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The Complex Truth About ‘Junk DNA’

quantamagazine.org

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Re: The Complex Truth About ‘Junk DNA’

#51

Post by ksaj »

shakil wrote: post #43

Any time I read about how some part of the body has no function, I try to remember that our understanding of the body is superficial at best, it was only a 100 years ago when getting your blood sucked by leeches was the standard of care for many conditions. Mother's milk was supposed to contain useless and indigestble substances till it turns out they were important for developing the baby's gut microbiota. Entire or…

That reminds me of both tonsils and the appendix - two body parts that are often referred to as "useless" even though they probably do some function we're just not aware of.

As for appendix, it seems to be home for bacteria that can cause dementia but are otherwise useful in the gut. I don't know if that's actually its purpose, but if so, it seems pretty important.

Re: The Complex Truth About ‘Junk DNA’

#52

Post by dekhn »

shakil wrote: post #43

Any time I read about how some part of the body has no function, I try to remember that our understanding of the body is superficial at best, it was only a 100 years ago when getting your blood sucked by leeches was the standard of care for many conditions. Mother's milk was supposed to contain useless and indigestble substances till it turns out they were important for developing the baby's gut microbiota. Entire or…

.... you know that leeches are used in modern medicine, right? Not for bloodletting, but many of the contexts that leeches were used for have enough overlap with bloodletting that it's actually best to assume that folks actually did use leeches to good effect.

The core of this ongoing debate is mainly about some regions, like Alu, which appear to truly have no function, and have little to no functional effect. I think scientists could still make a good faith experimental effort at attempting to salvage this idea, see Eddy's proposal about a "neutral genome" here: https://www.cell.com/current-biology/comments/S0960-9822(13)...

The fairest way to describe it is that scientists continually find that more and more DNA that was neglected as having zero functional (no observable, measurable, directed activity that is under evolutionary selection pressure) effect, does indeed affect the fitness of organisms in ways that are not accomodated by existing theories of gene expression or regulation. It seems unlikely, however, that we will ever truly be able to point to every single base pair in teh genome and say "it's under functional pressure", and if that's the case, it's easy to make the argument that some of it is "junk".

However, complex information processing systems like life don't really fall into simple classification, "junk" is really a subjective term, we should focus instead of measurable scientific phenomena like fitness.

Re: The Complex Truth About ‘Junk DNA’

#53

Post by dekhn »

ksaj wrote: post #51
shakil wrote: post #43

Any time I read about how some part of the body has no function, I try to remember that our understanding of the body is superficial at best, it was only a 100 years ago when getting your blood sucked by leeches was the standard of care for many conditions. Mother's milk was supposed to contain useless and indigestble substances till it turns out they were important for developing the baby's gut microbiota. Entire or…

That reminds me of both tonsils and the appendix - two body parts that are often referred to as "useless" even though they probably do some function we're just not aware of. As for appendix, it seems to be home for bacteria that can cause dementia but are otherwise useful in the gut. I don't know if that's actually its purpose, but if so, it seems pretty important.

The appendix is vestigial, not useless. It's fair to say it's vestigial, because you can remove it from large numbers of people and they don't die, which is very different from organs like the liver, heart, or lungs.

Re: The Complex Truth About ‘Junk DNA’

#56

Post by true_religion »

dekhn wrote: post #52
shakil wrote: post #43

Any time I read about how some part of the body has no function, I try to remember that our understanding of the body is superficial at best, it was only a 100 years ago when getting your blood sucked by leeches was the standard of care for many conditions. Mother's milk was supposed to contain useless and indigestble substances till it turns out they were important for developing the baby's gut microbiota. Entire or…

.... you know that leeches are used in modern medicine, right? Not for bloodletting, but many of the contexts that leeches were used for have enough overlap with bloodletting that it's actually best to assume that folks actually did use leeches to good effect. The core of this ongoing debate is mainly about some regions, like Alu, which appear to truly have no function, and have little to no functional effect. I thin…

Yes, the main problem with leeches in historical use was that medical theory believed disease was caused by a miasma and that drawing bad blood would cure the cause.

Today, we still use leeches but only for those cases where they can provably affect the cause.

Re: The Complex Truth About ‘Junk DNA’

#57

Post by simonblack »

Computer programs require both code and space for variables and also require 'defines' that don't show up as actual variables or actual code but tell both code and variables what their working values need to be.

Or maybe to put it in another way, in terms of usefulness, is that the 'junk DNA' holds the same significance as the programming header files do. Maybe we should be calling those data sequences of DNA as 'junk.h'.

I venture to say that maybe only 0.1% of the stuff we call 'Junk DNA' (or even none of it) is irrelevant.

Re: The Complex Truth About ‘Junk DNA’

#58

Post by miika »

“Some of it is essential for life, some seems useless, and some has its own agenda.”

It’s like you have a bookshelf filled with books. Some books you haven’t read, some were gifts, some were acquired, some you didn’t finish and some book you will read over and over again. All of them were kept for some reason.

I don’t believe nature would create something that’s completely useless. I just know that often I fail to see what the use might be.

Re: The Complex Truth About ‘Junk DNA’

#59

Post by dekhn »

true_religion wrote: post #56
dekhn wrote: post #52

Earlier quoted context omitted.

.... you know that leeches are used in modern medicine, right? Not for bloodletting, but many of the contexts that leeches were used for have enough overlap with bloodletting that it's actually best to assume that folks actually did use leeches to good effect. The core of this ongoing debate is mainly about some regions, like Alu, which appear to truly have no function, and have little to no functional effect. I thin…

Yes, the main problem with leeches in historical use was that medical theory believed disease was caused by a miasma and that drawing bad blood would cure the cause. Today, we still use leeches but only for those cases where they can provably affect the cause.

that's not really correct. we have a narrative for why leeches work, but it's not really a "provably affect the cause" sort of thing. We just know they eat dead tissue and suppress immune responses.

Re: The Complex Truth About ‘Junk DNA’

#60

Post by sockpuppet_12 »

JoeAltmaier wrote: post #49
ijidak wrote: post #33

Earlier quoted context omitted.

The idea of junk DNA never made sense to me. Having a list of proteins (coding DNA) does nothing to tell an organism how to combine those proteins to form working systems. It's like claiming that the parts list in an assembly manual is the only information of importance. And the step-by-step instructions are junk, because they don't describe a useful part in the box. Did we think that the whole organism just self-ass…

No creator necessary. Imagine a big machine run by paper tape. On the tape are two possible holes. Punch one and feed it in, the machine makes a man. Punch the other, it makes a mouse. Does the tape 'encode' the essence of 'human being'? (or even 'mouse'?) Of course not. The machine is a vital part of the equation. Likewise, dna in a jar is just a molecule. It has to have a cell, evolved over a billion years, ready t…

Yes you're right, we know that DNA is inert and used as a storage device by an organism.

What we don't know is how an organism with no intelligence (cell), could develop code (DNA), archive it, rehydrate it and then parse and copy it like someone with intelligence.

Without getting too deep into it, it's just not convincing anymore to appeal to vast amounts of time and random chance to do something which is fundamentally within the realms of engineering.

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