Researchers find surprising similarities between genetic and computer codes

Mar 29, 2013
'Survival of the fittest' now applies to computers
The package dependency network of Firefox shows the complex nature of technological systems. Picture credit: Dependency network of Firefox from Ubuntu Linux. Image created with the software Cytoscape. Credit: Tin Yau Pang

(Phys.org) —The term "survival of the fittest" refers to natural selection in biological systems, but Darwin's theory may apply more broadly than that. New research from the U.S. Department of Energy's Brookhaven National Laboratory shows that this evolutionary theory also applies to technological systems.

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.

Explore further: Bodies at sea: Ocean oxygen levels may impact scavenger response

More information: Universal distribution of component frequencies in biological and technological systems, www.pnas.org/content/early/201… /1217795110.abstract

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antialias_physorg
3.6 / 5 (12) Mar 29, 2013
The greatest similarity between DNA and computer programs I've run accross is: Legacy stuffgets passed on from generation to generation - often without any clear need.

It. Just. Won't. Die.
Lurker2358
2.6 / 5 (8) Mar 29, 2013
The greatest similarity between DNA and computer programs I've run accross is: Legacy stuffgets passed on from generation to generation - often without any clear need.

It. Just. Won't. Die.


Silly.

Ya think being immune to bubonic plague might be helpful again one day? Or maybe any number of other things that exist "somewhere" that YOU just don't know about?
Whydening Gyre
2.1 / 5 (7) Mar 29, 2013
Anti - Kinda like these ads to buy stuff that pop up in the comments section occasionally... Someday we're all gonna want to go out and by a Ed Hardy Bikini for $23.00
TheGhostofOtto1923
1.3 / 5 (11) Mar 29, 2013
The greatest similarity between DNA and computer programs I've run accross is: Legacy stuffgets passed on from generation to generation - often without any clear need.

It. Just. Won't. Die.
Right. And if god had written our DNA from scratch it wouldn't be so full of useless crap. More evidence that he ain't there.
Ya think being immune to bubonic plague might be helpful again one day? Or maybe any number of other things that exist "somewhere" that YOU just don't know about?
Who was ever immune to the plague? Silly.
Whydening Gyre
1.7 / 5 (6) Mar 29, 2013
The greatest similarity between DNA and computer programs I've run accross is: Legacy stuffgets passed on from generation to generation - often without any clear need.

It. Just. Won't. Die.
Right. And if god had written our DNA from scratch it wouldn't be so full of useless crap. More evidence that he ain't there.

Or that he's pretty much a scatter brained dyslexic.
brodix
1.3 / 5 (4) Mar 29, 2013
Mostly explained as bottom up. A spiritual absolute would be an elemental state, not an ideal form. Builds up, crashes, repeat.
TheGhostofOtto1923
1.5 / 5 (8) Mar 29, 2013
For instance lurker if gods creations were meant to be permanent and immutable, why did he include the mechanism of mutation? We can watch evolution working before our eyes.
Mostly explained as bottom up. A spiritual absolute would be an elemental state, not an ideal form. Builds up, crashes, repeat.
Lurkers god claims to be both. Alpha and omega.
Lurker2358
2.7 / 5 (13) Mar 29, 2013
Lurkers god claims to be both. Alpha and omega.


Straw man. The Bible does not claim humanity is immutable, nor does it claim creation itself is immutable. In fact, it quite says the opposite in many places regarding human nature, and the fate of humans, all life, and the universe itself.

"Alpha and Omega, the beginning and the end, the first and the last."

You are attempting to apply ordinary, temporal concepts to eternity.

You also, like Stephen Hawking, fail to realize the fact that there is nothing in logic or reason that requires "reality" to involve energy, mass, or space. The universe we exist in happens to be made of those properties, but there is no reason to assume they are fundamental to "reality" itself.

I'm talking about things which are barely conceivable, or even inconceivable to human beings, but they are conceivable to God, who can do those things if He so choose.

The "All possibilities contained in the tenth dimension" thing is faulty reasoning.
Alexander Riccio
1 / 5 (2) Mar 29, 2013
"The algorithmic origins of life"
christophe_galland1
3.7 / 5 (6) Mar 29, 2013
Back in 1995 Daniel Dennett wrote "Darwin's dangerous idea". We should not be so surprised to find here again that Darwinism is a universal concept applying to algorithmic processes such as life... and of course computer systems.

Unfortunately Darwin's dangerous idea is being fought by a constant supply of people including scientists who cannot accept that mind and design can emerge from mechanistic rules.
Lurker2358
2.1 / 5 (18) Mar 29, 2013
mind and design can emerge from mechanistic rules.


Who made the rules?

"In the beginning was the Logos, and the Logos was with God, and the Logos was God. He made all things and without him was not anything made that was made."

The problem Hawking has is he believes "1 - 1 equals 0" disproves creation, but he fails to see that his own statement shows that the "Logos" must pre-date the universe. After all, "1 - 1 equals 0" is a logical, mathematical statement. Thus "From nothing comes nothing", contrary to Hawking's "from nothing comes one plus negative one".

Hawking therefore fails to realize that a universe is less fundamental than Logos; that all possibilities come from the Logos, which is equated with God in the Bible. His own argument is a failed attempt to use a sub-set of logic to defeat Logos, which cannot be done, and none of YOU even admit his glaring failure.

You silly atheists lost from quite literally the beginning.
TheGhostofOtto1923
1.5 / 5 (8) Mar 29, 2013
The Bible does not claim humanity is immutable, nor does it claim creation itself is immutable
Of course he does. He says we and only we were created in his image. In addition:

John 1:3 (NIV)
3 Through him all things were made; without him nothing was made that has been made.

Man was made perfect and immortal but he sinned and so was condemned to suffer and die. And so it was only through sin that evolution could be possible because evolution requires death AND imperfection/mutation.

And by extension it seems that Adams original sin condemned the rest of life to mutation and evolution as well. Does this REALLY make sense to you?

Like I say if you had any respect for evidence you would see things differently. Science tells conclusively that the bible stories didn't HAPPEN. therefore the god who told them doesn't exist.
Logos
-is a Greek word. Why is the NT written in Greek when the people who claimed to have written it spoke Aramaic? (Because they didn't write it)
TheGhostofOtto1923
1.6 / 5 (7) Mar 29, 2013
You are attempting to apply ordinary, temporal concepts to eternity
Oh not me. Your god refers to 'beginning and end' a lot.

"This symbol [alpha and omega] was suggested by the Apocalypse, where many believe that Christ, as well as the Father, is "the First and the Last"; "the Alpha and Omega, the first and the last, the beginning and the end". Clement of Alexandria (2nd century, philosopher and commentator on pagan and Christian information) speaks of the Word as "the Alpha and the Omega of Whom alone the end becomes beginning, and ends again at the original beginning without any break"

-Your custom definition is another example of how Xian egomaniacs think some god exists for their benefit, and would for some reason allow them to redefine reality to make them feel better. For this is in essence what salvation IS, isn't it? Relief from pain?
Who made the rules?
Who wrote your book? A large number of liars. They had no idea how the universe functions.
jahbless
2 / 5 (4) Mar 29, 2013
Lurker, why you wasting your time man? These kids all know that logical deduction has no limitations (Godel be damned), and that God is an engineer whose methods of creation are, well, roughly identical to their own.

What you gonna bring in transcendental reality and make yourself look silly for? Lol! GhostofOtto has even clarified that John 1:3 excludes the possibility of human evolution! Stop talking man. The base materialists have made it clear that the rest of us are rank idiots. =)
jahbless
1 / 5 (3) Mar 29, 2013
[Double post -- delete]
TheGhostofOtto1923
1.6 / 5 (7) Mar 29, 2013
Stop talking man. The base materialists have made it clear that the rest of us are rank idiots. =)
Well no, evidence has made it clear. I and others feel it is our resonsibility to point this out.

Give up your fantasy worship before it kills us all.
Lurker2358
2.3 / 5 (6) Mar 29, 2013
Logos
-is a Greek word. Why is the NT written in Greek when the people who claimed to have written it spoke Aramaic? (Because they didn't write it.


Lol. ya ever read who it was addressed to? It was addressed to people at the time primarily who wrote and spoke Greek. In a couple cases, the Epistle is dictated to a translator.

The Israeli state was subjugate to Roman rule, but the eastern half of the Roman empire was Greek, and the SEPTUAGINT was the Greek translation of the Old Testament which the Jews commonly used throughout their Synagogues that they were allowed to have.

I'm not a historian, but you're completely ignorant.

By the way, Hebrew was the primary spoken language AMONG Jews at the time, and the texts shows that in several occasions.
komone
not rated yet Mar 29, 2013
Who made the rules?


Not sure why you think it must be a "who"? That seems to me to be a very weird assumption.
Lurker2358
2.3 / 5 (6) Mar 29, 2013
Luke 23:38 And a superscription also was written over him in letters of Greek, and Latin, and Hebrew, THIS IS THE KING OF THE JEWS.

If Aramaic was the common language, why wouldn't the governor have written in Aramaic?! he didn't. He wrote in Greek, Latin, and Hebrew.

Acts 22:40And when he had given him licence, Paul stood on the stairs, and beckoned with the hand unto the people. And when there was made a great silence, he spake unto them in the Hebrew tongue.

I believe there is contextual evidence to show Paul was fluent in at least all 3 of the languages listed above.
mikegonzalez2k
1.8 / 5 (5) Mar 29, 2013
Lurker you are an idiot, keep believing the entire universe is centered around humans. The world was not flat, and a higher being wouldn't put our race above all of the millions of others. That is simply egotistically ignorant of you to even consider that notion. Please take your ignorance elsewhere where other blind sheep like yourself can listen to you preach.
Lurker2358
2 / 5 (8) Mar 29, 2013
Oh not me. Your god refers to 'beginning and end' a lot.


I told you what that means, but you refuse to understand it.

Let me show you something else then, since you do not understand.

Deuteronomy 33:27
The eternal God is thy refuge...

1 Kings 8:27
But will God indeed dwell on the earth? behold, the heaven and heaven of heavens cannot contain thee; how much less this house that I have builded?

"I am the beginning and the end" does not mean that God has a beginning or end, silly. It means that REALITY starts and ends with God.

You think of the concept of eternity as something like an unending line, but God is much more than that. God is neither dimensional nor non-dimensional. God is the source of all things, including dimensionality and any abstract concepts you can think.

Last verse 23rd Psalm.

"Surely goodness and mercy shall follow me all the days of my life and I shall dwell in the house of the Lord FOR EVER."
Lurker2358
2 / 5 (8) Mar 29, 2013
Lurker you are an idiot, keep believing the entire universe is centered around humans. The world was not flat


the Bible never said it was flat. That is a false claim.

Job 26:7He stretcheth out the north over the empty place, and hangeth the earth upon nothing.

Which is absolutely true. Unlike the ancient greeks, his statement is true, which we KNOW, because we have satellites orbiting the Earth.

and a higher being wouldn't put our race above all of the millions of others.


Wow. The guy who doesn't believe in a higher being presumes to know what a higher being would do.

You are incredibly dishonest.

That is simply egotistically ignorant of you to even consider that notion.


...yet you enjoy that notion every day when you eat meat, or for that matter even fruits and veggies.

Every time you eat you practice a belief that you have some sort of moral right to consume another life form, therefore you in fact practice the same notion you claim to oppose.
mikegonzalez2k
1 / 5 (5) Mar 29, 2013
Your view of the universe is no different than the fools who believed in geocentrism. The universe doesn't revolve around us. You are not educated. You probably didn't even get through high school with a basic understand of mathematics and physics. Why are you even posting on a physics forum when your understand of physics is severely limited? Try sitting through a class in classical mechanics sometime where actual wise people are. Even you may learn something.
TheGhostofOtto1923
1.7 / 5 (6) Mar 29, 2013
If Aramaic was the common language, why wouldn't the governor have written in Aramaic?! he didn't. He wrote in Greek, Latin, and Hebrew
Well first off, it's a fable. 2nd, the NIV doesn't include these language qualifiers (why not?)

3rd, the governor obviously didn't write it as it was meant to mock jesus. 4th:

"However many critical scholars consider the "we" passages [in luke and acts] spurious or inserted and place the date c 80-90"

Acts 22:40And when he had given him licence, Paul
Acts? Why do you quote acts? It was written by people who lied about being eyewitnesses:

"...they believe Luke-Acts was written by an anonymous Christian author who may not have been an eyewitness to any of the events recorded within the text."

-And some 40% of works attributed to Paul are also forgeries. In other words you can't trust any of it because it is rife with lies and misconceptions.
komone
5 / 5 (2) Mar 29, 2013
All religious discussions aside (which seem to be to be a big diversion of little actual consequence), I find the results of this work unsurprising. It does play into my current best guess (i.e. model of the physical world) about what is "really" going on. We need a lot more evidence of this sort to figure out a really good and testable theory of information and physics (I personally believe that David Deutsch's Royal Society papers on this problem will resonate in future history - but that's just my opinion and belief right now).
TheGhostofOtto1923
1 / 5 (5) Mar 29, 2013
@lurker

Your references must be taken in the context of 1 and 2 Peter which your god chose to include in his canon despite the FACT that both are amateur forgeries.

The NT was written gens after the supposed life of Jesus by Greek scholars intent upon creating a religion to counter Jewish proselytism by vilifying them and specifically blaming them for the death of Jesus in John. It also incorporated various pagan conventions (godman, trinity, virgin birth, solar holidays, cannibal Eucharist, mary/ashtorah earth mother, etc) to facilitate the incorporation of euro and north African tribes.

Obviously the form of your shmorgasbord religion was entirely politically-motivated.
CQT
not rated yet Mar 29, 2013
...there is nothing in logic or reason that requires "reality" to involve energy, mass, or space. - Lurker

Phase space is independent of energy or mass. The article asserts that the authors of the research stated the order of information is the square root of the components to sustain that order (of information.) The way out is there are no constrictions as to what 'components' must be.

A 'structure' without components is where information about components is abandon without loss to the order.

Then you are left with self organization without a source.

The article is about the authors concepts which were abandoned in commentary to address matters for (or of) which I have far less understanding.
DavidW
1 / 5 (4) Mar 29, 2013
The greatest similarity between DNA and computer programs I've run accross is: Legacy stuffgets passed on from generation to generation - often without any clear need.

It. Just. Won't. Die.
Right. And if god had written our DNA from scratch it wouldn't be so full of useless crap. More evidence that he ain't there.

Or that he's pretty much a scatter brained dyslexic.


Or maybe before and after don't exist in that realm. I seems more logical that when we have thoughts that God has to be responsible based on a "cause and effect" proof, we have: A. Ignorantly ignored that we already realize is never proof that cause and effect operate out side of this realm, if such a place exists B. Not taken the time to consider the reality that there can be a god and that god could actually be innocent because we really have no evidence based on cause and effect to judge god.
aroc91
5 / 5 (3) Mar 29, 2013
After all, in AWT the main purpose of junk DNA is just to maintain the genetic incompatibility between species (the analogy of surface tension or dark matter for gravity field, btw).


It's like you just throw buzzwords together and hope it makes a coherent sentence. So you're saying the transverse vacuum density fluctuations interact with the metaphorical water ripples of the longitudinal surfaces to reverse entropy and enable life to exist?

I could generate random combinations of those words and recreate everything AWT proponents have every said on this site and none of it would mean anything. I'm sure you don't even know what you're saying 99% of the time.
DavidW
1 / 5 (3) Mar 29, 2013
OS's, code, robots, the lot, can never be more than a refection of what we really are. We cannot design them without instituting the real world reality in which we live by and operate in.

We are not like code. It is a reflection of us. That's all it is. We are the real thing. So, is Linux and the idea of community coding and prosperity for a better reflection of who we are? Is it a more ethical operating system choice? Is man actual at his core an animal that will naturally not kill when unnecessary, but instead is infected with so many lies that he does so anyway?

Their findings all point to the issue of the things we make can only be a reflection, are a reflection, and that we have a real mess on our hands. Expect to see the reflected faults of our actions, because they are there. These things we don't see under a microscope, but they are just as real. It's life!
Torbjorn_Larsson_OM
5 / 5 (2) Mar 29, 2013
Ha. Another hard strike against creationists. No wonder these crackpots surface in the comments, desperately flailing at the inevitable revelation of their folly as just that.

Creationists shouldn't comment on science, it is hilarious and it makes deconverts from religion, see Dawkins's Convert's Corner.

- "The amount of junk DNA would rather correspond the Windows system."

The analogy breaks down because while junk DNA is pseudogenes (former active genes) they can be routinely activated again (and there are examples). If a software programmer forgets to delete inactive code it is not reused.

- "Who made the rules?"

Physical laws are symmetries (sometimes broken), i.e. conservation of properties. That is necessary in order to have a large enough (isotropic, homogeneous) universe. So however it happened, this was forced in order to have observers. I.e. we can see it as a selection effect.
Torbjorn_Larsson_OM
5 / 5 (1) Mar 29, 2013
[cont] Reversely, an isotropic, homogeneous spacetime (so physically lawful universe) aka a Friedmann universe is a result of a spontaneous process. (Zero energy universe; admits for example inflation which would not happen else.)

This is what was suspected before WMAP 9 year and Planck 2 year data release confirmed it within the last few weeks.

So we now know that no magical agent ("who") made the universe or its laws at 7 sigma (Planck observation of inflation), beyond reasonable doubt. It just happened, and if it hadn't we wouldn't be here.

@aroc91: I think it is an AWT Eliza robot, parroting a nonsensical script. (Aether was rejected over a century ago.) =D
DavidW
1 / 5 (3) Mar 29, 2013
You....atheists....


Chill dude. You stepped over the line there. That's an important person. With the truth we feed that others may find health and strength.

DavidW
1 / 5 (6) Mar 30, 2013
you're completely ignorant.

Silly

You are incredibly dishonest.


Understanding the evidence in reality that God does exist does not mean we have a personal relationship with God. No matter how much we study, meditate, research, and articulate bible verses and that fact that we can provide endless evidence for the existence of God and that no one can really supply any valid evidence against such a belief, is not reason to attempt to place yourself above the truth and attempt to define others as something other than they are in the name of God!
Every time you eat you practice a belief that you have some sort of moral right to consume another life form

No! Taking what we NEED to survive must be allowed. Taking life for any reason that is not NEEDED support life is murder. Our basic nature does not cringe to pick an orange. Yet, it does when we others kill for pleasure alone. I wouldn't listen to you either. The seeds for truth do not grow well in lies
MandoZink
4.4 / 5 (7) Mar 30, 2013
Creationists have an interesting set of assumptions they must embrace:
There was a "who", there was a design, it was a rational act, it was intentional, it was logical and of course it had a beginning. These may be concepts our tiny minds require in the excruciatingly miniscule instant of infinity we currently existing in, but the universe doesn't really care. We pretty much just happen to be here now. No reason necessary. Lucky us.
TheGhostofOtto1923
1 / 5 (4) Mar 30, 2013
Understanding the evidence in reality that God does exist does not mean we have a personal relationship with God
Sorry your bad poetry and delusions of personal insight are no substitute for evidence. Evidence says A) the bookgods are all deception and lies and 2) your nonsense deist gods are at most, superfluous because from what we have found, the universe functions quite well all by itself.

Ever write song lyrics Dave? Perhaps your talents would be of some use to you there. Stuff like yours has made some people a lot of money.
http://www.steely...ics.html
DavidW
1 / 5 (5) Mar 30, 2013
It is well known by many that there are many questionable things written and that humans do make errors.

Truth and Life are self-evident witness on itself, the existence of God. Adding that such a reality requires an innocent God, and as such, is not debatable. God is real. I am not trying to get anyone to believe God exists. It's already real. It up to each person to open their heart to Truth and Life in all things. Creation itself is never more than self-evident witness of the Truth of God's love.
TheGhostofOtto1923
2 / 5 (4) Mar 30, 2013
Truth and Life are self-evident witness on itself, the existence of God. Adding that such a reality requires an innocent God, and as such, is not debatable
How can an innocent, truthful god exist who writes books full of willful deception and lies? That's just silly. No debating that is there?
Creation itself is never more than self-evident witness of the Truth of God's love
-And how can such a lovegod exist who would condemn people to everlasting torture just because they couldn't believe in him because he wrote books full of LIES?? That's not love Dave.
TheGhostofOtto1923
2 / 5 (4) Mar 30, 2013
"The seeds for truth do not grow well in lies" -where did I read this? Keats? Ginsberg? Cobain?
beyondApsis
5 / 5 (4) Mar 30, 2013
...we can provide endless evidence for the existence of God...


When did that happen? I didn't know actual physical evidence had been found. I do know there is vast archeological and anthropological evidence that humans have always borne superstition beliefs, including God, to explain what they could not understand. Over the millennia, thousands of belief systems have existed, until the organization of larger civilizations reinforced the currently prevailing ones, which then became major religions. They are different but have overlapping themes.

You are confusing "feeling really good about what I believe" for actual evidence.
beyondApsis
5 / 5 (4) Mar 30, 2013
...personal relationship with God...

is just an externally romanticized view of inner peace. It is no less satisfying, but it lacks the insight into the general human nature of the phenomenon, which is that we can all get in touch with "Truth and Life". For some it's skiing down a mountain, for others it's a feeling of superstitious mystery (religion), for others it's immersing oneself in the discovery of facts and realistic evidence (science). But believing what you "feel" and having it be being real are two very different things. That's where science has a definite edge.

I am quite sure that you still are not willing to comprehend that. I must ask, why are you actually here on this site?
TheGhostofOtto1923
1 / 5 (3) Mar 31, 2013
When did that happen? I didn't know actual physical evidence had been found
It hasn't. None. Only overwhelming contrary evidence to demonstrate conclusively that the bible stories never happened.

And so we can conclude that the books which describe them were not written by some omniscient, benevolent, or honest god.