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Researchers find surprising similarities between genetic and computer codes
Phys.org ^ | March 29, 2013 | NA

Posted on 04/06/2013 10:35:13 PM PDT by neverdem

Computational biologist Sergei Maslov of Brookhaven National Laboratory worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components "survive" in two complex systems: bacterial genomes and operating systems on Linux computers. Their work is published in the Proceedings of the National Academy of Sciences.

Maslov and Pang set out to determine not only why some specialized genes or computer programs are very common while others are fairly rare, but to see how many components in any system are so important that they can't be eliminated. "If a bacteria genome doesn't have a particular gene, it will be dead on arrival," Maslov said. "How many of those genes are there? The same goes for large software systems. They have multiple components that work together and the systems require just the right components working together to thrive.'"

Using data from the massive sequencing of bacterial genomes, now a part of the DOE Knowledgebase (KBase), Maslov and Pang examined the frequency of usage of crucial bits of genetic code in the of 500 and found a surprising similarity with the frequency of installation of 200,000 Linux packages on more than 2 million individual computers. Linux is an collaboration that allows designers to modify source code to create programs for public use.

The most frequently used components in both the biological and computer systems are those that allow for the most descendants. That is, the more a component is relied upon by others, the more likely it is to be required for full functionality of a system.

It may seem logical, but the surprising part of this finding is how universal it is. "It is almost expected that the frequency of usage of any component is correlated with how many other components depend on it," said Maslov. "But we found that we can determine the number of crucial components – those without which other components couldn't function – by a simple calculation that holds true both in biological systems and computer systems."

For both the bacteria and the computing systems, take the square root of the interdependent components and you can find the number of key components that are so important that not a single other piece can get by without them.

Maslov's finding applies equally to these complex networks because they are both examples of open access systems with components that are independently installed. "Bacteria are the ultimate BitTorrents of biology," he said, referring to a popular file-sharing protocol. "They have this enormous common pool of genes that they are freely sharing with each other. Bacterial systems can easily add or remove genes from their genomes through what's called horizontal gene transfer, a kind of file sharing between bacteria," Maslov said.

The same goes for Linux operating systems, which allow free installation of components built and shared by a multitude of designers independently of one another. The theory wouldn't hold true for, say, a Windows operating system, which only runs proprietary programs.

More information: Universal distribution of component frequencies in biological and technological systems, www.pnas.org/content/early/2013/03/21/1217795110.abstract


TOPICS: Culture/Society; News/Current Events; Technical
KEYWORDS: computationalbiology; genetics; operatingsystems

1 posted on 04/06/2013 10:35:13 PM PDT by neverdem
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To: neverdem

Bacterial genomes always bring to mind Nancy Pelosi


2 posted on 04/06/2013 10:40:33 PM PDT by woofie
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To: woofie

Perhaps except that they contain more usable information than she does.


3 posted on 04/06/2013 10:43:12 PM PDT by coloradan (The US has become a banana republic, except without the bananas - or the republic.)
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To: neverdem

It’s not at all surprising that complex systems created by biological systems would have commonality with complex biological systems.

What would be surprising is if there were none.


4 posted on 04/06/2013 11:11:22 PM PDT by Psycho_Bunny (Thought Puzzle: Describe Islam without using the phrase "mental disorder" more than four times.)
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To: El Gato; Ernest_at_the_Beach; Robert A. Cook, PE; lepton; LadyDoc; jb6; tiamat; PGalt; Dianna; ...
James Holmes' psychiatrist warned he may pose threat Sertraline was found in Holmes' apartment.

The Drug War on Boys-Beware of drug pushers in white coats

Experts: New diabetes treatment flushes sugar, calories out of body

Discovery in Neuroscience Could Help Re-Wire Appetite Control

FReepmail me if you want on or off my health and science ping list.

5 posted on 04/07/2013 12:05:14 AM PDT by neverdem ( Xin loi min oi)
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To: neverdem
“Everything should be made as simple as possible, but no simpler.” -- Albert Einstein.

Einstein's adage holds. The study provides a rough rule of thumb for when the system is approaching that state of simplicity beyond which breakage is expected.

6 posted on 04/07/2013 12:10:52 AM PDT by Myrddin
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To: neverdem; Hardraade

PING! And still counting! Hardraade, are you still keeping track of these hits?


7 posted on 04/07/2013 12:41:07 AM PDT by MestaMachine
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To: MestaMachine

Yep. That was in your writings a very long time ago, and it’s one of the more amazing ones.


8 posted on 04/07/2013 1:43:29 AM PDT by Hardraade (http://junipersec.wordpress.com (Vendetta))
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To: MestaMachine

Intelligent design......again.


9 posted on 04/07/2013 4:26:33 AM PDT by Erik Latranyi (When religions have to beg the gov't for a waiver, we are already under socialism.)
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To: neverdem
The most frequently used components in both the biological and computer systems are those that allow for the most descendants. That is, the more a component is relied upon by others, the more likely it is to be required for full functionality of a system.

An interesting thought occurred to me...

Like in Darwinian evolution...eons of random DNA mutations made us full functionally systems...at what point does computer systems being fully functional by randomness....

O'Wait...it doesn't...because it is missing a creator..

10 posted on 04/07/2013 4:43:40 AM PDT by Popman (Godlessness is always the first step to the concentration camp.)
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To: neverdem

I tell ya, the so-called “junk” DNA is really the data segment.


11 posted on 04/07/2013 4:50:52 AM PDT by NonValueAdded (If you can keep your head when all about you are losing theirs, you've likely misread the situation.)
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To: neverdem

———the more a component is relied upon by others, the more likely it is to be required for full functionality of a system-——

Or in Darwinian terms, the fittest survive. The rule is therefore survival of the fittest.


12 posted on 04/07/2013 4:59:42 AM PDT by bert ((K.E. N.P. N.C. +12 .....History is a process, not an event)
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To: Hardraade; MestaMachine

What are you guys referring to?


13 posted on 04/07/2013 5:48:52 AM PDT by 1010RD (First, Do No Harm)
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To: Popman
Like in Darwinian evolution...eons of random DNA mutations made us full functionally systems...at what point does computer systems being fully functional by randomness....

Good point. By the measure of strict evolutionists, one should be able to simply "shake" together random bits of code and get a fully functioning payroll system. Certainly that is simpler than a human being.

14 posted on 04/07/2013 6:25:03 AM PDT by Flick Lives (We're going to be just like the old Soviet Union, but with free cell phones!)
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To: Myrddin
Einstein's adage holds. The study provides a rough rule of thumb for when the system is approaching that state of simplicity beyond which breakage is expected.

Great comment - thanks for sharing...

15 posted on 04/07/2013 9:00:35 AM PDT by GOPJ (New AP term for Illegal Aliens IS Undocumented Democrats.... Jay Leno)
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To: Psycho_Bunny; neverdem; bert; Popman; GOPJ
Because our universe is a computer simulation:

In the beginning was the code

The Simulation Argument of Nick Bostrom

Strange Computer Code Discovered Concealed in Superstring Equations

16 posted on 04/07/2013 10:46:25 AM PDT by who_would_fardels_bear
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To: neverdem

Yeh, the libtards run script coded by the Rats. That one was easy.


17 posted on 04/07/2013 11:25:46 AM PDT by SgtHooper (The last thing I want to do is hurt you. But it's still on the list.)
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To: who_would_fardels_bear

Thanks for the links.


18 posted on 04/07/2013 12:37:19 PM PDT by neverdem ( Xin loi min oi)
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To: NonValueAdded
LISP is homoiconic. Code and data look the same. Tiny bits of syntax differentiate 'code mode' from 'data mode'. The use of methylation to mask a section of DNA may have a similar syntactic purpose

Many software metrics packages calculate dependencies. The object oriented versions throw in fan-in/fan-out. Calculating the proposed square root of those metrics would be an easy enhancement. As a management tool it might serve as a risk assessment to indicate that critical elements are still missing from a work in progress.

19 posted on 04/07/2013 12:40:37 PM PDT by Myrddin
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To: bert

>>”the fittest survive. The rule is therefore survival of the fittest.”

I still wonder how this is not tautological:
Those that survive are the fittest; therefore the fittest survive.


20 posted on 04/07/2013 2:24:24 PM PDT by D-fendr (Deus non alligatur sacramentis sed nos alligamur.)
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To: who_would_fardels_bear

Thanks for the links... interesting stuff...


21 posted on 04/08/2013 12:35:07 PM PDT by GOPJ (New AP term for Illegal Aliens IS Undocumented Democrats.... Jay Leno)
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