On BioScience and Life and Such

Junk, DNA, RNA, Brain, Biology and Possible Solutions

In Uncategorized on September 11, 2008 at 10:10 am

We and all other organisms are complicated biological structures made from very simple building blocks on an information template of DNA. Individual variations in DNA are rather easy to work out although you do need lots and lots of DNA sequencers, data-storage facilities and data comparison programs. Fact remains, – you basically only need time and money to do this.

We know that the DNA sequence itself is diverse enough to make every individual exclusive while retaining enough common features for speciation. So, DNA explains a lot, but the final functionality including the ability to adopt to changing environments, depends on the next levels of variation…

Take the Necker Cube below. As described by  Edge writer Nathan Myhrvold:

This is a perfectly good 2D picture, but we cannot help trying to force into being a 3D object. The 3D reconstruction problem is ill posed—there are two very different solutions, each of which is feasible. So, when you look at it you alternately see one then the other—you can feel it pop in, or pop out. Without a unique solution your brain flips between the possible solutions.

The analogy to biology is as follows:

Strictly speaking, the cube is two-dimensional. But, for all practical purposes it is a three-dimensional object. At the same time it’s three dimensional form shifts from one confirmation to the other.

The analogy to DNA is that while the written DNA-sequence is linear (two-dimensional) the resulting molecular three dimensional structure allows for transcription into RNA and interactions with proteins both at the DNA and RNA level. These interactions in turn can lead to effects that vary depending on the surrounding environment. The Necker cube is made out of 12 identical lines giving rise to two different three dimensional conformations. DNA is made out of four versions of millions of basepairs. Resulting in a vast number of possible final variations of effects.

Biology handles a chaotic and changing environment using simple building blocks to make flexible, hyper variable, intricate and complicated possible solutions. Knowing the DNA-sequence, the transcriptome and the proteome is basically just discovering the two first dimensions in a many-dimensional organism.

New ideas, approaches and tools are needed to explain how this seemingly chaotic system works. Dismissing reasons for the obvious complexity using terms like “junk-DNA” is not going to get us anywhere.

Instead, let’s start by acknowledging that we know very little. All we know is that function comes out of an apparent chaotic mixture of DNA protein and RNA. Let’s speculate that everything is there for a reason. Without reason you loose hope and visions and those are qualities that science is vitally dependent upon.

Illustration taken from http://wisebytes.net/illusions/

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  1. Dismissing reasons for the obvious complexity using terms like “junk-DNA” is not going to get us anywhere.

    Instead, let’s start by acknowledging that we know very little.

    I will do no such thing. We know a great deal about junk DNA. We know, for example, that 50% of our genome consists of defective transposons. There are many other reasons why scientists are confident that most of our genome has no function. You can read about it at Genomes and Junk DNA.

    I understand that you may not know these things but you make a big mistake in assuming that the term “junk” DNA is based on similar lack of knowledge.

  2. Larry, I understand from a recent discussion on the Adaptive Complexity Blog that you, T Ryan Gregory and Michael White have strong opinions on junk DNA. I can also easily see that there are a number of arguments supporting your notion of these stretches of DNA as “junk”. My problem is that I find such a view counterproductive. I cannot understand how dismissinig something as “junk” can do scientific progress any good. Why would anyone want to investigate further into junk ? And if you don’t investigate, aren’t you possibly missing out on something, maybe something important ?? I will repeat the analogy (on T Ryan Gregory’s onion test) I put on Michael White’s post:

    Say you are the first to discover Stonehenge. As a scientist you can choose between two approaches: 1) dismiss the stone-formation as a pile of rocks with no significance or 2) try to understand why they are arranged in this peculiar manner. This latter approach would require hypothesis and speculation on possible explanations. Using the onion test on the other hand, you would reach the conclusion that there are bigger piles of rock with no apparent function elsewhere, thus this pile of rock is no different. Consequently, using the onion test you would have stood in the way of scientific progress.

  3. I think your analogy is confusing.

    Let’s say you carefully examine the pile of rocks and conclude on the basis of all evidence available to you that it has a perfectly natural origin. The piles were not made by humans.

    Are you saying that you should keep that conclusion to yourself out of fear that it may inhibit further investigation?

    How would that work? Does one just give up publishing any paper that reaches such a conclusion?

    It would certainly have one effect that you may like. All the proponents of random genetic drift and evolution by accident would soon lose their grants and you adaptationists would have the field to yourselves. 🙂

  4. Larry.

    I have changed “assume” into “speculate” in the original post, you were right that this was an inaccurate phrasing.

    I find that your comment to the Stonehenge analogy says a lot. This is not about withholding scientific data, on the contrary. You certainly are entitled to publish your opinion on “junk” being “junk” and nothing else (you already have), and that is not the issue. The issue is that you keep criticizing others for speculating that this DNA has function, – why ?? What is that about ??

    There were and still are, good reasons to speculate on the origins of the Stonehenge formation, I find that there are good reasons to speculate on the function of “junk”-DNA/RNA as well (why is so much “junk” transcribed when we know that energy conservation is a major issue for all organisms ?). Speculating and asking questions like this does not make me an adaptionist, – please, please, stop calling me that…

    Hindsight will tell you that if you had examined Stonehenge and found no evidence of human involvement, you would have been wrong. I believe you may come to see that you are making a similar mistake with “junk”-DNA…

  5. I find that there are good reasons to speculate on the function of “junk”-DNA/RNA as well (why is so much “junk” transcribed when we know that energy conservation is a major issue for all organisms ?). Speculating and asking questions like this does not make me an adaptionist, – please, please, stop calling me that…

    You are speculating in the face of abundant evidence that the DNA has no function. You are even questioning whether pseudogenes might have a secret hidden function that has escaped our notice for three decades.

    That’s exactly what adaptionists do. They cannot accept scientific evidence suggesting that something may have evolved by chance and have no adaptive significance.

    The reason why I criticize those who question junk DNA is because the logic of their arguments is flawed. Not only do they ignore all the evidence in favor of the junk explanation, they exaggerate and misrepresent any “evidence” that refutes it.

    If you enjoy speculation so much then speculate on this …

    1. Why do pseudogenes and most of the transposon-related sequences look so much like broken genes?

    2. Why is the DNA sequence in most of our DNA not conserved?

    3. Why can we delete large segments of mammalian DNA with no observable effect?

    4. Why is there so much variations in repetitive DNA within a species? Some people have segments that are ten times longer than segments found in other people. Are all of the nucleotides in the longer segments functional?

    5. Why is the Fugu genome so much smaller than that of other fish?

    6. When two similar species differ in genome size by a factor of two—probably due to an ancient polyploidization—is the majority of DNA in both species functional?

    7. In the human lineage there are over one million Alu sequences. They all look like degenerate versions of 7SL RNA. Are all of these sequences functional? If so, what function could they be doing? And why do the human Alus look so different from the mouse ones?

    8. Most intron sequences do not seem to have a function. Why does the size of introns in the same gene vary so much in related species and why isn’t the sequence conserved in most cases?

  6. A challenge ? I’ll take you up on this and make a separate post answering to your list. For now, suffice it to say this:

    1. “You are speculating in the face of abundant evidence that the DNA has no function”

    I think there is an increasing body of evidence saying that much of this DNA has a function. Some of this documentation you can find in the links in the post, I’ll provide you with more when a respond to your list, including the “secret hidden function” of sequences in pseudogenes.

    2. “They cannot accept scientific evidence suggesting that something may have evolved by chance and have no adaptive significance”

    For the record I accept that all evolution is based on chance, but I also believe that the same chance events will remove most unnecessary DNA over time and consequently minimize the amount of “junk”. This, simply because minimizing junk would be advantageous….

    It follows then that we should be looking for possible function rather than dismissing it, but…

    3. You are assuming that I believe every single basepair has a discrete essential function. Both you and I understand very well that such a situation would have not allowed for evolution to occur. Some of this DNA clearly serves a buffering capacity. That does not however, mean it cannot have other functions as well.

  7. “New ideas, approaches and tools are needed to explain how this seemingly chaotic system works.”

    The expression “seemingly chaotic” may be used here in the colloquial sense roughly equivalent to “random” (without underlying mathematical rules, an undeterministic “mess”).

    Those familiar with informatics know that “chaotic” (and their complementary fractal) systems are completely deterministic and are ruled by strict (albeit not trivial) mathematical rules (call them “reasons” if you will).

    Principle of Recursive Genome Function (peer-reviewed journal article, full text made available in full, accompanied by a press release, etc) is found at http://www.junkdna.com/pellionisz_principle

    Regarding a side-question re-surfacing in blog debates “how is it that the fugu has 1/8 of the “junk” compared to e.g. the human genome”, the above Principle paper cites an earlier peer-reviewed journal giving an explanation in terms of the “fugu prediction of fractogene”.

    Pellionisz_at_junkdna.com

  8. […] This is good…..if it means what I mean: that labeling DNA of unknown function as “junk” by default is wrong. Which it most certainly is. For more on this topic, see my 6 post discussion with Larry Moran (1,2,3,4,5,6). […]

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