Science and Culture Today | Page 1210 | Discovering Design in Nature

[Editor’s Note: This is part three of a six-part response from microbiologist Don Ewert to Kathryn Applegate’s arguments that the vertebrate adaptive immune system is an example of Darwinian evolution in action. Part one can be found here, and part two is here.]

The second stage of B cell receptor development is initiated when a foreign protein enters our body and is detected by a circulating B cell using its cell surface antigen receptor (BCR). The BCRs that recognize these antigens improve their affinity (binding capacity) for the antigen by entering into a fine-tuning process called affinity maturation. This process ensures that highly effective antibody receptors are produced and released as cell-free antibodies into the circulation as the B cell completes its development. This increase in the strength of binding between a single antigenic determinant and an individual antibody combining site does not affect the specificity of the antibody, i.e. its ability to distinguish between small regions (epitopes) on the same antigen. Rather it allows for antibodies to remain bound to the foreign antigen for longer periods of time, thus giving the body a greater chance to clear the antigen-antibody complexes. The changes in the affinity of the receptor for an antigen results from the accumulation of nucleotide replacements that change the attractive and repulsive forces, mainly electrostatic forces, of the antigen combining site. The molecular mechanism for improving the affinity of the BCR is called somatic cell hypermutation (SHM), since the changes that are introduced in the DNA of the B cell (a somatic cell) cannot be passed on to the offspring of the animal.

[Editor’s Note: This is part two of a response from microbiologist Don Ewert to arguments from BioLogos’s Kathryn Applegate that our immune system shows the creative power Darwinian evolution. Part one can be found here.]

The intricate mechanism for generating antibody diversity from very few germline (existing) genes was discovered over thirty years ago. It involves shuffling gene segments and then fusing them to produce new combining sites for the antibody receptor displayed on individual B cells. How much of this process is pre-programmed and how much is random? Is this an example of the use of a “‘blind’ system to sustain and preserve life,” as Kathryn Applegate suggests? The evidence from decades of research reveals a complex network of highly regulated processes of gene expression that leave very little to chance, but permit the generation of receptor diversity without damaging the function of the immunoglobulin protein or doing damage to other sites in the genome.

The most remarkable aspect of antibody production is the mechanisms that generate the binding site of the antigen receptor. The antigen receptor of B cells are proteins called immunoglobulins. They have an antigen combining site at one end that binds to foreign proteins (variable or V region) and a tail, or constant region (C region), at the other end that controls the interaction with other components of the immune system that are responsible for eliminating the foreign invader. The variable end of the BCR heavy chain is generated by the shuffling and joining of gene segments from separate pools of V (45), D (23), and J (6) segments per cell and the random deletion and insertion of nucleotides at the joining sites. This process is duplicated on the second (light) chain of the immunoglobulin gene. The combined diversity generated by recombination which is limited by the number of gene segments and by nucleotide exchanges, which are unlimited, produces a potential repertoire of about 10¹¹ different receptor specificities. This process occurs during transcription of the DNA and involves a set of coordinated enzymatic reactions. The total number of available receptor specificities is limited by the number of B and T lymphocytes.

In my prior post, I explained that Kirk Fitzhugh, a scientist at the Natural History Museum of Los Angeles County (NHMLAC), wrongly claims that intelligent design (ID) is not testable. Fitzhugh’s error that ID is “immune to testing” is important. While he should have the academic freedom to believe and contend that ID is “immune to testing” and not scientific, he uses his claim that ID is not testable to justify suppressing ID. He anticipates this deficiency in his position, and thus writes: First, there’s the claim that science precludes expression of thought. In the context of ID, such a claim of overt suppression is inaccurate. Science is a process of acquiring ever-increasing causal understanding, and such a process has Read More ›

[Editor’s Note: Earlier this year, in a series of posts on the BioLogos website (“Adaptive Immunity: How Randomness Comes to the Rescue” and “Evolution and Immunity: Same Story“), Kathryn Applegate argued that the “random” processes of the vertebrate adaptive immune system serve as an example of how Darwinian mechanisms can generate biological complexity. Today, Discovery Institute presents part one of a response to Dr. Applegate from Donald L. Ewert, a research immunologist/virologist who spent much of his career studying the molecular and cell biology of the immune system, as well as theories about its evolution. Dr. Ewert received his Ph.D. from the University of Georgia in 1976. As a microbiologist, he operated a research laboratory at the Wistar Institute in Philadelphia for almost twenty years. The Wistar Institute is one of the world’s leading centers for biomedical research. His research, supported by National Institute of Health, National Science Foundation, and Department of Agriculture grants, has involved the immune system, viruses, and cellular biology.]

Introduction

In her articles on the BioLogos website, Kathryn Applegate attempts to show how the mechanisms used by the adaptive immune system to generate a diversity of antigen receptors are an example of Darwinian evolution. She focuses on aspects of these mechanisms that she characterizes as “blind” and “random,” stating, “Antibody production and evolution both involve mutation and selection.” She further claims that “the adaptive immune system harnesses the power of randomness to protect the body from assaults it has never seen before” and antibody “production requires randomness at multiple levels.” Applegate, however, frames her argument in theological terms, arguing that if “God uses natural processes — indeed, even a ‘blind’ system for generating massive amounts of diversity,” why could he not use the same mechanisms to “create life over long periods of time”?

My eight questions and answers for New Atheists have generated some amusing replies. Most just criticize me for asking, calling me ‘dishonest’ (that’s for my questions, not just for my answers). ‘No matter what, God didn’t do it’ is the typical reply.

One dyspeptic New Atheist was uncommonly amusing. Chuck O’Connor at Battling Confusion writes:

Michael Egnor (a fellow of the Discovery Institute – the PR organization that tries to deny biological evolution for the sake of Judeo/Christian creationism and theocracy – see their aims articulated in “The Wedge Strategy”) offers excellent evidence of this obsessive psychological quirk towards certainty when he creates a “strawman” argument against “New Atheism” at the Discovery Institute Web-site.

My “obsessive psychological quirk” was to ask important questions and to answer them coherently. After posting my questions, he asserts:

First off, Eignor’s [sic] unwillingness to enable comments at his blog post indicates he does not want to know what “New Atheists” believe.

We don’t take comments on ENV because much of what New Atheists believe is expressed in 4-letter parcels. They have their own blogs for that.

In the Hebrew version of Wikipedia, the page on intelligent design translates ID with the phrase “tichnun tivoni,” which means something like “intelligent planning.” And so it’s translated regularly too in Ha’aretz and other Israeli news sources. The Wiki page is well supplied with the usual distortions that you’d expect from Wikipedia in any language, but never mind that. The question of how to translate “intelligent design” into the language of the Bible is an interesting one. Is there an actual Biblical phrase that captures the idea?

In the journal Azure, published by the Shalem Center in Jerusalem, an essay on the “Secret of the Sabbath” indirectly suggests an answer. Rabbi Yosef Yitzhak Lifshitz reflects on the passage from the book of Exodus about the construction of the Tabernacle in the desert. Following the Exodus from Egypt, the Israelites were in the wilderness on their way to the land of Israel. Rather than having them construct a permanent Temple to worship in, God directed Moses to oversee the construction of a large movable tent for the same purpose. To carry out the work of designing the structure, God chose Betzalel and endowed him with “wisdom, understanding and knowledge…to perform all manner of workmanship” (35:31, 33).

The phrase given above as “workmanship,” melechet machshevet, really means purposive creativity — or, if you will, intelligent design. A helpful insight in the debate with theistic evolution advocates emerges from this observation.

As Rabbi Lifshitz explains, drawing on a long line of earlier commentators back to the Talmud and Midrash, the connection with the Sabbath goes as follows. When God gave the Sabbath to the Israelites, in the form of the Fourth Commandment, he was exceedingly sparing on the details of what actually constitutes the “work” (melachah) from which they were henceforth to rest on the Sabbath.

The Smithsonian Institution, a wonderful taxpayer-supported educational establishment, has a bad record when it comes to treating scientific Darwin-doubters with due respect for academic freedom and free speech. Now to this list of indictments add respect for intellectual property.

Readers will recall the Richard Sternberg affair, in which supervisors at the National Museum of Natural History (NMNH) persecuted an evolutionary biologist on staff just for editing a peer-reviewed research paper supportive of intelligent design. More recently, senior figures at the Smithsonian may have pressured the affiliated California Science Center to cancel a contract to show a Darwin-critical documentary, in what seems to be an instance of a public facility illegally regulating speech.

In both of those cases, the indications suggest it was the intention to squash a controversial viewpoint that motivated Smithsonian personnel. In the case of renowned lepidopterist Bernard d’Abrera, there’s no reason to believe that it was his Darwin-doubting itself that led to an act of startling brazenness.

Brazen…what? “Theft,” as d’Abrera calls it in his account published in a recent book in his series Butterflies of the World. He actually puts the word in quote marks since, he observes wryly, his attorney advised him that while it looks to the untrained eye exactly like theft, it wasn’t a criminal case, ending up instead in the Court of Federal Claims.

CSC research director Jay Richards takes aim at the latest pronouncement from Stephen Hawking today at The American: Stephen Hawking declared that our understanding of physics proves God did not create the universe. Is he right? Stephen Hawking holds the chair of mathematics at Cambridge University once held by Sir Isaac Newton. So when he declared that our understanding of physics shows that God did not create the universe, it was bound to get attention. Summarizing the thesis of his new book, The Grand Design (co-authored with Leonard Mlodinow), Hawking announced: “Because there is a law such as gravity, the universe can and will create itself from nothing. Spontaneous creation is the reason there is something rather than nothing, why Read More ›

In my prior post, I noted that for years I’ve owned a graduate assignment on evolutionary classification by LA County Museum of Natural History scientist Kirk Fitzhugh. After completing this “Classification” project, he went on to earn his PhD in biology and today is Curator of Polychaetes at the Natural History Museum of Los Angeles County (NHMLAC). Fitzhugh was part of the internal discussions at NHMLAC that I’ve been writing about, in which participants at one point planned to tell the California Science Center (CSC), “We urge you to cancel this event.” Fitzhugh, however, is not nearly so private about his disagreement with ID as some of his NHMLAC colleagues. It’s important to note that Dr. Fitzhugh should have every Read More ›