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Sixth DNA base discovered?

sciencedaily.com

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Re: Sixth DNA base discovered?

#21

Post by anigbrowl »

ars wrote: post #19
anigbrowl wrote: post #16

Earlier quoted context omitted.

I strongly disagree. You don't have to go into detail about them, but knowing the fact of their existence is fundamental. If you think there are only 4 bases and then later find out that there are others, the first reaction t that is to feel short-changed about your previous education and stupid about all the new stuff you have to absorb. If you are told there's 4 bases that seem to deliver 99.9% of the action and an…

> If you are told there's 4 bases that seem to deliver 99.9% of the action and another 20 or so which hardly get a look in How many blood types are there? Most people will say 4 (or 3, or 2 depending on how you define it). But there are actually far more of them, but the rest are rare or less important.

What point are you trying to make here? It costs very little effort to mention the existence of many more types, even while acknowledging that most of the time you're going to run across the most common four types.

On the other hand, suggesting that only 4 types exist is wrong. Anyone who is interested in biology is likely to waste a certain amount of time constructing theories based on a completely false premise, which is discouraging. That may sound trivial, but go look at festering debates involving a lot of pseudoscience, eg on the environment or evolution. People trot out arguments based on false premises as a matter of course, and I think that a you-don't-need-to-know approach to teaching science is part of the problem, because you end up with a lot of people who don't know what they don't know.

Re: Sixth DNA base discovered?

#22

Post by Balgair »

anigbrowl wrote: post #16
streptomycin wrote: post #8

Earlier quoted context omitted.

Because it's just not very important at that point. If you covered all the exceptions and special cases in biology, Bio 101 would never end. It'd be kind of like teaching string theory at the same time as F=M*A.

I strongly disagree. You don't have to go into detail about them, but knowing the fact of their existence is fundamental. If you think there are only 4 bases and then later find out that there are others, the first reaction t that is to feel short-changed about your previous education and stupid about all the new stuff you have to absorb. If you are told there's 4 bases that seem to deliver 99.9% of the action and an…

However, biology is chock full of exception cases. The 'Central Dogma' of DNA -> RNA -> Proteins is still largely true for most cases. However, we discover all the time exceptions to this rule. Same here for the different 'tags' you can give DNA bases. Yes, you can teach the undergrads this, but then you'd have to teach them all the edge cases and other tiny things we don't even really know exist but one study from 1987 in the GDR said that..... You get the idea.

You only have so much time in the class and you have to hit all the big points of the field in an intro class like this hypothetical one. DNA tagging is not important if you are going to have to take time away from the different amino acids and what the importance of serine is for folding, or some other part of it. Saying that you can just explain away the other edge cases, a part of science that is still highly variable is just throwing away the pedagogy and hard earned years of teaching the instructor already possesses.

Also, just getting those core concepts into the heads of most undergrads is tough enough already. Half of them don't come to class as is on a Friday afternoon, let alone the other classes they take and the lives they have to live. Depending on the class, many of them may not even be at all interested in the material as the class is just a GE or something. And don't get me started on pre-med majors....

At the end of the course, you want them to be able to just think that they can read an article like the OP and say to themselves: 'Yeah, ok, thats not what I learned in school, lets click on it.'

Re: Sixth DNA base discovered?

#23

Post by louthy »

streptomycin wrote: post #8
anigbrowl wrote: post #6

Earlier quoted context omitted.

I don't understand why you wouldn't set that sort of thing out at the basic level, even if it were accompanied with 'we understand ACGT quite well, the others are pretty mysterious and we're not sure if they matter as much.' Seems a bit like teaching English by focusing only on spelling but omitting any mention of punctuation or grammar for the first few years. Of course we don't try to teach that all at once, but ev…

Because it's just not very important at that point. If you covered all the exceptions and special cases in biology, Bio 101 would never end. It'd be kind of like teaching string theory at the same time as F=M*A.

> It'd be kind of like teaching string theory at the same time as F=M*A.

Would it be such a bad thing? I remember reading Richard Feynman's QED and thinking to myself: "I wish science lessons at school had started with this".

Re: Sixth DNA base discovered?

#24

Post by jacel »

anigbrowl wrote: post #6
karcass wrote: post #3

Earlier quoted context omitted.

Methylation and other base modifications (there are 20+ last I checked) are taught in upper-level biology courses. I guess the people who write biology texts consider this advanced material.

I don't understand why you wouldn't set that sort of thing out at the basic level, even if it were accompanied with 'we understand ACGT quite well, the others are pretty mysterious and we're not sure if they matter as much.' Seems a bit like teaching English by focusing only on spelling but omitting any mention of punctuation or grammar for the first few years. Of course we don't try to teach that all at once, but ev…

We do understand a lot of the base modifications pretty well, but that's all they are - modifications. I agree that it could be useful to introduce students to the concept of epigenetics, of which base pair modifications such as methyl-cytosine are just one aspect. But it is an aspect that is no more important than all of the other epigenetic mechanisms - so it should be taught in that context.

If you're interested in an overview of epigenetics, this is a great textbook chapter from Cold Spring Harbour Laboratory http://www.cshlpress.com/pdf/sample/epigen.pdf incidentally, James Watson, the co-discoverer of the structure of DNA, still works at CSHL.

Re: Sixth DNA base discovered?

#25

Post by dalke »

anigbrowl wrote: post #16
streptomycin wrote: post #8

Earlier quoted context omitted.

Because it's just not very important at that point. If you covered all the exceptions and special cases in biology, Bio 101 would never end. It'd be kind of like teaching string theory at the same time as F=M*A.

I strongly disagree. You don't have to go into detail about them, but knowing the fact of their existence is fundamental. If you think there are only 4 bases and then later find out that there are others, the first reaction t that is to feel short-changed about your previous education and stupid about all the new stuff you have to absorb. If you are told there's 4 bases that seem to deliver 99.9% of the action and an…

You do realize that your summary is equally wrong, yes?

There are indeed 118 recognized elements, but there are many more "types of atoms", only some of which are due to differences in proton count. There are also isotopes; tritium is a form type of hydrogen that is radioactive, and several times heavier than normal (1H) hydrogen.

Then there are charged atoms, including more esoteric forms where an inner shell electrons are removed instead of an outer.

And there are excited nuclei, like the metastable isotope technetium-99m. While chemically very similar to 99Tc, it emits gamma rays that make it a useful medical radiotracer.

That is, atoms differ not only because of the 'different combinations of subatomic particles', but also because of the specific energy states involved.

FWIW, there are the exotic atoms, like positronium (an electron-positron atom) and muonic atoms (where one of the electrons is replaced by a muon). These are still different combinations of subatomic particles.

Also, "smallest things we have managed to measure" becomes a meaningless phrase. Under current physics, an electron has no radius. It's a point particle, and no one is talking about strings which are smaller than a point. Instead, string theory proposes that the zero-dimensional point should be replaced by a one-dimensional string, or higher-dimensional branes. These should count as being larger objects than the current model for how electrons work.

We have oodles and boodles of frontiers to our scientific knowledge. No class can touch on every case. We have to give approximations and limited cases, as otherwise the result will be overwhelming.

For example, in geography class we ask students to identify the US on a map. We usually mean the 48 continental states plus Hawaii and Alaska. But the US also includes Puerto Rico, Guam, and other territories, including Kingman Reef and Bajo Nuevo Bank. Teachers have to figure out if it's more important for students to know that only the US considers Bajo Nuevo Bank to be part of the US[1], or if the students should instead learn more details about DNA, or string theory.

([1] While it could be an interesting segue into the International Court of Justice, Guano Act, the War of the Pacific, phosphate strip mining of Nauru, the Haber-Bosch process, and gas warfare in WWI, these are students who can't yet identify the lower 48 on the world map!)

Re: Sixth DNA base discovered?

#26

Post by anigbrowl »

dalke wrote: post #25
anigbrowl wrote: post #16

Earlier quoted context omitted.

I strongly disagree. You don't have to go into detail about them, but knowing the fact of their existence is fundamental. If you think there are only 4 bases and then later find out that there are others, the first reaction t that is to feel short-changed about your previous education and stupid about all the new stuff you have to absorb. If you are told there's 4 bases that seem to deliver 99.9% of the action and an…

You do realize that your summary is equally wrong, yes? There are indeed 118 recognized elements , but there are many more "types of atoms", only some of which are due to differences in proton count. There are also isotopes; tritium is a form type of hydrogen that is radioactive, and several times heavier than normal (1H) hydrogen. Then there are charged atoms, including more esoteric forms where an inner shell elect…

Yes, you should totally apply the standards for a textbook to an example of sketching scientific concepts that I composed in the space of 3 minutes. There's no middle ground between mentioning the most basic things and throwing in everything including the kitchen sink. I am a very bad person and I feel bad about it.

Re: Sixth DNA base discovered?

#27

Post by anigbrowl »

Balgair wrote: post #22
anigbrowl wrote: post #16

Earlier quoted context omitted.

I strongly disagree. You don't have to go into detail about them, but knowing the fact of their existence is fundamental. If you think there are only 4 bases and then later find out that there are others, the first reaction t that is to feel short-changed about your previous education and stupid about all the new stuff you have to absorb. If you are told there's 4 bases that seem to deliver 99.9% of the action and an…

However, biology is chock full of exception cases. The 'Central Dogma' of DNA -> RNA -> Proteins is still largely true for most cases. However, we discover all the time exceptions to this rule. Same here for the different 'tags' you can give DNA bases. Yes, you can teach the undergrads this, but then you'd have to teach them all the edge cases and other tiny things we don't even really know exist but one study from 1…

Saying that you can just explain away the other edge cases

I am not saying that. I'm just suggesting that it would be a good thing to allude to the fact of their existence in order to provide a glimpse of the wider context in which the basic concepts are introduced.

Re: Sixth DNA base discovered?

#28

Post by dalke »

anigbrowl wrote: post #26
dalke wrote: post #25

Earlier quoted context omitted.

You do realize that your summary is equally wrong, yes? There are indeed 118 recognized elements , but there are many more "types of atoms", only some of which are due to differences in proton count. There are also isotopes; tritium is a form type of hydrogen that is radioactive, and several times heavier than normal (1H) hydrogen. Then there are charged atoms, including more esoteric forms where an inner shell elect…

Yes, you should totally apply the standards for a textbook to an example of sketching scientific concepts that I composed in the space of 3 minutes. There's no middle ground between mentioning the most basic things and throwing in everything including the kitchen sink. I am a very bad person and I feel bad about it.

Yes, just like you should totally believe that your teachers are short-changing you by not summarizing perfectly the details they decided to not cover. And believing that you could remember all the details should they have done so.

Don't you feel horrible for never having been taught that contested unorganized, unincorporated United States territories like Bajo Nuevo Bank exist?

Your life must be upside down by first learning that the correct name for 'Brontosaurus' is 'Apatosaurus' and then to learn recently that it's now considered a valid genus of sauropod distinct from Apatosaurus.

You meant your example as a demonstration of how it's possible to teach string theory at the same time as F=MA. Otherwise, why did you even spend three minutes at the task? My response was to show that it isn't easy. If a teacher trips up over even a single point - eg, to explain that an atom is made of electrons, protons, and nucleus - then a future version of you will complain and say you were shortchanged, because there are atoms which are NOT made of those subatomic particles.

But few primary or secondary school teachers will know about these special cases, and for the vast majority of people it's useless information.

Re: Sixth DNA base discovered?

#29

Post by anigbrowl »

dalke wrote: post #28
anigbrowl wrote: post #26

Earlier quoted context omitted.

Yes, you should totally apply the standards for a textbook to an example of sketching scientific concepts that I composed in the space of 3 minutes. There's no middle ground between mentioning the most basic things and throwing in everything including the kitchen sink. I am a very bad person and I feel bad about it.

Yes, just like you should totally believe that your teachers are short-changing you by not summarizing perfectly the details they decided to not cover. And believing that you could remember all the details should they have done so. Don't you feel horrible for never having been taught that contested unorganized, unincorporated United States territories like Bajo Nuevo Bank exist? Your life must be upside down by first…

You meant your example as a demonstration of how it's possible to teach string theory at the same time as F=MA.

No I didn't. I think one should take a lot of time breaking down the details of F=MA and showing why it works and so forth. But I also think it's OK to allude to the existence of string theory early on when you're trying to establish the scope of what physics is about and why you might want to study it, even though it would probably take 10 years for someone to go from hearing about its existence to studying it directly.

Meanwhile, I'm grateful to have had some science teaches that were willing to identify some frontier areas of science by name, while admitting that they were beyond their own understanding (eg QM), and also so spend a bit (not too much) of class time letting us spitball ideas on things like time travel or anti-gravity in order to engage the subject imaginatively as well as meeting the specific curricular requirements.

Re: Sixth DNA base discovered?

#30

Post by ghshephard »

anigbrowl wrote: post #27
Balgair wrote: post #22

Earlier quoted context omitted.

However, biology is chock full of exception cases. The 'Central Dogma' of DNA -> RNA -> Proteins is still largely true for most cases. However, we discover all the time exceptions to this rule. Same here for the different 'tags' you can give DNA bases. Yes, you can teach the undergrads this, but then you'd have to teach them all the edge cases and other tiny things we don't even really know exist but one study from 1…

Saying that you can just explain away the other edge cases I am not saying that. I'm just suggesting that it would be a good thing to allude to the fact of their existence in order to provide a glimpse of the wider context in which the basic concepts are introduced.

Perhaps in an advanced biology course. But, given that you have limited time in class, and DNA is just one tiny, tiny component of a Bio 101 course, just getting across the concept of DNA, RNA, CGTA, Inheritance, and the implications to cell division is a victory.

Trying to teach, "Hey, there are four bases, but no, not really, you can also have methylated cytosines, What is methylation you ask...."

And then 25% of the class doesn't even grok the four bases concept because you got side tracked on a detail that is not relevant to baseline understanding.

Admittedly, you can be too simple. When I took grade 11/12 chemistry in 1986/1987 in British Columbia, Canada - they did not teach chirality, and I didn't hear about it until watching an episode of Breaking Bad. So I see how one can feel cheated out of some pretty core concepts...

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