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Monday, December 01, 2008

On the nature of life

A mechanic was removing a cylinder head from the motor of a motorcycle when he spotted a well known heart surgeon in his shop. The surgeon was there waiting for the service manager to come take a look at his bike. The mechanic shouted across the garage,

"Hey Doc, can I ask you a question?"

The surgeon, a bit surprised, walked over to the mechanic working on the motorcycle. The mechanic straightened up, wiped his hands on a rag and asked,

"So, Doc, look at this engine. I open its heart, take valves out, fix 'em, put 'em back in and when I finish, it works just like new. So how come I get such a small salary and you get the really big bucks, when you and I are doing basically the same work?"

The surgeon paused, smiled and leaned over and whispered to the mechanic ...

"Try doing it with the engine running!"

So why can't the patient's system just be shut down the way a machine is turned off? Doctors can indeed place a person's body on bypass, in a technical state of death, but they must in reality keep it alive. Once the cells die, the hope of recovery ends - and that is especially significant for brain cells. So the body cannot really just be shut off, the way a machine can.

From the pseudonymous Mike Gene's The Design Matrix: A Consilience of Clues:
Over time, any design is going to decay. If one wants a design to persist over time, there are only two options: a) continually intervene to deposit replacement designs or, b) design them such that they self-perpetuate. The self-perpetuation of a design is called replication or reproduction. There are good design reasons for using this strategy. Daniel Koshland, a scientist from the University of California, Berkeley, explains the importance of reproduction:

"This is not the only way the living system regenerates. The constant resynthesis of its proteins and body constituents is not quite perfect, so the small loss for each regeneration in the short run becomes a larger loss overall for all the processes in the long run, adding up to what we call aging. So living systems, at least the ones we know, use a clever trick to perfect the regeneration process-that is, they start over.. Starting over can be a cell dividing, in the case of Escherichia coli", or the birth of an infant for Homo sapiens. By beginning a new generation, the infant starts from scratch, and all the chemical ingredients, programs, and other constituents go back to the beginning to correct the inevitable decline of a continuously functioning metabolizing system. (emphasis added) [pp. 23-24]"

Reproduction is the means to forward a design into the future. Yet because of the inevitability of mutation, and its effects, replication over large spans of time will lead to evolution. It would thus seem that a good designer would take this "problem" and turn it into something to be exploited or used. This is just one example to illustrate that Intelligent Design and evolution may complement, rather than contradict each other. Lie itself could have been designed and evolution, by natural selection, would have subsequently followed. What's more, life might even have been designed in such away that Darwinian evolution was recruited to carry out distinct design objectives, meaning that evolution could have been "rigged by design." Or perhaps evolutionary mechanisms themselves may have been designed. How could we ever hope to address such fascinating possibilities?

How could we ever hope to address such fascinating possibilities? Well, we could try looking at the evidence.

Darwinian evolution would likely only work well in a living system or ecology if governed by an underlying mechanism that determines the desired end state (or, possibly, an acceptable range of end states).

For example, one might simulate Darwinian evolution for an airplane design - as long as we have ruled out outcomes like "wildly successful at replicating, but doesn't fly, and spreads massive ecological destruction worldwide, everywhere it goes."* The history of life on Earth suggests that something seems to inhibit such designs.

*And no, eco-nuts, don't write to tell me that humans cause ecological destruction worldwide. Quite the contrary. Humans have greatly increased the diversity of species,subspecies, and varieties worldwide (for good or ill), and are the only species that has ever attempted to prevent other species from extinction.

The only species (?) whose complete destruction we humans ever intentionally engineered was the smallpox virus. And about conserving the others, we are learning. So get a life, econuts!


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Thursday, June 05, 2008

And what's so bad about machines anyway?




Some people were not amused by my review of Christoph, Cardinal Schoenborn's book, Chance or Purpose?

One thing I had found surprising (and didn't make a secret of the fact) was the Cardinal's distaste for the idea that life forms could be compared with machines. He blamed the ID guys for that idea, which will be news to most biochemists.

Meanwhile, some people insist that only deists (people who think there is maybe a sort of God who wound up the world and let it go, but that's all, really) think that the design of life involves machines. Therefore it is a Bad Idea.

In reality - whatever we want to make of it - many elements of our physical life are much more like machines than they are like anything else. I have been reading Mike Gene’s book, The Design Matrix: A Consilience of Clues, which sets that out in detail. I strongly recommend Gene's book. By all means, sell your deluxe edition of Darwin's Origin of Species - with the gold-leafed illustration of “Ye Tree of Life” - and buy this one.

Here, for example, are some of the protein machines inside cells:

Examples: DNA processing machines

Replisome – replicates and repairs DNA (includes sliding clamps and clamp loaders)

Helices – unwinds and separates strands of DNA

Topoisomerase – untangles DNA strands that get knotted

Rad50 and RecA – fix DNA damage

RNA processing machines:

Transcriptosomes – massive complexes that make RNA copies of DNA genes

Splicesome “The function of the spliceosome is to cut the RNA into pieces, remove the sequences that are not part of the instruction for protein synthesis and splice he instruction pieces back together.” (Considered the most complex machine, 140 proteins, five RNA molecules.)

Editosome – “protein machines with more than twenty parts which function carefully select and precisely edit the protein synthesis instructions inherent in the ERNA molecule.”

Degradosomes and exosomes – degrade the RNA molecules when there is a problem with the instructions or when they are no longer needed.

(From pp. 90-91, but otherwise on and on)
Basically, it doesn’t matter what the Cardinal or the Deists or anybody at all think about machines.

Machines.Are.How.Life.Works.

Life is instantiated in machines. Any theory of life needs to just accept that and move on.

Re not liking the idea that our cells contain zillions of little machines: Years ago, an Ontario farmer was approached by someone who was upset by the fact that hens (like all birds) have only one orifice for the ejection of all body wastes, as well as for the laying of eggs.

He suggested that that individual complain to The Manufacturer ... Anti-Machinists may wish to do the same.

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