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New Causes of Autism Found in Noncoding DNA

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Re: New Causes of Autism Found in Noncoding DNA

#21

Post by dkoston »

Retric wrote: post #17
dkoston wrote: post #12

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them? /end venting

Junk DNA means non coding and without benifit. Due to the random nature of mutation such sequences are expected. However, verifying any specific sequence is useless is difficult. One important consideration is sequence length may have value even if the content is meaningless. Another is random sequences may aid long term adaptation even if they don’t currently do anything. So, if anything Junk is a fairly descriptive…

I don’t believe it exists without benefit. Nature can certainly phase parts of our system out over time (appendix) but to say it is without benefit is a bold statement. I’d argue that we simply don’t know the purpose and dismissing it as non-beneficial is arrogant or naive. Science should be based around evidence rather than lack of.

Re: New Causes of Autism Found in Noncoding DNA

#22

Post by dkoston »

mikeash wrote: post #18
dkoston wrote: post #12

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them? /end venting

As far as I can tell, the preferred scientific term is "non-coding DNA," with "junk DNA" being a sensational term that gets more traction in the media.

Here’s the Wikipedia quote:

> When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA".[1]

It’s not all non-coding DNA that is “junk”, just the stuff that “has no purpose”.

I’m arguing that it is much more likely that we don’t understand its purpose and should treat it as such rather than dismissing it as “junk”.

Re: New Causes of Autism Found in Noncoding DNA

#23

Post by alexandercrohde »

Would this mean gene-therapy could potentially undo autism?

Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing, and not just increased diagnoses, is there any candidate theory as to why mutations would be higher in developed countries recently?

Re: New Causes of Autism Found in Noncoding DNA

#24

Post by asdf21 »

alexandercrohde wrote: post #23

Would this mean gene-therapy could potentially undo autism? Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing, and not just increased diagnoses, is there any candidate theory as to why mutations would be higher in developed countries recently?

Older parents is the presumption.

Re: New Causes of Autism Found in Noncoding DNA

#25

Post by dnautics »

asdf21 wrote: post #24
alexandercrohde wrote: post #23

Would this mean gene-therapy could potentially undo autism? Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing, and not just increased diagnoses, is there any candidate theory as to why mutations would be higher in developed countries recently?

Older parents is the presumption.

assortative mating - a certain 'type' of person going to college and meeting people they reproduce with - is also implicated.

Re: New Causes of Autism Found in Noncoding DNA

#26

Post by strainer »

Retric wrote: post #17
dkoston wrote: post #12

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them? /end venting

Junk DNA means non coding and without benifit. Due to the random nature of mutation such sequences are expected. However, verifying any specific sequence is useless is difficult. One important consideration is sequence length may have value even if the content is meaningless. Another is random sequences may aid long term adaptation even if they don’t currently do anything. So, if anything Junk is a fairly descriptive…

But junk is perjorative word which suggests that it is entirely disposable even desirable to remove. That may turn out to be true but the experiment required to prove that thesis would require closely observing a biological systems evolution and disease evolution for some length of time, with "junk" DNA somehow removed and repressed. It may turn out to be a sort of filler with certain characteristics that work out to have repercussions for longer term genetic dynamics, and it may not. Since we cant tell yet, the name for it is very presumptive.

Re: New Causes of Autism Found in Noncoding DNA

#27

Post by stevenjohns »

dkoston wrote: post #21
Retric wrote: post #17

Earlier quoted context omitted.

Junk DNA means non coding and without benifit. Due to the random nature of mutation such sequences are expected. However, verifying any specific sequence is useless is difficult. One important consideration is sequence length may have value even if the content is meaningless. Another is random sequences may aid long term adaptation even if they don’t currently do anything. So, if anything Junk is a fairly descriptive…

I don’t believe it exists without benefit. Nature can certainly phase parts of our system out over time (appendix) but to say it is without benefit is a bold statement. I’d argue that we simply don’t know the purpose and dismissing it as non-beneficial is arrogant or naive. Science should be based around evidence rather than lack of.

What is the benefit of having an arch in the nose vs not having one? Or the benefit in light brown hair vs dark brown hair? Or the benefit in light brown eyes vs dark brown eyes?

How about the benefits in male pattern baldness where some of the hair on the scalp is affected by high levels of DHT and some aren't? How about diffused baldness where the way in which a person balds isn't in one particular place and is all over the scalp randomly?

These are all visual, observable examples. But when looking at individual genes, I'm sure you can appreciate that randomness inserts itself there as well - randomly, and not necessarily with any benefit. I don't think its arrogant or naive to appreciate that we are a set of random mutations, some of which have helped us become extremely successful in nature, but some of them don't have those benefits and only survived through luck or selection of other genes in the person they cohabited.

Re: New Causes of Autism Found in Noncoding DNA

#28

Post by tide_ad »

dkoston wrote: post #12

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them? /end venting

junk bonds

shrug

there was just a time when people threw that term around arbitrarily

Re: New Causes of Autism Found in Noncoding DNA

#29

Post by dnautics »

jballanc wrote: post #6
781 wrote: post #2

Stupid question from a noob: does gene location on a chromosome matter? If I swap gene A from chromosome 1 with gene B from chromosome 2, will this in general keep the cell viable and working the same way?

Gene location is extremely consequential, especially in Eukaryotes (everything that's not bacteria or bugs living near hydrothemal vents). A couple of things that are influenced by position: * First, and most immediate, are promoter/suppressor sequences. These are the bits of non-coding DNA that regulate when a gene is turned on or off. If you move a gene away from its promoter, it will not turn on and off at the rig…

I'm going to go against this and say no. We swap gene locations, all the time wholesale in mice, and usually the effect is limited. That doesn't get you a paper, so of course you publish when something... more interesting crops up.

It's just that there are many well-studied systems where where there are profound and severe effects that are singly extremely consequential, where you go "huh, wouldn't have guessed that" and the cause turns out to be really subtle.

If we're going with eukarya writ large, it's even less. Basically entire programs of plant husbandry is the industrial process of performing chromosomal translocation and overloading, and picking the one out a thousand? ten thousand? that reveals a commercially useful variant.

And yeast, well we've sliced and diced those chromosomes like no one's business (but it turns out they are particularly robust). I would go so far to say as "the general rule is that chromosomal location doesn't matter in yeast, with a handful of exceptions".

Conversely, there is one gene whose chromosomal location is basically invariant in prokarya, that's dnaA, which pretty much "has to be close to the ori".

Re: New Causes of Autism Found in Noncoding DNA

#30

Post by MagicPropmaker »

asdf21 wrote: post #24
alexandercrohde wrote: post #23

Would this mean gene-therapy could potentially undo autism? Also, since I believe it's now actually agreed upon that autism rates actually ARE increasing, and not just increased diagnoses, is there any candidate theory as to why mutations would be higher in developed countries recently?

Older parents is the presumption.

Another likely reason is increase in maternal obesity. See:

https://www.scientificamerican.com/article/maternal-obesity-...

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