This Circadian Clock Protein is Finely-Tuned (and a Bunch of Other Things)

Making Evolution Even More Ridiculous

That new paper on the circadian clock protein is not only an example of how evolution lacks theoretical content and so anything can be explained (“Many genes exhibit little codon-usage bias, which is thought to reflect a lack of selection for messenger RNA translation. Alternatively, however, non-optimal codon usage may be of biological importance.”) or of fine-tuning in biology (“Living organisms’ inner clocks are like Swiss watches with precisely manufactured spring mechanisms”). Nor is the paper merely an example of yet another falsification of evolutionary predictions (“The team … was perplexed when it found a paradoxical result”) or even of bad writing (“And that’s essentially a discovery”).

In addition to all those usual contradictions, the paper is another good example of the many signals in protein sequences and how crucial and fine-tuned they are. Coding genes specify the amino acid sequence in the resulting protein that is synthesized when the gene is expressed. Only a relatively few of the possible DNA gene sequences could code for a typical native protein, and these magical sequences are statistically impossible for evolution to find by known mechanisms.

Background

But that is not all. Coding genes carry all kinds of signals, in addition to the information that specifies the amino acid sequence. For instance, the gene’s DNA sequence is also implicated in the control of transcription—the gene copying process. And the gene’s DNA sequence determines the important stability of the DNA copy—the so-called mRNA strand, and the mRNA interactions with proteins such as splicing machinery.

Of course the gene sequence also determines the protein’s three-dimensional protein structure, the stability of that structure, the function of the protein, interactions of the protein with other proteins, instructions for transport, and so forth.

But on top of that information, the gene also contains signals that help to control the speed at which the new protein is synthesized. These signals have been found to be quite sophisticated and the resulting speed changes can cause the protein to take on a different conformation and influence the protein’s function and regulation.

And it appears that the DNA sequence can make the expression level of the protein sensitive to different environmental conditions. For instance, perhaps some proteins should have lower priority than other proteins, in certain conditions. That could be coded for in their respective gene sequences.

Also it has been discovered that gene sequences are cleverly arranged to complement the cell’s error correction mechanisms and so minimize copying errors.

One interaction that must be avoided is the propensity of proteins to stick to each other and form fibrils in what is known as an amyloid. As one researcher explained, “The amyloid state is more like the default state of a protein, and in the absence of specific protective mechanisms, many of our proteins could fall into it.” So the DNA gene sequence must avoid this problem.

Also, some genes are overlapping with other genes. In other words, the stretch of DNA where a gene resides may be shared with another gene entirely. So the genetic information is now doubled. And even if this is not the case, researchers are increasingly finding that genes perform multiple tasks. In what is known as gene sharing, the protein product of a gene may carry out several separate and distinct functions. As one researcher concluded, “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

One more thing

So a gene does not merely code for a protein. As difficult as it is for evolution to find a protein-coding gene sequence, it would be far more difficult to find a real gene because they carry so many more signals.

That brings us to the new paper on the circadian clock protein. For in addition to it demonstrating how evolution lacks theoretical content, fine-tuning in biology, yet another falsification of evolutionary predictions, and even of bad writing, the paper also shows just how important and sensitive are these layers of information.

In this case, the research found that speed at which the mRNA strand is translated into the protein amino acid sequence is finely-tuned. The DNA sequence contains signals to slow this process, and that is crucial. For otherwise the protein takes on a different conformation, is not properly regulated, and the circadian rhythms are lost.

It is not as though we find gradual pathways leading to ever more useful and fit designs. Instead, function is lost, even when relatively minor DNA sequence changes occur. The idea that such incredible designs spontaneously arose via evolution’s random chance events (no, selection doesn’t help, each event must be random with respect to need, multitudes of such events are needed, and we don’t generally find gradual pathways) continues to grow ever more unlikely.

Religion drives science and it matters.