DNA Data Storage

[Green Baron]

25 minutes ago, Cassel said:

Scientists should take care that the terms they use to describe discoveries are clear even to ordinary people.

That is impossible. Complex things cannot be described with simple words without simplifying to an extent that things are plainly wrong, at least can be misunderstood. If someone explains a complex thing with simple words, he may be trying to mislead you.

In this case, "junk DNA" is used in some publications where it can be expected that the reader understands that it means "a part which apparently doesn't code a protein sequence." (was that correct dear geneticists ? :-)) If you like, call it "non-coding dna sequence", just like wikepedia does. Which would be valid until a purpose might be found ;-)

Also, we must understand that for all life on earth there is a common ancestor and the basic encoding technique has not changed for hundreds of millions of years (maybe >2 billions). Some sequences may encode something in a different context, for another blueprint. Life isn't invented anew for every species and some sequences can be switched on and off, like for example number of fingers in the mammal skeleton, allowing for horses with 1 finger (+rudiments) or whales with many on the forelimb.

Edit: another example for the impossibility difficulties to explain complex things with simple words :-)

Edited March 25, 2019 by Green Baron

[Terwin]

23 minutes ago, Cassel said:

Scientists should take care that the terms they use to describe discoveries are clear even to ordinary people. They are getting salaries from the government just to work for the good of all of us. If such terms are created, it means that someone did his job wrong.

From 1972 to 1990 the idea that 'Selfish' or 'Junk' DNA was of no benefit to the organism was generally considered to be accurate.

I find it hard to fault someone for coining a term that was considered descriptive and accurate for almost 30 years after the term was coined.  (and it is still a handy short-hand for non-encoding DNA)

Edited March 25, 2019 by Terwin

[KSK]

48 minutes ago, Cassel said:

Scientists should take care that the terms they use to describe discoveries are clear even to ordinary people. They are getting salaries from the government just to work for the good of all of us. If such terms are created, it means that someone did his job wrong.

I sympathise with the sentiment behind this post but I also see a couple of problems with it.

A slight factual inaccuracy first - not all scientists draw a government salary. Quite a few of them are employed in the private sector. And yes - it is quite possible for private companies to do good, cutting edge science, even relatively blue skies science.

Next. Any profession at all has its own set of jargon. It might not mean much to people not in the profession but in context it makes perfect sense and conveys the necessary information in an accurate and concise way. So too with science. Scientific papers are written by scientists for other scientists. Also, to be frank, most scientific papers deal with the fine details - the stuff that isn't going to be that interesting to other scientists outside of their immediate field, let alone the general public. Trying to describe those fine details in layman terms, even informed layman terms - well you end up with something like this. 

But lastly - as other folks have already pointed out - by asking for clear terms from the outset, you're assuming that everything is known about the thing you're describing, or at least that what is known now will always and forever be correct. Which is simply not how science works.

Getting back on topic, you see this a lot in molecular biology. A new protein will quite often be given a name that reflects the details of how it was discovered. That name may not reflect its true function, it almost certainly won't reflect all its functions - because those functions aren't known and may take a long time - and multiple research grants to figure out. And unfortunately - 'I'll write this up in 10 years time once we've figured everything out and I can give this thing a more accurate name' simply isn't an option for most working scientists. Not that you would want them too either - much better to get those preliminary results out in the public domain where they can be checked, replicated and built upon by other scientists.

Postscript - scientists are also human. With all the quirks, foibles and occasionally misplaced senses of humour that that implies. Again, molecular biology is an excellent example - see, for example, the sonic hedgehog gene, or the RING (short for Really Interesting New Gene) ubiquitin ligases. 

Edited March 25, 2019 by KSK

[Cassel]

51 minutes ago, Green Baron said:

That is impossible. Complex things cannot be described with simple words without simplifying to an extent that things are plainly wrong

 "junk DNA"

Yea, isn't this that case? Complex thing were described by two words that makes it misleading.

[KSK]

22 minutes ago, Cassel said:

Yea, isn't this that case? Complex thing were described by two words that makes it misleading.

No - because when the term was coined it wasn't misleading. It didn't correspond to any protein coding DNA, most of it didn't correspond to any regulatory sequences or other functional sequences that were known at the time. Much of it looked like evolutionary debris - thousands of copies of transposons, old DNA that might have been a gene at one point but is now mutated beyond repair. In a word - junk.

If you prefer, you could use the more formal sounding (but equally uninformative) term, non-coding DNA. 

If we had known what it was for, it wouldn't have been labelled as junk. If we were labelling it now, we wouldn't label it as junk either. It's a classic example of science in action - the more we study something, the more we realise that our original picture of how it all works was woefully simplistic. That doesn't stop the original picture from still being useful - and its only until you do all that extra studying and research that you realise how simple it was.

 

Edited March 25, 2019 by KSK

[Cassel]

1 hour ago, KSK said:

Next. Any profession at all has its own set of jargon.
 

Jargon can use the dealer managers, athletes, but not scientists.

Quote

Scientific papers are written by scientists for other scientists.
 

And this is a big mistake, but how do scientists write in such a way that for an ordinary person it was difficult to understand what else to expect?
I used to hear a very good phrase at university, if you can not write something clearly, then you do not understand it yourself. In this way, I perceive scientists who create such terms.

Quote

But lastly - as other folks have already pointed out - by asking for clear terms from the outset, you're assuming that everything is known about the thing you're describing, or at least that what is known now will always and forever be correct. Which is simply not how science works.
 

So why are scientists so hard to admit to the average person that they do not know everything about everything?

 

19 minutes ago, KSK said:

No - because when the term was coined it wasn't misleading.

It was misleading, no one proved that it is a "junk fragment".

Quote

If you prefer, you could use the more formal sounding (but equally uninformative) term, non-coding DNA. 

If we had known what it was for, it wouldn't have been labelled as junk.

 

"Junk DNA" suggests that you know what this fragment is for and that its meaning is irrelevant. It does not suggest in any way that the meaning of this element is unknown to you. Scientists need to understand such basic issues.

non-coding DNA is also a misleading and meaningless name, because it tells you what this piece does not do, but does not say what it should do.

Edited March 25, 2019 by Cassel

[KSK]

19 minutes ago, Cassel said:

Jargon can use the dealer managers, athletes, but not scientists.

And this is a big mistake, but how do scientists write in such a way that for an ordinary person it was difficult to understand what else to expect?
I used to hear a very good phrase at university, if you can not write something clearly, then you do not understand it yourself. In this way, I perceive scientists who create such terms.

So why are scientists so hard to admit to the average person that they do not know everything about everything?

Just because you (or me for that matter) don't think something is clear, it doesn't necessarily mean it's not clear. It could mean that we don't know enough about the topic to even understand what we're being told. 

And to answer your last point - because the average person wants everything in nice simple terms, preferably with a yes or no answer attached. The average person has no patience for the vast majority of scientific answers which tend to be more along the lines of 'we don't know for sure but yes, if you make these assumptions, we think we know what happens for this subset of cases.'  Scientific answers also have a distressing habit of being proven wrong when additional evidence comes to light - which the average person has even less patience with. 

If the general public is prepared to lambast scientists for being honestly wrong, it should come as no surprise when they stop admitting to being wrong. It should also come as no surprise when public discourse over anything remotely complicated degenerates into entrenched positions and mudslinging. Because sometimes (most times?) there just isn't a nice simple answer.

Of course, as with any other field of endeavour, science does have its big egos who do think that eminence in their field means that they know everything about everything else. But from personal experience, I'm happy to say that they're far from being the norm.

Edited March 25, 2019 by KSK

[Green Baron]

28 minutes ago, Cassel said:

So why are scientists so hard to admit to the average person that they do not know everything about everything?

Nobody does this, that is a severe misunderstanding you must emancipate yourself from ;-) We all freely admit we do not know everything, and probably humankind as a whole might never know "everything". Even more, it may well be, that from a philosophical point of view, "everything" does not exist in an evolving universe. Or it has a limit, a do-not-use-after date printed on it because evolution has made some things different than before. There now is a new "everything" than before and if the rate of change is quicker than the rate of acquisition of knowledge about it, even the Red Queen could not catch up. Just a random thought ;-)

But we can be happy like a little child when we found something we think is worth presenting.

But i think this takes a wrong course. Do you always use a defined and well formed expression that describes exactly what you want to say ? Or do you say "this is like that, in order not to bore you i'll use the term foo". In a symposium, where time is limited to let's say 15min, would you prefer that the guy takes his time to describe in 3 dimensions what he is talking about when everybody else knows that the subject is "non-coding" or "junk DNA" ? It would be impossible to transport the his point.

 

But, well, now, that we have talked about it, we know what is meant with "junk DNA". We don't have to stay there any longer.

12 minutes ago, KSK said:

.... science does have its big egos ...

 

Oooh, i could tell stories about ancient genetics, but i leave it for fear of derailment.

Spoiler

 

Edited March 25, 2019 by Green Baron

[Cassel]

6 minutes ago, KSK said:

Just because you (or me for that matter) don't think something is clear, it doesn't necessarily mean it's not clear. It could mean that we don't know enough about the topic to even understand what we're being told. 

We write all the time about the wrong naming, not about the understanding of the mechanism behind the DNA is difficult and takes time, right?
If you have to devote time and have to start thinking like those who made up the term to understand the term, it means that something is wrong with science. It ceases to be generally available, and it was not supposed to serve only the elites? The language that is used by scientists increasingly detaches itself from reality.
 

6 minutes ago, KSK said:

And to answer your last point - because the average person wants everything in nice simple terms, preferably with a yes or no answer attached. The average person has no patience for the vast majority of scientific answers which tend to be more along the lines of 'we don't know for sure but yes, if you make these assumptions, we think we know what happens for this subset of cases.'  Scientific answers also have a distressing habit of being proven wrong when additional evidence comes to light - which the average person has even less patience with. 

 

And it is strange that ordinary people are discouraged when they see such terms? After all, to understand anything you have to remember many useless and misleading names. And it was enough to simply write an "unknown fragment of DNA".

[Cassel]

23 minutes ago, Green Baron said:

Oooh, i could tell stories about ancient genetics, but i leave it for fear of derailment.

  Reveal hidden contents

 

Not exactly, we write about writing data in DNA, but if we do not understand everything about DNA (as opposed to writing data in the form of zeros and ones on optical or magnetic discs), is this form of data storage safe?

24 minutes ago, Green Baron said:

But i think this takes a wrong course. Do you always use a defined and well formed expression that describes exactly what you want to say ?

Yes, if I want to communicate with someone.

24 minutes ago, Green Baron said:

Or do you say "this is like that, in order not to bore you i'll use the term foo".

If I do not want to bother someone, I use terms that he understands, but that does not change the meaning of what I'm talking about. In this case, I would say "a piece of DNA whose function is unknown."

 

[Green Baron]

You (or me) even have to devote time to grasp a simple concept like electrical energy, let alone DNA. Nothing comes from nothing, valid in the kitchen, experimental chemistry and computer gaming. Learning is fun. If only we could drink knowledge :-)

11 minutes ago, Cassel said:

Not exactly, we write about writing data in DNA, but if we do not understand everything about DNA (as opposed to writing data in the form of zeros and ones on optical or magnetic discs), is this form of data storage safe?

We (well, they, not i) perfectly understand the chemistry involved, to a degree that information can be encoded, written, stored and retrieved with relatively simple means. But we do not understand everything about how an organism is encoded in all its details. Like, in the 70s people knew how to store characters in a 7bit code called ASCII, but 3 dimensional animations stored and played in real time still were a mystery. Ok, a helpless analogy, maybe :-)

Ok, but now, to turn your argument on you ;-) what do you mean with "safe" ?

Edited March 25, 2019 by Green Baron

[KSK]

10 minutes ago, Cassel said:

We write all the time about the wrong naming, not about the understanding of the mechanism behind the DNA is difficult and takes time, right?
If you have to devote time and have to start thinking like those who made up the term to understand the term, it means that something is wrong with science. It ceases to be generally available, and it was not supposed to serve only the elites? The language that is used by scientists increasingly detaches itself from reality.

And it is strange that ordinary people are discouraged when they see such terms? After all, to understand anything you have to remember many useless and misleading names. And it was enough to simply write an "unknown fragment of DNA".

No - it means that if you want to understand something you have to take to the time to learn about it. This applies to everything in life. Science, law, politics, engineering, business, languages, agriculture, sport - everything. Likewise plumbing, car maintenance, doing your tax returns, public speaking - and any other life skill you care to mention.

If I hear a German person using a word I don't know, I can pretty much guarantee its because my German sucks, not that there's anything wrong with the German language. I can choose to be discouraged about that, or I can try and learn a bit of German. Maybe, if I'm prepared to put the effort in, I could learn more than a bit, perhaps even become fluent. Or I might decide that that would be too difficult and content myself with just knowing a bit more than I did before.

 

 

 

[Cassel]

17 minutes ago, KSK said:

No - it means that if you want to understand something you have to take to the time to learn about it. This applies to everything in life. Science, law, politics, engineering, business, languages, agriculture, sport - everything. Likewise plumbing, car maintenance, doing your tax returns, public speaking - and any other life skill you care to mention.

If I hear a German person using a word I don't know, I can pretty much guarantee its because my German sucks, not that there's anything wrong with the German language. I can choose to be discouraged about that, or I can try and learn a bit of German. Maybe, if I'm prepared to put the effort in, I could learn more than a bit, perhaps even become fluent. Or I might decide that that would be too difficult and content myself with just knowing a bit more than I did before.

 

If someone uses a word in a language that you do not understand, it means that they can not communicate with you properly and it does not mean that you have to learn something, only they have to improve their skills if they want to communicate with you.
And the professions in bold show the best that this way you creates artificial things that serve no purpose, only create new jobs for pseudo-experts who have to memorize some phrases. These things only slow down the development.

Science can not exist in isolation from ordinary people, science was meant to be for people, not for elites who will pretend to be smarter and claim to know everything better. Something like that will end badly.

A foreign language is a rather bad example, because learning a language can always be useful for example during a trip. But the terms that scientists give are so non-descriptive and misleading that learning them is a waste of time.

[KSK]

8 minutes ago, Cassel said:

If someone uses a word in a language that you do not understand, it means that they can not communicate with you properly and it does not mean that you have to learn something, only they have to improve their skills if they want to communicate with you.
And the professions in bold show the best that this way you creates artificial things that serve no purpose, only create new jobs for pseudo-experts who have to memorize some phrases. These things only slow down the development.

Science can not exist in isolation from ordinary people, science was meant to be for people, not for elites who will pretend to be smarter and claim to know everything better. Something like that will end badly.

A foreign language is a rather bad example, because learning a language can always be useful for example during a trip. But the terms that scientists give are so non-descriptive and misleading that learning them is a waste of time.

Ahh - I think your last post sums up why we're not going to agree about this. Taking each of your points in turn.

If somebody speaks to me in a language that I don't understand, then why is it up to that speaker to improve their communication skills? Why is it not up to me to improve mine?

I would argue that creating artificial things - in this case scientific terms - speeds up development by providing shortcuts for people to use. A trivial example - we're all quite happily referring to DNA here, rather than calling it deoxyribonucleic acid.

Newsflash - scientists are ordinary people. They just happen to enjoy and be good at science, which doesn't make them elites. Most scientists that I know would be utterly incompetent businesspeople for example - and I would argue that businesspeople will probably have a more direct impact on your life than scientists. Besides, as already pointed out on this thread, your 'scientists are pretending to be smarter than everyone else' meme is just plain wrong.

Learning a little science -and the terminology to go with it - is as useful as learning a little bit of a language. Knowing something about something is always better than knowing nothing about it - if nothing else it helps you understand what you don't know.  Leaving aside the argument as to whether scientific terminology is actually misleading, if you're simply dismissing it out of hand as a waste of time  then there's really no point having this discussion, since you're starting from a position where nothing I can say will change your mind.

[LordFerret]

8 hours ago, Cassel said:

Scientists should take care that the terms they use to describe discoveries are clear even to ordinary people. They are getting salaries from the government just to work for the good of all of us. If such terms are created, it means that someone did his job wrong.

Here's a term I like in Cosmology (for example) ... "uncertainties".  We have an entire science based on this (pretty much).

[Cassel]

11 hours ago, KSK said:

Ahh - I think your last post sums up why we're not going to agree about this. Taking each of your points in turn.

If somebody speaks to me in a language that I don't understand, then why is it up to that speaker to improve their communication skills? Why is it not up to me to improve mine?
 

That's why I wrote that language is a bad example. It's scientists who depend on ordinary people who keep their salaries from taxes if they create such a science, which an ordinary person (performing equally difficult profession, maybe it is worth stopping pretending that being a scientist today is something extraordinary) can not easily assimilate why ordinary people are supposed to spend on this "science" money?

11 hours ago, KSK said:

I would argue that creating artificial things - in this case scientific terms - speeds up development by providing shortcuts for people to use. A trivial example - we're all quite happily referring to DNA here, rather than calling it deoxyribonucleic acid.

See, you gave another example of the bad name "deoxyribonucleic acid" does not say anything about what it is used for. DNA is an abbreviation of a name that means nothing.
I do not know if you can look at names like a novice who does not know what the term refers to, if you have such a skill then you should see the problem that I see.

11 hours ago, KSK said:

Newsflash - scientists are ordinary people. They just happen to enjoy and be good at science, which doesn't make them elites. Most scientists that I know would be utterly incompetent businesspeople for example - and I would argue that businesspeople will probably have a more direct impact on your life than scientists. Besides, as already pointed out on this thread, your 'scientists are pretending to be smarter than everyone else' meme is just plain wrong.

Sure, but they pretend they are smarter that they really are, claiming that they know better how everyone should live and say they have a monopoly on knowledge and understanding about the phenomenon of the world around us. And they do not even know what the whole DNA chain is for.

 

11 hours ago, KSK said:

Learning a little science -and the terminology to go with it - is as useful as learning a little bit of a language. Knowing something about something is always better than knowing nothing about it - if nothing else it helps you understand what you don't know.  Leaving aside the argument as to whether scientific terminology is actually misleading, if you're simply dismissing it out of hand as a waste of time  then there's really no point having this discussion, since you're starting from a position where nothing I can say will change your mind.

Not true. Languages have been created for thousands of years, and scientific terminology has been brought to the limits of the absurd over the past 50 years.
The fact that the terminology is misleading is my opinion, I have no right to have an opinion other than yours?
As so-far you have not written anything that could change my opinion, you only give further examples of terms that are misleading or badly named.

The solution to this problem would be to create alternative, more descriptive names by some group of scientists.

6 hours ago, LordFerret said:

Here's a term I like in Cosmology (for example) ... "uncertainties".  We have an entire science based on this (pretty much).

Cosmology is a descriptive name, but it's probably because it has not been invented in the last 50 years.

[Green Baron]

@Cassel, there still is a problem in understanding.

DNA is a code. We can read and write it to code text for instance. No problem. Apart from that (and originally), it is used by nature to code proteins and in general life(tm). Parts of the DNA code that codes an organism are known, but not the whole code. The code for an organism is complex and we understand a growing part of it, but not all. Especially not side effects and dependencies. Like, you can read English, you understand parts of a text titled "King Henry VIII", but not all. The title is only a shortcut, it doesn't describe what's in the play, the time, the politics, the social interactions, personal reflections. For that, you must sit down and read it in whole. But everyone knows what "King henry VIII" is about when hearing the title, at least those who have studied literature. Would you rant at Shakespeare for not naming it good enough, misleading it for a simple theatre play, though you don't understand everything ? See what i mean ?

 

Language is a good example. Language is what makes you and me communicate. Language exist in many forms and versions, formal languages, natural languages, mathematics can be seen as the language of physics, symbolic languages, communication via signals, odours, ... In order to understand a language you must learn. Years. Decades. It never stops. If you are too lazy to do so, just leave the fun to others and honour them for their thriving and endeavours because, in contrary to your generalization of being useless and only spending other's money, these scientists and subsequently engineers enable your easy living, your pants (chemistry, agriculture. geoscience), your typing on the keyboard (physics, electronics, chemistry, petrology), your provisioning (economics, infrastructure, construction, geoscience in general), your ranting (physics, radiocommunications, networking, spaceflight, ...). Without the scientific foundations of engineering you'll be driving horse-(or ox-) coaches, eating things from the field (if the harvest was good enough), and wearing coarsely made rugs (if the big boy from the neighbourhood hasn't taken them from you).

In general, science lays the foundation and enables us to understand and manipulate the nature around us and also the living together of many people (philosophy, politics, economics, geography).

All things we use have been described and accumulated over centuries, and given names. These names are not perfect, but we know what we are talking about. You must learn to use them properly or you'll be chattering about things you don't understand (which we all do from time to time). Desoxyribonucleid acid is a name for complex thing whose description, experiments, applications and scientific history fills libraries. Do you want to bring a library every time you talk about it or just name it "DNA" ?

One day you may find a field of interest, whatever it'll be, and you'll see that people have worked on it before, found things, described them, given them names, abstractions, in order to enable the following generations to build upon their findings without having to go thorugh it over and again. That's how complex techniques like the one presented by the OP come into being.

Edited March 26, 2019 by Green Baron
streamlining

[kerbiloid]

17 hours ago, Cassel said:

Scientists should take care that the terms they use to describe discoveries are clear even to ordinary people.

To let the trash TV shows make their trash scientifically sounding? No way!
Who needs - he gets. Muggles' - for muggles.

15 hours ago, Cassel said:

16 hours ago, Green Baron said:

 "junk DNA"

Yea, isn't this that case? Complex thing were described by two words that makes it misleading.

I guess, most of those who don't get this term, doesn't care about DNA understanding at all.
They just know that DNA is a plastic spiral toy used by nerds to look wiser.

Also, we eat a junk food. It's still a food, nobody thinks it's useless.

15 hours ago, KSK said:

non-coding DNA

Advanced case: not-software_developing DNA.
Coders are programming noobs. Software developers are bigger ones.

15 hours ago, Cassel said:

Jargon can use the dealer managers, athletes, but not scientists.

All their language are one big jargon. Anyway nobody understands what are they talking about.
(Especially the chemists'. They have no human words other than "runs", "temperature", "normal conditions", and "the").

15 hours ago, Cassel said:

I used to hear a very good phrase at university, if you can not write something clearly, then you do not understand it yourself.

But it sometimes always requires to tell previous 9 seasons of the show, and the non-educated person starts sleeping at the 2nd and anyway forgets what was in the 1st.

So, it's just a declaration.

15 hours ago, Cassel said:

"Junk DNA" suggests that you know what this fragment is for and that its meaning is irrelevant.

Just "and some unclear crap between the genes" sounds less polite.
So, "junk DNA" is enough good.

13 hours ago, Cassel said:

Science can not exist in isolation from ordinary people

Ordinary people live in the world of magic. They need science only as a kind of magic. So, it does.

14 hours ago, KSK said:

If I hear a German person using a word I don't know, I can pretty much guarantee its because my German sucks, not that there's anything wrong with the German language.

Why not both? Why at all they couldn't make their language more understandable? (And German is still an easy one, compared to many others.)
Every nation mostly consisted of illiterate peasants when the languages were appearing. How and why did they invent all these monstrous constructions, and more of that - different in different languages?! 

1 hour ago, Cassel said:

It's scientists who depend on ordinary people who keep their salaries from taxes

Happily, it's the people who define and collect taxes whom the scientists depend on. So, they have to explain be trusted by them. 
A typical ordinary person would strangle himself for a dollar given to science.

1 hour ago, Cassel said:

bad name "deoxyribonucleic acid" does not say anything about what it is used for.

"deo" - "god-like", "nucleus" - a piece of stone to make a stone tool, "Xyribo" - probably some deity's or hero's name.
So, it's an ancient phrase meaning "the acid from the bagasse made by the god-like hero Xyribo's stone tool".

Or maybe some chemical, like "a deoxidized ribonucleic acid"

1 hour ago, Cassel said:

Sure, but they pretend they are smarter that they really are, claiming that they know better how everyone should live and say they have a monopoly on knowledge and understanding about the phenomenon of the world around us.

But this is really so, why not. Should they lie instead?

Edited March 26, 2019 by kerbiloid

[Terwin]

18 hours ago, Cassel said:

Jargon can use the dealer managers, athletes, but not scientists.

Indeed, no one should use jargon.

Shall I hop(open the door, sit inside, swing in my legs and close the door) in my(communally owned by my wife any myself for the last 4 years and fully paid off, so no bank ownership) car(2011 Nissan Alitma with a 4 cylinder 1.8 liter engine, front wheel drive, blue-tooth sound connection, auxiliary audio jack, quadraphonic sound, am/fm radio, glove box, seat-belts, airbags, including a sensor on the front passenger seat to optionally deactivate the front passenger airbag, roughly 97,000 miles, ......) to run(...) to the store(...) to get(...) some groceries(...)?

Quote

And this is a big mistake, but how do scientists write in such a way that for an ordinary person it was difficult to understand what else to expect?
I used to hear a very good phrase at university, if you can not write something clearly, then you do not understand it yourself. In this way, I perceive scientists who create such terms.

Last night I told a coworker 'I am having a problem with a t-list filter, could you take a look?  (url & login) Maintenance Manager > Asset Performance > Inspections > Dead Animal Report   Parent Work Order column'

And that coworker fully understood what I was talking about and how to access it.

Anyone not familiar with our system would require half a page to explain the problem, how to access it, and how it should be behaving.

 Fortunately, I knew my 'target audience' was familiar with the system and I could give him a short-hand version.

Your problem is, you want everyone to write with you as their target audience, especially those engaging in scientific research.  Sorry to tell you this, but you are not the target audience, nor should you be.

Quote

It was misleading, no one proved that it is a "junk fragment".

"Junk DNA" suggests that you know what this fragment is for and that its meaning is irrelevant. It does not suggest in any way that the meaning of this element is unknown to you. Scientists need to understand such basic issues.

non-coding DNA is also a misleading and meaningless name, because it tells you what this piece does not do, but does not say what it should do.

Science is not about 'proving' anything, it is about collecting evidence, counter examples, and making educated guesses to explain it all.

Newton never 'proved' gravity, he just described it to the best of his ability to measure it.

Einstein also never p'proved' gravity, he just came up with a better explanation that works in more situations. 

Indeed, still today it is not 'proven' that gravity is what keeps us from floating off the earth, or what keeps planets in their orbits, it is just a description of these phenomena which has proven useful for predicting future results.

If, as you recommend, Newton refused to write down his ideas on gravity without proof, and Einstein did the same, then we would not have Newtons three 'laws' or general relativity.

Personally, I prefer to have those who come up with novel ideas to write them down(preferably along with reasoning/evidence to support it) then for those ideas to get lost.

 

17 hours ago, Cassel said:

We write all the time about the wrong naming, not about the understanding of the mechanism behind the DNA is difficult and takes time, right?
If you have to devote time and have to start thinking like those who made up the term to understand the term, it means that something is wrong with science. It ceases to be generally available, and it was not supposed to serve only the elites? The language that is used by scientists increasingly detaches itself from reality.
 

And it is strange that ordinary people are discouraged when they see such terms? After all, to understand anything you have to remember many useless and misleading names. And it was enough to simply write an "unknown fragment of DNA".

'Unknown fragment of DNA' is not at all accurate, a more accurate description would be something like 'non-coding DNA fragment from inrons 3812 to 4273 inclusive in the white mouse genome 32-B'(but be sure to list each of the thousands of non-coding segments if you want to be fully accurate)

Also, the primary reason why the term 'junk DNA' is in the public lexicon, is not because Scientists put it there, but because some journalists took it out of context when publishing articles about DNA. 

 

17 hours ago, Cassel said:

Not exactly, we write about writing data in DNA, but if we do not understand everything about DNA (as opposed to writing data in the form of zeros and ones on optical or magnetic discs), is this form of data storage safe?

 

We have a general grasp about several functions performed by DNA, we are a long way from fully understanding everything about what it does and how it works.

Just from my basic knowledge about the possibility of lateral gene transference, I can say that if you had your thesis coded in DNA then accidentally spilled it into a pond you were walking past, it is entirely possible(if unlikely) that this would lead to the emergence of a super-bacteria which would eventually wipe out all mammalian life on the planet.

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If I do not want to bother someone, I use terms that he understands, but that does not change the meaning of what I'm talking about. In this case, I would say "a piece of DNA whose function is unknown."

Once again, you are not the target audience, the other scientists who fully understand the meanings of those terms are the target audience.

If you have problems with it, then you should learn the 'genetics research' sub-dialect which is already known by the entire target audience.  Much like Dante did not fail to communicate his Divine Comedy because it was written in Italian.  His intended audience could read Italian, and if you want to read it you either need to learn Italian or get a translated version.

16 hours ago, Cassel said:

If someone uses a word in a language that you do not understand, it means that they can not communicate with you properly and it does not mean that you have to learn something, only they have to improve their skills if they want to communicate with you.

True, but they are not trying to communicate with you, they are trying to communicate with their colleagues, and their colleagues understand all of the terms they are using.

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And the professions in bold show the best that this way you creates artificial things that serve no purpose, only create new jobs for pseudo-experts who have to memorize some phrases. These things only slow down the development.

Indeed, much like computer games are seen as serving no purpose by a great many people who consider them just a waste of time. 

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Science can not exist in isolation from ordinary people, science was meant to be for people, not for elites who will pretend to be smarter and claim to know everything better. Something like that will end badly.

Science, like most other things, has a sliding scale of complexity, and to have a more in-depth discussion, one must assume a certain level of familiarity with the subject.  Much like how I can mention the Vector, Terrier or Main-sail engines to you, and you already know that those are LFO engines and have an idea about their size, power, and efficiency along with how they are often used.

How easily could you describe your KSP rockets if you had to provide the thrust, ISP, fuel flow rate, fuel capacity, impact resistance, connection size, weight, etc. for every part?

As opposed to 'I used an asparagus lifter with 50 Vector stacks to get this monster into orbit'

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A foreign language is a rather bad example, because learning a language can always be useful for example during a trip. But the terms that scientists give are so non-descriptive and misleading that learning them is a waste of time.

If you knew every term and definition in English, then you would not be confused by these terms, for they are all in English and your failure to understand the full meaning of those terms is just because you are not familiar with that part of the English language.  

 

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See, you gave another example of the bad name "deoxyribonucleic acid" does not say anything about what it is used for. DNA is an abbreviation of a name that means nothing.
I do not know if you can look at names like a novice who does not know what the term refers to, if you have such a skill then you should see the problem that I see.

Indeed, much like the term 'Steel' does not indicate what it is used for.  'DNA' and 'Steel' describe specific chemical compounds which may be used for any of a large number of different purposes.

Are you saying 'Steel' is not a valid word to use? Would 'high carbon steel' or 'stainless steel' be better?

Indeed proper names can be confusing.  I am sure you have no idea who I am referring to when I say 'Christine' or 'Chris'(not him, the other one, no the other other one), or 'Christina'(not her, the other one).
And I am sure you would never use terms like 'hexafloride', 'hydrox', or 'hydrazine'

 

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Not true. Languages have been created for thousands of years, and scientific terminology has been brought to the limits of the absurd over the past 50 years.
The fact that the terminology is misleading is my opinion, I have no right to have an opinion other than yours?

Science has been pushing the boundaries of language for thousands of years.

You just think the last 50 years is absurd because that is the part you have context to understand.

500 years ago the terms 'microscopic' and 'microbe' were absurd and nonsensical, but then about 400 years ago the microscope was invented and they started naming different types of microscopic microbes.

Today those are just normal terms.

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As so-far you have not written anything that could change my opinion, you only give further examples of terms that are misleading or badly named.

It is impossible to change the opinion of some one who refuses to listen to you.

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The solution to this problem would be to create alternative, more descriptive names by some group of scientists.

They have done lots of that, but that is not the sort of thing that drives enough interest for journalists to report on it enough to get into the public lexicon.

I think your main problem is, you object to terms that were defined(and often mis-defined) by journalists who took the term from a scientific paper they did not properly understand, and then blaming the scientists for being confusing when they get quoted out of context.  I have no doubt that the scientists themselves are even more unhappy about the public being taught bad definitions for the terms they use then you are.

 

Edited March 26, 2019 by Terwin

[LordFerret]

@Cassel

I fail to understand your issue with the terminology used.  "Junk DNA" has a history to its definition and meaning.  For all intent of purpose, one could consider it a simple label for a placeholder;  It easily could have been called WhoKnowsWhat, or WhatEver, or Bob instead.  It doesn't matter the branch of science being discussed, pick any you wish, they are full of terms alien (mismatched) to common language and meaning... and to think about that, it's not limited to 'science'.

Because it's handy, from Wikipedia:

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Junk DNA

The term "junk DNA" became popular in the 1960s.^[37][38] According to T. Ryan Gregory, the nature of junk DNA was first discussed explicitly in 1972 by a genomic biologist, David Comings, who applied the term to all noncoding DNA.^[39] The term was formalized that same year by Susumu Ohno,^[40] who noted that the mutational load from deleterious mutations placed an upper limit on the number of functional loci that could be expected given a typical mutation rate. Ohno hypothesized that mammal genomes could not have more than 30,000 loci under selection before the "cost" from the mutational load would cause an inescapable decline in fitness, and eventually extinction. This prediction remains robust, with the human genome containing approximately 20,000 genes. Another source for Ohno's theory was the observation that even closely related species can have widely (orders-of-magnitude) different genome sizes, which had been dubbed the C-value paradox in 1971.^[6]

Though the fruitfulness of the term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and though some have recommended using more neutral terminology such as "noncoding DNA" instead;^[39] "junk DNA" remains a label for the portions of a genome sequence for which no discernible function has been identified and that through comparative genomics analysis appear under no functional constraint suggesting that the sequence itself has provided no adaptive advantage. Since the late 70s it has become apparent that the majority of non-coding DNA in large genomes finds its origin in the selfish amplification of transposable elements, of which W. Ford Doolittle and Carmen Sapienza in 1980 wrote in the journal Nature: "When a given DNA, or class of DNAs, of unproven phenotypic function can be shown to have evolved a strategy (such as transposition) which ensures its genomic survival, then no other explanation for its existence is necessary."^[41] The amount of junk DNA can be expected to depend on the rate of amplification of these elements and the rate at which non-functional DNA is lost.^[42] In the same issue of Nature, Leslie Orgel and Francis Crick wrote that junk DNA has "little specificity and conveys little or no selective advantage to the organism".^[43] The term occurs mainly in popular science and in a colloquial way in scientific publications, and it has been suggested that its connotations may have delayed interest in the biological functions of noncoding DNA.^[44]

Several lines of evidence indicate that some "junk DNA" sequences are likely to have unidentified functional activity and that the process of exaptation of fragments of originally selfish or non-functional DNA has been commonplace throughout evolution.^[45]

- https://en.wikipedia.org/wiki/Non-coding_DNA

[Green Baron]

There apparently has been a hearty discussion among geneticists around the concept of "junk DNA" and its amount in the human genome, after the ENCODE project claimed that 80% of the human DNA is functional, either directly encoding proteins or controlling the expressions of other parts of the genome. The last word has not been spoken yet :-)

Back to the case: if i understand it correctly, digital information is represented in the 4 bases, DNA synthesized and bottled. "Hey, don't spill my backup !"

Edited March 26, 2019 by Green Baron

[kerbiloid]

Spoiler

It isn't useless.

It's just an adware.

Even in DNA...

 

[KSK]

9 hours ago, Cassel said:

That's why I wrote that language is a bad example. It's scientists who depend on ordinary people who keep their salaries from taxes if they create such a science, which an ordinary person (performing equally difficult profession, maybe it is worth stopping pretending that being a scientist today is something extraordinary) can not easily assimilate why ordinary people are supposed to spend on this "science" money?

See, you gave another example of the bad name "deoxyribonucleic acid" does not say anything about what it is used for. DNA is an abbreviation of a name that means nothing.
I do not know if you can look at names like a novice who does not know what the term refers to, if you have such a skill then you should see the problem that I see.

Sure, but they pretend they are smarter that they really are, claiming that they know better how everyone should live and say they have a monopoly on knowledge and understanding about the phenomenon of the world around us. And they do not even know what the whole DNA chain is for.

Not true. Languages have been created for thousands of years, and scientific terminology has been brought to the limits of the absurd over the past 50 years.

The fact that the terminology is misleading is my opinion, I have no right to have an opinion other than yours?
As so-far you have not written anything that could change my opinion, you only give further examples of terms that are misleading or badly named.

The solution to this problem would be to create alternative, more descriptive names by some group of scientists.

Cosmology is a descriptive name, but it's probably because it has not been invented in the last 50 years.

Actually deoxyribonucleic acid is a pretty good descriptive name.

I'll admit that it doesn't tell you much about what it does but it does tell you quite a lot about what it is. It's an acid (obviously), it's found in the cell nucleus (hence nucleic acid) and it contains deoxyribose, which is particular monosaccharide. Or simple sugar if you prefer, although monosaccharide is more correct and avoids confusion with sucrose, which is what most people think of when they're talking about 'sugar'. Deoxyribose is also distinct from ribose (another monosaccharide) in that it has the same structure but is missing one oxygen atom (hence deoxy).

If I remember correctly, the reason that deoxyribonucleic acid is a poor functional name is that when it was first discovered, it's function wasn't known. (As I've already mentioned, this is pretty common in biology). There was a long running debate about whether the nucleic acids or nuclear proteins were responsible for carrying genetic information. It's also worth noting that the level of detail I'm going into above is pretty close to novice level. In the UK at least, it's the kind of detail you learn about if you stay at school past the age of 16 (and study biology of course).

There is a caveat of course - deoxyribonucleic acid  is only helpful as a descriptive name if one (let's keep this impersonal) knows what an acid is, or knows what the cell nucleus is. But a similar caveat is true of any almost scientific term (or any term in any other field). You can simplify your terminology all you like but at some point you need to assume some basic level of understanding. And imparting that basic understanding should be a task for the education system, or if one didn't study science at school, one's own responsibility to acquire. It shouldn't be the job of professional scientists to be teaching basic, school level science - apart from anything else, it would be a gross waste of taxpayer money.

Incidentally, I agree that science communication is important, both for the reason you mentioned and because I believe that having a more scientifically literate society is a good thing. Not least because it helps break down this idea of scientists as untouchable elites. As I said right at the start of this conversation, I do sympathise with the sentiment behind your original post. But I also think there's a limit as to how simplified science communication can and should be. In the end it becomes a choice - do you want the simple answer or the honest one?

Edited March 26, 2019 by KSK

[KSK]

TL:DR for my last post. 

I think it's okay for a scientist to start a layperson's explanation of DNA as 'a long coiled up molecule found in the cell nucleus'. I don't think it's reasonable to expect that scientist to explain what they mean by 'cell' or 'molecule'.

[kerbiloid]

And now let's have a deep breathe filling our blood with Oxyhemoglobin and recall the Metafuel of Life — Adenosine Triphosphate.

Edited March 26, 2019 by kerbiloid