Genetics

Transcription Factors 

Impact Individualism

A recent study done by researchers at Stanford University indicates a clear connection between how individual genes are expressed and the noncoding region of the genome, what used to be called Junk DNA. This isn't a big surprise considering that just 23,000 genes could not possibly represent all the complexity and variation in a human being, but this was the accepted thinking up until recently. This research goes a long way in confirming what many already suspected, the noncoding area of our genome represents a critical and controlling aspect of our development in the way it impacts expression.

IBM is a DRIVING FORCE of

PARADIGM SHIFTs in LIFE SCIENCES

Everybody knows that IBM is a huge, multi-national corporation that has revenue larger than some country's entire GDP. For those of us that are old enough, we can remember when IBM was schooled by Bill Gates and Microsoft, many wondered if IBM would ever recover. Well, not only have they recovered but are probably stronger than ever! This is company that is and has always been on the leading edge of science and not just computer technology but everything from cosmology to biology. This post attempts to outline what IBM is doing in the area of bioinformatics and computational biology.

DATABASES, WEB SERVICES AND TOOLS AVAILABLE

FOR BIOINFORMATICS

The diagram on the right represents R. palustries protein-protein interaction network that was discovered using a combination of mass spectometry and proprietary data analysis techniques, this represents just one of the many tools available to the bioinformatician. 

Database, Web Services and Tools

The focus of this post is exclusively related to bioinformatics information technology and more specifically database access and the use of web services and tools. I've posted a couple of articles recently that are related to this subject, they are located here, here and a more general article here. The fact of the matter is that both content and services are growing at a substantial pace when it comes to the life sciences, so much so that it is almost impossible to keep up.

DNA SEQUENCING

FASTER and CHEAPER

Making some real progress on an affordable method of DNA sequencing that ultimately everyone will benefit from. This technology is one of the places where the bridge between nanotechnology and genetics has been built and is structurally sound. In fact, nanotechnology is making as big an impact on the life sciences as the microscope did over 300 years ago.

The article (link below) discusses the recent work of some Arizona State University scientists that have created a method for faster, cheaper DNA sequencing. The goal is the infamous $1000 genome which we are rapidly approaching. Currently, there are only about 20 individuals that have had their genome sequenced.

The ultimate intention is to make sequencing part of a routine medical check-up, this seems to be a realistic goal for the not very distant future. This work is sponsored by the National Institutes of Health (NIH) from stimulus funds received for a National Human Genome Research Initiative. The money looks to be well spent, especially at ASU (what a fantastic school!).

This is actually quite amazing, the approach being used in analogous to threading a needle where the DNA is the thread and the scanner is the eye of the needle, reading each letter of DNA as it passes by. Previously the team had to use four separate eyes to read each of the letters (A, G, C, T), but now they are using carbon nanotubes, this technique has led to a single eye that can read all four letters.

GENETIC VARIANTS LINKED TO AGING

I thought this was old news but apparently not, seems that a recent discovery has linked genetic variants to biological aging. In a study just published in Nature, researchers from Kings College and University of Leicester released a new discovery that has implications in understanding cancer and other age related diseases - even death.

Our bodies age in two different ways, one is chronological and the other is biological. We are all familier with chronological age as defined by the number of birthdays someone has had. The biological age is a little different since it is more a measurement of cellular age than the age of the organism. That may seem a little confusing, let me explain.

On each chromosome there are structures called telomeres, all individuals have a certain amount (length) of telomeres they are born with. Some cell types, as they divide throughout the life of the organism, reduce the amount of telomerese length with each division. Comparing the length of telomeres in cells where this shortening doesn't occur to those where it does gives an indication of the biological age of the cells.

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Descriptive Model for Recursive Information Transfer

Simple Model for Recursive Information Transfer

OVERVIEW

This idea was submitted by Andras Pellionisz back in December of 2007 and the paper appeared June, 2008, available in full, for free here . The primary purpose of this paper is two fold:

1. Reversing two previous axioms in biology,
2. Introduces the idea of multidirectional recursion between DNA, RNA and Proteins.

Pellionisz refers to the two axioms as long standing dogmas in biology, originally put forth by Francis Crick in 1956 (his hand-drawn figure from 1956 is reproduced in the paper) and until very recently have been held onto by the establishment. Holding onto a paradigm is a common practice within institutions whether they are scientific, government or corporate based.

A primary argument of this principle is the fact that genomic research is as much a function of information technology as it is traditional biology, I agree. Once the genome was sequenced biology moved from the analog to the world of digital information, this is a good thing as it will allow biological systems to be understand at a much, much more rapid pace.

Pellionisz defines the history of this research in the following sequence:

Biocosm: A New Scientific Theory of Evolution: Intelligent Life is the Architect of the Universe

by Seth Shostak, James N Gardner

 (11 Amazon customer reviews)

Comment: "Fantastic book, well written and insightful"

Seth Shostak does the introduction to the book, obviously he has a high opinion of the author, the book and the theory. I think the world of Seth, he is a great guy and a testament to diligence. This was enough to get me to read the book, I hadn't heard of Gardner before this book.

Here is an excerpt from the website that was created in support of the book.

See the post below,  it shows a couple of very interesting correlations between mass and things like longevity, metabolic efficiency and energy used to pursue reproduction and existence. The biggest surpirse to me is the fact that someone came up with this correlation not just for single organisms but for entire colonies.

The research used bees, ants and termites as the colonies to study. In these studies they combined the mass of the entire colony to make the correlations, there not exactly the same but very, very close to those of a single organism. The research went further and used the queen as the sex organ and the rest of the colony as the body, turns out colonies spend as much time worrying about sex as individual organisms. This is interesting considering that colonies don't have to compete for sex, those details are worked out by the individuals function within the colony. You are either born to have sex or not!

It is a short read but somewhat significant in terms of the findings, identifying mathematical models that can emulate living organisms and systems will almost certainly create a better understanding through better and more complete computer simulations. Basically, no math no modeling.

Here is a link to a 12 part series about the miracles of water. David Sereda and George Noory talk it up for over an hour, Sereda rambles on about the amazing qualities and properties of water.

I've included links at the bottom to oher similar posts here, there is also a link to the video "Water, the Great Mystery" which came out earlier this year and Sereda (I believe) is a producer. Both of these represent some ridiculous claims, even though I clearly believe in the powers of water I do not believe much of the conjecture in the video and audio discussions.

There are some things I heard for the first time in the audio stream, for example I hadn't realized there were claims of water acting under the quantum phenomina of entanglement, but according to Sereda this is the case. There are lots of references to structure, for example in the context of holy water, but the reality is that the structure of water on any scale larger than nano cannot be determined.  So what they present as fact is of course conjecture and speculation.

These types of videos, in the end, are upsetting to me since they are clearly leaning on God and religion as the ultimate explanation for these anomolous properties that water has. They even go further by suggesting that structured water has cured people in days of deadly chronic diseases. It seems that any good thinking (Martin Chaplin for example) is or will be drowned out by these ridiculous statements and claimse

All that said, these are worth listening and watching because they do contain some truths and unfortunately there are not that many resources focused on the study of water (amazing isn't it?). Enjoy.