Biophysics

Mutations are used to explain evolution but also cause cancer. Biologists have discovered conditions for multiple mutations. Can we therefore infer that evolution via mutations is more likely? or that enhanced mutations will cause faster species degradation and extinction?

Biologists describe mechanism promoting multiple DNA mutations

DNA mutations—long known to fuel cancer as well as evolutionary changes in a living organism—had been thought to be rare events that occur randomly throughout the genome.

However, recent studies have shown that cancer development frequently involves the formation of multiple mutations that arise simultaneously and in close proximity to each other. . . .Anna Malkova, associate professor of biology in the UI College of Liberal Arts and Sciences, notes that the DNA repair pathway, known as break-induced replication (BIR), can promote clusters of DNA mutations.

“Previously, we have shown that double-strand DNA breaks, which can result from oxidation, ionizing radiation and replication errors, can be repaired by BIR,” says Malkova.

“During BIR, one broken DNA end is paired with an identical DNA sequence on another chromosome and initiates an unusual type of replication, which proceeds as a migrating bubble and is associated with the accumulation of large amounts of single-strand DNA,” she says.

In the Cell Reports study, researchers subjected yeast cells undergoing BIR to alkylating (cancer cell-killing agents) damage. “We found that the single-stranded DNA regions that accumulate during BIR are susceptible to damage that leads to the formation of mutation clusters,” explains Cynthia Sakofsky, postdoctoral fellow at the UI and one of two co-first authors on the paper. “These clusters are similar to those found in human cancer,” she says.

Importantly, say the researchers, the paper provides a mechanism to potentially explain how genetic changes form in human cancers. Thus, it will be critical for future research to determine whether BIR can form clustered mutations that lead to cancer in humans.

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The answer appears to be yes (at least for electrical and mechanical means, don’t know for sure about chemical and biological means). A physics professor assigned our class term papers of our choosing. Our goal was to learn something new. I chose to explore the effects of electricity and chemistry on nuclear processes. I thought the professor would take my head off for such a radical claim, so I determined to look at mainstream peer-reviewed literature on the topic. We all had to make presentations of our term papers in class, and the professor had a big smile after I gave mine, he said, “that was the topic of the night!” [The Vodka designation in the title indicates speculative ideas Read More ›

‘Quadruple helix’ DNA seen in human cells Balasubramanian’s group has been pursuing a four-stranded version of the molecule (DNA) that scientists have produced in the test tube now for a number of years. It is called the G-quadruplex. The “G” refers to guanine, one of the four chemical groups, or “bases”, that hold DNA together and which encode our genetic information (the others being adenine, cytosine, and thymine). The G-quadruplex seems to form in DNA where guanine exists in substantial quantities. . . . This revealed the four-stranded DNA arose most frequently during the so-called “s-phase” when a cell copies its DNA just prior to dividing. . . . If the G-quadruplex could be implicated in the development of some Read More ›

In order for a biological system to have more biological complexity, it often requires a substantial increase in thermodynamic entropy, not a reduction of it, contrary to many intuitions among creationists and IDists. This essay is part II of a series that began with Part 1 The physicist Fred Hoyle famously said: The chance that higher life forms might have emerged in this way is comparable to the chance that a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein. I agree with that assertion, but that conclusion can’t be formally derived from the 2nd law of thermodynamics (at least those forms of the 2nd law that are stated in many physics and engineering text Read More ›

The common belief is that adding disorder to a designed object will destroy the design (like a tornado passing through a city, to paraphrase Hoyle). Now if increasing entropy implies increasing disorder, creationists will often reason that “increasing entropy of an object will tend to destroy its design”. This essay will argue mathematically that this popular notion among creationists is wrong. The correct conception of these matters is far more nuanced and almost the opposite of (but not quite) what many creationists and IDists believe. Here is the more correct view of entropy’s relation to design (be it man-made or otherwise): 1. increasing entropy can increase the capacity for disorder, but it doesn’t necessitate disorder 2. increasing an object’s capacity Read More ›

In Bejan’s “Design in Nature”, Bejan promotes what he calls the “constructal law,” which states, “For a finite-size system to persist in time (to live), it must evolve in such a way that it provides easier access to the imposed currents that flow through it.” Bejan has denied that this relates at all to any ultimate form of design, but is this claim correct? In our next Engineering and Metaphysics video, Halsmer and Odom look into the constructal law and whether it indicates design, as well as other, new aspects the constructal law might be applicable to. If you are unable to see the video properly, the YouTube link is http://www.youtube.com/watch?v=eda6Mls1RBk

ID proponents and creationists should not use the 2nd Law of Thermodynamics to support ID. Appropriate for Independence Day in the USA is my declaration of independence and disavowal of 2nd Law arguments in support of ID and creation theory. Any student of statistical mechanics and thermodynamics will likely find Granville Sewell’s argument and similar arguments not consistent with textbook understanding of these subjects, and wrong on many levels. With regrets for my dissent to my colleagues (like my colleague Granville Sewell) and friends in the ID and creationist communities, I offer this essay. I do so because to avoid saying anything would be a disservice to the ID and creationist community of which I am a part.

 [Granville Sewell  responds to Sal Cordova here. ]

I’ve said it before, and I’ll say it again, I don’t think Granville Sewell 2nd law arguments are correct. An author of the founding book of ID, Mystery of Life’s Origin, agrees with me:

“Strictly speaking, the earth is an open system, and thus the Second Law of Thermodynamics cannot be used to preclude a naturalistic origin of life.”

Walter Bradley, Thermodynamics and the Origin of Life

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In today’s PhysOrg highlights, we hear about how yeast cells are able to communicate with one another via biochemical means. Using mathematical means to separate “noise” from information pathways. These beasts have “broadband”! “The mathematics provides variance decomposition techniques for dynamic systems,” said Dr Bowsher. “We were able to make rigorous connections between the concept of intrinsic noise in systems biology, the notion of information capacity used in communications engineering, and a correlation ratio introduced in the 1950s by Alfréd Rényi. We constructed a generalised signal-to-noise measure from the variance components to quantify the efficacy of information flow through a biochemical network.” Here’s a quote: The paper, which describes the application of this approach to yeast cells, shows that the Read More ›