What about fossil DNA?

[Brad Jensen]

I am new to the forum and I am presenting ideas that I have been thinking about in relation to dinosaurs and dinosaur fossils.

 

One idea that intrigues me is the idea of fossil DNA.

 

I don't mean physical nucleotides that might be found in or around dinosaur fossils.

 

I mean ancient DNA or RNA sequences that might be preserved in the "non-coding" DNA of the dinosaur descendants, birds.

 

DNA and RNA are basically scripting languages for building and activating proteins. When we think of evolution, we mostly think in terms of the evolution of organisms. But there is a meta-evolution of DNA and RNA themselves.

 

Among the other things I do, I write encryption and decryption programs.  These are ways to hide and reveal meaningful sequences of information, for later use.

 

It would make sense to me that mutations, particularly successful ones, should be preserved in the DNA record. Obviously they are, in evolutionary successful organisms. But what about when a new mutation appears and replaces an existing gene or set of genes  Why not transmute the no-longer-used coding genes and epigenes and store them,  within a set of markers, in the noncoding section of the DNA. Perhaps under certain environmental stresses, such as scarce food or overabundant food, the organism responds with mutation activation process that both create random new DNA sequences, as well as reactivating previously successful ones to try them out in the current environment.

 

Perhaps inside every ostrich, the fossil genes for one or many species of dinosaur lie waiting to be revealed.

 

While this might seem like a hint at intelligent design, languages can capture random changes and make them part of the structure over time.

 

A good example of this is the aging of most animals.  The process of the individual organism developing senescence was incorporated into our gene line many millions of years ago. The environmental advantage for it is that it allows younger organisms to compete successfully with older organisms, which allows more rapid evolution.  From the point of view of the individual organism, aging is an always deadly genetic disease. Without this programmed process, we might live extremely long lives. Molecules do not get tired, and chemicals do not run out of steam. 

 

In this view, every organism is a GMO. The process of evolution is enhanced and accelerated by as yet unknown genetically-driven designs.  Evolution is not a completely random process.

 

If this encoding exists it should show up with some investigation. 

 

I am sure the first billion years were the hardest. 

 

-Brad Jensen

 

 

[FranzBernhard]

Welcome to TFF from Austria!

 

There was at least one similar discussion here on TFF, about "building" a dinosaur out of a chicken. Here it is:

A question about chickenosaurus - General Discussion - The Fossil Forum

 

Franz Bernhard

Edited November 20, 2022 by FranzBernhard

[Brad Jensen]

10 hours ago, FranzBernhard said:

Welcome to TFF from Austria!

 

There was at least one similar discussion here on TFF, about "building" a dinosaur out of a chicken. Here it is:

A question about chickenosaurus - General Discussion - The Fossil Forum

 

Franz Bernhard

 The essential difference is that I am not talking about modifying active DNA, but about mining and retransforming 'fossilized' non-encoding DNA. I would also wonder if some nuclear DNA might be transformed and preserved in mitochondria. What we consider as instinctive behaviors has to be recorded and passed down somewhere. For a long time we believed acquired learning and behaviors could not be passed down genetically. But of course the mitochondria are passed from mother to child, and if the learnings of the mother are encoded in DNA, or some other as yet unsuspected method, in the mother's mitochondria, it could be a message in a bottle to the new generation. 

 

And of course, if fundamental thoughts and beliefs can be encoded in DNA or RNA, what is to prevent some future scientist from spreading a virus that infects us with the thought  that some current politician or rock star is an eloquent and compassionate genius? Or maybe turning us all back into dinosaurs, at least in attitude and behavior?

 

"Those who do not learn from dinosaurs, will be destined to have tiny arms and big teeth."

 

The future is the past, in new outfits.

 

Edited November 20, 2022 by Brad Jensen
duplication of words

[FranzBernhard]

5 minutes ago, Brad Jensen said:

The essential difference is that I am not talking about modifying active DNA, but about mining and retransforming 'fossilized' non-encoding DNA.

That was also my thought in that thread: How much dino is still in a chicken?

Tinkering with active DNA to create a dino-like animal from a chicken - well, one thing.

But digging out remaining dino-DNA, "renovate" it, if necessary, and bring that to life - that would be a story (in my eyes)!

Franz Bernhard

[jpc]

The chickenosaurus project is trying to do exactly what you are talking about... reactivating genes that are still in the chicken DNA to produce chick embryos with teeth and tails.

[JohnJ]

7 minutes ago, Brad Jensen said:

And of course, if fundamental thoughts and beliefs can be encoded in DNA or RNA, what is to prevent some future scientist from spreading a virus that infects us with the thought  that some current politician or rock star is an eloquent and compassionate genius? Or maybe turning us all back into dinosaurs, at least in attitude and behavior?

 

For purposes of this Forum, it would be appreciated if we keep the commentary focused on paleontology.  Thanks.

[digit]

2 hours ago, Brad Jensen said:

I would also wonder if some nuclear DNA might be transformed and preserved in mitochondria.

Human mtDNA (mitochondrial DNA) is tiny compared to the nuclear DNA--only 16,569 base pairs encoding for 13 proteins. I believe in the endosymbiotic origin of mitochondria--exogenous DNA from a primitive bacterial-like endosymbiont. Mitochondria are perfectly adapted for what they do--provide the cell with multiple metabolic tasks. They do not need to be re-tasked with preserving unused nuclear DNA--the nuclear DNA is more than up to that task already.

 

2 hours ago, Brad Jensen said:

What we consider as instinctive behaviors has to be recorded and passed down somewhere. For a long time we believed acquired learning and behaviors could not be passed down genetically. But of course the mitochondria are passed from mother to child, and if the learnings of the mother are encoded in DNA, or some other as yet unsuspected method, in the mother's mitochondria, it could be a message in a bottle to the new generation. 

Sorry, but doesn't even pass as good quality science fiction and even less great quality science. I thought we'd moved past the theories of giraffes straining to make their necks longer and then passing down "longer-necked" DNA to their descendants. We've also moved past the idea that acquired learning and behaviors can be passed down genetically. Surely, humans should be able to speak and read from birth were this to be the case. Our genetics make sure to pass down a nice diversity of variations with each generation. Natural selection is a non-random difference in the reproduction rate of various organisms based on minor differences in survival in particular environmental conditions. No "learnings" at all are passed down to offspring. If the mother's DNA had variations that allowed her to have more than her share of offspring then it is possible those same local adaptations to her environment may be passed down (though her nuclear DNA) to her more bountiful progeny. A male of a species that is able to command more territory and possibly mate with more females may also leave more progeny. This enhanced adaptation to the current local constraints could also be passed down to successive generations through his DNA contribution. There would be no way his genetic "fitness" could be passed down if it were taking place though mitochondrial "messages in bottles".

 

It's all fun to think about reactivating old atavistic genes on chickens and making "hen's teeth" not as rare as the adage would claim. This is the old "chickenosaurus" line of discussion which you will find a link to above. If you wish to argue new theories not based on science (encoding learned behaviors in the scant mtDNA) then there are other fictional or pseudo-science forums out there. Please don't misunderstand my reply as being rude, mean or demeaning in any way--I only wish to stress that this is a science-based forum and the ideas you are tossing around are decidedly outside the realm of existing proven science. We may enjoy from time to time on this forum discussing the merits of making dino-chickens or bringing back the mammoth, or life trying to imitate art in attempting to sequence dino-DNA (just don't start crowd-funding the dino-park just yet). If you wish to propose a theory where memories, thoughts, beliefs or behaviors get passed down in the tiny mtDNA then this is the wrong forum for that sort of fantasy.

 

If you do have an interest in mtDNA and evolution then I suggest you start with some Wikipedia articles on these and then do additional research online (or in the many books on the topics that explain the science so that laypeople are not buried with detail). There is a lot of great science established already and more details and layers being revealed continuously. Once you fully understand (or at least reasonably understand the basics) there will be no need for mitochondrial messages in bottles.

 

 

Cheers.

 

-Ken

[Brad Jensen]

5 hours ago, digit said:

Human mtDNA (mitochondrial DNA) is tiny compared to the nuclear DNA--only 16,569 base pairs encoding for 13 proteins. I believe in the endosymbiotic origin of mitochondria--exogenous DNA from a primitive bacterial-like endosymbiont. Mitochondria are perfectly adapted for what they do--provide the cell with multiple metabolic tasks. They do not need to be re-tasked with preserving unused nuclear DNA--the nuclear DNA is more than up to that task already.

 

Quote

 

Sorry, but doesn't even pass as good quality science fiction and even less great quality science. I thought we'd moved past the theories of giraffes straining to make their necks longer and then passing down "longer-necked" DNA to their descendants. We've also moved past the idea that acquired learning and behaviors can be passed down genetically. Surely, humans should be able to speak and read from birth were this to be the case. Our genetics make sure to pass down a nice diversity of variations with each generation. Natural selection is a non-random difference in the reproduction rate of various organisms based on minor differences in survival in particular environmental conditions. No "learnings" at all are passed down to offspring. If the mother's DNA had variations that allowed her to have more than her share of offspring then it is possible those same local adaptations to her environment may be passed down (though her nuclear DNA) to her more bountiful progeny. A male of a species that is able to command more territory and possibly mate with more females may also leave more progeny. This enhanced adaptation to the current local constraints could also be passed down to successive generations through his DNA contribution. There would be no way his genetic "fitness" could be passed down if it were taking place though mitochondrial "messages in bottles".

 

- Your point on mitochondria is taken, however  I did not restrict my thought to only DNA as a method of recording learned behavior. 

 

If you don't think behaviors such as foraging by ants or mating dances by birds are stored in DNA, where do you think they are recorded? Do you think all behavior is either random or socially acquired? And while human babies are not born knowing how to speak a specific language, they are born knowing how to learn and imitate one. At least that is what they taught us in physiological psychology some decades ago. It is most likely that all non-random behavior is recorded in some form of language, most certainly neurologically. Of course moist of our evidence for the encoding of learned experiences is positional thru brain area activation, and hypothesized thru synapse changes and perhaps synapse growth.  IS there a language and semantic storage system in the brain?  I expect that there is.    I would agree it is less proven that these recordings are preserved across generations in DNA. or in some other method.

 

 

Quote

It's all fun to think about reactivating old atavistic genes on chickens and making "hen's teeth" not as rare as the adage would claim.

This is the old "chickenosaurus" line of discussion which you will find a link to above.  If you wish to argue new theories not based on science (encoding learned behaviors in the scant mtDNA)

 

-Obviously I have not explained myself well. I am describing a possible encrypted archiving system for genes that would preserve combinations for possible future use mediated by the organism itself, not external genetic manipulation.

 

 

Quote

 

then there are other fictional or pseudo-science forums out there.

 

-please, you are isolating one small offhand conjecture from what I have said and building a bonfire on it.

 

-exploring the notion that non random behaviors are encoded and stored in some fashion that is passed thru inheritance is of interest to me as an information scientist

 

Quote

 

Please don't misunderstand my reply as being rude, mean or demeaning in any way

 

 

- of course, that is exactly what it is, but is amusing rather than offensive. "Thou crude and ignorant ruffian, get thee hence!".

 

 

Quote

--I only wish to stress that this is a science-based forum and the ideas you are tossing around are decidedly outside the realm of existing proven science.

Boy, I hope so. Fortunately the scientific method exists independently from those who would use it as a badge and a bludgeon.

 

Quote

 

We may enjoy from time to time on this forum discussing the merits of making dino-chickens or bringing back the mammoth, or life trying to imitate art in attempting to sequence dino-DNA (just don't start crowd-funding the dino-park just yet). If you wish to propose a theory where memories, thoughts, beliefs or behaviors get passed down in the tiny mtDNA then this is the wrong forum for that sort of fantasy.

-You have made your opinion abundantly clear, and you might even be right. IU certainly now agree that there is not enough genetic material for significant encoding of much of anything, from your description.

 

Quote

 

If you do have an interest in mtDNA and evolution then I suggest you start with some Wikipedia articles on these and then do additional research online (or in the many books on the topics that explain the science so that laypeople are not buried with detail). There is a lot of great science established already and more details and layers being revealed continuously. Once you fully understand (or at least reasonably understand the basics) there will be no need for mitochondrial messages in bottles.

-how wonderfully gracious of you to think so.

 

Non random information is stored in discrete entities preserved in a distinct order that are read and written by distinct mechanisms.

 

At this point, we do not know how this is done in organisms. 

 

Quote

 

Cheers.

 

-Ken

-Your non-random behavior is noted, will be recorded and remembered. It is wonderful to develop expert knowledge and skillfully apply it.  it can be useful to apply your reasoning abilities in an inclusive as well as exclusive fashion.

 

have any kind of day you want!

[FranzBernhard]

4 hours ago, Brad Jensen said:

Non random information is stored in discrete entities preserved in a distinct order that are read and written by distinct mechanisms.

At this point, we do not know how this is done in organisms. 

That is truly a point. As you pointed out, how is specific behavior passed on, if no learning from other beings is involved? Its called "instinct", but how is it passed from one generation to the next? Plenty room for research, I think.

Franz Bernhard

[Fossildude19]

While all of these "thought experiments" may be interesting (to some), at the end of the day, this is a FOSSIL FORUM.

Facts and Science are our main currencies here. While people can endlessly speculate on these "theories", the research behind them can be conducted elsewhere.

 

Mostly, we are here to talk about fossils.

 

[FossilDAWG]

It's hard to know where to start in addressing your post.  As a practicing molecular biologist at a major research university, though, I feel that I need to respond to some points.

 

I find it kind of insulting that you feel you have "discovered" the idea that the the genome contains "fossil DNA" that reflects the evolutionary history of a species.  Biologists have been using DNA sequences for several decades to reconstruct phylogenies and evolutionary histories.  In the past couple of decades it has become easier and easier to sequence entire genomes that are used in these (and many other) studies. 

 

There is no evidence at all that organisms make "backup copies" of their genome to archive their past history.  This idea makes no biological sense.  The genome has to be physically copied every time a cell divides.  This process is "expensive" in that all the nucleotides required have to be synthesized, and all the molecular machinery needed for copying the DNA, need to be made with each division.  This requires a lot of nutrients (molecular building blocks) and energy, and so it is costly which means it has a fitness cost.  Resources put to any use must have a fitness benefit that outweighs the cost.  Maintaining backup copies of the genome just in case the organism wants to "reinstall factory settings" somewhere down the road would divert a lot of resources away from reproduction (producing eggs/sperm for example) and other processes (for example maintaining an immune system) with a direct positive impact on fitness.

 

Behavior results from a physical structure, the brain, processing sensory information in the context of memory.  Genetics provides the information to be able to construct neural networks that carry out this processing.  Memory is formed by physical changes in these networks, by reinforcing some synaptic connections and trimming others.  In the case of humans, for example, we can learn language because our brains have evolved the appropriate neural nets that can respond to sensory input (hearing people speak) and context (what are people doing when they speak certain combinations of sounds) to form memories (physical changes in connections between neurons) that allow us to interpret those sounds (language) when we hear them again.  In other cases ("instinctive" behavior) the neural nets are more "hard-wired" so the connection between sensory input and output (behavior) is built in to the system.  Even there, the neural net can be modified by experience (learning) to some degree.  The process does not require some mysterious grand design or mysterious driving force.  It is well understood by well established biological principles.

 

While it may be "fun" to speculate about such things, it is only "useful" to do so after having spent the effort to learn at least a large fraction of the knowledge people have gained through hard work and rigorous experimentation.  There is a lot of important work still to be done studying the connections between genomes, history, and phenotypes (including behavior).  However is almost certain that "thought experiments" based on the assumption that living organisms function like computers designed by humans to serve human priorities (including backing up programs) will not lead to advances in understanding.

 

Don

[FranzBernhard]

20 minutes ago, FossilDAWG said:

There is no evidence at all that organisms make "backup copies" of their genome to archive their past history.

One question: These are not backup copies, but what about the multiple identical chromosome sets some organisms have? Whats the benefit? They copy them over and over again - for what? I have read that these copies are to "play with". I could be completely wrong with all this babbling, sorry then!

Thank you!
Franz Bernhard

[FossilDAWG]

Hi Franz,

 

I am not sure that I understand your question exactly.  There have been multiple instances where the entire genome has been duplicated during the evolution of many groups of organisms.  This is common in some plant lineages, but occurs in metazoans as well, including in the lineage leading to vertebrates,  Here is an interesting article that discusses the evolutionary significance of such duplications.  Although such events are rare accidents within a lineage, they may be evolutionarily important as they greatly expand the genetic raw material evolution may act on.  For example, if you suddenly have two copies of an essential gene, one copy may retain the original function and the second may diverge and acquire a novel function.  However, many genes may instead be silenced by becoming pseudogenes (genes with mutations that silence expression through frame shifts and/or premature stop codons).

 

While genome duplications can be important in the evolution of lineages of organisms, they are not at all similar to the "archiving of backup copies of the genome" suggested in the OP of this thread.  For one thing they are not static copies, they immediately begin to change and rapidly evolve.  They are transcriptionally active, i.e. they are "read" to make mRNA and ultimately proteins.  If organisms had a "need" (in terms of fitness) to store backup copies of their genome that would be a regular event instead of an extremely rare event, a specific molecular machinery would exist for that purpose (for which there is no evidence), and the archived copy would be protected from evolutionary changes and therefor would need to be transcriptionally silent.

 

I think it's a misnomer to say that extra copies of genes or chromosomes are to "play with".  They provide 'extra" genetic material that evolution may act on, silence, or delete.  "Play" suggests a deliberate or conscious process, and of course no organism has any way to treat it's genome as a toy.  Also the process is likely quite dangerous, and likely more often leads to death.  Expression of genes almost always requires a large degree of balance.  Duplicating a single chromosome, for example, leads to doubling of expression of the genes encoded on that chromosome and so doubling of concentrations of the encoded proteins.  Usually this is fatal, for example by causing developmental defects.  Sometimes the organism is viable but with consequences.  For example Down's syndrome results from an extra copy of chromosome 21.  If the entire genome is duplicated proteins may be expressed in the same proportions relative to one another but the total concentration will be higher, which is probably why there is strong selection (and so rapid evolution) to silence or delete the extra copies, or to acquire a novel function.

 

Don

[Brad Jensen]

7 hours ago, Fossildude19 said:

While all of these "thought experiments" may be interesting (to some), at the end of the day, this is a FOSSIL FORUM.

Facts and Science are our main currencies here. While people can endlessly speculate on these "theories", the research behind them can be conducted elsewhere.

 

Mostly, we are here to talk about fossils.

 

- I agree completely. The theory that I presented here says some things about fossils and the search for them. 

 

For example, if dinosaurs were lowland creatures, the search for new fossil bearing fields might be concentrated on areas that geologists think were low lying areas at the time before the extinction.

 

I also wonder if the US Navy has done deep radar searches off our coastlines and if these plots have been examined for evidence of fossils.

 

I do  think it is important to discuss whether dinosaurs could dance, or just stand around like nerds at a cocktail party trying not to fall down. When you mount that skeleton for display, are you being faithful to its actual posture, or are you making changes  because of conscious or unconscious assumptions? 

 

Having a mental context in mind while you are unearthing your bones of stone might lead to greater and more meaningful evidence from your observations, or to new observations that might have been previously overlooked.

 

What seems like "endless speculation" to you, I think of as a dispassionate analytical model building on a set of mostly agreed-upon facts or information points. These are the fossils I dig for,. I am talking about it here because I think that some small part of what I am saying will light some small spark that will help in the discovery and recovery of fossils.  I don't take up much bandwidth. 

 

Evolution is environment. If the dinosaurs all suddenly disappeared, it is because the environment they were superbly adapted to suddenly disappeared. What physical properties of the environment could those possibly be, and how could such a massive change happen in a short time on this Earth?

 

And how were other animals not submerged in the seeming chaos of this change? The logical conclusion is that they were adapted to a different environment than the dinosaurs were adapted to.

 

The only "unknown fact" at the time I formed this theory was about oxygen concentration at the time of the dinosaur extinction and it was a reasonable thing to infer with all the other data points that were available. And as it was, what I 'speculated' on was actually known to other researchers. 

 

I have been involved in forum participation and moderation since the mid 1980s, starting with dial up BBSes. There is a simple solution here, Don't read my posts or the post responses if you don't enjoy them. 

 

My intention for being here is to participate in the search for and recovery of fossils. Looking for the unknown within the known is endlessly fascinating.

 

Thank you for your response. 

 

 

 

 

 

 

Edited November 21, 2022 by Brad Jensen
missing and mis-typed words

[Fossildude19]

18 minutes ago, Brad Jensen said:

There is a simple solution here, Don't read my posts or the post responses if you don't enjoy them. 

 

Ah, if only I had that luxury. Alas, as an administrator, I do not.

As a former moderator, I am sure you understand this.

[Brad Jensen]

36 minutes ago, Fossildude19 said:

 

Ah, if only I had that luxury. Alas, as an administrator, I do not.

As a former moderator, I am sure you understand this.

I presently moderate Scrybyl.com, but since our forum principle is no post moderation, the task is easy.

[JohnJ]

8 minutes ago, Brad Jensen said:

I presently moderate Scrybyl.com, but since our forum principle is no post moderation, the task is easy.

 

Great.  Things are successfully different here.

[Brad Jensen]

1 hour ago, FossilDAWG said:

 

While genome duplications can be important in the evolution of lineages of organisms, they are not at all similar to the "archiving of backup copies of the genome" suggested in the OP of this thread.  For one thing they are not static copies, they immediately begin to change and rapidly evolve.  They are transcriptionally active, i.e. they are "read" to make mRNA and ultimately proteins.  If organisms had a "need" (in terms of fitness) to store backup copies of their genome that would be a regular event instead of an extremely rare event, a specific molecular machinery would exist for that purpose (for which there is no evidence), and the archived copy would be protected from evolutionary changes and therefor would need to be transcriptionally silent.

-Yes, I am suggesting the transformation of the gene copies so that they are "transcriptionaly silent".. It might be much easier to look for the content, and then if found, look for the mechanism.   I wonder if anyone has done longitudinal studies of individuals' non-coding DNA to see if there changes over time. 

1 hour ago, FossilDAWG said:

of course no organism has any way to treat it's genome as a toy. 

- except of course, humans.

1 hour ago, FossilDAWG said:

 

 

[Brad Jensen]

1 minute ago, JohnJ said:

 

Great.  Things are successfully different here.

I don't recommend it for 99% of forums. 

[JohnJ]

1 minute ago, Brad Jensen said:

I don't recommend it for 99% of forums. 

Noted.

[FossilDAWG]

3 minutes ago, Brad Jensen said:

-Yes, I am suggesting the transformation of the gene copies so that they are "transcriptionaly silent".. It might be much easier to look for the content, and then if found, look for the mechanism.   I wonder if anyone has done longitudinal studies of individuals' non-coding DNA to see if there changes over time.

I suggest you become familiar with some search engines.  Pubmed and Google Scholar are particularly useful and easy to use.  You should be able to find at least 1,000 peer-reviewed publications on the topic of transcriptional silencing and genome evolution.

[FossilNerd]

1 hour ago, Fossildude19 said:

 

Ah, if only I had that luxury. Alas, as an administrator, I do not.

As a former moderator, I am sure you understand this.

 

 

50 minutes ago, JohnJ said:

 

Great.  Things are successfully different here.

 

 

And we are all thankful for your, and the rest of the Admin team’s, efforts in keeping our little community a friendly, fossil and science focused, place of respite.

[JohnJ]

6 minutes ago, FossilNerd said:

keeping our little community a friendly, fossil and science focused, place of respite

 

That is due to the majority of our members... otherwise, we would all be herding cats, tyrannosaurs, or pseudogenes....  

[FranzBernhard]

11 hours ago, FossilDAWG said:

I am not sure that I understand your question exactly.  There have been multiple instances where the entire genome has been duplicated during the evolution of many groups of organisms.  This is common in some plant lineages, but occurs in metazoans as well, including in the lineage leading to vertebrates,  Here is an interesting article that discusses the evolutionary significance of such duplications.  Although such events are rare accidents within a lineage, they may be evolutionarily important as they greatly expand the genetic raw material evolution may act on.  For example, if you suddenly have two copies of an essential gene, one copy may retain the original function and the second may diverge and acquire a novel function.  However, many genes may instead be silenced by becoming pseudogenes (genes with mutations that silence expression through frame shifts and/or premature stop codons).

Yes, perfectly understood . And perfectly answered ! Thank you so much! And thank you also for the link. But any new ideas about this since then ?

Franz Bernhard

Edited November 22, 2022 by FranzBernhard