Science and Culture Today | Page 1200 | Discovering Design in Nature

There’s an outstanding review of Stephen Meyer’s Signature in the Cell by Terry Scambray in the New Oxford Review, which highlights a bit of relevant history for the reader on both Dr. Meyer and Darwin’s theory:

Signature in the Cell: DNA and the Evidence for Intelligent Design is a testament to the fact that, fortunately, such advice [“don’t ask questions”] never sank in with Meyer. After abandoning his life as a geophysicist in search of oil for Atlantic Richfield, and then earning a Cambridge doctorate, he continued to ask questions as he humbly but resolutely began his new quest: the search to understand the origins and basis of life.

This is, of course, an ancient quest. From then to now, most people have believed that the sublime order that we see in nature must have been designed. But Charles Darwin argued that design was an illusion: Nature alone, by a process of accidental trial and error over eons of time, had produced this ineffable harmony.

Despite the fact that Darwin’s theory of natural selection was accepted by most educated people, the theory itself was weakly supported from the beginning. It gained acceptance mainly for cultural rather than scientific reasons. Progressive ideas had gained dominance by the nineteenth century; correspondingly traditional institutions — mainly religion — were taking their lumps. Against this background, criticisms of Darwin were castigated as regressive and religiously motivated, despite their scientific objectivity and rigor. Such polemical treachery continues to this day.

I normally do not respond to criticisms and reviews of my work that are simply posted on the internet. Rather, I engage reviews, comments, and articles that appear in journals or prominent newspapers and magazines. The reason is that those printed venues usually ask noted scientists or philosophers to review books, so that they are very likely to contain the most pertinent and insightful comments. After all, if a book challenging Darwinian evolution is reviewed separately by the likes of Sean Carroll, Jerry Coyne, Michael Ruse, and Richard Dawkins, then the odds are good that they would have discovered any major errors, if such there be. However, if upon considering their criticisms, we see huffing and puffing instead of reasoned argument, or an attack on straw men instead of the actual arguments the author made, then we can conclude that the best minds in the field don’t have answers to the arguments the book presents. And if the best minds don’t have answers, it is quite likely that no one else has answers either.

That’s what happened when The Edge of Evolution was published in 2005. It received uniformly hostile reviews by prominent Darwinists. However, in my author’s blog on Amazon.com, at the time I engaged their criticisms and showed that virtually all of the reviews consisted of various degrees of bluster, question-begging, or attacks on straw men. What valid points remained I showed were minor and did not affect the main argument of the book: that while Darwinism can explain minor changes in life, there are strong reasons to think it does not explain much of the phenomenal complexity of the cell. Anyone who wishes to read those responses can do so at my blog and make their own judgments.

The question of the evolution of eukaryotic cells from prokaryotic ones has long been a topic of heated discussion in the scientific literature. It is generally thought that eukaryotes arose by some prokaryotic cells being engulfed and assimilated by other prokaryotic cells. Called endosymbiotic theory, there is some empirical basis for this. For example, mitochondria contain a single circular genome, carry out transcription and translation within its compartment, use bacteria-like enzymes/components, and replicate independently of host cell division and in a manner akin to bacterial binary fission.

Despite such evidence, however, when assessing the causal sufficiency of unguided processes, they — predictably — come up short. After all, it is all-too-easy to lapse into a long-discredited Lamarckian “inheritance-of-acquired-characteristics” mentality. It is important to bear in mind that, even if a cooperative assemblage of prokaryotes did by some fluke of luck arise, such an arrangement is of no evolutionary significance unless there is a genetic basis to ensure its propagation.

A second problem with this scenario is that mitochondria use a slight variation on the conventional genetic code (for example, the codon UGA is a stop codon in the conventional code, but encodes for Tryptophan in mitochondria). This implicates that the genes of the ingested prokaryotes would need to have been recoded on their way to the nucleus. The situation becomes even worse when one considers that, in eukaryotic cells, a mitochondrial protein is coded with an extra length of polypeptide which acts as a “tag” to ensure that the relevant protein is recognised as being mitochondrial and dispatched accordingly. The significant number of specific co-ordinated modifications which would be required to facilitate such a transition, therefore, arguably make it exhibitive of irreducible complexity.

[Editor’s Note: Today we present part five out of six in a series by microbiologist Donald L. Ewert. These posts are responding to the BioLogos Foundation’s blog where Kathryn Applegate argued that “random” processes that generate antibodies illustrate the creative power of Darwinian evolution. Previous installments of Dr. Ewert’s rebuttal can be found at the following links: Part One, Part Two, Part Three, and Part Four.]

Kathryn Applegate’s main point is that if “natural” processes — which she characterizes as “random” and “blind” — can be used to generate antibodies, the same mechanisms presumably could be used to “create life over long periods of time.”

The question addressed here is: Do the terms “random” and “blind” accurately describe the mechanisms for generating diversity via V(D)J rearrangement and affinity maturation by SHM? Based on our current knowledge about antibody development, briefly described above, I contend that what may appear to be a random process is actually highly orchestrated at many different levels — organismal (developmental), tissue (lymphoid tissues), cellular (B cells, helper T cells, antigen presenting cells), protein (MHC, enzymes, transcription factors, cytokines) and genetic (C and G placement, chromosomal accessibility). The function and structure of these highly specialized components must be coordinated to produce a specific antibody in response to an antigenic challenge. Independent developmental programs of the cell lineages, tissues, and organs must be controlled to ensure that their location and structure permit the interactions required for development of the B cell and antibody production. Therefore the combined functional and developmental aspects of antibody production involve a hierarchal matrix of regulatory controls that orchestrate the entire process. Antibody development is certainly not a “blind” or “random” process. What on the surface may seem like a random process is in fact an elegantly designed and regulated process.

[Editor’s Note: This is part four of a six-part series from microbiologist Donald L. Ewert responding to Kathryn Applegate, of the BioLogos Foundation, in her arguments that the vertebrate adaptive immune system illustrates the claimed creative the Darwinian mechanism. Previous parts of Ewert’s response can be found at the following links: Part One, Part Two, Part Three.]

Pathogen-directed activation of the immune response

The initiation of an immune response is designed so that the cellular and molecular components that are best equipped to deal with a pathogen are engaged. There are basically three response pathways. Non-protein antigens that have repeating carbohydrate units on their surface, such as are found on bacteria, can directly activate B cells. These B cell do not go through affinity maturation or class switch since multiple binding sites on the antigen make a strong bond with the B cell and the IgM class of antibody that is produced which has five receptors per molecule.

Responses to protein antigens fall into two classes, depending on whether the pathogen is intracellular or extracellular. Since intracellular antigens such as viruses are not accessible to circulating antibody, they activate cytotoxic T lymphocytes that are best equipped to kill them. This activation is directed by the Class I MHC antigen that is attached to the antigens as they are processed in cells. Extracellular proteins, which are best dealt with by circulating antibody, activate B cells to begin the process of affinity maturation and class switch that leads to the production of a monomeric IgG class of antibody. This latter pathway requires the assistance of a class of T lymphocytes called T helper cells (T_H) and the interaction of Class II MHC proteins.

As I was driving in to work, the local NPR station had on an interview with a guy who’s involved with gathering billions of seeds of various plant varieties into a “doomsday vault.” It is on a remote Norwegian island and intended as a precaution against the presumed devastations of global warming. There were few surprises in the conversation — the grim mood was well suited to the NPR target audience, which eats this stuff up — apart from one rather interesting question from a listener. The guest, Cary Fowler of the Global Crop Diversity Trust, was asked why his group bothers with seeds. In the future, won’t we be able to reconstitute life from the digital code of DNA?

Not necessarily, explained Fowler. He offered a few cryptic but telling comments about the complexities of gene expression, and how simply knowing the DNA sequence of a plant (or animal) may never be sufficient to generate life. Why? Part of the answer, implying a strong challenge to materialist explanations of life’s evolution, is suggested in a recent and illuminating essay, “Getting Over the Code Delusion,” in the Ethics and Public Policy Center journal, The New Atlantis.

Rare is the technical if otherwise quite accessible article that gives chills like this one does. Steve Talbott, a senior researcher at the Nature Institute, takes aim at the still-widespread illusion that DNA maps the construction of a living creature. In a 1992 essay, Nobel Prize-winning geneticist Walter Gilbert crowed that the time will come when a person will be able to say, of a human DNA sequence inscribed on a computer disk, “Here is a human being; it’s me!” How utterly naíve that has since been revealed to be.

Richard Dawkins calls DNA “a remarkable feat of digital information technology,” on the model of a computer albeit one that programs itself. Yet the burden of Talbott’s article is to show why the whole computer metaphor is inadequate. If you want a better one, the really apt metaphor would be drawn from the art of dance — or I’d say, music — with all that implies by way of purpose, agency, and expression.

I’ve received quite a bit of positive feedback about the responses to the Nature 15 Evolutionary Gems packet that we’ve been responding to since last summer. As a recap of this series, below are links to the 9 parts responding to what I’ve affectionately called “Nature‘s Evolution-Evangelism Packet.” Also, we’ve compiled the responses into a single PDF that can be used for educational purposes: Be sure to download the full PDF here. 

This month’s edition of Touchstone Magazine has a great column by the godfather of intelligent design, Phillip Johnson, offering his review of Stephen Meyer’s Signature in the Cell and his take on why the book has been met with such an uproar in the blogosphere: In another way, however, it is peculiar that there is such a furious and often ill-informed objection to a learned volume that isn’t even about the theory of biological evolution. The book advances well-reasoned arguments based on solid evidence about a prior problem — the origin of the cell’s information content — concerning which most scientists would concede that they know very little. The one thing that many of these scientists think they do know Read More ›

Scientific American recently reported on what has transpired since the completion of the Human Genome Project ten years ago. When the HGP was first announced in 2000, many scientists said that it would be the key to understanding disease and for developing cures. Ten years later, however, this has not been the case. The human genome project has aided in developing better research and technology, particularly in our abilities to sequence genes. It has also shown us that much of what we once considered junk DNA isn’t really junk at all. (See here, here, here, and here for past ENV discussions on junk DNA). However, scientists are coming to a sobering conclusion that perhaps their models and assumptions on the nature of disease may be mistaken.

Francis Collins is one of the world’s most prominent theistic evolutionists, and now a prominent piece of President Obama’s government. In this clip, God and Evolution contributors and other scholars respond to Francis Collins’ defense of theistic evolution in his book The Language of God. Display content from www.discovery.org Click here to display content from www.discovery.org. Always display content from www.discovery.org Open content directly In his book The Language of God: A Scientist Presents Evidence for Belief (2006) and other writings and interviews, Collins has described the paths that led him from atheism to religious belief and from an impatience with “messy” biology and a preference for the pristine realms of physics and chemistry to a fascination with DNA, RNA, Read More ›