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A computer scientist looks at DNA. - Comments

generationx's Avatar Comment 1 by generationx

No it's not, and who ever wrote this is an idiot. Why was this even posted on this site?

Thu, 16 Sep 2010 14:56:08 UTC | #519017

Schrodinger's Cat's Avatar Comment 2 by Schrodinger's Cat

" So now I come to a point where we have to ask ourselves two fundamental questions: if the mechanism behind DNA processing is uniform though all that lives, someone or something needs to have stopped the evolution process in it at a certain point. If DNA processing is not a product of evolution, something or someone needs to have created it. "

This argument is somewhat fallacious. It's a bit like reasoning " Why don't stars create heavier elements by some other means.....as the universe has had long enough to learn how to "

The answer is of course that stars do things the only way they CAN do them. And why should it be any different for life ? It's entirely possible, given the sheer complexity involved, that DNA processing is the way that it is......because self replication ( and hence the survival of any other method ) simply would not work any other way.

In engineering terms it may be analogous to the wheel. We're still getting around on a device which, though the materials may have changed, would not have been out of place in ancient history. The basic concept has remained unchanged for one very simple reason......it works !

Thu, 16 Sep 2010 15:01:39 UTC | #519027

AtheistEgbert's Avatar Comment 3 by AtheistEgbert

This is crazy. Please less crazy stuff from so-called atheists and more serious stuff.

Thu, 16 Sep 2010 15:03:56 UTC | #519028

JQisAwesome's Avatar Comment 4 by JQisAwesome

Is this another trollish thread that Richard selected "against strong advice from the other moderators?"

Thu, 16 Sep 2010 15:09:26 UTC | #519036

lilalindy's Avatar Comment 5 by lilalindy

A number of mechanisms have been used, with different levels of redundancy so, yes, they have been tried BUT the system we have now is so much better, compared to the others that is is effectively stable (it is the best by a long way so, without any almost as good competition, it survives). We can deduce that cells using it are so much better at passing on genes that they have all but wiped out other cells that use alternative systems.

Thu, 16 Sep 2010 15:12:32 UTC | #519039

Bliszs's Avatar Comment 6 by Bliszs

are you really a computer scientist

Thu, 16 Sep 2010 15:34:36 UTC | #519065

SaganTheCat's Avatar Comment 7 by SaganTheCat

se what happens when you spend too long in front of a VDU?

Thu, 16 Sep 2010 15:56:00 UTC | #519086

Jos Gibbons's Avatar Comment 8 by Jos Gibbons

Any change in the code would almost certainly render existing genes junk. Why would natural selection ever favour that? The universality of the code across all life is excellent evidence of universal common ancestry.

Thu, 16 Sep 2010 16:01:27 UTC | #519090

Budapest's Avatar Comment 9 by Budapest

What or who created it, I don’t know. I’m also not looking for any kind of God, I’m atheistic towards all the Gods made up by humans, but if there exists a scientific presumption for creation in reality we should look at it and take it into consideration.

In fact it’s a scientific obligation…

What a brilliant comment! Science is supposed to embrace freedom of enquiry. Galileo was considered heretic by Christians in his day, when he argued for the earth circling the sun and spent his last 8 years of life under house arrest.

It seems atheism has replaced the church in saying what can and cannot be accepted in science. The mere mention of a 'scientific presumption of creation' is decried as creationist, ignorant, unscientific. (As it clearly demonstrated by the comments in this forum.)

This stance is holding us back in science.

Religion has too much influence in politics and atheism has too much influence in science.

Updated: Thu, 16 Sep 2010 16:38:01 UTC | #519115

crookedshoes's Avatar Comment 10 by crookedshoes

No, No, No....

 Evolution favors that which works and DNA works.  There may have been an entire unpreserved "battle"  between precursors of DNA and DNA.  There is an entire RNA world hypothesis that is plausible and probably approaches reality.  The reason DNA is ubiquitous and universal is because it was what was present in that first single common ancestor.  Other "living things" at the time of the single common ancestor could have been based on some other code or replicator but, the "victory" of DNA sets the stage for it's current domination.  It simply speaks to how long ago DNA evolved; from our FIRST COMMON ANCESTOR.  It is the ultimate homology.  To say it hasn't changed, however, is a bit of an oversimplification.  Prokaryotes DNA is vastly different than Eukaryotes.  DNA has become considerably more complex.  The central dogma, however has not changed (and that is a bit oversimplified as well) because there is no PRESSURE for it to change; it works.

As for the brilliance of the statement: What or who created it, I don’t know. I’m also not looking for any kind of God, I’m atheistic towards all the Gods made up by humans, but if there exists a scientific presumption for creation in reality we should look at it and take it into consideration. In fact it’s a scientific obligation…

It is brilliant; in 1400. Since then it has been repeatedly shown that there is, in fact ZERO merit in a "scientific presumption for creation..." If all scientists operated under the atheistic flag I would agree that this type of thinking is very detrimental. However, not all scientists subscribe to the atheistic view. The comments on this forum are from atheists and scientists, and believers, and non scientists. To blanket state that these comments are representative of "ALL SCIENCE" is simply put; UNTRUE.

Thu, 16 Sep 2010 16:47:19 UTC | #519134

Alan4discussion's Avatar Comment 11 by Alan4discussion

I am no expert on genetics, but as (I believe) humans have 40% of the same genes as a cauliflower, and all life seems to have evolved from the same bacteria, perhaps the gene that was transplanted was an ancient one identical to the one it replaced. It is a very long time since plants and animals branched off the evolutionary tree and went their separate ways. Genetic enineers are transplanting genes all the time so we would need to read their reports to grasp details of this.

Thu, 16 Sep 2010 16:52:58 UTC | #519140

Balance_Maintained's Avatar Comment 12 by Balance_Maintained

Willem beware, you have challenged the herd and been found a troll, crazy, an idiot, lacking in reasoning and logic skills, and presumed a liar about your credentials. Welcome!! Life outside the herd is a wonderful thing. Lots of elbow room and all that.

However, scientific objectivity does not exist when scientist label themselves as atheist or creationist. However, you are posting on a atheist website, so one should expect a natural bias against anything that even remotely hints at design, intelligent or otherwise, in anyway shape or form.

@lilalindy I am curious as to these other mechanisms that have been tried. Do you have links with information on these as well as comparative data between that system and the current one? And, were they tried in nature or in a lab? Also, this is in direct contradiction to Schrodinger's Cat's statement, please clarify:

The answer is of course that stars do things the only way they CAN do them. And why should it be any different for life ? It's entirely possible, given the sheer complexity involved, that DNA processing is the way that it is......because self replication ( and hence the survival of any other method ) simply would not work any other way

Is that really the only way stars CAN do it? Do you have evidence to back up that sweeping statement? Just curious.

Thu, 16 Sep 2010 16:53:18 UTC | #519141

Bliszs's Avatar Comment 13 by Bliszs

It seems atheism has replaced the church in saying what can and cannot be accepted in science. The mere mention of a 'scientific presumption of creation' is decried as creationist, ignorant, unscientific. (As it clearly demonstrated by the comments in this forum.) This stance is holding us back in science.

no, what he is saying has no place in science and is scientifically wrong. i think you need to learn what science is. science may be speculative in certain aspects, it may explore new ideas, counter intuitive ideas, but this is just dumb.

Thu, 16 Sep 2010 16:54:24 UTC | #519142

Willem's Avatar Comment 14 by Willem

Evolution favors that which works and DNA works. There may have been an entire unpreserved "battle" between precursors of DNA

This is a contradiction, if there has been a battle between competing systems, this battle should go on up to date! Every generation would generate slightly differences in the way they interprete the digital information with no compatibility anymore...

The central dogma, however has not changed (and that is a bit oversimplified as well) because there is no PRESSURE for it to change; it works

This would falsify the evolution theory as there could exist a specie which didn’t evolve anymore since it was so strong and worked well… Evolution is an ongoing fact of nature..

So again my two statements keep on standing: If the mechanism behind DNA processing is uniform though all what lives, someone or something needs to have stopped the evolution process in it on a certain point. If DNA processing is not a product of evolution, something or someone needs to have created it.

Thu, 16 Sep 2010 17:31:08 UTC | #519175

Alan4discussion's Avatar Comment 15 by Alan4discussion

Budapest, you are making strange pronouncements on some sort of Atheism directing science, for which there is no evidence. I recall that recently on another thread, you made statements about posible new evidence disproving Darwin's Theory of Evolution by means of Natural Selection in "The Origin of Species" and much later asked for a definition of "a species"! I also needed to define "natural selection" in that discussion. While everyone is entitled to an opinion, it is difficult to have an informed debate when some of the participants do not appear to have done the basic homework on understanding the subject matter. Do you have any understanding of scientific method, peer review, or basic biology?

Thu, 16 Sep 2010 17:35:58 UTC | #519179

Willem's Avatar Comment 16 by Willem

Comment Removed by Author

Thu, 16 Sep 2010 17:38:36 UTC | #519180

rocket888's Avatar Comment 17 by rocket888

It is an interesting mystery how the DNA code evolved. What is particularly fascinating is how a two level code evolved. First we have the 4 letters, AGCT, that represent the bits, which are then encoded 3 at a time into "bytes", similar to the way the ASCII code is setup.

Now, ascii was pretty much a 7 bit code until it was expanded first to 8 bits and now to multiple bytes for international use.

So, DNA must have been preceded by a simpler code. The problem is nobody has found anything simpler either in fossils or in an alternative code.

There is one exception, however. Mitochondria have a slightly different coding for a few proteins. Since these were likely self sufficient bacteria at some previous era, the question is did this difference evolve AFTER they joined with other cells or are they a remnant of an older DNA code that has evolved?

Still, it's difficult to see just how such a complex code evolved from something simpler. An interesting mystery for certain. But then there was certainly a lot of time, since 80% of life was one celled or less.

My favorite read on this is the book "Seven clues to the origin of life" by A. G. Cairns-Smith.

Thu, 16 Sep 2010 18:08:43 UTC | #519211

Budapest's Avatar Comment 18 by Budapest

Comment 15 by Alan4discussion: I recall that recently on another thread, you made statements about posible new evidence disproving Darwin's Theory of Evolution by means of Natural Selection in "The Origin of Species" and much later asked for a definition of "a species"!

Not at all. I referred to an article in the July edition of The Times Eureka magazine which states that palaeontologists no longer accept Darwins model of incremental change. Fossils fit with the theory of Punctuated Equilibria, which proposes that species remain static for long periods of time (equilibria) and then something big happens (often global extinction) followed by evolution to a more advanced species.

I have never asked for a definition of 'species'. Rather I was asked twice by one member and I suggested he check a dictionary.

Thu, 16 Sep 2010 18:10:52 UTC | #519214

Budapest's Avatar Comment 19 by Budapest

Comment 17 by rocket888: My favorite read on this is the book "Seven clues to the origin of life" by A. G. Cairns-Smith.

Your comment about ASCII has peaked my interest. Thank you, I'll look for the book.

Thu, 16 Sep 2010 18:19:24 UTC | #519224

crookedshoes's Avatar Comment 20 by crookedshoes

Willem,

No contradiction at all. The battle would not necessarily go on to date. One thing competed the other to EXTINCTION. The RNA adapted to the subordinate role because it faced extinction otherwise. Some things go extinct. The ancestor of ours that had DNA did not. The other potential life was rendered extinct or changed (adapt or die)....It is going on right now, outside our windows. Survival means survival. Not all viable answers are selected. The one that survives is the viable one that is more efficient; more selected.

And again NO. I am not and have not here referred to a species. We are not discussing evolution of a species, we are talking about evolution of a FEATURE of living things, not living things. As for things that "do not evolve anymore" This is a misnomer. We have things like horseshoe crabs that appear through out the fossil record "unchanged".... BE CAREFUL!!! Fossils only show limited data. Horseshoe crabs' behavior, courtship rituals, bloodtypes, immune systems...etc... may have evolved vastly while the "shell" stayed the same.

You also are ignoring the FACT that prokaryotes' DNA is different than eukaryotes, a fact that causes your argument to fall flat. DNA HAS CHANGED. It just hasn't changed in the way your logic wants it to. Organic molecules spontaneously arise in early earth cnditions and SELF ASSEMBLE. Your two statements have fallen.

As rocket888points out, mitochondria do "read" the code differently. They are divergent in the exact area you are looking for. Also, the postulate of the RNA world predating the dawn of life is the likely "preDNA" you are looking for.

Thu, 16 Sep 2010 18:24:14 UTC | #519229

Roedy's Avatar Comment 21 by Roedy

As a computer scientist, DNA is downright miraculous. To encode behaviour and structure in traditional computer programming languages would take many orders of magnitude more information.

The thing that most puzzles me about DNA is why would a sequence at one point on a chromosome have a different effect than when it occurs elsewhere. Surely they would both synthesise the same proteins.

Unlike human language, DNA does not appear to be symbolic. It seems to directly encode the generated organic chemistry.

DNA seems to behave like positional keywords in computer languages, but that implies a convention assigning purposes to various slots on the chromosome. I have yet to hear an explanation of how these slots get assigned.

Perhaps is all just too complicated to have reached the lay public yet.

Thu, 16 Sep 2010 18:31:42 UTC | #519235

Balance_Maintained's Avatar Comment 22 by Balance_Maintained

@Crookedshoes - Do you have references for the following statements:

You also are ignoring the FACT that prokaryotes' DNA is different than eukaryotes, a fact that causes your argument to fall flat. DNA HAS CHANGED. It just hasn't changed in the way your logic wants it to. Organic molecules spontaneously arise in early earth conditions and SELF ASSEMBLE. Your two statements have fallen.

One thing competed the other to EXTINCTION. The RNA adapted to the subordinate role because it faced extinction otherwise.

Not questioning their validity, I just like to read the information from the source.

Thu, 16 Sep 2010 18:37:21 UTC | #519240

Sciros's Avatar Comment 23 by Sciros

This is a contradiction, if there has been a battle between competing systems, this battle should go on up to date!

On what basis do you make this assertion? Also explain what you mean when you say 'contradiction,' as you have not pointed one out.

Every generation would generate slightly differences in the way they interprete the digital information with no compatibility anymore...

Again, on what basis do you figure this? Why should the mechanism by which DNA drives an organism's development change across generations? Mind you, that mechanism needs to work in order for there to be a resulting organism in the first place.

This would falsify the evolution theory as there could exist a specie which didn’t evolve anymore since it was so strong and worked well…

Being "strong" and "working well" isn't going to keep a gene pool in any sort of stasis. There are other motivators for change. But indeed if an organism is so well suited to its environment that there are few pressures for major phenotypic adaptation, you'll not end up with many measurable phenotypic changes over the generations. That's why many living things have remained quite close to the same for millions of years and survive to this day.

So again my two statements keep on standing: If the mechanism behind DNA processing is uniform though all what lives, someone or something needs to have stopped the evolution process in it on a certain point.

This is obviously incorrect. All your claim would mean is that no other process has evolved, possibly because the chemistry involved is complex enough that even small changes end in failure from the get-go. You say you have a CS background. Then here's an elementary analogy. You have a .png file. Photoshop will interpret this file elegantly and display an image. Notepad can open a .png file, but you will see a bunch of gibberish. The interpretation is different and does not do what you need. If other interpretations produce gibberish, then the one that does work will invariably be the one that persists, if a working interpretation is necessary (which for DNA it is).

If DNA processing is not a product of evolution, something or someone needs to have created it.

But since it's a product of evolution, your point is moot.

Updated: Thu, 16 Sep 2010 18:43:41 UTC | #519242

Balance_Maintained's Avatar Comment 24 by Balance_Maintained

Also @Crookedshoes

According to this website:

For example, the DNA in the two cell types is precisely the same kind of DNA, and the genetic code for a prokaryotic cell is exactly the same genetic code used in eukaryotic cells.

So if you have a reference for your statement:

You also are ignoring the FACT that prokaryotes' DNA is different than eukaryotes, a fact that causes your argument to fall flat. DNA HAS CHANGED.

edit

The site does point out some differences but it is still DNA of the same kind and code.

Cheers

Updated: Thu, 16 Sep 2010 18:43:56 UTC | #519245

crookedshoes's Avatar Comment 25 by crookedshoes

Balance Maintained, You are making me alternately laugh and cry. Sure I have references for the difference in Prokaryotic vs. Eukaryotic DNA. These references are in EVERY SINGLE BIOLOGY TEXTBOOK AVAILABLE (short of the ones that have been doctored by Ray Comfort and his ilk.) Specifically, Prokaryotic DNA is circular not linear. It is not affiliated with histone protiens. It is not incorporated into a nucleus. Prokaryotic DNA is also regulated differently that Eukaryotic....Proks use operons as on off switches while Euks use more sophisticated methods for turning on and off their genes. Wait! There's more!!!!! Eukaryotes DNA has vast "junk" (not really considered junk anymore) but, Prokaryotes do not have "wasted" sequences. ALso there are vast triplet repeats and other repeats at the middle and ends of eukaryotic chromosomes that are called the centromere and telomere. Prokaryotes do not have these. Prokaryotes also can transfer their DNA to one another via several vehicles, one is called a plasmid. These are exclusively prokaryotic.

Even more: mitochondria and chloroplasts have their own DNA in their stroma and matrix....It is CIRCULAR and not affiliated with proteins!!! A smoking gun for Lynne Margulis' ENDOSYMBIOTIC THEORY.

Now the crying part: You learned this in high school biology. More tears: You quote this: For example, the DNA in the two cell types is precisely the same kind of DNA, and the genetic code for a prokaryotic cell is exactly the same genetic code used in eukaryotic cells.

This statement is somewhat misleading: the DNA is the same from the standpoint that the adenine, cytosine, guanine, and thymine nucleotides are consistent throughout DNA and universal. HOWEVER, all the changes I have listed above are all relevant, significant, and evolutionary. You seem to NEED the bases to change from ATCG to some other system of nucleotides for your satisfaction. THERE IS NO PRESSURE FOR THOSE BASES TO CHANGE. The pressure is in different directions. That doesn't mean it is not evolving. It is just not evolving in a way that satisfies your need.

The differences we are discussing are huge evolutionary differences. They revolve around the packaging and regulation of the DNA. And are the real basis behind the jump from single celled organisms to the multicellularity we see around us today. Hope this helps.

Thu, 16 Sep 2010 19:03:03 UTC | #519261

Alan4discussion's Avatar Comment 26 by Alan4discussion

Budapest: You have not answered my questions as to your qualifications or understanding for making sweeping statements about science! You seem to jump around fiddling with scraps of inconclusive information and then making it up! No one has said evolution proceeds at a uniform rate. It is well known that there is rapid expansion and evolution of remaining species after large extinction events.

There also seems to be a gulf in the level of understanding of computer code and of DNA code among participants in this thread. When computer code is mixed up or corrupted, as genes are in mutation, it would be most unusual to throw away millions computers until one was found where the mixed up code was an improvement as happens with mutated eggs, seeds, spores and bacteria. Computers are not self replicating. The analogies with well known commercial programs are therefore irrelevant! I also have doubts as to the relevance of computer programs which generate code, although I would be interested if any geneticists would like to comment. There is sound evidence that all present life evolved from a single source. I would speculate that there could have been others which were predated or driven to extinction by this one form, or they could simply not have been durable enough to leave a record.

Thu, 16 Sep 2010 19:06:44 UTC | #519265

God fearing Atheist's Avatar Comment 27 by God fearing Atheist

Two things: Luca and hill climbing

Evolution is a hill climbing algorithm. It will reach a local maximum, but there is no guarantee it will reach a global maximum. As a computer scientist you should understand it, but for everyone else I will explain. Suppose you are standing blindfold on a hilly terrain and need to reach a hill top. You tap the ground to the North, West, South and East to see which is the highest, take a step in that direction and repeat. You keep going until every direction is downhill. You are now at a local peak. Evolution works like that. The taps are random mutations and the "height" is the probability of survival (in the current environment).

Luca is the last universal common ancestor. If Luca had a genetic code that was at the top of a local fitness peak, then any mutation would be downhill (less fit), and therefore deselected by evolution. I.e. the genetic code has been stable for 3.5 billion years.

Prior to Luca there may have been many different genetic codes. They may have had equal fitness, and the Luca code just got lucky, or, more likely, the Luca code was fitter, and drove the others to extinction.

Note that once a gene is on a peak there is no way out. To escape to a fitter peak it has to cross a valley - a valley of death. The giraffe's laryngeal nerve is an example.

BTW Budapest

Comment 18 by Budapest :

hill climbing is the explanation for Punctuated Equilibria. Once an organism reaches a local peak in gene space it has nowhere to go. It will not change for hundreds of millions of years. However, the local peak is in relation to its current environment, so if that changes the location of the peak can change, and so the organism will start evolving again towards the new peak.

Updated: Thu, 16 Sep 2010 19:12:28 UTC | #519267

Sciros's Avatar Comment 28 by Sciros

Computers are not self replicating. The analogies with well known commercial programs are therefore irrelevant!

It was relevant enough if you understood the point the analogy was conveying. What's irrelevant is whether the programs are well known and commercial :-P

The analogy wasn't about changes leading to improvements. It was about one interpretation mechanism working and another not, when presented with identical input.

Thu, 16 Sep 2010 19:13:51 UTC | #519271

crookedshoes's Avatar Comment 29 by crookedshoes

God fearing, I really think highly of your "hill climbing" algorithm. I have seen Richard use "Mt. Improbable" and love that too. Thanks, I am gonna steal it from you, if you do not mind. crooked

Thu, 16 Sep 2010 19:18:27 UTC | #519277

EvolutivelySpeaking's Avatar Comment 30 by EvolutivelySpeaking

Willem,

Great ddiscovery! Hats off to pattern recognition. It appears you have noticed the same patterns within the DNA/RNA sequences as this other team of scientists have discovered. They mention a superset of instructions and subsets, one of which comprising ours. They also mention subroutines, which sounded to me similar to linked-list operations (push,pop..).

http://www.agoracosmopolitan.com/home/Frontpage/2007/01/08/01288.html

Someone needs to please run genetic programming routines on all available dna sequences, process the mutations in order to extract the routines inherent in the originals. This would be like using an atom smasher to find out what is inside.

I have been thinking the article above and now that you post this, these existing patterns need to be discovered. And the beauty is that the mechanisms of operation, such as basic edit, copy, paste, link and recompile of code will reveal itself.

The moment we can decode our dna, we can reconstruct our essence without dangerous and unnecessary subsets: the agressor gene, the aging gene and any other negatively impacted ones.

Go Willem, find some more high level programmers, maybe get a hold of Prof. Dorsey at the University of Mississippi (Genetic Programming genius), tell him Dirk and Adam said hello. He can help you with the GP aspects.

As to the nonsensical comments from the ignorant and indifferent sections of the peanut gallery, these are the best criticisms you can come up with? Come on, do some thinking and then hit the keyboard. Not impressive in terms of demonstrating logical thinking.

Thu, 16 Sep 2010 19:22:45 UTC | #519283