Evolution of de novo genes; a further nail in the coffin of intelligent design?

FrumiousBandersnatch

Well-Known Member
Mar 20, 2009
15,264
8,058
✟326,861.00
Faith
Atheist
Yet, we have to go outside of the observable when we look back to the origin of life and information.
We have to use an indirect approach - but the basic methodology still applies: hypotheses followed by experiment and observation. In this case, the hypotheses involve the chemistry of the precursors to life and the environment they occurred in.
 
  • Agree
Reactions: pitabread
Upvote 0

Oncedeceived

Senior Veteran
Jul 11, 2003
21,214
629
✟66,870.00
Faith
Christian
Marital Status
Married
We have to use an indirect approach - but the basic methodology still applies: hypotheses followed by experiment and observation. In this case, the hypotheses involve the chemistry of the precursors to life and the environment they occurred in.
The chemistry of precursors are the problem. I am sure that you are aware of the chicken or the egg dilemma. The environment is a hard one as well with many problems in regards to the longevity of chains within certain environments that were considered likely early in earth's history.
 
Upvote 0

Oncedeceived

Senior Veteran
Jul 11, 2003
21,214
629
✟66,870.00
Faith
Christian
Marital Status
Married
Sure, but in a similar context, hydrogen and oxygen atoms are needed prior to the formation of water molecules.
That is not information.

That doesn't necessarily mean there is anything symbolic there.
The bases of DNA are symbolic words. The sequence of the letters make up the words so to speak for mRNA to decode.



Define what you mean by "instructed". How do you think this process works exactly?
The genetic information contained within DNA is re-written which then instructs messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it provides the basis for the translation of DNA.



What do you mean by "put into the sequences"? What sequences are you talking about?
The sequences of the bases.
 
Upvote 0

FrumiousBandersnatch

Well-Known Member
Mar 20, 2009
15,264
8,058
✟326,861.00
Faith
Atheist
The chemistry of precursors are the problem. I am sure that you are aware of the chicken or the egg dilemma. The environment is a hard one as well with many problems in regards to the longevity of chains within certain environments that were considered likely early in earth's history.
That's why there is such a variety of work going on in this field. We solve problems, find explanations, and learn about the world, by observation and experiment, not by labelling things 'miracle'.
 
  • Agree
Reactions: pitabread
Upvote 0

pitabread

Well-Known Member
Jan 29, 2017
12,920
13,372
Frozen North
✟336,823.00
Country
Canada
Faith
Agnostic
Marital Status
Private
That is not information.

Well, why not?

In both cases we're talking about chemical reactions.

The bases of DNA are symbolic words. The sequence of the letters make up the words so to speak for mRNA to decode.

DNA bases aren't symbolic words. They are organic molecules.

There are no words in DNA, at least not in the context of a symbolic language like English.

Using analogies like language to explain concepts in DNA are one thing. But that doesn't make them one and the same.

The genetic information contained within DNA is re-written which then instructs messenger RNA (mRNA) by RNA polymerase.

But how does that work? What is the "instructing" that you think is happening here?

Be specific.

The sequences of the bases.

This still doesn't make sense in the context of, "the genetic information is stored information and then put into the sequences for a specific result."

The information we are talking about is the sequence (of nucleotides). It's one and the same.

I still don't know what you mean by "put into the sequences for a specific result".
 
Upvote 0

Oncedeceived

Senior Veteran
Jul 11, 2003
21,214
629
✟66,870.00
Faith
Christian
Marital Status
Married
No, DNA is nothing like computer hardware and software.

DNA is a biochemical molecule. The information storage in DNA is the particular nucleotide sequence that manifests that particular DNA molecule. In that respect, the "hardware" and "software" are one and the same.

In contrast, a computer is really just a fancy electrical circuit. Information can be stored in a computer in different means, but it's typically either via electrical charges or magnetic polarity. In a computer, the information can be decoupled from the storage medium. The latter can exist without the former.

The informational part of DNA consists of four molecular building blocks, often referred to simply by the letters A, C, T and G. Sequences of these letters spell out the manual for building the organism. The instructions are read out and implemented by complex molecular machinery with finely honed control mechanisms. Because the instructions are in code, they must first be decoded, or translated, by a mathematical procedure, before the cell can implement them. It took a few more years for scientists to crack the code and reveal the language of life, and several decades before DNA sequencing became commonplace.

The rapid progress made in molecular biology in the 1950s coincided with major advances in computing, and it was soon clear that the two subjects were intertwined. DNA, which serves as a database storage facility, is like the hard drive on a computer. The instructions etched into DNA and the associated readout and translation machinery resemble computer operating systems and software.

It turns out that the analogy goes far deeper. Human DNA codes for about 20,000 genes, but only a fraction of them are “expressed” at any one time. By expressed, I mean they get read out, causing a specific protein to be manufactured. Put simply, your genes are all there inside you, but they may be either “on” or “off” depending on circumstances. Genes are often linked via chemical messengers because a gene that codes for one protein may serve to switch others on or off. In this way, genes can form networks, sometimes of great complexity. It is the networks, rather than individual genes, that carry out the lion’s share of regulatory and control functions. In this respect, biology closely resembles electronics. Biologists routinely refer to the “wiring diagram” of gene networks, and have discovered that some arrangements form modules that can behave like the logic gates in a computer; by wiring together many such gates, cells are able to carry out complex computations.
Paul Davies What is life? | Paul Davies

Researchers find surprising similarities between genetic and computer codes
https://phys.org/news/2013-03-similarities-genetic-codes.html
 
Upvote 0

Oncedeceived

Senior Veteran
Jul 11, 2003
21,214
629
✟66,870.00
Faith
Christian
Marital Status
Married
That's why there is such a variety of work going on in this field. We solve problems, find explanations, and learn about the world, by observation and experiment, not by labelling things 'miracle'.
Why do you think I'm labelling things 'miracle'.
 
Upvote 0

FrumiousBandersnatch

Well-Known Member
Mar 20, 2009
15,264
8,058
✟326,861.00
Faith
Atheist
That is not information.
It certainly is.

The sequence of the letters make up the words so to speak for mRNA to decode.

The genetic information contained within DNA is re-written which then instructs messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it provides the basis for the translation of DNA.
There's no decoding - mRNA simply makes a 'mirror' copy; the process is called transcription, and the source DNA is called the template strand.
 
  • Agree
Reactions: pitabread
Upvote 0

Oncedeceived

Senior Veteran
Jul 11, 2003
21,214
629
✟66,870.00
Faith
Christian
Marital Status
Married
Not really. Even the comparison of transcription to an interpreter is pretty flaky - although the whole transcription process could be considered interpretation.

I graduated in Human Biology and spend around 12 years doing environmental physiology research and development before switching track to a career in software development, from assembler code, through C and C++, to Java. I'm retired now, but I keep up to date.

So you see I'm reasonably well qualified to say that DNA isn't really like computer code. It's an easy comparison to make because it's the closest analogy we have, but it's just an analogy.

It's easy and tempting to look at something complex or that's not understood and claim agency and purpose - and we seem primed to do that, but there are no well-defined criteria to make that judgement, and every time we've investigated such situations, we've discovered that the more we understand them the more they look natural and the less they look artificial. Labelling it as intelligent design is a dead-end non-explanation - it tells you nothing about the phenomenon you're trying to understand, and introduces a new entity for which there is no evidence or explanation - it raises more questions and answers none.

By continuing to investigate the origins of life, we've made a lot of new and remarkable discoveries - how cell membranes can spontaneously self-assemble, grow, and divide, how simple metabolic cycles can spontaneously arise, how RNA can act as both a template and an enzyme, and so-on. We don't yet know how DNA originated, but we're making progress.

Intelligence can construct ordered systems, but so can nature; complexity is an emergent property of low entropy systems with significant amounts of free energy. All of chemistry can be seen as the interactions between elements of a coded system where the electrons in the outer shell are instructional.

Well that's debatable - the earliest replicators (just a molecule that can duplicate itself or be duplicated) would probably not qualify for most definitions of 'life'; the first proto-cells likewise - they'd just swell and divide, splitting their contents. The major complexities would develop - evolve - over time.

There's always information.

A simple replicator doesn't even grow, it just makes copies or gets duplicated. As long as the duplication process is imperfect, it will evolve.

If you like. but everything can be considered to have and so encode information. Life is a particularly complex and indirect way of increasing entropy through oxidation; as Albert Szent-Györgyi said, "Life is nothing but an electron looking for a place to rest".

That's true only for complex life where individual creatures develop according to an inherited template. Simple replicators can form competitive ecosystems with a variety of roles and niches, without individual development or growth - plenty of time for that to develop later.
Thank you for your time on this response. I want to give it the time it deserves so I will get back when I can.
 
Upvote 0
This site stays free and accessible to all because of donations from people like you.
Consider making a one-time or monthly donation. We appreciate your support!
- Dan Doughty and Team Christian Forums

Speedwell

Well-Known Member
May 11, 2016
23,928
17,625
81
St Charles, IL
✟347,270.00
Country
United States
Faith
Other Religion
Marital Status
Married
That is the whole of the argument. No one at this time knows how it got there.
Evolutionary biologists have a pretty good idea--it's generated by a recursive process. If you don't like that then you're going to have to come up with something else. Otherwise you've got nothing.
 
Upvote 0

FrumiousBandersnatch

Well-Known Member
Mar 20, 2009
15,264
8,058
✟326,861.00
Faith
Atheist
Researchers find surprising similarities between genetic and computer codes
https://phys.org/news/2013-03-similarities-genetic-codes.html
The headline is misleading; the article describes statistical similarities in the way parts of the genetic code are used in metabolism and the modularity of complex systems such as operating systems. IOW it refers to the system organization, not the code:

"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."
 
Upvote 0

pitabread

Well-Known Member
Jan 29, 2017
12,920
13,372
Frozen North
✟336,823.00
Country
Canada
Faith
Agnostic
Marital Status
Private
Because the instructions are in code, they must first be decoded, or translated, by a mathematical procedure, before the cell can implement them.

I'm not sure what they mean by a "mathematical procedure". The translation process in DNA is chemical, not mathematical.

Unless these are referring to the modeling of the process itself. But a model is not the same thing as the process itself.

The rapid progress made in molecular biology in the 1950s coincided with major advances in computing, and it was soon clear that the two subjects were intertwined. DNA, which serves as a database storage facility, is like the hard drive on a computer. The instructions etched into DNA and the associated readout and translation machinery resemble computer operating systems and software.

In a literal sense, this is incorrect. Instructions aren't "etched" into DNA. They *are* the DNA.

I'm also not sure in what sense they think that translation processes resembling a computer OS and software. This seems to be a case of over-extending an analogy that doesn't work when you start to look at the literal differences of how each respective thing actually works.

Researchers find surprising similarities between genetic and computer codes
https://phys.org/news/2013-03-similarities-genetic-codes.html

This doesn't appear to be anything particularly revealing. All they are doing is drawing similarities between how there are common components in biology and common components in computer software.

Again, when you look into how these things work in a literal sense, the differences rapidly become apparent.
 
Upvote 0

FrumiousBandersnatch

Well-Known Member
Mar 20, 2009
15,264
8,058
✟326,861.00
Faith
Atheist
I'm not sure what they mean by a "mathematical procedure". The translation process in DNA is chemical, not mathematical.

Unless these are referring to the modeling of the process itself. But a model is not the same thing as the process itself.

In a literal sense, this is incorrect. Instructions aren't "etched" into DNA. They *are* the DNA.

I'm also not sure in what sense they think that translation processes resembling a computer OS and software. This seems to be a case of over-extending an analogy that doesn't work when you start to look at the literal differences of how each respective thing actually works.
Yes. Again, a number of clumsy analogies. I'm guessing this Paul Davies (physicist and astrobiologist) is the same guy lambasted for his theory about cancer.
 
Upvote 0
This site stays free and accessible to all because of donations from people like you.
Consider making a one-time or monthly donation. We appreciate your support!
- Dan Doughty and Team Christian Forums

Speedwell

Well-Known Member
May 11, 2016
23,928
17,625
81
St Charles, IL
✟347,270.00
Country
United States
Faith
Other Religion
Marital Status
Married
When an intelligent agent creates something, at some point he s going to have to start using physical forces to move material objects around. It doesn't matter whether you call it "ID" or "information." At some point he's going to have to move from intelligent design to intelligent construction. But that's the hand we never see. That's the hand the magician has in hs pocket while he pulls a rabbit out of a hat with the other.

All we are left with is a natural process which appears adequate to produce the results claimed for it. I want to see the other hand.
 
Upvote 0

Shemjaza

Regular Member
Site Supporter
Apr 17, 2006
6,220
3,838
45
✟926,829.00
Country
Australia
Faith
Atheist
Marital Status
Single
Politics
AU-Greens
When an intelligent agent creates something, at some point he s going to have to start using physical forces to move material objects around. It doesn't matter whether you call it "ID" or "information." At some point he's going to have to move from intelligent design to intelligent construction. But that's the hand we never see. That's the hand the magician has in hs pocket while he pulls a rabbit out of a hat with the other.

All we are left with is a natural process which appears adequate to produce the results claimed for it. I want to see the other hand.
"Now! Gentle audience... watch in wonder as the invisible magician pulls this rabbit out of a rabbit burrow!"
 
Upvote 0