DNA→RNA: What Do Students Think the Arrow Means? (2014) | Hacker News Reader

DNA→RNA: What Do Students Think the Arrow Means? (2014)

europepmc.org

93 pointsTomte71 comments

Wow. This is very nice work in which the authors find that about a third of undergrad students completely misunderstand the physical process underlying information flow from DNA to RNA.

I teach the central dogma of molecular biology to learners at multiple postgraduate levels. With the curse of knowledge, it never even occurred to me how wrongly people might get this.

I used to TA undergraduates in Molecular Bio. It was demoralizing to see how many answers to midterm and final exams were just regurgitated babble-stage nonsense. A hidden Markov model could have outscored half my students.

Well this is kind of what undergraduate studies are about, yeah? Not every student who wants to go into molecular biology is cut out for it. Hopefully when they meet a topic thats too hard and the grading is tough but fair they’ll put their efforts elsewhere.

Maybe we should be encouraged that half would really understand a Markov chain in biology?

The comment before didn't mean half know what a Markov chain is, instead that their knowledge is not better then one.

Only in the USA. Undergrad in the US is what high school is in most of the developed world -- a time for broad learning and exploration. Outside of the USA, if you're going to college, you're getting serious and fairly specific. In my experience, Americans take an extra four years or so to grow up, because they're allowed to. (I'm not saying this is good or bad.)

A lot of people from outside the US go to college in the US.

This was down last year with the pandemic, but apparently not as much as you'd think.

FYI I am a US citizen but studied did elementary school in Japan and USA, high school in Brazil and Sweden, undergrad in England, PhD in USA.

Normally, this is because they don't actually want to be there but the class is in the way to some other objective. So, what degree were you in the way of the students getting?

In addition, molecular biology may be the first "biology" class that an undergrad ever encounters where "memorization" isn't the point. That habit needs a while to get broken.

I HATED biology in high school--a bunch of useless memorization. Then I hit a molecular biology class and loved it--everything made sense. Of course, most of the students in the class reacted in precisely the opposite direction.

I was the same with school - no sciences for 11 & 12 because it was so dry

Then I completed a bachelors majoring in biochem and genetics under my own steam after I’d come to science in my own way and I couldn’t be happier with the path. There is such a big difference between the route, boring, dry way science is taught at school compared to the broader field of study. I even loved organic chem.

Don't AP Bio classes still cover some of this? I remember it being covered, at least at a high level, in my AP Bio class back when I was in 10th grade.

They still do, as someone who completed AP Bio a few months ago.

Good to know! I took it almost 30 years ago. (Yeah. I'm old.)

Having studied biology myself, I am also amazed by the level and the frequency of the misunderstandings that the authors found amongst students.

By the way, relevant XKCD: https://xkcd.com/2501/

In the interest of learning, could you provide some resources that explains the information flow?

I think I'm in the dangerous area of knowing enough about the subject to not recognise my own short comings, so I'd be grateful for any resources that helps me learn concepts I don't yet understand, or helps me understand, that I don't know enough about the subject to justify voicing an opinion

Google

The arrow just looks too much like the one used in chemistry.

I remember that it was a video like this that made it click for me in high school: https://www.youtube.com/watch?v=8M198uHJd_8

I've always found those articles studying common student misconceptions and their causes interesting . There's quite a lot of physics publications dealing with phenomenological primitives and concepts learned in other disciplines and how they influence students' learning of physics and might be misapplied. For example, this one describing common misconceptions about chemical bonding [1]

Some misconceptions are so strong and common that you might even get teachers that have and propagate them. I remember having a thermodynamics teacher who would insist it's impossible to reduce the entropy of a closed (rather than isolated) system, despite making it clear in their classes that you can reduce the entropy of such system by work and / or heat transfer.

[1] https://www.researchgate.net/publication/225227224_Some_Stud...

> reduce the entropy of a closed (rather than isolated) system

How do you define "closed" and "isolated"? In fact, this is the first time I'm hearing of a distinction between the two terms. In my experience, they are used synonymously.

In a closed system, matter cannot be exchanged between the system and the surroundings, but energy can be exchanged (in form of work or heat). In an isolated system, neither matter nor energy can be exchanged [1].

Those are the definitions used in thermodynamics, but they might be conflated into a single concept in other contexts/disciplines

[1] http://www.projects.bucknell.edu/LearnThermo/pages/Other%20T...

MC Hawking was wrong! He said "The earth is a not a closed system; it's powered by the sun!"

Anyway, that's not so much a misconception as it just terrible vocabulary.

Ultimately, many people don't understand what a function, mapping, transmutation, transcription, reclassification, or other process which takes items from one category and puts them in a new set of categories.

Programmers, especially in the data space, perform this activity _all the time_. It's almost as deeply ingrained as breathing. Many people who work in tech-adjacent areas get some kind of understanding of this as "business rules." But on all these fronts it is the application of mathematics, the logic and language of the structure of things.

For me, mathematics was always something that I was decent-but-limited at until I got a great teacher -- and then it all just clicked. I had this teacher at the early undergraduate level, but it was because of their absolute practicality that it all made sense. Prior instructors had focused on the _how_ to perform activities, but never really dug into the _what_ / definition of the activity. What the goal of the action was, and more importantly, how it could then be used as a tool in the toolkit.

What I have realized over time is that when things are difficult to explain, I find success by channeling the great math instructors I had in life.

I feel strongly that this relates to the DNA→RNA issue identified here. Simple abstraction, a game, you name it can help engage the _concept_ of reclassification, and then it becomes much simpler to apply the abstract concept to the specific process.

I've never heard of transmutation, transcription, reclassification, or category as data processing jargon.

Transmutation is for nuclear physicists, transcription is for court reporters, reclassification is for national security, and everything is categorical because people like the word.

How would they help with biology?

I have had some experience (among non-technical, non-bio co-workers) with what I suspect is the basic issue here (and I think the document link confirms this) - people just equate an "explanation" to connecting things with arrows and everybody kind of nods along while never agreeing on what the arrows mean.

It can be seen as antisocial if you - the recipient of the "knowledge" - question what they mean.

”Transform” is commonly used in the context of data wrangling.

Which is exactly the same wrong metaphor that the article is talking about. A transformation in data processing is a transcription in biochemistry creating something new without destroying the original), not a transformation in biochemistry (which destroys the original).

> everything is categorical because people like the word

> people just equate an "explanation" to connecting things with arrows and everybody kind of nods along while never agreeing on what the arrows mean

I bet you'd love category theory!

I can state categorically that I have read a little bit on category theory and neither fell in love nor remember it.

Well, transcription is a the transference of information between mediums. Spoken to written. Spoken to recorded media. Written to other written. But strangley not written to spoken, so the analogy breaks down there.

But if you have the understanding that transcription is a copying to another media, then the jargon makes perfect sense. People used to dictate and have a secretary transcribe. But we don't do that any more. And like the sound of a typewrighter the verb "transcribe" has drifted out of common parlance and might therefor gone a bit stale as an analogy.

> [transmutation] ... as data processing jargon

Nor have I for that specific context. As Whitman noted, people are large and contain multitudes. Reclassification and transcription are certainly common enough colloquialism even if not formal processes. It's all mappings[0] in the end.

> everybody kind of nods along while never agreeing on what the arrows mean.

Yes, this is what I said, and elucidated an abstraction process to convey complex technical information I both experienced and have used in practice.

[0] https://en.wikipedia.org/wiki/Map_(mathematics)

The point is that the physical process is not like programming or math -- there is a difference between "A becomes B" and "A is used to as a reference when creating B", which is conflated all the time in programming unless you are using linear types, which is rare. (Mutating a data structure doesn't give you a new type. Garbage collection does, but that's not part of the semantic model of a programming language).

I must be missing some important part of what you were trying to communicate.

It sounds as though you are saying "colloquialism[s]" have some value or relevance to technical understanding of a process.

It seems to me this is the primary means by which information gets lost because people think they know what is meant, but they don't.

It's the stumbling block that always reoccurs.

---- If someone says "map" and means function, then I know what a function is (I think).

If someone says "map" and means a higher order function, like in programming, then that's also something I think I know.

If someone wants to talk about morphisms that are not functions, then that sounds like it may be beyond my ability to follow.

But in any of the three cases, using the word "map" out of context fails to tell me which it is. Other associations, like the paper rand-mcnally map that I once used to drive across the country, are not helpful.

Apparently transcribe is a technical term too complicated for undergrads. I guess a third of college students have never read a transcript before leaving high school. Terrifying.

When I was a tutor at my community college, I learned pretty fast to explain concepts in as many different ways as I could until the concept “clicked”. Vocabulary is the gateway to understanding. From reading this paper, it seems like people didn’t know what transcribe means, so they miss that the name itself is an analogy and not solely a technical term.

It’s kind of frustrating that people are doing bad at biology because their English classes failed them.

Sounds like its the fault of the professors/TAs for not using an appropriate analogy.

I've graduated from high school and a bachelors program subsequently. That was all decades ago. I've never read a transcript in my life. Why would people do that generally, unless they had a job in transcription?

Because they missed a politician’s speech and read the transcript in the newspaper. Or read a transcript of a historical speech, like the Gettysburg Address.

Because they read their own medical records.

Because they want to watch television on low volume so they don’t wake the baby or partner, and turn the transcript on.

The fact that you have a university degree having never once done these things is indicative of an abysmal education system.

>Because they want to watch television on low volume so they don’t wake the baby or partner, and turn the transcript on.

Is calling subtitles "the transcript" a regional variation I've never heard before, or are you just stretching things to make a point?

No, and no. TV captions are not typically called transcripts, but they are in fact transcripts. They are not the script, because the director changes things and the actors ad lib. In fact, things get pretty dissonant when they try using the script as captions. Captions transcribe — copy language into a different form — the spoken dialogue into the written word.

I have done some of these things. But I didn't know all these things could be called transcript. Basically, I thought they were only for either academic records or recordings of court proceedings. Perhaps the whole terrifying thing with the high school students is actually just a big miscommunication.

If you look on US NPR website you will see transcripts of audio programs.

Now that I know this, I know that I've read many transcripts. And I now think that if someone claims not to have read a transcript, that it's more likely that they don't understand what a transcript is than that they actually haven't read a transcript.

its not about the word not being known, its about not knowing the specifics of the biochemistry underneath the metaphor.

The metaphor implies the biochemistry, at least somewhat. If you read the paper — anyone with a college degree should be able to understand it — most of the errors are about DNA being transformed into RNA. But the word transcribe means a copy is made! Maybe people also see the arrow as a chemical reaction product, being primed from HS chem, but arrows are used for other things. If you don’t know what transcribe means, you are likely to assume the wrong metaphor, I guess.

https://kraulis.wordpress.com/2015/11/04/why-do-so-many-scie... Also an interesting read about how the central dogma was never really meant to be presented in teh way that it is currently presented (really was meant to focus on "information" flow starting at DNA rather than show a definitive guide to the transformations between these molecules in a cell).

That's kind of mincing words: arguing that the Central Dogma isn't an incomplete description of the information system, it's just a complete description of the information of a subsystem.

So how does it really work? What does the arrow actually mean?

Is the point that the information on the DNA gets copied onto RNA while the DNA remains intact?

> Is the point that the information on the DNA gets copied onto RNA while the DNA remains intact?

Close, but I think it's more that the information gets used to assemble the RNA, and the resulting RNA also encodes information. Saying "copied onto RNA" can imply that the RNA previously existed in some kind of blank slate form.

So the arrow denotes a transfer/flow of information, but does not denote a chemistry 101 style reaction that changes a physical piece of DNA into a piece of RNA and then into a protein.

As an analogy - DNA is source code. The first arrow is the parser and creates RNA that is a reflection of the DNA. The second arrow (RNA to protein) is the compiler, taking the parsed code (RNA) and generating a program (protein) from it.

At no point is the source code consumed to create the program, akin to DNA.

Just semi related: I find it curious that 3 out of the 4 universities have the same percentage of minority students (12%). Is this figure a coincidence, or is it the result of some specific policy?

( I'm not American so I lack the context).

Most regional schools, as they get larger and larger, will have a student body that reflects the regional population fairly well. Three of these schools were private though, and small private schools especially can have idiosyncratic student populations. Apart from that, it's hard to say more without knowing which schools these were.

(A regional school is one that draws students mostly from the surrounding region instead of nationally/globally)

I don't have a direct answer to your question, but that's very close to the representation of black Americans in the total population. That number is cited colloquially as 15%.

> That number is cited colloquially as 15%.

What? No it isn't; it's cited colloquially as 12% or one in eight.

Compare https://en.wikipedia.org/wiki/Demographics_of_the_United_Sta...

A large chunk of top universities in the US have racial admittance quotas. Not saying that is the case for whatever universities you are looking at but it does exist.

(it's a PDF file)

HN could really use some kind of tag for when a submission goes to a file instead of a web page.

Why?

It would be useful for many. I have several computers that can browse the web but can't render PDF files (or run PDF.js).

Things don't have to be useful for everyone to be a good idea.

So my phone does what I expect it to do. When I open a link I might be opening it in another tab to read later, or switching to a different app while it loads, or something else. If it's a file I'm going to get a pop-up asking me what I want to do with it. Depending on where my finger was I might open the file with the wrong app or dismiss the pop-up making me either download it again or go find the file in a file manager. It also clutters up my Downloads folder with things I'm going to read or skim once and never look at again.

There is: https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...

It seems that the submitter hasn't applied it

There's no option for that when submitting. I think it's probably moderator-applied.

It's just text as part of the title. The submitter can do it (until the edit time runs out).

It usually happens automatically, but obviously not this time. That makes it very hard to think about it, because it mostly works.

My hypothesis is that HN's detection only looks for file extension, not content type headers, because it doesn't fetch the submission itself.

grzm is correct, it does not happen automatically. See https://news.ycombinator.com/newsguidelines.html.

There's a similar fundamental problem in maths education: What does "=" mean?

It's commonly reported that people are confused by = for assignment in programs, but one reason I tended towards programming and not math in school was that I had a hard time with the timeless nature of mathematical equality.

I found it intuitive that abstract things should happen in some order, whereas it was hard to imagine everything in a complex equation existing at once. How can anything be true if there's no time for it to become true? Etc.

This might be related to my being oriented more towards verbal processing and narratives.

I've been getting into formalizing math in computer proof assistants, and it made be realize equality was much more subtle than I had previously thought. Consider the sets {1, 2}, {2, 1}, {1, 2, 2}, and {n in Z | 1 <= n < 3}. These are not literally the same (since they're written differently; they're "intensionally" different), however, in math, sets are considered to be equal if they have the same elements (they're "extensionally" equivalent). These sets do happen to have the same elements (1 and 2) so they're all equal to each other. But you have to go through some process to construct an equality between pairs of sets to actually see this.

It's like how in many programming languages there are multiple kinds of equality. The most basic is that the variables refer to the same object in memory (i.e., a pointer comparison), which is hardly a computation at all. Others are more involved, like how in Python the `==` operator recursively checks for element-wise equality in data structures like lists, dictionaries, sets, and tuples. There is a concrete computation that demonstrates whether things are equal.

In math, there is no algorithm that can, in general, determine whether on not two things are actually equal. Given two objects, you might be able to come up with some ad hoc method to tell they're equal (which is a sort of computation -- proofs are programs). Math depends on a belief that these ad hoc equality proofs won't ever mutually contradict one another. Through this belief, we can pretend that there is exactly one Platonic ideal form of each thing somewhere out there in the mathematical universe.

(The almost-algorithm for determining equality, which is horribly slow but general, is to enumerate all possible proofs, checking one at a time to see if they prove or disprove the equality. Unfortunately, there are some concretely definable sets, similar to the machine you create for the halting problem, that this equality program will never decide are equal or not -- assuming math is consistent, that is. This is what the first Godel incompleteness theorem is about.)

This is true. I wrote a brief anecdote[1] about this. I was in the advanced math program as an undergraduate and one of the other students was telling me about how he always struggled with math throughout high school. Until one day, near the end of high school, he came to understand that the equal sign wasn't a symbol that is sometime written between steps of problem solving, but rather it meant that the values of the expressions on the two sides were equal to each other!

This realization changed everything for him. He ended up placing within the top Canada-wide in the Sir Issac Netwon high school physics contest, and ended up in the advanced mathematics classes with me.

[1] http://r6.ca/blog/20031202T032200Z.html

P.S. Today I'm doubtful that simply replacing an equal sign with an arrow like I suggested in 2003 would help all that much.

> Today I'm doubtful that simply replacing an equal sign with an arrow like I suggested in 2003 would help all that much.

Yes, I think the arrow would compound the problem. Learners already often think "=" means "and then".

What's missing: epigenetics as a feedback loop.

html link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041510/

This is so sad of an article.

I’ve got a degree in Computer Science and even I know what this DNA -> RNA process entails.

The trick I use to remember this is:

DNA: D means Disk

RNA: R means Ram

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