Darwin and DNA
 

I wrote in response to an earlier post that “Darwinists” and “Creationists” are so busy apologetically defending their respective paradigms that they miss some very interesting opportunities to change their beliefs. It appears both camps may be inattentionally blind.


Some very interesting ideas come from what is by far the most interesting paper I have examined this year in reading about evolution and genetics. The title is NeuroTheology: Brain, Science Spirituality, Religious Experience by Rhawn Joseph, Ph.D. I was able to download the PDF for free but have been unable to locate the link I used. (If I do locate it, I will post it.)


The Book:
Neurotheology: Brain, Science, Spirituality, Religious Experience


With scientific rigor, the author presents premises and argues the following summary:

1. All ‘evolved’ properties of past, present and future species exist a priori in DNA, in a non-activated (intron) form. What appears to be mutation is in fact the activation of a priori potential, coded in DNA. Speech in humans, for example. It was always there. It is also in mice, rats and dogs in an inactive ("intronic") state.


2. DNA components in an inactive state can and will conditionally respond to environmental factors. Environmental factors can activate genes existing a priori in a non-activated state. This can lead to what we currently call "evolved" features and even some all-new species. In all cases the potential for all polymorphism in living creatures lies dormant, pre-coded in their DNA until environmental factors activate it.

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As per the amazing claim that evolution is based on “random mutations” let us consider the so-called “language gene” known as FOXP2. This gene existed prior to the evolution of language, and is found in the genome of other mammals, including mice, rate, dogs, cats, chimopanzees and so on, but in a non-activated proteim-protected form. The gene was identified by Dr. Anthony P. Monaco of the University of Oxford. FOXP2 is believed to switch on other genes during the development of the brain thus giving rise to the neural circuitry which supports human language.

However, Dr. Svante Paabo and colleagues at the Max Planck Institute for Evolutionary Anthropology, reported in the August 2002 issue of NATURE, that the exact same gene exists in a non-activated form, in mice, chimpanzees and other primates (Enard et al 2002). According to Dr. Paabo, the FOXP2 gene has remained largely unaltered during the evolution of mammals. However, in humans this formerly silent gene became activated through changes in the shape of its protective protein coat. Protein prevents the activation of genes, and removal or alteration in the shape of this protein overcoat allows for the gene to be activated.


Thus, the “language gene” did not randomly evolve through random mutations. It existed prior to the evolution of humans and prior to the evolution of language, in a silent non-activated state.


The genetic code is for the most part universal (Strachan and Reed 1996; Watson et al 1992) and there is no evidence of randomness in its organization or expression—as demanded by Darwin’s theory.


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Skeptics might be wise to withhold judgement until they have examined this book and checked the current state of scientific research in this area of genetics.

Re: Darwin and DNA
 

I'm very skeptical. I'll give you a few reasons.

1. You need a direct lineage to hold onto a genetic lineage. Are nearest common ancester with dogs was much longer ago than that with chimps. Once there's a split, genetics alone can't hold onto this information unless there's something Lamarckian or absolutely revolutionary in genetics that has gone down and I missed it.
2. It sounds like some new agey BS to make us respect animals more. Sounds like the idea came before the evidence.
3. Nature abhors waste as a general rule. Specialization seems to be more useful than something akin to the backward compatability of windows 98 with windows 3.1. So, I doubt a bunch of those introns have all this latent potential encoded in them.

It's a compelling idea and I'm interested in the book, but I have serious doubts.

Even if there's some theory that intron DNA isn't just a bunch of junk and some regulatory genes and structurally useful DNA, I would prefer to have enough data to support this theory that there are review articles with a meta-analysis confirming this idea is likely. A couple papers along this line are not enough.

I have a friend doing post-doctoral work in genetics that I'll talk with about this idea as he keeps current in the field.

How is the referencing in the back of the book? Does it cite a lot of scientific literature from journals like Science, Nature, PNAS, Cell Genetics, etc. (I realize that the first two have fallen out of favor to some extent over the last few years)?

Re: Darwin and DNA
 

[ QUOTE ]

1. All ‘evolved’ properties of past, present and future species exist a priori in DNA, in a non-activated (intron) form. What appears to be mutation is in fact the activation of a priori potential, coded in DNA. Speech in humans, for example. It was always there. It is also in mice, rats and dogs in an inactive ("intronic") state.


2. DNA components in an inactive state can and will conditionally respond to environmental factors. Environmental factors can activate genes existing a priori in a non-activated state. This can lead to what we currently call "evolved" features and even some all-new species. In all cases the potential for all polymorphism in living creatures lies dormant, pre-coded in their DNA until environmental factors activate it.



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This is an argument presented by creationists who agree that evolution takes place but say it can happen only within constraints set by God at the time of creation. Ie no evolution can lead to organisms not already potentiated explicitly by the initial creation. This argument is part of the Jehovah's Witnesses portfolio of arguments, for example.

Re: Darwin and DNA
 

Oh crap, I didn't pay enough attention to the future part.

What terrific BS. It's like the X-files latent alien hybrid DNA thing, but way, way , way more implausible.

I can't believe I bothered to reply to that crap seriously. I want that 15 minutes back.

Re: Darwin and DNA
 

If you come across more research in this area I appreciate you posting or PM ing me the links as you find them. The entire subject of introns is wide open.

Introns comprise some 97% of the strand, and very little is understood about intronic DNA. The human genome is held in exons, comprising about 3% of the strand.

Current science labels intronic DNA 'junk DNA'. It is anything but. Introns contain non-random coding that no one to my knowledge has been able to read-- YET.

Re: Darwin and DNA
 

Creationist and God and Intelligent Design (ID) and so on...all these terms are buzz phrases intended to shunt the wide-open debate to a few well-defined ideological containers.

For example many say and believe and hammer the 'intelligent design' = "teach the kids Adam and Eve in high school" notion. That is a total distortion of ID.

For example look at the theory of
Cosmic Ancestry. Few traditional religionists would even look at the first three sentences of this theory. They would throw it out. Yet, it supports the ID notion.

Re: Darwin and DNA
 

[ QUOTE ]
If you come across more research in this area I appreciate you posting or PM ing me the links as you find them. The entire subject of introns is wide open.

Introns comprise some 97% of the strand, and very little is understood about intronic DNA. The human genome is held in exons, comprising about 3% of the strand.

Current science labels intronic DNA 'junk DNA'. It is anything but. Introns contain non-random coding that no one to my knowledge has been able to read-- YET.

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I'll let you know what I find. I can tell you don't know much about genetics though. I don't mean it as a slight either. I'm just being completely honest. Before we can intelligently discuss an issue like this one, you need to know the basics of genetics and of current research and knowledge in genetics. My background is limited to basic biology coursework in high school and in college as well as courses in molecular biology and cell biology with section devoted to genetics but you've already made a few mistakes.

I'm also disappointed you didn't answer any of my questions.

Beyond that you didn't deal with any of my concerns either.

It strikes me as all very suspect. I swear the closest thing you have to evidence here is Mr. Ed.

The Worship of Random, God of Darwinism
 

Now, the entire Darwinian model ( so called "evolution") depends upon randomness as it's bedrock foundation. It's randomness that causes mutation, and it is mutation that the evolution theory depends on as the change mechanism.

The randomness idea is comforting to those who might not believe in a plan of any Kind or Type. You know what I am getting at.

Randomness is the central underlying theorem of Darwinism.

To question randomness is to question everything in the theory. And it is a theory. It may partially explain some phenomena. It's just plain lazy to assume Darwin explains everything.

DNA is anything but random. Introns contain vast non-random sequences that are as yet undecoded. For now, we simply label introns JUNK DNA.

Introns science is in its infancy.

The idea that DNA contains all the coding a priori for what we currently call "random mutations" is at least as good as any competing theory that attempts to describe parts of the Way Things Really Work.

It continues to amaze me how dogmatic people can rabidly be about their current beliefs.

As for the origin of life on earth, consider:

Cosmic Ancestry

Few religionists (including the set of all dogmatic fundamentalists, darwinists, etc) will buy this. Or even consider it. The idea is a threat to their nice convenient worldview. The idea actually supports both camps. Imagine that.

This is just ONE THEORY of MANY theories that are competing for your attention.

And we know there is no perception without attention.

Re: Darwin and DNA
 

I'm not a biologist. I'm not an authority on DNA. I am a layman curious about genetics who reads. Alot.

Consequently I cannot answer your specific questions about genetics with any authority. This explains my request for links to genetic research you may find.

What I can do is raise some obvious questions. This forum seems a perfect place to do that.

Re: Darwin and DNA
 

Entertaining concepts but wrong. It's basically taking some interesting concepts in genetics and twisting them around.

Re: Darwin and DNA
 

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Entertaining concepts but wrong. It's basically taking some interesting concepts in genetics and twisting them around.

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No way man. When Dan figures out how to activate the magical pixie DNA so that I can have a talking dog, my life will be totally way cooler.

Re: The Worship of Random, God of Darwinism
 

This thread addresses your issues with the "randomness" in evolution.

No offense, but you're the dogmatic one here. You don't even understand genetics, yet you've chosen to misapply it.

You copy and paste nicely from quasiscientific sources, but you don't know what you're talking about and neither do the sources you've latched onto.

I've dealt with fruits of your sort before. It's not worth my time. You'll probably never learn enough genetics to know why the nonsense you're preaching is even wrong. And it would only take you a few weeks to learn it.

Give me my talking dog. Until then, Mr. Ed is as close as you get. And the series was cancelled decades ago.

Re: The Worship of Random, God of Darwinism
 

[ QUOTE ]
This thread addresses your issues with the "randomness" in evolution.

No offense, but you're the dogmatic one here. You don't even understand genetics, yet you've chosen to misapply it.

You copy and paste nicely from quasiscientific sources, but you don't know what you're talking about and neither do the sources you've latched onto.

I've dealt with fruits of your sort before. It's not worth my time. You'll probably never learn enough genetics to know why the nonsense you're preaching is even wrong. And it would only take you a few weeks to learn it.

Give me my talking dog. Until then, Mr. Ed is as close as you get. And the series was cancelled decades ago.

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I think this is harsh and uncalled for.
Especially considering our "debate" in the other thread where you're spouting some strange point that highlights deficiencies in your thinking about evolution. At no point did I say anything like this to you, despite the fact that the "sometimes a little information is worse than no information" idea goes on in your points in the other thread and it demonstrates a superficial knowledge of the way evolution works.
We're here to discuss things, and those of us with more information on certain subjects should educate, rather than insult, people with less information.

Re: Darwin and DNA
 

Intersting post, thanks. The more we try to approach things from different angles, the better off we'll be towards getting to the truth.

Re: The Worship of Random, God of Darwinism
 

You're entitled to your opinion.

I've discussed these types of things with people copying and pasting this kind of info before.
Copy and pasters usually don't even articulate their own arguments so there isn't much point to discussion.

And maybe you didn't read his post very carefully. His claim is that there is a talking gene in the dog hidden in intron DNA. If that's the case, someone should be able to express the gene and produce a talking dog. It's not as unreasonable or sarcastic as it may have sound. And I really do think a talking dog would be way cool. If he could produce a talking dog, it would go a long way toward proving the theory he copied and pasted was correct.

The guy talked like he had some insights into recent scientific developments in intronic DNA. He then demonstrated he doesn't even really understand what intronic DNA is or what scientific research had found about intronic DNA something like 6 years ago.

If you think I have deficiencies in this topic, why do you think I have some responsibility to impart knowledge to others? Do you advocate the spread of misinformation and fallacious reasoning? How inconsistent can you be?

Don't bother preaching to me about what you think I should do. And don't follow me into someone else's thread with your issues with me in another thread. It's self-centered and very inappropriate.

I willingly impart information on a routine basis as my post history demonstrates. In this case, I've decided the subject is uneducatable on this matter and simply likes ideas consistent with his religious beliefs. Surely, you realize that trying to convert the dogmatic is a futile process.

I'm the bigger loser here, btw, because I actually know that taking part in this discussion would be a waste of my time from past experience.

Re: Darwin and DNA
 

All properties of the past-present-future exist a prior in the "no boundary condition" based on Feynman's multiple history idea. This theory tied with evolutionary theories makes much more sense than what this guy is proposing. Also, i'm curious, does the scientific community house any credence in his theories, and if so, do they generally accept them as alterantives?

Re: The Worship of Random, God of Darwinism
 

So educate him on why this isn't possible without calling him names.

Don't flatter yourself that I followed you. I posted in this thread before the post of yours, in this thread, I had issues with. You merely seem like the most noticable bully in two of the threads I have commented in.

I just pointed out your bad behavior and gave an example on where you may have been guilty of the same behavior of the poster you were insulting.

Re: The Worship of Random, God of Darwinism
 

part1. No. You care. You do it.

part2. I'm always flattered by fans. Do you honestly believe you can bully in a forum post? Heh

part3. "may have been guilty of the same behavior" What behavior would that be? And what's this "may have" nonsense?

The guy implied I was dogmatic just because I concluded his theory was nonsense. I guess it's ok if he calls me names, eh? I was nice, but honest, until then. Then I stopped being nice. The only thing bad I did was call him a fruit. My comment about him never understanding genetics was based on the assumption that he'd never read about it, not that it was beyond his understanding. Truth be told, some people that latch onto quasi-scientific theories do so because they have trouble with mainstream science.

I don't know if Dan is such an individual, but I'm leaning toward not. I think Dan is just a sneaky religious type in disguise to be honest. Just trying to package his religious wares in scientific-sounding verbiage to offer proof to non-critical thinkers. This forum is sort of a poor candidate for that sort of thing, but it might go off really well in a conspirology forum. He essentially admitted already he is into intelligent design. Very common agenda.

The old forum I frequented had similar posters, but they were into anti-Semitic crap that talked about evil "Zionists" in the place of Jews. I much prefer people promoting intelligent design than hate, but I still don't appreciate people with disguised agendas.

Re: The Worship of Random, God of Darwinism
 

Why lower yourself to their level?
You're obviously in the right. Be civilized about it.

I'm not trying to get into a personal thing with you but the behavior I was talking about was the "genotype is more important than phenotype in natural selection"
That's a view, while not as ignorant as the talking dog thing, demonstrates a clear misconception of the subject at hand. Rather than me just saying "That's completely ridiculous and anyone who studies evolution will tell you so." I engaged in debate.
You called him a fruit.

Re: The Worship of Random, God of Darwinism
 

It's like Bill Hicks said: I don't mean to sound cold or cruel or viscious, but I am, so It comes out that
way.

You may find it hard to believe, but I can think of a worse things to call people than fruits. Scout's honor.

Re: The Worship of Random, God of Darwinism
 

I know, and I know it's frustrating, but that behavior often makes them get defensive and also takes away from your argument.

Re: The Worship of Random, God of Darwinism
 

[ QUOTE ]
It's like Bill Hicks said: I don't mean to sound cold or cruel or viscious, but I am, so It comes out that
way.

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[img]/images/graemlins/laugh.gif[/img]

Re: The Worship of Random, God of Darwinism
 

I think you mistook my post for being mad or something. I was just telling calling it like I saw it and had decided to dismiss his whole theory. I think I just used his mild insult as reasoning that it was fair throw him into the fruit basket. And I find the idea of a talking dog and Mr. Ed amusing.

Re: The Worship of Random, God of Darwinism
 

Bill Hicks fan???!!!

[img]/images/graemlins/laugh.gif[/img] [img]/images/graemlins/laugh.gif[/img] [img]/images/graemlins/laugh.gif[/img]

Re: The Worship of Random, God of Darwinism
 

[ QUOTE ]
Bill Hicks fan???!!!

[img]/images/graemlins/laugh.gif[/img] [img]/images/graemlins/laugh.gif[/img] [img]/images/graemlins/laugh.gif[/img]

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Quote:
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"I'm Jim Ficks, and I'm dead now... I jogged every day, ate nothing but tofu, swam 500 laps every morning.... and I'm dead! Yul Brenner drank, smoked, and got laid every night of his life. He's dead!.... [censored]! That Yul Brenner.... smoking, drinking, girls sittin' on his little cue-ball noggin every night of his life! And I'm running around a dewy track at dawn. And we're both f****n' dead." -- Bill Hicks - Relentless


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nuff said.

Re: Darwin and DNA
 

[ QUOTE ]
Some very interesting ideas come from what is by far the most interesting paper I have examined this year in reading about evolution and genetics . The title is NeuroTheology: Brain, Science Spirituality, Religious Experience by Rhawn Joseph, Ph.D. I was able to download the PDF for free but have been unable to locate the link I used. (If I do locate it, I will post it.)



[/ QUOTE ]

Unless you are an authority on either, that statement has little meaning.

Re: Darwin and DNA
 

Since I haven't read the book I won't comment on it much , other than to say it sounds very similar to some other arguments I've heard before, and I don't think it's valid.

Since the science seems to be missing in this thread, I'll offer a little primer on introns, for those that are interested. If you only learn one thing here, about introns or otherwise, I'll be happy.

DNA is composed to two main classes: coding regions and non-coding regions. Introns are in a subclass of coding regions - but first, lets define the (much more straight forward) coding regions.

Coding regions are composed of exons, and exons encode genes, and these are sequences of DNA that make protein. Lots of people forget this, or misunderstand it, and it's important. Genes encode protein. Protein includes "structural" protein, like the keratin in your hair, and also lots of little molecular machines that make and break stuff. They aren't magic wands that bequeath speech - there are a whole bunch of genes necessary for this, and not all of them are known. There is a middle man here called RNA - I'll get to that later.

Non-coding DNA includes stuff like strucutural DNA, that proteins can bind to, so your chromosomes stay in tact.

It also encodes regulatory DNA called "promoters". Promoters are sequences of DNA that tell the cells how much protein to make, and when. Not all genes are "on" all the time. You can think of promoters as sort of a dimmer switch for a light - on, off, and a bunch in between. Different cells, at different times, make different proteins.

Introns are short sequences of DNA found in between exons. Before making a protein, the DNA sequence of a gene is read by some of those little protein machines I mentioned earlier, and a RNA strand is made. The RNA initially contains both introns and exons. Then, the introns in the RNA are "spliced out" or removed by more protein machines. Then, more protein machines "read" the RNA, and make a protein.

Why there was this apparently useless DNA that just got removed was baffling to scientists initially, hence the name "junk DNA". It is no longer thought of as junk; several functions for introns are now known - I'll give you a couple. It wouldn't surprise me if even more is discovered later.

1. Alternative splicing: Sometimes, a gene will be spliced differently under different circumstances. In cell A, there might be three introns spliced out, and in cell B, there might only be two, but one of them is slightly bigger. Now there are two very similar, but slightly different proteins in different cells - and there has been an "economy of DNA" - only one gene! Cool, huh?

2. Introns are regulatory elements. This works in a couple of different ways - sometimes, an intron ban act like a promoter, or with a promoter, to turn a gene on or off. Sometimes, the intron can affect RNA stabilty, so the amount of RNA that gets made into protein can be affected.

There is a famous quote by a scientist (sorry, I forget who) said something like "Give me the regulatory elements of a man and the genes of a man, and I'll give you a man; give me the regulatory elements of a mouse and the genes of a man and I'll give you a mouse." I forget who said it. Anyway, at the time everyone thought he was nuts, but this is now (at least partially) accepted.

Of course, all this fuss about introns really has nothing to do with the validity of the argument, in my opinion. If you have questions about homologs and orthologs of genes, mutation rates, and selective pressures, let me know... I think these are more relevent.

Re: Darwin and DNA
 

Good quick summary.

To be a little more precise, exon DNA encodes proteins. A gene on the other hand is the unit of heritable information. As you mentioned genes may encode proteins (or parts thereof) or may have regulatory roles. There are genes with known functions in intron DNA. (I believe you know this, but you probably wrote your summary rather quickly)

Furthermore, it's not like there is some great mystery about the potential of intron DNA. There are established start codons and we've figured out the 64 combinations of DNA codons and whether they start or stop RNA transcription (the making of RNA from DNA) or code for one of the 20 amino acids.

Since the human genome project was completed (by both private and public entitites), we have a complete map of the human genome. Work since the project was completed has involved signficant annotation of the genomic data with proteomic data, information about what regions code for what proteins. When you actually find out what we know, it's a lot less mysterious and you can't so easily just point to the mysterious thing (psychics love talking about coupled particles and their "violation" of locality) and give it extraordinary power as the OP gives to intronic DNA. It's a classic rhetorical trick to lazily prove that which cannot be proven.

Obviously with 20 amino acids, start and stop codes, there are a full 42 unused codons, right? Wrong. There are redundant codons that code for the same amino acid. A codon consists of a group of 3 consecutive nucleotides on a DNA chromosome (not redundant here as some viruses use RNA as their source of heritable genetic material). There are 64 permutations of 3 nucleotides taken 4 at a time. Redundancy helps guard against problems related to the accidental change of one nucleotide for another.

The whole idea that there's a single gene for speech is simply preposterous.