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Computational biology

 
 
grant
13:28 / 25.02.03
You've heard of Moore's Law, right? That computer "intelligence" (speed/computational power) will double every so many years (until, some say, the physical limits of electrons traveling through silicon & copper have been reached - others say new technology will expand the limit to the speed of thought itself).

Moore's Law, meet Dickerson's Formula.

The deal: 24 years ago, Caltech chemistry professor Richard Dickerson came up with a mathematical formula describing the rate at which we're figuring out the structure of proteins - that is, the molecules the cells of our bodies are made of.

Quote: Dickerson, then a professor of physical chemistry at Caltech, noted that the number of protein crystal structures had risen from one solved by the end of 1961 to 23 solved by the end of 1977. His formula predicted that by March 2001, scientists would have solved the 3-D structures of a grand total of more than 12,000 proteins. He was very close.



The first protein structure solved by scientists in 1961 was myoglobin (inset). In the equation developed by Richard Dickerson for the number of new protein structures solved per year, n is the number of new structures in a given year, e is the natural logarithm 2.71828, and y is the year (for March 27, 2001, y = 2000.25).

Nobody knew how close until Arthur Arnone, a biochemistry professor at the University of Iowa, checked. Arnone found that the equation predicted that there would be 12,066 crystal structures solved by March 27, 2001. By that date, the Protein Data Bank (PDB), the international online repository of protein data, had posted 12,123 protein structures, only 57 more than Dickerson’s forecast. The Dickerson formula was accurate to within 0.5 percent.



Apparently, there's also an event horizon:

"I think that Dickerson’s equation is to protein structure what Moore’s Law is to semiconductor chips," said Arnone. "Even the time frames are the same. Dickerson’s equation and the current form of Moore’s Law were both derived in the late 1970s." Moore’s Law, created by Intel cofounder Gordon Moore, has forecast, with remarkable accuracy, that the number of transistors per square inch on integrated circuits would double about every 18 months.

Dickerson, now a professor of biochemistry at UCLA and a pioneer in X-ray crystallography, is astounded by his own predictions. "To move from the accidental to the ridiculous, if Dickerson’s Law holds, the year 2024 will see the production of 1 million new protein and nucleic acid structures, or 83,000 new structures per month," said Dickerson. "Somehow, I doubt that. Even the genomics and proteomics researchers who claim that their goal is to sequence all the DNA of an organism, and solve all the protein structures coded by that DNA, don’t go quite that far. But who knows? In short, I seem to have won the lottery. Pity there’s no jackpot."


What could it mean if we know how every protein on Earth is put together?

What will that point of singularity be like?

And if proteins can be subject to mathematical laws like this, can anything?
 
 
Thjatsi
05:16 / 26.02.03
"And if proteins can be subject to mathematical laws like this, can anything?"

Proteins aren't really that complex. They're basically a string of twenty different amino acids that are folded in a number of different ways, giving them many different diverse and impressive chemical properties. A single protein has nowhere near the level of complexity as a bacteria, brain, or ecological system.
 
 
Pepsi Max
04:39 / 27.02.03
grant> no need to be so breathless.

>And if proteins can be subject to mathematical laws like this, can >anything?

Yes. Lots of stuff grows exponentially. Human-generated scientific knowledge has grown expotentially since WWII (may be since the 18th century - human wisdom has not grown at a comparable rate) in certain areas - biotech and computing being the most noticeable (and the ones referenced here). And that's exactly what you'd expect in areas that haven't reached maturity yet.

Other areas are different - for instance the speed of cars hasn't increased greatly in the lat decade - but the complexity of their construction has.

>What could it mean if we know how every protein on Earth is put >together?

How is knowing proteins fundamentally different to knowing DNA genomes?

Now a different kettle of fish altogether is protein reverse-engineering. You decide on the properties of your compound (strong like keratin, an oxygen-binding agent like haemoglobin), design an amino-acid chain that achieves that, work back to the DNA chain and then feed it into bacteria or eukaryote. They then make heaps of your substance at minimal cost.
 
 
grant
21:14 / 27.02.03
Seems like it'd be a snap to build proteins to order once you've mapped out all the possibilities - which, according to the formula, should happen in our lifetimes.

Does DNA count as a protein? I honestly don't know.
 
 
Thjatsi
02:35 / 01.03.03
Actually, there's a concept called the Central Dogma of Molecular Biology. The basic idea is that DNA always forms RNA, which always forms a protein. Usually, it's taught with a nifty diagram like this:

DNA --> RNA --> Protein

So, lets say we have three bases in a string of DNA:

Adenine, Thymine, Guanine

or

ATG

This will almost always form the amino acid methionine. By the way, methionine is the starting point for just about every protein.

This process, and the codes that take you from DNA to RNA to Protein, are conserved across virtually every organism on the planet.

However, it is interesting to note that there are a few exceptions to the Central Dogma. First, viruses like HIV can use reverse transcriptase to go from RNA to DNA. Second, people have apparently gone straight from DNA to protein in lab settings. Third, you have prions, which can replicate without DNA or RNA. So, the name Central Dogma is a little tongue-in-cheek.

Send me a message and I'll e-mail you the powerpoint presentation I gave on this for my lab section.
 
  
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