PDA

View Full Version : Critique my article please?


sidney
July 20th, 2006, 12:20 AM
I've been asked to contribute a 300 word plus a picture article on my research for a departmental newsletter aimed at 15-18 year olds. I struggled to get it down below 1000 words, but I now have a 318 word draft. (They said they'll forgive the extra 18 words). But I don't know if it is even understandable now. I think that's small enough to just post here. Critiques, please? Thanks ....


Computer Simulation Models of Prebiotic Evolution of the Genetic Code

Sidney Markowitz

How did the Genetic Code emerge from whatever existed before there was life? My twelve-page PhD thesis proposal at http://www.cs.auckland.ac.nz/~sidney/sidneyphd.html describes how I will pursue the answers. Here, I'll explain what the question means, talking about proteins, genes, DNA/RNA, and the genetic code that ties them together.

The primary structural materials for living things are the many varieties of protein. A protein is a strand of hundreds of "beads", each one of 20 varieties of amino acids. The different chemical properties of the amino acids cause the strand to fold and twist resulting in an enormous variety of structures being possible.

Proteins are made by molecular factories following "blueprints" from genes, made of DNA or RNA which are strands of nucleotides. There are four types of nucleotides used in a gene. Think of amino acids as an alphabet of 20 letters used to "spell" proteins. The gene is like a code. Each three-nucleotide sequence, called a codon, represents one amino acid.

The "code book" for the genetic code is a group of proteins called the aminoacyl tRNA synthetases (AARS).

With rare exceptions, all life uses the same genetic code. This standard Genetic Code must have been established as life began.

The Genetic Code is implemented by AARSs, proteins built using genes that specify them using the Genetic Code. How could this circular system arise before it existed?

I am developing computer simulations that model simple systems in which there are RNA genes and proteins, but no fixed genetic code. If in the simulations a genetic code can evolve and come to dominate, it may provide some understanding into how the same thing could have happened in the world before there was life.

See http://en.wikipedia.org/wiki/Genetic_code for a more detailed introduction to the genetic code.

At http://www.dnaftb.org/dnaftb/ is a great high school level tutorial on Genetics.

davidh
July 20th, 2006, 02:41 AM
Usually when I read a news article, I don't expect to have to spend much effort in thinking about the logical or causal relationships between the thoughts expressed in it. And since the intended audience seems to be high school age students, I think they also mignt not be expected to put a lot of effort into analyzing the story.

So, in particular, it might be helpful to make the circularity of the question more explicit. For example, "the AARS are special kinds of proteins that guide the chemical linking of amino acids into chains, chains of amino acids exactly determined according to the sequences of nucleotide codons existing in the corresponding RNA chains, with the resulting sequences of amino acids then determining the structure and chemistry of ALL the proteins in each living creature, including the AARS proteins themselves. In a nutshell, you need proteins to make proteins."

I don't like that run-on sentence either. Maybe writing an abstract as as hard as being a diplomat or politician. Trying to convey precise meaning but still remain vague enough so as not to have to include overwhelming (or in the case of politics, too revealing) detail.

DH

davidh
July 20th, 2006, 02:55 AM
Just happened to think that it would really be interesting if one could discover the existence of "tipping points" during the process of doing simulation studies. That is, just as the "intelligent design" speculators come up with the idea of "irreducible complexity", one can just as well make a counter proposal of "transient tipping points" which may or may not be well preserved either in the fossil record or in commonly observed biochemical reactions of today. IOW, "irreducible complexity" is a euphemism for "I don't know" which is a sentence that is supposed to be always at the tip of the tongue both for honest scientists and honest people of faith

;)

DH

Peter Creasey
July 20th, 2006, 03:49 PM
a picture article on my research for a departmental newsletter aimed at 15-18 year olds. ... But I don't know if it is even understandable now. I think that's small enough to just post here. Critiques, please? Thanks ....

David, I am FAR removed from being 15 - 18 years old. I found myself constantly retracing as I tried to understand the gist of what you were describing. I believe 15 - 18 years old will lack the patience to expend even the minimal effort that I did.

I recommend that you somehow simplify your article with less esoteric structure and terminology.

Your PHD work sounds most impressive. Congratulations!

P.S. You might consider coming up with a tantalizing hook designed to stimulate further interest in your work!

sidney
July 20th, 2006, 10:53 PM
I recommend that you somehow simplify your article with less esoteric structure and terminology

What I get from both you and David is that it should be even simpler. With the 300 word limit, I can't use any more words to explain the same ideas more clearly. That implies dropping some of the content to make room for a more clear explanation of the rest. I'll consider that.

-- sidney

Jeff
July 21st, 2006, 12:52 PM
"Everything should be as simple as possible. But no simpler." - A. Einstein

sidney
July 21st, 2006, 03:38 PM
"Everything should be as simple as possible. But no simpler." - A. Einstein

That from the person who wrote an incomprehensible book on relativity for the layperson by testing it on his daughter who was too timid to admit to him that she could not understand any of it :)

-- sidney

Judy G. Russell
July 21st, 2006, 03:55 PM
Sidney, I have to agree with the others that it needs to be simplified. You might start thinking of starting out with something like this: "With very few exceptions, all life uses the same genetic code: the same combinations of genetic building blocks. What we don't know is how that genetic code came to be. My research is designed to use computer simulation to take some of the essential ingredients that the genetic code uses, put them into an environment without the genetic code, and see if the results help tell us how the genetic code developed."

davidh
July 21st, 2006, 05:49 PM
I remember about 45-50 years ago seeing articles in Scientific American about automata and self-replicating machines, or some such things, I think. I really don't know anything about that field, but I wonder if that theme might be a good angle to come at it from when writing an abstract for high-school age young people? Being "into" computers and sci-fi, it's probably something they could relate to.

DH

Lindsey
July 21st, 2006, 11:15 PM
What I get from both you and David is that it should be even simpler. With the 300 word limit, I can't use any more words to explain the same ideas more clearly. That implies dropping some of the content to make room for a more clear explanation of the rest. I'll consider that.
Yes, I think you can probably condense some of what is in paragraphs 2 and 3 by omitting some of the detail, and just making the point that genes provide the blueprints for assembling amino acids, and for assembling blocks of amino acids into proteins.

And I had some trouble parsing this key paragraph:

The Genetic Code is implemented by AARSs, proteins built using genes that specify them using the Genetic Code. How could this circular system arise before it existed?

It took me some puzzling to figure out that you were (I think) saying something along the line of: "So the code book (AARS) is made up of proteins, which are assembled using genes, which use the language of the Genetic Code, which requires AARS to decipher... Which came first, the Genetic Code or the proteins?"

Really, really interesting, Sidney!

--Lindsey

ndebord
July 21st, 2006, 11:15 PM
I've been asked to contribute a 300 word plus a picture article on my research for a departmental newsletter aimed at 15-18 year olds. I struggled to get it down below 1000 words, but I now have a 318 word draft. (They said they'll forgive the extra 18 words). But I don't know if it is even understandable now. I think that's small enough to just post here. Critiques, please? Thanks ....


Computer Simulation Models of Prebiotic Evolution of the Genetic Code

Sidney Markowitz

How did the Genetic Code emerge from whatever existed before there was life? My twelve-page PhD thesis proposal at http://www.cs.auckland.ac.nz/~sidney/sidneyphd.html describes how I will pursue the answers. Here, I'll explain what the question means, talking about proteins, genes, DNA/RNA, and the genetic code that ties them together.

The primary structural materials for living things are the many varieties of protein. A protein is a strand of hundreds of "beads", each one of 20 varieties of amino acids. The different chemical properties of the amino acids cause the strand to fold and twist resulting in an enormous variety of structures being possible.

Proteins are made by molecular factories following "blueprints" from genes, made of DNA or RNA which are strands of nucleotides. There are four types of nucleotides used in a gene. Think of amino acids as an alphabet of 20 letters used to "spell" proteins. The gene is like a code. Each three-nucleotide sequence, called a codon, represents one amino acid.

The "code book" for the genetic code is a group of proteins called the aminoacyl tRNA synthetases (AARS).

With rare exceptions, all life uses the same genetic code. This standard Genetic Code must have been established as life began.

The Genetic Code is implemented by AARSs, proteins built using genes that specify them using the Genetic Code. How could this circular system arise before it existed?

I am developing computer simulations that model simple systems in which there are RNA genes and proteins, but no fixed genetic code. If in the simulations a genetic code can evolve and come to dominate, it may provide some understanding into how the same thing could have happened in the world before there was life.

See http://en.wikipedia.org/wiki/Genetic_code for a more detailed introduction to the genetic code.

At http://www.dnaftb.org/dnaftb/ is a great high school level tutorial on Genetics.


==========================


Sidney,

I'll take a stab at this. Caveat. The hour is late and I'm running around more than a little right now. Anyhow, I have some experience as a rewrite man. These are just suggestions. Take them as you will.

Here, I'll explain what the question means and talk about proteins, genes, DNA/RNA and the genetic code that ties them together.

The many varieties of proteins are the primary structural materials for all living things.

each one MADE UP of 20 varieties of amino acids. (not sure I got your meaning here, so take this one with a grain of salt)

The next sentence also needs work, with the suggestion being finding out a way to end in a noun. Can't seem to come up with something at this hour.

Suggested transition. The common analogy used to describe DNA is an apt one: The building blocks of life.

Proteins are made by molecular factories that follow the "blueprints" provided by genes. Genes are like a code made up of DNA or RNA, which are strands of nucleotides. Each gene uses four types of nucleotides and each three-nucleotide sequences (called a codon) represents one amino acid. When you look at amino acids, it is like an alphabet made up of 20 letters used to "spell" proteins. (Actually don't have a clue what you're saying here, so if you can rewrite it please do so.)

When you look at the entire genetic code, its "code book" is a group of proteins called the aminoacyl tRNA systhetses (AARS). With rare exceptions, all life uses the EXACT same genetic code. This genetic code has been with us from the very beginning of life itself.

The conundrum is simple. How could the genetic code exist when it preexists proteins. (O.K. Once again, I don't have a clue what you're getting at here, but you need to make it clearer and more concise.)

By employing computer simulations that model simple systems in which there are RNA genes and proteins, but no fixed genetic code, I hope to provide some understanding about how it is that the same thing could happened in the world before there was life. (No clue, but this is how I would write this if I understood what the point was better.)