Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Scientists One Step Closer to Artificial Life and the Best Case for ID

Mary Shelley’s famous Gothic horror story presents a fascinating character: Victor Frankenstein. As a burgeoning scientist, Victor becomes obsessed with discovering the “principle” that distinguishes life from inanimate matter. After many long hours of study and laboratory work he uncovers “the cause of generation and life,” and becomes “capable of bestowing animation on lifeless matter.”

Frankenstein exercises his newfound ability by bringing a humanoid monster to life, only to abandon it in disgust. Victor’s moral failings lead to several tragic deaths at the hands of his creature, including those of his brother, his best friend, and, later, his wife on their wedding night. Even though the scientist and the creation are somewhat sympathetic figures, it’s not clear who’s the true monster—Victor, the creature, or both.

If there is a real life Frankenstein, he might very well be Craig Venter.

Venter stands as perhaps one of the most important scientists in the last decade or so. (In 2008, Time magazine voted him one of the world’s 100 most influential people.) As a major player in the emergence of the science of genomics, he is a scientific maverick who thinks big and has little patience for the red tape and bureaucracy that characterize many scientific programs. And like Victor, he is a polarizing figure, much admired and much hated by people within and outside the scientific community.

Recently, Venter founded a company called Synthetic Genomics. As with Shelley’s protagonist, Venter wants to create life in the laboratory. The new company is devoted to creating artificial, nonnatural life microbes that have commercial utility, particularly for the production of ethanol, hydrogen, and other forms of renewable energy. Once again, Venter has generated a mixture of excitement and horror among the scientific community, and the public at large.

Scientists like Venter who pursue the creation of artificial and synthetic life claim that these novel life-forms will benefit humanity. If they accomplish the desired breakthrough, it could go a long way toward resolving the energy and climate crises.

The very real prospect of scientists creating life in the lab raises all sorts of theological questions. Should human beings “play God”? Some conservative Christians worry that the genesis of novel life-forms by human hands eliminates the need for a Creator by substantiating the evolutionary paradigm. Many theists and atheists, alike, believe that if scientists can create life in the lab, then there is nothing special about any life. Therefore, the origin-of-life could have easily taken place on the early Earth without God’s necessary involvement.

The latest work by Venter’s team stands as another milestone in the quest to create an artificial life-form in the lab. Ironically, instead of supporting an evolutionary origin of life, this research demonstrates that life’s beginnings and transformation cannot happen apart from the work of an intelligent agent.

This week I will discuss the progress Venter and his team at Synthetic Genomics have made toward achieving their goal. In the next couple of weeks I’ll describe the details of their most recent accomplishment and will eventually explore the implications of this work for the intelligent design (creation)/evolution controversy.

The Path to Artificial Life

Venter and his coworkers became interested in creating artificial life as an outgrowth of another project. Initially, they were interested in determining the minimum genome for life. The term “genome” refers to an organism’s entire hereditary information, stored in the nucleotide sequences of DNA. The information housed in genomes exists in units called genes. These units contain the information that the cell’s machinery uses to make proteins.

Proteins take part in virtually every biochemical process and play critical roles in nearly every cell structure. Cataloging the number and types of proteins present in an organism gives biochemists important insight into its structures and operations. Venter’s team hopes that identifying the minimum genome will provide them with an understanding of life at its most fundamental level.

In their attempts to reach that target, Venter’s group has focused attention on a bacterium called Mycoplasma genitalium. This microbe has one of the smallest, if not the smallest, genome known to scientists. M. genitalium parasitizes the human genital and respiratory tracts. Its genome possesses about 480 gene products. Because its genome is so extensively pared-down, it’s ideally suited as a model system to determine the absolutely indispensable requirements for life—the “non-negotiable” biochemical systems that must be present for an entity to be recognized as a form of life.

The researchers reasoned that it is quite likely that the bare essential genome is much smaller than 480 gene products. It turns out that a significant fraction of this parasite’s genome is dedicated to mediating interactions between the parasite and its host and can be considered as nonessential to a strictly minimal life-form.

Using an experimental approach, Venter’s team worked to ascertain the minimum number of genes needed for life. Their protocols involved both the random and systematic mutation of M. genitalium genes to determine those that are indispensable for life. (Biochemists refer to these procedures as knock-out experiments.) If a gene is nonessential, M. genitalium will still grow after the gene is mutated.

Once the essential or minimum gene has been determined via the knock-out experiments, the scientists hope to confirm their result by preparing a synthetic minimal genome and introducing it into a cell to see if the cell with the transplanted genome grows. They realized that in the process of identifying the minimum genome, they came just a few short steps away from making artificial life in the lab.

Steps to Creating Artificial Life

Venter and collaborators’ approach to creating an artificial life-form is called a top-down strategy. It involves starting with a naturally occurring microbe and stripping it down to its bare genetic and biochemical essence, and then modifying it by adding nonnative genes to the minimal genome to generate a nonnatural form of life.

The major stages in this effort involve:

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.

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Parts 1 through 4 of this series described such features as information-processing systems, Gray codes, even parity codes, and error-minimization techniques in biological systems. A fifth feature (not part of this series) observed an analogy of a feedback control system found in dairy cows.

What do these apparent analogies of design in nature mean? Are they really analogues and how do they relate to the popular watchmaker argument?

William Paley’s Watchmaker Argument¹

British natural theologian William Paley (1743-1805) is famous for his so-called watchmaker argument. Paley argued that in contrast to a stone, a watch found on a remote path implies a watchmaker. Unlike the stone, the watch could not be constructed by the forces of nature. Paley further argued that organisms are similar to a watch in complexity (in fact, more complex); therefore, a Divine Designer can be inferred. (See here for more details about William Paley and his watchmaker argument.)

A contemporary of Paley, Scottish philosopher David Hume (1711-1776) offered several criticisms of Paley’s argument. In Hume’s estimation, the analogical argument between organisms and a watch was weak. Hume argued that the objects being compared (living organisms and a watch) were too dissimilar to constitute a good analogy; therefore, Paley’s argument would not stand. (See here and here for more information on David Hume and his objections to the design argument.)

Modern critics have added further reasons for doubting the legitimacy of the watchmaker argument. B. C. Johnson has argued that Paley did not use a strict-enough criterion for identifying design. For Paley, design was evident when a system contained several parts “framed and put together for a purpose.” Johnson, in contrast, says “we can identify a thing as designed, even when we do not know its purpose, only if it resembles the things we make to express our purposes.”²

Logician Patrick J. Hurley demonstrates the appropriate use of analogy. To build a strong analogy, Hurley reasons that one must find sufficiently numerous and relevant attributes in both halves of the analogy to establish an analogical relationship that supports the conclusion drawn. An analogy is more firmly established when the analogous systems are diverse and abundant.³

Have these criteria been established in the examples considered in this series?

As an engineer I would submit these reasons in arguing for an undeniable “yes”:

the genetic system is, by any objective standard, an information-processing system in the same way that our modern communication systems are;

the genetic information-processing system uses discrete, symbolic alphabets and sequences just as our modern digital communication systems do;

numerous and diverse analogies directly resemble our own designs in information-processing and error-control coding;

we have found these analogies to be strict and robust between the domains— analogies that highlight techniques that are aimed to minimize errors and maximize information transfer;

we have seen analogies of Gray codes, parity codes, and even feedback control systems (see here);

the genetic code has been found to be highly optimized, literally one-in-a-million in terms of its error-minimization capacities, and the very same code simultaneously conforms to a specific and unique mathematical structure that enables, in addition, the existence of code(s) operating along the DNA strands;

statistical studies of actual DNA reveal a signature that further suggests that codes similar to the parity code may well be in operation along the DNA strands.

Thus, twenty-first century insight into the genetic system has helped settle the centuries-old debate. The analogies discussed meet the objections raised and standards set by Hume, Johnson, and Hurley. Paley’s watchmaker argument is indeed reinvigorated with this new and powerful evidence coming from the intersection of molecular biology and information theory.

This evidence buttresses the divine design component of RTB’s creation model and finds a comfortable spot within the worldview of Christian theism.

Notes/References:

1. See here for further information on Paley’s argument, and objections raised, in the context of molecular motors.

2. Fazale Rana, “Hume vs. Paley: These “Motors” Settle the Debate,” Facts for Faith, no. 2 (Q2 2000).

3. Fazale Rana, “Hume vs. Paley: These “Motors” Settle the Debate.”

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.

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Anyone up for tic-tac-toe and genetics? It’s not exactly a game, but grab a cup of coffee and let’s explore the intriguing design in genetic systems.

In parts 1, 2, and 3 of this series, we observed three features of genetic systems that suggest design. In this article we look at isomorphic systems to find yet another analogy in the genetic code.

Analogy: Genetic Code-Like (GCL) Binary Representation

Recall the genetic code mapping table discussed in part 1 and part 2 of this series. This table describes the mapping between the 64 codons and the 20 amino acids.

Researchers in Venice, Italy, have identified a specific and unique number system and have used it to mathematically model the genetic code. In this work, the 64 codons and the 20 amino acids are assigned to numerical elements within the system, referred to as the genetic code-like (GCL) binary representation. The GCL binary representation is a unique model that holds true to the specific redundancy features in the natural genetic code mapping.¹ It is a mathematical model of the underlining physical/chemical processes related to genetic information processing—a so-called structural isomorphism.

An isomorphism is a one-to-one correspondence between the elements of two sets such that the result of an operation on elements of one set corresponds to the result of the analogous operation on their images in the other set. If two sets are isomorphic with respect to certain properties, then those properties that are true of one of the sets must also be true of the other.

For example, a six-sided die and a bag from which a number 1 through 6 is chosen are isomorphic. As another example, tic-tac-toe and the “game of 15” are isomorphic. In the game of 15, players take turns saying a number between 1 and 9. Numbers may not be repeated. Both players aim to say three numbers that add up to 15. Although perhaps not obvious, the defining characteristics of this number game are identical to those of tic-tac-toe. It turns out that both games are based on the well-known (to mathematicians) magic square.

The GCL binary representation and the genetic code are also isomorphic systems (sets). So, characteristics that are true of the GCL binary representation must also be true of the genetic code. (See here and here for more details of isomorphic systems.)

What are the characteristics of the GCL binary representation? The European researchers noted that this mathematical model exhibits:²

• Palindromic symmetry
• Parity symmetry
• Organized redundancy
• A rich mathematical structure

Such elegant symmetry, organization, and structure speak of a code that has been designed for a purpose—no mere afterthought of evolutionary chance events.

Also, the GCL binary representation makes possible the existence of error detection/correction codes that operate along the strands of DNA. A parity code (as discussed in part 3 of this series) is one example of such a technique.

If a parity code or similar technique functions along strands of DNA using the GCL binary representation, then dependence must exist in the genetic data along the strand. In other words, the data must be correlated to some degree.

Assuming the GCL binary representation and using two different robust statistical analysis methods, the research team discovered significant short- and long-range correlation peaks in actual DNA sequences. These results confirm that actual DNA sequences using this specific model satisfy a basic prerequisite for such error-minimizing techniques.

The team noted that “an error-control mechanism implies the organization of the redundancy in a mathematically structured way,” and that “[t]he genetic code exhibits a strong mathematical structure that is difficult to put in relation with biological advantages other than error correction.”

Thus, scientific advance has uncovered a peculiar and unique mathematical model that accounts for the key properties of the genetic code. This model exhibits symmetry, organized redundancy, and a mathematical structure that would be vital for the existence of error-coding techniques operating along the DNA strands. Actual DNA data tested using this model gives a strong hint that such further error-coding techniques may very well exist and provides impetus for future study in this area. Purposeful creation seems a reasonable conclusion.

Part 5 (the last entry) of this series will discuss the impact of these analogies on William Paley’s watchmaker argument.

Notes/References:

1. It describes exactly the 1st level of degeneracy (i.e., redundancy) in the natural genetic code (i.e., the number of codons which map to specific amino acids), and gives deep insight into the 2nd level of degeneracy (i.e., the association between specific codons and specific amino acids).

2. A full treatment of how the GCL binary representation displays these features is very technical and difficult to communicate without active use of visual aids. Nevertheless, this note is a brief attempt. See here for the necessary visual aid. Table 3 shows the actual GCL binary representation of the natural genetic code. The numerical elements in the model are associated with biochemical elements in the genetic code. The whole numbers 0–23 along the table edges map to amino acids. The 6-bit binary strings map to codons. The degeneracy number is shown in the center of the table, along with the amino acids coded for. The degeneracy number indicates how many different codons code for each particular amino acid. A careful inspection will show that all 64 codons are present, along with all 20 amino acids. Palindromic symmetry is seen as a reflection through the middle of the table in a left to right fashion. Palindromic amino acids are always associated in pairs. For example, tryptophan (Trp) and methionine (Met) are a pair of palindromic amino acids. Note that if the 6-bit codewords are folded on top of each other through the middle of the table, they form bitwise negated pairs, reflecting a very peculiar mathematical structure for palindromic symmetry. Also note the symmetry evident in the parity, again through the middle of the table. The light entries are odd parity (odd number of 1’s) and the dark entries are even parity (even number of 1’s). The interested reader is referred to the journal paper for further details.