What good is the concept of a “gene” if it excludes “junk DNA”?

_{Denyse O'Leary

May 3, 2014

'Junk DNA', News}

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Remember junk (non-coding) DNA?

Genes don’t consistently do what we once thought they would, so it’s time to reconsider what we mean when we say the word.

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Our concept of a gene is also challenged by the fact that much of the function in our DNA is located outside of conventionally defined genes. These “non-coding” functional DNA segments regulate when and where conventional protein-coding genes operate. For our biology, non-coding regulatory DNA elements are as consequential as genes, but their properties are even more difficult to define because their function isn’t based on the well-understood Genetic Code and their boundaries are even fuzzier than gene boundaries. As a result, non-coding regulatory DNA elements are much more difficult to count. One consortium of researchers put the number of regulatory DNA segments in the human genome between 580,000 and 2.9 million, while just last month a different consortium claimed that there are only 43,000. Regardless of how you count them, it’s clear that these non-gene regulatory DNA elements far outnumber conventional genes. It is hard not to wonder, then, what good is the concept of a gene if it doesn’t include most of our functional DNA?

In the aftermath of the Human Genome Project, biologists are struggling with the definition of a gene, but why should this matter to anyone else? It matters because the molecular concept of the gene that has dominated biomedical research for the last half-century is increasingly ill-suited for our efforts to understand the role of genetics in human biology. Giving a physical meaning to the concept of a gene was a triumph of 20th-century biology, but as it turns out, this scientific success hasn’t solved the problems we hoped it would.

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"In the aftermath of the Human Genome Project, biologists are struggling with the definition of a gene, but why should this matter to anyone else?" It matters because this narrow belief is the product of the foundational philosophy that produced it. The foundation is wrong, and it keeps leading researchers down the garden path. All they really had to do was ask a software developer. It is obvious to us that the volume of data found in the coding DNA was way the heck to little to define a human. The entire 3 gig of data in the human genome seems vastly too small to define a human. However, we also see some magnificent coding schemes going on allowing for the same piece of DNA to code for multiple proteins and protein variants. I have encountered at least a half dozen of these wizardly systems. This DNA code is far beyond the skill level of any modern-day programmer.Moose Dr_{May 3, 2014
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humbled @ 2
Can we also burn our copies of The selfish gene now?
Good riddance, but don't burn them all, leave some copies as reminders of the things they have said and written, so later they can't claim they never said them ;-) BTW, next time you stop by a bookstore where they have that or similar books in the science section, you may tell them those books belong in the 'cheap philosophy' section. If they respond that there's not such section, then tell them to keep the books in boxes until they have it ;-)Dionisio_{May 3, 2014
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Remember junk (non-coding) DNA?
Um, no. Regulatory elements are noncoding, but I don't know anyone who'd consider them junk. I'll ask you to read Dan Graur's posting "For the Zillionth Time: Junk DNA ? Non-Coding RNA", and pay special attention to the box labeled 1 on the diagram, and described in the notes as "Untranscribed functional DNA (e.g., DNA regulatory elements)".
For us other “we”, it also matters because it drives another nail into the coffin of evolution fiction.
This doesn't have anything to do with whether evolution is correct or not, it's a question of how best to organize our thinking about the heritable elements that make up the genome. The reality is complex and messy and hard to understand. In order to think about inheritance without being overwhelmed by that complexity, you have to abstract at least some of the complexity away. In the quoted article, Michael White is arguing that "Genes" aren't the best abstraction for this (at least as they're usually defined) -- that the concept oversimplifies too much. But changing how we think about the units oh heritability doesn't change whether evolution works or not. BTW, for an opposing view, I'll quote from Larry Moran's essay "What is a gene?":
There are regions upstream of the promoter that control whether or not the gene is transcribed. These regions are called regulatory regions. They may contain binding sites for various proteins that will attach there in order to enhance the binding of RNA polymerase to the promoter. One of the differences between my preferred definition of a gene and others is that some other definitions [e.g. what White appears to be recommending] include the promoter and the regulatory region. There are two problems with such definitions. First, they’re not consistent with standard usage when we talk about the regulation of gene expression. We don’t say that only “part” of a gene is transcribed, which would be correct if we included the regulatory region in our definition of a gene. How often have we heard anyone say that regulatory sequences control the expression of part of the gene? That doesn’t make sense. Second, by including regulatory sequences in the definition of a gene the actual extent of the gene becomes ill-defined. For most genes, we don’t know where all the regulatory sequences are located so we don’t know for sure where the gene begins or ends. Furthermore, there are some regulatory sequences, especially in eukaryotes, that are not contiguous with the gene and this leads to “genes” that are split into various pieces. It’s much easier to use a definition like “a DNA sequence that’s transcribed” because it defines a start and an end.
Note that Moran does not claim his definition is perfect; at the end, he gives several examples of DNA elements that don't fit his definition.Gordon Davisson_{May 3, 2014
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Can we also burn our copies of The selfish gene now?humbled_{May 3, 2014
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In the aftermath of the Human Genome Project, biologists are struggling with the definition of a gene, but why should this matter to anyone else? It matters because the molecular concept of the gene that has dominated biomedical research for the last half-century is increasingly ill-suited for our efforts to understand the role of genetics in human biology. Giving a physical meaning to the concept of a gene was a triumph of 20th-century biology, but as it turns out, this scientific success hasn’t solved the problems we hoped it would.
For us other "we", it also matters because it drives another nail into the coffin of evolution fiction. The hope that genes were a product of nature, thereby negating the need for a designer has gone "poof". Now we can have a conversation on what the real agenda of evolutionary biology is all about on a level playing field.awstar_{May 3, 2014
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