Blog: Dan E. Linstedt

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RNA and RNAi in Nanohousing

There has been renewed interest in RNAi and RNA lately in the biotech world (don't forget, biotech is a part of nanotech - or the other way around). RNA (or ribo-nucleaic acid) apparently has encoding and decoding instructions for gene sequences, RNAi apparently has the ability to block or inhibit specific gene sequences. See an introductory article here.

In this blog we will explore (theoretically anyhow) what this might mean to the nanohouse and DNA computing.

There are some neat pictures (simulated/generated) showing the DNA structure here. If you don't think nanohousing is being worked on, think again. Here's an IEEE link to a conference that occured in 2004.

Ok let's get started..
For quite a while I've blogged and written about convergence of form and function, along with convergence of industries: Bio, chemistry, technology, physics, etc.. Back in an early paper I wrote for B-Eye I predicted that the future technologist would have to have skills well beyond mere "technology" in order to survive (or face the threat of outsourcing). Well, form and function in Bio-tech are a BIG part of what make it work.

In the Nanohouse, we need to learn from this. The future nanohouse won't be JUST a data warehouse, or JUST an ODS, or JUST an OLTP system - no, it will be an "integrated data store" where the molecules collect "data" as history, when it pertains to the context in which it lives - assigned by "key" components of information that only it recognizes. Different parts of the DNA structure will represent different and distinct chemical keys - for storing different types of information.

Well that's all well and good, but we need functionality in the form of RNA and RNAi to act on the DNA strands that we "build". We also need catalyst type events to trigger interaction across the DNA sequences. Here's a quote from a Vienna RNA project that discusses this:

Biomolecules exhibit a close interplay between structure and function. Therefore the growing number of RNA molecules with complex functions, beyond that of encoding proteins, has brought increased demand for RNA structure prediction methods. While prediction of tertiary structure is usually infeasible, the area of RNA secondary structures is an example where computational methods have been highly successful.

Wow! So this means a Nanohouse is definitely feasible?
Yes - but it's still at least 5 to 10 years off before we understand enough to create one. However, the study of RNA and RNAi sequences along with the DNA strands is important, and will help build a foundation of knowledge from which the Nanohouse can be built.

Where does this impact my business today?
Quite frankly it doesn’t yet. How soon it does will depend on the advances in both Biotech and Nanotech sectors. I would speculate that if your top Information Technologists / Scientists and researchers are not yet involved in this field - they should be. The paradigm is already beginning to shift as we see applications of this technology be created in the labs around the world. Like any paradigm shift, this one will take time - and lots of it.

This is interesting, how does modeling take place in this element?
In order to answer this question, we must take a look at not just data visualization, but model visualization. Model visualization consists of putting data models into a 3D landscape, and combining them with hub-spoke like structures that resemble molecular connections (poor mans neural network), see the Data Vault data modeling references on this site.

How does this play with RNA and RNAi?
RNA can help with the interaction of the molecules, while RNAi can specifically block or inhibit interaction. But more than that, the dynamics of this interaction/blocking need to be scored and measured.

The first practical dynamic programming algorithms to predict the optimal secondary structure of an RNA sequence date back over 20 years (1). Since then they have been extended to allow prediction of suboptimal structures (2,3) and thermodynamic ensembles (4), which allow to assign a confidence level or ‘well definedness’ to the predictions (5).

So does this mean the Nanohouse is a "dynamic structure" model?
Interesting, the answer is it depends; dynamic structure in the sense of adding new DNA components, extracting, and connecting the DNA to other molecules, yes; but changing the core-structure underneath - no. RNA itself also has a structure, and the structure is rigid.

Recently, several methods have addressed the problem of predicting a consensus structure for a group of related RNA sequences (6–11). Such conserved structures are of particular interest, since conservation of structure in spite of sequence variation implies that the structure must be functionally important. By enhancing energy rules with sequence covariation these methods also obtain much better prediction accuracies.

In other words, the structure itself of the RNA stays the same - much the same as the structure of a neuron. Even though the memories change, the connections in the brain change, the thought patterns change, the basic structure of the neurons in the brain stay the same.

What does this mean to Nanohousing?
It means that the architecture of our structure must be consistent, repeatable, and redundant - but that the inter-relations, the functions, and the sequences can change (leading to a dynamic set of rules for inter-relationships, but a static structural based foundation from which to scale infinitely).

A stretch of the imagination might be to say:
The equivalent of ‘data mining activities’ has been found within the RNA and RNAi operations.

Can we beg, borrow and steal some of these concepts today?
Yes - we should be utilizing what we learn in these fields and applying it to our current modeling techniques and data warehouses.

* a close interplay between structure and function (the data model MUST be closely related to the functions in business)
* structure must be functionally important
* assign a confidence level or ‘well definedness’ to the relationship (dynamic relationships can be created, weighed, tested, and destroyed depending on viability to associative information)

You can find more on the Data Vault modeling technique (for free) here.

What do you think will happen in your Nanohouse?
Dan L

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