
Sixth DNA base discovered? - mmastrac
http://www.sciencedaily.com/releases/2015/05/150504101254.htm
======
TeMPOraL
"In the early 80s, to these four "classic" bases of DNA was added a fifth: the
methyl-cytosine (mC) derived from cytosine."

How come any biology course or book I've ever seen, whether high-school or
top-university level, only teaches about four bases?

~~~
karcass
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.

~~~
anigbrowl
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 even very simple books use things
like capital letters, commas, and periods so that kids get used to seeing them
early on.

~~~
streptomycin
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.

~~~
anigbrowl
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 another 20 or so which hardly get a look in,
then you have a basic overview of the field.

 _It 'd be kind of like teaching string theory at the same time as F=M_A.*

So what? 'All matter is made up of very tiny things called _atoms_. There are
118 different types of atoms that that we know about, which have many
interesting and surprising characteristics. Many atoms can be combined with
each other to form _molecules_. All atoms seem to be made out of different
combinations of _subatomic particles_ , which are the very smallest things we
have managed to measure, but which we only partially understand. Some
scientists think subatomic particles are made out of even tinier structures
called _strings_ , but nobody has managed to prove that one way or the other.'

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.

~~~
dalke
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!)

~~~
anigbrowl
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.

~~~
dalke
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.

~~~
anigbrowl
_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.

~~~
dalke
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](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.

~~~
anigbrowl
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.

~~~
dalke
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.

------
tokenadult
The comments illustrate why ScienceDaily is not a good source for submissions
to Hacker News. This has been discussed by many of us many times before
here.[1]

[1]
[https://news.ycombinator.com/item?id=7649650](https://news.ycombinator.com/item?id=7649650)

[https://news.ycombinator.com/item?id=8737181](https://news.ycombinator.com/item?id=8737181)

------
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...](http://sandwalk.blogspot.ie/2011/07/stop-press-scientists-discover-7th-
and.html)

------
ejstronge
I am always highly skeptical of Science Daily articles - this one sounds like
it was written by someone without further background knowledge than what was
given in a press release. Or, worse, this person far overstated what the cited
researchers claim

I think the 'layperson' summary of this article should be that the authors may
have found an unappreciated mechanism for gene expression [1-3; 3 articles
were published simultaneously].

As you may have heard, your genome comprises four 'letters', called the DNA
bases. Collections of these bases called genes encode proteins, molecular
structures that perform myriad functions. Indeed, everything that you can see
on a living organism is either protein or was created by a protein.

Genes have specific functions that are often limited in both time and space -
the protein encoded by a gene may only be needed in the embryonic pancreas,
for example. In the field of epigenetics, researchers try to understand the
causes of this tight control of gene activity, among other things.

The addition of methyl groups to DNA bases is a long appreciated way to
control gene activity - see ref. 4, which is an excellent, freely available
cell biology text. The DNA base cytosine is often modified to yield methyl-
cytosine, a methylated base with a well established role in the regulation of
gene expression; methyl-cytosine tends to mark genome areas with lower
probabilities of gene expression.

The authors find that methyl-adenine seems to play a role opposite to methyl-
cytosine, surprisingly. While the existence of methyl-adenine was known in
bacteria, its function in gene expression in more complicated organisms was
not known. Refs 1-3 don't show a causative role for methyl-adenine in
increasing gene expression but the correlations the authors report are likely
to be followed up.

In summary, the story behind this article is pretty exciting and could indeed
expand our understanding of epigenetics, cell biology and perhaps more.

One should remain _extremely_ skeptical of anything in Science Daily - always
go to the source.

[1]
[http://www.sciencedirect.com/science/article/pii/S0092867415...](http://www.sciencedirect.com/science/article/pii/S0092867415004274)

[2]
[http://www.sciencedirect.com/science/article/pii/S0092867415...](http://www.sciencedirect.com/science/article/pii/S0092867415004353)

[3]
[http://www.sciencedirect.com/science/article/pii/S0092867415...](http://www.sciencedirect.com/science/article/pii/S0092867415004225)

[4]
[http://www.ncbi.nlm.nih.gov/books/NBK26854/](http://www.ncbi.nlm.nih.gov/books/NBK26854/)

------
TheLoneWolfling
I wonder if the other two bases can be methylated? Though given they are
paired to bases that can be methylated...

Also, I hadn't heard of methylation being called another base. More of a
modifier/marker on the base.

~~~
tstactplsignore
Yes! Bacteria primarily methylate Adenine. [0]
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754416/](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754416/)

------
yellowapple
Pet peeve: headlines phrased as questions.

"Possible Sixth DNA Base Identified", as just one example, would have been a
phenomenally better headline that doesn't automatically invoke Betteridge's
law.

~~~
krick
I guess question mark is enough.

