Tuesday, October 19, 2010

When A Neutral Mutation Isn't

It has long been assumed in Darwinian circles that a neutral substitution in a protein is neutral in any given organism. In other words, a neutral substitution in a protein will be neutral in the human variant of that protein as well as the yeast variant of that protein, and in the amoeba variant of that protein, etc. So how did I found out that there is this assumption in Darwinian thinking? I peeked. Actually, I peeked a long time ago at Dr. Douglas Theobald's "29+ Evidences For Macroevolution (please do not ask me where he came up with the fascination with the number '29')." One of the things he said is telling of the assumption I described above. And this assumption is echoed by none other than Mr. Randy Crum! Since Mr. Crum actually describes it in more audience-friendly prose, I will quote Carumbas Blog yet again (click here to see Dr. Theobald's own words).
Thus sayeth Mr. Randy Crum (I will try to make this the last blog post where Mr. Crum takes flack, in case any of you are feeling sorry for him):

"In the last few decades, scientists have been able to sequence DNA and determine the specific amino acid sequences that make up proteins. Some of these proteins are very important and are present in all living things. But in many cases not every amino acid is necessary. Evolution predicts that differences will be explicable through evolutionary history.
The best way to explain this is through an example. The prototypical example is cytochrome-c.
Cytochrome c is an absolutely essential protein found in all organisms, including eukaryotes (organisms with cells that have a nucleus) and bacteria. It is necessary for life in all organisms because it allows mitochondria - the energy fuel of cells - to function.

Much of the cytochrome c protein is not needed (it is “functionally silent”). That part varies from organism to organism. Human cytochrome c has been confirmed to work in yeast - a single-celled organism - despite the fact that the naturally occurring cytochrome c found in yeast is very different from that found in humans (sharing only 38 amino acids)."

Okay I'll have to digress for a bit here. Mitochondria actually isn't the "energy fuel of cells" as Mr. Crum claims, but rather the ATP molecules are. 
Anyway this assumption I spoke of earlier is very prevalent in Darwinian circles. And what's wrong with this assumption? Well, to put it in terms that you would all understand, this assumption is simply wrong. 
The evidence from protein sequences convinces me of this. The error in this assumption is that it does not take into account organismal complexity, i.e. the number of different cell types in an organism. A yeast cell for example has only one type of cell, but the human organism has many different types of cells, from neurons to fat cells to erythrocytes. And this has rather profound implications. A neutral mutation in a yeast protein may not be neutral in humans. Here's why:
An ontogenic amino acid substitution in a human protein must be compatible with every one of the different cells found in the human organism (every cell, that is, that contains the protein; actin is prevalent in most human tissues, to name one example, while hemoglobin is found only in erythrocytes), while an amino acid substitution in a yeast protein must be compatible with only one cell type. 
An analogy may (in a theoretical sense) be useful here. Say you have protein A. And you have cell type X, Y, and Z. Any substitution mutation in protein A must be compatible with all three cell types. Meanwhile, if you only have cell type X, then protein A needs only to compatible with X (analogy a la Dr. Shi Huang). 

Now, the idea that a neutral mutation in yeast is not necessarily neutral in say, humans, is consistent with observations from cytochrome c sequences.
I compared the cytochrome c sequence of two unicellular organisms: Naegleria gruberi and Dictyostelium discoideum. To guard against any deletions, insertions, and what-not that might influence my sequence alignment I used the dot-matrix approach (Figure 1) as well as using ClustalX for the alignment.

The dot-matrix method found nothing that would significantly influence the alignment, although after correcting for gaps I achieved what I believe is the best alignment of the cytochrome c sequence of the two unicellular organisms (Figure 2).

Next, I aligned the cytochrome c sequence of two organisms as distant as the tuna and humans. The dot-matrix approach revealed a deletion as well as a higher degree of sequence similarity (Figure 3) than that between the two unicellular organisms. For a more quantifiable degree of sequence similarity between tuna and human cytochrome c, see Figure 4.

From the dot-matrix alignment and the ClustalX alignment one can see that there is obviously more sequence conservation in human and tuna cytochrome c than in the cytochrome c of the two unicellular organisms. This is what would be expected if a substitution in a unicellular organism was not necessarily neutral for a multicellular organism. I will add here that while human cytochrome c functions perfectly fine in yeast, no experiments have proven the reverse: I highly doubt that yeast cytochrome c would function in humans. I would predict that any protein from a multicellular organism would also function in a unicellular organism, but not vice versa.

Indeed, throughout the biological world we see conservation of protein sequences in multicellular organisms while there might often be a lack of conservation in unicellular organisms. Also, if one found a protein sequence that was conserved in unicellular organisms but not conserved in multicellular organisms then the entire idea I am proposing here would be proven utterly wrong. But there's not a single example of that, which would seem to validate this idea (an idea first proposed by Dr. Shi Huang I believe).
I suspect the Darwinians would respond with something like this: unicellular organisms reproduce faster than humans and tuna so they have had more time to accumulate neutral mutations. This however contradicts the notion of a constant clock, opening a can of worms for the Darwinian hypothesis.
So what are the implications of this? Namely, that one cannot really arbitrarily argue for a Darwinian origin of life forms on the basis of functional redundancy in proteins, since what is functionally redundant in one organism may not be in another.

I guess I'd better sit down and start working on a technical paper along these lines. And try not to feel sorry for you-know-who.


  1. Wow!!

    Excellent Job Livingstone!


  2. "It has long been assumed in Darwinian circles that a neutral substitution in a protein is neutral in any given organism. "
    -im not sure just how long that has been assumed (it isnt to my knowledge), but its known that 'neutral' mutations can and do affect expression differently in different organisms, for example codon preferences and utilisation affect regulation/expression.

    "I highly doubt that yeast cytochrome c would function in humans"
    -interesting, what is your logic behind that?

    "I suspect the Darwinians would respond with something like this: unicellular organisms reproduce faster than humans and tuna so they have had more time to accumulate neutral mutations."
    -or that we diverged a very long time ago.