Today’s New Reason To Believe

Keith McPherson

Keith McPherson received his Master of Science in Electrical Engineering from Georgia Institute of Technology in 1993, and currently works as an electrical engineer in Melbourne, FL, in the fields of communications and signal processing.

      -------------------------------

In part 1 of this series we learned how the genetic system is an information-processing system, and outlined several reasons why we could expect to find coding techniques in play to protect the genetic data. Such coding techniques are known and used by engineers to protect the data processed by many modern digital communications systems.

We now turn our attention to a few analogies of such coding techniques.

Analogy: Optimality of the Genetic Code and Gray Mapping

The first analogy will show from a qualitative and quantitative perspective that the genetic code is in fact an optimal (or near optimal) mapping from codons to amino acids. (See here for a table describing the genetic code.)

The genetic code seems optimized to the specific nucleotide error probabilities quite well, as is the case for a good code from an engineering perspective. For example, the first and third nucleotides of a codon (see here) are more likely to be misread during translation), and this error appears to be taken into account in the genetic code mapping. These most common errors, or mutations, translate the desired codon into a codon that codes either for the same amino acid, or for an amino acid that has very similar physicochemical properties, thus minimizing function loss. (This is similar to Gray codes used in digital communications.) Gray codes are a very fundamental concept used in virtually all digital communication systems.

More specifically, the genetic code seems to be specifically designed to code for the same or very similar amino acids for the most common types of substitution mutations (errors), thereby minimizing protein function loss. In like fashion, Gray codes used in engineering are specifically designed to code for the most similar bit patterns for the most common types of symbol errors, thereby minimizing information loss.

I noticed the similarity to Gray coding after reading a paper by Dr. Fazale Rana in 2002. The Gray code interpretation was highlighted by Manish Gupta in a paper published in 2006. Gupta plotted the 64 codons used in the genetic code in terms of nucleotide distance (see Figure 3 here), and remarked on the correspondence to Gray codes used in engineering. The concept of nucleotide distance and the illustrated plot establishes the validity of the Gray map interpretation.

Recall from part 1 that many genetic code mappings are possible due to the high level of redundancy. Therefore, from a qualitative perspective, and from an engineering perspective, the genetic code is superb, perhaps much better than one may expect from a naturalistic perspective.

Recent work shows just how remarkable the natural code is. (See here and here.) Researchers studying the error-minimizing properties of the genetic code noticed that prior work concluded that the natural code ranked in the top 0.02 percent for efficiency, but that the prior work overlooked bias in mutations.¹ When this bias is taken into account, the natural code makes a radical leap forward from the top 0.02 percent to literally one in a million.

Dr. Fazale Rana comments further on the error-minimizing properties of the genetic code:

The genetic code’s error-minimization properties are actually more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 1018 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of 1018 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature. ²

In summary, qualitative and quantitative evidence suggests that the natural genetic code is highly optimized and, in fact, tuned to the most common type of errors (mutations). In addition, this work highlights an underlying analogy between the genetic system and modern communications systems—the so-called Gray code.

The next article in this series will look at another coding analogy between modern digital communications systems and the genetic information-processing system.

Notes/References:

1. Bias includes the fact that not all codons are equally mistranslated to other codons, and that certain nucleotide positions within the codon are more prone to error. Purine/purine and pyrimidine/pyrimidine errors (transition mutations) are more common than purine/pyrimidine errors (transversion mutations), and the ranking of the positions is 3rd, 1st, and 2nd in terms of being more error prone.

2. Fazale Rana, “FYI: I.D. in DNA; Deciphering Design in the Genetic Code,” Facts for Faith, Quarter 1, 2002, 14-23.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Neanderthal Speech Gene May be Due to Contamination

Nobody really likes a potty mouth, including anthropologists. But it looks like these scientists will have to put up with “contaminated” language from Neanderthals, at least if the results of new work are valid. It appears as if the recovery of the so-called language gene from the remains of Neanderthals is not authentic, but instead may be due to contamination from human DNA.

The question of whether or not Neanderthals possessed language capacity has precipitated much controversy. Anatomical studies are ambiguous towards this end. (See Who Was Adam? for a detailed discussion.) To help resolve this issue a team from the Max Planck Institute turned to ancient DNA analysis to probe for the language gene in the Neanderthal genome.

In 2001, a research team from the United Kingdom reported that mutations in the FOXP2 gene cause severe language disorders. Presumably the FOXP2 protein plays a key role in controlling the development of brain and facial structures that support aspects of human language capacity.

An initial evolutionary analysis of the FOXP2 gene, conducted in 2002, indicated that the human variant arose about 200,000 years ago. Subsequent work, published later that year, placed the origin of the human FOXP2 gene at about 100,000 years ago. From an evolutionary standpoint, this is well after the time that humans and Neanderthals allegedly split from a common ancestor. Accordingly, Neanderthals should not possess a human-like FOXP2 gene and, therefore, language ability.

However, to everyone’s surprise, the team from the Max Planck Institute did isolate the human variant of the FOXP2 gene from a recently recovered Neanderthal specimen. This result was interpreted by some as evidence that Neanderthals had language. If so, it creates problems for the RTB human origins model, which predicts that Neanderthals and other hominids should behave in nonhuman ways, and, therefore, should not have the capacity for language.

Did Neanderthals possess language ability? At the time that the recovery of the Neanderthal language gene was announced I wrote:

The very real possibility exists that this result stems from contamination by human DNA. Clearly, the research team went to painstaking efforts to avoid contamination. Anthropologists suited up in clean room gowns and face masks to excavate the Neanderthal remains using sterilized tools. They designed the extraction protocol to avoid isolating any human DNA and ran the appropriate controls to ensure the Neanderthal DNA samples had no human contamination. In spite of these heroic efforts, the possibility of contamination cannot be ruled out. The team from the Max Planck Institute introduced contamination into the Neanderthal genome sample they were previously working with and wrongly interpreted this as evidence for human-Neanderthal interbreeding.

It looks like my initial assessment was right. A research team for the University of Chicago re-assessed the likelihood that Neanderthals possessed the human variant of FOXP2 by looking at the genetic variation associated with this gene among modern human populations. They concluded that the scenario proposed by the Max Planck workers—namely the human variant arose prior to the time that Neanderthal and human lineages diverged from a common ancestor—is inconsistent with the genetic patterns observed among modern humans. They also estimated that the human variant of FOXP2 arose about 42,000 years ago. This result falls in line with earlier estimates, which places the origin of the human variant between 100,000 and 200,000 years ago.

The Chicago scientists suggest two possible scenarios to explain the recovery of the human variant of the FOXP2 gene from Neanderthal remains. First, humans introduced the language gene into the Neanderthal gene pool through interbreeding. They assert that if low levels of interbreeding took place between humans and Neanderthals, this could account for the appearance of the human language gene in the Neanderthal genome. This conclusion is not well supported by other studies, which have failed to find any direct evidence for interbreeding.

The other possibility is that the DNA extracted from Neanderthals was contaminated with modern human DNA. Even though the Max Planck Institute scientists took every precaution to avoid contamination and even ran controls to ensure that their samples were free from contaminants, human DNA, which is ubiquitous, could have easily made its way into the sample. The team from the University of Chicago raises questions about the effectiveness of the control samples. They assert that the controls selected by the Max Planck team do not necessarily ensure contaminant-free Neanderthal DNA samples.

It is really beginning to look like Neanderthals didn’t have language capacity after all—just contaminated language. Now I’d like to know who’s going to volunteer to wash their mouths out with soap.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Does the Presence of a “Speech” Gene Mean Neanderthals Had Language? An article recently published in Current Biology has generated a lot of excitement about the possibility of Neanderthal language capacity. Scientists from the Max Planck Institute at Leipzig, Germany, announced the isolation of the so-called language gene from a Neanderthal specimen recently recovered in Spain. Some anthropologists interpret this discovery as evidence that Neanderthals had language. What does this mean for RTB’s biblically based human origins model?

Last week I provided some background information needed to understand the work of the Max Planck scientists. This week I will detail their findings and discuss the implications of their research for the RTB human origins model.

Controversy surrounds the question of whether or not Neanderthals possessed language capacity. Anatomical studies remain ambiguous. (See Who Was Adam? for a detailed discussion.) To help resolve this debate the team from the Max Planck Institute turned to ancient DNA analysis to probe for the language gene in the Neanderthal genome.

In 2001, a research team from the United Kingdom reported that mutations in the FOXP2 gene cause severe language disorders. Presumably the FOXP2 protein plays a key role in controlling the development of brain and facial structures that support aspects of human language capacity.

An initial evolutionary analysis of the FOXP2 gene, conducted in 2002, indicated that the human variant arose about 200,000 years ago. Subsequent work published later that year placed the origin of the human FOXP2 gene at about 100,000 years ago. From an evolutionary standpoint, this is well after the time that humans and Neanderthals allegedly split from a common ancestor. Accordingly, Neanderthals should not possess a human-like FOXP2 gene and, therefore, language ability.

To everyone’s surprise, the team from the Max Plank Institute isolated the human variant of the FOXP2 gene from a recently recovered Neanderthal specimen. Some have interpreted this result as evidence that Neanderthals had language. If so, what does this mean for the RTB human origins model which predicts that Neanderthals and other hominids should behave in non-human ways?

Did Neanderthals possess language ability? This conclusion is premature for a number of reasons.

First, the very real possibility exists that this result stems from contamination by human DNA. Clearly, the research team went to painstaking efforts to avoid contamination. Anthropologists suited up in clean room gowns and face masks and used sterilized tools to excavate the Neanderthal remains. They designed the extraction protocol to avoid isolating any human DNA and ran the appropriate controls to ensure the Neanderthal DNA samples had no human contamination. In spite of these heroic efforts, the possibility of contamination cannot be ruled out. The Max Planck researchers previously introduced contamination into a Neanderthal genome sample they were working with and wrongly interpreted this as evidence for human-Neanderthal interbreeding.

Even if these results are taken at face value, it still doesn’t mean that Neanderthals possessed language. As discussed last week, the presence of the FOXP2 gene is necessary for language in humans, but not sufficient. Myriad other genes must be present and properly expressed to give humans the ability to speak. To date, these other genes have not been identified in humans, let alone Neanderthals.

It is also conceivable that the Neanderthal FOXP2 gene is distinct from the human variant. The researchers did not isolate the entire FOXP2 gene. Instead they isolated the portion of the gene where the distinguishing features of the human variant reside. It could well be that when the entire gene is sequenced other regions it will display unique Neanderthal signatures.

Another troubling aspect of this study is that its results run contrary to other studies. For example, if Neanderthals had the human version of the FOXP2 gene, then from an evolutionary perspective the origin of the gene must have taken place prior to the time that Neanderthals and humans shared a common ancestor, which would be at least 500,000 to 750,000 years ago. Yet, as mentioned last week, evolutionary analyses place the origin of the human variant between 100,000 and 200,000 years ago. Additionally, the archeological evidence and brain-structure studies don’t support the existence of Neanderthal language. (See Who Was Adam? for details. Also, see a past TNRTB entry about Neanderthal division of labor.)

Did Neanderthals have language ability? In spite of the discovery of the so-called language gene in Neanderthals, the question still remains unresolved.

Still, the work by the scientists from the Max Planck Institute demonstrates the power and potential of ancient DNA studies to help us move toward resolving important scientific controversies.