Junk DNA – An Introduction

The popular South African magazine, Jewish Life, featured an article by me in its latest issue (March 2013). I reproduce it below.

***

Junk. Barren. Desert. Could these harsh terms have anything to do with human biology? In the latter part of the 20th century, as the intricacies of molecular genetics were being unfurled, a curious fact emerged. Much of our DNA does not contain instructions for manufacturing proteins, the workhorses of the cell. So if DNA doesn’t do what you thought it would do, it’s junk, right? The term Junk DNA was coined in 1972 by the biologist Susumu Ohno. He published an article wondering why there is “so much ‘junk DNA’ in our genome.”[1] In 1980, two papers appeared back-to-back in the journal Nature. Both argued that much genetic material has no function,[2] and the second article explicitly argued that much DNA in higher organisms is little better than junk.[3] In time, bleak terms like those at the beginning of this paragraph became ubiquitous in the discussion of human genetics.

But this terminology did not involve just an arcane point within genetics. Junk DNA was used to promote a much wider ideology. Many biologists claimed that most of our DNA is functionless detritus that accumulated in our cells as a by-product of merciless evolutionary processes. After all, what other explanation could there be for the existence in our genome of an ocean of inert genetic material? Here is one example of that argument. In 1998, the world’s foremost apostle for evolution, Richard Dawkins, wrote in the journal The Skeptic:

Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing… And there’s lots more DNA that doesn’t even deserve the name pseudogene… It consists of multiple copies of junk, “tandem repeats”, and other nonsense…[4]

Dawkins and other evolution junkies believe that there is no explanation for this apparently-superfluous material in our genomes, other than the admission that it is the residue of an evolutionary process:

Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.

Similarly, in Why Evolution Is True (published in 2009), the geneticist Jerry Coyne of the University of Chicago wrote that it is a “prediction” of neo-Darwinian theory that we will find the genome littered with useless “vestigial genes”. This sort of claim pervaded the literature for decades.

But that view has turned out to be spectacularly wrong. Since 1990 – but especially after completion of the Human Genome Project in 2003 – many hundreds of articles have appeared in the scientific literature documenting the various functions of non-coding DNA, and more are being published almost weekly. Far from consisting mainly of junk, our genome is increasingly revealing itself to be a multidimensional, integrated system in which “junk” DNA performs a wide variety of functions, often in a regulating or switching capacity, thus controlling critical cellular functions. The nail in the coffin for the “junk” paradigm was the ENCODE (Encyclopaedia of DNA Elements) project, a collaboration of 442 scientists in 32 laboratories. ENCODE mapped the part of the genome previously thought to be inert, and has thus far found function for more than 80% of the genome, which, it turns out, is a buzzing universe of biochemical activity. An article in the journal Science entitled ENCODE Project Writes Eulogy for Junk DNA began with: “This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases.”[5] The prediction made by the biologists Richard Sternberg and James Shapiro that one day, we will think of what used to be called junk DNA as a critical component of truly expert cellular control regimes,[6] is about to be fully borne out.

Let’s take a bird’s-eye view of this episode. For several decades, it seemed as if vast stretches of DNA did nothing. The consensus developed that this genetic material just accumulates in the genome like, well, like junk in a junkyard. This was portrayed, with strident triumphalism, as decisive evidence for biological evolution, but turned out to be completely wrong.

Some of the questions that motivated me to write Genesis and Genes (Feldheim, 2013) are reflected well through this type of historical episode. How often does a paradigm shift of this sort happen in science? How common is it for scientists to make absolute statements about physical phenomena that are not yet fully understood? How robust is the claim that some argument is supported by the consensus of scientists? And then there’s the Jewish angle. The Talmud teaches that everything that God created has a purpose.[7] Maharal (ca. 1520-1609), one of the greatest Jewish philosophers of the past half-millennium, wrote that even if we do not understand every feature of the human body, yet we are quite certain that nothing in it is superfluous.[8] Was that viewpoint ever compatible with the notion that our genomes are littered with junk? Most importantly, when evolutionary biologists proclaim, as they do often, that there is overwhelming evidence for evolution, is that evidence ever as hollow as the argument from junk DNA turned out to be?

I also wanted to explore how ignorance of the history of science distorts one’s ability to critically assess evidence for controversial ideas. Let’s look at one example. In the context of biology, one often hears a sound bite that originated with Theodosius Dobzhansky, one of the architects of the modern version of Darwinism. He wrote in 1973 that nothing in biology makes sense except in the light of evolution.[9] Imagine yourself as an impressionable student, hearing that nothing in your discipline makes sense unless you pay obeisance to a particular viewpoint. You would likely first come across this gem courtesy of your professor, an authority figure whose name is followed by an imposing alphabet soup of titles. The adage would be frequently repeated and become seared into your mind. Gradually, it would become part of your mental furniture, never given a second thought and never examined critically. But what if you had the benefit of some exposure to history? These days, continental drift (plate tectonics) is the theory that undergirds geology, oceanography and geophysics. But go back about sixty years, and those disciplines were held together by something called geosynclinal theory. Before it was ditched on history’s ash heap in favour of continental drift, geosynclinal theory was seen as the unifying concept in the earth sciences. As late as 1960, the authors of a geology-textbook could make the following breathtaking comment:

The geosynclinal theory is one of the great unifying principles in geology. In many ways its role in geology is similar to that of the theory of evolution, which serves to integrate the many branches of the biological sciences… Just as the doctrine of evolution is universally accepted among biologists, so also the geosynclinal origin of the major mountain systems is an established principle in geology.[10]

So this textbook equated evolution and geosynclinal theory in being quite indispensable to their respective disciplines, and yet, geosynclinal theory is dead and buried. The essential turned out to be transient. Would you be as credulous about evolution’s indispensability to biological research if you knew that similar claims have been made before and turned out to be totally wrong?

I also wanted to explore how scientists approach areas of their work that have obvious and profound philosophical implications, and how their worldview influences their work. In a book review of Carl Sagan’s The Demon-Haunted World, the prominent Harvard biologist Richard Lewontin made a comment that had all the subtlety of a cruise missile:

We take the side of science in spite of the patent absurdity of some of its constructs… in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism.

Professor Lewontin went on to assure his readers that,

It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create… a set of concepts that produce material explanations… Moreover, that materialism is an absolute, for we cannot allow a Divine Foot in the door.[11]

Crucially, I wanted to examine the claim that Judaism must be reconcilable with science. This is a notion that, although popular, is refuted by the historical experience of Junk DNA and similar historical episodes. A dogmatic insistence on marrying Judaism to every consensus position in science would force us to accept that the Torah be compatible with ideas that have been roundly discredited. If so, is there room to differentiate between Nature (what the world is really like) and science (the fallible human attempt to understand Nature)?

There are many more facets to Genesis and Genes, because its subject matter touches on the most fundamental questions about existence. Are human beings nothing more than meat on its path to putrefaction? Is there support in traditional sources for the notion that, somehow, God is involved in an evolutionary process? Do the Talmud and other traditional sources contain oblique references to hominids?

In an age of spiritual turmoil – one prominent figure in the kiruv-movement observed, “How can you teach people about their innate Godliness when they’re confused about their innate humanity?!” – I wrote Genesis and Genes with the conviction that its subject matter is more important than most, and that there is no alternative to being informed on the topic.

References:

[1] Susumu Ohno, So much ‘junk’ DNA in our genome”, Brookhaven Symposia in Biology 23 (1972):366-70. The entire article can be read here: http://www.junkdna.com/ohno.html
Retrieved 28th December 2011.
[2] W. Ford Doolittle and Carmen Sapienza, “Selfish Genes, the phenotype paradigm and genome evolution”, Nature 284 (1980): 601-603.
[3] Leslie E. Orgel and Francis H.C. Crick, “Selfish DNA: the ultimate parasite”, Nature 284 (1980): 604-607.
[4] Richard Dawkins, The Information Challenge, The Skeptic, Vol. 18 (4) December, 1998.
[5] ENCODE Project Writes Eulogy for Junk DNA, Elizabeth Pennisi, Science, Vol. 337 no. 6099 pages 1159-1161, 7 September 2012. The summary can be read here: http://www.sciencemag.org/content/337/6099/1159.summary.
Retrieved 2nd December 2012.
[6] Richard v. Sternberg and James A. Shapiro, “How Repeated Retroelements format genome function,” Cytogenetic and Genome Research, Vol. 110: 108–116 (2005).
[7] מסכת שבת דף עז עמוד ב: אמר רב יהודה אמר רב כל מה שברא הקב”ה בעולמו לא ברא דבר אחד לבטלה.
[8] מהר”ל תפארת ישראל פרק ח: וכבר אמרנו שאף אם אין ידוע לנו טעם וסבה של כל דבר ודבר שנמצא באדם למה הוא כך, מכל מקום ידוע לנו שאין דבר אחד לבטלה…
[9] The essay in which Dobzhansky made this statement was first published in the journal American Biology Teacher, volume 35, pages 125-129.
[10] Thomas H. Clark and Colin W. Stearn, The Geological Evolution of North America: A Regional Approach to Historical Geology, Ronald Press, 1960, page 43.
[11] Richard Lewontin, Billions and billions of demons (Review of The Demon-Haunted World: Science as a Candle in the Dark by Carl Sagan, 1997), The New York Review of Books, page 31, 9th January 1997.

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4 Responses to “Junk DNA – An Introduction”

  1. Matt Says:

    Oops, the quotation style I used somehow blocked out most of my text. Please disregard the previous post. Here is my full comment:

    ”..turned out to be completely wrong”

    I’m a bit confused. You often urge your readers to seek out established, reproducible science. Yet, here it seems that you are quoting new results from ENCODE without mentioning that they are controversial and yet unrepeated by other researchers:
    (http://blogs.nature.com/news/2012/09/fighting-about-encode-and-junk.html). What happened to your rule?

    Regardless of this 80% figure, between 5-8% of our genome consists of viral DNA which we improbably share with other primate cousins (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387345/)
    There are many other known instances of relic DNA such as the two telomeres (chromosomal end caps) in the the middle of the human chromosome 2 and at the fusion point of two primate chromosomes (http://www.pnas.org/content/88/20/9051.full.pdf). No matter how optimistic that 80% number is, one cannot stretch it to 100%.

    “I also wanted to explore how ignorance of the history of science distorts one’s ability to critically assess evidence for controversial ideas.”

    You very often accuse scientists of being ignorant of our own history. This not my experience, among my colleagues or among scientists from other fields. What is your basis for this assertion? Also, what exactly are your own credentials on the subject of science history?

    ”unless you pay obeisance to a particular viewpoint”

    Evolution is not a “viewpoint”, it is a collection of observations and a theoretical framework for understanding those observations. It is unfair to attribute authoritarianism to biology education. The biologists and educators I most admire couldn’t be further from authoritarian.

    I should also point out that presenting a theory as “unifying” or “essential” is not the same as asserting it to be absolute truth. The Dobzhansky quote is more of a description than an assertion. Regardless of whether or not evolutionary theory is revised or replaced at some future time, it is absolutely essential to our current understanding of biology as it stands now.

    “So this textbook equated evolution and geosynclinal theory in being quite indispensable to their respective disciplines, and yet, geosynclinal theory is dead and buried…Would you be as credulous about evolution’s indispensability to biological research if you knew that similar claims have been made before and turned out to be totally wrong?”

    It is impossible to understand the motions of the planets without Newtonian Mechanics. I recently advised a grad student to pay close attention to Classical Field Theory, as it is indispensable to modern physics. By your reasoning, should I presume that these are wrong simply because they are said to be indispensable? This sort of inference by association is fallacious. The fact that Theory A was wrong in the past has no direct bearing on whether or not Theory B is wrong. I agree that I would not want your readers to accept evolutionary theory merely based on an authoritative assertion. On the other hand, I would not want them to doubt evolution merely because you presented it alongside a failed theory. They should accept it or reject it based on an informed position regarding its scientific merits. No meta-scientific arguments are necessary.

  2. marc Says:

    Oh Matt,

    I think I know where you are coming from and in my opinion you are missing a critical piece of background to the whole point of what I believe Yoram is doing.

    I could be wrong of course….

    I shall tell you what I think despite the possibility that I am completly of target. Amonsgst some Orthodox Jews (especially those frequenting blogs!) there is an attitude – I would reveal my hand a little by calling it a sickness – that when ‘science ‘ forms a consensus it is true and one cannot voice an opinion different to that. Hence there are many that wish reinterpret Genesis I simply becaue ‘science’ says its not so.

    Your personal nuanced understanding of terms such as proof and evidence are not shared by some of our brethren.

    Hence it seems to me that a good deal of the book and the blog too is geared towards undermining this subservient attitude – therefore what you consider innuendo and avoiding the meat of the argument for many of us is the main argument – this is not some kind of childish point that in the past science was wrong so therefore it is wrong now too, it’s more subtle and more useful than that – it is that consensus is meaningless and only the evidence counts. furthermore the point is that just because science presently accpets certain assumptions it does not mean that we always have to without using our own critical faculties first. For you my friend this my be a no brainer, but not for so others.

    This is only my opinion, perhaps I’m completely wrong, but it seems therefore that you are perhaps sometimes arguing at cross purposes with Yoram.

    Kind regards,

    Marc

  3. Why Blogging is Bad For Science « Homologus Says:

    […] Junk DNA – An Introduction […]

  4. Teresa Says:

    Right away I am going away to do my breakfast, once having my breakfast coming again to read further news.

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