Thread: stochastic regulatory mechanisms

In another thread, this statement was made:

Originally Posted by spuriousmonkey

Because stochastic regulatory mechanisms for instance, wouldn't be deterministic.

Thu Oct 28, 2010
http://www.thescienceforum.com/viewt...r=asc&start=15

I've not been able to find what that expression means.

My biology book (2008) doesn't have the word "stochastic".

I recently watched a NOVA video "What Darwin Didn't Know" (2009).
There were many new and interesting things explained, but "stochastic" wasn't mentioned.

Could someone provide an explanation?

sto·chas·tic   
[stuh-kas-tik]
–adjective Statistics .
of or pertaining to a process involving a randomly determined sequence of observations each of which is considered as a sample of one element from a probability distribution.

— adj
1. statistics
a. (of a random variable) having a probability distribution, usually with finite variance
b. (of a process) involving a random variable the successive values of which are not independent
c. (of a matrix) square with non-negative elements that add to unity in each row
2. rare involving conjecture

stochastic
1662, "pertaining to conjecture," from Gk. stokhastikos "able to guess, conjecturing," from stokhazesthai "guess," from stokhos "a guess, aim, target, mark," lit. "pointed stick set up for archers to shoot at" (see sting). The sense of "randomly determined" is first recorded 1934, from Ger. Stochastik.

1. Involving or containing a random variable or variables.

2. Involving chance or probability.

Courtesy of [/url]www.dictionary.com

Tridimity

Originally Posted by tridimity

of or pertaining to a process involving a randomly determined sequence of observations each of which is considered as a sample of one element from a probability distribution.

Thanks, that's a great start.

Now where do we see this randomness happening in regulatory mechanisms?

You will have to do a bit better you best if you want to learn more. This isn't textbook or wikipedia stuff.

Read the literature, read between the lines, read some exotic papers, read some key papers. Put it all together.

Using the right key words in google scholar should give your hundreds of interesting papers though.

here is one for instance.

http://www.nature.com/nature/journal...ture08180.html

For me a revelation occurred after reading this:

http://www.ncbi.nlm.nih.gov/pubmed/17196993

J Theor Biol. 2007 Apr 21;245(4):610-26. Epub 2006 Nov 15.
Analytic formulas for discrete stochastic models of cell populations with both differentiation and de-differentiation.

And of course it all started a long time ago, see for instance this classic paper:

http://www.ncbi.nlm.nih.gov/pubmed/14104600

Proc Natl Acad Sci U S A. 1964 Jan;51:29-36.
A STOCHASTIC MODEL OF STEM CELL PROLIFERATION, BASED ON THE GROWTH OF SPLEEN COLONY-FORMING CELLS.
TILL JE, MCCULLOCH EA, SIMINOVITCH L.

that's right. 1964. It's actually a really interesting paper. I used the above two for a journal club once. Half the audience was captivated, the other half aggressive.

Stochastic regulation of cells and genes is often an obscure topic in the eyes of mainstream scientists. Although these mechanisms often can explain the unexplainable.

They are just not deterministic enough to fit the comfort zone of most scientists.

Originally Posted by spuriousmonkey

Read the literature, read between the lines, read some exotic papers, read some key papers. Put it all together.

Thanks for your references; they may be useful to some.
Personally, I'm not in a position to pay for web site articles or purchase the latest books.
I'm not a college grad but I understand most technical stuff when it's explained, especially when there are pictures.

So I was hoping someone could explain "stochastic regulatory mechanisms" in simple terms.

I get the impression that stochastic is the opposite of deterministic.

Originally Posted by spuriousmonkey

Because stochastic regulatory mechanisms for instance, wouldn't be deterministic.

The Wikipedia article seemed to say that "genetic determinism" (phenotype dictated entirely by genotype) is obsolete.
Instead, the phenotype is caused by or determined by "X":
1. strong influence of genes
2. environment
3. epigenetic mechanisms
http://en.wikipedia.org/wiki/Genetic_determinism

Define deterministic:
"of knowable outcome: having an outcome that can be predicted because all of its causes are either known or the same as those of a previous event"
http://encarta.msn.com/dictionary_18...rministic.html

This is where I don't understand.
There are countless regulatory mechanisms in processes such as DNA replication, cell divison, etc.. Don't they exist to accomplish a predictable outcome?

Obviously if an unknown factor such as a mutation occurs, the predicted outcome doesn't happen.
Is mutation considered a stochastic regulatory mechanism?

If not, could you please provide some examples that involve genetics?

Cell death is oftentimes described as being a 'stochastic' process. I.e. if you give a monolayer of cells in a cell culture dish the same apoptotic stimulus at exactly the same time point, they do not all die simultaneously. This fits with the definition of 'stochastic' as an antonym of 'deterministic'. Presumably, this is because not all cells are the same - certainly, there is variation between different cell-types and even between cells of the same cell-type. However, I don't know exactly why there is such great variation in their time of death, as it were.

Originally Posted by tridimity

Cell death is oftentimes described as being a 'stochastic' process. This fits with the definition of
'stochastic' as an antonym of 'deterministic'. Presumably, this is because not all cells are the same.

If all the cells received the same stimulus, I would think some cells would continue living if it's a stochastic process.
But if all the cells die, isn't that a predictable outcome?

What if some of the cells developed a defense mechanism against the apoptotic stimulus?
Like a person with an antidote when stung or bitten by a venomous creature.
Perhaps those cells wouldn't die.

Getting back to genetics, they say that a certain trait or disease is caused by X (gene, genes, whatever).

Originally Posted by spuriousmonkey

these disorders are shown to be caused by a mutation in a certain gene.

Do stochastic regulatory mechanisms intervene so the predicted disorder does not actually occur?
Are certain regulatory mechanisms always stochastic or does something change a "normal" regulatory mechanism?

What's happening?

who knows.

You could easily publish that if you had the answers. In the best journal.