Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Sixth DNA base discovered?

sciencedaily.com

Post reply on HN
Print view View original

31–40 of 40 posts

Re: Sixth DNA base discovered?

#31

Post by ghshephard »

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.

You were faced with exactly the same issue that a teacher was, you were limited in the time and space you had, so you tried to focus on the basic concepts. You failed to capture all of the detail, because of those limitations.

This is exactly why a teacher doesn't discuss DNA methylation in a Bio 101 course. When I'm just trying to grok DNA vs RNA, getting exposed to http://en.wikipedia.org/wiki/DNA_methylation is not going to help me, it's just going to confuse me.

But, if the teacher wanted to stretch the class a bit, perhaps diverting a bit of time to the intricacies of tRNA vs mRNA might make sense, and perhaps mention the existence of other biologically active RNAs. But, you have to draw a line somewhere, or you lose everyone. Bio 101 is a huge course, with thousands of concepts/terms to absorb. And the DNA component, with several dozen concepts, gets at most 1-2 hours of the curriculum.

DNA methylation falls below the line.

Re: Sixth DNA base discovered?

#32

Post by dalke »

anigbrowl wrote: post #29
dalke wrote: post #28

Earlier quoted context omitted.

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, eve…

If "No, I didn't" then what was your purpose in writing that example?

In any case, you wrote "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."

Either you will feel short-changed about all of the other things the teachers didn't tell you - did they tell you that atoms were made of electrons and a nucleus without mentioning exotic atoms? Did they tell you that noble gases don't chemically react with other molecules without mentioning things like xenon hexafluoride? Did they tell you that the pH goes from 0 to 14? Did they teach you that "the key to healthy eating is to enjoy a variety of nutritious foods from each of the 5 food groups" but not mention that a meat and fish diet is another way to eat healthy? Did they teach you that thrown objects (without wind resistance) fall in a parabola, without explaining that it's actually an approximation to an ellipse, which is an approximation to general relativity? Did they teach you that velocities add without explaining that it's an approximation only valid for low velocities? Did they teach you that DNA is right-handed when it forms a double helix, without telling you about Z-DNA? Did you learn that different parts of the tongue have different taste receptors when that's not actually true? Did they teach you that black holes absorb everything and neglect to mention Hawking radiation? Did they teach you that microwave ovens work by being tuned to the resonant frequency of water? Or that there is an physical correlation between left-brain/right-brain and creativity/analytical tasks?

If so, then by your definition your teachers short-changed you, and you no doubt feel pretty stupid right now.

If not, then your education was exceptional. http://pubs.acs.org/doi/pdf/10.1021/ed083p1465, for example, is a paper from the Journal of Chemical Education titled "Negative pH Does Exist". It says:

> The misconception that pH lies between 0 and 14 has been perpetuated in popular-science books (1–3), textbooks (4–8), revision guides (9), and reference books (10–16).

I find it unlikely to the point of laughability that your elementary grade math class mentioned that you can ignore relativistic affects when adding the speed of an airline passenger to the ground speed of the plane to compute the ground speed of the passenger. When you finally learned about special relativity, you might have felt like quite a fool for having previously only been taught about Newtonian mechanics.

Re: Sixth DNA base discovered?

#33

Post by anigbrowl »

dalke wrote: post #32
anigbrowl wrote: post #29

Earlier quoted context omitted.

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, eve…

If "No, I didn't" then what was your purpose in writing that example? In any case, you wrote "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." Either you will feel short-changed about all of the other things the teachers didn't tell you - did they t…

I explained my purpose in the second and third sentences. I really can't be bothered continuing this conversation as you seem more interested in scoring points with snarky remarks than in exploring ways to make science more interesting in school.

Re: Sixth DNA base discovered?

#34

Post by rgrannell1 »

This is very interesting, given that ScienceDaily reported the discovery of the seventh and eighth bases in 2011! Did they forget how to count, or do they just republish press releases without any understanding of the subject matter or actual journalism?

Source: http://sandwalk.blogspot.ie/2011/07/stop-press-scientists-di...

Re: Sixth DNA base discovered?

#35

Post by ars »

anigbrowl wrote: post #21
ars wrote: post #19

Earlier quoted context omitted.

> 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, w…

My point is just that there are huge number of biological corner cases that are skipped. It was just another example.

> and I think that a you-don't-need-to-know approach to teaching science is part of the problem

I agree actually, yet it's really hard to do for biology since it's not so much a science with axioms as archeology where you just look and see what there is.

So there's no way to actually say one way or another "this is all the types". Maybe no animal like that has been found. Or maybe it could be done with another type, but no such animals exist - so do you say there is another type or not?

Re: Sixth DNA base discovered?

#36

Post by ende »

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…

Maybe. Undergraduate biology typically sticks to the same set of model systems (Krebs Cycle, for example) even across different courses (microbiology, biochemistry, etc.) in order to reveal deeper levels of complexity within some focused context. You never really get all the edge cases at once though.

I think what most biology undergraduate programs need to add - and many have - is the equivalent of a "Programming Languages" course which adds a 'state of the diversity of the field' dimension to the usual micro-/macro- dimensions. CS (speaking very generally here) tends to either drill down into low level computation or up into high level abstraction, and Bio tends to drill down into sub-cellular/molecular or up into social/behavioral/evolutionary. In CS, a course in programming languages tends to offer a nice survey of the diverse extents of the field, and a similar survey of all of life's vast biodiversity would be a welcome addition to the undergraduate curriculum, imho.

Re: Sixth DNA base discovered?

#37

Post by dalke »

anigbrowl wrote: post #33
dalke wrote: post #32

Earlier quoted context omitted.

If "No, I didn't" then what was your purpose in writing that example? In any case, you wrote "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." Either you will feel short-changed about all of the other things the teachers didn't tell you - did they t…

I explained my purpose in the second and third sentences. I really can't be bothered continuing this conversation as you seem more interested in scoring points with snarky remarks than in exploring ways to make science more interesting in school.

You did not explain your purpose in spending 3 minutes to write a short and incorrect explanation of string theory. You described how you think in a school environment it is "OK to allude to the existence of string theory." I think it's reasonable to infer that you meant that explanation as an example of how a teacher might allude to string theory.

Regarding snarky comments, my goal was to reply to the snark present in "I am a very bad person and I feel bad about it." Since I do not believe that you feel that way about yourself. If you actually do feel bad about it, then I sincerely retract the tone of my response, and apologize for my poor interpretation.

Regarding "make science more interesting in school", that seems to be a shift in conversation. My comment was in regards to feeling "short-changed about your previous education and stupid about all the new stuff you have to absorb".

In the context of making "science more interesting in school" you wrote:

> Not talking about the existence of things when trying to introduce a field really stifles curiosity, by obscuring the fact that that there are many interesting avenues of inquiry that have yet to be explored.

This is incomplete. Many of the things we have brought up, from DNA methylation to obscure reef geography, are well explored. Your comment imply that only the globally unexplored is interesting to students, which simply isn't true. The issue is that it is not reasonable for all teachers to know all of the details about these topics, and be able to summarize them, in such a way that no student will ever feel that they have been slighted for being misinformed about a detail.

A great way to make science more interesting in school is to not cover all of the details and only hit the highlights. This coveys the main idea which is that these fields are comprehensible.

If instead teachers spend much of their time qualifying their statements, then most students will be overwhelmed with information. "Will this be on the test?" "No." "So why do we need to know it?" "Because it's good for you."

Call this the "Now eat your vegetables." or "It builds character" approach to teaching. I honestly do not believe this will make science more interesting.

Re: Sixth DNA base discovered?

#38

Post by TeMPOraL »

ars wrote: post #35
anigbrowl wrote: post #21

Earlier quoted context omitted.

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, w…

My point is just that there are huge number of biological corner cases that are skipped. It was just another example. > and I think that a you-don't-need-to-know approach to teaching science is part of the problem I agree actually, yet it's really hard to do for biology since it's not so much a science with axioms as archeology where you just look and see what there is. So there's no way to actually say one way or an…

So maybe it's time to teach, at some point in the class, that all those classifications in biology and other sciences are more or less arbitrary? That they're just approximations created for practical reasons, often adapted on the fly to fit a problem? Understanding this single concept would kill a lot of pseudo-scientific debates and prevent people from developing wrong ways of thinking, up to such ridiculous cases as modeling animals with Object-Oriented Programming you get in Software Engineering classes.

Re: Sixth DNA base discovered?

#39

Post by TeMPOraL »

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…

> 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

That's exactly how I felt when reading that headline and it's why I posted my comment.

> You don't have to give a big long-winded explanation, but there's nothing wrong with sketching out in very general terms where the frontiers of our scientific knowledge lie. Likewise you don't have to teach small children comparative linguistics, but it's a good thing to make them aware early on that there are many different languages that originate in different countries. Not talking about the existence of things when trying to introduce a field really stifles curiosity, by obscuring the fact that that there are many interesting avenues of inquiry that have yet to be explored.

I strongly agree. Discovering exceptions to the rigid belief structures I was being taught in school (and honeslty, even at university) was one of the things that made me stop believing in formal education (and realizing some of the teachers have no fucking clue what they're talking about). Teaching is not about forcing kids to memorize a bunch of facts; it's about creating mental models. You can say that kids just need to get the basic structure of the field, but a good structure has attachment points to which one can add something in the future.

Re: Sixth DNA base discovered?

#40

Post by dnautics »

ejstronge wrote: post #18
dnautics wrote: post #15

Earlier quoted context omitted.

Because methylcysteine and methyladenine aren't really fundamentally different from their unmethylated counterparts. In terms of the first order information content, they're identical. There differences are as regulatory annotations, but in terms of base pairing they're the same. I kind of cringed when I read that they are "fifth" and "sixth" base pairs because of the significant functional overlap with two of the ex…

> Because methylcysteine and methyladenine aren't really fundamentally different from their unmethylated counterparts... You mean methyl-cytosine; methyl-cysteine would be a derivative of the amino acid cysteine.

thanks.
Post reply on HN