Today’s New Reason To Believe

Posted by Dr. Fazale Rana

Nanobacteria Inorganic Material, Not Life

Common wisdom would say that someone who is less than six feet tall would never make it as a professional basketball player. Size matters in the NBA.

Size also matters to biochemists. Conventional wisdom places the lower bound on life at about 1 micron (give or take a few hundred nanometers). In 1999, the National Academy of Sciences sponsored a workshop on the minimal size requirements for life and concluded that life can’t exist if it’s less than 200 to 300 nanometers in size. This lower limit stems from the fact that the simplest conceivable living organism requires about 250 to 400 different proteins plus the genes and ribosomes needed to make them.

Some scientists, however, have challenged the prevailing view on these minimum size limits. They claim that they have evidence for bacteria well under 100 nanometers in size, so-called nanobacteria. Maybe size isn’t as important as biochemists think. There have been basketball players under six feet tall, like Calvin Murphy who had a successful career in the NBA even though he is only 5’ 9”. In fact, Murphy was elected to the Basketball Hall of Fame.

Even though nanobacteria are diminutive, they may make a big impact in a number of scientific arenas. Some biomedical researchers have implicated these putative nano-microbes in gallbladder and kidney stone formation, rheumatoid arthritis, some forms of cancer, and even Alzheimer’s disease. Some microbiologists claim to have detected nanobacteria in geological samples and have suggested that they may play a key role in some geochemical cycles. NASA scientists claimed that nanobacteria left behind fossil remains in the Martian meteorites ALH84001, opening up the possibility that life originated on Mars.

If nanobacteria exist then what are they? There is much debate about the identity of nanobacteria. Some claim that they are organisms that push the bounds of what we currently think is possible for life. Proponents of this view point out that before the discovery of extremophiles, few would have thought that life could exist, let alone thrive, under the extreme conditions of high temperatures and pressures, high concentrations of salt, or under highly acidic or alkaline conditions. Could it be that nanobacteria challenge our current understanding about the size requirements for life?

Some think that nanobacteria represent a transitional form of sorts. They speculate that these organisms are some type of primitive self-replicating system that connects contemporary life to more primitive life-forms.

Others think that nanobacteria represent a completely novel form of life—life as we don’t know it.

New work published in the Proceedings of the National Academy of Sciences sheds light on the identity of nanobacteria and has broad-reaching implications for such considerations as pathogenesis (origin of disease), the definition of life, the origin of life, and the possibility of life on Mars.

Evidence for Nanobacteria

Support for the existence of nanobacteria comes primarily from biomedical work and includes: 1) the ability to cultivate slow-growing cultures in growth media after inoculation from human serum; 2) the ability to raise antibodies to nanobacterial antigens; 3) bacteria-like appearance of nanobacteria when visualized with electron microscopy (such as uniform size, vesicular shapes that appear to be delineated by a membrane, structures that appear to capture cell division, and aggregation into colonies); and 4) the recovery of 16srRNA gene sequences associated with nanobacteria. In fact, a biotech company Nanobac Pharmaceuticals has recently been launched to commercialize diagnostic and treatment protocols for pathogenic nanobacteria.

An Early Challenge to Nanobacteria

In the midst of all the excitement about nanobacteria, some researchers have expressed skepticism about their bio-authenticity. For example a study published in 2000 argued that nanobacteria are actually inorganic deposits of hydroxyapatite. (See here for further discussion.) The results of this work, however, have been largely ignored.

A More Recent Challenge to Nanobacteria

A new study, just published, takes up where the older work left off. This new research affirms that nanobacteia are inorganic in nature, not biological entities. The researchers demonstrated, however, that instead of being hydroxyapatite, nanobacteria are calcium carbonate precipitates. These workers were able to grow nanobacteria-like particles from calcium carbonate that had uniform size and shapes, and appeared to be bound by a membrane with some appearing to undergo a cell-division process. These precipitates also aggregated into colony-like structures. The formation of these precipitates did require the presence of human serum. Presumably the proteins in the human serum controlled the morphology of the calcium carbonate deposits. It turns out that the response of the nanobacteria-like precipitates to antibodies seems to originate from human serum protein contaminants associated with the calcium carbonate.

Other results which favor the inorganic interpretation of nanobacteria include: 1) the failure to detect any DNA associated with the nanobacteria-like material; 2) the ability to generate growth after filtering the serum-inoculated growth medium through 0.1 micron pores; and 3) the ability to generate growth after irradiation with gamma-rays.

Implications

The implications of this latest work are profound. If nanobacteria are inorganic then:

• Nanobacteria do not cause disease.
• It appears that life can’t exist below about 250 to 300 nanometers in size. This means that life requires a significant level of complexity to even exist (250 to 400 different proteins plus the genes and ribosomes needed to make them).
• Nanobacteria are not a primitive self-replicating entity.
• The evidence for ancient life on Mars is negated.

The long and the short of it (no pun intended; well, actually, it was intended), nanobacteria are not life’s version of Calvin Murphy.

David H. Rogstad, Ph.D.

A couple of months ago I discussed an upgrade to the Arecibo Radio Telescope that would make it more effective for searching for intelligent life in outer space (SETI). That article included references to cases made, from a secular and a theistic point of view, for the improbability of finding intelligent life “out there.” These approaches call attention to the vast number of conditions that must be met for life to survive in any environment and the difficulty in meeting those conditions all at the same time. The authors’ conclusion is that Earth, which has supported advanced life over an extended period of time, may be unique in the observable universe. This idea is often referred to as the Rare Earth Hypothesis.

Andrew Watson of the University of East Anglia in the UK reports, in the February 1, 2008 issue of Astrobiology, on a mathematical study he performed that lends further support for the idea that intelligent life in the universe is rare. While he approaches the problem from a naturalistic perspective, his arguments have broad application. He begins by noting that advanced life has appeared late in Earth’s history, approximately 4 billion years after primitive life first appeared. And due to the increase of the Sun’s luminosity, Earth can support this life another billion years at most—a short time compared with the time since its origin.

On the ground of some general principles entailed in the stochastic (statistical, involving random variables) model used for his study, Watson then argues that the timing of the appearance of intelligent life will be governed by the necessity of life passing at least four very difficult evolutionary steps. The four stages he chose correspond to major steps apparent in the fossil record, including the emergence of single-celled bacteria, complex cells, specialized cells allowing complex life-forms, and intelligent life with an established language.

Watson argues that each step is independent of the other and can only take place after the previous steps in the sequence have occurred. He estimates the probability of each step occurring as 10 percent or less, so the chance of intelligent life emerging in an Earth-like environment is low, less than 0.01 percent over the four billion years of life’s history. On this ground he concludes that even with Earth-like conditions, there is still a very low probability that intelligent life will develop.

If we multiply this percentage by the extremely small probability for finding an Earth-like environment, then the likelihood for finding intelligent life anywhere else in the observable universe is virtually zero. This study argues against a random chance scenario, but fits well with the RTB creation model, where we expect that the appearance of life requires the direct hand of a creator who has placed it in this universe for a purpose.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Another Mechanism to Explain Origin of Homochirality Questioned

One of my teenage daughters is left-handed. And nobody in our family wants to sit next to her when we eat at the table. It’s not because she has bad manners. It’s because her left arm bumps into the right arm of the person seated next to her. When it comes to meal time, left-handed and right-handed people don’t go well together.

The same is true for life. Left-handed and right-handed molecules don’t mix well. The building blocks of proteins (amino acids), DNA (deoxyribose), and RNA (ribose) have to be exclusively in left-handed (amino acids) and right-handed (deoxyribose and ribose) configurations—a condition called homochirality—for life’s chemistry to be possible.

Because of its central importance, origin-of-life investigators focus a lot of attention on trying to account for the origin of homochirality, so far without much success. (In fact, I discussed this problem a few weeks ago.) New work*, however, has led a team of scientists to propose yet another mechanism to account for the genesis of homochirality. As with other proposals, this idea turns out to be unrealistic upon careful consideration.

To appreciate the discovery, I need to provide some background. For convenience, some of what follows is repeated from the earlier mentioned post on the origin of homochirality.

Homochirality

Some molecules are mirror images of each other. Molecular mirror images result when four different chemical constituents bind to a central carbon atom. (The central carbon atom is called the chiral carbon.) These chemical groups are oriented in space in one of two possible arrangements that turn out to be reflections of each other. As mirror images, these compounds cannot be overlaid on one another so that all the chemical groups coincide in space. Because they can’t be superposed, molecular mirror images (called enantiomers) are distinct chemical entities.

Some of the compounds that play key roles as life’s building blocks, such as amino acids, and the sugars deoxyribose and ribose are chiral compounds.

It turns out that the amino acids that comprise proteins and the sugars that are part of the constituents of DNA and RNA have uniform chirality, a condition biochemists call homochirality. In other words, all the amino acids in proteins have the same chirality. And all the sugars in DNA and RNA have identical chirality as well.

Homochirality is a strict requirement for life. Chirality dictates the three-dimensional positioning of chemical groups in space. And the spatial location of the chemical moieties (equal parts) plays an essential role in the interactions that stabilize the three-dimensional structure of proteins. (A protein’s structure determines its function.) As a case in point, for some proteins the incorporation of even one amino acid of the opposite mirror image into its backbone will disrupt the protein’s structure, and hence, function. Additionally, as Hugh Ross and I point out in Origins of Life, laboratory experiments demonstrate that the “wrong” enantiomeric form of a nucleotide inhibits the formation of DNA and RNA assembly.

Homochirality and the Origin of Life

In order to adequately explain the spontaneous emergence of life, origin-of-life researchers have to account for the origin of homochirality. This is no easy feat. While numerous proposed explanations for the genesis of homochirality have been advanced, none seem compelling and most are riddled with problems. (For a detailed discussion of some of the difficulties researchers encounter in their attempts to explain the origin of homochirality see Origins of Life.)

Part of this challenge stems from the fact that chemical reactions which generate chiral compounds from achiral starting materials produce a 50:50 mixture of both mirror images. (This type of mixture is called racemic.) In other words, chemical processes, as a rule of thumb, do not yield homochiral products—unless a chiral excess already exists at the outset for one of the reactants or the reaction catalyst.

Does Crystallization Lead to Homochirality?

A research team from Columbia University, headed up by Ronald Breslow, believes it can explain how homochirality emerged. These investigators have previously demonstrated that when amino acids crystallize out of solution in which there is a slight excess of one enantiomer, the ensuing crystal possesses a 50:50 mixture of the two enantiomers. On the other hand, the liquid phase becomes enriched with the enantiomer that initially was in slight excess. They have shown that a slight chiral excess of about 1% can quickly become amplified to about 90% after two rounds of crystallization. The reason for this enrichment stems from the reduced solubility of amino acid complexes formed when left-handed and right-handed versions combine compared to complexes formed from left-handed and left-handed forms (or right-handed and right-handed forms). The difference in solubility will cause the crystal to exclude the enantiomer that is initially in excess.

Based on this behavior, the Columbia team proposes the following scenario to explain how homochirality originated. First, they note that in meteorites like Murchison, a slight chiral excess has been detected for some amino acids recovered from the meteorite. Then they argue that meteorites delivering amino acids to early Earth would seed the oceans with a slight chiral excess of amino acids. As the oceans waters washed onto ancient shorelines and water evaporated, amino acid crystals would form, leaving behind an even greater chiral excess in the waters that returned to the oceans. Eventually, the amino acids in the oceans would be populated with nearly 100% of one enantiomer at the expense of the other. This end result, they claim, becomes the birth of homochirality as this chiral excess gets transferred to molecules taking part in the origin-of-life process.

At first glance this scenario seems quite reasonable. Closer examination, however, exposes a fundamental problem: chiral excess in Earth’s oceans will not promote homochirality in life molecules, but, in fact, detracts from it.

To illustrate, consider the reactions between amino acids to make peptides (small protein chains). Amino acids will not react with each other in water to form peptides. (In water the reverse reaction, in which peptides break down into the constitutive amino acids, is favored.) Origin-of-life researchers posit that this difficulty can be overcome if ocean waters deposit amino acids onto ancient shorelines. As the water evaporates, the reaction between amino acids becomes more likely. Additionally, the minerals on the shore can serve as catalysts promoting the reaction.

Herein lies the difficulty. According to the mechanism proposed by the Columbia chemists, the amino acids deposited on the shore will be a racemic mixture, displaying little if any chiral excess. The chirally enriched amino acids will be diluted out in the ocean waters and unable to react to form peptides.

In reality, the mechanism proposed by the Columbia scientists would inhibit the birth of homochirality, not promote it. Therefore, the homochirality problem still represents an “elbow-in-the-side” of chemical evolutionary explanations for the origin of life.

*This study made science news headlines when first published. I discussed the scientific and biblical implications of this research on the April 9, 2008 edition of our new podcast, RTB’s Science News Flash. This podcast offers a unique Christian perspective on headline-grabbing discoveries. A free subscription to this podcast is available through iTunes.