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Life - A distinctive characteristic of a living organism from dead organism or non-living thing, as specifically distinguished by the capacity to grow, metabolize, respond (to stimuli), adapt, and reproduce.
a self-replicating bacterium invented by Venter and his team that contains just 437 genes, a "genome smaller than that of any autonomously replicating cell found in nature"
Wouldn't at one point I guess this whole bio computer, figure out how to create life?
originally posted by: soficrow
a reply to: Protector
Nice post. Thanks. But...
You forgot to consider prions.
...the computer ...would just be running a program to select for our particular form of life.
A dangerous assumption.
Currently, the cost and time required for this process is somewhat prohibitive for consumer applications. It cost $7,000 to synthesize the DNA Erlich developed and another $2,000 to read it. The synthesis process took two weeks and the sequencing took about a day.
I have extremely limited knowledge of prions. I haven't run across them, yet, in bioinformatics. I don't really see where they'd be great in molecular computing. There are many other ways to manipulate molecules where you don't have to simultaneously worry about infection. Let's face it... almost no one wants to work in a biohazard environment.
Synthetic Biology Market worth $5,630.4 Million by 2018
Cell-free protein synthesis (also called in-vitro protein synthesis or abbreviated CFPS), is the production of protein using biological machinery without the use of living cells.
The three major end-users of CFPS systems are the pharmaceutical & biotechnological industry, contract research institutes, and academic & research institutes, of which pharmaceutical companies are dominant, followed by contract research institutes.
The living supercomputer
...HOW IS THE 'LIVING COMPUTER' MORE EFFICIENT?
* The agents (proteins) are available in large numbers at negligible cost.
* They are self-propelled and thus do not require a global, external driving force;
* Proteins operate independently of each other to ensure parallel exploration and have small dimensions to enable use in high-density networks with high computing power per unit area.
2012. The lure of molecular computing: While marketable products seem decades away, researchers are crystallizing theories and devices that will give biological organisms the power to compute
Pico-world dragnets: Computer-designed proteins recognize and bind small molecules
Computer-designed proteins that can recognize and interact with small biological molecules are now a reality. ...
“This is major step toward building proteins for use as biosensors or molecular sponges, or in synthetic biology — giving organisms new tools to perform a task,” said one of the lead researchers, Christine E. Tinberg, a postdoctoral fellow in biochemistry at the UW.
Protein Structure, Modelling and Applications
1. Why Is It Important to Study Proteins?
In the drama of life on a molecular scale, proteins are where the action is (1).
Proteins are molecular devices, in the nanometer scale, where biological function is exerted (1). They are the building blocks of all cells in our bodies and in all living creatures of all kingdoms. Although the information necessary for life to go on is encoded by the DNA molecule, the dynamic process of life maintenance, replication, defense and reproduction are carried out by proteins.
...[If... then...] the target protein 3D structure can be modeled based on one or on a combination of several template molecules (26). This is possible because homolog proteins descend from a common ancestor and are likely to present the same structure and function. Caution note: This is correct in general, but there are exceptions though. [sic]
...You can't really compare protein research, or even most synthetic biology research, with Prions.
In short, I wouldn't bet that Prions are a major part of upcoming molecular computing, nor protein research. It's more like a fringe technology sitting in the corner of a much larger and more well funded marketplace. But that's mostly speculation.
DNA samples stored at 4°C and RT showed varying degrees of evaporation but DNA was stable for up to 12 months at 4°C. Samples stored at room temperature totally evaporated by 6 months (Figure 2). At RT, DNA degradation was seen at 9 months. DNA stored in dry state at room temperature showed degradation at 3 months of storage (Figure 4).
Proteins do have a lot of weak spots. They can be transcribed or translated incorrectly. They can be denatured in a variety of ways. They can fold incorrectly. They can be deactivated depending on their receptors and the environment they are exposed to.
...prion polypeptides are intrinsically predisposed to non-physiological folding conformations that would account for their environmental durability
It is a commonplace observation that the prion forms of proteins are stable...
There are ...numerous other synthetic prions, consisting of sequences derived from those of prion-forming proteins modified by deletion, mutagenesis or by fusion with heterologous natural or artificial sequences for functional modification or as reporters.
But that relates to why they can do almost anything. They're amazingly flexible.
If I come across anything Prion related in the near future, I can revisit this thread.
originally posted by: Protector
a reply to: soficrow
I still think you're over-applying prion formation out of proteins. Proteins do not commonly denature into prions. Specific proteins found in the brain seem to convert into prions at an advanced age.
And I still think DNA is incredibly stable. I mean, it lasts for months and it's only a handful of atoms across. Sure, diamond's carbon structure has it beat, but I'm still impressed by DNA.
DNA Dethroned - Inheritance is Protein-Based.
...prions -and the traits they confer- can be inherited;
in humans, some are conserved over hundreds of millions of years.
Prion-like Protein Discovered in Bacteria
[…the emergence of prions predates the evolutionary split between eukaryotes and bacteria - and DNA]
DNA lasts for months. Not at all useful for building bio-computers, methinks. Prions, on the other hand, have been conserved over hundreds of millions of years.
When the team examined the human cognates (i.e. blood relatives) of the prion-proteins, the intrinsically disordered domains were conserved over hundreds of millions of years.
A team of Whitehead Institute and Stanford University scientists are redefining what it means to be a prion--a type of protein that can pass heritable traits from cell to cell by its structure instead of by DNA.
This property suggested a basis for inheritance of the altered protein. In a normal yeast life cycle the Sup35p stays soluble. However, in a [PSI+] strain the prion form aggregates. Lindquist describes this as a "renegade protein whose misfolding creates a surface that other proteins of the same type will add on to." The altered proteins can also be transferred from a mother to a daughter cell. Lindquist's group tied the in vivo process to the in vitro process by using mutations that affected the inheritance of the prions and also affected the protein's ability to form amyloids in vitro.
Though researchers have a simple biochemical model for prion formation, they still don't know the underlying mechanism of prion inheritance. The protein forms amyloid rich in b structures, and new proteins join on to it, but the driving force behind the molecular changes is a mystery.
"Protein-based genetic elements allow cells to have two different heritable phenotypic (physical) states with the same genome," comments Linquist. For example, it is biologically advantageous for cells to have [PSI] (the prion form) under some circumstances. A large yeast colony is likely to have one of these altered proteins ready to exploit a change in environment. On the other hand, if the environment doesn't change, the cell can drop out of the colony. "It is an ancient mechanism of inheritance, but a newly appreciated one," she adds.
originally posted by: Protector
a reply to: soficrow
...human DNA (and human ancestor DNA) has conserved the genetic encoding for proteins that become prions.
I assume (correct me if I'm wrong) that you believe the prions are being physically passed down because of this statement:
That's in relation to the epigenetic variations between cells. Prions aren't inherited separately from DNA. I don't know if you assumed they were or not.
Anyway, prions are not more resilient than DNA. They are created from DNA.
Epigenetic inheritance is an unconventional finding. It goes against the idea that inheritance happens only through the DNA code that passes from parent to offspring. It means that a parent's experiences, in the form of epigenetic tags, can be passed down to future generations.
As unconventional as it may be, there is little doubt that epigenetic inheritance is real.
In the early 2000's I ran across an interesting piece on some research going on across MULTIPLE universities including searchable databases with academic papers freely available.
Myself and 3 other people archived big chunks of data and the original article, including burning backups to Cd-rom.
The article: gone not even on way back
The papers: Same
The university websites: Same
OK so that's enough to make someone a bit shaky.
It gets worse!