Metaphors and “Metaphors”

Over at the THE EVOLUTION LIST, Allen MacNeill comments on a couple of excerpts from Chapter 3 of The Design Matrix. Allen writes:

The fundamental question in this ongoing debate is, how do we know an analogy really exists? For example, do we have any objective way to determine if one rock is analogous with another?

And

So, is there a way to verify if an analogy or metaphor is “real”?

And

In the brief example from Mike Gene’s The Design Matriz posted at the head of this thread, the implication is that the analogies we perceive between biological systems and those engineered by humans are “natural analogies”; that is, they are real analogies, and not simply a form of linguistic convenience. However, there is nothing about the finding of an analogy that necessarily verifies that the analogy is “natural” (i.e. “real”), as opposed to “semantic” (i.e. “imaginary”). This would be the case even if one found repeated analogies between complex systems engineered by humans and biological systems that evolved by natural selection. To verify that an analogy is “natural” requires an independent source of validation for the assertion that the analogy is “real” and not merely “semantic”. At this stage in my reasoning about this subject I am not at all sure how one would go about this.

Good points. Good questions. Let’s have a look.

EMail

For anyone interested, I changed my e-mail account.  
You can access the new one by clicking on the link at the bottom of this page.
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More text bunnahs!

A Rejected Book Cover

Localizing Function

More evidence that shows the importance of location for cellular function:

Like doctors making house calls, some DNA repair enzymes can relocate to the part of the cell that needs their help, a collaborative team of scientists at Emory University School of Medicine has found.

[…..]

One DNA repair enzyme they studied, Ntg1, moves to the nucleus or the mitochondria depending on where DNA damage is concentrated, the authors found. In contrast, a related enzyme, Ntg2, stays in the nucleus under all conditions.

Cells appear to direct Ntg1′s relocation by briefly attaching a small protein called SUMO to what needs to be moved around, the authors found. SUMO is found in fungi, plants and animals and is already being investigated by several research groups as a possible target for anti-cancer drugs.

- DNA repair mechanisms relocate in response to stress

Ah, yes. SUMO.

DM Outline IV

My continuing effort to organize blog entries into an outline so readers can better connect the dots (a consilience of clues).

A. Detecting Design

1. Science and Design

a. Outline the common definitions of ‘subjective’ and ‘objective.’

b. Identify problems with common definitions and propose George Cooper’s definition of objective - that which can be measured by all parties who should obtain the same result given an appropriate range of accuracy.

c. Draw upon the wisdom of one the great biologists, Jacques Monod, to explain why science cannot determine whether or not life was designed.

d. Demonstrate how archeology and forensics fail to give us reason to think that science can determine whether or not life was designed.

e. Explain how most proponents and critics of design are likely to think alike on one issue – they will find it uncomfortable to acknowledge that science cannot determine whether or not life was designed.

Conceptual Links Between Respiration and Photosynthesis

Let’s consider some conceptual links between the processes of aerobic respiration and photosynthesis.

Evolution of Bacterial Flagellum

I posted this on the original book blog back in the summer of 2008. Since then, the book blog was hacked and lost. So let me repost it again. A current update is appended at the end.

For the past several years, I have been focused on how one might facilitate the evolution of metazoa. But because of recent scientific discoveries, I should pause and comment on an old topic – the bacterial flagellum.

World’s largest snake?

If you look closely, I think you’ll see it’s a fake:

Electron transport: Front-loading and More

We’ve seen that the cytochrome oxidase, otherwise known as haem-copper oxygen reductase, plays the key role in aerobic respiration. There are actually three different versions of these protein complexes, known as type A, B, and C. The type A version is the one that is found in our mitochondria.

Researchers from France recently took a close look at these oxidases, surveying 673 complete genomes from both the archaeal and bacterial domains (Brochier-Armanet C, Talla E, Gribaldo S. 2009. The multiple evolutionary histories of dioxygen reductases: Implications for the origin and evolution of aerobic respiration. Mol Biol Evol. 26:285-97). They retrieved 1,640 examples, which indicates that many prokaryotes carry multiple versions of these oxidases.

Through careful genomic analyses, the researchers were able to track the evolutionary history of these three types of oxidases.

They found that type B oxidases likely originated among the archaebacteria and some copies have been laterally transferred to bacteria. Type C oxidases likely originated among the proteobacteria and transferred to other types of bacteria. But what about the type A oxidases, the type that are found in eukaryotic mitochondria (which are themselves the product of an earlier endosymbiosis)?

Commando Bunnahs

I’ve been super busy lately and hope to get back to the carrots this weekend (but no promises). In the meantime, you can sit back and enjoy my role in an upcoming movie.