DNA as a programming language

[Loudmouth]

Not only that, but the cell containing the DNA reminds me of a computer system.

• Information storage: DNA
• Processors: Enzymes
• Process spawning: Ribosomes
• Message handlers: RNA

A computer can make for a good analogy, but the analogy breaks down when you get to the nitty-gritty of the processes.

 

[ChetSinger]

The answer is yes. TTT codes for a different amino acid than AAA (or AAT, etc).

Thanks, you've corrected a misconception. I think I see now why pshun2404 mentioned 64 possible combinations. There are four possibilities per rung, and three rungs per specification, or 4^3. Do I have that right?

 

[sfs]

Thanks, you've corrected a misconception. I think I see now why pshun2404 mentioned 64 possible combinations. There are four possibilities per rung, and three rungs per specification, or 4^3. Do I have that right?

Yes, that is correct. In the usual genetic code, 3 of the 64 are stop codons, and the rest code for one of the 20 amino acids.

 

[[serious]]

Each rung in the ladder is always either an adenine/thymine pair or a cytosine/guanine pair. There are no other combinations, so it's binary. The rungs remind me of "bits" in a computer storage system, which always have one of two possible states.

Under that logic, nothing but binary exists. In base 10, for example, every digit is either greater or equal to 5, or less than 5.

 

[ChetSinger]

Under that logic, nothing but binary exists. In base 10, for example, every digit is either greater or equal to 5, or less than 5.

I've learned (see above) that the rungs are a base-4 code, not a base-2 one.

 

[stevevw]

Not a very good programming language. Every human generation contains, on average, about 60 mutations.
Over 25% of pregnancies end in miscarriage. Due, in part, to more severe "copying" errors.

And evolution claims that this process of random mutations and natural selection is able to create the amazing complexity and variety we see in all living things from basically nothing and less complex creatures. That living things become fitter and more viable as time goes on rather than more error prone and gradually less fitter. It gives a new meaning to survival of the fittest being the survival of those with the least mutations that cause the deterioration of living things.

 

[pat34lee]

You can copy a cd/dvd/BluRay millions of times without any errors. Whether the media contain music or code makes no difference.

Good software/hardware catches copy errors by reading the original and the copy and comparing the two.

Millions of times? On the same hardware? I think you discount wear and tear, random damage such as scratches from misuse or accident, bad reads or writes, etc. How about glitches and viruses? DNA has to deal with such problems and much more.

 

[ecco]

Millions of times? On the same hardware? I think you discount wear and tear, random damage such as scratches from misuse or accident, bad reads or writes, etc. How about glitches and viruses? DNA has to deal with such problems and much more.

So how do they produce millions of copies of movies on disks. How did they, not too long ago, produce millions of copies of music albums?

When a copying machine started producing errors it was replaced.

 

[ecco]

ecco said (RE: DNA): ↑

Not a very good programming language. Every human generation contains, on average, about 60 mutations.
Over 25% of pregnancies end in miscarriage. Due, in part, to more severe "copying" errors.

And evolution claims that this process of random mutations and natural selection is able to create the amazing complexity and variety we see in all living things from basically nothing and less complex creatures. That living things become fitter and more viable as time goes on rather than more error prone and gradually less fitter.

Yes it does. It isn't my problem that you don't understand the process.

The 25% of miscarriages don't carry on their genes to the next generation do they?

There are about 80,000,000 genes in the human genome.

The 60 or so mutations per generation are not necessarily disabling. If they are severely disabling, those genes also don't carry on to the next generation do they?

Of the remaining, some may provide a tiny bit better eyesight, or a tiny bit more strength, or a tiny bit more speed, or a tiny bit smarter brain or a tiny bit worse eyesight, or a tiny bit less strength, or a tiny bit less speed, or a tiny bit dumber brain. A TINY BIT!

Those individuals who got the "better" have a tiny bit more chance of producing offspring. A TINY BIT!

Those individuals who got the "worse" have a tiny bit less chance of producing offspring. A TINY BIT!

A TINY BIT!

It gives a new meaning to survival of the fittest being the survival of those with the least mutations that cause the deterioration of living things.

It's the same meaning that Darwin proposed a Century and a half ago. The only difference is that now his concept has been verified by Paleontologists, Biologists and Geneticists to name just a few.

If you were alive in 1700 you probably would have been arguing against heliocentricity. For all I know, you may still believe in geocentricity.

 

[pshun2404]

ecco said (RE: DNA): ↑






Yes it does. It isn't my problem that you don't understand the process.

The 25% of miscarriages don't carry on their genes to the next generation do they?

There are about 80,000,000 genes in the human genome.

The 60 or so mutations per generation are not necessarily disabling. If they are severely disabling, those genes also don't carry on to the next generation do they?

Of the remaining, some may provide a tiny bit better eyesight, or a tiny bit more strength, or a tiny bit more speed, or a tiny bit smarter brain or a tiny bit worse eyesight, or a tiny bit less strength, or a tiny bit less speed, or a tiny bit dumber brain. A TINY BIT!

Those individuals who got the "better" have a tiny bit more chance of producing offspring. A TINY BIT!

Those individuals who got the "worse" have a tiny bit less chance of producing offspring. A TINY BIT!

A TINY BIT!



It's the same meaning that Darwin proposed a Century and a half ago. The only difference is that now his concept has been verified by Paleontologists, Biologists and Geneticists to name just a few.

If you were alive in 1700 you probably would have been arguing against heliocentricity. For all I know, you may still believe in geocentricity.

Now now, you were doing so well...stooping to insult is both crass and very unprofessional...only one of creationist Darwin's ideas have really been useful (Natural Selection) and that has had to be refined....and nothing has shown the application of this in say changing creatures of one genus into creatures of an entirely different genus over time...speciation has only proved the genetic mechanism in producing variation of or in the same creature.

 

[stevevw]

In this peer-reviewed publication they find the "redundancy of the genetic code enables translational pausing". Which alone is fascinating, but in reading about how they found this out was the interesting part:

"Previously, evolutionary biologists have not been aware of the conceptual complexity required for genomic programming"

"We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties."

"Within the genome domain, executable operations format, read, write, copy, and maintain digital Functional Information (FI)"

"They reveal the ribosome, among other things, to be not only a machine, but an independent computer-mediated manufacturing system"

"We show in this paper that the bit patterns representing TP instructions follow logical and linguistic rules that support their use in a non-ambiguous way."

"We posit that the operation of the ribosome can be viewed as a type of physical multi-core processor in terms of concurrently executing amino acid elongation and pausing control to enable protein folding."

"The ribosome functions as a multi core processing protein synthesis machine."

"The ribosome can be thought of as an autonomous functional processor of data that it sees at its input."

"Such an iterative process nicely lends itself to an algorithmic process should geneticists experiment with writing their own genetic code."

"It has been shown that both the genetic code and TP code are decoupled allowing simultaneous decoding and dual functionality within the ribosome using the same alphabet (nucleotides) but different languages."

"The TP code also exhibits a syntax or grammar that obeys strict codon relationships that demonstrate language properties."


Not just a metaphor, it demonstrates language properties. And all that was just to show:
"The functionality of condonic redundancy denies the ill-advised label of “degeneracy.”
Because:
"Redundancy of the genetic code enables translational pausing"

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033003/

Here are some more peer reviewed papers on DNA being likened to a programming code or language.

Functional information and the emergence of biocomplexity
Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex) = -log2[F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function [greater than or equal to] Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree.
http://www.pnas.org/content/104/suppl_1/8574.full
double helix feature The digital code of DNA
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html
” MIT Professor of Mechanical Engineering Seth Lloyd
It’s been known since the structure of DNA was elucidated that DNA is very digital. There are four possible base pairs per site, two bits per site, three and a half billion sites, seven billion bits of information in the human DNA. There’s a very recognizable digital code of the kind that electrical engineers rediscovered in the 1950s that maps the codes for sequences of DNA onto expressions of proteins.
https://edge.org/conversation/seth_lloyd-seth-lloyd—life-what-a-concept

 

[stevevw]

ecco said (RE: DNA): ↑






Yes it does. It isn't my problem that you don't understand the process.

The 25% of miscarriages don't carry on their genes to the next generation do they?

There are about 80,000,000 genes in the human genome.

The 60 or so mutations per generation are not necessarily disabling. If they are severely disabling, those genes also don't carry on to the next generation do they?

Of the remaining, some may provide a tiny bit better eyesight, or a tiny bit more strength, or a tiny bit more speed, or a tiny bit smarter brain or a tiny bit worse eyesight, or a tiny bit less strength, or a tiny bit less speed, or a tiny bit dumber brain. A TINY BIT!

Those individuals who got the "better" have a tiny bit more chance of producing offspring. A TINY BIT!

Those individuals who got the "worse" have a tiny bit less chance of producing offspring. A TINY BIT!

A TINY BIT!

So if its such a TINY BIT as you say that doesn't happen that often how does this account for the massive amount of complexity and variety that has ever been and is seen in all living things today. What you have explained with those TINY BITS of better eyesight or being smarter or faster are abilities that already exist and therefore adjustments to stuff that has already got all the genetic info and function there. What about the new stuff that has to be made when it isn't there in the first place.

Considering that these are very complex abilities that involved massive amounts of intricate and complex biological abilities they just cant be mutated in one go. So if it is all about mutating these TINY BITS of vastly complex systems and features gradually how is there enough time or ability for those very rare mutations to build all that variety and complexity. If the majority of mutations are not going to add anything or have a selective value then how can evolution have the time to evolve that complexity and variety.

From what I have read and understand the majority of mutations do have a fitness cost. If anything they cause less fit living things and a loss of info rather than more fit and complex creatures. Even so if there is very rare mutations that only add TINY BITS of new functions and features that weren't there to begin with how would evolution account for such a massive amount of complexity and variety in the time available. How does a process that seems to take away be the same process that adds something better.

It's the same meaning that Darwin proposed a Century and a half ago. The only difference is that now his concept has been verified by Paleontologists, Biologists and Geneticists to name just a few

I have read that his theory is also being found to not be the main driving force for change in living things. That non adaptive forces such as HGT are more responsible.

If you were alive in 1700 you probably would have been arguing against heliocentricity. For all I know, you may still believe in geocentricity.

I follow the evidence but I dont assume that science knows everything and nor is it the be all and end all for everything. So I have more than science to use to look for the answers and dont restrict myself. Sometimes the answers may lie outside the boundaries of scientific thought and evidence.

 

[ecco]

pshun2404

....and nothing has shown the application of this in say changing creatures of one genus into creatures of an entirely different genus over time...speciation has only proved the genetic mechanism in producing variation of or in the same creature.

You, like many others, believe in micro evolution but not macro evolution. But you cannot see that they are one and the same. The only difference is the scale of time and the impact of environmental changes.

Stevevw

Considering that these are very complex abilities that involved massive amounts of intricate and complex biological abilities they just cant be mutated in one go. ... If the majority of mutations are not going to add anything or have a selective value ...

I certainly did not say “ the majority of mutations are not going to add anything”. I said (in part) "...some may provide a tiny bit better eyesight...Those individuals who got the "better" have a tiny bit more chance of producing offspring."

Stevevw

...how can evolution have the time to evolve that complexity and variety.

Three and a half billion years is a lot of time.

Stevevw

What about the new stuff that has to be made when it isn't there in the first place.

Change is new stuff.


We've gotten off topic, but...

All religious people pick and choose how much and what parts of scripture to take literally. Using christianity as an example...

• Some take all of scripture as 100% literal, OT and NT.
• Some take parts like Genesis as allegory.
• Some completely ignore the OT and just focus on Jesus.

Wherever this line falls, it defines the level of science that an individual accepts and what parts of science to disregard. Whenever personally held religious beliefs come in conflict with science, the religious beliefs will prevail.

There are tens of thousands of scientists who consider themselves to be christians and fully accept evolution. There are thousands of christian clergy who fully accept evolution. On the other end of the spectrum are people who will never accept parts or all of evolution because it conflicts with their “line in the sand”.

Case in point....

Stevevw

I follow the evidence but I dont assume that science knows everything and nor is it the be all and end all for everything. So I have more than science to use to look for the answers and dont restrict myself. Sometimes the answers may lie outside the boundaries of scientific thought and evidence.

I you look carefully at what parts of science you believe/disbelieve and what parts of scripture you believe/disbelieve, I think you will find a correlation.


I'll be out of town for a few days but I'll address your responses, if any, on Monday or Tuesday.

 

[pat34lee]

Those individuals who got the "better" have a tiny bit more chance of producing offspring. A TINY BIT!
Those individuals who got the "worse" have a tiny bit less chance of producing offspring. A TINY BIT!
A TINY BIT!

I agree totally.
Which is a problem for evolution.
What Darwin did not know is that
Mutations are 99.9% harmful or neutral at best
.1% or less beneficial
Which will add up faster?

 

[sfs]

I agree totally.
Which is a problem for evolution.
What Darwin did not know is that
Mutations are 99.9% harmful or neutral at best
.1% or less beneficial
Which will add up faster?

The beneficial ones. Well, actually the neutral ones, but since they mostly don't affect anything important, we can ignore them. The harmful ones are weeded out with great efficiency by natural selection, which leaves the beneficial mutations to accumulate. You can see this in a long-term evolution experiment: if you put bacteria, say, in a new environment, their fitness will get steadily better for a long time.

So no, this is not a problem for evolution.

 

[The Barbarian]

So no, this is not a problem for evolution.

Many bacteria, placed in a stressful environment, will start to mutate at higher rate. This kills most of them, but a few become more fit to that environment, and so natural selection encourages that response.

 

[[serious]]

I agree totally.
Which is a problem for evolution.
What Darwin did not know is that
Mutations are 99.9% harmful or neutral at best
.1% or less beneficial
Which will add up faster?

We can actually figure that out. Say we have a plate of 1 million bacteria. We will ignore neutral mutations, and assume there are 10 time the number of bad mutations as good. So 0.1% good, 1% bad. We'll say that on average a good mutation makes a bacteria 20% more successful, and a bad mutation makes it 20% worse. Let's grow the population to 1 trillion. We'll double the baseline each generation and adjust the good and bad off of that.
Generation 1: 10,000 bad, 1,000 good, and 989,000 neutral
Generation 2: 18,000 2,200 1,978,000
Generation 3: 32,400 4,840 3,956,000
Generation 4: 58,320 10,648 7,912,000
...
Generation 12: 6,426,841 5,843,183 2,025,472,000
Generation 13: 11,568,313 12,855,002 4,050,944,000
Generation 14: 20,822,964 28,281,005 8,101,888,000
...
Generation 20: 708,235,345 3,206,497,721 518,520,832,000
Generation 21: 1,274,823,622 7,054,294,987 1,037,041,664,000
Generation 22: 2,294,682,519 15,519,448,971 2,074,083,328,000

So 13 generations for the good to overtake the bad, and by the end of our run, the good was 7 times as common as the bad.

 

[[serious]]

The beneficial ones. Well, actually the neutral ones, but since they mostly don't affect anything important, we can ignore them. The harmful ones are weeded out with great efficiency by natural selection, which leaves the beneficial mutations to accumulate. You can see this in a long-term evolution experiment: if you put bacteria, say, in a new environment, their fitness will get steadily better for a long time.

So no, this is not a problem for evolution.

Even the neutral ones lose out in the end. In my example, that happens generation 74.

 

[sfs]

Even the neutral ones lose out in the end. In my example, that happens generation 74.

The neutral ones lose out if they're competing with beneficial ones(*); if they're not competing, then they will accumulate.

(*) Actually, most beneficial mutations are lost due to random drift.

 

[The Cadet]

• The data is binary.

Just FYI: the term you are looking for is "discrete".