Sunday, July 6, 2008

The acids in the nucleus.

What genes are? – part 1

During the 20th century, biologists started to understand the concept of genes, and the way basic chemicals can produce the diversity and phenomena of life. The big explosion of this knowledge was, when scientists proved that the material that is accountable to store and transfer the hidden data of how to create and maintain a living creatures, is coded in a complex, acidic molecules inside our cells nuclei.

These molecules are long chains of simple sugar molecule called ribose, in which each unit in the chain have a slightly different chemical structure. The ribose chains that were found in the nucleus were called Ribo – Nucleic – Acids (RNA) and Deoxy-ribo Nucleic Acids (DNA).
It the 1950’s, scientists understood the structure of these molecules, and from then to now, we gradually figuring out, how these molecules, store and use biological information.

So what is a gene?
A gene is a very old concept in modern biology that is a virtual unit of information that can be passed on to next generations. Today, we usually call to a unit of information written in the DNA language, which can be translated to one protein – a gene. I will explain that sentence later.

The language of life
It is funny to call to the basic molecules of life “nucleic acids”, since they do not have to be in the nucleus. Any creature on earth have DNA and RNA, from the simplest bacteria (which have no nucleus), to mammals and plants. And although the letters of the language are the same, there is huge different in the way different creatures use the universal language of DNA and RNA to store and retrieve information. In its basics, the DNA has 4 “letters” – four different ribose base molecules that can be combined to produce “words”. Part of the huge DNA molecules contains chains of three letter words that can be copied from the DNA to a RNA molecule and then each 3 letter word is translated with sophisticated machinery to long chains of different of amio-acids that build the small machinery of life. More about that later.

Storing the data
The information of how to build the small chemical machines of life is stored in the DNA, a very stable molecule. The DNA has two parallel chains, and each piece of information is actually backed up by the complementary chain. Advanced organisms usually store a backup of the entire gene repertoire in two different molecules. The information is carefully taking care of, by a big inventory of preserving and repairing machines. The DNA is held in every single cell. The information is passed on from generation to generation by duplicating the entire genetic material and passing half of it to the sibling.
We have to understand that most of the data stored in the DNA is not genes themselves, but a huge information on how to read them and when.

Reading the data
Like mentioned before, the data is read by a dedicated machines that knows how and when to translate the information to small molecular machines. Most of the genome contains information on where genes begin and end, when to read them, and in which organ. A lot of nano-machines (that the information to build them is also stored in genes), are used to read, and translate the data to the life processes.

The code of life
When we look on different organisms we can say that most of the gene repertoire was not dramatically changed from the ancient uni-cellular organisms to big animals. Many of life processes are the same. The change in many cases is in the code surrounded the genes, that dictate how and when to read these genes. For example, the hidden different between us and chimps, is probably not in the pool of genes, which is virtually identical, but in the control of how and when to use them.

Complicating things.
When we first solved the way genes are translated to the machinery of life (that will be explained in later articles), we thought that we can easily control the way genes are used, and if we will understand the genome, we will control the processes of life.
That was the beginning of “genetic engineering”. but soon we found out that things are much more complicated.
First, it turn out that most of the genome is not coding to “real genes”. Later we found that a lot of information is not stored in the DNA code, but in other form of data, like RNA, small molecules, and modification of the DNA. We found that genes can be edited after they were transcribed from the genome.
So today we stand with basic understanding of the information of life, but with many questions that have to be solved before we can really “genetically engineer” life.

So what biotechnology and genetic engineering really is?
Well, we do understand some of the way genes work, and we can use the information to manipulate living creatures to do what we want. How do we do so? – on this in later posts...

Let’s summarized:
1. Life’s data is stored in long molecular chains called DNA.
2. DNA is highly maintained and is the genetic material that passed between generations.
3. Part of the DNA contains the information on how to build the life machinery, and some contain the instructions of how to use this data.
4. The way the data is stored and read is very complex and we do not understand the whole picture yet.

Where to begin? - What genes are series

Where to begin?
When you start to think about scientific topic, it is very hard to know where to begin.
Bio-technology is a very broad subject, and if we where at school, we would start by learning basic biology and chemistry. However, this is not the purpose of this website.
So I think that we will skip the basics in biochemistry, and jump right to the most amazing discovery in the history of science - Our genes.

Biology as information science.
Instead of trying to define what life is and what genes are, and how we can make technology out of it, I'll jump right into the water and write a series, trying to explain why life is all about information, what genes are and how they work. I m sure that all of you already heard that we are build of cells, that we have genes that can be inherited, you might even heard something about DNA, RNA and other strange words like that.

The series will include the following:

1. The acids in the nucleus.
This part will discuss the basic (very basic, I promise) chemistry of data storage in our cells.

2. The assembly lines of biotech
We will see how nature invented the assembly lines and how it is use to make the coded information in our genes, becoming alive.

3. Information and us
We will talk about living creatures as information and how information can do all these staff.

4. Nanotechnology – a very old story
Here we will talk about the only real nanotechnology known today, the way it works, and what the connection to life.

What is biotech any way?

Maybe this question sounds strange to you, but before we can dive into the biotech science and practice, you have to understand what do I mean when I say "biotech".
Bio-technology, is a general term, referring to any kind of technology that uses living organisms or materials from living organisms.

The Wiktionary define biotechnology as:

"1. the use of living organisms (especially microorganisms) in industrial, agricultural, medical and other technological applications 2. the application of the principles and practices of engineering and technology to the life science"

I disagree with that. This definition is not enough. A huge amount of technologies uses bio materials, but does not considered as biotech - for example - riding on horses uses living organisms (horses), but is not considered biotech, so does egg produced by chickens.

So in order to call some technology "biotech" it must hold another quality. For my opinion this quality is science.
What distinguish regular technology that exploit biological processes, and biotechnology? - the understanding. In biotech, we use our advanced understanding of biology to create the technology. Usually this mean understanding the chemical processes behind the biological world.

In more details, bio-tech is usually referring to the following technologies:

1. Medical technology - when we use biological understanding to invent new medical procedures, drags, treatments or devices, it might be called "biotechnology".
2. Agricultural technology - Using our knowledge of plants and animals biology to create more advanced crops , live stocks and agricultural techniques.
3. Research techniques - some times we use bio-technology to invent new kind of research methods that creates new scientific data.
4. Chemical industry - Many useful materials can be produced by using biological principles and reactions. When using advanced biological methods to produce new materials, it is also bio-tech.
5. Food industry - Since all of our foods are essentially biological, a lot of modern food production practices uses bio-tech.
6. Energy industry - In recent years, a lot of efforts are invested in the research of renewable energy resources, and one of the important ways to achieve that is bio-tech.

What is the basic knowledge required for understanding bio-tech?
Biotechnology is eventually about understanding how biological processes work from two main angles: One is the chemical side of the process and the other is the way information is used to shape the machinery of life. Biology is about super advanced information processing and super efficient chemical reactions.
So, in order to understand bio-tech we will talk about these two aspects of biology and how understanding them, can help us engineer new technologies.
This site does not assume any previous knowledge of these subject, and it will explain any piece if science when it will be needed.

To conclude, it is quite hard to define what bio-tech is. but I think I passed on the main idea. hopefully, you'll keep reading the material on this site, and will get to know the subject and it aspects deeply.

D.H.