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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

#101

Post by klmr »

dkoston wrote: post #36
stevenjohns wrote: post #27

Earlier quoted context omitted.

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…

I can absolutely appreciate that we are a series of mutations. To say that there is no benefit or detriment to having an arched nose or not also seems naive. It’s likely that the shape of your nose can affect how much air passes to your lungs, how likely it is to be sun burnt or not, and many other things. Just because the values or benefits might be minuscule compared to other things doesn’t mean they do not exist.…

> To say that massive portions of our DNA “have no benefit” without having proof of such, seems naive to me.

What makes you think scientists have no proof? The whole reason we know junk DNA has no important function for cell biology is that there’s good evidence that says so. There’s some wiggle room with the details but the general picture of this won’t change, and this has been studied for a long time and is fairly well understood.

Re: New Causes of Autism Found in Noncoding DNA

#102

Post by mnw21cam »

klmr wrote: post #89
astazangasta wrote: post #51

Earlier quoted context omitted.

This is what my thesis is about (I titled it "Rehabilitating Junk DNA"). It isn't that complicated. Your resonance comment is gibberish, sorry. The DNA is a giant tape in base 4 (ATGC). There are programs written at random places on the tape that in a 64 bit encoding (i.e. triplets of quaternary bits). This is "coding sequence", about 1% of the genome (itself 3 gigabases, so 30 Mbases of coding sequence). A tape head…

Nice explanation but you seem to be saying that at most 3% (being generous) of DNA would be functional (if the rest is “random noise”). This number is over twice as small as the lowest estimate (~ 8%) of even the most fervent critics of ENCODE’s number. I’d love to hear a brief break-down of your reasons, if possible.

As an added complication, a decent proportion of DNA in the genome is meaningful at least in how long it is, because it separates two functional pieces of DNA that interact in 3D space due to the way the DNA wraps around other stuff. If you change the content of this DNA, it doesn't cause disease, but if you change the length, it does.

Re: New Causes of Autism Found in Noncoding DNA

#103

Post by bhouston »

klmr wrote: post #88
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?

> Would this mean gene-therapy could potentially undo autism? Almost certainly not. Autism is caused by developmental changes. This means that any gene therapy would have to start before the embryo development is even finished, i.e. in the mother’s womb. After that, it’s essentially too late. Think of it this way: Could gene therapy make an adult person taller or smaller? Despite the fact that height has a large gene…

It all depends on whether it is a structural thing that is established during fetal development, which can not be fixed post birth, or whether it is part of the brains's development post birth.

There is a shit ton of brain development post birth -- not structural (the growth of the initial neurons) but in weeding out pathways and reinforcing certain pathways. A lot of it is based on complex feedback between activity, neurochemical releases and receptors. All of that is fair game to change post birth.

Given that autism (like many other psychology labels) is a label for a diverse group of disorders which we can not fully tease apart accurately at this stage, it is likely true that some forms of autism can be treated post-birth, but others will not be.

Re: New Causes of Autism Found in Noncoding DNA

#104

Post by arkades »

hannob wrote: post #82
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?

> since I believe it's now actually agreed upon that autism rates actually ARE increasing why do you believe that? I'm not aware of any recent research that would point in that direction and disprove the very plausible hypothesis that the increase is an effect of changing diagnosis criteria and increased attention for the topic.

I’m also unfamiliar with any data to suggest the increase in rates is anything but a change in diagnostic criteria. And it’s my field, so I’d OP has data to share, I’d be very appreciative of a link.

Re: New Causes of Autism Found in Noncoding DNA

#105

Post by efa »

hannob wrote: post #82
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?

> since I believe it's now actually agreed upon that autism rates actually ARE increasing why do you believe that? I'm not aware of any recent research that would point in that direction and disprove the very plausible hypothesis that the increase is an effect of changing diagnosis criteria and increased attention for the topic.

Yes, I'd like to know where you are getting that the actual rates are increasing. My wife and I (parent's of a daughter with autism) laugh how every year they claim the numbers increase - 1/100, then 1/50, etc. These are numbers marketed by Autism Speaks and other organizations to make autism appear more wide spread and increase their funding. This does nothing but hurt people with more severe autism. Widening the net so wide so that any social difficulties is considered autism just reduces the availability of services for children with "real" autism. Autism is a spectrum, with people who are completely non-verbal constantly stemming to people with Asperger's Syndrome who excel but have some social difficulties. They really should be distinguished.

Re: New Causes of Autism Found in Noncoding DNA

#106

Post by dkoston »

klmr wrote: post #98
dkoston wrote: post #62

Earlier quoted context omitted.

Agreed, maybe I misspoke but I wasn’t aware of any place I said it did. “Junk DNA” is a well accepted term by the scientific community and public. https://www.scientificamerican.com/article/what-is-junk-dna-... Humorous take on my point: https://www.amazon.com/Junk-DNA-Journey-Through-Matter/dp/02... I think my main point was missed which is: “labeling something as non useful and leaving it out of the majority of DNA…

> labeling something as non useful and leaving it out of the majority of DNA sequencing as a result has made large swathes of the scientific community unaware of how non coding DNA works within the DNA ecosystem This is simply not true. Noncoding RNA and in particular regulatory regions have been known and studied for many decades. The reason we know less about them than about genes has multiple reasons, foremost the…

I have to disagree. Whole genome sequencing has only been prevalent in the past few years. I can agree that much of this has to do with the cost and complexity involved and the rise of new techniques and more computing power has opened up whole genome sequencing which has only been around since 2003 (1) and has been highly expensive and not used frequently until recently (2).

The majority of research I’ve come across in the past decade has been still focusing on DNA microarrays and qPCR which are focused on coding DNA. Perhaps I’m not seeing all the papers published for the studies you are familiar with and as such have a bias to believe that only a small portion of research is using NGS and is focused on non coding DNA.

1 https://www.yourgenome.org/facts/timeline-history-of-genomic... 2 https://academic.oup.com/hmg/article/25/R2/R157/2198171

Re: New Causes of Autism Found in Noncoding DNA

#108

Post by dkoston »

klmr wrote: post #101
dkoston wrote: post #36

Earlier quoted context omitted.

I can absolutely appreciate that we are a series of mutations. To say that there is no benefit or detriment to having an arched nose or not also seems naive. It’s likely that the shape of your nose can affect how much air passes to your lungs, how likely it is to be sun burnt or not, and many other things. Just because the values or benefits might be minuscule compared to other things doesn’t mean they do not exist.…

> To say that massive portions of our DNA “have no benefit” without having proof of such, seems naive to me. What makes you think scientists have no proof? The whole reason we know junk DNA has no important function for cell biology is that there’s good evidence that says so. There’s some wiggle room with the details but the general picture of this won’t change, and this has been studied for a long time and is fairly…

Whole genome sequencing on humans has only existed for 16 years (1). In 2003, the cost was prohibitive until NGS (next generation sequencing) techniques became commercialized. We can definitely disagree here as 15 years of research which in my worldview is focused mostly on coding DNA and karyotyping doesn’t seem like much to draw this conclusion. There’s plenty of decades old science that has shifted or been rewritten due to the rise of new techniques related to faster computing power.

It’s quite possible that I’m biased based on the labs I’m familiar with and papers I’ve been reading. I just haven’t seen the focus that you are talking about.

1 https://www.yourgenome.org/facts/timeline-history-of-genomic...

Re: New Causes of Autism Found in Noncoding DNA

#109

Post by klmr »

dkoston wrote: post #108
klmr wrote: post #101

Earlier quoted context omitted.

> To say that massive portions of our DNA “have no benefit” without having proof of such, seems naive to me. What makes you think scientists have no proof? The whole reason we know junk DNA has no important function for cell biology is that there’s good evidence that says so. There’s some wiggle room with the details but the general picture of this won’t change, and this has been studied for a long time and is fairly…

Whole genome sequencing on humans has only existed for 16 years (1). In 2003, the cost was prohibitive until NGS (next generation sequencing) techniques became commercialized. We can definitely disagree here as 15 years of research which in my worldview is focused mostly on coding DNA and karyotyping doesn’t seem like much to draw this conclusion. There’s plenty of decades old science that has shifted or been rewritt…

Junk DNA has already been studied before whole-genome sequencing existed, and evidence from NGS not only hasn’t overturned that research, it has largely corroborated it. And as for personal biases, I’m a staunch defender of the ENCODE research so I’m certainly not biased in favour of the concept of junk DNA.

Re: New Causes of Autism Found in Noncoding DNA

#110

Post by klmr »

dkoston wrote: post #106
klmr wrote: post #98

Earlier quoted context omitted.

> labeling something as non useful and leaving it out of the majority of DNA sequencing as a result has made large swathes of the scientific community unaware of how non coding DNA works within the DNA ecosystem This is simply not true. Noncoding RNA and in particular regulatory regions have been known and studied for many decades. The reason we know less about them than about genes has multiple reasons, foremost the…

I have to disagree. Whole genome sequencing has only been prevalent in the past few years. I can agree that much of this has to do with the cost and complexity involved and the rise of new techniques and more computing power has opened up whole genome sequencing which has only been around since 2003 (1) and has been highly expensive and not used frequently until recently (2). The majority of research I’ve come across…

Well my own research has focused completely on noncoding DNA. So yes. It exists.
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