Wednesday, September 18, 2013

Breaking News!!! Wikipedia Is Wrong! (about the Central Dogma)

I shuddered when I spotted Razib's latest post in my aggregator [see The Central Dogma goes YouTube]. "Oh, no!" I thought, "Am I going to have to point him to my post on The Central Dogma of Molecular Biology?

Imagine my surprise when I saw that he has a link to the Wikipedia article on the Central Dogma. I said to myself, "This will set him straight because I wrote some of that article."

Oops! The Wikipedia article on the Central Dogma of Molecular Biology has been changed. Apparently I haven't looked at it for nine years since the important change was made by someone named Kierano back on September 15, 2006. Kierano describes himself (in 2011) as a Ph.D. student in bioinformatics.

Here's the opening paragraphs from before Sept. 15, 2006.
The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The central dogma is often misunderstood. It is frequently confused with the standard pathway of information flow from "DNA to RNA to protein". There are notable exceptions to the normal pathway of information flow and these are often mistakenly referred to as exceptions to the central dogma.

The standard information flow pathway can be summarized in a very short and oversimplified manner as "DNA makes RNA makes proteins, which in turn facilitate the previous two steps as well as the replication of DNA", or simply "DNA → RNA → protein". This process is therefore broken down into three steps: transcription, translation, and replication. By new knowledge of the RNA processing, a fourth step must be included: splicing.
This has undergone some edits from what I originally wrote but the main idea is there. Strictly speaking, the Central Dogma of Molecular Biology (Crick version) says only that once information gets into protein it can't flow back to nucleic acid. I thought it was important to explain the main misconception; namely, that the Central Dogma means DNA to RNA to protein. This should be referred to as "the standard information flow pathway" or something similar.

The rest of the Wikipedia article talks about transcription and translation which, strictly speaking, are not part of the Central Dogma. However, the misconception is so widespread that many people expect these to be described under "Central Dogma."

The new version posted on Sept. 15, 2006 says ...
The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The dogma is a framework for understanding the transfer of information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of information-carrying biopolymers: DNA and RNA (both nucleic acids), and protein. There are 9 possible direct transfers of information that can occur between these. The dogma classes these into 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under abnormal conditions), and 3 unkown transfers (believed to never occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA, (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).

The central dogma is occasionally misunderstood as being a statement of absolute fact. If taken as such, it can be criticised, as there are well-described exceptions. It is also criticised by some systems biologists as being too reductionist.
This is the beginning of a change in emphasis. Kierano removed my statement that the basic meaning of the Central Dogma is often misunderstood. It's clear that he misunderstands it.

On March 10, 2012 someone named Nbauman addd the following statement; "Or, as Marshall Nirenberg said, 'DNA makes RNA makes protein.'" Nbauman cautioned that this was a reliable published source and should not be removed from the Wikipedia article. As far as I can tell Nbauman is not a scientist and has no training in science. In fact, she seems proud of the fact that she is ignorant of the subjects she edits. She does not seem to have noticed that her "authority" (Nirenberg) conflicts with another authority (Francis Crick).

Here's the complete version as of this morning. It's going to change as soon as I get around to it.
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It was first stated by Francis Crick in 1958[1] and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.
Or, as Marshall Nirenberg said, "DNA makes RNA makes protein."[3]

To appreciate the significance of the concept, note that Crick had misapplied the term "dogma" in ignorance. In evolutionary or molecular biological theory, either then or subsequently, Crick's proposal had nothing to do with the correct meaning of "dogma". He subsequently documented this error in his autobiography.

The dogma is a framework for understanding the transfer of sequence information between sequential information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and 3 unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).


10 comments :

  1. I checked the NIH website cited by NBauman and it's an exhibit about Marshall Nirenberg, not authored by Nirenberg. The NIH website neither stated nor implied that Nirenberg actually said it - in fact, that statement was in the glossary. When I tried to find out if Nirenberg really did say it, every website that says he did linked back to the Wikipedia article. This is one of the most aggravating aspects of Wikipedia, one piece of misinformation posted to Wikipedia gets propagated all over the Internet.

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    1. Attributing bon mots to an authority is a very old practice ("As Plato says somewhere...", "To quote Aristotle..."). Hippocrates never said, "Primum non nocere" (or anything in Greek to that effect), William of Ockham never said, "Entia non sunt multiplicanda praeter necessitatem", and Voltaire never said, "L'étymologie est une science où les voyelles ne font rien et les consonnes fort peu de chose".

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  2. Wikipedia is the Wild West. The comments of the knowledgeable, who usually are busy people, are quickly reversed by those with contrary agendas and nothing better to do. Caveat lector!

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  3. I just came across something that may affect debates about the central dogma, or junk DNA:

    http://www.sciencedaily.com/releases/2013/09/130918132446.htm

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  4. IMO the Venters and Pugh article doesn't change much since even the authors admit the following in their conclusion:

    The finding that these initiation complexes are largely limited to locations having well-defined core promoters and measured TSSs indicates that they are functional and specific, but it remains to be determined to what end.
    (emphasis mine)

    Thus, they found out it is more that noise starts at certain positions in the genome that are reminiscent of promoters than at other positions. But this doesn't mean that transcripts initiated at these sites are functional.

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  5. Wikipedians often engage in scientific-sounding fuckwitery. Rather than engage with the ideas, we see people trotting out silly arguments about the meaning and application of the word dogma, or a near techno-babble that completely avoids the basic issue.

    It's actually a bit reminiscent of pseudo-science, as far as pseudo-science attempts to emulate the accouterments and authority of science (a la Hansson, and others, in "Philosophy of Pseudoscience)

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  6. I can't believe how widespread this misconception is. I'm a third-year undergraduate in Molecular Biology & Genetics and indeed the incorrect version is what is taught in textbooks and repeated in class. I was made aware of the history behind the Central Dogma from this blog, and have since read the key papers. One of the textbooks I'm currently reading describes the Sequence Hypothesis and says something like it's been refuted but still a solid foundation. You'd think more people in the field would have read Crick's writing on this. I posted to a link to one of the explanatory posts from this blog a class discussion board recently. I think it's really quite important to know and is much more than a simple misnomer. It's shaped a lot of the dialogue in the field throughout history and the way discoveries are framed and publicized.

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    1. It's sad to admit how few of my colleagues (post-docs and PhD students) have never read a paper published before the 1990s. No wonder we seem to keep re-inventing the wheel.

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