-Allen, M., Min, R., Miotto, B., Monahan, H., Moqtaderi, Z., Mu, X., O’Geen, H., Ouyang, Z., Patacsil, D., Pei, B., Raha, D., Ramirez, L., Reed, B., Rozowsky, J., Sboner, A., Shi, M., Sisu, C., Slifer, T., Witt, H., Wu, L., Xu, X., Yan, K., Yang, X., Yip, K., Zhang, Z., Struhl, K., Weissman, S., Gerstein, M., Farnham, P., Snyder, M., Tenenbaum, S., Penalva, L., Doyle, F., Karmakar, S., Landt, S., Bhanvadia, R., Choudhury, A., Domanus, M., Ma, L., Moran, J., Patacsil, D., Slifer, T., Victorsen, A., Yang, X., Snyder, M., White, K., Auer, T., Centanin, L., Eichenlaub, M., Gruhl, F., Heermann, S., Hoeckendorf, B., Inoue, D., Kellner, T., Kirchmaier, S., Mueller, C., Reinhardt, R., Schertel, L., Schneider, S., Sinn, R., Wittbrodt, B., Wittbrodt, J., Weng, Z., Whitfield, T., Wang, J., Collins, P., Aldred, S., Trinklein, N., Partridge, E., Myers, R., Dekker, J., Jain, G., Lajoie, B., Sanyal, A., Balasundaram, G., Bates, D., Byron, R., Canfield, T., Diegel, M., Dunn, D., Ebersol, A., Frum, T., Garg, K., Gist, E., Hansen, R., Boatman, L., Haugen, E., Humbert, R., Jain, G., Johnson, A., Johnson, E., Kutyavin, T., Lajoie, B., Lee, K., Lotakis, D., Maurano, M., Neph, S., Neri, F., Nguyen, E., Qu, H., Reynolds, A., Roach, V., Rynes, E., Sabo, P., Sanchez, M., Sandstrom, R., Sanyal, A., Shafer, A., Stergachis, A., Thomas, S., Thurman, R., Vernot, B., Vierstra, J., Vong, S., Wang, H., Weaver, M., Yan, Y., Zhang, M., Akey, J., Bender, M., Dorschner, M., Groudine, M., MacCoss, M., Navas, P., Stamatoyannopoulos, G., Kaul, R., Dekker, J., Stamatoyannopoulos, J., Dunham, I., Beal, K., Brazma, A., Flicek, P., Herrero, J., Johnson, N., Keefe, D., Lukk, M., Luscombe, N., Sobral, D., Vaquerizas, J., Wilder, S., Batzoglou, S., Sidow, A., Hussami, N., Kyriazopoulou-Panagiotopoulou, S., Libbrecht, M., Schaub, M., Kundaje, A., Hardison, R., Miller, W., Giardine, B., Harris, R., Wu, W., Bickel, P., Banfai, B., Boley, N., Brown, J., Huang, H., Li, Q., Li, J., Noble, W., Bilmes, J., Buske, O., Hoffman, M., Sahu, A., Kharchenko, P., Park, P., Baker, D., Taylor, J., Weng, Z., Iyer, S., Dong, X., Greven, M., Lin, X., Wang, J., Xi, H., Zhuang, J., Gerstein, M., Alexander, R., Balasubramanian, S., Cheng, C., Harmanci, A., Lochovsky, L., Min, R., Mu, X., Rozowsky, J., Yan, K., Yip, K. and Birney, E. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414) 57-74.

 

 

One thought on “What the junk?!

  1. Just because we cannot account for the purpose of something, does not make it meaningless. Things like transposons, viruses which integrate into the human genome, genes which are very transiently expressed, epigenetic control of transcription and translation, etc. may one day fill our knowledge of what the human genome contains. I think it’s too early to say that most of what humans pack in their trunk is junk 🙂

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