IEEE spectrum Oct 2008 p 18:
article: Unsticking MEMS

says they get stuck because of the casimir effect; when they get too close together, reduces number of photons that can form between parts to the length of the wavelength of the distance between those parts; so, many more photons pressing on the outsides force the parts together, making a form of friction called: stiction;

so, are there no photons in e-coli?

if there are, why don’t they get stuck when they are 1 to 2 orders of magnitude smaller?

they plan to fix the problem by coating surfaces with metamaterials, which are “specifically designed to have properties that *do not occur naturally*, such as bending light the wrong way. Did e-coli also solve the problem by evolving “naturally” non-natural properties?

Thoughts?

“In engineered systems various possible contingencies are anticipated and processes are put in place to deal with them if and when any particular contingency actually arises in the future.

These forward looking predetermined responses are “front loaded” – put in place before they are actually needed.”

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I think this is reasonable…but what is also reasonable is that creatures were created with intelligence…the were created with minds…they were created with the ability to perceive environments, learn from them, and make the appropriate biological changes in response. Consciousness is basically just being aware of one’s surroundings. So it only makes since that consciousness (since all living organisms surely have it in one degree or another) play a role in biological change. The genome, then, isn’t the main player in biological change — the mind is. The genome is just a follower, an effect of a deeper cause. That’s my 2 cents anyway.

Yes, I am talking about post #13. Thank you. There are still a few missing, but I think it is because of my bad editing. All the links are in this post (2x:)).

My links disappeared

Are you talking about comment #13, which should now be viewable? First time posters are held in moderation as well as comments with 10+ links.

These forward looking predetermined responses are “front loaded” – put in place before they are actually needed.

Chance & necessity is a reactive process that cannot plan ahead. Intelligent design is a proactive process that can plan ahead.

I suspect a good example of this is Desulforudis Audaxviator, a bacteria recently discovered living without oxygen, in temperatures around 60°C but able to survive as long as it has a small amount of water flowing through radioactive rocks. The discovers believe it could survive on mars!

How does an organism develop the ability to utilise radioactivity without dying out first? At 60°C? With no oxygen?

As many DNA sequences are available to the public I think that, when software and computing power are up to it, many front loaded sequences will come to light from home users, not scientists, because they are looking for them. Seek and you shall find.

For example the Mnx gene. What does it do:
It is involved in the development of the pancreas and motor neurons.
1) Zebrafish mnx genes in endocrine and exocrine pancreas formation.
2) The Mnx homeobox gene class defined by HB9, MNR2 and amphioxus AmphiMnx.

The HB9 homeobox gene has been cloned from several vertebrates and is implicated in motor neuron differentiation. In the chick, a related gene, MNR2, acts upstream of HB9 in this process. Here we report an amphioxus homologue of these genes and show that it diverged before the gene duplication yielding HB9 and MNR2. AmphiMnx RNA is detected in two irregular punctate stripes along the developing neural tube, comparable to the distribution of ‘dorsal compartment’ motor neurons, and also in dorsal endoderm and posterior mesoderm. We propose a new homeobox class, Mnx, to include AmphiMnx, HB9, MNR2 and their Drosophila and echinoderm orthologues; we suggest that vertebrate HB9 is renamed Mnx1 and MNR2 be renamed Mnx2.

And here is some interesting research:
<a Directed Evolution of Motor Neurons from Genetically Engineered Neural Precursors.

Stem cell-based therapies hold therapeutic promise for degenerative motor neuron diseases such as amyotrophic lateral sclerosis and for spinal cord injury. Fetal neural progenitors present less risk of tumor formation than embryonic stem (ES) cells but inefficiently differentiate into motor neurons, in line with their low expression of motor neuron-specific transcription factors and poor response to soluble external factors. To overcome this limitation, we genetically engineered fetal rat spinal cord neurospheres to express the transcription factors HB9, Nkx6.1 and Ngn2. Enforced expression of the three factors rendered neural precursors responsive to sonic hedgehog and retinoic acid and directed their differentiation into cholinergic motor neurons that projected axons and formed contacts with co-cultured myotubes. When transplanted in the injured adult rat spinal cord, a model of acute motor neuron degeneration, the engineered precursors transiently proliferated, colonized the ventral horn, expressed motor neuron-specific differentiation markers and projected cholinergic axons in the ventral root. We conclude that genetic engineering can drive the differentiation of fetal neural precursors into motor neurons which efficiently engraft in the spinal cord. The strategy thus holds promise for cell replacement in motor neuron and related diseases.

What did these guys do? They enforced the expression of 3 genes associated with neuronal development in order to direct the development of motor neurons. Sonic hedgehog also played a role.
So four genes played a role:
1. HB9
2. Nkx6.1
3. Ngn2
4. Sonic hedgehog

Are similar genes present in the Trichoplax genome?
1. HB9 (mnx)
Yes (see above).

2. Nkx6.1
Here is the <a human Nk6 gene.
And here is <athe Trichoplax version.

3. Ngn2
Here is the <ahuman neurogenin 2 (ngn2) gene.
And here <ais the Trichoplax version.
A quick <aBLAST (blastp) the human genome shows this sequence to be closely related to ngn2 (E-value = 3^-8).

4. Sonic hedgehog (shh)
Here is the human shh gene.
This gene seems to absent in from the Trichoplax genome, however, the <apresence of shh in Monosiga brevicollis (unicellular eukaryote that diverged before Trichoplax) suggest the possibility of gene loss in this lineage.

Wonder what will happen if shh is co-expressed and together with mnx, Nk6 and ngn2 in Trichoplax, or whether these genes will function like their counterparts in higher animals.

A complex array of neurologically associated developmental pathways present in this eumetazoan that has no nerves, sensory cells and muscle cells, and there is more…

Is there any simple example you could give of front-loading in a biological organism or something?

Search for “nylonase”. Make sure you understand what a frameshift is – that’ll enable you to understand how unlikely the non-frontloaded story is.

However, as we are seeing more and more with discovery’s like the importance of epigenetics in the development of organisms there are many layers yet to be peeled back.

For example, if a organisms DNA sequence contains X bytes it could be said that only X-Y bytes could be frontloads, where Y is the number of bytes needed to build the organism in question. So X-Y is the maximal amount of potential front loaded information and so if we can measure the speed at which the frontloaded information is enabled we can estimate that duration. From what I’ve read (assuming Lenski’s results were trustworthy at any level) the rate appears to be very slow.

Of course, it won’t be for a long time that such a determination could be made, if ever. And when it is my response will simply be “there’s another layer you’ve not looked at”. It might be the gluons and quarks making up the atoms that contain the information required, we simply don’t know sufficent information at the momement to rule anything out which is why it’s so fustrating to see science on the path it currently is. OK, I doubt it’ll be a the level of individual quarks, but you get my meaning.

Sure, progress is being made but how much faster could that progress be made if we take the prior commitment to “no intelligence required” away?