Discovery Institute recently released a stunning animation (different from the one above) of the mechanics of ATP synthase, a biomechanical power generator found almost ubiquitously across life. The video above offers another glimpse of the engineering prowess of this amazing molecular machine.

There exists three main types of membrane-embedded ATPases: F-type, V-type and P-type. I will discuss here the F-type ATPases (also called ATP synthase). V-type ATPases facilitate the acidification of intracellular organelles, and use the energy from adenosine triphosphate (ATP) hydrolysis to pump protons into cells and organelles (Beyenbach and Wieczorek, 2006). P-type ATPases are involved in the pumping of cations, also using the energy of ATP hydrolysis (Bublitz et al., 2011; Kuhlbrandt, 2004). The F-type ATPase discussed here is unique inasmuch as it, rather than hydrolysing ATP, actively synthesizes it using the energy from the flow of protons down an electrochemical gradient. There are also A-type ATPases which are found in archaea and perform a similar function to F-type ATPases (Bickel-Sandkötter et al., 1998).

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Atheist philosopher A.C. Grayling, whose debate with Peter S. Williams I wrote about yesterday, recently published a new book, The God Argument: The Case Against Religion and for Humanism. I was particularly interested in reading Chapter 11, which is devoted to the subject of creationism and intelligent design. The chapter contains so many errors and is so poorly researched that one hardly knows where to begin. Continue reading →

The video above features a short excerpt from a debate between well-known atheist philosopher A.C. Grayling (famous for conveniently “forgetting” having debated William Lane Craig) and Christian philosopher Peter S. Williams. Their subject: the fine-tuning of the universe’s initial conditions to support complex life, bearing on the case for intelligent design. Williams articulates the argument from specified complexity, using the analogy of an ATM bank machine. A bank pin number is a very specific combination of four digits (some banks allow more), and there is a total of ten digits (0-9) on an ATM keypad. There is thus only one four-digit combination out of a total of 10,000 (10^4) combinatorial possibilities that will allow the money to be retrieved from the machine. Since ATM machines typically allow only three attempts before denying access to one’s bank account, it is vastly more probable than not that the machine will not be cracked by chance. This is analogous to the kind of specified complexity that is of interest to ID theorists.

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The video above shows the process by which bacterial cells reproduce themselves. Looks simple, doesn’t it? It’s only a colony of cells elongating before splitting in two. Don’t be fooled — appearances can be deceiving. As is so common throughout biology, the apparent simplicity at the macro level masks remarkable complexity at the micro or molecular level.

In eukaryotes, cell division occurs by either meiosis (sex cells) or mitosis (somatic cells). Bacteria, however, undergo neither of those processes (they are asexual and contain no membrane-enclosed organelles or nuclei). Bacterial cell division occurs by a process known as binary fission. Rod-shaped bacteria (e.g. Escherichia coli or Salmonella typhimurium) elongate to twice their original length. This is followed by invagination of the cell membrane, and the formation of a septal ring in the middle (Vicente et al., 2006; Weiss, 2004). The elongated bacterial cell splits down the middle, forming two daughter cells. Some bacteria exhibit variations on this mechanism. For example, inCaulobacter, no septum is formed (Poindexter and Hagenzieker, 1981) and its division is asymmetrical(Judd et al., 2003).

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I’ve been reading the recently published book Microbes and Evolution: The World that Darwin Never Saw, which combines my two primary areas of interest: microbiology and evolution. Chapter 38 of the book is written by Kelly Hughes and David Blair of the University of Utah, two of the world’s leading experts on bacterial flagellar assembly. Having followed the work of Kelly Hughes and his colleagues for a few years, I hold their work in the highest regard. I myself have a deep fascination with the subject of bacterial gene expression. I was intrigued, therefore, when I discovered the title of Hughes and Blair’s chapter: “Irreducible Complexity? Not!” Continue reading →

In previous articles (see here and here), I’ve been reviewing the molecular nano-machinery needed for the replication of DNA. Before DNA polymerase is able to synthesize the new complementary strands, it needs to be given access to the nucleotides of the single-stranded template DNA. The internal base pairing in the double helix must therefore be broken and the helix unwound. Generally, the initial opening of the double helix (at the origin of replication) is performed by an initiator protein (Stenlund, 2003). DNA helicases can melt base pairs using the energy released during the process of binding, hydrolysis and release of ATP.

DNA helicase travels ahead of the replication fork, continuously opening and unwinding the DNA double helix to provide the template needed by the DNA Polymerase. With a rotational speed of up to 10,000 rotations per minute, the helicase rivals the rotational speed of jet engine turbines. When I first encountered and studied the mechanisms of DNA replication in my early undergraduate days, I was stunned by its complexity and elegance. I later came to the realization, however, that my initial conception of the sophistication of these molecular machines was a gross underestimation. The closer I inspected the nanomachinery responsible for information processing in the cell, the more I felt a sense of astonishment and marvel. You could write an entire book about each and every one of the numerous nanomachines needed for successful DNA replication. Indeed, such a book on DNA helicases and related DNA motors was recently published. Continue reading →

In a previous article, I gave a brief overview of the complex molecular mechanisms governing DNA replication. Now, I will focus specifically on the replication enzyme DNA polymerase.

DNA polymerase is the enzyme responsible for synthesizing new strands of DNA, complementary to the sequence of the template strand. The unidirectional DNA polymerase progresses along the template strand in a 3′-5′ direction, since it requires a pre-existing 3′-OH group for the adding of nucleotides. The daughter strand is, consequently, synthesized in a 5′-3′ direction (opposite to the direction of movement of the polymerase since the two strands have an anti-parallel orientation). Continue reading →

Recently I have been reviewing some literature on the elegant molecular mechanisms by which DNA is replicated. As an undergraduate biology student, I recall being struck by their sheer complexity, sophistication, and intrinsic beauty. As I read about such a carefully orchestrated process, involving so many specific enzymes and protein complexes, and its extraordinary accuracy, it was almost as though the word “design” jumped off the pages of my textbook and slapped me in the face. The rate of DNA replication has been measured as a whopping 749 nucleotides per second (McCarthy et al., 1976) and the error rate for accurate polymerases is believed to be in the range of 10^-7 and 10^-8, based on studies of E. coli and bacteriophage DNA replication (Schaaper, 1993).

In this article, I want to provide here a brief overview of the central processes involved in DNA replication.

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