'Junk DNA'

Inessential does not mean non-functional! Gene guns, transposons, some polyploids, programmed apoptosis, etc.

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Strictly speaking gene guns are inessential for living organisms, but does being inessential for life make this tool of genetic engineering non-functional? If there are tools for innovation and exploration, they might not be essential, but does that mean they are non-functional? Of course not!

In like manner transposons and some forms of polyploidy might not strictly speaking be essential, but they might be important for evolutionary innovations and may useful for exploring and innovating. As James Shapiro suggested, the statistics suggest living organisms have some capability for natural genetic engineering, and if they are natural genetic engineers, tools like transposons and some forms of polyploidy may be functional because they are used as part of the process of natural engineering.

Why do I think transposons are functional? I posed the following question on reddit/r/creation:

There has been discussion about whether transposons are junk. Without transposase enzymes to make transposons possible, we wouldn’t have transposons.

So the question to die-hard junk-DNA advocates who insist transposons are mostly inessential junk, why should transposases evolve in the first place and why should they be maintained?

A quick google shows hardly any attempt at an evolutionary explanation. Contrast this with the verbose treatment of the evolution of tetrapods.

So, what are the precursors to transposases, and what were the intermediate steps, and what were the intermediate functions. Did we co-opt a mechanism that enables parasitic behavior of transposons?

Why should transposons evolve?

The wiki entry on transposase is noticeably silent on an evolutionary explanation of their origin. One will get a few google hits on “phylogeny of transposase” but they are not at all informative to what the ancestor of transposase looked like. For all we can tell, the data suggests it just popped out of nowhere ex nihilo. 🙂

Needless to say, I didn’t get any pro-evolutionary explanations for the origin of transposases.

Most B-cells variants in the human immune maturation process die. Like shotgun pellets, the expectation is that many will miss, but some will find utility. They die from a process called apoptosis:

Apoptosis (/ˌæ.pəpˈtoʊ.sɪs/;[2][3] from Ancient Greek ἀπό apo, “away from” and πτῶσις ptōsis, “falling”) is the process of programmed cell death (PCD) that may occur in multicellular organisms.[4] Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation.

In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular injury, in general apoptosis confers advantages during an organism’s lifecycle. For example, the separation of fingers and toes in a developing human embryo occurs because cells between the digits apoptose. Unlike necrosis, apoptosis produces cell fragments called apoptotic bodies that phagocytic cells are able to engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage.[5]
Apoptosis (/ˌæ.pəpˈtoʊ.sɪs/;[2][3] from Ancient Greek ἀπό apo, “away from” and πτῶσις ptōsis, “falling”) is the process of programmed cell death (PCD) that may occur in multicellular organisms.[4] Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation.

In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular injury, in general apoptosis confers advantages during an organism’s lifecycle. For example, the separation of fingers and toes in a developing human embryo occurs because cells between the digits apoptose. Unlike necrosis, apoptosis produces cell fragments called apoptotic bodies that phagocytic cells are able to engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage.[5]

Wikipedia

So if something is programmed to die does that mean it is non-functional? No!

Many B Cells die by design! It does not make them junk!

B cells exist as clones. All B cells derive from a particular cell, and, thus, the antibodies that their differentiated progenies (see below) produce can recognize and/or bind the same specific surface components composed of biological macromolecules (epitope) of given antigen. Such clonality has important consequences, as immunogenic memory relies on it. The great diversity in immune response comes about because there are up to 109 clones with specificities for recognizing different antigens. A single B cell or a clone of cells with shared specificity, upon encountering its specific antigen, divides to produce many B cells. Most of such B cells differentiate into plasma cells that secrete antibodies into blood that bind the same epitope that elicited proliferation in the first place. A small minority survives as memory cells that can recognize only the same epitope. However, with each cycle, the number of surviving memory cells increases. The increase is accompanied by affinity maturation, which induces the survival of B cells that bind to the particular antigen with high affinity. This subsequent amplification with improved specificity of immune response is known as secondary immune response. B cells that have not been activated by antigen are known as naive lymphocytes; those that have met their antigen become activated, and have differentiated further into fully functional lymphocytes are known as effector B lymphocytes.

If we were to guage the value of B cells by the number of DNA variants that are tossed and never used, using Dan Gruar’s metric, B cell DNA is junk and therefore non-functional!

B cells work at the organismal level and it is possible transposons serve an analogous role at the population level. The value of transposons at the population level is acknowledged in mainstream literature. From looking at evolutionary literature, I credit them with asserting the innovative value of transposons and polyploidy. Maybe most of the experiments and trial are designed to miss in order that one solution may be found. Variation and selection of B Cells, transposon and polyploidal systems are design features, not ultimately design explanations. Natural selection is a design feature which does not explain its own origin.

PS
Here is a video of a gene gun.

[youtube VqklR_8YRfA]

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