Today’s New Reason To Believe

A few weeks ago we reported on the discovery of a new planet circling an M-type dwarf star named Gliese 581 in the constellation Libra. This discovery received a lot of attention in the news because its distance from the parent star fell within the “habitability zone,” where it is possible that liquid water could exist on the planet’s surface and, hence, the planet could support life. As we pointed out in our report, the researchers had to make a number of assumptions to reach this conclusion, but the discovery was exciting nonetheless.

In the meantime, new work has been done on this planetary system. A team of scientists working out of the Potsdam Institute for Climate Impact Research have investigated the system for habitability (see here for a press release, and here for their paper) using planetary formation and climate models that are thought to hold true for these types of systems.

They have concluded that the original planet, Gl 581c, which was suggested as the best candidate for Earth-like conditions is, in fact, likely to have a dense atmosphere with a corresponding high temperature at its surface. So, even though the planet resides at an appropriate distance from its parent star, the thick atmosphere raises the temperature beyond what would be necessary to support life. A similar situation exists in our own solar system with the planet Venus, where its dense atmosphere and consequent high temperature precludes its habitability.

On the other hand, these same researchers investigated another planet (Gl 581d) in the same system that had previously been rejected as habitable because of its greater distance from the parent star. While this planet would normally be too cold on the surface, its denser atmosphere brings that temperature into a region of habitability.

One of the conditions that trouble both of these planets is “tidal lock,” where their distance from the parent star is so close that the action of the stars gravity causes the same side of the planet to always face the star. Consequently, even Gl 581d will have a face that is too hot and an opposite face that is too cold; the only zone where life could possibly exist would be near the transition region between these two faces.

The authors acknowledge that tidal lock—along with many other problems—suggests the search for a home planet for mankind is no easy task. However, the results so far are tantalizing for the scientist looking for planets that can harbor life. As concluded in our earlier report, we expect that further research will, in fact, establish the uniqueness of the Earth and its parent star as a place where advanced life can exist and, therefore, provide further support for the RTB creation model.

For further discussion of habitable planets around M-dwarf stars, see here.

DNA Researchers Uncover Evidence that Overlapping Genes Are Widespread in Mammal Genomes

I have never cared much for puzzles, but I know some people can’t get enough of them. (Although admittedly, I’ve gotten hooked on Sudoku.)

Whether you are a fan of the Sunday Puzzle or not, I have a word challenge for you. This game illustrates the concept of overlapping genes and hopefully will help you appreciate why I think biochemical systems represent the most profound evidence for intelligent design.

The Challenge

The rules for this game are straightforward. Come up with a sentence (or even a word) that will yield another meaningful sentence (or word) if the reading frame is shifted by either one or two letters to the right or left. For example:

Original sentence:

    The boy went to the store.

Reading frame shifted by one letter to the left:

    T heb oyw entt ot hes tore.

Reading frame shifted by two letters:

    Th ebo ywe ntto th est ore.

I have yet to come up with a sentence that works. Yet, solutions to this type of puzzle abound in the genomes of a wide range of organisms in the form of overlapping genes.

A Biochemistry Primer

Genes are segments of DNA that house the information the cell’s machinery uses to manufacture proteins.

Genes consist of a sequence of nucleotides (or genetic letters), abbreviated A, G, C, and T, linked together to form a molecular chain. The specific sequence of nucleotides dictates the amino acid sequence of the protein encoded by a particular gene.

The cell’s machinery builds proteins using twenty different amino acids. The specific amino acid sequence determines the way the protein chain folds into a complex and precise three-dimensional structure. The overall shape of the protein dictates its function.

The set of rules the cell’s machinery uses to relate the nucleotide sequence of a gene to the amino acid sequence of a protein is called the genetic code. The fundamental unit in the genetic code is a sequence of three nucleotides, referred to as a codon. There are sixty-four codons in the genetic code, since there are four different nucleotides found in DNA (4 ³ =64). The coding assignments of the genetic code are redundant in some cases, since sixty-four codons specify twenty amino acids. Some amino acids are signified by a single codon only. Other amino acids are connoted by several different codons.

To illustrate how the genetic code translates information stored in DNA into information functionally expressed by proteins, consider the short messenger RNA nucleotide sequence: UCU CCU GCA AUU CGU AU. (To make proteins, the cell’s machinery first copies the information housed in the gene by assembling a chain-like molecule called messenger RNA [mRNA]. Like DNA, mRNA consists of a sequence of nucleotides. The cell’s machinery uses the same nucleotides to make mRNA as DNA with one exception: U is used in place of a T.)

    Position:   123
                UCU CCU GCA AUU CGU AU

If the cell’s biochemical apparatus uses a reading frame that begins at the first position, the resulting protein will have the sequence: serine-proline-alanine-isoleucine-arginine, since UCU signifies serine, CCU signifies proline, etc. If the reading frame starts at the second position in the nucleotide sequence, an entirely different protein will be generated with the sequence: leucine-leucine-glutamine-phenylalanine-valine. Shifting the reading frame to the third nucleotide position yields a peptide with the sequence: serine-cysteine-asparagine-serine-tyrosine.

As evinced by this example, there are only three possible reading frames for a nucleotide sequence. Three very different proteins can be encoded by a single nucleotide sequence, simply by shifting the reading frame by either 1 or 2 nucleotides.

Biochemists believe that in most cases only one reading frame is used in living systems, and the nonoverlapping, “one gene, one protein” relationship holds. This expectation stems from repeated observations that when a gene’s reading frame shifts as a result of a mutation, it almost always leads to catastrophic results. These so-called frameshift mutations result when nucleotides are accidentally inserted or deleted from a gene. And, as made evident in the above example with the model nucleotide sequence, a frameshift produces a protein with a radically different amino acid sequence. The mutant protein almost always is nonfunctional junk.

Frameshift mutations stand in contrast to substitution mutations, which involve the replacement of one nucleotide with another. This type of mutation merely replaces the one amino acid in the polypeptide chain with another. All other amino acids remain unchanged. Substitution mutations can be catastrophic, but more often than not these types of errors have limited, if any, effect on protein function because the gene’s reading frame hasn’t changed.

Overlapping Genes

But in some cases two reading frames are used, and two genes overlap onto the same nucleotide sequence. In the late 1970s biochemists studying the bacteriophage fX174 (a virus that infects the bacterium, Escherichia coli) made a startling discovery: the genome of this bacteriophage directs the production of more proteins than it should, based on the size of its DNA. Researchers resolved this paradox when they demonstrated that some of the fX174 genes overlap (for example, see Nature 264 1976: 34-41).

This conclusion was quite unsettling at that time. Biochemists had considered the relationship “one gene, one protein” to be absolute and a cornerstone of molecular biology. Since the work on the bacteriophage fX174 genome biochemists have identified overlapping genes in other viruses, as well as in bacteria, insects, fish, and mammals. In each case, overlapping genes are read by the cell’s machinery using a different reading frame.

Researchers noted that in most cases overlapping genes occur in some of the smallest, most compact genomes in nature (viruses and parasitic bacteria, like Mycoplasma genitalium.) The prevailing thinking was that the occurrence of overlapping genes in more-complex creatures was a rarity because they represent a costly arrangement for the organism. Mutations to one gene also mutate the overlapping partner.

A new study challenges this biochemical orthodoxy. A team of American and European scientists uncovered evidence that overlapping genes may well be widespread in mammal genomes. They point out that:

the skepticism surrounding eukaryotic dual coding is unwarranted: rather than being artifacts, overlapping reading frames are often hallmarks of fascinating biology.

This study provides motivation for molecular biologists to search for more examples of overlapping genes in mammals and other complex organisms. The new expectation is that more and more examples will be found.

The apparent widespread occurrence of overlapping genes doesn’t make much sense from an evolutionary perspective, because of the cost they represent to the organism. This cost is only worth it if there is a rationale for overlapping genes. The research team notes that the overlapping genes they uncovered seem to be involved in biochemical multitasking.

Even though it is not a direct analogy to the overlapping genes found in the genome of organisms, the “overlapping sentence” word challenge highlights how difficult it is to come up with a sequence of letters (or in biochemical systems: nucleotides and amino acids) that house overlapping messages, even when an intelligent agent diligently seeks out a solution. Yet, solutions to this biochemical conundrum seem to abound throughout nature. For me, the only explanation for overlapping genes is the work of a Creator. It’s hard to imagine how undirected evolutionary processes could produce overlapping genes.

For more reasons why biochemical information points to the work of a Creator, see Fazale Rana, “FYI: ID in DNA,” Facts for Faith (issue 8, 2002).

Last month’s multiverse discussion focused on one of its less controversial aspects—the idea that the universe extends beyond the limits of our observations. The uniformity we see in our universe (the cosmic microwave background radiation being the best example) strongly argues for this point. The issue then becomes how large the actual universe is. Using the maximum curvature detected by WMAP and a simple assumption that the universe closes back on itself, a minimum size for the whole universe roughly equals 1000 times the size of the observable universe. (For a discussion of these terms see my initial multiverse article.)

Somewhat more controversial is the idea of a spatially infinite universe—a result that derives from the current formulations of how inflation works. As discussed last month, a spatially infinite universe dramatically impacts the apologetic significance of some fine-tuning arguments, although it would still comfortably fit within a Christian worldview.

As it currently stands, any experimental verification of inflation’s details lay far in the future so the conclusion of a spatially infinite universe remains a more philosophical issue at this point. In such light, I thought it relevant to highlight some philosophical arguments against a spatially infinite universe advanced by William Lane Craig. Craig uses them to support the Kalam cosmological argument but they apply here as well.

An article in Scientific American gives more details of the relevant science, but the point pertinent to this discussion involves a transformation of the infinite future expansion of our bubble into an actual spatially infinite universe. Craig argues that actual infinities of the type invoked here cannot exist because they lead to absurdities.

He outlines a few examples of absurdities arising in dynamical infinities in this article published in the Canadian Journal of Philosophy:

1. Consider an infinite hotel full of guests. Now suppose another infinite group arrives and asks for rooms. If the owner has each guest move to the room twice their current value (1 to 2, 2 to 4, 3 to 6,…), this leaves open the infinite number of odd-numbered rooms. So a completely full hotel can accommodate an infinite number of new guests.

2. Consider two planets where one orbits twice as fast as the other. After an infinite time, each planet has accumulated an identical number (the infinite value aleph-null, ) of orbits. However, during every possible finite time interval, the faster planet accumulates twice as many orbits as the slower.

3. In the previous example, one could ask the question of whether the number of completed orbits is even or odd. After an infinite time the number of orbits is a value referred to as aleph-null. An even number is a multiple of two; an odd number is one more than a multiple of 2. But, = (2 x ) = (2 x + 1). So the number of orbits after infinite time is both odd and even.

These examples highlight that basic rules which we take for granted cannot apply in physically existing infinites. Either we must rewrite basic arithmetic rules (addition, subtraction, multiplication, division, and comparison) or such infinities do not exist. I have glossed over many details, but the objections Craig raises are worth a serious look as a response to infinite, dynamic universes. Additionally, scientists typically regard infinities as a sign that they have entered a region where their theories are no longer valid.

So, there may be good philosophical reasons to reject the notion that we live in a spatially infinite universe. Even so, the issue of the actual spatial extent of our universe still remains. It could still be so large as to negate the apologetical significance of the fine-tuning arguments. However, that scenario also poses some significant philosophical issues that I will address next time.