Sixth DNA base discovered?
sciencedaily.com
sciencedaily.com
How come any biology course or book I've ever seen, whether high-school or top-university level, only teaches about four bases?
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.
It'd be kind of like teaching string theory at the same time as F=MA.*
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.
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.
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.
> 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?
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.'
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.
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...
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!)
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.
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.
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.
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.
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.
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.
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".
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.
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.
It's definitely not true that "we're not sure if base modifications matter much". We know they matter; you can get quite different results from the same genetic change in a maternal chromosome vs a paternal chromosome.
Anyway, I assume methylation was covered in her curriculum at some point, either as a biology undergrad or a med student. So your answer is either "because you're not reading the right books" or possibly "because methyl-cytosine is clearly a variety of cytosine, which is one of the four 'classic' bases".
Yeah, that's what I'm talking about. I've heard about methylation before (frankly, I can't remember if we had this in high school, but I encountered the topic briefly later in life), but never in terms of a "fifth base".
When DNA is replicated, methyl-cytosine pairs with guanine just like cytosine does. The only way to maintain the 'methylation marks' is to add a methyl group back on to the newly synthesized cytosine. When DNA is converted into RNA, which is then converted into protein, whether a cytosine has a methyl group attached makes no difference to the final protein.
So whether a cytosine is methylated or not doesn't change the DNA sequence you inherit from your parents. It doesn't change the structure of the protein produced from that gene. What it can do, is change when and where that gene is expressed - which can make a huge difference to the behaviour of the cell.
For instance, a gene such as BRCA1 could be 'turned off' because too many cytosines are methylated, and this could cause a cell to become cancerous. Or a lack of methylation could cause too much c-Myc to be produced, which could result in the same outcome. But then, there many other genetic regulatory mechanisms that can do that as well - such as histone modifications, chromatin structure, transcription factors, and probably methyl-adenine too! All these mechanisms interact to ensure genes are turned on and off at the right time and place, and this field is known as 'epigenetics'.
Methyl-cytosine is a modified version of cytosine that is a very important part of epigenetics, but since it is almost irrelevant to other aspects of genetics, I would argue that you could not consider it a 'fifth base'. Having read the paper, methyl-adenine is the same - interesting new aspect of epigenetics and gene regulation, but not a new base. Also, this paper doesn't exactly 'discover' it, we found methyl-adenine in bacteria in the 60s....
If you want to read about truly new bases, scientists actually synthesised an entirely new pair of bases last year, that can replicate and encode RNA and proteins! A seriously cool step forward in synthetic life http://www.nature.com/news/first-life-with-alien-dna-1.15179
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 existing ones.
You mean methyl-cytosine; methyl-cysteine would be a derivative of the amino acid cysteine.
Source: http://sandwalk.blogspot.ie/2011/07/stop-press-scientists-di...
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...
[2] http://www.sciencedirect.com/science/article/pii/S0092867415...
[3] http://www.sciencedirect.com/science/article/pii/S0092867415...
Also, I hadn't heard of methylation being called another base. More of a modifier/marker on the base.
"Possible Sixth DNA Base Identified", as just one example, would have been a phenomenally better headline that doesn't automatically invoke Betteridge's law.