What is DNA and how does it work?

Sep 4, 2012


Discussion by: JonPerry

At a recent Richard Dawkins convention, I (an animator) met hip hop artist Anthony Danzl. Over a quick chat after the convention we realized that both of us were feeling a need to branch out a bit and do something in science education. I had been lazily working on a genetics animation for a while and we decided to finish it together to see what we could do with our powers combined.

Our first video “What is DNA and how does it work” was up on YouTube a few weeks later. There was a great response from viewers and it was immediately picked up by several teachers for use in the classroom.

Due to the positive response we’ve decided to keep moving forward. We just put up a website and published a second video called “What is a Gene“. We have plans to create an entire series on genetics and evolution.

Thank you Richard Dawkins for inadvertently introducing Anthony and me. It’s been great so far and the future looks promising!

I’m curious to know, what other projects have been started by people meeting at Richard Dawkins conventions?

26 comments on “What is DNA and how does it work?

  • 1
    Sjoerd Westenborg says:

    I would just like to say I liked the video. Great as a teaching tool indeed! I know for the sake of simplicity you couldn’t elaborate too much, but please go with recipe and not blueprint.



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  • 2
    JonPerry says:

    Thanks for the feedback. I’ll keep that in mind for future videos. I agree that a recipe is a more accurate analogy. In these videos we have to simplify a lot and it’s difficult to decide which points should be explained thoroughly, what should be glossed over, and what should be left out. I love hearing what others think. 

    We really struggled to simply define a Gene in the video “What is a Gene”. After several days of debate we finally went with “A segment of DNA which codes for protein”. This definition of course is not perfectly accurate as some genes make RNA that never goes on to produce protein and some virus genes are not even made of DNA.

    In spite of these rare but important exceptions, we settled on our definition because it described the vast majority of genes and was easy for new students to understand. We figure that though our definition is slightly inaccurate, it is not misleading and would not impede a student from learning and accepting a more detailed definition if they decided to learn more about genetics. 

    I’m curious to hear what others think of how we simplified the definition of a gene. Is it accurate enough to satisfy critics? Down the road when we get into evolution our work will be intensely scrutinized for accuracy by the creationists/ID folks. It’s very important that we develop a solid system for simplifying concepts while still being accurate and totally honest.



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  • From my understanding of Dawkins and Williams, it’s incorrect to describe a gene as a physical structure. A gene is information. As the video rightly states, genes are code and can’t be seen.  Subsequent descriptions, however, belie the gene’s invisible nature by showing pictures of them! If metaphor was intended, it needs to be clarified in the video because from my perspective, kids are going to think genes are simply “too tiny” to be seen instead of understanding they can’t be seen in principle.

    The hardware/software analogy for DNA/genes  is not only understandable for kids, it’s accurate.

    Mike



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  • 4
    inquisador says:

    This is splendidly done. The careful wording and vivid illustration is beneficial to understanding, and conveys a lot of information in a short time.

    Well done Jon, but have you noticed the typo on ‘what is DNA’ at 2:53?

    Mike;

    I am one of those who thinks DNA is too tiny to be seen!  Could you possibly please explain further why it is invisible in nature?  I’m confused.

    Thanks.



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  • inquisador,

    DNA can be physically visualized accurately (polymer chain, nucleotide, molecules) because it is an object. It is the gene that cannot be seen. It can’t be seen not because it’s tiny, but rather because it is not an object. It is information. In other words, DNA is the tangible “vehicle,” whereas the gene is the message.

    This is how I understand it.

    Mike



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  • 7
    JonPerry says:

    Yes, their are two version of the video up, the earlier version has the typo. Both are up on Youtube. I wanted to take down the one with the typo but it was embed on multiple websites so I have them both up for now.



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  • 8
    JonPerry says:

     Mike, I think you understand it correctly but are looking at it slightly differently than we are. A gene is like a word, it’s not recognizable to anyone who can not read but is clear as day to anyone who does read.

    Genes are like words that cells can read. Researchers are now learning how to read them too.

    A word is made of letters, a gene is made of physical nucleotides. A starting nucleotide, an ending nucleotide, and all the nucleotides in-between.

    A strand of DNA is made of millions and millions of nucleotides. Some stretches of DNA are random gibberish, some stretches of DNA are genes. If you or I were to look at a strand of DNA, we simply wouldn’t know where genes start and end because we have not be trained in how to read or recognize them. They are invisible to us, hidden among the gibberish, but they do have a physical start and a physical end.



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  • 9
    ganggan says:

    Some comments for you to consider.
    Video “DNA”
    1. Spell out RNA.
    2. Show amino acids transferred to the ribosome; otherwise, it looks like a magic of turning RNA into protein.
    3. Newly synthesized proteins do not immediately form the shapes after translation. 

    Video “Gene”
    1. Promoter and terminator are usually not considered as parts of a gene. A gene is a stretch of DNA that is transcribed in to RNA, equivalent to the transcription unit.



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  • 10
    Sample says:

    Let’s ignore DNA.

    I agree that saying “letters are to words as nucleotides are to genes” is a common understanding but I understand that to be a controversial correlation, false even. Rather than risk plagiarizing this point–because my understanding is shaped primarily from a very short essay–allow me to post a brief paragraph ot two rather than try to reinvent the wheel:

    Evolutionary biologists have failed to realize that they work with two more
    or less incommensurable domains: that of information and that of matter. I
    address this problem in my 1992 book, Natural Selection: Domains, Levels, and
    Challenges. These two domains will never be brought together in any kind of
    the sense usually implied by the term “reductionism.” You can speak of galaxies
    and particles of dust in the same terms, because they both have mass and charge
    and length and width. You can’t do that with information and matter. Information
    doesn’t have mass or charge or length in millimeters. Likewise, matter doesn’t
    have bytes. You can’t measure so much gold in so many bytes. It doesn’t have
    redundancy, or fidelity, or any of the other descriptors we apply to
    information. This dearth of shared descriptors makes matter and information two
    separate domains of existence, which have to be discussed separately, in their
    own terms.

    The gene is a package of information, not an object. The pattern of base
    pairs in a DNA molecule specifies the gene. But the DNA molecule is the medium,
    it’s not the message. Maintaining this distinction between the medium and the
    message is absolutely indispensable to clarity of thought about evolution. [George C. Williams as quoted in The Third Culture: Beyond the Scientific Revolution by John Brockman 1995]

    I remain beholden to this interpretation of genes though I welcome correction if this 1995 assertion is no longer an accepted scientific view. Until then, I must respectfully reject the “letters are to words as nucleotides are to genes” as not merely an inadequate analogy but a fundamentally incorrect one.

    Mike



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  • 11
    JonPerry says:

     Ganggan, thanks for the suggestions.

    1. By this do you mean we should spell out Ribonucleic acid? We decided against spelling out Ribonucleic acid (or saying the word) because we try to only introduce a max of 3 “big” words in each video. That might be a rule we should reconsider for this video however since we spelled out Deoxyribonucleic acid for them. It might be good for them to see the comparison.

    We found the two things that turn people off to science are math and big words. We try to leave them out of our scripts as much as possible.

    2. We actually created a draft version of this video with tRNA bringing amino acids to the ribosome as it built the protein. It was a mess to look at so we dropped the tRNA to clean it up a bit. Now that you mention this though, I imagine it may be good to at least show the amino acids being sucked into the ribosome.

    3. Not all proteins go through post-translational modification but most animal proteins do. We left post-translational modification out of this video because we already filled the viewers mind with so much information. We might make a future video that talks specifically about post-translational modification. One is not currently in the outline but it’s a good idea.

    1. (gene video) Including the promoter region and terminator of a gene as part of a gene was again, something we debated a bit about before putting it into the video. Different text books define genes differently which is frustrating and somewhat disappointing. The strength of including promoters and terminators in the definition of a gene is that a gene is popularly defined (and commonly defined in most textbooks) as a “basic unit of biological inheritance”. A lone transcription unit is useless to a cell without a promoter region and terminator and therefore, does not function as a basic unit of inheritance.



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  • 12
    JonPerry says:

     Something to add here, one of the main problems with including promotion and termination units in the definition of a gene is that some virus genes don’t have them. They use the promoters of their host instead of creating their own.



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  • 13
    inquisador says:

    Mike,

    Thanks for the explanation. I get it now. 

    I also get that the distinction between information and medium may be awkward to maintain at times, as we refer to stretches of DNA in terms of the information it conveys as genes.

    Do we read a book or do we read the information it contains? And if the latter then why do we say the former?



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  • inquisador,

    I’ve thought about your question on and off for about thirty minutes. I’d like to ask how any response to it (from me or others) would affect the distinction between information and medium? The answer to that, it seems to me, is it wouldn’t. I’m curious, why do you ask it?

    If you think a level of understanding can be added to the gene discussion by contemplating your question, I am all ears!

    Mike



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  • 15
    inquisador says:

    Mike,

    The reason I asked my question is that I remained a little confused by something you said and I wanted to explore that a bit to clear it up in my mind. It was this:

    “I remain beholden to this interpretation of genes though I welcome correction if this 1995 assertion is no longer an accepted scientific view. Until then, I must respectfully reject the “letters are to words as nucleotides are to genes” as not merely an inadequate analogy but a fundamentally incorrect one. “

    I was not sure in what sense this analogy is incorrect. It seemed like a reasonable one to me. Although now that I look at it again I can see the problem with it. 

    Yes, it is inadequate and incorrect. I see that the terms do not match up. Something I missed earlier.
    Sorry to be an irritant.

    Thanks for your patience. No reply necessary to my previous question. 

    I think you have already added to my level of understanding.



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  • 16
    Sample says:

    I appreciated your question. I spent my entire dog walk yesterday contemplating tangents arising from the posts on this particular discussion in addition to laughing at my goofy pup’s antics. Cheers.

    Mike



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  • 18
    JonPerry says:

    Mike, I’m having trouble following the main idea behind your objection to the gene video and your objection to the “word  to gene” analogy. Not knowing how else to respond I just want to clarify some things about genes.

    A gene’s only purpose (or trick or whatever you want to call it), is to be transcribed into RNA. That’s it. 

    The purpose of most RNA strands (though there are some exceptions) is to be translated into a protein or a group of proteins by a ribosome. For this reason, most researchers will tell you that a gene’s job is to make a protein or group of proteins.

    A gene has both a physical aspect and an informational aspect.

    Physical aspect: A gene is made of a countable number of nucleotides. A nucleotide is a physical object. If a particular gene is 200 nucleotides long, then that gene can be physically measured and weighed. It can even be physically removed from one DNA strand and physically inserted into another.

    Informational aspect: The sequence of nucleotides in a gene contain information which can be read by various chemical structures in the cell. In a simple protein coding gene, the transcription unit of the gene is transcribed into mRNA, and in a simple mRNA strand (one with no introns) every 3 nucleotides in the RNA are called codons. Ribosomes use mRNA instructions to build proteins. Robosomes translate one mRNA codon into one amino acid when building a protein chain. 

    Here is a translation key that shows which three nucleotides translate to which of the 20 amino acids: http://en.wikipedia.org/wiki/G

    The DNA video shows the RNA to protein process in action: http://www.youtube.com/watch?v

    The protein coding information in a gene can be physically measured. 3 nucleotids = 1 amino acid. Williams warning against reductionism which you quoted above does not apply here when studying how an individual gene builds an individual protein. Reductionism actually works here to help us understand how proteins are built.

    Proteins built by genes, however, then interact with other chemicals inside the body and other proteins built by other genes. These highly complicated and poorly understood chemical interactions are what eventually cause organisms to develop defining traits such as long noses or short noses, blue eyes or brown eyes, and so on. A person’s traits are not coded for by individual genes. Our physical traits come about through the collective work of multiple genes who each do their own little part. 

    Within the complex chemistry of life, there are mass amounts of “information”. This information is nearly impossible to measure and understand because it’s so interconnected. This is where Williams’ warning about the dangers of “reductionism” becomes extremely important and valid. The whole is far greater than the sum of its parts. If you break it down into parts, it will stop working. If you look to closely, you will miss the big picture.

    Individual genes, however, are fairly simple to understand. They can be physically measured in length, and much of the protein coding information they contain is easy for researchers to understand, manipulate, reverse engineer, and so on.  

    As far as the gene to word analogy goes, it would probably be better to say that letters are like  nucleotides, words are like codons (not genes), sentences or paragraphs are like genes.

    Hope that wasn’t too confusing. I wrote this sort of fast and I typically need to draw things to explain them. I’m not a good writer. 

    Cheers
    Jon



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  • 19
    Sample says:

    Let’s say your next video is called, “What is a Meme?” Memes do not exist without brains. Would you animate neurons and glial cells to describe what a meme is? How would you draw a meme? I think your video unnecessarily distracts from its mission by describing a gene’s effects  (protein building, etc.) and the physical structures that genes emerge from (nucleotides) rather than what a gene is: information.

    I’m concerned one of us is misunderstanding or misrepresenting Williams’ position.  

    Mike



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  • 20
    inquisador says:

    “Let’s say your next video is called, “What is a Meme?” Memes do not exist without brains. Would you animate neurons and glial cells to describe what a meme is?”

    Yes, why not?  

    Another excellent analogy.



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  • 21
    Sample says:

    inquisador,

    I can’t tell if you are posting clever satire or not. I’ll assume you aren’t. 

    You ask, “why not?”  A brain is subject to matryoshka-like reductionism (brain–>cell–>molecule–>atom–>quark) but a meme is not. Well, I suppose one could pattern a meme’s “birth, life, and death” and reverse engineer that into an analogous reductionism of sorts, but it would not be strictly synonymous with material reductionism.

    Mike



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  • 22
    inquisador says:

    I may be naive but not satirical. 

    Jon; once again, great videos. Brilliant and thought-provoking. More please.

    And don’t be afraid of packing in too much information. These are ideal for repeat watching, in conjunction with textbook reading, discovering more detail each time.



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  • Well, in your body you have 4 letters A, T, C, and G. If you get a really powerful magnifying glass or microscope you can actually see these letters strung out throughout the length of your body. Geneticists read the genome like a book. 



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  • I’d like to reiterate that I am not objecting to the term gene. I am not objecting to the term gene being used to represent information that is encoded by base pairs. I am not objecting to identifying with stretches of base pairs, having beginnings and endings, as representing genes. 

    My understanding is that the information that is conveyed by the base pairs can only be metaphorically represented by identifying the physical medium that contains the information. 

    Rather than thinking of another analogy to help clarify my point, let’s consider what Williams said: 

    Just the fact that fifteen years ago I started using a computer may have had something to do with my ideas here. The constant process of transferring information from one physical medium to another and then being able to recover that same information in the original medium brings home the separability of information and matter. In biology, when you’re talking about things like genes and genotypes and gene pools, you’re talking about information, not physical objective reality. They’re patterns.

    I’m reaching the limitations of my explanatory powers regarding my objection to representing genes in a manner that does not explain their fundamental informational identity. When I watch the video titled, “What is a gene” I come away not learning what it is but rather, only what it does. I just think that for a video titled as such, I should be educated at least as much on the former as the latter. Of course that is a stylistic opinion. However, fleshing out this discussion has not convinced me that we are nearer to agreeing on all the particulars. I do look forward to more discussion about it because if I’m wrong, I’d like to be convinced of it. 🙂

    Mike



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